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Title: Conformational flexibility of fork-remodeling helicase Rad5 shown by full-ensemble hybrid methods

Abstract

Several pathways exist to bypass DNA damage during replication. One such pathway is template switching. The Rad5 protein plays two important roles in template switching: it is an E3 ubiquitin ligase that catalyzes PCNA poly-ubiquitylation and it is a helicase that converts replication forks to chicken foot structures. To understand the structure, conformational flexibility, and mechanism of Rad5, we used a full-ensemble hybrid method combining Langevin dynamics simulations and small-angle X-ray scattering. From these studies, we generated the first experimentally validated, high-resolution structural model of Rad5. We found that Rad5 is more compact and less extended than is suggested by its large amount of predicted intrinsic disorder. Thus, Rad5 likely has a novel intra-molecular interaction that limits the range of conformational space it can sample. We provide evidence for a novel interaction between the HIRAN and the helicase domains of Rad5, and we discuss the biological and mechanistic implications of this.

Authors:
ORCiD logo [1]; ORCiD logo [1]
  1. Univ. of Iowa, Iowa City, IA (United States). College of Medicine
Publication Date:
Research Org.:
Argonne National Laboratory (ANL), Argonne, IL (United States). Advanced Photon Source (APS)
Sponsoring Org.:
National Institute of General Medical Sciences (NIGMS); National Institute of Environmental Health Sciences (NIEHS); National Institutes of Health (NIH); USDOE Office of Science (SC)
OSTI Identifier:
1581819
Grant/Contract Number:  
GM081433; F30ES028078; AC02-06CH11357; 9 P41 GM103622; 1S10OD018090-01
Resource Type:
Accepted Manuscript
Journal Name:
PLoS ONE
Additional Journal Information:
Journal Volume: 14; Journal Issue: 10; Journal ID: ISSN 1932-6203
Publisher:
Public Library of Science
Country of Publication:
United States
Language:
ENGLISH
Subject:
59 BASIC BIOLOGICAL SCIENCES

Citation Formats

Gildenberg, Melissa S., and Washington, M. Todd. Conformational flexibility of fork-remodeling helicase Rad5 shown by full-ensemble hybrid methods. United States: N. p., 2019. Web. doi:10.1371/journal.pone.0223875.
Gildenberg, Melissa S., & Washington, M. Todd. Conformational flexibility of fork-remodeling helicase Rad5 shown by full-ensemble hybrid methods. United States. https://doi.org/10.1371/journal.pone.0223875
Gildenberg, Melissa S., and Washington, M. Todd. Fri . "Conformational flexibility of fork-remodeling helicase Rad5 shown by full-ensemble hybrid methods". United States. https://doi.org/10.1371/journal.pone.0223875. https://www.osti.gov/servlets/purl/1581819.
@article{osti_1581819,
title = {Conformational flexibility of fork-remodeling helicase Rad5 shown by full-ensemble hybrid methods},
author = {Gildenberg, Melissa S. and Washington, M. Todd},
abstractNote = {Several pathways exist to bypass DNA damage during replication. One such pathway is template switching. The Rad5 protein plays two important roles in template switching: it is an E3 ubiquitin ligase that catalyzes PCNA poly-ubiquitylation and it is a helicase that converts replication forks to chicken foot structures. To understand the structure, conformational flexibility, and mechanism of Rad5, we used a full-ensemble hybrid method combining Langevin dynamics simulations and small-angle X-ray scattering. From these studies, we generated the first experimentally validated, high-resolution structural model of Rad5. We found that Rad5 is more compact and less extended than is suggested by its large amount of predicted intrinsic disorder. Thus, Rad5 likely has a novel intra-molecular interaction that limits the range of conformational space it can sample. We provide evidence for a novel interaction between the HIRAN and the helicase domains of Rad5, and we discuss the biological and mechanistic implications of this.},
doi = {10.1371/journal.pone.0223875},
journal = {PLoS ONE},
number = 10,
volume = 14,
place = {United States},
year = {Fri Oct 18 00:00:00 EDT 2019},
month = {Fri Oct 18 00:00:00 EDT 2019}
}

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Cited by: 5 works
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