Coarse-grained molecular dynamics of tetrameric transmembrane peptide bundles within a lipid bilayer

Chemistry and Physics of Lipids

Volumn 163, Issue 6, 2010, Pages 530-537

  Nguyen, Thuy Hien T ^a   Rao, Niny Z ^b   Schroeder, William M ^a   Moore, Preston B ^a  

^a University of the Sciences in Philadelphia   (United Kingdom)

^b THOMAS JEFFERSON UNIVERSITY   (United States)

Author keywords

All atom; DMPC bilayer; Ion channel; LS2 peptide; Tetramer bundle; WALP peptide

Indexed keywords

ION CHANNEL; MEMBRANE PROTEIN; PEPTIDE; PEPTIDE LS2; PEPTIDE WALP; UNCLASSIFIED DRUG; DIMYRISTOYLPHOSPHATIDYLCHOLINE; LIPID BILAYER;

ARTICLE; HYDROPHILICITY; HYDROPHOBICITY; LIPID BILAYER; MOLECULAR DYNAMICS; PRIORITY JOURNAL; PROTEIN STRUCTURE; SIMULATION; CHEMISTRY; THERMODYNAMICS;

DIMYRISTOYLPHOSPHATIDYLCHOLINE; LIPID BILAYERS; MEMBRANE PROTEINS; MOLECULAR DYNAMICS SIMULATION; PEPTIDES; THERMODYNAMICS;

EID: 77954217918     PISSN: 00093084     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.chemphyslip.2010.04.007     Document Type: Article

References (62)

