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Molecular dynamics simulation of hydration in myoglobin
1Department of Biochemistry, University of New Mexico, Albuquerque 87545, USA.
Proteins
|May 1, 1995
Summary
Molecular dynamics simulations reveal that only 4 of 89 bound water molecules remain stable around carbon monoxide myoglobin. Most hydration sites show dynamic water molecule exchange, indicating significant protein-water interface mobility.
Area of Science:
- Biophysics
- Structural Biology
- Computational Chemistry
Background:
- Neutron diffraction studies identified 89 bound water molecules in carbon monoxide myoglobin.
- Understanding protein hydration is crucial for comprehending protein function and dynamics.
Purpose of the Study:
- To evaluate the stability and dynamics of water molecules bound to carbon monoxide myoglobin.
- To investigate the hydrogen bonding interactions between protein and water molecules.
Main Methods:
- Utilized molecular dynamics (MD) simulations with the CHARMM software package.
- Initiated simulation from a myoglobin structure obtained via neutron diffraction analysis.
- Performed 50 picoseconds (ps) of Newtonian dynamics after system solvation, minimization, and equilibration.
Main Results:
- Only 4 out of 89 initially identified water molecules remained continuously bound throughout the 50 ps simulation.
- The majority of solvent molecules exhibited high mobility, with dynamic breaking and reforming of hydrogen bonds.
- At any given moment, 73 hydration sites were occupied by water molecules, though not always the same ones.
Conclusions:
- The bound water molecules in carbon monoxide myoglobin are largely dynamic, not static.
- Protein hydration shells are highly mobile, with constant exchange of water molecules.
- Neutron diffraction provides a static snapshot, while MD simulations reveal the dynamic nature of protein-water interactions.