CRC 1093 - Publications

Joint publications of CRC members Selected Publications

2019

I. Hadrovic, P. Rebmann, F.-G. Klärner, G. Bitan, T. Schrader: Molecular Lysine Tweezers Counteract Aberrant Protein Aggregation. Frontiers in Chemistry, Mini Review, 01 October 2019. doi: 10.3389/fchem.2019.00657

S. Köcher, S. Resch, T. Kessenbrock, L. Schrapp, M. Ehrmann, M. Kaiser: From dolastatin 13 to cyanopeptolins, micropeptins, and lyngbyastatins: the chemical biology of Ahp-cyclodepsipeptides. Nat Prod Rep. 2019 Aug 27. doi: 10.1039/c9np00033j.

L. Bartsch, M. Bartel, J. Iglesias Fernandez, Y. Ruiz Blanco, C. Beuck, J. Briels, A. Gigante, N. Toetsch, P. Bayer , E. Sanchez-Garcia , C. Ottmann, C. Schmuck : Multivalent ligands with tailor-made anion binding motif as stabilizers of protein-protein interactions. Chembiochem. 2019 Jun 6. doi: 10.1002/cbic.201900288.

S. B. van der Meer, K. Loza, K. Wey, M. Heggen, C. Beuck, P. Bayer, M. Epple: Click chemistry on the surface of ultrasmall gold nanoparticles (2 nm) for covalent ligand attachment followed by NMR spectroscopy”, Langmuir 2019, 35, 6288-6296.

J. Bongard, A. L. Schmitz, A. Wolf, G. Zischinsky, M. Pieren, B. Schellhorn, K. Bravo-Rodriguez, J. Schillinger, U. Koch, P. Nussbaumer, B. Klebl, J. Steinmann, J. Buer, E. Sanchez-Garcia, M. Ehrmann, M. Kaiser: Chemical validation of DegS as a target for the development of antibiotics with a novel mode of action. ChemMedChem 10.1002/cmdc.201900193.

L. Rojas-Sanchez, V. Sokolova, S. Riebe, J. Voskuhl, M. Epple: Covalent Surface Functionalization of Calcium Phosphate Nanoparticles with Fluorescent Dyes by Copper-Catalysed and by Strain-Promoted Azide-Alkyne Click Chemistry. ChemNanoMat 2019, 5, 436 –446, DOI: 10.1002/cnma.201800509

R. Kosinski, A. Mukhortava, W. Pfeifer, A. Candelli, P. Rauch, B. Saccà: Sites of high local frustration in DNA origami. Nat Commun. 2019 Mar 5;10(1):1061. doi: 10.1038/s41467-019-09002-6.

T. Ruks, C. Beuck, T. Schaller, F. C. Niemeyer, M. Zähres, K. Loza, M. Heggen, U. Hagemann, C. Mayer, P. Bayer, M. Epple: Solution NMR spectroscopy with isotope-labelled cysteine (13C, 15N) reveals the surface structure of L-cysteine-coated ultrasmall gold nanoparticles (1.8 nm). Langmuir 2019, 35 (3), 767-778 DOI: 10.1021/acs.langmuir.8b03840

V. Sokolova, L. Rojas-Sánchez, N. Białas, N. Schulze, M. Epple: Calcium phosphate nanoparticle-mediated transfection in 2D and 3D mono- and co-culture cell models. Acta Biomaterialia 2019, 84 391–401

2018

M. Weith, J. Seiler, J. van den Boom, M. Kracht, J. Hülsmann, I. Primorac, J. Del Pino Garcia, F. Kaschani, M. Kaiser, A. Musacchio, M. Bollen, H. Meyer: Ubiquitin-Independent Disassembly by a p97 AAA-ATPase Complex Drives PP1 Holoenzyme Formation. Mol Cell. 2018 Nov 15;72(4):766-777.e6. doi: 10.1016/j.molcel.2018.09.020.

V. Halder, J. Oeljeklaus, G. Heilmann, J.H. Krahn, Y. Liu, Y. Xiong, M. Schlicht, J. Schillinger, B. Kracher, M. Ehrmann, E. Kombrink, F. Kaschani, M. Kaiser: Identification of the Natural Product Rotihibin A as a TOR Kinase Signaling Inhibitor by Unbiased Transcriptional Profiling. Chemistry. 2018 Aug 27;24(48):12500-12504. doi: 10.1002/chem.201802647.

