Simulation study of interactions and reactivities between NADH cytochrome b5 reductase and cytochrome b5

Journal of Molecular Liquids

Volumn 147, Issue 1-2, 2009, Pages 139-144

  Asada, Toshio ^a   Nagase, Shigeru ^b   Nishimoto, Kichisuke ^c   Koseki, Shiro ^a  

^a Osaka Prefecture University   (Japan)

^b INSTITUTE FOR MOLECULAR SCIENCE   (Japan)

^c NONE   (Japan)

Author keywords

Molecular dynamics; Mutagenesis; NADH cytochrome; Quantum mechanical molecular mechanical calculations

Indexed keywords

BINDING FREE ENERGIES; CONTACT AREAS; CYTOCHROME B5; DOCKING COMPLEXES; DOCKING MODELS; ELECTROSTATIC INTERACTIONS; ENZYMATIC ACTIVITIES; MOLECULAR-DYNAMICS SIMULATIONS; NADH-CYTOCHROME; NON-POLAR; PROTEIN INTERACTIONS; QM/MM CALCULATIONS; QUANTUM MECHANICAL/MOLECULAR MECHANICAL CALCULATIONS; REACTION MECHANISMS; SIMULATION STUDIES; STEADY STATE; VACUUM STATE; VAN DER WAALS INTERACTIONS;

ACTIVATION ENERGY; DOCKING; FREE ENERGY; HEMOGLOBIN; HYDRATES; MOLECULAR DYNAMICS; MOLECULAR MECHANICS; MUTAGENESIS; PORPHYRINS; REACTION KINETICS; VAN DER WAALS FORCES; VIBRATIONS (MECHANICAL);

BINDING ENERGY;

EID: 67349145536     PISSN: 01677322     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.molliq.2009.01.006     Document Type: Article

References (23)

1. Iyanagi T. Biochemistry 16 (1977) 2725
2. Nishida H., Inaka K., Yamanaka M., Kaida S., Kobayashi K., and Miki K. Biochemistry 34 (1995) 2763
3. Bewley M.C., Marohnic C.C., and Barber M.J. Biochemistry 40 (2001) 13574
4. Hultquist D.E., and Passon P.G. Nat. New Biol. 229 (1971) 252
5. Strittmatter P., Hackett C.S., Korza G., and Ozols J. J. Biol. Chem. 265 (1990) 21709
6. Kawano M., Shirabe K., Nagai T., and Takeshita M. Biochem. Biophys. Res. Commun. 245 (1998) 666
7. Shirabe K., Nagai T., Yubisui T., and Takeshita M. Biochim. Biophys. Acta. 1384 (1998) 16
8. Bando S., Takano T., Yubisui T., Shirabe K., Takeshita M., and Nakagawa A. Acta. Cryst. D 60 (2004) 1929
9. Iyanagi T., Watanabe S., and Anan K.F. Biochemistry 23 (1984) 1418
10. Asada T., Nagase S., Nishimoto K., and Koseki S. J. Phys. Chem. B 112 (2008) 5718
11. Massova I., and Kollman P.A. J. Am. Chem. Soc. 121 (1999) 8133
12. Wu J., Gan J.H., Xia Z.X., Wang Y.H., Wang W.H., Xue L.L., Xie Y., and Huang Z.X. Proteins 40 (2000) 249
13. Case D.A., Pearlman D.A., Caldwell J.W., Cheatham W.J., Thomas E., Ross W.S., Simmerling C., Darden T., Merz K.M., Stanton R.V., Cheng A., Vincent J.J., Crowley M., Tsui V., Gohlke H., Radmer R., Duan Y., Pitera J., Massova I., Seibel G.L., Singh U.C., Weiner P., and Kollman P.A. Amber-7. University of California at San Francisco, San Francisco (2002)
14. Jorgensen W.L., Chandrasekhar J., Madura J.D., Impey R.W., and Klein M.L. J. Chem. Phys. 79 (1983) 926
15. Ph.D. thesis, University of California, Davis (1984). http://www.pharmacy.manchester.ac.uk/ bryce/amber/
16. Massova I., and Kollman P.A. Pers. Drug Discov. Design 18 (2000) 113
17. Srinivasan J., Miller J., Kollman P.A., and Case D.A. J. Biomol. Struct. Dyn. 16 (1998) 671
18. Sitkoff D., Sharpe K.A., and Honig B. J. Phys. Chem. 98 (1994) 1978
19. Kuhn B., and Kollman P.A. J. Am. Chem. Soc. 122 (2000) 3909
20. Sanner M.F., Olson A.J., and Spehner J.C. Biopolymers 38 (1996) 305
21. Frisch M.J., Trucks G.W., Schlegel H.B., Scuseria G.E., Robb M.A., Cheeseman J.R., Montgomery J.A., Vreven T., Kudin K.N., Burant J.C., Millam J.M., Iyengar S.S., Tomasi J., Barone V., Mennucci B., Cossi M., Scalmani G., Rega N., Petersson G.A., Nakatsuji H., Hada M., Ehara M., Toyota K., Fukuda R., Hasegawa J., Ishida M., Nakajima T., H onda Y., Kitao O., Nakai H., Klene M., Li X., Knox J.E., Hratchian H.P., Cross J.B., Bakken V., Adamo C., Jaramillo J., Gomperts R., Stratmann R.E., Yazyev O., Austin A.J., Cammi R., Pomelli C., Ochterski J.W., Ayala P.Y., Morokuma K., Voth G.A., Salvador P., Dannenberg J.J., Zakrzewski V.G., Dapprich S., Daniels A.D., Strain M.C., Farkas O., Malick D.K., Rabuck A.D., Raghavachari K., Foresman J.B., Ortiz J.V., Cui Q., Baboul A.G., Clifford S., Cioslowski J., Stefanov B.B., Liu G., Liashenko A., Piskorz P., Komaromi I., Martin R.L., and Fox D.J. Gaussian 03 (2004), Gaussian, Inc., Wallingford CT
22. Page C.C., Moser C.C., Chen X., and Dutton P.L. Nature 402 (1999) 47
23. Wraight C.A. Biochim. Biophys. Acta. 1757 (2006) 886