Malaysian Journal of Analytical Sciences Vol 23 No 4 (2019): 613 - 624

DOI: 10.17576/mjas-2019-2304-07

 

 

 

 

INTERACTION STUDIES OF PUTATIVE CHEMICAL LIGANDS IN BINDING SITES OF THERMOSTABLE LIPASE FROM Geobacillus zalihae STRAIN T1

 

(Kajian Interaksi Ligan Kimia pada Tapak Pengikatan Lipase Termostabil daripada Geobacillus zalihae Stren T1)

 

Mohd Basyaruddin Abdul Rahman^1,2* and Muhammad Alif Mohammad Latif ^1,2,3

 

¹Integrated Chemical BioPhysics Research

²Department of Chemistry, Faculty of Science

³Centre of Foundation Studies for Agricultural Science

Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia

 

*Corresponding author:  basya@upm.edu.my

 

 

Received: 19 August 2018; Accepted: 3 July 2019

 

 

Abstract

Industrial biotechnology focusing on the usage of enzyme as the catalyst in many chemical reactions, however enzyme stability remains a major challenge. Enzyme can be modified via genetic or chemical methods by manipulating its structure. A potential biocatalyst based on lipase enzyme was designed by in silico approach. The enzyme-ligand interactions between selected chemical ligands and a thermostable lipase from Geobacillus zalihae strain T1 were studied by using molecular docking, AutoDock 3.0.5. The T1 lipase structure (PDB ID: 2DSN) was predicted to have 65 pockets in the structure, with nine of them have the potential binding sites for ligands based on their surface area, volume and number of residues. The characteristics of each selected binding site and chemical ligands were analyzed. Types of enzyme-ligand interactions involved in binding sites were determined and co-related with the final docked energies. All these discoveries may prove useful for designing novel binding sites, in particular as new biocatalyst.

 

Keywords:  thermostable lipase, binding site, protein-ligand interaction, docking, biocatalyst

 

Abstrak

Industri bioteknologi memberi tumpuan kepada penggunaan enzim sebagai pemangkin dalam banyak tindak balas kimia, namun mengekalkan kestabilan enzim menjadi cabaran utama. Enzim boleh diubah melalui kaedah genetik atau kimia dengan memanipulasi struktur asasnya. Biokatalis yang berpotensi berdasarkan enzim lipase direka bentuk dengan menggunakan pendekatan berkomputer. Interaksi enzim-ligand antara ligan kimia dipilih dan lipase termostabil dari Geobacillus zalihae stren T1 telah dikaji dengan menggunakan pendokkan molekul, AutoDock 3.0.5. Struktur lipase T1 (PDB ID: 2DSN) diramalkan mempunyai 65 poket dalam struktur, dengan sembilan daripadanya mempunyai tapak pengikat yang berpotensi untuk ligan berdasarkan luas permukaan, jumlah dan bilangan residu. Ciri-ciri setiap tapak pengikat dan ligan kimia tersebut dipilih untuk dianalisis. Jenis-jenis interaksi enzim-ligan yang terlibat dalam tapak pengikat telah ditentukan dan berkait dengan tenaga berlabuh yang paling akhir. Semua penemuan ini terbukti bermanfaat bagi membentuk tapak mengikat novel, khususnya sebagai biokatalis yang baru.

 

Kata kunci:  lipase termostabil, tapak pengikat, interaksi protein-ligan, pendokkan, biokatalis

 

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