ArticleBiopolymers2015
Empirical estimation of local dielectric constants: Toward atomistic design of collagen mimetic peptides.
Article in Biopolymers, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed.
- Molecular Modelling in Bioactive Peptide Discovery and Characterisation.Biomolecules · 2025Review
- Design of a minimal di-nickel hydrogenase peptide.Science advances · 2023Article
- More than skin deep: cyclic peptides as wound healing and cytoprotective compounds.Frontiers in cell and developmental biology · 2023Review
- Computational design of a sensitive, selective phase-changing sensor protein for the VX nerve agent.Science advances · 2022Article
- De novo metalloprotein design.Nature reviews. Chemistry · 2022Article
- Biophysical analysis of the structural evolution of substrate specificity in RuBisCO.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- Structural and Dynamic Properties of Allergen and Non-Allergen Forms of Tropomyosin.Structure (London, England : 1993) · 2018Article
- Computer-aided design of amino acid-based therapeutics: a review.Drug design, development and therapy · 2018Review
- Article
- Metal Stabilization of Collagen and de Novo Designed Mimetic Peptides.Biochemistry · 2015Article
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Authors and funding
2 authors.
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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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