Membrane-Protein Interactions in a Generic Coarse-Grained Model for Lipid Bilayers

West B, Brown FLH, Schmid F (2009)
Biophysical Journal 96(1): 101-115.

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DOI
Autor*in
West, BeateUniBi; Brown, Frank L. H.; Schmid, Friederike
Einrichtung
Fakultät für Physik
SFB 613 Physik von Einzelmolekülprozessen/mol.Erkennung in organ.Sys.
Abstract / Bemerkung
We study membrane-protein interactions and membrane-mediated protein-protein interactions by Monte Carlo simulations of a generic coarse-grained model for lipid bilayers with cylindrical hydrophobic inclusions. The strength of the hydrophobic force and the hydrophobic thickness of the proteins are systematically varied. The results are compared with analytical predictions of two popular analytical theories: The Landau-de Gennes theory and the elastic theory. The elastic theory provides an excellent description of the fluctuation spectra of pure membranes and successfully reproduces the deformation profiles of membranes around single proteins. However, its prediction for the potential of mean force between proteins is not compatible with the simulation data for large distances. The simulations show that the lipid-mediated interactions are governed by five competing factors: direct interactions; lipid-induced depletion interactions; lipid bridging; lipid packing; and a smooth long-range contribution. The mechanisms leading to hydrophobic mismatch interactions are critically analyzed.
Erscheinungsjahr
2009
Zeitschriftentitel
Biophysical Journal
Band
96
Ausgabe
1
Seite(n)
101-115
ISSN
0006-3495
Page URI
https://pub.uni-bielefeld.de/record/1633781

Zitieren

West B, Brown FLH, Schmid F. Membrane-Protein Interactions in a Generic Coarse-Grained Model for Lipid Bilayers. Biophysical Journal. 2009;96(1):101-115.
West, B., Brown, F. L. H., & Schmid, F. (2009). Membrane-Protein Interactions in a Generic Coarse-Grained Model for Lipid Bilayers. Biophysical Journal, 96(1), 101-115. https://doi.org/10.1529/biophysj.108.138677
West, Beate, Brown, Frank L. H., and Schmid, Friederike. 2009. “Membrane-Protein Interactions in a Generic Coarse-Grained Model for Lipid Bilayers”. Biophysical Journal 96 (1): 101-115.
West, B., Brown, F. L. H., and Schmid, F. (2009). Membrane-Protein Interactions in a Generic Coarse-Grained Model for Lipid Bilayers. Biophysical Journal 96, 101-115.
West, B., Brown, F.L.H., & Schmid, F., 2009. Membrane-Protein Interactions in a Generic Coarse-Grained Model for Lipid Bilayers. Biophysical Journal, 96(1), p 101-115.
B. West, F.L.H. Brown, and F. Schmid, “Membrane-Protein Interactions in a Generic Coarse-Grained Model for Lipid Bilayers”, Biophysical Journal, vol. 96, 2009, pp. 101-115.
West, B., Brown, F.L.H., Schmid, F.: Membrane-Protein Interactions in a Generic Coarse-Grained Model for Lipid Bilayers. Biophysical Journal. 96, 101-115 (2009).
West, Beate, Brown, Frank L. H., and Schmid, Friederike. “Membrane-Protein Interactions in a Generic Coarse-Grained Model for Lipid Bilayers”. Biophysical Journal 96.1 (2009): 101-115.

38 Zitationen in Europe PMC

Daten bereitgestellt von Europe PubMed Central.

