Simulasi Dinamika Molekul Protein 1GB1 Menggunakan Not Just Another Molecular Dynamcs Program (NAMD)

Abstract

Protein 1GB1 helps Streptomyces griseus to avoid host defense by immunoglobulin binding site properties. The aim of this study are to learn the mechanism of unfolding and molecular dynamics of protein 1GB1 by temperature variance based on some parameters. Coordinate file of 1GB1 that given by NMR (Nuclear Magnetic Resonance) can be downloaded from Protein Data Bank, then it was processed by some steps such as minimization, heating, equilibration and production run using PBC (Periodic Boundary Condition) and PME (Particle Mesh Ewald) methods. Simulation running at 325K, 350K, 375K, 400K, 450K dan 500K. Except simulation 1 ns at 500K, all simulations running for 10 ns. Some parameters shown unfolding process of 1GB1 at 900 ps in 500 K simulation. Secondary structures that broke for the first time is alpha-helix that converted to turn and coil.