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

International Tables for Crystallography (2006). Vol. F, ch. 4.3, pp. 100-110   | 1 | 2 |
doi: 10.1107/97809553602060000662

Chapter 4.3. Application of protein engineering to improve crystal properties

D. R. Daviesa* and A. Burgess Hickmana

aLaboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0560, USA
Correspondence e-mail:


Bell, J. A., Wilson, K. P., Zhang, X.-J., Faber, H. R., Nicholson, H. & Matthews, B. W. (1991). Comparison of the crystal structure of bacteriophage T4 lysozyme at low, medium, and high ionic strengths. Proteins, 10, 10–21.
Braig, K., Otwinowski, Z., Hegde, R., Boisvert, D. C., Joachimiak, A., Horwich, A. L. & Sigler, P. B. (1994). The crystal structure of the bacterial chaperonin GroEL at 2.8 Å. Nature (London), 371, 578–586.
Budisa, N., Steipe, B., Demange, P., Eckerskorn, C., Kellermann, J. & Huber, R. (1995). High-level biosynthetic substitution of methionine in proteins by its analogs 2-aminohexanoic acid, selenomethionine, telluromethionine and ethionine in Escherichia coli. Eur. J. Biochem. 230, 788–796.
Bujacz, G., Jaskolski, M., Alexandratos, J., Wlodawer, A., Merkel, G., Katz, R. A. & Skalka, A. M. (1995). High resolution structure of the catalytic domain of avian sarcoma virus integrase. J. Mol. Biol. 253, 333–346.
Carugo, O. & Argos, P. (1997). Protein–protein crystal-packing contacts. Protein Sci. 6, 2261–2263.
Cowie, D. B. & Cohen, G. N. (1957). Biosynthesis by Escherichia coli of active altered proteins containing selenium instead of sulfur. Biochim. Biophys. Acta, 26, 252–261.
Dale, G. E., Broger, C., Langen, H., D'Arcy, A. & Stüber, D. (1994). Improving protein solubility through rationally designed amino acid replacements: solubilization of the trimethoprim-resistant type S1 dihydrofolate reductase. Protein Eng. 7, 933–939.
D'Arcy, A. (1994). Crystallizing proteins – a rational approach? Acta Cryst. D50, 469–471.
Dasgupta, S., Iyer, G. H., Bryant, S. H., Lawrence, C. E. & Bell, J. A. (1997). Extent and nature of contacts between protein molecules in crystal lattices and between subunits of protein oligomers. Proteins, 28, 494–514.
Dayhoff, M. O. (1978). Atlas of protein sequence and structure, Vol. 5, Suppl. 3, p. 363. Washington DC: National Biomedical Research Foundation.
Donahue, J. P., Patel, H., Anderson, W. F. & Hawiger, J. (1994). Three-dimensional structure of the platelet integrin recognition segment of the fibrinogen γ chain obtained by carrier protein-driven crystallization. Proc. Natl Acad. Sci. USA, 91, 12178–12182.
Doublié, S. (1997). Preparation of selenomethionyl proteins for phase determination. Methods Enzymol. 276, 523–530.
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.
Fermi, G. & Perutz, M. F. (1981). Atlas of molecular structures in biology, Vol. 2. Oxford: Clarendon Press.
Golden, B. L., Ramakrishnan, V. & White, S. W. (1993). Ribosomal protein L6: structural evidence of gene duplicaton from a primitive RNA binding protein. EMBO J. 12, 4901–4908.
Goldgur, Y., Dyda, F., Hickman, A. B., Jenkins, T. M., Craigie, R. & Davies, D. R. (1998). Three new structures of the core domain of HIV-1 integrase: an active site that binds magnesium. Proc. Natl Acad. Sci. USA, 95, 9150–9154.
Heinz, D. W. & Matthews, B. W. (1994). Rapid crystallization of T4 lysozyme by intermolecular disulfide cross-linking. Protein Eng. 7, 301–307.
Hendrickson, W. A. (1991). Determination of macromolecular structures from anomalous diffraction of synchrotron radiation. Science, 254, 51–58.
