Lid Conformational Dynamics of Rhizomucor miehei Lipase by Targeted Molecular Dynamics Approach

• Main Author: ABDILLAH MUTHAHARIRI ( NIM : 10510055 ), YUSRAN
• Format: Final Project
• Language: Indonesia
• Online Access: https://digilib.itb.ac.id/gdl/view/24832
• Institution: Institut Teknologi Bandung

Lipase is known as one of the highly demanded commercial enzymes. As a result, molecular investigations on lipase in order to seek novel variants to fullfil industrial needs still intensively carried out. One of the trending topics on lipase is the dynamics of lid segment that has been known play crucial role in catalytic activity of lipase. In this study, we investigated the detailed mechanism of lid movement by in silico approach. We used Rhizomucor miehei lipase (RmL), which has 265 residues in total and has a single lid located at residues 85 up to 91. In this study, we investigated the detailed mechanism of the lid opening and closing by targeted molecular dynamics (TMD) method. Using this method, we can elucidate key residues playing important role in regulating the lid movement. The crystal structure of the RmL in the closed and the open lid forms used in our simulation were derived from protein data bank encoded as 3TGL and 4TGL, respectively. Each structure of the RmL was explicitely solvated with TIP3P water model and equilibrated with NPT ensamble at 300 K and 1 atm, followed by 8 ns free dynamics run. Variations of initial target structures for TMD simulations were retrieved from each nanosecond coordinate in the free dynamics simulations trajectory, thereby resulting 9 initial target structures. TMD simulation were run for 500 ps for both closing and opening lid movements with the applied external force about 0.125 kcal/(mol.Å2). The closing lid movement simulation showed that Arg86, Asp61, Asp113, and Glu117 played important role to regulate the movement of the lid. The regulation of its movement was controlled by electrostatic interactions between Arg86 and Asp61, Asp113, and Glu117. Such electrostatic interactions restrained the lid closing movement. The opening lid movement simulation showed that Asp91, His108, and Lys109 played important role to regulate the movement of the lid. The electrostatics interactions between Asp91 and His108/Lys109 regulate its opening movement. Such electrostatic interactions promoted the lid opening movement. Our TMD simulation thus showed that the opening dan closing lid of RmL were regulated by electrostatics interactions.