Active site geometry stabilization of a presenilin homolog by the lipid bilayer promotes intramembrane proteolysis
- German Center for Neurodegenerative Diseases, Germany
- Technical University of Munich, Germany
- Osaka Medical and Pharmaceutical University, Japan
- Helmholtz Zentrum München, Germany
- Ludwig-Maximilians-Universität München, Germany
Abstract
Cleavage of membrane proteins in the lipid bilayer by intramembrane proteases is crucial for health and disease. Although different lipid environments can potently modulate their activity, how this is linked to their structural dynamics is unclear. Here we show that the carboxy-peptidase-like activity of the archaeal intramembrane protease PSH, a homolog of the Alzheimer's disease-associated presenilin/γ-secretase is impaired in micelles and promoted in a lipid bilayer. Comparative molecular dynamics simulations revealed that important elements for substrate binding such as transmembrane domain 6a of PSH are more labile in micelles and stabilized in the lipid bilayer. Moreover, consistent with an enhanced interaction of PSH with a transition-state analog inhibitor, the bilayer promoted the formation of the enzyme´s catalytic active site geometry. Our data indicate that the lipid environment of an intramembrane protease plays a critical role in structural stabilization and active site arrangement of the enzyme-substrate complex thereby promoting intramembrane proteolysis.
Data availability
For all figures the source data are provided in the respective source data files. The coordinate and trajectory files of all simulations can be accessed at Zenodo: https://doi.org/10.5281/zenodo.6487373
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Recognition of the amyloid precursor protein by human γ-secretaseRCSB Protein Data Bank, 6IYC.
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Structure of a presenilin family intramembrane aspartate proteaseRCSB Protein Data Bank, 4HYG.
Article and author information
Author details
Funding
Deutsche Forschungsgemeinschaft (263531414 / FOR2290)
- Martin Zacharias
- Harald Steiner
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Reviewing Editor
- M Joanne Lemieux, University of Alberta, Canada
Version history
- Received: December 3, 2021
- Preprint posted: January 10, 2022 (view preprint)
- Accepted: May 16, 2022
- Accepted Manuscript published: May 17, 2022 (version 1)
- Version of Record published: July 14, 2022 (version 2)
Copyright
© 2022, Feilen et al.
This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.
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Active site geometry stabilization of a presenilin homolog by the lipid bilayer promotes intramembrane proteolysis
eLife 11:e76090.
https://doi.org/10.7554/eLife.76090
Further reading
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Numerous lipids are heterogeneously distributed among organelles. Most lipid trafficking between organelles is achieved by a group of lipid transfer proteins (LTPs) that carry lipids using their hydrophobic cavities. The human genome encodes many intracellular LTPs responsible for lipid trafficking and the function of many LTPs in defining cellular lipid levels and distributions is unclear. Here, we created a gene knockout library targeting 90 intracellular LTPs and performed whole-cell lipidomics analysis. This analysis confirmed known lipid disturbances and identified new ones caused by the loss of LTPs. Among these, we found major sphingolipid imbalances in ORP9 and ORP11 knockout cells, two proteins of previously unknown function in sphingolipid metabolism. ORP9 and ORP11 form a heterodimer to localize at the ER-trans-Golgi membrane contact sites, where the dimer exchanges phosphatidylserine (PS) for phosphatidylinositol-4-phosphate (PI(4)P) between the two organelles. Consequently, loss of either protein causes phospholipid imbalances in the Golgi apparatus that result in lowered sphingomyelin synthesis at this organelle. Overall, our LTP knockout library toolbox identifies various proteins in control of cellular lipid levels, including the ORP9-ORP11 heterodimer, which exchanges PS and PI(4)P at the ER-Golgi membrane contact site as a critical step in sphingomyelin synthesis in the Golgi apparatus.
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- Biochemistry and Chemical Biology
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