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


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.


OmpX A8-35 Surfactants Dynamics 





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












Electron microscopy


Full width at half-maximum


Molecular dynamics


Membrane protein


Outer membrane protein X from Escherichia coli


Principal component analysis


Reverse coarse-grain


Root mean squared fluctuations


The fast twitch sarcoplasmic calcium pump


  1. Althoff T, Mills DJ, Popot J-L, Kühlbrandt W (2011) Arrangement of electron transport chain components in bovine mitochondrial supercomplex I1III2IV1. EMBO J 30:4652–4664CrossRefPubMedPubMedCentralGoogle Scholar
  2. Böckmann RA, Caflisch A (2005) Spontaneous formation of detergent micelles around the outer membrane protein OmpX. Biophys J 88:3191–3204CrossRefPubMedPubMedCentralGoogle Scholar
  3. Catoire LJ, Zoonens M, van Heijenoort C et al (2009) Inter- and intramolecular contacts in a membrane protein/surfactant complex observed by heteronuclear dipole-to-dipole cross-relaxation. J Magn Reson 197:91–95CrossRefPubMedGoogle Scholar
  4. Catoire LJ, Zoonens M, van Heijenoort C et al (2010) Solution NMR mapping of water-accessible residues in the transmembrane beta-barrel of OmpX. Eur Biophys J 39:623–630CrossRefPubMedGoogle Scholar
  5. Champeil P, Menguy T, Tribet C et al (2000) Interaction of amphipols with sarcoplasmic reticulum Ca2+-ATPase. J Biol Chem 275:18623–18637CrossRefPubMedGoogle Scholar
  6. Charvolin D, Picard M, Huang L-S, et al. (2014) Solution behavior and crystallization of cytochrome bc1 in the presence of amphipols. J Membrane Biol. doi:10.1007/s00232-014-9694-4
  7. Choutko A, Glättli A, Fernández C et al (2011) Membrane protein dynamics in different environments: simulation study of the outer membrane protein X in a lipid bilayer and in a micelle. Eur Biophys J 40:39–58CrossRefPubMedGoogle Scholar
  8. Dahmane T, Rappaport F, Popot J-L (2013) Amphipol-assisted folding of bacteriorhodopsin in the presence or absence of lipids: functional consequences. Eur Biophys J 42:85–101CrossRefPubMedGoogle Scholar
  9. Etzkorn M, Zoonens M, Catoire LJ et al (2014) How amphipols embed membrane proteins: global solvent accessibility and interaction with a flexible protein terminus. J Membr Biol. doi:10.1007/s00232-014-9657-9
  10. Fernández C, Adeishvili K, Wüthrich K (2001) Transverse relaxation-optimized NMR spectroscopy with the outer membrane protein OmpX in dihexanoyl phosphatidylcholine micelles. Proc Natl Acad Sci USA 98:2358–2363CrossRefPubMedPubMedCentralGoogle Scholar
  11. Giusti F, Popot J-L, Tribet C (2012) Well-defined critical association concentration and rapid adsorption at the air/water interface of a short amphiphilic polymer, amphipol A8-35: a study by Förster resonance energy transfer and dynamic surface tension measurements. Langmuir 28:10372–10380CrossRefPubMedGoogle Scholar
  12. Giusti F, Rieger J, Catoire LJ et al (2014) Synthesis, characterization and applications of a perdeuterated amphipol. J Membr Biol. doi: 10.1007/s00232-014-9656-x
  13. Gohon Y, Pavlov G, Timmins P et al (2004) Partial specific volume and solvent interactions of amphipol A8-35. Anal Biochem 334:318–334CrossRefPubMedGoogle Scholar
  14. Gohon Y, Giusti F, Prata C et al (2006) Well-defined nanoparticles formed by hydrophobic assembly of a short and polydisperse random terpolymer, amphipol A8-35. Langmuir 22:1281–1290CrossRefPubMedGoogle Scholar
  15. Gohon Y, Dahmane T, Ruigrok RWH et al (2008) Bacteriorhodopsin/amphipol complexes: structural and functional properties. Biophys J 94:3523–3537CrossRefPubMedPubMedCentralGoogle Scholar
  16. Hagn F, Etzkorn M, Raschle T, Wagner G (2013) Optimized phospholipid bilayer nanodiscs facilitate high-resolution structure determination of membrane proteins. J Am Chem Soc 135:1919–1925. doi:10.1021/ja310901f CrossRefPubMedPubMedCentralGoogle Scholar
  17. Hess B, Kutzner C, van der Spoel D, Lindahl E (2008) GROMACS 4: algorithms for highly efficient, load-balanced, and scalable molecular simulation. J Chem Theory Comput 4:435–447CrossRefPubMedGoogle Scholar
  18. Humphrey W, Dalke A, Schulten K (1996) VMD: visual molecular dynamics. J Mol Graph 14:33–38CrossRefPubMedGoogle Scholar
