Summary
Macromolecular X-ray crystallography is an important and powerful technique in drug discovery, used by pharmaceutical companies in the discovery process of new medicines. The detailed analysis of crystal structures of protein–ligand complexes allows the study of the specific interactions of a particular drug with its protein target at the atomic level. It is used to design and improve drugs. The starting point of these studies is the preparation of suitable crystals of complexes with potential ligands, which can be achieved by using different strategies described in this chapter. In addition, an introduction to X-ray crystallography is given, highlighting the fundamental steps necessary to determine the three-dimensional structure of protein–ligand complexes, as well as some of the tools and criteria to validate crystal structures available in databases.
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References
Dror, O., Lasker, K., Nussinov, R., and Wolfson, H. (2007). EMatch: an efficient method for aligning atomic resolution subunits into intermediate-resolution cryo-EM maps of large macromolecular assemblies. Acta Crystallogr. D Biol. Crystallogr. 63, 42–49
Sigworth, F. J. (2007). From cryo-EM, multiple protein structures in one shot. Nat. Methods 4, 20–21
Hassell, A. M., An, G., Bledsoe, R. K., Bynum, J. M., Carter, H. L., III, Deng, S. J., Gampe, R. T., Grisard, T. E., Madauss, K. P., Nolte, R. T., Rocque, W. J., Wang, L., Weaver, K. L., Williams, S. P., Wisely, G. B., Xu, R., and Shewchuk, L. M. (2007). Crystallization of protein-ligand complexes. Acta Crystallogr. D Biol. Crystallogr. 63, 72–79
Chung, C. W. (2007). The use of biophysical methods increases success in obtaining liganded crystal structures. Acta Crystallogr. D Biol. Crystallogr. 63, 62–71
Niesen, F. H., Berglund, H., and Vedadi, M. (2007). The use of differential scanning fluorimetry to detect ligand interactions that promote protein stability. Nat. Protoc. 2, 2212–2221
Senisterra, G.A. (2006). Screening for ligands using a generic and high-throughput light-scattering assay. J. Biomol. Screen. 11, 940–948
Vedadi, M., Niesen, F. H., Allali-Hassani, A., Fedorov, O. Y., Finerty, P. J., Wasney, G. A., Yeung, R., Arrowsmith, C., Ball, L. J., Berglund, H., Hui, R., Marsden, B. D., Nordlund, P., Sundstrom, M., Weigelt, J., and Edwards, A. M. (2006). Chemical screening methods to identify ligands that promote protein stability, protein crystallization, and structure determination. Proc. Natl. Acad. Sci. U.S.A. 103, 15835–15840
Brown, W., Ed. (1993). Dynamic Light Scattering: The Method and Some Applications, Vol. 49. Monographs on the Physics and Chemistry of Materials. Oxford University Press, USA
Schmitz, K. S. (1990). An Introduction to Dynamic Light Scattering by Macromolecules. Academic Press, Boston
Feng, B. Y., Shelat, A., Doman, T. N., Guy, R. K., and Shoichet, B. K. (2005). High-throughput assays for promiscuous inhibitors. Nat. Chem. Biol. 1, 146–148
McNae, I. W., Kan, D., Kontopidis, G., Patterson, A., Taylor, P., Worrall, L., and Walkinshaw, M. D. (2005). Studying protein-ligand interactions using protein crystallography. Crystallogr. Rev. 11, 61–71
Matthews, B. W. (1968). Solvent content of protein crystals. J. Mol. Biol. 33, 491–497
Vilenchik, L. Z., Griffith, J. P., St Clair, N., Navia, M. A., and Margolin, A. L. (1998). Protein crystals as novel microporous materials. J. Am. Chem. Soc. 120, 4290–4294
Lusty, C. J. (1999). A gentle vapor-diffusion technique for cross-linking of protein crystals for cryocrystallography. J. Appl. Crystallogr. 32, 106–112
Danley, D. E. (2006). Crystallization to obtain protein-ligand complexes for structure-aided drug design. Acta Crystallogr. D Biol. Crystallogr. 62, 569–575
Skarzynski, T. and Thorpe, J. (2006). Industrial perspective on X-ray data collection and analysis. Acta Crystallogr. D Biol. Crystallogr. 62, 102–107
Hiller, N., Fritz-Wolf, K., Deponte, M., Wende, W., Zimmermann, H., and Becker, K. (2006). Plasmodium falciparum glutathione S-transferase – structural and mechanistic studies on ligand binding and enzyme inhibition. Protein Sci. 15, 281–289
Williams, S. P. and Sigler, P. B. (1998). Atomic structure of progesterone complexed with its receptor. Nature 393, 392–396
