ArticleLangmuir : the ACS journal of surfaces and colloids2017
A New DelPhi Feature for Modeling Electrostatic Potential around Proteins: Role of Bound Ions and Implications for Zeta-Potential.
Article in Langmuir : the ACS journal of surfaces and colloids, 2017. 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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10 citing papers in PubMed.
- Comparative Assessment of Cellular Responses to Microscale Silica Morphologies in Human Gastrointestinal Cells: Insights for Occupational Health.International journal of environmental research and public health · 2024Article
- Exploring the Limits of the Generalized CHARMM and AMBER Force Fields through Predictions of Hydration Free Energy of Small Molecules.Journal of chemical information and modeling · 2024Article
- Computational Study of the pH-Dependent Ionic Environment around β-Lactoglobulin.The journal of physical chemistry. B · 2022Article
- BION-2: Predicting Positions of Non-Specifically Bound Ions on Protein Surface by a Gaussian-Based Treatment of Electrostatics.International journal of molecular sciences · 2020Article
- Capturing the Effects of Explicit Waters in Implicit Electrostatics Modeling: Qualitative Justification of Gaussian-Based Dielectric Models in DelPhi.Journal of chemical information and modeling · 2020Article
- DelPhi Suite: New Developments and Review of Functionalities.Journal of computational chemistry · 2019Article
- Specificity of protein-DNA interactions in hypersaline environment: structural studies on complexes of Halobacterium salinarum oxidative stress-dependent protein hsRosR.Nucleic acids research · 2019Article
- Explicit ions/implicit water generalized Born model for nucleic acids.The Journal of chemical physics · 2018Article
- Protein surface functionalisation as a general strategy for facilitating biomimetic mineralisation of ZIF-8.Chemical science · 2018Article
- Prediction of pKa Values for Neutral and Basic Drugs based on Hybrid Artificial Intelligence Methods.Scientific reports · 2018Article
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4 authors.
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Abstract
A new feature of the popular software DelPhi is developed and reported, allowing for computing the surface averaged electrostatic potential (SAEP) of macromolecules. The user is given the option to specify the distance from the van der Waals surface where the electrostatic potential will be outputted. In conjunction with DelPhiPKa and the BION server, the user can adjust the charges of titratable groups according to specific pH values, and add explicit ions bound to the macromolecular surface. This approach is applied to a set of four proteins with "experimentally" delivered zeta (ζ)-potentials at different pH values and salt concentrations. It has been demonstrated that the protocol is capable of predicting ζ-potentials in the case of proteins with relatively large net charges. This protocol has been less successful for proteins with low net charges. The work demonstrates that in the case of proteins with large net charges, the electrostatic potential should be collected at distances about 4 Å away from the vdW surface and explicit ions should be added at a binding energy cutoff larger than 1-2kT, in order to accurately predict ζ-potentials. The low salt conditions substantiate this effect of ions on SAEP.
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