Linked Life Data

17326079

Source:http://linkedlifedata.com/resource/pubmed/id/17326079

Statements in which the resource exists as a subject.
PredicateObject
rdf:type
lifeskim:mentions
pubmed:issue
2
pubmed:dateCreated
2007-4-30
pubmed:abstractText
The negatively charged phosphates of nucleic acids are often paired with positively charged residues upon binding proteins. It was thus counter-intuitive when previous Poisson-Boltzmann (PB) calculations gave positive energies from electrostatic interactions, meaning that they destabilize protein-nucleic acid binding. Our own PB calculations on protein-protein binding have shown that the sign and the magnitude of the electrostatic component are sensitive to the specification of the dielectric boundary in PB calculations. A popular choice for the boundary between the solute low dielectric and the solvent high dielectric is the molecular surface; an alternative is the van der Waals (vdW) surface. In line with results for protein-protein binding, in this article, we found that PB calculations with the molecular surface gave positive electrostatic interaction energies for two protein-RNA complexes, but the signs are reversed when the vdW surface was used. Therefore, whether destabilizing or stabilizing effects are predicted depends on the choice of the dielectric boundary. The two calculation protocols, however, yielded similar salt effects on the binding affinity. Effects of charge mutations differentiated the two calculation protocols; PB calculations with the vdW surface had smaller deviations overall from experimental data.
pubmed:grant
pubmed:language
eng
pubmed:journal
pubmed:citationSubset
IM
pubmed:chemical
pubmed:status
MEDLINE
pubmed:month
Jun
pubmed:issn
0006-3525
pubmed:author
pubmed:copyrightInfo
Copyright 2007 Wiley Periodicals, Inc.
pubmed:issnType
Print
pubmed:day
5
pubmed:volume
86
pubmed:owner
NLM
pubmed:authorsComplete
Y
pubmed:pagination
112-8
pubmed:dateRevised
2008-11-21
pubmed:meshHeading
pubmed:year
2007
pubmed:articleTitle
Do electrostatic interactions destabilize protein-nucleic acid binding?
pubmed:affiliation
Institute of Molecular Biophysics, School of Computational Science, Florida State University, Tallahassee, FL 32306, USA.
pubmed:publicationType
Journal Article, Research Support, N.I.H., Extramural