Relaxation to native conformation of a bond-fluctuating protein chain with hydrophobic and polar nodes

Physical Review E - Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics

Volumn 70, Issue 5, 2004, Pages 4-

  Bjursell, Johan ^a   Pandey, R B ^b  

^a GEORGE MASON UNIVERSITY   (United States)

^b UNIVERSITY OF SOUTHERN MISSISSIPPI   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CHEMICAL BONDS; COMPUTER SIMULATION; CONFORMATIONS; HYDROPHOBICITY; LATTICE CONSTANTS; MATHEMATICAL MODELS; MICROSCOPIC EXAMINATION; MOLECULAR DYNAMICS; MOLECULAR STRUCTURE; MOLECULAR WEIGHT; MONTE CARLO METHODS; RELAXATION PROCESSES;

CONFORMATIONAL RELAXATION; POLAR NODES; POWER-LAW DECAY; PROTEIN CHAINS;

PROTEINS;

PROTEIN;

AMINO ACID SEQUENCE; ARTICLE; BINDING SITE; CHEMICAL MODEL; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER SIMULATION; ELECTRICITY; HYDROPHOBICITY; METHODOLOGY; MOLECULAR GENETICS; MONTE CARLO METHOD; MOTION; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN FOLDING; SEQUENCE ANALYSIS; STATISTICAL MODEL; STRUCTURE ACTIVITY RELATION;

AMINO ACID SEQUENCE; BINDING SITES; COMPUTER SIMULATION; ELECTROSTATICS; HYDROPHOBICITY; MODELS, CHEMICAL; MODELS, MOLECULAR; MODELS, STATISTICAL; MOLECULAR SEQUENCE DATA; MONTE CARLO METHOD; MOTION; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN FOLDING; PROTEINS; SEQUENCE ANALYSIS, PROTEIN; STRUCTURE-ACTIVITY RELATIONSHIP;

EID: 41349114797     PISSN: 1063651X     EISSN: None     Source Type: Journal    
DOI: 10.1103/PhysRevE.70.052904     Document Type: Article

References (25)

1. C.K. Mathews, K.E. van Holde, and K.G. Ahern, Biochemistry, 3rd ed. (Addison-Wesley/Longman, Reading, MA, 2000).
2. P.C. Turner, A.G. McLennan, A.D. Bates, and M.R. H. White, Molecular Biology, 2nd ed. (BIOS/Springer-Verlag, New York, 2000).
3. C. Branden and J. Tooze, Introduction to Protein Structure, 2nd ed. (Garland, New York, 1999).
4. D. Baker, Nature (London)NATUAS0028-083610.1038/35011000 405, 39 (2000).
5. A.I. Jewett, V.S. Pande, and K.W. Plaxco, J. Mol. Biol.JMOBAK0022-283610.1016/S0022-2836(02)01356-6 326, 247 (2003).
6. B. Gillespie and K.W. Plaxco, Annu. Rev. Biochem.ARBOAW0066-415410.1146/annurev.biochem.73.011303.073904 73, 837 (2004).
7. J.E. Kohn (unpublished).
8. J.R. Banavar, O. Gonzalez, J.H. Maddocks, and A. Maritan, J. Stat. Phys.JSTPBS0022-471510.1023/A:1021010526495 110, 35 (2003).
9. J.R. Banavar and A. Maritan, Rev. Mod. Phys.RMPHAT0034-686110.1103/RevModPhys.75.23 75, 23 (2003), and references therein.
10. K.M. Fiebig and K.A. Dill, J. Chem. Phys.JCPSA60021-960610.1063/1.464068 98, 3475 (1993).
11. K. Yue, Proc. Natl. Acad. Sci. U.S.A.PNASA60027-8424 92, 312 (1995).
12. J.D. Bryngelson, J.N. Onuchic, N.D. Socci, and P.G. Wolynes, Proteins18PLAF0887-3585 21, 167 (1995).10.1002/prot.340210302
13. C. Tang, Physica APHYADX0378-437110.1016/S0378-4371(00)00413-1 288, 31 (2000).
14. E.I. Shakhnovich, Phys. Rev. Lett.PRLTAO0031-900710.1103/PhysRevLett.72.3907 72, 3907 (1994).
15. U.H.E. Hansmann and L.T. Wille, Phys. Rev. Lett.PRLTAO0031-900710.1103/PhysRevLett.88.068105 88, 068105 (2002).
16. U.H.E. Hansmann and Y. Okamoto, Curr. Opin. Struct. Biol.COSBEF0959-440X10.1016/S0959-440X(99)80025-6 9, 177 (1999).
17. U.H.E. Hansmann, Physica APHYADX0378-4371 321, 152 (2003).10.1016/S0378-4371(02)01764-8
18. S. Takada, Proteins18PLAF0887-358510.1002/1097-0134(20010101)42:1<85::AID-PROT90>3.0.CO;2-3 42, 85 (2001).
19. C.-M. Chen and C.-C. Chen, Biophys. J.BIOJAU0006-3495 84, 1902 (2003).10.1016/S0006-3495(03)74998-4
20. U.H.E. Hansmann, Comput. Sci. Eng.CSENFA1521-9615 5, 64 (2003).10.1109/MCISE.2003.1166554
21. Monte Carlo and Molecular Dynamics Simulations in Polymer Science, edited by K. Binder (Oxford University Press, New York, 1995).
22. A. Baumgaertner, in The Monte Carlo Method in Condensed Matter Physics, 2nd ed., edited by K. Binder, Topics in Applied Physics Vol. 71 (Springer, Berlin, 1995).
23. G.M. Foo and R.B. Pandey, Phys. Rev. EPLEEE81063-651X10.1103/PhysRevE.57.5802 57, 5802 (1998).
24. G.M. Foo and R.B. Pandey, J. Chem. Phys.JCPSA60021-960610.1063/1.476661 109, 1162 (1998).
25. G.M. Foo and R.B. Pandey, Macromol. Theory Simul.MTHSEK1022-1344 8, 571 (1998).