Repressor-operator complexes

Anderson, J.E., Ptashne, M., Harrison, S.C. A phage repressor-operator complex at 7 A resolution. Nature 316 S96-601, 1985. 

Pabo, C.O., et al. Conserved residues make similar contacts in two repressor-operator complexes. Science 247 1210-1213, 1990. 

Repressor Concentration in E. coli The dissociation constant for a particular repressor-operator complex is very low, about 10 13 M. An E. coli cell (volume 2 X 10 12 mL) contains 10 copies of the repressor. Calculate the cellular concentration of the repressor protein. How does this value compare with the dissociation constant of the repressor-operator complex What is the significance of this result ... 

Figure 5-39 (A) Stereoscopic ribbon representation of the E. coli methionine repressor-operator complex. Two subunits form a dimer with a double-stranded antiparallel 3 ribbon that fits into the major groove of the DNA in the B form. One strand is shaded more darkly than the other.

Anderson, J. E., M. Ptashne, and S. C. Harrison, Structure of the repressor-operator complex of bacteriophage 434. Nature 306 846-852, 1987. 

Fig. 9. Two hydrogen bonding motifs found in the lambda repressor-operator complex. Taken from Ref. 50...

Several crystal structure analyses of individual repressors and of repressor-operator complexes disclosed a recurrent template on the protein side. It consists of an a-helix/turn/a-helix motif with an almost invariant glycine in the turn region [707-710]. Most of the repressors so far investigated display such a motif but the interactions with the operator DNA, which occur in the major groove are individually different. Here we consider more closely the well-documented complexes between the N-terminal fragment of the repressor from phage 434 and its specific operator DNA [711], and the ternary complex formed between tryptophan repressor, tryptophan and DNA [712, 713]. 

Otwinowski Z, Schevitz RW, Zhang R-G, Lawson CL, Joachimiak A, Marmorstein RQ, Luisi BF, Sigler PB (1988) Crystal structure of trp repressor/operator complex at atomic resolution. Nature 335 321-329... 

Jayaram B, DiCapua FM, Beveridge DL (1991) A theoretical study of polyelectrolyte effects in protein-DNA interactions Monte Carlo free energy simulations on the ion atmosphere contribution to the thermodynamics of lambda repressor-operator complex formation. J Am Chem Soc 113 5211-5221... 

The trp repressor-operator complex exhibits no direct hydrogen bonds from the protein to the DNA bases but has three water molecules that mediate the necessary contacts for specific recognition between protein and DNA, so exemplifying well the importance water has in the process of recognition (26). Water-mediated links are also important in nuclear hormone receptors such as the estrogen receptor-DNA complex. 

Wibowo FR, Rauch C, Trieb M, Wellenzohn B, Liedl KR. Water-mediated contacts in the trp-repressor operator complex recognihon process. Biopolymers 2004 73 668-681. 

Figure 1 NMR Experiments used to assign the trp repressor-operator complex (11,24).

W.S. Somers and S.E. Phillips. 1992. Crystal structure of the met repressor-operator complex at 2.8 A resolution reveals... 

Repressor-operator complex of bacteriophage 434 Xentronics MWPC (Film) 166.0 139.0 1422 7.0 (3.2) Anderson, Ptashne and Harrison (1987)... 

Phage 434 repressor-operator complex bromine derivative Xentronics MWPC 148.3 27.7... 

Assume that the dissociation constant K for the repressor-operator complex is 10 M... 

Calculate the rate constant fe iss for the dissociation of the repressor-operator complex. What is the tyj (half-time of dissociation, or half-life) of the repressor-operator complex ... 

Since the repressor concentration is much higher than the dissociation constant for the repressor/operator complex (10 M), the single molecule will be bound to (operator) DNA. 

When the operon concentration is fixed at a very low level such that the total repressor concentration is always much greater than the total operator concentration, any lack of complete repression must be a measure of the dissociation of the repressor-operator complex. Provided the operon concentration can be sufficiently reduced, one should obtain an accurate measure of the formation constant of the repressor-operator complex under these conditions. Figure 8 shows the results of such an experiment in which the extent of repression is measured as a function of repressor concentration. Except for the zero point, the total repressor concentration is maintained at least ten times as high as that of the total operon, so that Rj k R, where Rt represents the total repressor concentration and R represents the free repressor concentration. From the formation constant, for the simplest reaction involving the reaction of one repressor molecule with one operon molecule, we have... 

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