ArticleJournal of chemical theory and computation2013
On the Dielectric "Constant" of Proteins: Smooth Dielectric Function for Macromolecular Modeling and Its Implementation in DelPhi.
Article in Journal of chemical theory and computation, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 204 papers.
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204 citing papers in PubMed, 549 citations in OpenAlex.
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- Unraveling the Catalytic Mechanism and Substrate Selectivity of HDAC10: A Dual-Filter Approach for Polyamine Deacetylation.JACS Au · 2025Article
- Prediction of aggregation in monoclonal antibodies from molecular surface curvature.Scientific reports · 2025Article
144 more citing papers are in PubMed but not listed here.
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
Abstract
Implicit methods for modeling protein electrostatics require dielectric properties of the system to be known, in particular, the value of the dielectric constant of protein. While numerous values of the internal protein dielectric constant were reported in the literature, still there is no consensus of what the optimal value is. Perhaps this is due to the fact that the protein dielectric constant is not a "constant" but is a complex function reflecting the properties of the protein's structure and sequence. Here, we report an implementation of a Gaussian-based approach to deliver the dielectric constant distribution throughout the protein and surrounding water phase by utilizing the 3D structure of the corresponding macromolecule. In contrast to previous reports, we construct a smooth dielectric function throughout the space of the system to be modeled rather than just constructing a "Gaussian surface" or smoothing molecule-water boundary. Analysis on a large set of proteins shows that (a) the average dielectric constant inside the protein is relatively low, about 6-7, and reaches a value of about 20-30 at the protein's surface, and (b) high average local dielectric constant values are associated with charged residues while low dielectric constant values are automatically assigned to the regions occupied by hydrophobic residues. In terms of energetics, a benchmarking test was carried out against the experimental p
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.