Cells produce a great number of different protein complexes, each of which is made up of many individual proteins. These protein complexes, like ribosomes, are what controls almost all of a cell’s life-sustaining biological functions. Biologists have succeeded in determining the structure of many of protein complexes, but very little is known about how the individual protein complexes assemble and how they dynamically change over time.
We developed an innovative method called KARMA to study these questions, which stands for kinetic analysis of incorporation rates in macromolecular assemblies. Similar to geological fossils dating, KARMA uses the content of isotope-labeled molecules to measure the age of cellular proteins. This makes it possible to track the dynamic changes of protein complex assemblies, even for very large complexes and with a high temporal resolution.
Well heard-of illnesses like Alzheimer’s disease, Parkinson disease or diabetes originate from miss-assembled protein complexes, aggregates. Such aggregates form due to the loss of proteostasis control – a tendency that our cells constantly keep proteins and protein complexes in a working condition. We will use the power of KARMA to study how does a set of protein complexes that safeguard other cellular proteins keeps itself functional and prevents protein miss-assembly. We will also look at the reasons why health-treating protein aggregates, like the ones causing Alzheimer’s disease, form in our cells. Besides these very important questions our work will enable researchers to understand a wide range of dynamic processes like COVID and other infections.
To be properly functional, cells must keep myriad protein molecules and their complexes in a working condition, which is known as proteostasis. Loss of proteostasis is detrimental. For example, well heard-of illnesses including Alzheimer’s disease, Parkinson disease or diabetes originate from the cell's inability to keep the functional state of proteins. To understand the mechanisms of proteostasis and origins of its failure it is important to characterise the fate of cellular proteins (protein dynamics) including when and how they fold, assemble into multiprotein complexes, get modified and eliminated.
Surprisingly, our knowledge of the protein dynamics is very fragmentary. For instance, the assembly mechanisms were studied for only a handful of ~4000 protein complexes present in mammals alone! To gain insight into the mechanisms of proteostasis, we propose to implement an innovative method entitled kinetic analysis of incorporation rates in macromolecular assemblies (KARMA), which would allow us to elucidate protein dynamics in the context of live cells.
Using KARMA and budding yeast - a very powerful model system - we will address challenging questions in the field of proteostasis: How does the proteostasis network – the guardian of cellular proteins - keeps itself functional? How are vital cellular structures affected by the proteostasis failure? How exactly do disease-causing protein aggregates form in live cells?
The implementation of KARMA requires an interdisciplinary effort at the intersection of biochemistry, quantitative mass-spectrometry and analysis of metabolic processes. KARMA is a very generic technique that can be used in various organisms not only to tackle the control of proteostasis but also to answer questions ranging from the formation of protein complexes to the mechanisms of viral infection.