Molecular dynamics studies of AChBP with nicotine and carbamylcholine: The role of water in the binding pocket

Protein Engineering, Design and Selection

Volumn 20, Issue 7, 2007, Pages 353-359

  Amiri, Shiva ^a   Sansom, Mark S P ^a   Biggin, Philip C ^a  

^a UNIVERSITY OF OXFORD   (United Kingdom)

Author keywords

Computational; Conformational change; Cys loop receptor; Nicotinic acetylcholine receptor; Simulation

Indexed keywords

CONFORMATIONAL CHANGE; CYS-LOOP RECEPTOR; NEUROTRANSMITTER RECEPTORS; NICOTINIC ACETYLCHOLINE RECEPTOR;

BINDING SITES; COMPUTER SIMULATION; CONFORMATIONS; LIGANDS; MOLECULAR DYNAMICS;

PROTEINS;

ACETYLCHOLINE BINDING PROTEIN; BINDING PROTEIN; CARBACHOL; NICOTINE; NICOTINIC RECEPTOR; UNCLASSIFIED DRUG; WATER;

ARTICLE; BINDING SITE; LIGAND BINDING; MOLECULAR DYNAMICS; PRINCIPAL COMPONENT ANALYSIS; PRIORITY JOURNAL; PROTEIN ANALYSIS; SIMULATION;

BINDING SITES; CARBACHOL; CARRIER PROTEINS; LIGANDS; MODELS, MOLECULAR; NICOTINE; WATER;

EID: 34548206866     PISSN: 17410126     EISSN: 17410134     Source Type: Journal    
DOI: 10.1093/protein/gzm029     Document Type: Article

References (50)

