CGDB: A database of membrane protein/lipid interactions by coarse-grained molecular dynamics simulations

Molecular Membrane Biology

Volumn 25, Issue 8, 2008, Pages 662-669

  Chetwynd, Alan P ^a   Scott, Kathryn A ^a   Mokrab, Younes ^a   Sansom, Mark S P ^a  

^a UNIVERSITY OF OXFORD   (United Kingdom)

Author keywords

Coarse grained; Membrane protein; Molecular dynamics

Indexed keywords

ARACHIDONATE 5 LIPOXYGENASE ACTIVATING PROTEIN; DILAUROYLPHOSPHATIDYLCHOLINE; DIPALMITOYLPHOSPHATIDYLCHOLINE; DISTEAROYLPHOSPHATIDYLCHOLINE; MECHANOSENSITIVE CHANNEL OF SMALL CONDUCTANCE PROTEIN; MEMBRANE PROTEIN; UNCLASSIFIED DRUG; VOLTAGE GATED POTASSIUM CHANNEL;

ARTICLE; LIPID BILAYER; MOLECULAR DYNAMICS; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN LIPID INTERACTION; PROTEIN STRUCTURE; SIMULATION;

CARRIER PROTEINS; COMPUTER SIMULATION; DATABASES, PROTEIN; ESCHERICHIA COLI PROTEINS; ION CHANNELS; LIPID BILAYERS; MEMBRANE PROTEINS; MODELS, MOLECULAR; POTASSIUM CHANNELS; PROTEIN INTERACTION DOMAINS AND MOTIFS;

EID: 57049124381     PISSN: 09687688     EISSN: 14645203     Source Type: Journal    
DOI: 10.1080/09687680802446534     Document Type: Article

References (50)

