Teaching Principles of Enzyme Structure, Evolution, and Ca- talysis Using Bioinformatics
The study of enzyme function has greatly benefited from the increase in the number of gene sequences and the development of bioinformatics tools that allow for the rapid search of these vast sets of data, the integration of their results, and the linking of information regarding en- zyme families, function, chemical mechanism, and structures of homologous enzymes. Similarly, the development of free- ly available threading programs, which provide a 3-dimen- sional (3D) structural model of an enzyme of interest, have facilitated structural and functional studies that contribute to the understanding of the chemical mechanism of a target enzyme. These tools can also be used to teach basic prin- ciples of chemical biology, molecular evolution, and enzyme structure and function in silico. A training exercise for senior undergraduate students interested in working with enzymes is presented in this article. The exercise includes the use of bioinformatics programs to identify a target protein from a partial gene sequence, identify its family, and obtain a 3D model. The second part of the exercise consists of search- ing the literature database to provide a plausible chemical mechanism based on the available data from homologous enzymes.