Computational 'microscopy' of cellular membranes.

作者: Helgi I. Ingólfsson , Clément Arnarez , Xavier Periole , Siewert J. Marrink

DOI: 10.1242/JCS.176040

关键词:

摘要: Computational 'microscopy' refers to the use of computational resources simulate dynamics a molecular system. Tuned cell membranes, this technique is able capture interplay between lipids and proteins at spatio-temporal resolution that unmatched by other methods. Recent advances allow us zoom out from individual atoms molecules supramolecular complexes subcellular compartments contain tens millions particles, complexity crowded environment real membranes. This Commentary gives an overview main concepts describes state-of-the-art methods used model membrane processes. We illustrate power modelling approaches providing few in-depth examples large-scale simulations move up descriptions into arena. end with outlook towards complete in silico.

参考文章(179)
William G. Hoover, Canonical dynamics: Equilibrium phase-space distributions Physical Review A. ,vol. 31, pp. 1695- 1697 ,(1985) , 10.1103/PHYSREVA.31.1695
Nathan Schmid, Andreas P. Eichenberger, Alexandra Choutko, Sereina Riniker, Moritz Winger, Alan E. Mark, Wilfred F. van Gunsteren, Definition and testing of the GROMOS force-field versions 54A7 and 54B7 European Biophysics Journal. ,vol. 40, pp. 843- 856 ,(2011) , 10.1007/S00249-011-0700-9
Sanja Pöyry, Oana Cramariuc, Pekka A. Postila, Karol Kaszuba, Marcin Sarewicz, Artur Osyczka, Ilpo Vattulainen, Tomasz Róg, Atomistic Simulations Indicate Cardiolipin to have an Integral Role in the Structure of the Cytochrome bc1 Complex Biochimica et Biophysica Acta. ,vol. 1827, pp. 769- 778 ,(2013) , 10.1016/J.BBABIO.2013.03.005
Heidi Koldsø, David Shorthouse, Jean Hélie, Mark S. P. Sansom, Lipid Clustering Correlates with Membrane Curvature as Revealed by Molecular Simulations of Complex Lipid Bilayers PLoS Computational Biology. ,vol. 10, pp. e1003911- ,(2014) , 10.1371/JOURNAL.PCBI.1003911
Wataru Shinoda, Russell DeVane, Michael L Klein, Zwitterionic Lipid Assemblies: Molecular Dynamics Studies of Monolayers, Bilayers, and Vesicles Using a New Coarse Grain Force Field Journal of Physical Chemistry B. ,vol. 114, pp. 6836- 6849 ,(2010) , 10.1021/JP9107206
Benjamin A. Hall, Judith P. Armitage, Mark S. P. Sansom, Mechanism of Bacterial Signal Transduction Revealed by Molecular Dynamics of Tsr Dimers and Trimers of Dimers in Lipid Vesicles PLoS Computational Biology. ,vol. 8, pp. e1002685- ,(2012) , 10.1371/JOURNAL.PCBI.1002685
Fabrizio Marinelli, Lior Almagor, Reuben Hiller, Moshe Giladi, Daniel Khananshvili, José D. Faraldo-Gómez, Sodium recognition by the Na+/Ca2+ exchanger in the outward-facing conformation Proceedings of the National Academy of Sciences of the United States of America. ,vol. 111, pp. 201415751- ,(2014) , 10.1073/PNAS.1415751111
Gary S Ayton, Will G Noid, Gregory A Voth, Multiscale modeling of biomolecular systems: in serial and in parallel. Current Opinion in Structural Biology. ,vol. 17, pp. 192- 198 ,(2007) , 10.1016/J.SBI.2007.03.004
Janamejaya Chowdhary, Edward Harder, Pedro E. M. Lopes, Lei Huang, Alexander D. MacKerell, Benoît Roux, A polarizable force field of dipalmitoylphosphatidylcholine based on the classical Drude model for molecular dynamics simulations of lipids. Journal of Physical Chemistry B. ,vol. 117, pp. 9142- 9160 ,(2013) , 10.1021/JP402860E