A5029977238- Protein Structure and Dynamics
- Enzyme Structure and Function
- vaccines and immunoinformatics approaches
- Immunotherapy and Immune Responses
- NMR spectroscopy and applications
- Advanced NMR Techniques and Applications
- Monoclonal and Polyclonal Antibodies Research
- RNA and protein synthesis mechanisms
- Mass Spectrometry Techniques and Applications
- Toxin Mechanisms and Immunotoxins
- Metabolomics and Mass Spectrometry Studies
- Glycosylation and Glycoproteins Research
- Ubiquitin and proteasome pathways
- Advanced MRI Techniques and Applications
- Ion channel regulation and function
- Natural Language Processing Techniques
- Venomous Animal Envenomation and Studies
- Molecular spectroscopy and chirality
- Bacterial Genetics and Biotechnology
- ATP Synthase and ATPases Research
- Hemoglobin structure and function
- Electron Spin Resonance Studies
- Chemical Reactions and Isotopes
- Chemical Reaction Mechanisms
- Bioinformatics and Genomic Networks
University of Freiburg
2020-2023
Weihenstephan-Triesdorf University of Applied Sciences
2016-2017
Technical University of Munich
2016-2017
Medigene (Germany)
2017
Goethe University Frankfurt
2008-2014
Frankfurt Institute for Advanced Studies
2011-2013
University of Helsinki
2008
University of Gothenburg
2006-2008
Goethe Institute
2008
University of Basel
2000-2004
The WeNMR ( http://www.wenmr.eu ) project is a European Union funded international effort to streamline and automate analysis of Nuclear Magnetic Resonance (NMR) Small Angle X-Ray scattering (SAXS) imaging data for atomic near-atomic resolution molecular structures. Conventional calculation structure requires the use various software packages, considerable user expertise ample computational resources. To facilitate NMR spectroscopy SAXS in life sciences consortium has established standard...
An approach is described for joint interleaved recording, real-time processing, and analysis of NMR data sets. The method employs multidimensional decomposition to find common information in a set conventional triple-resonance spectra recorded the nonlinear sampling mode, builds model hyperdimensional (HD) spectrum. While preserving sensitivity per unit measurement time allowing maximal spectral resolution, reduces collection on average by 2 orders magnitude compared method. 7-10 dimensional...
Based on the 1H-15N NMR spectroscopy data, three-dimensional structure and internal dynamic properties of ribosomal protein L7 from Escherichia coli were derived. The dimer in solution can be described as a set three distinct domains, tumbling rather independently linked via flexible hinge regions. dimeric N-terminal domain (residues 1-32) consists two antiparallel α-α-hairpins forming symmetrical four-helical bundle, whereas identical C-terminal domains 52-120) adopt compact α/β-fold. There...
Lately, pre-trained language models advanced the field of natural processing (NLP). The introduction Bidirectional Encoders for Transformers (BERT) and its optimized version RoBERTa have had significant impact increased relevance models. First, research in this mainly started on English data followed by trained with multilingual text corpora. However, current shows that are inferior to monolingual Currently, no German single model is yet published, which we introduce work (GottBERT). portion...
A target-oriented approach for the acquisition of information in biomolecular NMR spectroscopy is being developed. This combines concurrent data accumulation, processing, and monitoring spectral quality. Real-time estimation parameters allows to be stopped when results are complete have a specified precision. The technique based on multidimensional decomposition, which can process incomplete data. An incremental nonuniform sampling scheme ensures optimization resolution sensitivity. To...
Abstract Large‐scale initiatives for obtaining spatial protein structures by experimental or computational means have accentuated the need critical assessment of structure determination and prediction methods. These include blind test projects such as (CASP) nuclear magnetic resonance (CASD‐NMR). An important aim is to establish validation criteria that can reliably assess accuracy a new structure. Various quality measures derived from coordinates been proposed. A universal structural method...