Membrane-Mediated Cooperativity of Proteins.
Weikl TR., Annu Rev Phys Chem 69(), 2018
PMID: 29490203
Directed Supramolecular Organization of N-BAR Proteins through Regulation of H0 Membrane Immersion Depth.
Kahraman O, Langen R, Haselwandter CA., Sci Rep 8(1), 2018
PMID: 30401832
Hydrodynamics of bilayer membranes with diffusing transmembrane proteins.
Callan-Jones A, Durand M, Fournier JB., Soft Matter 12(6), 2016
PMID: 26725841
Architecture and Function of Mechanosensitive Membrane Protein Lattices.
Kahraman O, Koch PD, Klug WS, Haselwandter CA., Sci Rep 6(), 2016
PMID: 26771082
Monte Carlo study of the frame, fluctuation and internal tensions of fluctuating membranes with fixed area.
Shiba H, Noguchi H, Fournier JB., Soft Matter 12(8), 2016
PMID: 26796575
Curvature correction to the mobility of fluid membrane inclusions.
Daniels DR., Eur Phys J E Soft Matter 39(10), 2016
PMID: 27771858
Mechanics of membrane fusion/pore formation.
Fuhrmans M, Marelli G, Smirnova YG, Müller M., Chem Phys Lipids 185(), 2015
PMID: 25087882
A hybrid molecular dynamics/fluctuating hydrodynamics method for modelling liquids at multiple scales in space and time.
Korotkin I, Karabasov S, Nerukh D, Markesteijn A, Scukins A, Farafonov V, Pavlov E., J Chem Phys 143(1), 2015
PMID: 26156468
Multiscale modelling to understand the self-assembly mechanism of human β2-adrenergic receptor in lipid bilayer.
Ghosh A, Sonavane U, Joshi R., Comput Biol Chem 48(), 2014
PMID: 24291490
More than the sum of its parts: coarse-grained peptide-lipid interactions from a simple cross-parametrization.
Bereau T, Wang ZJ, Deserno M., J Chem Phys 140(11), 2014
PMID: 24655203
Poisson's Ratio and Young's Modulus of Lipid Bilayers in Different Phases.
Jadidi T, Seyyed-Allaei H, Tabar MR, Mashaghi A., Front Bioeng Biotechnol 2(), 2014
PMID: 25152882
Effect of hydrophobic mismatch on domain formation and peptide sorting in the multicomponent lipid bilayers in the presence of immobilized peptides.
Liang Q, Wu QY, Wang ZY., J Chem Phys 141(7), 2014
PMID: 25149801
Phase behaviors and membrane properties of model liposomes: temperature effect.
Wu HL, Sheng YJ, Tsao HK., J Chem Phys 141(12), 2014
PMID: 25273473
A polarizable coarse-grained water model for dissipative particle dynamics.
Peter EK, Pivkin IV., J Chem Phys 141(16), 2014
PMID: 25362324
The role of membrane-mediated interactions in the assembly and architecture of chemoreceptor lattices.
Haselwandter CA, Wingreen NS., PLoS Comput Biol 10(12), 2014
PMID: 25503274
Effect of capsid confinement on the chromatin organization of the SV40 minichromosome.
Saper G, Kler S, Asor R, Oppenheim A, Raviv U, Harries D., Nucleic Acids Res 41(3), 2013
PMID: 23258701
Coarse-grained computer simulation of dynamics in thylakoid membranes: methods and opportunities.
Schneider AR, Geissler PL., Front Plant Sci 4(), 2013
PMID: 24478781
Coarse-Grained Models for Protein-Cell Membrane Interactions.
Bradley R, Radhakrishnan R., Polymers (Basel) 5(3), 2013
PMID: 26613047
The shape and free energy of a lipid bilayer surrounding a membrane inclusion.
