Molecular dynamics simulation of solvated azurin: correlation between surface solvent accessibility and water residence times.
A system containing the globular protein azurin and 3,658 water molecules has been simulated to investigate the influence on water dynamics exerted by a protein surface. Evaluation of water mean residence time for elements having different secondary structure did not show any correlation. Identically, comparison of solvent residence time for atoms having different charge and polarity did not show any clear trend. The main factor influencing water residence time in proximity to a specific site was found to be its solvent accessibility. In detail for atoms belonging to lateral chains and having solvent-accessible surface lower than approximately 16 A(2)a relation is found for which charged and polar atoms are surrounded by water molecules characterized by residence times longer than the non polar ones. The involvement of the low accessible protein atom in an intraprotein hydrogen bond further modulates the length of the water residence time. On the other hand for surfaces having high solvent accessibility, all atoms, independently of their character, are surrounded by water molecules which rapidly exchange with the bulk solvent. Proteins 2000;39:56-67.
Luise
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INFM and Department of Biology, University of Rome "Tor Vergata," Rome, Italy.
Falconi
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M
Desideri
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D001400:Azurin / Q000737:chemistry*; D003198:Computer Simulation; D008958:Models, Molecular; D017433:Protein Structure, Secondary; D012984:Software; D012996:Solutions; D012997:Solvents; D013499:Surface Properties; D014867:Water
D012996:Solutions; D012997:Solvents; D014867:Water; D001400:Azurin