tailieunhanh - Báo cáo khoa học: Refined solution structure and backbone dynamics of the archaeal MC1 protein

The 3D structure of methanogen chromosomal protein 1 (MC1), deter-mined with heteronuclear NMR methods, agrees with its function in terms of the shape and nature of the binding surface, whereas the 3D structure determined with homonuclear NMR does not. | IFEBS Journal Refined solution structure and backbone dynamics of the archaeal MC1 protein Francoise Paquet Karine Loth Herve Meudal Francoise Culard Daniel Genest and Gerard Lancelot Centre de Biophysique Moleculaire CNRS UPR 4301 Orleans France Keywords arm bulges DNA-binding protein molecular dynamics MD simulation NMR relaxation Correspondence F. Paquet Centre de Biophysique Moleculaire CNRS UPR 4301 Rue Charles-Sadron F-45071 Orleans Cedex 2 France Fax 33 2 38631517 Tel 33 2 38257692 E-mail Database Structuraldata are available in the Protein Data Bank database under the accession number 2KHL Received 26 July 2010 revised 15 September 2010 accepted 20 October 2010 doi The 3D structure of methanogen chromosomal protein 1 MC1 determined with heteronuclear NMR methods agrees with its function in terms of the shape and nature of the binding surface whereas the 3D structure determined with homonuclear NMR does not. The structure features five loops which show a large distribution in the ensemble of 3D structures. Evidence for the fact that this distribution signifies internal mobility on the nanosecond time scale was provided by using 15N-relaxation and molecular dynamics simulations. Structural variations of the arm 11 residues induced large shape anisotropy variations on the nanosecond time scale that ruled out the use of the model-free formalism to analyze the relaxation data. The backbone dynamics analysis of MC1 was achieved by comparison with 20 ns molecular dynamics trajectories. Two b-bulges showed that hydrogen bond formation correlated with u and w dihedral angle transitions. These jumps were observed on the nanosecond time scale in agreement with a large decrease in 15N-NOE for Gly17 and Ile89. One water molecule bridging NH Glu87 and CO Val57 through hydrogen bonding contributed to these dynamics. Nanosecond slow motions observed in loops LP3 35-42 and LP5 67-77 reflected the lack of .