Rice University's “deep-learning extended depth-of-field microscope,” or DeepDOF. (representational image)
A team at Rice University has developed a strategy to zoom in on tiny protein segments inside living cells.
The method reveals subtle environmental changes that could signal the earliest stages of diseases such as Alzheimer’s, Parkinson’s, and cancer. The findings also point to new ways of screening drugs that target protein aggregation disorders.
The researchers engineered a fluorescent probe, called AnapTh, into precise protein subdomains. This probe monitors real-time changes that conventional techniques often miss.
By tracking localized shifts, scientists can see how distinct regions of the same protein behave differently as they begin to aggregate.
“We essentially built a molecular magnifying glass,” said Han Xiao, professor of chemistry and director of Rice’s SynthX Center. “This allows us to visualize subtle environmental changes that previously went unnoticed.”
The team based its design on the idea that early local changes appear before visible clumping.
AnapTh, a fluorescent amino acid, shifts its emission spectrum depending on the surrounding microenvironment. Using genetic code expansion, the scientists inserted the probe at chosen sites without disrupting protein folding or function.
This approach gave them spatial resolution and real-time monitoring that existing tools could not match.
“We wanted a method to light up just one spot in a protein and watch what happens around it in live cells,” said Mengxi Zhang, a graduate student and co-first author. “When aggregation starts, some parts become denser and more hydrophobic, while others remain unchanged.”
Applying the technique to disease-related proteins revealed a surprising pattern. Aggregation did not happen uniformly.
Some subdomains showed higher fluorescence intensity and spectral shifts, marking denser and chemically altered environments. Others remained unchanged.
Diagram of mice and cell sensors tracking epigenetic changes. Credit – Rice University
This finding challenges older models that described aggregation as uniform.
Instead, the evidence shows aggregation begins at discrete “hot spots” and then spreads. These early localized misfolding events may become future biomarkers or serve as therapeutic entry points.
The results reshape how scientists view protein aggregation.
They highlight a process that is both uneven and dynamic, with specific sites driving the earliest disease-related changes. This new perspective provides fresh insight into the molecular triggers of neurodegeneration.
Protein aggregation underlies devastating disorders such as Alzheimer’s plaques, Parkinson’s Lewy bodies, and misfolded proteins in cancer.
Understanding where and how these changes begin gives researchers a clearer path toward treatments. The discovery offers a sharper lens for studying how small errors in folding a spiral into major health threats.
Testing drugs at earliest stages
The Rice team also demonstrated how the platform could help drug discovery. By detecting early subdomain changes, the tool can track disease progression with more sensitivity.
Researchers can also identify compounds that intervene before aggregation spreads.
“This platform gives us a jump start,” said Shudan Yang, a graduate student and co-first author. “Now we can test potential inhibitors and see at the very first sign of trouble whether they prevent local misfolding.”
That level of precision, Yang added, is exactly what drug development needs.
The approach could shorten timelines for drug screening and sharpen targeting of disease-specific weak spots.
Co-authors of the study include Rice researchers Shikai Jin, Yuda Chen, Yiming Guo, Yu Hu, and Peter Wolynes.
The study is published in the journal Nature Chemical Biology.
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