A new structural framework for integrating replication protein A into DNA processing machinery

Journal Article · Tue Jan 01 00:00:00 EST 2013 · Nucleic Acids Research

DOI:https://doi.org/10.1093/nar/gks1332· OSTI ID:1067297

Brosey, Chris A ^[1]; Yan, Chunli ^[2]; Tsutakawa, Susan E ^[3]; Heller, William T ^[4]; Rambo, Robert P ^[3]; Tainer, John A ^[5]; Ivanov, Ivaylo ^[2]; Chazin, Walter J ^[1]

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1. Vanderbilt University
2. Georgia State University, Atlanta
3. Lawrence Berkeley National Laboratory (LBNL)
4. ORNL
5. Lawrence Berkeley National Laboratory, The Scripps Research Institite and The Skaggs Institute

By coupling the protection and organization of ssDNA with the recruitment and alignment of DNA processing factors, Replication Protein A (RPA) lies at the heart of dynamic multi-protein DNA processing machinery. Nevertheless, how RPA manages to coordinate the biochemical functions of its eight domains remains unknown. We examined the structural biochemistry of RPA s DNA binding activity, combining small-angle x-ray and neutron scattering with all-atom molecular dynamics simulations to investigate the architecture of RPA s DNA-binding core. It has been long held that RPA engages ssDNA in three stages, but our data reveal that RPA undergoes two rather than three transitions as it binds ssDNA. In contrast to previous models, RPA is more compact when fully engaged on 20-30 nucleotides of ssDNA than when DNA-free, and there is no evidence for significant population of a highly compacted structure in the initial 8-10 nucleotide binding mode. These results provide a new framework for understanding the integration of ssDNA into DNA processing machinery and how binding partners may manipulate RPA architecture to gain access to the substrate.

• Research Organization: Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). High Flux Isotope Reactor (HFIR); Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Spallation Neutron Source (SNS); Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Center for Structural Molecular Biology (CSMB)
• Sponsoring Organization: USDOE Office of Science (SC)
• DOE Contract Number: DE-AC05-00OR22725
• OSTI ID: 1067297
• Journal Information: Nucleic Acids Research, Vol. 41, Issue 4; ISSN 0305--1048
• Country of Publication: United States
• Language: English