Structure and dynamics of an amphiphilic peptide in a lipid bilayer: A molecular dynamics study

Biophysical Journal

Volumn 73, Issue 6, 1997, Pages 3039-3055

  Belohorcová, Katarína ^a   Davis, James H ^a   Woolf, Thomas B ^c   Roux, Benoît ^b  

^a UNIVERSITY OF GUELPH   (Canada)

^b UNIVERSITÉ DE MONTRÉAL   (Canada)

^c JOHNS HOPKINS UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

MEMBRANE PROTEIN;

ARTICLE; DYNAMICS; LIPID BILAYER; MOLECULAR DYNAMICS; PEPTIDE ANALYSIS; SIMULATION; STRUCTURE ANALYSIS;

EID: 0030733344     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0006-3495(97)78332-2     Document Type: Article

References (65)

1. Alper, H. E., and T. R. Stouch. 1995. Orientation and diffusion of a drug analogue in biomembranes: molecular dynamics simulations. J. Phys. Chem. 99:5724-5731.
2. Bassolino-Klimas, D., H. E. Alper, and T. R. Stouch. 1993. Solute diffusion in lipid bilayer membranes: an atomic level study. Biochemistry. 32:12624-12637.
3. Bassolino-Klimas, D., H. E. Alper, and T. R. Stouch. 1995. Mechanism of solute diffusion through lipid bilayer membranes by molecular dynamics simulation. J. Am. Chem. Soc. 117:4118-4129.
4. Brooks, B. R., R. E. Bruccoleri, B. D. Olafson, D. J. States, S. Swaminathan, and M. Karplus. 1983. CHARMM: a program for macromolecular energy, minimization, and dynamics calculations. J. Comput. Chem. 4:187-217.
5. Brooks, C. L., and M. Karplus. 1989. Solvent effects on protein motion and protein effects on solvent motion. J. Mol. Biol 208:159-181.
6. Brooks, C. L., M. Karplus, and B. M. Pettitt. 1988. Proteins: A Theoretical Perspective of Dynamics, Structure and Thermodynamics. I. Prigogine and S. A. Rice, editors. Advances in Chemical Physics, Vol. LXXI. John Wiley and Sons, New York.
7. Cantor, C. R., and P. R. Schimmel. 1980. Biophysical Chemistry. Part I. The Conformations of Biological Macromolecules. W. H. Freeman and Co., San Francisco.
8. Creighton, T. E. 1983. Proteins: Structures and Molecular Principles. W. H. Freeman and Co., New York.
9. Damodaran, K. V., and K. M. Merz, Jr. 1995. Interaction of the fusion inhibiting peptide carbobenzoxy-D-Phe-L-Phe-Gly with N-methyldioleoylphosphatidylethanolamine lipid bilayers. J. Am. Chem. Soc. 117: 6561-6571.
10. Damodaran, K. V., K. M. Merz, Jr., and B. P. Gaber. 1995. Interaction of small peptides with lipid bilayers. Biophys. J. 69:1299-1308.
11. Davis, J. H., D. M. Clare, R. S. Hodges, and M. Bloom. 1983. Interaction of a synthetic amphiphilic polypeptide and lipids in a bilayer structure. Biochemistry. 22:5298-5305.
12. Deisenhofer, J., and H. Michel. 1989. The photosynthetic reaction center from the purple bacterium Rhodopseudomonas viridis. Science. 245: 1463-1473.
13. De Loof, H., S. C. Harvey, J. P. Segrest, and R. W. Pastor. 1991. Mean field stochastic boundary molecular dynamics simulation of a phospholipid in a membrane. Biochemistry. 30:2099-2113.
14. Dunbrack, R. L., and M. Karplus. 1993. Backbone-dependent rotamer library for proteins. Application to side-chain prediction. J. Mol. Biol. 230:543-574.
15. Edholm, O., O. Berger, and F. Jähnig. 1995. Structure and fluctuations of bacteriorhodopsin in the purple membrane: a molecular dynamics study. J. Mol. Biol. 250:94-111.
16. Edholm, O., and J. Johansson. 1987. Lipid bilayer polypeptide interactions studied by molecular dynamics simulation. Eur. Biophys. J. 14:203-209.
17. Ermler, U., G. Fritzsch, S. Buchanan, and H. Michel. 1992. In Research in Photosynthesis. N. Murata, editor. Kluwer, Dordrecht, the Netherlands. 341-347.
18. Gennis, R. B. 1989. Biomembranes: Molecular Structure and Function. Springer Verlag, New York.
19. Grigorieff, N., T. A. Ceska, K. H. Downing, J. M. Baldwin, and R. Henderson. 1996. Electron-crystallographic refinement of the structure of bacteriorhodopsin. J. Mol. Biol. 259:393-421.
20. Haile, J. M. 1992. Molecular Dynamics Simulations: Elementary Methods. John Wiley and Sons, New York.
