Searching for New Z-DNA/Z-RNA Binding Proteins Based on Structural Similarity to Experimentally Validated Zα Domain.
Beaudoin, Christopher A
Int J Mol Sci
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Bartas, M., Slychko, K., Brázda, V., Červeň, J., Beaudoin, C. A., Blundell, T. L., & Pečinka, P. (2022). Searching for New Z-DNA/Z-RNA Binding Proteins Based on Structural Similarity to Experimentally Validated Zα Domain.. Int J Mol Sci, 23 (2) https://doi.org/10.3390/ijms23020768
Z-DNA and Z-RNA are functionally important left-handed structures of nucleic acids, which play a significant role in several molecular and biological processes including DNA replication, gene expression regulation and viral nucleic acid sensing. Most proteins that have been proven to interact with Z-DNA/Z-RNA contain the so-called Zα domain, which is structurally well conserved. To date, only eight proteins with Zα domain have been described within a few organisms (including human, mouse, Danio rerio, Trypanosoma brucei and some viruses). Therefore, this paper aimed to search for new Z-DNA/Z-RNA binding proteins in the complete PDB structures database and from the AlphaFold2 protein models. A structure-based similarity search found 14 proteins with highly similar Zα domain structure in experimentally-defined proteins and 185 proteins with a putative Zα domain using the AlphaFold2 models. Structure-based alignment and molecular docking confirmed high functional conservation of amino acids involved in Z-DNA/Z-RNA, suggesting that Z-DNA/Z-RNA recognition may play an important role in a variety of cellular processes.
Bioinformatics, Protein binding, Z-dna, Z-rna, Zα Domain, RNA-Binding Proteins, DNA-Binding Proteins, DNA, Z-Form, RNA, Binding Sites, Amino Acid Sequence, Nucleic Acid Conformation, Protein Conformation, Protein Binding, Structure-Activity Relationship, Models, Molecular, Protein Interaction Domains and Motifs, Molecular Dynamics Simulation, Molecular Docking Simulation
External DOI: https://doi.org/10.3390/ijms23020768
This record's URL: https://www.repository.cam.ac.uk/handle/1810/334260
Attribution 4.0 International
Licence URL: https://creativecommons.org/licenses/by/4.0/