Literature DB >> 19362465

Systematic multiscale simulation of membrane protein systems.

Gary S Ayton1, Gregory A Voth.   

Abstract

Current multiscale simulation approaches for membrane protein systems vary depending on their degree of connection to the underlying molecular scale interactions. Various approaches have been developed that include such information into coarse-grained models of both the membrane and the proteins. By contrast, other approaches employ parameterizations obtained from experimental data. Mesoscopic models operate at larger scales and have also been employed to examine membrane remodeling, protein inclusions, and ion channel gating. When bridged together such that molecular-level information is propagated between the different scales, a systematic multiscale methodology for membrane protein systems can be achieved.

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Year:  2009        PMID: 19362465      PMCID: PMC4693605          DOI: 10.1016/j.sbi.2009.03.001

Source DB:  PubMed          Journal:  Curr Opin Struct Biol        ISSN: 0959-440X            Impact factor:   6.809


  48 in total

1.  A consistent model for thermal fluctuations and protein-induced deformations in lipid bilayers.

Authors:  Grace Brannigan; Frank L H Brown
Journal:  Biophys J       Date:  2005-12-02       Impact factor: 4.033

2.  Membrane remodeling from N-BAR domain interactions: insights from multi-scale simulation.

Authors:  Gary S Ayton; Philip D Blood; Gregory A Voth
Journal:  Biophys J       Date:  2007-02-26       Impact factor: 4.033

Review 3.  Multiscale modeling of biomolecular systems: in serial and in parallel.

Authors:  Gary S Ayton; Will G Noid; Gregory A Voth
Journal:  Curr Opin Struct Biol       Date:  2007-03-23       Impact factor: 6.809

4.  Nonequilibrium membrane fluctuations driven by active proteins.

Authors:  Lawrence C-L Lin; Nir Gov; Frank L H Brown
Journal:  J Chem Phys       Date:  2006-02-21       Impact factor: 3.488

5.  The multiscale coarse-graining method. II. Numerical implementation for coarse-grained molecular models.

Authors:  W G Noid; Pu Liu; Yanting Wang; Jhih-Wei Chu; Gary S Ayton; Sergei Izvekov; Hans C Andersen; Gregory A Voth
Journal:  J Chem Phys       Date:  2008-06-28       Impact factor: 3.488

6.  Systematic multiscale parameterization of heterogeneous elastic network models of proteins.

Authors:  Edward Lyman; Jim Pfaendtner; Gregory A Voth
Journal:  Biophys J       Date:  2008-07-25       Impact factor: 4.033

7.  Mixed atomistic and coarse-grained molecular dynamics: simulation of a membrane-bound ion channel.

Authors:  Qiang Shi; Sergei Izvekov; Gregory A Voth
Journal:  J Phys Chem B       Date:  2006-08-10       Impact factor: 2.991

8.  Multiscale coarse-graining and structural correlations: connections to liquid-state theory.

Authors:  W G Noid; Jhih-Wei Chu; Gary S Ayton; Gregory A Voth
Journal:  J Phys Chem B       Date:  2007-03-30       Impact factor: 2.991

9.  The multiscale coarse-graining method. I. A rigorous bridge between atomistic and coarse-grained models.

Authors:  W G Noid; Jhih-Wei Chu; Gary S Ayton; Vinod Krishna; Sergei Izvekov; Gregory A Voth; Avisek Das; Hans C Andersen
Journal:  J Chem Phys       Date:  2008-06-28       Impact factor: 3.488

10.  The interaction of phospholipase A2 with a phospholipid bilayer: coarse-grained molecular dynamics simulations.

Authors:  Chze Ling Wee; Kia Balali-Mood; David Gavaghan; Mark S P Sansom
Journal:  Biophys J       Date:  2008-05-09       Impact factor: 4.033

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  37 in total

1.  Characterizing protein energy landscape by self-learning multiscale simulations: application to a designed β-hairpin.

Authors:  Wenfei Li; Shoji Takada
Journal:  Biophys J       Date:  2010-11-03       Impact factor: 4.033

2.  PRIMO: A Transferable Coarse-grained Force Field for Proteins.

Authors:  Parimal Kar; Srinivasa Murthy Gopal; Yi-Ming Cheng; Alexander Predeus; Michael Feig
Journal:  J Chem Theory Comput       Date:  2013-08-13       Impact factor: 6.006

3.  Protein-mediated transformation of lipid vesicles into tubular networks.

Authors:  Mijo Simunovic; Carsten Mim; Thomas C Marlovits; Guenter Resch; Vinzenz M Unger; Gregory A Voth
Journal:  Biophys J       Date:  2013-08-06       Impact factor: 4.033

Review 4.  Efficient Exploration of Membrane-Associated Phenomena at Atomic Resolution.

Authors:  Josh V Vermaas; Javier L Baylon; Mark J Arcario; Melanie P Muller; Zhe Wu; Taras V Pogorelov; Emad Tajkhorshid
Journal:  J Membr Biol       Date:  2015-05-22       Impact factor: 1.843

Review 5.  Modeling and simulation of ion channels.

Authors:  Christopher Maffeo; Swati Bhattacharya; Jejoong Yoo; David Wells; Aleksei Aksimentiev
Journal:  Chem Rev       Date:  2012-10-04       Impact factor: 60.622

6.  Impact of membrane lipid composition on the structure and stability of the transmembrane domain of amyloid precursor protein.

Authors:  Laura Dominguez; Leigh Foster; John E Straub; D Thirumalai
Journal:  Proc Natl Acad Sci U S A       Date:  2016-08-24       Impact factor: 11.205

Review 7.  Lipid simulations: a perspective on lipids in action.

Authors:  Ilpo Vattulainen; Tomasz Rog
Journal:  Cold Spring Harb Perspect Biol       Date:  2011-04-01       Impact factor: 10.005

Review 8.  Multiscale simulations of protein-facilitated membrane remodeling.

Authors:  Aram Davtyan; Mijo Simunovic; Gregory A Voth
Journal:  J Struct Biol       Date:  2016-06-17       Impact factor: 2.867

9.  Transmembrane fragment structures of amyloid precursor protein depend on membrane surface curvature.

Authors:  Laura Dominguez; Stephen C Meredith; John E Straub; David Thirumalai
Journal:  J Am Chem Soc       Date:  2014-01-08       Impact factor: 15.419

Review 10.  Multiscale simulation of protein mediated membrane remodeling.

Authors:  Gary S Ayton; Gregory A Voth
Journal:  Semin Cell Dev Biol       Date:  2009-11-13       Impact factor: 7.727

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