Playing Evolution: Making Enzymes from Scratch

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In researching almost any topic in biology I am consistently amazed at how natural selection produces things so well suited for their specific roles. From an animal perfectly filling an ecological niche, to an organ efficiently performing a biological task, to a molecule precisely providing the ideal chemistry for its function. It is truly astounding how a process that moves along through random mutation events can result in perfectly coordinated systems at every level. Although natural evolution results in sublimely well-tuned components for every biological system, it also takes a stupendously long time to go about its business. Enter the twenty-first century scientist. While scientists in nanorobotics and materials science are making game-changing leaps and bounds in our ability to manipulate ourselves and our environment, enzyme engineers are starting to give them a run for their money. Have a tough chemical job to do? One that has never been done before? Why not engineer a brand-spanking-new custom enzyme to catalyze your worries away?

            Many of the enzymes that exist naturally are made of protein. The protein itself is a long chain made of different amino acids linked together. You can think of it kind of like a long charm bracelet: the links of the chain form the structure of the chain, while different charms on each of the links make each part of it unique. With proteins, there are 20 types of amino acids or “charms” to choose from that can be strung together in different combinations.

           

            Much like how a ball of wool doesn’t do you a heck of a lot of good on a cold day, a enzyme doesn’t do much at all as one long strand. Mittens or a scarf, however, can be very functional, and so can an enzyme when it is tangled up into a very specific shape. In fact, it is the three dimensional shape that gives a folded enzyme its ability to perform chemistry. So how do enzymes stay folded in the right shape? Going back to the charm bracelet example, some charms (amino acids) can interact specifically with each other to reinforce specific shapes. The “chain” itself also has a tendency to form certain structures: telephone chord-like coils (alpha-helices) and flat sheets formed by the chain doubling back over itself repeatedly (beta-sheets). Additionally, over one third of all proteins contain atoms of iron, zinc, copper, or other metals. By interacting strongly with specific groups of amino acids, these metals can lock part of an enzyme structure in place, helping the rest of the enzyme to also hold its active shape.

            If the interactions that keep an enzyme folded properly and functional seem complex, that’s because they are. A single enzyme has hundreds of individual interactions between individual amino acids and metal groups, some of which can be removed or replaced, and some of which are vitally important either to keep the enzyme in the right shape, or to perform specific chemical functions. Scientists have been trying to tease this apart for years by deleting or swapping out specific amino acids in natural enzymes and observing the effects of these changes. Much like tinkering with an engine vs. building one from scratch, however, you can only learn so much about how something works without creating one of your own. This is exactly what a group of scientists from the University of Michigan reported recently in Nature Chemistry. These intrepid researchers designed an enzyme from scratch: designing a structural “scaffold” (complete with a structure-stabilizing metal) into which they incorporated a small area capable of performing similar chemistry to one of our body’s own enzymes. By testing which enzyme design concepts make the chemistry faster or slower, these researchers are testing and applying the basic principals we currently think govern how all enzymes work.

            Designing enzymes from scratch to perform tasks that natural enzymes already perform is almost the definition of reinventing the wheel. It is, however, incredibly valuable in at least two respects: it demonstrates that we understand how enzymes work well enough to design them from the bottom up, and it opens the door to engineering brand new enzymes that catalyze chemistry not found in nature. Imagine creating an enzyme that quickly breaks down Styrofoam or other long-lasting pollutants. Enzymes are the most powerful chemists in nature, and if we can design their abilities, rather than simply co-opting them, they can be our most powerful industrial and biotechnological tools as well.