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Molecular simulation and modelling

The BPTI-Trypsin complex has a pre-bound state

The BPTI-Trypsin complex has a pre-bound state

Reviews

  • L. Wehahn, B. G. Keller "Fluorinated Protein-Ligand Complexes - A Computational Perspective" J. Phys. Chem. B (2024), 128, 6014-6027. https://doi.org/10.1021/acs.jpcb.4c01493
  • B. G. Keller, L. Donati,  S. Aleksić, ”Markov state models in drug design” in "Biomolecular Simulations in Structure-Based Drug Discovery", Wiley-VCH, Weinheim (2019), edited by F.L. Gervasio, V. Spiwok
  • B. G. Keller, “Moleküle in Bewegung,” Nachrichten aus der Chemie, 66,  325–326 (2018)
  • C. Rakers, M. Bermudez, B. G. Keller, J. R. M. Mortier,  G. Wolber, “Computational close up on protein-protein interactions: how to unravel the invisible using molecular dynamics simulations?,” WIREs Comput Mol Sci,5, 345–359 (2015). https://doi.org/10.1002/wcms.1222

Proteins

  • L.M. Finn, R. Cummer, B. Castagner, B.G. Keller "Clostridioides difficile Toxins Unhinged: Allosterically Switchable Network Orients β-flap" bioRxiv (2024) https://doi.org/10.1101/2024.08.08.607137
  • M.T. Wenz, M. Bertazzon, J. Sticht, S. Aleksić, D. Gjorgjevikj, C. Freund, B.G. Keller "Target recognition in tandem WW domains: complex structures for parallel and antiparallel ligand orientation in h-FBP21 tandem WW" J. Chem. Inf. 62 (2022), 6586-6601. https://doi.org/10.1021/acs.jcim.1c01426
  • J.-O. Joswig, J. Anders, H. Zhang, C. Rademacher, B.G. Keller “The molecular basis for the pH-dependent calcium affinity of the pattern recognition receptor langerin” J. Biol. Chem (2021) 296 p. 100718. https://doi.org/10.1016/j.jbc.2021.100718
  • D. Schumacher, O. Lemke, J. Helma, L. Gerszonowicz, V. Waller, T. Stoschek, P. M. Durkin, N. Budisa, H. Leonhardt, B. G. Keller,  C. P. R. Hackenberger, “Broad substrate tolerance of tubulin tyrosine ligase enables one-step site-specific enzymatic protein labeling,” Chem Sci, 8, 3471–3478 (2017) https://doi.org/10.1039/C7SC00574A
  • J. Hanske, S. Aleksić, M. Ballaschk, M. Jurk, E. Shanina, M. Beerbaum, P. Schmieder, B. G. Keller,  C. Rademacher, “Intradomain Allosteric Network Modulates Calcium Affinity of the C-Type Lectin Receptor Langerin,” J. Am. Chem. Soc.,138,  12176–12186 (2016). https://doi.org/10.1021/jacs.6b05458

Cyclic Peptides

  • G. Yao, S. Kosol, M. Wenz, E. Irran, B.G. Keller, O. Trapp, R.D. Süßmuth "The occurrence of ansamers in the synthesis of cyclic peptide" Nat. Commun. (2022) 13, 6488. https://doi.org/10.1038/s41467-022-34125-8
  • G. Yao, C.H. Knittel, S. Kosol, M. Wenz, B.G. Keller, H. Gruß, A. Braun, C. Lutz, T. Hechler, A. Pahl, R.D. Süssmuth “Iodine-mediated tryptathionine formation facilitates the synthesis of novel amanitines” J. Am. Chem. Soc (2021) 142, p. 14322-14331. https://doi.org/10.1021/jacs.1c06565
  • G. Yao, J.-O. Joswig, B. G. Keller, R. D. Süssmuth, “Total Synthesis of the Death Cap Toxin Phalloidin: Atropoisomer Selectivity Explained by Molecular-Dynamics Simulations.,” Chemistry – A European Journal, 25, 8030–8034  (2019). https://doi.org/10.1002/chem.201901888
  • J. Witek, S. Wang, B. Schroeder, R. Lingwood, A. Dounas, H.-J. Roth, M. Fouché, M. Blatter, O. Lemke, B. Keller,  S. Riniker, “Rationalization of the Membrane Permeability Differences in a Series of Analogue Cyclic Decapeptides.,” J. Chem. Inf. Model.,59, 294–308 (2019). https://doi.org/10.1021/acs.jcim.8b00485
  • J. Witek, M. Mühlbauer, B. G. Keller, M. Blatter, A. Meissner, T. Wagner,  S. Riniker, “Interconversion Rates between Conformational States as Rationale for the Membrane Permeability of Cyclosporines.,” ChemPhysChem,  7, 608 (2017). https://doi.org/10.1002/cphc.201700995
  • J. Witek, B. G. Keller, M. Blatter, A. Meissner, T. Wagner,  S. Riniker, “Kinetic Models of Cyclosporin A in Polar and Apolar Environments Reveal Multiple Congruent Conformational States,” J. Chem. Inf. Model., 56, 1547–1562 (2016). https://doi.org/10.1021/acs.jcim.6b00251

