Taras V. Pogorelov, Josh V. Vermaas, Mark J. Arcario, and Emad Tajkhorshid.
Partitioning of amino acids into a model membrane: Capturing the
interface.
Journal of Physical Chemistry B, 118:1481-1492, 2014.
POGO2014-ET
Energetics of protein side chain partitioning between aqueous solution and cellular
membranes is of fundamental importance for correctly capturing the membrane binding
and specific protein–lipid interactions of peripheral membrane proteins. We recently
reported a highly mobile membrane mimetic (HMMM) model that accelerates lipid
dynamics by modeling the membrane interior partially as a fluid organic solvent while
retaining a literal description of the lipid head groups and the beginning of the tails. While
the HMMM has been successfully applied to study spontaneous insertion of a number of
peripheral proteins into membranes, a quantitative characterization of the energetics of
membrane–protein interactions in HMMM membranes has not been performed. We report
here the free energy profiles for partitioning of 10 protein side chain analogues into a
HMMM membrane. In the interfacial and headgroup regions of the membrane, the side
chain free energy profiles show excellent agreement with profiles previously reported for
conventional membranes with fulltail lipids. In regions where the organic solvent is
prevalent, the increased dipole and fluidity of the solvent generally result in a less accurate
description, most notably overstabilization of aromatic and polar amino acids. As an
additional measure of the ability of the HMMM model to describe membrane–protein
interactions, the watertomembrane interface transfer energies were analyzed and found to
be in agreement with the previously reported experimental and computational
hydrophobicity scales. We discuss strengths and weaknesses of HMMM in describing
protein–membrane interactions as well as further development of model membranes.
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