Computational Biology Lecture 21: Protein folding and threading

As was the case with RNA folding, the goal is to determine the three-dimensional structure of a protein based on its amino acid sequence. There is a strong belief that the amino acid sequence completely and uniquely determines the folding. This is reinforced by the following experiment: Unfold a protein (by exerting a certain temperature) and then release it such that no other substances are present. The protein immediately folds back to the three-dimensional structure it had before, thus called its native structure. The folding process takes less than a second. Therefore, it appears that all information necessary for the protein to achieve its native structure is contained in the amino acid sequence (this is not true for all proteins because there are some that need auxiliary molecules to fold). Before discussing the protein folding prediction, we describe the main components of the protein three-dimensional structure, known as protein secondary structures. These are α-helices, β-sheets, and loops.