ZINC FINGER PEPTIDES

Zinc fingers are polypeptides that are part of small protein domains in which the zinc complex structure contributes to the overall stability of the domain. However, zinc fingers are structurally diverse polypeptides and a variety of zinc finger peptide motifs or zinc finger structural motifs have now been identified and classified. Since the discovery of the first zinc finger polypeptides or proteins intensive research has revealed over the years that zinc fingers are involved in a broad range of cellular processes. For example, zinc fingers are a part of nuclear receptor proteins including receptors for steroid hormones, thyroid hormone, and retinoic acid, and many others. In summary zinc binding polypeptide motifs are ubiquitous structures found in a multitude of proteins.

In a typical zinc finger, as present in natural transcription factors, a zinc ion is held by a pair of histidines and a pair of cysteines. This zinc ion amino acid complex stabilizes the packing of an anti-parallel β-sheet against an α-helix. The α-helix is also called the “recognition helix”. This helix interacts with a triplet of bases in the DNA indicating that the DNA recognition is a one to one interaction between the three amino acids in the protein helix and the nucleotide bases. Apparently zinc fingers can function as independent modules. In recent years the engineering of unique non-natural zinc fingers has led to the development of the zinc finger technology.

A comprehensive classification of zinc finger spatial structures was published by Krishna et al. in 2003. According to this classification scheme each available zinc finger structure can be placed into one of eight fold groups that are based on the structural properties in the vicinity of the zinc-binding site. The majority of zinc fingers are found in the three fold groups, C2H2-like finger, treble clef finger and the zinc ribbon.

A whole family of synthetic peptides that interact with zinc ions have been modeled and designed using zinc figure domains. This has led to the production of fluorescent peptide-based sensor molecules for divalent zinc. The design for the chemosensor relies on a synthetic peptide sequence template covalently attached to a fluorescence reporter which is sensitive to metal induced changes in the conformation of the polypeptide construct.

Zinc is a metallic element with the atomic number 30 and a molecular weight of 65.37. Zinc is an important and essential element in many organisms including human. A number of zinc salts are used in medicine and many proteins use zinc as a cofactor.

Zinc-finger Proteins

The transcription factor IIIA (TF_IIIA) was the first well-characterized eukaryotic positive-acting regulator protein. The cloning and sequencing of the gene encoding for this transcription factor, TF_IIIA, led to the discovery of a recurring cysteine and/or histidine amino acid residue motif spaced at regular intervals along the amino acid sequence of this protein. The protein was found to have nine repeated domains that contain cysteines and histidines spaced at regular intervals. These amino acids can bind zinc ions. In addition, it was found that the purified native protein contained an amount of zinc equal to the cystine-histidine clusters present in the transcription factor. These findings led to the proposal that TF_IIIA contains ‘zinc finger” folds that protrude from the surface of the protein and bind to DNA. In the proposed zinc-finger folded structure of TF_IIIA the repeated domains form loops in such as way that zinc ions are bound between a pair of cysteines and a pair of histidines. Furthermore, a phenylalanine or tyrosine residue and a leucine residue occur at nearly constant positions in the peptide loops. Mutational studies showed that these amino acid residues are required for DNA binding. Many regulatory proteins have now been found to contain zinc fingers, and because of the rapid growth of structural information on proteins and their folding a multitude of structures are now available for study.