In-silico Analysis of Peroxidase from Raphanus Sativus
Authors: Saikia Shilpa , Yadav Meera , Yadav Hardeo Singh 
Published: January 2025

Background::

In-silico study plays an important role in bioinformatics. It is a fastexpanding
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.

Method::

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, mcresol,
p-cresol, hydroquinone, catechol, resorcinol, benzaldehyde and aniline were analysed by
molecular docking technique.

Result::

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 wetlab
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.