Publications
The Research Training Group (RTG) “Bioactive Peptides – Innovative Aspects of Synthesis and Biosynthesis” was established in 2019. Publications based on the RTG projects are listed below. Publications of the participating research departments are listed on their respective websites.
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53. Koller T, Berger MJ, Morici M, Paternoga H, Bulatov T, Di Stasi A, Dang T, Mainz A, Raulf K, Crowe-McAuliffe C, Scocchi M, Mardiro M, Beckert B, Vázquez-Laslop N, Mankin AS , Süssmuth RD, Wilson DN (2024). A Paenilamicins are context-specific translocation inhibitors of protein synthesis. Nat Chem Biol., online ahead of print - doi: 10.1038/s41589-024-01752-9
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52. Baade B, Michaelis M, Prestel A, Paone C, Klishin N, Scheinost L, Nedielkov R, Hauck CR and Möller HM (2024). A flexible loop in the paxillin LIM3 domain mediates direct binding to integrin β3. PLOS Biology, in print - doi: 10.1371/journal.pbio.3002757.
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51. Schäfer JL and Keller BG (2024). Implementation of Girsanov Reweighting in OpenMM and
Deeptime. J. Phys. Chem. B., 128(25), 6014-6027. doi: 10.1021/acs.jpcb.4c01702
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50. Said N, Finazzo M, Hilal T, Wang B, Selinger TL, Gjorgjevikj D, Artsimovitch I and Wahl MC (2024). Sm-like protein Rof inhibits transcription termination factor ρ by binding site obstruction and conformational insulation. Nat. Commun. 15(1), 3186. doi: 10.1038/s41467-024-47439-6.
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49. Piemontese E, Herfort A, Perevedentseva Y, Möller HM, and Seitz O (2024). Multiphosphorylation-Dependent Recognition of Anti-pS2 Antibodies against RNA Polymerase II C‑Terminal Domain Revealed by Chemical Synthesis. J. Am. Chem. Soc., 146, 12074-12086. doi: 10.1021/jacs.4c01902.
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48. Arafiles JVV, Franke J, Franz L, Gómez-González J, Kemnitz-Hassanin K, and Hackenberger CPR (2023). Cell-Surface-Retained Peptide Additives for the Cytosolic Delivery of Functional Proteins.
J. Am. Chem.Soc, 145, 24535-24548. doi: 10.1021/jacs.3c05365.
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47. Kosol S, Rostock L, Barsig J, Tabarelli T, Hommernick K, Kulike M, Eulberg T, Seidel M, Behroz I, Kleebauer L, Grätz S, Mainz A, Süssmuth RD (2023). Transcription activation by the resistance protein AlbA as a tool to evaluate derivatives of the antibiotic albicidin. Chem. Sci.,
doi: 10.1039/d3sc00955f.
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46. Sigurdsson A, Martins BM, Düttmann SA, Jasyk M, Dimos-Röhl B, Schöpf F, Gemander M, Knittel CH, Schnegotzki R, Schmid B, Kosol S, Pommerening L, González-Viegas M, Seidel M, Hügelland M, Leimkühler S, Dobbek H, Mainz A, SüssmuthRD (2023). Discovery of the lanthipeptide curvocidin and structural insights into its trifunctional synthetase CuvL. Angew. Chem. Int. Ed. e202302490.
doi: 10.1002/anie.202302490.
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45. Kapp-Joswig J-O, Keller BG (2023). CommonNNClustering - A Python Package for Generic Common-Nearest-Neighbor Clustering. Chem. Inf. Model. 63, 1093–1098. doi: 10.1021/acs.jcim.2c01493
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44. Gorenflos Lopez JL, Schmieder P, Kemnitz-Hassanin K, Asikoglu HC, Celik A, Stieger CE, Fiedler D, Hinderlich S, Hackenberger CPR (2023). Real-time monitoring of the sialic acid biosynthesis pathway by NMR. Chem. Sci. 14, 3482-3492. doi: 10.1039/d2sc06986e.
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43. Yao G, Kosol S, Wenz MT, Irran E, Keller BG, Trapp O, Süssmuth RD (2022) The occurrence of ansamers in the synthesis of cyclic peptides. Nat. Commun. 13, 6488.
doi: 10.1038/s41467-022-34125-8
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42. Feurstein C, Meyer V, Jung S (2022) Structure–Activity Predictions From Computational Mining of Protein Databases to Assist Modular Design of Antimicrobial Peptides. Front.Microbiol. 13.
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41. Trunschke S, Piemontese E, Fuchs O, Abboud A, Seitz O (2022) Enhancing Auxiliary-mediated Native Chemical Ligation at Challenging Junctions with Pyridine Scaffolds. Chem. Eur. J., e202202065. doi: 10.1002/chem.202202065.
