Studi Perubahan Sifat Struktur dan Termodinamik Pelipatan Protein Model H0P Menggunakan Simulasi Monte Carlo dengan Algoritma Wang-Landau

Abstract

Protein folding is a process of folding a protein from a one-dimensional form into a three-dimensional shape as its functional form, and this process is very challenging to be experimentally investigated due to the highly complex shape of proteins. Therefore, a simplified protein shape model and a method for simulating protein folding are needed. The model used in this research is the H0P model, where the protein-forming amino acids are mapped into 3 monomers: 'H' for hydrophobic, '0' for neutral, and 'P' for polar. In this study, the protein folding was simulated using Monte Carlo (MC) simulation with the Wang-Landau (WL) Algorithm. The purpose of the WL algorithm is to directly calculate the density of states (DOS), then calculate thermodynamic quantities such as specific heat (Cv), and structural quantities such as radius of gyration (Rg) and tortuosity (τ). Based on the curves of Cv(T), Rg(T), and τ(T) changes, it was found that protein folding undergoes two processes, namely coil-globule collapse and folding transition.