Molecular dynamics simulation exploration of cooperative migration mechanism of calcium ions in sarcoplasmic reticulum Ca2+-ATPase

Journal of Computational Chemistry

Volumn 30, Issue 13, 2009, Pages 2136-2145

  Huang, Yongqi ^a   Li, Huifang ^a   Bu, Yuxiang ^a  

^a SHANDONG UNIVERSITY   (China)

Author keywords

Ca2+ atpase; Calcium pump; Cooperative binding; Molecular dynamics simulation

Indexed keywords

ACTIVE TRANSPORT; ATOMIC LEVELS; BINDING ABILITIES; BINDING PROCESS; BINDING STATE; CA2+-ATPASE; CALCIUM IONS; CONCENTRATION GRADIENTS; COOPERATIVE BINDING; COOPERATIVE MECHANISMS; DYNAMICAL PROCESS; ELECTROSTATIC ATTRACTIONS; ELECTROSTATIC REPULSION; FOUR AMINO ACIDS; MIGRATION MECHANISMS; MOLECULAR DYNAMICS SIMULATION; MOLECULAR DYNAMICS SIMULATIONS; P-TYPE; SARCOPLASMIC RETICULUM; STRUCTURAL REARRANGEMENT; X-RAY STRUCTURE;

AMINES; AMINO ACIDS; BINDING ENERGY; CALCIUM; CALCIUM ALLOYS; CYTOLOGY; DYNAMICS; ELECTROSTATICS; IONS; MOLECULAR DYNAMICS; MOLECULAR MECHANICS; ORGANIC ACIDS; PUMPS;

BINDING SITES;

ADENOSINE TRIPHOSPHATASE; CALCIUM;

ARTICLE; BIOLOGICAL MODEL; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER SIMULATION; METABOLISM; QUANTUM THEORY; SARCOPLASMIC RETICULUM;

ADENOSINE TRIPHOSPHATASES; CALCIUM; COMPUTER SIMULATION; MODELS, BIOLOGICAL; MODELS, MOLECULAR; QUANTUM THEORY; SARCOPLASMIC RETICULUM;

EID: 69949142492     PISSN: 01928651     EISSN: 1096987X     Source Type: Journal    
DOI: 10.1002/jcc.21219     Document Type: Article

References (37)

1. Møller, J. V.; Juul, B.; leMaire, M. Biochim Biophys Acta 1996, 1286, 1.
2. MacLennan, D. H.; Rice, W. J.; Green, N. M. J Biol Chem 1997, 272, 28815.
3. Lee, A. G.; East, J. M. Biochem J 2001, 356, 665.
4. Ma, H.; Lewis, D.; Xu, Cl; Inesi, G.; Toyoshima, C Biochemistry 2005, 44, 8090.
5. Yu, X.; Carroll, S.; Rigaud, J. L.; Inesi, G. Biophys J 1993, 64, 1232.
6. Makinose, M. FEBS Lett 1973, 37, 140.
7. Post, R. L.; Hegyvary, C.; Kume, S. J Biol Chem 1972, 247, 6530.
8. Toyoshima, C.; Nakasako, M.; Nomura, H.; Ogawa, H. Nature 2000, 405, 647.
9. Sørensen, T. L.-M.; Møller, J. V.; Nissen, P. Science 2004, 304, 1672.
10. Toyoshima, C.; Mizutani, T. Nature 2004, 430, 529.
11. Toyoshima, C.; Nomura, H. Nature 2002, 418, 605.
12. Toyoshima, C.; Nomura, H.; Tsuda, T. Nature 2004, 432, 361.
13. Olesen, C.; Sørensen, T. L.-M.; Nielsen, R. C.; Møller, J. V.; Nissen, P. Science 2004, 306, 2251.
14. Takahashi, M.; Kondou, Y.; Toyoshima, C Proc Nati Acad Sci USA 2007, 104, 5800.
15. Obara, K.; Miyashita, N.; Xu, C.; Toyoshima, I.; Sugita, Y.; Inesi, G.; Toyoshima, C Proc Nati Acad Sci USA 2005, 102, 14489.
16. Clarke, D. M.; Maruyama, K.; Loo, T. W.; Leberer, E.; Inesi, G.; MacLennan, D. H. J Biol Chem 1989, 264, 11246.
17. Daiho, T.; Yamasaki, K.; Saino, T.; Kamidochi, M.; Satoh, K.; Iizuka, H.; Suzuki, H. J Biol Chem 2001, 276, 32771.
18. Zhang, Z.; Lewis, D.; Strock, C.; Inesi, G.; Nakasako, M.; Nomura, H.; Toyoshima, C. Biochemistry 2000, 39, 8758.
19. Peinelt, C.; Apell, H.-J. Biophys J 2005, 89, 2427.
20. (a) Xiang, F.; Bu, Y.; Ai, H.; Li, P. J. Phys Chem B 2004, 108, 17628;
21. (b) Li, H.; Bu, Y.; Yan, S.; Li, P.; Cukier, R. I. J Phys Chem B 2006, 110, 11005;
22. (c) Xiang, F.; Li, P.; Yan, S. H.; Sun, L. X.; Cukier, R. I.; Bu, Y. N J Chem 2006, 30, 890;
23. (d) Liu, H. C.; Zhang, L.; Li, P.; Cukier, R. I.; Bu, Y. Chem Phys Chem 2007, 8, 304.
24. Inesi, G.; Kurzmack, M.; Coan, C.; Lewis, D. E. J Biol Chem 1980, 255, 3025.
25. McIntosh, D. B. Nat Struct Biol 2000, 7, 532.
26. Einholm, A. P.; Vilsen, B.; Andersen, J. P. J Biol Chem 2004, 279, 15888.
27. Toyoshima, C.; Inesi, G. Annu Rev Biochem 2004, 73, 269.
28. Inesi, G.; Ma, H.; Lewis, D.; Xu, C. J Biol Chem 2004, 279, 31629.
29. Falson, P.; Menguy, T.; Corre, F.; Bouneau, L.; de Gracia, A. G.; Soulié, S.; Centeno, F.; Møller, J. V.; Champeil, P.; le Maire, M. J Biol Chem 1997, 272, 17258.
30. Menguy, T.; Corre, F.; Bouneau, L.; Deschamps, S.; Møller, J. V.; Champeil, P.; le Maire, M.; Falson, P. J Biol Chem 1998, 273, 20134.
31. Zhang, Z.; Lewis, D.; Sumbilla, C.; Inesi, G.; Toyoshima, C. J Biol Chem 2001, 276, 15232.
32. Shrivastava, H.; Sanaom, M. S. P. Biophys J 2000, 78, 557.
33. de Groot, B. L.; Grubmüller, H. Science 2001, 294, 2353.
34. Costa, V.; Carloni, P. Proteins 2003, 50, 104.
35. Lin, Y.; Cao, Z.; Mo, Y. J Am Chem Soc 2006, 128, 10876.
36. Gumbart, J.; Wang, Y.; Aksimentiev, A.; Tajkhorshid, E.; Schulten, K. Curr Opin Struct Boil 2005, 15, 423.
37. Menguy, T.; Corre, F.; Juul, B.; Bouneau, L.; Lafitte, D.; Derrick, P. J.; Sharma, P. S.; Falson, P.; Levine, B. A.; Møller, J. V.; le Maire, M. J Biol Chem 2002, 277, 13016.