Interpreting protein/DNA interactions: distinguishing specific from non-specific and electrostatic from non-electrostatic components.

ABSTRACT: We discuss the effectiveness of existing methods for understanding the forces driving the formation of specific protein-DNA complexes. Theoretical approaches using the Poisson-Boltzmann (PB) equation to analyse interactions between these highly charged macromolecules to form known structures are contrasted with an empirical approach that analyses the effects of salt on the stability of these complexes and assumes that release of counter-ions associated with the free DNA plays the dominant role in their formation. According to this counter-ion condensation (CC) concept, the salt-dependent part of the Gibbs energy of binding, which is defined as the electrostatic component, is fully entropic and its dependence on the salt concentration represents the number of ionic contacts present in the c

SUBMITTER: Privalov PL 

PROVIDER: S-EPMC3074165 | biostudies-literature | 2011 Apr

REPOSITORIES: biostudies-literature