Extension of the Highly Mobile Membrane Mimetic to Transmembrane Systems through Customized in Silico Solvents

Vermaas, Josh V.; Pogorelov, Taras V.; Tajkhorshid, Emad

doi:10.1021/acs.jpcb.6b11378

Title: Extension of the Highly Mobile Membrane Mimetic to Transmembrane Systems through Customized in Silico Solvents

Journal Article · Tue Feb 28 00:00:00 EST 2017 · Journal of Physical Chemistry. B, Condensed Matter, Materials, Surfaces, Interfaces and Biophysical Chemistry

DOI:https://doi.org/10.1021/acs.jpcb.6b11378· OSTI ID:1480280

Vermaas, Josh V. ^[1]; Pogorelov, Taras V. ^[1]; Tajkhorshid, Emad ^[1]

Univ. of Illinois at Urbana-Champaign, IL (United States)

Typically, the mechanics of the protein–lipid interactions of transmembrane proteins are difficult to capture with conventional atomic molecular dynamics, due to the slow lateral diffusion of lipids restricting sampling to states near the initial membrane configuration. The highly mobile membrane mimetic (HMMM) model accelerates lipid dynamics by modeling the acyl tails nearest to the membrane center as a fluid organic solvent while maintaining an atomic description of the lipid headgroups and short acyl tails. The HMMM has been applied to many peripheral protein systems; however, the organic solvent used to date caused deformations in transmembrane proteins by intercalating into the protein and disrupting interactions between individual side chains. We ameliorate the effect of the solvent on transmembrane protein structure through the development of two new in silico Lennard-Jones solvents. The parameters for the new solvents were determined through an extensive parameter search in order to match the bulk properties of alkanes in a highly simplified model. Using these new solvents, we substantially improve the insertion free energy profiles of 10 protein side chain analogues across the entire bilayer. Furthermore, we reduce the intercalation of solvent into transmembrane systems, resulting in native-like transmembrane protein structures from five different topological classes within a HMMM bilayer. The parametrization of the solvents, in addition to their computed physical properties, is discussed. By combining high lipid lateral diffusion with intact transmembrane proteins, we foresee the developed solvents being useful to efficiently identify membrane composition inhomogeneities and lipid binding caused by the presence of membrane proteins.

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Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States). National Energy Research Scientific Computing Center (NERSC)

Sponsoring Organization:: USDOE National Nuclear Security Administration (NNSA); National Institutes of Health (NIH)

Grant/Contract Number:: FG02-97ER25308; AC02-05CH11231

OSTI ID:: 1480280

Journal Information:: Journal of Physical Chemistry. B, Condensed Matter, Materials, Surfaces, Interfaces and Biophysical Chemistry, Vol. 121, Issue 15; ISSN 1520-6106

Publisher:: American Chemical SocietyCopyright Statement

Country of Publication:: United States

Language:: English

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Cited by: 12 works

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