title: Model of a DNA-protein complex of the architectural monomeric protein MC1 from Euryarchaea.
abstract: In Archaea the two major modes of DNA packaging are wrapping by histone proteins or bending by architectural non-histone proteins. To supplement our knowledge about the binding mode of the different DNA-bending proteins observed across the three domains of life, we present here the first model of a complex in which the monomeric Methanogen Chromosomal protein 1 (MC1) from Euryarchaea binds to the concave side of a strongly bent DNA. In laboratory growth conditions MC1 is the most abundant architectural protein present in Methanosarcina thermophila CHTI55. Like most proteins that strongly bend DNA, MC1 is known to bind in the minor groove. Interaction areas for MC1 and DNA were mapped by Nuclear Magnetic Resonance (NMR) data. The polarity of protein binding was determined using paramagnetic probes attached to the DNA. The first structural model of the DNA-MC1 complex we propose here was obtained by two complementary docking approaches and is in good agreement with the experimental data previously provided by electron microscopy and biochemistry. Residues essential to DNA-binding and -bending were highlighted and confirmed by site-directed mutagenesis. It was found that the Arg25 side-chain was essential to neutralize the negative charge of two phosphates that come very close in response to a dramatic curvature of the DNA.
authors.affiliation: Centre de Biophysique Moléculaire, Centre National de la Recherche Scientifique UPR 4301, Université d'Orléans, Orleans, France.
authors.forename: Françoise
authors.initials: F
authors.lastname: Paquet
authors.affiliation: Faculté des Sciences Pharmaceutiques et Biologiques, Institut de Génétique et Développement de Rennes, Centre National de la Recherche Scientifique UMR 6290, Université de Rennes1, Rennes, France.
authors.forename: Olivier
authors.initials: O
authors.lastname: Delalande
authors.affiliation: Centre de Biophysique Moléculaire, Centre National de la Recherche Scientifique UPR 4301, Université d'Orléans, Orleans, France.
authors.forename: Stephane
authors.initials: S
authors.lastname: Goffinont
authors.affiliation: Centre de Biophysique Moléculaire, Centre National de la Recherche Scientifique UPR 4301, Université d'Orléans, Orleans, France.
authors.forename: Françoise
authors.initials: F
authors.lastname: Culard
authors.affiliation: Centre de Biophysique Moléculaire, Centre National de la Recherche Scientifique UPR 4301, Université d'Orléans, Orleans, France.
authors.forename: Karine
authors.initials: K
authors.lastname: Loth
authors.affiliation: Centre de Biophysique Moléculaire, Centre National de la Recherche Scientifique UPR 4301, Université d'Orléans, Orleans, France.
authors.forename: Ulysse
authors.initials: U
authors.lastname: Asseline
authors.affiliation: Centre de Biophysique Moléculaire, Centre National de la Recherche Scientifique UPR 4301, Université d'Orléans, Orleans, France.
authors.forename: Bertrand
authors.initials: B
authors.lastname: Castaing
authors.affiliation: Centre de Biophysique Moléculaire, Centre National de la Recherche Scientifique UPR 4301, Université d'Orléans, Orleans, France.
authors.forename: Celine
authors.initials: C
authors.lastname: Landon
mesh_terms: D019843:Archaeal Proteins / Q000737:chemistry* / Q000378:metabolism*; D001483:Base Sequence; D004247:DNA / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D008958:Models, Molecular; D062105:Molecular Docking Simulation; D009690:Nucleic Acid Conformation; D011485:Protein Binding; D011487:Protein Conformation; D012261:Ribonucleoproteins / Q000737:chemistry* / Q000378:metabolism*; D055672:Static Electricity; D013499:Surface Properties
chemical_list: D019843:Archaeal Proteins; C051211:HMb protein, Methanosarcina; D012261:Ribonucleoproteins; D004247:DNA