Monte-Carlo Simulations of Peptide-Membrane Interactions: Web-Server

Short peptides interact with biological membranes in many ways. For example, antimicrobial peptides destabilize bacterial cell membrane, while fusion peptides of viral proteins promote membrane fusion. Short peptides may mimic the interaction of integral membrane proteins with the membrane and thus are a convenient model system to study the folding and insertion of membrane proteins into the hydrophobic environment of the membrane. Along with various experimental techniques, computational methods are also used in research of peptides-membranes interactions. We have previously developed a Monte Carlo (MC) simulations model for the investigation of linear α-helical peptides with membranes. This model was tested on an assortment of peptides, such as Magainin2, penetratine, M2δ peptide (a transmembrane segment from the acetylcholine receptor δ-subunit), melittin and NK-2 and its derivatives. The results of the simulations correlated very well with empiric data. Moreover, these computations were used to guide further experimental efforts. Encouraged by these studies, we are establishing a web-server to allow external users to perform simulations of their peptides of interest in membrane and water environments. The server will provide a possibility to choose the amino acid sequence of the peptide, the ratio of zwitterionic-to-acidic lipids and width of the bilayer, and the ionic strength. The results will include the free energy of membrane-association of the peptide, its helical content upon membrane interaction as well as its predicted location in the membrane.