Our digestive system needs enzymes to break down the food we eat and allow it to be efficiently absorbed through the small intestine, entering the bloodstream and nourishing cells and organs. Processed food has enzymes for speeding up the chemical reactions. However, these molecules have more to offer than just a good meal. Penny Beuning, a professor of chemistry and chemical biology at the Northeastern University believes that by understanding the working of enzymes, we can know about its applications in things like human health or biofuels. Learning more about how enzymes facilitate chemical reactions, we can know about new ways to target harmful bacteria and improve our own bodies. At the same time, this can help researchers engineer new, more efficient enzymes for producing food, cleaning up environmental contamination, or manufacturing fuels from renewable sources.
With a combination of computational predictions and experimental testing, Beuning and her colleagues are trying to make it easier to determine what a particular enzyme does. For instance, amino acids get strung together like beads on a necklace. These long chains of amino acids then spiral and fold into tangled-looking proteins. The chemical properties of the various amino acids, and their positions within the three-dimensional structure, determine whether an enzyme will make copies of your DNA for new cells or help you digest milk. The researchers need to focus on those amino acids that are relevant to an enzyme’s role as a catalyst, speeding up chemical reactions and not look at every amino acids.
Mary Jo Ondrechen, the principal investigator for the project, has developed a method for predicting which amino acids are involved in the chemical reactions. The next logical step to take would be to try and predict the individual roles of the amino acids. If arrangements of amino acids that indicate a particular function can be identified, chemical fingerprint can be used to figure out what other enzymes do. Thus, machine learning algorithms will be used to predict the roles of specific amino acids in a family of enzymes called glycoside hydrolases, which interact with sugars. Then experiments will be conducted in Beuning’s lab to check those predictions.
“The genomic data set for humans, and now thousands of other species, is a treasure trove. We have a lot to learn, and a lot to gain from understanding it”, says Ondrechen.
Shahjadi Jemim Rahman
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