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Paramagnetic‑iterative relaxation matrix approach: extracting PRE‑restraints from NOESY spectra for 3D structure elucidation of biomolecules

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Supporting Information for the publication "Paramagnetic-Iterative Relaxation Matrix Approach – Extracting PRE-Restraints from NOESY Spectra for 3D Structure Elucidation of Biomolecules" published in Journal of Biomolecular NMR. Files and scipts can be found at:


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G-quadruplexes are important drug targets in anticancer research. In our group, we apply NMR spectroscopy to investigate structural polymorphism of G-quadruplexes as well as real-time NMR to gain insight into folding pathways (Bessi et al., Angew Chem 2015). Further, we solve NMR structures of the holo and apo states of physiologically relevant G quadruplex drug targets (Wirmer-Bartoschek et al., Angew Chem 2017), and we apply state-of-the-art NMR methods to investigate G4-ligand interactions (Bessi et al., ACS Chem Biol. 2012).

Membrane Proteins

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We investigate light-absorbing complexes such as rhodopsin in order to understand how our eyes sense light. In particular, we apply time-resolved NMR spectroscopy to investigate branched photo-cycles (Chatterjee et al., Angew Chem. 2014). We also contribute to structural characterization of the respiratory chain complexes by synthesis of specific inhibitors (Zickermann et al., Science 2015).

Structure-based drug design

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By integrated structural biology (NMR, X-ray) and biophysics (MST, ITC CD), chemical synthesis and cell biology, we contribute to the development of new drug candidates, especially in the field of cancer (C. Herbert et al.,Cancer Cell 2013; Vogtherr et al., Angew. Chem. 2005).

RNA-based regulation

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As recently discovered, RNA plays a central role in cellular regulation of transcription (Steinert et al., eLife 2017) and translation (Reining et al., Nature 2013). We investigate how riboswitch RNAs sense changes in metabolite concentration and how they kinetically influence gene expression.

Protein folding and misfolding

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Regarding protein folding, we are able to analyse the starting point of folding, the unfolded state of proteins, by NMR spectroscopy (Klein-Seetharaman et al., Science 2002) as well as kinetics of folding and misfolding (Schlepckow et al., Angew. Chem. 2013) and the structure of the folded state.

Development of New NMR Techniques for Monitoring of Protein Folding with Atomic Resolution

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We have developed two independent methods to study structural transitions and reactions by time-resolved NMR spectroscopy with millisecond dead-time. Therefore, on one hand, we use a rapid mixing system inside the active volume in the probe, which we developed in cooperation with BRUKER. In addition, we have developed a method to laser-trigger cofactor dependent reactions inside the NMR tube which we established. These studies are supported by a wide variety of other spectroscopic techniques including stopped-flow fluorescence, CD, FTIR and EPR to gain further insight in structural characteristics during the folding process. At the moment we are focusing on the structural characterization of transient intermediates in protein folding. We are studying the kinetics of the natural structural changes of a-lactalbumine and calmoduline upon ion addition in cellular conditions, the binding kinetics of calmoduline to the calcium-pump receptor peptides and the refolding from denaturating reagents of calmodulin, a-lactalbumine, lysozyme and ubiquitin.

NMR studies of the structure and dynamics of the ribosomal protein L11 from Thermotoga maritima.

L11 is highly conserved ribosomal protein and its interaction with the ribosomal RNA segment from 23S subunit is considered to undergo an „induced fit“-conformational adjustment of both the protein and the RNA with respect to their conformations in the unbound state (Leulliot and Varani, 2001; Draper et al., 1996). Furthermore, the conformational dynamics of L11 are thought to play an important role in the binding process.

Comparison of the NMR Spectroscopy Solution Structure of Pyranosyl-RNA and Its Nucleo-delta-peptide Analogue

For all biological systems, nature has chosen ribo- and deoxyribonucleic acids as its genetic building block. In order to understand this selectivity, the structures of the potential alternatives to the natural nucleic acids have to be investigated. We have determined the solution structures of pRNA and Nucleo-d-peptides by NMR spectroscopy. The structures pose important questions about the origin of helicity, stacking and inclination of these oligomers.

Matlab scripts

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