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

Published version
Peer-reviewed

Type

Article

Change log

Authors

Slychko, Kristyna 
Červeň, Jiří 
Beaudoin, Christopher A 

Abstract

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.

Description

Keywords

Z-DNA, Z-RNA, Zα domain, bioinformatics, protein binding, Amino Acid Sequence, Binding Sites, DNA, Z-Form, DNA-Binding Proteins, Models, Molecular, Molecular Docking Simulation, Molecular Dynamics Simulation, Nucleic Acid Conformation, Protein Binding, Protein Conformation, Protein Interaction Domains and Motifs, RNA, RNA-Binding Proteins, Structure-Activity Relationship

Journal Title

Int J Mol Sci

Conference Name

Journal ISSN

1661-6596
1422-0067

Volume Title

23

Publisher

MDPI AG
Sponsorship
Wellcome Trust (200814/Z/16/Z)