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

Melissa S Gildenberg; M Todd Washington

doi:10.1371/journal.pone.0223875

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

Journal article

Open access

Peer reviewed

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

Melissa S Gildenberg and M Todd Washington

PloS one, Vol.14(10), pp.e0223875-e0223875

2019

DOI: 10.1371/journal.pone.0223875

PMCID: PMC6799953

PMID: 31626633

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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.

DNA Replication

DNA Damage

DNA Helicases - chemistry

DNA Helicases - genetics

DNA Helicases - metabolism

Molecular Dynamics Simulation

Protein Conformation

Protein Domains

Recombinant Proteins - biosynthesis

Recombinant Proteins - chemistry

Recombinant Proteins - isolation & purification

Saccharomyces cerevisiae - metabolism

Saccharomyces cerevisiae Proteins - chemistry

Saccharomyces cerevisiae Proteins - genetics

Saccharomyces cerevisiae Proteins - metabolism

Scattering, Small Angle

X-Ray Diffraction

Details

Title: Subtitle: Conformational flexibility of fork-remodeling helicase Rad5 shown by full-ensemble hybrid methods
Creators: Melissa S Gildenberg - University of Iowa
M Todd Washington - University of Iowa
Resource Type: Journal article
Publication Details: PloS one, Vol.14(10), pp.e0223875-e0223875
DOI: 10.1371/journal.pone.0223875
PMID: 31626633
PMCID: PMC6799953
NLM abbreviation: PLoS One
ISSN: 1932-6203
eISSN: 1932-6203
Grant note: P41 GM103622 / NIGMS NIH HHS F30 ES028078 / NIEHS NIH HHS R01 GM081433 / NIGMS NIH HHS T32 GM007337 / NIGMS NIH HHS P30 CA086862 / NCI NIH HHS S10 OD018090 / NIH HHS
Language: English
Date published: 2019
Academic Unit: Radiation Oncology; Biochemistry and Molecular Biology
Record Identifier: 9984230422802771

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