Active site geometry stabilization of a presenilin homolog by the lipid bilayer promotes intramembrane proteolysis

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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

The following previously published data sets were used

1. Zhou
2. R
3. Yang
4. G
5. Guo
6. X
7. Zhou
8. Q
9. Lei
10. J
11. Shi
12. Y
(2019) Recognition of the amyloid precursor protein by human γ-secretase
RCSB Protein Data Bank, 6IYC.

https://www.rcsb.org/structure/6IYC
1. Li
2. X
3. Dang
4. S
5. Yan
6. C
7. Gong
8. X
9. Wang
10. J
11. Shi
12. Y
(2013) Structure of a presenilin family intramembrane aspartate protease
RCSB Protein Data Bank, 4HYG.

https://www.rcsb.org/structure/4HYG

Article and author information

Author details

Lukas P Feilen

German Center for Neurodegenerative Diseases, Munich, Germany

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0001-8221-6742
Shu-Yu Chen

Physics Department T38, Technical University of Munich, Garching, Germany

Competing interests
The authors declare that no competing interests exist.
Akio Fukumori

Department of Pharmacotherapeutics II, Osaka Medical and Pharmaceutical University, Takatsuki, Japan

Competing interests
The authors declare that no competing interests exist.
Regina Feederle

Institute for Diabetes and Obesity, Helmholtz Zentrum München, Munich, Germany

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0002-3981-367X
Martin Zacharias

Physics Department T38, Technical University of Munich, Garching, Germany

Competing interests
The authors declare that no competing interests exist.
Harald Steiner

Biomedical Center (BMC), Ludwig-Maximilians-Universität München, Munich, Germany

For correspondence
harald.steiner@med.uni-muenchen.de

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0003-3935-0318

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.

Copyright

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.