A New DelPhi Feature for Modeling Electrostatic Potential
around Proteins: Role of Bound Ions and Implications for Zeta-Potential
Version 2 2017-02-20, 13:06
Version 1 2017-02-20, 13:03
Posted on 2017-02-20 - 13:06
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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Chakravorty, Arghya; Jia, Zhe; Li, Lin; Alexov, Emil (2017). A New DelPhi Feature for Modeling Electrostatic Potential
around Proteins: Role of Bound Ions and Implications for Zeta-Potential. ACS Publications. Collection. https://doi.org/10.1021/acs.langmuir.6b04430
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AUTHORS (4)
AC
Arghya Chakravorty
ZJ
Zhe Jia
LL
Lin Li
EA
Emil Alexov