Hendrickson, W. A., Horton, J. R. & LeMaster, D. M. (1990). Selenomethionyl proteins produced for analysis by multiwavelength anomalous diffraction (MAD): a vehicle for direct determination of three-dimensional structure. EMBO J. 9, 1665–1672.
Hendrickson, W. A. & Ogata, C. M. (1997). Phase determination from multiwavelength anomalous diffraction measurements. Methods Enzymol. 276, 494–523.
Hickman, A. B., Dyda, F. & Craigie, R. (1997). Heterogeneity in recombinant HIV-1 integrase corrected by site-directed mutagenesis: the identification and elimination of a protease cleavage site. Protein Eng. 10, 601–606.
Hizi, A. & Hughes, S. H. (1988). Expression of the Moloney murine leukemia virus and human immunodeficiency virus integration proteins in Escherichia coli. Virology, 167, 634–638.
Hoffman, D. W., Davies, C., Gerchman, S. E., Kycia, J. H., Porter, S. J., White, S. W. & Ramakrishnan, V. (1994). Crystal structure of prokaryotic ribosomal protein L9: a bi-lobed RNA-binding protein. EMBO J. 13, 205–212.
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.
Jenkins, T. M., Hickman, A. B., Dyda, F., Ghirlando, R., Davies, D. R. & Craigie, R. (1995). Catalytic domain of human immunodeficiency virus type 1 integrase: identification of a soluble mutant by systematic replacement of hydrophobic residues. Proc. Natl Acad. Sci. USA, 92, 6057–6061.
Karle, J. (1980). Some developments in anomalous dispersion for the structural investigation of macromolecular systems in biology. Int. J. Quantum Chem. Symp. 7, 357–367.
Kuge, M., Fujii, Y., Shimizu, T., Hirose, F., Matsukage, A. & Hakoshima, T. (1997). Use of a fusion protein to obtain crystals suitable for X-ray analysis: crystallization of a GST-fused protein containing the DNA-binding domain of DNA replication-related element-binding factor, DREF. Protein Sci. 6, 1783–1786.
Kwong, P. D., Wyatt, R., Robinson, J., Sweet, R. W., Sodroski, J. & Hendrickson, W. A. (1998). Structure of an HIV gp120 envelope glycoprotein in complex with the CD4 receptor and a neutralizing human antibody. Nature (London), 393, 648–659.
Lawson, D. M., Artymiuk, P. J., Yewdall, S. J., Smith, J. M. A., Livingstone, J. C., Treffry, A., Luzzago, A., Levi, S., Arosio, P., Cesareni, G., Thomas, C. D., Shaw, W. V. & Harrison, P. M. (1991). Solving the structure of human H ferritin by genetically engineering intermolecular crystal contacts. Nature (London), 349, 541–544.
Leahy, D. J., Erickson, H. P., Aukhil, I., Joshi, P. & Hendrickson, W. A. (1994). Crystallization of a fragment of human fibronectin: introduction of methionine by site-directed mutagenesis to allow phasing via selenomethionine. Proteins, 19, 48–54.
McElroy, H. E., Sisson, G. W., Schoettlin, W. E., Aust, R. M. & Villafranca, J. E. (1992). Studies on engineering crystallizability by mutation of surface residues of human thymidylate synthase. J. Cryst. Growth, 122, 265–272.
Martinez, C., De Geus, P., Lauwereys, M., Matthyssens, G. & Cambillau, C. (1992). Fusarium solani cutinase is a lipolytic enzyme with a catalytic serine accessible to solvent. Nature (London), 356, 615–618.
Martínez-Hackert, E., Harlocker, S., Inouye, M., Berman, H. M. & Stock, A. M. (1996). Crystallization, X-ray studies, and site-directed cysteine mutagenesis of the DNA-binding domain of OmpR. Protein Sci. 5, 1429–1433.
Matthews, B. W. (1993). Structural and genetic analysis of protein stability. Annu. Rev. Biochem. 62, 139–160.
