Principal Investigator Michael Landreh
Mass spectrometry of protein interactions from cancer to memory
All biological processes can be described as biomolecules “talking” to each other, providing cargo, information, or transportation. These events usually take the from of a direct physical contact, i.e. a non-covalent interaction, in which one molecule, most often a protein, binds to one or more partners, inducing a change in the three-dimensional structure. In this manner, proteins can keep in touch with their environment to control their function. For example, upon sensing a change in pH, sider silk proteins lock each other into infinite chains to form very stable scaffolds, and membrane proteins can recognise individual lipid molecules in their environment to tune their activity accordingly. Aberrant, -faulty- interactions, on the other hand, interfere with these processes and are therefore often associated with diseases. Some proteins interact with themselves and form toxic structures such as amyloid fibrils that eventually lead to degeneration of the affected tissue, as seen in e.g Alzheimer's disease. Similarly, destabilization and aggregation of the tumour suppressor p53 and its targets leads loss of cell cycle control and impaired DNA damage repair, giving rise to cancer. Therefore, it is important to understand how exactly proteins “talk” to each other, and use this information to find ways to prevent interactions from going wrong.
Our group focuses on the use of mass spectrometry (MS), a technique that allows us to determine the exact weight of biomolecules, to study how proteins recognise and bind their partners. MS is well-suited for the study of transient interactions, large complexes and even unstable proteins, all of which are refractory to other structural biology methods like NMR and X-ray crystallography. For this purpose, we combine several complementary approaches:
- In “native” MS, we gently transfer proteins together with their binding partners from physiological solutions into the vacuum inside the mass spectrometer and measure the weight and stability of the resulting complex. This reveals what type of interaction holds the partners together, and how many (and which) molecules are involved.
- Hydrogen/deuterium exchange MS measures the incorporation of a chemical label (Deuterium) into the protein. Deuterium is incorporated into flexible and exposed parts of the protein. By measuring the resulting increase in weight, we are able to determine the stability and folding state of a protein, and even locate binding sites for tother proteins.
- MS-based proteomics allows us to identify individual proteins from complex mixtures based on their unique mass “fingerprints”. Using individual proteins as bait, we are able to fish out their specific interaction partners and map upstream and downstream targets.
The combination of all three techniques provides direct insights into several aspects of an interaction, but also generates constraints that can be used to direct computational modelling.
Monitoring intracellular interactions for drug development. Protein-protein interactions are commonly studied in vitro using isolated, purifed proteins. We are combining intracellular HDX-MS and native MS to preserve conformational signatures of protein complexes inside bacterial cells for read-out by MS. Using the interactions between the tumor suppressor p53 and its downstream partners as a target system, we want to follow e.g. the effects of drugs on protein-protein interactions in a cellular environment. The goal is to integrate intracellular structural biology with proteome-wide screening methods for drug target engagement such as CETSAs that can be applied in targeted drug discovery.
Structure, stability, and interactions of prion-like proteins in memory formation. Aggregation-prone proteins are related to a number of diseases such as neurodegenerative disorders, hereditary cancers, and interstitial lung disease, yet remain among the most challenging targets for structural biology. We are using the power of structural mass spectrometry to understand how the ability of a group of prion-like proteins to assemble into large cellular structures facilitates long-term memory formation.
The aims of this project are two-fold: 1. We want to unravel the role of each part of these complex multi-domain proteins in switching from a soluble, inactive state to an amyloid-like structure without undergoing toxic, uncontrolled aggregation normally observed for prion proteins. 2. We are interested in how self-assembly affects the interactome of memnons, such as their ability to bind RNAs and anti-amyloid chaperones. Using MS-based structure and interaction maps, we hope to derive models for self-assembly and its impact on the cellular processes that can shed light on how structural changes in a small family of proteins can elicit something as complex as memory formation.
We also collaborate with David Drew (Stockholm U) on membrane protein-lipid interactions, Erik Marklund (Uppsala) on integrating MS and MD simulations, Carol Robinson (Oxford) on MS method development, and Jan Johansson (KI) and Anna Rising (SLU) on strategies against amyloid formation, and the biology of spider silk production.
Neurodegenerative diseases and protein aggregation disorders
Mass spectrometric method development