Structural and functional prediction of DNA glycosylases as well as their phylogenetic relationship by bioinformatic methods
DOI:
https://doi.org/10.37636/recit.v7n4e372Keywords:
Oxidative stress, Genotoxicity, Repair, DNA, in silicoAbstract
Nitrogenous bases are a component of DNA nucleotides and can be altered by both external and internal factors. The base excision repair (BER) mechanism is responsible for removing damaged bases through the action of various enzymes. In this study, we performed an in-silico analysis of the gene and protein sequences of glycosylases responsible for eliminating altered bases: MPG, OGG1, NEIL1, MUTYH, and NTHL1, which participate in the BER mechanism of Homo sapiens. We used various bioinformatics tools to characterize the guanine and cytosine (G≡C) content of the genes, the secondary and tertiary structures of the glycosylases, protein motifs, and the phylogenetic relationships between the glycosylases. Gene and amino acid sequences were downloaded from GenBank, and the online software tools GENSCAN, Gor4, Phyre2, InterPro, and MEGA were used. The G≡C content percentages obtained were 63.80%, 63.50%, 61.33%, 60.48%, and 59.20% for MPG, NTHL1, NEIL1, MUTYH, and OGG1, respectively. Secondary structure analysis of the proteins showed that NTHL1 has the highest percentage (43.42%) of alpha helix, OGG1 has the highest percentage (16.23%) of extended chain structure, and NEIL1 has the highest percentage of random coil (57.69%). Additionally, we performed the prediction of tertiary structure and domains in proteins, where the HhH domain was observed in OGG1, MUTYH, and NTHL1. The phylogenetic tree revealed the evolutionary relationships among the studied genes, with the OGG1 gene being the common ancestor. These findings are important for understanding the molecular structure of glycosylases and provide valuable information that can be utilized in both experimental and biotechnological studies, as well as in understanding the evolutionary function of DNA repair and in the design of therapeutic strategies involving glycosylases.
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