Premium
Empirical estimation of local dielectric constants: Toward atomistic design of collagen mimetic peptides
Author(s) -
Pike Douglas H.,
Nanda Vikas
Publication year - 2015
Publication title -
peptide science
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.556
H-Index - 125
eISSN - 1097-0282
pISSN - 0006-3525
DOI - 10.1002/bip.22644
Subject(s) - solvation , dielectric , chemistry , electrostatics , computational chemistry , molecular dynamics , solvent models , solvent , molecule , static electricity , chemical physics , solvent effects , thermodynamics , organic chemistry , quantum mechanics , physics
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 peptides for which experimentally determined stabilities are available. Computing local dielectric constants using atomistic protein models and the assumption of additive atomic polarizabilities is a rapid and potentially useful method for improving electrostatics and solvation calculations that can be applied in the computational design of peptides. © 2015 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 104: 360–370, 2015.