Constant-pH Brownian Dynamics Simulations of a Protein near a Charged Surface.

ABSTRACT: We have developed a rigid-body Brownian dynamics algorithm that allows for simulations of a globular protein suspended in an ionic solution confined by a charged planar boundary, with an explicit treatment of pH-dependent protein protonation equilibria and their couplings to the electrostatic potential of the plane. Electrostatic interactions are described within a framework of the continuum Poisson-Boltzmann model, whereas protein-plane hydrodynamic interactions are evaluated based on analytical expressions for the position- and orientation-dependent near-wall friction tensor of a spheroid. The algorithm was applied to simulate near-surface diffusion of lysozyme in solutions having pH in the range 4-10 and ionic strengths of 10 and 150 mM. As a reference, we performed Brownian dynamics si

SUBMITTER: Antosiewicz JM 

PROVIDER: S-EPMC7689933 | biostudies-literature | 2020 Nov

REPOSITORIES: biostudies-literature