title: Integrating multi-scale data on homologous recombination into a new recognition mechanism based on simulations of the RecA-ssDNA/dsDNA structure.
abstract: RecA protein is the prototypical recombinase. Members of the recombinase family can accurately repair double strand breaks in DNA. They also provide crucial links between pairs of sister chromatids in eukaryotic meiosis. A very broad outline of how these proteins align homologous sequences and promote DNA strand exchange has long been known, as are the crystal structures of the RecA-DNA pre- and postsynaptic complexes; however, little is known about the homology searching conformations and the details of how DNA in bacterial genomes is rapidly searched until homologous alignment is achieved. By integrating a physical model of recognition to new modeling work based on docking exploration and molecular dynamics simulation, we present a detailed structure/function model of homology recognition that reconciles extremely quick searching with the efficient and stringent formation of stable strand exchange products and which is consistent with a vast body of previously unexplained experimental results.
authors.affiliation: School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138, USA.
authors.forename: Darren
authors.initials: D
authors.lastname: Yang
authors.affiliation: Laboratoire de Biochimie Théorique, CNRS UPR 9080, Univ Paris Diderot, Sorbonne Paris Cité, IBPC, Paris, France.
authors.forename: Benjamin
authors.initials: B
authors.lastname: Boyer
authors.affiliation: Laboratoire de Biochimie Théorique, CNRS UPR 9080, Univ Paris Diderot, Sorbonne Paris Cité, IBPC, Paris, France.
authors.forename: Chantal
authors.initials: C
authors.lastname: Prévost
authors.affiliation: Department of Physics, Harvard University, Cambridge, MA 02138, USA.
authors.forename: Claudia
authors.initials: C
authors.lastname: Danilowicz
authors.affiliation: Department of Physics, Harvard University, Cambridge, MA 02138, USA prentiss@fas.harvard.edu.
authors.forename: Mara
authors.initials: M
authors.lastname: Prentiss
mesh_terms: D020029:Base Pairing; D059371:DNA, B-Form / Q000737:chemistry* / Q000378:metabolism; D004277:DNA, Single-Stranded / Q000737:chemistry* / Q000378:metabolism; D059765:Homologous Recombination; D056004:Molecular Dynamics Simulation; D011485:Protein Binding; D011938:Rec A Recombinases / Q000737:chemistry* / Q000378:metabolism
chemical_list: D059371:DNA, B-Form; D004277:DNA, Single-Stranded; D011938:Rec A Recombinases