Zinc fingers are protein folds that bind to zinc ions and DNA/RNA, regulating gene expression and virus assembly. They consist of an alpha helix and beta sheet held in place by cystine and histidine residues. Zinc finger nucleases can cut DNA at specific points, while engineered zinc fingers can be used as artificial transcription factors. Zinc fingers in viral proteins, such as HIV-1, are potential targets for antiviral compounds. Selective inhibitors for retroviral zinc finger proteins are achievable.
A zinc finger is a finger-shaped protein fold made up of specific amino acids in the protein that bind to a zinc ion. These proteins often bind to DNA and RNA because their shape allows for tight domain interaction with DNA and RNA nucleotides. Their nucleotide-binding properties allow them to function in gene expression regulation and virus assembly.
There are several types of zinc finger structures, but the most common version consists of an alpha helix and a beta sheet, the two most common secondary structures in proteins, on either side of at least one zinc ion. The alpha helix and beta sheet are held in place by cystine and histidine residues, coordinating the zinc ion via their nitrogen and sulfur atoms. The zinc finger binds to DNA and through the interaction of amino acids at its periphery with base pairs in the center of the DNA double helix. It is a compact protein domain and its small size allows it to be very close to DNA base pairs.
These proteins are the most common transcription factors in living organisms. A transcription factor is a protein that binds to DNA and controls the transfer of genetic information to RNA. The fact that these proteins target DNA has made them candidates for targeted redesign in order to target DNA sequences of interest.
For example, a zinc finger nuclease (ZFN) is a synthetic protein that has an engineered zinc finger binding domain fused to a restriction endonuclease or DNA cleavage enzyme. ZFN can be used to cut DNA at specific points and is a useful tool to promote site-specific recombination of DNA. Engineered zinc fingers can also be used as artificial transcription factors.
Zinc finger domains are found in some viral proteins, including the neocapsid (NC) protein of human immunodeficiency virus-1 (HIV-1). NC is an attractive antiviral target because it is important for viral assembly and is highly conserved. Inhibitors that specifically target the zinc fingers of viral and retroviral proteins could be used to prevent the virus from replicating. Obtaining antiviral compounds of this nature is an active area of biomedical research.
These proteins play an important role in the normal metabolism of cells. To be effective, antiretroviral compounds must specifically target retroviral zinc finger proteins. These retroviral proteins have distinct amino acid sequences and structural differences from zinc finger cell proteins, so obtaining selective inhibitors is an achievable goal.
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