Protein Phase Transitions in Health and Disease

Our lab aims at understanding how genetic changes between individuals can or cannot result in disease by quantifying the impact mutations have on protein aggregation and toxicity. 

We are particularly interested in amino acid sequences that can adopt different conformations and undergo a process of self-assembly which results in distinct physical states.

Protein self-assembly  

The aggregation of proteins into insoluble amyloid fibrils is a key process in the pathogenesis of a number of neurodegenerative conditions, such as Parkinson’s disease or Amyotrophic Lateral Sclerosis. However, examples of functional amyloid are also widespread in nature, especially across bacteria and fungi. Our work aims at systematically deciphering the sequence-dependencies of the process of aggregation in both functional and pathological contexts.  

Proteins can also self-assemble into a more dynamic and reversible state through a process of condensation which is thought to contribute to the organization of the intracellular space. However, also for proteins that undergo liquid-demixing to form biomolecular condensates, the balance between function and dysfunction is far from clear. It is also unknown if and how condensates are precursors of insoluble amyloid-like states, and to which extent proteins are structured once in the liquid state.  

Quantifying the impact of mutations at scale 

In order to understand how mutations affect these delicate equilibria and to elucidate when and why a sequence starts aggregating or becomes toxic for the cell, our lab integrates experimental and computational approaches in different model systems. Recently, we have developed different Multiplexed Assays of Variant Effects (MAVEs) to quantify the toxicity and aggregation propensity of hundreds of thousands of protein sequences in vivo. By capturing the full landscape of the effects of mutations in a specific protein sequence we can guide clinicians to better diagnose and treat human disease, but we also reach a comprehensive mechanistic understanding of the process of amyloid formation and protein-induced toxicity. This translates in the possibility of rationally developing better targeted therapeutics, as well as in a set of fundamental principles that can guide protein design in bioengineering. 

Developing novel strategies to report on protein conformation  

In collaboration with the Lehner lab we also develop combinatorial mutagenesis approaches to study the interactions between mutations. We then use such genetic interactions to report on the conformation different proteins adopt as they start aggregating. Overall, we aim at generating exhaustive datasets that will give mechanistic insights on the process of protein aggregation, while also reporting on specific conformations and mechanisms leading to cellular toxicity.  The massive amount of data we generate is used to train new models of protein aggregation. Our strategy is also amenable to tackle many intrinsically disordered proteins, which are particularly difficult to study in vitro. In this perspective, in vivo selection approaches such as the ones we develop can provide a unique opportunity to investigate these sequences in a systematic way. 

Map of the effect of mutations on toxicity of the TDP-43 Prion-like Domain.

Percentage of substitutions and insertions increasing or decreasing amyloid formation of the Amyloid-Beta peptide, visualized on the cross-section of ex-vivo fibrils (7Q4M).

• Thermo MaxQ 8000

• Priyanka Narayan
  NIH-NIDDK
• Xavier Salvatella
  IRB, Barcelona
• Fran Supek
  IRB, Barcelona
• Ben Lehner
  CRG, Barcelona
• Luke McAlary /Justin Yerbury
  University of Wollongong, Australia