Intra-protein hydrogen bonding is dynamically stabilized by electronic polarization

Journal of Chemical Physics

Volumn 130, Issue 11, 2009, Pages

  Duan, Li L ^b   Mei, Ye ^a   Zhang, Qing G ^b   Zhang, John Z H ^a,c  

^a EAST CHINA NORMAL UNIVERSITY   (China)

^b SHANDONG NORMAL UNIVERSITY   (China)

^c NEW YORK UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMBER; BINDING SITES; DYNAMICS; HYDROGEN; MOLECULAR DYNAMICS; PHOTOLITHOGRAPHY; POLARIZATION; PROTEINS; STABILITY;

ATOMIC CHARGES; BETA SHEETS; COMPUTATIONAL RESULTS; DYNAMICAL STABILITIES; ELECTRONIC POLARIZATION EFFECTS; ELECTRONIC POLARIZATIONS; HYDROGEN BONDINGS; LOCAL STRUCTURES; MD SIMULATIONS; MOLECULAR FRACTIONATION WITH CONJUGATE CAPS; MOLECULAR-DYNAMICS SIMULATIONS; NATIVE STRUCTURES; POISSON-BOLTZMANN; PROTEIN STRUCTURES; QUANTUM-MECHANICAL CALCULATIONS; SECONDARY STRUCTURES; SIMULATION TIME; STABILIZING EFFECTS;

HYDROGEN BONDS;

PROTEIN;

ARTICLE; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER SIMULATION; HYDROGEN BOND; PROTEIN CONFORMATION; PROTEIN SECONDARY STRUCTURE; PROTEIN STABILITY; QUANTUM THEORY; STATIC ELECTRICITY; TIME;

COMPUTER SIMULATION; HYDROGEN BONDING; MODELS, MOLECULAR; PROTEIN CONFORMATION; PROTEIN STABILITY; PROTEIN STRUCTURE, SECONDARY; PROTEINS; QUANTUM THEORY; STATIC ELECTRICITY; TIME FACTORS;

EID: 63149159310     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.3089723     Document Type: Article

References (39)

