Krähenbühl Barbara, El Bakkali Issam, Schmidt Elena, Güntert Peter, Wider Gerhard (2014), Automated NMR resonance assignment strategy for RNA via the phosphodiester backbone based on high-dimensional through-bond APSY experiments., in Journal of biomolecular NMR
, 59(2), 87-93.
Walczak Michal J., Puorger Chasper, Glockshuber Rudi, Wider Gerhard (2014), Intramolecular Donor Strand Complementation in the E. coli Type 1 Pilus Subunit FimA Explains the Existence of FimA Monomers As Off-Pathway Products of Pilus Assembly That Inhibit Host Cell Apoptosis, in JOURNAL OF MOLECULAR BIOLOGY
, 426(3), 542-549.
Krähenbühl Barbara, Boudet Julien, Wider Gerhard (2013), 4D experiments measured with APSY for automated backbone resonance assignments of large proteins., in Journal of biomolecular NMR
, 56(2), 149-54.
Krähenbühl B, Wider G (2012), Automated Projection Spectroscopy (APSY) for the Assignment of NMR Resonances of Biological Macromolecules, in CHIMIA
, 66(10), 767-771.
Krahenbuhl B, Hofmann D, Maris C, Wider G (2012), Sugar-to-base correlation in nucleic acids with a 5D APSY-HCNCH or two 3D APSY-HCN experiments, in JOURNAL OF BIOMOLECULAR NMR
, 52(2), 141-150.
Krahenbuhl B, Hiller S, Wider G (2011), 4D APSY-HBCB(CG)CDHD experiment for automated assignment of aromatic amino acid side chains in proteins, in JOURNAL OF BIOMOLECULAR NMR
, 51(3), 313-318.
Hiller S, Wider G (2011), Automated Projection Spectroscopy and Its Applications, in Top. Curr. Chem.
, 316, 21-48.
Nuclear magnetic resonance (NMR) spectroscopy in solution has found wide spread applications in physical, chemical, biological and medical sciences. A prerequisite for the detailed analysis of the information content of NMR spectra are individual assignments of resonances to specific nuclei (atoms). In biological applications, the necessary data is usually obtained from a number of multi-dimensional NMR experiments which correlate coherences of 1H, 13C and 15N nuclei in doubly 13C,15N isotope-labeled macromolecules. Often, the data cannot be analyzed by automated computer programs and full resonance assignments can only be obtained interactively by an experienced NMR spectroscopist. The aim of this research project is the development of efficient methods for NMR spectroscopy applied to biological macromolecules. Recently, in collaboration with Prof. Wüthrich (ETH-Z), we introduced a new technique, APSY (automated projection spectroscopy), which is based on projection NMR spectroscopy. APSY was shown to provide data that can reliably be analyzed by automated programs. For example, for protein spectra fully automated assignments of resonances of nuclei in the backbone and in aliphatic side chains could be obtained.In this proposal we want to further develop the APSY methodology and extend its applicability. In a first step, the available APSY techniques for resonance assignments in protein spectra will be complemented by APSY experiments for automated assignment of resonances of aromatic side chain nuclei. With the successful implementation of these experiments a set of APSY experiments will be available for complete and automated assignment of resonances in spectra of small and medium size proteins. For larger proteins transverse relaxation reduces the sensitivity of NMR spectra and usually these proteins are perdeuterated to reduce relaxation. We want to extend the applicability of the APSY technology to this class of proteins. For maximal sensitivity APSY experiments will be designed that use the concept of transverse relaxation optimizes spectroscopy (TROSY). The result of this development will be a set of APSY experiments for automated resonance assignment of nuclei in the polypeptide backbone (including the ?-carbon) of deuterated 13C,15N-labeled proteins.Based on the experience gained with the use of APSY with proteins we want to apply the APSY technique to another class of macromolecules: RNA and DNA. The assignment of resonances in RNA (DNA) is often challenging especially for automated routines because of the small dispersion of resonances in RNA (DNA) spectra. The application of APSY with denatured proteins has shown that this method can deal very well with poorly resolved spectra. Based on APSY correlation experiments in the bases, sugar and the oligonucleotide backbone we will design a suite of APSY experiments for automated sequence-specific assignments of resonances in spectra of 13C,15N-labeled RNA (DNA). The outcome of this work will provide experimental procedures for automated resonance assignment in spectra of biological macromolecules. The methodology will make the application of NMR spectroscopy with this class of molecules more efficient by alleviating a major bottleneck in the analysis of NMR data. We anticipate that this methodology progress will have a considerable impact on current biophysical research with NMR spectroscopy.