STUDY OF ALPHA-AMYLASES HALOTHERMOTRIX ORENII PROTEIN STABILITY IN VARIOUS SALT CONCENTRATIONS BY MOLECULAR DYNAMIC SIMULATION

• Main Author: FADLIYANSYAH RAMADHAN (NIM : 10507087); Pembimbing : Dr. Rukman Hertadi
• Format: Final Project
• Language: Indonesia
• Online Access: https://digilib.itb.ac.id/gdl/view/15591
• Institution: Institut Teknologi Bandung

Halophile’s microorganisms have been well-known as one type of microorganisms exhibited high adaptability to live under the high salinity environment. Halothermotrix orenii is one of the species of bacteria in the halophile’s group. In this work, we are interested to study how the protein isolated from the bacteria can stable under high salt concentration. We selected alpha-amylase A (Amy A) as the protein target for our study. We performed molecular dynamics approach to elucidate the key factors responsible for the stability of Amy A under various salinity concentrations. As a comparison, mesophile’s alpha-amylase from Pseudomonas stutzeri was selected. The simulations of both halophile and mesophile proteins were run under two different salt concentration e.i. 0 and 3 M NaCl. For each salt concentration, the simulations were performed in two different set of temperatures, namely 300 K and 400 K. The result from the simulation at 300 K clearly exhibited the difference in RMSD profiles of both type of proteins. In two different salt concentrations, RMSD of halophile alpha-amylase showed obviously distinct profiles but it was almost indistinguishable in mesophile’s α-amylase. This result was justified with the simulation at 400K, which showed wider difference of RMSD value for halophile’s alpha-amylase in both salt concentrations but mesophile’s one was still less affected even at this temperature. Analysis of solvent accessible surface area (SASA) for the exposed non-polar residues showed the surface area enlargement when halophile’s alpha-amylase dissolved in 0 M NaCl at 400 K. On the contrary, the non-polar SASA of the meshopile protein was relatively similar under various salinity and temperatures. Further molecular analysis to the simulation trajectory of the halophile’s alpha-amylase at 0 M NaCl revealed the event causing in stability of the protein at this condition. The movement of coil chain located between domain A and B in the halophiles proteins was found to be a trigger for the instability of the protein’s conformation. This event was occurred due to the electrostatic repulsion among common charge residues, namely between Lys166 and Lys169, as well as among Asp162-Arg174-Asp167, as a result, the coil was unable to return to its initial position. Therefore, our simulation can show the salinity effect to the conformation of halophile’s alpha-amylase.