A Comparative Study for Rhodopsin Protein Folding Problem

Abstract

Proteins are very important components in any living cells. A number of diseases such as Retinitis pigmentosa, Stargadt-like macular degeneration and Doyne Honeycomb Retinal Dystrophy (DHRD) diseases are shown to result from misfunctioning of proteins. Protein folding problem is a way to predict the best and optimal 3D molecular structure (tertiary structure) of a protein which is then considered to be a sign for the protein's proper functionality. This comparative study's purpose is to calculate the protein's energy using the Empirical Conformational Energy Program for Peptides (ECEPP) package and experiments were performed on the Rhodopsin proteinusing three different evolutionary algorithms in order to find the best energy in parallel with the best structure for the protein and a comparison for the results obtained from the three algorithms was performed. It was found that the best result was -11.8 obtained from the Extended Compact Genetic Algorithm (ECGA). ECGA has proved from the obtained results to be the best algorithm from the chosen algorithms in the comparative study in obtaining the Rhodpsin protein's energy and its equivalent structure.