In Silico Studies on Catalases From Plant Sources

Abstract

Introduction In the era of genomics, bioinformatics has become highly significant, assisting in the genome-wide discovery and characterization of potential genomic regions of different enzymes for a variety of industrial applications. Catalases are unique among environmental biocatalysts due to their high catalytic rate and thermostability. Therefore, present communication deals with the bioinformatics analysis on the characterization of the protein sequence of catalases from diverse plant sources and subjected to assessment of homology, multiple sequence alignment, construction of the phylogenetic tree, amino acid composition, physiochemical properties, motif search, secondary and tertiary structure prediction and its Ramachandran plot . Method In the present study, a total of 65 protein sequences of catalases from diverse plant sources were retrieved from the NCBI database and subjected to bioinformatics assessment for homology search, multiple sequence alignment, phylogenetic tree construction, motif search, and prediction of structural analysis using different in silico analytical tools available. Result The protein sequence of many enzymes have been assessed and analyzed using bioinformatics tools. The diversity of plant sources for catalases was found to be largest for Oryza sativa.The amino acid residue variability in the 65 catalase protein sequences studied ranged from 90 to 533. The molecular weights varied between 10322.46 to 61366.87 daltons, while the pI values varied between 4.53 to 7.95. Thermostability and hydrophilicity were identified in abundance in these proteins, as shown by their relatively high aliphatic index and negative GRAVY values, respectively. The phylogenetic tree displayed unique clusters for each plant genus, and numerous accessions of the same genus were clustered together, suggesting similarity at the sequence level.The prediction of the secondary structure of the catalase showed the predominance of random coil followed by the alpha helix. Ramachandran plot showed that most of the amino acid residues is in the core region which represent the favourable/allowed combination of phi-psi values. The dark region with maximum residues, correspond to no steric hinderance, ie these are the allowed regions for α- helical and β-sheet conformations. Conclusion Five motifs were consistently identified across all sequences, indicating that they were related to the plant catalase PLN02609 family. Plant catalase PLN02609 is found in three kingdoms of life and is known to perform a number of biosynthetic and degradative functions. By analysing plant catalase protein sequences using bioinformatics, it is possible to molecularly clone critical genes and anticipate gene regulatory networks and whole-cell dynamics. Ramachandran plot showed that most of the amino acid residues are in the core region which represent the favourable comformation of amino acid residues of the catalase. In silico study of protein sequences elucidates the various catalytic sites, allowing for potential modification to achieve desired properties.