Construction of an implicit membrane environment for the lattice Monte Carlo simulation of transmembrane protein

Biophysical Chemistry

Volumn 147, Issue 1-2, 2010, Pages 35-41

  Chen, Yantao ^a   Wang, Mingliang ^a   Zhang, Qianling ^a   Liu, Jianhong ^a  

^a SHENZHEN UNIVERSITY   (China)

Author keywords

Implicit membrane environment; Lattice chain; Monte Carlo simulation; Protein folding; Transmembrane protein

Indexed keywords

MEMBRANE PROTEIN;

ARTICLE; BIOLOGICAL MODEL; CHIRALITY; COMPUTER SIMULATION; CONFORMATIONAL TRANSITION; CONTROLLED STUDY; CRYSTAL STRUCTURE; DNA HELIX; FEASIBILITY STUDY; HYDROGEN BOND; HYDROPHOBICITY; INFLUENZA VIRUS A; LIPID MEMBRANE; MEMBRANE MODEL; MEMBRANE POTENTIAL; MONTE CARLO METHOD; PRIORITY JOURNAL; PROCESS MODEL; PROTEIN CONFORMATION; PROTEIN DOMAIN; PROTEIN FOLDING; SARS CORONAVIRUS; STATISTICAL MODEL; THERMODYNAMICS;

COMPUTER SIMULATION; HYDROGEN BONDING; HYDROPHOBICITY; MEMBRANE LIPIDS; MEMBRANE PROTEINS; MEMBRANES, ARTIFICIAL; MODELS, MOLECULAR; MONTE CARLO METHOD; PROTEIN FOLDING; THERMODYNAMICS; VIRAL ENVELOPE PROTEINS; VIRAL MATRIX PROTEINS;

INFLUENZA A VIRUS; SARS CORONAVIRUS;

EID: 75549091941     PISSN: 03014622     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.bpc.2009.12.008     Document Type: Article

References (45)

