How Machine Learning Is Propelling Structural Biology

 As a structural biologist, he is studying this process on the smallest scale: the trillions of atoms that must synchronize their work to make it happen.

“I don’t see a big difference between solving a 5,000-piece jigsaw puzzle and the research we are doing in my lab,” says Farming, an assistant professor of cell biology in the Blavat Nik Institute at Harvard Medical School. “We are trying to figure out what this process looks like visually, and from there we can form ideas about how it works.”

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Nearly all cells in the human body contain the same genetic material, but what tissue types those cells become during development — whether they become liver or skin, for example — is largely driven by gene expression, which dictates which genes are turned on and off. Gene expression is regulated by a process called transcription — the focus of Farming's work. During transcription, molecular machines read instructions contained in the genetic blueprint stored inside DNA, and create RNA, the molecule that carries out the instructions. Other molecular machines read RNA and use this information to make proteins that fuel almost all activities in the body.

The human genome is present in almost every cell, and if you stretched out the DNA that makes up the genome, it would be roughly two meters, or six and a half feet long. But this two-meter-long molecule has to fit inside the nucleus of a cell, which is only a few microns in size. This is the equivalent of taking a fishing line that stretches from Boston to New Haven, Connecticut, or about 150 miles, and trying to squeeze it into a soccer ball. To achieve this, our cells compact DNA  into a structure called chromatin, but then molecular machines can no longer access the genomic information on DNA. This creates a conflict, because DNA needs to be compact enough to fit inside a cell’s nucleus, but molecular machines have to be able to access the genomic information on DNA. We are especially interested in visualizing the process of how a molecular machine called RNA polymerase II gains access to genomic information and transcribes DNA into RNA.

To do this, we introduce genetic material that codes for a human molecular machine of interest into an insect or bacterial cell, so the cell makes a lot of that machine. Then, we use purification techniques to separate the machine from the cell so we can study it in isolation. However, it gets complicated because often we are not just interested in a single molecular machine, which we also refer to as a protein. There are thousands of proteins that interact with each other to regulate transcription, so we have to repeat this process thousands of times to understand these protein-protein interactions.


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