The potassium ion channel: Comparison of linear scaling semiempirical and molecular mechanics representations of the electrostatic potential

Journal of Physical Chemistry B

Volumn 105, Issue 50, 2001, Pages 12674-12679

  Bliznyuk, Andrey A ^a   Rendell, Alistair P ^a   Allen, Toby W ^a   Chung, Shin Ho ^a  

^a AUSTRALIAN NATIONAL UNIVERSITY   (Australia)

Author keywords

[No Author keywords available]

Indexed keywords

ION PERMEATION;

AMINO ACIDS; BINDING ENERGY; BIOCHEMISTRY; ELECTROMAGNETIC WAVE POLARIZATION; ELECTROSTATICS; MOLECULAR DYNAMICS; PARAMETER ESTIMATION; POSITIVE IONS; POTASSIUM; PROTEINS; WATER;

QUANTUM THEORY;

EID: 0035924827     PISSN: 10895647     EISSN: None     Source Type: Journal    
DOI: 10.1021/jp013069h     Document Type: Article

References (32)

1. Peterson, I.; Liljefors, T. Reviews in Computational Chemistry; VCH Publishes: New York, 1996; Vol. 9, pp 167-189.
2. Cornell, W.D.; Cieplak, P.; Bayly, C.I.; Gould, I.R.; Merz, K.M., Jr.; Ferguson, D.M.; Spellmeyer, D.C.; Fox, T.; Cadwell, J.W.; Kollman, P.A. J. Am. Chem. Soc., 1995, 117, 5179.
3. Jorgensen, W.L.; Tirado-Rives, J. J. Am. Chem. Soc., 1988, 110, 1664.
4. Mackerell, A.D.; Bashford, D.; Bellott, M.; Dunbrack, R.L.; Evanseck, J.D.; Field, M.J.; Fischer, S.; Gao, J.; Guo, H.; Ha, S.; Josephmccarthy, 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.
5. Kollman, P.A.; Massova, I.; Reyes, C.; Kuhn, B.; Huo, S.H.; Chong, L.; Lee, M.; Lee, T.; Duan, Y.; Wang, W.; Donini, O.; Cieplak, P.; Srinivasan, J.; Case, D.A.; Cheatham, T.E. Acc. Chem. Res. 2000, 33, 889.
6. Gao, J. Reviews in Computational Chemistry; VCH Publishes: New York, 1996; Vol. 7, pp 119-185.
7. Ordejon, P. Comput. Mater. Sci. 1998, 12, 157.
8. Stewart, J.J.P. Int. J. Quantum Chem. 1996, 58, 133.
9. Lee, T.; York, D.M.; Yang, W. J. Chem. Phys. 1996, 105, 2744.
10. Daniels, A.D.; Milliam, J.M.; Scuseria, G.E. J. Chem. Phys. 1997, 107, 425.
11. Dixon, S.L.; Merz, K.M. Jr. J. Chem. Phys. 1997, 107, 879.
12. Wang, B.; Ford, G.P. J. Comput. Chem. 1993, 14, 1101.
13. Doyle, D.A.; Cabral, J.M.; Pfuetzner, R.A.; Kuo, A.; Gulbis, J.M.; Cohen, S.L.; Chair, B.T.; MacKinnon, R. Science 1998, 280, 69.
14. Miller, C. Genome Biol. 2000, 1 4.
15. Tieleman, D.P.; Biggin, P.C.; Smith, G.R.; Sansom, M.S.P. Biochim. Biophys. Acta, in press.
16. Schrempf, H.; Schmidt, O.; Kummerlen, R.; Muller, D.; Betzler, M.; Steinkamp, T.; Wagner, R. EMBO J. 1995, 14, 5170.
17. Allen, T.W.; Bliznyuk, A.; Rendell, A.P.; Kuyucak, S.; Chung, S.-H. J. Chem. Phys. 2000, 112, 8191.
18. Luzhkov, V.B.; Aqvist J. Biochim. Biophys. Acta 2000, 1481, 360.
19. Allen, T.W.; Kuyucak, S.; Chung, S.-H. Biophys. J. 1999, 77, 2502.
20. Aqvist, J.; Luzhkov, V. Nature 2000, 404, 881.
21. Berneche, S.; Roux, B. Biophys. J.. 2000, 78, 2900.
22. Biggin, P.C.; Smith, G.R.; Shrivastava, I.; Choe, S.; Sansom, M.S.P. Biochim. Biophys. Acta 2001, 1510, 1.
23. Brooks B.R., Bruccolerim, R.E.; Olafson, B.D.; States, D.J.; Swaminathan, S.; and Karplus, M. J. Comput. Chem. 1983, 4, 187.
24. Neria, E.; Fischer, S.; Karplus, M. J. Chem. Phys. 1996, 105, 1902.
25. Stewart, J.J.P. MOPAC 2000; Fujitsu Limited: Tokyo, 1999.
26. Perozo, E.; Cortes, D.M.; Cuello, L.G. Science 1999, 285, 73.
27. Lazaridis, T.; Karplus, M. Proteins 1999, 35, 133.
28. Frisch, M.J.; Trucks, G.W.; Schlegel, H.B.; Scuseria, G.E.; Robb, M.A.; Cheeseman, J.R.; Zakrzewski, V.G.; Montgomery, J.A., Jr.; Stratmann, R.E.; Burant, J.C.; Dapprich, S.; Millam, J.M.; Daniels, A.D.; Kudin, K.N.; Strain, M.C.; Farkas, O.; Tomasi, J.; Barone, V.; Cossi, M.; Cammi, R.; Mennucci, B.; Pomelli, C.; Adamo, C.; Clifford, S.; Ochterski, J.; Petersson, G.A.; Ayala, P.Y.; Cui, Q.; Morokuma, K.; Malick, D.K.; Rabuck, A.D.; Raghavachari, K.; Foresman, J.B.; Cioslowski, J.; Ortiz, J.V.; Baboul, A.G.; Stefanov, B.B.; Liu, G.; Liashenko, A.; Piskorz, P.; Komaromi, I.; Gomperts, R.; Martin, R.L.; Fox, D.J.; Keith, T.; Al-Laham, M.A.; Peng, C.Y.; Nanayakkara, A.; Gonzalez, C.; Challacombe, M.; Gill, P.M.W.; Johnson, B.; Chen, W.; Wong, M.W.; Andres, J.L.; Gonzalez, C.; Head-Gordon, M.; Replogle, E.S.; Pople, J.A. Gaussian 98, Revision A.7; Gaussian, Inc.: Pittsburgh, PA, 1998.
29. Berendsen, H.J.C.; Grigera, J.R.; Straatsma, T.P. J. Phys. Chem. 1987, 91, 6269.
30. Stern, H.A.; Kaminski, G.A.; Banks, J.L.; Zhou, R.; Berne, B.J.; Frieshner, R.A. J. Phys. Chem. B 1999, 103, 4730.
31. Winn, P.J.; Ferenczy, G.G.; Reynolds, C.A. J. Comput. Chem. 1999, 20, 704.
32. Gane, P.J.; Dean, P.M. Curr. Opin. Struct. Biol. 2000, 10, 401.