Matias, P. M., Donner, P., Coelho, R., Thomaz, M., Peixoto, C., Macedo, S., Otto, N., Joschko, S., Scholz, P., Wegg, A., Basler, S., Schafer, M., Egner, U., and Carrondo, M. A. (2000). Structural evidence for ligand specificity in the binding domain of the human androgen receptor. Implications for pathogenic gene mutations. J. Biol. Chem. 275, 26164–26171
Hope, H. (1988). Cryocrystallography of biological macromolecules: a generally applicable method. Acta Crystallogr B 44 (Pt 1), 22–26
Garman, E. F. and Schneider, T. R. (1997). Macromolecular cryocrystallography. J. Appl. Crystallogr. 30, 211–237
Read, R. J. (1999). Detecting outliers in non-redundant diffraction data. Acta Crystallogr. D Biol. Crystallogr. 55, 1759–1764
Otwinowsky, Z. (1991). CCP4 Daresbury Study Weekend Proceedings
Brunger, A. T., Adams, P. D., Clore, G. M., DeLano, W. L., Gros, P., Grosse-Kunstleve, R. W., Jiang, J. S., Kuszewski, J., Nilges, M., Pannu, N. S., Read, R. J., Rice, L. M., Simonson, T., and Warren, G. L. (1998). Crystallography & NMR system: a new software suite for macromolecular structure determination. Acta Crystallogr. D Biol. Crystallogr. 54, 905–921
delaFortelle, E. and Bricogne, G. (1997). Maximum-likelihood heavy-atom parameter refinement for multiple isomorphous replacement and multiwavelength anomalous diffraction methods. Meth. Enzymol. 276, 472–494
Terwilliger, T. C. and Berendzen, J. (1999). Automated MAD and MIR structure solution. Acta Crystallogr. D Biol. Crystallogr. 55, 849–861
Tong, L. and Rossmann, M. G. (1990). The locked rotation function. Acta Crystallogr. A 46, 783–792
Navaza, J. (1994). Amore – an automated package for molecular replacement. Acta Crystallogr. A 50, 157–163
Kissinger, C. R., Gehlhaar, D. K., and Fogel, D. B. (1999). Rapid automated molecular replacement by evolutionary search. Acta Crystallogr. D Biol. Crystallogr. 55, 484–491
Read, R. J. (2001). Pushing the boundaries of molecular replacement with maximum likelihood. Acta Crystallogr. D Biol. Crystallogr. 57, 1373–1382
Long, F., Vagin, A. A., Young, P., and Murshudov, G. N. (2007). BALBES: a molecular-replacement pipeline. Acta Crystallogr. D Biol. Crystallogr. 64, 125–132
Engh, R. A. and Huber, R. (1991). Accurate bond and angle parameters for X-ray protein-structure refinement. Acta Crystallogr. A 47, 392–400
Engh, R. A. and Huber, R. (2001). Structure quality and target parameters. In: Rossmann, M. G., and Arnold, E. (eds.) International Tables for Crystallography, Vol. F. Kluwer, Dordrecht, The Netherlands, pp. 382–392
Hendrickson, W. A. (1985). Stereochemically restrained refinement of macromolecular structures. Methods Enzymol. 115, 252–270
Parkinson, G., Vojtechovsky, J., Clowney, L., Brunger, A. T., and Berman, H. M. (1996). New parameters for the refinement of nucleic acid-containing structures. Acta Crystallogr. D Biol. Crystallogr. 52, 57–64
Priestle, J. P. (2003). Improved dihedral-angle restraints for protein structure refinement. J. Appl. Crystallogr. 36, 34–42
Brunger, A. T. (1992). X-Plor Version 3.1: A System for X-ray Crystallography and NMR, Yale University Press, New Haven
Emsley, P., and Cowtan, K. (2004). Coot: model-building tools for molecular graphics. Acta Crystallogr. D Biol. Crystallogr. 60, 2126–2132
Kleywegt, G. J. (2000). Validation of protein crystal structures. Acta Crystallogr. D Biol. Crystallogr. 56, 249–265
Berman, H. M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T. N., Weissig, H., Shindyalov, I. N., and Bourne, P. E. (2000). The Protein Data Bank. Nucleic Acids Res. 28, 235–242
Terwilliger, T. C., Klei, H., Adams, P. D., Moriarty, N. W., and Cohn, J. D. (2006). Automated ligand fitting by core-fragment fitting and extension into density. Acta Crystallogr. D Biol. Crystallogr. 62, 915–922
Adams, P. D., Grosse-Kunstleve, R. W., Hung, L. W., Ioerger, T. R., McCoy, A. J., Moriarty, N. W., Read, R. J., Sacchettini, J. C., Sauter, N. K., and Terwilliger, T. C. (2002). PHENIX: building new software for automated crystallographic structure determination. Acta Crystallogr. D Biol. Crystallogr. 58, 1948–1954
Murshudov, G. N., Vagin, A. A., and Dodson, E. J. (1997). Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallogr. D Biol. Crystallogr. 53, 240–255
Blanc, E., Roversi, P., Vonrhein, C., Flensburg, C., Lea, S. M., and Bricogne, G. (2004). Refinement of severely incomplete structures with maximum likelihood in BUSTER-TNT. Acta Crystallogr. D Biol. Crystallogr. 60, 2210–2221