Mazzoni, M. R., Malinski, J. A. & Hamm, H. E. (1991). Structural analysis of rod GTP-binding protein, Gt. J. Biol. Chem. 266, 14072–14081.
Mittl, P. R. E., Berry, A., Scrutton, N. S., Perham, R. N. & Schulz, G. E. (1994). A designed mutant of the enzyme glutathione reductase shortens the crystallization time by a factor of forty. Acta Cryst. D50, 228–231.
Nagai, K., Oubridge, C., Jessen, T. H., Li, J. & Evans, P. R. (1990). Crystal structure of the RNA-binding domain of the U1 small nuclear ribonucleoprotein A. Nature (London), 348, 515–520.
Nilsson, B., Forsberg, G., Moks, T., Hartmanis, M. & Uhlén, M. (1992). Fusion proteins in biotechnology and structural biology. Curr. Opin. Struct. Biol. 2, 569–575.
Noel, J. P., Hamm, H. E. & Sigler, P. B. (1993). The 2.2 Å crystal structure of transducin-α complexed with GTPγS. Nature (London), 366, 654–663.
Oubridge, C., Ito, N., Teo, C.-H., Fearnley, I. & Nagai, K. (1995). Crystallisation of RNA-protein complexes II. The application of protein engineering for crystallisation of the U1A protein–RNA complex. J. Mol. Biol. 249, 409–423.
Peat, T. S., Frank, E. G., Woodgate, R. & Hendrickson, W. A. (1996). Production and crystallization of a selenomethionyl variant of UmuD′, an Escherichia coli SOS response protein. Proteins, 25, 506–509.
Price, S. R. & Nagai, K. (1995). Protein engineering as a tool for crystallography. Curr. Opin. Biotech. 6, 425–430.
Privé, G. G., Verner, G. E., Weitzman, C., Zen, K. H., Eisenberg, D. & Kaback, H. R. (1994). Fusion proteins as tools for crystallization: the lactose permease from Escherichia coli. Acta Cryst. D50, 375–379.
Scott, C. A., Garcia, K. C., Stura, E. A., Peterson, P. A., Wilson, I. A. & Teyton, L. (1998). Engineering protein for X-ray crystallography: the murine major histocompatibility complex class II molecule I-A. Protein Sci. 7, 413–418.
Stoll, V. S., Manohar, A. V., Gillon, W., Macfarlane, E. L. A., Hynes, R. C. & Pai, E. F. (1998). A thioredoxin fusion protein of VanH, a D-lactate dehydrogenase from Enterococcus faecium: cloning, expression, purification, kinetic analysis, and crystallization. Protein Sci. 7, 1147–1155.
Sun, D.-P., Alber, T., Bell, J. A., Weaver, L. H. & Matthews, B. W. (1987). Use of site-directed mutagenesis to obtain isomorphous heavy-atom derivatives for protein crystallography: cysteine-containing mutants of phage T4 lysozyme. Protein Eng. 1, 115–123.
Windsor, W. T., Walter, L. J., Syto, R., Fossetta, J., Cook, W. J., Nagabhushan, T. L. & Walter, M. R. (1996). Purification and crystallization of a complex between human interferon γ receptor (extracellular domain) and human interferon γ. Proteins, 26, 108–114.
Yang, W., Hendrickson, W. A., Crouch, R. J. & Satow, Y. (1990). Structure of ribonuclease H phased at 2 Å resolution by MAD analysis of the selenomethionyl protein. Science, 249, 1398–1405.
Yang, W., Hendrickson, W. A., Kalman, E. T. & Crouch, R. J. (1990). Expression, purification, and crystallization of natural and selenomethionyl recombinant ribonuclease H from Escherichia coli. J. Biol. Chem. 265, 13553–13559.
Zhang, G., Liu, Y., Qin, J., Vo, B., Tang, W.-J., Ruoho, A. E. & Hurley, J. H. (1997). Characterization and crystallization of a minimal catalytic core domain from mammalian type II adenylyl cyclase. Protein Sci. 6, 903–908.
Zhang, X., Wozniak, J. A. & Matthews, B. W. (1995). Protein flexibility and adaptability seen in 25 crystal forms of T4 lysozyme. J. Mol. Biol. 250, 527–552.