Molecular dynamics simulations of the TrkH membrane protein

Biochemistry

Volumn 51, Issue 8, 2012, Pages 1559-1565

  Domene, Carmen ^a   Furini, Simone ^a,b  

^a UNIVERSITY OF OXFORD   (United Kingdom)

^b UNIVERSITY OF SIENA   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

ACTIVE TRANSPORT; COORDINATION NUMBER; CRYSTALLOGRAPHIC STRUCTURE; INTRACELLULAR SIDE; MEMBRANE PROTEINS; MOLECULAR DYNAMICS SIMULATIONS; PASSIVE DIFFUSIONS; SELECTIVITY FILTER; TRANS-MEMBRANE PROTEINS; UMBRELLA SAMPLING;

BINDING SITES; CELL MEMBRANES; CYTOLOGY; MOLECULAR DYNAMICS;

PROTEINS;

MEMBRANE PROTEIN; POTASSIUM CHANNEL; PROTEIN TRKH; SODIUM ION; UNCLASSIFIED DRUG;

ARTICLE; BINDING SITE; MOLECULAR DYNAMICS; PRIORITY JOURNAL; PROTEIN STRUCTURE; SIMULATION;

BINDING SITES; CRYSTALLOGRAPHY, X-RAY; MEMBRANE TRANSPORT PROTEINS; MODELS, MOLECULAR; MOLECULAR DYNAMICS SIMULATION; POTASSIUM; POTASSIUM CHANNELS; PROTEIN CONFORMATION; VIBRIO PARAHAEMOLYTICUS;

EID: 84857539138     PISSN: 00062960     EISSN: 15204995     Source Type: Journal    
DOI: 10.1021/bi201586n     Document Type: Article

References (33)

