Abstract

The structural and functional investigation of a hypothetical protein HP (KZV07215.1) from Saccharomyces cerevisiae (SC) has shed light on how fungal adaptation to unusual conditions and metabolic modifications occur. In this study, we performed a comprehensive in silico characterization of a mitochondrial hypothetical protein (KZV07215.1), encoded by the WN66_06778 gene, to elucidate its putative structure and function. Physicochemical profiling revealed a moderately acidic, hydrophobic, and highly stable 58.7-kDa protein with an isoelectric point of 6.55. According to the results of functional annotating programs like InterProScan, NCBI-CDD Search, and Pfam, the desired product is a cytochrome c oxidase (COX) protein of the respiratory system. Its 3D configuration was determined using the homology modeling technique by I-TASSER (TM-score estimation of 0.98 ± 0.05). Following the GalaxyRefine, a stable 3D structure was confirmed by PROCHECK, QMEAN (value of −3.36), QMEANDisCo Global (score of 0.77 ± 0.05), and ERRAT (score of 92.381). FTSite confirms the site of activity of the hypothesized structure. Molecular docking revealed substantial binding affinities with HEA compounds, yielding docking scores of −159.90 kcal/mol (HP-HEA III), ensuring robust and stable interactions. these findings strongly support the annotation of KZV07215.1 as a COX-I-like protein involved in electron transport chain complex IV activity. This work highlights the value of computational pipelines for functional annotation of uncharacterized mitochondrial proteins and suggests potential implications for understanding respiratory regulation and bioenergetic disorders.

Key words: Saccharomyces cerevisiae, mitochondrial DNA (mtDNA), hypothetical protein, cytochrome c oxidase like subunit I, molecular docking.