Genomes as Resources for Biocatalysis

Enantioselectivity and Enzyme-Substrate Docking Studies of a Ketoreductase from Sporobolomyces salmonicolor (SSCR) and Saccharomyces cerevisiae (YOL151w)

Models for two ketoreductases were created and used to predict the stereoselectivity of the enzymes. One was based on the crystal structure of Sporobolomyces salmonicolor. This model was used to predict the stereoselectivity for 46 ketone reductions using this enzyme; only 6 were incorrectly predicted. The stereochemistries of the products were compared to the experimental values found in the literature. The Prelog rules were also used to predict the stereoselectivity for this enzyme; however the Prelog rules seem to be highly substrate dependent. As a result, predicting stereoselectivity of KREDs is more complicated than is allowed for with just substrate size and geometry. This enzyme showed Prelog docking geometry for 13 substrates if the enzyme is assumed to prefer an anti-Prelog docking geometry. For SSCR the molecular modeling proved to be a better method for predicting stereoselectivity of the enzymes. The second model was a homology model for YOL151w based on the enzyme crystal structure of Sporobolomyces salmonicolor carbonyl reductase, SSCR. In this homology model, 14 compounds were docked and the predicted stereochemistry was compared to the literature values. Of these, 5 were incorrectly predicted.

Computational enzyme design

Recent developments in computational chemistry and biology have come together in the "inside-out" approach to enzyme engineering. Proteins have been designed to catalyze reactions not previously accelerated in nature. Some of these proteins fold and act as catalysts, but the success rate is still low. The achievements and limitations of the current technology are highlighted and contrasted to other protein engineering techniques. On its own, computational "inside-out" design can lead to the production of catalytically active and selective proteins, but their kinetic performances fall short of natural enzymes. When combined with directed evolution, molecular dynamics simulations, and crowd-sourced structure-prediction approaches, however, computational designs can be significantly improved in terms of binding, turnover, and thermal stability.

Using biocatalysis to integrate organic chemistry into a molecular biology laboratory course

Current cutting-edge biomedical investigation requires that the researcher have an operational understanding of several diverse disciplines. Biocatalysis is a field of science that operates at the crossroads of organic chemistry, biochemistry, microbiology, and molecular biology, and provides an excellent model for interdisciplinary research. We have developed an inquiry-based module that uses the mutagenesis of the yeast reductase, YDL124w, to study the bioorganic synthesis of the taxol side-chain, a pharmacologically important molecule. Using related structures, students identify regions they think will affect enzyme stereoselective, design and generate site-specific mutants, and then characterize the effect of these changes on enzyme activity. This laboratory activity gives our students experience, working in a scientific discipline outside of biology and exposes them to techniques and equipment they do not normally work with in a molecular biology course. These inter-disciplinary experiences not only show the relevance of other sciences to biology, but also give our students the ability to communicate more effectively with scientists outside their discipline.

Strategies for discovery and improvement of enzyme function: state of the art and opportunities

Developments in biocatalysis have been largely fuelled by consumer demands for new products, industrial attempts to improving existing process and minimizing waste, coupled with governmental measures to regulate consumer safety along with scientific advancements. One of the major hurdles to application of biocatalysis to chemical synthesis is unavailability of the desired enzyme to catalyse the reaction to allow for a viable process development. Even when the desired enzyme is available it often forces the process engineers to alter process parameters due to inadequacies of the enzyme, such as instability, inhibition, low yield or selectivity, etc. Developments in the field of enzyme or reaction engineering have allowed access to means to achieve the ends, such as directed evolution, de novo protein design, use of non‐conventional media, using new substrates for old enzymes, active‐site imprinting, altering temperature, etc. Utilization of enzyme discovery and improvement tools therefore provides a feasible means to overcome this problem. Judicious employment of these tools has resulted in significant advancements that have leveraged the research from laboratory to market thus impacting economic growth; however, there are further opportunities that have not yet been explored. The present review attempts to highlight some of these achievements and potential opportunities.