Extent and nature of contacts between protein molecules in crystal lattices and between subunits of protein oligomers

Proteins: Structure, Function and Genetics

Volumn 28, Issue 4, 1997, Pages 494-514

  Dasgupta, Swagata ^a,d   Iyer, Ganesh H ^a   Bryant, Stephen H ^b   Lawrence, Charles E ^c   Bell, Jeffrey A ^a  

^a Research Rensselaer Polytechnic Institute   (United States)

^b NATIONAL INSTITUTES OF HEALTH   (United States)

^c WADSWORTH CENTER   (United States)

^d INDIAN INSTITUTE OF TECHNOLOGY   (India)

Author keywords

Contact patches; Hydrophobic interaction; Molecular recognition; Potential of mean force; Protein crystallization; Protein interfaces; Salt bridges

Indexed keywords

AMINO ACID SEQUENCE; ARTICLE; CRYSTAL STRUCTURE; CRYSTALLIZATION; HYDROPHOBICITY; MOLECULAR INTERACTION; PRIORITY JOURNAL; PROTEIN STRUCTURE;

CRYSTALLIZATION; MODELS, MOLECULAR; OLIGOPEPTIDES; PROTEIN STRUCTURE, SECONDARY; PROTEINS;

EID: 0030877077     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/(SICI)1097-0134(199708)28:4<494::AID-PROT4>3.0.CO;2-A     Document Type: Article

References (56)

