International
Tables for
Crystallography
Volume F
Crystallography of biological macromolecules
Edited by E. Arnold, D. M. Himmel and M. G. Rossmann

International Tables for Crystallography (2012). Vol. F, ch. 1.3, pp. 13-38   | 1 | 2 |
doi: 10.1107/97809553602060000806

Chapter 1.3. Macromolecular crystallography and medicine

W. G. J. Hola* and C. L. M. J. Verlindea

aBiomolecular Structure Center, Department of Biological Structure, Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195–7742, USA
Correspondence e-mail:  hol@gouda.bmsc.washington.edu

Macromolecular crystallography is discussed in terms of its impact on medicine, and selected examples of protein structures of medical relevance are provided. The application of crystallography to the study of genetic diseases is covered, as well as the role of crystallography in the development of novel pharmaceuticals.

1.3.1. Introduction

| top | pdf |

In the last hundred years, crystallography has contributed immensely to the expansion of our understanding of the atomic structure of matter as it extends into the three spatial dimensions in which we describe the world around us. At the beginning of this century, the first atomic arrangements in salts, minerals and low-molecular-weight organic and metallo-organic compounds were unravelled. Then, initially one by one, but presently as an avalanche, the molecules of life were revealed in full glory at the atomic level with often astonishing accuracy, beginning in the 1950s when fibre diffraction first helped to resolve the structure of DNA, later the structures of polysaccharides, fibrous proteins, muscle and filamentous viruses. Subsequently, single-crystal methods became predominant and structures solved in the 1960s included myoglobin, haemoglobin and lysozyme, all of which were heroic achievements by teams of scientists, often building their own X-ray instruments, pioneering computational methods, and improving protein purification and crystallization procedures. Quite soon thereafter, in 1978, the three-dimensional structures of the first viruses were determined at atomic resolution. Less than ten years later, the mechanisms and structures of membrane proteins started to be unravelled. Presently, somewhere between five and ten structures of proteins are solved each day, about 85% by crystallographic procedures and about 15% by NMR methods. It is quite possible that within a decade the Protein Data Bank (PDB; Bernstein et al., 1977[link]) will receive a new coordinate set for a protein, RNA or DNA crystal structure every half hour. The resolution of protein crystal structures is improving dramatically and the size of the structures tackled is sometimes enormous: a virus with over a thousand subunits has been solved at atomic resolution (Grimes et al., 1995[link]) and the structure of the ribosome is on its way (Ban et al., 1999[link]; Cate et al., 1999[link]; Clemons et al., 1999[link]).

Macromolecular crystallography, discussed here in terms of its impact on medicine, is clearly making immense strides owing to a synergism of progress in many scientific disciplines including:

  • (a) Computer hardware and software: providing unprecedented computer power as well as instant access to information anywhere on the planet via the internet.

  • (b) Physics: making synchrotron radiation available with a wide range of wavelengths, very narrow bandwidths and very high intensities.

  • (c) Materials science and instrumentation: revolutionizing X-ray intensity measurements, with currently available charge-coupled-device detectors allowing protein-data collection at synchrotrons in tens of minutes, and with pixel array detectors on the horizon which are expected to collect a complete data set from a typical protein within a few seconds.

  • (d) Molecular biology: allowing the cloning, overexpression and modification of genes, with almost miraculous ease in many cases, resulting in a wide variety of protein variants, thereby enabling crystallization of `impossible' proteins.

  • (e) Genome sequencing: determining complete bacterial genomes in a matter of months. With several eukaryote genomes and the first animal genome already completed, and with the human genome expected to be completed to a considerable degree by 2000, protein crystallographers suddenly have an unprecedented choice of proteins to study, giving rise to the new field of structural genomics.

  • (f) Biochemistry and biophysics: providing a range of tools for rapid protein and nucleic acid purification by size, charge and affinity, and for characterization of samples by microsequencing, fluorescence, mass spectrometry, circular dichroism and dynamic light scattering procedures.

  • (g) Chemistry, in particular combinatorial chemistry: discovering by more and more sophisticated procedures high affinity inhibitors or binders to drug target proteins which are of great interest by themselves, while in addition such compounds tend to improve co-crystallization results quite significantly.

  • (h) Crystallography itself: constantly developing new tools including direct methods, multi-wavelength anomalous-dispersion phasing techniques, maximum-likelihood procedures in phase calculation and coordinate refinement, interactive graphics and automatic model-building programs, density-modification methods, and the extremely important cryo-cooling techniques for protein and nucleic acid crystals, to mention only some of the major achievements in the last decade.

Numerous aspects of these developments are treated in great detail in this volume of International Tables.

1.3.2. Crystallography and medicine

| top | pdf |

Knowledge of accurate atomic structures of small molecules, such as vitamin B12, steroids, folates and many others, has assisted medicinal chemists in their endeavours to modify many of these molecules for the combat of disease. The early protein crystallographers were well aware of the potential medical implication of the proteins they studied. Examples are the studies of the oxygen-carrying haemoglobin, the messenger insulin, the defending antibodies and the bacterial-cell-wall-lysing lysozyme. Yet, even by the mid-1980s, there were very few crystallographic projects which had the explicit goal of arriving at pharmaceutically active compounds (Hol, 1986[link]). Since then, however, we have witnessed an incredible increase in the number of projects in this area with essentially every major pharmaceutical company having a protein crystallography unit, while in academia and research institutions the potential usefulness of a protein structure is often combined with the novelty of the system under investigation. In one case, the HIV protease, it might well be that, worldwide, the structure has been solved over one thousand times – in complex with hundreds of different inhibitory compounds (Vondrasek et al., 1997[link]).

Impressive as these achievements are, this seems to be only the beginning of medicinal macromolecular crystallography. The completion of the human genome project will provide an irresistible impetus for `human structural genomics': the determination, as rapidly and systematically as possible, of as many human protein structures as possible. The genome sequences of most major infectious agents will be completed five years hence, if not sooner. This is likely to be followed up by `selected pathogen structural genomics', which will provide a wealth of pathogen protein structures for the design of new pharmaceuticals and probably also for vaccines.

This overview, written in late 1999, aims to convey some feel of the current explosion of `crystallography in medicine'. Ten, perhaps even five, years ago it might have been feasible to make an almost comprehensive list of all protein structures of potentially direct medical relevance. Today, this is virtually impossible. Here we mention only selected examples in the text with apologies to the crystallographers whose projects should also have been mentioned, and to the NMR spectroscopists and electron microscopists whose work falls outside the scope of this review. Tables 1.3.3.1[link] and 1.3.4.1[link] to 1.3.4.5[link] provide more information, yet do not claim to cover comprehensively this exploding field. Also, not all of the structures listed were determined with medical applications in mind, though they might be exploited for drug design one day. These tables show at the same time tremendous achievements as well as great gaps in our structural knowledge of proteins from humans and human pathogens.

1.3.3. Crystallography and genetic diseases

| top | pdf |

Presently, an immense number of genetic diseases have been characterized at the genetic level and archived in OMIM [On-line Mendelian Inheritance in Man. Center for Medical Genetics, Johns Hopkins University (Baltimore, MD) and the National Center for Biotechnology Information, National Library of Medicine (Bethesda, MD), 1999. URL: http://www.ncbi.nlm.nih.gov/omim/ ], with many more discoveries to occur in the next decades. Biomolecular crystallography has been very successful in explaining the cause of numerous genetic diseases at the atomic level. The stories of sickle cell anaemia, thalassemias and other deficiencies of haemoglobin set the stage (Dickerson & Geis, 1983[link]), followed by numerous other examples (Table 1.3.3.1[link]). Given the frequent occurrence of mutations in humans, it is likely that for virtually every structure of a human protein, a number of genetic diseases can be rationalized at the atomic level. Two investigations from the authors' laboratory may serve as examples:

  • (i) The severity of various cases of galactosialidosis – a lysosomal storage disease – could be related to the predicted effects of the amino-acid substitutions on the stability of human protective protein cathepsin A (Rudenko et al., 1998[link]).

    Table 1.3.3.1| top | pdf |
    Crystal structures and genetic diseases

    Crystal structureDiseaseReference
    Acidic fibroblast growth factor receptor Familial Pfeiffer syndrome [1]
    Alpha-1-antitrypsin Alpha-1-antitrypsin deficiency [2]
    Antithrombin III Hereditary thrombophilia [3], [4]
    Arylsulfatase A Leukodystrophy [5]
    Aspartylglucosaminidase Aspartylglusominuria [6]
    Beta-glucuronidase Sly syndrome [7]
    Branched-chain alpha-keto acid dehydrogenase Maple syrup urine syndrome, type Ia [39]
    Carbonic anhydrase II Guibaud–Vainsel syndrome, Marble brain disease [8]
    p53 Cancer [9], [10]
    Ceruloplasmin Hypoceruloplasminemia [11]
    Complement C3 C3 complement component 3 deficiency [12]
    Cystatin B Progressive myoclonus epilepsy [13]
    Factor VII Factor VII deficiency [14]
    Factor VIII Factor VIII deficiency [40]
    Factor X Factor X deficiency (Stuart–Prower factor deficiency) [15]
    Factor XIII Factor XIII deficiency [16]
    Fructose-1,6-bisphosphate aldolase Fructose intolerance (fructosemia) [41]
    Gelsolin Amyloidosis V [17]
    Growth hormone Growth hormone deficiency [18]
    Haemochromatosis protein HFE Hereditary haemochromatosis [19]
    Haemoglobin Beta-thalassemia, sickle-cell anaemia [20]
    Tyrosine hydroxylase Hereditary Parkinsonism [21]
    Hypoxanthine–guanine phosphoribosyltransferase Lesch–Nyhan syndrome [22]
    Insulin Hyperproinsulinemia, diabetes [42]
    Isovaleryl–coenzyme A dehydrogenase Isovaleric acid CoA dehydrogenase deficiency [23]
    Lysosomal protective protein Galactosialidosis [24]
    Ornithine aminotransferase Ornithine aminotransferase deficiency [25]
    Ornithine transcarbamoylase Ornithine transcarbamoylase deficiency [43]
    p16INK4a tumour suppressor Cancer [26]
    Phenylalanine hydroxylase Phenylketonuria [27]
    Plasminogen Plasminogen deficiency [28], [29], [30]
    Protein C Protein C deficiency [31]
    Purine nucleotide phosphorylase Purine nucleotide phosphorylase deficiency [32]
    Serum albumin Dysalbuminemic hyperthyroxinemia [33]
    Superoxide dismutase (Cu, Zn-dependent) Familial amyotrophical lateral sclerosis [34]
    Thrombin Hypoprothrombinemia, dysprothrombinemia [35]
    Transthyretrin Amyloidosis I [36]
    Triosephosphate isomerase Triosephosphate isomerase deficiency [37]
    Trypsinogen Hereditary pancreatitis [38]

    References: [1] Blaber et al. (1996)[link]; [2] Loebermann et al. (1984)[link]; [3] Carrell et al. (1994)[link]; [4] Schreuder et al. (1994)[link]; [5] Lukatela et al. (1998)[link]; [6] Oinonen et al. (1995)[link]; [7] Jain et al. (1996)[link]; [8] Liljas et al. (1972)[link]; [9] Cho et al. (1994)[link]; [10] Gorina & Pavletich (1996)[link]; [11] Zaitseva et al. (1996)[link]; [12] Nagar et al. (1998)[link]; [13] Stubbs et al. (1990)[link]; [14] Banner et al. (1996)[link]; [15] Padmanabhan et al. (1993)[link]; [16] Yee et al. (1994)[link]; [17] McLaughlin et al. (1993)[link]; [18] DeVos et al. (1992)[link]; [19] Lebron et al. (1998)[link]; [20] Harrington et al. (1997)[link]; [21] Goodwill et al. (1997)[link]; [22] Eads et al. (1994)[link]; [23] Tiffany et al. (1997)[link]; [24] Rudenko et al. (1995)[link]; [25] Shah et al. (1997)[link]; [26] Russo et al. (1998)[link]; [27] Erlandsen et al. (1997)[link]; [28] Mulichak et al. (1991)[link]; [29] Mathews et al. (1996)[link]; [30] Chang, Mochalkin et al. (1998)[link]; [31] Mather et al. (1996)[link]; [32] Ealick et al. (1990)[link]; [33] He & Carter (1992)[link]; [34] Parge et al. (1992)[link]; [35] Bode et al. (1989)[link]; [36] Blake et al. (1978)[link]; [37] Mande et al. (1994)[link]; [38] Gaboriaud et al. (1996)[link]; [39] Ævarsson et al. (2000[link]); [40] Pratt et al. (1999[link]); [41] Gamblin et al. (1990[link]); [42] Bentley et al. (1976[link]); [43] Shi et al. (1998[link]).
  • (ii) The modification of Tyr393α to Asn in the branched-chain 2-oxo acid dehydrogenase occurs at the interface of the α and β subunits in this [\alpha_{2}\beta_{2}] heterotetramer, providing a nice explanation of the `mennonite' variants of maple syrup urine disease (MSUD) (Ævarsson et al., 2000[link]).

Impressive as the insights obtained into the causes of diseases like these might be, there is almost a sense of tragedy associated with this detailed understanding of a serious, sometimes fatal, afflictions at the atomic and three-dimensional level: there is often so little one can do with this knowledge. There are at least two, very different, reasons for this. The first reason is that turning a malfunctioning protein or nucleic acid into one that functions properly is notoriously difficult. Treatment would generally require the oral use of small molecules that somehow counteract the effect of the mutation, i.e. the administration of the small molecule has to result in a functional complex of the drug with the mutant protein. This is in almost all cases far more difficult than finding compounds that block the activity of a protein or nucleic acid – which is the way in which most current drugs function. The second reason for the paucity of drugs for treating genetic diseases is very different in nature: the number of patients suffering from a particular mutation responsible for a genetic disease is very small in most cases. This means that market forces do not encourage funding the expensive steps of testing the toxicity and efficacy of potentially pharmaceutically active compounds. One of several exceptions is sickle cell anaemia, where significant efforts have been made to arrive at pharmaceutically active agents (Rolan et al., 1993[link]). In this case the mutation Glu6βVal leads to deoxyhaemoglobin polymerization via the hydrophobic valine. In spite of several ingenious approaches based on the allosteric properties of haemoglobin (Wireko & Abraham, 1991[link]), no successful compound seems to be on the horizon yet for the treatment of sickle cell anaemia.

More recently, the spectacular molecular mechanisms underlying genetic serpin deficiency diseases have been elucidated. A typical example is α1-antitrypsin deficiency, which leads to cirrhosis and emphysema. Normal α1-antitrypsin, a serine protease inhibitor, exposes a peptide loop as a substrate for the cognate proteinase in its active but metastable conformation. After cleavage of the loop, the protease becomes trapped as an acyl-enzyme with the serpin, and the cleaved serpin loop inserts itself as the central strand of one of the serpin β-sheets, accompanied by a dramatic change in protein stability. In certain mutant serpins, however, the exposed loop is conformationally more metastable and occasionally inserts itself into the β-sheet of a neighbouring serpin molecule, thereby forming serpin polymers with disastrous consequences for the patient (Carrell & Gooptu, 1998[link]). In vitro, the polymerization of α1-antitrypsin can be reversed with synthetic homologues of the exposed peptide loop (Skinner et al., 1998[link]). This approach might be useful for other `conformational diseases', which include Alzheimer's and other neurodegenerative disorders.

Another frequently occurring genetic disease is cystic fibrosis. Here we face a more complex situation than that in the case of sickle cell anaemia: a range of different mutations causes a malfunctioning of the same ion channel, which, consequently, leads to a range of severity of the disease (Collins, 1992[link]). Protein crystallography is currently helpful in an indirect way in alleviating the problems of cystic fibrosis patients, not by studying the affected ion channel itself, but by revealing the structure of leukocyte elastase (Bode et al., 1986[link]), an enzyme responsible for much of the cellular damage associated with cystic fibrosis (Birrer, 1995[link]). On the basis of the elastase structure, inhibitors were developed to combat the effects of the impaired ion channel (Warner et al., 1994[link]). Also, structures of key enzymes of Pseudomonas aeruginosa, a bacterium affecting many cystic fibrosis patients, form a basis for the design of therapeutics to treat infections by this pathogen. Yet, to the best of our knowledge, no compound has been developed so far that repairs the malfunctioning ion channel.

However, in some cases there might be more opportunities than assumed so far. Several mutations leading to genetic diseases result in a lack of stability of the affected protein. In instances when the mutant protein is still stable enough to fold, small molecules could conceivably be discovered that bind `anywhere' to a pocket of these proteins, thereby stabilizing the protein. The same small molecule could even be able to increase the stability of proteins with different mildly destabilizing mutations. Such an approach, though not trivial by any means, might be worth pursuing. Proof of principle of this concept has recently been provided for several unstable p53 mutants, where the same small molecule enhanced the stability of different mutants (Foster et al., 1999[link]).

Of course, mutations that destroy cofactor binding or active sites, or destroy proper recognition of partner proteins, will be extremely difficult to correct by small molecules targeting the affected protein. In such instances, gene therapy is likely to be the way by which our and the next generation may be able to improve the lives of future generations.

1.3.4. Crystallography and development of novel pharmaceuticals

| top | pdf |

The impact of detailed knowledge of protein and nucleic acid structures on the design of new drugs has already been significant, and promises to be of tremendous importance in the next decades. The first structure of a known major drug bound to a target protein was probably that of methotrexate bound to dihydrofolate reductase (DHFR) (Matthews et al., 1977[link]). Even though the source of the enzyme was bacterial while methotrexate is used as a human anticancer agent, this protein–drug complex structure was nevertheless a hallmark achievement. It is generally accepted that the first protein-structure-inspired drug actually reaching the market was captopril, which is an antihypertensive compound blocking the action of angiotensin-converting enzyme, a metalloprotease. In this case, the structure of zinc-containing carboxypeptidase A was a guide to certain aspects of the chemical modification of lead compounds (Cushman & Ondetti, 1991[link]). This success has been followed up by numerous projects specifically aimed at the design of new inhibitors, or activators, of carefully selected drug targets.

Structure-based drug design (SBDD) (Fig. 1.3.4.1[link]) is the subject of several books and reviews that summarize projects and several success stories up until the mid-1990s (Kuntz, 1992[link]; Perutz, 1992[link]; Verlinde & Hol, 1994[link]; Whittle & Blundell, 1994[link]; Charifson, 1997[link]; Veerapandian, 1997[link]). Possibly the most dramatic impact made by SBDD has been on the treatment of AIDS, where the development of essentially all of the protease inhibitors on the market in 1999 has been guided by, or at least assisted by, the availability of numerous crystal structures of protease–inhibitor complexes.

[Figure 1.3.4.1]

Figure 1.3.4.1 | top | pdf |

The structure-based drug design cycle.

The need for a large number of structures is common in all drug design projects and is due to several factors. One is the tremendous challenge for theoretical predictions of the correct binding mode and affinity of inhibitors to proteins. The current force fields are approximate, the properties of water are treacherous, the flexibility of protein and ligands lead quickly to a combinatorial explosion, and the free-energy differences between various binding modes are small. All this leads to the need for several experimental structures in a structure-based drug design cycle (Fig. 1.3.4.1[link]). In this cycle, numerous disciplines are interacting in multiple ways. Many institutions, small and large, are following in one way or another this paradigm to speed up the lead discovery, lead optimization and even the bioavailability improvement steps in the drug development process. Moreover, a very powerful synergism exists between combinatorial chemistry and structure-based drug design. Structure-guided combinatorial libraries can utilize knowledge of ligand target sites in the design of the library [see e.g. Ferrer et al. (1999[link]), Eckert et al. (1999[link]) and Minke et al. (1999[link])]. Once tight-binding ligands are found by combinatorial methods, crystal structures of library compound–target complexes provide detailed information for new highly specific libraries.

The fate of a drug candidate during clinical tests can hinge on a single methyl group – just as a point mutation can alter the benefit of a wild-type protein molecule into the nightmare of a life-long genetic disease. Hence, many promising inhibitors eventually fail to be of benefit to patients. Nevertheless, knowledge of a series of protein structures in complex with inhibitors is of immense value in the design and development of future pharmaceuticals. In the following sections some examples will be looked at.

1.3.4.1. Infectious diseases

| top | pdf |

1.3.4.1.1. Viral diseases

| top | pdf |

Some icosahedral pathogenic viruses have all their capsid proteins elucidated, while for the more complex viruses like influenza virus, hepatitis C virus (HCV) and HIV, numerous individual protein structures have been solved (Table 1.3.4.1[link]). However, not all 14 native proteins of the HIV genome have yet surrendered to the crystallographic community, nor to the NMR spectroscopists or the high-resolution electron microscopists, our partners in experimental structural biology (Turner & Summers, 1999[link]). Nevertheless, the structures of HIV protease, reverse transcriptase and fragments of HIV integrase and of HIV viral core and surface proteins are of tremendous value for developing novel anti-AIDS therapeutics [Arnold et al., 1996[link]; Lin et al., 1998[link]; Wlodawer & Vondrasek, 1998[link]; see also references in Table 1.3.4.1(a)[link]]. A similar situation occurs for hepatitis C virus. The protease structure of this virus has been solved recently (simultaneously by four groups!), as well as its helicase structure, providing platforms on the basis of which the design of novel drugs is actively pursued (Le et al., 1998[link]).

Table 1.3.4.1| top | pdf |
Important human pathogenic viruses and their proteins

(a) RNA viruses

(i) Single-stranded

FamilyExampleProtein structures solvedReference
Arenaviridae Lassa fever virus None  
Bunyaviridae Hantavirus None  
Caliciviridae Hepatitis E virus, Norwalk virus None  
Coronaviridae Corona virus None  
Deltaviridae Hepatitis D virus Oligomerization domain of antigen [1]
Filoviridae Ebola virus GP2 of membrane fusion glycoprotein [2]
Flaviviridae Dengue NS3 protease [3]
Hepatitis C NS3 protease [4], [5]
RNA helicase [6]
Yellow fever None  
Tick-borne encephalitis virus Envelope glycoprotein [7]
Orthomyxoviridae Influenza virus Neuraminidase [8]
Haemagglutinin [9]
Matrix protein M1 [10]
Paramyxoviridae Measles, mumps, parainfluenza, respiratory syncytial virus None  
Picornaviridae Hepatitis A virus 3C protease [11]
Poliovirus Capsid [12]
RNA-dependent polymerase [13]
Rhinovirus Capsid [14]
3C protease [15]
Echovirus Capsid [16]
Retroviridae HIV Capsid protein [17]
Matrix protein [18]
Protease [19], [20], [21]
Reverse transcriptase [22], [23], [47], [48], [49]
Integrase [24]
gp120 [25]
NEF [26]
gp41 [27]
Rhabdovirus Rabies virus None  
Togaviridae Rubella None  

(ii) Double-stranded

FamilyExampleProtein structures solvedReference
Reoviridae Rotavirus None  

(b) DNA viruses

(i) Single-stranded

FamilyExampleProtein structures solvedReference
Parvoviridae B 19 virus None  

(ii) Double-stranded

FamilyExampleProtein structures solvedReference
Adenoviridae Adenovirus Protease [28]
Capsid [29]
Knob domain of fibre protein [30]
Hepadnaviridae Hepatitis B Capsid [31]
Herpesviridae Cytomegalovirus Protease [32], [33], [34]
Epstein–Barr virus Domains of nuclear antigen 1 [35]
BCRF1 [36]
Herpes simplex Protease [37]
Thymidine kinase [38]
Uracyl-DNA glycosylase [39]
Core of VP16 [40]
Varicella zoster Protease [42]
Papovaviridae Papillomavirus DNA-binding domain of E2 [43]
Activation domain of E2 [44]
Poxviridae Smallpox virus None  
Vaccinia virus (related to smallpox but non-pathogenic) Methyltransferase VP39 [45]
Domain of topoisomerase [46]

References: [1] Zuccola et al. (1998)[link]; [2] Weissenhorn et al. (1998)[link]; [3] Murthy et al. (1999)[link]; [4] Love et al. (1996)[link]; [5] Yan et al. (1998)[link]; [6] Yao et al. (1997)[link]; [7] Rey et al. (1995)[link]; [8] Varghese et al. (1983)[link]; [9] Wilson et al. (1981)[link]; [10] Sha & Luo (1997)[link]; [11] Allaire et al. (1994)[link]; [12] Hogle et al. (1985)[link]; [13] Hansen et al. (1997)[link]; [14] Rossmann et al. (1985)[link]; [15] Matthews et al. (1994)[link]; [16] Filman et al. (1998)[link]; [17] Worthylake et al. (1999)[link]; [18] Hill et al. (1996)[link]; [19] Navia, Fitzgerald et al. (1989)[link]; [20] Wlodawer et al. (1989)[link]; [21] Erickson et al. (1990)[link]; [22] Rodgers et al. (1995)[link]; [23] Ding et al. (1995)[link]; [24] Dyda et al. (1994)[link]; [25] Kwong et al. (1998)[link]; [26] Lee et al. (1996)[link]; [27] Chan et al. (1997)[link]; [28] Ding et al. (1996)[link]; [29] Roberts et al. (1986)[link]; [30] Xia et al. (1994)[link]; [31] Wynne et al. (1999)[link]; [32] Tong et al. (1996)[link]; [33] Qiu et al. (1996)[link]; [34] Shieh et al. (1996)[link]; [35] Bochkarev et al. (1995)[link]; [36] Zdanov et al. (1997)[link]; [37] Hoog et al. (1997)[link]; [38] Wild et al. (1995)[link]; [39] Savva et al. (1995)[link]; [40] Liu et al. (1999)[link]; [42] Qiu et al. (1997)[link]; [43] Hegde & Androphy (1998)[link]; [44] Harris & Botchan (1999)[link]; [45] Hodel et al. (1996)[link]; [46] Sharma et al. (1994)[link]; [47] Kohlstaedt et al. (1992[link]); [48] Jacobo-Molina et al. (1993[link]); [49] Ren et al. (1995[link]).

