Interaction of Piscidin-1 with zwitterionic versus anionic membranes: A comparative molecular dynamics study

Journal of Biomolecular Structure and Dynamics

Volumn 31, Issue 12, 2013, Pages 1393-1403

  Rahmanpour, Arezoo ^a   Ghahremanpour, Mohammad Mehdi ^a   Mehrnejad, Faramarz ^b   Moghaddam, Majid Erfani ^c  

^a AZARBAIJAN SHAHID MADANI UNIVERSITY   (Iran)

^b UNIVERSITY OF TEHRAN   (Iran)

^c TARBIAT MODARES UNIVERSITY   (Iran)

Author keywords

Antimicrobial peptides; Membrane; Molecular dynamics simulation; Peptide drugs

Indexed keywords

1 PALMITOYLOLEOYLGLYCEROPHOSPHOCHOLINE; AMPHOLYTE; ANION; GLYCEROL; GLYCEROPHOSPHORYLCHOLINE; PALMITOYLOLEOYLPHOSPHTIDYLGLYCEROL; PISCIDIN 1; POLYPEPTIDE ANTIBIOTIC AGENT; SOLVENT; UNCLASSIFIED DRUG;

ARTICLE; CELL MEMBRANE; LIPID BILAYER; LIPID COMPOSITION; LIPID MEMBRANE; MEMBRANE BIOLOGY; MOLECULAR DYNAMICS; MOLECULAR MODEL; PRIORITY JOURNAL; PROTEIN FUNCTION; PROTEIN LIPID INTERACTION; PROTEIN TRANSPORT;

ANIMALS; ANIONS; ANTIMICROBIAL CATIONIC PEPTIDES; CELL MEMBRANE; FISH PROTEINS; LIPID BILAYERS; MODELS, MOLECULAR; MOLECULAR CONFORMATION; MOLECULAR DYNAMICS SIMULATION; PHOSPHATIDYLCHOLINES; PHOSPHATIDYLGLYCEROLS; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN STRUCTURE, TERTIARY;

EID: 84887007593     PISSN: 07391102     EISSN: 15380254     Source Type: Journal    
DOI: 10.1080/07391102.2012.737295     Document Type: Article

References (54)

