Viscosity dependence of protein dynamics.
The influence of solvent viscosity on protein dynamics was investigated with molecular dynamics simulations of factor Xa in two solvents differing only in viscosity, by a factor of 10. We obtained this viscosity change by changing the masses of the solvent atoms by a factor of 100. Equilibrium properties of the protein, that is, the average structure, its fluctuations, and the secondary structure, show no significant dependence on the solvent viscosity. The dynamic properties of the protein, that is, the atom-positional correlation times and torsional angle transitions, however, depend on the solvent viscosity. The protein appears to be much more mobile in the solvent of lower viscosity. It feels the influence of the solvent not only on the surface but even in its core. With increasing solvent viscosity, the positional relaxation times of atoms in the protein core increase as much as those of atoms on the protein surface, and the relative increase in the core is even larger than on the surface.
Walser
R
R
Laboratory of Physical Chemistry, Swiss Federal Institute of Technology Zürich, Zürich, Switzerland.
van Gunsteren
W F
WF
D019295:Computational Biology; D003198:Computer Simulation; D015951:Factor Xa / Q000737:chemistry*; D008958:Models, Molecular; D011487:Protein Conformation; D012997:Solvents / Q000737:chemistry; D014783:Viscosity
D012997:Solvents; D015951:Factor Xa