Importance of individual side chains for the stability of a protein fold: Computational alanine scanning of the insulin monomer

Journal of Computational Chemistry

Volumn 27, Issue 15, 2006, Pages 1843-1857

  Zoete, Vincent ^a   Meuwly, Markus ^b  

^a SWISS INSTITUTE OF BIOINFORMATICS   (Switzerland)

^b UNIVERSITY OF BASEL   (Switzerland)

Author keywords

Binding free energy; Computational alanine scanning; Insulin; MM GBSA; Protein structural stability

Indexed keywords

COMPUTATIONAL METHODS; COMPUTER SIMULATION; ELECTROSTATICS; ESTIMATION; FREE ENERGY; INSULIN; MOLECULAR DYNAMICS; MONOMERS; THERMODYNAMIC STABILITY; VAN DER WAALS FORCES;

BINDING FREE ENERGY; COMPUTATIONAL ALANINE SCANNING; COMPUTATIONAL MUTATIONS TO ESTIMATE PROTEIN STABILITY (CMEPS); PROTEIN STRUCTURAL STABILITY;

PROTEINS;

ALANINE; INSULIN;

ARTICLE; CHEMICAL STRUCTURE; CHEMISTRY; COMPARATIVE STUDY; COMPUTER SIMULATION; MUTATION; PROTEIN CONFORMATION; PROTEIN FOLDING; THERMODYNAMICS;

ALANINE; COMPUTER SIMULATION; INSULIN; MODELS, MOLECULAR; MUTATION; PROTEIN CONFORMATION; PROTEIN FOLDING; THERMODYNAMICS;

EID: 33750539273     PISSN: 01928651     EISSN: 1096987X     Source Type: Journal    
DOI: 10.1002/jcc.20512     Document Type: Article

References (58)

