Centre for Biological Signalling Studies

Mix and Match: How Signalling Molecules recognize their Partners

Researchers develop a new method that allows them to understand how phosphatase enzymes distinguish their substrates

The phosphatases PP1 and PP2A play key roles in the regulation of essential biological processes such as heartbeat, learning, and cell division. Dysregulation of these enzymes contributes to the development and progression of many diseases, such as cancer and heart failure. A research team headed by Prof. Maja Köhn from the Clusters of Excellence for biological signalling studies BIOSS and CIBSS at the University of Freiburg, together with collaborators from the European Molecular Biology Laboratory (EMBL) Heidelberg and the Technical University Munich (TUM), has developed a new mass spectrometry-based method that sheds light on the complex biological mechanisms controlling phosphatase activity. This method, which has now been published in the journal Nature Communications, will also be broadly applicable to investigate the regulation of other types of enzymes.


Phosphatases and Kinases: an uneven balance

Through a process called dephosphorylation, phosphatases remove phosphate groups from proteins. Through the opposite process of phosphorylation, another type of enzymes, so-called kinases, attach phosphate groups. Phosphate groups act as molecular switches for the control of cellular signalling processes. Intriguingly, nature has developed completely different solutions to the same problem of substrate recognition on the kinase and phosphatase side: While hundreds of individually regulated kinases exist in our cells that each phosphorylate only specific proteins, few phosphatases are there to counteract them. This raises the question how the selective dephosphorylation of so many different proteins can be accurately controlled by the cell. Researchers already knew that additional regulatory proteins seem to be the key to the problem. Nevertheless, the role of the phosphatases’ structure and its binding to the substrate has long been under debate.


A multi-layered system

PP1 and PP2A selectively remove phosphate groups from the amino acids serine and threonine – certain building blocks of proteins. With their newly developed mass spectrometry-based method, the researchers found that the binding preferences of PP1 and PP2A differ and influence their specificity to certain proteins. “We have now developed an approach to synthesize thousands of different amino acid combinations in a single reaction tube,” Maja Köhn explains the process. “We can then test whether PP1 or PP2A phosphatase recognize these substrates.” The researchers found that both enzymes differ in which amino acid sequences they recognize. They then confirmed the biological relevance of these observations: The results reveal a multi-layered system for dephosphorylation reactions in basic cellular processes, with binding specificity being one of several regulatory mechanisms. “This will help to explain erroneous dephosphorylation reactions in diseases such as heart failure, Alzheimer’s and cancer, allowing for new drug discovery strategies.” Köhn says.


Correspondence: Prof. Maja Köhn (


Original study:

Hoermann et al. (2020): Dissecting the sequence determinants for dephosphorylation by the catalytic subunits of phosphatases PP1 and PP2A. In: Nature Communications. DOI: 10.1038/s41467-020-17334-x