Repressor dimers

Figure 7-15 shows the time evolution of the temperature, total energy, and potential energy for a 300 ps simulation of the tetracycline repressor dimer in its induced (i.e., hgand-bound) form. Starting from the X-ray structure of the monomer in a complex with one molecule of tetracycline and a magnesium ion (protein database... 

Figure 8.14 Overall view of the complex between 434 repressor fragment and a palindromic synthetic 14mer of DNA (see Table 8.2). The two binding sites of the repressor dimer to the DNA are identical.

Individual operator sites are denoted O if vacant, or R2 if occupied by a repressor dimer. Pairwise interactions between adjacent occupied sites are denoted ( ) AG 2 and AG23 the free energies of cooperative interaction between adjacent occupied sites, defined as the difference between AG, for any species and the sum of the intrinsic free enei es of binding to occupied sites. 

An example for such an arrangement is the Met repressor of E. coli. The palindromic recognition sequence of the MeO repressor occurs in 2-5 copies on the DNA. The repressor itself binds as a dimer on one copy of the recognition sequence. Protein-protein interactions mediate cooperative binding of the repressor dimers to the adjacent copies of the recognition sequence. 

When tryptophan is lacking, a trp repressor protein (encoded by the trpR operon) is synthesized. The trp repressor dimer is inactive, cannot bind to the trp operator and so the trp operon is transcribed to produce the enzymes that then synthesize tryptophan for the cell. When tryptophan is present, tryptophan synthesis is not needed. In this situation, acting as a corepressor, tryptophan binds to the repressor and activates it so that the repressor now binds to the trp operator and stops transcription of the trp operon. 

In the crystal structure [711], a dimes formed by two N-terminal 434 repressor fragments is bound to the 20 base pairs DNA duplex so that the complex has overall 2-fold rotational symmetry. The polypeptide chain is folded into five a-helices HI to H5, with helices H2 and H3 forming the helix/turn/helix motif (Fig. 20.16). Helices H3 and H3 of the 434 repressor dimer insert into two successive major grooves of the operator DNA whereas the N-termini of the flanking helices H2, H4 and H2 H4 contact the sugar-phosphate backbones. 

Inspection of the complete E. coli genome sequence reveals two sites within 500 bp of the primary operator site that approximate the sequence of the operator. Other lac repressor dimers can bind to these sites, particularly when aided by cooperative interactions with the lac repressor dimer at the primary operator site. No other sites that closely match sequence of the lac operator site are present in the rest of the E. coli genome sequence. Thus, the DNA-binding specificity of the lac repressor is sufficient to specify a nearly unique site within the E. coli genome. 

Figure 31.5. Structure of the LAC Repressor. A lac repressor dimer is shown bound to DNA. A part of the structure that mediates the formation of lac repressor tetramers is not shown.

Fig. 7. Water at protein-DNA interfaces. Four protein-DNA complexes are shown with the DNA placed in front of the molecular surface of the protein, colored according to the electrostatic potential (red, negative blue, positive). The complexes are with the lambda repressor dimer (limb) three zinc fingers from the Zif268 transcription factor (laay) the human TATA box-binding protein (Icdw) and the dimeric E2 domain of papilloma virus (2bop). Red spheres represent interface water molecules. Figure taken from Nadassy et al. (1999) and drawn with GRASP (see web sites).

The relative changes in ID spectra of both aromatic and aliphatic regions at 1 kbar with respect to 1 bar indicated that there must be some changes in structure of Arc repressor prior to its dissociation. In this pressure range, there is no dissociation of 1 mM Arc repressor dimer according to the fluorescence emission and polarization experiments. ... 

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