Literature DB >> 18848917

Multiscale simulations of heterogeneous model membranes.

Sagar A Pandit1, H Larry Scott.   

Abstract

This review will focus on computer modeling aimed at providing insights into the existence, structure, size, and thermodynamic stability of localized domains in membranes of heterogeneous composition. Modeling the lateral organization within a membrane is problematic due to the relatively slow lateral diffusion rate for lipid molecules so that microsecond or longer time scales are needed to fully model the formation and stability of a raft in a membrane. Although atomistic simulations currently are not able to reach this scale, they can provide data on the intermolecular forces and correlations that are involved in lateral organization. These data can be used to define coarse grained models that are capable of predictions of lateral organization in membranes. In this paper, we review modeling efforts that use interaction data from MD simulations to construct coarse grained models for heterogeneous bilayers. In this review we will discuss MD simulations done with the aim of gaining the information needed to build accurate coarse-grained models. We will then review some of the coarse-graining work, emphasizing modeling that has resulted from or has a basis in atomistic simulations.

Entities:  

Mesh:

Substances:

Year:  2008        PMID: 18848917      PMCID: PMC2664294          DOI: 10.1016/j.bbamem.2008.09.004

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


  60 in total

1.  Theory of the effect of unsaturation on the main-chain transition.

Authors:  M Scoville-Simonds; M Schick
Journal:  Phys Rev E Stat Nonlin Soft Matter Phys       Date:  2003-01-28

2.  Molecular view of hexagonal phase formation in phospholipid membranes.

Authors:  Siewert-Jan Marrink; Alan E Mark
Journal:  Biophys J       Date:  2004-09-17       Impact factor: 4.033

3.  Coupling field theory with mesoscopic dynamical simulations of multicomponent lipid bilayers.

Authors:  J Liam McWhirter; Gary Ayton; Gregory A Voth
Journal:  Biophys J       Date:  2004-09-03       Impact factor: 4.033

Review 4.  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

5.  Chain ordering in liquid crystals. II. Structure of bilayer membranes.

Authors:  S Marcelja
Journal:  Biochim Biophys Acta       Date:  1974-10-29

6.  Molecular simulations of mesoscopic bilayer phases.

Authors:  Marieke Kranenburg; Maddalena Venturoli; Berend Smit
Journal:  Phys Rev E Stat Nonlin Soft Matter Phys       Date:  2003-06-18

7.  Coarse-grained model for phospholipid/cholesterol bilayer employing inverse Monte Carlo with thermodynamic constraints.

Authors:  Teemu Murtola; Emma Falck; Mikko Karttunen; Ilpo Vattulainen
Journal:  J Chem Phys       Date:  2007-02-21       Impact factor: 3.488

8.  Lateral organization in lipid-cholesterol mixed bilayers.

Authors:  Sagar A Pandit; George Khelashvili; Eric Jakobsson; Ananth Grama; H L Scott
Journal:  Biophys J       Date:  2006-10-27       Impact factor: 4.033

9.  Cholesterol surrogates: a comparison of cholesterol and 16:0 ceramide in POPC bilayers.

Authors:  Sagar A Pandit; See-Wing Chiu; Eric Jakobsson; Ananth Grama; H L Scott
Journal:  Biophys J       Date:  2006-10-27       Impact factor: 4.033

10.  A 13C and 2H nuclear magnetic resonance study of phosphatidylcholine/cholesterol interactions: characterization of liquid-gel phases.

Authors:  T H Huang; C W Lee; S K Das Gupta; A Blume; R G Griffin
Journal:  Biochemistry       Date:  1993-12-07       Impact factor: 3.162

View more
  11 in total

1.  Self-consistent mean-field model for palmitoyloleoylphosphatidylcholine-palmitoyl sphingomyelin-cholesterol lipid bilayers.

Authors:  Paul W Tumaneng; Sagar A Pandit; Guijun Zhao; H L Scott
Journal:  Phys Rev E Stat Nonlin Soft Matter Phys       Date:  2011-03-31

2.  Molecular dynamic simulation study of cholesterol and conjugated double bonds in lipid bilayers.

Authors:  Guijun Zhao; P V Subbaiah; Evan Mintzer; See-Wing Chiu; Eric Jakobsson; H L Scott
Journal:  Chem Phys Lipids       Date:  2011-10-01       Impact factor: 3.329

3.  Molecular simulation of rapid translocation of cholesterol, diacylglycerol, and ceramide in model raft and nonraft membranes.

Authors:  W F Drew Bennett; D Peter Tieleman
Journal:  J Lipid Res       Date:  2012-01-13       Impact factor: 5.922

4.  The Phase Behavior and Organization of Sphingomyelin/Cholesterol Membranes: A Deuterium NMR Study.

Authors:  Amir Keyvanloo; Mehran Shaghaghi; Martin J Zuckermann; Jenifer L Thewalt
Journal:  Biophys J       Date:  2018-03-27       Impact factor: 4.033

5.  Dual-resolution molecular dynamics simulation of antimicrobials in biomembranes.

Authors:  Mario Orsi; Massimo G Noro; Jonathan W Essex
Journal:  J R Soc Interface       Date:  2010-12-03       Impact factor: 4.118

6.  Atomistic simulations of bicelle mixtures.

Authors:  Yong Jiang; Hao Wang; James T Kindt
Journal:  Biophys J       Date:  2010-06-16       Impact factor: 4.033

Review 7.  Phase separation in biological membranes: integration of theory and experiment.

Authors:  Elliot L Elson; Eliot Fried; John E Dolbow; Guy M Genin
Journal:  Annu Rev Biophys       Date:  2010       Impact factor: 12.981

8.  Cholesterol induces specific spatial and orientational order in cholesterol/phospholipid membranes.

Authors:  Hector Martinez-Seara; Tomasz Róg; Mikko Karttunen; Ilpo Vattulainen; Ramon Reigada
Journal:  PLoS One       Date:  2010-06-17       Impact factor: 3.240

9.  The ELBA force field for coarse-grain modeling of lipid membranes.

Authors:  Mario Orsi; Jonathan W Essex
Journal:  PLoS One       Date:  2011-12-16       Impact factor: 3.240

10.  Lipid interactions of an actinoporin pore-forming oligomer.

Authors:  Aliasghar Sepehri; Binod Nepal; Themis Lazaridis
Journal:  Biophys J       Date:  2021-02-20       Impact factor: 4.033

View more

北京卡尤迪生物科技股份有限公司 © 2022-2023.