Full text loading...
- ISSN: 1570-1646
- E-ISSN: 1875-6247
-
In-silico Analysis of Peroxidase from Raphanus Sativus
- Source: Current Proteomics, Volume 21, Issue 5, Dec 2024, p. 523 - 542
-
- 19 Sep 2024
- 04 Dec 2024
- 03 Jan 2025
Abstract
Background
In-silico study plays an important role in bioinformatics. It is a fast-expanding field to modelling, predicting and explaining biological activity at the molecular level using computational methods. Peroxidases are heme or non-heme-containing key antioxidant enzyme belonging to the oxidoreductase family. They can bioremediate the different environmental pollutants such as dioxins, petroleum hydrocarbons, synthetic dyes, herbicides, pesticides, chlorinated hydrocarbons, different phenolic and nonphenolic compounds etc. The current work aims to extend knowledge among researchers in better understanding structure of peroxidase purified from Raphanus sativus by analysing it’s physicochemical properties, secondary structure prediction, and 3D modelling of protein sequences and its validation using a variety of conventional computational methods.
Objective
Using bioinformatics techniques, it is feasible to figure out the relationship between sequence, structure, and function using enzyme protein sequences. To improve catalytic efficacy, thermostability, structure prediction, and validation, in-silico studies of the protein sequences of several industrially important enzymes have been performed recently.
Methods
The physical and chemical parameters of radish peroxidase was analysed by using protparam tool-Expasy. SOPMA, SWISS MODEL, PROCHECK, ERRAT and Verify3D tools were used for structural analysis and validation of peroxidase protein sequence of Raphanus Sativus. The Molecular Evolutionary Genetics Analysis (MEGA 11) tool was used to align the protein sequences automatically and manually using the query sequence and peroxidase from various plant sources. Interaction of Radish peroxidase with the different organic substrates like guaiacol, o-cresol, m-cresol, p-cresol, hydroquinone, catechol, resorcinol, benzaldehyde and aniline were analysed by molecular docking technique.
Results
This research gave critical information regarding the properties and functioning of Raphanus sativus peroxidase. The computational molecular weight for the query protein sequence of radish peroxidase was found to be 37.503 KDa. The analysis of secondary structure prediction using SOPMA tool revealed that random coil (Cc) was present in the highest percentage as 39.18%. From the instability index (II) value and the aliphatic index value it was confirmed that the protein was slightly unstable but thermally stable in a wide range of temperature. The phylogenetic tree constructed by Molecular Evolutionary Genetics Analysis (MEGA 11) server revealed that the peroxidase and other plant peroxidases had been evolved from a common ancestor. Molecular docking analysis revealed that all the ligand had binding energy > -4.0 Kcal/mol. The interaction involved in the docking of radish peroxidase with selected ligands were conventional hydrogen bond, pi-cation, alkyl, pi-alkyl, pi-pi stacked, pi-sigma, carbon hydrogen bond, pi-lone pair.
Conclusion
In summary, these in-silico investigations provide a strong basis for carrying out wet-lab experiments to boost production, research for novel sources with a metagenomics strategy and attempt directed evolution to include desired functional features. From this study, we found the active site of the enzyme and the key amino acid residues that are used in the enzyme-ligand interaction. The novel information presented in this work will promote proteomics research and the development of novel bioinformatics techniques. The investigation of enzyme-ligand interactions will aid in the creation of a fresh approach to the synthesis of organic molecules.
©
2024 Bentham Science Publishers