Dynamics of water confined in the interdomain region of a multidomain protein.
Molecular dynamics simulations are performed to study the dynamics of interfacial water confined in the interdomain region of a two-domain protein, BphC enzyme. The results show that near the protein surface the water diffusion constant is much smaller and the water-water hydrogen bond lifetime is much longer than that in bulk. The diffusion constant and hydrogen bond lifetime can vary by a factor of as much as 2 in going from the region near the hydrophobic domain surface to the bulk. Water molecules in the first solvation shell persist for a much longer time near local concave sites than near convex sites. Also, the water layer survival correlation time shows that on average water molecules near the extended hydrophilic surfaces have longer residence times than those near hydrophobic surfaces. These results indicate that local surface curvature and hydrophobicity have a significant influence on water dynamics.
Department of Chemistry, Columbia University, New York, New York 10027, USA.
Lan
L
Hua
Xuhui
X
Huang
Ruhong
R
Zhou
B J
BJ
Berne
D003198:Computer Simulation; D004058:Diffusion; D049308:Dioxygenases / Q000737:chemistry*; D006860:Hydrogen Bonding; D011487:Protein Conformation; D017510:Protein Folding; D013499:Surface Properties; D013997:Time Factors; D014867:Water / Q000737:chemistry*
D014867:Water; D049308:Dioxygenases; C074272:2,3-dihydroxybiphenyl oxygenase