A quite spectacular example of how structural knowledge can lead to the synthesis of powerful inhibitors is provided by influenza virus neuraminidase. The structure of a neuraminidase–transition-state analogue complex suggested the addition of positively charged amino and guanidinium groups to the C4 position of the analogue, which resulted, in one step, in a gain of four orders of magnitude in binding affinity for the target enzyme (von Itzstein et al., 1993[link]).

1.3.4.1.2. Bacterial diseases

| top | pdf |

A very large number of structures of important drug target proteins of bacterial origin have been solved crystallographically (Table 1.3.4.2[link]). Currently, the most important single infectious bacterial agent is Mycobacterium tuberculosis, with three million deaths and eight million new cases annually (Murray & Salomon, 1998[link]). The crystal structures of several M. tuberculosis potential and proven drug target proteins have been elucidated (Table 1.3.4.2[link]). The complete M. tuberculosis genome has been sequenced recently (Cole et al., 1998[link]), and this will undoubtedly have a tremendous impact on future drug development.

Table 1.3.4.2| top | pdf |
Protein structures of important human pathogenic bacteria

OrganismDisease(s)Protein structures solvedReference
Staphylococcus aureus Abscesses Alpha-haemolysin [1]
Endocarditis Aureolysin [2]
Gastroenteritis Beta-lactamase [3]
Toxic shock syndrome Collagen adhesin [4]
7,8-Dihydroneopterin aldolase [5]
Dihydropteroate synthetase [6]
Enterotoxin A [7]
Enterotoxin B [8]
Enterotoxin C2 [9]
Enterotoxin C3 [10]
Exfoliative toxin A [11]
Ile-tRNA-synthetase [12]
Kanamycin nucleotidyltransferase [13]
Leukocidin F [14]
Nuclease [15]
Staphopain [16]
Staphylokinase [17]
Toxic shock syndrome toxin-1 [18]
Staphylococcus epidermidis Implant infections None  
Enterococcus faecalis Urinary tract and biliary tract infections NADH peroxidase [19]
(Streptococcus faecalis)   Histidine-containing phosphocarrier protein [20]
Streptococcus mutans Endocarditis Glyceraldehyde-3-phosphate dehydrogenase [21]
Streptococcus pneumoniae Pneumonia Penicillin-binding protein PBP2x [22]
Meningitis, upper respiratory tract infections Dpnm DNA adenine methyltransferase [23]
Streptococcus pyogenes Pharyngitis Inosine monophosphate dehydrogenase [24]
Scarlet fever, toxic shock syndrome, immunologic disorders (acute glomerulonephritis and rheumatic fever) Pyrogenic exotoxin C [25]
Bacillus anthracis Anthrax Anthrax protective antigen [26]
Bacillus cereus Food poisoning Beta-amylase [27]
Beta-lactamase II [28]
Neutral protease [29]
Oligo-1,6-glucosidase [30]
Phospholipase C [31]
Clostridium botulinum Botulism Neurotoxin type A [32]
Clostridium difficile Pseudomembranous colitis None  
Clostridium perfringens Gas gangrene Alpha toxin [33]
Food poisoning Perfringolysin O [34]
Clostridium tetani Tetanus Toxin C fragment [35]
Corynebacterium diphtheriae Diphtheria Toxin [36]
Toxin repressor [37]
Listeria monocytogenes Meningitis, sepsis Phosphatidylinositol-specific phospholipase C [38]
Actinomyces israelii Actinomycosis None  
Nocardia asteroides Nocardiosis None  
Neisseria gonorrhoeae Gonorrhea Type 4 pilin [39]
Carbonic anhydrase [40]
Neisseria meningitidis Meningitis Dihydrolipoamide dehydrogenase [41]
Bordetella pertussis Whooping cough Toxin [42]
Virulence factor P.69 [43]
Brucella sp. Brucellosis None  
Campylobacter jejuni Enterocolitis None  
Enterobacter cloacae Urinary tract infection, pneumonia Beta-lactamase: class C [44]
UDP-N-acetylglucosamine enolpyruvyltransferase [45]
Escherichia coli      
 ETEC (enterotoxigenic) Traveller's diarrhoea Heat-labile enterotoxin [46]
Heat-stable enterotoxin (is a peptide) [47]
 EHEC (enterohaemorrhagic) HUS Verotoxin-1 [48]
 EPEC (enteropathogenic) Diarrhoea None  
 EAEC (enteroaggregative) Diarrhoea None  
 EIEC (enteroinvasive) Diarrhoea None  
 UPEC (uropathogenic)   FimH adhesin [49]
FimC chaperone [49]
PapD [50]
 NMEC (neonatal meningitis) Meningitis None  
Franciscella tularensis Tularemia None  
Haemophilus influenzae Meningitis, otitis media, pneumonia Diaminopimelate epimerase [51]
6-Hydroxymethyl-7,8-dihydropterin pyrophosphokinase [52]
Ferric iron binding protein Mirp [53]
Klebsiella pneumoniae Urinary tract infection, pneumonia, sepsis β-Lactamase SHV-1 [54]
Legionella pneumophila Pneumonia None  
Pasteurella multocida Wound infection None  
Proteus mirabilis Pneumonia, urinary tract infection Catalase [55]
Glutathione S-transferase [56]
Proteus vulgaris Urinary tract infections Pvu II DNA-(cytosine N4) methyltransferase [57]
Pvu II endonuclease [58]
Tryptophanase [59]
Salmonella typhi Typhoid fever None, but many for S. typhimurium linked with zoonotic disease  
Salmonella enteridis Enterocolitis None  
Serratia marcescens Pneumonia, urinary tract infection Serralysin [60]
Aminoglycoside 3-N-acetyltransferase [61]
Chitinase A [62]
Chitobiase [63]
Endonuclease [64]
Hasa (haemophore) [65]
Prolyl aminopeptidase [66]
Shigella sp. Dysentery Chloramphenicol acetyltransferase [67]
Shiga-like toxin I [68]
Vibrio cholerae Cholera Cholera toxin [69], [70]
DSBA oxidoreductase [71]
Neuraminidase [104]
Yersinia enterocolitica Enterocolitis Protein-Tyr phosphatase YOPH [72]
Yersinia pestis Plague None  
Pseudomonas aeruginosa Wound infection, urinary tract infection, pneumonia, sepsis Alkaline metalloprotease [73]
Amidase operon [74]
Azurin [75]
Cytochrome 551 [76]
Cytochrome c peroxidase [77]
Exotoxin A [78]
p-Hydroxybenzoate hydroxylase [79]
Hexapeptide xenobiotic acetyltransferase [80]
Mandelate racemase [81]
Nitrite reductase [82]
Ornithine transcarbamoylase [83]
Porphobilinogen synthase [84]
Pseudolysin [85]
Burkholderia cepacia Wound infection, urinary tract infection, pneumonia, sepsis Biphenyl-cleaving extradiol dioxygenase [86]
cis-Biphenyl-2,3-dihydrodiol-2,3-dehydrogenase [87]
Dialkylglycine decarboxylase [88]
Lipase [89]
Phthalate dioxygenase reductase [90]
Stenotrophomonas maltophilia (= Pseudomonas maltophilia) Sepsis None  
Bacteroides fragilis Intra-abdominal infections Beta-lactamase type 2 [91]
Mycobacterium leprae Leprosy Chaperonin-10 (GroES homologue) [92]
RUVA protein [93]
Mycobacterium tuberculosis Tuberculosis 3-Dehydroquinate dehydratase [94]
Dihydrofolate reductase [95]
Dihydropteroate synthase [96]
Enoyl acyl-carrier-protein reductase (InhA) [97]
Mechanosensitive ion channel [98]
Quinolinate phosphoribosyltransferase [99]
Superoxide dismutase (iron dependent) [100]
Iron-dependent repressor  
Mycobacterium bovis Tuberculosis Tetrahydrodipicolinate-N-succinyltransferase [102]
Chlamydia psitacci Psittacosis None  
Chlamydia pneumoniae Atypical pneumonia None  
Chlamydia trahomatis Ocular, respiratory and genital infections None  
Coxiella burnetii Q fever None  
Rickettsia sp. Rocky Mountain spotted fever None  
Borrelia burgdorferi Lyme disease Outer surface protein A [103]
Leptospira interrogans Leptospirosis None  
Treponema pallidum Syphilis None  
Mycoplasma pneumoniae Atypical pneumonia None  

References: [1] Song et al. (1996)[link]; [2] Banbula et al. (1998)[link]; [3] Herzberg & Moult (1987)[link]; [4] Symersky et al. (1997)[link]; [5] Hennig et al. (1998)[link]; [6] Hampele et al. (1997)[link]; [7] Sundstrom et al. (1996)[link]; [8] Papageorgiou et al. (1998)[link]; [9] Papageorgiou et al. (1995)[link]; [10] Fields et al. (1996)[link]; [11] Vath et al. (1997)[link]; [12] Silvian et al. (1999)[link]; [13] Pedersen et al. (1995)[link]; [14] Pedelacq et al. (1999)[link]; [15] Loll & Lattman (1989)[link]; [16] Hofmann et al. (1993)[link]; [17] Rabijns et al. (1997)[link]; [18] Prasad et al. (1993)[link]; [19] Yeh et al. (1996)[link]; [20] Jia et al. (1993)[link]; [21] Cobessi et al. (1999)[link]; [22] Pares et al. (1996)[link]; [23] Tran et al. (1998)[link]; [24] Zhang, Evans et al. (1999)[link]; [25] Roussel et al. (1997)[link]; [26] Petosa et al. (1997)[link]; [27] Mikami et al. (1999)[link]; [28] Carfi et al. (1995)[link]; [29] Pauptit et al. (1988)[link]; [30] Watanabe et al. (1997)[link]; [31] Hough et al. (1989)[link]; [32] Lacy et al. (1998)[link]; [33] Naylor et al. (1998)[link]; [34] Rossjohn, Feil, McKinstry et al. (1997)[link]; [35] Umland et al. (1997)[link]; [36] Choe et al. (1992)[link]; [37] Qiu et al. (1995)[link]; [38] Moser et al. (1997)[link]; [39] Parge et al. (1995)[link]; [40] Huang, Xue et al. (1998)[link]; [41] Li de la Sierra et al. (1997)[link]; [42] Stein et al. (1994)[link]; [43] Emsley et al. (1996)[link]; [44] Lobkovsky et al. (1993)[link]; [45] Schonbrunn et al. (1996)[link]; [46] Sixma et al. (1991)[link]; [47] Ozaki et al. (1991)[link]; [48] Stein et al. (1992)[link]; [49] Choudhury et al. (1999)[link]; [50] Sauer et al. (1999)[link]; [51] Cirilli et al. (1993)[link]; [52] Hennig et al. (1999)[link]; [53] Bruns et al. (1997)[link]; [54] Kuzin et al. (1999)[link]; [55] Gouet et al. (1995)[link]; [56] Rossjohn, Polekhina et al. (1998)[link]; [57] Gong et al. (1997)[link]; [58] Athanasiadis et al. (1994)[link]; [59] Isupov et al. (1998)[link]; [60] Baumann (1994)[link]; [61] Wolf et al. (1998)[link]; [62] Perrakis et al. (1994)[link]; [63] Tews et al. (1996)[link]; [64] Miller et al. (1994)[link]; [65] Arnoux et al. (1999)[link]; [66] Yoshimoto et al. (1999)[link]; [67] Murray et al. (1995)[link]; [68] Ling et al. (1998)[link]; [69] Merritt et al. (1994)[link]; [70] Zhang et al. (1995)[link]; [71] Hu et al. (1997)[link]; [72] Stuckey et al. (1994)[link]; [73] Miyatake et al. (1995)[link]; [74] Pearl et al. (1994)[link]; [75] Adman et al. (1978)[link]; [76] Almassy & Dickerson (1978)[link]; [77] Fulop et al. (1995)[link]; [78] Allured et al. (1986)[link]; [79] Gatti et al. (1994)[link]; [80] Beaman et al. (1998)[link]; [81] Kallarakal et al. (1995)[link]; [82] Nurizzo et al. (1997)[link]; [83] Villeret et al. (1995)[link]; [84] Frankenberg et al. (1999)[link]; [85] Thayer et al. (1991)[link]; [86] Han et al. (1995)[link]; [87] Hulsmeyer et al. (1998)[link]; [88] Toney et al. (1993)[link]; [89] Kim et al. (1997)[link]; [90] Correll et al. (1992)[link]; [91] Concha et al. (1996)[link]; [92] Mande et al. (1996)[link]; [93] Roe et al. (1998)[link]; [94] Gourley et al. (1999)[link]; [95] Li et al. (2000[link]); [96] Baca et al. (2000[link]); [97] Dessen et al. (1995)[link]; [98] Chang, Spencer et al. (1998)[link]; [99] Sharma et al. (1998)[link]; [100] Cooper et al. (1995)[link]; [102] Beaman et al. (1997)[link]; [103] Li et al. (1997)[link]; [104] Crennell et al. (1994[link]).

The crystal structures of many bacterial dihydrofolate reductases, the target of several antimicrobials including trimethoprim, have also been reported. Recently, the atomic structure of dihydropteroate synthase (DHPS), the target of sulfa drugs, has been elucidated, almost 60 years after the first sulfa drugs were used to treat patients (Achari et al., 1997[link]; Hampele et al., 1997[link]).

A very special set of bacterial proteins are the toxins. Some of these have dramatic effects, with even a single molecule able to kill a host cell. These toxins outsmart and (mis)use many of the defence systems of the host, and their structures are often most unusual and fascinating, as recently reviewed by Lacy & Stevens (1998[link]). The structures of the toxins are actively used for the design of proph­ylactics and therapeutic agents to treat bacterial diseases [see e.g. Merritt et al. (1997[link]), Kitov et al. (2000[link]) and Fan et al. (2000[link])]. It is remarkable that the properties of these devastating toxins are also used, or at least considered, for the treatment of disease, such as in the engineering of diphtheria toxin to create immunotoxins for the treatment of cancer and the deployment of cholera toxin mutants as adjuvants in mucosal vaccines. Knowledge of the three-dimensional structures of these toxins assists in the design of new thera­peut­ically useful proteins.

1.3.4.1.3. Protozoan infections

| top | pdf |

A major cause of death and worldwide suffering is due to infections by several protozoa, including:

  • (a) Plasmodium falciparum and related species, causing various forms of malaria;

  • (b) Trypanosoma cruzi, the causative agent of Chagas' disease in Latin America;

  • (c) Trypanosoma brucei, causing sleeping sickness in Africa;

  • (d) Some eleven different Leishmania species, responsible for several of the most horribly disfiguring diseases known to mankind.

Drug resistance, combined with other factors, has been the cause of a major disappointment for the early hopes of a `malaria eradication campaign'. Fortunately, new initiatives have been launched recently under the umbrella of the `Malaria roll back' program and the `Multilateral Initiative for Malaria' (MIM). We are facing a formidable challenge, however, since the parasite is very clever at evading the immune response of the human host. Drugs are the mainstay of current treatments and may well be so for a long time to come. Protein crystallographic studies of Plasmodium proteins are hampered by the unusual codon usage of the Plasmodium species, coupled with a tendency to contain insertions of numerous hydrophilic residues in the polypeptide chain (Gardner et al., 1998[link]) which provide sometimes serious obstacles to obtaining large amounts of Plasmodium proteins for structural investigations.

However, the structures of an increasing number of potential drug targets from these protozoan parasites are being unravelled. These include the variable surface glycoproteins (VSGs) and glycolytic enzymes of Trypanosoma brucei, crucial malaria proteases, and the remarkable trypanothione reductase (Table 1.3.4.3[link]). The structures of nucleotide phosphoribosyl transferases of a variety of protozoan parasites have also been elucidated. Moreover, the structure of DHFR from Pneumocystis carinii, the major opportunistic pathogen in AIDS patients in the United States, has been determined. Several of these structures are serving as starting points for the development of new drugs.

Table 1.3.4.3| top | pdf |
Protein structures of important human pathogenic protozoa, fungi and helminths

(a) Protozoa

OrganismDiseaseProtein structures solvedReference
Acanthamoeba sp. Opportunistic meningoencephalitis, corneal ulcers Actophorin [1]
Profilin [2]
Cryptosporidium parvum Cryptosporidiosis None  
Entamoeba histolytica Amoebic dysentery, liver abscesses None  
Giardia lamblia Giardiasis None  
Leishmania sp. Leishmaniasis Adenine phosphoribosyltransferase [3]
Dihydrofolate reductase-thymidylate synthase [4]
Glyceraldehyde-3-phosphate dehydrogenase [5]
Leishmanolysin [6]
Nucleoside hydrolase [7]
Pyruvate kinase [8]
Triosephosphate isomerase [9]
Plasmodium sp. Malaria Fructose-1,6-bisphosphate aldolase [10]
Lactate dehydrogenase [11]
MSP1 [12]
Plasmepsin II [13]
Purine phosphoribosyltransferase [14]
Triosephosphate isomerase [15]
Pneumocystis carinii Pneumonia Dihydrofolate reductase [16]
Toxoplasma gondii Toxoplasmosis HGXPRTase [17]
UPRTase [18]
Trichomonas vaginalis Trichomoniasis None  
Trypanosoma brucei Sleeping sickness Fructose-1,6-bisphosphate aldolase [19]
Glyceraldehyde-3-phosphate dehydrogenase [20]
6-Phosphogluconate dehydrogenase [21]
Phosphoglycerate kinase [22]
Triosephosphate isomerase [23]
VSG [24]
Trypanosoma cruzi Chagas' disease Cruzain (cruzipain) [25]
Glyceraldehyde-3-phosphate dehydrogenase [26]
Hypoxanthine phosphoribosyltransferase [27]
Triosephosphate isomerase [28]
Trypanothione reductase [29]
Tyrosine aminotransferase [30]

(b) Fungi

OrganismDiseaseProtein structures solvedReference
Aspergillus fumigatus Aspergillosis Restrictocin [31]
Blastomyces dermatidis Blastomycosis None  
Candida albicans Candidiasis Dihydrofolate reductase [32]
N-Myristoyl transferase [33]
Phosphomannose isomerase [34]
Secreted Asp protease [35]
Coccidiodes immitis Coccidioidomycosis None  
Cryptococcus neoformans Cryptococcosis None  
Histoplasma capsulatum Histoplasmosis None  
Mucor sp. Mucormycosis None  
Paracoccidioides brasiliensis Paracoccidioidomycosis None  
Rhizopus sp. Phycomycosis Lipase II [36]
Rhizopuspepsin [37]
RNase Rh [38]

(c) Helminths

OrganismDiseaseProtein structures solvedReference
Clonorchis sinensis Clonorchiasis None  
Fasciola hepatica Fasciolasis Glutathione S-transferase [39]
Fasciolopsis buski Fasciolopsiasis None  
Paragominus westermani Paragonimiasis None  
Schistosoma sp. Schistosomiasis Glutathione S-transferase [39], [40]
Hexokinase [41]
Diphyllobotrium latum Diphyllobothriasis None  
Echinococcus granulosus Unilocular hydatid cyst disease None  
Taenia saginata Taeniasis None  
Taenia solium Taeniasis None  
Ancylostoma duodenale Old World hookworm disease None  
Anisakis Anisakiasis None  
Ascaris lumbricoides Ascariasis Haemoglobin [42]
Major sperm protein [43]
Trypsin inhibitor [44]
Enterobius vermicularis Pinworm infection None  
Necator New World hookworm disease None  
Strongyloides stercoralis Strongyloidiasis None  
Trichinella spiralis Trichinosis None  
Trichuris trichiura Whipworm infection None  
Brugia malayi Filariasis Peptidylprolyl isomerase [45], [46]
Dracunculus medinensis Guinea worm disease None  
Loa loa Loiasis None  
Onchocerca volvulus River blindness None  
Toxocara canis Visceral larva migrans None  
Wuchereria bancrofti Lymphatic filariasis (elephantiasis) None  

References: [1] Leonard et al. (1997)[link]; [2] Liu et al. (1998)[link]; [3] Phillips et al. (1999)[link]; [4] Knighton et al. (1994)[link]; [5] Kim et al. (1995)[link]; [6] Schlagenhauf et al. (1998)[link]; [7] Shi, Schramm & Almo (1999)[link]; [8] Rigden et al. (1999)[link]; [9] Williams et al. (1999)[link]; [10] Kim et al. (1998)[link]; [11] Read et al. (1999)[link]; [12] Chitarra et al. (1999)[link]; [13] Silva et al. (1996)[link]; [14] Shi, Li et al. (1999)[link]; [15] Velanker et al. (1997)[link]; [16] Champness et al. (1994)[link]; [17] Schumacher et al. (1996)[link]; [18] Schumacher et al. (1998)[link]; [19] Chudzik et al. (2000[link]); [20] Vellieux et al. (1993)[link]; [21] Phillips et al. (1998)[link]; [22] Bernstein et al. (1998)[link]; [23] Wierenga et al. (1987)[link]; [24] Freymann et al. (1990)[link]; [25] McGrath et al. (1995)[link]; [26] Souza et al. (1998)[link]; [27] Focia et al. (1998)[link]; [28] Maldonado et al. (1998)[link]; [29] Lantwin et al. (1994)[link]; [30] Blankenfeldt et al. (1999)[link]; [31] Yang & Moffat (1995)[link]; [32] Whitlow et al. (1997)[link]; [33] Weston et al. (1998)[link]; [34] Cleasby et al. (1996)[link]; [35] Cutfield et al. (1995)[link]; [36] Kohno et al. (1996)[link]; [37] Suguna et al. (1987)[link]; [38] Kurihara et al. (1992)[link]; [39] Rossjohn, Feil, Wilce et al. (1997)[link]; [40] McTigue et al. (1995)[link]; [41] Mulichak et al. (1998)[link]; [42] Yang et al. (1995)[link]; [43] Bullock et al. (1996)[link]; [44] Huang et al. (1994)[link]; [45] Mikol et al. (1998)[link]; [46] Taylor et al. (1998)[link].

1.3.4.1.4. Fungi

| top | pdf |

In general, the human immune system is able to keep the growth of fungi under control, but in immuno-compromised patients (e.g. as a result of cancer chemotherapy, HIV infection, transplantation patients receiving immunosuppressive drugs, genetic disorders) such organisms are given opportunities they usually do not have. Candida albicans is an opportunistic fungal organism which causes serious complications in immuno-compromised patients. Several of its proteins have been structurally characterized (Table 1.3.4.3[link]) and provide opportunities for the development of selectively active inhibitors.

1.3.4.1.5. Helminths

| top | pdf |

Worms affect the lives of billions of human beings, causing serious morbidity in many ways. Onchocerca volvolus is the cause of river blindness, which resulted in the virtual disappearance of entire villages in West Africa, until ivermectin appeared. This remarkable compound dramatically reduced the incidence of the disease, even though it does not kill the adult worms. Therefore, a biological clock is ticking, waiting until resistance occurs against this single compound available for treatment. Schistosoma species are responsible for a wide variety of liver diseases and are spreading continuously since irrigation schemes provide a perfect environment for the intermediate snail vector. Other medically important helminths are Wuchereria bancrofti and Brugia malayi. Only a few protein structures from these very important disease-causing organisms have been unravelled so far (Table 1.3.4.3[link]).

1.3.4.2. Resistance

| top | pdf |

Resistance to drugs in infectious organisms, as well as in cancers, is a fascinating subject, since it demonstrates the action and reaction of biological systems in response to environmental challenges. Life, of course, has been evolving to do just that – and the arrival of new chemicals, termed `drugs', on the scene is nothing new to organisms that are the result of evolutionary processes involving billions of years of chemical warfare. Populations of organisms span a wide range of variation at the genetic and protein levels, and the chance that one of the variants is able to cope with drug pressure is nonzero. The variety of mechanisms observed to be responsible for drug resistance is impressive (Table 1.3.4.4[link]).

Table 1.3.4.4| top | pdf |
Mechanisms of resistance

Overexpress target protein
Mutate target protein
Use other protein with same function
Remove target altogether
Overexpress detoxification enzyme
Mutate detoxification enzyme
Create new detoxification enzyme
Mutate membrane porin protein
Remove or underexpress membrane porin protein
Overexpress efflux pumps
Mutate efflux pumps
Create/steal new efflux pumps
Improve DNA repair
Mutate prodrug conversion enzyme

Crystallography has made major contributions to the detailed molecular understanding of resistance in the case of detoxification, mutation and enzyme replacement mechanisms. Splendid examples are:

  • (a) The beta-lactamases: These beta-lactam degrading enzymes, of which there are four classes, are produced by many bacteria to counteract penicillins and cephalosporins, the most widely used antibiotics on the planet. No less than 53 structures of these enzymes reside in the PDB.

  • (b) HIV protease mutations: Tens of mutations have been characterized structurally. Many alter the active site at the site of mutation, thereby preventing drug binding. Other mutations rearrange the protein backbone, reshaping entire pockets in the binding site (Erickson & Burt, 1996[link]).

  • (c) HIV reverse transcriptase mutations: Via structural studies, at least three mechanisms of drug resistance have been elucidated: direct alteration of the binding sites for the nucleoside analogue or non-nucleoside inhibitors, mutations that change the position of the DNA template, and mutations that induce conformational changes that propagate into the active site (Das et al., 1996[link]; Hsiou et al., 1998[link]; Huang, Chopra et al., 1998[link]; Ren et al., 1998[link]; Sarafianos et al., 1999[link]).

  • (d) Resistance to vancomycin: In non-resistant bacteria, vancomycin stalls the cell-wall synthesis by binding to the D-Ala-D-Ala terminus of the lipid–PP-disaccharide–pentapeptide substrate of the bacterial transglycosylase/transpeptidase, thereby sterically preventing the approach of the substrate. Resistant bacteria, however, have acquired a plasmid-borne transposon encoding for five genes, vanS, vanR, vanH, vanA and vanX, that allows them to synthesise a substrate ending in D-Ala-D-lactate. This minute difference, an oxygen atom replacing an NH, leads to a 1000-fold reduced affinity for vancomycin, explaining the resistance (Walsh et al., 1996[link]). Thus far, the structures of vanX (Bussiere et al., 1998[link]) and D-Ala-D-Ala ligase as a model for vanA (Fan et al., 1994[link]) have been solved. They provide an exciting basis for arriving at new antibiotics against vancomycin-resistant bacteria.

