In silico analysis of cellulase enzymes from Bacillus subtilis, Aspergillus niger and Trichoderma reesei with molecular docking techniques
Yanty maryanty, Sri rulianah, Dwina moentamaria
Chemical Engineering major Politeknik Negeri Malang, Soekarno – Hatta street no.09 Malang – East Java, Indonesia. 65123
Abstract
Molecular docking technique in in silico analysis of cellulase enzymes from Bacillus subtilis, Aspergillus niger and Trichoderma reesei was performed using Autodock Vina in the PyRx 9.5 program. The proteins used are Beta-1,4 endoglucanase from Asperillus niger (PDB ID 5I77), endoglucanase 1 from Trichoderma reesei (PDB ID 1EG1), Beta-1,4 endoglucanase from Bacillus subtilis (3PZT) and the ligand used is Cellulose (Pubchemerm reesei) ID 16211032). The PyMol 2.3.1 program is used to visualize the docking results, while the LigPlot 2.1 program is used to see the amino acid interactions that occur. Docking conducted in this study is blind docking by mimicking the interaction of target proteins and ligand control. Docking is a method for predicting the strength of interactions between receptors and ligands, based on binding affinity values. The more negative the value, the stronger the interaction that occurs between receptors and ligands. Compared with the results of cellulase docking enzymes, docking between richorderma reesei cellulose and cellulose gives the best results. Binding affinity scores (kcal / mol) Bacillus subtilis, Trichoderma receii, Aspergillus niger are -5.9, -6.2, -5.9, respectively. After knowing the value of binding affinity, it is necessary to do further analysis, to see the interaction of amino acids between proteins and ligands, using the LigPlot program. The results of the interaction of Bacillus subtilis, Trichoderma reseei, Aspergillus niger in hidrophobic binding are His235, Ala263, Tyr231, Trp207, Leu133; Tyr146, Trp320, Pro107, Gln174, Asp172; Ser233, Tyr227, Ser196 and Hydrogen Bonding Gln209, Glu169, Ser264, Glu298, His65, Trp291; Glu196, Glu201, Arg108, Ser318, Ser106, Tyr38; Gly232, Trp197, Asp163, Trp201, respectively.
Keywords: Docking technique, Bacillus subtilis, Trichoderma reseei, Aspergillus niger, binding affinity
Topic: Chemical Engineering