Molecular dynamics studies of protein and peptide folding and unfolding

Proteins are fascinating. As objects in three-dimensional space, they are sometimes elegant and always complex molecules, yet they consist of only 20 different amino acid building blocks. The function of proteins is determined by their three-dimensional structure, and the majority of biological processes involve one or more protein molecules. The mechanism of the evolutionary development of specific proteins is one of the unsolved problems of biology. Most proteins are very sensitive to their environment; small temperature or pH changes can alter both their stability and their ability to function. The native structure of a protein is determined by the amino acid sequence (Anfinsen, 1972). In solution, many proteins have been shown to refold by themselves under conditions that lead to a stable native state, but in vivo the folding process can be very complicated and often involves other proteins, such as chaperones (Gething and Sambrook, 1992).