Protein-induced membrane disorder: A molecular dynamics study of melittin in a dipalmitoylphosphatidylcholine bilayer

Biophysical Journal

Volumn 78, Issue 3, 2000, Pages 1359-1375

  Bachar, Michal ^a   Becker, Oren M ^a  

^a TEL AVIV UNIVERSITY   (Israel)

Author keywords

[No Author keywords available]

Indexed keywords

DIPALMITOYLPHOSPHATIDYLCHOLINE; MELITTIN; PROTEIN;

AMINO TERMINAL SEQUENCE; ARTICLE; HYDRATION; HYDROPHILICITY; MEMBRANE DAMAGE; MOLECULAR DYNAMICS; PHOSPHOLIPID BILAYER; PROTEIN STRUCTURE; PROTON TRANSPORT;

EID: 0034091671     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0006-3495(00)76690-2     Document Type: Article

References (63)

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. Bachar, M., and O. M. Becker. 1999. Melittin at a membrane/water interface: effects on water orientation and water penetration. J. Chem. Phys. 111:8672-8685.
3. 1H-NMR study in methanol. Eur. J. Biochem. 173:139-146.
4. Belohorcova, K., J. H. Davis, T. B. Woolf, and B. Roux. 1997. Structure and dynamics of an amphiphilic peptide in a lipid bilayer: a molecular dynamics study. Biophys. J. 73:3039-3055.
5. Berger, O., O. Edholm, and F. Jahnig. 1997. Molecular dynamics simulations of a fluid bilayer of dipalmitoylphosphatidylcholine at full hydration, constant pressure, and constant temperature. Biophys. J. 72: 2002-2013.
6. Berneche, S., M. Nina, and B. Roux. 1998. Molecular dynamics simulation of melittin in a dimyristoylphosphatidylcholine bilayer membrane. Biophys. J. 75:1603-1618.
7. Bradrick, T. D., A. Philippetis, and S. Georghiou. 1995. Stopped-flow fluorometric study of the interaction of melittin with phospholipid bilayers: importance of the physical state of the bilayer and the acyl chain length. Biophys. J. 69:1999-2010.
8. Bradshaw, J. P., C. E. Dempsey, and A. Watts. 1994. A combined x-ray and neutron diffraction study of selectively deuterated melittin in phospholipid bilayers: effect of pH. Mol. Membr. Biol. 11:79-86.
9. Brooks, B. R., R. E. Bruccoleri, B. D. Olafson, D. J. States, S. Swaminathan, and M. Karplys. 1983. CHARMM: a program for macromolecular energy, minimization, and dynamics calculations. J. Comput. Chem. 4:187-217.
10. Chiu. S.-W., M. Clark, S. Subramanian, H. L. Scott, and E. Jakobsson. 1995. Incorporation of surface tension into molecular dynamics simulations at interfaces: a fluid phase lipid bilayer membrane. Biophys. J. 69:1230-1245.
11. Damodaran, K. V., and K. M. Merz, Jr. 1994. Computer simulation of lipid systems. In Reviews in Computational Chemistry. K. B. Lipkowitz and D. B. Boyd, Editors. VCH Publishers, New York.
12. Damodaran, K. V., K. M. Merz, Jr., and B. P. Gaber. 1995. Interaction of small peptides with lipid bilayers. Biophys. J. 69:1299-1308.
13. DeGrado, W. F., G. F. Musso, M. Lieber, E. T. Kaiser, and F. J. Kezdy. 1982. Kinetics and mechanism of hemolysis induced by melittin and by a synthetic melittin analogue. Biophys. J. 37:329-338.
14. 2H NMR and ESR study using designed transmembrane α-helical peptides and gramicidin A. Biochemistry. 37:9333-9345.
15. Dempsey, C. E. 1990. The actions of melittin on membranes. Biochim. Biophys. Acta. 1031:143-161.
16. Devaux, P. F., and M. Siegneuret. 1985. Specificity of lipid-protein interactions as determined by spectroscopic techniques. Biochim. Biophys. Acta. 822:63-125.
17. Douliez, J. P., A. Leonard, and E. J. Dufourc. 1995. Restatement of order parameters in biomembranes: calculation of C-C bond order parameters from C-D quadrupolar splittings. Biophys. J. 68:1727-1739.
18. Ducarme, P., M. Rahman, and B. Brasseur. 1998. IMPALA: a simple restraint field to simulate the biological membrane in molecular structure studies. Proteins. 30:357-371.
