Book of Abstracts: Albany 2003
June 17-21 2003
On the Role of DNA Looping in the Regulation of Lac operon in Escherichia coli
DNA transcription frequently involves binding of multiple structural and regulatory proteins to promoter sites on DNA followed by deformation of the spacer DNA and formation of a looped nucleo-protein complex, the structure of which determines the transcription efficiency. Recently obtained experimental information about the sequence-dependence of DNA structure and deformability has stimulated development of methods for computational modeling of the structure of such complex protein-DNA assemblies. Presented will be results of application of such methods to the study of the mechanism of repression of the Lac operon in Escherichia coli. The Lac operon is activated by the catabolite activator protein (CAP) and repressed by the Lac repressor protein (LacR, which interacts with two operator sites in the promoter region and mediates the formation of a DNA loop. Although the dependence of repression on the distance between LacR binding sites has been measured, the configuration of the loop and its role in the repressive mechanism is unknown. Our calculations show that simultaneous binding of LacR and CAP to their natural binding sites in the lac promoter is sterically permissible but energetically unfavorable. The simultaneous binding of LacR and RNA polymerase (RNAP) to DNA is sterically permissible if the LacR tetramer adopts an extended form in which the DNA binding domains lie at opposing ends and the four-helix dimerization domain occupies the middle. Moreover, this configuration of LacR induces a bend in the DNA that brings the upstream element of the promoter close to the a-subunits of RNAP and may thereby enhance the RNAP binding strength and account for the suspected LacR and RNAP binding cooperativity.
1Department of Chemistry & Chemical Biology