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

Biopolymers
Douglas H Pike, Vikas Nanda

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 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.

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Citations

Aug 1, 2015·Biochemistry·Avanish S ParmarVikas Nanda
Jun 28, 2016·Current Opinion in Structural Biology·Haiyan Liu, Quan Chen
Apr 27, 2016·PloS One·Yoshiaki MaedaHiroshi Matsui
Aug 8, 2019·Proteins·Jose K James, Vikas Nanda
Aug 10, 2020·Biotechnology and Applied Biochemistry·Joshua A ManciniVikas Nanda
Sep 24, 2019·Current Pharmaceutical Design·Neha S MauryaAshutosh Mani
Nov 18, 2020·Proceedings of the National Academy of Sciences of the United States of America·Saroj PoudelPaul G Falkowski
Jun 30, 2017··Ofer M. ShirSandeep V. Belure

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