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:
-
- 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}
}
Web of Science
Works referenced in this record:
The Chromodomains of the Chd1 Chromatin Remodeler Regulate DNA Access to the ATPase Motor
journal, September 2010
- Hauk, Glenn; McKnight, Jeffrey N.; Nodelman, Ilana M.
- Molecular Cell, Vol. 39, Issue 5
ZDOCK server: interactive docking prediction of protein-protein complexes and symmetric multimers
journal, February 2014
- Pierce, B. G.; Wiehe, K.; Hwang, H.
- Bioinformatics, Vol. 30, Issue 12
Yeast Rad5 Protein Required for Postreplication Repair Has a DNA Helicase Activity Specific for Replication Fork Regression
journal, October 2007
- Blastyák, András; Pintér, Lajos; Unk, Ildiko
- Molecular Cell, Vol. 28, Issue 1
Replication of damaged DNA by translesion synthesis in human cells
journal, November 2004
- Lehmann, Alan R.
- FEBS Letters, Vol. 579, Issue 4
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
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
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
Determination of the regularization parameter in indirect-transform methods using perceptual criteria
journal, August 1992
- Svergun, D. I.
- Journal of Applied Crystallography, Vol. 25, Issue 4, p. 495-503
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
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
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
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
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
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
Probability-based protein identification by searching sequence databases using mass spectrometry data
journal, December 1999
- Perkins, David N.; Pappin, Darryl J. C.; Creasy, David M.
- Electrophoresis, Vol. 20, Issue 18
HLTF’s Ancient HIRAN Domain Binds 3′ DNA Ends to Drive Replication Fork Reversal
journal, June 2015
- Kile, Andrew C.; Chavez, Diana A.; Bacal, Julien
- Molecular Cell, Vol. 58, Issue 6
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
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
Translesion synthesis: Y-family polymerases and the polymerase switch
journal, July 2007
- Lehmann, A.; Niimi, A.; Ogi, T.
- DNA Repair, Vol. 6, Issue 7
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
Role of yeast Rad5 and its human orthologs, HLTF and SHPRH in DNA damage tolerance
journal, March 2010
- Unk, Ildiko; Hajdú, Ildikó; Blastyák, András
- DNA Repair, Vol. 9, Issue 3
Control of spontaneous and damage-induced mutagenesis by SUMO and ubiquitin conjugation
journal, September 2003
- Stelter, Philipp; Ulrich, Helle D.
- Nature, Vol. 425, Issue 6954
Ubiquitin signalling in DNA replication and repair
journal, June 2010
- Ulrich, Helle D.; Walden, Helen
- Nature Reviews Molecular Cell Biology, Vol. 11, Issue 7
Prediction of disordered regions in proteins based on the meta approach
journal, April 2008
- Ishida, T.; Kinoshita, K.
- Bioinformatics, Vol. 24, Issue 11
Structural basis for ATP-dependent chromatin remodelling by the INO80 complex
journal, April 2018
- Eustermann, Sebastian; Schall, Kevin; Kostrewa, Dirk
- Nature, Vol. 556, Issue 7701
EUKARYOTIC TRANSLESION SYNTHESIS DNA POLYMERASES: Specificity of Structure and Function
journal, June 2005
- Prakash, Satya; Johnson, Robert E.; Prakash, Louise
- Annual Review of Biochemistry, Vol. 74, Issue 1
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
Eukaryotic translesion synthesis: Choosing the right tool for the job
journal, November 2018
- Powers, Kyle T.; Washington, M. Todd
- DNA Repair, Vol. 71
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
Structure and dynamics of the yeast SWR1-nucleosome complex
journal, October 2018
- Willhoft, Oliver; Ghoneim, Mohamed; Lin, Chia-Liang
- Science, Vol. 362, Issue 6411
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
Translesion DNA synthesis in eukaryotes: A one- or two-polymerase affair
journal, August 2002
- Prakash, S.
