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. In the case of eukaryotic membrane zervamicin stayed in the water and located parallel to the membrane surface. We compared hydrogen bonds between peptide and lipids and concluded that interactions of ZrvIIB with prokaryotic membrane are stronger than those with eukaryotic one. Also it was shown that two zervamicin molecules formed dimer and penetrated deeper in the area of lipid headgroups.

Graphical abstractFigure optionsDownload full-size imageDownload as PowerPoint slideResearch highlights► Zervamicin molecule interacts with lipid headgroups but does not penetrate the hydrophobic core of the bilayer. ► Interaction of ZrvIIB with prokaryotic membrane is stronger than with eukaryotic one. ► Two zervamicin molecules can form dimmer, which penetrates deeper into the area of lipid headgroups.