Dataset / Data from: Multiscale Modeling Shows How 2'-deoxy-ATP Rescues Ventricular Function in Heart …

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Title: Data from: Multiscale Modeling Shows How 2'-deoxy-ATP Rescues Ventricular Function in Heart Failure
Contributor: Hock, Marcus T.
Date Created and/or Issued: 2020 to 2022
Contributing Institution: UC San Diego, Research Data Curation Program
Collection: Data from: Multiscale Modeling Shows How 2'-deoxy-ATP Rescues Ventricular Function in Heart Failure
Rights Information: Under copyright
Constraint(s) on Use: This work is protected by the U.S. Copyright Law (Title 17, U.S.C.). Use of this work beyond that allowed by "fair use" or any license applied to this work requires written permission of the copyright holder(s). Responsibility for obtaining permissions and any use and distribution of this work rests exclusively with the user and not the UC San Diego Library. Inquiries can be made to the UC San Diego Library program having custody of the work.
Use: This work is available from the UC San Diego Library. This digital copy of the work is intended to support research, teaching, and private study.
Rights Holder and Contact: UC Regents
Description: This collection contains the molecular dynamics simulations of the myosin motor protein from the PNAS paper "Multiscale modeling shows how 2'-deoxy-ATP rescues ventricular function in heart failure". The molecular dynamics simulations were carried in triplicate out with either ATP (ADP.Pi) bound to the pre-powerstroke scallop myosin (PDB: 1QVI), or dATP (dADP.Pi) for 2 microseconds. The simulations were carried out to understand how dATP influences myosin structure and function, and acts as a possible heart failure therapeutic. The uploaded trajectories include the topology file for the ATP and dATP structures, with frames saved every 10 ps. The explicit water has been removed from the simulations in order to save space. Please see the manuscript for a complete description of the molecular dynamics simulations carried out. These trajectories are also used as inputs to create molecular Markov State models, to discretize the conformations of myosin into distinct metastable states. This analysis is carried out in python Jupyter notebooks, in the github associated with the manuscript and this collection.
Simulations carried out with compute time resources provided by Extreme Science and Engineering Discovery Environment (XSEDE) resource COMET through allocation TG-MCB200100 (to M.R.). XSEDE was supported by the National Science Foundation grant number ACI-1548562. This work was supported by National Institutes of Health grants GM31749 (to G.A.H.), HL154624 (to D.A.B.), HL128368 and P30 AR074990 (to M.R.), HL137100 (to A.D.M.) and P41 GM103426 (to A.D.M. and J.A.M.) and Wu Tsai Human Performance Alliance and the Joe and Clara Tsai Foundation (to A.D.M.). This material is based upon work supported by the National Science Foundation Graduate Research Fellowship Program under Grant No. DGE-2038238 (to A.E.T.), the UC President's Dissertation Year Fellowship (to A.E.T.), and an American Heart Association Pre-doctoral Fellowship award ID 906494 (to M.T.H.). Partial funding for M.C.C. was provided by Award Number T32HL007828 from the National Heart, Lung, and Blood Institute. K.J.M. is supported by the Simula-UCSD-University of Oslo Research and Ph.D. training (SUURPh) program, an international collaboration in computational biology and medicine funded by the Norwegian Ministry of Education and Research.
Research Data Curation Program, UC San Diego, La Jolla, 92093-0175 (https://lib.ucsd.edu/rdcp)
Teitgen, Abigail E.; Hock, Marcus T.; McCabe, Kimberly J.; Childers, Matthew C.; Huber, Gary A.; Marzban, Bahador; Beard, Daniel A.; McCammon, J. Andrew; Regnier, Michael; McCulloch. Andrew D. (2024). Data from: Multiscale Modeling Shows How 2'-deoxy-ATP Rescues Ventricular Function in Heart Failure. UC San Diego Library Digital Collections. https://doi.org/10.6075/J00G3KCC
Type: dataset
Identifier: ark:/20775/bb83062613
Language: English
Subject: 2'-deoxyadenosine triphosphate (dATP)
DATP
Cardiovascular medicine
Amber
Bay scallop
Multiscale modeling
Myosin
Markov state model (MSM)
Molecular dynamics (MD)
Biomedical and clinical sciences
Argopecten irradians

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