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40. Scholz S, Kerestetzopulou S, Wiebach V, Schnegotzki R, Schmid B, Reyna-Gonzáles E, Ling D, Süssmuth RD, Dittmann E, Baunach M (2022) One-Pot Chemoenzymatic Synthesis of Microviridin Analogs Containing Functional Tags. ChemBioChem 23, e202200345. doi: 10.1002/cbic.202200345.
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39. Stieger CE, Park Y, de Geus MAR, Kim D, Huhn C, Slenczka JS, Ochtrop P, Müchler JM, Süssmuth RD, Broichhagen J, Baik M-H, Hackenberger CPR (2022) DFT-guided discovery of ethynyl-triazolyl-phosphinates as modular electrophiles for chemoselective cysteine bioconjugation and profiling. Angew. Chem. Int. Ed. 61, e202205348. doi: 10.1002/anie.202205348.
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38. Bilbrough T, Piemontese E, Seitz O (2022) Dissecting the role of protein phosphorylation: a chemical biology toolbox. Chem. Soc. Rev. 51, 5691-5730. doi: 10.1039/D1CS00991E.
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37. Kolbowski L, Lenz S, Fischer L, Sinn LR, O'Reilly FJ, Rappsilber J (2022) Improved peptide backbone fragmentation is the primary advantage of MS-cleavable crosslinkers. Anal. Chem. 94, 7779-7786. doi: 10.1021/acs.analchem.1c05266.
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36. Dang T, Loll B, Müller S, Skobalj R, Ebeling J, Bulatov T, Gensel S, Göbel J, Wahl MC, Genersch E, Mainz A, Süssmuth RD (2022) Molecular basis of antibiotic self-resistance in a bee larvae pathogen. Nat. Commun. 13, 2349. doi: 10.1038/s41467-022-29829-w.
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35. Feurstein C, Meyer V, Jung S (2022) Structure–Activity Predictions From Computational Mining of Protein Databases to Assist Modular Design of Antimicrobial Peptides. Front. Microbiol. 13:812903, doi: 10.3389/fmicb.2022.812903.
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34. Krumbholz J, Ishida K, Baunach M, Teikari JE, Rose MM, Sasso S, Hertweck C, Dittmann E (2022) Deciphering chemical mediators regulating specialized metabolism in a symbiotic cyanobacterium. Angew. Chem. Int. Ed. 61, doi: 10.1002/anie.202204545.
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33. Wenz MT, Bertazzon M, Sticht J, Aleksić S, Gjorgjevikj D, Freund C, Keller BG (2022) Target recognition in tandem WW domains: complex structures for parallel and antiparallel ligand orientation in h-FBP21 tandem WW. J. Chem. Inf. Model. doi: 10.1021/acs.jcim.1c01426.
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32. Schnegotzki R, Wiebach V, Sánchez-Hidalgo M, Tietzmann M, zur Bonsen AB, Genilloud O, Süssmuth RD (2022) Total Synthesis and Biosynthesis of Cyclodepsipeptide Cochinmicin I. Org. Lett. 24(12), 2344-2348. DOI: 10.1021/acs.orglett.2c00525.
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31. Sinn LR, Giese SH, Stuiver M, Rappsilber J (2022) Leveraging Parameter Dependencies in high-field asymmetric waverform ion-mobility spectrometry and size exclusion chromatography for proteome-wide crosslinking mass spectrometry. Anal. Chem. 94, 11, 4627–4634, doi: 10.1021/acs.analchem.1c04373.
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30. Schnegotzki R, Koopman J, Grimme S, Süssmuth RD (2022) Quantum Chemistry-based Molecular Dynamics Simulations as a Tool for the Assignment of ESI-MS/MS Spectra of Drug Molecules. Chemistry 28(27), doi: 10.1002/chem.202200318.
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29. Mittermeier M, Wang B, Said N, Gjorgjevikj D, Wahl MC, Artsimovitch I (2022) A non-native C-terminal extension of the β' subunit compromises RNA polymerase and Rho functions Mol. Microbiol. 117, 871-85. doi: 10.1111/mmi.14879.
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28. Baltzer S, Bulatov T, Schmied C, Krämer A, Berger BT, Oder A, Walker-Gray R, Kuschke C, Zühlke K, Eichhorst J, Lehmann M, Knapp S, Weston J, von Kries JP, Süssmuth RD, Klussmann E (2022) Aurora Kinase A is involved in Controlling the Localization of Aquaporin-2 in Renal Principal Cells. Int. J. Mol. Sci. 23(2), 763, doi: 10.3390/ijms23020763.
