Hydrogen-deuterium exchange reveals a dynamic DNA-binding map of replication protein A.
Journal
Nucleic acids research
ISSN: 1362-4962
Titre abrégé: Nucleic Acids Res
Pays: England
ID NLM: 0411011
Informations de publication
Date de publication:
22 02 2021
22 02 2021
Historique:
accepted:
28
12
2020
revised:
21
12
2020
received:
04
09
2020
pubmed:
15
1
2021
medline:
4
3
2021
entrez:
14
1
2021
Statut:
ppublish
Résumé
Replication protein A (RPA) binds to single-stranded DNA (ssDNA) and interacts with over three dozen enzymes and serves as a recruitment hub to coordinate most DNA metabolic processes. RPA binds ssDNA utilizing multiple oligosaccharide/oligonucleotide binding domains and based on their individual DNA binding affinities are classified as high versus low-affinity DNA-binding domains (DBDs). However, recent evidence suggests that the DNA-binding dynamics of DBDs better define their roles. Utilizing hydrogen-deuterium exchange mass spectrometry (HDX-MS), we assessed the ssDNA-driven dynamics of the individual domains of human RPA. As expected, ssDNA binding shows HDX changes in DBDs A, B, C, D and E. However, DBD-A and DBD-B are dynamic and do not show robust DNA-dependent protection. DBD-C displays the most extensive changes in HDX, suggesting a major role in stabilizing RPA on ssDNA. Slower allosteric changes transpire in the protein-protein interaction domains and linker regions, and thus do not directly interact with ssDNA. Within a dynamics-based model for RPA, we propose that DBD-A and -B act as the dynamic half and DBD-C, -D and -E function as the less-dynamic half. Thus, segments of ssDNA buried under the dynamic half are likely more readily accessible to RPA-interacting proteins.
Identifiants
pubmed: 33444457
pii: 6097544
doi: 10.1093/nar/gkaa1288
pmc: PMC7897470
doi:
Substances chimiques
DNA, Single-Stranded
0
RPA1 protein, human
0
Replication Protein A
0
RPA2 protein, human
EC 2.7.7.7
Types de publication
Journal Article
Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
1455-1469Subventions
Organisme : NIGMS NIH HHS
ID : R01 GM130746
Pays : United States
Organisme : NIGMS NIH HHS
ID : R01 GM133967
Pays : United States
Organisme : NIGMS NIH HHS
ID : R15 GM110671
Pays : United States
Organisme : NIGMS NIH HHS
ID : P20 GM103474
Pays : United States
Informations de copyright
© The Author(s) 2021. Published by Oxford University Press on behalf of Nucleic Acids Research.
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