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Dynamic coupling between coordinates in a model for biomolecular isomerization.

Ao Ma1, Ambarish Nag, Aaron R Dinner

  • 1Department of Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, The University of Chicago, 5640 S. Ellis Avenue, Chicago, Illinois 60637, USA.

The Journal of Chemical Physics
|April 22, 2006
PubMed
Summary
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Understanding complex reactions requires projecting dynamics onto meaningful coordinates. This study shows both the potential of mean force and diffusion tensor are essential for quantitatively describing alanine dipeptide dynamics.

Area of Science:

  • Chemical Physics
  • Computational Chemistry
  • Biomolecular Dynamics

Background:

  • Complex chemical reactions require dimensionality reduction to understand system dynamics.
  • Previous work introduced an automatic method for identifying coordinates related to stable-state commitment probabilities.
  • This method was successfully applied to the alanine dipeptide's C(7eq)-->alpha(R) biomolecular isomerization.

Purpose of the Study:

  • To explore approximate methods for estimating diffusion tensors in restrained systems.
  • To quantitatively assess the importance of the potential of mean force and diffusion tensor in describing system dynamics.
  • To investigate the role of off-diagonal elements in the diffusion tensor for coupled coordinates.

Main Methods:

  • Estimating diffusion tensors for systems with one and two-dimensional restraints.

Related Experiment Videos

  • Applying an extension of Kramers theory for unimolecular reaction rates.
  • Analyzing the alanine dipeptide's C(7eq)-->alpha(R) transition dynamics.

    • Main Results:

    • Both the potential of mean force and the diffusion tensor are crucial for quantitative description of alanine dipeptide dynamics.
    • Off-diagonal elements of the diffusion tensor are significant, indicating coupling between coordinates.
    • Hydrodynamic-like response of remaining degrees of freedom influences coordinate coupling.

    Conclusions:

    • Accurate modeling of biomolecular dynamics necessitates consideration of both potential of mean force and diffusion tensor.
    • Coordinate coupling, influenced by solvent dynamics, plays a vital role in reaction pathways.
    • The developed methods provide a quantitative framework for analyzing complex chemical systems.