Dimer-dimer stacking interactions are important for nucleic acid binding by the archaeal chromatin protein Alba.
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 Arg59 and Phe60. 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 Phe60 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.
Jelinska
Clare
C
Centre for Biomolecular Sciences, University of St Andrews, Fife KY169ST, U.K.
Petrovic-Stojanovska
Biljana
B
Ingledew
W John
WJ
White
Malcolm F
MF
D019843:Archaeal Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D015153:Blotting, Western; D002843:Chromatin / Q000235:genetics / Q000378:metabolism; D018360:Crystallography, X-Ray; D019641:DNA, Archaeal / Q000235:genetics / Q000378:metabolism*; D004268:DNA-Binding Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D019281:Dimerization; D004578:Electron Spin Resonance Spectroscopy; D024202:Electrophoretic Mobility Shift Assay; D016297:Mutagenesis, Site-Directed; D009154:Mutation / Q000235:genetics; D009696:Nucleic Acids / Q000235:genetics / Q000378:metabolism*; D011485:Protein Binding; D011487:Protein Conformation
D019843:Archaeal Proteins; D002843:Chromatin; D019641:DNA, Archaeal; D004268:DNA-Binding Proteins; D009696:Nucleic Acids; C444360:Sso10b protein, Sulfolobus solfataricus