Literature DB >> 26194872

Biomembranes in atomistic and coarse-grained simulations.

Kristyna Pluhackova1, Rainer A Böckmann.   

Abstract

The architecture of biological membranes is tightly coupled to the localization, organization, and function of membrane proteins. The organelle-specific distribution of lipids allows for the formation of functional microdomains (also called rafts) that facilitate the segregation and aggregation of membrane proteins and thus shape their function. Molecular dynamics simulations enable to directly access the formation, structure, and dynamics of membrane microdomains at the molecular scale and the specific interactions among lipids and proteins on timescales from picoseconds to microseconds. This review focuses on the latest developments of biomembrane force fields for both atomistic and coarse-grained molecular dynamics (MD) simulations, and the different levels of coarsening of biomolecular structures. It also briefly introduces scale-bridging methods applicable to biomembrane studies, and highlights selected recent applications.

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Year:  2015        PMID: 26194872     DOI: 10.1088/0953-8984/27/32/323103

Source DB:  PubMed          Journal:  J Phys Condens Matter        ISSN: 0953-8984            Impact factor:   2.333


  20 in total

1.  A Coiled-Coil Peptide Shaping Lipid Bilayers upon Fusion.

Authors:  Martin Rabe; Christopher Aisenbrey; Kristyna Pluhackova; Vincent de Wert; Aimee L Boyle; Didjay F Bruggeman; Sonja A Kirsch; Rainer A Böckmann; Alexander Kros; Jan Raap; Burkhard Bechinger
Journal:  Biophys J       Date:  2016-11-15       Impact factor: 4.033

2.  Phosphatidylinositol-3,5-bisphosphate lipid-binding-induced activation of the human two-pore channel 2.

Authors:  Sonja A Kirsch; Andreas Kugemann; Armando Carpaneto; Rainer A Böckmann; Petra Dietrich
Journal:  Cell Mol Life Sci       Date:  2018-04-28       Impact factor: 9.261

3.  Investigating the Structure of Multicomponent Gel-Phase Lipid Bilayers.

Authors:  Remco Hartkamp; Timothy C Moore; Christopher R Iacovella; Michael A Thompson; Pallav A Bulsara; David J Moore; Clare McCabe
Journal:  Biophys J       Date:  2016-08-23       Impact factor: 4.033

4.  Membrane phase transition during heating and cooling: molecular insight into reversible melting.

Authors:  Liping Sun; Rainer A Böckmann
Journal:  Eur Biophys J       Date:  2017-07-19       Impact factor: 1.733

5.  Molecular Dynamics of the Association of L-Selectin and FERM Regulated by PIP2.

Authors:  Fude Sun; Carsten F E Schroer; Lida Xu; Huiwei Yin; Siewert J Marrink; Shi-Zhong Luo
Journal:  Biophys J       Date:  2018-04-24       Impact factor: 4.033

Review 6.  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

Review 7.  The Multifaceted Role of SNARE Proteins in Membrane Fusion.

Authors:  Jing Han; Kristyna Pluhackova; Rainer A Böckmann
Journal:  Front Physiol       Date:  2017-01-20       Impact factor: 4.566

8.  Prediction of Thylakoid Lipid Binding Sites on Photosystem II.

Authors:  Floris J Van Eerden; Manuel N Melo; Pim W J M Frederix; Siewert J Marrink
Journal:  Biophys J       Date:  2017-12-19       Impact factor: 4.033

9.  Unperturbed hydrocarbon chains and liquid phase bilayer lipid chains: a computer simulation study.

Authors:  Alexander L Rabinovich; Alexander P Lyubartsev; Dmitrii V Zhurkin
Journal:  Eur Biophys J       Date:  2017-07-11       Impact factor: 1.733

10.  Statistically derived asymmetric membrane potentials from α-helical and β-barrel membrane proteins.

Authors:  Julia Koehler Leman; Richard Bonneau; Martin B Ulmschneider
Journal:  Sci Rep       Date:  2018-03-13       Impact factor: 4.379

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