Specificity zinc fingers

Hurt JA, Thibodeau SA, Hirsh AS, Pabo CO, Joung JK (2003) Highly specific zinc finger proteins obtained by directed domain shuffling and cell-based selection. Proc Natl Acad Sci USA 100 12271-12276... 

Generation of targeted donble-strand DNA breaks by the use of specific Zinc-finger endonuclease induces homologous recombination that facilitates gene targeting. In the future it will be... 

It has also been possible to determine the x-ray structures of classic zinc finger motifs from several proteins bound to specific DNA fragments. We will here describe one such structure containing three zinc fingers from a mouse protein, Zif 268, which is expressed at an early developmental stage of the mouse. Nikola Pavletich and Carl Pabo at the Johns Hopkins University School of Medicine, Baltimore, determined the x-ray structure to 2.1 A resolution of a recombinant polypeptide derived from Zif 268 bound to a 10-base... 

The 12 residues between the second cysteine zinc ligand and the first histidine ligand of the classic zinc finger motif form the "finger region". Structurally, this region comprises the second p strand, the N-terminal half of the helix and the two residues that form the turn between the p strand and the helix. This is the region of the polypeptide chain that forms the main interaction area with DNA and these interactions are both sequence specific. 

Figure 10.4 Detailed view of the binding of the second zinc finger of Zif 268 to DNA. Two side chains, Arg 46 and His 49, form sequence-specific interactions with DNA. There are also three nonspecific interactions between phosphate groups of the DNA and the side chains of Arg 42, Ser 45, and His 53.

Figure 10.5 Comparison of the sequence-specific binding to DNA of six different zinc fingers. Residues in the N-terminus of the a helix in the finger regions are numbered 1 to 6. The residue immediately preceding the a helix is numbered -1. Amino acid residues and nucleotides that make sequence-specific contacts are colored. In spite of the structural similarities between the zinc fingers and their overall mode of binding, there is no simple rule that governs which bases the fingers contact.

Fig. 6.3 Molecular model of the domains of the chimeric nuclease (constituted by an hybrid between a non-specific DNA cleavage domain and a zinc finger recognition domain) and DNA. The cleavage domain sits behind...

The specificity involved in the control of transcription requires that regulatory proteins bind with high affinity to the correct region of DNA. Three unique motifs— the helix-turn-helix, the zinc finger, and the leucine... 

Bulyk, M. L., Huang, X., Choo, Y., and Church, G. M. (2001). Exploring the DNA-binding specificities of zinc fingers with DNA microarrays. Proc. Natl. Acad. Sci. USA 98, 7158-7163. 

The lack of zinc can also be a problem in biological systems and is responsible for disease states. For example, nitric oxide-dependent apoptosis can be induced in motor neurons by zinc-deficient SOD, and in some cases of amyotrophic lateral sclerosis, zinc-deficient SOD may participate in this type of oxidative mechanism involving nitric oxide.969 One form of hereditary human hair loss or alopecia was mapped to a specific gene and a mutation found in affected individuals. The gene encodes a single zinc finger transcription factor protein with restricted expression in the brain and skin.970 Zinc has been implicated in Alzheimer s via beta amyloid formation, and a role has been attributed for the cerebral zinc metabolism in the neuropathogenesis of Alzheimer s disease.971... 

Fig. 1.6. Binding domain to DNA. ERs contain two structures called zinc fingers, typical of proteins that interact with DNA. One zinc atom forms four links of coordination with four cysteine residues of the protein structure, which occupy nearby positions, thus leaving a loop of some 15 to 22 aminoacids. The zinc fingers of the receptor are capable of interacting with specific sequences of DNA, the hormone response elements, with which they establish hydrogen bridges and form stable structures...

The zinc fingers are common structures among the transcription factors. Nevertheless, the coordination with zinc is more frequently produced between two histidine residues and two neighboring cysteines than when it is among four cysteine residues, as occurs in the nuclear hormone receptors. The zinc fingers provide an optimum architecture for the mutual recognition between specific sequences of amino acids and nucleotides. In the case of the nuclear receptors, the interaction occurs between particular amino acids of the DBD and guanine residues of the DNA sequence (Fig. 1.7). 

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