Enhanced Wang Landau sampling of adsorbed protein conformations

Journal of Chemical Physics

Volumn 136, Issue 11, 2012, Pages

  Radhakrishna, Mithun ^a   Sharma, Sumit ^b   Kumar, Sanat K ^a  

^a Department of Earth and Environmental Sciences   (United States)

^b Princeton University   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CONFIGURATIONAL BIAS; FOLDED CONFORMATION; FOLDING PROCESS; FOLDING TRANSITION; HYDROPHOBIC CONTACT; HYDROPHOBIC SURFACES; HYDROPHOBIC-POLAR PROTEINS; NATIVE STATE; PROTEIN CONFORMATION; PROTEIN FRAGMENTATION; RANDOM COIL; SECONDARY STRUCTURES; WANG-LANDAU SAMPLING;

ADSORPTION; COMPUTER SIMULATION; PROTEIN FOLDING; PROTEINS; SURFACE CHEMISTRY;

HYDROPHOBICITY;

PROTEIN;

ADSORPTION; ALGORITHM; ARTICLE; CHEMICAL PHENOMENA; CHEMISTRY; MOLECULAR DYNAMICS; PROTEIN CONFORMATION; SURFACE PROPERTY;

ADSORPTION; ALGORITHMS; HYDROPHOBIC AND HYDROPHILIC INTERACTIONS; MOLECULAR DYNAMICS SIMULATION; PROTEIN CONFORMATION; PROTEINS; SURFACE PROPERTIES;

EID: 84859262916     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.3691669     Document Type: Article

References (39)

