A combined molecular dynamic simulation and urea 14N NMR relaxation study of the urea-lysozyme system

Spectrochimica Acta - Part A: Molecular and Biomolecular Spectroscopy

Volumn 75, Issue 3, 2010, Pages 953-959

  Lindgren, Matteus ^a   Sparrman, Tobias ^a   Westlund, Per Olof ^a  

^a UMEÅ UNIVERSITY   (Sweden)

Author keywords

14N urea NMR relaxation; Molecular dynamics simulation; Urea lysozyme system

Indexed keywords

14N-UREA NMR-RELAXATION; CHEMICAL DENATURATION; DENATURED PROTEINS; FAST DYNAMICS; FIELD DEPENDENCE; FOLDED PROTEINS; LONG RESIDENCE TIME; MD SIMULATION; MODEL PARAMETERS; MOLECULAR DYNAMIC SIMULATIONS; MOLECULAR DYNAMICS SIMULATION; MOLECULAR DYNAMICS SIMULATIONS; NMR RELAXATION; NMR RELAXATION EXPERIMENTS; NMR RELAXATION RATES; PARAMETER FITTING; PARAMETER SET; PROTEIN INTERFACES; PROTEIN SURFACE; RELAXATION MODELS; RELAXATION RATES; ROTATIONAL DYNAMICS; SIMPLE MODEL; SOLVATION SHELL; SPIN-RELAXATION RATES; UNFOLDED PROTEINS; WATER MODELS;

COMPUTER SIMULATION; DENATURATION; DYNAMICS; METABOLISM; MOLECULAR DYNAMICS; MOLECULAR MECHANICS; NUCLEAR MAGNETIC RESONANCE; PROTEINS;

UREA;

ANTIINFECTIVE AGENT; LYSOZYME; UREA; WATER;

ANIMAL; ARTICLE; CHEMICAL STRUCTURE; CHEMISTRY; CHICKEN; METABOLISM; MOLECULAR DYNAMICS; NUCLEAR MAGNETIC RESONANCE; PROTEIN CONFORMATION; PROTEIN DENATURATION; PROTEIN FOLDING;

ANIMALS; ANTI-INFECTIVE AGENTS; CHICKENS; MODELS, MOLECULAR; MOLECULAR DYNAMICS SIMULATION; MURAMIDASE; NUCLEAR MAGNETIC RESONANCE, BIOMOLECULAR; PROTEIN CONFORMATION; PROTEIN DENATURATION; PROTEIN FOLDING; UREA; WATER;

EID: 76349102557     PISSN: 13861425     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.saa.2009.11.054     Document Type: Article

References (29)

1. Ramsden W. J. Physiol. 28 (1902) xxiii-xxvi
2. Tanford C. Adv. Protein Chem. 24 (1970) 1-95
3. Frank H., and Franks F. J. Chem. Phys. 48 (1968) 4746-4757
4. Finer E.G., Franks F., and Tait M.J. J. Am. Chem. Soc. 94 (1972) 4424-4429
5. Robinson D., and Jencks W. J. Am. Chem. Soc. 87 (1965) 2462-2469
6. Bagno A., Lovato G., Scorrano G., and Wijnen J.W. J. Phys. Chem. 97 (1993) 4601-4607
7. Shimizu A., Fumino K., Yukiyasu K., and Taniguchi Y. J. Mol. Liq. 85 (2000) 269-278
8. Modig K., Kurian E., Prendergast F.G., and Halle B. Protein Sci. 12 (2003) 2768-2781
9. Halle B. Philos. Trans. R. Soc. Lond. B 359 (2004) 1207-1224
10. Liepinsh E., and Otting G. J. Am. Chem. Soc. 116 (1994) 9670
11. Han L., Zhou R., Thirumalai D., and Berne B.J. Proc. Natl. Acad. Sci. U.S.A. 105 (2008) 16928-16933
12. Bennion B.J., and Daggett V. Proc. Natl. Acad. Sci. U.S.A. 100 (2003) 5142-5147
13. Roy S., and Dey J. J. Colloid Interface Sci. 290 (2005) 526-532
14. Nilsson S., Piculell L., and Malmsten M. J. Phys. Chem. 94 (1990) 5149
15. Brooks B.R., et al. J. Comput. Chem. 4 (1983) 187-217
16. MacKerell A.D., et al. J. Phys. Chem. B102 (1998) 3586-3616
17. Caballero-Herrera A., and Nilsson L. J. Mol. Struct. Theochem. 758 (2006) 139-148
18. Timasheff S.N., and Xie G. Biophys. Chem. 105 (2003) 421-448
19. Sasahara K., Sakurai M., and Nitta K. J. Mol. Biol. 291 (1999) 693-701
20. Pace C.N. Methods Enzymol. 131 (1986) 266-280
21. Piculell L., and Halle B. J. Chem. Soc. Faraday Trans. 1 82 (1986) 401-414
22. Kawahara K., and Tanford C. J. Biol. Chem. 241 (1966) 3228-3232
23. B. Halle, V.P. Denisov, in: N.R. Krishna, L.J. Berliner (Eds.), Biological Magnetic Resonance, vol. 17, Kluwer Academic, Plenum Press New York, 1999, pp. 419-484.
24. Halle B., and Wennerström H. J. Chem. Phys. 75 (1981) 1928-1943
25. Piculell L., and Halle B. J. Chem. Soc. Faraday Trans. 1 82 (1986) 415-429
26. Halle B., Denisov V.P., Modig K., Davidovic M., Bucjner J., and Kiefhaber T. Protein Folding Handbook, Part 1 (2005), Wiley VCH Verlag, GmbH& Co. KGaA (Chapter 8)
27. Kakalis L.T., and Baianu I.C. Arch. Biochem. Biophys. 267 (1988) 829-842
28. Nilsson L., and Mekka P. J. Chem. Phys. 105 (2001) 9954-9960
29. Makhatadze G.I., and Privalov P.L. J. Mol. Biol. 226 (1992) 491-505