AlphaFold helps researchers discover how protein mutations cause disease and how to prevent it
Luigi Vitagliano is Director of Research at the Biostructures and Bioimaging Institute in Naples, Italy. He shares his story on AlphaFold.
Being a structural biologist in the age of AlphaFold is like the early days of gold mining. Before this technology, everyone did the painstaking work of finding individual gold nuggets, cleaning them and looking at them one by one. Then, suddenly, a gold mine appeared. We couldn’t believe our luck.
For 30 years, I have been studying the proteins encoded in our DNA. Inside most human cells, there are somewhere between 20,000 and 100,000 different proteins. In some cases, the way the sequence of amino acids in a protein takes its shape, also known as “protein folding,” can be fraught with abnormalities, and these are linked to many diseases.
Recently, I examined a family of human proteins known as the potassium channel tetramerization domain (KCTD) proteins, which are particularly poorly understood. What is particularly interesting about mutations in these proteins – caused by genetic mutations – is the range of diseases they are associated with: from schizophrenia to autism and leukemia to colon cancers as well as brain disorders and movement.
As new proteins are continuously produced within cells, old or defective ones must be removed. There are 25 kinds of KCTD proteins in humans, and four-fifths of them seek out other proteins and mark them for degradation and destruction. This process is called ubiquitination and is essential for maintaining cell health and preventing disease.
When KCTD proteins do not function properly, the consequences can be debilitating for our health. However, there is much we do not understand about them. About a fifth of the KCTD proteins inside cells were a mystery to scientists like me: we had no idea what they did and therefore how to prevent them from mutating and causing disease. Until now, we have had very little structural information about them, which has been a major obstacle to KCTD research.
The structures predicted by AlphaFold revealed that during evolution their structures remained very similar despite having very different genetic codes. This was a breakthrough. Previously, we relied on genetics to assess similarities or differences between proteins. Based on the genes alone, we thought these proteins would be very different.
Using AlphaFold, we were able to create a new evolutionary family tree based on the shape of these proteins rather than their genetic sequence. Evolutionary trees are usually built using genetic information, but do not take structural similarities into account. Structure is related to function, so using this approach is exciting—it could reveal all kinds of mysteries about which KCTD proteins have similar functions and how those functions evolved over time.
I used AlphaFold to examine and compare the structure of all 25 KCTD proteins for similarities and differences, to determine which parts of these proteins are important. To our delight, the predicted structures of AlphaFold appeared to be very accurate.
For example, we already knew that one part of the KCTD proteins—the BTB domain—was similar among all family members, so we assumed that this was the most important part. AlphaFold has revealed many more additional structural similarities between these proteins and opened up a whole new realm of exploration.
For 60 years – including my 30 years working in this field – we have tried and failed to find the connection between sequences and structures. Entire generations of eminent scientists could not solve this problem. Then, almost miraculously, this solution appeared. All of our data, the structural information for all KCTD family members, comes from AlphaFold. Without it, this study could not have been done at all.
My feeling was that AlphaFold was a dream. If someone had told me that in two years we would have over 200 million protein structures, I would not have believed it. Now, what lies in the coming decades is learning exactly what these proteins do. There is much more excitement and discovery ahead.