Computational Signaling Protein Dynamics and Geometric Mass Relations in Biomolecular Diffusion.

ABSTRACT: We present an atomistic level computational investigation of the dynamics of a signaling protein, monocyte chemoattractant protein-1 (MCP-1), that explores how simulation geometry and solution ionic strength affect the calculated diffusion coefficient. Using a simple extension of noncubic finite size diffusion correction expressions, it is possible to calculate experimentally comparable diffusion coefficients that are fully consistent with those determined from cubic box simulations. Additionally, increasing the concentration of salt in the solvent environment leads to changes in protein dynamics that are not explainable through changes in solvent viscosity alone. This work in accurate computational determination of protein diffusion coefficients led us to investigate molecular-weight-base

SUBMITTER: Fennell CJ 

PROVIDER: S-EPMC5985777 | biostudies-literature | 2018 May

REPOSITORIES: biostudies-literature