Analisis Kestabilan Protein 1GB1 Menggunakan Simulasi Dinamika Molekul

Abstract

A mechanism to explain the stability of the protein is still a major problem that is not fully understood. One of the problem is understanding the high thermal stability of 1GB1 protein. The thermal stability of 1GB1 protein can be analyzed using molecular dynamics simulation technique. The aim of this research is to learn molecular dynamics and thermal stability of 1GB1 protein in the range of simulation up to 100 ns. Simulation process consists of the preparation, minimization, heating, equilibration, and production run. The initial coordinate file 1GB1 can be downloaded from Protein Data Bank. The influence of thermal that given by this simulation are 450K and 475K for 100 ns, while 500K is bounded for 2 ns. For 475K simulation, the unfolding process occured at 95 ns indicated by the dissappearance of some secondary structure. For 500K simulation, the unfolding process occured at 745 ps indicated by the dissappearance of most of the secondary structure (collapsing of α-helix and β-hairpin structure).