Conformation Analysis of T1 Lipase on Alcohols Solvent using Molecular Dynamics Simulation

International Conference on Energy Sciences 2016

能源学;物理学

Putri, A.M.^1 ; Sumaryada, T.^2,3 ; Wahyudi, S.T.^1

Biophysics Division, Department of Physics, Bogor Agricultural University, Jalan Meranti Kampus IPB, Dramaga Bogor

16680, Indonesia^1

Computational Biophysics and Molecular Modeling Research Group (CBMoRG), Department of Physics, Bogor Agricultural University, Jalan Meranti Kampus IPB, Dramaga Bogor

16680, Indonesia^2

Tropical Biopharmaca Research Center, Jalan Taman Kencana No. 3, Bogor

16128, Indonesia^3

关键词: Alcohol solvent;    Conformation analysis;    Molecular dynamics simulations;    Nonpolar amino acids;    Root mean square deviations;    Solvent accessible surface areas;    T1 lipase;    Transesterification reaction;   

Others  :  https://iopscience.iop.org/article/10.1088/1742-6596/877/1/012007/pdf
DOI  :  10.1088/1742-6596/877/1/012007

来源: IOP

【 摘 要 】

Biodiesel usually is produced commercially via a transesterification reaction of vegetable oil with alcohol and alkali catalyst. The alkali catalyst has some drawbacks, such as the soap formation during the reaction. T1 Lipase enzyme had been known as a thermostable biocatalyst which is able to produce biodiesel through a cleaner process. In this paper the performance of T1 lipase enzyme as catalyst for transesterification reaction in pure ethanol, methanol, and water solvents were studied using a Molecular Dynamics (MD) Simulation at temperature of 300 K for 10 nanoseconds. The results have shown that in general the conformation of T1 lipase enzyme in methanol is more dynamics as shown by the value of root mean square deviation (RMSD), root mean squared fluctuation (RMSF), and radius of gyration. The highest solvent accessible surface area (SASA) total was also found in methanol due to the contribution of non-polar amino acid in the interior of the protein. Analysis of MD simulation has also revealed that the enzyme structure tend to be more rigid in ethanol environment. The analysis of electrostatic interactions have shown that Glu359-Arg270 salt-bridge pair might hold the key of thermostability of T1 lipase enzyme as shown by its strong and stable binding in all three solvents.