Antimicrobial peptides are an abundant and diverse group of molecules that are produced by many tissues and cell types in a variety of invertebrate, plant and animal species. Their amino acid composition, amphipathicity, cationic charge and size allow them to attach to and insert into membrane bilayers to form pores by 'barrel-stave', 'carpet' or 'toroidal-pore' mechanisms. Although these models are helpful for defining mechanisms of antimicrobial peptide activity, their relevance to how peptides damage and kill microorganisms still need to be clarified. Recently, there has been speculation that transmembrane pore formation is not the only mechanism of microbial killing. In fact several observations suggest that translocated peptides can alter cytoplasmic membrane septum formation, inhibit cell-wall synthesis, inhibit nucleic-acid synthesis, inhibit protein synthesis or inhibit enzymatic activity. In this review the different models of antimicrobial-peptide-induced pore formation and cell killing are presented.

Antimicrobial peptides: pore formers or metabolic inhibitors in bacteria?

Structure of lipid bilayers

Many biologically interesting phenomena occur on a time scale that is too long to be studied by atomistic simulations. These phenomena include the dynamics of large proteins and self-assembly of biological materials. Coarse-grained (CG) molecular modeling allows computer simulations to be run on length and time scales that are 2–3 orders of magnitude larger compared to atomistic simulations, providing a bridge between the atomistic and the mesoscopic scale. We developed a new CG model for proteins as an extension of the MARTINI force field. Here, we validate the model for its use in peptide-bilayer systems. In order to validate the model, we calculated the potential of mean force for each amino acid as a function of its distance from the center of a dioleoylphosphatidylcholine (DOPC) lipid bilayer. We then compared amino acid association constants, the partitioning of a series of model pentapeptides, the partitioning and orientation of WALP23 in DOPC lipid bilayers and a series of KALP peptides in dimyris...

The MARTINI Coarse-Grained Force Field: Extension to Proteins

Endosomal escape pathways for delivery of biologicals

https://www.cell.com/biophysj/pdf/S0006-3495(09)00791-7.pdf

CHARMM-GUI Membrane Builder for Mixed Bilayers and Its Application to Yeast Membranes

The condensing effect of cholesterol in lipid bilayers.

We suggest a physical mechanism by which antimicrobial peptides spontaneously induce stable pores in membranes. Peptide binding to a lipid bilayer causes an internal stress, or internal membrane tension, that can be sufficiently strong to create pores. Like detergents, peptides have a high affinity for the rim of the pore. Binding to the rims reduces the line tension and decreases the number of peptides causing the internal membrane tension. Consequently, the pore radius is stable. The pore formation resembles a phase transition.

/pdf/molecular-mechanism-of-peptide-induced-pores-in-membranes-3qur8mj7os.pdf

Molecular mechanism of Peptide-induced pores in membranes.

Antimicrobial peptides are known to form pores in cell membranes. We study this process in model bilayers of various lipid compositions. We use two of the best-studied peptides, alamethicin and melittin, to represent peptides making two types of pores, that is, barrel-stave pores and toroidal pores. In both cases, the key control variable is the concentration of the bound peptides in the lipid bilayers (expressed in the peptide-lipid molar ratio, P/L). The method of oriented circular dichroism (OCD) was used to monitor the peptide orientation in bilayers as a function of P/L. The same samples were scanned by X-ray diffraction to measure the bilayer thickness. In all cases, the bilayer thickness decreases linearly with P/L and then levels off after P/L exceeds a lipid-dependent critical value, (P/L)*. OCD spectra showed that the helical peptides are oriented parallel to the bilayers as long as P/L < (P/L)*, but as P/L increases over (P/L)*, an increasing fraction of peptides changed orientation to become perpendicular to the bilayer. We analyzed the data by assuming an internal membrane tension associated with the membrane thinning. The free energy containing this tension term leads to a relation explaining the P/L-dependence observed in the OCD and X-ray diffraction measurements. We extracted the experimental parameters from this thermodynamic relation. We believe that they are the quantities that characterize the peptide-lipid interactions related to the mechanism of pore formation. We discuss the meaning of these parameters and compare their values for different lipids and for the two different types of pores. These experimental parameters are useful for further molecular analysis and are excellent targets for molecular dynamic simulation studies.

/pdf/energetics-of-pore-formation-induced-by-membrane-active-55862wxepy.pdf

Energetics of pore formation induced by membrane active peptides

http://hwhuang.rice.edu/pdfs/Chen2003.pdf

Evidence for membrane thinning effect as the mechanism for peptide-induced pore formation.

How antimicrobial peptides form pores in membranes is of interest as a fundamental membrane process. However, the underlying molecular mechanism, which has potential applications in therapeutics, nonviral gene transfer, and drug delivery, has been in dispute. We have resolved this mechanism by observing the time-dependent process of pore formation in individual giant unilamellar vesicles (GUVs) exposed to a melittin solution. An individual GUV first expanded its surface area at constant volume and then suddenly reversed to expanding its volume at constant area. The area expansion, the volume expansion, and the point of reversal all match the results of equilibrium measurements performed on peptide–lipid mixtures. The mechanism includes a negative feedback that makes peptide-induced pores stable with a well defined size, contrary to the suggestion that peptides disintegrate the membrane in a detergent-like manner.

/pdf/mechanism-and-kinetics-of-pore-formation-in-membranes-by-8m0eh13ln1.pdf

Fang-Yu Chen

Papers

The condensing effect of cholesterol in lipid bilayers.

Molecular mechanism of Peptide-induced pores in membranes.

Energetics of pore formation induced by membrane active peptides

Evidence for membrane thinning effect as the mechanism for peptide-induced pore formation.

Mechanism and kinetics of pore formation in membranes by water-soluble amphipathic peptides