A new feature of the popular software DelPhi, that computes the electrostatic field around solutes including biomolecules, is developed and reported, allowing for computing the surface averaged electrostatic potential (SAEP) around them. 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 equally useful softwares - 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 proteins with “experimentally” delivered zeta-potentials at different pH values and salt concentrations. It has been demonstrated that the protocol is capable of predicting zeta-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 cut-off larger than 1-2 kT, in order to accurately predict zeta-potentials.

New DelPhi feature for modeling electrostatic potential around proteins: Role of bound ions and implications for zeta-potential

254th National Meeting (2017)

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