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A New DelPhi Feature for Modeling Electrostatic Potential around Proteins: Role of Bound Ions and Implications for Zeta-Potential

Chakravorty, Arghya, Jia, Zhe, Li, Lin, Alexov, Emil
Langmuir 2017 v.33 no.9 pp. 2283-2295
computer software, energy, ions, models, pH, prediction, proteins, van der Waals forces, zeta potential
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.