1. Dimer–dimer stacking interactions are important for nucleic acid binding by the archaeal chromatin protein Alba
- Author
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Malcolm F. White, Biljana Petrovic-Stojanovska, W. John Ingledew, Clare Jelinska, Centre for Biomolecular Sciences, University of St Andrews [Scotland], BBSRC, EPSRC, University of St Andrews. Scottish Oceans Institute, University of St Andrews. School of Biology, and University of St Andrews. Biomedical Sciences Research Complex
- Subjects
ssRNA, single-stranded RNA ,Protein Conformation ,Dimer ,SSH10B ,Electrophoretic Mobility Shift Assay ,Plasma protein binding ,Crystallography, X-Ray ,Biochemistry ,chemistry.chemical_compound ,Protein structure ,Nucleic Acids ,cw-ESR, continuous wave ESR ,0303 health sciences ,Alba ,dsDNA, double-stranded DNA ,Distance ,030302 biochemistry & molecular biology ,Life Sciences ,Acetylation ,Chromatin ,DNA-Binding Proteins ,DNA, Archaeal ,Mechanism ,SDSL, site-directed spin labelling ,Dimerization ,Research Article ,Protein Binding ,archaea ,Archaeal Proteins ,Blotting, Western ,SIR2 ,Biology ,HSQC, heteronuclear single-quantum coherence ,EMSA, electrophoretic mobility-shift assay ,FRET, fluorescence resonance energy transfer ,DNA-binding ,03 medical and health sciences ,ssDNA, single-stranded DNA ,Electrophoretic mobility shift assay ,Molecular Biology ,ESR ,030304 developmental biology ,Electron Spin Resonance Spectroscopy ,RNA ,Cell Biology ,Archaea ,NMR ,DEER, double electron–electron resonance ,chemistry ,site-directed spin labelling ,Site-directed spin labelling ,Mutation ,Mutagenesis, Site-Directed ,Nucleic acid ,Biophysics ,DNA - Abstract
Archaea use a variety of small basic proteins to package their DNA. One of the most widespread and highly conserved is the Alba (Sso10b) protein. Alba interacts with both DNA and RNA in vitro, and we show in the present study that it binds more tightly to dsDNA (double-stranded DNA) than to either ssDNA (single-stranded DNA) or RNA. The Alba protein is dimeric in solution, and forms distinct ordered complexes with DNA that have been visualized by electron microscopy studies; these studies suggest that, on binding dsDNA, the protein forms extended helical protein fibres. An end-to-end association of consecutive Alba dimers is suggested by the presence of a dimer-dimer interface in crystal structures of Alba from several species, and by the strong conservation of the interface residues, centred on Are and Phe(60). In the present study we map perturbation of the polypeptide backbone of Alba upon binding to DNA and RNA by NMR, and demonstrate the central role of Phe(60) in forming the dimer dimer interface. Site-directed spin labelling and pulsed ESR are used to confirm that an end-to-end, dimer dimer interaction forms in the presence of dsDNA. Publisher PDF
- Published
- 2010
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