21. Helfand, E. 1978. Brownian dynamics study of transitions in a polymer chain of bistable oscillators. J. Chem. Phys. 69:1010-1018.
22. Heller, H., M. Schaefer, and K. Schulten. 1993. Molecular dynamics simulation of a bilayer of 200 lipids in the gel and in the liquid-crystal phases. J. Phys. Chem. 97:8343-8360.
23. Hirst, J. D., and C. L. Brooks, III. 1995. Molecular dynamics of isolated helices of myoglobin. Biochemistry. 34:7614-7621.
24. Huang, P., and G. H. Loew. 1995. Interaction of an amphiphilic peptide with a phospholipid bilayer surface by molecular dynamics simulation study. J. Biomol. Struct. Dyn. 12:937-956.
25. Huschilt, J. C., B. Millman, and J. H. Davis. 1989. Orientation of α-helical peptides in a lipid bilayer. Biochim. Biophys. Acta. 979:139-141.
26. Jenkins, G. M., and D. G. Watts. 1968. Spectral Analysis and Its Applications. Holden-Day, San Fransisco.
27. Jorgensen, W. L. 1981. Quantum and statistical mechanical studies of liquids. 10. Transferable intermolecular potential functions for water, alcohols and ethers. Application to liquid water. J. Am. Chem. Soc. 103:335-345.
28. Jorgensen, W. L., J. Chandrasekhar, J. D. Madura, R. W. Impey, and M. L. Klein. 1983. Comparison of simple potential functions for simulating liquid water. J. Chem. Phys. 79:926-935.
29. Kovacs, H., A. E. Mark, J. Johansson, and W. F. van Gunsteren. 1995. The effect of environment on the stability of an integral membrane helix: molecular dynamics simulations of surfactant protein C in chloroform, methanol and water. J. Mol. Biol. 247:808-822.
30. Kühlbrandt, W., D. N. Wang, and Y. Fujiyoshi. 1994. Atomic model of plant light-harvesting complex by electron crystallography. Nature. 367: 614-621.
31. Langlais, D. B. 1994. Internuclear distance measurements using rotational resonance. Ph.D. thesis. University of Guelph, Guelph, Ontario, Canada.
32. Lewis, B. A., and D. M. Engelman. 1983. Lipid bilayer thickness varies linearly with acyl chain length in fluid phosphatidylcholine vesicles. J. Mol. Biol. 166:211-217.
33. Loncharich, R. J., B. R. Brooks, and R. W. Pastor. 1992. Langevin dynamics of peptides: the frictional dependence of isomerization rates of N-acetylalanyl-N-methylamide. Biopolymers. 32:523-535.
34. Mackerell, A. D., D. Bashford, M. Bellot, R. L. Dunbrack, M. J. Field, S. Fischer, J. Gao, H. Guo, D. Joseph, S. Ha, L. Kuchnir, K. Kuczera, F. T. K. Lau, C. Mattos, S. Michnick, D. T. Nguyen, T. Ngo, B. Prodhom, B. Roux, B. Schlenkrich, J. Smith, R. Stote, J. Straub, J. Wiorkiewicz-Kuczera, and M. Karplus. 1992. Self-consistent parametrization of biomolecules for molecular modelling and condensed phase simulations. Biophys. J. 61:A143.
35. Marrink, S. J., and H. J. C. Berendsen. 1994. Simulation of water transport through a lipid membrane. J. Phys. Chem. 98:4155-4168.
36. Mouritsen, O. G., and M. Bloom. 1993. Models of lipid-protein interactions in membranes. Annu. Rev. Biophys. Biomol. Struct. 22:145-171.
37. Nagle, J. F. 1993. Area/lipid of bilayers from NMR. Biophys. J. 64: 1476-1481.
38. Nezil, F. A., and M. Bloom. 1992. Combined influence of cholesterol and synthetic amphiphilic peptides upon bilayer thickness in model membranes. Biophys. J. 61:1176-1183.
39. Pastor, R. W. 1994. Molecular dynamics and Monte Carlo simulations of lipid bilayer. Curr. Opin. Struct. Biol. 4:486-492.
40. Pastor, R. W., and S. E. Feller. 1996. Time scales of lipid dynamics and molecular dynamics. In Biological Membranes: A Molecular Perspective from Computation and Experiment. K. M. Merz, Jr., and B. Roux, editors. Birkhäuser, Boston. 3-29.
41. Pastor, R. W., R. H. Venable, and M. Karplus. 1991. Model for the structure of the lipid bilayers. Proc. Natl. Acad. Sci. USA. 88:892-896.
42. Pauling, L., and R. B. Corey. 1951. The structure of synthetic polypeptides. Proc. Natl. Acad. Sci. USA. 37:241-250.
