Researchers solve structure of ‘flipping’ cellular machine

New understanding of crucial molecular enzyme could lead to Alzheimer’s and cancer therapies.

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A new study from the Scripps Research Institute (CA, USA) and the University of California, Berkeley (CA, USA) has demonstrated how a critical molecular enzyme starts in a tucked-in somersault position and ‘flips’ when it encounters the right target. Their findings shed light on the process by which cells eliminate disease promoting proteins, and could lead to the development of novel therapeutics to combat cancer and Alzheimer’s disease.

“Having an atomic-resolution structure and a better understanding of this mechanism gives us the ability to someday design therapeutics to combat cancer and neurodegeneration,” explained co-senior author on the study, Gabriel Lander.

The study provides new information on the proteasome, a molecular machine that serves as a recycling center in cells, breaking down spent or damaged proteins or eliminating the harmful misfolded proteins observed in certain diseases. This research is the first study in nearly 20 years to solve a significant component of the proteasome at a near-atomic resolution.

The breakthrough was made possible by recent advances in cryo-electron microscopy. Using this technology, the researchers investigated a part of the proteasome that contains the deubiquitinase enzyme Rpn11. Rpn11 is responsible for cleaving molecular tags from proteins to be recycled in the proteasome, and without it, the protein tags would clog the proteasome, killing the cell.

From previous research, the team understood that Rpn11 and its associated proteins latch onto the proteasome, forming a lid. The lid complex can exist separately from the proteasome, which can be problematic, as if Rpn11 cleaves tags from proteins that have not reached the proteasome these proteins could avoid recycling and cause disease. The team wanted to identify the mechanism by which nature avoided this problem.

Corey Dambacher, one of the first authors of the study, described their discovery: “There's a sophisticated network of interactions that pin the Rpn11 deubiquitinase against neighboring subunits to keep it inhibited in the isolated proteasome lid.” Mark Herzik Jr, one of the other first authors, added, “In order for Rpn11 to perform its job, it has to flip out of this inhibited conformation.”

The researchers also showed that, in order to flip out of the conformation at the proteasome, the proteins surrounding Rpn11 pivot and rotate, binding to the proteasome and releasing the active site from its nook. The system is finely tuned, but there may be ways to manipulate it; the study collaborators made small mutations to the proteins accompanying Rpn11, and found that any small change will release the active site, even when the lid is floating away from the proteasome.

The understanding of the mechanism could help to guide future therapies to remove damaged or misfolded proteins, such as in Parkinson’s, Alzheimer’s or several cancers.


Dambacher, C. M., Worden, E. J., Herzik, M. A., Martin, A., & Lander, G. C. Atomic structure of the 26S proteasome lid reveals the mechanism of deubiquitinase inhibition. eLife. (2016);

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Stella Bennett

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