Abstract Helix formation of an S‐peptide analog, comprising the first 20 residues Ribonuclease A and two additional N‐terminal residues, was studied by measuring hydrogen bond (H‐bond) h3 J NC′ scalar couplings as a function 2,2,2‐trifluoroethanol (TFE) concentration. The give direct evidence for closing individual backbone N‐H•••O = C H‐bonds during TFE‐induced secondary structure. Whereas no correlations could be detected without TFE, α‐helical (i,i +4) H‐bond were observed amides A5 to...
Modified ubiquitin sequences, each completed with a His tag and TEV cleavage site, were designed to enhance the expression of protein/peptide targets. With this new system we have been able characterize several peptide-protein interactions by ITC NMR CD spectroscopic methods, including LIR domains autophagy modifiers.
A 600 MHz 1H NMR study of toxin OSK1, blocker small-conductance Ca2+-activated K+ channels, is presented. The unambiguous sequential assignment all the protons was obtained using TOCSY, DQF-COSY, and NOESY experiments at pH 3.0 (10, 30, 45 degrees C) in aqueous solution. 3J(N alpha), 3J(alphabeta) vicinal spin coupling constants were determined high-resolution spectra. cross-peak volumes spectra used to define local structure protein by program HABAS generate torsion angle interproton...
Adoptive immunotherapy offers great potential for treating many types of cancer but its clinical application is hampered by cross-reactive T cell responses in healthy human tissues, representing serious safety risks patients. We previously developed a computational tool called Expitope assessing cross-reactivity (CR) antigens based on tissue-specific gene expression. However, transcript abundance only indirectly indicates protein The recent availability proteome-wide information now...
Abstract Native state hydrogen exchange of cold shock protein A (CspA) has been characterized as a function the denaturant urea and stabilizing agent trimethylamine N ‐oxide (TMAO). The structure CspA five strands β‐sheet. Strands β1‐β4 have strongly protected amide protons that, based on experiments urea, through simple all‐or‐none global unfolding mechanism. By contrast, protection from strand β5 is too weak to measure in water. Strand bonded β3 β4, both which afford strong solvent...
Simple peak-picking algorithms, such as those based on lineshape fitting, perform well when peaks are completely resolved in multidimensional NMR spectra, but often produce wrong intensities and frequencies for overlapping peak clusters. For example, NOESY-type spectra have considerable overlaps leading to significant intensity errors, which can result erroneous structural restraints. Precise critical unambiguous resonance assignments. To alleviate this problem, a more sophisticated...
Cross-reactivity (CR) or invocation of autoimmune side effects in various tissues has important safety implications adoptive immunotherapy directed against selected antigens. The ability to predict CR (on-target and off-target toxicities) may help the early selection safer therapeutically relevant target antigens.We developed a methodology for calculation quantitative any defined peptide epitope. Using this approach, we performed assessment 4 groups 283 currently known human MHC-class-I...
Adequate digital resolution and signal sensitivity are two critical factors for protein structure determinations by solution NMR spectroscopy. The prime objective obtaining high is to resolve peak overlap, especially in NOESY spectra with thousands of signals where the analysis needs be performed on a large scale. Achieving maximum usually limited practically available measurement time. We developed method utilizing non-uniform sampling balancing sensitivity, large-scale effect accuracy...
A novel approach is developed to address the challenge of annotating with phenotypic effects those exome variants for which relevant empirical data are lacking or minimal. The predictive annotation method implemented as a stacked ensemble supervised base-learners, including distributed random forest and gradient boosting machines. Ensemble models were trained cross-validated on evidence-based categorical variant effect annotations from ClinVar database, applied 84 million non-synonymous...
A new approach is suggested for delineating the structural and functional amino acid residues in proteins with known three‐dimensional structure, basing on involvement of intramolecular hydrophobic hydrophilic interactions additional information about conservativity residues. The applied to families homologous neurotoxins cardiotoxins. results obtained concerning role both toxins accord well similarity their fold, but different mechanisms action. Current can be used detailed characterization...