Conformational Flexibility of Ubiquitin-Modified and SUMO-Modified PCNA Shown by Full-Ensemble Hybrid Methods

Kyle T Powers; Emily D Lavering; M Todd Washington

doi:10.1016/j.jmb.2018.10.017

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Conformational Flexibility of Ubiquitin-Modified and SUMO-Modified PCNA Shown by Full-Ensemble Hybrid Methods

Journal article

Open access

Peer reviewed

Conformational Flexibility of Ubiquitin-Modified and SUMO-Modified PCNA Shown by Full-Ensemble Hybrid Methods

Kyle T Powers, Emily D Lavering and M Todd Washington

Journal of molecular biology, Vol.430(24), pp.5294-5303

12/07/2018

DOI: 10.1016/j.jmb.2018.10.017

PMCID: PMC6453135

PMID: 30381149

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https://doi.org/10.1016/j.jmb.2018.10.017View

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Abstract

Ubiquitin-modified proliferating cell nuclear antigen (PCNA) and small ubiquitin-like modifier (SUMO)-modified PCNA regulate DNA damage tolerance pathways. X-ray crystal structures of these proteins suggested that they do not have much conformational flexibility because the modifiers have preferred binding sites on the surface of PCNA. By contrast, small-angle X-ray scattering analyses of these proteins suggested that they have different degrees of conformational flexibility, with SUMO-modified PCNA being more flexible. These conclusions were based on minimal-ensemble hybrid approaches, which produce unrealistic models by representing flexible proteins with only a few static structures. To overcome the limitations of minimal-ensemble hybrid approaches and to determine the degree of conformational flexibility of ubiquitin-modified PCNA and SUMO-modified PCNA, we utilized a novel full-ensemble hybrid approach. We carried out molecular simulations and small-angle X-ray scattering analyses of both proteins and obtained outstanding agreement between the full ensembles generated by the simulations and the experimental data. We found that both proteins have a high degree of conformational flexibility. The modifiers occupy many positions around the back and side of the PCNA ring. Moreover, we found no preferred ubiquitin-binding or SUMO-binding sites on PCNA. This conformational flexibility likely facilitates the recognition of downstream effector proteins and the formation of PCNA tool belts.

Binding Sites

Crystallography, X-Ray

DNA Damage

Models, Molecular

Proliferating Cell Nuclear Antigen - chemistry

Proliferating Cell Nuclear Antigen - metabolism

Protein Binding

Protein Conformation

Scattering, Small Angle

Small Ubiquitin-Related Modifier Proteins - chemistry

Small Ubiquitin-Related Modifier Proteins - metabolism

Ubiquitin - chemistry

Ubiquitin - metabolism

X-Ray Diffraction

Details

Title: Subtitle: Conformational Flexibility of Ubiquitin-Modified and SUMO-Modified PCNA Shown by Full-Ensemble Hybrid Methods
Creators: Kyle T Powers - University of Iowa
Emily D Lavering - University of Iowa
M Todd Washington - University of Iowa
Resource Type: Journal article
Publication Details: Journal of molecular biology, Vol.430(24), pp.5294-5303
DOI: 10.1016/j.jmb.2018.10.017
PMID: 30381149
PMCID: PMC6453135
ISSN: 0022-2836
eISSN: 1089-8638
Grant note: P41 GM103622 / NIGMS NIH HHS R01 GM081433 / NIGMS NIH HHS P30 CA086862 / NCI NIH HHS S10 OD018090 / NIH HHS
Language: English
Date published: 12/07/2018
Academic Unit: Radiation Oncology; Biochemistry and Molecular Biology
Record Identifier: 9984293090402771

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