Sensitivity of polar solvation dynamics to the secondary structures of aqueous proteins and the role of surface exposure of the probe

Journal of the American Chemical Society

Volumn 127, Issue 11, 2005, Pages 4071-4075

  Bandyopadhyay, Sanjoy ^a   Chakraborty, Sudip ^a   Balasubramanian, Sundaram ^b   Bagchi, Biman ^c  

^a INDIAN INSTITUTE OF TECHNOLOGY   (India)

^b JAWAHARLAL NEHRU CENTRE FOR ADVANCED SCIENTIFIC RESEARCH   (India)

^c INDIAN INSTITUTE OF SCIENCE   (India)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACIDS; COMPUTER SIMULATION; MOLECULAR DYNAMICS; MOLECULAR STRUCTURE; SURFACE WATERS;

ORIENTATIONAL DYNAMICS; POLAR SOLVATION DYNAMICS; SECONDARY STRUCTURES; SURFACE WATER MOLECULES;

PROTEINS;

AMINO ACID; PROTEIN; SURFACE WATER;

ARTICLE; CALCULATION; CORRELATION FUNCTION; MOLECULAR DYNAMICS; MOLECULAR PROBE; PROTEIN SECONDARY STRUCTURE; SENSITIVITY ANALYSIS; SOLVATION; SURFACE PROPERTY; WATER STRUCTURE;

BINDING SITES; COMPUTER SIMULATION; ELECTRODES; GOLD; MODELS, CHEMICAL; MODELS, MOLECULAR; NEUROFILAMENT PROTEINS; PEPTIDE FRAGMENTS; PROTEIN STRUCTURE, SECONDARY; PROTEIN STRUCTURE, TERTIARY; SURFACE PROPERTIES; WATER;

EID: 15744389630     PISSN: 00027863     EISSN: None     Source Type: Journal    
DOI: 10.1021/ja042847r     Document Type: Article

References (45)