1. Skou, J. C. (1998) The influence of some cations on an adenosine triphosphatase from peripheral nerves (Reprinted from Biochim. Biophys. Acta, vol 23, pg 394-401, 1957) J. Am. Soc. Nephrol. 9 (11) 2170-2177
2. + uptake systems; CRC Press, Boca Raton, FL.
3. + transport in Escherichia coli K-12 J. Biol. Chem. 252 (4) 1394-1401
4. Cao, Y., Jin, X. S., Huang, H., Derebe, M. G., Levin, E. J., Kabaleeswaran, V., Pan, Y. P., Punta, M., Love, J., Weng, J., Quick, M., Ye, S., Kloss, B., Bruni, R., Martinez-Hackert, E., Hendrickson, W. A., Rost, B., Javitch, J. A., Rajashankar, K. R., Jiang, Y. X., and Zhou, M. (2011) Crystal structure of a potassium ion transporter, TrkH Nature 471 (7338) 336-340
5. Maser, P., Hosoo, Y., Goshima, S., Horie, T., Eckelman, B., Yamada, K., Yoshida, K., Bakker, E. P., Shinmyo, A., Oiki, S., Schroeder, J. I., and Uozumi, N. (2002) Glycine residues in potassium channel-like selectivity filters determine potassium selectivity in four-loop-per-subunit HKT transporters from plants Proc. Natl. Acad. Sci. U.S.A. 99 (9) 6428-6433
6. Nimigean, C. M. and Allen, T. W. (2011) Origins of ion selectivity in potassium channels from the perspective of channel block J. Gen. Physiol. 137 (5) 405-413
7. +-channels J. Mol. Biol. 409 (5) 867-878
8. + ions Biophys. J. 101 (7) 1623-1631
9. + channel Proteins 74 (2) 437-448
10. + channel Nature 414 (6859) 73-77
11. + ion conduction through Kv1.2 Biophys. J. 91 (6) L2-L4
12. Aqvist, J. and Luzhkov, V. (2000) Ion permeation mechanism of the potassium channel Nature 404 (6780) 881-884
13. Furini, S. and Domene, C. (2009) Atypical mechanism of conduction in potassium channels Proc. Natl. Acad. Sci. U.S.A. 106 (38) 16074-16077
14. + KcsA channel structure J. Mol. Biol. 389 (3) 637-645
15. Torrie, G. M. and Valleau, J. P. (1974) Monte-Carlo free-energy estimates using non-Booltzman sampling: Application to subcritical Lennard-Jones fluid Chem. Phys. Lett. 28 (4) 578-581
16. Domene, C. and Furini, S. (2009) Examining ion channel properties using free-energy methods Methods Enzymol. 466, 155-177
17. Kumar, S., Bouzida, D., Swendsen, R. H., Kollman, P. A., and Rosenberg, J. M. (1992) The weighted histogram analysis method for free-energy calculations on biomolecules. 1. The method J. Comput. Chem. 13, 1011-1021
18. Phillips, J. C., Braun, R., Wang, W., Gumbart, J., Tajkhorshid, E., Villa, E., Chipot, C., Skeel, R. D., Kale, L., and Schulten, K. (2005) Scalable molecular dynamics with NAMD J. Comput. Chem. 26 (16) 1781-1802
19. MacKerell, A. D., Bashford, D., Bellott, 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., Wirkiewicz-Kuczera, J., Yin, D., and Karplus, M. (1998) All-atom empirical potential for molecular modeling and dynamics studies of proteins J. Phys. Chem. B 102 (18) 3586-3616
20. - from statistical perturbation theory Chem. Phys. 129 (2) 193-200
21. Roux, B. and Berneche, S. (2002) On the potential functions used in molecular dynamics simulations of ion channels Biophys. J. 82 (3) 1681-1684
22. Feller, S. E., Zhang, Y. H., Pastor, R. W., and Brooks, B. R. (1995) Constant-pressure molecular dynamics simulation: The Langevin piston method J. Chem. Phys. 103 (11) 4613-4621
23. Essmann, U., Perera, L., Berkowitz, M. L., Darden, T., Lee, H., and Pedersen, L. G. (1995) A smooth particle mesh Ewald method J. Chem. Phys. 103 (19) 8577-8593
24. Miyamoto, S. and Kollman, P. A. (1992) Settle: An analytical version of the Shake and Rattle algorithm for wigid water molecules J. Comput. Chem. 13 (8) 952-962
25. Cordero-Morales, J. F., Cuello, L. G., Zhao, Y., Jogini, V., Cortes, D. M., Roux, B., and Perozo, E. (2006) Molecular determinants of gating at the potassium-channel selectivity filter Nat. Struct. Mol. Biol. 13 (4) 311-318
26. Cordero-Morales, J. F., Jogini, V., Chakrapani, S., and Perozo, E. (2011) A multipoint hydrogen-bond network underlying KcsA C-type inactivation Biophys. J. 100 (10) 2387-2393
27. + selectivity filter Nature 414 (6859) 37-42
28. Domene, C., Klein, M. L., Branduardi, D., Gervasio, F. L., and Parrinello, M. (2008) Conformational changes and gating at the selectivity filter of potassium channels J. Am. Chem. Soc. 130 (29) 9474-9480
29. Furini, S. and Domene, C. (2009) Atypical mechanism of conduction in potassium channels Proc. Natl. Acad. Sci. U.S.A. 106 (38) 16074-16077
30. Allen, T. W., Kuyucak, S., and Chung, S. H. (1999) Molecular dynamics study of the KcsA potassium channel Biophys. J. 77 (5) 2502-2516
31. Kuyucak, S., Andersen, O. S., and Chung, S. H. (2001) Models of permeation in ion channels Rep. Prog. Phys. 64 (11) 1427-1472
32. Illingworth, C. J. and Domene, C. (2009) Many-body effects and simulations of potassium channels Proc. R. Soc. London, Ser. A 465 (2106) 1701-1716
33. + channels J. Chem. Theory Comput. 6 (12) 3780-3792