Statistical properties of liquid protein-water molecular system dynamics

  • Jutharath Voraprateep

    Student thesis: Doctoral ThesisDoctor of Philosophy


    It is considered an established fact that water plays the major role in protein
    motion, there is a close connection between the water dynamics and the
    protein conformational dynamics.

    We report on statistical analysis of such conformational dynamics obtained
    using classical molecular dynamics simulations with explicit water. We
    investigate specific moments in time when one of the dihedral angles of
    a simulated protein (a peptide dialanine) makes a large amplitude change
    causing a conformational transition in the peptide. We are interested in
    finding statistical correlations between the values of the angle at the moment
    of transition and several moments in advance of the transition (between
    0.0 and 50.1ps). We also investigate how these correlations change when
    conditioned on the presence of water at different locations in space around
    the peptide. The challenge is in a large number of parameters that influence
    the conformational dynamics, which leads to multivariate probabilities. As
    statistical tools, we use pair-copulas and the Kendall's tau correlation.

    Copulas are a special way of representing multivariate probabilities. Paircopulas
    construction (PCC) decomposes a multivariate probability density
    into bivariate copulas, so-called pair-copulas. D-vine is one of graphical
    models that give a specific way of decomposing the probability density.
    The dependency structure is determined by the bivariate copulas and a
    nested set of trees using pair-copula. For this research, we apply the D-vine
    to study the statistical correlations between variables describing molecular
    conformation of a peptide and the properties of water molecules surrounding
    the peptide.

    We have found that the dynamics of peptides conformation possesses temporal
    correlations well in advance of the moments of conformational transitions.
    Moreover, when conditioned on the presence of water molecules
    at a few very specific locations in the first hydration shell of the peptide,
    these correlations become stronger and longer in time. This quantifies the
    influence of water on the conformational transitions and specifies water
    molecules that appear critical for the peptide to make successful conformational
    Date of Award20 Jun 2017
    Original languageEnglish
    SupervisorDmitry Nerukh (Supervisor)

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