Paul A. Sims
Enzymology, Biocatalysis and Biochemical Education
I am interested in the structure and function relationships of enzymes. Currently, we are studying the enzymes adhP (an alcohol dehydrogenase) and tartronate semialdehyde reductase (TSAR). We are working with Dr. Leonard Thomas of the OU Macromolecular X-ray Crystallography Laboratory to determine the structures of these enzymes. In addition, we also perform kinetic analyses, which help us understand the order of addition of substrates and the order of release of products (i.e., the kinetic mechanism). The structural studies complement the results of the kinetic analyses by providing (potentially) the identities of important active site residues. We test hypotheses about the roles of active-site residues by using site-directed mutagenesis to change these residues. We then purify the site-specific variants and test their catalytic activity. Collectively, these studies help us to determine the chemical mechanism, which is a description of the active-site residues that participate in the sequence of bond breaking and bond formation. This process provides us with a reasonably complete understanding of the catalytic functioning of these enzymes. Other research focuses on developing instructional and laboratory activities for undergraduate biochemistry courses. For example, we developed an inexpensive and relatively green method of purifying genomic DNA for use in large undergraduate laboratories; we developed a computer activity in which spreadsheets are used to estimate the isoelectric point of proteins; and we created worksheets that help students understand the pentose phosphate pathway and the Calvin cycle, two notoriously complicated biochemical pathways.
Ribbon representation of the crystal structure of TSAR showing bound NAD and tartrate in stick form. Image courtesy Dr. Leonard Thomas
Close up of the active site of TSAR showing part of the Fo–Fc electron density map of bound NAD. Image courtesy Dr. Leonard Thomas
Research keywords: enzymology; biocatalysis; biochemical education