Simulated annealing in protein folding

Abstract

Proteins are the fundamental molecules of living cells. They are roughly linear chains of subunits called amino acids. There are 20 biologically interesting amino acids, and thus a protein molecule can be thought of as a word constituted from 20-letter alphabet. In a living cell there are different types of proteins, performing different tasks. Proteins are created by a genetic code determined by the DNA of the cell. The DNA molecules are located in the cell nucleus. A messenger RNA carries the code for a particular type of proteins from the nuclear DNA, and it acts as a template for the formation of that protein, assembling (by catalytic reactions) the protein chain from amino acids in the cell. Each amino acid in the protein chain is associated to a triple of DNA base pair. The linear chain of a protein is called the primary structure. These chains actually fold into complicated 3-dimensional structures called secondary and tertiary structures. The folded structure is highly sensitive to the particular amino acids present; it invariably holds the key to the biological functions of the protein.