title: Coupling between inter-helical hydrogen bonding and water dynamics in a proton transporter.
abstract: Long-distance proton transfers by proton pumps occurs in discrete steps that may involve the direct participation of protein sidechains and water molecules, and coupling of protonation changes to structural rearrangements of the protein matrix. Here we explore the role of inter-helical hydrogen bonding in long-distance protein conformational coupling and dynamics of internal water molecules. From molecular dynamics simulations of wild type and nine different bacteriorhodopsin mutants we find that both intra- and inter-helical hydrogen bonds are important determinants of the local protein structure, dynamics, and water interactions. Based on molecular dynamics and bioinformatics analyses, we identify an aspartate/threonine inter-helical hydrogen-bonding motif involved in controlling the local conformational dynamics. Perturbation of inter-helical hydrogen bonds can couple to rapid changes in water dynamics.
authors.affiliation: Department of Artificial Intelligence, University of Granada, E-18071 Granada, Spain.
authors.forename: Coral
authors.initials: C
authors.lastname: del Val
authors.affiliation: University Medical Center Utrecht, Department of Radiotherapy, Heidelberglaan 100, 3584 CX Utrecht, The Netherlands.
authors.forename: Luiza
authors.initials: L
authors.lastname: Bondar
authors.affiliation: Theoretical Molecular Biophysics, Institute of Theoretical Physics, Department of Physics, Freie Universität Berlin, Arnimallee 14, D-14195 Berlin, Germany. Electronic address: nbondar@zedat.fu-berlin.de.
authors.forename: Ana-Nicoleta
authors.initials: AN
authors.lastname: Bondar
mesh_terms: D000595:Amino Acid Sequence; D019943:Amino Acid Substitution; D001436:Bacteriorhodopsins / Q000737:chemistry* / Q000235:genetics; D001665:Binding Sites; D016384:Consensus Sequence; D006860:Hydrogen Bonding; D056004:Molecular Dynamics Simulation; D008969:Molecular Sequence Data; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D014867:Water / Q000737:chemistry*
chemical_list: D014867:Water; D001436:Bacteriorhodopsins
keywords: Hydrogen bonding; Proton transfer; Water dynamics