Intramembrane proteases recognize and cleave their substrates within the plane of the membrane. By this these unusual proteases influence a large number of important biological functions and are involved in the development of various serious diseases, such as Alzheimer's disease, virus infections and immunodeficiencies. Despite more than a decade of research, we do neither know the full repertoire of intramembrane protease substrates, nor the molecular prerequisites that qualify a substrate as such. It is therefore largely unclear what structurally differentiates substrates from non-substrates. On the one hand, the known substrates exhibit a tremendous diversity of primary structures. On the other hand, only a fraction of single-span proteins is known as substrates and point mutations within them can strongly interfere with their proteolysis. This puzzling discrepancy between seemingly promiscuous and clearly sequence-specific proteolysis of substrates indicates that the latter share structural features that allow for specific recognition and cleavage by a given protease.

Together we pursue an interdisciplinary approach that
i) aims to identify previously unknown substrates for the different types of intramembrane proteases and
ii) shows, for some exemplary cases, how proteolysis is linked to the substrate / enzyme interaction and to the structural and conformational flexibility of the transmembrane helices.
 
The Chair of Biochemistry and Molecular Biology is involved in this joint project with the sub-project "Substrate recognition and processing by Signal Peptide Peptidase-like 2 (SPPL2) family”.
The aim of this sub-project is the identification and validation of new substrates for the family of SPPL2 proteases which belong to the class of intramembrane aspartyl proteases. Furthermore, we use mass spectrometry to analyze the cleavage sites of the SPPL2 protease in known and new substrates and investigate the exact cleavage mechanism.
Initial results suggest a multi-step cleavage mechanism for substrate processing by SPPL2 proteases. An intramembrane protease apparently achieves substrate/non-substrate discrimination at several levels. Determining the role of soluble and transmembrane domains at these different levels is the mission of this proposal.