A happy cell is a balance cell, but for every stupendously twist protein it creates; it must tear the old ones asunder. That means untangling a convoluted pretzel-like mass for recycling. Cdc48 plays a critical role in unraveling the spent proteins. Cdc48 is like a Swiss army knife of the cell and can interact with so many different substrates. Until now we didn’t have an understanding exactly of how it works.”Peter Shen, Ph.D., assistant professor in Biochemistry at University of Utah Health and senior author on the paper.

Undulations as it unfolds proteins

Shen led a multi-institutional team of researchers to identify key structures of Cdc48; to visualize its undulations as it unfolds proteins. The results are available online in issue of Science. “We set out to do this because we care how molecular machines work,” said Shen. “We decided to hone-in on Cdc48 due to clinical relevance.”

For years, researchers have known that a single-point mutation in Cdc48 can cascade into serious diseases; including amyotrophic lateral sclerosis (ALS) and Charcot-Marie-Tooth disease type 2Y. “Human Cdc48 is link to multiple diseases and is the target of efforts to develop therapeutics; for the treatment of cancers,” said Christopher Hill, DPhil., distinguish; professor of Biochemistry at U of U Health and co-corresponding author on the study. “The structure that we have determine; can be use to advance efforts to develop more effective inhibitors and therapeutics.”

In the study, the research team purified Cdc48 directly from yeast cells (Saccharomyces cerevisiae) and took snapshots of the purify particles in different configurations; after it was flash frozen using cryogenic electron microscopy (cryo-EM). “The cells are already doing the hard work for us by making these complexes,” Shen said. “Because this method is so fast; we have capture Cdc48 in the act of unfolding a protein substrate.”

Conveyor belt-like movement

Using this approach, the research team demonstrate how Cdc48 unfolds the protein by threading it through a central pore of the complex; using a hand-over-hand conveyor belt-like movement. The recycle tangle they were imaging was a mystery until collaborators at Brigham Young University applied mass spectrometry proteomics; to the same harvested complex to unmask the anonymous proteinan inactive protein phosphatase 1 complex.

Shen believes these results are applicable to human cells, because Cdc48 is highly conserve.”We believe the structure we solved here will look very similar to what our bodies are expressing right now,” he said. The research team was unable to visualize the entire complex because Cdc48; interacts with multiple binding partners almost simultaneously.

This efficient multitasking blurs the reconstruction; however, Shen wants to continue to explore how Cdc48; manages to bind with so many partners at roughly the same time. “The coolest part is this demonstrates that we can take a protein directly; out of their cells and image them in their native state,” Shen said. “I think this is the future of the cryo-EM field.”