Tjörnhammar R, Edholm O., Chem Phys Lipids 169(), 2013
PMID: 23333873
Directional interactions and cooperativity between mechanosensitive membrane proteins.
Haselwandter CA, Phillips R., Europhys Lett 101(6), 2013
PMID: 25309021
Monolayer curvature stabilizes nanoscale raft domains in mixed lipid bilayers.
Meinhardt S, Vink RL, Schmid F., Proc Natl Acad Sci U S A 110(12), 2013
PMID: 23487780
Limited perturbation of a DPPC bilayer by fluorescent lipid probes: a molecular dynamics study.
Ackerman DG, Heberle FA, Feigenson GW., J Phys Chem B 117(17), 2013
PMID: 23548205
Thermal fluctuations in shape, thickness, and molecular orientation in lipid bilayers. II. Finite surface tensions.
Watson MC, Morriss-Andrews A, Welch PM, Brown FL., J Chem Phys 139(8), 2013
PMID: 24007028
Thermal fluctuations and bending rigidity of bilayer membranes.
Tarazona P, Chacón E, Bresme F., J Chem Phys 139(9), 2013
PMID: 24028128
Hierarchical Order Parameters for Macromolecular Assembly Simulations I: Construction and Dynamical Properties of Order Parameters.
Singharoy A, Sereda Y, Ortoleva PJ., J Chem Theory Comput 8(4), 2012
PMID: 22661911
Bilayer elasticity at the nanoscale: the need for new terms.
Bitbol AF, Constantin D, Fournier JB., PLoS One 7(11), 2012
PMID: 23144862
A generic force field for protein coarse-grained molecular dynamics simulation.
Gu J, Bai F, Li H, Wang X., Int J Mol Sci 13(11), 2012
PMID: 23203075
Solvent-free coarse-grained lipid model for large-scale simulations.
Noguchi H., J Chem Phys 134(5), 2011
PMID: 21303161
Modeling the release kinetics of poorly water-soluble drug molecules from liposomal nanocarriers.
Loew S, Fahr A, May S., J Drug Deliv 2011(), 2011
PMID: 21773045
Continuum simulations of biomembrane dynamics and the importance of hydrodynamic effects.
Brown FL., Q Rev Biophys 44(4), 2011
PMID: 21729348
Quantitative modeling of membrane deformations by multihelical membrane proteins: application to G-protein coupled receptors.
Mondal S, Khelashvili G, Shan J, Andersen OS, Weinstein H., Biophys J 101(9), 2011
PMID: 22067146
Thermal fluctuations in shape, thickness, and molecular orientation in lipid bilayers.
Watson MC, Penev ES, Welch PM, Brown FL., J Chem Phys 135(24), 2011
PMID: 22225175
Multiscale simulation of protein mediated membrane remodeling.
Ayton GS, Voth GA., Semin Cell Dev Biol 21(4), 2010
PMID: 19922811
Lipid membranes with transmembrane proteins in shear flow.
Khoshnood A, Noguchi H, Gompper G., J Chem Phys 132(2), 2010
PMID: 20095714
Coarse-grained simulations of membranes under tension.
Neder J, West B, Nielaba P, Schmid F., J Chem Phys 132(11), 2010
PMID: 20331316
Molecular simulation of the effect of cholesterol on lipid-mediated protein-protein interactions.
de Meyer FJ, Rodgers JM, Willems TF, Smit B., Biophys J 99(11), 2010
PMID: 21112287
Toy amphiphiles on the computer: What can we learn from generic models?
Schmid F., Macromol Rapid Commun 30(9-10), 2009
PMID: 21706660
Systematic multiscale simulation of membrane protein systems.
Ayton GS, Voth GA., Curr Opin Struct Biol 19(2), 2009
PMID: 19362465

