The zinc finger (ZF) are structural motifs present in many eukaryotic proteins. They belong to the group of metalloproteins, as they are capable of binding the zinc metal ion, which they require for their operation. More than 1,500 ZF domains are predicted to exist in about 1,000 different proteins in humans.
The term zinc finger or “zinc finger” was first coined in 1985 by Miller, McLachlan, and Klug, while studying in detail the small DNA-binding domains of the Xenopus laevis transcriptional factor TFIIIA, described by other authors some years earlier..
Graphic representation of the zinc finger motif in proteins (Thomas Splettstoesser (www.scistyle.com), via Wikimedia Commons)
Proteins with ZF motifs are among the most abundant in the genome of eukaryotic organisms and participate in a diversity of essential cellular processes, among which are gene transcription, protein translation, metabolism, the folding and assembly of other proteins and lipids., programmed cell death, among others.
Structure
The structure of the ZF motifs is extremely conserved. Usually these repeated regions have 30 to 60 amino acids, the secondary structure of which is found as two antiparallel beta sheets that form a hairpin and an alpha helix, which is denoted as ββα.
Said secondary structure is stabilized by hydrophobic interactions and by the coordination of a zinc atom given by two cysteine and two histidine residues (Cys 2 His 2). However, there are ZFs that can coordinate more than one zinc atom and others where the order of the Cys and His residues varies.
The ZFs can be repeated in a batch, linearly configured in the same protein. All have similar structures, but can be chemically differentiated from each other by variations of amino acid residues key to the fulfillment of their functions.
A common feature among ZFs is their ability to recognize DNA or RNA molecules of different lengths, which is why they were initially considered only as transcriptional factors.
In general, recognition is of 3bp regions in DNA and is achieved when the ZF domain protein presents the alpha helix to the major groove of the DNA molecule.
Classification
There are different ZF motifs that differ from each other by their nature and the different spatial configurations achieved by the coordination bonds with the zinc atom. One of the classifications is as follows:
C
This is a commonly found motif in ZFs. Most C 2 H 2 motifs are specific for interaction with DNA and RNA, however, they have been observed to participate in protein-protein interactions. They have between 25 and 30 amino acid residues and are found within the largest family of regulatory proteins in mammalian cells.
Primary structure of a C2H2 zinc finger domain, including the bonds that coordinate the zinc ion and with a "hand and finger" background (AngelHerraez, via Wikimedia Commons)
C
They interact with RNA and some other proteins. They are seen mainly as part of some retrovirus capsid proteins, assisting in the packaging of viral RNA just after replication.
C
Proteins with this motif are enzymes responsible for DNA replication and transcription. A good example of these can be the T4 and T7 phage coarse enzymes.
C
This family of ZF comprises transcription factors that regulate the expression of important genes in numerous tissues during cell development. GATA-2 and 3 factors, for example, are involved in hematopoiesis.
C
These domains are typical of yeast, specifically the GAL4 protein, which activates the transcription of genes involved in the use of galactose and melibiose.
Zinc Fingers (C
These particular structures possess 2 subtypes of ZF domains (C 3 HC 4 and C 3 H 2 C 3) and are present in numerous animal and plant proteins.
They are found in proteins such as RAD5, involved in DNA repair in eukaryotic organisms. They are also found in RAG1, essential for the reconfiguration of immunoglobulins.
H
This domain of ZF is highly conserved in the integrases of retroviruses and retrotransposons; by binding to the target protein it causes a conformational change in it.
Features
Proteins with ZF domains serve a variety of purposes: they can be found on ribosomal proteins or on transcriptional adapters. They have also been detected as an integral part of the structure of yeast RNA polymerase II.
They appear to be involved in intracellular zinc homeostasis and in the regulation of apoptosis or programmed cell death. In addition, there are some ZF proteins that function as chaperones for the folding or transport of other proteins.
Binding to lipids and a critical role in protein-protein interactions are also prominent functions of the ZF domains in some proteins.
Biotechnological importance
Over the years, the structural and functional understanding of the ZF domains has allowed great scientific advances that involve the use of their characteristics for biotechnological purposes.
Since some ZF proteins have high specificity for certain DNA domains, much effort is currently invested in the design of specific ZFs, which can provide valuable advances in gene therapy in humans.
Interesting biotechnological applications also arise from the design of proteins with genetically engineered ZFs. Depending on the desired purpose, some of these can be modified by the addition of "poly zinc" finger peptides, which are capable of recognizing virtually any DNA sequence with high affinity and specificity.
Nuclease-modified genomic editing is one of the most promising applications today. This type of editing offers the possibility to carry out studies on genetic function directly in the model system of interest.
Genetic engineering using modified ZF nucleases has captured the attention of scientists in the field of genetic improvement of cultivars of plants of agronomic importance. These nucleases have been used to correct an endogenous gene that produces herbicide resistant forms in tobacco plants.
Nucleases with ZF have also been used for the addition of genes in mammalian cells. The proteins in question were used to generate a set of isogenic mouse cells with a set of defined alleles for an endogenous gene.
Such a process has a direct application in the tagging and creation of new allelic forms to study structure and function relationships in native conditions of expression and in isogenic environments.
References
- Berg, JM (1990). Zinc finger domains: hypotheses and current knowledge. Annual Review of Biophysics and Biophysical Chemistry, 19 (39), 405–421.
- Dreier, B., Beerli, R., Segal, D., Flippin, J., & Barbas, C. (2001). Development of zinc finger domains for recognition of the 5'-ANN-3 'family of DNA sequences and their use in the construction of artificial transcription factors. JBC, (54).
- Gamsjaeger, R., Liew, CK, Loughlin, FE, Crossley, M., & Mackay, JP (2007). Sticky fingers: zinc-fingers as protein-recognition motifs. Trends in Biochemical Sciences, 32 (2), 63–70.
- Klug, A. (2010). The Discovery of Zinc Fingers and Their Applications in Gene Regulation and Genome Manipulation. Annual Review of Biochemistry, 79 (1), 213–231.
- Kluska, K., Adamczyk, J., & Krȩzel, A. (2017). Metal binding properties of zinc fingers with a naturally altered metal binding site. Metallomics, 10 (2), 248–263.
- Laity, JH, Lee, BM, & Wright, PE (2001). Zinc finger proteins: New insights into structural and functional diversity. Current Opinion in Structural Biology, 11 (1), 39–46.
- Miller, J., McLachlan, AD, & Klug, A. (1985). Repetitive zinc-binding domains in the protein transcription factor IIIA from Xenopus oocytes. Journal of Trace Elements in Experimental Medicine, 4 (6), 1609–1614.
- Urnov, FD, Rebar, EJ, Holmes, MC, Zhang, HS, & Gregory, PD (2010). Genome editing with engineered zinc finger nucleases. Nature Reviews Genetics, 11 (9), 636–646.