IFIB – Interfakultäres Institut für Biochemie

Publications

2019

Seidel J., Meisinger T., Sindlinger J., Pieloch P., Finkemeier I., Schwarzer D.: Peptide-based 2-aminophenylamide probes for targeting endogenous class I HDAC complexes. Chembiochem (2019); Epub ahead of print

2018

Hagmann V., Sommer S., Fabian P., Bierlmeier J., van Treel N., Mootz H. D., Schwarzer D., Azevedo J. E., Dodt G.: Chemically monoubiquitinated PEX5 binds to the components of the peroxisomal docking and export machinery. Sci. Rep. 8 (2018); 16014

Ernst C., Heidrich J., Sessler C, Sindlinger J., Schwarzer D., Koch P., and Boeckler F. M.: Switching Between Bicyclic and Linear Peptides - The Sulfhydryl-Specific Linker TPSMB Enables Reversible Cyclization of Peptides. Front. Chem. 6 (2018); 484

Ernst C., Sindlinger J., Schwarzer D., Koch P., and Boeckler F. M.: The Symmetric Tetravalent Sulfhydryl-Specific Linker NATBA Facilitates a Combinatorial “Tool Kit” Strategy for Phage Display-Based Selection of Functionalized Bicyclic Peptides. ACS Omega 3 (2018); 12361-12368

Fischle W., Schwarzer D.: Chemistry meets epigenetics: from chromatin tools to small molecules affecting the readout of our genomes. Curr. Opin. Chem. Biol. 45 (2018); vii-ix

Koskela M. M., Brünje A., Ivanauskaite A., Grabsztunowicz M., Lassowskat I., Neumann U., Dinh T. V., Sindlinger J., Schwarzer D., Wirtz M., Tyystjärvi E., Finkemeier I., Mulo P.: Chloroplast Acetyltransferase NSI Is Required for State Transitions in Arabidopsis thaliana. Plant Cell 30 (2018); 1695-1709

Füßl M., Lassowskat I., Née G., Koskela M. M., Brünje A., Tilak P., Giese J., Leister D., Mulo P., Schwarzer D., Finkemeier I.: Beyond Histones: New Substrate Proteins of Lysine Deacetylases in Arabidopsis Nuclei. Front. Plant Sci. 9 (2018); 461

2017

Hartl M., Füßl M., Boersema P. J., Jost J.-O., Kramer K., Bakirbas A., Sindlinger J., Plöchinger M., Leister D., Uhrig G., Moorhead G. G. B., Cox J., Salvucci M. E., Schwarzer D., Mann M., Finkemeier I.: Lysine acetylome profiling uncovers novel histone deacetylase substrate proteins in Arabidopsis. Mol. Syst. Biol. 13 (2017); 949

Schmohl L., Bierlmeier J., von Kügelgen N., Kurz L., Reis P., Barthels F., Mach P., Schutkowski M., Freund C., Schwarzer D.: Identification of sortase substrates by specificity profiling. Bioorg Med Chem. 25 (2017); 5002-5007

Schmohl L., Bierlmeier J., Gerth F., Freund C., Schwarzer D.: Engineering sortase A by screening a second-generation library using phage display. J Pept Sci. 23 (2017); 631-635

2016

Liokatis S., Klingberg R., Tan S., Schwarzer D.: Differentially Isotope-Labeled Nucleosomes to Study Asymmetric Histone Modification Crosstalk by Time-Resolved NMR Spectroscopy. Angew Chem Int Ed Engl. 55 (2016); 8262-5

Hiragami-Hamada K., Soeroes S., Nikolov M., Wilkins B., Kreuz S., Chen C., De La Rosa-Velázquez I.A., Zenn H.M., Kost N., Pohl W., Chernev A., Schwarzer D., Jenuwein T., Lorincz M., Zimmermann B., Walla P.J., Neumann H., Baubec T., Urlaub H., Fischle W.: Dynamic and flexible H3K9me3 bridging via HP1b dimerization establishes a plastic state of condensed chromatin. Nat Commun. 7 (2016); 11310

Sindlinger J., Bierlmeier J., Geiger L.C., Kramer K., Finkemeier I., Schwarzer D.: Probing the structure-activity relationship of endogenous histone deacetylase complexes with immobilized peptide-inhibitors. J Pept Sci. 22 (2016); 352-9

Fischle W., Schwarzer D.: Probing Chromatin-modifying Enzymes with Chemical Tools. ACS Chemical Biology 11 (2016) 689-705; review

