Volume 23, Issue 2
Accurate PKa Computation Using Matched Interface and Boundary (MIB) Method Based Poisson-Boltzmann Solver

Jingzhen Hu, Shan Zhao & Weihua Geng

Commun. Comput. Phys., 23 (2018), pp. 520-539.

Published online: 2018-02

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  • Abstract

The pKa values are important quantities characterizing the ability of protein active sites to give up protons. pKa can be measured using NMR by tracing chemicalshifts of some special atoms, which is however expensive and time-consuming. Alternatively, pKa can be calculated numerically by electrostatic free energy changes subject to the protonation and deprotonation of titration sites. To this end, the PoissonBoltzmann (PB) model is an effective approach for the electrostatics. However, numerically solving PB equation is challenging due to the jump conditions across the dielectric interfaces, irregular geometry of the molecular surface, and charge singularities. Our recently developed matched interface and boundary (MIB) method treats these challenges rigorously, resulting in a solid second order MIBPB solver. Since the MIBPB solver uses Green’s function based regularization of charge singularities by decomposing the solution into a singular component and a regularized component, it is particularly efficient in treating the accuracy-sensitive, numerous, and complicated charge distributions from the pKa calculation. Our numerical results demonstrate that accurate free energies and pKa values are achieved at coarse grid rapidly. In addition, the resulting software, which pipelines the entire pKa calculation procedure, is available to all potential users from the greater bioscience community.

  • Keywords

pKa, acid dissociation constant, Poisson-Boltzmann, finite difference, charge singularity.

  • AMS Subject Headings

92C40, 35J66

  • Copyright

COPYRIGHT: © Global Science Press

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@Article{CiCP-23-520, author = {}, title = {Accurate PKa Computation Using Matched Interface and Boundary (MIB) Method Based Poisson-Boltzmann Solver}, journal = {Communications in Computational Physics}, year = {2018}, volume = {23}, number = {2}, pages = {520--539}, abstract = {

The pKa values are important quantities characterizing the ability of protein active sites to give up protons. pKa can be measured using NMR by tracing chemicalshifts of some special atoms, which is however expensive and time-consuming. Alternatively, pKa can be calculated numerically by electrostatic free energy changes subject to the protonation and deprotonation of titration sites. To this end, the PoissonBoltzmann (PB) model is an effective approach for the electrostatics. However, numerically solving PB equation is challenging due to the jump conditions across the dielectric interfaces, irregular geometry of the molecular surface, and charge singularities. Our recently developed matched interface and boundary (MIB) method treats these challenges rigorously, resulting in a solid second order MIBPB solver. Since the MIBPB solver uses Green’s function based regularization of charge singularities by decomposing the solution into a singular component and a regularized component, it is particularly efficient in treating the accuracy-sensitive, numerous, and complicated charge distributions from the pKa calculation. Our numerical results demonstrate that accurate free energies and pKa values are achieved at coarse grid rapidly. In addition, the resulting software, which pipelines the entire pKa calculation procedure, is available to all potential users from the greater bioscience community.

}, issn = {1991-7120}, doi = {https://doi.org/10.4208/cicp.OA-2017-0078}, url = {http://global-sci.org/intro/article_detail/cicp/10536.html} }
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