Dielectric relaxation in proteins: the computational perspective.
In photoexcitation and electron transfer, a new dipole or charge is introduced, and the structure is adjusted. This adjustment represents dielectric relaxation, which is the focus of this review. We concentrate on a few selected topics. We discuss linear response theory, as a unifying framework and a tool to describe non-equilibrium states. We review recent, molecular dynamics simulation studies that illustrate the calculation of dynamic and thermodynamic properties, such as Stokes shifts or reorganization free energies. We then turn to the macroscopic, continuum electrostatic view. We recall the physical definition of a dielectric constant and revisit the decomposition of the free energy into a reorganization and a static term. We review some illustrative continuum studies and discuss some difficulties that can arise with the continuum approach. In conclusion, we consider recent developments that will increase the accuracy and broaden the scope of all these methods.
Simonson
Thomas
T
Laboratoire de Biochimie (UMR CNRS 7654), Department of Biology, Ecole Polytechnique, 91128 Palaiseau, France. thomas.simonson@polytechnique.edu
D003198:Computer Simulation; D004583:Electrons; D008954:Models, Biological; D017510:Protein Folding; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism*
D011506:Proteins