skip to main content
OSTI.GOV title logo U.S. Department of Energy
Office of Scientific and Technical Information

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

ORCiD logo; ORCiD logo;
Publication Date:
Research Org.:
Argonne National Lab. (ANL), Argonne, IL (United States). Advanced Photon Source (APS)
Sponsoring Org.:
National Institutes of Health (NIH)
OSTI Identifier:
Resource Type:
Journal Article
Journal Name:
Additional Journal Information:
Journal Volume: 14; Journal Issue: 10; Journal ID: ISSN 1932-6203
Public Library of Science
Country of Publication:
United States

Citation Formats

Gildenberg, Melissa S., Washington, M. Todd, and Zhang, Yanbin. 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, & Zhang, Yanbin. Conformational flexibility of fork-remodeling helicase Rad5 shown by full-ensemble hybrid methods. United States. doi:10.1371/journal.pone.0223875.
Gildenberg, Melissa S., Washington, M. Todd, and Zhang, Yanbin. Fri . "Conformational flexibility of fork-remodeling helicase Rad5 shown by full-ensemble hybrid methods". United States. doi:10.1371/journal.pone.0223875.
title = {Conformational flexibility of fork-remodeling helicase Rad5 shown by full-ensemble hybrid methods},
author = {Gildenberg, Melissa S. and Washington, M. Todd and Zhang, Yanbin},
abstractNote = {},
doi = {10.1371/journal.pone.0223875},
journal = {PLoS ONE},
issn = {1932-6203},
number = 10,
volume = 14,
place = {United States},
year = {2019},
month = {10}

Works referenced in this record:

Eukaryotic translesion synthesis: Choosing the right tool for the job
journal, November 2018

Conformational Flexibility of Ubiquitin-Modified and SUMO-Modified PCNA Shown by Full-Ensemble Hybrid Methods
journal, December 2018

  • Powers, Kyle T.; Lavering, Emily D.; Washington, M. Todd
  • Journal of Molecular Biology, Vol. 430, Issue 24
  • DOI: 10.1016/j.jmb.2018.10.017

Structure and dynamics of the yeast SWR1-nucleosome complex
journal, October 2018

The Chromodomains of the Chd1 Chromatin Remodeler Regulate DNA Access to the ATPase Motor
journal, September 2010

ZDOCK server: interactive docking prediction of protein-protein complexes and symmetric multimers
journal, February 2014

The C-terminal region of translesion synthesis DNA polymerase η is partially unstructured and has high conformational flexibility
journal, January 2018

  • Powers, Kyle T.; Elcock, Adrian H.; Washington, M. Todd
  • Nucleic Acids Research, Vol. 46, Issue 4
  • DOI: 10.1093/nar/gky031

Yeast Rad5 Protein Required for Postreplication Repair Has a DNA Helicase Activity Specific for Replication Fork Regression
journal, October 2007

Replication of damaged DNA by translesion synthesis in human cells
journal, November 2004

Eukaryotic Translesion Polymerases and Their Roles and Regulation in DNA Damage Tolerance
journal, March 2009

  • Waters, L. S.; Minesinger, B. K.; Wiltrout, M. E.
  • Microbiology and Molecular Biology Reviews, Vol. 73, Issue 1
  • DOI: 10.1128/MMBR.00034-08

Y-family DNA polymerases in mammalian cells
journal, April 2009

  • Guo, Caixia; Kosarek-Stancel, J. Nicole; Tang, Tie-Shan
  • Cellular and Molecular Life Sciences, Vol. 66, Issue 14
  • DOI: 10.1007/s00018-009-0024-4

Translesion DNA synthesis in eukaryotes: A one- or two-polymerase affair
journal, August 2002

PrDOS: prediction of disordered protein regions from amino acid sequence
journal, May 2007

  • Ishida, T.; Kinoshita, K.
  • Nucleic Acids Research, Vol. 35, Issue Web Server
  • DOI: 10.1093/nar/gkm363

CRYSOL – a Program to Evaluate X-ray Solution Scattering of Biological Macromolecules from Atomic Coordinates
journal, December 1995

  • Svergun, D.; Barberato, C.; Koch, M. H. J.
  • Journal of Applied Crystallography, Vol. 28, Issue 6
  • DOI: 10.1107/S0021889895007047

Determination of the regularization parameter in indirect-transform methods using perceptual criteria
journal, August 1992

PCNA, the Maestro of the Replication Fork
journal, May 2007

Crystal structure of the PRC1 ubiquitylation module bound to the nucleosome
journal, October 2014

  • McGinty, Robert K.; Henrici, Ryan C.; Tan, Song
  • Nature, Vol. 514, Issue 7524
  • DOI: 10.1038/nature13890

The ClusPro web server for protein–protein docking
journal, January 2017

PRIMUS: a Windows PC-based system for small-angle scattering data analysis
journal, September 2003

  • Konarev, Petr V.; Volkov, Vladimir V.; Sokolova, Anna V.
  • Journal of Applied Crystallography, Vol. 36, Issue 5, p. 1277-1282
  • DOI: 10.1107/S0021889803012779

Structure of the SWI2/SNF2 chromatin-remodeling domain of eukaryotic Rad54
journal, April 2005

  • Thomä, Nicolas H.; Czyzewski, Bryan K.; Alexeev, Andrei A.
  • Nature Structural & Molecular Biology, Vol. 12, Issue 4
  • DOI: 10.1038/nsmb919

