STUDY OF STABILITY AND DYNAMICS OF LIPASE ENCAPSULATED IN POLY (3-HYDROXYBUTYRATE) SYSTEM BY USING MOLECULAR DYNAMIC SIMULATION

• Main Author: Sandwika Jaya, Kurnia
• Format: Final Project
• Language: Indonesia
• Subjects: Kimia
• Online Access: https://digilib.itb.ac.id/gdl/view/64924
• Institution: Institut Teknologi Bandung

Lipases are widely used in industry as a biocatalyst in mediating reactions of lipids convertion various product such as fatty acid and biodiesel. Nevertheless, biocatalysts like lipase are mostly a delicate molecule that easy to denature after a short periode of their application and most of them are difficult to be renatured. One of ways to overcome such sortcoming is by encapsulating enzymes with a particular biopolymer to provide protection from direct impact of environmental condition that may denature the enzyme. In addition, the encapsulation of enzymes will allow us to recover them so that they can be used in other reactions. One of the polymer materials that is widely used as an enzyme encapsulator is poly (3-hydroxybutyrate) or PHB. The aim of this study is to investigate the effect of PHB encapsulation to the stability and dynamics of lipase at atomic level by performing molecular dynamics (MD) simulations in various thermal perturbation levels. In this study, lipase structure of Candida rugosa was selected as a model enzyme because its 3D structure has been available in protein data bank with pdb code of 1CRL, while for PHB structure, it was build and optimized manually using MarvinSketch. All MD simulations were performed by using GROMACS 2018, with the force field of CHARMM36 for potential energy calculations. In order to study the encapsulation effect, simulations were carried out on PHB-free lipasess and PHB-encapsulated lipase. Thermal perturbations toward the stability and dynamics of both states of lipase were simulated by performing MD at 300 K, 350 K, and 400 K. All simulations were carried out up to 100 ns with the integration time step of 2 fs. MD trajectory analysis showed that PHB- encapsulated lipase has better stability against thermal perturbation than that of PHB-free lipase. PHB apparently become a shield against thermal perturbation, thereby protecting the lipase against such perturbation. Lipase from Candida rugosa has lid substructure that its dynamics must be maintain for the enzyme activity. Focusing the analysis to the dynamic of the lid substructure showed that PHB encapsulation still maintain its dynamics motion of this substructure suggesting that the encapsulation will not significantly affecting its activity. All of analyses above revealed that PHB is compatible biopolymer for lipase encapsulation.