Scientists capture the misfolding of rogue proteins in action

Sumeet Kulkarni

Researchers at the National Center for Biological Sciences (NCBS), Bengaluru, have used a combination of techniques to unravel the mystery of how prions misfold. Prions are proteins that undergo structural changes to form compound assemblies called amyloid fibrils, which can lead to fatal infectious neurodegenerative diseases like the Mad Cow disease and other Transmissible Spongiform Encelopathies in mammals.

Prion protein expressed in E. coli, purified and fibrillized at pH 7
Prion protein expressed in E. coli, purified and fibrillized at pH 7  (Photo: Image by Roger Moore, Rocky Mountain Laboratories; NIAID [CC BY 2.0 (])

Proteins are the building blocks of life. But imagine if a protein could morph into a completely different, rogue avatar of itself at the flick of a switch. Even worse, imagine this dysfunction spreading to similar proteins in the neighbourhood of the affected protein, eventually damaging the surrounding tissue. 

Ishita Sengupta is an Assistant Professor at the Indian Institute of Technology (IIT), Kanpur, who studies prions, the villainous proteins in this plot. Nearly seven decades after their discovery, there is still a lot of mystery surrounding prions. The high-resolution structure of the misfolded, aggregated and infectious form of the prion protein has still not been solved,” Sengupta notes. 

Over the course of her post-doctoral work in Jayant Udgaonkar’s lab at the National Center for Biological Sciences (NCBS), Bengaluru, Sengupta used a combination of experimental techniques to get a detailed, step-by-step understanding of how prions operate.

The term infectious disease’ brings to mind the picture of a pathogen that spreads it, like a bacterium, a fungus, or a virus. All of these depend on nucleic acids, i.e. DNA or RNA, to replicate as they propagate between organisms and spread disease. That is why the discovery of the prion, a protein created by our own body which seemed to be the sole agent for the spread of certain diseases, was so enigmatic. 

We don’t really know what role prions play in our bodies. Like all proteins, they are made up of a string of amino acids which fold into a characteristic shape. Under the influence of various physical and chemical forces, this string of amino acids may self-assemble into two main kinds of structures: spiral-pasta-like alpha-helices, and flat-noodle-shaped beta-sheets. 

Protein secondary structures
Protein Secondary structures: Alpha-helix and Beta-sheet (Modified from illustration by Thomas Shafee [CC BY-SA 4.0 (https://​cre​ativecom​mons​.org/​l​i​c​e​n​s​e​s​/​b​y​-​s​a/4.0)])

The prion protein does not have the ability to cause disease in its normal configuration, which is a complex 3‑dimensional structure primarily composed of spiral alpha-helices. Under certain kinds of triggers, it can misfold into a completely different shape and form aggregated structures called amyloid fibrils, which have more flat beta-sheets. Not all misfolded prions lead to disease — but when they do, such amyloid fibrils have been shown to be highly correlated with severe tissue damage. Despite being very rare, all prion diseases are fatal and there is no known cure.

We do not know for certain what triggers prion proteins to misfold. However, if we can understand how these triggers cause small changes in the prion molecule, and if we have a timeline of the sequence of these changes, then we can start thinking about how to address the corresponding diseases,” says Neelanjana Sengupta, an associate professor at the Indian Institute of Science Education and Research (IISER) Kolkata, who was not involved with this study.

To investigate this process, the researchers tagged different chemical parts of the mouse prion protein. Using a technique called Fluorescence Resonance Energy Transfer, the researchers tracked energy changes within the molecule. This allowed them to monitor extremely minute changes in the relative distance between the tagged protein parts. The experiments were performed under acidic conditions, which are believed to facilitate prion misfolding in living systems. 

It was known that unlike their original alpha-helical form, misfolded prions in aggregated structures have a greater proportion of flat beta-sheets. This study provides a greater resolution of what the resulting structure looks like and also provides fresh insights on how this process unfolds. For the first time, the researchers were actually able to pinpoint which parts of the protein changed their shape, and exactly when they did so. Detailed surveillance of every way in which these rogues operate is crucial to developing strategies to stop them.

This may just be the first step towards drug development, Ishita notes. Since our experiments have been performed in-vitro with purified proteins, drawing conclusions about disease-relevance from these results would be premature,” she warns. 

However, the innovative fashion in which this series of standard biochemical techniques have been combined can also inspire research on misfolding pathways for other proteins responsible for other neurodegenerative diseases like Alzheimer’s and Parkinson’s disease.

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Written By

Sumeet Kulkarni is a graduate student studying Astrophysics at the University of Mississippi. Since his undergraduate days at IISER Pune, he has harboured a keen interest in writing and public engagement through creative expressions of scientific ideas.