Interactions of cationic-hydrophobic peptides with lipid bilayers: a Monte Carlo simulation method.
We present a computational model of the interaction between hydrophobic cations, such as the antimicrobial peptide, Magainin2, and membranes that include anionic lipids. The peptide's amino acids were represented as two interaction sites: one corresponds to the backbone alpha-carbon and the other to the side chain. The membrane was represented as a hydrophobic profile, and its anionic nature was represented by a surface of smeared charges. Thus, the Coulombic interactions between the peptide and the membrane were calculated using the Gouy-Chapman theory that describes the electrostatic potential in the aqueous phase near the membrane. Peptide conformations and locations near the membrane, and changes in the membrane width, were sampled at random, using the Metropolis criterion, taking into account the underlying energetics. Simulations of the interactions of heptalysine and the hydrophobic-cationic peptide, Magainin2, with acidic membranes were used to calibrate the model. The calibrated model reproduced structural data and the membrane-association free energies that were measured also for other basic and hydrophobic-cationic peptides. Interestingly, amphipathic peptides, such as Magainin2, were found to adopt two main membrane-associated states. In the first, the peptide resided mostly outside the polar headgroups region. In the second, which was energetically more favorable, the peptide assumed an amphipathic-helix conformation, where its hydrophobic face was immersed in the hydrocarbon region of the membrane and the charged residues were in contact with the surface of smeared charges. This dual behavior provides a molecular interpretation of the available experimental data.
Shental-Bechor
Dalit
D
Department of Biochemistry, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, Israel.
Haliloglu
Turkan
T
Ben-Tal
Nir
N
D000595:Amino Acid Sequence; D000818:Animals; D023181:Antimicrobial Cationic Peptides / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D055592:Biophysical Phenomena; D001703:Biophysics; D002352:Carrier Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D002412:Cations; D057846:Cell-Penetrating Peptides; D057927:Hydrophobic and Hydrophilic Interactions; D066298:In Vitro Techniques; D008051:Lipid Bilayers / Q000737:chemistry* / Q000378:metabolism*; D054806:Magainins; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009010:Monte Carlo Method; D010455:Peptides / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D011485:Protein Binding; D012997:Solvents; D055672:Static Electricity; D013816:Thermodynamics; D029867:Xenopus Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism
D023181:Antimicrobial Cationic Peptides; D002352:Carrier Proteins; D002412:Cations; D057846:Cell-Penetrating Peptides; D008051:Lipid Bilayers; D054806:Magainins; D010455:Peptides; D012997:Solvents; D029867:Xenopus Proteins; C053301:magainin 2 peptide, Xenopus; C414409:penetratin