83 References

Daten bereitgestellt von Europe PubMed Central.

Biomembranes—Molecular Structure and Function
Gennis R.B.., 1989
Developmental clustering of ion channels at and near the node of Ranvier.
Rasband MN, Trimmer JS., Dev. Biol. 236(1), 2001
PMID: 11456440
The effects of bilayer thickness and tension on gramicidin single-channel lifetime.
Elliott JR, Needham D, Dilger JP, Haydon DA., Biochim. Biophys. Acta 735(1), 1983
PMID: 6194820
Curvature and hydrophobic forces drive oligomerization and modulate activity of rhodopsin in membranes.
Botelho AV, Huber T, Sakmar TP, Brown MF., Biophys. J. 91(12), 2006
PMID: 17012328
Models of lipid-protein interactions in membranes.
Mouritsen OG, Bloom M., Annu Rev Biophys Biomol Struct 22(), 1993
PMID: 8347987
Theoretical analysis of protein organization in lipid membranes
Gil T., Ipsen J.H., Mouritsen O.G., Sabra M.C., Sperotto M.M.., 1998
Modelling of proteins in membranes.
Sperotto MM, May S, Baumgaertner A., Chem. Phys. Lipids 141(1-2), 2006
PMID: 16620797
The state of lipid rafts: from model membranes to cells.
Edidin M., Annu Rev Biophys Biomol Struct 32(), 2003
PMID: 12543707
Physical properties of the fluid lipid-bilayer component of cell membranes: a perspective.
Bloom M, Evans E, Mouritsen OG., Q. Rev. Biophys. 24(3), 1991
PMID: 1749824
Hydrophobic mismatch between proteins and lipids in membranes
Killian J.A.., 1998
Is the protein/lipid hydrophobic matching principle relevant to membrane organization and functions?
Dumas F, Lebrun MC, Tocanne JF., FEBS Lett. 458(3), 1999
PMID: 10570923
Experimental evidence for hydrophobic matching and membrane-mediated interactions in lipid bilayers containing gramicidin.
Harroun TA, Heller WT, Weiss TM, Yang L, Huang HW., Biophys. J. 76(2), 1999
PMID: 9929495
Organization of model helical peptides in lipid bilayers: insight into the behavior of single-span protein transmembrane domains.
Sharpe S, Barber KR, Grant CW, Goodyear D, Morrow MR., Biophys. J. 83(1), 2002
PMID: 12080125
Protein-lipid interactions studied with designed transmembrane peptides: role of hydrophobic matching and interfacial anchoring
De M.R.R., Killian J.A.., 2003
Theoretical study of protein--lipid interactions in bilayer membranes.
Owicki JC, Springgate MW, McConnell HM., Proc. Natl. Acad. Sci. U.S.A. 75(4), 1978
PMID: 273895
Theory of protein-lipid and protein-protein interactions in bilayer membranes.
Owicki JC, McConnell HM., Proc. Natl. Acad. Sci. U.S.A. 76(10), 1979
PMID: 291895
Lipids do influence protein function-the hydrophobic matching hypothesis revisited.
Jensen MO, Mouritsen OG., Biochim. Biophys. Acta 1666(1-2), 2004
PMID: 15519316
Mattress model of lipid-protein interactions in membranes.
Mouritsen OG, Bloom M., Biophys. J. 46(2), 1984
PMID: 6478029
A molecular model for lipid-protein interaction in membranes: the role of hydrophobic mismatch.
Fattal DR, Ben-Shaul A., Biophys. J. 65(5), 1993
PMID: 8298013
Lipid chain packing and lipid-protein interaction in membranes
Fattal D.R., Ben-Shaul A.., 1995
Stresses in lipid membranes and interactions between inclusions
Kralchevski P.A., Paunov V.N., Denkov N.D., Nagayama K.., 1995
Interaction between two cylindrical inclusions in a symmetric lipid bilayer
Bohinc K., Kralj-Iglic V., May S.., 2003
Deformation free energy of bilayer membrane and its effect on gramicidin channel lifetime.
Huang HW., Biophys. J. 50(6), 1986
PMID: 2432948
Elasticity of lipid bilayer interacting with amphiphilic helical peptides
Huang H.W.., 1995
Theoretical analysis of hydrophobic matching and membrane-mediated interactions in lipid bilayers containing gramicidin.
Harroun TA, Heller WT, Weiss TM, Yang L, Huang HW., Biophys. J. 76(6), 1999
PMID: 10354442
Energetics of inclusion-induced bilayer deformations.
Nielsen C, Goulian M, Andersen OS., Biophys. J. 74(4), 1998
PMID: 9545056
Inclusion-induced bilayer deformations: effects of monolayer equilibrium curvature.
Nielsen C, Andersen OS., Biophys. J. 79(5), 2000
PMID: 11053132
Membrane induced interactions between inclusions
Dan N., Pincus P., Safran S.A.., 1993
Membrane induced interactions between inclusions
Dan N., Berman A., Pincus P., Safran S.A.., 1994
Interaction between inclusions embedded in membranes.
Aranda-Espinoza H, Berman A, Dan N, Pincus P, Safran S., Biophys. J. 71(2), 1996
PMID: 8842204
