ArticleJournal of the American Chemical Society2013
Protein dielectric constants determined from NMR chemical shift perturbations.
Article in Journal of the American Chemical Society, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 39 papers.
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Who cites it
39 citing papers in PubMed.
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- NMR spectroscopy charges into protein surface electrostatics.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- Novel phosphatidylinositol 4-kinases III beta (PI4KIIIβ) inhibitors discovered by virtual screening using free energy models.Journal of computer-aided molecular design · 2020Article
- Variations in Proteins Dielectric Constants.ChemistryOpen · 2020Article
- Identification of the Interactions Interference Between the PH and START Domain of CERT by Limonoid and HPA Inhibitors.Frontiers in molecular biosciences · 2020Article
- Random coil chemical shifts for serine, threonine and tyrosine phosphorylation over a broad pH range.Journal of biomolecular NMR · 2019Article
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- Driving Forces of Translocation Through Bacterial Translocon SecYEG.The Journal of membrane biology · 2018Article
- A reevaluation of the origin of the rate acceleration for enzyme-catalyzed hydride transfer.Organic & biomolecular chemistry · 2017Review
- Development of constant-pH simulation methods in implicit solvent and applications in biomolecular systems.Biophysical reviews · 2017Review
- Model for screened, charge-regulated electrostatics of an eye lens protein: Bovine gammaB-crystallin.Physical review. E · 2017Article
- Substituent Effects on Carbon Acidity in Aqueous Solution and at Enzyme Active Sites.Synlett : accounts and rapid communications in synthetic organic chemistry · 2017Article
- A simple model for electrical charge in globular macromolecules and linear polyelectrolytes in solution.The Journal of chemical physics · 2017Article
- The impact of viral RNA on the association free energies of capsid protein assembly: bacteriophage MS2 as a case study.Journal of molecular modeling · 2017Article
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8 authors.
Funding
Abstract
Understanding the connection between protein structure and function requires a quantitative understanding of electrostatic effects. Structure-based electrostatic calculations are essential for this purpose, but their use has been limited by a long-standing discussion on which value to use for the dielectric constants (ε(eff) and ε(p)) required in Coulombic and Poisson-Boltzmann models. The currently used values for ε(eff) and ε(p) are essentially empirical parameters calibrated against thermodynamic properties that are indirect measurements of protein electric fields. We determine optimal values for ε(eff) and ε(p) by measuring protein electric fields in solution using direct detection of NMR chemical shift perturbations (CSPs). We measured CSPs in 14 proteins to get a broad and general characterization of electric fields. Coulomb's law reproduces the measured CSPs optimally with a protein dielectric constant (ε(eff)) from 3 to 13, with an optimal value across all proteins of 6.5. However, when the water-protein interface is treated with finite difference Poisson-Boltzmann calculations, the optimal protein dielectric constant (ε(p)) ranged from 2 to 5 with an optimum of 3. It is striking how similar this value is to the dielectric constant of 2-4 measured for protein powders and how different it is from the ε(p) of 6-20 used in models based on the Poisson-Boltzmann equation when calculating thermodynamic parameters. Because the value of ε(p) = 3 is obtained by analysis of NMR chemical shift perturbations instead of thermodynamic parameters such as pK(a) values, it is likely to describe only the electric field and thus represent a more general, intrinsic, and transferable ε(p) common to most folded proteins.
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