Differential flexibility of the secondary structures of lysozyme and the structure and ordering of surrounding water molecules

Journal of Chemical Physics

Volumn 134, Issue 11, 2011, Pages

  Sinha, Sudipta Kumar ^a   Bandyopadhyay, Sanjoy ^a  

^a INDIAN INSTITUTE OF TECHNOLOGY   (India)

Author keywords

[No Author keywords available]

Indexed keywords

AQUEOUS SOLUTIONS; ATOMISTIC MOLECULAR DYNAMICS SIMULATIONS; BISTABLES; EXPERIMENTAL STUDIES; EXPLICIT WATER; HELICAL SEGMENTS; HEN EGG WHITE LYSOZYME; PROTEIN MOLECULES; PROTEIN SEGMENTS; ROOM TEMPERATURE; SECONDARY STRUCTURES; WATER MOLECULE;

ENZYMES; HYDROLASES; MOLECULAR DYNAMICS;

MOLECULES;

LYSOZYME; WATER;

AMINO ACID SEQUENCE; ARTICLE; CHEMISTRY; MOLECULAR DYNAMICS; MOLECULAR GENETICS; PROTEIN DENATURATION; PROTEIN SECONDARY STRUCTURE; THERMODYNAMICS;

AMINO ACID SEQUENCE; MOLECULAR DYNAMICS SIMULATION; MOLECULAR SEQUENCE DATA; MURAMIDASE; PROTEIN DENATURATION; PROTEIN STRUCTURE, SECONDARY; THERMODYNAMICS; WATER;

EID: 79953183645     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.3560442     Document Type: Article

References (60)

