The Journal of Membrane Biology

, Volume 247, Issue 9–10, pp 883–895 | Cite as

Molecular Dynamics Simulations of a Membrane Protein/Amphipol Complex

  • Jason D. Perlmutter
  • Jean-Luc Popot
  • Jonathan N. Sachs
Article

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.

Keywords

OmpX A8-35 Surfactants Dynamics 

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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Copyright information

© Springer Science+Business Media New York 2014

Authors and Affiliations

  • Jason D. Perlmutter
    • 1
  • Jean-Luc Popot
    • 2
  • Jonathan N. Sachs
    • 3
  1. 1.Department of PhysicsBrandeis UniversityWalthamUSA
  2. 2.Laboratoire de Biologie Physico-Chimique des Protéines MembranairesUMR 7099, CNRS/Université Paris 7, Institut de Biologie Physico-Chimique (FRC 550)ParisFrance
  3. 3.Department of Biomedical EngineeringUniversity of MinnesotaMinneapolisUSA

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