Effects of antimicrobial peptide revealed by simulations: Translocation, pore formation, membrane corrugation and Euler buckling

International Journal of Molecular Sciences

Volumn 14, Issue 4, 2013, Pages 7932-7958

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

^a BEIJING NORMAL UNIVERSITY   (China)

^b WEST VIRGINIA UNIVERSITY   (United States)

Author keywords

Antimicrobial peptides; Dissipative particle dynamics; Membrane

Indexed keywords

LIPID; MEMBRANE PROTEIN; POLYPEPTIDE ANTIBIOTIC AGENT; ANTIMICROBIAL CATIONIC PEPTIDE; LIPID BILAYER;

ARTICLE; BINDING AFFINITY; CELL VIABILITY; CHANNEL GATING; COMPLEX FORMATION; DISSIPATIVE PARTICLE DYNAMICS STIMULATION; EULER BUCKLING; HYDROPHILICITY; HYDROPHOBICITY; MATHEMATICAL ANALYSIS; MEMBRANE BIOLOGY; MEMBRANE CORRUGATION; MEMBRANE POTENTIAL; MOLECULAR DYNAMICS; MOLECULAR SIZE; PROTEIN LIPID INTERACTION; PROTEIN LOCALIZATION; PROTEIN TRANSPORT; STRUCTURE ANALYSIS; CHEMICAL MODEL; CHEMISTRY; LIPID BILAYER;

ANTIMICROBIAL CATIONIC PEPTIDES; LIPID BILAYERS; MODELS, CHEMICAL;

EID: 84876314138     PISSN: 16616596     EISSN: 14220067     Source Type: Journal    
DOI: 10.3390/ijms14047932     Document Type: Article

References (27)

1. Alberts, B.; Johnson, A.; Lewis, J.; Raff, M.; Roberts, K.; Walter, P. Molecular Biology of Cell; Garland Science: New York, NY, USA, 2002.
2. Zasloff, M. Antimicrobial peptides of multicellular organisms. Nature 2002, 415, 389-395.
3. Brogden, K.A. Antimicrobial peptides: Pore formers or metabolic inhibitors in bacteria? Nat. Rev. Microbiol. 2005, 3, 238-250.
4. Matsuzaki, K. Why and how are peptide-lipid interactions utilized for self-defense? Magainins and tachyplesins as archetypes. Biochim. Biophys. Acta 1999, 1462, 1-10.
5. Shai, Y. Mechanism of the binding, insertion and destabilization of phospholipid bilayer membranes by alpha-helical antimicrobial and cell non-selective membrane-lytic peptide. Biochim. Biophys. Acta 1999, 1462, 55-70.
6. Yang, L.; Weiss, T.M.; Lehrer, R.I.; Huang, H.W. Crystalization of antimicrobial pores in membranes: Magainin and protegrin. Biophys. J. 2000, 79, 2002-2009.
7. Bobone, S.; Gerelli, Y.; de Zotti, M.; Bocchinfuso, G.; Farrotti, A.; Orioni, B.; Sebastiani, F.; Latter, E.; Penfold, J., Senesi, R.; et al. Membrane thickness and the mechanism of action of the short peptaibol trichogin GA IV. Biochim. Biophys. Acta 2013, 1828, 1013-1024.
8. Yang, L.; Harroun, T.A.; Weiss, T.M.; Ding, T.M.; Huang, H.W. Barrel-Stave model or toroidal model? A case study on melittin pores. Biophys. J. 2001, 81, 1475-1485.
9. Yamaguchi, S.; Huster, D.; Waring, A.; Lehrer, R.I.; Kearney, W.; Tack, B.F.; Hong, M. Orientation and dynamics of an antimicrobial peptide in the lipid bilayer by solid-state NMR spectroscopy. Biophys. J. 2001, 81, 2203-2214.
10. Tsai, C.-W.; Hsu, N.-Y.; Wang, C.-H.; Lu, C.-Y.; Chang, Y.; Tsai, H.-H. G.; Ruaan, R.-C. Coupling molecular dynamics simulations with experiments for the rational design of Indolicidin-analogous antimicrobial peptides. J. Mol. Biol. 2009, 392, 837-854.
11. Gao, L.; Fang, W. Effects of induced tension and electrostatic interactions on the mechanisms of antimicrobial peptide translocation across lipid bilayer. Soft Matt. 2009, 5, 3312-3318.
12. Chen, L.; Gao, L.; Fang, W.; Golubovic, L. How the antimicrobial peptides kill bacteria: Computational physics insights. Commum. Comput. Phys. 2012, 11, 709-725.
13. Fantner, G.E.; Barbero, R.J.; Gray, D.S.; Belcher, A.M.; Kinetics of antimicrobial peptide activity measured on individual bacterial cells using high-speed atomic force microscopy. Nat. Nanotech. 2010, 5, 280-285.
14. Meincken, M.; Holroyd, D.L.; Rautenbach, M. Atomic force microscopy study of the effect of antimicrobial peptides on the cell envelope of Escherichia coli. Antimicrob. Agents Chemother. 2005, 49, 4085-4092.
15. Espanol, P.; Warren, P.B. Statistical mechanics of dissipative particle dynamics. Europhys. Lett. 1995, 30, 191-196.
16. Groot, R.D.; Warren, P.B. Dissipative particle dynamics: Bridging the gap between atomistic and mesoscopic simulation. J. Chem. Phys. 1997, 107, 4423-4435.
17. Groot, R.D. Electrostatic interactions in dissipative particle dynamics-simulation of polyelectrolytes and anionic surfactants.J. Chem. Phys. 2003, 118, 11265-11277.
18. Gao, L.; Fang, W. Communications: Self-energy and corresponding virial contribution of electrostatic interactions in dissipative particle dynamics: Simulations of cationic lipid bilayers. J. Chem. Phys. 2010, 132, 031102-031104.
19. Jakobsen, A.F. Constant-pressure and constant-surface tension simulations in dissipative particle dynamics. J. Chem. Phys. 2005, 122, 124901:1-124901:8.
20. Gao, L.; Shillcock, J.C.; Lipowsky, R. Improved dissipative particle dynamics simulations of lipid bilayers. J. Chem. Phys. 2007, 126, 015101:1-015101:8.
21. Golubovic, L.; Moldovan, D.; Peredera, A. Dynamics of Euler buckling instability. Phys. Rev. Lett. 1998, 81, 3387-3390.
22. Moldovan, D.; Golubovic, L. Buckling dynamics of compressed thin sheets (membranes). Phys. Rev. Lett. 1999, 82, 2884-2887.
23. Tsapis, N.; Ober, R.; Chafotte, A.; Warschawski, D.E.; Everett, J.; Kauffmann, J.; Kahn, P.; Waks, M.; Urbach, W. Modification of the elastic constants of a peptide-decorated lamellar phase. Langmuir 2002, 18, 4384-4392.
24. Golubovic, L.; Lubensky, T.C. Steric entropy and phase equilibria in microemulsions. Europhys. Lett. 1989, 10, 513-518.
25. Golubovic, L.; Lubensky, T.C. Smectic elastic constants of lamellar fluid membrane phases: Crumpling effects. Phys. Rev. B 1989, 39, 12110-12133.
26. Golubovic, L. Passages and droplets in lamellar fluid membrane phases. Phys. Rev. E 1994, 50, R2419-R2422.
27. Moldovan, D.; Golubovic, L. Tethered membranes far from equilibrium: Buckling dynamics. Phys. Rev. E 1999, 60, 4377-4384.