Automated builder and database of protein/membrane complexes for molecular dynamics simulations

PLoS ONE

Volumn 2, Issue 9, 2007, Pages

  Jo, Sunhwan ^a   Kim, Taehoon ^a   Im, Wonpil ^a  

^a UNIVERSITY OF KANSAS   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

GLOBULAR PROTEIN; MEMBRANE PROTEIN; DIMYRISTOYLPHOSPHATIDYLCHOLINE; PROTEIN;

ARTICLE; COMPUTER INTERFACE; COMPUTER PROGRAM; COMPUTER SIMULATION; LIPID BILAYER; MOLECULAR DYNAMICS; PROTEIN DATABASE; PROTEIN FUNCTION; PROTEIN INTERACTION; WEB BROWSER; CELL MEMBRANE; CHEMICAL STRUCTURE; CHEMISTRY;

CELL MEMBRANE; DATABASES, PROTEIN; DIMYRISTOYLPHOSPHATIDYLCHOLINE; LIPID BILAYERS; MODELS, MOLECULAR; MOLECULAR DYNAMICS SIMULATION; PROTEINS;

EID: 41149134824     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0000880     Document Type: Article

References (36)

1. Jordan JD, Landau EM, Iyengar R (2000) Signaling networks: the origins of cellular multitasking. Cell 103: 193-200.
2. Hunter T (2000) Signaling-2000 and beyond. Cell 100: 113-127.
3. Fu D, Libson A, Miercke LJ, Weitzman C, Nollert P, et al. (2000) Structure of a glycerol-conducting channel and the basis for its selectivity. Science 290: 481-486.
4. Khademi S, O'Connell J 3rd, Remis J, Robles-Colmenares Y, Miercke LJ, et al. (2004) Mechanism of ammonia transport by Amt/MEP/Rh: structure of AmtB at 1.35 A. Science 305: 1587-1594.
5. Yellen G (2002) The voltage-gated potassium channels and their relatives. Nature 419: 35-42.
6. Jiang Y, Lee A, Chen J, Cadene M, Chait BT, et al. (2002) Crystal structure and mechanism of a calcium-gated potassium channel. Nature 417: 515-522.
7. Murata K, Mitsuoka K, Hirai T, Walz T, Agre P, et al. (2000) Structural determinants of water permeation through aquaporin- 1. Nature 407: 599-605.
8. Dong J, Yang G, McHaourab HS (2005) Structural basis of energy transduction in the transport cycle of MsbA. Science 308: 1023-1028.
9. Elston T, Wang H, Oster G (1998) Energy transduction in ATP synthase. Nature 391: 510-513.
10. Alberts B (2002) Molecular biology of the cell. New York: Garland Science. pp xxxiv, 1463, [1486].
11. Wallin E, von Heijne G (1998) Genome-wide analysis of integral membrane proteins from eubacterial, archaean, and eukaryotic organisms. Protein Sci 7: 1029-4038.
12. Terstappen GC, Reggiani A (2001) In silico research in drug discovery. Trends Pharmacol Sci 22: 23-26.
13. White S Membrane Proteins of Known 3D Structure. http:// blanco.biomol.uci.edu/MembraneΡoteins×al.html.
14. Berman HM, Battistuz T, Bhat TN, Bluhm WF, Bourne PE, et al. (2002) The Protein Data Bank. Acta Crystallogr D Biol Crystallogr 58: 899-907.
15. de Groot BL, Grubmuller H (2001) Water permeation across biological membranes: mechanism and dynamics of aquaporin-1 and GIpF. Science 294: 2353-2357.
16. Chakrabarti N, Tajkhorshid E, Roux B, Pomes R (2004) Molecular basis of proton blockage in aquaporins. Structure 12: 65-74.
17. Roux B, Schulten K (2004) Computational studies of membrane channels. Structure 12: 1343-1351.
18. Noskov SY, Berneche S, Roux B (2004) Control of ion selectivity in potassium channels by electrostatic and dynamic properties of carbonyl ligands. Nature 431: 830-834.
