High-Res Video Shows Exactly How Proteins Become Untangled

If you zoom way way in, it’s apparent that your body is a fine-tuned assembly line, manufacturing countless proteins that serve as the building blocks for all of your cellular machinery. Normally, these proteins are synthesized with incredible precision, but sometimes mistakes happen and they come together in the wrong shape. These misfolded proteins, if not properly dealt with, can help cause serious diseases, like Alzheimer’s Disease, type 2 diabetes, and Parkinson’s Disease.

When this happens, specific proteins will dive into the misfolded clump and pull it apart — either to try again and make it right or eradicate it altogether. After 10 years of experimentation, a team of biochemists from University of Pennsylvania’s Perelman School of Medicine managed to get a closer look at one of these proteins, known as Hsp104, and how it works in hopes of exploiting it in a new form of medicine.

Their research, published this week in Science, let researchers analyze the structure and activity of Hsp104 down to its individual atoms.

Their high-resolution video of the protein in action revealed how the protein works. Researchers already knew what Hsp104 did, but they weren’t quite sure how. Hsp104 grabs onto one strand from a clump of misfolded proteins and works its way down, eventually pulling it loose from the tangle like a single strand of spaghetti. Researchers liken the process to how a ratchet wrench works.

As of yet, there are no medical treatments out there that pull apart misfolded proteins. While the team from Perelman School of Medicine have already managed to alter Hsp104’s makeup in such a way that it works faster than normal, it’s too early to apply their findings in a new medication.

“It appears to pull substrates through stepwise, like a ratchet,” says senior study author Daniel Southworth, Ph.D., an assistant professor at the University of Michigan Life Sciences Institute. “We can see how the proteins in the machine rearrange between different states to grab onto the next site on the substrate.”

To do so, the protein relies on its six identical components that grab onto strand one at a time.

“The study helps us to understand how cells can break apart toxic protein aggregates to restore protein function,” says James Shorter, one of the paper’s co-authors. “Finally having a clear picture of this remarkable nanomachine will empower our designs for therapeutic versions that work in humans.”

The ultimate goal would be to engineer a version of Hsp104 — which is common throughout the tree of life but not found in any animals — as a medication that would break up clusters of faulty proteins, like the amyloid plaques that develop in Alzheimer’s Disease, and speed up the brain’s degeneration. By understanding the mechanism by which Hsp104 acts, the scientists hope to engineer a protein that can do the same to the clumps of protein common in neurodegenerative diseases.

Abstract:

Hsp100 polypeptide translocases are conserved AAA+ machines that maintain proteostasis by unfolding aberrant and toxic proteins for refolding or proteolytic degradation. The Hsp104 disaggregase from S. cerevisiae solubilizes stress-induced amorphous aggregates and amyloid. The structural basis for substrate recognition and translocation is unknown. Using a model substrate (casein), we report cryo-EM structures at near-atomic resolution of Hsp104 in different translocation states. Substrate interactions are mediated by conserved, pore-loop tyrosines that contact an 80 Å-long unfolded polypeptide along the axial channel. Two protomers undergo a ratchet-like conformational change that advances pore-loop-substrate interactions by two-amino acids. These changes are coupled to activation of specific ATPase sites and, when transmitted around the hexamer, reveal a processive rotary translocation mechanism and a remarkable flexibility in Hsp104-catalyzed disaggregation.