1. Protein-Solvent Interaction, edited by, R. B. Gregory, (Marcel Dekker, New York, 1995).
2. N. Nandi and B. Bagchi, J. Phys. Chem. 100, 13914 (1996). 10.1021/jp960134s
3. N. Nandi and B. Bagchi, J. Phys. Chem. B 101, 10954 (1997). 10.1021/jp971879g
4. B. Bagchi, Chem. Rev. 105, 3197 (2005). 10.1021/cr020661+ (Pubitemid 41430808)
5. X. J. Jordinades, M. J. Lang, X. Song, and G. R. Fleming, J. Phys. Chem. B. 103, 7995 (1999). 10.1021/jp9910993
6. S. K. Pal, J. Peon, B. Bagchi, and A. H. Zewail, J. Phys. Chem. B 106, 12376 (2002). 10.1021/jp0213506
7. S. Guha, K. Sahu, D. Roy, S. K. Mondal, S. Roy, and K. Bhattacharyya, Biochemistry 44, 8940 (2005). 10.1021/bi0473915 (Pubitemid 40943211)
8. K. Sahu, S. K. Mondal, S. Ghosh, D. Roy, P. Sen, and K. Bhattacharyya, J. Phys. Chem. B 110, 1056 (2006). 10.1021/jp0538924 (Pubitemid 43164732)
9. W. Qiu, Y.-T. Kao, L. Zhang, Y. Yang, L. Wang, W. E. Stites, D. Zhong, and A. H. Zewail, Proc. Natl. Acad. Sci. U.S.A. 103, 13979 (2006). 10.1073/pnas.0606235103 (Pubitemid 44452967)
10. T. Li, A. A. Hassanali, Y.-T. Kao, D. Zhong, and S. J. Singer, J. Am. Chem. Soc. 129, 3376 (2007). 10.1021/ja0685957 (Pubitemid 46449368)
11. P. Abbyad, X. Shi, W. Childs, T. B. McAnaney, B. E. Cohen, and S. G. Boxer, J. Phys. Chem. B 111, 8269 (2007). 10.1021/jp0709104 (Pubitemid 47184403)
12. C. Mattea, J. Qvist, and B. Halle, Biophys. J. 95, 2951 (2008). 10.1529/biophysj.108.135194
13. B. Halle and L. Nilsson, J. Phys. Chem. B 113, 8210 (2009). 10.1021/jp9027589
14. S. Ebbinghaus, S. J. Kim, M. Heyden, X. Yu, U. Heugen, M. Gruebele, D. M. Leitner, and M. Havenith, Proc. Natl. Acad. Sci. U.S.A. 104, 20749 (2007). 10.1073/pnas.0709207104
15. B. Born, H. Weingrtner, E. Brndermann, and M. Havenith, J. Am. Chem. Soc. 131, 3752 (2009). 10.1021/ja808997y
16. J. H. Roh, J. E. Curtis, S. Azzam, V. N. Novikov, I. Peral, Z. Chowdhuri, R. B. Gregory, and A. P. Sokolov, Biophys. J. 91, 2573 (2006). 10.1529/biophysj.106.082214 (Pubitemid 44515024)
17. S. Khodadadi, S. Pawlus, and A. P. Sokolov, J. Phys. Chem. B 112, 14273 (2008). 10.1021/jp8059807
18. D. Russo, R. K. Murarka, J. R. D. Copley, and T. Head-Gordon, J. Phys. Chem. B 109, 12966 (2005). 10.1021/jp051137k (Pubitemid 40999823)
19. C. Malardier-Jugroot, M. E. Johnson, R. K. Murarka, and T. Head-Gordon, Phys. Chem. Chem. Phys. 10, 4903 (2008). 10.1039/b806995f
20. S. Perticaroli, L. Comez, M. Paolantoni, P. Sassi, L. Lupi, D. Fioretto, A. Paciaroni, and A. Morresi, J. Phys. Chem. B 114, 8262 (2010). 10.1021/jp101896f
21. A. R. Bizzarri and S. Cannistraro, J. Phys. Chem. B 106, 6617 (2002). 10.1021/jp020100m (Pubitemid 35281745)
22. M. Marchi, F. Sterpone, and M. Ceccarelli, J. Am. Chem. Soc. 124, 6787 (2002). 10.1021/ja025905m (Pubitemid 34602673)
23. F. Merzel and J. C. Smith, Proc. Natl. Acad. Sci. U.S.A. 99, 5378 (2002). 10.1073/pnas.082335099 (Pubitemid 34411556)
24. N. Smolin and R. Winter, J. Phys. Chem. B 108, 15928 (2004). 10.1021/jp047579y
25. L. Hua, X. Huang, R. Zhou, and B. J. Berne, J. Phys. Chem. B 110, 3704 (2006). 10.1021/jp055399y
26. F. Pizzitutti, M. Marchi, F. Sterpone, and P. J. Rossky, J. Phys. Chem. B 111, 7584 (2007). 10.1021/jp0717185 (Pubitemid 47166814)
27. M. Tarek and D. J. Tobias, Biophys. J. 79, 3244 (2000). 10.1016/S0006-3495(00)76557-X
28. M. Tarek and D. J. Tobias, Phys. Rev. Lett. 88, 138101 (2002). 10.1103/PhysRevLett.88.138101
29. H. Xu and B. J. Berne, J. Phys. Chem. B 105, 11929 (2001). 10.1021/jp012749h (Pubitemid 35338348)
30. S. Bandyopadhyay, S. Chakraborty, and B. Bagchi, J. Am. Chem. Soc. 127, 16660 (2005). 10.1021/ja054462u (Pubitemid 41740417)
31. S. Chakraborty and S. Bandyopadhyay, J. Phys. Chem. B 111, 7626 (2007). 10.1021/jp072350e (Pubitemid 47166819)
