title: Intrinsically disordered C-terminal tails of E. coli single-stranded DNA binding protein regulate cooperative binding to single-stranded DNA.
abstract: The homotetrameric Escherichia coli single-stranded DNA binding protein (SSB) plays a central role in DNA replication, repair and recombination. E. coli SSB can bind to long single-stranded DNA (ssDNA) in multiple binding modes using all four subunits [(SSB)65 mode] or only two subunits [(SSB)35 binding mode], with the binding mode preference regulated by salt concentration and SSB binding density. These binding modes display very different ssDNA binding properties with the (SSB)35 mode displaying highly cooperative binding to ssDNA. SSB tetramers also bind an array of partner proteins, recruiting them to their sites of action. This is achieved through interactions with the last 9 amino acids (acidic tip) of the intrinsically disordered linkers (IDLs) within the four C-terminal tails connected to the ssDNA binding domains. Here, we show that the amino acid composition and length of the IDL affects the ssDNA binding mode preferences of SSB protein. Surprisingly, the number of IDLs and the lengths of individual IDLs together with the acidic tip contribute to highly cooperative binding in the (SSB)35 binding mode. Hydrodynamic studies and atomistic simulations suggest that the E. coli SSB IDLs show a preference for forming an ensemble of globular conformations, whereas the IDL from Plasmodium falciparum SSB forms an ensemble of more extended random coils. The more globular conformations correlate with cooperative binding.
authors.affiliation: Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, 660 South Euclid Avenue, St. Louis, MO 63110, USA.
authors.forename: Alexander G
authors.initials: AG
authors.lastname: Kozlov
authors.affiliation: Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, 660 South Euclid Avenue, St. Louis, MO 63110, USA.
authors.forename: Elizabeth
authors.initials: E
authors.lastname: Weiland
authors.affiliation: Department of Biomedical Engineering and Center for Biological Systems Engineering, Washington University in St. Louis, 1 Brookings Drive, St. Louis, MO 63130, USA.
authors.forename: Anuradha
authors.initials: A
authors.lastname: Mittal
authors.affiliation: Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, 660 South Euclid Avenue, St. Louis, MO 63110, USA.
authors.forename: Vince
authors.initials: V
authors.lastname: Waldman
authors.affiliation: Department of Chemistry and Biochemistry, Utah State University, 0300 Old Main Hill, Logan, UT 84322, USA.
authors.forename: Edwin
authors.initials: E
authors.lastname: Antony
authors.affiliation: Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, 660 South Euclid Avenue, St. Louis, MO 63110, USA.
authors.forename: Nicole
authors.initials: N
authors.lastname: Fazio
authors.affiliation: Department of Biomedical Engineering and Center for Biological Systems Engineering, Washington University in St. Louis, 1 Brookings Drive, St. Louis, MO 63130, USA. Electronic address: pappu@wustl.edu.
authors.forename: Rohit V
authors.initials: RV
authors.lastname: Pappu
authors.affiliation: Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, 660 South Euclid Avenue, St. Louis, MO 63110, USA. Electronic address: lohman@biochem.wustl.edu.
authors.forename: Timothy M
authors.initials: TM
authors.lastname: Lohman
mesh_terms: D004260:DNA Repair / Q000235:genetics; D004261:DNA Replication / Q000235:genetics; D004277:DNA, Single-Stranded / Q000378:metabolism*; D004268:DNA-Binding Proteins / Q000235:genetics / Q000378:metabolism*; D004926:Escherichia coli / Q000235:genetics / Q000378:metabolism*; D029968:Escherichia coli Proteins / Q000235:genetics / Q000378:metabolism*; D064267:Intrinsically Disordered Proteins / Q000378:metabolism; D008958:Models, Molecular; D010963:Plasmodium falciparum / Q000235:genetics / Q000378:metabolism*; D011485:Protein Binding / Q000502:physiology; D011487:Protein Conformation; D017384:Sequence Deletion / Q000235:genetics
chemical_list: D004277:DNA, Single-Stranded; D004268:DNA-Binding Proteins; D029968:Escherichia coli Proteins; D064267:Intrinsically Disordered Proteins; C476430:SSB protein, E coli
keywords: DNA repair; DNA replication; cooperativity; regulation; simulations