“Some people breed cats and dogs. I breed molecules.” – Frances Arnold, Nobel Prize in Chemistry, 2018
Last week, it was announced that the 2018 Nobel Prize in Chemistry had been awarded to three scientists:
Frances Arnold, for the directed evolution of enzymes; and
George Smith and Sir Gregory Winter for the phage display of peptides and antibodies.
But what does this mean? I know when I first read about it I had no idea at all what it was or why it was so important or relevant.
It turns out that the underlying principle is beautifully simple – but also a long way from how scientists usually work.
Science is a very logical subject. Scientists set out to try and find the answer to a question (or solution to a problem), and sometimes they succeed and sometimes they don’t. Invariably, they find numerous other questions (and answers) along the way. Deliberate random chance is not something scientists tend to use as an investigative method. And yet, that is exactly what these scientists have done.
Let’s begin with Frances Arnold’s work. (I’ll save the work of Smith and Winter for a future post.)
A protein which can detect pressure changes in the ear, allowing us to hear. A small change to the order of amino acids anywhere in the protein could change its rather complicated shape sufficiently that it was no longer able to do its job. © Johan Jarnestad/The Royal Swedish Academy of Sciences
Enzymes are nature’s catalysts, substances which make chemical reactions faster by providing an alternative lower-energy pathway for them to take, sometimes to the extent that a reaction can happen which otherwise would require too much energy to proceed under a particular set of conditions (e.g. the rather specific conditions inside the human body). Enzymes are also proteins, extremely complex molecules made of several thousand amino acids joined together in a particular order to make a chain that will fold into a particular 3D shape. That particular shape will catalyse a particular reaction under particular conditions. A small change here or there, and the shape you get – and the effect it has on other molecules – can be radically different. All the enzymes in our bodies are coded for in our DNA, but creating enzymes from scratch has long been a problem for scientists.
Frances Arnold realised that using the traditional scientific approach of logic and rationality wasn’t going to work for developing new enzymes. It would be like looking for a needle in a haystack – difficult, time-consuming, and with little chance of success. So she took her inspiration from nature. Enzymes are a fundamental part of biology, and life exists solely because nature has managed to solve a whole multitude of complex chemical problems, many involving enzymes. Evolution has been creating species adapted to particular conditions ever since life began, so there are organisms which can survive extreme cold or extreme heat, extreme dryness, extreme pressures (deep ocean), extreme salt levels… From fish with antifreeze proteins in their blood which allows them to swim (and survive!) in the polar oceans, to an underwater molecular glue that allows mussels to stick themselves to rocks. (It’s the same principle as bacteria developing antibiotic resistance.)
Evolution is the continuous and gradual development of something, generally by small changes that, put together over time, lead to bigger changes. Biologically, it is how species become better adapted for survival, and how new species are created. Within a population of a species, there is inherent and natural variation between the members. The vast majority of that variation is inconsequential when it comes to survival, but every so often, a particular feature may make a particular individual more likely to survive and reproduce (and reproduce more). Over many generations, that favourable characteristic can become present in the majority of members of the population.
My three cats are all very recognisable as cats, however there is also a lot of variation between them. Variation between members of a species is a part of nature. Horace is much bigger than Sid, so if finding food required squeezing into small spaces, Sid would stand a much better chance of survival. In deep snow though, Horace would because his legs are longer.
In effect, evolution is nature’s own way of optimising enzymes for a particular set of reaction conditions.
All this variation comes from chance genetic mutations. Frances Arnold hypothesised that introducing random variation into the genetic code for the enzyme would create random variation in the protein produced, and that some of these may perform better under a particular set of conditions than the original enzyme. Over successive iterations of the process, a much better variant could then be produced: directed evolution.
- Create random mutations in the genetic code for the enzyme.
- Put the mutated genes into bacteria, which will then produce many different variants of the enzyme.
- Select from the enzymes produced those which most closely meet the required criteria.
- Introduce a second round of genetic mutations into that most successful variant.
- Repeat the selection process for an even better variant of the original enzyme.
- Repeat for a third generation.
Frances Arnold began with the enzyme subtilisin, trying to make it function in an organic solvent, rather than water. Subtilisin breaks down casein (an protein in milk), so she used this as her test for selection – in a solution containing 35% DMF (dimethyl formamide, an organic solvent), instead of just water. By the third generation, she had found a variant of subtilisin that worked 256 times better in DMF than the original enzyme! The genetic code for this variant had a combination of 10 different mutations – it could never have been predicted.
Mutations can occur anywhere within the genetic code – it’s completely random.
After just a few cycles of directed evolution, enzymes can be produced that are thousands of times more effective than the original.
It’s like looking for a needle in haystack, but with the help of a magnet.
It has huge benefits for a wide range of applications: pharmaceuticals (compounds manufactured for use as medicines), plastics, biofuels, and many other things besides. These are processes which have previously relied on strong solvents, corrosive acids, and heavy metals. New processes using enzymes don’t require these, as well as being faster and producing fewer by-products. What’s not to like about a method that is faster, safer, and more environmentally sound?! Enzymes developed using directed evolution are now being used to transform simple sugars (readily available) into isobutanol, an energy-rich compound which can be used for producing both biofuels and greener plastics.
In doing this work, Frances Arnold demonstrated the power of chance and directed selection in research, rather than relying on human rationality. In her own words, “Twenty five years ago, it was considered the lunatic fringe. Scientists didn’t do that. Gentlemen didn’t do that. But since I’m an engineer and not a gentleman, I had no problem with that.”
Professor Dame Carol Robinson, someone I feel very privileged to have met when I was a student, and president of the Royal Society of Chemistry, said, with reference to this year’s Nobel Prizes in Chemistry: “It would have been hard to predict the outcome of this research at the start – this speaks to the need for basic research.”
What Professor Arnold did was considered completely mad when she started doing it – it was so completely different to how scientists had previously worked. But that didn’t mean that it was wrong, and look where it ended up! It just goes to show, if you can dream it, you might just be able to make it a reality.
What are you going to discover?