Depth dependent dynamics in the hydration shell of a protein.
We study the dynamics of hydration water/protein association in folded proteins using lysozyme and myoglobin as examples. Extensive molecular dynamics simulations are performed to identify underlying mechanisms of the dynamical transition that corresponds to the onset of amplified atomic fluctuations in proteins. The results indicate that the number of water molecules within a cutoff distance of each residue scales linearly with protein depth index and is not affected by the local dynamics of the backbone. Keeping track of the water molecules within the cutoff sphere, we observe an effective residence time, scaling inversely with depth index at physiological temperatures while the diffusive escape is highly reduced below the transition. A depth independent orientational memory loss is obtained for the average dipole vector of the water molecules within the sphere when the protein is functional. While below the transition temperature, the solvent is in a glassy state, acting as a solid crust around the protein, inhibiting any large scale conformational fluctuations. At the transition, most of the hydration shell unfreezes and water molecules collectively make the protein more flexible.
Servantie
J
J
Faculty of Engineering and Natural Sciences, Sabanci University, Orhanli 34956 Tuzla, Istanbul 34956, Turkey. cservantie@sabanciuniv.edu
Atilgan
C
C
Atilgan
A R
AR
D000465:Algorithms; D004058:Diffusion; D056004:Molecular Dynamics Simulation; D009113:Muramidase / Q000737:chemistry; D009211:Myoglobin / Q000737:chemistry; D018583:Pliability; D011506:Proteins / Q000737:chemistry*; D012997:Solvents / Q000737:chemistry; D013696:Temperature; D014867:Water / Q000737:chemistry*
D009211:Myoglobin; D011506:Proteins; D012997:Solvents; D014867:Water; D009113:Muramidase