Literature DB >> 27327264

Multiscale simulations of protein-facilitated membrane remodeling.

Aram Davtyan1, Mijo Simunovic2, Gregory A Voth3.   

Abstract

Protein-facilitated shape and topology changes of cell membranes are crucial for many biological processes, such as cell division, protein trafficking, and cell signaling. However, the inherently multiscale nature of membrane remodeling presents a considerable challenge for understanding the mechanisms and physics that drive this process. To address this problem, a multiscale approach that makes use of a diverse set of computational and experimental techniques is required. The atomistic simulations provide high-resolution information on protein-membrane interactions. Experimental techniques, like electron microscopy, on the other hand, resolve high-order organization of proteins on the membrane. Coarse-grained (CG) and mesoscale computational techniques provide the intermediate link between the two scales and can give new insights into the underlying mechanisms. In this Review, we present the recent advances in multiscale computational approaches established in our group. We discuss various CG and mesoscale approaches in studying the protein-mediated large-scale membrane remodeling.
Copyright © 2016 Elsevier Inc. All rights reserved.

Entities:  

Keywords:  BAR proteins; Coarse-grained simulations; Membrane remodeling; Mesoscale simulations; Molecular dynamics

Mesh:

Substances:

Year:  2016        PMID: 27327264      PMCID: PMC5031523          DOI: 10.1016/j.jsb.2016.06.012

Source DB:  PubMed          Journal:  J Struct Biol        ISSN: 1047-8477            Impact factor:   2.867


  65 in total

1.  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

2.  Multiscale computer simulation of the immature HIV-1 virion.

Authors:  Gary S Ayton; Gregory A Voth
Journal:  Biophys J       Date:  2010-11-03       Impact factor: 4.033

Review 3.  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

Review 4.  Membrane curvature and mechanisms of dynamic cell membrane remodelling.

Authors:  Harvey T McMahon; Jennifer L Gallop
Journal:  Nature       Date:  2005-12-01       Impact factor: 49.962

5.  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 6.  When Physics Takes Over: BAR Proteins and Membrane Curvature.

Authors:  Mijo Simunovic; Gregory A Voth; Andrew Callan-Jones; Patricia Bassereau
Journal:  Trends Cell Biol       Date:  2015-10-28       Impact factor: 20.808

7.  Reconstructing protein remodeled membranes in molecular detail from mesoscopic models.

Authors:  Edward Lyman; Haosheng Cui; Gregory A Voth
Journal:  Phys Chem Chem Phys       Date:  2011-04-18       Impact factor: 3.676

8.  Effect of chain length and unsaturation on elasticity of lipid bilayers.

Authors:  W Rawicz; K C Olbrich; T McIntosh; D Needham; E Evans
Journal:  Biophys J       Date:  2000-07       Impact factor: 4.033

9.  A Hybrid Approach for Highly Coarse-grained Lipid Bilayer Models.

Authors:  Anand Srivastava; Gregory A Voth
Journal:  J Chem Theory Comput       Date:  2013-01-08       Impact factor: 6.006

10.  Membrane tension controls the assembly of curvature-generating proteins.

Authors:  Mijo Simunovic; Gregory A Voth
Journal:  Nat Commun       Date:  2015-05-26       Impact factor: 14.919

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  8 in total

1.  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

2.  On the role of external force of actin filaments in the formation of tubular protrusions of closed membrane shapes with anisotropic membrane components.

Authors:  Luka Mesarec; Wojciech Góźdź; Samo Kralj; Miha Fošnarič; Samo Penič; Veronika Kralj-Iglič; Aleš Iglič
Journal:  Eur Biophys J       Date:  2017-05-09       Impact factor: 1.733

3.  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 4.  Systems biology of cellular membranes: a convergence with biophysics.

Authors:  Morgan Chabanon; Jeanne C Stachowiak; Padmini Rangamani
Journal:  Wiley Interdiscip Rev Syst Biol Med       Date:  2017-05-05

5.  Biophysics of membrane curvature remodeling at molecular and mesoscopic lengthscales.

Authors:  N Ramakrishnan; Ryan P Bradley; Richard W Tourdot; Ravi Radhakrishnan
Journal:  J Phys Condens Matter       Date:  2018-05-22       Impact factor: 2.333

Review 6.  Computational Modeling of Realistic Cell Membranes.

Authors:  Siewert J Marrink; Valentina Corradi; Paulo C T Souza; Helgi I Ingólfsson; D Peter Tieleman; Mark S P Sansom
Journal:  Chem Rev       Date:  2019-01-09       Impact factor: 72.087

7.  Scaffolding the cup-shaped double membrane in autophagy.

Authors:  Amir Houshang Bahrami; Mary G Lin; Xuefeng Ren; James H Hurley; Gerhard Hummer
Journal:  PLoS Comput Biol       Date:  2017-10-24       Impact factor: 4.475

8.  On the Role of Curved Membrane Nanodomains, and Passive and Active Skeleton Forces in the Determination of Cell Shape and Membrane Budding.

Authors:  Luka Mesarec; Mitja Drab; Samo Penič; Veronika Kralj-Iglič; Aleš Iglič
Journal:  Int J Mol Sci       Date:  2021-02-26       Impact factor: 5.923

  8 in total

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