Stützer A., Liokatis S., Kiesel A., Schwarzer D., Sprangers R., Söding J., Selenko P., Fischle W.: Modulations of DNA Contacts by Linker Histones and Post-translational Modifications Determine the Mobility and Modifiybility of Nucleosomal H3 Tails. Molecular Cell 61 (2016) 247–259

Seidel J., Klockenbusch C., Schwarzer D.: Investigating deformylase and deacylase activity of mammalian and bacterial sirtuins. Chembiochem 17 (2016) 398-402

Dose A., Sindlinger J., Bierlmeier J., Bakirbas A., Schulze-Osthoff K., Einsele-Scholz S., Hartl M., Essmann F., Finkemeier I., Schwarzer D.: Interrogating Substrate Selectivity and Comaprison of Endogenous Histone Deacetylase Complexes with Chemical Probes. Angew Chem Int Ed Engl. 55 (2016) 1192-1195

2015

Fischle W., Mootz H., Schwarzer D.: Synthetic histone code. Curr Opin Chem Biol. 28 (2015) 131-140; Review

Jost O., Hanswillemenke A., Schwarzer D.: A miniaturized readout strategy for endogenous histone deacetylase activity. Mol Biosyst. 11 (2015) 1820-1823

Thongwichian R., Kosten J., Benary U., Rose H.M., Stuiver M., Theillet F.X., Dose A., Koch B., Yokoyama H., Schwarzer D., Wolf J., Selenko P.: A Multiplexed NMR-Reporter Approach to Measure Cellular Kinase and Phosphatase Activities in Real-Time. J Am Chem Soc. 137 (2015) 6468-6471

Fischle W., Schwarzer D., Mootz H.D.: Chemical biology: Chromatin chemistry goes cellular. Nat Chem. 5 (2015) 371-373; Review

Schmohl L., Wagner F. R., Schümann M., Krause E., Schwarzer D.: Semisynthesis and Initial Characterization of Sortase A Mutants Containing Selenocysteine and Homocysteine. Bioorg. Med Chem. 15 (2015) 2883-2889

Klingberg R., Jost J.O., Schümann M., Gelato K.A., Fischle W., Krause E., Schwarzer D.: Analysis of phosphorylation-dependent protein-protein interactions of histone H3. ACS Chem Biol. 10 (2015) 138-145

2014

Schmohl L., Schwarzer D.: Sortase-mediated ligations for the site-specific modification of proteins. Curr Opin Chem Biol. 22 (2014) 122-128; Review

Abel S., Geltinger B., Heinrich N., Michl D., Klose A., Beyermann M., Schwarzer D.: Semisynthesis and optimization of G protein-coupled receptor mimics. J Pept Sci. 20 (2014) 831-836

Gelato K.A., Tauber M., Ong M.S., Winter S., Hiragami-Hamada K., Sindlinger J., Lemak A., Bultsma Y., Houliston S., Schwarzer D., Divecha N., Arrowsmith C.H., Fischle W.: Accessibility of Different Histone H3-Binding Domains of UHRF1 Is Allosterically Regulated by Phosphatidylinositol 5-Phosphate. Mol Cell. 54 (2014) 905-919

Schmohl L., Schwarzer D.: Chemo-enzymatic three-fragment assembly of semisynthetic proteins. J Pept Sci. 20 (2014) 145-151

2013

Lang D., Schümann M., Gelato K., Fischle W., Schwarzer D., Krause E.: Probing the acetylation code of histone H4. Proteomics 13 (2013) 2989-2997

Teschke T., Geltinger B., Dose A., Freund C., Schwarzer D.: Probing the recognition of post-translational modifications by combining sortase-mediated ligation and phage-assisted selection. ACS Chem Biol. 8 (2013) 1692-1697

Finkemeier I., Schwarzer D.: Lysin-Acetylierung: eine altbekannte Proteinmodifikation in neuem Licht. BIOspektrum. 7 (2013) 810–812; Review

2012

Dose A., Jost J.O., Spieß A.C., Henklein P., Beyermann M., Schwarzer D.: Facile synthesis of colorimetric histone deacetylase substrates. Chem Commun. 48 (2012) 9525-9527

Munari F., Soeroes S., Zenn H.M., Schomburg A., Kost N., Schroeder S., Klingberg R., Rezaei-Ghaleh N., Stuetzer A., Gelato K.A., Walla P.J., Becker S., Schwarzer D., Zimmermann B., Fischle W., Zweckstetter M.: Methylation of K9 in histone H3 directs alternative modes of highly dynamic interaction of heterochromatin protein hHP1β with the nucleosome. J Biol Chem. 287 (2012) 33756-33765

