How the antimicrobial peptides kill bacteria: Computational physics insights

Communications in Computational Physics

Volumn 11, Issue 3, 2012, Pages 709-725

  Chen, Licui ^a   Gao, Lianghui ^a   Fang, Weihai ^a   Golubovic, Leonardo ^b  

^a BEIJING NORMAL UNIVERSITY   (China)

^b WEST VIRGINIA UNIVERSITY   (United States)

Author keywords

Antimicrobial peptide; Bilayer membrane; Dissipative particle dynamics

Indexed keywords

EID: 84855171050     PISSN: 18152406     EISSN: 19917120     Source Type: Journal    
DOI: 10.4208/cicp.071210.240511a     Document Type: Article

References (27)

1. B. Alberts, A. Johnson, J. Lewis, M. Raff, K. Roberts, and P. Walter, Molecular Biology of Cell, Garland Science, New York, 2002.
2. T. H. Denmark, Themed issue: Membrane biophysics, Soft Matt., 5 (2009), pp. 3145-3147.
3. M. Zasloff, Antimicrobial peptides of multicellular organisms, Nature (London, United Kingdom), 415 (2002), pp. 389-395. (Pubitemid 34100944)
4. K. A. Brogden, Antimicrobial peptides: Pore formers or metabolic inhibitors in bacteria? Nat. Rev. Microbiol., 3 (2005), pp. 238-250. (Pubitemid 40298223)
5. K. Matsuzaki, Why and how are peptide-lipid interactions utilized for self-defense? Magainins and tachyplesins as archetypes, Biochim. Biophys. Acta., 1462 (1999), pp. 1-10.
6. Y. Shai, Mechanism of the binding, insertion and destabilization of phospholipid bilayer membranes by α-helical antimicrobial and cell non-selective membrane-lytic peptides, Biochim. Biophys. Acta., 1462 (1999), pp. 55-70.
7. L. Yang, T. M. Weiss, R. I. Lehrer, and H. W. Huang, Crystalization of antimicrobial pores in membranes: Magainin and protegrin, Biophys. J., 79 (2000), pp. 2002-2009.
8. P. La Rocca, P. C. Biggin, and D. P. Tieleman, Simulation studies of the interaction of antimicrobial peptides and lipid bilayers, Biochim. Biophys. Acta., 1462 (1999), pp. 185-200.
9. J. H. Lin and A. Baumgaertner, Stability of a melittin pore in a lipid bilayer: A molecular dynamics study, Biophys. J., 78 (2000), pp. 1714-1724. (Pubitemid 30183570)
10. H. Leontiadou, A. E. Mark, and S. J. Marrink, Antimicrobial peptide in action, J. Am. Chem. Soc., 128 (2006), pp. 12156-12161.
11. H. D. Herce and A. E. Garcia, Molecular dynamics simulations suggest a mechanism for translocation of the HIV-1 Tat peptide across lipid membranes, Proc. Natl. Acad. Sci. U. S. A., 104 (2007), pp. 20805-20810.
12. F. Jean-Francois, J. Elezgaray, P. Berson, P. Vacher, and E. J. Duforc, Pore formation induced by an antimicrobial peptide: Electrostatic effects, Biophys. J., 95 (2008), pp. 5748-5756.
13. C. F. Lopez, S. O. Nielsen, P. B. Moore, and M. L. Klein, Understanding nature's design for ananosyringe, Proc. Natl. Acad. Sci. U. S. A., 101 (2004), pp. 4431-4434.
14. C. F. Lopez, S. O. Nielsen, P. B. Moore, and M. L. Klein, Structure and dynamics of model pore insertion into a membrane, Biophys. J., 88 (2005), pp. 3083-3094. (Pubitemid 40586563)
15. C. F. Lopez, S. O. Nielsen, G. Srinivas, W. F. DeGrado, and M. L. Klein, Probing membrane insertion activity of antimicrobial polymers via coarse-grain molecular dynamics, J. Chem. Theor. Comput., 2 (2006), pp. 649-655.
16. M. Venturoli, B. Smit, and M. M. Sperotto, Simulation studies of protein-induced bilayer deformations, and lipid-induced protein tilting, on a mesoscopic model for lipid bilayers with embedded proteins, Biophys. J., 88 (2005), pp. 1778-1798. (Pubitemid 40983847)
17. G. Illya, and M. Deserno, Coarse-grained simulation studies of peptide-induced pore formation, Biophys. J., 95 (2008), pp. 4163-4173.
18. L. Gao and W. Fang, Effects of induced tension and electrostatic interactions on the mechanisms of antimicrobial peptide translocation across lipid bilayer, Soft Matt., 5 (2009), pp. 3312-3318.
19. P. Espanol and P. B. Warren, Statistical mechanics of dissipative particle dynamics, Europhys. Lett., 30 (1995), pp. 191-196.
20. R. D. Groot and P. B. Warren, Dissipative particle dynamics: Bridging the gap between atomistic and mesoscopic simulation, J. Chem. Phys., 107 (1997), pp. 4423-4435. (Pubitemid 127611597)
21. R. D. Groot and K. L. Rabone, Mesoscopic simulation of cell membrane damage, morphology change and rupture by nonionic surfactants, Biophys. J., 81 (2001), pp. 725-736. (Pubitemid 32721448)
22. G. J. Martyna, D. J. Tobias, and M. L. Klein, Constant pressure molecular dynamics algorithms, J. Chem. Phys., 101 (1994), pp. 4177-4189.
23. A. F. Jakobsen, Constant-pressure and constant-surface tension simulations in dissipative particle dynamics, J. Chem. Phys., 122 (2005), pp. 124901.
24. R. D. Groot, Electrostatic interactions in dissipative particle dynamics-simulation of polyelectrolytes and anionic surfactants, J. Chem. Phys., 118 (2003), pp. 11265-11277.
25. P. H. Hunenberger, Calculation of the group-based pressure in molecular simulations. I. A general formulation including Ewald and particle-particle- particle-mesh electrostatics, J. Chem. Phys., 116 (2002), pp. 6880-6897. (Pubitemid 34537071)
26. L. Gao and W. Fang, Communications: Self-energy and corresponding virial contribution of electrostatic interactions in dissipative particle dynamics: Simulations of cationic lipid bilayers, J. Chem. Phys., 132 (2010), pp. 031102-031104.
27. G. E. Fantner, R. J. Barbero, D. S. Gray and A. M. Belcher, Kinetics of antimicrobial peptide activity measured on individual bacterial cells using high-speed atomic force microscopy, Nat. Nanotech., 5 (2010), pp. 280-285.