ArticleBiophysical journal2003
Comparison of calculation and experiment implicates significant electrostatic contributions to the binding stability of barnase and barstar.
Article in Biophysical journal, 2003. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 57 papers.
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Who cites it
57 citing papers in PubMed, 133 citations in OpenAlex.
- The Intrinsic Radius as a Key Parameter in the Generalized Born Model to Adjust Protein-Protein Electrostatic Interaction.International journal of molecular sciences · 2023Article
- A newly introduced salt bridge cluster improves structural and biophysical properties of de novo TIM barrels.Protein science : a publication of the Protein Society · 2022Article
- Energetics and kinetics of substrate analog-coupled staphylococcal nuclease folding revealed by a statistical mechanical approach.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- The de Rham-Hodge Analysis and Modeling of Biomolecules.Bulletin of mathematical biology · 2020Article
- Designed Mutations Alter the Binding Pathways of an Intrinsically Disordered Protein.Scientific reports · 2019Article
- Electrostatic Interactions in Protein Structure, Folding, Binding, and Condensation.Chemical reviews · 2018Review
- "Martinizing" the Variational Implicit Solvent Method (VISM): Solvation Free Energy for Coarse-Grained Proteins.The journal of physical chemistry. B · 2017Article
- Electrostatic effects on the folding stability of FKBP12.Protein engineering, design & selection : PEDS · 2016Article
- Parameter optimization in differential geometry based solvation models.The Journal of chemical physics · 2015Article
- Problems of robustness in Poisson-Boltzmann binding free energies.Journal of chemical theory and computation · 2015Article
- Poisson-Boltzmann versus Size-Modified Poisson-Boltzmann Electrostatics Applied to Lipid Bilayers.The journal of physical chemistry. B · 2014Article
- Variational Implicit Solvation with Poisson-Boltzmann Theory.Journal of chemical theory and computation · 2014Article
- Sensitivities to parameterization in the size-modified Poisson-Boltzmann equation.The Journal of chemical physics · 2014Article
- Using the concept of transient complex for affinity predictions in CAPRI rounds 20-27 and beyond.Proteins · 2013Article
- Molecular dynamics simulations of highly crowded amino acid solutions: comparisons of eight different force field combinations with experiment and with each other.Journal of chemical theory and computation · 2013Article
- Variational Implicit-Solvent Modeling of Host-Guest Binding: A Case Study on Cucurbit[7]uril|Journal of chemical theory and computation · 2013Article
- Poisson-Boltzmann Calculations: van der Waals or Molecular Surface?Communications in computational physics · 2013Article
- Using DelPhi capabilities to mimic protein's conformational reorganization with amino acid specific dielectric constants.Communications in computational physics · 2013Article
- Biomolecular electrostatics and solvation: a computational perspective.Quarterly reviews of biophysics · 2012Review
- Nucleation of sickle hemoglobin mixed with hemoglobin A: experimental and theoretical studies of hybrid-forming mixtures.Biophysical journal · 2011Article
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
The contributions of electrostatic interactions to the binding stability of barnase and barstar were studied by the Poisson-Boltzmann model with three different protocols: a), the dielectric boundary specified as the van der Waals (vdW) surface of the protein along with a protein dielectric constant (epsilon (p)) of 4; b), the dielectric boundary specified as the molecular (i.e., solvent-exclusion (SE)) surface along with epsilon (p) = 4; and c), "SE + epsilon (p) = 20." The "vdW + epsilon (p) = 4" and "SE + epsilon (p) = 20" protocols predicted an overall electrostatic stabilization whereas the "SE + epsilon (p) = 4" protocol predicted an overall electrostatic destabilization. The "vdW + epsilon (p) = 4" protocol was most consistent with experiment. It quantitatively reproduced the observed effects of 17 mutations neutralizing charged residues lining the binding interface and the measured coupling energies of six charge pairs across the interface and reasonably rationalized the experimental ionic strength and pH dependences of the binding constant. In contrast, the "SE + epsilon (p) = 4" protocol predicted significantly larger coupling energies of charge pairs whereas the "SE + epsilon (p) = 20" protocol did not predict any pH dependence. This study calls for further scrutiny of the different Poisson-Boltzmann protocols and demonstrates potential danger in drawing conclusions on electrostatic contributions based on a particular calculation protocol.
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Registered trials
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