Liokatis S., Stützer A., Elsässer S.J., Theillet F.-X., Klingberg R., van Rossum B., Schwarzer D., Allis C.D., Fischle W., Selenko P.: Phosphorylation of histone H3 Ser10 establishes a hierarchy for subsequent intramolecular modification events. Nat Struct Mol Biol. 19 (2012) 819-823

Bekei B., Rose H.M., Herzig M., Dose A., Schwarzer D., Selenko P.: In-cell NMR in Mammalian cells: part 1. Methods Mol Biol. 895 (2012) 43-54

Schwarzer D.: Die Chemische Biologie beschreitet neue Wege in der Chromatinforschung. BIOspektrum. 3 (2012) 248–250; Review

Theillet F.X., Liokatis S., Jost J.O., Bekei B., Rose H.M., Binolfi A., Schwarzer D., Selenko P.: Site-specific mapping and time-resolved monitoring of lysine methylation by high-resolution NMR spectroscopy. J Am Chem Soc. 134 (2012) 7616-7619

Lebrun P., Raze D., Fritzinger B., Wieruszeski J.M., Biet F., Dose A., Carpentier M., Schwarzer D., Allain F., Lippens G., Locht C.: Differential contribution of the repeats to heparin binding of HBHA, a major adhesin of Mycobacterium tuberculosis. PLoS One. 7 (2012) e32421

Broncel M., Krause E., Schwarzer D., Hackenberger C.P.: The Alzheimer's Disease Related Tau Protein as a New Target for Chemical Protein Engineering. Chemistry. 18 (2012) 2488-2492

Schwarzer D., Ludwig C., Thiel I.V., Mootz H.D.: Probing intein-catalyzed thioester formation by unnatural amino acid substitutions in the active site. Biochemistry. 51 (2012) 233-242

Seeliger D., Soeroes S., Klingberg R., Schwarzer D., Grubmüller H., Fischle W.: Quantitative Assessment of Protein Interaction with Methyl-Lysine Analogues by Hybrid Computational and Experimental Approaches. ACS Chem Biol. 7 (2012) 150-154

2011

Piotukh K., Geltinger B., Heinrich N., Gerth F., Beyermann M., Freund C., Schwarzer D.: Directed evolution of sortase A mutants with altered substrate selectivity profiles. J Am Chem Soc. 133 (2011) 17536-17539

Stojic L., Jasencakova Z., Prezioso C., Stutzer A., Bodega B., Pasini D., Klingberg R., Mozzetta C., Margueron R., Puri P.L., Schwarzer D., Helin K., Fischle W., Orlando V.: Chromatin regulated interchange between polycomb repressive complex 2 (PRC2)-Ezh2 and PRC2-Ezh1 complexes controls myogenin activation in skeletal muscle cells. Epigenetics Chromatin. 4 (2011) 16

Dose A., Liokatis S., Theillet F.X., Selenko P., Schwarzer D.: NMR profiling of histone deacetylase and acetyl-transferase activities in real time. ACS Chem Biol. 20 (2011) 419-424

2010

Tsai W.W., Wang Z., Yiu T.T., Akdemir K.C., Xia W., Winter S., Tsai C.Y., Shi X., Schwarzer D., Plunkett W., Aronow B., Gozani O., Fischle W., Hung M.C., Patel D.J, Barton M.C.: TRIM24 links a noncanonical histone signature to breast cancer. Nature. 468 (2010) 927-932

Liokatis S., Dose A., Schwarzer D., Selenko P.: Simultaneous Detection of Protein Phosphorylation and Acetylation by High-Resolution NMR Spectroscopy. J Am Chem Soc. 132 (2010) 14704-14705

Schwarzer D.: Chemical tools in chromatin research. J Pept Sci. 16 (2010) 530–537; Review

Hackenberger C.P.R., Arndt H.D., Schwarzer D.: Semisynthese: Werkzeug für die Chemische Biologie. Chemie in Unserer Zeit. 44 (2010) 198-206; Review

Arndt H.D, Hackenberger C.P.R., Schwarzer D.: Semisynthese: Chemie mit den Molekülen der Natur. Chemie in Unserer Zeit. 44 (2010) 130-137; Review

2009

Ludwig C., Schwarzer D., Zettler J., Garbe D., Janning P., Czeslik C., Mootz H.D.: Semisynthesis of proteins using split inteins. Methods Enzymol. 462 (2009) 77-96; Review

Schwarzer D.: Hacking the genetic code of mammalian cells. Chembiochem. 10 (2009) 1602-1604; Review

