Journal:MicroPubl Biol:000763

Quaternary structure analysis of IRE1

Samirul Bashir, Debnath Pal, Ozaira Qadri, Mariam Banday, and Khalid Majid Fazili ^[1]

Molecular Tour
IRE1, a sensor protein found in the endoplasmic reticulum (ER) of eukaryotic cells. IRE1 is involved in the Unfolded Protein Response (UPR), a cellular stress response pathway that helps cells cope with the stress caused by the accumulation of unfolded proteins in the ER. Structurally IRE1 has a sensory N-terminal domain towards the ER lumen, a C-terminal catalytic domain towards the cytosol, and a linker region connecting the two domains. The activation of IRE1 requires dimerization/oligomerization in the lumenal domain, which functionally activates the catalytic C-terminal domain. The quaternary structure of IRE1 lumenal dimer was deduced from the crystal structure published earlier, which suggested that a large stable interface is formed through a beta-sheet spreading across the dimer subunits. However, there are two problems with this form of the quaternary structure. First, the presence of a strong interface implies that a large activation and deactivation energy may be needed to alter the monomer-dimer equilibrium, which may not be adequate for a sensor protein. Second, the end-to-end distance of the C-termini of the lumenal domain between two monomers is 62.8 Å, which requires a cytoplasmic domain with same distance. However, this structure does not fit well with experimental data.

To address these issues, we present an alternative quaternary structural model for dimerization of IRE1 lumenal domain. In this model, the lumenal domain dimer has a side-by-side orientation, which is less stable than the previous model and has a shorter distance of 42.8 Å. A corresponding C-terminal domain that matches it, has a N-terminal separation of 41.7 Å, which has been suggested to be the correct dimerization state of the IRE1 C-terminal domain. In our model, the dimer form of the lumenal domain is less stable with an interface area of 1130 Å and theoretical interaction and dissociation free energy values of -12.3 and 0.3 kcal/mol, respectively. On the other hand, other quaternary structure of IRE1 is more stable, with an interface area of 1730 Å and theoretical interaction and dissociation free energy values of -15.2 and 7.2 kcal/mol, respectively. The dimer form, however, still has a reasonably large interface area and low dissociation free energy, which means it can easily switch between a monomer and dimer state. Additionally, the lumenal-C-terminal domain separation of approximately 40 Å is more likely to stabilize the full IRE1 protein in its functional form.

Furthermore, the head-tail dimer is stabilized by enthalpic contributions from 7 hydrogen bonds and 3 salt bridges. In contrast, the side-by-side dimer is stabilized by entropic forces from 33 hydrogen bonds and 32 salt bridges, giving it a positive interaction free energy. This suggests that the stability of the side-by-side dimer is highly dependent on its immediate environment. The head-tail dimer, on the other hand, is more stable due to enthalpic contributions and requires more energy to switch its dimerization state. The side-by-side dimer is better suited to act as a sensor protein. Overall, our model of the IRE1 lumenal dimer is consistent with the potential side-by-side orientation of the cytoplasmic dimer.

References

1. ↑ doi: https://dx.doi.org/10.17912/micropub.biology.000763