1. Jeffrey, G. A.; Saenger, W. Hydrogen Bonding in Biological Systems; Springer-Verlag: New York, 1991.
2. Xu, H.; Berne, B. J. J. Phys. Chem. B 2001, 105, 11929-11932.
3. Jordinades, X. J.; Lang, M. J.; Song, X.; Fleming, G. R. J. Phys. Chem. B. 1999, 103, 7995-8005. Fleming, G. R. Proc. Natl. Acad. Sci. U.S.A. 1998, 95, 15161-15162.
4. Jordinades, X. J.; Lang, M. J.; Song, X.; Fleming, G. R. J. Phys. Chem. B. 1999, 103, 7995-8005. Fleming, G. R. Proc. Natl. Acad. Sci. U.S.A. 1998, 95, 15161-15162.
5. Bhattacharyya, K. Acc. Chem. Res. 2003, 36, 95-101. Pal, S. K.; Mandal, D.; Sukul, D.; Sen, S.; Bhattacharyya, K. J. Phys. Chem. B. 2001, 105, 1438-1441. Sen, P.; Mukherjee, S.; Dutta, P.; Halder, A.; Mandal, D.; Banerjee, R.; Roy, S.; Bhattacharyya, K. J. Phys. Chem. B 2003, 107, 14563-14568.
6. Bhattacharyya, K. Acc. Chem. Res. 2003, 36, 95-101. Pal, S. K.; Mandal, D.; Sukul, D.; Sen, S.; Bhattacharyya, K. J. Phys. Chem. B. 2001, 105, 1438-1441. Sen, P.; Mukherjee, S.; Dutta, P.; Halder, A.; Mandal, D.; Banerjee, R.; Roy, S.; Bhattacharyya, K. J. Phys. Chem. B 2003, 107, 14563-14568.
7. Bhattacharyya, K. Acc. Chem. Res. 2003, 36, 95-101. Pal, S. K.; Mandal, D.; Sukul, D.; Sen, S.; Bhattacharyya, K. J. Phys. Chem. B. 2001, 105, 1438-1441. Sen, P.; Mukherjee, S.; Dutta, P.; Halder, A.; Mandal, D.; Banerjee, R.; Roy, S.; Bhattacharyya, K. J. Phys. Chem. B 2003, 107, 14563-14568.
8. Pal, S. K.; Peon, J.; Zewail, A. H. Proc. Natl. Acad. Sci. U.S.A. 2002, 99, 1763-1768. Pal, S. K.; Peon, J.; Bagchi, B.; Zewail, A. H. J. Phys. Chem. A 2002, 106, 12376-12395.
9. Pal, S. K.; Peon, J.; Zewail, A. H. Proc. Natl. Acad. Sci. U.S.A. 2002, 99, 1763-1768. Pal, S. K.; Peon, J.; Bagchi, B.; Zewail, A. H. J. Phys. Chem. A 2002, 106, 12376-12395.
10. Pethig, R. Annu. Rev. Phys. Chem. 1992, 43, 177-205. Bhattacharyya, K.; Bagchi, B. J. Phys. Chem. A 2000, 104, 10603-10613. Nandi, N.; Bhattacharyya, K.; Bagchi, B. Chem. Rev. 2000, 100, 2013-2045. Bagchi, B. Annu. Rep. Prog. Chem., Sect. C: Phys. Chem. 2003, 99, 127-175.
11. Pethig, R. Annu. Rev. Phys. Chem. 1992, 43, 177-205. Bhattacharyya, K.; Bagchi, B. J. Phys. Chem. A 2000, 104, 10603-10613. Nandi, N.; Bhattacharyya, K.; Bagchi, B. Chem. Rev. 2000, 100, 2013-2045. Bagchi, B. Annu. Rep. Prog. Chem., Sect. C: Phys. Chem. 2003, 99, 127-175.
12. Pethig, R. Annu. Rev. Phys. Chem. 1992, 43, 177-205. Bhattacharyya, K.; Bagchi, B. J. Phys. Chem. A 2000, 104, 10603-10613. Nandi, N.; Bhattacharyya, K.; Bagchi, B. Chem. Rev. 2000, 100, 2013-2045. Bagchi, B. Annu. Rep. Prog. Chem., Sect. C: Phys. Chem. 2003, 99, 127-175.
13. Pethig, R. Annu. Rev. Phys. Chem. 1992, 43, 177-205. Bhattacharyya, K.; Bagchi, B. J. Phys. Chem. A 2000, 104, 10603-10613. Nandi, N.; Bhattacharyya, K.; Bagchi, B. Chem. Rev. 2000, 100, 2013-2045. Bagchi, B. Annu. Rep. Prog. Chem., Sect. C: Phys. Chem. 2003, 99, 127-175.
14. Mashimo, S.; Umehara, T.; Kuwabara, S.; Yagihara, S. J. Phys. Chem. 1989, 93, 4963-4967. Fukuzaki, M.; Miura, N.; Shinyashiki, N.; Kurita, D.; Shioya, S.; Haida, M.; Mashimo, S. J. Phys. Chem. 1995, 99, 431-435.
15. Mashimo, S.; Umehara, T.; Kuwabara, S.; Yagihara, S. J. Phys. Chem. 1989, 93, 4963-4967. Fukuzaki, M.; Miura, N.; Shinyashiki, N.; Kurita, D.; Shioya, S.; Haida, M.; Mashimo, S. J. Phys. Chem. 1995, 99, 431-435.
16. Borbat, P. P.; Mchaourab, H. S.; Freed, J. H. J. Am. Chem. Soc. 2002, 124, 5304-5314. Liang, Z. C.; Freed, J. H. J. Phys. Chem. B 1999, 103, 6384-6396.
17. Borbat, P. P.; Mchaourab, H. S.; Freed, J. H. J. Am. Chem. Soc. 2002, 124, 5304-5314. Liang, Z. C.; Freed, J. H. J. Phys. Chem. B 1999, 103, 6384-6396.
18. Levitt, M.; Sharon, R. Proc. Natl. Acad. Sci. U.S.A. 1988, 85, 7557-7561.
19. Tarek, M.; Tobias, D. J. J. Am. Chem. Soc. 1999, 121, 9740-9741. Tarek, M.; Tobias, D. J. Biophys. J. 2000, 79, 3244-3257. Tarek, M.; Tobias, D. J. Phys. Rev. Lett. 2002, 88, 138101.
20. Tarek, M.; Tobias, D. J. J. Am. Chem. Soc. 1999, 121, 9740-9741. Tarek, M.; Tobias, D. J. Biophys. J. 2000, 79, 3244-3257. Tarek, M.; Tobias, D. J. Phys. Rev. Lett. 2002, 88, 138101.
