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Protein hydration elucidated by molecular dynamics simulation

P J Steinbach1, B R Brooks

  • 1Laboratory of Structural Biology, National Institutes of Health, Betheda, MD 20892.

Proceedings of the National Academy of Sciences of the United States of America
|October 1, 1993
PubMed
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Molecular dynamics simulations reveal that 350 water molecules fully hydrate myoglobin, stabilizing its structure and influencing its transitions. This hydration affects protein motion and conformational changes, aligning with experimental findings.

Area of Science:

  • Biophysics
  • Computational Biology
  • Structural Biology

Background:

  • Myoglobin hydration is crucial for its function and stability.
  • Previous studies have suggested varying numbers of water molecules hydrating myoglobin.
  • Understanding protein hydration is key to deciphering protein dynamics.

Purpose of the Study:

  • To determine the precise number of water molecules hydrating myoglobin using molecular dynamics simulations.
  • To investigate the role of these water molecules in protein conformation, transitions, and dynamics.
  • To compare simulation results with experimental data from X-ray and neutron diffraction.

Main Methods:

  • Extensive molecular dynamics (MD) simulations were performed.
  • Simulations covered a wide range of hydration conditions.

Related Experiment Videos

  • Analysis focused on water molecule distribution, protein conformation, and transition rates.

    • Main Results:

    • Myoglobin is fully hydrated by 350 water molecules, consistent with experimental data.
    • Hydrating water molecules form clusters, interacting with charged groups and leaving some surface areas uncovered.
    • Hydration at 300 K stabilizes carboxymyoglobin conformation, reduces torsional transitions, and promotes alternative surface conformations.
    • Simulations reproduced the experimentally observed glass transition near 220 K, correlating with increased dihedral angle transitions.
    • Protein hydration enhances anharmonic motion above 220 K.

    Conclusions:

    • 350 water molecules play a significant role in myoglobin's structural stability and dynamics.
    • Protein hydration influences the glass transition and enhances anharmonic motions.
    • MD simulations provide a valuable tool for understanding protein hydration and its effects.