title: Mechanism of conformational coupling in SecA: Key role of hydrogen-bonding networks and water interactions.
abstract: SecA uses the energy yielded by the binding and hydrolysis of adenosine triphosphate (ATP) to push secretory pre-proteins across the plasma membrane in bacteria. Hydrolysis of ATP occurs at the nucleotide-binding site, which contains the conserved carboxylate groups of the DEAD-box helicases. Although crystal structures provide valuable snapshots of SecA along its reaction cycle, the mechanism that ensures conformational coupling between the nucleotide-binding site and the other domains of SecA remains unclear. The observation that SecA contains numerous hydrogen-bonding groups raises important questions about the role of hydrogen-bonding networks and hydrogen-bond dynamics in long-distance conformational couplings. To address these questions, we explored the molecular dynamics of SecA from three different organisms, with and without bound nucleotide, in water. By computing two-dimensional hydrogen-bonding maps we identify networks of hydrogen bonds that connect the nucleotide-binding site to remote regions of the protein, and sites in the protein that respond to specific perturbations. We find that the nucleotide-binding site of ADP-bound SecA has a preferred geometry whereby the first two carboxylates of the DEAD motif bridge via hydrogen-bonding water. Simulations of a mutant with perturbed ATP hydrolysis highlight the water-bridged geometry as a key structural element of the reaction path.
authors.affiliation: Theoretical Molecular Biophysics, Department of Physics, Freie Universitaet Berlin, Arnimallee 14, D-14195 Berlin, Germany.
authors.forename: Stefan
authors.initials: S
authors.lastname: Milenkovic
authors.affiliation: Theoretical Molecular Biophysics, Department of Physics, Freie Universitaet 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: D000251:Adenosine Triphosphatases / Q000737:chemistry* / Q000235:genetics; D000255:Adenosine Triphosphate / Q000737:chemistry* / Q000235:genetics; D020816:Amino Acid Motifs; D001412:Bacillus subtilis / Q000201:enzymology* / Q000235:genetics; D001426:Bacterial Proteins / Q000737:chemistry* / Q000235:genetics; D006860:Hydrogen Bonding; D026901:Membrane Transport Proteins / Q000737:chemistry* / Q000235:genetics; D056004:Molecular Dynamics Simulation; D009154:Mutation; D017434:Protein Structure, Tertiary; D000069816:SEC Translocation Channels; D000081416:SecA Proteins; D013329:Structure-Activity Relationship; D014867:Water / Q000737:chemistry*
chemical_list: D001426:Bacterial Proteins; D026901:Membrane Transport Proteins; D000069816:SEC Translocation Channels; D014867:Water; D000255:Adenosine Triphosphate; D000251:Adenosine Triphosphatases; D000081416:SecA Proteins
keywords: ATP hydrolysis; Hydrogen-bond maps; Molecular dynamics; Protein dynamics; Protein motor