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Title: Determining Atomistic SAXS Models of Tri-Ubiquitin Chains from Bayesian Analysis of Accelerated Molecular Dynamics Simulations

Abstract

Small-angle X-ray scattering (SAXS) has become an increasingly popular technique for characterizing the solution ensemble of flexible biomolecules. However, data resulting from SAXS is typically low-dimensional and is therefore difficult to interpret without additional structural knowledge. In theory, molecular dynamics (MD) trajectories can provide this information, but conventional simulations rarely sample the complete ensemble. Here, we demonstrate that accelerated MD simulations can be used to produce higher quality models in shorter time scales than standard simulations, and we present an iterative Bayesian Monte Carlo method that is able to identify multistate ensembles without overfitting. This methodology is applied to several ubiquitin trimers to demonstrate the effect of linkage type on the solution states of the signaling protein. Here, we observe that the linkage site directly affects the solution flexibility of the trimer and theorize that this difference in plasticity contributes to their disparate roles in vivo.

Authors:
 [1];  [2];  [1];  [3]; ORCiD logo [4]; ORCiD logo [1]
+ Show Author Affiliations
  1. Illinois Inst. of Technology, Chicago, IL (United States)
  2. Univ. of Massachusetts, Amherst, MA (United States); Univ. of Wisconsin, Madison, WI (United States)
  3. Univ. of Wisconsin, Madison, WI (United States)
  4. Univ. of Massachusetts, Amherst, MA (United States)
Publication Date:
Research Org.:
Argonne National Laboratory (ANL), Argonne, IL (United States)
Sponsoring Org.:
USDOE Office of Science (SC); National Inst. of Health; National Science Foundation (NSF)
OSTI Identifier:
1395364
Grant/Contract Number:  
AC02-06CH11357; R15GM114758; R35GM119647; R01GM110543; P41GM103622; ACI-1053575
Resource Type:
Accepted Manuscript
Journal Name:
Journal of Chemical Theory and Computation
Additional Journal Information:
Journal Volume: 13; Journal Issue: 6; Journal ID: ISSN 1549-9618
Publisher:
American Chemical Society
Country of Publication:
United States
Language:
ENGLISH
Subject:
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY; scattering; peptides and proteins; cluster chemistry; X-ray scattering; computer simulations

Citation Formats

Bowerman, Samuel, Rana, Ambar S. J. B., Rice, Amy, Pham, Grace H., Strieter, Eric R., and Wereszczynski, Jeff. Determining Atomistic SAXS Models of Tri-Ubiquitin Chains from Bayesian Analysis of Accelerated Molecular Dynamics Simulations. United States: N. p., 2017. Web. doi:10.1021/acs.jctc.7b00059.
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Bowerman, Samuel, Rana, Ambar S. J. B., Rice, Amy, Pham, Grace H., Strieter, Eric R., & Wereszczynski, Jeff. Determining Atomistic SAXS Models of Tri-Ubiquitin Chains from Bayesian Analysis of Accelerated Molecular Dynamics Simulations. United States. https://doi.org/10.1021/acs.jctc.7b00059
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Bowerman, Samuel, Rana, Ambar S. J. B., Rice, Amy, Pham, Grace H., Strieter, Eric R., and Wereszczynski, Jeff. Mon . "Determining Atomistic SAXS Models of Tri-Ubiquitin Chains from Bayesian Analysis of Accelerated Molecular Dynamics Simulations". United States. https://doi.org/10.1021/acs.jctc.7b00059. https://www.osti.gov/servlets/purl/1395364.
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@article{osti_1395364,
title = {Determining Atomistic SAXS Models of Tri-Ubiquitin Chains from Bayesian Analysis of Accelerated Molecular Dynamics Simulations},
author = {Bowerman, Samuel and Rana, Ambar S. J. B. and Rice, Amy and Pham, Grace H. and Strieter, Eric R. and Wereszczynski, Jeff},
abstractNote = {Small-angle X-ray scattering (SAXS) has become an increasingly popular technique for characterizing the solution ensemble of flexible biomolecules. However, data resulting from SAXS is typically low-dimensional and is therefore difficult to interpret without additional structural knowledge. In theory, molecular dynamics (MD) trajectories can provide this information, but conventional simulations rarely sample the complete ensemble. Here, we demonstrate that accelerated MD simulations can be used to produce higher quality models in shorter time scales than standard simulations, and we present an iterative Bayesian Monte Carlo method that is able to identify multistate ensembles without overfitting. This methodology is applied to several ubiquitin trimers to demonstrate the effect of linkage type on the solution states of the signaling protein. Here, we observe that the linkage site directly affects the solution flexibility of the trimer and theorize that this difference in plasticity contributes to their disparate roles in vivo.},
doi = {10.1021/acs.jctc.7b00059},
journal = {Journal of Chemical Theory and Computation},
number = 6,
volume = 13,
place = {United States},
year = {Mon May 08 00:00:00 EDT 2017},
month = {Mon May 08 00:00:00 EDT 2017}
}
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https://doi.org/10.1021/acs.jctc.7b00059
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