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27. Bulatov T, Gensel S, Mainz A, Dang T, Koller TO, Voigt K, Ebeling J, Wilson DN, Genersch E, Süssmuth RD (2022) Total Synthesis and Biological Evaluation of Paenilamicins from the Honey Bee Pathogen Paenibacillus larvae. J. Am. Chem. Soc. 144, 1, 288-296, doi: 10.1021/jacs.1c09616.
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26. Schneider AFL, Kallen J, Ottl J, Reid JC, Ripoche S, Ruetz S, Stachyra TM, Hintermann S, Dumelin CE, Hackenberger CPR, Marzinzik AL (2021) Discovery, X-Ray Structure and CPP-Conjugation Enabled Uptake of p53/MDM2 Macrocyclic Peptide Inhibitors. RSC Chem. Biol. 2, 1661-1668. doi: 10.1039/D1CB00056J.
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25. Zborovsky L & Kleebauer L, Seidel M, Kostenk A, von Eckardstein L, Gombert FO, Weston JD, Süssmuth RD (2021) Improvement of the antimicrobial potency, pharmacokinetic and pharmacodynamic properties of albicidin by incorporation of nitrogen atoms. Chemical Science 12, doi: 10.1039/d1sc04019g
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24. Grass LM, Wollenhaupt J, Barthel T, Parfentev I, Urlaub H, Loll B, Klauck E, Antelmann H, Wahl MC (2021) Large-scale ratcheting in a bacterial DEAH/RHA-type RNS helicase that modulates antibiotics susceptibility Proc Natl Aced Sci USA 118, 30, e2100370118, doi: 10.1073/pnas.2100370118
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23. Yao G, Knittel CH, Kosol S, Wenz MT, Keller BG, Gruß H, Braun AC, Lutz C, Hechler T, Pahl A, Süssmuth RD (2021) Iodine-Mediated Tryptathionine Formation Facilitates the Synthesis of Amanitins. J. Am. Chem. Soc. 143, doi: 10.1021/jacs.1c06565
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22. Kleebauer L, Zborovsky L, Hommernick K, Seidel M, Weston J, Süssmuth RD (2021) Overcoming AlbD protease resistance and improving potency: Synthesis and bioactivity of antibacterial albicidin analogues with amide bond isosteres. Org. Lett. 23, doi: 10.1021/acs.orglett.1c02312
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21. Schneider AFL, Benz L, Lehmann M, Hackenberger CPR (2021) Cell-Permeable Nanobodies Allow Dual-Color Super-Resolution Microscopy in Untransfected Living Cells. Angew. Chem. Int. Ed. 60, 2-8, DOI: 10.1002/anie.202103068
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20. Lenz S, Sinn L, O´Reilly FJ, Fischer L, Wegner F, Rappsilber J (2021) Reliable identification of protein-protein interactions by crosslinking mass spectrometry. Nat. Comm. 12:3564, doi:10.1038/s41467-021-23666
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19. Stieger CE, Franz L, Körlin F, Hackenberger CPR (2021) Diethynyl Phosphinates for Cysteine-Selective Protein Labeling and Disulfide Rebridging. Angew. Chem. Int. Ed. 60, 1-7. doi:0.1002/anie.202100683
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18. Giese SH, Sinn L, Wegner F, Rappsilber J (2021) Retention time prediction using neural networks increases identifications in crosslinking mass spectrometry. Nat. Comm. 12: 3237, doi:10.1038/s41467-021-23441-0
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17. Schneider AFL, Kithil M, Cardoso MC, Lehmann M, Hackenberger CPR (2021) Cellular uptake of large biomolecules enabled by cell-surface-reactive cell-penetrating peptide additives.
Nature Chemistry 13, doi: 10.1038/s41557-021-00661-x
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16. Said N, Hilal T, Sunday ND, Kathri A, Bürger J, Mielke T, Belugorov BA, Loll B, Sen R, Artsimovitch I, Wahl MC (2021) Steps toward translocation-independent RNApolymerase inactivation by terminator ATPaser. Science 371 (6524), doi: 10.1126/science.abd1673
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15. Joswig JO, Anders J, Zhang H, Rademacher C, Keller BG (2021) The molecular basis for the pH-dependent calcium affinity of the pattern recognition receptor langerin. J. Biol. Chem. 296, 100718, doi: 10.1016/j.jbc.2021.100718.
