Engineering Af1521 improves ADP-ribose binding and identification of ADP-ribosylated proteins

Kathrin Nowak, Florian Rosenthal, Tobias Karlberg, Mareike Bütepage, Ann-Gerd Thorsell, Birgit Dreier, Jonas Grossmann, Jens Sobek, Ralph Imhof, Bernhard Lüscher, Herwig Schüler, Andreas Plückthun, Deena M. Leslie Pedrioli and Michael O. Hottiger ()
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Kathrin Nowak: University of Zurich
Florian Rosenthal: University of Zurich
Tobias Karlberg: Karolinska Institute
Mareike Bütepage: RWTH Aachen University
Ann-Gerd Thorsell: Karolinska Institute
Birgit Dreier: University of Zurich
Jonas Grossmann: Functional Genomics Center Zurich, ETH Zurich and University of Zurich
Jens Sobek: Functional Genomics Center Zurich, ETH Zurich and University of Zurich
Ralph Imhof: University of Zurich
Bernhard Lüscher: RWTH Aachen University
Herwig Schüler: Karolinska Institute
Andreas Plückthun: University of Zurich
Deena M. Leslie Pedrioli: University of Zurich
Michael O. Hottiger: University of Zurich

Nature Communications, 2020, vol. 11, issue 1, 1-14

Abstract: Abstract Protein ADP-ribosylation is a reversible post-translational modification that regulates important cellular functions. The identification of modified proteins has proven challenging and has mainly been achieved via enrichment methodologies. Random mutagenesis was used here to develop an engineered Af1521 ADP-ribose binding macro domain protein with 1000-fold increased affinity towards ADP-ribose. The crystal structure reveals that two point mutations K35E and Y145R form a salt bridge within the ADP-ribose binding domain. This forces the proximal ribose to rotate within the binding pocket and, as a consequence, improves engineered Af1521 ADPr-binding affinity. Its use in our proteomic ADP-ribosylome workflow increases the ADP-ribosylated protein identification rates and yields greater ADP-ribosylome coverage. Furthermore, generation of an engineered Af1521 Fc fusion protein confirms the improved detection of cellular ADP-ribosylation by immunoblot and immunofluorescence. Thus, this engineered isoform of Af1521 can also serve as a valuable tool for the analysis of cellular ADP-ribosylation under in vivo conditions.

Date: 2020
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DOI: 10.1038/s41467-020-18981-w

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