  • (e) DHFR: Some bacteria resort to the `ultimate mutation' in order to escape the detrimental effects of antibiotics. They simply replace the entire targeted enzyme by a functionally identical but structurally different enzyme. A prime example is the presence of a dimeric plasmid-encoded DHFR in certain trimethoprim-resistant bacteria. The structure proved to be unrelated to that of the chromosomally encoded monomeric DHFR (Narayana et al., 1995[link]).

Clearly, the structural insight gained from these studies provides us with avenues towards methods for coping with the rapid and alarming spread of resistance against available antibiotics that threatens the effective treatment of bacterial infections of essentially every person on this planet. This implies that we will constantly have to be aware of the potential occurrence of mono- and also multi-drug resistance, which has profound consequences for drug-design strategies for essentially all infectious diseases. It requires the development of many different compounds attacking many different target proteins and nucleic acids in the infectious agent. It appears to be crucial to use, from the very beginning, several new drugs in combination so that the chances of the occurrence of resistance are minimal. Multi-drug regimens have been spectacularly successful in the case of leprosy and HIV. Obviously, the development of vaccines is by far the better solution, but it is not always possible. Antigenic variation, see e.g. the influenza virus, requires global vigilance and constant re-engineering of certain vaccines every year. Moreover, for higher organisms, and even for many bacterial species like Shigella (Levine & Noriega, 1995[link]), with over 50 serotypes per species, the development of successful vaccines has, unfortunately, proved to be very difficult indeed. For sleeping sickness, the development of a vaccine is generally considered to be impossible. It is most likely, therefore, that world health will depend for centuries on a wealth of therapeutic drugs, together with many other measures, in order to keep the immense number of pathogenic organisms under control.

1.3.4.3. Non-communicable diseases

| top | pdf |

Of this large and diverse category of human afflictions we have already touched upon genetic disorders in Section 1.3.3[link] above. Other major types of non-communicable diseases include cancer, aging disorders, diabetes, arthritis, and cardiovascular and neurological illnesses. The field of non-communicable diseases is immense. Describing in any detail the current projects in, and potential impact of, protein and nucleic acid crystallography on these diseases would need more space than this entire volume on macromolecular crystallography. Hence, only a few selected examples out of the hundreds which could be described can be discussed here. Table 1.3.4.5[link] lists many examples of human protein structures elucidated without any claim as to completeness – it is simply impossible to keep up with the fountain of structures being determined at present. Yet, such tables do provide, it is hoped, an overview of what has been achieved and what needs to be done.

Table 1.3.4.5| top | pdf |
Important human protein structures in drug design

Proteins from other species that might have been studied as substitutes for human ones were left out because of space limitations. We apologize to the researchers affected.

Pharmacological categoryProteinReference
Synaptic and neuroeffector junctional function None  
Central nervous system function None  
Inflammation Fibroblast collagenase (MMP-1) (also important in cancer) [1], [2], [3], [4]
Gelatinase [5], [6]
Stromelysin-1 (MMP-3) (also important in cancer) [7], [8], [9], [10], [11]
Matrilysin (MMP-7) (also important in cancer) [12]
Neutrophil collagenase (MMP-8) (also important in cancer) [13], [14], [15], [16]
Collagenase-3 (MMP-13) [17]
Human neutrophil elastase (also important for cystic fibrosis) [18], [19], [20]
Interleukin-1 beta converting enzyme (ICE) [21], [22]
p38 MAP kinase [23], [24]
Phospholipase A2 [25], [26], [27]
Renal and cardiovascular function Renin [28]
Gastrointestinal function None  
Cancer 17-Beta-hydroxysteroid dehydrogenase [29], [30]
BRCT domain (BRCA1 C-terminus) [31]
Bcr-Abl kinase [32]
Cathepsin B [33]
Cathepsin D [34], [35]
CDK2 [36]
CDK6 [37]
DHFR [38], [39]
Acidic fibroblast growth factor (FGF) [40]
FGF receptor tyrosine kinase domain [41]
Glycinamide ribonucleotide formyl transferase [42]
Interferon-beta [43]
MMPs: see Inflammation  
p53 [44], [45]
p60 Src [46]
Purine nucleoside phosphorylase [47]
ras p21 [48], [49], [50], [51]
Serine hydroxymethyltransferase [52]
S-Adenosylmethionine decarboxylase [53]
Thymidylate synthase [54]
Topoisomerase I [55], [56]
Tumour necrosis factor [57]
Interleukin 1-alpha [58]
Interleukin 1-beta [59]
Interleukin 1-beta receptor [60], [61]
Interleukin 8 [62]
Immunomodulation Calcineurin [63]
Cathepsin S [64]
Cyclophilin [65], [66], [67]
Immunophilin FKBP12 [68], [69], [70]
Inosine monophosphate dehydrogenase [71]
Interferon-gamma [72], [73]
Lymphocyte-specific kinase Lck [74]
PNP [47]
Syk kinase [75]
Tumour necrosis factor [57]
ZAP Tyr kinase [76]
Interleukin 2 [77]
Interleukin 5 [78]
Haematopoiesis Erythropoietin receptor [79], [80]
Coagulation AT III [81], [82], [83], [84]
Factor III [85], [86]
Factor VII [87]
Factor IX [88]
Factor X [89]
Factor XIII [90]
Factor XIV [91]
Fibrinogen: fragment [92], [93]
Plasminogen activator inhibitor (PAI) [94], [95], [96]
Thrombin [97], [98], [99]
tPA [100]
Urokinase-type plasminogen activator [101]
von Willebrand factor [102], [103], [104]
Hormones and hormone receptors Insulin [105]
Insulin receptor [106], [107]
Human growth hormone + receptor [108]
Oestrogen receptor [109], [110]
Progesterone receptor [111]
Prolactin receptor [112]
Ocular function Carbonic anhydrase [113]
Genetic diseases See Table 1.3.3.1[link]  
Drug binding Human serum albumin [114], [115]
Drug metabolism Glutathione S-transferase A-1 [116], [117]
Glutathione S-transferase A4–4 [118]
Glutathione S-transferase Mu-1 [119]
Glutathione S-transferase Mu-2 [120]
Neurodegeneration Aldose reductase [121]
JNK3 [122]
Osteoporosis Cathepsin K [123], [64]
Src SH2 [126]
Various Interferon-alpha 2b [124]
Bcl-xL [125]

References: [1] Borkakoti et al. (1994)[link]; [2] Lovejoy, Cleasby et al. (1994)[link]; [3] Lovejoy, Hassell et al. (1994)[link]; [4] Spurlino et al. (1994)[link]; [5] Libson et al. (1995)[link]; [6] Gohlke et al. (1996)[link]; [7] Becker et al. (1995)[link]; [8] Dhanaraj et al. (1996)[link]; [9] Esser et al. (1997)[link]; [10] Gomis-Ruth et al. (1997)[link]; [11] Finzel et al. (1998)[link]; [12] Browner et al. (1995)[link]; [13] Bode et al. (1994)[link]; [14] Reinemer et al. (1994)[link]; [15] Stams et al. (1994)[link]; [16] Betz et al. (1997)[link]; [17] Gomis-Ruth et al. (1996)[link]; [18] Bode et al. (1986)[link]; [19] Wei et al. (1988)[link]; [20] Navia, McKeever et al. (1989)[link]; [21] Walker et al. (1994)[link]; [22] Rano et al. (1997)[link]; [23] Wilson et al. (1996)[link]; [24] Tong et al. (1997)[link]; [25] Scott et al. (1991)[link]; [26] Wery et al. (1991)[link]; [27] Kitadokoro et al. (1998)[link]; [28] Sielecki et al. (1989)[link]; [29] Ghosh et al. (1995)[link]; [30] Breton et al. (1996)[link]; [31] Zhang et al. (1998)[link]; [32] Nam et al. (1996)[link]; [33] Musil et al. (1991)[link]; [34] Baldwin et al. (1993)[link]; [35] Metcalf & Fusek (1993)[link]; [36] De Bondt et al. (1993)[link]; [37] Russo et al. (1998)[link]; [38] Oefner et al. (1988)[link]; [39] Davies et al. (1990)[link]; [40] Blaber et al. (1996)[link]; [41] McTigue et al. (1999)[link]; [42] Varney et al. (1997)[link]; [43] Karpusas et al. (1997)[link]; [44] Cho et al. (1994)[link]; [45] Gorina & Pavletich (1996)[link]; [46] Xu et al. (1997)[link]; [47] Ealick et al. (1990)[link]; [48] DeVos et al. (1988)[link]; [49] Pai et al. (1989)[link]; [50] Krengel et al. (1990)[link]; [51] Scheffzek et al. (1997)[link]; [52] Renwick et al. (1998)[link]; [53] Ekstrom et al. (1999)[link]; [54] Schiffer et al. (1995)[link]; [55] Redinbo et al. (1998)[link]; [56] Stewart et al. (1998)[link]; [57] Banner et al. (1993)[link]; [58] Graves et al. (1990)[link]; [59] Priestle et al. (1988)[link]; [60] Schreuder et al. (1997)[link]; [61] Vigers et al. (1997)[link]; [62] Baldwin et al. (1991)[link]; [63] Kissinger et al. (1995)[link]; [64] McGrath et al. (1998)[link]; [65] Kallen et al. (1991)[link]; [66] Ke et al. (1991)[link]; [67] Pfuegl et al. (1993)[link]; [68] Van Duyne, Standaert, Karplus et al. (1991)[link]; [69] Van Duyne, Standaert, Schreiber & Clardy (1991)[link]; [70] Van Duyne et al. (1993)[link]; [71] Colby et al. (1999)[link]; [72] Ealick et al. (1991)[link]; [73] Walter et al. (1995)[link]; [74] Zhu et al. (1999)[link]; [75] Futterer et al. (1998)[link]; [76] Meng et al. (1999)[link]; [77] Brandhuber et al. (1987)[link]; [78] Milburn et al. (1993)[link]; [79] Livnah et al. (1996)[link]; [80] Livnah et al. (1998)[link]; [81] Carrell et al. (1994)[link]; [82] Schreuder et al. (1994)[link]; [83] Skinner et al. (1997)[link]; [84] Skinner et al. (1998)[link]; [85] Muller et al. (1994)[link]; [86] Muller et al. (1996)[link]; [87] Banner et al. (1996)[link]; [88] Rao et al. (1995)[link]; [89] Padmanabhan et al. (1993)[link]; [90] Yee et al. (1994)[link]; [91] Mather et al. (1996)[link]; [92] Pratt et al. (1997)[link]; [93] Spraggon et al. (1997)[link]; [94] Mottonen et al. (1992)[link]; [95] Aertgeerts et al. (1995)[link]; [96] Xue et al. (1998)[link]; [97] Bode et al. (1989)[link]; [98] Rydel et al. (1990)[link]; [99] Rydel et al. (1994)[link]; [100] Laba et al. (1996)[link]; [101] Spraggon et al. (1995)[link]; [102] Bienkowska et al. (1997)[link]; [103] Huizinga et al. (1997)[link]; [104] Emsley et al. (1998)[link]; [105] Ciszak & Smith (1994)[link]; [106] Hubbard et al. (1994)[link]; [107] Hubbard (1997)[link]; [108] DeVos et al. (1992)[link]; [109] Schwabe et al. (1993)[link]; [110] Brzozowski et al. (1997)[link]; [111] Williams & Sigler (1998)[link]; [112] Somers et al. (1994)[link]; [113] Kannan et al. (1975)[link]; [114] He & Carter (1992)[link]; [115] Curry et al. (1998)[link]; [116] Sinning et al. (1993)[link]; [117] Cameron et al. (1995)[link]; [118] Bruns et al. (1999)[link]; [119] Tskovsky et al. (1999)[link]; [120] Raghunathan et al. (1994)[link]; [121] Wilson et al. (1992)[link]; [122] Xie et al. (1998)[link]; [123] Thompson et al. (1997)[link]; [124] Radhakrishnan et al. (1996)[link]; [125] Muchmore et al. (1996)[link]; [126] Waksman et al. (1993[link]).

1.3.4.3.1. Cancers

| top | pdf |

Over a hundred different cancers have been described and clearly the underlying defect, loss of control of cell division, can be the result of many different shortcomings in different cells. The research in this area proceeds at a feverish pace, yet the development, discovery and design of effective but safe anti-cancer agents are unbelievably difficult challenges. The modifications needed to turn a normal cell into a malignant one are very small, hence the chance of arriving at `true' anti-cancer drugs that exploit such small differences between normal and abnormal cells is exceedingly small. Nevertheless, such selective anti-cancer agents would leave normal cells essentially unaffected and are therefore the holy grail of cancer therapy. Few if any such compounds have been found so far, but cancer therapy is benefiting from a gradual increase in the number of useful compounds. Many have serious side effects, weaken the immune system and are barely tolerated by patients. However, they rescue large numbers of patients and hence it is of interest that many targets of these compounds, proteins and DNA molecules, have been structurally elucidated by crystallographic methods – often in complex with the cancer drug. The mode of action of many anti-cancer compounds is well understood, e.g. methotrexate targeting dihydrofolate reductase, and fluorouracil targeting thymidilate synthase. These are specific enzyme inhibitors acting along principles well known in other areas of medicine. Several anti-cancer drugs display unusual modes of action, such as:

  • (a) the DNA intercalators daunomycin (Wang et al., 1987[link]) and adriamycin (Zhang et al., 1993[link]);

  • (b) cisplatin, which forms DNA adducts (Giulian et al., 1996[link]);

  • (c) taxol, which not only binds to tubulin but also to bcl-2, thereby blocking the machinery of cancer cells in two entirely different ways (Amos & Lowe, 1999[link]);

  • (d) camptothecin analogues, such as irinotecan and topotecan, which have the unusual property of prolonging the lifetime of a covalent topoisomerase–DNA complex, generating major road blocks on the DNA highway and causing DNA breakage and cell death;

  • (e) certain compounds function as minor-groove binders, e.g. netropsin and distamycin (Kopka et al., 1985[link]);

  • (f) completely new drugs which were developed based on the structures of matrix metalloproteinases, purine nucleotide phosphorylase and glycinamide ribonucleotide formyltransferase and which are in clinical trials (Jackson, 1997[link]).

Meanwhile, it is sad that crystallography has not yet made any contribution to the molecular understanding of multi-drug resistance in cancer. The resistance is caused by cellular pumps that efficiently pump out the drugs, often leading to failed chemotherapy (Borst, 1999[link]). On the other hand, the structures of major oncogenic proteins such as p21 (DeVos et al.[link], 1988; Pai et al., 1989[link]; Krengel et al., 1990[link]; Scheffzek et al., 1997[link]) and p53 (Cho et al., 1994[link]; Gorina & Pavletich, 1996[link]) are of tremendous importance for future structure-based design of anti-neoplastic agents.

1.3.4.3.2. Diabetes

| top | pdf |

The hallmark characteristic of type I diabetes is a lack of insulin. A major therapeutic approach to this problem is insulin replacement therapy. Unfortunately, the insulin requirements of the body vary dramatically during the course of a day, with high concentrations needed at meal times and a basal level during the rest of the day. Only monomeric insulin is active at the insulin receptor level, but insulin has a natural tendency to form dimers and hexamers that dissociate upon dilution. Thanks to the three-dimensional insight obtained from dozens of insulin crystal structures, as wild-type (Hodgkin, 1971[link]), mutants (Whittingham et al., 1998[link]) and in complex with zinc ions and small molecules such as phenol (Derewenda et al., 1989[link]), it has been possible to fine-tune the kinetics of insulin dissociation. The resulting availability of a variety of insulin preparations with rapid or prolonged action profiles has improved the quality of life of millions of people (Brange, 1997[link]).

1.3.4.3.3. Blindness

| top | pdf |

The main causes of blindness worldwide are cataract, trachoma, glaucoma and onchocerciasis (Thylefors et al., 1995[link]). Trachoma and onchocerciasis are parasitic diseases that destroy the architecture of the eye; they were discussed in Section 1.3.4.1[link]. The other two are discussed here. During cataract development, the lens of the eye becomes non-transparent as a result of aggregation of crystallins, preventing image formation. Crystal structures of several mammalian beta- and gamma-crystallins are known, but no human ones yet. In glaucoma, the optic nerve is destroyed by high intra-ocular pressure. One way to lower the pressure is to inhibit carbonic anhydrase II, a pivotal enzyme in maintaining the intra-ocular pressure. On the basis of the carbonic anhydrase crystal structure, researchers at Merck Research Laboratories were able to guide the optimization of an S-thienothiopyran-2-sulfonamide lead into a marketed drug for glaucoma: dorzolamide (Baldwin et al., 1989[link]).

1.3.4.3.4. Cardiovascular disorders

| top | pdf |

Thrombosis is a major cause of morbidity and mortality, especially in the industrial world. Hence, major effort is expended by pharmaceutical industries in the development of new classes of anti-coagulants with fewer side effects than available drugs, such as heparins and coumarins. Because blood coagulation is the result of an amplification cascade of enzymatic reactions, many potential targets are available. At present most of the effort is directed towards thrombin (Weber & Czarniecki, 1997[link]) and factor Xa (Ripka, 1997[link]), responsible for the penultimate step and the step immediately preceding it in the cascade, respectively. Thrombin is especially fascinating owing to the presence of at least three subsites: a primary specificity pocket with the catalytic serine-protease machinery, an exosite for recognizing extended fibrinogen and an additional pocket for binding heparin. This knowledge has led to the design of bivalent inhibitors which occupy two sites with ultra-high affinity and exquisite specificity. Several of these agents are in clinical trials (Pineo & Hull, 1999[link]).

1.3.4.3.5. Neurological disorders

| top | pdf |

Even a quick glance at Table 1.3.4.5[link] shows that crystallography contributes to new therapeutics for numerous human afflictions and diseases. Yet there are major gaps in our understanding of protein functions, in particular of those involved in development and in neurological functions. These proteins are the target of many drugs obtained by classical pre-crystal-structure methods. These proven drug targets are very often membrane proteins involved in neuronal functions, and the diseases concerned are some of the most prevalent in mankind. A non-exhaustive list includes cerebrovascular disease (strokes), Parkinson's, epilepsy, schizophrenia, bipolar disease and depression.

Some of these diseases are heart-breaking afflictions, where parents have to accept the suicidal tendencies of their children, often with fatal outcomes; where partners have to endure the tremendous mood swings of their bipolar spouses and have to accept extreme excesses in behaviour; where a happy evening of life is turned into the gradual and sad demise of human intellect due to the progression of Alzheimer's, or to the loss of motor functions due to Parkinson's, or into the tragic stare of a victim of deep depression. Human nature, in all its shortcomings, has the tendency to try to help such tragic victims, but drugs for neurological disorders are rare, drug regimens are difficult to optimize and the commitment to follow a drug regimen – often for years, and often with major side effects – is a next to impossible task in many cases. New, better drugs are urgently needed and hence the structure determinations of the `molecules of the brain' are major scientific as well as medical challenges of the next decades. Such molecules will shed light on some of the deepest mysteries of humanity, including memory, cognition, desire, sleep etc. At the same time, such structures will provide opportunities for treating those suffering from neurodegenerative diseases due to age, genetic disposition, allergies, infections, traumas and combinations thereof. Such `CNS protein structures' are one of the major challenges of biomacromolecular crystallography in the 21st century.

1.3.4.4. Drug metabolism and crystallography

| top | pdf |

As soon as a drug enters the body, an elaborate machinery comes into action to eliminate this foreign and potentially harmful molecule as quickly as possible. Two steps are usually distinguished in this process: phase I metabolism, in which the drug is functionalized, and phase II metabolism, in which further conjugation with endogenous hydrophilic molecules takes place, so that excretion via the kidneys can occur. Whereas this `detoxification' process is essential for survival, it often renders promising inhibitors useless as drug candidates. Hence, structural knowledge of the proteins involved in metabolism could have a significant impact on the drug development process.

Thus far, only the structures of a few proteins crucial for drug distribution and metabolism have been elucidated. Human serum albumin binds hundreds of different drugs with micromolar dissociation constants, thereby altering drug levels in the blood dramatically. The structure of this important carrier molecule has been solved in complex with several drug molecules and should one day allow the prediction of the affinity of new chemical entities for this carrier protein, and thereby deepen our understanding of the serum concentrations of new candidate drugs (Carter & Ho, 1994[link]; Curry et al., 1998[link]; Sugio et al., 1999[link]). Human oxidoreductases and hydrolases of importance in drug metabolism with known structure are: alcohol dehydrogenase (EC 1.1.1.1) (Hurley et al., 1991[link]), aldose reductase (EC 1.1.1.21) (Wilson et al., 1992[link]), glutathione reductase (NADPH) (EC 1.6.4.2) (Thieme et al., 1981[link]), catalase (EC 1.11.1.6) (Ko et al., 2000[link]), myeloperoxidase (EC 1.11.1.7) (Choi et al., 1998[link]) and beta-glucuronidase (EC 3.2.1.31) (Jain et al., 1996[link]). Recently, the first crystal structure of a mammalian cytochrome P-450, the most important class of xenobiotic metabolizing enzymes, has been reported (Williams et al.[link], 2000).

Of the conjugation enzymes, only glutathione S-transferases (EC 2.5.1.18) have been characterized structurally: A1 (Sinning et al., 1993[link]), A4–4 (Bruns et al., 1999[link]), MU-1 (Patskovsky et al., 1999[link]), MU-2 (Raghunathan et al., 1994[link]), P (Reinemer et al., 1992[link]) and THETA-2 (Rossjohn, McKinstry et al., 1998[link]). Tens of structures await elucidation in this area (Testa, 1994[link]).

1.3.4.5. Drug manufacturing and crystallography

| top | pdf |

The development of drugs is a major undertaking and one of the hallmarks of modern societies. However, once a safe and effective therapeutic agent has been fully tested and approved, manufacturing the compound on a large scale is often the next major challenge. Truly massive quantities of penicillin and cephalosporin are produced worldwide, ranging from 2000 to 7000 tons annually (Conlon et al., 1995[link]). In the production of semi-synthetic penicillins, the enzyme penicillin acylase plays a very significant role. This enzyme catalyses the hydrolysis of penicillin into 6-aminopenicillanic acid. Its crystal structure has been elucidated (Duggleby et al., 1995[link]) and may now be used for protein-engineering studies to improve its properties for the biotechnology industry. The production of cephalosporins could benefit in a similar way from knowing the structure of cephalosporin acylase (CA), since the properties of this enzyme are not optimal for use in production plants. Therefore, the crystal structure determination of CA could provide a basis for improving the substrate specificity of CA by subsequent protein-engineering techniques. Fortunately, a first CA structure has been solved recently (Kim et al., 2000[link]), with many other structures expected to be solved essentially simultaneously. Clearly, crystallography can be not only a major player in the design and optimization of therapeutic drugs, but also in their manufacture.

1.3.5. Vaccines, immunology and crystallography

| top | pdf |

Vaccines are probably the most effective way of preventing disease. An impressive number of vaccines have been developed and many more are under development (National Institute of Allergy and Infectious Diseases, 1998[link]). Smallpox has been eradicated thanks to a vaccine, and polio is being targeted for eradication in a worldwide effort, again using vaccination strategies. To the best of our knowledge, crystal structures of viruses, viral capsids or viral proteins have not been used in developing the currently available vaccines. However, there are projects underway that may change this.

For instance, the crystal structure of rhinovirus has resulted in the development of compounds that have potential as antiviral agents, since they stabilize the viral capsid and block, or at least delay, the uncoating step in viral cell entry (Fox et al., 1986[link]). These rhinovirus capsid-stabilizing compounds are, in a different project, being used to stabilize poliovirus particles against heat-induced denaturation in vaccines (Grant et al., 1994[link]). This approach may be applicable to other cases, although it has not yet resulted in commercially available vaccine-plus-stabilizer cocktails. However, it is fascinating to see how a drug-design project may be able to assist vaccine development in a rather unexpected manner.

Three-dimensional structural information about viruses is also being used to aid in the development of vaccines. Knowledge of the architecture of and biological functions of coat proteins has been used to select loops at viral surfaces that can be replaced with antigenic loops from other pathogens for vaccine-engineering purposes (e.g. Burke et al., 1988[link]; Kohara et al., 1988[link]; Martin et al., 1988[link]; Murray et al., 1998[link]; Arnold et al., 1994[link]; Resnick et al., 1995[link]; Smith et al., 1998[link]; Arnold & Arnold, 1999[link]; Zhang, Geisler et al., 1999[link]). The design of human rhinovirus (HRV) and poliovirus chimeras has been aided by knowing the atomic structure of the viruses (Hogle et al., 1985[link]; Rossmann et al., 1985[link]; Arnold & Rossmann, 1988[link]; Arnold & Rossmann, 1990[link]) and detailed features of the neutralizing immunogenic sites on the virion surfaces (Sherry & Rueckert, 1985[link]; Sherry et al., 1986[link]). In this way, one can imagine that in cases where the atomic structures of antigenic loops in `donor' immunogens are known as well as the structure of the `recipient' loop in the virus capsid protein, optimal loop transplantation might become possible. It is not yet known how to engineer precisely the desired three-dimensional structures and properties into macromolecules. However, libraries of macromolecules or viruses constructed using combinatorial mutagenesis can be searched to increase the likelihood of including structures with desired architecture and properties such as immunogenicity. With appropriate selection methods, the rare constructs with desired properties can be identified and `fished out'. Research of this type has yielded some potently immunogenic presentations of sequences transplanted on the surface of HRV (reviewed in Arnold & Arnold, 1999[link]). For reasons not quite fully understood, presenting multiple copies of antigens to the immune system leads to an enhanced immune response (Malik & Perham, 1997[link]). It is conceivable that, eventually, it might even be possible for conformational epitopes consisting of multiple `donor' loops to be grafted onto `recipient capsids' while maintaining the integrity of the original structure. Certainly, such feats are difficult to achieve with present-day protein-engineering skills, but recent successes in protein design offer hope that this will be feasible in the not too distant future (Gordon et al., 1999[link]).