21. Tarek, M.; Tobias, D. J. J. Am. Chem. Soc. 1999, 121, 9740-9741. Tarek, M.; Tobias, D. J. Biophys. J. 2000, 79, 3244-3257. Tarek, M.; Tobias, D. J. Phys. Rev. Lett. 2002, 88, 138101.
22. Makarov, V.; Andrews, K. A.; Pettitt, B. M. Biopolymers 1998, 45, 469-478. Makarov, V.; Pettitt, B. M.; Feig, M. Acc. Chem. Res. 2002, 35, 376-384.
23. Makarov, V.; Andrews, K. A.; Pettitt, B. M. Biopolymers 1998, 45, 469-478. Makarov, V.; Pettitt, B. M.; Feig, M. Acc. Chem. Res. 2002, 35, 376-384.
24. Marchi, M.; Sterpone, F.; Ceccarelli, M. J. Am. Chem. Soc. 2002, 124, 6787-6791.
25. Zhou, H. X.; Wlodek, S. T.; McCammon, J. A. Proc. Natl. Acad. Sci. U.S.A. 1998, 95, 9280-9283.
26. Bizzarri, A. R.; Cannistraro, S. J. Phys. Chem. B 2002, 106, 6617-6633.
27. Bandyopadhyay, S.; Chakraborty, S.; Balasubramanian, S.; Pal, S.; Bagchi, B. J. Phys. Chem. B 2004, 108, 12608-12616.
28. Pierce D. W.; Boxer, S. G. Biophys. J. 1995, 68, 1583-1591.
29. Balasubramanian, S.; Bagchi, B. J. Phys. Chem. B 2001, 105, 12529-12533. Pal, S.; Balasubramanian, S.; Bagchi, B. J. Chem. Phys. 2002, 117, 2852-2859.
30. Balasubramanian, S.; Bagchi, B. J. Phys. Chem. B 2001, 105, 12529-12533. Pal, S.; Balasubramanian, S.; Bagchi, B. J. Chem. Phys. 2002, 117, 2852-2859.
31. McKnight, C. J.; Matsudaira, P. T.; Kim, P. S. Nat. Struct. Biol. 1997, 4, 180-184. McKnight, C. J.; Doering, D. S.; Matsudaira, P. T.; Kim, P. S. J. Mol. Biol. 1996, 260, 126-134.
32. McKnight, C. J.; Matsudaira, P. T.; Kim, P. S. Nat. Struct. Biol. 1997, 4, 180-184. McKnight, C. J.; Doering, D. S.; Matsudaira, P. T.; Kim, P. S. J. Mol. Biol. 1996, 260, 126-134.
33. Doering, D. S.; Matsudaira, P. Biochemistry 1996, 35, 12677-12685. Pope, B.; Way, M.; Matsudaira, P. T.; Weeds, A. FEBS Lett. 1994, 338, 58-62.
34. Doering, D. S.; Matsudaira, P. Biochemistry 1996, 35, 12677-12685. Pope, B.; Way, M.; Matsudaira, P. T.; Weeds, A. FEBS Lett. 1994, 338, 58-62.
35. Duan, Y.; Kollman, P. A. Science 1998, 282, 740-744. Duan, Y.; Wang, L.; Kollman, P. A. Proc. Natl. Acad. Sci. U.S.A. 1998, 95, 9897-9902.
36. Duan, Y.; Kollman, P. A. Science 1998, 282, 740-744. Duan, Y.; Wang, L.; Kollman, P. A. Proc. Natl. Acad. Sci. U.S.A. 1998, 95, 9897-9902.
37. Nandi, N.; Bagchi, B. J. Phys. Chem. 1996, 100, 13914-13919. Nandi, N.; Bagchi, B. J. Phys. Chem. B 1997, 101, 10954-10961.
38. Nandi, N.; Bagchi, B. J. Phys. Chem. 1996, 100, 13914-13919. Nandi, N.; Bagchi, B. J. Phys. Chem. B 1997, 101, 10954-10961.
39. MacKerell, A. D., Jr.; Bashford, D.; Bellott, M.; Dunbraek, R. L., Jr.; 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., III.; Roux, B.; Schlenkrich, M.; Smith, J. C.; Stole, R.; Straub, J.; Watanabe, M.; Wiorkiewicz-Kuczera, J.; Yin, D.; Karplus, M. J. Phys. Chem. B 1998, 102, 3586-3616.
40. Jorgensen, W. L.; Chandrasekhar, J.; Madura, J. D.; Impey, R. W.; Klein, M. L. J. Chem. Phys. 1983, 79, 926-935.
41. Jimenez, R.; Fleming, G. R.; Kumar, P. V.; Maroncelli, M. Nature 1994, 369, 471-473. Roy, S.; Bagchi, B. J. Chem. Phys. 1993, 99, 9938-9943. Nandi, N.; Roy, S.; Bagchi, B. J. Chem. Phys. 1995, 102, 1390-1397. Stratt, R. M.; Maroncelli, M. J. Phys. Chem. 1996, 100, 12981-12996.
42. Jimenez, R.; Fleming, G. R.; Kumar, P. V.; Maroncelli, M. Nature 1994, 369, 471-473. Roy, S.; Bagchi, B. J. Chem. Phys. 1993, 99, 9938-9943. Nandi, N.; Roy, S.; Bagchi, B. J. Chem. Phys. 1995, 102, 1390-1397. Stratt, R. M.; Maroncelli, M. J. Phys. Chem. 1996, 100, 12981-12996.
43. Jimenez, R.; Fleming, G. R.; Kumar, P. V.; Maroncelli, M. Nature 1994, 369, 471-473. Roy, S.; Bagchi, B. J. Chem. Phys. 1993, 99, 9938-9943. Nandi, N.; Roy, S.; Bagchi, B. J. Chem. Phys. 1995, 102, 1390-1397. Stratt, R. M.; Maroncelli, M. J. Phys. Chem. 1996, 100, 12981-12996.
44. Jimenez, R.; Fleming, G. R.; Kumar, P. V.; Maroncelli, M. Nature 1994, 369, 471-473. Roy, S.; Bagchi, B. J. Chem. Phys. 1993, 99, 9938-9943. Nandi, N.; Roy, S.; Bagchi, B. J. Chem. Phys. 1995, 102, 1390-1397. Stratt, R. M.; Maroncelli, M. J. Phys. Chem. 1996, 100, 12981-12996.
45. Balasubramanian, S.; Pal, S.; Bagchi, B. Phys. Rev. Lett. 2002, 89, 115505.