19. Dufourc, E. J., I. C. P. Smith, and J. Dufourcq. 1986. Molecular details of melittin-induced lysis of phospholipid membranes as revealed by deuterium and phosphorus NMR. Biochemistry. 25:6448-6455.
20. Feller, S. E., and R. W. Pastor. 1996. On simulating lipid bilayers with an applied surface tension: periodic boundary conditions and undulations. Biophys. J. 71:1350-1355.
21. Feller, S. E., R. W. Pastor, A. Rojnickarin, S. Bogusz, and B. R. Brooks. 1996. Effect of electrostatic force truncation on interfacial and transport properties of water. J. Phys. Chem. 100:17011-17020.
22. Feller, S. E., R. M. Venable, and R. W. Pastor. 1997. Computer simulations of a DPPC phospholipid bilayer: structural changes as a function of molecular surface area. Langmuir. 13:6555-6561.
23. Feller, S. E., Y. Zhang, R. W. Pastor, and B. R. Brooks. 1995. Constant pressure molecular dynamics simulation: the Langevin piston method. J. Chem. Phys. 103:4613-4621.
24. Geve, G., and D. March. 1987. Phospholipid Bilayers: Physical Principles and Models. Wiley Interscience, New York.
25. Gevod, V. S., and K. S. Birdi. 1984. Melittin and the 8-26 fragment: differences in ionophoric properties as measured by monolayer method. Biophys. J. 45:1079-1083.
26. Habermann, E., and H. Kowallek. 1970. Modification of amino groups and tryptophan in melittin as an aid to recognition of structure-activity relationships. Hoppe Seylers Z. Physiol. Chem. 351:884-890.
27. 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.
28. Jost, P., O. H. Griffith, R. A. Capaldi, and G. Vanderkooi. 1973. Evidence for boundary lipid in membrane. Proc. Natl. Acad. Sci. USA. 70: 480-484.
29. Koynova, R., and M. Caffrey. 1998. Phases and phase transitions of the phosphatidylcholines. Biochim. Biophys. Acta. 1376:91-145.
30. Lopez Cascales, J. J., J. Garcia de la Torre, S. J. Marrink, and H. J. C. Berendsen. 1996. Molecular dynamics simulation of a charged biological membrane. J. Chem. Phys. 104:2713-2720.
31. MacKerell Jr., A. D., D. Bashford, M. Bellott, R. L. Dunbrack, Jr., J. D. Evanseck, M. J. Field, S. Fischer, J. Gao, H. Guo, S. Ha, D. Joseph-McCarthy, L. Kuchnir, K. Kuczera, F. T. K. Lau, C. Mattos, S. Michnick, T. Ngo, D. T. Nguyen, B. Prodhom, W. E. Reiher III, B. Roux, M. Schlenkrich, J. C. Smith, R. Stole, J. Straub, M. Watanabe, J. Wiorkiewicz-Kuczera, D. Yin, and M. Karplus. 1998, All-atom empirical potential for molecular modeling and dynamics studies of proteins. J. Phys. Chem. B. 102:3586-3616.
32. Manjunatha-Kini, R., and H. J. Evans. 1989. A common cytolytic region in myotoxins, hemolysins, cardiotoxins and antibacterial peptides. Int. J. Pept. Protein Res. 34:277-286.
33. Marrink, S. J. 1994. Permeation of Small Molecules across Lipid Membranes. Ph.D. thesis, University of Groningen.
34. Marrink, S. J., and H. J. C. Berendsen. 1994. Simulation of water transport through a lipid membrane. J. Phys. Chem. 98:4155-4168.
35. Marrink, S. J., O. Berger, P. Tieleman, and F. Jahnig. 1998. Adhesion forces of lipids in a phospholipid membrane studied by molecular dynamics simulations. Biophys. J. 74:931-943.
36. Marrink, S. J., R. M. Sok, and H. J. C. Berendsen. 1996. Free volume properties of a simulated lipid membrane. J. Chem. Phys. 104: 9090-9099.
37. Milik, M., and J. Skolnick. 1993. Insertion of peptide chains into lipid membranes: an off-lattice Monte Carlo dynamics model. Proteins Struct. Funct. Genet. 15:10-25.
38. Monette, M., and M. Lafleur. 1995. Modulation of melittin-induced lysis by surface charge density of membranes. Biophys. J. 68:187-195.
39. Mouritsen, O. G. 1991. Theoretical models of phospholipid phase transition. Chem. Phys. Lipids. 57:178-194.
40. Mouritsen, O. G., and R. L. Biltonen. 1993. Protein-lipid interactions and membrane heterogeneity. In Protein-Lipid Interactions. A. Watts, editor. Elsevier, London. 1-39.
