title: Head to head dimer model; an alternative model for the strand exchange reaction by RecA protein of Escherichia coli.
abstract: The RecA protein of E coli promotes a strand exchange reaction in vitro which appears to be similar to homologous genetic recombination in vivo. A model for the mechanism of strand transfer reaction by RecA protein has been proposed by Howard-Flanders et al based on the assumption that the RecA monomer has two distinctive DNA binding sites both of which can bind to ssDNA as well as dsDNA. Here, I propose an alternative model based on the assumption that RecA monomer has a single domain for binding to a polynucleotide chain with a unique polarity. In addition, the model is based on a few mechanical assumptions that, in the presence of ATP, two RecA molecules form a head to head dimer as the basic binding unit to DNA, and that the binding of RecA protein to a polynucleotide chain induces a structural change of RecA protein that causes a higher state of affinity for another RecA molecule that is expressed as cooperativy. The model explains many of the biochemical capabilities of RecA protein including the polar polymerization of RecA protein on single stranded DNA and polar strand transfer of DNA by the protein as well as the formation of a joint DNA molecule in a paranemic configuration. The model also presents the energetics in the strand transfer reaction.
authors.affiliation: Laboratory of Genetics, Department of Biology, Faculty of Science, Osaka University, Japan.
authors.forename: T
authors.initials: T
authors.lastname: Horii
mesh_terms: D000255:Adenosine Triphosphate / Q000494:pharmacology; D001665:Binding Sites; D004247:DNA / Q000378:metabolism*; D004277:DNA, Single-Stranded / Q000378:metabolism; D004926:Escherichia coli / Q000032:analysis*; D046911:Macromolecular Substances; D008954:Models, Biological; D011487:Protein Conformation; D011938:Rec A Recombinases / Q000737:chemistry / Q000378:metabolism*; D011995:Recombination, Genetic; D012689:Sequence Homology, Nucleic Acid
chemical_list: D004277:DNA, Single-Stranded; D046911:Macromolecular Substances; D000255:Adenosine Triphosphate; D004247:DNA; D011938:Rec A Recombinases