Scientists Unlock 3D Structure of Key Protein in Cellular Damage Response, Paving Way for Targeted Therapies
Baltimore, MD – In a breakthrough that could revolutionize the growth of treatments for cellular stress and related diseases, researchers at Johns hopkins University and the Ludwig-Maximilians-University Munich (LMU) have unveiled the first detailed 3D structure of the ZAK protein. This protein plays a critical role in a cell’s ability to detect and respond to damage, particularly from stressors like UV irradiation. The findings, published November 19 in Nature, offer unprecedented insight into the protein’s activation mechanism and open new avenues for designing specialized therapies.
“in order to develop drugs to target this pathway, we needed to understand how ZAK actually works at a molecular level,” explained Dr. Brenda Schulman, a professor of biochemistry at Johns Hopkins and lead author of the study.
The ZAK protein’s role is intimately linked to ribosomes, the cellular machinery responsible for translating genetic code into proteins.When cells encounter stress – from UV light exposure to nutrient depletion or toxins – ribosomes can stall during this process, leading to “traffic jams” and the production of incomplete or abnormal proteins.This triggers a cellular stress response pathway mediated by ZAK.
“The way the cell knows there’s a problem is through ribosomes,” stated a lead researcher, whose team previously demonstrated in 2020 that ribosome collisions activate the ZAK protein.
The new experiments aimed to elucidate precisely how ZAK proteins interact with ribosomes to sense translational errors and initiate a signaling cascade. Researchers utilized lab-cultured human cells,engineering them to overproduce inactivated ZAK proteins. By inducing ribosome collisions with a specific drug, they were able to activate ZAK and isolate samples for analysis.
Cryo-EM Reveals Protein Architecture
Collaborating with LMU scientists, the johns Hopkins team employed cryo-electron microscopy (cryo-EM) to visualize the activated ZAK protein and define its 3D structure. After two years and hundreds of samples, a breakthrough came via a text message from a graduate student at LMU, indicating a promising result revealing a significant portion of the ZAK protein’s architecture.
The analysis revealed a surprising characteristic of the ZAK protein: more than half of it is indeed predicted to be unstructured, described by researchers as “like spaghetti.” The structured portions, though, appear to act as “tentacles” to detect collided ribosomes, forming a bridge between the stalled ribosomal complexes.
Key Interactions Identified
The research team identified specific interactions between the ZAK protein and the ribosome. The C terminus of ZAK consistently binds to the ribosome, while collision-specific interactions occur with ribosomal rRNA known as expansion segments. Moreover, a region called the RIM interacts with RACK1 on the ribosome to activate ZAK when collisions occur.
These findings have significant implications for the development of kinase inhibitors.Kinases, like ZAK, regulate cellular processes by adding chemical groups to other proteins. Current kinase-targeting drugs often bind to locations that cause unwanted side effects.
“Now, we know more about the makeup of these specialized sites in the ZAK protein and can be more specific in developing drugs that target it,” the lead researcher explained.
Future Research Directions
the research team plans to further refine the ZAK protein’s structural map,aiming to capture the complete structure and understand its behaviour when not connected to colliding ribosomes. This deeper understanding could unlock even more targeted therapeutic strategies.
The research was supported by the Howard Hughes Medical Institute, the European Research Council, the National Key R&D program of China, the National Natural Science Foundation of China, the National Institutes of Health, the National Science Foundation, the Damon Runyon Cancer Research Foundation, The Johns Hopkins University provost’s Postdoctoral Fellowship Program and the Dermatology Foundation’s Dermatologist Investigator Research Fellowship.
DOI: 10.1038/s41586-025-09772-8