1. Creighton, T. E. Proteins: Structures and Molecular Properties. W. H. Freeman: New York, 1993.
2. Freire, E. Methods Enzymol 1995, 259, 144.
3. Pace, C. N. Methods Enzymol 1986, 131, 266.
4. Aqvist, J.; Luzhkov, V. B.; Brandsal, B. O. Acc Chem Res 2002, 35, 358.
5. Tame, J. R. H. J Comput-Aided Mol Des 1999, 13, 99.
6. Hansson, T.; Oostenbrink, C.; van Gunsteren, W. F. Curr Opin Struct Biol 2002, 12, 190.
7. Brems, D. N.; Alter, L. A.; Beckage, M. J.; Chance, R. E.; DiMarchi, R. D.; Green, L. K.; Long, H. B.; Pekar, A. H.; Shields, J. E.; Frank, B. Protein Eng 1992, 5, 527.
8. Kitagawa, K.; Ogawa, H.; Burke, G. T.; Chanley, J. D.; Katsoyannis, P. G. Biochemistry 1984, 23, 1405.
9. Nakagawa, S. H.; Tager, H. S. J Biol Chem 1986, 261, 7332.
10. Nakagawa, S. H.; Tager, H. S. Biochemistry 1992, 31, 3204.
11. Mirmira, R. G.; Tager, H. S. J Biol Chem 1989, 264, 6349.
12. Mirmira, R. G.; Nakagawa, S. H.; Tager, H. S. J Biol Chem 1991, 266, 1428.
13. Keller, D.; Clausen, R.; Josefsen, K.; Led, J. J. Biochemistry 2001, 40, 10732.
14. Kristensen, C.; Kjeldsen, T.; Wiberg, F. C.; Schaffer, L.; Hach, M.; Havelund, S.; Bass, J.; Steiner, D. F.; Andersen, A. S. J Biol Chem 1997, 272, 12978.
15. Kollman, P. A.; Massova, I.; Reyes, C.; Kuhn, B.; Huo, S.; Chong, L.; Lee, M.; Lee, T.; Duan, Y.; Wang, W.; Donini, O.; Cieplak, P.; Srinivasan, J.; Case, D. A.; Cheatham, T. E., III. Acc Chem Res 2000, 33, 889.
16. Srinivasan, J.; Cheatham, T. E., III; Cieplak, P.; Kollman, P. A.; Case, D. A. J Am Chem Soc 1998, 120, 9401.
17. Gohlke, H.; Kiel, C.; Case, D. A. J Mol Biol 2003, 330, 891.
18. Guerois, R.; Nielsen, J. E.; Serrano, L. J Mol Biol 2002, 320, 369.
19. Schymkowitz, J.; Borg, J.; Stricher, F.; Nys, R.; Rousseau, F.; Serrano, L. Nucleic Acids Res 2005, 33, W382.
20. Bernstein, F. C.; Koetzle, T. F.; Williams, G. J.; Meyer, E. E., Jr.; Brice, M. D.; Rodgers, J. R.; Kennard, O.; Shimanouchi, T.; Tasumi, M. J Mol Biol 1977, 112, 535.
21. Berman, H. M.; Battistuz, T.; Bhat, T. N.; Bluhm, W. F.; Bourne, P. E.; Burkhardt, K.; Feng, Z.; Gilliland, G. L.; Iype, L.; Jain, S.; Fagan, P.; Marvin, J.; Padilla, D.; Ravichandran, V.; Schneider, B.; Thanki, N.; Weissig, H.; Westbrook, J. D.; Zardecki, C. Acta Cryst 2002, D58, 899.
22. Baker, E. N.; Blundell, T. L.; Cutfield, J. F.; Cutfield, S. M.; Dodson, E. J.; Dodson, G. G.; Crowfoot Hodgkin, D. M.; Hubbard, R. E.; Isaacs, N. W; Reynolds, C. D.; Sakabe, K.; Sakabe, N.; Vijayan, N. M. Philos Trans R Soc London B Biol Sci 1988, 319, 369.
23. Jorgensen, W. L.; Chandrasekhar, J.; Madura,J. D.; Impey, R. W.; Klein, M. L. J Chem Phys 1983, 79, 926.
24. Brooks, B. R.; Bruccoleri, R.; Olafson, B. D.; States, D. J.; Swaminathan, S.; Karplus, M. J Comput Chem 1983, 4, 187.
25. MacKerell, A. D.; Bashford, D.; Bellott, M.; Dunbrack,R. L.; 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.; Roux, B.; Schlenkrich, M.; Smith, J. C.; Stote, R.; Straub, J.; Watanabe, M.; Wiorkiewicz-Kuczera, J.; Yin, D.; Karplus, M. J Phys Chem B 1998, 102, 3586.
26. Brooks, C. L., III; Karplus, M.; Pettitt, B. M. Protein. A Theoritical Perspective of Dynamics, Structure, and Thermodynamics (Advances in Chemical Physics, Vol. 71); Wiley-Interscience: New York, 1988.
27. Zoete, V.; Meuwly, M.; Karplus, M. J Mol Biol 2004, 342, 913.
28. Jaramillo, A.; Wernisch, L.; Hery, S.; Wodak, S. J. Comb Chem High Throughput Screen 2001, 4, 643.
29. Lazaridis, T.; Karplus, M. Proteins 1999, 35, 133.
30. Lazaridis, T.; Karplus, M. Curr Opin Struct Biol 2000, 10, 139.
31. Lazaridis, T.; Karplus, M. Biophys Chem 2003, 100, 367.
32. Hasel, W.; Hendrikson, T. F.; Still, W. C. Tetrahedron Comput Methodol 1988, 1, 103.
33. Still, W. C.; Tempczyk, A.; Hawley, R. C.; Hendrickson, T. J Am Chem Soc 1990, 112, 6127.
34. Lee, M. S.; Salsbury, F. R., Jr.; Brooks, C. L., III. J Chem Phys 2002, 116, 10606.
35. Lee, M. S.; Feig, M.; Salsbury, F. R., Jr.; Brooks, C. L., III. J Comput Chem 2003, 24, 1348.
36. Zoete, V.; Meuwly, M.; Karplus, M. Proteins 2005, 61, 79.
37. Davis, M. E.; Madura, J. D.; Luty, B. A.; McCammon, J. A. Comput Phys Commun 1991, 62, 187.
38. McQuarrie, D. A. Statistical Mechanics; Harper & Row: New York, 1976.
39. Tidor, B.; Karplus, M. J Mol Biol 1994, 238, 405.
40. Laskowski, R. A. Mol Graphics 1995, 13, 323.
41. Mauguen, Y.; Hartley, R. W.; Dodson, E. J.; Dodson, G. G.; Bricogne, G.; Chothia, C.; Jack, A. Nature 1982, 297, 162.
42. O'Neill, J. W.; Kim, D. E.; Baker, D.; Zhang, K. Y. Acta Crystallogr D: Biol Crystallogr 2001, 57, 480.
43. Kim, D. E.; Fisher, C.; Baker, D. J Mol Biol 2001, 298, 971.
44. Serrano, L.; Kellis, J. T., Jr.; Cann, P.; Matouschek, A.; Fersht, A. R. J Mol Biol 1992, 224, 783.
45. Huo, S.; Massova, I.; Kollman, P. A. J Comput Chem 2002, 23, 15.
46. Nakagawa, S. H.; Tager, H. S.; Steiner, D. F. Biochemistry 2000, 39, 15826.
47. Kitagawa, K.; Ogawa, H.; Burke, G. T.; Chanley, J. D.; Katsoyannis, P. G. Biochemistry 1984, 23, 4444.
48. Erikson, A. E.; Baase, W. A.; Zhang, W. A.; Heinz, X. J.; Blaber, M.; Baldwin, E. P.; Matthews, B. W. Science 1991, 255, 178.
49. Gohlke, H.; Klebe, G. Curr Opin Struct Biol 2001, 11, 231.
50. Koradi, R.; Billeter, M.; Wüthrich, K. J Mol Graphics 1996, 14, 51.
51. Chen, H.; Shi, M.; Guo, Z. Y; Tang, Y. H.; Qiao, Z. S.; Liang, Z. H.; Feng, Y. M. Protein Eng 2000, 13, 779.
52. Hua, Q. X.; Shoelson, S. E.; Kochoyan, M.; Weiss, M. A. Nature 1991, 354, 238.
53. Xu, B.; Hua, Q. X.; Nakagawa, S. H.; Jia, W.; Chu, Y. C.; Katsoyannis, P. G.; Weiss, M. A. Protein Sci 2002, 11, 104.
54. Zhang, Y.; Whittingham, J. L.; Turkenburg, J. P.; Dodson, E. J.; Brange, J.; Dodson, G. G. Acta Crystallogr D: Biol Crystallogr 2002, 58, 186.
55. Derewenda, U.; Derewenda, Z.; Dodson, E. J.; Dodson, G. G.; Bing, X.; Markussen, J. J Mol Biol 1991, 220, 425.
56. Cutfield, J.; Cutneid, S.; Dodson, E.; Dodson, G.; Hodgkin, D.; Reynolds, C. Hoppe-Seylers Z Physiol Chem 1981, 6, 755.
57. Ludvigsen, S.; Olsen, H. B.; Kaarsholm, N. C. J Mol Biol 1998, 279, 1.
58. Tai, K.; Murdock, S.; Wu, B.; Ng, M. H.; Johnston, S.; Fangohr, H.; Cox, S. J.; Jeffreys, P.; Essex, J. W.; Sansom, M. S. Org Biomol Chem 2004, 2, 3219.