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14. Behroz I, Kleebauer L, Hommernick K, Seidel M, Grätz S, Mainz A, Weston JB, Süssmuth RD (2021) Acetylenic Replacement of Albicidin’s Methacrylamide Residue Circumvents Detrimental (E)‐(Z)‐Photoisomerization and Preserves Antibacterial Activity. Chemistry 27, doi: 10.1002/chem.202100523
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13. Roske JJ, Lui S, Loll B, Neu U, Wahl MC (2021) A skipping rope translocation mechanism in awidespread family of DNA repair helicases. Nucleic Acid Research 49 (1), doi: 10.1093/nar/gkaa1174
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12. Baumann AL, Schwagerus S, Broi K, Kemnitz-Hassain K, Stieger CE, Trieloff N, Schmieder P, Hackenberger CPR (2020) Chemically induced vinylphosphono- thiolate electrophiles for thiol-thiol bioconjugations. J. Am. Chem. Soc. 142 (20), 9544–9552, doi: 10.1021/jacs.0c03426.
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11. Pei HH, Hilal T, Chen ZA, Huang YH, Gao Y, Said N, Loll B, Rappsilber J, Belogurov GA, Artsimovitch I, Wahl MC (2020) The δ subunit and NTPase HelD institute a two-pronged mechanism for RNA polymerase recycling. Nat Commun. 11(1):6418. doi: 10.1038/s41467-020-20159-3.
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10. Agostini F, Sinn LR, Petras D, Kubyshkin V, Berger AA, Schipp CJ, Dorrestein PC, Rappsilber J, Budisa N, Koksch B (2020) Multiomics Analysis Provides Insight into the Laboratory Evolution of Escherichia coli toward the Metabolic Usage of Fluorinated Indoles. ACS Cent. Sci. 7(1):81-92, doi: 10.1021/acscentsci.0c00679.
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9. O'Reilly FJ, Xue L, Graziadei A, Sinn LR, Lenz S, Tegunov D, Blötz C, Singh N, Hagen WJH, Cramer P, Stülke J, Mahamid J, Rappsilber J (2020) In-cell architecture of an actively transcribing-translating expressome. Science. 369(6503):554-557, doi: 10.1126/science.abb3758.
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8. Wiebach V, Mainz A, Schnegotzki R, Siegert MAJ, Hügelland M, Pliszka N, Süssmuth RD (2020) An Amphipathic Alpha-Helix Guides Maturation of the Ribosomally-Synthesized Lipolanthines. Angew Chem 59, 16777-16785, doi: 10.1002/anie.202003804
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7. Siegert MJ, Knittel CH, Süssmuth RD (2020) A Convergent Total Synthesis of Death Cap Toxin α-Amanitin. Angew Chem Int Ed Engl. 59(14), 5500-5504. doi: 10.1002/anie.201914620.
Corresponding cover picture: doi: 10.1002/anie.202001279
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6. Wahl MC, Sen R (2019) Exploiting phage strategies to modulate bacterial transcription. Transcription 10, 222-230. doi: 10.1080/21541264.2019.1684137
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5. Apel C, Kasper MA, Stieger CE, Hackenberger CPR, Christmann M (2019) Protein Modification of Lysine with 2-(2-Styrylcyclopropyl)ethanol. Org. Lett. 21, 10043–10047. doi: 10.1021/acs.orglett.9b03982
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4. Cairns T, Feurstein C, Zheng X, Zheng P, Sun J, Meyer V (2019) Functional exploration of co-expression networks identifies a nexus for modulating protein and citric acid titres in Aspergillus niger submerged culture. Fungal Biol Biotechnol. 6, 18. doi: 10.1186/s40694-019-0081-x
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3. Cairns T, Feurstein C, Zheng X, Zheng P, Sun J, Meyer V (2019) A quantitative image analysis pipeline for the characterization of filamentous fungal morphologies as a tool to uncover targets for morphology engineering: a case study using apID in Aspergillus niger. Biotechnol Biofuels. 12, 1-17. doi: 10.1186/s13068-019-1473-0
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2. Dehm D, Krumbholz J, Baunach M, Wiebach V, Hinrichs K, Guljamow A, Tabuchi T, Jenke-Kodama H, Süssmuth RD, Dittmann E (2019) Unlocking the Spatial Control of Secondary Metabolism Uncovers Hidden Natural Product Diversity in Nostoc punctiforme. ACS Chem. Biol. 14, 1271–1279. doi: 10.1021/acschembio.9b00240
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1. Yao G, Joswig JO, Keller BG, Süßmuth RD (2019) Total Synthesis of the Death Cap Toxin Phalloidin: Atropoisomer Selectivity Explained by Molecular‐Dynamics Simulations. Chem. Eur. J. 25, 8030-8034. doi:10.1002/chem.201901888
