title: Structural dynamics of E. coli single-stranded DNA binding protein reveal DNA wrapping and unwrapping pathways.
abstract: Escherichia coli single-stranded (ss)DNA binding (SSB) protein mediates genome maintenance processes by regulating access to ssDNA. This homotetrameric protein wraps ssDNA in multiple distinct binding modes that may be used selectively in different DNA processes, and whose detailed wrapping topologies remain speculative. Here, we used single-molecule force and fluorescence spectroscopy to investigate E. coli SSB binding to ssDNA. Stretching a single ssDNA-SSB complex reveals discrete states that correlate with known binding modes, the likely ssDNA conformations and diffusion dynamics in each, and the kinetic pathways by which the protein wraps ssDNA and is dissociated. The data allow us to construct an energy landscape for the ssDNA-SSB complex, revealing that unwrapping energy costs increase the more ssDNA is unraveled. Our findings provide insights into the mechanism by which proteins gain access to ssDNA bound by SSB, as demonstrated by experiments in which SSB is displaced by the E. coli recombinase RecA.
authors: Department of Physics, Center for the Physics of Living Cells, Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, United States.
authors: Sukrit
authors: S
authors: Suksombat
authors: Department of Physics, Center for the Physics of Living Cells, Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, United States.
authors: Rustem
authors: R
authors: Khafizov
authors: Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, United States.
authors: Alexander G
authors: AG
authors: Kozlov
authors: Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, United States.
authors: Timothy M
authors: TM
authors: Lohman
authors: Department of Physics, Center for the Physics of Living Cells, Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, United States.
authors: Yann R
authors: YR
authors: Chemla
mesh_terms: D004269:DNA, Bacterial / Q000737:chemistry* / Q000378:metabolism; D004277:DNA, Single-Stranded / Q000737:chemistry* / Q000378:metabolism; D004268:DNA-Binding Proteins / Q000737:chemistry* / Q000378:metabolism*; D004926:Escherichia coli / Q000737:chemistry / Q000378:metabolism*; D029968:Escherichia coli Proteins / Q000737:chemistry* / Q000378:metabolism*; D007700:Kinetics; D008856:Microscopy, Fluorescence; D009690:Nucleic Acid Conformation; D052898:Optical Tweezers; D011485:Protein Binding; D011487:Protein Conformation
chemical_list: D004269:DNA, Bacterial; D004277:DNA, Single-Stranded; D004268:DNA-Binding Proteins; D029968:Escherichia coli Proteins; C476430:SSB protein, E coli
keywords: E. coli; biophysics; energy landscape; optical tweezers; protein-nucleic acid interaction; single molecule; single stranded DNA binding protein; structural biology