title: Oscillatory Diffusion and Second-Order Cyclostationarity in Alanine Tripeptide from Molecular Dynamics Simulation.
abstract: Molecular dynamics (MD) simulation distinctly describes motions of biomolecules at high resolution and can potentially be used to explain allosteric mechanism in subcellular processes. Statistical methods are necessary to realize this potential because MD simulations generate a large volume of data and because the analysis is never efficient, objective, or thorough without using appropriate statistical approaches. Tracing the flow of information within a biomolecule requires not only a description of an overall mechanism but also a multiscale statistical description from atomic interactions to the overall mechanism. The foundation of this multiscale description, in general, is a measure of correlation between motions of atoms or residues, as reflected by dynamic cross-correlation, Pearson correlation, or mutual information. However, these correlations can be inadequate because they assume wide sense stationarity, which means that the instantaneous average and correlation of a particular property are time-independent. Consequently, these measures of correlation cannot account for correlation between motions of different frequencies, since frequency implies oscillation and variation over time. Here, we characterize the nonstationarity in the form of pure oscillatory instantaneous variance in the signed dihedral angular accelerations (SDAA) along the main chain of alanine tripeptide in MD simulations by power spectrum, corrected squared envelope spectrum (CSES), and cross-CSES. This oscillation has a physical interpretation of an oscillatory diffusion. The fraction of this oscillation in all motions is as high as about 40% at some frequencies. This shows that oscillatory instantaneous variance exists in the SDAA and that significant correlation may not be accounted for in current correlation analysis. This oscillation is also found to transmit between dihedral angles. These results could have implications in the understanding of the dynamics of biomolecules.
authors.affiliation: Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University , Atlanta, Georgia 30302-3965, United States.
authors.forename: Ka Chun
authors.initials: KC
authors.lastname: Ho
authors.affiliation: Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University , Atlanta, Georgia 30302-3965, United States.
authors.forename: Donald
authors.initials: D
authors.lastname: Hamelberg
mesh_terms: D000409:Alanine / Q000737:chemistry*; D004058:Diffusion; D056004:Molecular Dynamics Simulation; D009842:Oligopeptides / Q000737:chemistry* / Q000378:metabolism
chemical_list: D009842:Oligopeptides; D000409:Alanine