Complete atomistic model of a bacterial cytoplasm for integrating physics, biochemistry, and systems biology

Journal of Molecular Graphics & Modelling
Michael FeigYuji Sugita

Abstract

A model for the cytoplasm of Mycoplasma genitalium is presented that integrates data from a variety of sources into a physically and biochemically consistent model. Based on gene annotations, core genes expected to be present in the cytoplasm were determined and a metabolic reaction network was reconstructed. The set of cytoplasmic genes and metabolites from the predicted reactions were assembled into a comprehensive atomistic model consisting of proteins with predicted structures, RNA, protein/RNA complexes, metabolites, ions, and solvent. The resulting model bridges between atomistic and cellular scales, between physical and biochemical aspects, and between structural and systems views of cellular systems and is meant as a starting point for a variety of simulation studies.

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Citations

Jan 17, 2016·Current Opinion in Structural Biology·Alberto PerezKen A Dill
Sep 10, 2015·Biological Chemistry·David Gnutt, Simon Ebbinghaus
Jan 12, 2016·Wiley Interdisciplinary Reviews. Computational Molecular Science·Jaewoon JungYuji Sugita
Apr 8, 2015·Current Opinion in Structural Biology·Juan R PerillaKlaus Schulten
Jun 4, 2016·Journal of Molecular Biology·Wonpil ImIlya A Vakser
Jul 6, 2016·Journal of Chemical Information and Modeling·Michael Feig
Sep 16, 2016·Journal of Chemical Theory and Computation·Jaewoon JungYuji Sugita
Oct 25, 2016·Journal of Molecular Graphics & Modelling·Samir S Roy, Manju Kapoor
Oct 5, 2016·Philosophical Transactions. Series A, Mathematical, Physical, and Engineering Sciences·Jesper TegnérDavid Gomez-Cabrero
Jul 1, 2017·The Journal of Physical Chemistry. B·Michael FeigYuji Sugita
Nov 8, 2016·Molecular BioSystems·Shu-Ichi Nakano, Naoki Sugimoto
Jul 13, 2019·Annual Review of Cell and Developmental Biology·Michael Feig, Yuji Sugita
Dec 17, 2018·The Journal of Chemical Physics·Jeffery B Klauda
Oct 22, 2019·Frontiers in Molecular Biosciences·Vijay Phanindra Srikanth KompellaRicardo L Mancera
Aug 28, 2020·Frontiers in Bioengineering and Biotechnology·Lucia MarucciChristopher Woods
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Feb 28, 2018·Current Opinion in Biotechnology·Lukas Andreas Widmer, Jörg Stelling
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Aug 9, 2017·Journal of Chemical Theory and Computation·Philipp S SchmalhorstMateusz Sikora
Dec 10, 2019·Journal of Chemical Information and Modeling·Leandro Oliveira BortotDavid van der Spoel
Jan 18, 2018·The Journal of Physical Chemistry. B·David S GoodsellArthur J Olson
Nov 15, 2021·Journal of Molecular Biology·Martina MaritanDavid S Goodsell

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