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Water's Contribution to the Energetic Roughness from Peptide Dynamics.

Quentin Johnson1, Urmi Doshi1, Tongye Shen1

  • 1Department of Chemistry and the Center for Biotechnology and Drug Design, Georgia State University, Atlanta, Georgia 30302-4098, Department of Biochemistry, Cellular & Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996, and Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830.

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Water significantly impacts protein dynamics by altering the energy landscape. This study quantifies water

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Area of Science:

  • Biophysics
  • Computational Biology
  • Protein Dynamics

Background:

  • Protein function is intrinsically linked to molecular dynamics and interactions with surrounding water.
  • Water molecule ordering and reordering influence protein energy landscapes and dynamics.
  • Understanding water's role is crucial for accurate biomolecular simulations.

Purpose of the Study:

  • To quantify the contribution of water to the ruggedness of protein energy landscapes.
  • To develop and apply a model for extracting water's effect on energy landscape roughness.
  • To evaluate the impact of water models on biomolecular dynamics.

Main Methods:

  • Molecular dynamics simulations of a peptide substrate analogue.
  • Development and implementation of a model based on the Ornstein-Uhlenbeck process.
  • Application of Zwanzig's theory of diffusion on a rough potential.

Main Results:

  • Water contributes significant additional roughness to protein energy landscapes.
  • At lower temperatures, this water-induced roughness can become comparable to kBT.
  • This roughness can substantially slow down protein dynamics.

Conclusions:

  • Water's contribution to energy landscape ruggedness is a critical factor in protein dynamics.
  • The choice of water model in atomistic simulations directly impacts biomolecular system dynamics.
  • Findings have implications for enzyme function, particularly how substrate landscapes change in different environments.