New and efficient poisson-Boltzmann solver for interaction of multiple proteins

Eng Hui Yap, Teresa Head-Gordon

Research output: Contribution to journalArticle

18 Citations (Scopus)

Abstract

We derive a new numerical approach to solving the linearized Poisson-Boltzmann equation (PBE) by representing the protein surface as a collection of spheres in which the surface charges can then be iteratively solved by new analytical multipole methods previously introduced by us [Lotan, I.; Head-Gordon, T. J. Chem. Theory Comput. 2006, 2, 541.]. We show that our Poisson-Boltzmann semianalytical method, PB-SAM, realizes better accuracy, more flexible memory management, and at reduced cost relative to either finite difference or boundary element method PBE solvers. We provide two new benchmarks of PBE solution accuracy to test the numerical PBE solutions based on (1) arrays of up to hundreds of spherical low dielectric geometries with asymmetric charges in which mutual polarization is treated exactly and (2) two overlapping spheres with increasing charge asymmetry by solving the PB-SAM method to very high pole order. We illustrate the strength of the PB-SAM approach by computing the potential profile of an array of 60 T1-particle forming monomers of the bromine mosaic virus.

Original languageEnglish (US)
Pages (from-to)2214-2224
Number of pages11
JournalJournal of Chemical Theory and Computation
Volume6
Issue number7
DOIs
StatePublished - Jul 13 2010
Externally publishedYes

Fingerprint

Boltzmann equation
proteins
Proteins
interactions
Bromine
boundary element method
viruses
Surface charge
bromine
Boundary element method
Viruses
multipoles
Poles
Membrane Proteins
poles
monomers
Monomers
asymmetry
Polarization
costs

ASJC Scopus subject areas

  • Physical and Theoretical Chemistry
  • Computer Science Applications

Cite this

New and efficient poisson-Boltzmann solver for interaction of multiple proteins. / Yap, Eng Hui; Head-Gordon, Teresa.

In: Journal of Chemical Theory and Computation, Vol. 6, No. 7, 13.07.2010, p. 2214-2224.

Research output: Contribution to journalArticle

Yap, Eng Hui ; Head-Gordon, Teresa. / New and efficient poisson-Boltzmann solver for interaction of multiple proteins. In: Journal of Chemical Theory and Computation. 2010 ; Vol. 6, No. 7. pp. 2214-2224.
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