New research with implications for drug discovery allows visualization of the smallest protein clusters

Penn engineers have developed a new way to visualize the smallest clumps of proteins, bypassing the physical limitations of light-powered microscopes and opening new avenues for detecting proteins involved in diseases like Alzheimer’s and test new treatments.

In an article published in Cellular systems, Lukasz Bugaj, assistant professor of bioengineering, describes the creation of CluMPS, or Clusters Magnified by Phase Separation, a molecular tool that activates by forming visible blobs in the presence of clusters of target proteins as small as a few nanometers. Essentially, CluMPS works like an on/off switch that responds to the presence of protein clumps that it is programmed to detect.

Normally, Bugaj explains, detecting such clusters requires laborious techniques. “With CluMPS, you don’t need anything other than a standard laboratory microscope.” The tool fuses with the target protein to form condensates an order of magnitude larger than the protein clumps themselves that resemble colored drops from a lava lamp. “We believe that the simplicity of the approach is one of its main advantages,” says Bugaj. “You don’t need specialized skills or equipment to quickly see if there are small clumps in your cells.”

To treat diseases like Alzheimer’s, ALS and even cancer, the ability to detect such small protein clumps promises to be a fundamental advance, allowing researchers to determine whether drugs actually eliminate disease-causing clumps. ‘a target protein in a cell.

“You need a very clear signal,” explains Bugaj, to know whether a treatment has worked or not. “It’s very obvious when you have a gigantic cluster, but if you have small clusters, it’s much more difficult. We can now amplify this signal and see which drugs actually dissolve the clusters.”

In addition to opening new avenues for drug discovery, CluMPS will allow researchers to understand how proteins work in new ways, leading to a deeper and more sophisticated rendering of the cells themselves. “There’s a whole landscape of protein clustering that’s happening on a small scale, that’s important, but we don’t know it yet,” Bugaj says.

One of the challenges overcome by CluMPS is that the light waves themselves are larger than the smaller protein clusters, making it very difficult to visualize these clusters without specialized techniques. “The wavelength of blue light is around 400 nanometers,” Bugaj explains. “You can’t actually determine the location of anything smaller than half that wavelength with a conventional microscope,” making protein clusters tens of nanometers wide almost invisible.

To develop CluMPS, Bugaj and his lab teamed up with Elizabeth Rhoades, professor of chemistry at Penn Arts & Sciences, whose lab helped validate that CluMPS actually detected groups of target proteins instead of generating false positives. “This was a really rewarding collaboration for us,” says Rhoades, “because it allowed us to apply the methods commonly used by our lab to help validate this powerful new tool in living cells. It was exciting to see how how well we could differentiate between clusters and single proteins.

Thomas R. Mumford, a doctoral student at Bugaj Lab and lead author of the paper, played a key role in brainstorming and performing the necessary experiments.

“It was crucial to characterize how the underlying features of protein groups interacted with CluMPS to trigger condensation,” says Mumford, to allow future users of the technology to understand precisely how it worked.

“It was up to us to demonstrate that we were indeed detecting small clusters,” adds Bugaj. “One of the most rewarding aspects was working with Tom and the Rhoades lab to think about new types of experiments that would make this point convincingly.”