Salt effects on protein-DNA interactions: The λcI repressor and EcoRI endonuclease

Vinod K. Misra, Jonathan L. Hecht, Kim A. Sharp, Richard A. Friedman, Barry Honig

Research output: Contribution to journalArticlepeer-review

157 Scopus citations

Abstract

In this paper, finite-difference solutions to the nonlinear Poisson-Boltzmann (NLPB) equation are used to calculate the salt dependent contribution to the electrostatic DNA binding free energy for both the λcI repressor and the EcoRI endonuclease. For the protein-DNA systems studied, the NLPB method describee nonspecific univalent salt dependent effects on the binding free energy which are in excellent agreement with experimental results. In these systems, the contribution of the ion atmosphere to the binding free energy substantially destabilizes the protein-DNA complexes. The magnitude of this effect involves a macromolecular structure dependent redistribution of both cations and anions around the protein and the DNA which is dominated by long range electrostatic interactions. We find that the free energy associated with global ion redistribution upon binding is more important than changes associated with local protein-DNA interactions (ion-pairs) in determining salt effects. The NLPB model reveals how long range salt effects can play a significant role in the relative stability of protein-DNA complexes with different structures.

Original languageEnglish
Pages (from-to)264-280
Number of pages17
JournalJournal of Molecular Biology
Volume238
Issue number2
DOIs
StatePublished - 1994

Keywords

  • Binding energy
  • DNA
  • DNA binding
  • Electrostatics
  • Salt

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