In Silico Characterization of a Hypothetical Protein from Pseudomonas aeruginosa LESB58: A Structural and Functional Perspective
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Background
Pseudomonas aeruginosa LESB58 is an omnipresent opportunistic bacteria that causes both acute and persistent infections in immunocompromised people. This bacteria is now on the WHO’s red list, meaning that new medicines are desperately needed for treatment. Although the bacterial genome is known, many hypothetical proteins have unidentified activities. Annotating hypothetical proteins can be critical steps toward discovering new druggable targets and treatments. In this work, a hypothetical protein of the Pseudomonas aeruginosa LESB58 strain (accession no. CAW29855.1, 284 amino acids) was chosen for in-depth structural and functional research.
Methods & Results
The target hypothetical protein’s subcellular location and other physicochemical characteristics were estimated to indicate that it is cytoplasmic. Using bioinformatics tools, it was determined that the target protein had the conserved domain of the phenazine biosynthesis protein family. Multiple sequence alignment of the target protein’s homologous sequence was produced, which helped to create a phylogenetic tree and identify the target protein’s common ancestor. The extended strand was mostly present in the secondary structure produced by PSI-PRED. Using a template protein (PDB ID: 1uok.1.A), a 3D model of the target protein was predicted using the SWISS-MODEL service based on the homology modeling idea. After energy reduction via the YASARA tool, which increases the structure’s stability the SWISS-MODEL structure was evaluated and validated using multiple tools. The RMSD value of 0.347 Å was produced by superimposing the target with the template protein using UCSF Chimera, indicating a dependable three-dimensional structure. PrankWeb server anticipated and visualized the modeled structure’s active site. The target proteins with non-homologous protein against the human proteome and human antitargets are finally predicted by a pipeline builder, suggest that this protein may be a possible therapeutic target.
Conclusion
By helping P. aeruginosa evade the host’s immune system and form biofilms that contribute to antibiotic resistance and worsen infections, this protein can boost P. aeruginosa pathogenicity. The study’s results, which examine both functional and structural features, might help in the creation of novel antibacterial drug targets and Pseudomonas aeruginosa LSB58 medications.
