OpenAWSEM with Open3SPN2: A fast, flexible, and accessible framework for large-scale coarse-grained biomolecular simulations

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dc.citation.articleNumbere1008308
dc.citation.issueNumber2
dc.citation.journalTitlePLOS Computational Biology
dc.citation.volumeNumber17
dc.contributor.authorLu, Wei
dc.contributor.authorBueno, Carlos
dc.contributor.authorSchafer, Nicholas P.
dc.contributor.authorMoller, Joshua
dc.contributor.authorJin, Shikai
dc.contributor.authorChen, Xun
dc.contributor.authorChen, Mingchen
dc.contributor.authorGu, Xinyu
dc.contributor.authorDavtyan, Aram
dc.contributor.authorPablo, Juan J. de
dc.contributor.authorWolynes, Peter G.
dc.contributor.orgCenter for Theoretical Biological Physics
dc.date.accessioned2021-04-21T15:46:22Z
dc.date.available2021-04-21T15:46:22Z
dc.date.issued2021
dc.description.abstractWe present OpenAWSEM and Open3SPN2, new cross-compatible implementations of coarse-grained models for protein (AWSEM) and DNA (3SPN2) molecular dynamics simulations within the OpenMM framework. These new implementations retain the chemical accuracy and intrinsic efficiency of the original models while adding GPU acceleration and the ease of forcefield modification provided by OpenMM’s Custom Forces software framework. By utilizing GPUs, we achieve around a 30-fold speedup in protein and protein-DNA simulations over the existing LAMMPS-based implementations running on a single CPU core. We showcase the benefits of OpenMM’s Custom Forces framework by devising and implementing two new potentials that allow us to address important aspects of protein folding and structure prediction and by testing the ability of the combined OpenAWSEM and Open3SPN2 to model protein-DNA binding. The first potential is used to describe the changes in effective interactions that occur as a protein becomes partially buried in a membrane. We also introduced an interaction to describe proteins with multiple disulfide bonds. Using simple pairwise disulfide bonding terms results in unphysical clustering of cysteine residues, posing a problem when simulating the folding of proteins with many cysteines. We now can computationally reproduce Anfinsen’s early Nobel prize winning experiments by using OpenMM’s Custom Forces framework to introduce a multi-body disulfide bonding term that prevents unphysical clustering. Our protein-DNA simulations show that the binding landscape is funneled towards structures that are quite similar to those found using experiments. In summary, this paper provides a simulation tool for the molecular biophysics community that is both easy to use and sufficiently efficient to simulate large proteins and large protein-DNA systems that are central to many cellular processes. These codes should facilitate the interplay between molecular simulations and cellular studies, which have been hampered by the large mismatch between the time and length scales accessible to molecular simulations and those relevant to cell biology.
dc.identifier.citationLu, Wei, Bueno, Carlos, Schafer, Nicholas P., et al.. "OpenAWSEM with Open3SPN2: A fast, flexible, and accessible framework for large-scale coarse-grained biomolecular simulations." <i>PLOS Computational Biology,</i> 17, no. 2 (2021) Public Library of Science: https://doi.org/10.1371/journal.pcbi.1008308.
dc.identifier.digitaljournal-pcbi-1008308
dc.identifier.doihttps://doi.org/10.1371/journal.pcbi.1008308
dc.identifier.urihttps://hdl.handle.net/1911/110303
dc.language.isoeng
dc.publisherPublic Library of Science
dc.rightsThis is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
dc.rights.urihttps://creativecommons.org/licenses/by/4.0/
dc.titleOpenAWSEM with Open3SPN2: A fast, flexible, and accessible framework for large-scale coarse-grained biomolecular simulations
dc.typeJournal article
dc.type.dcmiText
dc.type.publicationpublisher version
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