Molecular dynamics of C-peptide of ribonuclease A studied by replica-exchange Monte Carlo method and diffusion theory

Chemical Physics Letters

Volumn 380, Issue 5-6, 2003, Pages 609-619

  La Penna, Giovanni ^a   Mitsutake, Ayori ^b   Masuya, Masato ^c   Okamoto, Yuko ^d,e  

^a CNR   (Italy)

^b KEIO UNIVERSITY   (Japan)

^c KAGOSHIMA UNIVERSITY   (Japan)

^d INSTITUTE FOR MOLECULAR SCIENCE   (Japan)

^e GRADUATE UNIVERSITY FOR ADVANCED STUDIES   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

C PEPTIDE; RIBONUCLEASE A;

ALGORITHM; ARTICLE; DIFFUSION; EXPERIMENT; MATHEMATICAL COMPUTING; MOLECULAR DYNAMICS; MONTE CARLO METHOD; NUCLEAR MAGNETIC RESONANCE; NUCLEAR OVERHAUSER EFFECT; PROTON NUCLEAR MAGNETIC RESONANCE; STATISTICAL ANALYSIS;

EID: 0142248393     PISSN: 00092614     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.cplett.2003.07.031     Document Type: Article

References (31)

1. Mitsutake A., Okamoto Y. J. Chem. Phys. 112:2000;10638.
2. Okamoto Y., Masuya M., Nabeshima M., Nakazawa T. Chem. Phys. Lett. 299:1999;17.
3. Go M. Nature. 291:1981;90.
4. Okamoto Y. Comp. Phys. Commun. 142:2001;55.
5. Mitsutake A., Sugita Y., Okamoto Y. Biopolymers (Pept. Sci.). 60:2001;96.
6. Fausti S., La Penna G., Paoletti J., Genest D., Lancelot G., Perico A. J. Biomol. NMR. 27:2001;333.
7. La Penna G., Carbone P., Carpentiero R., Rapallo A., Perico A. J. Chem. Phys. 114:2001;1876.
8. Shoemaker K.R., Kim P.S., Brems D.N., Marqusee S., York E.J., Chaiken I.M., Stewart J.M., Baldwin R.L. Proc. Natl. Acad. Sci. USA. 82:1985;2349.
9. Osterhout J.J. Jr., Baldwin R.L., York E.J., Stewart J.M., Dyson H.J., Wright P.E. Biochemistry. 28:1989;7059.
10. Brüschweiler R., Morikis D., Wright P.E. J. Biomol. NMR. 5:1995;353.
11. Okamoto Y., Fukugita M., Nakazawa T., Kawai H. Protein Eng. 4:1991;639.
12. Soman K.V., Karimi A., Case D.A. Biopolymers. 33:1993;1567.
13. Schaefer M., Bartels C., Karplus M. J. Mol. Biol. 284:1998;835.
14. Hansmann U.H.E., Okamoto Y. J. Phys. Chem. B. 103:1999;1595.
15. Lipari G., Szabo A. J. Am. Chem. Soc. 104:1982;4546.
16. Hukushima K., Nemoto K. J. Phys. Soc. Jpn. 65:1996;1604.
17. Sugita Y., Okamoto Y. Chem. Phys. Lett. 314:1999;141.
18. A. Mitsutake, M. Kinoshita, Y. Okamoto, F. Hirata, submitted for publication.
19. Sugita Y., Kitao A., Okamoto Y. J. Chem. Phys. 113:2000;6042.
20. Cavanagh J., Fairbrother W.J., Palmer III A.G., Skelton N.J. Protein NMR Spectroscopy. 1996;Academic Press, San Diego.
21. Rose M.E. Elementary Theory of Angular Momentum. 1957;John Wiley & Sons, New York.
22. La Penna G., Pratolongo R., Perico A. Macromolecules. 32:1999;506.
23. Perico A., Pratolongo R. Macromolecules. 30:1997;5958.
24. Sippl M.J., Némethy G., Scheraga H.A. J. Phys. Chem. 88:1984;6231. and references therein.
25. Okamoto Y. Biopolymers. 34:1994;529.
26. Ooi T., Oobatake M., Némethy G., Scheraga H.A. Proc. Natl. Acad. Sci. USA. 84:1987;3086.
27. M. Masuya, manuscript in preparation, see also < http://biocomputing. cc/.
28. Pastor R.W., Karplus M. J. Phys. Chem. 92:1988;2636.
29. Kostov K.S., Freed K.F. J. Chem. Phys. 106:1997;771.
30. Tilton R.F. Jr., Dewan J.C., Petsko G.A. Biochemistry. 31:1992;2469.
31. Koradi R., Billeter M., Wüthrich K. J. Mol. Graphics. 14:1996;51. the program is http://www.mol.biol.ethz.ch/wuthrich/software/molmol/.