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

Autoři: Melissa S. Gildenberg aff001;  M. Todd Washington aff001
Působiště autorů: Department of Biochemistry, University of Iowa College of Medicine, Iowa City, Iowa, United States of America aff001
Vyšlo v časopise: PLoS ONE 14(10)
Kategorie: Research Article
doi: 10.1371/journal.pone.0223875


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.

Klíčová slova:

Biochemical simulations – Biophysical simulations – Cross-linking – DNA damage – DNA replication – Helicases – Simulation and modeling – Small-angle scattering


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