New tool dramatically speeds up research into enzymes

Researchers at Stanford University have developed a new tool they say dramatically speeds up the study of enzymes. The new tool allows thousands of very small experiments to run simultaneously on a single polymer chip. It was designed specifically to allow scientists to study enzymes faster and more comprehensively than possible in the past.Enzymes are protein molecules comprised of amino acid chains that speed up or catalyze the conversion of one type of molecule into another. Enzymes enable reactions inside the body, including digestion and fermentation, and all other chemical events happening inside of cells. Without enzymes to speed up these reactions, they would happen extraordinarily slowly.

Researchers say a chemical reaction that would take longer than a lifetime of the universe to happen on its own can occur in seconds, thanks to enzymes. Since enzymes are so important, a lot is known about them, including their structure and the chemical groups they use to perform their reactions. However, details surrounding how forms of enzymes connect to the functions and how they're able to perform biochemical transitions at such high speed and specificity aren't understood.

The new tool is dubbed HT-MEK, which is short for High-Throughput Microfluidic Enzyme Kinetics. HT-MEK promises to compress the years of work into just a few weeks by enabling thousands of enzyme experiments to be carried out simultaneously. Study co-leader Dan Herschlag says that limits in the ability of scientists to perform enough experiments have prevented science from truly dissecting and understanding enzymes.

HT-MEK could reveal clues about how distant parts of enzymes work together to perform their tasks by allowing scientists to deeply probe beyond the small "active site" of an enzyme where substrate binding occurs. One researcher says it's like taking a flashlight, and rather than shining in on the active site alone, they're shining it over the entire enzyme. HT-MEK leverages two existing technologies to speed up the analysis of enzymes, including microfluidics and cell-free protein synthesis. The device is automated, allowing scientists to use printers to deposit microscopic spots of synthetic DNA coding for the enzyme they want on a slide.

They're then able to align nanoliter-sized chambers filled with the protein starter mix over the spots. The team used the new technology on a well-studied enzyme called PafA. They found mutations beyond the active site affected its ability to catalyze chemical reactions and that most of the amino acids making up the enzyme had effects.