In all eukaryotes, the Unfolded Protein Response (UPR) is a molecular program that maintains the protein folding homeostasis in the endoplasmic reticulum (ER). The UPR plays a crucial role in health and disease. Stress sensors proteins on the ER membrane activate the UPR. The evolutionary most conserved sensor is the protein IRE1, which activates the UPR by forming dimers and larger assemblies. In particular, IRE1's luminal domain (LD) interacts with unfolded proteins and these interactions promote oligomerization by an unresolved mechanism. The direct binding mode of peptides is still not understood.
My work aims to elucidate the structure and assembly mechanism of large supramolecular assemblies of human IRE1 and probe its binding to unfolded proteins. These events are crucial for IRE1's functions but are not yet understood.
We employed a multiscale approach, performing atomistic and coarse-grained (CG) molecular dynamic (MD) simulations.
For investigating the formation of clusters of dimers of IRE1, we used the coarse-grained Martini 3 force field. We obtained encouraging results: hIRE cLD dimers can form clusters where contacts are mediated by disordered regions.
Peptide binding experiments, in atomistic and CG, were successful and led us to propose a new model for the direct binding of peptides and unfolded proteins.
Further analysis will be needed to extrapolate relevant dimer-dimer conformations from our simulations and to assess the effect of peptides on the dynamics of hIRE1 cLD dimer.