19. Petrache HI, Grossfield A, MacKenzie KR, Engelman DM, Woolf TB (2000) Modulation of glycophorin A transmembrane helix interactions by lipid bilayers: molecular dynamics calculations. J Mol Biol 302: 727-746.
20. Woolf TB, Roux B (1994) Molecular dynamics simulation of the gramicidin channel in a phospholipid bdayer. Proc Natl Acad Sci U S A 91: 11631-11635.
21. Woolf TB, Roux B (1996) Structure, energetics, and dynamics of lipid-protein interactions: A molecular dynamics study of the gramicidin A channel in a DMPC bilayer. Proteins 24: 92-114.
22. Shen C, Bassolino D, Stouch T (1997), Transmembrane helix structure, dynamics, and interactions: multi-nanosecond molecular dynamics simulations. Biophys J 73: 3-20.
23. Tieleman DP, Berendsen HJ (1998) A molecular dynamics study of the pores formed by Escherichia coli OmpF porin in a fully hydrated palmitoyloleoylphosphatidylcholine bilayer. Biophys J 74: 2786-2801.
24. Faraldo-Gomez JD, Smith GR, Sansom MS (2002) Setting up and optimization of membrane protein simulations. Eur Biophys J 31: 217-227.
25. Lomize MA, Lomize AL, Pogozheva ID, Mosberg HI (2006) OPM: orientations of proteins in membranes database. Bioinformatics 22: 623-625.
26. Nagle JF, Tristram-Nagle S (2000) Structure of lipid bilayers. Biochim Biophys Acta 1469: 159-195.
27. Im W, Roux B (2002) Ions and counterions in a biological channel: a molecular dynamics simulation of OmpF porin from Escherichia coli in an explicit membrane with 1 M, KCI aqueous salt solution. J Mol Biol 319: 1177-1197.
28. Brooks BR, Bruccoleri RE, Olafson BD, States DJ, Swaminathan S, et al. (1983) CHARMM: a program for macromolecular energy, minimization, and dynamics calculations. J Comp Chem 4: 187-217.
29. MacKerell AD, Bashford D, Bellott M, Dunbrack RL, Evanseck JD, et al. (1998) All-atom empirical potential for molecular modeling and dynamics studies of proteins. Journal of Physical Chemistry B 102: 3586-3616.
30. Mackerell AD Jr, Feig M, Brooks CL 3rd (2004) Extending the treatment of backbone energetics in protein force fields: limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations. J Comput Chem 25: 1400-1415.
31. Jorgensen WL, Chandrasekhar J, Madura JD, Impey RW, Klein ML (1983) Comparison of Simple Potential Functions for Simulating Liquid Water. Journal of Chemical Physics 79: 926-935.
32. Klauda JB, Brooks BR, MacKerell AD, Venable RM, Pastor RW (2005) An ab initio study on the torsional surface of alkanes and its effect on molecular simulations of alkanes and a DPPC bilayer. Journal of Physical Chemistry B 109: 5300-5311.
33. Feller SE, Zhang YH, Pastor RW (1995) Computer-Simulation of Liquid/ Liquid Interfaces .2. Surface-Tension Area Dependence of a Bilayer and Monolayer. Journal of Chemical Physics 103: 10267-10276.
34. Dolan EA, Venable RM, Pastor RW, Brooks BR (2002) Simulations of membranes and other interfacial systems using P2(1) and Pc periodic boundary conditions. Biophys J 82: 2317-2325.
35. Van Der Spoel D, Lindahl E, Hess B, Groenhof G, Mark AE, et al. (2005) GROMACS: fast, flexible, and free. J Comput Chem 26: 1701-1718.
36. Phillips JC, Braun R, Wang W, Gumbart J, Tajkhorshid E, et al. (2005) Scalable molecular dynamics with NAMD. J Comput Chem 26: 1781-1802.