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. 14-15   | 1 | 2 |

Section 1.3.3. Crystallography and genetic diseases

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

1.3.3. Crystallography and genetic diseases

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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.

References

Birrer, P. (1995). Proteases and antiproteases in cystic fibrosis: pathogenetic considerations and therapeutic strategies. Respiration, 62, S25–S28.
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.
Carrell, R. W. & Gooptu, B. (1998). Conformational changes and diseases – serpins, prions and Alzheimer's. Curr. Opin. Struct. Biol. 8, 799–809.
Collins, F. S. (1992). Cystic fibrosis: molecular biology and therapeutic implications. Science, 256, 774–779.
Dickerson, R. E. & Geis, I. (1983). Hemoglobin. Menlo Park: Benjamin Cummings Publishing Co.
Foster, B. A., Coffey, H. A., Morin, M. J. & Rastinejad, F. (1999). Pharmacological rescue of mutant p53 conformation and function. Science, 286, 2507–2510.
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.
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.
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.
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.
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.
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.








































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