Insight into the role of hydration on protein dynamics.
The potential energy surface of a protein is rough. This intrinsic energetic roughness affects diffusion, and hence the kinetics. The dynamics of a system undergoing Brownian motion on this surface in an implicit continuum solvent simulation can be tuned via the frictional drag or collision frequency to be comparable to that of experiments or explicit solvent simulations. We show that the kinetic rate constant for a local rotational isomerization in stochastic simulations with continuum solvent and a collision frequency of 2 ps(-1) is about 10(4) times faster than that in explicit water and experiments. A further increase in the collision frequency to 60 ps(-1) slows down the dynamics, but does not fully compensate for the lack of explicit water. We also show that the addition of explicit water does not only slow down the dynamics by increasing the frictional drag, but also increases the local energetic roughness of the energy landscape by as much as 1.0 kcal/mol.
Hamelberg
Donald
D
Howard Hughes Medical Institute, Center for Theoretical Biological Physics, Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, California 92093, USA. dhamelberg@mccammon.ucsd.edu
Shen
Tongye
T
McCammon
J Andrew
JA
D003198:Computer Simulation; D007536:Isomerism; D010455:Peptides / Q000737:chemistry*; D011487:Protein Conformation; D013269:Stochastic Processes; D013816:Thermodynamics; D014867:Water / Q000737:chemistry*
D010455:Peptides; D014867:Water