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Communication

Searching for New Z-DNA/Z-RNA Binding Proteins Based on Structural Similarity to Experimentally Validated Zα Domain

1
Department of Biology and Ecology, Faculty of Science, University of Ostrava, 710 00 Ostrava, Czech Republic
2
Department of Biophysical Chemistry and Molecular Oncology, Institute of Biophysics of the Czech Academy of Sciences, 612 65 Brno, Czech Republic
3
Department of Biochemistry, Sanger Building, University of Cambridge, Tennis Court Rd., Cambridge CB2 1GA, UK
*
Author to whom correspondence should be addressed.
Academic Editors: Maurizio Battino, Vaclav Brazda and Richard Bowater
Int. J. Mol. Sci. 2022, 23(2), 768; https://doi.org/10.3390/ijms23020768
Received: 30 November 2021 / Revised: 3 January 2022 / Accepted: 5 January 2022 / Published: 11 January 2022
(This article belongs to the Special Issue Impacts of Molecular Structure on Nucleic Acid-Protein Interactions)
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. View Full-Text
Keywords: Z-DNA; Z-RNA; Zα domain; protein binding; bioinformatics Z-DNA; Z-RNA; Zα domain; protein binding; bioinformatics
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MDPI and ACS Style

Bartas, M.; Slychko, K.; Brázda, V.; Červeň, J.; Beaudoin, C.A.; Blundell, T.L.; Pečinka, P. Searching for New Z-DNA/Z-RNA Binding Proteins Based on Structural Similarity to Experimentally Validated Zα Domain. Int. J. Mol. Sci. 2022, 23, 768. https://doi.org/10.3390/ijms23020768

AMA Style

Bartas M, Slychko K, Brázda V, Červeň J, Beaudoin CA, Blundell TL, Pečinka P. Searching for New Z-DNA/Z-RNA Binding Proteins Based on Structural Similarity to Experimentally Validated Zα Domain. International Journal of Molecular Sciences. 2022; 23(2):768. https://doi.org/10.3390/ijms23020768

Chicago/Turabian Style

Bartas, Martin, Kristyna Slychko, Václav Brázda, Jiří Červeň, Christopher A. Beaudoin, Tom L. Blundell, and Petr Pečinka. 2022. "Searching for New Z-DNA/Z-RNA Binding Proteins Based on Structural Similarity to Experimentally Validated Zα Domain" International Journal of Molecular Sciences 23, no. 2: 768. https://doi.org/10.3390/ijms23020768

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