2D depiction of nonbonding interactions for protein complexes

Journal of Computational Chemistry

Volumn 30, Issue 6, 2009, Pages 940-951

  Zhou, Peng ^a   Tian, Feifei ^b   Shang, Zhicai ^a  

^a ZHEJIANG UNIVERSITY   (China)

^b CHONGQING UNIVERSITY   (China)

Author keywords

2D GraLab; Molecular graphics; Nonbonding energetics; PostScript; Protein protein interaction

Indexed keywords

2D-GRALAB; BINDING SPECIFICITIES; CONFORMATIONAL ENTROPY; DESOLVATION; DISULFIDE BONDS; GEOMETRIC CHARACTERISTICS; HYDROPHOBIC CONTACT; INPUT FILES; INTERACTION INFORMATION; INTERACTION MODES; NON-BONDING INTERACTIONS; NONBONDING ENERGETICS; POSTSCRIPT; PROTEIN BINDING; PROTEIN COMPLEXES; PROTEIN ENGINEERING; PROTEIN STRUCTURES; PROTEIN-PROTEIN INTERACTION; PROTEIN-PROTEIN INTERACTIONS; SALT BRIDGES; SCHEMATIC REPRESENTATIONS; VAN DER WAALS INTERACTIONS;

BIOCHEMICAL ENGINEERING; BIOCHEMISTRY; GENETIC ENGINEERING; HYDROGEN; HYDROGEN BONDS; VAN DER WAALS FORCES;

MOLECULAR GRAPHICS;

DISULFIDE; INORGANIC SALT; MULTIPROTEIN COMPLEX;

ARTICLE; CHEMISTRY; COMPUTER GRAPHICS; COMPUTER PROGRAM; ENTROPY; HYDROGEN BOND; HYDROPHOBICITY; METABOLISM; PROTEIN BINDING; PROTEIN CONFORMATION;

COMPUTER GRAPHICS; DISULFIDES; ENTROPY; HYDROGEN BONDING; HYDROPHOBICITY; MULTIPROTEIN COMPLEXES; PROTEIN BINDING; PROTEIN CONFORMATION; SALTS; SOFTWARE;

EID: 65449123873     PISSN: 01928651     EISSN: 1096987X     Source Type: Journal    
DOI: 10.1002/jcc.21109     Document Type: Article

References (67)

1. Chothia, C.; Janin, J. Nature 1974, 256, 705.
2. Jones, S.; Thornton, J. M. Proc Natl Acad Sci USA 1996, 93, 13.
3. Luscombe, N. M.; Laskowski, R. A.; Westhead, D. R.; Milburn, D.; Jones, S.; Karmirantzoua, M.; Thornton, J. M. Acta Crystallogr D 1998,54, 1132.
4. DeLano, W. L. The PyMOL Molecular Graphics System; DeLano Scientific: San Carlos, CA, 2002.
5. Petrey, D.; Honig, B. Methods Enzymol 2003, 374, 492.
6. Humphrey, W.; Dalke, A.; Schulten, K. J Mol Graphics 1996, 14, 33.
7. Gabdoulline, R. R.; Wade, R. C.; Walther, D. Nucleic Acids Res 2003, 31, 3349.
8. Gabdoulline, R. R.; Hoffmann, R.; Leitner, F.; Wade, R. C. Bioinformatics 2003, 19, 1723.
9. Wade, R. C.; Gabdoulline, R. R.; De Rienzo, F. Int J Quantum Chem 2001, 83, 122.
10. Wallace, A. C.; Laskowski, R. A.; Thornton, J. M. Protein Eng 1995, 8, 127.
11. Stierand, K.; Maaß, P. C.; Rarey, M. Bioinformatics 2006, 22, 1710.
12. Clark, A. M.; Labute, P. J Chem Inf Model 2007, 47, 1933.
13. Luscombe, N. M.; Laskowski, R. A.; Thorntonm J. M. Nucleic Acids Res 1997, 25, 4940.
14. Salerno, W. J.; Seaver, S. M.; Armstrong, B. R.; Radhakrishnan, I. Nucleic Acids Res 2004, 32, W566.
15. Fischer, T. B.; Holmes, J. B.; Miller, I. R.; Parsons, J. R.; Tung, L.; Hu, J. C.; Tsai, J. J Struct Biol 2006, 153, 103.
16. Keskin, O.; Ma, B.; Nussinov, R. J Mol Biol 2005, 345, 1281.
17. Glaser, F.; Steinberg, D. M.; Vakser, I. A.; Ben-Tal, N. Proteins 2001, 43, 89.
18. Gray, J. J.; Moughon, S.; Wang, C.; Kuhlman, O. S. B.; Rohl, C. A.; Baker, D. J Mol Biol 2003, 331, 281.
19. Cootes, A. P.; Curmi, P. M. G.; Cunningham, R.; Donnelly, C.; Torda, A. E. Proteins 1998, 32, 175.
20. Ofran, Y.; Rost, B. J Mol Biol 2003, 325, 377.
21. Bahadur, R. P.; Chakrabarti, P.; Rodier, F.; Janin, J. J Mol Biol 2004, 336, 943.
22. Word, J. M.; Lovell, S. C.; Richardson, J. S.; Richardson, D. C. J Mol Biol 1999, 285, 1735.
23. McDonald, I. K.; Thornton, J. M. J Mol Biol 1994, 238, 777.
24. Word, J. M.; Lovell, S. C.; LaBean, T. H.; Taylor, H. C.; Zalis, M. E.; Presley, B. K.; Richardson, J. S.; Richardson, D. C. J Mol Biol 1999,285, 1711.
25. Sanner, M. F.; Olson, A. J.; Spehner, J.-C. Biopolymers 1996, 38, 305.
26. Rocchia, W.; Alexov, E.; Honig, B. J Phys Chem B 2001, 105, 6507.
27. Laskowski, R. A.; MacArthur, M. W.; Moss, D. S.; Thornton, J. M. J Appl Crystallogr 1993, 26, 283.
28. Canutescu, A. A.; Shelenkov, A. A.; Dunbrack, R. L., Jr. Protein Sci 2003, 12, 2001.
29. Brunger, A. T.; Kuriyan, J.; Karplus, M. Science 1987, 235, 458.
30. Boobbyer, D. N. A.; Goodford, P. J.; McWhinnie, P. M.; Wade, R. C. J Med Chem 1989, 32, 1083.
31. Goodford, P. J. J Med Chem 1985, 28, 849.
32. Brooks, B. R.; Bruccoleri, R. E.; Olafson, B. D.; States, D. J.; Swaminathan, S.; Karplus, M. J Comput Chem 1983, 4, 187.
33. Huey, R.; Morris, G. M.; Olson, A. J.; Goodsell, D. S. J Comput Chem 2007, 28, 1145.
34. Hill, T. L. J Chem Phys 1948, 16, 399.
35. Hirschfelder, J.; Roseveare, W. J Phys Chem 1939, 43, 15.
36. Cornell, W. D.; Cieplak, P.; Bayly, C. I.; Gould, I. R.; Merz, K. M., Jr.; Ferguson, D. M.; Spellmeyer, D. C.; Fox, T.; Caldwell, J. W.; Kollman, P. A. J Am Chem Soc 1995, 117, 5179.
37. Bondi, A. J Phys Chem 1964, 68, 441.
38. Chothia, C. Nature 1975, 254, 304.
39. Li, A. J.; Nussinov, R. Proteins 1998, 32, 111.
40. Eisenberg, D.; McLachlan, A. D. Nature 1986, 319, 199.
41. Juffer, A. H.; Eisenhaber, F.; Hubbard, S. J.; Walther, D.; Argos, P. Protein Sci 1995, 4, 2499.
42. Kim, A. Amino Acid Side Chain Contributions to Free Energy of Transfer of Tripeptides from Water to Octanol [Dissertation]; University of California: San Francisco, California, 1990.
43. Schiffer, C. A.; Caldwell, J. W.; Kollman, P. A.; Stroud, R. M. Mol Simul 1993, 10, 121.
44. Zhou, H.; Zhou, Y. Proteins 2002, 49, 483.
45. Kumar, S.; Nussinov, R. Chembiochem 2002, 3, 604.
46. Kumar, S.; Nussinov, R. J Mol Biol 1999, 293, 1241.
47. Sarakatsannis, J. N.; Duan, Y. Proteins 2005, 60, 732.
48. Hendsch, Z. S.; Tidor, B. Protein Sci 1994, 3, 211.
49. Klapper, I.; Hagstrom, R.; Fine, R.; Sharp, K.; Honig, B. Proteins 1986, 1, 47.
50. Hendsch, Z. S.; Sindelar, C. V.; Tidor, B. J Phys Chem B 1998, 102, 4404.
51. Sitkoff, D.; Sharp, K. A.; Honig, B. J Phys Chem 1994, 98, 1978.
52. Weiner, S. J.; Kollman, P. A.; Case, D. A.; Singh, U. C.; Ghio, C.; Alagona, G.; Profeta, S., Jr.; Weiner, P. J Am Chem Soc 1984, 106, 765.
53. MacKerell Juniorperiod, A. D.; Bashford, D.; Bellott, M.; Dunbrack, R. L., Jr.; Evanseck, J. D.; Field, M. J.; Fischer, S.; Gao, J.; Guo, H.; Ha, S.; Joseph-McCarthy, D.; Kuchnir, L.; Kuczera, K.; Lau, F. T. K.; Mattos, C.; Michnick, S.; Ngo, T.; Nguyen, D. T.; Prodhom, B.; Reiher, W. E., III; Roux, B.; Schlenkrich, M.; Smith, J. C.; Stote, R.; Straub, J.; Watanabe, M.; Wiórkiewicz-Kuczer, J.; Yin, D.; Karplus, M. J Phys Chem B 1998, 102, 3586.
54. Kumar, S.; Nussinov, R. Biophys J 2002, 83, 1595.
55. Brady, G. P.; Sharp, K. A. Curr Opin Struct Biol 1997, 7, 215.
56. Doig, A. J.; Sternberg, M. J. E. Protein Sci 1995, 4, 2247.
57. Creamer, T. P. Proteins 2000, 40, 443.
58. Koehl, P.; Delarue, M. J Mol Biol 1994, 239, 249.
59. Karplus, M.; Ichiye, T.; Pettitt, B. M. Biophys J 1987, 52, 1083.
60. Chellgren, B. W.; Creamer, T. P. Proteins 2006, 62, 411.
61. Zhang, J.; Liu, J. S. PLoS Comput Biol 2006, 2, 1586.
62. Lovell, S. C.; Word, J. M.; Richardson, J. S.; Richardson, D. C. Proteins 2000, 40, 389.
63. Dunbrack, R. L., Jr. Curr Opin Struct Biol 2002, 12, 431.
64. Zhang, C.; Vasmatzis, G.; Cornette, J. L.; DeLisi, C. J Mol Biol 1997, 267, 707.
65. McGaughey, G. B.; Gagné, M.; Rappé, A. K. J Biol Chem 1998, 273, 15458.
66. Cho, K.; Lee, K.; Lee, K. H.; Kim, D.; Lee, D. Proteins 2006, 65, 593.
67. Baldwin, R. L. J Mol Biol 2007, 371, 283.