Method Developed to Profile Protein Complexes

Cells are filled with many different types of proteins that interact with each other and often work together in groups. These groups are called complexes and are molecular machines that only function properly when their individual components interact. Which proteins interact with each other and how also depends on the state of the body. Under normal conditions in a healthy body, two proteins might join together. If the conditions change due to cellular stress, proteins can change their interaction partners, which can be problematic.

Understanding these interactions is vital for developing targeted treatments that can restore cellular equilibrium and is the focus of a recently published study in Nature Biotechnology. According to co-author Cathy Marulli, "Altered interactions between proteins can lead to diseases such as Alzheimer's, Parkinson's or cancer." Understanding these interactions is vital for developing targeted treatments that can restore cellular equilibrium.

To study this intricate network, Marulli and other scientists from ETH Zurich combined serial ultrafiltration with limited proteolysis-coupled mass spectrometry to create FLiP–MS, a new structural proteomics workflow. FLiP-MS allows researchers to analyze the complete interaction network of proteins, known as the interactome, directly within complex cellular environments.

The team identified around 6,000 interaction interfaces between proteins and used these as markers to assess changes in protein interactions under different conditions. Their study revealed significant alterations in protein complexes during cellular stress.

One key finding was the importance of a protein complex called SAGA in the yeast cell's interaction network. Marulli likens SAGA to a DJ at a party, noting that its removal dramatically affects other protein interactions.

The method developed can also be applied to many organisms. “For each species we want to study, we just need to develop a new set of binding markers to be able to use this method to study protein interactions in mouse or human cells,” says Marulli. The next logical step is therefore to determine the interaction markers for the interactome of human cells in order to analyze defective protein interactions in a single step.

This research has broad implications. The method can be adapted to study protein interactions in other organisms, including humans, potentially leading to new diagnostic tools and insights into disease mechanisms. It also opens doors for pharmaceutical research, as understanding protein interaction sites could guide the development of new drugs with fewer side effects.