title: Molecular modelling, dynamics simulation and characterization of antifungal chitinase from Sechium edule.
abstract: Chitinases are varied sized proteins which have the ability to degrade chitin and are present in a huge range of organisms like fungi, yeasts, arthropods, humans etc. and have been getting increased attention due to their biocontrol properties. In silico analysis sheds light on the extensive properties of this plant protein. In this paper, a particular antifungal protein Chitinase sourced from Sechium edule from East Khasi Hills, Meghalaya was characterized using an array of bioinformatics tools. The modelled protein showed conserved domains characteristic to glycosyl hydrolase, family 18 superfamily. Likewise, a part of the conserved domain area fits in with xylanase inhibitor Xip-1 and the class ΙΙΙ plant chitinases, for example, concanavalin B, hevamine, which have a GH18 area. The modelled wild type protein exhibited secondary characteristics comprising of 48.8% helix, 62.2% sheets and 13.8% turns, displaying an aliphatic index of 80.53 and instability index of 48.88 inferring upon the fact that the protein is relatively unstable without its appropriate environment. The paper functions as the first attempt to portray molecular dynamics simulation of Chitinase from Sechium edule reinforced by modelling and thorough characteristic analysis of the protein by employing parameters like Ramachandran Plot, Chou and Fasman Secondary Structure prediction, ProtParam etc. Further approaches like protein engineering and activity analysis suggested.
authors.affiliation: Centre for Advanced Studies in Botany, North Eastern Hill University, Umshing Mawkynroh, Shillong 793022, India.
authors.forename: Bipasha
authors.initials: B
authors.lastname: Bhattacharjee
authors.affiliation: Centre for Advanced Studies in Botany, North Eastern Hill University, Umshing Mawkynroh, Shillong 793022, India.
authors.forename: Neeta
authors.initials: N
authors.lastname: Pathaw
authors.affiliation: Centre for Advanced Studies in Botany, North Eastern Hill University, Umshing Mawkynroh, Shillong 793022, India.
authors.forename: Nikhil K
authors.initials: NK
authors.lastname: Chrungoo
authors.affiliation: Department of Biotechnology and Bioinformatics, North Eastern Hill University, Umshing Mawkynroh, Shillong 793022, India. Electronic address: atanubioinfo@gmail.com.
authors.forename: Atanu
authors.initials: A
authors.lastname: Bhattacharjee
mesh_terms: D000935:Antifungal Agents / Q000737:chemistry; D002688:Chitinases / Q000737:chemistry*; D019662:Cucurbitaceae / Q000145:classification / Q000201:enzymology*; D007194:India; D008958:Models, Molecular; D056004:Molecular Dynamics Simulation; D015202:Protein Engineering; D040681:Structural Homology, Protein
chemical_list: D000935:Antifungal Agents; D002688:Chitinases
keywords: Bioinformatics; Chitinase; Molecular docking; Under researched plants of North-East India