Mms2-Ubc13-Dependent and -Independent Roles of Rad5 Ubiquitin Ligase in Postreplication Repair and Translesion DNA Synthesis in Saccharomyces cerevisiae
journal, August 2006

  • Gangavarapu, V.; Haracska, L.; Unk, I.
  • Molecular and Cellular Biology, Vol. 26, Issue 20
  • DOI: 10.1128/MCB.01260-06

Modeling Conformationally Flexible Proteins With X-ray Scattering and Molecular Simulations
journal, January 2019

  • Powers, Kyle T.; Gildenberg, Melissa S.; Washington, M. Todd
  • Computational and Structural Biotechnology Journal, Vol. 17
  • DOI: 10.1016/j.csbj.2019.04.011

A new structural framework for integrating replication protein A into DNA processing machinery
journal, January 2013

  • Brosey, Chris A.; Yan, Chunli; Tsutakawa, Susan E.
  • Nucleic Acids Research, Vol. 41, Issue 4
  • DOI: 10.1093/nar/gks1332

ATSAS 2.1 – towards automated and web-supported small-angle scattering data analysis
journal, April 2007

  • Petoukhov, Maxim V.; Konarev, Peter V.; Kikhney, Alexey G.
  • Journal of Applied Crystallography, Vol. 40, Issue s1
  • DOI: 10.1107/S0021889807002853

The Phyre2 web portal for protein modeling, prediction and analysis
journal, May 2015

  • Kelley, Lawrence A.; Mezulis, Stefans; Yates, Christopher M.
  • Nature Protocols, Vol. 10, Issue 6
  • DOI: 10.1038/nprot.2015.053

Y-family DNA polymerases and their role in tolerance of cellular DNA damage
journal, February 2012

  • Sale, Julian E.; Lehmann, Alan R.; Woodgate, Roger
  • Nature Reviews Molecular Cell Biology, Vol. 13, Issue 3
  • DOI: 10.1038/nrm3289

Probability-based protein identification by searching sequence databases using mass spectrometry data
journal, December 1999

Crystal structure of the full Swi2/Snf2 remodeler Mot1 in the resting state
journal, October 2018

HLTF’s Ancient HIRAN Domain Binds 3′ DNA Ends to Drive Replication Fork Reversal
journal, June 2015

SWISS-MODEL: modelling protein tertiary and quaternary structure using evolutionary information
journal, April 2014

  • Biasini, Marco; Bienert, Stefan; Waterhouse, Andrew
  • Nucleic Acids Research, Vol. 42, Issue W1
  • DOI: 10.1093/nar/gku340

An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database
journal, November 1994

  • Eng, Jimmy K.; McCormack, Ashley L.; Yates, John R.
  • Journal of the American Society for Mass Spectrometry, Vol. 5, Issue 11
  • DOI: 10.1016/1044-0305(94)80016-2

The Rad5 helicase activity is dispensable for error-free DNA post-replication repair
journal, April 2014

BioXTAS RAW , a software program for high-throughput automated small-angle X-ray scattering data reduction and preliminary analysis
journal, August 2009

  • Nielsen, S. S.; Toft, K. Noergaard; Snakenborg, D.
  • Journal of Applied Crystallography, Vol. 42, Issue 5
  • DOI: 10.1107/S0021889809023863

Translesion synthesis: Y-family polymerases and the polymerase switch
journal, July 2007

Striking Effects of Hydrodynamic Interactions on the Simulated Diffusion and Folding of Proteins
journal, January 2009

  • Frembgen-Kesner, Tamara; Elcock, Adrian H.
  • Journal of Chemical Theory and Computation, Vol. 5, Issue 2
  • DOI: 10.1021/ct800499p

Role of yeast Rad5 and its human orthologs, HLTF and SHPRH in DNA damage tolerance
journal, March 2010

Control of spontaneous and damage-induced mutagenesis by SUMO and ubiquitin conjugation
journal, September 2003

Ubiquitin signalling in DNA replication and repair
journal, June 2010

  • Ulrich, Helle D.; Walden, Helen
  • Nature Reviews Molecular Cell Biology, Vol. 11, Issue 7
  • DOI: 10.1038/nrm2921

Prediction of disordered regions in proteins based on the meta approach
journal, April 2008

Structural basis for ATP-dependent chromatin remodelling by the INO80 complex
journal, April 2018

journal, June 2005

Principles of ubiquitin and SUMO modifications in DNA repair
journal, March 2009

Nucleosome–Chd1 structure and implications for chromatin remodelling
journal, October 2017

  • Farnung, Lucas; Vos, Seychelle M.; Wigge, Christoph
  • Nature, Vol. 550, Issue 7677
  • DOI: 10.1038/nature24046

RAD6-dependent DNA repair is linked to modification of PCNA by ubiquitin and SUMO
journal, September 2002

  • Hoege, Carsten; Pfander, Boris; Moldovan, George-Lucian
  • Nature, Vol. 419, Issue 6903
  • DOI: 10.1038/nature00991

Variations on a theme: Eukaryotic Y-family DNA polymerases
journal, May 2010

  • Washington, M. Todd; Carlson, Karissa D.; Freudenthal, Bret D.
  • Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics, Vol. 1804, Issue 5
  • DOI: 10.1016/j.bbapap.2009.07.004