A consistent model for thermal fluctuations and protein-induced deformations in lipid bilayers.
Brannigan G, Brown FL., Biophys. J. 90(5), 2005
PMID: 16326916
Contributions of Gaussian curvature and nonconstant lipid volume to protein deformation of lipid bilayers.
Brannigan G, Brown FL., Biophys. J. 92(3), 2006
PMID: 17098794
Influence of hydrophobic mismatch and palmitoylation on the association of transmembrane alpha-helical peptides with detergent-resistant membranes.
van Duyl BY, Rijkers DT, de Kruijff B, Killian JA., FEBS Lett. 523(1-3), 2002
PMID: 12123808
Interfacial anchor properties of tryptophan residues in transmembrane peptides can dominate over hydrophobic matching effects in peptide-lipid interactions.
de Planque MR, Bonev BB, Demmers JA, Greathouse DV, Koeppe RE 2nd, Separovic F, Watts A, Killian JA., Biochemistry 42(18), 2003
PMID: 12731875
Statistical thermodynamic analysis of peptide and protein insertion into lipid membranes.
Ben-Shaul A, Ben-Tal N, Honig B., Biophys. J. 71(1), 1996
PMID: 8804596
Protein inclusion in lipid membranes: a theory based on the hypernetted chain integral equation.
Lague P, Zuckermann MJ, Roux B., Faraday Discuss. (111), 1998
PMID: 10822607
Lipid-mediated interactions between intrinsic membrane proteins: a theoretical study based on integral equations.
Lague P, Zuckermann MJ, Roux B., Biophys. J. 79(6), 2000
PMID: 11106595
Lipid-mediated interactions between intrinsic membrane proteins: dependence on protein size and lipid composition.
Lague P, Zuckermann MJ, Roux B., Biophys. J. 81(1), 2001
PMID: 11423413
A molecular model for lipid-mediated interaction between proteins in membranes
May S., Ben-Shaul A.., 2000
Protein-membrane interaction: effect of myelin basic protein on the dynamics of oriented lipids
Natali F., Relini A., Gliozzi A., Rolandi R., Cavatorta P.., 2003
Orientation and lipid-peptide interactions of gramicidin A in lipid membranes: polarized attenuated total reflection infrared spectroscopy and spin-label electron spin resonance.
Kota Z, Pali T, Marsh D., Biophys. J. 86(3), 2004
PMID: 14990479
Theories on structural perturbations of lipid bilayers
May S.., 2000
Long-range forces in heterogeneous fluid membranes
Goulian M., Bruinsma R., Pincus P.., 1993
Inhomogeneous fluid membranes: Segregation, ordering, and effective rigidity.
Netz RR, Pincus P., Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Topics 52(4), 1995
PMID: 9963884
Fluctuation-induced interactions between rods on membranes and interfaces
Golestanian R., Goulian M., Kardar M.., 1996
Fluctuation-induced aggregation of rigid membrane inclusions
Weikl T.R.., 2001
Aggregation and vesiculation of membrane proteins by curvature-mediated interactions.
Reynwar BJ, Illya G, Harmandaris VA, Muller MM, Kremer K, Deserno M., Nature 447(7143), 2007
PMID: 17522680
Microscopic membrane elasticity and interactions among membrane inclusions: interplay between the shape, dilation, tilt and tilt-difference modes
Fournier J.-B.., 1999
Structure of symmetric and asymmetric "ripple" phases in lipid bilayers.
Lenz O, Schmid F., Phys. Rev. Lett. 98(5), 2007
PMID: 17358906
Peptides and proteins in membranes: what can we learn via computer simulations?
Efremov RG, Nolde DE, Konshina AG, Syrtcev NP, Arseniev AS., Curr. Med. Chem. 11(18), 2004
PMID: 15379706
Molecular simulations of lipid-mediated protein-protein interactions.
de Meyer FJ, Venturoli M, Smit B., Biophys. J. 95(4), 2008
PMID: 18487292
Protein attraction in membranes induced by lipid fluctuations.
Sintes T, Baumgartner A., Biophys. J. 73(5), 1997
PMID: 9370422
Coarse-grained transmembrane proteins: hydrophobic matching, aggregation, and their effect on fusion.
Smeijers AF, Pieterse K, Markvoort AJ, Hilbers PA., J Phys Chem B 110(27), 2006
PMID: 16821889
The MARTINI force field: coarse grained model for biomolecular simulations.
Marrink SJ, Risselada HJ, Yefimov S, Tieleman DP, de Vries AH., J Phys Chem B 111(27), 2007
PMID: 17569554
A generic model for lipid monolayers, bilayers, and membranes
Schmid F., Düchs D., Lenz O., West B.., 2007
Short grafted chains: Monte Carlo simulations of a model for monolayers of amphiphiles
Stadler C., Lange H., Schmid F.., 1999
Phase behavior of amphiphilic monolayers: theory and simulations
Düchs D., Schmid F.., 2001
A simple computer model for liquid lipid bilayers
Lenz O., Schmid F.., 2005