32. S. Chakraborty, S. K. Sinha, and S. Bandyopadhyay, J. Phys. Chem. B 111, 13626 (2007). 10.1021/jp0746401 (Pubitemid 350275467)
33. S. K. Sinha, S. Chakraborty, and S. Bandyopadhyay, J. Phys. Chem. B 112, 8203 (2008). 10.1021/jp8000724
34. A. A. Golosov and M. Karplus, J. Phys. Chem. B 111, 1482 (2007). 10.1021/jp065493u (Pubitemid 46339079)
35. M. Agarwal, H. R. Kushwaha, and C. Chakravarty, J. Phys. Chem. B 114, 651 (2010). 10.1021/jp909090u
36. F. Sterpone, G. Stirnemann, J. T. Hynes, and D. Laage, J. Phys. Chem. B 114, 2083 (2010). 10.1021/jp9119793
37. D. N. LeBard and D. V. Matyushov, J. Phys. Chem. B 114, 9246 (2010). 10.1021/jp1006999
38. H. Acharya, S. Vembanur, S. N. Jamadagni, and S. Garde, Faraday Discuss. 146, 353 (2010). 10.1039/b927019a
39. H. G. Nagendra, N. Sukumar, and M. Vijayan, Proteins: Struct., Funct., Genet. 32, 229 (1998). 10.1002/(SICI)1097-0134(19980801)32:2229::AID-PROT93.0. CO;2-F
40. A. J. Kirby, Nat. Struct. Biol. 8, 737 (2001). 10.1038/nsb0901-737 (Pubitemid 32803584)
41. J. C. Phillips, R. Braun, W. Wang, J. Gumbart, E. Tajkhorshid, E. Villa, C. Chipot, R. D. Skeel, L. Kale, and K. Schulten, J. Comput. Chem. 26, 1781 (2005). 10.1002/jcc.20289 (Pubitemid 43078511)
42. S. E. Feller, Y. Zhang, R. W. Pastor, and B. R. Brooks, J. Chem. Phys. 103, 4613 (1995). 10.1063/1.470648
43. M. P. Allen and D. J. Tildesley, Computer Simulation of Liquids (Clarendon, Oxford, 1987).
44. T. Darden, D. York, and L. Pedersen, J. Chem. Phys. 98, 10089 (1993). 10.1063/1.464397
45. A. D. MacKerell Jr., D. Bashford, M. Bellott, R. L. Dunbrack Jr., J. D. Evanseck, M. J. Field, S. Fischer, J. Gao, H. Guo, S. Ha, D. Joseph-McCarthy, L. Kuchnir, K. Kuczera, F. T. K. Lau, C. Mattos, S. Michnick, T. Ngo, D. T. Nguyen, B. Prodhom, W. E. Reiher III, B. Roux, M. Schlenkrich, J. C. Smith, R. Stote, J. Straub, M. Watanabe, J. Wiorkiewicz-Kuczera, D. Yin, and M. Karplus, J. Phys. Chem. B 102, 3586 (1998). 10.1021/jp973084f
46. W. L. Jorgensen, J. Chandrasekhar, J. D. Madura, R. W. Impey, and M. L. Klein, J. Chem. Phys. 79, 926 (1983). 10.1063/1.445869
47. A. Yokota, K. Hirai, H. Miyauchi, S. Iimura, Y. Noda, K. Inoue, K. Akasaka, H. Tachibana, and S. Segawa, Biochemistry 43, 6663 (2004). 10.1021/bi049967w (Pubitemid 38697566)
48. M. Buck, J. Boyd, C. Redfield, D. A. MacKenzie, D. J. Jeenes, D. B. Archer, and C. M. Dobson, Biochemistry 34, 4041 (1995). 10.1021/bi00012a023
49. S. M. Le Grand and K. M. Merz, J. Comput. Chem. 14, 349 (1993). 10.1002/jcc.540140309
50. D. I. Svergun, S. Richard, M. H. J. Koch, Z. Sayers, S. Kuprin, and G. Zacai, Proc. Natl. Acad. Sci. U.S.A. 95, 2267 (1998). 10.1073/pnas.95.5.2267 (Pubitemid 28145930)
51. J. R. Errington and P. G. Debenedetti, Nature (London) 409, 318 (2001). 10.1038/35053024 (Pubitemid 32151231)
52. P. Kumar, S. V. Buldyrev, and H. E. Stanley, Proc. Natl. Acad. Sci. U.S.A. 106, 22130 (2009). 10.1073/pnas.0911094106
53. P. L. Chau and A. J. Hardwick, Mol. Phys. 93, 511 (1998). 10.1080/002689798169195
54. M. Simone, G. Brirganti, and P. Londei, Phys. Rev. Lett. 92, 158101 (2004). 10.1103/PhysRevLett.92.158101
55. S. Lee, P. G. Debenedetti, and J. R. Errington, J. Chem. Phys. 122, 204511 (2005). 10.1063/1.1917745 (Pubitemid 40858512)
56. R. Sharma, S. N. Chakraborty, and C. Chakravarty, J. Chem. Phys. 125, 204501 (2006). 10.1063/1.2390710 (Pubitemid 44847680)
57. A. Mudi and C. Chakravarty, J. Phys. Chem. B 110, 8422 (2006). 10.1021/jp056003l
58. M. Buck, S. Bouguet-Bonnet, R. W. Pastor, and A. D. MacKerell Jr., Biophys. J. 90, L36 (2006). 10.1529/biophysj.105.078154
59. A. D. MacKerell Jr., M. Feig, and C. L. Brooks III, J. Am. Chem. Soc. 126, 698 (2004). 10.1021/ja036959e (Pubitemid 38114337)
60. A. D. MacKerell Jr., J. Comput. Chem. 25, 1584 (2004). 10.1002/jcc.20082