1. Bernstein, F.C., Koetzle, T.F., Williams, G.J.B., Meyer Jr., E.F., Brice, M.D., Rogers, J.R., Kennard, O., Shimanouchi, T., Tasumi, M. The Protein Data Bank: A computer-based archival file for macromolecular structures. J. Mol. Biol. 112:535-542, 1977.
2. Abola, E., Bernstein, F.C., Bryant, S.H., Koetzle, T.F., Weng, J. Protein Data Bank. In: Allen, F.H., Bergerhoff, G., Sievers, R. "Crystallographic Databases: Information Content, Software Systems, Scientific Applications." Bonn/ Cambridge/Chester: Data Commission of the International Union of Crystallography, 1987:107-132.
3. Crosio, M.P., Rodier, F., Jullien, M. Packing forces in ribonuclease crystals. FEBS Lett, 271:152-156, 1990.
4. Svensson, L.A., Dill, J., Sjölin, L., Wlodawer, A., Toner, M., Bacon, D., Moult, J., Veerapandian, B., Gilliland, G.L. The crystal packing interactions of two different crystal forms of bovine ribonuclease A. J. Crystal Growth 110:119-130, 1991.
5. Crosio, M.P., Janin, J., Jullien, M. Crystal packing in six crystal forms of pancreatic ribonuclease. J. Mol. Biol. 228:243-251, 1992.
6. Radha Kishan, K.V., Zeelen, J.P., Noble, M.E.M., Borchert, T.V., Wierenga, R.K. Comparison of the structures and the crystal contacts of trypanosomal triosephosphate isomerase in four different crystal forms. Protein Sci. 3:779-787, 1994.
7. Zhang, X.J., Wozniak, J.A., Matthews, B.W. Protein flexibility and adaptability seen in 25 crystal forms of T4 lysozyme. J. Mol. Biol. 250:527-552, 1995.
8. Takahashi, T., Endo, S., Nagayama, K. Stabilization of protein crystals by electrostatic interactions as revealed by a numerical approach. J. Mol. Biol. 234:421-432, 1993.
9. Matthews, B.W. Solvent content of protein crystals. J. Mol. Biol. 33:491-497, 1968.
10. Islam, S.A., Weaver, D.L. Molecular interactions in protein crystals: Solvent accessible surface and stability. Proteins 8:1-5, 1990.
11. Frey, M., Genovesio-Taverne, J.C., Fontecilla-Camps, J.C. Molecular packing and morphology of protein crystals. J. Phys. D. Appl. Phys. 24:105-110, 1991.
12. Janin, J., Rodier, F. Protein-protein interactions at crystal contacts. Proteins 23:580-587, 1995.
13. Janin, J., Miller, S., Chothia, C. Surface, subunit interfaces and interior of oligomeric proteins. J. Mol. Biol. 204:155-164, 1988.
14. Argos, P. An investigation of protein subunit and domain interfaces. Protein Eng. 2:101-113, 1988.
15. Miller, S. The structure of interfaces between subunits of dimeric and tetrameric proteins. Protein Eng. 3:77-83, 1989.
16. Jones, S., Thornton, J.M. Protein-protein interactions: A review of protein dimer structures. Prog. Biophys. Mol. Biol. 63:31-65, 1995.
17. Miller, S., Lesk, A.M., Janin, J., Chothia, C. The accessible surface area and stability of oligomeric proteins. Nature 328:834-836, 1987.
18. Tsai, C.-J., Lin, S.L., Wolfson, H.J., Nussinov, R. Studies of protein-protein interfaces: A statistical analysis of the hydrophobic effect. Protein Sci. 6:53-64, 1997.
19. Korn, A.P., Burnett, R.M. Distribution and complementarity of hydropathy in multisubunit proteins. Proteins 9:37-55, 1991.
20. Neet, K.E., Timm, D.E. Conformational stability of dimeric proteins: Quantitative studies by equilibrium denaturation. Protein Sci. 3:2167-2174, 1994.
21. Boberg, J., Salakoski, T., Vihinen, M. Selection of a representative set of structures from the Brookhaven Protein Data Bank. Proteins 14:265-276, 1992.
22. Hobohm, U., Scarf, M., Schneider, R., Sander, C. Selection of representative protein data sets. Protein Sci. 1:409-417, 1992.
23. Hobohm, U., Sander, C. Enlarged representative set of protein structures. Protein Sci. 3:522-524, 1994.
24. Becker, R.A., Chambers, J.M., Wilks, A.R. "The New 'S' Language: A Programming Environment for Data Analysis and Graphics." Pacific Grove, CA: Wadsworth, 1988.
25. Bryant, S.H. PKB: A program system and data base for analysis of protein structure. Proteins 5:233-247, 1989.
26. Liebman, M.N., Venanzi, C.A., Weinstein, H. Structural analysis of carboxypeptidase A and its complexes with inhibitors as a basis for modeling enzyme recognition and specificity. Biopolymers 24:1721-1758, 1985.
27. Morris, A.L., Hutchinson, E.G., MacArthur, M.W., Thornton, J.M. Stereochemical quality of protein structure coordinates. Proteins 12:345-364, 1992.
28. Tronrud, D.E., Ten Eyck, L.F., Matthews, B.W. An efficient general-purpose least-squares refinement program for macromolecular structures. Acta Crystallogr. A 43:489-503, 1987.
29. Lee, B., Richards, F.M. The interpretation of protein structure: Estimation of static accessibility. J. Mol. Biol. 55:379-400, 1971.
30. Shrake, A., Rupley, J.A. Environment and exposure to solvent of protein atoms: Lysozyme and insulin. J. Mol. Biol. 79:351-371, 1973.
31. Bryant, S.H., Lawrence, C.E. The frequency of ion-pair substructures in proteins is quantitatively related to electrostatic potential: A statistical model for non-bonded interactions. Proteins 9:108-119, 1991.
32. Bryant, S.H., Lawrence, C.E. An empirical energy function for threading protein sequence through the folding motif. Proteins 16:92-112, 1993.
33. Fienberg, S.E. "The Analysis of Cross-Classified Categorical Data." Cambridge, MA: MIT Press, 1980.
34. Padmaja, N., Ramakumar, S., Viswamitra, M.A. Space-group frequencies of proteins and of organic compounds with more than one formula unit in the asymmetric unit. Acta Crystallogr. A46:725-730, 1990.
35. Brock, C.P., Dunitz, J.D. Towards a grammar of crystal packing. Chem. Mater. 6:1118-1127, 1994.
36. Wukovitz, S.W., Yeates, T.O. Why protein crystals favour some space-groups over others. Nature Struct. Biol. 2:1062-1067, 1995.
37. McPherson, A. "The Preparation and Analysis of Protein Crystals." Malabar, FL: Robert E. Kreieger Publishing, 1989:174-179.
38. McPherson, A. A brief history of protein crystal growth. J. Crystal Growth 110:1-10, 1991.
39. Creighton, T.E. An empirical approach to protein conformation stability and flexibility. Biopolymers 22:49-58, 1983.
40. Lawrence, M.C., Colman, P.M. Shape complementarity at protein/protein interfaces. J. Mol. Biol. 234:946-950, 1993.
41. Hubbard, S.J., Argos, P. Cavities and packing at protein interfaces. Protein Sci. 3:2194-2206, 1994.
42. Cherfils, J., Duquerroy, S., Janin, J. Protein-protein recognition analyzed by docking simulation. Proteins 11:271-280, 1991.
43. Helmer-Citterich, M., Tramontano, A. PUZZLE: A new method for automated protein docking based on surface shape complementarity. J. Mol. Biol. 235:1021-1031, 1994.
44. Zielenkiewicz, P., Rabczenko, A. Protein-protein recognition: Method for finding complementary surfaces of interacting proteins. J. Theor. Biol. 111:17-30, 1984.
45. Jiang, F., Kim, S.H. "Soft docking": Matching of molecular surface cubes. J. Mol. Biol. 219:79-102, 1991.
46. Bacon, D.J., Moult, J. Docking by least-squares fitting of molecular surface patterns. J. Mol. Biol. 225:849-858, 1992.
47. Meng, E.C., Shoichet, B.K., Kuntz, I.D. Automated docking with grid-based energy evaluation. J. Comput. Chem. 13:505-524, 1992.
48. Shoichet, B.K., Kuntz, I.D. Protein docking and complementarity. J. Mol. Biol. 221:327-346, 1991.
49. Shoichet, B.K., Kuntz, I.D. Matching chemistry and shape in molecular docking. Protein Eng. 6:723-732, 1993.
50. Walls, P.H., Sternberg, M.J.E. New algorithm to model protein recognition based on surface complementarity: Applications to antibody antigen docking. J. Mol. Biol. 228:277-297, 1992.
51. Cherfils, J., Janin, J. Protein docking algorithms: Simulating molecular recognition. Curr. Opin. Struct. Biol. 3:265-269, 1993.
52. Kabsch, W., Sander, C. Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 22:2577-2637, 1983.
53. Musafia, B., Buchner, V., Arad, D. Complex salt bridges in proteins: Statistical analysis of structure and function. J. Mol. Biol. 254:761-770, 1995.
54. Patro, S.Y., Przybycien, T.M. Simulations of kinetically irreversible protein aggregate structure. Biophys. J. 66:1-16, 1994.
55. Patro, S.Y., Przybycien, T.M. Simulations of reversible protein aggregate and crystal structure. Biophys. J. 70: 2888-2902, 1996.
56. 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. Solving the structure of human H ferritin by genetically engineering intermolecular crystal contacts. Nature 349: 541-544, 1991.