Literature DB >> 26853937

Continuum descriptions of membranes and their interaction with proteins: Towards chemically accurate models.

David Argudo1, Neville P Bethel1, Frank V Marcoline1, Michael Grabe2.   

Abstract

Biological membranes deform in response to resident proteins leading to a coupling between membrane shape and protein localization. Additionally, the membrane influences the function of membrane proteins. Here we review contributions to this field from continuum elastic membrane models focusing on the class of models that couple the protein to the membrane. While it has been argued that continuum models cannot reproduce the distortions observed in fully-atomistic molecular dynamics simulations, we suggest that this failure can be overcome by using chemically accurate representations of the protein. We outline our recent advances along these lines with our hybrid continuum-atomistic model, and we show the model is in excellent agreement with fully-atomistic simulations of the nhTMEM16 lipid scramblase. We believe that the speed and accuracy of continuum-atomistic methodologies will make it possible to simulate large scale, slow biological processes, such as membrane morphological changes, that are currently beyond the scope of other computational approaches. This article is part of a Special Issue entitled: Membrane Proteins edited by J.C. Gumbart and Sergei Noskov.
Copyright © 2016 Elsevier B.V. All rights reserved.

Entities:  

Keywords:  Bilayer; Biological membrane; Electrostatics; Hydrophobic mismatch; Transmembrane protein

Mesh:

Substances:

Year:  2016        PMID: 26853937      PMCID: PMC4877259          DOI: 10.1016/j.bbamem.2016.02.003

Source DB:  PubMed          Journal:  Biochim Biophys Acta        ISSN: 0006-3002


  132 in total

Review 1.  How proteins produce cellular membrane curvature.

Authors:  Joshua Zimmerberg; Michael M Kozlov
Journal:  Nat Rev Mol Cell Biol       Date:  2006-01       Impact factor: 94.444

2.  The BAR domain superfamily: membrane-molding macromolecules.

Authors:  Adam Frost; Vinzenz M Unger; Pietro De Camilli
Journal:  Cell       Date:  2009-04-17       Impact factor: 41.582

3.  Continuum approaches to understanding ion and peptide interactions with the membrane.

Authors:  Naomi R Latorraca; Keith M Callenberg; Jon P Boyle; Michael Grabe
Journal:  J Membr Biol       Date:  2014-03-21       Impact factor: 1.843

4.  Mixed fluid bilayers: Effects of confinement.

Authors: 
Journal:  Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Topics       Date:  1994-10

5.  A comparison of coarse-grained and continuum models for membrane bending in lipid bilayer fusion pores.

Authors:  Jejoong Yoo; Meyer B Jackson; Qiang Cui
Journal:  Biophys J       Date:  2013-02-19       Impact factor: 4.033

6.  Dynamic sorting of lipids and proteins in membrane tubes with a moving phase boundary.

Authors:  Michael Heinrich; Aiwei Tian; Cinzia Esposito; Tobias Baumgart
Journal:  Proc Natl Acad Sci U S A       Date:  2010-04-05       Impact factor: 11.205

7.  A novel method for measuring the bending rigidity of model lipid membranes by simulating tethers.

Authors:  Vagelis A Harmandaris; Markus Deserno
Journal:  J Chem Phys       Date:  2006-11-28       Impact factor: 3.488

8.  Theoretical analysis of hydrophobic matching and membrane-mediated interactions in lipid bilayers containing gramicidin.

Authors:  T A Harroun; W T Heller; T M Weiss; L Yang; H W Huang
Journal:  Biophys J       Date:  1999-06       Impact factor: 4.033

9.  Three-dimensional stress field around a membrane protein: atomistic and coarse-grained simulation analysis of gramicidin A.

Authors:  Jejoong Yoo; Qiang Cui
Journal:  Biophys J       Date:  2013-01-08       Impact factor: 4.033

10.  A continuum method for determining membrane protein insertion energies and the problem of charged residues.

Authors:  Seungho Choe; Karen A Hecht; Michael Grabe
Journal:  J Gen Physiol       Date:  2008-05-12       Impact factor: 4.086

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  15 in total

1.  Atomistic insight into lipid translocation by a TMEM16 scramblase.

Authors:  Neville P Bethel; Michael Grabe
Journal:  Proc Natl Acad Sci U S A       Date:  2016-11-21       Impact factor: 11.205

2.  New Continuum Approaches for Determining Protein-Induced Membrane Deformations.

Authors:  David Argudo; Neville P Bethel; Frank V Marcoline; Charles W Wolgemuth; Michael Grabe
Journal:  Biophys J       Date:  2017-05-23       Impact factor: 4.033

3.  A Membrane Burial Potential with H-Bonds and Applications to Curved Membranes and Fast Simulations.

Authors:  Zongan Wang; John M Jumper; Sheng Wang; Karl F Freed; Tobin R Sosnick
Journal:  Biophys J       Date:  2018-10-23       Impact factor: 4.033

4.  Characterization of Lipid-Protein Interactions and Lipid-Mediated Modulation of Membrane Protein Function through Molecular Simulation.

Authors:  Melanie P Muller; Tao Jiang; Chang Sun; Muyun Lihan; Shashank Pant; Paween Mahinthichaichan; Anda Trifan; Emad Tajkhorshid
Journal:  Chem Rev       Date:  2019-04-12       Impact factor: 60.622

Review 5.  Molecular simulations of cellular processes.

Authors:  Fabio Trovato; Giordano Fumagalli
Journal:  Biophys Rev       Date:  2017-11-28

6.  Emerging Diversity in Lipid-Protein Interactions.

Authors:  Valentina Corradi; Besian I Sejdiu; Haydee Mesa-Galloso; Haleh Abdizadeh; Sergei Yu Noskov; Siewert J Marrink; D Peter Tieleman
Journal:  Chem Rev       Date:  2019-02-13       Impact factor: 60.622

7.  Gramicidin A Channel Formation Induces Local Lipid Redistribution II: A 3D Continuum Elastic Model.

Authors:  Alexander J Sodt; Andrew H Beaven; Olaf S Andersen; Wonpil Im; Richard W Pastor
Journal:  Biophys J       Date:  2017-03-28       Impact factor: 4.033

Review 8.  Continuum Electrostatics Approaches to Calculating pKas and Ems in Proteins.

Authors:  M R Gunner; N A Baker
Journal:  Methods Enzymol       Date:  2016-06-20       Impact factor: 1.600

Review 9.  The Role of the Membrane in Transporter Folding and Activity.

Authors:  Melanie Ernst; Janice L Robertson
Journal:  J Mol Biol       Date:  2021-06-15       Impact factor: 6.151

Review 10.  The Mechanics and Thermodynamics of Tubule Formation in Biological Membranes.

Authors:  Arijit Mahapatra; Can Uysalel; Padmini Rangamani
Journal:  J Membr Biol       Date:  2021-01-19       Impact factor: 2.426

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