- Genes & Development, Vol. 16, Issue 15
PCNA, the Maestro of the Replication Fork
journal, May 2007
- Moldovan, George-Lucian; Pfander, Boris; Jentsch, Stefan
- Cell, Vol. 129, Issue 4
The ClusPro web server for protein–protein docking
journal, January 2017
- Kozakov, Dima; Hall, David R.; Xia, Bing
- Nature Protocols, Vol. 12, Issue 2
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
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
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
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
The Rad5 helicase activity is dispensable for error-free DNA post-replication repair
journal, April 2014
- Ball, Lindsay G.; Xu, Xin; Blackwell, Susan
- DNA Repair, Vol. 16
Principles of ubiquitin and SUMO modifications in DNA repair
journal, March 2009
- Bergink, Steven; Jentsch, Stefan
- Nature, Vol. 458, Issue 7237
Nucleosome–Chd1 structure and implications for chromatin remodelling
journal, October 2017
- Farnung, Lucas; Vos, Seychelle M.; Wigge, Christoph
- Nature, Vol. 550, Issue 7677
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
SWISS-MODEL: modelling protein tertiary and quaternary structure using evolutionary information
text, January 2014
- Biasini, Marco; Bienert, Stefan; Waterhouse, Andrew
- Oxford University Press
Crystal structure of the PRC1 ubiquitylation module bound to the nucleosome
text, January 2014
- S., Tan,; R. C., Henrici,; R. K., McGinty,
- Nature Publishing Group
Byonic: Advanced Peptide and Protein Identification Software
journal, December 2012
- Bern, Marshall; Kil, Yong J.; Becker, Christopher
- Current Protocols in Bioinformatics, Vol. 40, Issue 1
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
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
PCNA, the Maestro of the Replication Fork
journal, May 2007
- Moldovan, George-Lucian; Pfander, Boris; Jentsch, Stefan
- Cell, Vol. 129, Issue 4
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
Translesion synthesis: Y-family polymerases and the polymerase switch
journal, July 2007
- Lehmann, A.; Niimi, A.; Ogi, T.
- DNA Repair, Vol. 6, Issue 7
Role of yeast Rad5 and its human orthologs, HLTF and SHPRH in DNA damage tolerance
journal, March 2010
- Unk, Ildiko; Hajdú, Ildikó; Blastyák, András
- DNA Repair, Vol. 9, Issue 3
The Rad5 helicase activity is dispensable for error-free DNA post-replication repair
journal, April 2014
- Ball, Lindsay G.; Xu, Xin; Blackwell, Susan
- DNA Repair, Vol. 16
Eukaryotic translesion synthesis: Choosing the right tool for the job
journal, November 2018
- Powers, Kyle T.; Washington, M. Todd
- DNA Repair, Vol. 71
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
Yeast Rad5 Protein Required for Postreplication Repair Has a DNA Helicase Activity Specific for Replication Fork Regression
journal, October 2007
- Blastyák, András; Pintér, Lajos; Unk, Ildiko
- Molecular Cell, Vol. 28, Issue 1
The Chromodomains of the Chd1 Chromatin Remodeler Regulate DNA Access to the ATPase Motor
journal, September 2010
- Hauk, Glenn; McKnight, Jeffrey N.; Nodelman, Ilana M.
- Molecular Cell, Vol. 39, Issue 5
HLTF’s Ancient HIRAN Domain Binds 3′ DNA Ends to Drive Replication Fork Reversal
journal, June 2015
- Kile, Andrew C.; Chavez, Diana A.; Bacal, Julien
- Molecular Cell, Vol. 58, Issue 6
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
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
Control of spontaneous and damage-induced mutagenesis by SUMO and ubiquitin conjugation
journal, September 2003
- Stelter, Philipp; Ulrich, Helle D.
- Nature, Vol. 425, Issue 6954
The ClusPro web server for protein–protein docking
journal, January 2017
- Kozakov, Dima; Hall, David R.; Xia, Bing
- Nature Protocols, Vol. 12, Issue 2
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
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
Phosphate dysregulation via the XPR1–KIDINS220 protein complex is a therapeutic vulnerability in ovarian cancer
journal, April 2022
- Bondeson, Daniel P.; Paolella, Brenton R.; Asfaw, Adhana
- Nature Cancer, Vol. 3, Issue 6
Prediction of disordered regions in proteins based on the meta approach
journal, April 2008
- Ishida, T.; Kinoshita, K.
- Bioinformatics, Vol. 24, Issue 11
ZDOCK server: interactive docking prediction of protein-protein complexes and symmetric multimers
journal, February 2014
- Pierce, B. G.; Wiehe, K.; Hwang, H.
- Bioinformatics, Vol. 30, Issue 12
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
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
Translesion DNA synthesis in eukaryotes: A one- or two-polymerase affair
journal, August 2002
- Prakash, S.
- Genes & Development, Vol. 16, Issue 15
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
EUKARYOTIC TRANSLESION SYNTHESIS DNA POLYMERASES: Specificity of Structure and Function
journal, June 2005
- Prakash, Satya; Johnson, Robert E.; Prakash, Louise
- Annual Review of Biochemistry, Vol. 74, Issue 1
Crystal structure of the full Swi2/Snf2 remodeler Mot1 in the resting state
journal, October 2018
- Butryn, Agata; Woike, Stephan; Shetty, Savera J.
- eLife, Vol. 7