Dimer:dimer stacking Interactions are important for nucleic acid binding by the archaeal chromatin protein Alba

Clare Jelinska , Biljana Petrovic-Stojanovska , William John Ingledew , Malcolm F White (1)

1 Centre for Biomolecular Sciences

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 here that it binds more tightly to dsDNA than to either ssDNA or RNA. The Alba protein is dimeric in solution, and forms distinct ordered complexes with DNA that have been visualised 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 Arg-59 and Phe-60. Here 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 electron spin resonance are used to confirm that an end-to-end, dimer:dimer interaction forms in the presence of dsDNA.

Mots clés: Life Sciences

Clare Jelinska, Biljana Petrovic-Stojanovska, William John Ingledew, Malcolm F White. Dimer:dimer stacking Interactions are important for nucleic acid binding by the archaeal chromatin protein Alba. Biochemical Journal, 2010, 427 (1), pp.49-55. ⟨10.1042/BJ20091841⟩. ⟨hal-00479285⟩