  19. Huynh KW, Cohen MR, Moiseenkova-Bell VY (2014) Application of amphipols for structure-functional analysis of TRP channels. J Membr Biol. doi:10.1007/s00232-014-9684-6
  20. Kim PS, Baldwin RL (1982) Influence of charge on the rate of amide proton exchange. Biochemistry (Mosc) 21:1–5. doi:10.1021/bi00530a001 CrossRefGoogle Scholar
  21. Kyte J, Doolittle RF (1982) A simple method for displaying the hydropathic character of a protein. J Mol Biol 157:105–132CrossRefPubMedGoogle Scholar
  22. Liao M, Cao E, Julius D, Cheng Y (2013) Structure of the TRPV1 ion channel determined by electron cryo-microscopy. Nature 504:107–112CrossRefPubMedPubMedCentralGoogle Scholar
  23. Liao M, Cao E, Julius D, Cheng Y (2014) Single particle electron cryo-microscopy of a mammalian ion channel. Curr Opin Struct Biol 27:1–7. doi:10.1016/ CrossRefPubMedGoogle Scholar
  24. Marrink SJ, Risselada HJ, Yefimov S et al (2007) The MARTINI force field: coarse grained model for biomolecular simulations. J Phys Chem B 111:7812–7824CrossRefPubMedGoogle Scholar
  25. Martinez KL, Gohon Y, Corringer P-J et al (2002) Allosteric transitions of Torpedo acetylcholine receptor in lipids, detergent and amphipols: molecular interactions vs. physical constraints. FEBS Lett 528:251–256CrossRefPubMedGoogle Scholar
  26. Periole X, Cavalli M, Marrink S-J, Ceruso MA (2009) Combining an elastic network with a coarse-grained molecular force field: structure, dynamics, and intermolecular recognition. J Chem Theory Comput 5:2531–2543CrossRefPubMedGoogle Scholar
  27. Perlmutter JD, Drasler WJ II, Xie W et al (2011) All-atom and coarse-grained molecular dynamics simulations of a membrane protein stabilizing polymer. Langmuir 27:10523–10537CrossRefPubMedPubMedCentralGoogle Scholar
  28. Picard M, Dahmane T, Garrigos M et al (2006) Protective and inhibitory effects of various types of amphipols on the Ca2+-ATPase from sarcoplasmic reticulum: a comparative study. Biochemistry 45:1861–1869CrossRefPubMedGoogle Scholar
  29. Planchard N, Point É, Dahmane T et al (2014) The use of amphipols for solution NMR studies of membrane proteins: advantages and constraints as compared to other solubilizing media. J Membr Biol. doi:10.1007/s00232-014-9654-z
  30. Pocanschi CL, Popot J-L, Kleinschmidt JH (2013) Folding and stability of outer membrane protein A (OmpA) from Escherichia coli in an amphipathic polymer, amphipol A8-35. Eur Biophys J 42:103–118CrossRefPubMedGoogle Scholar
  31. Popot J-L (2010) Amphipols, nanodiscs, and fluorinated surfactants: three nonconventional approaches to studying membrane proteins in aqueous solutions. Annu Rev Biochem 79:737–775CrossRefPubMedGoogle Scholar
  32. Popot J-L, Berry EA, Charvolin D et al (2003) Amphipols: polymeric surfactants for membrane biology research. Cell Mol Life Sci 60:1559–1574CrossRefPubMedGoogle Scholar
  33. Popot J-L, Althoff T, Bagnard D et al (2011) Amphipols from A to Z. Annu Rev Biophys 40:379–408CrossRefPubMedGoogle Scholar
  34. Swift J (1726) Travels into several remote nations of the world. In four parts. By Lemuel Gulliver, first a surgeon, and then a captain of several ships. Benjamin Motte, LondonGoogle Scholar
  35. Tehei M, Giusti F, Zaccai G, Popot J-L (2014) Thermal fluctuations in amphipol A8-35 particles measured by neutron scattering. J Membr Biol (under review)Google Scholar
  36. Tribet C, Audebert R, Popot JL (1996) Amphipols: polymers that keep membrane proteins soluble in aqueous solutions. Proc Natl Acad Sci USA 93:15047–15050CrossRefPubMedPubMedCentralGoogle Scholar
  37. Vogt J, Schulz GE (1999) The structure of the outer membrane protein OmpX from Escherichia coli reveals possible mechanisms of virulence. Structure 7:1301–1309CrossRefPubMedGoogle Scholar
  38. Zoonens M, Popot J-L (2014) Amphipols for each season. J Membr Biol. doi:10.1007/s00232-014-9666-8
  39. Zoonens M, Catoire LJ, Giusti F, Popot J-L (2005) NMR study of a membrane protein in detergent-free aqueous solution. Proc Natl Acad Sci USA 102:8893–8898CrossRefPubMedPubMedCentralGoogle Scholar
  40. Zoonens M, Giusti F, Zito F, Popot J-L (2007) Dynamics of membrane protein/amphipol association studied by Förster resonance energy transfer: implications for in vitro studies of amphipol-stabilized membrane proteins. Biochemistry 46:10392–10404CrossRefPubMedGoogle Scholar

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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