Chemistry Seminar with Dr. Alireza Ghanbarpour from WashU at 4:00pm

Join us on October 17th for Dr. Ghanbarpour's seminar, titled "Decoding the Secrets of AAA+ Protease Specificity"

From bacteria to humans, intracellular degradation is mainly mediated by ATP-dependent AAA+ proteases, including ClpXP and FtsH, which degrade abnormal proteins and reshape the proteome as cells respond to environmental stress or attacks by pathogens(1, 2). Selective degradation depends on initial protease recognition of an unstructured degron sequence, typically at a terminus of a target protein, followed by ATP-powered unfolding of any native structure proximal to the degron and processive translocation of the unfolded polypeptide into a sequestered proteolysis chamber (3, 4). As degradation is irreversible, rigorous regulation is essential to avoid unintended proteolysis. Achieving such precision in a crowded cell is no small feat. How do AAA+ proteases achieve a high level of specificity but adapt their activities in response to environmental or developmental needs? Part of the answer is accessory adaptor proteins, which selectively facilitate or inhibit substrate recognition, but how adaptors function is poorly understood. My research investigates substrate specificity and adaptor function for two AAA+ proteases: membrane-bound FtsH, with special roles in membrane-protein degradation, and ClpXP, a cytoplasmic enzyme, employing a multidisciplinary approach that combines structural biology, in vitro reconstitution, biochemistry, and cellular assays. I will discuss cryo-EM structures and experiments that show that the conformation of the axial channel of ClpX is one determinant of substrate specificity(2, 5), that reveal how an adaptor protein delivers a substrate to ClpX axial channel to enhance specificity (2), and that uncover a large complex of FtsH with additional membrane proteins that form a nautilus-like structure around the protease(6), suggesting a novel model for substrate selection by membrane anchored AAA proteases.

1. A. Ghanbarpour, X. Fei, T. A. Baker, J. H. Davis, R. T. Sauer, The SspB adaptor drives structural changes in the AAA+ ClpXP protease during ssrA-tagged substrate delivery. Proceedings of the National Academy of Sciences 120, e2219044120 (2023).

2. A. Ghanbarpour et al., A closed translocation channel in the substrate-free AAA+ ClpXP protease diminishes rogue degradation. Nature Communications 14, 7281 (2023).

3. T. A. Baker, R. T. Sauer, ClpXP, an ATP-powered unfolding and protein-degradation machine. Biochimica et Biophysica Acta (BBA) - Molecular Cell Research 1823, 15-28 (2012).

4. S. A. Mahmoud, P. Chien, Regulated Proteolysis in Bacteria. Annual Review of Biochemistry 87, 677-696 (2018).

5. A. Ghanbarpour, R. T. Sauer, J. H. Davis, A proteolytic AAA+ machine poised to unfold a protein substrate. bioRxiv, 2023.2012.2014.571662 (2023).

6. A. Ghanbarpour et al., An asymmetric nautilus-like HflK/C assembly controls FtsH proteolysis of membrane proteins. bioRxiv, 2024.2008.2009.604662 (2024