1. P.J. Bond, and M.S.P. Sansom The simulation approach to bacterial outer membrane proteins (Review) Mol. Membr. Biol. 21 2004 151 161
2. P.J. Bond, and M.S. Sansom Insertion and assembly of membrane proteins via simulation J. Am. Chem. Soc. 128 2006 2697 2704
3. P.J. Bond, J. Holyoake, A. Ivetac, S. Khalid, and M.S. Sansom Coarse-grained molecular dynamics simulations of membrane proteins and peptides J. Struct. Biol. 157 2007 593 605
4. R. Chang, G.S. Ayton, and G.A. Voth Multiscale coupling of mesoscopic-and atomistic-level lipid bilayer simulations J. Chem. Phys. 122 2005 244716-244716
5. M.R.R. de Planque, B.B. Bonev, J.A.A. Demmers, D.V. Greathouse, R.E. Koeppe, F. Separovic, A. Watts, and J.A. Killian Interfacial anchor properties of tryptophan residues in transmembrane peptides can dominate over hydrophobic matching effects in peptide-lipid interactions Biochemistry (N.Y.) 42 2003 5341 5348
6. A.H. de Vries, A.E. Mark, and S.J. Marrink The binary mixing behavior of phospholipids in a bilayer: a molecular dynamics study J. Phys. Chem. B 108 2004 2454 2463
7. W.F. Degrado, Z.R. Wasserman, and J.D. Lear Protein design, a minimalist approach Science 243 1989 622 628
8. K.C. Duff, and R.H. Ashley The transmembrane domain of influenza-a M2 protein forms amantadine-sensitive proton channels in planar lipid bilayers Virology 190 1992 485 489
9. B. Ensing, and E.J. Baerends Reaction path sampling of the reaction between iron(II) and hydrogen peroxide in aqueous solution J. Phys. Chem. A 106 2002 7902 7910
10. B. Ensing, M. De Vivo, M. Liu, P.B. Moore, and M.L. Klein Metadynamics as a tool for exploring free energy landscapes of chemical reactions Acc. Chem. Res. 39 2006 73 81
11. D.J. Estes, S. Memarsadeghi, S.K. Lundy, F. Marti, D.D. Mikol, D.A. Fox, and M. Mayer High-throughput profiling of ion channel activity in primary human lymphocytes Anal. Chem. 80 2008 3728 3735
12. D. Evans, and B. Holian The Nose-Hoover thermostat J. Chem. Phys. 83 1985 4069 4074
13. S. Fernandez-Lopez, H.S. Kim, E.C. Choi, M. Delgado, J.R. Granja, A. Khasanov, K. Kraehenbuehl, G. Long, D.A. Weinberger, K.M. Wilcoxen, and M.R. Ghadiri Antibacterial agents based on the cyclic d,l-alpha-peptide architecture Nature 412 2001 452 455
14. I. Horia, Petrache, M. Daniel, Zuckerman, N. Jonathan, Sachs, J.A. Killian, E. Roger, I.I. Koeppe, and T.B. Woolf Hydrophobic matching mechanism investigated by molecular dynamics simulations Langmuir 18 2002 1340 1351
15. K.P. Howard, J.D. Lear, and W.F. DeGrado Sequence determinants of the energetics of folding of a transmembrane four-helix-bundle protein Proc. Natl. Acad. Sci. U.S.A. 99 2002 8568 8572
16. G. Hummer, J.C. Rasaiah, and J.P. Noworyta Water conduction through the hydrophobic channel of a carbon nanotube Nature 414 2001 188 190
17. T. Husslein, P.B. Moore, Q.F. Zhong, D.M. Newns, P.C. Pattnaik, and M.L. Klein Molecular dynamics simulation of a hydrated diphytanol phosphatidylcholine lipid bilayer containing an alpha-helical bundle of four transmembrane domains of the Influenza A virus M2 protein Faraday Discus. 1998 201 208
18. Y.X. Jiang, A. Lee, J.Y. Chen, M. Cadene, B.T. Chait, and R. MacKinnon The open pore conformation of potassium channels Nature 417 2002 523 526
19. J.A. Killian Synthetic peptides as models for intrinsic membrane proteins FEBS Lett. 555 2003 134 138
20. M.L. Klein, and W. Shinoda Large-scale molecular dynamics simulations of self-assembling systems Science 321 2008 798 800
21. Krzysztof Palczewski, Takashi Kumasaka, Tetsuya Hori, Craig A. Behnke, Hiroyuki Motoshima, Brian A. Fox, Isolde le Trong, David C. Teller, Tetsuji Okada, Ronald E. Stenkamp, Masaki Yamamoto, Masashi Miyano, 2000. Science Crystal structure of rhodopsin: a G protein-coupled receptor, 289, 739-745.
22. A. Laio, and M. Parrinello Escaping free-energy minima PNAS 99 2002 12562 12566
23. J.D. Lear, Z.R. Wasserman, and W.F. DeGrado Synthetic amphiphilic peptide models for protein ion channels Science 240 1988 1177 1181
24. J.D. Lear, H. Gratkowski, and W.F. DeGrado De novo design, synthesis and characterization of membrane-active peptides Biochem. Soc. Trans. 29 2001 559 564
25. R.H. Li, N. Mitra, H. Gratkowski, G. Vilaire, R. Litvinov, C. Nagasami, J.W. Weisel, J.D. Lear, W.F. DeGrado, and J.S. Bennett Activation of integrin alpha IIb beta 3 by modulation of transmembrane helix associations Science 300 2003 795 798
26. C.F. Lopez, M. Montal, J.K. Blasie, M.L. Klein, and P.B. Moore Molecular dynamics investigation of membrane-bound bundles of the channel-forming transmembrane domain of viral protein U from the human immunodeficiency virus HIV-1 Biophys. J. 83 2002 1259 1267
27. C.F. Lopez, S.O. Nielsen, P.B. Moore, J.C. Shelley, and M.L. Klein Self-assembly of a phospholipid Langmuir monolayer using coarse-grained molecular dynamics simulations J. Phys.: Condens. Matter 14 2002 9431 9444
28. C.F. Lopez, P.B. Moore, J.C. Shelley, M.Y. Shelley, and M.L. Klein Computer simulation studies of biomembranes using a coarse grain model Comput. Phys. Commun. 147 2002 1 6
29. C.F. Lopez, S.O. Nielsen, P.B. Moore, and M.L. Klein Understanding nature's design for a nanosyringe Proc. Natl. Acad. Sci. U.S.A. 101 2004 4431 4434
30. C.F. Lopez, S.O. Nielsen, B. Ensing, P.B. Moore, and M.L. Klein Structure and dynamics of model pore insertion into a membrane Biophys. J. 88 2005 3083 3094