1. Arinaminpathy,Y., Sansom,M.S.P. and Biggin,P.C. (2006) Mol. Pharm., 69, 11-18.
2. Ashcroft,F.M. (2000) Ion Channels and Disease. Academic Press, San Diego, p. 481.
3. Berendsen,H.J.C., Postma,J.P.M., van Gunsteren,W.F., DiNola,A. and Haak,J.R. (1984) J. Chem. Phys., 81, 3684-3690.
4. Berendsen,H.J.C., van der Spoel,D. and van Drunen,R. (1995) Comp. Phys. Commun., 95, 43-56.
5. Bourne,Y., Talley,T.T., Hansen,S.B., Taylor,P. and Marchot,P. (2005) EMBO J., 24, 1512-1522.
6. Brejc,K., van Dijk,W.J., Klassen,R.V., Schuurmans,M., van Der Oost,J., Smit,A.B. and Sixma,T.K. (2001) Nature, 411, 269-276.
7. Brejc,K., van Dijk,W.J., Smit,A.B. and Sixma,T.K. (2002) Novartis Found Symp., 245, 22-29.
8. Celie,P.H. et al. (2005a) Nat. Struct. Mol. Biol., 12, 582-588.
9. Celie,P.H., Klassen,R.V., van Rossum-Fikkert,S.H., van Elk,R., van Nierop,P., Smit,A.B. and Sixma,T.K. (2005b) J. Biol. Chem., 280, 26457-26466.
10. Celie,P.H., van Rossum-Fikkert,S.H., van Dijk,W.J., Brejc,K., Smit,A.B. and Sixma,T.K. (2004) Neuron, 41, 907-914.
11. Cheng,X., Lu,B., Grant,B., Law,R.J. and McCammon,J.A. (2006) J. Mol. Biol., 355, 310-324.
12. Cymes,G.D., Grosman,C. and Auerbach,A. (2002) Biochemistry, 41, 5548-5555.
13. Darden,T., York,D. and Pedersen,L. (1993) J. Chem. Phys., 98, 10089-10092.
14. De Fusco,M., Becchetti,A., Patrignani,A., Annesi,G., Gambardella,A., Quattrone,A., Ballabio,A., Wanke,E. and Casari,G. (2000) Nat. Genet., 26, 275-276.
15. Faraldo-Gomez,J.D., Forrest,L.R., Baaden,M., Bond,P.J., Domene,C., Patargias,G., Cuthbertson,J. and Sansom,M.S.P. (2004) Proteins Struct. Funct. Genet., 57, 783-791.
16. Gao,F., Bren,N., Burghardt,T.P., Hansen,S.B., Henchman,R.H., Taylor,P., McCammon,J.A. and Sine,S.M. (2005) J. Biol. Chem., 280, 8443-8451.
17. Graton,J., Berthelot,M., Gal,J., Girard,S., Laurence,C., Lebreton,J., Le Questel,J., Maria,P. and Naus,P. (2002) J. Am. Chem. Soc., 124, 10552-10562.
18. Grosman,C. (2003) Biochemistry, 41, 5548-5555.
19. Hansen,S.B., Sulzenbacher,G., Huxford,T., Marchot,P., Taylor,P. and Bourne,Y. (2005) EMBO J., 1-12.
20. Hehre,W.J.Y. and Kluzinger,P. (1997) A guide to molecular mechanics and molecular orbital calculations in Spartan. Wavefunction Inc., Irvine, CA.
21. Henchman,R.H., Wang,H.L., Sine,S.M., Taylor,P. and McCammon,J.A. (2005) Biophys. J., 88, 2564-2576.
22. Henchman,R.H., Wang,H.-L., Sine,S.M., Taylor,P. and McCammon,J.A. (2003) Biophys. J., 85, 3007-3018.
23. Hermans,J., Berendsen,H.J.C., van Gunsteren,W.F. and Postma,J.P.M. (1984) Biopolymers, 23, 1513-1518.
24. Hess,B., Bekker,J., Berendsen,H.J.C. and Fraaije,J.G.E.M. (1997) J. Comp. Chem., 18, 1463-1472.
25. Hogg,R.C. and Bertrand,D. (2004) Curr. Drug Targets CNS Neurol. Disord., 3, 123-130.
26. Humphrey,W., Dalke,A. and Schulten,K. (1996) J. Molec. Graph., 14, 33-38.
27. Karlin,A. (2002) Nat. Rev. Neurosci., 102, 102-114.
28. Kaye,L.S., Sansom,M.S.P. and Biggin,P.C. (2006) J. Biol. Chem., 281, 12736-12742.
29. Law,R.J., Henchman,R.H. and McCammon,J.A. (2005) Proc. Natl Acad. Sci. USA, 102, 6813-6818.
30. Lester,H.A., Dibas,M.I., Dahan,D.S., Leite,J.F. and Dougherty,D.A. (2004) Trends Neurosci., 27, 329-336.
31. Lindahl,E., Hess,B. and van der Spoel,D. (2001) J. Mol. Model, 7, 306-317.
32. Miyazawa,A., Fujiyoshi,Y. and Unwin,N. (2003) Nature, 424, 949-955.
33. Nicke,A. (2004) Eur. J. Biochem., 271, 2293.
34. Nose,S. (1984) Mol. Phys., 52, 255-268.
35. Pankow,J.F., Barsanti,K.C. and Peyton,D.H. (2003) Chem. Res. Toxic., 16, 23-27.
36. Parinello,M. and Rahman,A. (1981) J. Appl. Phys., 52, 7182-7190.
37. Pettersen,E.F., Goddard,T.D., Huang,C.C., Couch,G.S., Greenblatt,D.M., Meng,E.C. and Ferrin,T.E. (2004) J. Comp. Chem., 25, 1605-1612.
38. Schuettelkopf,A.W. and van Aalten,D.M.F. (2004) Acta Cryst. D, 60, 1355-1363.
39. Sixma,T.K. and Smit,A.B. (2003) Annu. Rev. Biophys. Biomol. Struct., 32, 311-334.
40. Smit,A.B., Brejc,K., Syed,N.I. and Sixma,T.K. (2003) Ann. N. Y. Acad. Sci., 998, 81-92.
41. Smit,A.B., et al. (2001) Nature, 411, 261-268.
42. Speranskiy,K. and Kurnikova,M. (2004) J. Chem. Phys., 121, 1516-1524.
43. Speranskiy,K. and Kurnikova,M. (2005) Biochemistry, 44, 11508-11517.
44. Steinlein,O.K. (2001) Am. J. Med. Genet., 106, 139-145.
45. Ulens,C., Hogg,R.C., Celie,P.H., Bertrand,D., Tsetlin,V., Smit,A.B. and Sixma,T.K. (2006) Proc. Natl Acad. Sci. USA, 103, 3615-3620.
46. Unwin,N. (2002) Novartis Found Symp., 245, 5-15.
47. Unwin,N. (2005) J. Mol. Biol., 346, 967-989.
48. van Gunsteren,W.F., Krüger,P., Billeter,S.R., Mark,A.E., Eising,A.A., Scott,W.R.P., Hüneberger,P.H. and Tironi,I.G. (1996). Biomolecular simulation: the GROMOS96 manual and user guide. Groningen/Zürich: Biomos/Hochschulverlag AG an der ETH Zürich.
49. Wallace,A.C., Laskowski,R.A. and Thornton,J.M. (1995) Prot. Eng., 8, 127-134.
50. Zhang,D., Gullingsrud,J. and McCammon,J.A. (2006) J. Am. Chem. Soc., 128, 3019-3026.