Biophysical Principles of Specificity and Stability of Protein-DNA Interactions: Application to RNA Polymerase (Eσ70)-Promoter Interactions
Protein-DNA interactions are competitive noncovalent interactions. The rate and extent of complex formation at a specific site is affected not only by macromolecular concentration variables but also by the concentrations of low molecular weight competitors, especially electrolyte ions (Record and Mossing, 1987). Given this situation, how can one characterize the contributions of various noncovalent interactions to the stability and specificity of these complexes and to their mechanisms of formation and/or dissociation? What is the relevance of this information to understanding the regulation of these interactions in the control of gene expression? Regulation may occur at either a kinetic or thermodynamic level. For example, the control of initiation of transcription by E. coli RNA polymerase (Eσ70) occurs at the level of the kinetics of formation of open complexes at these promoters (kinetic control) (cf. McClure (1985) and references therein). The control of expression of the lac operon by lac repressor in conjunction with specific effectors (inducers) apparently occurs at the thermodynamic level (thermodynamic control): the equilibrium degree of occupancy of the operator site by repressor is thought to be the key factor regulating transcription of the lac genes (cf. vonHippel, 1979; Sellitti et al., 1987).
KeywordsNoncovalent Interaction Hydrophobic Effect Standard Free Energy Change Polyelectrolyte Effect Open Complex Formation
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