Paper Citing NAMD - Abstract
Bonhenry, Daniel; Tarek, Mounir; Dehez, Francois
Effects of Phospholipid Composition on the Transfer of a Small Cationic Peptide Across a Model Biological Membrane
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 9:5675-5684, DEC 2013
The transfer of a lysine amino acid analogue across phospholipid membrane models was investigated using molecular-dynamics simulations. The evolution of the protonation state of this small peptide as a function of its position inside the membrane was studied by determining the local pK(a) by means of free-energy calculations. Permeability and mean-first-passage time were evaluated and showed that the transfer occurs on the submillisecond time scale. Comparative studies were conducted to evaluate changes in the pK(a) arising from differences in the phospholipid chemical structure. We compared, hence, the effect of an ether vs an ester linkage of the lipid headgroup as well as linear vs branched lipid tails. The study reveals that protonated lysine residues can be buried further inside an ether lipid membrane than an ester lipid membrane, while branched lipids are found to stabilize less the charged form compared to their unbranched lipid chain counterparts.
