Dimer binding to DNA

Figure 39-13. A schematic representation of the three-dimensional structure of Cro protein and its binding to DNA by its helix-turn-helix motif. The Cro monomer consists of three antiparallel p sheets (P1-P3) and three a-helices (a,-a3).The helix-turn-helix motif is formed because the aj and U2 helices are held at about 90 degrees to each other by a turn offour amino acids. The helix of Cro is the DNA recognition surface (shaded). Two monomers associate through the antiparallel P3 sheets to form a dimer that has a twofold axis of symmetry (right). A Cro dimer binds to DNA through its helices, each of which contacts about 5 bp on the same surface of the major groove. The distance between comparable points on the two DNA a-helices is 34 A, which is the distance required for one complete turn of the double helix. (Courtesy of B Mathews.)...

Thyroid hormone binds to receptors in the nucleus that control the expression of genes responsible for many metabolic processes. The T3 receptor exists in two monomeric forms alpha and beta. When activated by T3, the a and (3 monomers combine to form ao, PP, or aP dimers. These Tj-activated dimers bind to DNA response elements and control the synthesis of RNA, which codes for specific proteins that mediate the actions of thyroid hormones. 

This model of Cro binding to DNA was arrived at by intuition and clever model building. Its validity was considerably strengthened when the same features were subsequently found in the DNA-binding domains of the lambda-repressor molecule. The helix-turn-helix motif with a recognition helix is present in the repressor, and moreover the repressor DNA-binding domains dimerize in the crystals in such a way that the recognition helices are separated by 34 A as in Cro. 

The homeodomain frequently binds to DNA as a monomer, in contrast to procaryotic DNA-binding proteins containing tbe belix-turn-helix motif, which usually bind as dimers. In vitro tbe homeodomain binds specifically to... 

The individual domains of the two receptors both have structures similar to that of the glucocorticoid receptor, and they bind to DNA in a similar way, with their recognition helices in the major groove. The dimer contacts are, however, totally different. In the glucocorticoid receptor, which binds to a palindromic DNA sequence like the 434 repressor described in Chapter 8, the domains interact symmetrically in a head-to-head fashion equivalent... 

Subsequently Stephen Harrison s group determined the x-ray structure of a PPRl-DNA complex and showed that the zinc cluster domain of PPRl and its mode of binding to DNA was very similar to that of GAL4, and that PPRl also dimerized through a coiled-coil region. However, the linker region... 

Figure 10.28 Schematic diagram of the binding of the transcription factor Max to DNA. The two monomers of Max (blue and green) form a dimer through both the helix-loop-helLx regions which form a four-helix bundle like MyoD, and the zipper regions, which are arranged in a coiled coil. The N-terminal basic regions bind to DNA in a way similar to GCN4 and MyoD. (Adapted from A.R. Ferre-D Amare et al., Nature 363 38-4S, 1993.)...

Dimeric complexes like [Cl(NH3)Pt H2N(CH2)4NH2 Pt(NH3)Cl]Cl2 are also being investigated as they bind to DNA in a different way to that involved in cisplatin binding and are active in cisplatin-resistant human tumour cells. They are more potent than cisplatin in lung cancer models in vivo and are likely to go on clinical trials in the near future [204],... 

The core unit of the chromatin, the nucleosome, consists of histones arranged as an octamer consisting of a (H3/ H4)2-tetramer complexed with two histone H2A/H2B dimers. Accessibility to DNA-binding proteins (for replication, repair, or transcription) is achieved by posttranslational modifications of the amino-termini of the histones, the histone tails phosphorylation, acetylation, methylation, ubiquitination, and sumoyla-tion. Especially acetylation of histone tails has been linked to transcriptional activation, leading to weakened interaction of the core complexes with DNA and subsequently to decondensation of chromatin. In contrast, deacetylation leads to transcriptional repression. As mentioned above, transcriptional coactivators either possess HAT activity or recruit HATs. HDACs in turn act as corepressors. 

Fig. 3.6 Polyamide-DNA binding motifs targeting longer DNA sequences. Overlapped and slipped homodimers depending on the sequence context, six-ring polyamides with central p-Ma residues can bind to DNA as fully overlapped homodimers, recognizing 11 bp, or as slipped homodimers, recognizing 13 bp. Extended hairpin extended conformation increases binding site size (to 9 bp) and enhances binding affinity. Cooperative dimer a cooperatively binding hairpin polyamide can...