AUTHOR UNKNOWN, 0
Monte Carlo simulation studies of lipid order parameter profiles near integral membrane proteins.
Sperotto MM, Mouritsen OG., Biophys. J. 59(2), 1991
PMID: 2009352
Simulation studies of protein-induced bilayer deformations, and lipid-induced protein tilting, on a mesoscopic model for lipid bilayers with embedded proteins.
Venturoli M, Smit B, Sperotto MM., Biophys. J. 88(3), 2005
PMID: 15738466

AUTHOR UNKNOWN, 0
Calculation of deformation energies and conformations in lipid membranes containing gramicidin channels.
Helfrich P, Jakobsson E., Biophys. J. 57(5), 1990
PMID: 1692748

AUTHOR UNKNOWN, 0

AUTHOR UNKNOWN, 0
Coupling between membrane tilt-difference and dilation: a new “ripple” instability and multiple crystalline inclusions phases
Fournier J.-B.., 1998
Influence of rigid inclusions on the bending elasticity of a lipid membrane.
Fosnaric M, Iglic A, May S., Phys Rev E Stat Nonlin Soft Matter Phys 74(5 Pt 1), 2006
PMID: 17279913
Conformational chain statistics in a model lipid bilayer: comparison between mean field and Monte Carlo calculations
Harries D., Ben-Shaul A.., 1997
Mobility and elasticity of self-assembled membranes
Goetz R., Gompper G., Lipowsky R.., 1999
Mesoscopic undulations and thickness fluctuations in lipid bilayers from molecular dynamics simulations.
Lindahl E, Edholm O., Biophys. J. 79(1), 2000
PMID: 10866968
Effect of undulations on surface tension in simulated bilayers
Marrink S.J., Mark A.E.., 2001
Thermal fluctuations in a lamellar phase of a binary amphiphile-solvent mixture: a molecular-dynamics study
Loison C., Mareschal M., Kremer K., Schmid F.., 2003
Statistical Thermodynamics of Surfaces, Interfaces, and Membranes
Safran S.A.., 1994
The statistical mechanical theory of transport processes. IV. The equations of hydrodynamics
Irving J.H., Kirkwood J.G.., 1950
Computer simulations of bilayer membranes: self-assembly and interfacial tension
Goetz R., Lipowsky R.., 1998
Spatial and energetic-entropic decomposition of surface tension in lipid bilayers from molecular dynamics simulations
Lindahl E., Edholm O.., 2000

AUTHOR UNKNOWN, 0

AUTHOR UNKNOWN, 0
Elastic curvature constants of lipid monolayers and bilayers.
Marsh D., Chem. Phys. Lipids 144(2), 2006
PMID: 17045578
Molecular dynamics simulations of rhodopsin in different one-component lipid bilayers.
Cordomi A, Perez JJ., J Phys Chem B 111(25), 2007
PMID: 17530884
Phase behavior and induced interdigitation in bilayers studied with dissipative particle dynamics
Kranenburg M., Venturoli M., Smit B.., 2003

AUTHOR UNKNOWN, 0
Liquid phases of Langmuir monolayers
Schmid F., Schick M.., 1995
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