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Related Experiment Videos

Viscosity dependence of protein dynamics.

R Walser1, W F van Gunsteren

  • 1Laboratory of Physical Chemistry, Swiss Federal Institute of Technology Zürich, Zürich, Switzerland.

Proteins
|January 11, 2001
PubMed
Summary

Protein dynamics are significantly impacted by solvent viscosity. Molecular dynamics simulations reveal that while protein structure remains stable, its internal movements slow down considerably in more viscous solvents, affecting both surface and core regions.

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Area of Science:

  • Biophysics
  • Computational Chemistry
  • Molecular Dynamics

Background:

  • Solvent properties critically influence biomolecular behavior.
  • Understanding solvent effects on protein dynamics is crucial for various biological processes.
  • Factor Xa is a key enzyme in the coagulation cascade.

Purpose of the Study:

  • To investigate the influence of solvent viscosity on the dynamics of the protein factor Xa.
  • To determine how changes in viscosity affect both equilibrium and dynamic properties of the protein.
  • To explore the extent to which solvent viscosity impacts protein core versus surface dynamics.

Main Methods:

  • Utilized molecular dynamics (MD) simulations.
  • Simulated factor Xa in two solvents with a 10-fold difference in viscosity.

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  • Achieved viscosity difference by altering solvent atom masses by a factor of 100.

    • Main Results:

    • Protein equilibrium properties (average structure, fluctuations, secondary structure) were independent of solvent viscosity.
    • Protein dynamic properties, including atom-positional correlation times and torsional angle transitions, were viscosity-dependent.
    • Proteins exhibited greater mobility in lower viscosity solvents; core atom relaxation times increased with viscosity, even more so than surface atoms.

    Conclusions:

    • Solvent viscosity significantly modulates protein dynamics, not just surface interactions but also internal core motions.
    • Increased solvent viscosity leads to slower protein dynamics, with a pronounced effect on the protein's core.
    • These findings highlight the importance of considering solvent viscosity in simulations and understanding protein function.