M. Hayduk , S. Riebe, J. Voskuhl: Phosphorescence Through Hindered Motion of Pure Organic Emitters. Chemistry. 2018 Aug 22;24(47):12221-12230. doi: 10.1002/chem.201800521.

Schillinger J, Severin K, Kaschani F, M. Kaiser, M. Ehrmann: HTRA1-Dependent Cell Cycle Proteomics. J. Proteome Res. 2018 Aug 3;17(8):2679-2694. doi: 10.1021/acs.jproteome.8b00129. Epub 2018 Jul 13.

C. Heid, A. Sowislok, T. Schaller, F. Niemeyer, F.G. Klärner, T. Schrader: Molecular Tweezers with Additional Recognition Sites. Chemistry. 2018 Aug 6;24(44):11332-11343. doi: 10.1002/chem.201801508. Epub 2018 Jul 17.

M. Nshanian, C. Lantz, P. Wongkongkathep, T. Schrader, F.-G. Klärner, A. Blümke, C. Despres, M. Ehrmann, C. Smet-Nocca, G. Bitan, J. A. Loo: Native Top-Down Mass Spectrometry and Ion Mobility Spectrometry of the Interaction of Tau Protein with a Molecular Tweezer Assembly Modulator. J. Am. Soc. Mass Spectrom. 2018. DOI: 10.1007/s13361-018-2027-6

K. Bravo-Rodriguez, B. Hagemeier, L. Drescher, M. Lorenz, J. Rey, M. Meltzer, F. Kaschani, M. Kaiser, M. Ehrmann: Utilities for Mass Spectrometry Analysis of Proteins: Fast post processing of mass spectrometry data. Rapid Commun Mass Spectrom. 2018 Jul 31. doi: 10.1002/rcm.8243.

E. Yilmaz, D. Bier, X. Guillory, J. Briels, Y. B. Ruiz-Blanco, E. Sanchez-Garcia, C. Ottmann, M. Kaiser: Mono- and Bivalent 14-3-3 Inhibitors for Characterizing Supramolecular "Lysine Wrapping" of Oligoethylene Glycol (OEG) Moieties in Proteins. Chemistry. 2018 Jun 20. doi: 10.1002/chem.201801074.

M. Hayduk, S. Riebe, K. Rudolph, S. Schwarze, F. van der Vight, C. G. Daniliuc, G. Jansen, J. Voskuhl: Molecular Recognition of Spermine using Aggregation-Induced Emission. Israel Journal of Chemistry. 2018 58(8) June 2018 DOI: 10.1002/ijch.201800037

F. Trusch, L. Loebach, S. Wawra, E. Durward, A. Wuensch, N. A. Iberahim, I. de Bruijn, K. MacKenzie, A. Willems, A. Toloczko, J. Diéguez-Uribeondo, T. Rasmussen, T. Schrader, P. Bayer, C. J. Secombes & P. van West: Cell entry of a host-targeting protein of oomycetes requires gp96. Nature Commun. 2018, 9, 2347. doi: 10.1038/s41467-018-04796-3.

J.Bongard, M. Lorenz, I. R. Vetter , P. Stege, A. T. Porfetye, A. L. Schmitz, F. Kaschani, A. Wolf, U. Koch, P. Nussbaumer, B. Klebl, M. Kaiser, M. Ehrmann: Identification of Noncatalytic Lysine Residues from Allosteric Circuits via Covalent Probes. ACS Chem. Biol. 2018, Article ASAP, DOI: 10.1021/acschembio.8b00101 Publication Date (Web): April 16, 2018

S. Mittal, K. Bravo-Rodriguez, E. Sanchez-Garcia: Mechanism of Inhibition of Beta Amyloid Toxicity by Supramolecular Tweezers. J. Phys. Chem. B. 2018 Apr 19;122(15):4196-4205. doi: 10.1021/acs.jpcb.7b10530. Epub 2018 Apr 9.

M. Li, S. Mosel, S. K. Knauer, C. Schmuck: A dipeptide with enhanced anion binding affinity enables cell uptake and protein delivery. Org Biomol Chem. 2018 Mar 28;16(13):2312-2317. doi: 10.1039/c7ob02721d.