Immense efforts have been made by numerous crystallographers to unravel the structures of molecules involved in the unbelievably complex, powerful and fascinating immune system. Many of the human proteins studied are listed in Table 1.3.4.5[link] with, as specific highlights, the structures of immunoglobulins (Poljak et al., 1973[link]), major histocompatibility complex (MHC) molecules (Bjorkman et al., 1987[link]; Brown et al., 1993[link]; Fremont et al., 1992[link]; Bjorkman & Burmeister, 1994[link]), T-cell receptors (TCR) and MHC:TCR complexes (Garboczi et al., 1996[link]; Garcia et al., 1996[link]), an array of cytokines and chemokines, and immune cell-specific kinases such as lck (Zhu et al., 1999[link]). This knowledge is being converted into practical applications, for instance by humanising non-human antibodies with desirable properties (Reichmann et al., 1988[link]) and by creating immunotoxins.

The interactions between chemokines and receptors, and the complicated signalling pathways within each immune cell, make it next to impossible to predict the effect of small compounds interfering with a specific protein–protein interaction in the immune system (Deller & Jones, 2000[link]). However, great encouragement has been obtained from the discovery of the remarkable manner by which the immunosuppressor FK506 functions: this small molecule brings two proteins, FKB12 and calcineurin, together, thereby preventing T-cell activation by calcineurin. The structure of this remarkable ternary complex is known (Kissinger et al., 1995[link]). Such discoveries of unusual modes of action of therapeutic compounds are the foundation for new concepts such as `chemical dimerizers' to activate signalling events in cells such as apoptosis (Clackson et al., 1998[link]).

In spite of the gargantuan task ahead aimed at unravelling the cell-to-cell communication in immune action, it is unavoidable that the next decades will bring us unprecedented insight into the many carefully controlled processes of the immune system. In turn, it is expected that this will lead to new therapeutics for manipulating a truly wonderful defence system in order to assist vaccines, to decrease graft rejection processes in organ transplants and to control auto-immune diseases that are likely to be playing a major role in cruelly debilitating diseases such as rheumatoid arthritis and type I diabetes.

1.3.6. Outlook and dreams

| top | pdf |

At the beginning of the 1990s, Max Perutz inspired many researchers with a passion for structure and a heart for the suffering of mankind with a fascinating book entitled Protein Structure – New Approaches to Disease and Therapy (Perutz, 1992[link]). The explosion of medicinal macromolecular crystallography since then has been truly remarkable. What should we expect for the next decades?

In the realm of safe predictions we can expect the following:

  • (a) High-throughput macromolecular crystallography due to the developments outlined in Section 1.3.1[link], leading to the new field of `structural genomics'.

  • (b) Crystallography of very large complexes. While it is now clear that an atomic structure of a complex of 58 proteins and three RNA molecules, the ribosome, is around the corner, crystallographers will widen their horizons and start dreaming of structures like the nuclear pore complex, which has a molecular weight of over 100 000 000 Da.

  • (c) A steady flow of membrane protein structures. Whereas Max Perutz could only list five structures in his book of 1992, there are now over 40 PDB entries for membrane proteins. Most of them are transmembrane proteins: bacteriorhodopsin, photoreaction centres, light-harvesting complexes, cytochrome bc1 complexes, cytochrome c oxidases, photosystem I, porins, ion channels and bacterial toxins such as haemolysin and LukF. Others are monotopic membrane proteins such as squalene synthase and the cyclooxygenases. Clearly, memb­rane protein crystallography is gaining momentum at present and may open the door to atomic insight in neurotransmitter pharmacology in the next decade.

What if we dream beyond the obvious? One day, medicinal crystallography may contribute to:

  • (a) The design of submacromolecular agonists and antagonists of proteins and nucleic acids in a matter of a day by integrating rapid structure determinations, using only a few nanograms of protein, with the power of combinatorial and, in particular, computational chemistry.

  • (b) `Structural toxicology' based on `human structural genomics'. Once the hundreds of thousands of structures of human proteins and complexes with other proteins and nucleic acids have been determined, truly predictive toxicology may become possible. This will not only speed up the drug-development process, but may substantially reduce the suffering of animals in preclinical tests.

  • (c) The creation of completely new classes of drugs to treat addiction, organ regeneration, aging, memory enhancement etc.

One day, crystallography will have revealed the structure of hundreds of thousands of proteins and nucleic acids from human and pathogen, and their complexes with each other and with natural and designed low-molecular-weight ligands. This will form an extraordinarily precious database of knowledge for furthering the health of humans. Hence, in the course of the 21st century, crystallography is likely to become a major driving force for improving health care and disease prevention, and will find a well deserved place in future books describing progress in medicine, sometimes called `The Greatest Benefit to Mankind' (Porter, 1999[link]).

Acknowledgements

We wish to thank Heidi Singer for terrific support in preparing the manuscript, and Drs Alvin Kwiram, Michael Gelb, Seymour Klebanov, Wes Van Voorhis, Fred Buckner, Youngsoo Kim and Rein Zwierstra for valuable comments.

