[Effect of Pro11-Ala11 amino acid substitution on structural and functional properties of antimicrobial peptide buforin 2].

Molecular dynamics simulations were used to investigate spatial structure of antimicrobial peptide buforin 2 in water and in toroidal transmembrane pores. It is shown that Pro11-Ala11 amino acid substitution contributes to stabilization of the helix and enables the peptide to form stable transmembrane toroidal pore. The results obtained correlate with the changes observed when modified buforin 2 interacts with cells.

Interaction of zervamicin IIB with lipid bilayers. Molecular dynamics study.

In this work we have studied the interaction of zervamicin IIB (ZrvIIB) with the model membranes of eukaryotes and prokaryotes using all-atom molecular dynamics. In all our simulations zervamicin molecule interacted only with lipid headgroups but did not penetrate the hydrophobic core of the bilayers. During the interaction with the prokaryotic membrane zervamicin placed by its N-termini towards the lipids and rotated at an angle of 40° relatively to the bilayer surface.

[Comparative studies of structural properties of melittin in water and trifluroethanol/water mixture by the molecular dynamics method].

The structural properties and dynamic behavior of the antimicrobial peptide melittin in hydrophobic and polar environments have been investigated. The main characteristics of the secondary structure of melittin in different media have been analyzed, and compared with the data on the ideal alpha-helix. It has been shown that melittin is an alpha-helix bent in the region of residue Pro14; in this case, the N-terminus of the peptide tends to unfold, while the C-terminal segment (residues 14-23) retains the helical structure for 20 ns of the simulation.