31. M. Makowski, E. Sobolewski, C. Czaplewski, A. Liwo, S. Oldziej, J.H. No, and H.A. Scheraga Simple physics-based analytical formulas for the potentials of mean force for the interaction of amino acid side chains in water. 3. Calculation and parameterization of the potentials of mean force of pairs of identical hydrophobic side chains J. Phys. Chem. B 111 2007 2925 2931
32. F.M. Marassi, and S.J. Opella NMR structural studies of membrane proteins Curr. Opin. Struct. Biol. 8 1998 640 648
33. S.J. Marrink, and A.E. Mark Molecular dynamics simulation of the formation, structure, and dynamics of small phospholipid vesicles J. Am. Chem. Soc. 125 2003 15233 15242
34. Moore, P.B., 2005. CM3D.
35. P.B. Moore, Q.F. Zhong, T. Husslein, and M.L. Klein Simulation of the HIV-1 Vpu transmembrane domain as a pentameric bundle FEBS Lett. 431 1998 143 148
36. M. Nanias, C. Czaplewski, and H.A. Scheraga Replica exchange and multicanonical algorithms with the coarse-grained UNRES force field J. Chem. Theory Comput. 2 2006 513 528
37. D.M. Newns, Q.F. Zhong, P.B. Moore, T. Husslein, P. Pattnaik, and M.L. Klein Molecular dynamics study of structure and gating of low molecular weight ion channels Parallel Comput. 26 2000 965 976
38. C.G. Nichols, and T.P. Flagg Ion channels Genetics 2009
39. S.O. Nielsen, C.F. Lopez, P.B. Moore, J.C. Shelley, and M.L. Klein Molecular dynamics investigations of lipid Langmuir monolayers using a coarse-grain model J. Phys. Chem. B 107 2003 13911 13917
40. S.O. Nielsen, C.F. Lopez, I. Ivanov, P.B. Moore, J.C. Shelley, and M.L. Klein Transmembrane peptide-induced lipid sorting and mechanism of l-alpha-to-inverted phase transition using coarse-grain molecular dynamics Biophys. J. 87 2004 2107 2115
41. S.O. Nielsen, B. Ensing, V. Ortiz, P.B. Moore, and M.L. Klein Lipid bilayer perturbations around a transmembrane nanotube: a coarse grain molecular dynamics study Biophys. J. 88 2005 3822 3828
42. S. Oiki, W. Danho, V. Madison, and M. Montal M2-delta, a candidate for the structure lining the ionic channel of the nicotinic cholinergic receptor Proc. Natl. Acad. Sci. U.S.A. 85 1988 8703 8707
43. S. Oiki, W. Danho, and M. Montal Channel protein engineering-synthetic 22-mer peptide from the primary structure of the voltage-sensitive sodium-channel forms ionic channels in lipid bilayers Proc. Natl. Acad. Sci. U.S.A. 85 1988 2393 2397
44. R.B. Ross, and Sanat Mohanty Multiscale Simulation Methods for Nanomaterials 2008 73
45. M.S.P. Sansom, I.H. Shrivastava, K.M. Ranatunga, and G.R. Smith Simulations of ion channels-watching ions and water move Trends Biochem. Sci. 25 2000 368 374
46. J.C. Shelley, M.Y. Shelley, R.C. Reeder, S. Bandyopadhyay, P.B. Moore, and M.L. Klein Simulations of phospholipids using a coarse grain model J. Phys. Chem. B 105 2001 9785 9792
47. A.M. Slovic, H. Kono, J.D. Lear, J.G. Saven, and W.F. DeGrado Computational design of water-soluble analogues of the potassium channel KcsA Proc. Natl. Acad. Sci. U.S.A. 101 2004 1828 1833
48. A.F. Smeijers, K. Pieterse, A.J. Markvoort, and P.A. Hilbers Coarse-grained transmembrane proteins: hydrophobic matching, aggregation, and their effect on fusion J. Phys. Chem. B 110 2006 13614 13623
49. R.C. Stevens High-throughput protein crystallization Curr. Opin. Struct. Biol. 10 2000 558 563
50. R.J. Sugrue, and A.J. Hay Structural characteristics of the M2 protein of influenza-a viruses-evidence that it forms a tetrameric channel Virology 180 1991 617 624
51. T. Takahashi, J. Sugiura, and K. Nagayama Comparison of all atom, continuum, and linear fitting empirical models for charge screening effect of aqueous medium surrounding a protein molecule J. Chem. Phys. 116 2002 8232 8237
52. L. Thogersen, B. Schiott, T. Vosegaard, N.C. Nielsen, and E. Tajkhorshid Peptide aggregation and pore formation in a lipid bilayer: a combined coarse-grained and all atom molecular dynamics study Biophys. J. 95 2008 4337 4347
53. D.P. Tieleman, P.C. Biggin, G.R. Smith, and M.S.P. Sansom Simulation approaches to ion channel structure-function relationships Q. Rev. Biophys. 34 2001 473 561
54. J. Torres, A. Kukol, and I.T. Arkin Mapping the energy surface of transmembrane helix-helix interactions Biophys. J. 81 2001 2681 2692
55. V.M. Unger Electron cryomicroscopy methods Curr. Opin. Struct. Biol. 11 2001 548 554
56. C. Wang, R.A. Lamb, and L.H. Pinto Direct measurement of the influenza-a virus M(2) protein ion-channel activity in mammalian-cells Virology 205 1994 133 140
57. L. Yang, T.A. Harroun, T.M. Weiss, L. Ding, and H.W. Huang Barrel-stave model or toroidal model? A case study on melittin pores Biophys. J. 81 2001 1475 1485
58. H. Yin, J.S. Slusky, B.W. Berger, R.S. Walters, G. Vilaire, R.I. Litvinov, J.D. Lear, G.A. Caputo, J.S. Bennett, and W.F. DeGrado Computational design of peptides that target transmembrane helices Science 315 2007 1817 1822
59. Q. Zhong, P.B. Moore, D.M. Newns, and M.L. Klein Molecular dynamics study of the LS3 voltage-gated ion channel FEBS Lett. 427 1998 267 270
60. Q.F. Zhong, T. Husslein, P.B. Moore, D.M. Newns, P. Pattnaik, and M.L. Klein The M2 channel of influenza A virus: a molecular dynamics study FEBS Lett. 434 1998 265 271
61. Q.F. Zhong, Q. Jiang, P.B. Moore, D.M. Newns, and M.L. Klein Molecular dynamics simulation of a synthetic ion channel Biophys. J. 74 1998 3 10
62. Q.F. Zhong, P.B. Moore, and M.L. Klein Formation and stability of the LS3 synthetic ion channel Abstr. Pap. Am. Chem. Soc. 215 1998 U565-U565