R. Pöhler, J. H. Krahn, J. van den Boom, G. Dobrynin, F. Kaschani, H.-M. Eggenweiler, F. T. Zenke, M. Kaiser, H. Meyer: A Non-Competitive Inhibitor of VCP/p97 and VPS4 RevealsConserved Allosteric Circuits in Type I and II AAA ATPases. Angew Chem Int Ed Engl. 2018 Volume 57, Issue 6, February 5, DOI: 10.1002/anie.201711429

M. Ehlers, J. N. Grad, S. Mittal, D. Bier, M. Mertel, L. Ohl, M. Bartel, J. Briels, M. Heimann, C. Ottmann, E. Sanchez-Garcia, D. Hoffmann, C. Schmuck: Rational Design, Binding Studies, and Crystal-Structure Evaluation of the First Ligand Targeting the Dimerization Interface of the 14-3-3ζ Adapter Protein. Chembiochem. 2018 Mar 16;19(6):591-595. doi: 10.1002/cbic.201700588.

J. Stelzer, C. Vallet, A. Sowa, D. Gonzalez‐Abradelo, S. Riebe, C. G. Daniliuc, M. Ehlers, C. A. Strassert, S. Knauer, J. Voskuhl: On the Influence of Substitution Patterns in Thioether‐Based Luminophores with Aggregation‐Induced Emission Properties. Chemistry Select. 2018 First published: 25 January 2018, doi 10.1002/slct.201702900

B. Zakeri, S. Niebling, A. G. Martinéz, P. Sokkar, E. Sanchez-Garcia, C. Schmuck, S. Schlücker: Molecular recognition of carboxylates in the protein leucine zipper by a multivalent supramolecular ligand: residue-specific, sensitive and label-free probing by UV resonance Raman spectroscopy. Phys Chem Chem Phys. 2018 Jan 17;20(3):1817-1820. doi: 10.1039/c7cp04971d.

J. N. Grad, A. Gigante, C. Wilms, J. N. Dybowski, L. Ohl, C. Ottmann, C. Schmuck, D. Hoffmann: Locating Large, Flexible Ligands on Proteins. J Chem Inf Model. 2018 Jan 11. doi: 10.1021/acs.jcim.7b00413.

J. Wissler, M. Wehmeyer, S. Bäcker, S. Knauer , S. Schlücker : Simultaneous Rayleigh/Mie and Raman/Fluorescence Characterization of Molecularly Functionalized Colloids by Correlative Single-Particle Real-Time Imaging in Suspension. Anal Chem. 2018 Jan 2;90(1):723-728. doi: 10.1021/acs.analchem.7b02528

W. Pfeifer, P. Lill, C. Gatsogiannis, B. Saccà: Hierarchical Assembly of DNA Filaments with Designer Elastic Properties. ACS Nano. 2018 Jan 23;12(1):44-55. doi: 10.1021/acsnano.7b06012

2017

D. Bier, S. Mittal, K. Bravo-Rodriguez, A. Sowislok, X. Guillory, J. Briels, C. Heid, M. Bartel, B. Wettig, L. Brunsveld, E. Sanchez-Garcia, T. Schrader, C. Ottmann: The Molecular Tweezer CLR01 Stabilizes a Disordered Protein-Protein Interface. J Am Chem Soc. 2017 Nov 15;139(45):16256-16263. doi: 10.1021/jacs.7b07939. Epub 2017 Nov 2.

A. Hogeweg , A. Sowislok , T. Schrader, C. Beuck : An NMR Method To Pinpoint Supramolecular Ligand Binding to Basic Residues on Proteins. Angew Chem Int Ed Engl. 2017 Nov 13;56(46):14758-14762. doi: 10.1002/anie.201707950. Epub 2017 Oct 13.

