Influence of point mutations on the flexibility of cytochrome b 5: Molecular dynamics simulations of holoproteins

Biopolymers

Volumn 83, Issue 3, 2006, Pages 297-312

  Cheng, Qinyi ^a   Benson, David R ^a   Rivera, Mario ^a   Kuczera, Krzysztof ^a  

^a UNIVERSITY OF KANSAS   (United States)

Author keywords

Cytochrome b5; Heme binding; Isoforms; Molecular dynamics simulations; Mutants; Stability

Indexed keywords

HEME BINDING; ISOFORMS; MUTANTS;

BIOCHEMISTRY; BIOLOGICAL MEMBRANES; COMPUTER SIMULATION; CYTOLOGY; HYDROPHOBICITY; MOLECULAR DYNAMICS;

PROTEINS;

APOPROTEIN; CYTOCHROME B5; HEME; HOLOPROTEIN DERIVATIVE; POLYPEPTIDE; PROTEIN; SOLVENT; UNCLASSIFIED DRUG;

ARTICLE; MOLECULAR DYNAMICS; MOLECULAR INTERACTION; POINT MUTATION; PROTEIN SECONDARY STRUCTURE; PROTEIN STABILITY; PROTEIN STRUCTURE; STRUCTURE ANALYSIS;

ANIMALS; CATTLE; COMPUTER SIMULATION; CYTOCHROMES B5; ENDOPLASMIC RETICULUM; MEMBRANE PROTEINS; MITOCHONDRIAL PROTEINS; MODELS, MOLECULAR; MOLECULAR STRUCTURE; PLIABILITY; POINT MUTATION; PROTEIN CONFORMATION; PROTEIN ISOFORMS; RATS;

BOS TAURUS; MAMMALIA;

EID: 33749326083     PISSN: 00063525     EISSN: 10970282     Source Type: Journal    
DOI: 10.1002/bip.20563     Document Type: Article

References (37)

