Understanding water: molecular dynamics simulations of myoglobin.
Molecular dynamics simulations were performed on CO myoglobin to evaluate the stability of the bound water molecules as determined in a neutron diffraction analysis. The myoglobin structure derived from the neutron analysis provided the starting coordinate set used in the simulation. The simulations show that only a few water molecules are tightly bound to protein atoms, while most solvent molecules are labile, breaking and reforming hydrogen bonds. Comparison between myoglobin in solution and in a single crystal highlighted some of the packing effects on the solvent structure and shows that water solvent plays an indispensable role in protein dynamics and structural stability. The described observations explain some of the differences in the experimental results of protein hydration as observed in NMR, neutron and X-ray diffraction studies.
Gu
W
W
Los Alamos National Laboratory, New Mexico 87545, USA.
Garcia
A E
AE
Schoenborn
B P
BP
D003198:Computer Simulation; D003461:Crystallography / Q000379:methods; D006860:Hydrogen Bonding; D009682:Magnetic Resonance Spectroscopy; D008958:Models, Molecular; D009211:Myoglobin / Q000737:chemistry*; D009502:Neutrons; D011487:Protein Conformation; D012542:Scattering, Radiation; D012984:Software; D014867:Water; D014961:X-Ray Diffraction
D009211:Myoglobin; C018013:carboxymyoglobin; D014867:Water