The use of 1H-1H nuclear Overhauser effects (NOE) for structural studies of uniformly deuterated polypeptide chains in large structures is investigated by model calculations and NMR experiments. Detailed analysis of the evolution of the magnetization during 1H-1H NOE experiments under slow-motion conditions shows that the maximal 1H-1H NOE transfer is independent of the overall rotational correlation time, even in the presence of chemical exchange with the bulk water, provided that the mixing time is adjusted for the size of the structure studied. 1H-1H NOE buildup measurements were performed for the 472-kDa complex of the 72-kDa cochaperonin GroES with a 400-kDa single-ring variant of the chaperonin GroEL (SR1). These experiments demonstrate that multidimensional NOESY experiments with cross-correlated relaxation-enhanced polarization transfer and transverse relaxation-optimized spectroscopy elements can be applied to structures of molecular masses up to several hundred kilodaltabs, which opens new possibilities for studying functional interactions in large maromolecular assemblies in solution.
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http://dx.doi.org/10.1073/pnas.0607141103 | DOI Listing |
J Biomol NMR
April 2023
Department of Biochemistry, Molecular Biology & Biophysics, University of Minnesota, 6-155 Jackson Hall, 312 Church St. SE, Minneapolis, MN, 55455, USA.
The nuclear Overhauser effect (NOE) is one of NMR spectroscopy's most important and versatile parameters. NOE is routinely utilized to determine the structures of medium-to-large size biomolecules and characterize protein-protein, protein-RNA, protein-DNA, and protein-ligand interactions in aqueous solutions. Typical [H,H] NOESY pulse sequences incorporate water suppression schemes to reduce the water signal that dominates H-detected spectra and minimize NOE intensity losses due to unwanted polarization exchange between water and labile protons.
View Article and Find Full Text PDFMagn Reson (Gott)
August 2022
Laboratory of Physical Chemistry, ETH, Swiss Federal Institute of Technology, HCI F217, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland.
Exact nuclear Overhauser enhancement (eNOE) yields highly accurate, ensemble averaged H-H distance restraints with an accuracy of up to 0.1 Å for the multi-state structure determination of proteins as well as for nuclear magnetic resonance molecular replacement (MR) to determine the structure of the protein-ligand interaction site in a time-efficient manner. However, in the latter application, the acquired eNOEs lack the obtainable precision of 0.
View Article and Find Full Text PDFMagn Reson (Gott)
September 2021
Department of Biochemistry, Duke University School of Medicine, Durham, NC, USA.
In duplex DNA, Watson-Crick A-T and G-C base pairs (bp's) exist in dynamic equilibrium with an alternative Hoogsteen conformation, which is low in abundance and short-lived. Measuring how the Hoogsteen dynamics varies across different DNA sequences, structural contexts and physiological conditions is key for identifying potential Hoogsteen hot spots and for understanding the potential roles of Hoogsteen base pairs in DNA recognition and repair. However, such studies are hampered by the need to prepare C or N isotopically enriched DNA samples for NMR relaxation dispersion (RD) experiments.
View Article and Find Full Text PDFMagn Reson (Gott)
April 2021
Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
Resonance assignment and structural studies of larger proteins by nuclear magnetic resonance (NMR) can be challenging when exchange broadening, multiple stable conformations, and H back-exchange of the fully deuterated chain pose problems. These difficulties arise for the SARS-CoV-2 Main Protease, a homodimer of 2 306 residues. We demonstrate that the combination of four-dimensional (4D) TROSY-NOESY-TROSY spectroscopy and 4D NOESY-NOESY-TROSY spectroscopy provides an effective tool for delineating the H-H dipolar relaxation network.
View Article and Find Full Text PDFMagn Reson Chem
December 2019
Institute of Chemical Process Fundamentals of the CAS, Prague 6, Czech Republic.
The connectivities of all atoms in ascorbigen A, an important metabolite, were determined unambiguously for the first time. The connectivity between carbon atoms was established by 2D INADEQUATE, and one-bond C- C coupling constants were determined for all pairs of directly connected carbon atoms except for two strongly coupled carbon pairs. The C- C coupling in one of the pairs was proved by a modification of standard INADEQUATE; however, the signals from the other pair were too weak to be observed.
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