Dense liquid droplets act as cellular computers

AAn emerging field explores how groups of molecules condense inside cells, how oil droplets come together and separate from water in a salad dressing.

In human cells, “liquid-liquid phase separation” occurs because similar large molecules coalesce into dense droplets separated from the more dilute parts of the fluid cell interior. Previous work had suggested that evolution exploited the natural formation of these “condensates” to organize cells, providing, for example, isolated spaces for the construction of cellular machinery.

In addition, abnormal and condensed groups, also called “tangled”, of molecules in the droplets are almost always present in the cells of patients with neurodegenerative diseases, including Alzheimer’s disease. Although no one knows why such condensates form, a new theory argues that the biophysical properties of cell interiors change as people age, in part due to “molecular clutter” packing more molecules together. in the same spaces to affect phase separation.

Researchers liken condensates to microprocessors, computers embedded in circuits, because both recognize and calculate responses based on incoming information. Despite the presumed impact of physical changes on liquid processors, the field has struggled to clarify the mechanisms linking phase separation, condensate formation, and chemical signal-based computation, which occur on a much larger scale. small, according to the researchers. Indeed, natural condensates have so many functions that experiments find it difficult to delimit them.

To address this challenge, researchers from NYU Grossman School of Medicine and the German Center for Neurodegenerative Diseases built an artificial system that revealed how the formation of condensates alters the action at the molecular level of enzymes called kinases, an example of chemical calculation. Kinases are protein switches that influence cellular processes by phosphorylating – attaching a molecule called a phosphate group – to target molecules.

The new analysis, published online September 14 in molecular cellfound that the formation of artificial condensates during phase separation provided more “sticky” regions where medically important kinases and their targets could interact and trigger phosphorylation signals.

“The results of our study show that physical changes like crowding can lead to the formation of condensates that are converted into biochemical signals, as if the condensates were squishy computers,” says lead study author Liam J. Holt, PhD, Fellow of the Institute for Systems Genetics at NYU. Langone Health.

Among the kinases studied considered to be more active in a crowded, condensed environment was cyclin-dependent kinase 2, known to phosphorylate the microtubule-binding protein Tau. Tangled condensates of Tau are frequently found in the brain cells of patients with Alzheimer’s disease.

“Our experiments suggest that the formation of more Tau condensates results in more Tau phosphorylation,” adds Dr. Holt, who is also an associate professor in the Department of Biochemistry and Molecular Pharmacology. “Whether these mechanisms lead to more brain cell death and whether their reversal could constitute a new therapeutic approach will be important questions in our future work.

Specifically, the study found that when Tau and cyclin-dependent kinase condense together into dense droplets, there was a threefold acceleration of phosphorylation at a cluster of sites on Tau (the AT8 epitope) linked to Alzheimer’s disease.

Engineering of a biosensor

In seeking to design useful versions of these computers, the research team tested several engineered condensates, synthesizing different scaffold molecules to see which were the best sample kinases – MAPK3, Fus3 and Cyclin-Dependent Kinase 1 (Cdk1 ) – as well as their targets to increase signaling. Condensates form when scaffolding molecules interlock with droplets. The team found that in their model, the clumping together of large biomolecules into droplets inside single-celled living organisms called yeast made phosphorylation reactions hundreds of times faster.

The study also revealed that the formation of condensates allowed the included kinases to phosphorylate more types of molecules, and without the presence of the usually required molecular shapes. This suggests that condensates in crowded cells create altered stone types, some potentially linked to disease, the authors say.

Going forward, the research team is looking to build on an earlier study from Dr. that build other large proteins in cells. The team plans to investigate whether compounds known to inhibit mTORC1 can reduce Tau crowding and phosphorylation.

Finally, the research team hopes their findings will advance the design of other cellular computers that respond to physical forces. This could include introducing engineered processors into immune cells that would be activated to attack cancer cells as they seek to squeeze into tissues made dense by tumor growth.

Along with Dr. Holt, study authors from NYU Langone Health’s Institute of Systems Genetics were Dajun Sang and Tong Shu. Other authors were Christian Pantoja, Alain Ibanez from Opakua and Markus Zweckstetter from the German Center for Neurodegenerative Diseases (DZNE), Göttingen, Germany. Zweckstetter is also a professor at the Max Planck Institute for Multidisciplinary Sciences, Department of NMR-Based Structural Biology.

The study was funded by grants R01 GM132447, R37 CA240765, and TR01 NS127186 from the National Institutes of Health. The American Cancer Society, the Pershing Square Sohn Cancer Award, the Chan Zuckerberg Initiative, the Department of Defense Multidisciplinary University Research Initiative (MURI) competition, the Deutsche Akademischer Austauschdienst (DAAD), and the European Council for research also supported the work.

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