Organoarsenic probes to study proteins by NMR spectroscopy

Arsenical probes enable structural studies of proteins. We report the first organoarsenic probes for nuclear magnetic resonance (NMR) spectroscopy to study proteins in solutions. These probes can be attached to irregular loop regions. A lanthanide-binding tag induces sizable pseudocontact shifts in protein NMR spectra of a magnitude never observed for small paramagnetic probes before.

DEER-PREdict: Software for efficient calculation of spin-labeling EPR and NMR data from conformational ensembles

Owing to their plasticity, intrinsically disordered and multidomain proteins require descriptions based on multiple conformations, thus calling for techniques and analysis tools that are capable of dealing with conformational ensembles rather than a single protein structure. Here, we introduce DEER-PREdict, a software program to predict Double Electron-Electron Resonance distance distributions as well as Paramagnetic Relaxation Enhancement rates from ensembles of protein conformations. DEER-PREdict uses an established rotamer library approach to describe the paramagnetic probes which are bound covalently to the protein.DEER-PREdict has been designed to operate efficiently on large conformational ensembles, such as those generated by molecular dynamics simulation, to facilitate the validation or refinement of molecular models as well as the interpretation of experimental data. The performance and accuracy of the software is demonstrated with experimentally characterized protein systems: HIV-1 protease, T4 Lysozyme and Acyl-CoA-binding protein. DEER-PREdict is open source (GPLv3) and available at github.com/KULL-Centre/DEERpredict and as a Python PyPI package pypi.org/project/DEERPREdict.

Non-Destructive Analysis of Mummification Balms in Ancient Egypt, Based on EPR of Vanadyl and Organic Radical Markers of Bitumen

The black matter employed in funeral context by ancient Egyptian is a complex mixture of plant-based compounds with variable amounts of bitumen. Asphaltene, the most resistant component of bitumen, contain Vanadyl porphyrins and carbonaceous radicals which can be used as paramagnetic probes to investigate embalming materials without sample preparation. Electron Paramagnetic Resonance (EPR) at X-band, combining in-phase and out-of-phase detection schemes, provides new information in a non-destructive way about the presence, the origin, and the evolution of bitumen in these complex materials. It is found that the relative EPR intensity of radicals and vanadyl porphyrins is sensitive to the origin of the bitumen. The presence of non-porphyrinic vanadyl complexes in historical samples is likely due to the complexation of VO2+ ions by carboxylic functions at the interface between bitumen and other biological components of the embalming matter. The absence of such oxygenated vanadyl complex in natural bitumen and in one case of historical human mummy acquired by a museum in the 19th century reveals a possible, non-documented, ancient restoration of this mummy by pure bitumen. The linear correlation between in-phase and out-of phase EPR intensities of radicals and vanadyl porphyrins in balms and in natural bitumen, reveals a nanostructuration of radicals and vanadyl porphyrin complexes, which was not affected by the preparation of the balm. This points to the remarkable chemical stability of paramagnetic probes in historical bitumen in ancient Egypt.

Non-Destructive Analysis of Mummification Balms in Ancient Egypt, Based on EPR of Vanadyl and Organic Radical Markers of Bitumen

The black matter employed in funeral context by ancient Egyptian is a complex mixture of plant-based compounds with variable amounts of bitumen. Asphaltene, the most resistant component of bitumen, contain Vanadyl porphyrins and carbonaceous radicals which can be used as paramagnetic probes to investigate embalming materials without sample preparation. Electron Paramagnetic Resonance (EPR) at X-band, combining in-phase and out-of-phase detection schemes, provides new information in a non-destructive way about the presence, the origin, and the evolution of bitumen in these complex materials. It is found that the relative EPR intensity of radicals and vanadyl porphyrins is sensitive to the origin of the bitumen. The presence of non-porphyrinic vanadyl complexes in historical samples is likely due to the complexation of VO2+ ions by carboxylic functions at the interface between bitumen and other biological components of the embalming matter. The absence of such oxygenated vanadyl complex in natural bitumen and in one case of historical human mummy acquired by a museum in the 19th century reveals a possible, non-documented, ancient restoration of this mummy by pure bitumen. The linear correlation between in-phase and out-of phase EPR intensities of radicals and vanadyl porphyrins in balms and in natural bitumen, reveals a nanostructuration of radicals and vanadyl porphyrin complexes, which was not affected by the preparation of the balm. This points to the remarkable chemical stability of paramagnetic probes in historical bitumen in ancient Egypt.

DEER-PREdict: Software for Efficient Calculation of Spin-Labeling EPR and NMR Data from Conformational Ensembles

Owing to their plasticity, intrinsically disordered and multidomain proteins require descriptions based on multiple conformations, thus calling for techniques and analysis tools that are capable of dealing with conformational ensembles rather than a single protein structure. Here, we introduce DEER-PREdict, a software to predict Double Electron-Electron Resonance distance distributions as well as Paramagnetic Relaxation Enhancement rates from ensembles of protein conformations. DEER-PREdict uses an established rotamer library approach to describe the paramagnetic probes which are bound covalently to the protein. DEER-PREdict has been designed to operate efficiently on large conformational ensembles, such as those generated by molecular dynamics simulation, to facilitate the validation or refinement of molecular models as well as the interpretation of experimental data. The performance and accuracy of the software is demonstrated with experimentally characterized protein systems: HIV-1 protease, T4 Lysozyme and Acyl-CoA-binding protein. DEER-PREdict is open source (GPLv3) and available at github.com/KULL-Centre/DEERpredict and as a Python PyPI package pypi.org/project/DEERPREdict.

A ratiometric 19F MR-based method for the quantification of Ca2+ using responsive paramagnetic probes

A custom made lanthanide complex with a high number of fluorine atoms was used to develop a quantitative method to assess calcium ion concentration by means of 19F chemical shift imaging.

Exploring exchange processes in proteins by paramagnetic perturbation of NMR spectra

The effects induced by extrinsic paramagnetic probes on protein NMR spectra, widely used for surface mapping, can also be exploited to detect the sites of slow and intermediate exchange due to structural or intermolecular interaction dynamics.