1. Y. Ueda, H. Taketomi, and N. G, Biopolymers 17 (6), 1531 (1978). 10.1002/bip.1978.360170612
2. A. E. Garcia and J. N. Onuchic, Proc. Natl. Acad. Sci. U.S.A. 100 (24), 13898 (2003). 10.1073/pnas.2335541100 (Pubitemid 37499163)
3. K. A. Dill, Biochemistry 24 (6), 1501 (1985). 10.1021/bi00327a032
4. Z. Y. Guo and D. Thirumalai, and J. D. Honeycutt, J. Chem. Phys. 97 (1), 525 (1992). 10.1063/1.463600
5. B. Berger and T. Leighton, J. Comput. Biol. 5 (1), 27 (1998); 10.1089/cmb.1998.5.27
6. P. Crescenzi, D. Goldman, C. Papadimitriou, A. Piccolboni, and M. Yannakakis, J. Comput. Biol. 5 (3), 423 (1998). 10.1089/cmb.1998.5.423
7. J. I. Siepmann and D. Frenkel, Mol. Phys. 75 (1), 59 (1992). 10.1080/00268979200100061
8. G. M. Torrie and J. P. Valleau, J. Comput. Phys. 23 (2), 187 (1977). 10.1016/0021-9991(77)90121-8
9. S. Kumar, D. Bouzida, R. H. Swendsen, P. A. Kollman, and J. M. Rosenberg, J. Comput. Chem. 13 (8), 1011 (1992); 10.1002/jcc.540130812
10. A. M. Ferrenberg and R. H. Swendsen, Phys. Rev. Lett. 63 (12), 1195 (1989). 10.1103/PhysRevLett.63.1195
11. T. Wust and D. P. Landau, Phys. Rev. Lett. 102 (17), 178101 (2009). 10.1103/PhysRevLett.102.178101
12. J. M. Deutsch, J. Chem. Phys. 106 (21), 8849 (1997); 10.1063/1.473943
13. N. Lesh, M. Mitzenmacher, and S. Whitesides, Proceedings of the Seventh Annual International Conference on Research in Computational Molecular Biology (ACM, Berlin, Germany, 2003), pp. 188.
14. V. Castells and P. R. Van Tassel, J. Chem. Phys. 122 (8), 084707 (2005). 10.1063/1.1849772 (Pubitemid 41047503)
15. K. Yue, K. M. Fiebig, P. D. Thomas, H. S. Chan, E. I. Shakhnovich, and K. A. Dill, Proc. Natl. Acad. Sci. U.S.A. 92 (1), 325 (1995). 10.1073/pnas.92.1. 325
16. Y. W. Li, T. Wüst, and D. P. Landau, Comput. Phys. Commun. 182, 1896 (2011). 10.1016/j.cpc.2010.12.049
17. G. Anand, S. Sharma, A. K. Dutta, S. K. Kumar, and G. Belfort, Langmuir 26 (13), 10803 (2010). 10.1021/la1006132
18. G. Anand, S. Sharma, S. K. Kumar, and G. Belfort, Langmuir 25 (9), 4998 (2009); 10.1021/la803771d
19. A. Sethuraman, G. Vedantham, T. Imoto, T. Przybycien, and G. Belfort, Proteins: Struct., Funct., Bioinf. 56 (4), 669 (2004); 10.1002/prot.20183 (Pubitemid 39063310)
20. G. Anand, F. M. Zhang, R. J. Linhardt, and G. Belfort, Langmuir 27 (5), 1830 (2011); 10.1021/la1041794
21. G. Anand, S. N. Jamadagni, S. Garde, and G. Belfort, Langmuir 26 (12), 9695 (2010). 10.1021/la100363m
22. S. Sharma, B. J. Berne, and S. K. Kumar, Biophys. J. 99 (4), 1157 (2010). 10.1016/j.bpj.2010.05.030
23. Z. Y. Zhuang, A. I. Jewett, S. Kuttimalai, G. Bellesia, S. Gnanakaran, and J. E. Shea, Biophys. J. 100 (5), 1306 (2011). 10.1016/j.bpj.2010.12.3735
24. K. Yue and K. A. Dill, Proc. Natl. Acad. Sci. U.S.A. 92 (1), 146 (1995); 10.1073/pnas.92.1.146
25. T. Cellmer, D. Bratko, J. M. Prausnitz, and H. Blanch, Proc. Natl. Acad. Sci. U.S.A. 102 (33), 11692 (2005); 10.1073/pnas.0505342102 (Pubitemid 41170788)
26. E. I. Shakhnovich and A. M. Gutin, Protein Eng. 6 (8), 793 (1993). 10.1093/protein/6.8.793
27. G. Bellesia, A. I. Jewett, and J. E. Shea, Protein Sci. 19 (1), 141 (2010). 10.1002/pro.288
28. M. Ramirez-Alvarado, T. Kortemme, F. J. Blanco, and L. Serrano, Bioorg Med. Chem. 7 (1), 93 (1999); 10.1016/S0968-0896(98)00215-6 (Pubitemid 29097698)
29. S. Kamtekar and M. H. Hecht, FASEB J. 9 (11), 1013 (1995);
30. H. Y. Xiong, B. L. Buckwalter, H. M. Shieh, and M. H. Hecht, Proc. Natl. Acad. Sci. U.S.A. 92 (14), 6349 (1995); 10.1073/pnas.92.14.6349
31. M. W. West and M. H. Hecht, Protein Sci. 4 (10), 2032 (1995). 10.1002/pro.5560041008
32. A. D. Swetnam and M. P. Allen, Phys. Chem. Chem. Phys. 11 (12), 2046 (2009). 10.1039/b818067a
33. J. I. Siepmann and D. Frenkel, Mol. Phys. 75 (1), 59 (1992). 10.1080/00268979200100061
34. A. W. P. Vermeer, C. E. Giacomelli, and W. Norde, Biochim. Biophys. Acta 1526 (1), 61 (2001). 10.1016/S0304-4165(01)00101-5 (Pubitemid 32245772)
35. C. E. Giacomelli and W. Norde, Biomacromolecules 4 (6), 1719 (2003). 10.1021/bm034151g (Pubitemid 37455585)
36. M. R. Wattenbarger, H. S. Chan, D. F. Evans, V. A. Bloomfield, and K. A. Dill, J. Chem. Phys. 93 (11), 8343 (1990). 10.1063/1.459317
37. T. S. Jain and J. J. de Pablo, J. Chem. Phys. 116 (16), 7238 (2002). 10.1063/1.1463422 (Pubitemid 34537103)
38. N. Rathore and J. J. de Pablo, J. Chem. Phys. 116 (16), 7225 (2002). 10.1063/1.1463059 (Pubitemid 34537101)
39. N. Rathore, T. A. Knotts, and J. J. de Pablo, J. Chem. Phys. 118 (9), 4285 (2003). 10.1063/1.1542598