Chapter 9: DNA-protein interactions in bacteria. The main contents of this chapter include all of the following: The λ family of repressors, the trp repressor, general considerations on Protein–DNA interactions, DNA-binding proteins: action at a distance,.and other contents. | Molecular Biology Fifth Edition Chapter 9 DNA-Protein Interactions in Bacteria Lecture PowerPoint to accompany Robert F. Weaver Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. The l Family of Repressors Repressors have recognition helices that lie in the major groove of the appropriate operator Specificity of this binding depends on amino acids in the recognition helices 9- Binding Specificity of Repressor-DNA Interaction Site Repressors of l-like phage have recognition helices that fit sideways into the major groove of the operator DNA Certain amino acids on the DNA side of the recognition helix make specific contact with bases in the operator These contacts determine the specificity of protein-DNA interactions Changing these amino acids can change the specificity of the repressor 9- Probing Binding Specificity by Site-Directed Mutagenesis Key amino acids in the recognition helices of 2 repressors are proposed These amino acids are | Molecular Biology Fifth Edition Chapter 9 DNA-Protein Interactions in Bacteria Lecture PowerPoint to accompany Robert F. Weaver Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. The l Family of Repressors Repressors have recognition helices that lie in the major groove of the appropriate operator Specificity of this binding depends on amino acids in the recognition helices 9- Binding Specificity of Repressor-DNA Interaction Site Repressors of l-like phage have recognition helices that fit sideways into the major groove of the operator DNA Certain amino acids on the DNA side of the recognition helix make specific contact with bases in the operator These contacts determine the specificity of protein-DNA interactions Changing these amino acids can change the specificity of the repressor 9- Probing Binding Specificity by Site-Directed Mutagenesis Key amino acids in the recognition helices of 2 repressors are proposed These amino acids are largely different between the two repressors 9- l Repressor The l repressor has an extra motif, an amino-terminal arm that aids binding by embracing the DNA Cro and l repressor share affinity for the same operators, but have microspecificities for OR1 or OR3 These specificities are determined by interactions between different amino acids in the recognition helices of the 2 proteins and different base pairs in the 2 operators 9- High-Resolution Analysis of l Repressor-Operator Interactions General Structural Features Recognition helices of each repressor monomer nestle into the DNA major grooves in the 2 half-sites Helices approach each other to hold the two monomers together in the repressor dimer DNA is similar in shape to B-form DNA Bending of DNA at the two ends of the DNA fragment as it curves around the repressor dimer 9- Hydrogen bonds between repressor and base pairs in the major groove 9- Amino Acid/DNA Backbone Interactions Hydrogen bond at Gln 33 maximizes