41. Nagle, J. F., R. Zhang, S. Tristram-Nagle, W. Sun, H. I. Petrache, and R. M. Suter. 1996. X-ray structure determination of fully hydrated L alpha phase dipalmitoylphosphatidylcholine bilayers. Biophys. J. 70: 1419-1431.
42. Pastor, R. W. 1994. Molecular dynamics and Monte Carlo simulations of lipid bilayers. Curr. Opin. Struct. Biol. 4:486-492.
43. Pastore, A., T. S. Harvey, C. E. Dempsey, and I. D. Campbell. 1989. The dynamic properties of melittin in solution: investigation by NMR and molecular dynamics. Eur. Biophys. J. 16:363-367.
44. Ruggiero, A., and B. Hudson. 1989. Critical density fluctuations in lipid bilayers detected by fluorescence lifetime heterogeneity. Biophys. J. 55:1111-1124.
45. Schlenkrich, M., J. Brickman, A. D. MacKerell, and M. Karplus. 1996. An empirical potential energy function for phospholipids: criteria for parameter optimization and applications. In Biological Membranes: A Molecular Perspective from Computation and Experiment. K. Merz and B. Roux, editors. Birkhäuser, Boston, MA.
46. Scott, H. L. 1986. Monte Carlo calculations of order parameter profiles in models of lipid-protein interactions in bilayers. Biochemistry. 25: 6122-6126.
47. Scott, H. L., and S. Kalaskar. 1989. Lipid chains and cholesterol in model membranes: a Monte Carlo study. Biochemistry. 28:3687-3691.
48. Seelig, A., and J. Seelig. 1974. The dynamic structure of fatty acyl chains in a phospholipid bilayer measured by deuterium magnetic resonance. Biochemistry. 13:4839-4845.
49. Shen, L. Y., D. Bassolino, and T. Stouch. 1997. Transmembrane helix structure, dynamics, and interactions: multi-nanosecond molecular dynamics simulations. Biophys. J. 73:3-20.
50. Terwilliger, T. C., and D. Eisenberg. 1982. The structure of melittin. II, Interpretation of the structure. J. Biol. Chem. 257:6016-6022.
51. Tieleman, D. P., and H. J. C. Berendsen. 1996. Molecular dynamics simulations of a fully hydrated dipalmitoyl phosphatidylcholine bilayer with different macroscopic boundary conditions and parameters. J. Chem. Phys. 105:4871-4880.
52. Tieleman, D. P., and H. J. C. Berendsen. 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.
53. Tieleman, D. P., L. R. Forrest, M. S. P. Sansom, and H. J. C. Berendsen. 1998. Lipid properties and the orientation of aromatic residues in OmpF, influenza M2 and alamethicin systems: molecular dynamic simulations. Biochemistry. 37:17554 -17561.
54. Tieleman, D. P., S. J. Marrink, and H. J. C. Berendsen. 1997. A computer perspective of membranes: molecular dynamics studies of lipid bilayer systems. Biochim. Biophys. Acta. 1331:235-270.
55. Tieleman, D. P., M. S. P. Sansom, and H. J. C. Berendsen. 1999. Alamethicin helices in a bilayer and in solution: molecular dynamics simulations. Biophys. J. 76:40-49.
56. Tosteson, M. T., S. J. Holmes, M. Razin, and D. C. Tosleson. 1985. Permeation of ions in membranes. J. Membr. Bitil. 87:35-44.
57. van der Ploeg, P., and H. J. C. Berendsen. 1982. Molecular dynamics of a bilayer membrane. J. Chem. Phys. 76:3271-3276.
58. Vogel, H. 1987. Comparison of the conformation and orientation of alamethicin and melittin in lipid membranes. Biochemistry. 26:4562-4572.
59. Vogel, H., and F. Jähnig. 1986. The structure of melittin in membranes. Biophys. J. 50:573-582.
60. 13C NMR characterization of the structure and dynamics of synthetic melittin and melittin analogues in lipid environments. Biochemistry. 31:1301-1313.
61. Woolf, T. B. 1997. Molecular dynamics of individual alpha-helices of bacleriorhodopsin in dimyristoyl phosphatidylcholine. 1. Structure and dynamics. Biophys. J. 73:2376-2392.
62. Woolf, T. B. 1998. Molecular dynamics of individual alpha-helices of bacteriorhodopsin in dimyristoyl phosphatidylcholine. 2. Interaction energy analysis. Biophys. J. 74:115-131.
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.