J. Wissler, S. Bäcker, A. Feis, S. Knauer , S. Schlücker : Site-Specific SERS Assay for Survivin Protein Dimer: From Ensemble Experiments to Correlative Single-Particle Imaging. Small. 2017 July 4. doi: 10.1002/smll.201700802

A. Scheer, S. Knauer, R. Verhaegh: Survivin expression pattern in the intestine of normoxic and ischemic rats. BMC Gastroenterology 2017 Jun. 14. DOI: 10.1186/s12876-017-0625-6

S. Riebe, C. Vallet, F. van der Vight, D. Gonzalez-Abradelo, C. Wölper, C. A. Strassert, G. Jansen, S. Knauer, J. Voskuhl: Aromatic Thioethers as novel Luminophores with Aggregation‐ Induced Fluorescence and Phosphorescence. Chem. Eur. J. 2017 Jun 29. doi: 10.1002/chem.201701867

P. de Vink, J. Briels, T. Schrader, L. Milroy, L. Brunsveld, C. Ottmann: Cucurbit[8]uril and 14-3-3 based binary bivalent supramolecular-protein assembly platform and co-crystal structure. Angew Chem Int Ed Engl. 2017 May 16. doi: 10.1002/anie.201701807

M. Kopp , S. Kollenda, M. Epple: Nanoparticle-protein interactions: Therapeutic approaches and supramolecular chemistry. Acc. Chem. Res. 2017, 50 (6), pp 1383–1390, doi: 10.1021/acs.accounts.7b00051

T. Vöpel, K. Bravo-Rodriguez, S. Mittal, S. Vachharajani, D. Gnutt, A. Sharma, A. Steinhof, O. Fatoba, G. Ellrichmann, M. Nshanian, C. Heid, J. A. Loo, F. G. Klärner, T. Schrader, G. Bitan, E. E. Wanker, S. Ebbinghaus E. Sanchez-Garcia: Inhibition of Huntingtin Exon-1 Aggregation by the Molecular Tweezer CLR01. J. Am. Chem. Soc. 2017 Apr 26;139(16):5640-5643. doi: 10.1021/jacs.6b11039. Epub 2017 Apr 13

P. Gilles, K. Wenck, I. Stratmann, M. Kirsch , D. A. Smolin, T. Schaller, H. de Groot, A. Kraft, T. Schrader: High-Affinity Copolymers Inhibit Digestive Enzymes by Surface Recognition. Biomacromolecules. 2017 Jun 12;18(6):1772-1784. doi: 10.1021/acs.biomac.7b00162. Epub 2017 May 9

S. Koecher, J. Rey, J. Bongard, A. N. Tiaden, M. Meltzer, P. Richards, M. Ehrmann, M. Kaiser: Tailored Ahp-cyclodepsipeptides as potent non-covalent serine protease inhibitors. Angew. Chem. Int. Ed. 2017 May 17. doi: 10.1002/anie.201701771

E.-C. Schöneweiß, B. Saccà: The collective behavior of spring-like motifs tethered to a DNA origami nanostructure. Nanoscale. 2017, 9, 4486

C. Wilch, P. Talbiersky, U. Berchner-Pfannschmidt, T. Schaller, M. Kirsch , F.-G. Klärner, T. Schrader: Molecular tweezers inhibit PARP-1 by a new Mechanism. Eur. J. Org. Chem. 2017. DOI: 10.1002/ejoc.201601596 - very important paper.

M. Kopp, O. Rotan, C. Papadopoulos, N. Schulze, H. Meyer, M. Epple: Delivery of the autofluorescent protein R-phycoerythrin by calcium phosphate nanoparticles into four different eukaryotic cell lines (HeLa, HEK293T, MG-63, MC3T3): Highly efficient, but leading to endolysosomal proteolysis in HeLa and MC3T3 cells. PLOS ONE 2017, June 6, https://doi.org/10.1371/journal.pone.0178260

P. Jana, K. Samanta, S. Bäcker, E. Zellermann, S. Knauer C. Schmuck: Efficient Gene Transfection through Inhibition of β-Sheet (Amyloid Fiber) Formation of a Short Amphiphilic Peptide by Gold Nanoparticles. Angew Chem Int Ed Engl. 2017, Apr 10. doi: 10.1002/anie.201700713

S. Chernousova , M. Epple: Live-cell imaging to compare the transfection and gene silencing efficiency of calcium phosphate nanoparticles and a liposomal transfection agent. Gene Therapy. 2017, 24, 282–289; doi:10.1038/gt.2017.13

A. Sprengel, P. Lill, P. Stegemann, K. Bravo-Rodriguez, E.-C. Schöneweiß, M. Merdanovic, D. Gudnason, M. Aznauryan, L. Gamrad, S. Barcikowski, E. Sanchez-Garcia , V. Birkedal, C. Gatsogiannis, M. Ehrmann , B. Saccà: Tailored protein encapsulation into a DNA host using geometrically organized supramolecular interactions. Nat. Comm. 2017. doi: 10.1038/ncomms14472

A. C. Faesen, M. Thanasoula, S. Maffini, C. Breit, F. Müller, S. van Gerwen, T. Bange, A. Musacchio: Basis of catalytic assembly of the mitotic checkpoint complex. Nature. 2017, Feb 23; 542, 498–502.