1. Wallin E, von Heijne G. 1998. Genome-wide analysis of integral membrane proteins from eubacterial, archean, and eukaryotic organisms. Prot Sci 7:1029-1038.
2. Cornelius F. 2001. Modulation of Na,K-ATPase and Na-ATPase activity by phospholipids and cholesterol. I. Steady-state kinetics. Biochemistry 40:8842-8851.
3. 2+-ATPase reconstituted with short-chain or long-chain phosphatidylcholines. Biochem J 304:569-575.
4. Sunshine C, McNamee MG. 1994. Lipid modulation of nicotinic acetylcholine-receptor function - the role of membrane lipid-composition and fluidity. Biochim Biophys Acta 1191:59-64.
5. Baldwin PA, Hubbell WL. 1985. Effects of lipid environment on the light-induced conformational-changes of rhodopsin. 1. Absence of metarhodopsin-II production in dimyristoylphosphatidylcholine recombinant membranes. Biochemistry 24:2624-2632.
6. Baldwin PA, Hubbell WL. 1985. Effects of lipid environment on the light-induced conformational-changes of rhodopsin. 2. Roles of lipid chain-length, unsaturation, and phase state. Biochemistry 24:2633-2639.
7. Caffrey M, Feigenson GW. 1981. Fluorescence quenching in model membranes. 3. Relationship between calcium adenosine-triphosphatase enzyme-activity and the affinity of the protein for phosphatidylcholines with different acyl chain characteristics. Biochemistry 20:1949-1961.
8. Lee AG. 2004. How lipids affect the activities of integral membrane proteins. Biochim Biophys Acta 1666:62-87.
9. Lange C, Nett JH, Trumpower BL, Hunte C. 2001. Specific roles of protein-phospholipid interactions in the yeast cytochrome bc(1) complex structure. EMBO J 20:6591-6600.
10. Fyfe PK, Isaacs NW, Cogdell RJ, Jones MR. 2004. Disruption of a specific molecular interaction with a bound lipid affects the thermal stability of the purple bacterial reaction centre. Biochim Biophys Acta 1608:11-22.
11. Fyfe PK, McAuley KE, Roszak AW, Isaacs NW, Codgell RJ, Jones MR. 2001. Probing the interface between membrane proteins and membrane lipids by X-ray crystallography. Trends Biochem Sci 26:106-112.
12. Hunte C, Richers S. 2008. Lipids and membrane protein structures. Curr Opin Struct Biol 18:406-411.
13. Feller SE, Gawrisch K, Woolf TB. 2003. Rhodopsin exhibits a preference for solvation by polyunsaturated docosohexaenoic acid. J Am Chem Soc 125:4434-4435.
14. Grossfield A, Feller SE, Pitman MC. 2006. A role for direct interactions in the modulation of rhodopsin by omega-3 polyunsaturated lipids. Proc Natl Acad Sci USA 103:4888-4893.
15. Grossfield A, Feller SE, Pitman MC. 2007. Convergence of molecular dynamics simulations of membrane proteins. Proteins: Struct Func Bioinf 67:31-40.
16. Marrink SJ, de Vries AH, Mark AE. 2004. Coarse grained model for semiquantitative lipid simulations. J Phys Chem B 108:750-760.
17. Marrink SJ, Risselada J, Yefimov S, Tieleman DP, de Vries AH. 2007. The MARTINI forcefield: coarse grained model for biomolecular simulations. J Phys Chem B 111:7812-7824.
18. Monticelli L, Kandasamy SK, Periole X, Larson RG, Tieleman DP, Marrink SJ. 2008. The MARTINI coarse grained force field: extension to proteins. J Chem Theor Comp 4:819-834.
19. Basyn F, Charloteaux B, Thomas A, Brasseur R. 2001. Prediction of membrane protein orientation in lipid bilayers: a theoretical approach. J Mol Graphics Modelling 20:235-244.
20. Basyn F, Spies B, Bouffioux O, Thomas A, Brasseur R. 2003. Insertion of X-ray structures of proteins in membranes. J Mol Graphics Modelling 22:11-21.
21. Ducarme P, Rahman N, Brasseur R. 1998. IMPALA: a simple restraint field to simulate the biological membrane in structure studies. Prot Struct Func Genet 30:357-371.
22. Im W, Feig M, Brooks CL. 2003. An implicit membrane generalized Born theory for the study of structure, stability, and interactions of membrane proteins. Biophys J 85:2900-2918.
23. Ulmschneider MB, Sansom MSP, Di Nola A. 2005. Properties of integral membrane protein structures: derivation of an implicit membrane potential. Proteins: Struct Funct Bioinf 59:252-265.
24. Ulmschneider MB, Sansom MSP, Di Nola A. 2006. Evaluating tilt angles of membrane-associated helices: comparison of computational and NMR techniques. Biophys J 90:1650-1660.
25. Sansom MSP, Scott KA, Bond PJ. 2008. Coarse grained simulation: a high throughput computational approach to membrane proteins. Biochem Soc Transac 36:27-32.
26. Scott KA, Bond PJ, Ivetac A, Chetwynd AP, Khalid S, Sansom MSP. 2008. Coarse-grained MD simulations of membrane protein-bilayer self-assembly. Structure 16:621-630.
27. Andersen OS, Koeppe RE. 2007. Bilayer thickness and membrane protein function: an energetic perspective. Ann Rev Biophys Biomol Struct 36:107-130.
28. Powl AM, East JM, Lee AG. 2007. Different effects of lipid chain length on the two sides of a membrane and the lipid annulus of MscL. Biophys J 93:113-122.
29. Dixon RAF, Diehl RE, Opas E, Rands E, Vickers PJ, Evans JF, Gillard JW, Miller DK. 1990. Requirement of a 5-lipoxygenase-activating protein for leukotriene synthesis. Nature 343:282-284.
30. Miller DK, Gillard JW, Vickers PJ, Sadowski S, Leveille C, Mancini JA, Charleson P, Dixon RAF, Fordhutchinson AW, Fortin R, Gauthier JY, Rodkey J, Rosen R, Rouzer C, Sigal IS, Strader CD, Evans JF. 1990. Identification and isolation of a membrane-protein necessary for leukotriene production. Nature 343:278-281.
31. Steinbacher S, Bass R, Strop P, Rees DC. 2007. Structures of the prokaryotic mechanosensitive channels MscL and MscS. In: Mechanosensitive Ion Channels, Part A pp 1-24.
32. EdwardsMD, Booth IR, Miller S. 2004. Gating the bacterial mechanosensitive channels: MscS a new paradigm? Curr Opin Microbiol 7:163-167.
33. Ferguson AD, McKeever BM, Xu SH, Wisniewski D, Miller DK, Yamin TT, Spencer RH, Chu L, Ujjainwalla F, Cunningham BR, Evans JF, Becker JW. 2007. Crystal structure of inhibitor-bound human 5-lipoxygenase-activating protein. Science 317:510-512.
34. + channel. Nature 423:33-41.
35. Ramsey IS, Moran MM, Chong JHA, Clapham DE. 2006. A voltage-gated proton-selective channel lacking the pore domain. Nature 440:1213-1216.
36. Schmidt D, Jiang QX, MacKinnon R. 2006. Phospholipids and the origin of cationic gating charges in voltage sensors. Nature 444:775-779.
37. Freites JA, Tobias DJ, von Heijne G, White SH. 2005. Interface connections of a transmembrane voltage sensor. Proc Natl Acad Sci USA 102:15059-15064.
38. Treptow W, Tarek M. 2006. Environment of the gating charges in the Kv1.2 Shaker potassium channel. Biophys J 90:L64-66.
39. Bond PJ, Sansom MSP. 2007. Bilayer deformation by the Kv channel voltage sensor domain revealed by self-assembly simulations. Proc Natl Acad Sci USA 104:2631-2636.
40. Sands ZA, Sansom MSP. 2007. How does a voltage-sensor interact with a lipid bilayer? Simulations of a potassium channel domain. Structure 15:235-244.
41. + channel in a membrane environment. Biophys J 93:3070-3082.
42. Bond PJ, Sansom MSP. 2006. Insertion and assembly of membrane proteins via simulation. J Amer Chem Soc 128:2697-2704.
43. Lindahl E, Hess B, van der Spoel D. 2001. GROMACS 3.0: a package for molecular simulation and trajectory analysis. J Molec Model 7:306-317.
44. Berendsen HJC, Postma JPM, van Gunsteren WF, DiNola A, Haak JR. 1984. Molecular dynamics with coupling to an external bath. J Chem Phys 81:3684-3690.
45. Granseth E, von Heijne G, Elofsson A. 2005. A study of the membrane-water interface region of membrane proteins. J Mol Biol 346:377-385.
46. + channel in a lipid membrane-like environment. Nature 450:376-382.
47. Periole X, Huber T, Marrink SJ, Sakmar TP. 2007. G protein-coupled receptors self-assemble in dynamics simulations of model bilayers. J Am Chem Soc 129:10126-10132.
48. Yeagle PL, Bennett M, Lemaitre V, Watts A. 2007. Transmembrane helices of membrane proteins may flex to satisfy hydrophobic mismatch. Biochim Biophys Acta 1768:530-537.
49. Atilgan AR, Durell SR, Jernigan RL, Demirel MC, Keskin O, Bahar I. 2001. Anisotropy of fluctuation dynamics of proteins with an elastic network model. Biophys J 80:505-515.
50. Hilf RJC, Dutzler R. 2008. X-ray structure of a prokaryotic pentameric ligand-gated ion channel. Nature 452:375-379.