Enzymes Are the Engines of Life — Machine Learning Tools Could Help Scientists Design New Ones to Tackle Disease and Climate Change

Enzymes are molecular machines that carry out the chemical reactions that sustain all life, an ability that has captured the attention of scientists like me.

Consider muscle movement. Your body releases a molecule called acetylcholine to trigger your muscle cells to contract. If acetylcholine sticks around for too long, it can paralyze your muscles — including your heart muscle cells — and, well, that’s that. This is where the enzyme acetylcholinesterase comes in. This enzyme can break down thousands of acetylcholine molecules per second to ensure muscle contraction is stopped, paralysis avoided, and life continued. Without this enzyme, it would take a month for a molecule of acetylcholine to break down on its own — about 10 billion times slower.

You can imagine why enzymes are of particular interest to scientists looking to solve modern problems. What if there were a way to break down plastic, capture carbon dioxide, or destroy cancer cells as fast as acetylcholinesterase breaks down acetylcholine? If the world needs to take action quickly, enzymes are a compelling candidate for the job — if only researchers could design them to handle those challenges on demand.

Designing enzymes, unfortunately, is very hard. It’s like working with an atom-sized Lego set, but the instructions were lost and the thing won’t hold together unless it’s assembled perfectly. Newly published research from our team suggests that machine learning can act as the architect on this Lego set, helping scientists build these complex molecular structures accurately.

What’s an Enzyme?

Let’s take a closer look at what makes up an enzyme.

Enzymes are proteins — large molecules that do the behind-the-scenes work that keep all living things alive. These proteins are made up of amino acids, a set of building blocks that can be stitched together to form long strings that get knotted up into specific shapes.

The specific structure of a protein is key to its function in the same way that the shapes of everyday objects are. For example, much like a spoon is designed to hold liquid in a way that a knife simply can’t, the enzymes involved in moving your muscles aren’t well suited for photosynthesis in plants.

For an enzyme to function, it adopts a shape that perfectly matches the molecule it processes, much like a lock matches a key. The unique grooves in the enzyme — the lock — that interact with the target molecule — the key — are found in a region of the enzyme known as the active site.

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