Thermal denaturing of mutant lysozyme with both the OPLSAA and the CHARMM force fields

Journal of the American Chemical Society

Volumn 128, Issue 41, 2006, Pages 13388-13395

  Eleftheriou, Maria ^a   Germain, Robert S ^a   Royyuru, Ajay K ^a   Zhou, Ruhong ^a,b  

^a IBM T J WATSON RESEARCH CENTER   (United States)

^b Och Spine at New York Presbyterian Hospitals   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

COMPUTER SIMULATION; MOLECULAR DYNAMICS; PROTEINS; SUPERCOMPUTERS; UREA;

BIOMOLECULAR SIMULATIONS; MUTANT LYSOZYME; PROTEIN STRUCTURE; THERMAL DENATURING;

MUTAGENESIS;

LYSOZYME; MUTANT PROTEIN; UREA;

ALPHA HELIX; ARTICLE; CHARMM FORCE FIELD; ENZYME DENATURATION; ENZYME STABILITY; ENZYME STRUCTURE; GENE MUTATION; HEN; HIGH TEMPERATURE; MOLECULAR DYNAMICS; MOLECULAR MODEL; NONHUMAN; OPLSAA FORCE FIELD; PROTEIN DOMAIN; PROTEIN FOLDING; QUALITATIVE ANALYSIS; REPRODUCIBILITY; THERMAL ANALYSIS; WILD TYPE;

ANIMALS; CHICKENS; COMPUTER SIMULATION; ELECTROSTATICS; ENERGY TRANSFER; GLYCINE; HEAT; MURAMIDASE; MUTATION; PROTEIN DENATURATION; PROTEIN STRUCTURE, SECONDARY; SPECTRUM ANALYSIS; TIME FACTORS; TRYPTOPHAN;

EID: 33750060447     PISSN: 00027863     EISSN: None     Source Type: Journal    
DOI: 10.1021/ja060972s     Document Type: Article

References (35)

1. Kagan, B. L.; Dobson, C. M. Science 2005, 307, 42-43.
2. Klein-Seetharaman, J.; Oikawa, M.; Grimshaw, S. B.; Wirmer, J.; Duchardt, E.; Ueda, T.; Imoto, T.; Smith, L. J.; Dobson, C. M.; Schwalbe, H. Science 2002, 295, 1719-1722.
3. Dumoulin, M.; Last, A.; Desmyter, A.; Decanniere, K.; Canet, D.; Spencer, A.; Archer, D.; Muyldermans, S.; Wyns, L.; Matagne, A.; Redfield, C.; Robinson, C.; Dobson, C. M. Nature 2003, 424, 783-788.
4. Chili, F.; Stefani, M.; Taddei, N.; Ramponi, G.; Dobson, C. M. Nature 2003, 424, 805-808.
5. Fersht, A. R.; Daggett, V. Cell 2002, 108, 573-582.
6. Fersht, A. R. Structure and Mechanism in Protein Science; W. H. Freeman and Co.: New York, 1999.
7. Brooks, C. L.; Onuchic, J. N.; Wales, D. J. Science 2001, 293, 612-613.
8. Dobson, C. M.; Sali, A.; Karplus, M. Angew. Chem., Int. Ed. 1998, 37, 868-893.
9. Brooks, C. L.; Gruebele, M.; Onuchic, J. N.; Wolynes, P. G. Proc. Natl. Acad. Sci. U.S.A. 1998, 95, 11037.
10. Duan, Y.; Kollman, P. A. Science 1998, 282, 740.
11. Zhou, R.; Huang, X.; Margulius, C. J.; Berne, B. J. Science 2004, 305, 1605-1609.
12. Liu, P.; Huang, X.; Zhou, R.; Berne, B. J. Nature 2005, 437, 159-162.
13. Snow, C. D.; Nguyen, H.; Pande, V. S.; Gruebele, M. Nature 2002, 420, 102.
14. Garcia, A. E.; Onuchic, J. N. Proc. Natl. Acad. Sci. U.S.A. 2003, 100, 13898-13903.
15. Kokubo, H.; Okamoto, Y. Chem. Phys. Lett. 2004, 392, 168-175.
16. Daggett, V.; M., L. Mol. Biol. 1994, 252, 600.
17. Daggett, V. Curr. Opin. Struct. Biol. 2000, 10, 160.
18. Brooks, C. L. Curr. Opin. Struct. Biol. 1998, 8, 222.
19. Jorgensen, W. L.; Maxwell, D.; Tirado-Rives, J. J. Am. Chem. Soc. 1996, 118, 11225-11236.
20. Berendsen, H. J. C.; Postma, J. P. M.; van Gunsteren, W. F.; Hermans, J. In Intermolecular forces; Pullman, B., Ed.; Reidel: Dordrecht, 1981; pp 331-342.
21. Brooks, B. R.; Bruccoeri, R. E.; Olafson, B. D.; States, D. J.; Swaminathan, S.; Karplus, M. J. Comput. Chem. 1983, 4, 187.
22. Neria, E.; Fischer, S.; Karplus, M. J. Chem. Phys. 1996, 105, 1902-1921.
23. Jorgensen, W. L.; Chandrasekhar, J.; Madura, J.; Impey, R. W.; Klein, M. L. J. Chem. Phys. 1983, 79, 926-935.
24. Essman, U.; Perera, L.; Berkowitz, M. L.; Darden, T.; Lee, H.; Pedersen, L. G. J. Chem. Phys. 1995, 103, 8577.
25. Swope, W. C.; Anderson, H. C.; Berens, P. H.; Wilson, K. R. J. Chem. Phys. 1982, 76, 637.
26. Fitch, B. G.; Germain, R. S.; Mendell, M.; Pitera, J.; Pitman, M.; Rayshubskiy, A.; Sham, Y.; Suits, F.; Swope, W.; Ward, T. J.; Zhestkov, Y.; Zhou, R. J. Parallel Distri. Comput. 2003, 63, 759-773.
27. Allen, F.; et al. IBM Syst. J. 2001, 40, 310-327.
28. Moraitakis, G.; Goodfellow, J. Biophys. J. 2003, 84, 2149-2158.
29. Hu, H.; Elstner, M.; Hermans, J. Proteins 2003, 50, 451-463.
30. Dinner, A. R.; Lazaridis, T.; Karplus, M. Proc. Natl. Acad. Sci. U.S.A. 1999, 96, 9068-9073.
31. Zhou, R.; Berne, B. J.; Germain, R. Proc. Natl. Acad. Sci. U.S.A. 2001, 98, 14931-14936.
32. Venclovas, C.; Zenla, A.; Fidelis, K.; Moult, J. Proteins 1999, S3, 231-237.
33. de Bakker, P. I.; Hunenberger, P. H.; McCammon, J. A. J. Mol. Biol. 1999, 285, 1811-1830.
34. Frishman, D.; Argos, P. Proteins 1995, 23, 566-579.
35. Zhou, R. Proc. Natl. Acad. Sci. U.S.A. 2003, 100, 13280-13285.