1. Aittoniemi, J., de Wet, H., Ashcroft, F. M., & Sansom, M. S. (2010). Asymmetric switching in a homodimeric ABC transporter: A simulation study. PLoS Computational Biology, 6(4), e1000762.
2. Allen, W. J., Lemkul, J. A., & Bevan, D. R. (2009). GridMAT-MD: A grid-based membrane analysis tool for use with molecular dynamics. Journal of Computational Chemistry, 30, 1952-1958.
3. Bechinger, B. (2004). Membrane-lytic peptides. Critical Reviews in Plant Sciences, 23, 271-292.
4. Berendsen, H. J. C., Postma, J. P. M., van Gunsteren, W. F., Di Nola, A., & Haak, J. R. (1984). Molecular dynamics with coupling to an external bath. Journal of Chemical Physics, 81, 3684-3690.
5. Berendsen, J. C., van der Spoel, D., & van Drunen, R. (1995). GROMACS: A message-passing parallel molecular dynamic implementation. Computer Physics Communications, 91, 43-56.
6. Bradshow, J. P. (2003). Cationic antimicrobial peptides: Issues for potential clinical use. Biodrugs, 17, 233-240.
7. Brogden, K. (2005). Antimicrobial peptides: Pore formers or metabolic inhibitors in bacteria? Nature Reviews Microbiology, 3, 238-250. (Pubitemid 40298223)
8. Campagna, S., Saint, N., Molle, G., & Aumelas, A. (2007). Structure and mechanism of action of the antimicrobial peptide piscidin. Biochemistry, 46, 1771-1778.
9. Chekmenev, E. Y., Vollmar, B. S., & Cotton, M. (2006). Investigating molecular recognition and biological function at interfaces using piscidins, antimicrobial peptides from fish. Biochimica et Biophysica Acta, 1758, 1359-1372. (Pubitemid 44467864)
10. Chen, F., & Huang, H. W. (2003). Evidence for membrane thinning effect as the mechanism for peptide-induced pore formation. Biophysical Journal, 84, 3751-3575.
11. Cheng, J. T., Hale, J. D., Elliott, M., Hancock, R. E., & Straus, S. K. (2011). The importance of bacterial membrane composition in the structure and function of aurein 2.2 and selected variants. Biochimica et Biophysica Acta, 1808, 622-633.
12. Chinchar, V. G., Bryan, L., & Rollins-Smith, L. (2004). Inactivation of viruses infecting ectothermic animals by amphibian and piscine antimicrobial peptides. Virology, 323, 268-275. (Pubitemid 38748474)
13. Darden, T., York, D., & Pedersen, L. (1993). Particle mesh Ewald: An N-log (N) method for Ewald sums in large systems. Journal of Computational Chemistry, 18, 1463-1472.
14. De Angelis, A. A., Grant, C. V., Baxter, M. K., McGavin, J. A., Opella, S. J., & Cotton, M. L. (2011). Amphipathic antimicrobial piscidin in magnetically aligned lipid bilayers. Biophysical Journal, 101, 1086-1094.
15. Delano, W. L. (2002). The PYMOL molecular graphics system. San Carlos, CA: Delano Scientific. http://www.pymol.org
16. Douliez, J. P., Leonard, A., & Dufourc, E. J. (1995). Restatement of order parameters in biomembranes: Calculation of C-C bond order parameters from C-D quadrupolar splittings. Biophysical Journal, 68, 1727-1739.
17. Dowhan, W. (1997). Molecular basis for membrane phospholipid diversity: Why are there so many lipids? Annual Review of Biochemistry, 66, 199-232. (Pubitemid 27274656)
18. Essmann, U., Perera, L., Berkowitz, M. L., Darden, T., Lee, H., & Pedersen, L. G. (1995). A smooth particle mesh Ewald method. Journal of Chemical Physics, 103, 8577-8592.
19. Fleming, E., Maharaj, N. P., Chen, J. L., & Nelson, R. B. (2008). Effect of lipid composition on buforin II structure and membrane entry. Proteins, 73, 480-491.
20. Hess, B., Bekker, H., Berendsen, H. J. C., & Fraaije, J. G. E. M. (1997). LINCS: A linear constraints solver for molecular simulation. Journal of Computational Chemistry, 18, 1463-1472. (Pubitemid 127637344)
21. Hoover, W. G. (1985). Canonical dynamics: Equilibrium phasespace distributions. Physical Review A, 31, 1695-1697.
22. Hoskin, D. W., & Ramamoorthy, A. (2008). Studies on anticancer activities of antimicrobial peptides. Biochimica et Biophysica Acta, 1778, 357-375.
23. Hsu, J. C., & Yip, C. M. (2007). Molecular dynamics simulations of indolicidin association with model lipid bilayers. Biophysical Journal, 92, L100-L102. (Pubitemid 46910525)
24. Humphrey, W., Dalke, A., & Schulten, K. (1996). VMD: Visual molecular dynamics. Journal of Molecular Graphics, 14, 33-38. (Pubitemid 26152973)
25. Johansson, A. C., & Lindahl, E. (2009). The role of lipid composition for insertion and stabilization of amino acids in membranes. Journal of Chemical Physics, 130, 185101-1-185101-8.
26. Kandasamy, S. K., & Larson, R. G. (2004). Binding and insertion of alpha-helical anti-microbial peptides in POPC bilayers studied by molecular dynamics simulations. Chemistry and Physics of Lipids, 132, 113-132. (Pubitemid 39458325)
27. Kandasamy, S. K., & Larson, R. G. (2006). Effect of salt on the interactions of antimicrobial peptides with zwitterionic lipid bilayers. Biochimica et Biophysica Acta, 1758, 1274-1284. (Pubitemid 44436074)
28. Kukol, A. (2009). Lipid models for united-atom molecular dynamics simulations of proteins. Journal of Chemical Theory and Computation, 5, 615-626.
