Evolution of protein lipograms: A bioinformatics problem

Abstract

A protein lacking one of the 20 common amino acids is a protein lipogram. This open-ended problem-based learning assignment deals with the evolution of proteins with biased amino acid composition. It has students query protein and metabolic databases to test the hypothesis that natural selection has reduced the frequency of each amino acid specifically in the enzymes required for its biosynthesis. Student groups work in parallel on different amino acids and share strategies. Aside from content objectives that integrate knowledge of protein structure, function, synthesis, and evolution, this problem incorporates oral and written presentations, statistical analysis, and substantial decision making. The point of the problem described here is that a deficiency or absence of a particular amino acid in a protein may be more than a chance occurrence and may be driven by natural selection. The challenge is to demonstrate the difference. © 2006 by The International Union of Biochemistry and Molecular Biology.