1. Lederer, F.; Ghrir, R.; Guiard, B.; Cortial, S.; Ito, A. Eur J Biochem 1983, 132, 95-102.
2. Kuroda, R.; Ikenoue, T.; Honsho, M.; Tsujimoto, S.; Mitoma, J.; Ito, A. J Biol Chem 1998, 273, 31097-31102.
3. Durley, R. C. E.; Mathews, F. S. Acta Cryst 1996, D52, 65-76.
4. Rodriguez-Maranon, M. J.; Qiu, F.; Stark, R. E.; White, S. P.; Zhang, X.; Foundling, S. I.; Rodriguez, V.; Schilling, C. L., III; Bunce, R. A.; Rivera, M. Biochemistry 1996, 35, 16378-16390.
5. Altuve, A.; Wang, L.; Benson, D. R.; Rivera, M. Biochem Biophys Res Commun 2004, 314, 602-609.
6. Rivera, M.; Seetharaman, R.; Girdhar, D.; Wirtz, M.; Zhang, X.; Wang, X.; White, S. Biochemistry 1998, 37, 1485-1494.
7. Rivera, M.; Wells, M. A.; Walker, F. A. Biochemistry 1994, 33, 2161-2170.
8. Silchenko, S.; Sippel, M. L.; Kuchment, O.; Benson, D. R.; Mauk, A. G.; Altuve, A.; Rivera, M. Biochem Biophys Res Commun 2000, 271, 467-472.
9. Altuve, A.; Silchenko, S.; Lee, K.-H.; Kuczera, K.; Terzyan, S.; Zhang, X.; Benson, D. R.; Rivera, M. Biochemistry 2001, 40, 9469-9483.
10. Cowley, A. B.; Altuve, A.; Kuchment, O.; Terzyan, S.; Zhang, X.; Rivera, M.; Benson, D. R. Biochemistry 2002, 41, 11566-11581.
11. Cowley, A. B.; Rivera, M.; Benson, D. R. Protein Sci 2004, 13, 2316-2329.
12. Cowley, A. B.; Sun, N.; Rivera, M.; Benson, D. R. Biochemistry 2005, 44, 14606-14615.
13. Storch, E. M.; Daggett, V. Biochemistry 1995, 34, 9682.
14. Lee, K.-H.; Kuczera, K. Biopolymers 2003, 69, 260-269.
15. Cowley, A. B.; Kennedy, M. L.; Silchenko, S.; Lukat-Rodgers, G. S.; Rodgers, K. R.; Benson, D. R. Inorg Chem 2006, 45, in press.
16. Simeonov, M.; Altuve, A.; Massiah, M. A.; Wang, A.; Eastman, M. A.; Benson, D. R.; Rivera, M. Biochemistry 2005, 44, 9308-9319.
17. Sun, N.; Wang, A.; Cowley, A. B.; Altuve, A.; Rivera, M.; Benson, D. R. Protein Eng Design Selection 2005, 18, 571-579.
18. Brooks, B. R.; Bruccoleri, R. E.; Olafson, B. D.; States, D. J.; Swaminathan, S.; Karplus, M. J Comput Chem 1983, 4, 187-217.
19. MacKerell, A. D.; Bashford, D.; Bellott, M.; Dunbrack, R. L.; Evanseck, J. D.; Field, M. J.; Fischer, S.; Gao, J.; Guo, H.; Ha, S.; Joseph-McCarthy, D.; Kuchnir, L.; Kuczera, K.; Lau, F. T. K.; Mattos, C.; Michnick, S.; Ngo, T.; Nguyen, D. T.; Prodhom, B.; Reiher, W. E.; Roux, B.; Schlenkrich, M.; Smith, J. C.; Stote, R.; Straub, J.; Watanabe, M.; Wiorkiewicz-Kuczera, J.; Yin, D.; Karplus, M. J Phys Chem B 1998, 102, 3586-3616.
20. Jorgensen, W. L.; Chandrasekhar, J.; Madura, J. D.; Impey, R. W.; Klein, M. L. J Chem Phys 1983, 79, 926-935.
21. Arnesano, F.; Banci, L.; Bertini, I.; Felli, I. C. Biochemistry 1998, 37, 173-184.
22. Brunger, A. T.; Karplus, M. Proteins 1988, 4, 148-156.
23. Grubmueller, H. SOLVATE. 1.0, Ludwig-Maximilians University: Munich, 1996.
24. Leach, A. R. Molecular Modeling. Principles and Applications; Longman: Harlow, UK, 1996.
25. Allen, M. P.; Tildesley, D. J. Computer-Simulations of Liquids; Oxford Science Publications: London, 1987.
26. Ryckaert, J. P.; Ciccotti, G.; Berendsen, H. J. C. J Comp Phys 1977, 23, 327-341.
27. Feller, S. E.; Zhang, Y.; Pastor, R. W.; Brooks, B. R. J Chem Phys 1995, 103, 4613-4621.
28. Essmann, U.; Perera, L.; Berkowitz, M. L.; Darden, T.; Lee, H.; Pedersen, L. G. J Chem Phys 1995, 103, 8577-8593.
29. Lee, B.; Richards, F. M. J Mol Biol 1971, 55, 379-400.
30. Kraulis, P. J. J Appl Cryst 1991, 24, 945-949.
31. Aqvist, J. Comp Chem 1986, 10, 97-99.
32. Zhang, Q.; Cao, C.; Wang, Z.-Q.; Wang, Y.-H.; Wu, H.; Huang, Z.-X. Protein Sci 2004, 13, 2161-2169.
33. Muskett, F. W.; Whitford, D. Unpublished results.
34. Storch, E. M.; Daggett, V. Biochemistry 1996, 35, 11596-11604.
35. Moore, C. D.; Lecomte, J. T. J. Biochemistry 1990, 29, 1984-1989.
36. Moore, C. D.; Lecomte, J. T. J. Biochemistry 1993, 32, 199-207.
37. Mukhopadhyay, K.; Lecomte, J. T. J. Biochemistry 2004, 43, 12227-12236.