2008

Hackenberger C.P.R., Schwarzer D.: Chemoselective Ligation and Modification Strategies for Peptides and Proteins. Angew Chem Int Ed. 47 (2008) 10030-10074; Review

Ludwig C., Schwarzer D., Mootz H.D.: Interaction studies and alanine scanning analysis of a semi-synthetic split intein reveal thiazoline ring formation from an intermediate of the protein splicing reaction. J Biol Chem. 283 (2008) 25264-25272

2007

Mootz H.D., Schwarzer D.: Biochemie und Molekular Biologie 2006. Nachrichten aus der Chemie. 55 (2007) 276-279; Review

2006

Schwarzer D., Zhang Z., Zheng W., Cole P.A.: Negative Regulation of a Protein Tyrosine Phosphatase by Tyrosine Phosphorylation. J Am Chem Soc. 128 (2006) 4192-4193

2005

Schwarzer D., Cole P.A.: Protein semisynthesis and expressed protein ligation: chasing a protein's tail. Curr Opin Chem Biol. 9 (2005) 561-569; Review

Shen K., Hines A.C., Schwarzer D., Pickin K.A., Cole P.A.: Protein kinase structure and function analysis with chemical tools. Biochim Biophys Acta. Proteins and Proteomics. 1754 (2005) 65-78; Review

Zheng W., Schwarzer D., Lebeau A., Weller J.L., Klein D.C., Cole P.A.: Cellular stability of serotonin N-acetyltransferase conferred by phosphonodifluoromethylene alanine (Pfa) substitution for Ser-205. J Biol Chem. 280 (2005) 10462-10467

2004

Linne U., Schwarzer D., Schroeder G., Marahiel M.A.: Mutational analysis of a type II thioesterase associated with nonribosomal peptide synthesis. Eur J Biochem. 271 (2004) 1536-1545

2003

Richardt A., Kemme T., Wagner S., Schwarzer D., Marahiel M.A., Hovemann B.T.: Ebony: a novel nonribosomal peptide synthetase for beta-alanine conjugation with biogenic amines in Drosophila. J Biol Chem. 278 (2003) 41160-41166

Schwarzer D., Finking R., Marahiel M.A.: Nonribosomal Peptides: From Genes to Products. Nat Prod Rep. 20 (2003) 275-287; Review

2002

Schwarzer D., Mootz H.D., Linne U., Marahiel M.A.: Regeneration of misprimed nonribosomal peptide synthetases by type II thioesterases. Proc Natl Acad Sci. U.S.A. 99 (2002) 14083-14089

Mootz H.D., Kessler N., Linne U., Eppelmann K., Schwarzer D., Marahiel M.A.: Decreasing the ring-size of a nonribosomal peptide antibiotic by in frame module deletion in the biosynthetic genes. J Am Chem Soc. 124 (2002) 10980-10981

Mootz H.D., Schwarzer D., Marahiel M.A.: Ways of assembling complex natural products on modular nonribosomal peptide synthetases. ChemBioChem. 3 (2002) 490-504; Review

Bruner S.D., Weber T., Kohli R.M., Schwarzer D., Marahiel M.A., Walsh C.T., Stubbs M.T.: Structural basis for the cyclization of the lipopeptide antibiotic surfactin by the thioesterase domain SrfTE. Structure. 10 (2002) 301-310

2001

Schwarzer D., Mootz H.D., Marahiel M.A.: Exploring the impact of different thioesterase domains for the design of hybrid peptide synthetases. Chem Biol. 8 (2001) 997-1010

Kohli R.M., Trauger J.W., Schwarzer D., Marahiel M.A., Walsh C.T.: Generality of peptide cyclization catalyzed by isolated thioesterase domains of nonribosomal peptide synthetases. Biochemistry. 40 (2001) 7099-7108

Schwarzer D., Marahiel M.A.: Multimodular biocatalysts for natural product assembly. Naturwissenschaften 88 (2001) 93-101; Review

2000

Mootz H.D., Schwarzer D., Marahiel M.A.: Construction of hybrid peptide synthetases by module and domain fusions. Proc Natl Acad Sci. U.S. A. 97 (2000) 5848-5853

Book Chapters

Hackenberger C.R.P., Bode J.W., Schwarzer D.: Chemoselective Peptide Ligation: A Privileged Tool for Protein Synthesis. (Chapter 13) Amino Acids, Peptides and Proteins in Organic Chemistry, Wiley-VCH, Andrew B. Huges (ed.) (2011) 445-494

Schwarzer D.: Histone Acetylation. Encyclopedia of Molecular Pharmacology, 2nd Ed., Springer Berlin Heidelberg (2008) 592-595