1. A. T. Hagler, E. Huler, and S. Lifson, J. Am. Chem. Soc. JACSAT 0002-7863 10.1021/ja00824a004 96, 5319 (1974).
2. B. R. Brooks, R. E. Bruccoleri, B. D. Olafson, D. J. States, S. Swaminathan, and M. Karplus, J. Comput. Chem. JCCHDD 0192-8651 10.1002/jcc.540040211 4, 187 (1983).
3. G. Nemethy, M. S. Pottle, and H. A. Scheraga, J. Phys. Chem. JPCHAX 0022-3654 10.1021/j100234a011 87, 1883 (1983).
4. H. J. C. Berendsen, J. P. M. Postma, W. F. v. Gunsteren, A. diNola, and J. R. Haak, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.448118 81, 3684 (1984).
5. D. A. Pearlman, D. A. Case, J. W. Caldwell, W. S. Ross, T. E. Cheatham III, S. DelBolt, G. Seibel, and P. Kollman, Comput. Phys. Commun. CPHCBZ 0010-4655 10.1016/0010-4655(95)00041-D 91, 1 (1995).
6. S. A. Adcock and J. A. McCammon, Chem. Rev. (Washington, D.C.) CHREAY 0009-2665 10.1021/cr040426m 106, 1589 (2006).
7. D. W. Zhang and J. Z. H. Zhang, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.1591727 119, 3599 (2003).
8. X. He, Y. Mei, Y. Xiang, D. W. Zhang, and J. Z. H. Zhang, Proteins: Struct., Funct., Bioinf. 61, 423 (2005).
9. Y. Mei, X. He, Y. Xiang, D. W. Zhang, and J. Z. H. Zhang, Proteins: Struct., Funct., Bioinf. 59, 489 (2005).
10. Y. Mei, D. W. Zhang, and J. Z. H. Zhang, J. Phys. Chem. A JPCAFH 1089-5639 10.1021/jp045109y 109, 2 (2005).
11. Y. Mei, C. G. Ji, and J. Z. H. Zhang, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.2345201 125, 094906 (2006).
12. Y. Mei, E. L. Wu, K. L. Han, and J. Z. H. Zhang, Int. J. Quantum Chem. IJQCB2 0020-7608 10.1002/qua.20875 106, 1267 (2006).
13. L. L. Duan, Y. Tong, Y. Mei, Q. G. Zhang, and J. Z. H. Zhang, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.2770720 127, 145101 (2007).
14. B. Honig, K. A. Sharp, and A. -S. Yang, J. Phys. Chem. JPCHAX 0022-3654 10.1021/j100108a002 97, 1101 (1993).
15. D. J. Tannor, B. Marten, R. Murphy, R. A. Friesner, D. Stikoff, A. Nicholls, M. Ringalda, W. A. Goddard III, and B. Honig, J. Am. Chem. Soc. JACSAT 0002-7863 10.1021/ja00105a030 116 11875 (1994).
16. M. Perutz, Science SCIEAS 0036-8075 10.1126/science.694508 201, 1187 (1978).
17. A. Warshel and S. Russell, Q. Rev. Biophys. 17, 283 (1984). 0033-5835
18. J. B. Matthew, Annu. Rev. Biophys. Biophys. Chem. ARBCEY 0883-9182 10.1146/annurev.bb.14.060185.002131 14, 387 (1985).
19. M. E. Davis and J. A. McCammon, Chem. Rev. (Washington, D.C.) CHREAY 0009-2665 10.1021/cr00101a005 90, 509 (1990).
20. B. Honig and A. Nicholls, Science SCIEAS 0036-8075 10.1126/science. 7761829 268, 1144 (1995).
21. C. G. Ji, Y. Mei, and J. Z. H. Zhang, Biophys. J. BIOJAU 0006-3495 10.1529/biophysj.108.131110 95, 1080 (2008).
22. C. G. Ji and J. Z. H. Zhang, J. Am. Chem. Soc. JACSAT 0002-7863 10.1021/ja807374x 130, 17129 (2008).
23. H. Ming, Y. Kato, K. Miyazono, K. Ito, M. Kamo, K. Nagata, and M. Tanokura, Proteins: Struct., Funct., Bioinf. 69, 204 (2007). 1367-4803
24. J. -M. Lancelin, L. Guilhaudis, I. Krimm, M. J. Blackledge, D. Marion, and J. -P. Jacquot, Proteins 41, 334 (2000).
25. H. Yamawaki and B. C. Berk, Curr. Opin. Nephrol. Hypertens. 12, 149 (2005). 1062-4821
26. A. T. Alexandrescu, W. Jahnke, R. Wiltscheck, and M. J. J. Blommers, J. Mol. Biol. JMOBAK 0022-2836 10.1006/jmbi.1996.0422 260, 570 (1996).
27. J. L. Markley, A. P. Hinck, S. N. Loh, K. Prehoda, D. Truckses, W. F. Walkenhorst, and J. Wang, Pure Appl. Chem. PACHAS 0033-4545 10.1351/ pac199466010065 66, 65 (1994).
28. J. Pooart, T. Torikata, and T. Araki, Biosci., Biotechnol., Biochem. 68, 159 (2004). 0916-8451
29. J. B. Garrett, L. S. Mullins, and F. M. Raushel, Protein Sci. 5, 204 (1996). 0961-8368
30. D. Bang, N. Chopra, and S. B. H. Kent, J. Am. Chem. Soc. 126, 1377 (2004). 0002-7863
31. J. P. Ryckaert, G. Ciccotti, and H. J. C. Berendsen, J. Comput. Phys. JCTPAH 0021-9991 10.1016/0021-9991(77)90098-5 23, 327 (1977).
32. K. A. Dill, Biochemistry BICHAW 0006-2960 10.1021/bi00483a001 29, 7133 (1990).
33. B. Honig and A. S. Yang, Adv. Protein Chem. 46, 27 (1995). 0065-3233
34. J. K. Myers and C. N. Pace, Biophys. J. 71, 2033 (1996). 0006-3495
35. B. D. Hames, N. M. Hooper, and J. D. Houghton, Instant Notes in Biochemistry (BIOS Scientific, Oxford, 1997).
36. W. Kabsch and C. Sander, Biopolymers BIPMAA 0006-3525 10.1002/bip.360221211 22, 2577 (1983).
37. J. L. Gao, F. J. Luque, and M. Orozco, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.464126 98, 2975 (1993).
38. W. S. Xie and J. L. Gao, J. Chem. Theory Comput. JCTCCE 1549-9618 10.1021/ct700167b 3, 1890 (2007).
39. W. S. Xie, L. C. Song, D. G. Truhlar, and J. L. Gao, J. Phys. Chem. B 112, 14124 (2008). 1520-6106