title: Protein-DNA interfaces: a molecular dynamics analysis of time-dependent recognition processes for three transcription factors.
abstract: We have studied the dynamics of three transcription factor-DNA complexes using all-atom, microsecond-scale MD simulations. In each case, the salt bridges and hydrogen bond interactions formed at the protein-DNA interface are found to be dynamic, with lifetimes typically in the range of tens to hundreds of picoseconds, although some interactions, notably those involving specific binding to DNA bases, can be a hundred times longer lived. Depending on the complex studied, this dynamics may or may not lead to the existence of distinct conformational substates. Using a sequence threading technique, it has been possible to determine whether DNA sequence recognition is sensitive or not to such conformational changes, and, in one case, to show that recognition appears to be locally dependent on protein-mediated cation distributions.
authors.affiliation: MMSB UMR 5086 CNRS/University of Lyon I, Institut de Biologie et Chimie des Protéines, 7 passage du Vercors, Lyon 69367, France.
authors.forename: Loïc
authors.initials: L
authors.lastname: Etheve
authors.affiliation: MMSB UMR 5086 CNRS/University of Lyon I, Institut de Biologie et Chimie des Protéines, 7 passage du Vercors, Lyon 69367, France.
authors.forename: Juliette
authors.initials: J
authors.lastname: Martin
authors.affiliation: MMSB UMR 5086 CNRS/University of Lyon I, Institut de Biologie et Chimie des Protéines, 7 passage du Vercors, Lyon 69367, France richard.lavery@ibcp.fr.
authors.forename: Richard
authors.initials: R
authors.lastname: Lavery
mesh_terms: D001483:Base Sequence; D001665:Binding Sites; D004247:DNA / Q000737:chemistry* / Q000378:metabolism; D004268:DNA-Binding Proteins / Q000737:chemistry* / Q000378:metabolism; D006801:Humans; D006860:Hydrogen Bonding; D062105:Molecular Docking Simulation; D056004:Molecular Dynamics Simulation; D009690:Nucleic Acid Conformation; D059372:Nucleotide Motifs; D056510:Position-Specific Scoring Matrices; D011485:Protein Binding; D011487:Protein Conformation; D055748:SOXB1 Transcription Factors / Q000737:chemistry / Q000378:metabolism; D035181:TATA-Box Binding Protein / Q000737:chemistry / Q000378:metabolism; D014157:Transcription Factors / Q000737:chemistry / Q000378:metabolism
chemical_list: D004268:DNA-Binding Proteins; D055748:SOXB1 Transcription Factors; D035181:TATA-Box Binding Protein; D014157:Transcription Factors; D004247:DNA