Detailed analysis of the lambda repressor led to the important concept that transcription regulatory proteins have several functional domains. For example, lambda repressor binds to DNA with high affinity. Repressor monomers form dimers, dimers interact with each other, and repressor interacts with RNA polymerase. The protein-DNA interface and the three protein-protein interfaces all involve separate and distinct domains of the repressor molecule. As will be noted below (see Figure 39—17), this is a characteristic shared by most (perhaps all) molecules that regulate transcription. 

Fig. 1.5. Activation of the native receptor by thehormone. The hormone-receptor interaction determines a very strong bond that attracts distant amino acid residues, which alters the three-dimensional structure of the receptor. As a consequence, the receptor loses its affinity for the proteins that were originally close but that no longer find their zones of contact with the receptor. Simultaneously, the receptor reorganizes other hormone-dependent zones it acquires dimerization capacity and exhibits a capacity to bind to DNA and to transcription factors. The interaction with antiestrogens also produces a conformational change, which can give rise or not to the formation of dimers, in any case with a different conformation...

The interaction between the receptor dimer and DNA is produced in an orderly manner. First, the dimer is placed in the main furrow of the double helix, and the first monomer interacts with the first pentamer of the HRE in the main furrow of the double helix. Later the second molecule of the receptor dimer binds to the second pentamer. The distance between both pentamers is minimum from zero to five nucleotides, depending on the type of receptor. This implies that the dimer assures a sufficiently compact and symmetrical structure among both receptor molecules, so that a similar intimacy can be produced in the association with the palindrome. 

In another recent example, Hashimoto reported photoaffinity experiments on retinoic acid receptors (RAR). Retinoic acid plays a critical role in cell proliferation and differentiation. RARs belong to the superfamily of nuclear/ thyroid hormone receptors. They consist of six transmembrane domains (A-F) which is a general feature of these receptors. The A/B domains have an autonomous transactivation function while the C-domain contains the Zn-finger, which binds to DNA. The large E-domain participates in ligand binding, dimerization, and ligand dependent transactivation. Finally, D- and F-domains help the orientation and stabilization of the E-domain. 

Figure 8.3 Model of two Fur dimers binding to opposite sides of canonical B-DNA. The twofold symmetry between the Fur dimers follows the symmetry of the DNA sequence. (From Pohl et al., 2003. Reproduced with permission of Blackwell Publishing Ltd.)...

Other multinuclear protein-zinc interactions may be implicated for the GAL4 protein in vivo. For example, since the GAL4 dimer binds to palindromic DNA sequences (Giniger et al, 1985), one possibility is that the dimer interface of the intact protein could comprise three zinc ions tetrahedrally coordinated by the 12 cysteines of two GAL4 monomers... 

The leucine zipper itself does not participate in the recognition it is only utilized for dimerization of the proteins. The N-terminal end of the basic leucine zipper motif is relatively unstructured in the absence of DNA. A helical structure is induced upon binding to DNA allowing specific contacts to the recognition sequence. Dimer formation is a prerequisite for the exact positioning of the N-terminal basic end in the major groove of the DNA. Analogous to the dimeric structure of the protein, the DNA sequence displays 2-fold synunetry (see 1.2.4). 

Fig. 1.19. Tetramerization of the Lac repressor and loop formation of the DNA. The Lac repressor from E. coli binds as a dimer to the two-fold symmetric operator seqnence, whereby each of the monomers contacts a half-site of a recognition sequence. The Lac operon of E. coli possesses three operator sequences Of, 02 and 03, aU three of which are required for complete repression. Of and 03 are separated by 93 bp, and only these two sequences are displayed in the figure above. Between Of and 03 is a binding site for the CAP protein and the contact surface for the RNA polymerase. The Lac repressor acts as a tetramer. It is therefore assumed that two dimers of the repressor associate to form the active tetramer, whereby one of the two dimers is bound to 03, the other dimer binds to Of. The intervening DNA forms a so-caUed repression loop. After Lewis et al., 1996.

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