The Effect of Amino-acid Gyration on Protein Conformation

Abstract

Proteins are basically polymers of amino acids that are linked together through peptide bonds. The biological function of a given protein depends on its native structure, which has the lowest free energy level; hence finding out the structure is very important. The de novo protein method for predicting the structure of proteins has been proved to be nondeterministic polynomial time (NP)-hard even with short lattices. In order to facilitate a study of the factors influencing conformation of a protein to its native structure, we develop a Monte Carlo model of protein conformation on square lattice. We studied the effect of amino-acid gyration on the native conformation of a protein. We found that this model is very effective and gives compact structures for isotropic gyration.