Roversi, P., Blanc, E., Vonrhein, C., Evans, G., and Bricogne, G. (2000). Modelling prior distributions of atoms for macromolecular refinement and completion. Acta Crystallogr. D Biol. Crystallogr. 56, 1316–1323
Jones, T. A., Zou, J. Y., Cowan, S. W., and Kjeldgaard, M. (1991). Improved methods for building protein models in electron-density maps and the location of errors in these models. Acta Crystallogr. A 47, 110–119
Evans, P. R. (2007). An introduction to stereochemical restraints. Acta Crystallogr. D Biol. Crystallogr. 63, 58–61
Kleywegt, G. J., Henrick, K., Dodson, E. J., and van Aalten, D. M. F. (2003). Pound-wise but penny-foolish: how well do micromolecules fare in macromolecular refinement? Structure 11, 1051–1059
Kleywegt, G. J. (2007). Crystallographic refinement of ligand complexes. Acta Crystallogr. D Biol. Crystallogr. 63, 94–100
Feng, Z. K., Chen, L., Maddula, H., Akcan, O., Oughtred, R., Berman, H. M., and Westbrook, J. (2004). Ligand Depot: a data warehouse for ligands bound to macromolecules. Bioinformatics 20, 2153–2155
Schuttelkopf, A. W. and van Aalten, D. M. F. (2004). PRODRG: a tool for high-throughput crystallography of protein-ligand complexes. Acta Crystallogr. D Biol. Crystallogr. 60, 1355–1363
vanAalten, D. M. F., Bywater, R., Findlay, J. B. C., Hendlich, M., Hooft, R. W. W., and Vriend, G. (1996). PRODRG, a program for generating molecular topologies and unique molecular descriptors from coordinates of small molecules. J. Comput. Aided Mol. Des. 10, 255–262
Gasteiger, J., Rudolph, C., and Sadowski, J. (1992). Automatic Generation of 3D-Atomic Coordinates for Organic Molecules. Tetrahedron Comput. Method. 3, 537–547
Peat, T. S., Christopher, J. A., and Newman, J. (2005). Tapping the protein data bank for crystallization information. Acta Crystallogr. D Biol. Crystallogr. 61, 1662–1669
Perrakis, A., Morris, R., and Lamzin, V. S. (1999). Automated protein model building combined with iterative structure refinement. Nat. Struct. Biol. 6, 458–463
Evrard, G. X., Langer, G. G., Perrakis, A., and Lamzin, V. S. (2007). Assessment of automatic ligand building in ARP/wARP. Acta Crystallogr. D Biol. Crystallogr. 63, 108–117
Levinson, N. M., Kuchment, O., Shen, K., Young, M. A., Koldobskiy, M., Karplus, M., Cole, P. A., and Kuriyan, J. (2006). A Src-like inactive conformation in the Abl tyrosine kinase domain. PLoS. Biol. 4, 753–767
Kleywegt, G. J. and Jones, T. A. (1998). Databases in protein crystallography. Acta Crystallogr. D Biol. Crystallogr. 54, 1119–1131
Bragg, W. H. and Bragg, W. L. (1913). The reflection of X-rays by crystals. Proc. R. soc. Lond. Ser. A-Contain. Pap. Math. Phys. Character 88, 428–428
Sheldrick, G. M. (1995). Structure solution by iterative peaklist optimization and tangent expansion in-space group P1. Acta Crystallogr. B 51, 423–431
Weeks, C. M. and Miller, R. (1999). Optimizing Shake-and-Bake for proteins. Acta Crystallogr. D Biol. Crystallogr. 55, 492–500
Ten Eyck, L. F. and Watenpaugh, K. D. (2006). Introduction to refinement. In: Rossmann, M. G., and Arnold, E. (eds.) Crystallography of Biological Macromolecules, Vol. F. Kluwer, Dordrecht, The Netherlands, pp. 369–374
Wang, B. C. (1985). Resolution of phase ambiguity in macromolecular crystallography. Meth. Enzymol. 115, 90–112
Leslie, A. G. W. (1987). A reciprocal-space method for calculating a molecular envelope using the algorithm of Wang, B.C. Acta Crystallogr. A 43, 134–136
Hodel, A., Kim, S. H., and Brunger, A. T. (1992). Model bias in macromolecular crystal-structures. Acta Crystallogr. A 48, 851–858
Read, R. J. (1986). Improved Fourier coefficients for maps using phases from partial structures with error. Acta Crystallogr. A 42, 140–149
Potterton, E., McNicholas, S., Krissinel, E., Cowtan, K., and Noble, M. (2002). The CCP4 molecular-graphics project. Acta Crystallogr. D Biol. Crystallogr. 58, 1955–1957
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The authors acknowledge Dr. Shabir Najmudin and Dr. Abhik Mukhopadhyay for critical reading of the manuscript.
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Carvalho, A.L., Trincão, J., Romão, M.J. (2010). X-Ray Crystallography in Drug Discovery. In: Roque, A. (eds) Ligand-Macromolecular Interactions in Drug Discovery. Methods in Molecular Biology, vol 572. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-60761-244-5_3
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