Research background

Around a third of all human proteins are made in the endoplasmic reticulum (ER), where they must fold correctly before being sent to their destinations in and beyond the cell. Molecular chaperones such as BiP guide this process, helping new proteins fold and preventing misfolded ones from accumulating. When the folding capacity of the ER is overwhelmed, cells activate the unfolded protein response (UPR), a signalling network that restores balance or, if stress persists, triggers cell death. Failures in ER protein homeostasis contribute to diseases including neurodegeneration, diabetes and cancer. My group uses structural biology and biochemsitry to understand how ER chaperones work and how they sense and signal stress.

 

Key discoveries

A new model for how cells sense ER stress
My group proposed a new model for how the unfolded protein response (UPR) is switched on. Using purified proteins in a reconstituted system, we showed that the ER chaperone BiP binds the UPR sensors IRE1 and PERK through its nucleotide-binding domain rather than its substrate-binding domain, as had been assumed, and that this interaction is ATP-independent. When misfolded proteins accumulate, an allosteric change in BiP causes it to release IRE1 and PERK, triggering the stress response (Carrara et al., eLife 2015; Kopp et al., eLife2018).

Although binding does not require ATP, we went on to show that ATP primes BiP’s complexes with IRE1 and PERK to detect misfolded proteins, and that these sensors block the recruitment of BiP’s co-chaperones. Together these switch BiP from its usual role as a chaperone into a dedicated ER stress sensor (Kopp et al., Nat. Struct. Mol. Biol. 2019).

We also determined crystal structures of the PERK luminal domain, which revealed that it forms transient tetramers during ER stress signalling (Carrara et al., EMBO Journal 2015).

How the UPR signal is passed on
We determined the structure of the cytosolic kinase and RNase domains of human IRE1 in a face-to-face arrangement, revealing how IRE1 molecules phosphorylate each other in trans. We further showed that specific phosphorylation events generated by this trans-autophosphorylation activate IRE1’s RNase splicing activity, linking IRE1’s two enzymatic functions (Ali et al., EMBO Journal 2011; Prischi et al., Nat. Commun. 2014).

A near-native structural biology platform for ER chaperone complexes
More recently, my group developed a new approach for determining the structures of ER chaperone complexes in a near-native state, isolated directly from human (HEK) cells rather than reconstituted from purified components. Using this approach, we found that the architecture of a previously uncharacterised “hook” domain points to a role in substrate binding, leading us to propose a model for how these chaperone complexes engage their client proteins (Ben-Khoud et al., bioRxiv 2025). We are now using this platform to uncover how ER chaperone complexes carry out protein quality control in the ER.

Research areas

ER chaperones

The endoplasmic reticulum (ER) is a major site for protein folding and maturation within the within the Eukaryotic cell. Proteins that reside within the ER along with proteins destined for the Golgi, plasma membrane, and extra cellular space are synthesized by ribosomes that are attached to the ER membrane. The newly translated polypeptide chain is acted upon by protein folding and post translational modification machinery that include molecular chaperones, glycosylating enzymes and oxidoreductases. The sole ER Hsp 70 chaperone, referred to as BiP, is an abundant protein that plays a major role in protein folding within this compartment. BiP action is influenced by its co-chaperones and other regulators (such as GRP170), which act to stimulate BiP activity - thereby driving protein folding.

The cooperation between chaperones and other post translational modifying enzymes ensure successful preservation of protein structure and therefore its function. We seek to understand - at the molecular level - how these processes regulate protein homeostasis, and how their aberrant function could affect cell fitness.

Unfolded protein response
The ER is the first compartment of the secretory pathway and is therefore critically important in specialized secretory cells, such as insulin鈥憄roducing β cells and antibody鈥憄roducing plasma cells. A sudden increase in the demand for secretory protein production places substantial pressure on the ER’s folding and maturation capacity, potentially leading to the accumulation of misfolded proteins. This condition, known as ER stress, is toxic to cells.
To restore homeostasis, cells activate a compensatory signaling pathway that enhances ER folding capacity to match the increased load. This pathway, termed the unfolded protein response (UPR), is mediated primarily by three transmembrane sensors: IRE1, PERK, and ATF6. These activator proteins span the ER membrane, with domains in both the ER lumen and the cytosol, enabling signal transmission between compartments. The UPR monitors misfolded proteins and coordinates both transcriptional responses in the nucleus and translational adjustments in the cytosol to rebalance ER function. Although the overall physiological framework of the UPR is well established, the precise molecular mechanisms governing signal detection and transmembrane propagation remain incompletely understood.