CORDIS - EU research results

Three-dimensional dynamic views of proteomes as a novel readout for physiological and pathological alterations

Project description

It may be the quality and not the quantity that counts when it comes to proteins

Proteins are ubiquitous, mediating structural and functional roles in all cells. Their dysfunction is intimately involved in disease and one important way to assess their activity is to screen for their expression (proteomics assays looking at the entire complement of proteins expressed by an organism). However, many disease processes may alter protein function – intricately related to structure – without altering expression. The EU-funded project Proteomes-in-3D is testing a novel methodology to measure altered structures within the entire proteome of an organism and determine whether they are correlated with complex phenotypes. The team is focusing on protein aggregates or superassemblies (SAs), given that SAs are involved in both normal and disease processes. In addition, they will create an atlas of structural proteome dynamics from data generated throughout the project to provide a firm foundation for future studies of the structural proteome.


Protein expression screens are routinely used to identify biological processes deregulated upon disease development or upon specific cellular perturbations. Generating molecular hypotheses from these ‘omic data remains challenging, however, and many molecular events that modulate protein function do not involve altered protein levels. With this project, I propose a new paradigm. I propose that by measuring altered structures of proteins on a global scale, we can capture altered functional states of proteins and proteomes. I propose that the new approach will support the generation of testable molecular hypotheses from global data and the development of new frameworks for the modelling of biological systems.

Building on a unique mass spectrometric approach my lab developed, which captures protein structural changes on a proteome-wide scale, we will assess the performance of the global structural readout at analyzing complex phenotypes. We will apply it to a biomedical problem of interest to my lab: the functional and pathological implications of protein aggregates or superassemblies (SAs).

Protein aggregates form not only during disease but also under physiological conditions. These structures regulate important normal processes and contribute to cellular architecture. Using the new structural approach, we will identify and characterize networks of novel functional SAs in E. coli, mouse, and human proteomes. We will assess how genomic variation, environment and age modulate protein structures and SA assembly and how SAs are linked to phenotypes. Last, we will translate our approach to a clinical setting and ask whether altered protein structures can serve as biomarkers of disease, specifically Parkinson’s disease and how SAs underlie Parkinson’s subtypes. We will collect the wealth of dynamic structural data generated through this project into an Atlas of Structural Proteome Dynamics and use the data to shed new light on features of the structural proteome.

Host institution

Net EU contribution
€ 2 000 000,00
Raemistrasse 101
8092 Zuerich

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Schweiz/Suisse/Svizzera Zürich Zürich
Activity type
Higher or Secondary Education Establishments
Total cost
€ 2 000 000,00

Beneficiaries (1)