References

Achari, A., Somers, D. O., Champness, J. N., Bryant, P. K., Rosemond, J. & Stammers, D. K. (1997). Crystal structure of the anti-bacterial sulfonamide drug target dihydropteroate synthase. Nature Struct. Biol. 4, 490–497.
Adman, E. T., Stenkamp, R. E., Sieker, L. C. & Jensen, L. H. (1978). A crystallographic model for azurin at 3 Å resolution. J. Mol. Biol. 123, 35–47.
Aertgeerts, K., De Bondt, H. L., De Ranter, C. J. & Declerck, P. J. (1995). Mechanisms contributing to the conformational and functional flexibility of plasminogen activator inhibitor-1. Nature Struct. Biol. 2, 891–897.
Ævarsson, A., Chuang, J. L., Wynn, R. M., Turley, S., Chuang, D. T. & Hol, W. G. J. (2000). Crystal structure of human branched-chain α-ketoacid dehydrogenase and the molecular basis of multienzyme complex deficiency in maple syrup urine disease. Struct. Fold. Des. 8, 277–291.
Allaire, M., Chernaia, M. M., Malcolm, B. A. & James, M. N. (1994). Picornaviral 3C cysteine proteinases have a fold similar to chymotrypsin-like serine proteinases. Nature (London), 369, 72–76.
Allured, V. S., Collier, R. J., Carroll, S. F. & McKay, D. B. (1986). Structure of exotoxin A of Pseudomonas aeruginosa at 2.0-Å resolution. Proc. Natl Acad. Sci. USA, 83, 1320–1324.
Almassy, R. J. & Dickerson, R. E. (1978). Pseudomonas cytochrome c551 at 2.0 Å resolution: enlargement of the cytochrome c family. Proc. Natl Acad. Sci. USA, 75, 2674–2678.
Amos, L. A. & Lowe, J. (1999). How Taxol stabilises microtubule structure. Chem. Biol. 6, R65–R69.
Arnold, E., Das, K., Ding, J., Yadav, P. N., Hsiou, Y., Boyer, P. L. & Hughes, S. H. (1996). Targeting HIV reverse transcriptase for anti-AIDS drug design: structural and biological considerations for chemotherapeutic strategies. Drug Des. Discov. 13, 29–47.
Arnold, E. & Rossmann, M. G. (1988). The use of molecular-replacement phases for the refinement of the human rhinovirus 14 structure. Acta Cryst. A44, 270–283.
Arnold, E. & Rossmann, M. G. (1990). Analysis of the structure of a common cold virus, human rhinovirus 14, refined at a resolution of 3.0 Å. J. Mol. Biol. 211, 763–801.
Arnold, G. F. & Arnold, E. (1999). Using combinatorial libraries to develop vaccines. ASM News, 65, 603–610.
Arnold, G. F., Resnick, D. A., Li, Y., Zhang, A., Smith, A. D., Geisler, S. C., Jacobo-Molina, A., Lee, W., Webster, R. G. & Arnold, E. (1994). Design and construction of rhinovirus chimeras incorporating immunogens from polio, influenza, and human immunodeficiency viruses. Virology, 198, 703–708.
Arnoux, P., Haser, R., Izadi, N., Lecroisey, A., Delepierre, M., Wandersman, C. & Czjzek, M. (1999). The crystal structure of HasA, a hemophore secreted by Serratia marcescens. Nature Struct. Biol. 6, 516–520.
Athanasiadis, A., Vlassi, M., Kotsifaki, D., Tucker, P. A., Wilson, K. S. & Kokkinidis, M. (1994). Crystal structure of PvuII endonuclease reveals extensive structural homologies to EcoRV. Nature Struct. Biol. 1, 469–475.
Baca, A. M., Sirawaraporn, R., Turley, S., Athappilly, F., Sirawaraporn, W. & Hol, W. G. J. (2000). Crystal structure of Mycobacterium tuberculosis 6-hydroxymethyl-1,8-dihydropteroate synthase in complex with pterin monophosphate: new insight into the enzymatic mechanism and sulfa-drug action. J. Mol. Biol. 302, 1193–1212.
Baldwin, E. T., Bhat, T. N., Gulnik, S., Hosur, M. V., Sowder, R. C. I., Cachau, R. E., Collins, J., Silva, A. M. & Erickson, J. W. (1993). Crystal structures of native and inhibited forms of human cathepsin D: implications for lysosomal targeting and drug design. Proc. Natl Acad. Sci. USA, 90, 6796–6800.
Baldwin, E. T., Weber, I. T., St Charles, R., Xuan, J. C., Appella, E., Yamada, M., Matsushima, K., Edwards, B. F., Clore, G. M. & Gronenborn, A. M. (1991). Crystal structure of interleukin 8: symbiosis of NMR and crystallography. Proc. Natl Acad. Sci. USA, 88, 502–506.
Baldwin, J. J., Ponticello, G. S., Anderson, P. S., Christy, M. E., Murcko, M. A., Randall, W. C., Schwam, H., Sugrue, M. F., Springer, J. P., Gautheron, P., Grove, J., Mallorga, P., Viader, M. P., McKeever, B. M. & Navia, M. A. (1989). Thienothiopyran-2-sulfonamides: novel topically active carbonic anhydrase inhibitors for the treatment of glaucoma. J. Med. Chem. 32, 2510–2513.
Ban, N., Nissen, P., Hansen, J., Capel, M., Moore, P. B. & Steitz, T. A. (1999). Placement of protein and RNA structures into a 5 Å-resolution map of the 50S ribosomal subunit. Nature (London), 400, 841–847.
Banbula, A., Potempa, J., Travis, J., Fernandez-Catalan, C., Mann, K., Huber, R., Bode, W. & Medrano, F. (1998). Amino-acid sequence and three-dimensional structure of the Staphylococcus aureus metalloproteinase at 1.72 Å resolution. Structure, 6, 1185–1193.
Banner, D. W., D'Arcy, A., Chene, C., Winkler, F. K., Guha, A., Konigsberg, W. H., Nemreson, Y. & Kirchhofer, D. (1996). The crystal structure of the complex of blood coagulation factor VIIa with soluble tissue factor. Nature, 380, 41–46.
Banner, D. W., D'Arcy, A., Janes, W., Gentz, R., Schoenfeld, H. J., Broger, C., Loetscher, H. & Lesslauer, W. (1993). Crystal structure of the soluble human 55 kd TNF receptor–human TNF beta complex: implications for TNF receptor activation. Cell, 7, 431–445.
Baumann, U. (1994). Crystal structure of the 50 kDa metallo protease from Serratia marcescens. J. Mol. Biol. 242, 244–251.
Beaman, T. W., Binder, D. A., Blanchard, J. S. & Roderick, S. L. (1997). Three-dimensional structure of tetrahydrodipicolinate N-succinyltransferase. Biochemistry, 36, 489–494.
Beaman, T. W., Sugantino, M. & Roderick, S. L. (1998). Structure of the hexapeptide xenobiotic acetyltransferase from Pseudomonas aeruginosa. Biochemistry, 37, 6689–6696.
Becker, J. W., Marcy, A. I., Rokosz, L. L., Axel, M. G., Burbaum, J. J., Fitzgerald, P. M., Cameron, P. M., Esser, C. K., Hagmann, W. K., Hermes, J. D. & Springer, J. P. (1995). Stromelysin-1: three dimensional structure of the inhibited catalytic domain and of the C-truncated proenzyme. Protein Sci. 4, 1966–1976.
Bentley, G., Dodson, E., Dodson, G., Hodgkin, D. & Mercola, D. (1976). Structure of insulin in 4-zinc insulin. Nature (London), 261, 166–168.
Bernstein, B. E., Williams, D. M., Bressi, J. C., Kuhn, P., Gelb, M. H., Blackburn, G. M. & Hol, W. G. J. (1998). A bisubstrate analog induces unexpected conformational changes in phosphoglycerate kinase from Trypanosoma brucei. J. Mol. Biol. 279, 1137–1148.
Bernstein, F. C., Koetzle, T. F., Williams, G. J., Meyer, E. F. Jr, Brice, M. D., Rodgers, J. R., Kennard, O., Shimanouchi, T. & Tasumi, M. (1977). The Protein Data Bank. A computer-based archival file for macromolecular structures. Eur. J. Biochem. 80, 319–324.
Betz, M., Huxley, P., Davies, S. J., Mushtaq, Y., Pieper, M., Tschesche, H., Bode, W. & Gomis-Ruth, F. X. (1997). 1.8-Å crystal structure of the catalytic domain of human neutrophil collagenase (matrix metalloproteinase-8) complexed with a peptidomimetic hydroxamate primed-side inhibitor with a distinct selectivity profile. Eur. J. Biochem. 247, 356–363.
Bienkowska, J., Cruz, M., Atiemo, A., Handin, R. & Liddington, R. (1997). The von Willebrand factor A3 domain does not contain a metal ion-dependent adhesion site motif. J. Biol. Chem. 272, 25162–25167.
Birrer, P. (1995). Proteases and antiproteases in cystic fibrosis: pathogenetic considerations and therapeutic strategies. Respiration, 62, S25–S28.
Bjorkman, P. J. & Burmeister, W. P. (1994). Structures of two classes of MHC molecules elucidated: crucial differences and similarities. Curr. Opin. Struct. Biol. 4, 852–856.
Bjorkman, P. J., Saper, M. A., Samraoui, B., Bennett, W. S., Strominger, J. L. & Wiley, D. C. (1987). Structure of human class I histocompatibility antigen, HLA-A2. Nature (London), 329, 506–512.
Blaber, M., DiSalvo, J. & Thomas, K. A. (1996). X-ray crystal structure of human acidic fibroblast growth factor. Biochemistry, 35, 2086–2094.
Blake, C. C., Geisow, M. J., Oatley, S. J., Rerat, B. & Rerat, C. (1978). Structure of prealbumin: secondary, tertiary and quaternary interactions determined by Fourier refinement at 1.8 Å. J. Mol. Biol. 121, 339–356.
Blankenfeldt, W., Nowicki, C., Montemartini-Kalisz, M., Kalisz, H. M. & Hecht, H. J. (1999). Crystal structure of Trypanosoma cruzi tyrosine aminotransferase: substrate specificity is influenced by cofactor binding mode. Protein Sci. 8, 2406–2417.
Bochkarev, A., Barwell, J. A., Pfuetzner, R. A., Furey, W. Jr, Edwards, A. M. & Frappier, L. (1995). Crystal structure of the DNA-binding domain of the Epstein–Barr virus origin-binding protein EBNA 1. Cell, 83, 39–46.
Bode, W., Mayr, I., Baumann, U., Huber, R., Stone, S. R. & Hofsteenge, J. (1989). The refined 1.9 Å crystal structure of human alpha-thrombin: interaction with D-Phe-Pro-Arg chloromethylketone and significance of the Tyr-Pro-Pro-Trp insertion segment. EMBO J. 8, 3467–3475.
Bode, W., Reinemer, P., Huber, R., Kleine, T., Schnierer, S. & Tschesche, H. (1994). The X-ray crystal structure of the catalytic domain of human neutrophil collagenase inhibited by a substrate analogue reveals the essentials for catalysis and specificity. EMBO J. 13, 1263–1269.
Bode, W., Wei, A. Z., Huber, R., Meyer, E., Travis, J. & Neumann, S. (1986). X-ray crystal structure of the complex of human leukocyte elastase (PMN elastase) and the third domain of the turkey ovomucoid inhibitor. EMBO J. 5, 2453–2458.
Borkakoti, N., Winkler, F. K., Williams, D. H., D'Arcy, A., Broadhurst, M. J., Brown, P. A., Johnson, W. H. & Murray, E. J. (1994). Structure of the catalytic domain of human fibroblast collagenase complexed with an inhibitor. Nature Struct. Biol. 1, 106–110.
Borst, P. (1999). Multidrug resistance: a solvable problem? Ann. Oncol. 10, S162–S164.
Brandhuber, B. J., Boone, T., Kenney, W. C. & McKay, D. B. (1987). Three-dimensional structure of interleukin-2. Science, 238, 1707–1709.
Brange, J. (1997). The new era of biotech insulin analogues. Diabetologia, 40, S48–S53.
Breton, R., Housset, D., Mazza, C. & Fontecilla-Camps, J. C. (1996). The structure of a complex of human 17-beta-hydroxysteroid dehydrogenase with estradiol and NADP+ identifies two principal targets for the design of inhibitors. Structure, 4, 905–915.
Brown, J. H., Jardetzky, T. S., Gorga, J. C., Stern, L. J., Urban, R. G., Strominger, J. L. & Wiley, D. C. (1993). Three-dimensional structure of the human class II histocompatibility antigen HLA-DR1. Nature (London), 364, 33–39.
Browner, M. F., Smith, W. W. & Castelhano, A. L. (1995). Matrilysin-inhibitor complexes: common themes among metalloproteases. Biochemistry, 34, 6602–6610.
Bruns, C. M., Hubatsch, I., Ridderstrom, M., Mannervik, B. & Tianer, J. A. (1999). Human glutathione transferase A4–4 crystal structures and mutagenesis reveal the basis of high catalytic efficiency with toxic lipid peroxidation products. J. Mol. Biol. 288, 427–439.
Bruns, C. M., Nowalk, A. J., Arvai, A. S., McTigue, M. A., Vaughan, K. G., Mietzner, T. A. & McRee, D. E. (1997). Structure of Hemophilus influenzae Fe(+3)-binding protein reveals convergent evolution within a superfamily. Nature Struct. Biol. 4, 919–924.
Brzozowski, A. M., Pike, A. C., Dauter, Z., Hubbard, R. E., Bonn, T., Engstrom, O., Ohman, L., Greene, G. L., Gustafsson, J. A. & Carlquist, M. (1997). Molecular basis of agonism and antagonism in the oestrogen receptor. Nature (London), 389, 753–758.
Bullock, T. L., Roberts, T. M. & Stewart, M. (1996). 2.5 Å resolution crystal structure of the motile major sperm protein (MSP) of Ascaris suum. J. Mol. Biol. 263, 284–296.
Burke, K. L., Dunn, G., Ferguson, M., Minor, P. D. & Almond, J. W. (1988). Antigen chimaeras of poliovirus as potential new vaccines. Nature (London), 332, 81–82.
Bussiere, D. E., Pratt, S. D., Katz, L., Severin, J. M., Holzman, T. & Park, C. H. (1998). The structure of VanX reveals a novel amino-dipeptidase involved in mediating transposon-based vancomycin resistance. Mol. Cell, 2, 75–84.
Cameron, A. D., Sinning, I., L'Hermite, G., Olin, B., Board, P. G., Mannervik, B. & Jones, T. A. (1995). Structural analysis of human alpha-class glutathione transferase A1–1 in the apo-form and in complexes with ethacrynic acid and its glutathione conjugate. Structure, 3, 717–727.
Carfi, A., Pares, S., Duee, E., Galleni, M., Duez, C., Frere, J. M. & Dideberg, O. (1995). The 3-D structure of a zinc metallo-beta-lactamase from Bacillus cereus reveals a new type of protein fold. EMBO J. 14, 4914–4921.
Carrell, R. W. & Gooptu, B. (1998). Conformational changes and diseases – serpins, prions and Alzheimer's. Curr. Opin. Struct. Biol. 8, 799–809.
Carrell, R. W., Stein, P. E., Fermi, G. & Wardell, M. R. (1994). Biological implications of a 3 Å structure of dimeric antithrombin. Structure, 2, 257–270.
Carter, D. C. & Ho, J. X. (1994). Structure of serum albumin. Adv. Protein Chem. 45, 153–203.
Cate, J. H., Yusupov, M. M., Zusupova, G. Z., Earnest, T. N. & Noller, H. F. (1999). X-ray crystal structures of 70S ribosome functional complexes. Science, 285, 2095–2104.
Champness, J. N., Achari, A., Ballantine, S. P., Bryant, P. K., Delves, C. J. & Stammers, D. K. (1994). The structure of Pneumocystis carinii dihydrofolate reductase to 1.9 Å resolution. Structure, 2, 915–924.
Chan, D. C., Fass, D., Berger, J. M. & Kim, P. S. (1997). Core structure of gp41 from the HIV envelope glycoprotein. Cell, 89, 263–273.
Chang, G., Spencer, R. H., Lee, A. T., Barclay, M. T. & Rees, D. C. (1998). Structure of the MscL homolog from Mycobacterium tuberculosis: a gated mechanosensitive ion channel. Science, 282, 2220–2226.
Chang, Y., Mochalkin, I., McCance, S. G., Cheng, B., Tulinsky, A. & Castellino, F. J. (1998). Structure and ligand binding determinants of the recombinant kringle 5 domain of human plasminogen. Biochemistry, 37, 3258–3271.
Charifson, P. S. (1997). Practical Application of Computer-Aided Drug Design. New York: Marcel Dekker Inc.
Chitarra, V., Holm, I., Bentley, G. A., Petres, S. & Longacre, S. (1999). The crystal structure of C-terminal merozoite surface protein 1 at 1.8 Å resolution, a highly protective malaria vaccine candidate. Mol. Cell, 3, 457–464.
Cho, Y., Gorina, S., Jeffrey, P. D. & Pavletich, N. P. (1994). Crystal structure of a p53 tumor suppressor–DNA complex: understanding tumorigenic mutations. Science, 265, 346–355.
Choe, S., Bennett, M. J., Fujii, G., Curmi, P. M., Kantardjieff, K. A., Collier, R. J. & Eisenberg, D. (1992). The crystal structure of diphtheria toxin. Nature, 357, 216–222.
Choi, H. J., Kang, S. W., Yang, C. H., Rhee, S. G. & Ryu, S. E. (1998). Crystal structure of a novel human peroxidase enzyme at 2.0 Å resolution. Nature Struct. Biol. 5, 400–406.
Choudhury, D., Thompson, A., Stojanoff, V., Langermann, S., Pinkner, J., Hultgren, S. J. & Knight, S. D. (1999). X-ray structure of the Fim-C-FimH chaperone–adhesin complex from uropathogenic Escherichia coli. Science, 285, 1061–1066.
Chudzik, D. M., Michels, P. A., de Walque, S. & Hol, W. G. J. (2000). Structures of type 2 peroxisomal targeting signals in two trypanosomatid aldolases. J. Mol. Biol. 300, 697–707.
Cirilli, M., Zheng, R., Scapin, G. & Blanchard, J. S. (1993). Structural symmetry: the three-dimensional structure of Haemophilus influenzae diaminopimelate epimerase. Biochemistry, 37, 16452–16458.
Ciszak, E. & Smith, G. D. (1994). Crystallographic evidence for dual coordination around zinc in the T3R3 human insulin hexamer. Biochemistry, 33, 1512–1517.
Clackson, T., Yang, W., Rozamus, L. W., Hatada, M., Amara, J. F., Rollins, C. T., Stevenson, L. F., Magari, S. R., Wood, S. A., Courage, N. L., Lu, X., Cerasoli, F. J., Gilman, M. & Holt, D. A. (1998). Redesigning an FKBP–ligand interface to generate chemical dimerizers with novel specificity. Proc. Natl Acad. Sci. USA, 95, 10437–10442.
Cleasby, A., Wonacott, A., Skarzynski, T., Hubbard, R. E., Davies, G. J., Proudfoot, A. E., Bernard, A. R., Payton, M. A. & Wells, T. N. (1996). The X-ray crystal structure of phosphomannose isomerase from Candida albicans at 1.7 Å resolution. Nature Struct. Biol. 3, 470–479.
Clemons, W. M. J., May, J. L., Wimberly, B. T., McCutcheon, J. P., Capel, M. S. & Ramakrishnan, V. (1999). Structure of a bacterial 30S ribosomal subunit at 5.5 Å resolution. Nature (London), 400, 833–840.
Cobessi, D., Tete-Favier, F., Marchal, S., Azza, S., Branlant, G. & Aubry, A. (1999). Apo and holo crystal structures of an NADP-dependent aldehyde dehydrogenase from Streptococcus mutans. J. Mol. Biol. 290, 161–173.
Colby, T. D., Vanderveen, K., Strickler, M. D., Markham, G. D. & Goldstein, B. M. (1999). Crystal structure of human type II inosine monophosphate dehydrogenase: implications for ligand binding and drug design. Proc. Natl Acad. Sci. USA, 96, 3531–3536.
Cole, S. T., Brosch, R., Parkhill, J., Garnier, T., Churcher, C., Harris, D., Gordon, S. V., Eiglmeier, K., Gas, S., Barry, C. E. III, Tekaia, F., Badcock, K., Basham, D., Brown, D., Chillingworth, T., Connor, R., Davies, R., Devlin, K., Feltwell, T., Gentles, S., Hamlin, N., Holroyd, S., Hornby, T., Jagels, K., Krogh, A., McLean, J., Moule, S., Murphy, L., Oliver, K., Osborne, J., Quail, M. A., Rajandream, M. A., Rogers, J., Rutter, S., Seeger, K., Skelton, J., Squares, R., Squares, S., Sulston, J. E., Taylor, K., Whitehead, S. & Barrell, B. G. (1998). Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence. Nature (London), 393, 537–544.
Collins, F. S. (1992). Cystic fibrosis: molecular biology and therapeutic implications. Science, 256, 774–779.
Concha, N. O., Rasmussen, B. A., Bush, K. & Herzberg, O. (1996). Crystal structure of the wide-spectrum binuclear zinc beta-lactamase from Bacteroides fragilis. Structure, 4, 823–836.
Conlon, H. D., Baqai, J., Baker, K., Shen, Y. Q., Wong, B. L., Noiles, R. & Rausch, C. W. (1995). 2-step immobilized enzyme conversion of cephalosporin-c to 7-aminocephalosporanic acid. Biotechnol. Bioeng. 46, 510–513.
Cooper, J. B., McIntyre, K., Badasso, M. O., Wood, S. P., Zhang, Y., Garbe, T. R. & Young, D. (1995). X-ray structure analysis of the iron-dependent superoxide dismutase from Mycobacterium tuberculosis at 2.0 Å resolution reveals novel dimer–dimer interactions. J. Mol. Biol. 246, 531–544.
Correll, C. C., Batie, C. J., Ballou, D. P. & Ludwig, M. L. (1992). Phthalate dioxygenase reductase: a modular structure for electron transfer from pyridine nucleotides to [2Fe–2S]. Science, 258, 1604–1610.
Crennell, S., Garman, E., Laver, G., Vimr, E. & Taylor, G. (1994). Crystal structure of Vibrio cholerae neuraminidase reveals dual lectin-like domains in addition to the catalytic domain. Structure, 2, 535–544.
Curry, S., Mandelkow, H., Brick, P. & Franks, N. (1998). Crystal structure of human serum albumin complexed with fatty acid reveals an asymmetric distribution of binding sites. Nature Struct. Biol. 5, 827–835.
Cushman, D. W. & Ondetti, M. A. (1991). History of the design of captopril and related inhibitors of angiotensin converting enzyme. Hypertension, 17, 589–592.
Cutfield, S. M., Dodson, E. J., Anderson, B. F., Moody, P. C., Marshall, C. J., Sullivan, P. A. & Cutfield, J. F. (1995). The crystal structure of a major secreted aspartic proteinase from Candida albicans in complexes with two inhibitors. Structure, 3, 1261–1271.
Das, K., Ding, J., Hsiou, Y., Clark, A. D. Jr, Moereels, H., Koymans, L., Andries, K., Pauwels, R., Janssen, P. A. J., Boyer, P. L., Clark, P., Smith, R. H. Jr, Kroeger Smith, M. B., Michejda, C. J., Hughes, S. H. & Arnold, E. (1996). Crystal structures of 8-Cl and 9-Cl TIBO complexed with wild-type HIV-1 RT and 8-Cl TIBO complexed with the Tyr181Cys HIV-1 RT drug-resistant mutant. J. Mol. Biol. 264, 1085–1100.
Davies, J. F., Delcamp, T. J., Prendergast, N. J., Ashford, V. A., Freisheim, J. H. & Kraut, J. (1990). Crystal structures of recombinant human dihydrofolate reductase complexed with folate and 5-deazafolate. Biochemistry, 29, 9467–9479.
De Bondt, H. L., Rosenblatt, J., Jancarik, J., Jones, H. D., Morgan, D. O. & Kim, S. H. (1993). Crystal structure of cyclin-dependent kinase 2. Nature (London), 363, 595–602.
Deller, M. C. & Jones, E. Y. (2000). Cell surface receptors. Curr. Opin. Struct. Biol. 10, 213–219.
Derewenda, U., Derewenda, Z., Dodson, E. J., Dodson, G. G., Reynolds, C. D., Smith, G. D., Sparks, C. & Swenson, D. (1989). Phenol stabilizes more helix in a new symmetrical zinc insulin hexamer. Nature (London), 338, 594–596.
Dessen, A., Quemard, A., Blanchard, J. S., Jacobs, W. R. J. & Sacchettini, J. C. (1995). Crystal structure and function of the isoniazid target of Mycobacterium tuberculosis. Science, 267, 1638–1641.
DeVos, A. M., Tong, L., Milburn, M. V., Matias, P. M., Jancarik, J., Noguchi, S., Nishimura, S., Miura, K., Ohtsuka, E. & Kim, S. H. (1988). Three-dimensional structure of an oncogene protein: catalytic domain of human c-H-ras p21. Science, 239, 888–893.
DeVos, A. M., Ultsch, M. & Kossiakoff, A. A. (1992). Human growth hormone and extracellular domain of its receptor: crystal structure of the complex. Science, 255, 306–312.
Dhanaraj, V., Ye, Q.-Z., Johnson, L. L., Hupe, D. J., Otwine, D. F., Dunbar, J. B. J., Rubin, J. R., Pavlovsky, A., Humblet, C. & Blundell, T. L. (1996). X-ray structure of a hydroxamate inhibitor complex of stromelysin catalytic domain and its comparison with members of the zinc metalloproteinase superfamily. Structure, 4, 375–386.
Dickerson, R. E. & Geis, I. (1983). Hemoglobin. Menlo Park: Benjamin Cummings Publishing Co.
Ding, J., Das, K., Tantillo, C., Zhang, W., Clark, A. D. Jr, Jessen, S., Lu, X., Hsiou, Y., Jacobo-Molina, A., Andries, K., Pauwels, R., Moereels, H., Koymans, L., Janssen, P. A. J., Smith, R. H. Jr, Kroeger Koepke, M., Michejda, C. J., Hughes, S. H. & Arnold, E. (1995). Structure of HIV-1 reverse transcriptase in a complex with the non-nucleoside inhibitor alpha-APA R 95845 at 2.8 Å resolution. Structure, 3, 365–379.
Ding, J., McGrath, W. J., Sweet, R. M. & Mangel, W. F. (1996). Crystal structure of the human adenovirus proteinase with its 11 amino acid cofactor. EMBO J. 15, 1778–1783.
Duggleby, H. J., Tolley, S. P., Hill, C. P., Dodson, E. J., Dodson, G. & Moody, P. C. (1995). Penicillin acylase has a single-amino-acid catalytic centre. Nature (London), 373, 264–268.
Dyda, F., Hickman, A. B., Jenkins, T. M., Engelman, A., Craigie, R. & Davies, D. R. (1994). Crystal structure of the catalytic domain of HIV-1 integrase: similarity to other polynucleotidyl transferases. Science, 266, 1981–1986.
Eads, J. C., Scapin, G., Xu, Y., Grubmeyer, C. & Sacchettini, J. C. (1994). The crystal structure of human hypoxanthine-guanine phosphoribosyltransferase with bound GMP. Cell, 78, 325–334.
Ealick, S. E., Cook, W. J., Vijay-Kumar, S., Carson, M., Nagabhushan, T. L., Trotta, P. P. & Bugg, C. E. (1991). Three-dimensional structure of recombinant human interferon-gamma. Science, 252, 698–702.
Ealick, S. E., Rule, S. A., Carter, D. C., Greenhough, T. J., Babu, Y. S., Cook, W. J., Habash, J., Helliwell, J. R., Stoeckler, J. D., Parks, R. E. J., Chen, S. F. & Bugg, C. E. (1990). Three-dimensional structure of human erythrocytic purine nucleoside phosphorylase at 3.2-Å resolution. J. Biol. Chem. 265, 1812–1820.
Eckert, D. M., Malashkevish, V. N., Hong, L. H., Carr, P. A. & Kim, P. S. (1999). Inhibiting HIV-1 entry: discovery of D-peptide inhibitors that target the gp41 coiled-coil pocket. Cell, 99, 103–115.
Ekstrom, J. L., Mathews, I. I., Stanley, B. A., Pegg, A. E. & Ealick, S. E. (1999). The crystal structure of human S-adenosylmethionine decarboxylase at 2.25 Å resolution reveals a novel fold. Struct. Fold. Des. 7, 583–595.
Emsley, J., Cruz, M., Handin, R. & Liddington, R. (1998). Crystal structure of the von Willebrand factor A1 domain and implications for the binding of platelet glycoprotein Ib. J. Biol. Chem. 273, 10396–10401.
Emsley, P., Charles, I. G., Fairweather, N. F. & Isaacs, N. W. (1996). Structure of Bordetella pertussis virulence factor P.69 pertactin. Nature (London), 381, 90–92.
Erickson, J., Neidhart, D. J., VanDrie, J., Kempf, D. J., Wang, X. C., Norbeck, D. W., Plattner, J. J., Rittenhouse, J. W., Turon, M., Wideburg, N., Kohlbrenner, W. E., Simmer, R., Helfrich, R., Paul, D. A. & Knigge, M. (1990). Design, activity, and 2.8 Å crystal structure of a C2 symmetric inhibitor complexed to HIV-1 protease. Science, 249, 527–533.
Erickson, J. W. & Burt, S. K. (1996). Structural mechanisms of HIV drug resistance. Annu. Rev. Pharmacol. Toxicol. 36, 545–571.
Erlandsen, H., Fusetti, F., Martinez, A., Hough, E., Flatmark, T. & Stevens, R. C. (1997). Crystal structure of the catalytic domain of human phenylalanine hydroxylase reveals the structural basis for phenylketonuria. Nature Struct. Biol. 4, 995–1000.
Esser, C. K., Bugianesi, R. L., Caldwell, C. G., Chapman, K. T., Durette, P. L., Girotra, N. N., Kopka, I. E., Lanza, T. J., Levorse, D. A., Maccoss, M., Owens, K. A., Ponpipom, M. M., Simeone, J. P., Harrison, R. K., Niedzwiecki, L., Becker, J. W., Marcy, A. I., Axel, M. G., Christen, A. J., McDonnell, J., Moore, V. L., Olsqewski, J. M., Saphos, C., Visco, D. M., Shen, F., Colletti, A., Kriter, P. A. & Hagmann, W. K. (1997). Inhibition of stromelysin-1 (MMP-3) by P1′-biphenylylethyl carboxyalkyl dipeptides. J. Med. Chem. 40, 1026–1040.
Fan, C., Moews, P. C., Walsh, C. T. & Knox, J. R. (1994). Vancomycin resistance: structure of D-alanine:D-alanine ligase at 2.3 Å resolution. Science, 266, 439–443.
Fan, E., Zhang, Z., Minke, W. E., Hou, Z., Verlinde, C. L. M. J. & Hol, W. G. J. (2000). A 105 gain in affinity for pentavalent ligands of E. coli heat-labile enterotoxin by modular structure-based design. J. Am. Chem. Soc. 122, 2663–2664.