43. 2H-NMR. Eur. Biophys. J. 12:1-11.
44. Picot, D., P. J. Loll, and R. M. Garavito. 1994. The X-ray structure of the membrane protein prostaglandin H2 synthase-1. J. Mol. Biol. 227: 493-509.
45. Prosser, R. S., and J. H. Davis. 1994. Dynamics of an integral membrane protein: a deuterium NMR relaxation study of gramicidin. Biophys. J. 66:1429-1440.
46. Prosser, R. S., J. H. Davis, C. Mayer, K. Weisz, and G. Kothe. 1992. Deuterium NMR relaxation studies of peptide-lipid interactions. Biochemistry. 31:9355-9363.
47. Ramakrishnan, C., and K. V. Soman. 1982. Identification of secondary structures in globular proteins - a new algorithm. Int. J. Pept. Protein Res. 20:218-237.
48. Roux, B., and T. B. Woolf. 1996. Molecular dynamics of Pf1 coat protein in a phospholipid bilayer. In Biological Membranes: A Molecular Perspective from Computation and Experiment. K. M. Merz, Jr., and B. Roux, editors. Birkhäuser, Boston. 555-587.
49. Ryckaert, J.-P., G. Ciccotti, and H. J. C. Berendsen. 1977. Numerical integration of the Cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes. J. Comput. Phys. 23: 327-341.
50. Shen, L., D. Bassolino, and T. Stouch. 1997. Structure and interaction of a transmembrane polyalanine alpha-helix with a DMPC bilayer studied by multi-nanosecond molecular dynamics simulation. Biophys. J. 73:3-20.
51. Song, L., M. R. Hobaugh, C. Shustak, S. Cheley, H. Bayley, and J. E. Gouaux. 1996. Structure of staphylococcal α-hemolysin, a heptameric transmembrane pore. Science. 274:1859-1866.
52. Stouch, T. R. 1993. Lipid membrane structure and dynamics studied by all-atom molecular dynamics simulations of hydrated phospholipid bilayers. Mol. Sim. 10:335-362.
53. Stowell, M. H. B., and D. C. Rees. 1995. Structure and stability of membrane proteins. Adv. Protein Chem. 46:279-311.
54. Sundaralingam, M. 1972. Molecular structures and conformations of the phospholipids and sphingomyelins. Ann. N.Y. Acad. Sci. 195:324-355.
55. van Gunsteren, W. F., P. H. Hünenberger, A. E. Mark, P. E. Smith, and I. G. Tironi. 1995. Computer simulation of protein motion. Comput. Phys. Commun. 91:305-319.
56. van Gunsteren, W. F., and A. E. Mark. 1992. On the interpretation of biochemical data by molecular dynamics computer simulation. Eur. J. Biochem. 204:947-961.
57. Venable, R. M., Y. Zhang, B. J. Hardy, and R. W. Pastor. 1993. Molecular dynamics simulations of a lipid bilayer and of hexadecane: an investigation of membrane fluidity. Science. 262:223-226.
58. Verlet, L. 1967. Computer experiments on classical fluids. I. Thermodynamical properties of Lennard-Jones molecules. Phys. Rev. 159:98-103.
59. Weiss, M. S., and G. E. Schulz. 1992. Structure of porin refined at 1.8 angstroms resolution. Nature. 367:243-249.
60. Woolf, T. B. 1996. Molecular dynamics simulations of individual bacteriorhodopsin helices in explicit DMPC. Biophys. J. 70:A377.
61. Woolf, T. B., and B. Roux. 1994a. Molecular dynamics simulation of the gramicidin channel in a phospholipid bilayer. Proc. Natl. Acad. Sci. USA. 91:11631-11635.
62. Woolf, T. B., and B. Roux. 1994b. Conformational flexibility of o-phosphorylcholine and o-phosphorylethanolamine: a molecular dynamics study of solvation effects. J. Am. Chem. Soc. 116:5916-5926.
63. Woolf, T. B., and B. Roux. 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.
64. Zhang, Y. P., R. N. A. H. Lewis, R. S. Hodges, and R. N. McElhaney. 1992a. FTIR spectroscopic studies of the conformation and amide hydrogen exchange of a peptide model of the hydrophobic transmembrane α-helices of membrane proteins. Biochemistry. 31:11572-11578.
65. Zhang, Y. P., R. N. A. H. Lewis, R. S. Hodges, and R. N. McElhaney. 1992b. Interaction of a peptide model of a hydrophobic transmembrane α-helical segment of a membrane protein with phosphatidylcholine bilayers: differential scanning calorimetric and FTIR spectroscopic studies. Biochemistry. 31:11579-11588.