What Is the Dielectric Constant of a Protein When Its Backbone Is Fixed?

Abstract

Monte Carlo (MC) simulations with a fixed protein backbone but mobile sidechains are common for acid/base constants and protein design. To characterize the fluctuations in these models, estimating the Fröhlich-Kirkwood dielectric constant can give physical insight and allow comparison both with models that are more rigorous (fully flexible) and ones that are simpler (Poisson-Boltmann without any explicit protein flexibility). MC simulations of two small proteins yield protein dielectric constants of 12 and 14, about 70% of the result from MD (16 and 22). Thus, the consistency between the fully explicit MD and partly explicit MC is only fair.