Ferrer, M., Kapoor, T. M., Strassmaier, T., Weissenhorn, W., Skehel, J. J., Oprian, D., Schreiber, S. L., Wiley, D. C. & Harrison, S. C. (1999). Selection of gp41-mediated HIV-1 cell entry inhibitors from biased combinatorial libraries of non-natural binding elements. Nature Struct. Biol. 6, 953–960.
Fields, B. A., Malchiodi, E. L., Li, H., Ysern, X., Stauffacher, C. V., Schlievert, P. M., Karjalainen, K. & Mariuzza, R. A. (1996). Crystal structure of a T-cell receptor beta-chain complexed with a superantigen. Nature (London), 384, 188–192.
Filman, D. J., Wien, M. W., Cunningham, J. A., Bergelson, J. M. & Hogle, J. M. (1998). Structure determination of echovirus 1. Acta Cryst. D54, 1261–1272.
Finzel, B. C., Baldwin, E. T., Bryant, G. L. J., Hess, G. F., Wilks, J. W., Trepod, C. M., Mott, J. E., Marshall, V. P., Petzold, G. L., Poorman, R. A., O'Sullivan, T. J., Schostarez, H. J. & Mitchell, M. A. (1998). Structural characterizations of nonpeptidic thiadiazole inhibitors of matrix metalloproteinases reveal the basis for stromelysin selectivity. Protein Sci. 7, 2118–2126.
Focia, P. J., Craig, S. P. III, Nieves-Alicea, R., Fletterick, R. J. & Eakin, A. E. (1998). A 1.4 Å crystal structure for the hypoxanthine phosphoribosyltransferase of Trypanosoma cruzi. Biochemistry, 37, 15066–15075.
Foster, B. A., Coffey, H. A., Morin, M. J. & Rastinejad, F. (1999). Pharmacological rescue of mutant p53 conformation and function. Science, 286, 2507–2510.
Fox, M. P., Otto, M. J. & McKinlay, M. A. (1986). Prevention of rhinovirus and poliovirus uncoating by WIN 51711, a new antiviral drug. Antimicrob. Agents Chemother. 30, 110–116.
Frankenberg, N., Erskine, P. T., Cooper, J. B., Shoolingin-Jordan, P. M., Jahn, D. & Heinz, D. W. (1999). High resolution crystal structure of a Mg2+-dependent porphobilinogen synthase. J. Mol. Biol. 289, 591–602.
Fremont, D. H., Matsumura, M., Stura, E. A., Peterson, P. A. & Wilson, I. A. (1992). Crystal structures of two viral peptides in complex with murine MHC class I H-2Kb. Science, 257, 919–927.
Freymann, D., Down, J., Carrington, M., Roditi, I., Turner, M. & Wiley, D. (1990). 2.9 Å resolution structure of the N-terminal domain of a variant surface glycoprotein from Trypanosoma brucei. J. Mol. Biol. 216, 141–160.
Fulop, V., Ridout, C. J., Greenwood, C. & Hajdu, J. (1995). Crystal structure of the di-haem cytochrome c peroxidase from Pseudomonas aeruginosa. Structure, 3, 1225–1233.
Futterer, K., Wong, J., Grucza, R. A., Chan, A. C. & Waksman, G. (1998). Structural basis for Syk tyrosine kinase ubiquity in signal transduction pathways revealed by the crystal structure of its regulatory SH2 domains bound to a dually phosphorylated ITAM peptide. J. Mol. Biol. 281, 523–537.
Gaboriaud, C., Serre, L., Guy-Crotte, O., Forest, E. & Fontecilla-Camps, J. C. (1996). Crystal structure of human trypsin 1: unexpected phosphorylation of Tyr151. J. Mol. Biol. 259, 995–1010.
Gamblin, S. J., Cooper, B., Millar, J. R., Davies, G. J., Littlechild, J. A. & Watson, H. C. (1990). The crystal structure of human muscle aldolase at 3.0 Å resolution. FEBS Lett. 264, 282–286.
Garboczi, D. N., Ghosh, P., Utz, U., Fan, Q. R., Biddison, W. E. & Wiley, D. C. (1996). Structure of the complex between human T-cell receptor, viral peptide and HLA-A2. Nature (London), 384, 134–141.
Garcia, K. C., Degano, M., Stanfield, R. L., Brunmark, A., Jackson, M. R., Petereson, P. A., Teyton, L. & Wilson, I. A. (1996). An αβ T cell receptor structure at 2.5 Å and its orientation in the TCR–MHC complex. Science, 274, 209–219.
Gardner, M. J., Tettelin, H., Carucci, D. J., Cummings, L. M., Aravind, L., Koonin, E. V., Shallom, S., Mason, T., Yu, K., Fujii, C., Pederson, J., Shen, K., Jing, J., Aston, C., Lai, Z., Schwartz, D. C., Pertea, M., Salzburg, S., Zhou, L., Sutton, G. G., Clayton, R., White, O., Smith, H. O., Fraser, C. M., Adams, M. D., Venter, J. C. & Hoffman, S. L. (1998). Chromosome 2 sequence of the human malaria parasite Plas­modium falciparum. Science, 282, 1126–1132.
Gatti, D. L., Palfey, B. A., Lah, M. S., Entsch, B., Massey, V., Ballou, D. P. & Ludwig, M. L. (1994). The mobile flavin of 4-OH benzoate hydroxylase. Science, 266, 110–114.
Ghosh, D., Pletnev, V. Z., Zhy, D. W., Wawrzak, Z., Duax, W. L., Pangborn, W., Labrie, F. & Lin, S. W. (1995). Structure of human estrogenic 17-beta-hydroxysteroid dehydrogenase at 2.20-Å resolution. Structure, 3, 503–513.
Giulian, D., Corpuz, M., Richmond, B., Wendt, E. & Hall, E. R. (1996). Activated microglia are the principal glial source of thromboxane in the central nervous system. Neurochem. Int. 29, 65–76.
Gohlke, U., Gomis-Ruth, F. X., Crabbe, T., Murphy, G., Docherty, A. J. & Bode, W. (1996). The C-terminal (haemopexin-like) domain structure of human gelatinase A (MMP2): structural implications for its function. FEBS Lett. 378, 126–120.
Gomis-Ruth, F. X., Gohlke, U., Betz, M., Knauper, V., Murphy, G., Lopez-Otin, C. & Bode, W. (1996). The helping hand of collagenase-3 (MMP-13): 2.7 Å crystal structure of its C-terminal haemopexin-like domain. J. Mol. Biol. 264, 556–566.
Gomis-Ruth, F. X., Maskos, K., Betz, M., Bergner, A., Huber, R., Suzuki, K., Yoshida, N., Nagase, H., Brew, K., Bourenkov, G. P., Bartunik, H. & Bode, W. (1997). Mechanism of inhibition of the human matrix metalloproteinase stromelysin-1 by TIMP-1. Nature (London), 389, 77–81.
Gong, W., O'Gara, M., Blumenthal, R. M. & Cheng, X. (1997). Structure of pvu II DNA-(cytosine N4) methyltransferase, an example of domain permutation and protein fold assignment. Nucleic Acids Res. 25, 2702–2715.
Goodwill, K. E., Sabatier, C., Marks, C., Raag, R., Fitzpatrick, P. F. & Stevens, R. C. (1997). Crystal structure of tyrosine hydroxylase at 2.3 Å and its implications for inherited neurodegenerative diseases. Nature Struct. Biol. 4, 578–585.
Gordon, D. B., Marshall, S. A. & Mayo, S. L. (1999). Energy functions for protein design. Curr. Opin. Struct. Biol. 9, 509–513.
Gorina, S. & Pavletich, N. P. (1996). Structure of the p53 tumor suppressor bound to the ankyrin and SH3 domains of 53BP2. Science, 274, 1001–1005.
Gouet, P., Jouve, H. M. & Dideberg, O. (1995). Crystal structure of Proteus mirabilis PT catalase with and without bound NADPH. J. Mol. Biol. 249, 933–954.
Gourley, D. G., Shrive, A. K., Polikarpov, I., Krell, T., Coggins, J. R., Hawkins, A. R., Isaacs, N. W. & Sawyer, L. (1999). The two types of 3-dehydrogenase have distinct structures but catalyze the same overall reaction. Nature Struct. Biol. 6, 521–525.
Grant, R. A., Hiemath, C. N., Filman, D. J., Syed, R., Andries, K. & Hogle, J. M. (1994). Structures of poliovirus complexes with anti-viral drugs: implications for viral stability and drug design. Curr. Biol. 4, 784–797.
Graves, B. J., Hatada, M. H., Hendrickson, W. A., Miller, J. K., Madison, V. S. & Satow, Y. (1990). Structure of interleukin 1 alpha at 2.7-Å resolution. Biochemistry, 29, 2679–2684.
Grimes, J., Basak, A. K., Roy, P. & Stuart, D. (1995). The crystal structure of bluetongue virus VP7. Nature (London), 373, 167–170.
Hampele, I. C., D'Arcy, A., Dale, G. E., Kostrewa, D., Nielsen, J., Oefner, C., Page, M. G., Schonfeld, H. J., Stuber, D. & Then, R. L. (1997). Structure and function of the dihydropteroate synthase from Staphylococcus aureus. J. Mol. Biol. 268, 21–30.
Han, S., Eltis, L. D., Timmis, K. N., Muchmore, S. W. & Bolin, J. T. (1995). Crystal structure of the biphenyl-cleaving extradiol dioxygenase from a PCB-degrading pseudomonad. Science, 270, 976–980.
Hansen, J. L., Long, A. M. & Schultz, S. C. (1997). Structure of the RNA-dependent RNA polymerase of poliovirus. Structure, 5, 1109–1122.
Harrington, D. J., Adachi, K. & Royer, W. E. Jr (1997). The high resolution crystal structure of deoxyhemoglobin S. J. Mol. Biol. 272, 398–407.
Harris, S. F. & Botchan, M. R. (1999). Crystal structure of the human papillomavirus type 18 E2 activation domain. Science, 284, 1673–1677.
He, X. M. & Carter, D. C. (1992). Atomic structure and chemistry of human serum albumin. Nature (London), 358, 209–215.
Hegde, R. S. & Androphy, E. J. (1998). Crystal structure of the E2 DNA-binding domain from human papillomavirus type 16: implications for its DNA binding-site selection mechanism. J. Mol. Biol. 284, 1479–1489.
Hennig, M., Dale, G. E., D'Arcy, A., Danel, F., Fischer, S., Gray, C. P., Jolidon, S., Muller, F., Page, M. G., Pattison, P. & Oefner, C. (1999). The structure and function of the 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase from Haemophilus influenzae. J. Mol. Biol. 287, 211–219.
Hennig, M., D'Arcy, A., Hampele, I. C., Page, M. G., Oefner, C. & Dale, G. E. (1998). Crystal structure and reaction mechanism of 7,8-dihydroneopterin aldolase from Staphylococcus aureus. Nature Struct. Biol. 5, 357–362.
Herzberg, O. & Moult, J. (1987). Bacterial resistance to beta-lactam antibiotics: crystal structure of beta-lactamase from Staphylococcus aureus PC1 at 2.5 Å resolution. Science, 236, 694–701.
Hill, C. P., Worthylake, D., Bancroft, D. P., Christensen, A. M. & Sundquist, W. I. (1996). Crystal structures of the trimeric human immunodeficiency virus type 1 matrix protein: implications for membrane association and assembly. Proc. Natl Acad. Sci. USA, 93, 3099–3104.
Hodel, A. E., Gershon, P. D., Shi, X. & Quiocho, F. A. (1996). The 1.85 Å structure of vaccinia protein VP39: a bifunctional enzyme that participates in the modification of both mRNA ends. Cell, 85, 247–256.
Hodgkin, D. C. (1971). Insulin molecules: the extent of our knowledge. Pure Appl. Chem. 26, 375–384.
Hofmann, B., Schomburg, D. & Hecht, H. J. (1993). Crystal structure of a thiol proteinase from Staphylococcus aureus V-8 in the E-64 inhibitor complex. Acta Cryst. A49, C-102.
Hogle, J. M., Chow, M. & Filman, D. J. (1985). Three-dimensional structure of poliovirus at 2.9 Å resolution. Science, 229, 1358–1365.
Hol, W. G. J. (1986). Protein crystallography and computer graphics – toward rational drug design. Angew. Chem. Int. Ed. Engl. 25, 767–778.
Hoog, S. S., Smith, W. W., Qiu, X., Janson, C. A., Hellmig, B., McQueney, M. S., O'Donnell, K., O'Shannessy, D., DiLella, A. G., Debouck, C. & Abdel-Meguid, S. S. (1997). Active site cavity of herpesvirus proteases revealed by the crystal structure of herpes simplex virus protease/inhibitor complex. Biochemistry, 36, 14023–14029.
Hough, E., Hansen, L. K., Birknes, B., Jynge, K., Hansen, S., Hordvik, A., Little, C., Dodson, E. & Derewenda, Z. (1989). High-resolution (1.5 Å) crystal structure of phospholipase C from Bacillus cereus. Nature (London), 338, 357–360.
Hsiou, Y., Das, K., Ding, J., Clark, A. D. Jr, Kleim, J. P., Rosner, M., Winkler, I., Riess, G., Hughes, S. H. & Arnold, E. (1998). Structures of Tyr188Leu mutant and wild-type HIV-1 reverse transcriptase complexed with the non-nucleoside inhibitor HBY 097: inhibitor flexibility is a useful design feature for reducing drug resistance. J. Mol. Biol. 284, 313–323.
Hu, S. H., Peek, J. A., Rattigan, E., Taylor, R. K. & Martin, J. L. (1997). Structure of TcpG, the DsbA protein folding catalyst from Vibrio cholerae. J. Mol. Biol. 268, 137–146.
Huang, H., Chopra, R., Verdine, G. L. & Harrison, S. C. (1998). Structure of a covalently trapped catalytic complex of HIV-1 reverse transcriptase: implications for drug resistance. Science, 282, 1669–1675.
Huang, K., Strynadka, N. C., Bernard, V. D., Peanasky, R. J. & James, M. N. (1994). The molecular structure of the complex of Ascaris chymotrypsin/elastase inhibitor with porcine elastase. Structure, 2, 679–689.
Huang, S., Xue, Y., Sauer-Eriksson, E., Chirica, L., Lindskog, S. & Jonsson, B. H. (1998). Crystal structure of carbonic anhydrase from Neisseria gonorrhoeae and its complex with the inhibitor acetazolamide. J. Mol. Biol. 283, 301–310.
Hubbard, S. R. (1997). Crystal structure of the activated insulin receptor tyrosine kinase in complex with peptide substrate and ATP analog. EMBO J. 16, 5572–5581.
Hubbard, S. R., Wei, L., Ellis, L. & Hendrickson, W. A. (1994). Crystal structure of the tyrosine kinase domain of the human insulin receptor. Nature (London), 372, 746–754.
Huizinga, E. G., Martijn van der Plas, R., Kroon, J., Sixma, J. J. & Gros, P. (1997). Crystal structure of the A3 domain of human von Willebrand factor: implications for collagen binding. Structure, 5, 1147–1156.
Hulsmeyer, M., Hecht, H. J., Niefind, K., Hofer, B., Eltis, L. D., Timmis, K. N. & Schomburg, D. (1998). Crystal structure of cis-biphenyl-2,3-dihydrodiol-2,3-dehydrogenase from a PCB degrader at 2.0 Å resolution. Protein Sci. 7, 1286–1293.
Hurley, T. D., Bosron, W. F., Hamilton, J. A. & Amzel, L. M. (1991). Structure of human beta 1 beta 1 alcohol dehydrogenase: catalytic effects of non-active-site substitutions. Proc. Natl Acad. Sci. USA, 88, 8149–8153.
Isupov, M. N., Antson, A. A., Dodson, E. J., Dodson, G. G., Dementieva, I. S., Zakomirdina, L. N., Wilson, K. S., Dauter, Z., Lebedev, A. A. & Harutyunyan, E. H. (1998). Crystal structure of tryptophanase. J. Mol. Biol. 276, 603–623.
Itzstein, M. von, Wu, W. Y., Kok, G. B., Pegg, M. S., Dyason, J. C., Jin, B., Van Phan, T., Smythe, M. L., White, H. F., Oliver, S. W., Colman, P. M., Varghese, J. N., Ryan, D. M., Woods, J. M., Bethell, R. C., Hotham, V. J., Cameron, J. M. & Penn, C. R. (1993). Rational design of potent sialidase-based inhibitors of influenza virus replication. Nature (London), 363, 418–423.
Jackson, R. C. (1997). Contributions of protein structure-based drug design to cancer chemotherapy. Semin. Oncol. 24, 164–172.
Jacobo-Molina, A., Ding, J., Nanni, R. G., Clark, A. D. Jr, Lu, X., Tantillo, C., Williams, R. L., Kamer, G., Ferris, A. L., Clark, P., Hizi, A., Hughes, S. H. & Arnold, E. (1993). Crystal structure of human immunodeficiency virus type 1 reverse transcriptase complexed with double-stranded DNA at 3.0 Å resolution shows bent DNA. Proc. Natl Acad. Sci. USA, 90, 6320–6324.
Jain, S., Drendel, W. B., Chen, Z. W., Mathews, F. S., Sly, W. S. & Grubb, J. H. (1996). Structure of human beta-glucuronidase reveals candidate lysosomal targeting and active-site motifs. Nature Struct. Biol. 3, 375–381.
Jia, Z., Vandonselaar, M., Quail, J. W. & Delbaere, L. T. (1993). Active-centre torsion-angle strain revealed in 1.6 Å-resolution structure of histidine-containing phosphocarrier protein. Nature (London), 361, 94–97.
Kallarakal, A. T., Mitra, B., Kozarich, J. W., Gerlt, J. A., Clifton, J. G., Petsko, G. A. & Kenyon, G. L. (1995). Mechanism of the reaction catalyzed by mandelate racemase: structure and mechanistic properties of the K166R mutant. Biochemistry, 34, 2788–2797.
Kallen, J., Spitzfaden, C., Zurini, M. G. M., Wider, G., Widmer, H., Wuethrich, K. & Walkinshaw, M. D. (1991). Structure of human cyclophilin and its binding site for cyclosporin A determined by X-ray crystallography and NMR spectroscopy. Nature (London), 353, 276–279.
Kannan, K. K., Notstrand, B., Fridborg, K., Lovgren, S., Ohlsson, A. & Petef, M. (1975). Crystal structure of human erythrocyte carbonic anhydrase B. Three-dimensional structure at a nominal 2.2-Å resolution. Proc. Natl Acad. Sci. USA, 72, 51–55.
Karpusas, M., Nolte, M., Benton, C. B., Meier, W., Lipscomb, W. N. & Goelz, S. (1997). The crystal structure of human interferon beta at 2.2-Å resolution. Proc. Natl Acad. Sci. USA, 94, 11813–11818.
Ke, H., Zydowsky, L. D., Liu, J. & Walsh, C. T. (1991). Crystal structure of recombinant human T-cell cyclophilin A at 2.5-Å resolution. Proc. Natl Acad. Sci. USA, 88, 9483–9487.
Kim, H., Certa, U., Döbelli, H., Jakob, P. & Hol, W. G. J. (1998). Crystal structure of fructose-1,6-bisphosphate aldolase from the human malaria parasite Plasmodium falciparum. Biochemistry, 37, 4388–4396.
Kim, H., Feil, I. K., Verlinde, C. L. M. J., Petra, P. H. & Hol, W. G. J. (1995). Crystal structure of glycosomal glyceraldehyde-3-phosphate dehydrogenase from Leishmania mexicana: implication for structure-based drug design and a new position for the inorganic phosphate binding site. Biochemistry, 34, 14975–14986.
Kim, K. K., Song, H. K., Shin, D. H., Hwang, K. Y. & Suh, S. W. (1997). The crystal structure of a triacylglycerol lipase from Pseudomonas cepacia reveals a highly open conformation in the absence of a bound inhibitor. Structure, 5, 173–185.
Kim, Y., Yoon, K.-H., Khang, Y., Turley, S. & Hol, W. G. J. (2000). The 2.0 Å crystal structure of cephalosporin acylase. Struct. Fold. Des. 8, 1059–1068.
Kissinger, C. R., Parge, H. E., Knighton, D. R., Lewis, C. T., Pelletier, L. A., Tempczyk, A., Kalish, V. J., Tucker, K. D., Showalter, R. E., Moomaw, E. W., Gastinel, L. N., Habuka, N., Chen, X., Maldonado, F., Barker, J. E., Bacquet, R. & Villafranca, J. E. (1995). Crystal structures of human calcineurin and the human FKBP12-FK506-calcineurin complex. Nature (London), 378, 641–644.
Kitadokoro, K., Hagishita, S., Sato, T., Ohtan, M. & Miki, K. (1998). Crystal structure of human secretory phospholipase A2-IIA complex with the potent indolizine inhibitor 120–1032. J. Biochem. 123, 619–623.
Kitov, P. I., Sadowska, J. M., Mulvey, G., Armstrong, G. D., Ling, H., Pannu, N. S., Read, R. J. & Bundle, D. R. (2000). Shiga-like toxins are neutralized by tailored multivalent carbohydrate ligands. Nature (London), 403, 669–672.
Knighton, D. R., Kan, C. C., Howland, E., Janson, C. A., Hostomska, Z., Welsh, K. M. & Matthews, D. A. (1994). Structure of and kinetic channelling in bifunctional dihydrofolate reductase-thymidylate synthase. Nature Struct. Biol. 1, 186–194.
Ko, T.-P., Safo, M. K., Musayev, F. N., Di Salvo, M. L., Wang, C., Wu, S.-H. & Abraham, D. J. (2000). Structure of human erythrocyte catalase. Acta Cryst. D56, 241–245.
Kohara, M., Abe, S., Komatsu, T., Tago, K., Arita, M. & Nomoto, A. (1988). A recombinant virus between the Sabin 1 and Sabin 3 vaccine strains of poliovirus as a possible candidate for a new type 3 poliovirus live vaccine strain. J. Virol. 62, 2828–2835.
Kohlstaedt, L. A., Wang, J., Friedman, J. M., Rice, P. A. & Steitz, T. A. (1992). Crystal structure at 3.5 Å resolution of HIV-1 reverse transcriptase complexed with an inhibitor. Science, 256, 1783–1790.
Kohno, M., Funatsu, J., Mikami, B., Kugimiya, W., Matsuo, T. & Morita, Y. (1996). The crystal structure of lipase II from Rhizopus niveus at 2.2 Å resolution. J. Biochem. 120, 505–510.
Kopka, M. L., Yoon, C., Goodsell, D., Pjura, P. & Dickerson, R. E. (1985). The molecular origin of DNA-drug specificity in netropsin and distamycin. Proc. Natl Acad. Sci. USA, 82, 1376–1380.
Krengel, U., Petsko, G. A., Goody, R. S., Kabsch, W. & Wittinghofer, A. (1990). Refined crystal structure of the triphosphate conformation of H-ras p21 at 1.35-Å resolution: implications for the mechanism of GTP hydrolysis. EMBO J. 9, 2351–2359.
Kuntz, I. D. (1992). Structure-based strategies for drug design and discovery. Science, 257, 1078–1082.
Kurihara, H., Mitsui, Y., Ohgi, K., Irie, M., Mizuno, H. & Nakamura, K. T. (1992). Crystal and molecular structure of RNase Rh, a new class of microbial ribonuclease from Rhizopus niveus. FEBS Lett. 306, 189–192.
Kuzin, A. P., Nukaga, M., Nukaga, Y., Hujer, A. M., Bonomo, R. A. & Knox, J. R. (1999). Structure of the SHV-1 beta-lactamase. Biochemistry, 38, 5720–5727.
Kwong, P. D., Wyatt, R., Robinson, J., Sweet, R. W., Sodroski, J. & Hendrickson, W. A. (1998). Structure of an HIV gp120 envelope glycoprotein incomplex with the CD4 receptor and a neutralizing human antibody. Nature (London), 393, 648–659.
Laba, D., Bauer, M., Huber, R., Fischer, S., Rudolph, R., Kohnert, U. & Bode, W. (1996). The 2.3 Å crystal structure of the catalytic domain of recombinant two-chain human tissue-type plasminogen activator. J. Mol. Biol. 258, 117–135.
Lacy, D. B. & Stevens, R. C. (1998). Unraveling the structure and modes of action of bacterial toxins. Curr. Opin. Struct. Biol. 8, 778–784.
Lacy, D. B., Tepp, W., Cohen, A. C., DasGupta, B. R. & Stevens, R. C. (1998). Crystal structure of botulinum neurotoxin type A and implications for toxicity. Nature Struct. Biol. 5, 898–902.
Lantwin, C. B., Schlichting, I., Kabsch, W., Pai, E. F. & Krauth-Siegel, R. L. (1994). The structure of Trypanosoma cruzi trypanothione reductase in the oxidized and NADPH reduced state. Proteins, 18, 161–173.
Le, H. V., Yao, N. & Weber, P. C. (1998). Emerging targets in the treatment of hepatitis C infection. Emerg. Ther. Targets, 2, 125–136.
Lebron, J. A., Bennett, M. J., Vaughn, D. E., Chirino, A. J., Snow, P. M., Mintier, G. A., Feder, J. N. & Bjorkman, P. J. (1998). Crystal structure of the hemochromatosis protein HFE and characterization of its interaction with transferrin receptor. Cell, 93, 111–123.
Lee, C. H., Saksela, K., Mirza, U. A., Chait, B. T. & Kuriyan, J. (1996). Crystal structure of the conserved core of HIV-1 Nef complexed with a Src family SH3 domain. Cell, 85, 931–942.
Leonard, S. A., Gittis, A. G., Petrella, E. D., Pollard, T. D. & Lattman, E. E. (1997). Crystal structure of the actin-binding protein actophorin from Acanthamoeba. Nature Struct. Biol. 4, 369–373.
Levine, M. M. & Noriega, F. (1995). A review of the current status of enteric vaccines. Papua New Guinea Med. J. 38, 325–331.
Li, H., Dunn, J. J., Luft, B. J. & Lawson, C. L. (1997). Crystal structure of Lyme disease antigen outer surface protein A complexed with an Fab. Proc. Natl Acad. Sci. USA, 94, 3584–3589.
Li, R., Sirawaraporn, P., Chitnumsub, P., Sirawaraporn, W. & Hol, W. G. J. (2000). Three-dimensional structure of M. tuberculosis dihydrofolate reductase reveals opportunities for the design of novel tuberculosis drugs. J. Mol. Biol. 295, 307–323.
Li de la Sierra, I., Pernot, L., Prange, T., Saludjian, P., Schiltz, M., Fourme, R. & Padron, G. (1997). Molecular structure of the lipoamide dehydrogenase domain of a surface antigen from Neisseria meningitidis. J. Mol. Biol. 269, 129–141.
Libson, A. M., Gittis, A. G., Collier, I. E., Marmer, B. L., Goldberg, G. I. & Lattman, E. E. (1995). Crystal structure of the haemopexin-like C-terminal domain of gelatinase A. Nature Struct. Biol. 2, 938–942.
Liljas, A., Kannan, K. K., Bergsten, P. C., Waara, I., Fridborg, K., Strandberg, B., Carlbom, U., Jarup, L., Lovgren, S. & Petef, M. (1972). Crystal structure of human carbonic anhydrase C. Nat. New Biol. 235, 131–137.
Lin, J. H., Ostovic, D. & Vacca, J. P. (1998). The integration of medicinal chemistry, drug metabolism, and pharmaceutical research and development in drug discovery and development. The story of Crixivan, an HIV protease inhibitor. Pharm. Biotechnol. 99, 233–255.
Ling, H., Boodhoo, A., Hazes, B., Cummings, M. D., Armstrong, G. D., Brunton, J. L. & Read, R. J. (1998). Structure of the shiga-like toxin I B-pentamer complexed with an analogue of its receptor Gb3. Biochemistry, 37, 1777–1788.
Liu, S., Fedorov, A. A., Pollard, T. D., Lattman, E. E., Almo, S. C. & Magnus, K. A. (1998). Crystal packing induces a conformational change in profilin-I from Acanthamoeba castellanii. J. Struct. Biol. 123, 22–29.
Liu, Y., Gong, W., Huang, C. C., Herr, W. & Cheng, X. (1999). Crystal structure of the conserved core of the herpes simplex virus transcriptional regulatory protein VP16. Genes Dev. 13, 1692–1703.
Livnah, O., Johnson, D. L., Stura, E. A., Farrell, F. X., Barbone, F. P., You, Y., Liu, K. D., Goldsmith, M. A., He, W., Krause, C. D., Petska, S., Jolliffe, L. K. & Wilson, I. A. (1998). An antagonist peptide-EPO receptor complex suggests that receptor dimerization is not sufficient for activation. Nature Struct. Biol. 5, 993–1004.
Livnah, O., Stura, E. A., Johnson, D. L., Middleton, S. A., Mulcahy, L. S., Wrighton, N. C., Dower, W. J., Jolliffe, L. K. & Wilson, I. A. (1996). Functional mimicry of a protein hormone by a peptide agonist: the EPO receptor complex at 2.8 Å. Science, 273, 464–471.
Lobkovsky, E., Moews, P. C., Liu, H., Zhao, H., Frere, J. M. & Knox, J. R. (1993). Evolution of an enzyme activity: crystallographic structure at 2-Å resolution of cephalosporinase from the ampC gene of Enterobacter cloacae P99 and comparison with a class A penicillinase. Proc. Natl Acad. Sci. USA, 90, 11257–11261.
Loebermann, H., Tokuoka, R., Deisenhofer, J. & Huber, R. (1984). Human alpha 1-proteinase inhibitor. Crystal structure analysis of two crystal modifications, molecular model and preliminary analysis of the implications for function. J. Mol. Biol. 177, 531–557.
Loll, P. J. & Lattman, E. E. (1989). The crystal structure of the ternary complex of staphylococcal nuclease, Ca2+, and the inhibitor pdTp, refined at 1.65 Å. Proteins, 5, 183–201.
Love, R. A., Parge, H. E., Wickersham, J. A., Hostomsky, Z., Habuka, N., Moomaw, E. W., Adachi, T. & Hostomska, Z. (1996). The crystal structure of hepatitis C virus NS3 proteinase reveals a trypsin-like fold and a structural zinc binding site. Cell, 87, 331–342.
Lovejoy, B., Cleasby, A., Hassell, A. M., Longley, K., Luther, M. A. W. D., McGeehan, G., McElroy, A. B., Drewry, D., Lambert, M. H. & Jordan, S. R. (1994). Structure of the catalytic domain of fibroblast collagenase complexed with an inhibitor. Science, 263, 375–377.
Lovejoy, B., Hassell, A. M., Luther, M. A., Weigl, D. & Jordan, S. R. (1994). Crystal structures of recombinant 19-kDa human fibroblast collagenase complexed to itself. Biochemistry, 33, 8207–8217.
Lukatela, G., Krauss, N., Theis, K., Selmer, T., Gieselmann, V., von Figura, K. & Saenger, W. (1998). Crystal structure of human arylsulfatase A: the aldehyde function and the metal ion at the active site suggest a novel mechanism for sulfate ester hydrolysis. Biochemistry, 37, 3654–3664.
McGrath, M. E., Eakin, A. E., Engel, J. C., McKerrow, J. H., Craik, C. S. & Fletterick, R. J. (1995). The crystal structure of cruzain: a therapeutic target for Chagas' disease. J. Mol. Biol. 247, 251–259.
McGrath, M. E., Palmer, J. T., Bromme, D. & Somoza, J. R. (1998). Crystal structure of human cathepsin S. Protein Sci. 7, 1294–1302.