1. Wallin E., von Heijne G. Genome-wide analysis of integral membrane proteins from eubacterial, archaean, and eukaryotic organisms. Protein Sci. 1998, 7:1029-1038.
2. White S.H., Wimley W.C. Membrane protein folding and stability: physical principles. Annu. Rev. Biophys. Biomolec. Struct. 1999, 28:319-365.
3. Bowie J.U. Solving the membrane protein folding problem. Nature 2005, 438:581-589.
4. Elofsson A., von Heijne G. Membrane protein structure: prediction versus reality. Annu. Rev. Biochem. 2007, 76:125-140.
5. Oberai A., Ihm Y., Kim S., Bowie J.U. A limited universe of membrane protein families and folds. Protein Sci. 2006, 15:1723-1734.
6. White S.H. Biophysical dissection of membrane proteins. Nature 2009, 459:344-346.
7. Ash W.L., Zlomislic M.R., Oloo E.O., Tieleman D.P. Computer simulations of membrane proteins. Biochim. Biophys. Acta-Biomembr. 2004, 1666:158-189.
8. Ayton G.S., Voth G.A. Systematic multiscale simulation of membrane protein systems. Curr. Opin. Struct. Biol. 2009, 19:138-144.
9. Kolinski A., Skolnick J. Reduced models of proteins and their applications. Polymer 2004, 45:511-524.
10. Tozzini V. Coarse-grained models for proteins. Curr. Opin. Struct. Biol. 2005, 15:144-150.
11. Kim S.Y., Lee J. Folding simulations of small proteins. Biophys. Chem. 2005, 115:195-200.
12. Zhang L., Lu D.N., Liu Z. How native proteins aggregate in solution: a dynamic Monte Carlo simulation. Biophys. Chem. 2008, 133:71-80.
13. Chen Y.T., Zhou Y.Q., Ding J.D. The helix-coil transition re-visited. Proteins 2007, 69:58-68.
14. Marrink S.J., Risselada H.J., Yefimov S., Tieleman D.P., de Vries A.H. The MARTINI force field: coarse grained model for biomolecular simulations. J. Phys. Chem. B 2007, 111:7812-7824.
15. Bond P.J., Holyoake J., Ivetac A., Khalid S., Sansom M.S.P. Coarse-grained molecular dynamics simulations of membrane proteins and peptides. J. Struct. Biol. 2007, 157:593-605.
16. Feig M. Implicit membrane models for membrane protein simulation. Methods in Molecular Biology [M] 2008, 181-196. Humana Press Inc. A. Kukol (Ed.).
17. Im W., Feig M., Brooks C.L. An implicit membrane generalized Born theory for the study of structure, stability, and interactions of membrane proteins. Biophys. J. 2003, 85:2900-2918.
18. Ulmschneider M.B., Ulmschneider J.P., Sansom M.S.P., Di Nola A. A generalized Born implicit-membrane representation compared to experimental insertion free energies. Biophys. J. 2007, 92:2338-2349.
19. Chen C.M., Chen C.C. Computer simulations of membrane protein folding: structure and dynamics. Biophys. J. 2003, 84:1902-1908.
20. Sperotto M.M., May S., Baumgaertner A. Modelling of proteins in membranes. Chem. Phys. Lipids 2006, 141:2-29.
21. Torres J., Wang J.F., Parthasarathy K., Liu D.X. The transmembrane oligomers of coronavirus protein E. Biophys. J. 2005, 88:1283-1290.
22. Lemaitre V., Willbold D., Watts A., Fischer W.B. Full length Vpu from HIV-1: combining molecular dynamics simulations with NMR spectroscopy. J. Biomol. Struct. Dyn. 2006, 23:485-496.
23. Levesque K., Finzi A., Binette J., Cohen E.A. Role of CD4 receptor down-regulation during HIV-1 infection. Curr. HIV Res. 2004, 2:51-59.
24. Kochendoerfer G.G., Salom D., Lear J.D., Wilk-Orescan R., Kent S.B.H., DeGrado W.F. Total chemical synthesis of the integral membrane protein influenza A virus M2: role of its C-terminal domain in tetramer assembly. Biochemistry 1999, 38:11905-11913.
25. Tobler K., Kelly M.L., Pinto L.H., Lamb R.A. Effect of cytoplasmic tail truncations on the activity of the M-2 ion channel of influenza A virus. J. Virol. 1999, 73:9695-9701.
26. Liu D.X., Yuan Q., Liao Y. Coronavirus envelope protein: a small membrane protein with multiple functions. Cell. Mol. Life Sci. 2007, 64:2043-2048.
27. Rota P.A., Oberste M.S., et al. Characterization of a novel coronavirus associated with severe acute respiratory syndrome. Science 2003, 300:1394-1399.
28. Torres J., Parthasarathy K., Lin X., Saravanan R., Kukol A., Liu D.X. Model of a putative pore: the pentameric alpha-helical bundle of SARS coronavirus E protein in lipid bilayers. Biophys. J. 2006, 91:938-947.
29. Pinto L.H., Lamb R.A. The M2 proton channels of influenza A and B viruses. J. Biol. Chem. 2006, 281:8997-9000.
30. Stouffer A.L., Acharya R., Salom D., Levine A.S., Di Costanzo L., Soto C.S., Tereshko V., Nanda V., Stayrook S., DeGrado W.F. Structural basis for the function and inhibition of an influenza virus proton channel. Nature 2008, 451:596-U513.
31. Schnell J.R., Chou J.J. Structure and mechanism of the M2 proton channel of influenza A virus. Nature 2008, 451:591-U512.
32. Sheu S.Y., Schlag E.W., Selzle H.L., Yang D.Y. Hydrogen bonds in membrane proteins. J. Phys. Chem. B 2009, 113:5318-5326.
33. Mokrab Y., Stevens T.J., Mizuguchi K. Lipophobicity and the residue environments of the transmembrane alpha-helical bundle. Proteins 2009, 74:32-49.
34. Kyte J., Doolittle R.F. A simple method for displaying the hydropathic character of a protein. J. Mol. Biol. 1982, 157:105-132.
35. Carmesin I., Kremer K. The bond fluctuation method: a new effective algorithm for the dynamics of polymers in all spatial dimensions. Macromolecules 1988, 21:2819-2823.
36. Deutsch H.P., Binder K. Inter-diffusion and self-diffusion in polymer mixtures: a Monte Carlo study. J. Chem. Phys. 1991, 94:2294-2304.
37. Verdier P.H., Stockmayer W.H. Monte Carlo calculations on the dynamics of polymers in dilute solution. J. Chem. Phys. 1962, 36:227-235.
38. Hilhorst H.J., Deutch J.M. Analysis of Monte Carlo results on the kinetics of lattice polymer chains with excluded volume. J. Chem. Phys. 1975, 63:5153-5161.
39. Mukherjee A., Bagchi B. Correlation between rate of folding, energy landscape, and topology in the folding of a model protein HP-36. J. Chem. Phys. 2003, 118:4733-4747.
40. Buchete N.V., Straub J.E., Thirumalai D. Continuous anisotropic representation of coarse-grained potentials for proteins by spherical harmonics synthesis. J. Molec. Graph. Model. 2004, 22:441-450.
41. Metropolis N., Rosenbluth A.W., Rosenbluth M.N., Teller A.H., Teller E. Equation of state calculations by fast computing machines. J. Chem. Phys. 1953, 21:1087-1092.
42. Parlett B.N. The Symmetric Eigenvalue Problem 1980, Prentice Hall, Englewood Cliffs, New Jersey.
43. Kabsch W., Sander C. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 1983, 22:2577-2637.
44. Bowie J.U. Helix packing in membrane proteins. J. Mol. Biol. 1997, 272:780-789.
45. Ulmschneider M.B., Sansom M.S.P., Di Nola A. Evaluating tilt angles of membrane-associated helices: comparison of computational and NMR techniques. Biophys. J. 2006, 90:1650-1660.