Molecular modelling and dynamics of Kaurene Synthase involved in Stevia Rebaudiana (Accession MS007) Terpene Biosynthesis

Samsulrizal, Nurul Hidayah and Meenakshi Sundram, Tamil Chelvan and Abdul Hamid, Azzmer Azzar (2023) Molecular modelling and dynamics of Kaurene Synthase involved in Stevia Rebaudiana (Accession MS007) Terpene Biosynthesis. Asia Pacific Journal of Molecular Biology and Biotechnology (APJMBB), 31 ((2) suppl.). p. 82. ISSN 0128-7451 E-ISSN 2672-7277

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Abstract

Introduction: This paper presents the study on protein modelling, substrate docking and molecular dynamics of kaurene synthase involved in Stevia Rebaudiana MS007 (stevia). Kaurene synthase (KS) is a key enzyme in terpene biosynthesis pathway, and its activity is essential for biosynthesis of the sweetening compounds (i.e stevioside and rebaudioside) in stevia. Method: The KS gene was isolated and subsequently characterized using sequence homology and Multiple Sequence Alignment (MSA). The gene was translated and then subjected to protein modeling and molecular dynamics analysis. The molecular modelling approach involved the use of protein modelling tools to analyze the structure of the KS genes. Autodock Tools and Vina was used to perform molecular docking of KS, with ent-copalyl diphosphate ligand (ECDP) and GROMACS for molecular dynamics simulations of the KS enzyme complex. Result: Through these analyses, model predicted by AlphaFold was chosen as it has highest ERRAT value: 94.3369. As for substrate docking, 4 modes were generated and mode 1 was chosen as it has the lowest affinity energy (kcal/mol) value which is -10.6 kcal mol-1. In molecular dynamics simulation, KS enzyme was considered a stable enzyme since the RMSD value of the protein was below 4Å. The minimum distance between KS and ECDP was below 3Å which also show its complex interaction was good and strong. Conclusion: The results of this study provide insight into the mechanisms of terpene biosynthesis in stevia and can be used to develop biotechnological strategies for improving the production of sweetening compounds in stevia.

Item Type:	Article (other)
Subjects:	Q Science > Q Science (General) S Agriculture > SB Plant culture
Kulliyyahs/Centres/Divisions/Institutes (Can select more than one option. Press CONTROL button):	Kulliyyah of Science > Department of Plant Science
Depositing User:	Dr Nurul Hidayah Samsulrizal
Date Deposited:	28 Aug 2023 16:10
Last Modified:	28 Aug 2023 16:26
URI:	http://irep.iium.edu.my/id/eprint/106232

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