McLaughlin, P. J., Gooch, J. T., Mannherz, H. G. & Weeds, A. G. (1993). Structure of gelsolin segment 1-actin complex and the mechanism of filament severing. Nature (London), 364, 685–692.
McTigue, M. A., Wickersham, J. A., Pinko, C., Showalter, R. E., Parast, C. V., Tempczyk-Russell, A., Gehring, M. R., Mroczkowski, B., Kan, C. C., Villafranca, J. E. & Appelt, K. (1999). Crystal structure of the kinase domain of human vascular endothelial growth factor receptor 2: a key enzyme in angiogenesis. Struct. Fold. Des. 7, 319–330.
McTigue, M. A., Williams, D. R. & Tainer, J. A. (1995). Crystal structure of a schistosomal drug and vaccine target: glutathione S-transferase from Schistosoma japonica and its complex with the leading antischistosomal drug praziquantel. J. Mol. Biol. 246, 21–27.
Maldonado, E., Soriano-Garcia, M., Moreno, A., Cabrera, N., Garza-Ramos, G., de Gomez-Puyou, M., Gomez-Puyou, A. & Perez-Montfort, R. (1998). Differences in the intersubunit contacts in triose­phosphate isomerase from two closely related pathogenic trypan­osomes. J. Mol. Biol. 283, 193–203.
Malik, P. & Perham, R. N. (1997). Simultaneous display of different peptides on the surface of filamentous bacteriophage. Nucleic Acids Res. 25, 915–916.
Mande, S. C., Mainfroid, V., Kalk, K. H., Goraj, K., Marital, J. A. & Hol, W. G. J. (1994). Crystal structure of recombinant human triosephosphate isomerase at 2.8 Å resolution. Protein Sci. 3, 810–821.
Mande, S. C., Mehra, F., Bloom, B. R. & Hol, W. G. J. (1996). Structure of the heat shock protein chaperonin-10 of Mycobacterium leprae. Science, 271, 203–207.
Martin, A., Wychowski, C., Couderc, T., Crainic, R., Hogle, J. & Girard, M. (1988). Engineering a poliovirus type 2 antigenic site on a type 1 capsid results in a chimaeric virus which is neurovirulent for mice. EMBO J. 7, 2839–2847.
Mather, T., Oganesseyan, V., Hof, P., Huber, R., Foundling, S., Esmon, S. & Bode, W. (1996). The 2.8 Å crystal structure of Gla-domainless activated protein C. EMBO J. 15, 6822–6831.
Mathews, I. I., Vanderhoff-Hanaver, P., Castellino, F. J. & Tulinsky, A. (1996). Crystal structures of the recombinant kringle 1 domain of human plasminogen in complexes with the ligands epsilon-aminocaproic acid and trans-4-(aminomethyl)cyclohexane-1-carboxylic acid. Biochemistry, 35, 2567–2576.
Matthews, D. A., Alden, R. A., Bolin, J. T., Freer, S. T., Hamlin, R., Xuong, N., Kraut, J., Poe, M., Williams, M. & Hoogsteen, K. (1977). Dihydrofolate reductase: X-ray structure of the binary complex with methotrexate. Science, 197, 452–455.
Matthews, D. A., Smith, W. W., Ferre, R. A., Condon, B., Budahazi, G., Sisson, W., Villafranca, J. E., Janson, C. A., McElroy, H. E., Gribskov, C. L. & Worland, S. (1994). Structure of human rhinovirus 3C protease reveals a trypsin-like polypeptide fold, RNA-binding site, and means for cleaving precursor polyprotein. Cell, 77, 761–771.
Meng, W., Sawasdikosol, S., Burakoff, S. J. & Eck, M. J. (1999). Structure of the amino-terminal domain of Cbl complexed to its binding site on ZAP-70 kinase. Nature (London), 398, 84–90.
Merritt, E. A., Sarfaty, S., van den Akker, F., L'hoir, C., Martial, J. A. & Hol, W. G. J. (1994). Crystal structure of cholera toxin B-pentamer bound to receptor GM1 pentasaccharide. Protein Sci. 3, 166–175.
Merritt, E. A., Sarfaty, S., Feil, I. K. & Hol, W. G. J. (1997). Structural foundation for the design of receptor antagonists targeting E. coli heat-labile enterotoxin. Structure, 5, 1485–1499.
Metcalf, P. & Fusek, M. (1993). Two crystal structures for cathepsin D: the lysosomal targeting signal and active site. EMBO J. 12, 1293–1302.
Mikami, B., Adachi, M., Kage, T., Sarikaya, E., Nanmori, T., Shinke, R. & Utsumi, S. (1999). Structure of raw starch-digesting Bacillus cereus beta-amylase complexed with maltose. Biochemistry, 38, 7050–7061.
Mikol, V., Ma, D. & Carlow, C. K. (1998). Crystal structure of the cyclophilin-like domain from the parasitic nematode Brugia malayi. Protein Sci. 7, 1310–1316.
Milburn, M. V., Hassell, A. M., Lambert, M. H., Jordan, S. R., Proudfoot, A. E. I., Graber, P. & Wells, T. N. C. (1993). A novel dimer configuration revealed by the crystal structure at 2.4-Å resolution of human interleukin-5. Nature (London), 363, 172–176.
Miller, M. D., Tanner, J., Alpaugh, M., Benedik, M. J. & Krause, K. L. (1994). 2.1 Å structure of Serratia endonuclease suggests a mechanism for binding to double-stranded DNA. Nature Struct. Biol. 1, 461–468.
Minke, W. E., Hong, F., Verlinde, C. L. M. J., Hol, W. G. J. & Fan, E. (1999). Using a galactose library for exploration of a novel hydrophobic pocket in the receptor binding site of the E. coli heat-labile enterotoxin. J. Biol. Chem. 274, 33469–33473.
Miyatake, H., Hata, Y., Fujii, T., Hamada, K., Morihara, K. & Katsube, Y. (1995). Crystal structure of the unliganded alkaline protease from Pseudomonas aeruginosa IFO3080 and its conformational changes on ligand binding. J. Biochem. (Tokyo), 118, 474–479.
Moser, J., Gerstel, B., Meyer, J. E., Chakraborty, T., Wehland, J. & Heinz, D. W. (1997). Crystal structure of the phosphatidylinositol-specific phospholipase C from the human pathogen Listeria monocytogenes. J. Mol. Biol. 273, 269–282.
Mottonen, J., Strand, A., Symersky, J., Sweet, R. M., Danley, D. E., Gioghegan, K. F., Gerard, R. D. & Goldsmith, E. J. (1992). Structural basis of latency in plasminogen activator inhibitor-1. Nature (London), 355, 270–273.
Muchmore, S. W., Sattler, M., Liang, H., Meadows, R. P., Harlan, J. E., Yoon, H. S., Nettesheim, D., Chang, B. S., Thompson, C. B., Wong, S. L., Ng, S. L. & Fesik, S. W. (1996). X-ray and NMR structure of human Bcl-xL, an inhibitor of programmed cell death. Nature (London), 381, 335–341.
Mulichak, A. M., Tulinsky, A. & Ravichandran, K. G. (1991). Crystal and molecular structure of human plasminogen kringle 4 refined at 1.9-Å resolution. Biochemistry, 30, 10576–10588.
Mulichak, A. M., Wilson, J. E., Padmanabhan, K. & Garavito, R. M. (1998). The structure of mammalian hexokinase-1. Nature Struct. Biol. 5, 555–560.
Muller, Y. A., Ultsch, M. H. & DeVos, A. M. (1996). The crystal structure of the extracellular domain of human tissue factor refined to 1.7-Å resolution. J. Mol. Biol. 256, 144–159.
Muller, Y. A., Ultsch, M. H., Kelley, R. F. & DeVos, A. M. (1994). Structure of the extracellular domain of human tissue factor: location of the factor VIIa binding site. Biochemistry, 33, 10864–10870.
Murray, C. J. & Salomon, J. A. (1998). Modeling the impact of global tuberculosis control strategies. Proc. Natl Acad. Sci. USA, 95, 13881–13886.
Murray, I. A., Cann, P. A., Day, P. J., Derrick, J. P., Sutcliffe, M. J., Shaw, W. V. & Leslie, A. G. (1995). Steroid recognition by chloramphenicol acetyltransferase: engineering and structural analysis of a high affinity fusidic acid binding site. J. Mol. Biol. 254, 993–1005.
Murray, M. G., Kuhn, R. J., Arita, M., Kawamura, N., Nomoto, A. & Wimmer, E. (1988). Poliovirus type 1/type 3 antigenic hybrid virus constructed in vitro elicits type 1 and type3 neutralizing antibodies in rabbits and monkeys. Proc. Natl Acad. Sci. USA, 85, 3203–3207.
Murthy, H. M., Clum, S. & Padmanabhan, R. (1999). Dengue virus NS3 serine protease. Crystal structure and insights into interaction of the active site with substrates by molecular modeling and structural analysis of mutational effects. J. Biol. Chem. 274, 5573–5580.
Musil, D., Zucic, D., Turk, D., Engh, R. A., Mayr, I., Huber, R., Popovic, T., Turk, V., Towatari, T., Katunuma, N. & Bode, W. (1991). The refined 2.15 Å X-ray crystal structure of human liver cathepsin B: the structural basis for its specificity. EMBO J. 10, 2321–2330.
Nagar, B., Jones, R. G., Diefenbach, R. J., Isenman, D. E. & Rini, J. M. (1998). X-ray crystal structure of C3d: a C3 fragment and ligand for complement receptor 2. Science, 280, 1277–1281.
Nam, H. J., Haser, W. G., Roberts, T. M. & Frederick, C. A. (1996). Intramolecular interactions of the regulatory domains of the Bcr-Abl kinase reveal a novel control mechanism. Structure, 4, 1105–1114.
Narayana, N., Matthews, D. A., Howell, E. E. & Nguyen-huu, X. (1995). A plasmid-encoded dihydrofolate reductase from trimethoprim-resistant bacteria has a novel D2-symmetric active site. Nature Struct. Biol. 2, 1018–1025.
National Institute of Allergy and Infectious Diseases (1998). The Jordan Report: Accelerated Development of Vaccines. NIAID, Bethesda, MD.
Navia, M. A., Fitzgerald, P. M., McKeever, B. M., Leu, C. T., Heimbach, J. C., Herber, W. K., Sigal, I. S., Darke, P. L. & Springer, J. P. (1989). Three-dimensional structure of aspartyl protease from human immunodeficiency virus HIV-1. Nature (London), 337, 615–620.
Navia, M. A., McKeever, B. M., Springer, J. P., Lin, T. Y., Williams, H. R., Fluder, E. M., Dorn, C. P. & Hoogsteen, K. (1989). Structure of human neutrophil elastase in complex with a peptide chloromethyl ketone inhibitor at 1.84-Å resolution. Proc. Natl Acad. Sci. USA, 86, 7–11.
Naylor, C. E., Eaton, J. T., Howells, A., Justin, N., Moss, D. S., Titball, R. W. & Basak, A. K. (1998). Structure of the key toxin in gas gangrene. Nature Struct. Biol. 5, 738–746.
Nurizzo, D., Silvestrini, M. C., Mathieu, M., Cutruzzola, F., Bourgeois, D., Fulop, V., Hajdu, J., Brunori, M., Tegoni, M. & Cambillau, C. (1997). N-terminal arm exchange is observed in the 2.15 Å crystal structure of oxidized nitrite reductase from Pseudomonas aeruginosa. Structure, 5, 1157–1171.
Oefner, C., D'Arcy, A. & Winkler, F. K. (1988). Crystal structure of human dihydrofolate reductase complexed with folate. Eur. J. Biochem. 174, 377–385.
Oinonen, C., Tikkanen, R., Rouvinen, J. & Peltonen, L. (1995). Three-dimensional structure of human lysosomal aspartylglucosaminidase. Nature Struct. Biol. 2, 1102–1108.
Ozaki, H., Sato, T., Kubota, H., Hata, Y., Katsube, Y. & Shimonishi, Y. (1991). Molecular structure of the toxin domain of heat-stable enterotoxin produced by a pathogenic strain of Escherichia coli. A putative binding site for a binding protein on rat intestinal epithelial cell membranes. J. Biol. Chem. 266, 5934–5941.
Padmanabhan, K., Padmanabhan, K. P., Tulinsky, A., Park, C. H., Bode, W., Huber, R., Blankenship, D. T., Cardin, A. D. & Kisiel, W. (1993). Structure of human des(1–45) factor Xa at 2.2-Å resolution. J. Mol. Biol. 232, 947–966.
Pai, E. F., Kabsch, W., Krengel, U., Holmes, K. C., John, J. & Wittinghofer, A. (1989). Structure of the guanine-nucleotide-binding domain of the Ha-ras oncogene product p21 in the triphosphate conformation. Nature (London), 341, 209–214.
Papageorgiou, A. C., Acharya, K. R., Shapiro, R., Passalacqua, E. F., Brehm, R. D. & Tranter, H. S. (1995). Crystal structure of the superantigen enterotoxin C2 from Staphylococcus aureus reveals a zinc-binding site. Structure, 3, 769–779.
Papageorgiou, A. C., Tranter, H. S. & Acharya, K. R. (1998). Crystal structure of microbial superantigen staphylococcal enterotoxin B at 1.5 Å resolution: implications for superantigen recognition by MHC class II molecules and T-cell receptors. J. Mol. Biol. 277, 61–79.
Pares, S., Mouz, N., Petillot, Y., Hakenbeck, R. & Dideberg, O. (1996). X-ray structure of Streptococcus pneumoniae PBP2x, a primary penicillin target enzyme. Nature Struct. Biol. 3, 284–289.
Parge, H. E., Forest, K. T., Hickey, M. J., Christensen, D. A., Getzoff, E. D. & Tainer, J. A. (1995). Structure of the fibre-forming protein pilin at 2.6 Å resolution. Nature (London), 378, 32–38.
Parge, H. E., Hallewell, R. A. & Tainer, J. A. (1992). Atomic structures of wild-type and thermostable mutant recombinant human Cu,Zn superoxide dismutase. Proc. Natl Acad. Sci. USA, 89, 6109–6113.
Patskovsky, Y. V., Patskovska, L. N. & Listowsky, I. (1999). Functions of His107 in the catalytic mechanism of human glutathione s-transferase hGSTM1a-1a. Biochemistry, 38, 1193–1202.
Pauptit, R. A., Karlsson, R., Picot, D., Jenkins, J. A., Niklaus-Reimer, A. S. & Jansonius, J. N. (1988). Crystal structure of neutral protease from Bacillus cereus refined at 3.0 Å resolution and comparison with the homologous but more thermostable enzyme thermolysin. J. Mol. Biol. 199, 525–537.
Pearl, L., O'Hara, B., Drew, R. & Wilson, S. (1994). Crystal structure of AmiC: the controller of transcription antitermination in the amidase operon of Pseudomonas aeruginosa. EMBO J. 13, 5810–5817.
Pedelacq, J. D., Maveyraud, L., Prevost, G., Bab-Moussa, L., Gonzalez, A., Coucelle, E., Shepard, W., Monteil, H., Samama, J. P. & Mourey, L. (1999). The structure of a Staphylococcus aureus leucocidin component (LukF-PV) reveals the fold of the water-soluble species of a family of transmembrane pore-forming toxins. Struct. Fold. Des. 7, 277–287.
Pedersen, L. C., Benning, M. M. & Holden, H. M. (1995). Structural investigation of the antibiotic and ATP-binding sites in kanamycin nucleotidyltransferase. Biochemistry, 34, 13305–13311.
Perrakis, A., Tews, I., Dauter, Z., Oppenheim, A. B., Chet, I., Wilson, K. S. & Vorgias, C. E. (1994). Crystal structure of a bacterial chitinase at 2.3 Å resolution. Structure, 2, 1169–1180.
Perutz, M. (1992). Protein Structure. New Approaches to Disease and Therapy. New York: W. H. Freeman & Co.
Petosa, C., Collier, R. J., Klimpel, K. R., Leppla, S. H. & Liddington, R. C. (1997). Crystal structure of the anthrax toxin protective antigen. Nature (London), 385, 833–838.
Pfuegl, G., Kallen, J., Schirmer, T., Jansonius, J. N., Zurini, M. G. M. & Walkinshaw, M. D. (1993). X-ray structure of a decameric cyclophilin–cyclosporin crystal complex. Nature (London), 361, 91–94.
Phillips, C., Dohnalek, J., Gover, S., Barrett, M. P. & Adams, M. J. (1998). A 2.8 Å resolution structure of 6-phosphogluconate dehydrogenase from the protozoan parasite Trypanosoma brucei: comparison with the sheep enzyme accounts for differences in activity with coenzyme and substrate analogues. J. Mol. Biol. 282, 667–681.
Phillips, C. L., Ullman, B., Brennan, R. G. & Hill, C. P. (1999). Crystal structures of adenine phosphoribosyltransferase from Leishmania donovani. EMBO J. 18, 3533–3545.
Pineo, G. F. & Hull, R. D. (1999). Thrombin inhibitors as anticoagulant agents. Curr. Opin. Hematol. 6, 298–303.
Poljak, R. J., Amzel, L. M., Avey, H. P., Chen, B. L., Phizackerley, R. P. & Saul, F. (1973). Three-dimensional structure of the Fab′ fragment of a human immunoglobulin at 2.8-Å resolution. Proc. Natl Acad. Sci. USA, 70, 3305–3310.
Porter, R. (1999). The Greatest Benefit to Mankind: a Medical History of Humanity. New York: W. W. Norton and Co., Inc.
Prasad, G. S., Earhart, C. A., Murray, D. L., Novick, R. P., Schlievert, P. M. & Ohlendorf, D. H. (1993). Structure of toxic shock syndrome toxin 1. Biochemistry, 32, 13761–13766.
Pratt, K. P., Cote, H. C., Chung, D. W., Stenkamp, R. E. & Davie, E. W. (1997). The primary fibrin polymerization pocket: three-dimensional structure of a 30-kDa C-terminal gamma chain fragment complexed with the peptide Gly-Pro-Arg-Pro. Proc. Natl Acad. Sci. USA, 94, 7176–7181.
Pratt, K. P., Shen, B. W., Takeshima, K., Davie, E. W., Fujikawa, K. & Stoddard, B. L. (1999). Structure of the C2 domain of human factor VIII at 1.5 Å resolution. Nature (London), 402, 439–442.
Priestle, J. P., Schar, H. P. & Grutter, M. G. (1988). Crystal structure of the cytokine interleukin-1 beta. EMBO J. 7, 339–343.
Qiu, X., Culp, J. S., DiLella, A. G., Hellmig, B., Hoog, S. S., Janson, C. A., Smith, W. W. & Abdel-Meguid, S. S. (1996). Unique fold and active site in cytomegalovirus protease. Nature (London), 383, 275–279.
Qiu, X., Janson, C. A., Culp, J. S., Richardson, S. B., Debouck, C., Smith, W. W. & Abdel-Meguid, S. S. (1997). Crystal structure of varicella-zoster virus protease. Proc. Natl Acad. Sci. USA, 94, 2874–2879.
Qiu, X., Verlinde, C. L. M. J., Zhang, S., Schmitt, M. P., Holmes, R. K. & Hol, W. G. J. (1995). Three-dimensional structure of the diphtheria toxin repressor in complex with divalent cation co-repressors. Structure, 3, 87–100.
Rabijns, A., De Bondt, H. L. & De Ranter, C. (1997). Three-dimensional structure of staphylokinase, a plasminogen activator with therapeutic potential. Nature Struct. Biol. 4, 357–360.
Radhakrishnan, R., Walter, L. J., Hruza, A., Reichert, P., Trotta, P. P., Nagabhushan, T. L. & Walter, M. R. (1996). Zinc mediated dimer of human interferon-alpha 2b revealed by X-ray crystallography. Structure, 4, 1453–1463.
Raghunathan, S., Chandross, R. J., Kretsinger, R. H., Allison, T. J., Penington, C. J. & Rule, G. S. (1994). Crystal structure of human class mu glutathione transferase GSTM2–2. Effects of lattice packing on conformational heterogeneity. J. Mol. Biol. 238, 815–832.
Rano, T. A., Timkey, T., Peterson, E. P., Rotonda, J., Nicholson, D. W., Becker, J. W., Chapman, K. T. & Thornberry, N. A. (1997). A combinatorial approach for determining protease specificities: application to interleukin-1 beta converting enzyme (ICE). Chem. Biol. 4, 149–155.
Rao, Z., Handford, P., Mayhew, M., Knott, V., Brownlee, G. G. & Stuart, D. (1995). The structure of a Ca(2+)-binding epidermal growth factor-like domain: its role in protein–protein interactions. Cell, 82, 131–141.
Read, J. A., Wilkinson, K. W., Tranter, R., Sessions, R. B. & Brady, R. L. (1999). Chloroquine binds in the cofactor binding site of Plasmodium falciparum lactate dehydrogenase. J. Biol. Chem. 274, 10213–10218.
Redinbo, M. R., Stewart, L., Kuhn, P., Champoux, J. J. & Hol, W. G. J. (1998). Crystal structures of human topoisomerase I in covalent and noncovalent complexes with DNA. Science, 279, 1504–1513.
Reichmann, L., Clark, M., Waldmann, H. & Winter, G. (1988). Reshaping human antibodies for therapy. Nature (London), 332, 323–327.
Reinemer, P., Dirr, H. W., Ladenstein, R., Huber, R., Lo Bello, M., Federici, G. & Parker, M. W. (1992). Three-dimensional structure of class pi glutathione S-transferase from human placenta in complex with S-hexylglutathione at 2.8 Å resolution. J. Mol. Biol. 227, 214–226.
Reinemer, P., Grams, F., Huber, R., Kleine, T., Schnierer, S., Piper, M., Tschesche, H. & Bode, W. (1994). Structural implications for the role of the N terminus in the `superactivation' of collagenases. A crystallographic study. FEBS Lett. 338, 227–233.
Ren, J., Esnouf, R., Garman, E., Somers, D., Ross, C., Kirby, I., Keeling, J., Darby, G., Jones, Y., Stuart, D. & Stammers, D. (1995). High resolution structures of HIV-1 RT from four RT-inhibitor complexes. Nature Struct. Biol. 2, 293–302.
Ren, J., Esnouf, R. M., Hopkins, A. L., Jones, E. Y., Kirby, I., Keeling, J., Ross, C. K., Larder, B. A., Stuart, D. I. & Stammers, D. K. (1998). 3-Azido-3′-deoxythymidine drug resistance mutations in HIV-1 reverse transcriptase can induce long range conformational changes. Proc. Natl Acad. Sci. USA, 95, 9518–9523.
Renwick, S. B., Snell, K. & Baumann, U. (1998). The crystal structure of human cytosolic serine hydroxymethyltransferase: a target for cancer chemotherapy. Structure, 15, 1105–1116.
Resnick, D. A., Smith, A. D., Geisler, S. C., Zhang, A., Arnold, E. & Arnold, G. F. (1995). Chimeras from a human rhinovirus 14–human immunodeficiency virus type 1 (HIV-1) V3 loop seroprevalence library induce neutralizing responses against HIV-1. J. Virol. 69, 2406–2411.
Rey, F. A., Heinz, F. X., Mandl, C., Kunz, C. & Harrison, S. C. (1995). The envelope glycoprotein from tick-borne encephalitis virus at 2 Å resolution. Nature (London), 375, 291–298.
Rigden, D. J., Phillips, S. E., Michels, P. A. & Fothergill-Gilmore, L. A. (1999). The structure of pyruvate kinase from Leishmania mexicana reveals details of the allosteric transition and unusual effector specificity. J. Mol. Biol. 291, 615–635.
Ripka, W. C. (1997). Design of antithrombotic agents directed at factor Xa. In Structure-Based Drug Design, edited by P. Veerapandian, pp. 265–294. New York: Marcel Dekker.
Roberts, M. M., White, J. L., Grutter, M. G. & Burnett, R. M. (1986). Three-dimensional structure of the adenovirus major coat protein hexon. Science, 232, 1148–1151.
Rodgers, D. W., Bamblin, S. J., Harris, B. A., Ray, S., Culp, J. S., Hellmig, B., Woolf, D. J., Debouck, C. & Harrison, S. C. (1995). The structure of unliganded reverse transcriptase from the human immunodeficiency virus type 1. Proc. Natl Acad. Sci. USA, 92, 1222–1226.
Roe, S. M., Barlow, T., Brown, T., Oram, M., Keeley, A., Tsaneva, I. R. & Pearl, L. H. (1998). Crystal structure of an octameric RuvA–Holliday junction complex. Mol. Cell, 2, 361–372.
Rolan, P. E., Parker, J. E., Gray, S. J., Weatherley, B. C., Ingram, J., Leavens, W., Wootton, R. & Posner, J. (1993). The pharmacokinetics, tolerability and pharmacodynamics of tucaresol (589C80; 4[2-formyl-3-hydroxyphenoxymethyl] benzoic acid), a potential anti-sickling agent, following oral administration to healthy subjects. Br. J. Clin. Pharmacol. 35, 419–425.
Rossjohn, J., Feil, S. C., McKinstry, W. J., Tweten, R. K. & Parker, M. W. (1997). Structure of a cholesterol-binding, thiol-activated cytolysin and a model of its membrane form. Cell, 89, 685–692.
Rossjohn, J., Feil, S. C., Wilce, M. C. J., Sexton, J. L., Spithill, T. W. & Parker, M. W. (1997). Crystallization, structural determination and analysis of a novel parasite vaccine candidate: Fasciola hepatica glutathione S-transferase. J. Mol. Biol. 273, 857–872.
Rossjohn, J., McKinstry, W. J., Oakley, A. J., Verger, D., Flanagan, J., Chelvanayagam, G., Tan, K. L., Board, P. G. & Parker, M. W. (1998). Human theta class glutathione transferase: the crystal structure reveals a sulfate-binding pocket within a buried active site. Structure, 6, 309–322.
Rossjohn, J., Polekhina, G., Feil, S. C., Allocati, N., Masulli, M., De Illio, C. & Parker, M. W. (1998). A mixed disulfide bond in bacterial glutathione transferase: functional and evolutionary implications. Structure, 6, 721–734.
Rossmann, M. G., Arnold, E., Erickson, J. W., Frankenberger, E. A., Griffith, J. P., Hecht, H. J., Johnson, J. E., Kamer, G., Luo, M., Mosser, A. G., Rueckert, R. R., Sherry, B. & Vriend, G. (1985). Structure of a human common cold virus and functional relationship to other picornaviruses. Nature (London), 317, 145–153.
Roussel, A., Anderson, B. F., Baker, H. M., Fraser, J. D. & Baker, E. N. (1997). Crystal structure of the streptococcal superantigen SPE-C: dimerization and zinc binding suggest a novel mode of interaction with MHC class II molecules. Nature Struct. Biol. 4, 635–643.
Rudenko, G., Bonten, E., d'Azzo, A. & Hol, W. G. J. (1995). Three-dimensional structure of the human `protective protein': structure of the precursor form suggests a complex activation mechanism. Structure, 3, 1249–1259.
Rudenko, G., Bonten, E., Hol, W. G. J. & d'Azzo, A. (1998). The atomic model of the human protective protein/cathepsin A suggests a structural basis for galactosialidosis. Proc. Natl Acad. Sci. USA, 95, 621–625.
Russo, A. A., Tong, L., Lee, J. O., Jeffrey, P. D. & Pavletich, N. P. (1998). Structural basis for inhibition of the cyclin-dependent kinase Cdk6 by the tumour suppressor p16INK4a. Nature (London), 395, 237–243.
Rydel, T. J., Ravichandran, K. G., Tulinsky, A., Bode, W., Huber, R., Roitsch, C. & Fenton, J. W. I. (1990). The structure of a complex of recombinant hirudin and human alpha-thrombin. Science, 249, 277–280.
Rydel, T. J., Yin, M., Padmanabhan, K. P., Blankenship, D. T., Cardin, A. D., Correa, P. E., Fenton, J. W. I. & Tulinsky, A. (1994). Crystallographic structure of human gamma-thrombin. J. Biol. Chem. 269, 22000–22006.
Sarafianos, S. G., Das, K., Ding, J., Boyer, P. L., Hughes, S. H. & Arnold, E. (1999). Touching the heart of HIV-1 drug resistance: the fingers close down on the dNTP at the polymerase active site. Chem. Biol. 6, R137–R146.
Sauer, F. G., Futterer, K., Pinkner, J. S., Dodson, K. W., Hultgren, S. J. & Waksman, G. (1999). Structural basis of chaperone function and pilus biogenesis. Science, 285, 1058–1061.
Savva, R., McAuley-Hecht, K., Brown, T. & Pearl, L. (1995). The structural basis of specific base-excision repair by uracil-DNA glycosylase. Nature (London), 373, 487–493.
Scheffzek, K., Ahmadian, M. R., Kabsch, W., Wiesmuller, L., Lautwein, A., Schmitz, F. & Wittinghofer, A. (1997). The Ras–RasGAP complex: structural basis for GTPase activation and its loss in oncogenic Ras mutants. Science, 277, 333–338.
Schiffer, C. A., Clifton, I. J., Davisson, V. J., Santi, D. V. & Stroud, R. M. (1995). Crystal structure of human thymidylate synthase: a structural mechanism for guiding substrates into the active site. Biochemistry, 34, 16279–16287.
Schlagenhauf, E., Etges, R. & Metcalf, P. (1998). The crystal structure of the Leishmania major surface proteinase leishmanolysin (gp63). Structure, 6, 1035–1046.
Schonbrunn, E., Sack, S., Eschenberg, S., Perrakis, A., Krekel, F., Amrhein, N. & Mandelkow, E. (1996). Crystal structure of UDP-N-acetylglucosamine enolpyruvyltransferase, the target of the antibiotic fosfomycin. Structure, 4, 1065–1075.
Schreuder, H., Tardif, C., Trump-Kallmeyer, S., Soffientini, A., Sarubbi, E., Akeson, A., Bowlin, T., Yanofsky, S. & Barrett, R. W. (1997). A new cytokine-receptor binding mode revealed by the crystal structure of the IL-1 receptor with an antagonist. Nature (London), 386, 194–200.
Schreuder, H. A., de Boer, B., Dijkema, R., Mulders, J., Theunissen, H. J. M., Grootenhuis, P. D. J. & Hol, W. G. J. (1994). The intact and cleaved human antithrombin III complex as a model for serpin-proteinase interactions. Nature Struct. Biol. 1, 48–54.
Schumacher, M. A., Carter, D., Ross, D. S., Ullman, B. & Brennan, R. G. (1996). Crystal structures of Toxoplasma gondii HGXPRTase reveal the catalytic role of a long flexible loop. Nature Struct. Biol. 3, 881–887.
