Impact of a Poisson-Boltzmann electrostatic restraint on protein structures refined at medium resolution

Andrei Korostelev, Marcia O. Fenley, Michael Chapman

Research output: Contribution to journalArticle

5 Citations (Scopus)

Abstract

The Poisson-Boltzmann formulism has been developed as a restraint for electrostatic interactions during the crystallographic refinement of macromolecules. It accounts implicitly for the effects of solvent and mobile ions, which are usually not included as restraints in the refinement of experimental structures. The electrostatic restraint has been implemented by combining software for numerically solving the three-dimensional Poisson-Boltzmann equation with a package for stereochemically restrained refinement. Its application to medium-resolution protein structures leads to a reduced free R factor, overfitting and to improved interactions in salt bridges and between polar or charged amino acids and the solvent. In contrast, Coulombic and screened Coulombic treatments did not lead to significant gains. The work leads to a modest improvement in refinement methods, confirmation that the Poisson-Boltzmann formulism is more consistent with experimental structure than the Coulombic approach, and to a reduction in the discrepancy between experimental and electrostatically optimized atomic models.

Original languageEnglish (US)
Pages (from-to)1786-1794
Number of pages9
JournalActa Crystallographica Section D: Biological Crystallography
Volume60
Issue number10
DOIs
StatePublished - Oct 2004
Externally publishedYes

Fingerprint

Static Electricity
Electrostatics
electrostatics
proteins
Boltzmann equation
R Factors
Coulomb interactions
Macromolecules
Proteins
Software
Salts
Ions
macromolecules
Amino Acids
amino acids
interactions
salts
computer programs
ions

ASJC Scopus subject areas

  • Clinical Biochemistry
  • Biochemistry, Genetics and Molecular Biology(all)
  • Biochemistry
  • Biophysics
  • Condensed Matter Physics
  • Structural Biology

Cite this

Impact of a Poisson-Boltzmann electrostatic restraint on protein structures refined at medium resolution. / Korostelev, Andrei; Fenley, Marcia O.; Chapman, Michael.

In: Acta Crystallographica Section D: Biological Crystallography, Vol. 60, No. 10, 10.2004, p. 1786-1794.

Research output: Contribution to journalArticle

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