Lipid bilayers, interactions with gramicidins

Prenner EJ, Lewis RNAH, McElhaney RN. The interaction of the antimicrobial peptide gramicidin S with lipid bilayer model and biological membranes. Biochim. Biophys. Acta 1999 1462 201-221. Papahadjonponlos D, Moscarello M, Eylar EH, Isaac T. Effects of proteins on thermotropic phase transitions of phospholipid membranes. Biochim. Biophys. Acta 1975 401 317-335. 

MD simulations of ionophore/channel molecules intercalated into a lipid bilayer would require a large number of lipid molecules to ensure that the ionophore/channel molecule does not interact with its periodic images. Still, comparisons between boundary and bulk lipids may have to be done from independent simulations to get an accurate view of how these molecules affea bilayer dynamics. Typical channels like gramicidin show ion transport times of —10 s, which is a time scale that is presently unattainable in typical MD simulations. However, one can obtain insights into the molecular aspects of the energy barriers involved in the translocation of small molecules and ions from PMF calculations, particularly when there is no ambiguity about the path of the solute movement. Moreover, short time scale (10 s) simulations can... 

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