title: Interrogating Substrate Selectivity and Composition of Endogenous Histone Deacetylase Complexes with Chemical Probes.
abstract: Histone deacetylases (HDACs) regulate the function and activity of numerous cellular proteins by removing acetylation marks from regulatory lysine residues. We have developed peptide-based HDAC probes that contain hydroxamate amino acids of various lengths to replace modified lysine residues in the context of known acetylation sites. The interaction profiles of all human HDACs were studied with three sets of probes, which derived from different acetylation sites, and sequence context was found to have a strong impact on substrate recognition and composition of HDAC complexes. By investigating K382 acetylation of the tumor suppressor p53 as an example, we further demonstrate that the interaction profiles reflect the catalytic activities of respective HDACs. These results underline the utility of the newly established probes for deciphering not only activity, but also substrate selectivity and composition of endogenous HDAC complexes, which can hardly be achieved otherwise.
authors.affiliation: Chemische Biologie, Interfakultäres Institut für Biochemie, Universität Tübingen, Hoppe-Seyler-Strasse 4, 72076, Tübingen, Germany.
authors.forename: Alexander
authors.identifier: http://orcid.org/0000-0001-9054-8165
authors.initials: A
authors.lastname: Dose
authors.affiliation: Chemische Biologie, Interfakultäres Institut für Biochemie, Universität Tübingen, Hoppe-Seyler-Strasse 4, 72076, Tübingen, Germany.
authors.forename: Julia
authors.identifier: http://orcid.org/0000-0002-7265-8093
authors.initials: J
authors.lastname: Sindlinger
authors.affiliation: Chemische Biologie, Interfakultäres Institut für Biochemie, Universität Tübingen, Hoppe-Seyler-Strasse 4, 72076, Tübingen, Germany.
authors.forename: Jan
authors.identifier: http://orcid.org/0000-0002-7261-4744
authors.initials: J
authors.lastname: Bierlmeier
authors.affiliation: Plant Proteomics, Max-Planck-Institut für Pflanzenzüchtungsforschung, Carl-von-Linné Weg 10, 50829, Köln, Germany.
authors.forename: Ahmet
authors.initials: A
authors.lastname: Bakirbas
authors.affiliation: Molekulare Medizin, Interfakultäres Institut für Biochemie, Universität Tübingen, Hoppe-Seyler-Strasse 4, 72076, Tübingen, Germany.|Deutsches Konsortium für Translationale Krebsforschung (DKTK) und, Deutsches Krebsforschungszentrum, 69120, Heidelberg, Germany.
authors.forename: Klaus
authors.initials: K
authors.lastname: Schulze-Osthoff
authors.affiliation: Molekulare Medizin, Interfakultäres Institut für Biochemie, Universität Tübingen, Hoppe-Seyler-Strasse 4, 72076, Tübingen, Germany.
authors.forename: Stephanie
authors.initials: S
authors.lastname: Einsele-Scholz
authors.affiliation: Plant Proteomics, Max-Planck-Institut für Pflanzenzüchtungsforschung, Carl-von-Linné Weg 10, 50829, Köln, Germany.|Mass Spectrometry Facility, Max F. Perutz Laboratories (MFPL), Universität Wien, Vienna Biocenter (VBC), Dr. Bohr-Gasse 3, 1030, Wien, Austria.
authors.forename: Markus
authors.identifier: http://orcid.org/0000-0002-4970-7336
authors.initials: M
authors.lastname: Hartl
authors.affiliation: Molekulare Medizin, Interfakultäres Institut für Biochemie, Universität Tübingen, Hoppe-Seyler-Strasse 4, 72076, Tübingen, Germany.
authors.forename: Frank
authors.initials: F
authors.lastname: Essmann
authors.affiliation: Plant Proteomics, Max-Planck-Institut für Pflanzenzüchtungsforschung, Carl-von-Linné Weg 10, 50829, Köln, Germany.|Institut für Biologie und Biotechnologie, Universität Münster, Schlossplatz 7, 48149, Münster, Germany.
authors.forename: Iris
authors.identifier: http://orcid.org/0000-0002-8972-4026
authors.initials: I
authors.lastname: Finkemeier
authors.affiliation: Chemische Biologie, Interfakultäres Institut für Biochemie, Universität Tübingen, Hoppe-Seyler-Strasse 4, 72076, Tübingen, Germany. dirk.schwarzer@uni-tuebingen.de.
authors.forename: Dirk
authors.identifier: http://orcid.org/0000-0002-7477-3319
authors.initials: D
authors.lastname: Schwarzer
mesh_terms: D002460:Cell Line; D006655:Histone Deacetylases / Q000378:metabolism*; D006801:Humans; D013058:Mass Spectrometry; D015335:Molecular Probes; D013379:Substrate Specificity; D053719:Tandem Mass Spectrometry
chemical_list: D015335:Molecular Probes; D006655:Histone Deacetylases
keywords: HDAC; activity-based protein profiling; chemical probes; lysine acetylation; proteomics