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 Frohlich-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.
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https://hal-polytechnique.archives-ouvertes.fr/hal-00984670
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Submitted on : Monday, April 28, 2014 - 4:27:43 PM
Last modification on : Wednesday, March 27, 2019 - 3:56:02 PM

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Thomas Simonson. What Is the Dielectric Constant of a Protein When Its Backbone Is Fixed?. Journal of Chemical Theory and Computation, American Chemical Society, 2013, 9 (10), pp.4603-4608. ⟨10.1021/ct400398e⟩. ⟨hal-00984670⟩

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