Fluorine in Biomolecules

  • L. Wehahn, B. G. Keller "Pre-bound State Discovered in the Unbinding Pathway of Fluorinated Variants of the Trypsin-BPTI Complex Using Random Acceleration Molecular Dynamics Simulations" J. Chem. Inf. Model. (2024) 64, 5194-5206. https://doi.org/10.1021/acs.jcim.4c00338
  • M. Müll, F. Pourmasoumi, L. Wehrhan, O. Nosovska, P. Stephan, H. Zeihe, I. Vilotijevic, B. G. Keller, H. Kries "Biosynthetic incorporation of fluorinated amino acids into the nonribosomal peptide gramicidin S" RSC Chem. Biol. (2023), 4 692-697. https://doi.org/10.1039/D3CB00061C
  • L. Wehrhan, J. Leppkes, N. Dimos, B. Loll, B. Koksch, B.G. Keller ”Water network in the binding pocket of fluorinated BPTI-Trypsin complexes - insights from simulation and experiment” J. Phys. Chem. B (2022) 126, 9985–9999. https://doi.org/10.1021/acs.jpcb.2c05496
  • M. Tiemann, E. Nawrotzky, P. Schmieder, L. Wehrhan, S. Bergemann,V. Martos, C. Arkona, B.G. Keller; J. Rademann "A Formylglycine-Peptide for the Site-Directed Identification of Phosphotyrosine-Mimetic Fragments" Chem. Eur. J. 3 (2022), p. 773-782. https://doi.org/10.1002/chem.202201282
  • J. Leppkes, N. Dimos, B. Loll, T. Hohmann, M. Dyrks, A. Wieseke, B.G. Keller, B. Koksch "Fluorine-induced polarity increases inhibitory activity of BPTI towards chymotrypsin" RSC Chem. Bio. 3 (2022), p. 773-782. https://doi.org/10.1039/D2CB00018K
  • M. Accorsi, M. Tiemann, L. Wehrhan, L.M. Finn, R. Cruz, M. Rautenberg, F. Emmerling, J. Heberle, B.G. Keller, J. Rademann "Pentafluorophosphato‐Phenylalanines: Amphiphilic Phosphotyrosine Mimetics Displaying Fluorine‐Specific Protein Interactions" Angew. Chem. Int. Ed. (2022), e202203579. https://doi.org/10.1002/anie.202203579

Biomimetic Hydrogels

  • J. Proksch, M.C.S. Dal Colle, F. Heinz, R.F. Schmidt, J. Gottwald, M. Delbianco, B.G. Keller, M. Gradzielski, U. Alexiev, B. Koksch "Impact of glycan nature on structure and viscoelastic properties of glycopeptide hydrogels" J. Pept. Sci. (2024), 30, e3599. https://doi.org/10.1002/psc.3599
  • F. Heinz, J. Proksch, R.F. Schmidt, B. Koksch, M. Gradzielski, B.G. Keller "How chromophore labels shape the structure and dynamics of a peptide hydrogel" Biomacromolecules (2024), 25, 1262–1273. https://doi.org/10.1021/acs.biomac.3c01225

Other molecules

  • J. Wahl, A. Ahsanullah, H. Zupan, F. Gottschalk, A. Nerlich, C. Arkona, A.C. Hocke, B.G. Keller, J. Rademann "Chemically Stable Diazo Peptides as Selective Probes of Cysteine Proteases in Living Cells" Angew. Chem. Int. Ed. (2024), e202411006 https://doi.org/10.1002/anie.202411006
  • A. Loges, M. Manni, M. Louvel, M. Wilke, S. Jahn, E. Welter, M. Borchert, S. Qiao, S. Klemme, B. G. Keller, T. John "Complexation of Zr and Hf in fluoride-rich hydrothermal aqueous fluids and its significance for high field strength element fractionation" Geochim. Cosmochim. Acta (2024), 366 167-181. https://doi.org/10.1016/j.gca.2023.12.013
  • P. Kiran, S. Bhatia, D. Lauster, S. Aleksić, C. Fleck, N. Peric, W. Maison, S. Liese, B. G. Keller, A. Herrmann,  R. Haag, “Exploring Rigid and Flexible Core Trivalent Sialosides for Influenza Virus Inhibition,” Chemistry – A European Journal,  24, 19373–19385 (2018). https://doi.org/10.1002/chem.201804826
  • J. Hormann, J. Malina, O. Lemke, M. J. Hülsey, S. Wedepohl, J. Potthoff, C. Schmidt, I. Ott, B. G. Keller, V. Brabec,  N. Kulak, “Multiply Intercalator-Substituted Cu(II) Cyclen Complexes as DNA Condensers and DNA/RNA Synthesis Inhibitors,” Inorganic Chemistry, 57, 5004–5012 (2018). https://doi.org/10.1021/acs.inorgchem.8b00027