beta_helix Staff Lv 1
Over the past few decades, enzymes have found their way into the spotlight for performing difficult chemical reactions in the laboratory and industrial settings. This interest is driven by their ability to efficiently catalyze reactions in water at room temperature with incredible efficiencies (rate enhancements of up to 1019). In addition enzymes have stringent specificities for the substrates they take in and the products they put out. While over 280,000 enzymes have been currently identified in nature, there are still many reactions that researches commonly use in the laboratory for which there is no known enzyme to catalyze the reaction. One such reaction is the Diels-Alder reaction. The reaction was discovered in 1928 and won a Nobel prize in 1950. Since then it has become a cornerstone reaction for organic chemistry and can be found in every introductory organic chemistry text as well as many patents in the pharmaceuticals, materials, fine chemicals, and agrochemical industries.
In this puzzle we present an enzyme we have designed that is able to catalyze the Diels-Alder reaction. Currently it has low levels of activity but we believe that by increasing the number of contacts to the ligand we can increase its activity. To do this we have engineered a partial helix that has shown some increase in activity, but we believe YOU CAN MAKE IT BETTER! The goal of this puzzle is to stabilize this helix and make a more ordered secondary structure motif (e.g. Helix-Loop-Helix). Your results will be selected based on the lowest energy and best secondary structures. The top designs will be tested in the laboratory for their ability to catalyze this reaction.
