Studying the effect of site-specific hydrophobicity and polarization on hydrogen bond energy of protein using a polarizable method

Journal of Chemical Theory and Computation

Volumn 8, Issue 6, 2012, Pages 2157-2164

  Ji, Chang G ^a,b   Xiao, Xudong ^a,b   Zhang, John Z H ^a,b,c  

^a EAST CHINA NORMAL UNIVERSITY   (China)

^b EAST CHINA NORMAL UNIVERSITY   (China)

^c NEW YORK UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84862189032     PISSN: 15499618     EISSN: 15499626     Source Type: Journal    
DOI: 10.1021/ct300252d     Document Type: Article

References (44)

1. Anfinsen, C. B. Science 1973, 181, 223
2. Creighton, T. Science 1988, 240, 267
3. Baldwin, R. L. J. Mol. Biol. 2007, 371, 283
4. Pace, C. N. Nat. Struct. Mol. Biol. 2009, 16, 681
5. Bolen, D. W.; Rose, G. D. Annu. Rev. Biochem. 2008, 77, 339
6. Klotz, I. M.; Farnham, S. B. Biochemistry 1968, 7, 3879
7. Baldwin, R. L. J. Biol. Chem. 2003, 278, 17581
8. Yang, A.-S.; Hitz, B.; Honig, B. J. Mol. Biol. 1996, 259, 873
9. Yang, A.-S.; Honig, B. J. Mol. Biol. 1995, 252, 351
10. Yang, A.-S.; Honig, B. J. Mol. Biol. 1995, 252, 366
11. Fernández, A.; Berry, R. S. Biophys. J. 2002, 83, 2475
12. Fernández, A.; Zhang, X.; Chen, J. In Progress in Molecular Biology and Translational Science; Conn, P. M., Ed.; Academic Press: 525 B Street, Suite 1900, San Diego, CA, USA, 2008; Vol. 83, p 53.
13. Némethy, G.; Steinberg, I. Z.; Scheraga, H. A. Biopolymers 1963, 1, 43
14. Deechongkit, S.; Dawson, P. E.; Kelly, J. W. J. Am. Chem. Soc. 2004, 126, 16762
15. Deechongkit, S.; Nguyen, H.; Powers, E. T.; Dawson, P. E.; Gruebele, M.; Kelly, J. W. Nature 2004, 430, 101
16. Jager, M.; Deechongkit, S.; Koepf, E. K.; Nguyen, H.; Gao, J.; Powers, E. T.; Gruebele, M.; Kelly, J. W. Pept. Sci. 2008, 90, 751
17. Gao, J.; Bosco, D. A.; Powers, E. T.; Kelly, J. W. Nat. Struct. Mol. Biol. 2009, 16, 684
18. Choudhary, A.; Raines, R. T. ChemBioChem 2011, 12, 1801
19. Scheike, J. A.; Baldauf, C.; Spengler, J.; Albericio, F.; Pisabarro, M. T.; Koksch, B. Angew. Chem., Int. Ed. 2007, 46, 7766
20. Levitt, M. Nat. Struct. Biol. 2001, 8, 392
21. Cieplak, P.; Dupradeau, F. Y.; Duan, Y.; Wang, J. M. J. Phys.: Condens. Matter 2009, 21, 333102
22. Ji, C. G.; Zhang, J. Z. H. J. Phys. Chem. B 2011, 115, 12230
23. Ji, C. G.; Zhang, J. Z. H. J. Am. Chem. Soc. 2008, 130, 17129
24. Ji, C. G.; Zhang, J. Z. H. J. Phys. Chem. B 2009, 113, 13898
25. Ji, C. G.; Zhang, J. Z. H. J. Phys. Chem. B 2009, 113, 16059
26. Ji, C. G.; Mei, Y.; Zhang, J. Z. H. Biophys. J. 2008, 95, 1080
27. Pauling, L.; Delbruck, M. Science 1940, 92, 77
28. Cieplak, P.; Caldwell, J.; Kollman, P. J. Comput. Chem. 2001, 22, 1048
29. Patel, S.; Brooks, C. L. J. Comput. Chem. 2004, 25, 1
30. Patel, S.; Mackerell, A. D.; Brooks, C. L. J. Comput. Chem. 2004, 25, 1504
31. Lamoureux, G.; MacKerell, J. A. D.; Roux, B. J. Chem. Phy. 2003, 119, 5185
32. Xie, W.; Orozco, M.; Truhlar, D. G.; Gao, J. J. Chem. Theory. Comput. 2009, 5, 459
33. Berendsen, H. J. C.; Grigera, J. R.; Straatsma, T. P. J. Phys. Chem. 1987, 91, 6269
34. Zhao, Y.; Truhlar, D. G. Acc. Chem. Res. 2008, 41, 157
35. Banks, J. L.; Kaminski, G. A.; Zhou, R.; Mainz, D. T.; Berne, B. J.; Friesner, R. A. J. Chem. Phys. 1999, 110, 741
36. Chelli, R.; Procacci, P.; Righini, R.; Califano, S. J. Chem. Phys. 1999, 111, 8569
37. Ranganathan, R.; Lu, K. P.; Hunter, T.; Noel, J. P. Cell 1997, 89, 875
38. Darden, T.; York, D.; Pedersen, L. J. Chem. Phys. 1993, 98, 10089
39. Andersen, H. C. J. Comput. Phys. 1983, 52, 24
40. Hornak, V.; Abel, R.; Okur, A.; Strockbine, B.; Roitberg, A.; Simmerling, C. Proteins: Struct., Funct., Bioinf. 2006, 65, 712
41. Case, D. A.; Cheatham, T. E.; Darden, T.; Gohlke, H.; Luo, R.; Merz, K. M.; Onufriev, A.; Simmerling, C.; Wang, B.; Woods, R. J. J. Comput. Chem. 2005, 26, 1668
42. Tomlinson, J. H.; Ullah, S.; Hansen, P. E.; Williamson, M. P. J. Am. Chem. Soc. 2009, 131, 4674
43. Dill, K. A. Biochemistry 1990, 29, 7133
44. Pace, C. N.; Hermans, J. Crit. Rev. Biochem. Mol. Biol. 1975, 3, 1