title: Hierarchical Biomolecular Dynamics: Picosecond Hydrogen Bonding Regulates Microsecond Conformational Transitions.
abstract: Biomolecules exhibit structural dynamics on a number of time scales, including picosecond (ps) motions of a few atoms, nanosecond (ns) local conformational transitions, and microsecond (μs) global conformational rearrangements. Despite this substantial separation of time scales, fast and slow degrees of freedom appear to be coupled in a nonlinear manner; for example, there is theoretical and experimental evidence that fast structural fluctuations are required for slow functional motion to happen. To elucidate a microscopic mechanism of this multiscale behavior, Aib peptide is adopted as a simple model system. Combining extensive molecular dynamics simulations with principal component analysis techniques, a hierarchy of (at least) three tiers of the molecule's free energy landscape is discovered. They correspond to chiral left- to right-handed transitions of the entire peptide that happen on a μs time scale, conformational transitions of individual residues that take about 1 ns, and the opening and closing of structure-stabilizing hydrogen bonds that occur within tens of ps and are triggered by sub-ps structural fluctuations. Providing a simple mechanism of hierarchical dynamics, fast hydrogen bond dynamics is found to be a prerequisite for the ns local conformational transitions, which in turn are a prerequisite for the slow global conformational rearrangement of the peptide. As a consequence of the hierarchical coupling, the various processes exhibit a similar temperature behavior which may be interpreted as a dynamic transition.
authors.affiliation: Biomolecular Dynamics, Institute of Physics, Albert Ludwigs University , Freiburg, 79104 Germany.
authors.forename: Sebastian
authors.initials: S
authors.lastname: Buchenberg
authors.affiliation: Biomolecular Dynamics, Institute of Physics, Albert Ludwigs University , Freiburg, 79104 Germany.
authors.forename: Norbert
authors.initials: N
authors.lastname: Schaudinnus
authors.affiliation: Biomolecular Dynamics, Institute of Physics, Albert Ludwigs University , Freiburg, 79104 Germany.|Freiburg Institute for Advanced Studies (FRIAS), Albert Ludwigs University , Freiburg, 79104 Germany.
authors.forename: Gerhard
authors.initials: G
authors.lastname: Stock
mesh_terms: D006860:Hydrogen Bonding; D056004:Molecular Dynamics Simulation; D010455:Peptides / Q000737:chemistry*; D025341:Principal Component Analysis; D011487:Protein Conformation; D013696:Temperature; D013816:Thermodynamics; D013997:Time Factors
chemical_list: D010455:Peptides