Internship and thesis proposals
Computational investigation of the molecular mechanism of Ca2+-dependent allosteric activation of the EndoU ribonuclease

Domaines
Biophysics

Type of internship
Théorique, numérique
Description
EndoU is a ribonuclease (RNA-cleaving enzyme) found both in bacteria and eukaryotes, including humans. Its activity is regulated, in eukaryotes, by Ca2+ ions. Recently, S. Campagne’s experimental team in Bordeaux used a combination of several biochemical experiments to suggest a molecular mechanism for this Ca2+ triggered activation. They evidenced a change in EndoU conformation upon Ca2+ binding and identified several binding sites for Ca2+, whose importance was confirmed by mutation experiments. These experiments thus suggest a Ca2+-dependent allosteric activation of EndoU, but the molecular mechanism allowing for signal communication between the catalytic site and distant Ca2+ binding sites remains to be fully characterized. To goal of the project is to uncover the molecular details of this Ca2+-activated allosteric behavior, using molecular simulations. Specific strategies to characterize the Ca2+-induced rearrangement pathways will be implemented and combined with state-of-the-art force fields for ions. Given the high flexibility of the EndoU-RNA complex, enhanced sampling techniques will also be used to properly characterize the conformational ensemble of the complex in different conditions.

Contact
Elise Duboué-Dijon
Laboratory : LBT - UPR9080
Team : Laboratoire de Biochimie Théorique
Team Website
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