29. Lauth, X., Shike, H., Burns, J. C., Westerman, M. E., Ostland, V. E., Carlberg, J. M., ? Bulet, P. (2002). Discovery and characterization of two isoforms of moronecidin, a novel antimicrobial peptide from hybrid striped bass. Journal of Biological Chemistry, 277, 5030-5039. (Pubitemid 34968543)
30. Lee, S. A., Kim, Y. K., Lim, S. S., Zhu, W. L., Ko, H., Shin, S. Y., ? Kim, Y. (2007). Solution structure and cell selectivity of piscidin 1 and its analogues. Biochemistry, 46, 3653-3663. (Pubitemid 46493466)
31. Lindahl, E., Hess, B., & van der spoel, D. (2001). Gromacs 3.0: A package for molecular simulation and trajectory analysis. Journal of Molecular Modeling, 26, 1701-1718.
32. Mehrnejad, F., & Zarei, M. (2010). Molecular dynamics simulation study of the interaction of piscidin 1 with DPPC bilayers: Structure-activity relationship. Journal of Biomolecular Structure & Dynamics, 27, 551-560.
33. Miller, K. R. (1979). Structure of a bacterial photosynthetic membrane. Proceedings of the National Academy of Sciences of the USA, 76, 6415-6419. (Pubitemid 10163409)
34. Mukherjee, S., & Maxfield, F. R. (2004). Membrane domains. Annual Review of Cell and Developmental Biology, 20, 839-866. (Pubitemid 39488660)
35. Nośe, S., & Klein, M. L. (1983). Constant pressure molecular dynamics for molecular systems. Molecular Physics, 50, 1055-1076.
36. Papo, N., & Shai, Y. (2005). Host defense peptides as new weapons in cancer treatment. Cellular and Molecular Life Sciences, 62, 784-790. (Pubitemid 40655628)
37. Parrinello, M., & Rahman, A. (1981). Polymorphic transitions in single crystals: A new molecular dynamics method. Journal of Applied Physics, 52, 7182-7190. (Pubitemid 12456820)
38. Powers, J. P., & Hancock, R. E. (2003). Relationship between peptide structure and antibacterial activity. Peptides, 24, 1681-1691. (Pubitemid 38198075)
39. Sengupta, D., Leontiadou, H., Mark, A. E., & Marrink, S. J. (2008). Toroidal pores formed by antimicrobial peptides shows significant disorder. Biochimica et Biophysica Acta, 1778, 2308-2317.
40. Shepherd, C. M., Vogel, H. J., & Tieleman, D. P. (2003). Interactions of the designed antimicrobial peptide MB21 and truncated dermaseptin S3 with lipid bilayers: Moleculardynamics simulations. Biochemical Journal, 370, 233-243. (Pubitemid 36259436)
41. Silphaduang, U., & Noga, E. J. (2001). Peptide antibiotics in mast cells of fish. Nature, 414, 268-269. (Pubitemid 33097794)
42. Singer, S. J., & Nicolson, G. L. (1972). The fluid mosaic model of the structure of cell membranes. Science, 175, 720-731.
43. Tang, M., Waring, A. J., & Hong, M. (2007). Phosphatemediated arginine insertion into lipid membranes and pore formation by a cationic membrane peptide from solid-state NMR. Journal of the American Chemical Society, 37, 11438-11446. (Pubitemid 47555563)
44. Tieleman, D. P., Forrest, L. R., Sansom, M. S. P., & Berendsen, H. J. C. (1998). Lipid properties and the orientation of aromatic residues in OmpF, Influenza M2 and Alamethicin systems: Molecular dynamics simulations. Biochemistry, 37, 17554-17561.
45. Tieleman, D. P., Marrink, S. J., & Berendsen, H. J. A. (1997). Computer perspective of membranes: Molecular dynamics studies of lipid bilayer systems. Biochimica et Biophysica Acta, 1331, 235-270. (Pubitemid 28015516)
46. Van Der Spoel, D., Lindahl, E., Hess, B., Groenhof, G., Mark, A. E., & Berendsen, H. J. (2005). GROMACS: Fast flexible and free. Journal of Computational Chemistry, 16, 1701-1718.
47. Van Gunsteren, W. F., Billeter, S. R., Eising, A. A., Hunenberger, P. H., Kruger, P., Mark, A. E., Scott, W. R. P., & Tironi, I. G. (1996). Biomolecular simulation: The GROMOS96 manual and user guide. Zürich: vdf Hochschulverlag AG an der ETH Zürich.
48. Wessman, P., Morin, M., Reijmar, K., & Edwards, K. (2010). Effect of ?-helical peptides of liposome structure: A comparative study of melittin and alamethicin. Journal of Colloid and Interface Science, 386, 127-135.
49. Wiggins, P. A., & Nelson, P. C. (2006). Generalized theory of semiflexible polymers. Physical Review E, 73, 031906.
50. Wymore, T., Gao, X. F., & Wong, T. C. (1999). Molecular dynamics simulation of the structure and dynamics of a dodecylphosphocholine micelle in aqueous solution. Journal of Molecular Structure, 195, 485-486.
51. Yang, Y., Cao, J., & Shi, Y. (2004). Identification and characterization of a gene encoding human LPGAT1, an endoplasmic reticulum-associated lysophosphatidylglycerol acyltransferase. Journal of Biological Chemistry, 279, 55866-55874. (Pubitemid 40066594)
52. Yeaman, M. R., & Yount, N. Y. (2003). Mechanisms of antimicrobial peptide action and resistance. Pharmacological Reviews, 55, 27-55. (Pubitemid 36268398)
53. Zasloff, M. (2002). Antimicrobial peptides of multicellular organisms. Nature, 415, 389-395. (Pubitemid 34100944)
54. Zhao, W., Róg, T., Gurtovenko, A. A., Vattulainen, I., & Karttunen, M. (2007). Atomic-scale structure and electrostatics of anionic palmitoyloleoyl phosphtidylglycerol lipid bilayers with Na+ counterions. Biophysical Journal, 92, 1114-1124. (Pubitemid 46203173)