C. Gerke, M. F. Ebbesen, D. Jansen, S. Boden, T. Freichel, L. Hartmann: Sequence-controlled glycopolymers via step-growth polymerization of precision glycomacromolecules for lectin receptor clustering. Biomacromolecules. 2017, DOI: 10.1021/acs.biomac.6b01657

O. Rotan, K. N. Severin, S. Pöpsel, A. Peetsch, M. Merdanovic, M. Ehrmann, M. Epple: Uptake of the proteins HTRA1 and HTRA2 by cells mediated by calcium phosphate nanoparticles. Beilstein J. Nanotechn. 2017, 8, 381–393.

D. Pan, K. Klare, A. Petrovic, A. Take, K. Walstein, P. Singh, A. Rondelet, A. W. Bird, A. Musacchio: CDK-regulated dimerization of M18BP1 on a Mis18 hexamer is necessary for CENP-A loading. Elife. 2017, Jan 6; 6. pii: e23352. doi: 10.7554/eLife.23352.

M. Nemec, D. Hoffmann: Quantitative assessment of molecular dynamics sampling for flexible systems. J Chem Theory Comput. 2017 Jan 13. doi: 10.1021/acs.jctc.6b00823.

C. Papadopoulos, P. Kirchner, M. Bug, D. Grum, L. Koerver, N. Schulze, R. Poehler, A. Dressler, S. Fengler, K. Arhzaouy, V. Lux, M. Ehrmann, C. C. Weihl , H. Meyer: VCP/p97 cooperates with YOD1, UBXD1 and PLAA to drive clearance of ruptured lysosomes by autophagy. EMBO J. 2017, 36:135-150

Publications 2014-2017 First Funding Period

Complete list of publications

Chemical Ligands and Methods Publications Area A

Sorted by project:

  • Project A1
    Protein-recognition by supramolecular ligands from focused combinatorial libraries (Carsten Schmuck)
  • Project A2
    Natural products as starting structures for the development of supramolecular ligands (Markus Kaiser)
  • Project A3
    Designed copolymers and molecular tweezers for protein surface recognition (Thomas Schrader)
  • Project A5
    Protein-specific nanoparticles for cellular uptake (Matthias Epple)
  • Project A6
    DNA-based nanocontainers for predesigned spatial confinement of proteins (Barbara Saccà)
  • Project A7
    Pareto-optimization of protein-surface targeting supramolecular binders with hetero-avidity (Daniel Hoffmann)
  • Project A8
    Exploring protein-recognition by supramolecular binders with MD and QM/MM methods (Elsa Sánchez-Garcia)
  • Project A9
    Raman spectroscopic monitoring of protein recognition by supramolecular ligands (Sebastian Schlücker)
  • Project A10
    Novel luminophores with aggregation induced emission properties for protein recognition (Jens Voskuhl)
  • Project A11
    Precision macromolecules for the sequence-controlled presentation of supramolecular ligands (Laura Hartmann)

Biological Targets Publications Area B

Sorted by project:

  • Project B1
    Supramolecular ligands modulate assembly and function of HtrA proteases (Michael Ehrmann)
  • Project B2
    Probing mechanisms of the Cdc48/p97 segregase with designed supramolecular ligands (Hemmo Meyer)
  • Project B4
    Modulation of 14-3-3 protein-protein interactions by supramolecular chemistry (Christian Ottmann)
  • Project B5
    Dissection and modulation of (patho)biological Survivin functions by supramolecular ligands (Shirley Knauer)
  • Project B6
    Targeting centromer recruitment of mitotic regulators by supramolecular ligands (Andrea Musacchio)
  • Project B7
    Manipulation of the kinetochore-microtubule interface by supramoleular ligands (Stefan Westermann)

Central Service Projects Publications Area Z

Sorted by project: