Average assignment method for predicting the stability of protein mutants

Biopolymers

Volumn 82, Issue 1, 2006, Pages 80-92

  Saraboji, K ^b   Gromiha, M Michael ^a   Ponnuswamy, M N ^b  

^a NATIONAL INSTITUTE OF ADVANCED INDUSTRIAL SCIENCE AND TECHNOLOGY AIST   (Japan)

^b UNIVERSITY OF MADRAS   (India)

Author keywords

Amino acid substitution; Average assignment method; Free energy change; Protein mutants; Thermal stability

Indexed keywords

AMINO ACIDS; CORRELATION METHODS; FREE ENERGY; SUBSTITUTION REACTIONS; THERMODYNAMIC STABILITY;

AMINO ACID SUBSTITUTION; AVERAGE ASSIGNMENT METHOD; FREE ENERGY CHANGE; PROTEIN MUTANTS;

PROTEINS;

MUTANT PROTEIN; SOLVENT;

AMINO ACID SUBSTITUTION; ARTICLE; DATA BASE; DENATURATION; PROTEIN SECONDARY STRUCTURE; PROTEIN STABILITY; THERMOSTABILITY;

AMINO ACID SUBSTITUTION; AMINO ACIDS; DATABASES, PROTEIN; GENOMIC INSTABILITY; PREDICTIVE VALUE OF TESTS; PROTEIN DENATURATION; PROTEIN STRUCTURE, SECONDARY; PROTEINS; SOLVENTS; THERMODYNAMICS;

EID: 33646053131     PISSN: 00063525     EISSN: 10970282     Source Type: Journal    
DOI: 10.1002/bip.20462     Document Type: Article

References (52)

1. Bash, P.; Singh, U. C.; Langridge, R.; Kollman, P. A. Science 1987, 236, 564-568.
2. Tidor, B.; Karplus, M. Biochemistry 1991, 30, 3217-3228.
3. Sugita, Y.; Kitao, A. Biophys J 1998, 75, 2178-2187.
4. Takano, K.; Yutani, K. Protein Eng 2001, 14, 525-528.
5. Wang, Y.; Lal, L.; Li, S.; Han, Y.; Tang, Y. Protein Eng 1996, 19, 479-484.
6. Lee, C.; Levitt, M. Nature 1991, 352, 448-451.
7. van Gunsteren, W. F.; Mark, A. E. J Mol Biol 1992, 227, 389-395.
8. Lee, C. J Mol Biol 1994, 236, 918-939.
9. Damborsky, J.; Bohac, M.; Prokop, M.; Kutty, M.; Koca, J. Protein Eng 1998, 11, 901-907.
10. Pikkemaat, M. G.; Linssen, A. B. M.; Berendsen, H. J. C.; Janssenl, D. B. Protein Eng 2002, 15, 185-192.
11. Miyazawa, S.; Jernigan, R. L. Protein Eng 1994, 7, 1209-1220.
12. Bordner, A. J.; Abagyan, R. A. Proteins 2004, 57, 400-413.
13. Topham, C. M.; Srinivasan, N.; Blundell, T. L. Protein Eng 1997, 10, 7-21.
14. Takano, K.; Ota, M.; Ogasahara, K.; Yamagata, Y.; Nishikawa, K.; Yutani, K. Protein Eng 1999, 12, 663-672.
15. Gilis, D.; Rooman, M. J Mol Biol 1996, 257, 1112-1126.
16. Gills, D.; Rooman, M. J Mol Biol 1997, 272, 276-290.
17. Khatun, J.; Khare, S. D.; Nikolay, V.; Dokholyan, N. V. J Mol Biol 2004, 336, 1223-1238.
18. Gromiha, M. M.; Oobatake, M.; Kono, H.; Uedaira, H.; Sarai, A. J Protein Chem 1999, 18, 565-578.
19. Capriotti, E.; Fariselli, P.; Casadio, R. Bioinformatics 2004, 20, i63-i68.
20. Gromiha, M. M. An, J.; Kono, H.; Oobatake, M.; Uedaira, H.; Sarai, A. Nucleic Acids Res 1999, 27, 286-268.
21. Gromiha, M. M.; Oobatake, M.; Kono, H.; Uedaira, H.; Sarai, A. J Biomol Struct Dynam 2000, 18, 281-295.
22. Gromiha, M. M.; Oobatake, M.; Kono, H.; Uedaira, H.; Sarai, A. Biopolymers 2002, 64, 210-220.
23. Guerois, R.; Nielsen, J. E.; Serrano, L. J Mol Biol 2002, 320, 369-387.
24. Zhou, H.; Zhou, Y. Proteins 2002, 49, 483-492.
25. Chan, C. H.; Liang, H. K.; Hsiao, N. W.; Ko, M. T.; Lyu, P. C.; Hwang, J. K. Proteins 2004, 57, 684-691.
26. Gilis, D.; Rooman, M. Protein Eng 2000, 13, 849-856.
27. Gromiha, M. M.; Oobatake, M.; Kono, H.; Uedaira, H.; Sarai, A. Protein Eng 1999, 12, 549-555.
28. Gromiha, M. M. Polymer 2003, 44, 4061-4066.
29. Saraboji, K.; Gromiha, M. M.; Ponnuswamy, M. N. Comp Biol Chem 2005, 29, 25-35.
30. Bava, K. A.; Gromiha, M. M.; Uedaira, H.; Kitajima, K.; Sarai, A. Nucleic Acids Res 2004, 32, D120-D121, Database issue.
31. Eisenhaber F, Argos P: Improved strategy in analytical surface calculation for molecular system- handling of singularities and computational efficiency. J Comp Chem 1993, 14: 1272-1280.
32. Momany, F. A.; McGuire, R. F.; Burgess, A. W.; Scheraga, H. A. J Phys Chem 1975, 79, 2361-2381.
33. Hecht, M. H.; Sturtevant, J. M.; Sauer, R. T. Proteins 1986, 1, 43-46.
34. Pinker, R. J.; Lin, L.; Rose, G. D.; Kallenbach, N. R. Protein Sci 1993, 2, 1099-10105.
35. Haruki, M.; Noguchi, E.; Nakai, C.; Liu, Y. Y.; Oobatake, M.; Itaya, M.; Kanaya, S. Eur J Biochem 1994, 220, 623-631.
36. Milla, M. E.; Brown, B. M.; Sauer, R. T. Nat Struct Biol 1994, 1, 518-523.
37. Takano, K.; Ogasahara, K.; Kaneda, H.; Yamagata, Y.; Fujii, S.; Kanaya, E.; Kikuchi, M.; Oobatake, M.; Yutani, K. J Mol Biol 1995, 254, 62-76.
38. Takano, K.; Yamagata, Y.; Fujii.; S.; Yutani, K. Biochemistry 1997, 36, 688-698.
39. Masumoto, K.; Ueda, T.; Motoshima, H.; Imoto, T. Protein Eng 2000; 13, 691-695.
40. Kellis, J. T., Jr.; Nyberg, K.; Fersht, A. R. Biochemistry 1989, 28, 4914-4922.
41. Eriksson, A. E.; Baase, W. A.; Zhang, X. J.; Heinz, D. W.; Blaber, M.; Baldwin, E. P.; Matthews, B. W. Science 1992, 255, 178-183.
42. Jackson, S. E.; Moracci, M.; el Masry, N.; Johnson, C. M.; Fersht, A. R. Biochemistry 1993, 32, 11259-11269.
43. Takano, K.; Yamagata, Y.; Yutani, K. J Mol Biol 1998, 280, 749-761.
44. Capriotti, E.; Fariselli, P.; Calabrese, R.; Casadio, R. Bioinformatics 2005, 21(Supplement 2), ii54-ii58.
45. Lazaridis, T.; Karplus, M. Curr Opin Struct Biol 2000, 10, 139-145.
46. Yutani, K.; Ogasahara, K.; Tsujita, T.; Sugino, Y. Proc Natl Acad Sci USA 1987, 84, 4441-4444.
47. Matthews, B. W. Adv Protein Chem 1995, 46, 249-278.
48. Shortle, D.; Stites, W. E.; Meeker, A. K. Biochemistry 1990, 29, 8033-8041.
49. Lee, B.; Richards, F. M. J Mol Biol 1971, 55, 379-400.
50. Kabsch, W.; Sander, C. Biopolymers 1983, 22, 2577-2637.
51. Eisenhaber, F.; Argos, P. J Comp Chem 1993, 14, 1272-1280.
52. Gromiha, M. M.; Ahmad, S. Curr Comput Aided Drug Design 2005, 1, 223-235.