ch09_20403358.pptVIP

The trp repressor requires tryptophan to force the recognition helices of the repressor dimer into the proper position for interacting with the trp operator. 2) trp Repressor–Operator Interactions As we have seen, the trp repressor points directly into the DNA major groove, rather than lying sideways in it the way the λ repressor does. Thus, it is harder to understand how direct amino acid/DNA base interactions could occur with this repressor. The recognition helix (E, red) in the trp repressor points into the major groove of the operator, rather than lying sideways in it. It also shows the contacts between amino acids on the D and E helices (numbered 68-90) and phosphates in the DNA backbone (numbered 1 to 4 on one strand and -7 to -9 on the other). The black oval represents the axis of rotational symmetry between the two operator half-sites. 2900 ?2 25/1; 18/12 Two water molecules (red) appear to form hydrogen bonds with two amino acids (Thr 83 and Gln 68) and two sites on the operator (adenine-7 and phosphate-8). Without the water molecules, the protein and DNA atoms would be too far apart to form hydrogen bonds with one another. The trp repressor binds to the trp operator in a less-direct way than the λ family of repressors bind to their operators. The recognition helix of the trp repressor points directly into the major groove of the operator, which allows only one direct contact between an amino acid and a base. All the other interactions are either direct contacts between amino acids and DNA backbone phosphates, or indirect contacts through water molecules. 9.3 General Considerations on Protein–DNA Interactions 1) Hydrogen Bonding Capabilities of the Four Different Base Pairs 2) The Role of DNA Shape in Specific Binding to Proteins 3) The Importance of Multimeric DNA-Binding Proteins What contributes to the specificity of binding between a protein and a specific stretch of DNA? The examples we have seen so far suggest two answers: (1) specific intera