Prediction of and Experimental Support for the Three-Dimensional Structure of Replication Protein A

Replication protein A (RPA) is a heterotrimeric, multidomain, single-stranded DNA binding protein that is essential for DNA replication, repair, and recombination. Crystallographic and NMR studies on RPA protein fragments have provided structures for all domains; however, intact heterotrimeric RPA h...

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Bibliographic Details
Published in:	Biochemistry (Easton) Vol. 48; no. 33; pp. 7892 - 7905
Main Authors:	Nuss, Jonathan Eric, Sweeney, Deacon John, Alter, Gerald Michael
Format:	Journal Article
Language:	English
Published:	United States American Chemical Society 25-08-2009
Subjects:	Binding, Competitive Computational Biology - methods Computer Simulation Crystallography, X-Ray Humans Hydrolysis Ligands Models, Molecular Phosphorylation Predictive Value of Tests Protein Binding Protein Precursors - chemistry Protein Precursors - metabolism Protein Structure, Tertiary Protein Subunits - chemistry Protein Subunits - metabolism Replication Protein A - chemistry Replication Protein A - metabolism Thermodynamics
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Summary:	Replication protein A (RPA) is a heterotrimeric, multidomain, single-stranded DNA binding protein that is essential for DNA replication, repair, and recombination. Crystallographic and NMR studies on RPA protein fragments have provided structures for all domains; however, intact heterotrimeric RPA has resisted crystallization, and a complete protein structure has not yet been described. In this study, computational methods and experimental reactivity information (MRAN) were used to model the complete structure of RPA. To accomplish this, models of RPA’s globular domains and its domain-linking regions were docked in various orders. We also determined rates of proteolytic cleavage and amino acid side chain chemical modifications in native, solution state RPA. These experimental data were used to select alternate modeling intermediates and final structural models, leading to a single model most consistent with our results. Using molecular dynamics simulations and multiple rounds of simulated annealing, we then relaxed this structural model and examined its flexibility. The family of resultant models is consistent with other, previously published, critical lines of evidence and with experimental reactivity data presented herein.
Bibliography:	ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23
ISSN:	0006-2960 1520-4995
DOI:	10.1021/bi801896s