Literature DB >> 30623647

Computational Modeling of Realistic Cell Membranes.

Siewert J Marrink1, Valentina Corradi2, Paulo C T Souza1, Helgi I Ingólfsson3, D Peter Tieleman2, Mark S P Sansom4.   

Abstract

Cell membranes contain a large variety of lipid types and are crowded with proteins, endowing them with the plasticity needed to fulfill their key roles in cell functioning. The compositional complexity of cellular membranes gives rise to a heterogeneous lateral organization, which is still poorly understood. Computational models, in particular molecular dynamics simulations and related techniques, have provided important insight into the organizational principles of cell membranes over the past decades. Now, we are witnessing a transition from simulations of simpler membrane models to multicomponent systems, culminating in realistic models of an increasing variety of cell types and organelles. Here, we review the state of the art in the field of realistic membrane simulations and discuss the current limitations and challenges ahead.

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Year:  2019        PMID: 30623647      PMCID: PMC6509646          DOI: 10.1021/acs.chemrev.8b00460

Source DB:  PubMed          Journal:  Chem Rev        ISSN: 0009-2665            Impact factor:   72.087


  643 in total

1.  The effect of membrane curvature on the conformation of antimicrobial peptides: implications for binding and the mechanism of action.

Authors:  Rong Chen; Alan E Mark
Journal:  Eur Biophys J       Date:  2011-01-26       Impact factor: 1.733

2.  Multiple interactions between an Arf/GEF complex and charged lipids determine activation kinetics on the membrane.

Authors:  Deepti Karandur; Agata Nawrotek; John Kuriyan; Jacqueline Cherfils
Journal:  Proc Natl Acad Sci U S A       Date:  2017-09-18       Impact factor: 11.205

3.  Membrane proteins diffuse as dynamic complexes with lipids.

Authors:  Perttu S Niemelä; Markus S Miettinen; Luca Monticelli; Henrik Hammaren; Pär Bjelkmar; Teemu Murtola; Erik Lindahl; Ilpo Vattulainen
Journal:  J Am Chem Soc       Date:  2010-06-09       Impact factor: 15.419

4.  The molecular face of lipid rafts in model membranes.

Authors:  H Jelger Risselada; Siewert J Marrink
Journal:  Proc Natl Acad Sci U S A       Date:  2008-11-05       Impact factor: 11.205

5.  A new force field for simulating phosphatidylcholine bilayers.

Authors:  David Poger; Wilfred F Van Gunsteren; Alan E Mark
Journal:  J Comput Chem       Date:  2010-04-30       Impact factor: 3.376

Review 6.  Computational approaches for modeling GPCR dimerization.

Authors:  Xuan-Yu Meng; Mihaly Mezei; Meng Cui
Journal:  Curr Pharm Biotechnol       Date:  2014       Impact factor: 2.837

7.  Interaction of the antimicrobial peptide polymyxin B1 with both membranes of E. coli: a molecular dynamics study.

Authors:  Nils A Berglund; Thomas J Piggot; Damien Jefferies; Richard B Sessions; Peter J Bond; Syma Khalid
Journal:  PLoS Comput Biol       Date:  2015-04-17       Impact factor: 4.475

Review 8.  Membrane-Mediated Oligomerization of G Protein Coupled Receptors and Its Implications for GPCR Function.

Authors:  Stefan Gahbauer; Rainer A Böckmann
Journal:  Front Physiol       Date:  2016-10-25       Impact factor: 4.566

9.  Closely related, yet unique: Distinct homo- and heterodimerization patterns of G protein coupled chemokine receptors and their fine-tuning by cholesterol.

Authors:  Stefan Gahbauer; Kristyna Pluhackova; Rainer A Böckmann
Journal:  PLoS Comput Biol       Date:  2018-03-12       Impact factor: 4.475

10.  Interaction of the human erythrocyte Band 3 anion exchanger 1 (AE1, SLC4A1) with lipids and glycophorin A: Molecular organization of the Wright (Wr) blood group antigen.

Authors:  Antreas C Kalli; Reinhart A F Reithmeier
Journal:  PLoS Comput Biol       Date:  2018-07-16       Impact factor: 4.475

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  120 in total

1.  Trimerization of dopamine transporter triggered by AIM-100 binding: Molecular mechanism and effect of mutations.

Authors:  Mary Hongying Cheng; Luca Ponzoni; Tatiana Sorkina; Ji Young Lee; She Zhang; Alexander Sorkin; Ivet Bahar
Journal:  Neuropharmacology       Date:  2019-06-20       Impact factor: 5.250

2.  A Crucial Role for Side-Chain Conformation in the Versatile Charge Selectivity of Cys-Loop Receptors.

Authors:  Tyler J Harpole; Claudio Grosman
Journal:  Biophys J       Date:  2019-04-02       Impact factor: 4.033

3.  Large-Scale Molecular Dynamics Simulations of Cellular Compartments.

Authors:  Eric Wilson; John Vant; Jacob Layton; Ryan Boyd; Hyungro Lee; Matteo Turilli; Benjamín Hernández; Sean Wilkinson; Shantenu Jha; Chitrak Gupta; Daipayan Sarkar; Abhishek Singharoy
Journal:  Methods Mol Biol       Date:  2021

4.  Protein Structure Prediction and Design in a Biologically Realistic Implicit Membrane.

Authors:  Rebecca F Alford; Patrick J Fleming; Karen G Fleming; Jeffrey J Gray
Journal:  Biophys J       Date:  2020-03-14       Impact factor: 4.033

Review 5.  Molecular dynamics simulations in photosynthesis.

Authors:  Nicoletta Liguori; Roberta Croce; Siewert J Marrink; Sebastian Thallmair
Journal:  Photosynth Res       Date:  2020-04-15       Impact factor: 3.573

6.  Ultrafast Dynamics at Lipid-Water Interfaces.

Authors:  Jennifer C Flanagan; Mason L Valentine; Carlos R Baiz
Journal:  Acc Chem Res       Date:  2020-08-31       Impact factor: 22.384

7.  Molecular Structure of Sphingomyelin in Fluid Phase Bilayers Determined by the Joint Analysis of Small-Angle Neutron and X-ray Scattering Data.

Authors:  Milka Doktorova; Norbert Kučerka; Jacob J Kinnun; Jianjun Pan; Drew Marquardt; Haden L Scott; Richard M Venable; Richard W Pastor; Stephen R Wassall; John Katsaras; Frederick A Heberle
Journal:  J Phys Chem B       Date:  2020-06-16       Impact factor: 2.991

8.  Gangliosides Destabilize Lipid Phase Separation in Multicomponent Membranes.

Authors:  Yang Liu; Jonathan Barnoud; Siewert J Marrink
Journal:  Biophys J       Date:  2019-09-06       Impact factor: 4.033

Review 9.  Structural and functional consequences of reversible lipid asymmetry in living membranes.

Authors:  Milka Doktorova; Jessica L Symons; Ilya Levental
Journal:  Nat Chem Biol       Date:  2020-11-16       Impact factor: 15.040

10.  Physical Characterization of Triolein and Implications for Its Role in Lipid Droplet Biogenesis.

Authors:  Siyoung Kim; Gregory A Voth
Journal:  J Phys Chem B       Date:  2021-06-17       Impact factor: 2.991

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