Molecular Dynamics Simulation To Study Unfolding Mechanism of Protein L As a Result of Heating and Dissolving In 8 M Urea Solution

• Main Author: (NIM 10504073), SUHARTA
• Format: Final Project
• Language: Indonesia
• Online Access: https://digilib.itb.ac.id/gdl/view/12683
• Institution: Institut Teknologi Bandung

Protein folding mechanism is an important aspect in biochemistry due to its close relation with its function. The folding mechanism can be studied at molecular level as a result of the unfolding simulation with molecular dynamics approach with an assumption that it's pathways are the reverse of the unfolding ones. In the current work domain B1 of protein L isolated from Peptostreptococcus magnus was used as a model for the study of the folding/unfolding process. Unfolding simulations of protein L were performed at 400 K and 500 K both in water and urea 8 M. The simulation results showed that the unfolding process in water and urea 8 M at 500 K occurred with similar mechanism, in which the unfolding began with the destabilization of B-hairpin at C terminal area. For the case of the simulation at 400 K, the protein unfolding was only observed in the urea 8 M. In this simulation, the unfolding was occurred relativelly faster when hydrogen bonds in B-pararel strands were disrupted. Our simulation also revealed that unfolding mechanism of protein L was occurred in two state transitions. Based on the reverse events in the unfolding mechanisms, we proposed that the folding mechanism of protein L apparently similar to the nucleation condensation model. Our simulation, thus, can provide insight into mechanisms of unfolding/folding process of protein L at molecular level.