Dioxygenase from Aspergillus fumigatus MC8: molecular modelling and in silico studies on enzyme–substrate interactions

Abstract

Flavoenzymes have been extensively studied for their structural and mechanistic properties because they find potential application as industrial biocatalysts. They are attractive for biocatalysis because of the selectivity, controllability and efficiency of their reactions. Some of these enzymes catalyse the oxidative modification of protein substrates. Among them oxygenases (monoxoygenases and dioxygenases) are of special interest because they are highly entantio as well as regio-selective and can be used for oxyfunctionalisation. Dioxygenase enzymes catalyse oxygenation reactions in which both di-oxygen atoms are incorporated into the product. A dioxygenase enzyme purified from Aspergillus fumigatus MC8 was subjected to protein digestion followed by peptide sequencing. The sequence analysis of the peptide fragments resulted in identifying its match with that of an extracellular dioxygenase sequence from the same species of fungus existing in the protein database. The sequence was submitted to protein homology/analogy recognition engine online server for homology modelling and the 3D structure was predicted. Subsequently, the in silico studies of the enzyme–substrate (protein–ligand) interaction were carried out by using the method of molecular docking simulations wherein the modelled dioxygenase enzyme (protein) was docked with the substrates (ligands), catechin and epicatechin.

Keywords:

• dioxygenase
• peptide sequencing
• homology modelling
• molecular docking

Acknowledgements

KR is thankful to the Département Soutien et Formation des communautés scientifiques du sud (DSF), Institut de Recherche pour le Développement (IRD), France, for the doctoral fellowship. The facilities provided by the Bioinformatics Division of the Department of Microbiology and Biotechnology, School of Life Sciences, Kannur University, India, is greatly acknowledged. The service provided by the Centre d'Analyses Protéomics, Faculté de Medicine, Hospital Nord, Marseille, France, in getting the peptide sequence data is greatly acknowledged. The article is dedicated to the loving memory of Dr Christopher AUGUR, Research Officer, IRD, Marseille, France.

Notes

1. Present address: Molecular Cell Biology Unit (MCBU), Department of Biology, Lund University, Biology Building A, Sölvegatan 35, SE-223 62 Lund, Sweden.

Additional information

Notes on contributors

Krishnankutty Roopesh

1