Schumacher, M. A., Carter, D., Scott, D. M., Roos, D. S., Ullman, B. & Brennan, R. G. (1998). Crystal structures of Toxoplasma gondii uracil phosphoribosyltransferase reveal the atomic basis of pyrimidine discrimination and prodrug binding. EMBO J. 17, 3219–3232.
Schwabe, J. W. E., Chapman, L., Finch, J. T. & Rhodes, D. (1993). The crystal structure of the estrogen receptor DNA-binding domain bound to DNA: how receptors discriminate between their response elements. Cell, 75, 567–578.
Scott, D. L., White, S. P., Browning, J. L., Rosa, J. J., Gelb, M. H. & Sigler, P. B. (1991). Structures of free and inhibited human secretory phospholipase A2 from inflammatory exudate. Science, 254, 1007–1010.
Sha, B. & Luo, M. (1997). Structure of a bifunctional membrane-RNA binding protein, influenza virus matrix protein M1. Nature Struct. Biol. 4, 239–244.
Shah, S. A., Shen, B. W. & Brunger, A. T. (1997). Human ornithine aminotransferase complexed with L-canaline and gabaculine: structural basis for substrate recognition. Structure, 5, 1067–1075.
Sharma, A., Hanai, R. & Mondragon, A. (1994). Crystal structure of the amino-terminal fragment of vaccinia virus DNA topoisomerase I at 1.6 Å resolution. Structure, 2, 767–777.
Sharma, V., Grubmeyer, C. & Sacchettini, J. C. (1998). Crystal structure of quinolinic acid phosphoribosyltransferase from Mycobacterium tuberculosis: a potential TB drug target. Structure, 6, 1587–1599.
Sherry, B., Mosser, A. G., Colonno, R. J. & Rueckert, R. R. (1986). Use of monoclonal antibodies to identify four neutralization immunogens on a common cold picornavirus, human rhinovirus 14. J. Virol. 57, 246–257.
Sherry, B. & Rueckert, R. (1985). Evidence for at least two dominant neutralization antigens on human rhinovirus 14. J. Virol. 53, 137–143.
Shi, D., Morizono, H., Ha, Y., Aoyagi, M., Tuchman, M. & Allewell, N. M. (1998). 1.85-Å resolution crystal structure of human ornithine transcarbamoylase complexed with N-phosphonacetyl-L-ornithine. Catalytic mechanism and correlation with inherited deficiency. J. Biol. Chem. 273, 34247–34254.
Shi, W., Li, C. M., Tyler, P. C., Furneaux, R. H., Cahill, S. M., Girvin, M. E., Grubmeyer, C., Schramm, V. L. & Almo, S. C. (1999). The 2.0 Å structure of malarial purine phosphoribosyltransferase in complex with a transition-state analogue inhibitor. Biochemistry, 38, 9872–9880.
Shi, W., Schramm, V. L. & Almo, S. C. (1999). Nucleoside hydrolase from Leishmania major. Cloning, expression, catalytic properties, transition state inhibitors, and the 2.5-Å crystal structure. J. Biol. Chem. 274, 21114–21120.
Shieh, H. S., Kurumbail, R. G., Stevens, A. M., Stegeman, R. A., Sturman, E. J., Pak, J. Y., Wittwer, A. J., Palmier, M. O., Wiegand, R. C., Holwerda, B. C. & Stallings, W. C. (1996). Three-dimensional structure of human cytomegalovirus protease. Nature (London), 383, 279–282.
Sielecki, A. R., Hayakawa, K., Fujinaga, M., Murphy, M. E. P., Fraser, M., Muir, A. K., Carilli, C. T., Lewicki, J. A., Baxter, J. D. & James, M. N. G. (1989). Structure of recombinant human renin, a target for cardiovascular-active drugs, at 2.5-Å resolution. Science, 243, 1346–1351.
Silva, A. M., Lee, A. Y., Gulnik, S. V., Maier, P., Collins, J., Bhat, T. N., Collins, P. J., Cachau, R. E., Luker, K. E., Gluzman, I. Y., Francis, S. E., Oksman, A., Goldberg, D. E. & Erickson, J. W. (1996). Structure and inhibition of plasmepsin II, a hemoglobin-degrading enzyme from Plasmodium falciparum. Proc. Natl Acad. Sci. USA, 93, 10034–10039.
Silvian, L. F., Wang, J. & Steitz, T. A. (1999). Insights into editing from an ile-tRNA synthetase structure with tRNAile and mupirocin. Science, 285, 1074–1077.
Sinning, I., Kleywegt, G. J., Cowan, S. W., Reinemer, P., Dirr, H. W., Huber, R., Gilliland, G. L., Armstrong, R. N., Ji, X., Board, P. G., Olin, B., Mannervik, B. & Jones, T. A. (1993). Structure determination and refinement of human alpha class glutathione transferase A1–1, and a comparison with the mu and pi class enzymes. J. Mol. Biol. 232, 192–212.
Sixma, T. K., Pronk, S. E., Kalk, K. H., Wartna, E. S., van Zanten, B. A. M., Witholt, B. & Hol, W. G. J. (1991). Crystal structure of a cholera toxin-related heat-labile enterotoxin from E. coli. Nature (London), 351, 371–377.
Skinner, R., Abrahams, J. P., Whisstock, J. C., Lesk, A. M., Carrell, R. W. & Wardell, M. R. (1997). The 2.6 Å structure of antithrombin indicates a conformational change at the heparin binding site. J. Mol. Biol. 266, 601–609.
Skinner, R., Chang, W. S. W., Jin, L., Pei, X. Y., Huntington, J. A., Abrahams, J. P., Carrell, R. W. & Lomas, D. A. (1998). Implications for function and therapy of a 2.9 Å structure of binary-complexed antithrombin. J. Mol. Biol. 283, 9–14.
Smith, A. D., Geisler, S. C., Chen, A. A., Resnick, D. A., Roy, B. M., Lewi, P. J., Arnold, E. & Arnold, G. F. (1998). Human rhinovirus type 14:human immunodeficiency virus type 1 (HIV-1) V3 loop chimeras from a combinatorial library induce potent neutralizing antibody responses against HIV-1. J. Virol. 72, 651–659.
Somers, W., Ultsch, M., DeVos, A. M. & Kossiakoff, A. A. (1994). The X-ray structure of a growth hormone–prolactin receptor complex. Nature (London), 372, 478–481.
Song, L., Hobaugh, M. R., Shustak, C., Cheley, S., Bayley, H. & Gouaux, J. E. (1996). Structure of staphylococcal alpha-hemolysin, a heptameric transmembrane pore. Science, 274, 1859–1866.
Souza, D. H., Garratt, R. C., Araujo, A. P., Guimaraes, B. G., Jesus, W. D., Michels, P. A., Hannaert, V. & Oliva, G. (1998). Trypanosoma cruzi glycosomal glyceraldehyde-3-phosphate dehydrogenase: structure, catalytic mechanism and targeted inhibitor design. FEBS Lett. 424, 131–135.
Spraggon, G., Everse, S. J. & Doolittle, R. F. (1997). Crystal structures of fragment D from human fibrinogen and its crosslinked counterpart from fibrin. Nature (London), 389, 455–462.
Spraggon, G., Phillips, C., Nowak, U. K., Ponting, C. P., Saunders, D., Dobson, C. M., Stuart, D. I. & Jones, E. Y. (1995). The crystal structure of the catalytic domain of human urokinase-type plasminogen activator. Structure, 3, 681–691.
Spurlino, J. C., Smallwood, A. M., Carlton, D. D., Banks, T. M., Vavra, K. J., Johnson, J. S., Cook, E. R., Falvo, J., Wahl, R. D., Pulvino, T. A., Wendoloski, J. J. & Smith, D. L. (1994). 1.56-Å structure of mature truncated human fibroblast collagenase. Proteins, 19, 98–109.
Stams, T., Spurlino, J. C., Smith, D. L., Wahl, R. C., Ho, T. F., Qoronfleh, M. H., Banks, T. M. & Rubin, B. (1994). Structure of human neutrophil collagenase reveals large S1′ specificity pocket. Nature Struct. Biol. 1, 119–123.
Stein, P. E., Boodhoo, A., Armstrong, G. D., Cockle, S. A., Klein, M. H. & Read, R. J. (1994). The crystal structure of pertussis toxin. Structure, 2, 45–57.
Stein, P. E., Boodhoo, A., Tyrrell, G. J., Brunton, J. L. & Read, R. J. (1992). Crystal structure of the cell-binding B oligomer of verotoxin-1 from E. coli. Nature (London), 355, 748–750.
Stewart, L., Redinbo, M. R., Qiu, X., Hol, W. G. J. & Champoux, J. J. (1998). A model for the mechanism of human topoisomerase I. Science, 279, 1534–1541.
Stubbs, M. T., Laber, B., Bode, W., Huber, R., Jerala, R., Lenarcic, B. & Turk, V. (1990). The refined 2.4 Å X-ray crystal structure of recombinant human stefin B in complex with the cysteine proteinase papain: a novel type of proteinase inhibitor interaction. EMBO J. 9, 1939–1947.
Stuckey, J. A., Schubert, H. L., Fauman, E. B., Zhang, Z. Y., Dixon, J. E. & Saper, M. A. (1994). Crystal structure of Yersinia protein tyrosine phosphatase at 2.5 Å and the complex with tungstate. Nature (London), 370, 571–575.
Sugio, S., Kashima, A., Mochizuki, S., Noda, M. & Kobayashi, K. (1999). Crystal structure of human serum albumin at 2.5 Å resolution. Protein Eng. 12, 439–446.
Suguna, K., Bott, R. R., Padlan, E. A., Subramanian, E., Sheriff, S., Cohen, G. H. & Davies, D. R. (1987). Structure and refinement at 1.8 Å resolution of the aspartic proteinase from Rhizopus chinensis. J. Mol. Biol. 196, 877–900.
Sundstrom, M., Hallen, D., Svensson, A., Schad, E., Dohlsten, M. & Abrahmsen, L. (1996). The co-crystal structure of staphylococcal enterotoxin type A with Zn2+ at 2.7 Å resolution. Implications for major histocompatibility complex class II binding. J. Biol. Chem. 271, 32212–32216.
Symersky, J., Patti, J. M., Carson, M., House-Pompeo, K., Teale, M., Moore, D., Jin, L., Schneider, A., DeLucas, L. J., Hook, M. & Narayana, S. V. (1997). Structure of the collagen-binding domain from a Staphylococcus aureus adhesin. Nature Struct. Biol. 4, 833–838.
Taylor, P., Page, A. P., Kontopidis, G., Husi, H. & Walkinshaw, M. D. (1998). The X-ray structure of a divergent cyclophilin from the nematode parasite Brugia malayi. FEBS Lett. 425, 361–366.
Testa, B. (1994). Drug metabolism. In Burger's Medicinal Chemistry and Drug Discovery, 5th ed., edited by M. E. Wolf, Vol. 1. New York: John Wiley & Sons.
Tews, I., Perrakis, A., Oppenheim, A., Dauter, Z., Wilson, K. S. & Vorgias, C. E. (1996). Bacterial chitobiase structure provides insight into catalytic mechanism and the basis of Tay–Sachs disease. Nature Struct. Biol. 3, 638–648.
Thayer, M. M., Flaherty, K. M. & McKay, D. B. (1991). Three-dimensional structure of the elastase of Pseudomonas aeruginosa at 1.5-Å resolution. J. Biol. Chem. 266, 2864–2871.
Thieme, R., Pai, E. F., Schirmer, R. H. & Schulz, G. E. (1981). Three-dimensional structure of glutathione reductase at 2 Å resolution. J. Mol. Biol. 152, 763–782.
Thompson, S. K., Halbert, S. M., Bossard, M. J., Tomaszek, T. A., Levy, M. A., Zhao, B., Smith, W. W., Abdel-Meguid, S. S., Janson, C. A., D'Alessio, K. J., McQueney, M. S., Amegadzie, B. Y., Hanning, C. R., DesJarlais, R. L., Briand, J., Sarkar, S. K., Huddleston, M. J., James, C. F., Carr, S. A., Garges, K. T., Shu, A., Heys, J. R., Bradbeer, J., Zembryki, D. & Veber, D. F. (1997). Design of potent and selective human cathepsin K inhibitors that span the active site. Proc. Natl Acad. Sci. USA, 94, 14249–14254.
Thylefors, B., Negrel, A. D., Pararajasegaram, R. & Dadzie, K. Y. (1995). Global data on blindness. Bull. WHO, 73, 115–121.
Tiffany, K. A., Roberts, D. L., Wang, M., Paschke, R., Mohsen, A. W., Vockley, J. & Kim, J. J. (1997). Structure of human isovaleryl-CoA dehydrogenase at 2.6 Å resolution: structural basis for substrate specificity. Biochemistry, 36, 8455–8464.
Toney, M. D., Hohenester, E., Cowan, S. W. & Jansonius, J. N. (1993). Dialkylglycine decarboxylase structure: bifunctional active site and alkali metal sites. Science, 261, 756–759.
Tong, L., Pav, S., White, D. M., Rogers, S., Crane, K. M., Cywin, C. L., Brown, M. L. & Pargellis, C. A. (1997). A highly specific inhibitor of human p38 MAP kinase binds in the ATP pocket. Nature Struct. Biol. 4, 311–316.
Tong, L., Qian, C., Massariol, M. J., Bonneau, P. R., Cordingley, M. G. & Lagace, L. (1996). A new serine-protease fold revealed by the crystal structure of human cytomegalovirus protease. Nature (London), 383, 272–275.
Tran, P. H., Korszun, Z. R., Cerritelli, S., Springhorn, S. S. & Lacks, S. A. (1998). Crystal structure of the DpnM DNA adenine methyltransferase from the Dpnii restriction system of Streptococcus pneumoniae bound to S-adenosylmethionine. Structure, 6, 1563–1575.
Tskovsky, Y. V., Patskovska, L. N. & Listowsky, I. (1999). Functions of His107 in the catalytic mechanism of human glutathione s-transferase hGSTM1a-1a. Biochemistry, 38, 1193–1202.
Turner, B. G. & Summers, M. F. (1999). Structural biology of HIV. J. Mol. Biol. 285, 1–32.
Umland, T. C., Wingert, L. M., Swaminathan, S., Furey, W. F., Schmidt, J. J. & Sax, M. (1997). Structure of the receptor binding fragment HC of tetanus neurotoxin. Nature Struct. Biol. 4, 788–792.
Van Duyne, G. D., Standaert, R. F., Karplus, P. A., Schreiber, S. L. & Clardy, J. (1991). Atomic structure of FKBP-FK506, an immunophilin–immunosuppressant complex. Science, 252, 839–842.
Van Duyne, G. D., Standaert, R. F., Karplus, P. A., Schreiber, S. L. & Clardy, J. (1993). Atomic structures of the human immunophilin FKBP-12 complexes with FK506 and rapamycin. J. Mol. Biol. 229, 105–124.
Van Duyne, G. D., Standaert, R. F., Schreiber, S. L. & Clardy, J. (1991). Atomic structure of the rapamycin human immunophilin FKBP-12 complex. J. Am. Chem. Soc. 113, 7433–7434.
Varghese, J. N., Laver, W. G. & Colman, P. M. (1983). Structure of the influenza virus glycoprotein antigen neuraminidase at 2.9 Å resolution. Nature (London), 303, 35–40.
Varney, M. D., Palmer, C. L., Romines, W. H. R., Boritzki, T., Margosiak, S. A., Almassy, R., Janson, C. A., Bartlett, C., Howland, E. J. & Ferre, R. (1997). Protein structure-based design, synthesis, and biological evaluation of 5-thia-2,6-diamino-4(3H)-oxopyrimidines: potent inhibitors of glycinamide ribonucleotide transformylase with potent cell growth inhibition. J. Med. Chem. 40, 2502–2524.
Vath, G. M., Earhart, C. A., Rago, J. V., Kim, M. H., Bohach, G. A., Schlievert, P. M. & Ohlendorf, D. H. (1997). The structure of the superantigen exfoliative toxin A suggests a novel regulation as a serine protease. Biochemistry, 36, 1559–1566.
Veerapandian, P. (1997). Editor. Structure-Based Drug Design. New York: Marcel-Dekker.
Velanker, S. S., Ray, S. S., Gokhale, R. S., Suma, S., Balaram, P. & Murthy, M. R. (1997). Triosephosphate isomerase from Plasmodium falciparum: the crystal structure provides insights into antimalarial drug design. Structure, 5, 751–761.
Vellieux, F. M., Hajdu, J., Verlinde, C. L., Groendijk, H., Read, R. J., Greenhough, T. J., Campbell, J. W., Kalk, K. H., Littlechild, J. A., Watson, H. C. & Hol, W. G. J. (1993). Structure of glycosomal glyceraldehyde-3-phosphate dehydrogenase from Trypanosoma brucei determined from Laue data. Proc. Natl Acad. Sci. USA, 90, 2355–2359.
Verlinde, C. L. M. J. & Hol, W. G. J. (1994). Structure-based drug design: progress, results and challenges. Structure, 2, 577–587.
Vigers, G. P., Anderson, L. J., Caffes, P. & Brandhuber, B. J. (1997). Crystal structure of the type-I interleukin-1 receptor complexed with interleukin-1beta. Nature (London), 386, 190–194.
Villeret, V., Tricot, C., Stalon, V. & Dideberg, O. (1995). Crystal structure of Pseudomonas aeruginosa catabolic ornithine transcarbamoylase at 3.0-Å resolution: a different oligomeric organization in the transcarbamoylase family. Proc. Natl Acad. Sci. USA, 92, 10762–10766.
Vondrasek, J., van Buskirk, C. P. & Wlodawer, A. (1997). Database of three-dimensional structure of HIV proteinases. Nature Struct. Biol. 4, 8.
Waksman, G., Shoelson, S. E., Pant, N., Cowburn, D. & Kuriyan, J. (1993). Binding of a high affinity phosphotyrosyl peptide to the Src SH2 domain: crystal structures of the complexed and peptide-free forms. Cell, 72, 779–790.
Walker, N. P. C., Talanian, R. V., Brady, K. D., Dang, L. C., Bump, N. J., Ferenz, C. R., Franklin, S., Ghayur, T., Hackett, M. C., Hammill, L. D., Herzog, L., Hugunin, M., Houy, W., Mankovich, J. A., McGuiness, L., Orlewicz, E., Paskind, M., Pratt, C. A., Reis, P., Summani, A., Terranova, M. & Welch, J. P. (1994). Crystal structure of the cysteine protease interleukin-1 beta-converting enzyme: a (p20/p10)2 homodimer. Cell, 78, 343–352.
Walsh, C. T., Fisher, S. L., Park, I. S., Prahalad, M. & Wu, Z. (1996). Bacterial resistance to vancomycin: five genes and one missing hydrogen bond tell the story. Chem. Biol. 3, 21–28.
Walter, M. R., Windsor, W. T., Nagabhushan, T. L., Lundell, D. J., Lunn, C. A., Zauodny, P. J. & Narula, S. K. (1995). Crystal structure of a complex between interferon-gamma and its soluble high-affinity receptor. Nature (London), 376, 230–235.
Wang, A. H., Ughetto, G., Quigley, G. J. & Rich, A. (1987). Interactions between an anthracycline antibiotic and DNA: molecular structure of daunomycin complexed to d(CpGpTpApCpG) at 1.2 Å resolution. Biochemistry, 26, 1152–1163.
Warner, P., Green, R. C., Gomes, B. & Strimpler, A. M. (1994). Non-peptidic inhibitors of human leukocyte elastase. 1. The design and synthesis of pyridone-containing inhibitors. J. Med. Chem. 37, 3090–3099.
Watanabe, K., Hata, Y., Kizaki, H., Katsube, Y. & Suzuki, Y. (1997). The refined crystal structure of Bacillus cereus oligo-1,6-glucosidase at 2.0 Å resolution: structural characterization of proline-substitution sites for protein thermostabilization. J. Mol. Biol. 269, 142–153.
Weber, P. C. & Czarniecki, M. (1997). Structure-based design of thrombin inhibitors. In Structure-Based Drug Design, edited by P. Veerapandian, pp. 247–264. New York: Marcel Dekker.
Wei, A. Z., Mayr, I. & Bode, W. (1988). The refined 2.3-Å crystal structure of human leukocyte elastase in a complex with a valine chloromethyl ketone inhibitor. FEBS Lett. 234, 367–373.
Weissenhorn, W., Carfi, A., Lee, K. H., Skehel, J. J. & Wiley, D. C. (1998). Crystal structure of the Ebola virus membrane fusion subunit, GP2, from the envelope glycoprotein ectodomain. Mol. Cell, 2, 605–616.
Wery, J. P., Schevitz, R. W., Clawson, D. K., Bobbitt, J. L., Dow, E. R., Gamboa, G., Goodson, T. J., Hermann, R. B., Kramer, R. M., McClure, D. B., Mihelich, E. D., Putnam, J. E., Sharp, J. D., Stark, D. H., Teater, C., Warrick, M. W. & Jones, N. D. (1991). Structure of recombinant human rheumatoid arthritic synovial fluid phospholipase A2 at 2.2-Å resolution. Nature (London), 352, 79–82.
Weston, S. A., Camble, R., Colls, J., Rosenbrock, G., Taylor, I., Egerton, M., Tucker, A. D., Tunnicliffe, A., Mistry, A., Macia, F., de La Fortelle, E., Irwin, J., Bricogne, G. & Pauptit, R. A. (1998). Crystal structure of the anti-fungal target N-myristoyl transferase. Nature Struct. Biol. 5, 213–221.
Whitlow, M., Howard, A. J., Stewart, D., Hardman, K. D., Kuyper, L. F., Baccanari, D. P., Fling, M. E. & Tansik, R. L. (1997). X-ray crystallographic studies of Candida albicans dihydrofolate reductase. High resolution structure of the holoenzyme and an inhibited ternary complex. J. Biol. Chem. 272, 30289–30298.
Whittingham, J. L., Edwards, D. J., Antson, A. A., Clarkson, J. M. & Dodson, G. G. (1998). Interactions of phenol and m-cresol in the insulin hexamer, and their effect on the association properties of B28 pro Asp insulin analogues. Biochemistry, 37, 11516–11523.
Whittle, P. J. & Blundell, T. L. (1994). Protein structure-based drug design. Annu. Rev. Biophys. Biomol. Struct. 23, 349–375.
Wierenga, R. K., Kalk, K. H. & Hol, W. G. J. (1987). Structure determination of the glycosomal triosephosphate isomerase from Trypanosoma brucei brucei at 2.4 Å resolution. J. Mol. Biol. 198, 109–121.
Wild, K., Bohner, T., Aubry, A., Folkers, G. & Schulz, G. E. (1995). The three-dimensional structure of thymidine kinase from herpes simplex virus type 1. FEBS Lett. 368, 289–292.
Williams, J. C., Zeelen, J. P., Neubauer, G., Vriend, G., Backmann, J., Michels, P. A., Lambeir, A. M. & Wierenga, R. K. (1999). Structural and mutagenesis studies of leishmania triosephosphate isomerase: a point mutation can convert a mesophilic enzyme into a superstable enzyme without losing catalytic power. Protein Eng. 12, 243–250.
Williams, P. A., Cosme, J., Sridhar, V., Johnson, E. F. & McRee, D. E. (2000). Mammalian microsomal cytochrome P450 monooxygenase: structural adaptations for membrane binding and functional diversity. Mol. Cell, 5, 121–131.
Williams, S. P. & Sigler, P. B. (1998). Atomic structure of progesterone complexed with its receptor. Nature (London), 393, 392–396.
Wilson, D. K., Bohren, K. M., Gabbay, K. H. & Quiocho, F. A. (1992). An unlikely sugar substrate site in the 1.65 Å structure of the human aldose reductase holoenzyme implicated in diabetic complications. Science, 257, 81–84.
Wilson, I. A., Skehel, J. J. & Wiley, D. C. (1981). Structure of the haemagglutinin membrane glycoprotein of influenza virus at 3 Å resolution. Nature (London), 289, 366–373.
Wilson, K. P., Fitzgibbon, M. J., Caron, P. R., Griffith, J. P., Chen, W., McCaffrey, P. G., Chambers, S. P. & Su, M. S. (1996). Crystal structure of p38 mitogen-activated protein kinase. J. Biol. Chem. 271, 27696–27700.
Wireko, F. C. & Abraham, D. J. (1991). X-ray diffraction study of the binding of the antisickling agent 12C79 to human hemoglobin. Proc. Natl Acad. Sci. USA, 88, 2209–2211.
Wlodawer, A., Miller, M., Jaskolski, M., Sathyanarayana, B. K., Baldwin, E., Weber, I. T., Selk, L. M., Clawson, L., Schneider, J. & Kent, S. B. (1989). Conserved folding in retroviral proteases: crystal structure of a synthetic HIV-1 protease. Science, 245, 616–621.
Wlodawer, A. & Vondrasek, J. (1998). Inhibitors of HIV-1 protease: a major success of structure-assisted drug design. Annu. Rev. Biophys. Biomol. Struct. 27, 249–284.
Wolf, E., Vassilev, A., Makino, Y., Sali, A., Nakatani, Y. & Burley, S. K. (1998). Crystal structure of a GCN5-related N-acetyltransferase: Serratia marcescens aminoglycoside 3-N-acetyltransferase. Cell, 94, 439–449.
Worthylake, D. K., Wang, H., Yoo, S., Sundquist, W. I. & Hill, C. P. (1999). Structures of the HIV-1 capsid protein dimerization domain at 2.6 Å resolution. Acta Cryst. D55, 85–92.
Wynne, S. A., Crowther, R. A. & Leslie, A. G. (1999). The crystal structure of the human hepatitis B virus capsid. Mol. Cell, 3, 771–780.
Xia, D., Henry, L. J., Gerard, R. D. & Deisenhofer, J. (1994). Crystal structure of the receptor-binding domain of adenovirus type 5 fiber protein at 1.7 Å resolution. Structure, 2, 1259–1270.
Xie, X., Gu, Y., Fox, T., Coll, J. T., Fleming, M. A., Markland, W., Caron, P. R., Wilson, K. P. & Su, M. S. (1998). Crystal structure of JNK3: a kinase implicated in neuronal apoptosis. Structure, 6, 983–991.
Xu, W., Harrison, S. C. & Eck, M. J. (1997). Three-dimensional structure of the tyrosine kinase c-Src. Nature (London), 385, 595–602.
Xue, Y., Bjorquist, P., Inghardt, T., Linschoten, M., Musil, D., Sjolin, L. & Deinum, J. (1998). Interfering with the inhibitory mechanism of serpins: crystal structure of a complex formed between cleaved plasminogen activator inhibitor type 1 and a reactive-centre loop peptide. Structure, 6, 627–636.
Yan, Y., Li, Y., Munshi, S., Sardana, V., Cole, J. L., Sardana, M., Steinkuehler, C., Tomei, L., De Francesco, R., Kuo, L. C. & Chen, Z. (1998). Complex of NS3 protease and NS4A peptide of BK strain hepatitis C virus: a 2.2 Å resolution structure in a hexagonal crystal form. Protein Sci. 7, 837–847.
Yang, J., Kloek, A. P., Goldberg, D. E. & Mathews, F. S. (1995). The structure of Ascaris hemoglobin domain I at 2.2 Å resolution: molecular features of oxygen avidity. Proc. Natl Acad. Sci. USA, 92, 4224–4228.
Yang, X. & Moffat, K. (1995). Insights into specificity of cleavage and mechanism of cell entry from the crystal structure of the highly specific Aspergillus ribotoxin, restrictocin. Structure, 4, 837–852.
Yao, N., Hesson, T., Cable, M., Hong, Z., Kwong, A. D., Le, H. V. & Weber, P. C. (1997). Structure of the hepatitis C virus RNA helicase domain. Nature Struct. Biol. 4, 463–467.
Yee, V. C., Pedersen, L. C., LeTrong, I., Bishop, P. D., Stenkamp, R. E. & Teller, D. C. (1994). Three-dimensional structure of a transglutaminase: human blood coagulation factor XIII. Proc. Natl Acad. Sci. USA, 91, 7296–7300.
Yeh, J. I., Claiborne, A. & Hol, W. G. J. (1996). Structure of the native cystein-sulfenic acid redox center of enterococcal NADH peroxidase refined at 2.8 Å resolution. Biochemistry, 35, 9951–9957.
Yoshimoto, T., Kabashima, T., Uchikawa, K., Inoue, T., Tanaka, N., Nakamura, K. T., Tsuru, M. & Ito, K. (1999). Crystal structure of prolyl aminopeptidase from Serratia marcescens. J. Biochem. (Tokyo), 126, 559–565.
Zaitseva, I., Zaitsev, V., Card, G., Moshkov, K., Bax, B., Ralph, A. & Lindley, P. (1996). The X-ray structure of human serum ceruloplasmin at 3.1 Å: nature of the copper centres. J. Biol. Inorg. Chem. 1, 15–23.
Zdanov, A., Schalk-Hihi, C., Menon, S., Moore, K. W. & Wlodawer, A. (1997). Crystal structure of Epstein–Barr virus protein BCRF1, a homolog of cellular interleukin-10. J. Mol. Biol. 268, 460–467.
Zhang, A., Geisler, S. C., Smith, A. D., Resnick, D. A., Li, M. L., Wang, C. Y., Looney, D. J., Wong-Staal, F., Arnold, E. & Arnold, G. F. (1999). A disulfide-bound HIV-1 V3 loop sequence on the surface of human rhinovirus 14 induces neutralizing responses against HIV-1. J. Biol. Chem. 380, 365–374.
Zhang, H., Gao, Y. G., van der Marel, G. A., van Boom, J. H. & Wang, A. H. (1993). Simultaneous incorporations of two anticancer drugs into DNA. The structures of formaldehyde-cross-linked adducts of daunorubicin-d(CG(araC)GCG) and doxorubicin-d(CA(araC)GTG) complexes at high resolution. J. Biol. Chem. 268, 10095–10101.
Zhang, R., Evans, G., Rotella, F. J., Westbrook, E. M., Beno, D., Huberman, E., Joachimiak, A. & Collart, F. R. (1999). Characteristics and crystal structure of bacterial inosine-5′-monophosphate dehydrogenase. Biochemistry, 38, 4691–4700.
Zhang, R. G., Scott, D. L., Westbrook, M. L., Nance, S., Spangler, B. D., Shipley, G. G. & Westbrook, E. M. (1995). The three-dimensional crystal structure of cholera toxin. J. Mol. Biol. 251, 563–573.
Zhang, X., Morera, S., Bates, P. A., Whitehead, P. C., Coffer, A. I., Hainbucher, K., Nash, R. A., Sternberg, M. J., Lindahl, T. & Freemont, P. S. (1998). Structure of an XRCC1 BRCT domain: a new protein–protein interaction module. EMBO J. 17, 6404–6411.
Zhu, X., Kim, J. L., Newcomb, J. R., Rose, P. E., Stover, D. R., Toledo, L. M., Zhao, H. & Morgenstern, K. A. (1999). Structural analysis of the lymphocyte-specific kinase Lck in complex with non-selective and Src family selective kinase inhibitors. Struct. Fold. Des. 7, 651–661.
Zuccola, H. J., Rozzelle, J. E., Lemon, S. M., Erickson, B. W. & Hogle, J. M. (1998). Structural basis of the oligomerization of hepatitis delta antigen. Structure, 6, 821–830.








































to end of page
to top of page