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BOYLE ERICA 13/SCI03/005 BCH 415- BIO INORGANIC CHEMISTRY. ASSIGNMENT: WRITE ON ZINC FINGERS. The zinc finger is a common structural motif in many protein DNA binding domains. It is found in roughly 3%(!) of all proteins and performs a diverse range of functions not limited to enhancing or inhibiting one specific gene. They are one of several domains that evolved to solve the problem of sequence specific binding of nucleic acids. A zinc ion coordinates with the protein and helps stabilize an alpha helix that can recognize DNA in a sequence specific manner. The common thread among these domains is a requirement for a coordinated zinc ion and a sequence specific interaction with nucleic acids like DNA or RNA (usually), but the structure of the other domains determines how the protein uses this interaction to perform its cellular functions. The Structure Zinc finger domains take advantage of the coordination of a zinc ion to cysteine and histidine side chains (in the "classic zinc finger" but there are other uncommon variations as well) to stabilize a short alpha helix and two beta sheets. The alpha helix is oriented in such a way that it fits neatly into the major groove of DNA where it orients side chains towards the unique functional groups on the edge of DNA bases. Side chains on the zinc finger helices (the "finger") hydrogen bond with only the correct DNA base, and thus bind to DNA in a sequence specific manner. The following are images of a single zinc finger protein (Zif268, pdb ID: 1ZAA [1]) with three zinc finger domains (green) coordinated to zinc ions (gray) by the side chains of two cysteines and two histidines (blue). Each zinc finger domain has an alpha helix whose side chains (yellow) interact with individual bases in the major groove of double stranded DNA (orange) through hydrogen bonding interactions (red). Notice the coordination chemistry of the zinc ion with the cysteines in the loop and the histidines in the alpha helix. This coordination chemistry stabilizes the "finger" and allows it to contact DNA. Also notice that multiple zinc finger domains can wrap around the DNA with each contacting the major groove. Looking down the center of DNA shows the yellow side chains of the zinc finger protein pointing in towards the DNA along the major groove. Zooming in on the major groove shows the sequence specific interactions between zinc finger side chains and the major groove functional groups of the purines in the DNA. These hydrogen bond contacts are lost if the sequence of the DNA doesn't exactly match the side chains of the zinc finger and vice versa. The Function The structure of the zinc finger explains its common function in stabilizing the recognition helix that confers sequence specific recognition of nucleic acids. Zinc fingers are easily modified protein motifs; minor changes to the amino acids in the helix with side chains that contact DNA can alter the sequence specificity. Nature has found many uses for these short, highly specific, easily modifiable and evolvable, sequence motifs when a protein needs to recognize a specific RNA or DNA sequence to function properly. They are especially common domains in transcription factors that must recognize specific DNA sequences upstream of a target gene to either inhibit or enhance binding of RNA polymerase or other transcription factors. They can either enhance or inhibit the transcription of the gene into mRNA depending on where they bind and which other proteins they recruit. Other functions that proteins with zinc finger domains are used for in the cell: The transcription factor TFIIIA has up to 9 zinc fingers that interact with the promoter sequence of DNA where it recruits RNA polymerase and induces transcription of the 5S rRNA gene. The SLUG and SNAIL zinc finger proteins bind at an E-box sequence on DNA and repress transcription of E-cadherins by blocking the access of other transcription factors that would otherwise promote its transcription. The PARP protein has two zinc finger domains that bind specifically to DNA sites with single strand breaks and a catalytic domain that repairs the damage. Tristetraprolin (aka ZFP36) is a translational regulator whose zinc finger domain binds to specific sequences of AU-rich elements in the 3' untranslated region of mRNAs and targets them for degradation. Zinc-finger antiviral protein (ZAP) binds specific sequences of viral mRNAs and recruits the RNA exosome to break them down before they are translated. The Future Zinc finger domains are so easy to modify while retaining sequence specificity for DNA that bioengineers have been able to design zinc fingers that bind to most three base pair sequence with high specificity.[2] Most recent work on zinc fingers focuses on engineering them to perform novel biological functions to specific DNA sequences (restriction endonucleases, inhibitors to fight viral mRNAs, and more). References: 1. Pavletich, N. & Pabo, C. Zinc finger-DNA recognition: crystal structure of a Zif268-DNA complex at 2.1 A. Science 252, 809-817 (1991). 2. Segal, D.J. Toward controlling gene expression at will: Selection and design of zinc finger domains recognizing each of the 5’-GNN-3’DNA target sequences. Proceedings of the National Academy of Science 96, 2758-2763(1999). 3. http://quora.com