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taylorvich [soylentnews.org] writes:

https://spectrum.ieee.org/ai-protein-localization [ieee.org]

A new deep-learning model can now predict how proteins sort themselves inside the cell. The model has uncovered a hidden layer of molecular code that shapes biological organization, adding new dimensions of complexity to our understanding of life and offering a powerful biotechnology tool for drug design and discovery.

Previous AI systems in biology, such as the Nobel Prize-winning AlphaFold, have focused on predicting protein structure. But this new system, dubbed ProtGPS, allows scientists to predict not just how a protein is built, but where it belongs inside the cell. It also empowers scientists to engineer proteins with defined distributions, directing them to cellular locations with surgical precision.

“Knowledge of where a protein goes is entirely complementary to how it folds,” says Henry Kilgore, a chemical biologist at the Whitehead Institute for Biomedical Research in Cambridge, Mass., who co-led the research. Together, these properties shape its function and interactions within the cell. These insights—and the machine learning tools that make them possible—“will come to have a substantial impact on drug development programs,” he says.

Kilgore and his colleagues described the new tool in a paper published 6 February in the journal Science.

Over the past few years, AI tools like AlphaFold have revolutionized structural biology by predicting protein shapes—much like the instruction manual that comes with a piece of IKEA furniture, showing how to assemble the chair or bed. But it turns out knowing a protein’s structure isn’t enough to understand its function. ProtGPS fills in this missing piece by determining where each molecular piece of “furniture” belongs within the cell’s open-plan interior.

Some proteins have clear destinations. Researchers have known for decades that proteins headed for places like the nucleus or mitochondria—structures enclosed by membranes and walled off from the rest of the cell—carry short signaling tags that guide them.

But much of the cell is an open environment, where proteins rely on more subtle cues to sort themselves into what are called biomolecular condensates—dynamic, liquid-like clusters that help regulate gene activity, manage cellular stress, and contribute to disease. And just as a cozy armchair might naturally fit into a reading nook, proteins follow intrinsic molecular placement rules that guide them to specialized condensates suited to particular functions.

ProtGPS has now begun to decode these rules, uncovering hidden features in the sequence of amino acids that form the backbone of all proteins—intrinsic sorting cues that determine whether and where a protein will localize within different condensates in the cell.

Original Submission