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Molecular Dynamics Simulations of a Membrane Protein/Amphipol Complex

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Abstract

Amphipathic polymers known as “amphipols” provide a highly stabilizing environment for handling membrane proteins in aqueous solutions. A8-35, an amphipol with a polyacrylate backbone and hydrophobic grafts, has been extensively characterized and widely employed for structural and functional studies of membrane proteins using biochemical and biophysical approaches. Given the sensitivity of membrane proteins to their environment, it is important to examine what effects amphipols may have on the structure and dynamics of the proteins they complex. Here we present the first molecular dynamics study of an amphipol-stabilized membrane protein, using Escherichia coli OmpX as a model. We begin by describing the structure of the complexes formed by supplementing OmpX with increasing amounts of A8-35, in order to determine how the amphipol interacts with the transmembrane and extramembrane surfaces of the protein. We then compare the dynamics of the protein in either A8-35, a detergent, or a lipid bilayer. We find that protein dynamics on all accessible length scales is restrained by A8-35, which provides a basis to understanding some of the stabilizing and functional effects of amphipols that have been experimentally observed.

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Abbreviations

2D:

Two-dimensional

A8-35:

A poly(sodium acrylate)-based amphipol comprising ~35 % of free carboxylates, ~25 % of octyl chains, ~40 % of isopropyl groups

APol:

Amphipol

CG:

Coarse-grain

DDM:

n-Dodecyl-β-d-maltopyranoside

DHPC:

Dihexanoylphosphatidylcholine

DOPC:

Dioleoylphosphatidylcholine

EM:

Electron microscopy

FWHM:

Full width at half-maximum

MD:

Molecular dynamics

MP:

Membrane protein

OmpX:

Outer membrane protein X from Escherichia coli

PCA:

Principal component analysis

RCG:

Reverse coarse-grain

RMSF:

Root mean squared fluctuations

SERCA1a:

The fast twitch sarcoplasmic calcium pump

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Acknowledgments

Particular thanks are due to L. J. Catoire, M. Tehei, and G. Zaccai for discussions about the manuscript, as well as to a referee for useful comments. Computational resources were provided by the Minnesota Supercomputing Institute (MSI). This work was also supported by the French Centre National de la Recherche Scientifique.

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Authors and Affiliations

  1. Department of Physics, Brandeis University, 415 South Street, Waltham, MA, 02453, USA

    Jason D. Perlmutter

  2. Laboratoire de Biologie Physico-Chimique des Protéines Membranaires, UMR 7099, CNRS/Université Paris 7, Institut de Biologie Physico-Chimique (FRC 550), 13 rue Pierre et Marie Curie, 75005, Paris, France

    Jean-Luc Popot

  3. Department of Biomedical Engineering, University of Minnesota, 312 Church Street SE, Minneapolis, MN, 55455, USA

    Jonathan N. Sachs

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  1. Jason D. Perlmutter
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Correspondence to Jason D. Perlmutter.

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Perlmutter, J.D., Popot, JL. & Sachs, J.N. Molecular Dynamics Simulations of a Membrane Protein/Amphipol Complex. J Membrane Biol 247, 883–895 (2014). https://doi.org/10.1007/s00232-014-9690-8

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