Researchers Uncover Complex Substrate Profile for Enzyme Action

The γ-secretase enzyme can cleave more than 150 membrane proteins. These include the amyloid precursor protein, which produces deposits linked to Alzheimer’s disease, and the Notch1 protein, which is involved in cell communication and cancer development.

Until recently, the mechanism by which γ-secretase recognizes its target proteins was unclear. Unlike many other proteases, γ-secretase does not identify substrates based on specific amino acid sequences.

An interdisciplinary team from LMU's Biomedical Center, the Technical University of Munich (TUM), and the German Center for Neurodegenerative Diseases (DZNE) has now clarified aspects of this process.

The researchers found that the enzyme’s substrates share a complex physicochemical profile, which plays a key role in their recognition and cleavage.

New Technique Makes Hidden Features Visible

To investigate this, the scientists developed a method called Comparative Physicochemical Profiling (CPP). This technique compares the physicochemical features of known substrates to those of reference proteins. It helps identify distinct patterns that characterize γ-secretase targets.

They also used explainable artificial intelligence (XAI) to highlight the properties of γ-secretase substrates.

The substrates of γ-secretase possess a specific physicochemical profile, which spans the entire transmembrane domain and adjacent sequence regions.

Harald Steiner, Study Lead and Professor, Ludwig Maximilian University of Munich

The analysis showed that, near the cleavage site, substrates can shift from a helical structure to a more extended shape. This finding is supported by experimental data from enzyme-substrate complexes.

We wanted to understand what actually defines a substrate, and not just generate a black-box prediction. The use of explainable AI has given us precisely this transparency.

Dr. Stephan Breimann, Study Lead Author and Associate Professor, Technical University of Munich

Perspectives for Research and Application

Using CPP, the researchers identified several previously unknown substrates of γ-secretase. Some of these proteins are involved in immune regulation and cancer-related processes.

The researchers believe that their approach has broader applications beyond γ-secretase.

“We see a new approach in here for also decoding the interplay of sequence, structure, and function in other proteases—or, say, in receptors,” explained Steiner.

In the future, these insights could support the development of targeted therapies. This may include small-molecule drugs, peptides, or antibodies designed with greater specificity.

Over time, the findings may contribute to creating more precise therapeutic agents for a variety of diseases.