Empirical estimation of local dielectric constants: Toward atomistic design of collagen mimetic peptides.

ABSTRACT: One of the key challenges in modeling protein energetics is the treatment of solvent interactions. This is particularly important in the case of peptides, where much of the molecule is highly exposed to solvent due to its small size. In this study, we develop an empirical method for estimating the local dielectric constant based on an additive model of atomic polarizabilities. Calculated values match reported apparent dielectric constants for a series of Staphylococcus aureus nuclease mutants. Calculated constants are used to determine screening effects on Coulombic interactions and to determine solvation contributions based on a modified Generalized Born model. These terms are incorporated into the protein modeling platform protCAD, and benchmarked on a data set of collagen mimetic peptid

SUBMITTER: Pike DH 

PROVIDER: S-EPMC5389890 | biostudies-literature | 2015 Jul

REPOSITORIES: biostudies-literature