The GNAT: A new tool for processing NMR data

Castañar, Laura; Poggetto, Guilherme Dal; Colbourne, Adam A.; Nilsson, Mathias

doi:10.1002/mrc.4717

Cited by 72 publications

(76 citation statements)

References 119 publications

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“…Tetramethylsilane (TMS) was used in all NMR experiments as internal standard and chemical shift ( δ ) values are given in ppm. General NMR Analysis Toolbox (GNAT, v1.2, Free Software Foundation, Inc., Boston, MA, USA) was used for the analyses of NMR experiments [ 43 ]. Low resolution mass spectra were obtained on a Thermofisher LCQ DECA XP ion trap mass spectrometer or a Waters-Micromass ZQ-Single quadrupole mass spectrometer.…”

Section: Methodsmentioning

confidence: 99%

NHS-Functionalized THP Derivative for Efficient Synthesis of Kit-Based Precursors for 68Ga Labeled PET Probes

et al. 2021

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Hexadentate tris(3,4-hydroxypyridinone) ligands (THP) complex Fe3+ at very low iron concentrations and their high affinities for oxophilic trivalent metal ions have led to their development for new applications as bifunctional chelators for the radiometal gallium-68 (68Ga). THP-peptide bioconjugates rapidly and quantitatively complex 68Ga at room temperature, neutral pH, and micromolar ligand concentrations, making them amenable to kit-based radiosynthesis of 68Ga PET radiopharmaceuticals. With the aim to produce an N-hydroxysuccinimide-(NHS)-THP reagent for kit-based 68Ga-labeling and PET imaging, THP-derivatives were designed and synthesized to exploit the advantages of NHS chemistry for coupling with peptides, proteins, and antibodies. The more stable five-carbon atoms linker product was selected for a proof-of-concept conjugation and radiolabeling study with an anti-programmed death ligand 1 (PD-L1) camelid single domain antibody (sdAb) under mild conditions and further evaluated for site-specific amide bond formation with a synthesized glucagon-like peptide-1 (GLP-1) targeting peptide using solid-phase synthesis. The obtained THP-GLP-1 conjugate was tested for its 68Ga chelating ability, demonstrating to be a promising candidate for the detection and monitoring of GLP-1 aberrant malignancies. The obtained sdAb-THP conjugate was radiolabeled with 68Ga under mild conditions, providing sufficient labeling yields after 5 min, demonstrating that the novel NHS-THP bifunctional chelator can be widely used to easily conjugate the THP moiety to different targeting molecules (e.g., antibodies, anticalins, or peptides) under mild conditions, paving the way to the synthesis of different imaging probes with all the advantages of THP radiochemistry.

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Section: Methodsmentioning

confidence: 99%

NHS-Functionalized THP Derivative for Efficient Synthesis of Kit-Based Precursors for 68Ga Labeled PET Probes

et al. 2021

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“…The gradient range used for each temperature was 500 to 26,500 DAC units in increments of 1000 DAC (1 DAC = 0.001744 G/cm), with 27 equal increments per experiment. The diffusion data were processed, and the corresponding hydrodynamic radius ( R H ) was estimated for each experiment using the program General NMR Analysis Toolbox (GNAT) [40,41,42]. From the estimated R H values, the radius of gyration was calculated using the scaling relation, Rg = 0.65 × R H , following Gaussian chain approximation.…”

Section: Methodsmentioning

confidence: 99%

The Ensemble of Conformations of Antifreeze Glycoproteins (AFGP8): A Study Using Nuclear Magnetic Resonance Spectroscopy

2019

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The primary sequence of antifreeze glycoproteins (AFGPs) is highly degenerate, consisting of multiple repeats of the same tripeptide, Ala–Ala–Thr*, in which Thr* is a glycosylated threonine with the disaccharide beta-d-galactosyl-(1,3)-alpha-N-acetyl-d-galactosamine. AFGPs seem to function as intrinsically disordered proteins, presenting challenges in determining their native structure. In this work, a different approach was used to elucidate the three-dimensional structure of AFGP8 from the Arctic cod Boreogadus saida and the Antarctic notothenioid Trematomus borchgrevinki. Dimethyl sulfoxide (DMSO), a non-native solvent, was used to make AFGP8 less dynamic in solution. Interestingly, DMSO induced a non-native structure, which could be determined via nuclear magnetic resonance (NMR) spectroscopy. The overall three-dimensional structures of the two AFGP8s from two different natural sources were different from a random coil ensemble, but their “compactness” was very similar, as deduced from NMR measurements. In addition to their similar compactness, the conserved motifs, Ala–Thr*–Pro–Ala and Ala–Thr*–Ala–Ala, present in both AFGP8s, seemed to have very similar three-dimensional structures, leading to a refined definition of local structural motifs. These local structural motifs allowed AFGPs to be considered functioning as effectors, making a transition from disordered to ordered upon binding to the ice surface. In addition, AFGPs could act as dynamic linkers, whereby a short segment folds into a structural motif, while the rest of the AFGPs could still be disordered, thus simultaneously interacting with bulk water molecules and the ice surface, preventing ice crystal growth.

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“…Benchtop NMR with WATERGATE W5 was able to 323 detect lipidic intracellular concentrations at 9 mg.L À1 and to quan- whose width depends on the quality of the fit, which is particularly critical when peaks are overlapped such as in complex mixtures. To deal with this limitation, the processing of DOSY data has been the subject of numerous multivariate signal processing developments, notably by the group of Nilsson and co-workers [41,42].…”

Section: Introductionmentioning

confidence: 99%

Gradient-based pulse sequences for benchtop NMR spectroscopy

Gouilleux

Farjon

Giraudeau

2020

Journal of Magnetic Resonance

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Benchtop NMR spectroscopy has been on the rise for the last decade, by bringing high-resolution NMR in 30 environments that are not easily compatible with high-field NMR. Benchtop spectrometers are accessible, 31 low cost and show an impressive performance in terms of sensitivity with respect to the relatively low 32 associated magnetic field (40-100 MHz). However, their application is limited by the strong and ubiqui-33 tous peak overlaps arising from the complex mixtures which are often targeted, often characterized by a 34 great diversity of concentrations and by strong signals from non-deuterated solvents. Such limitations 35 can be addressed by pulse sequences making clever use of magnetic field gradient pulses, capable of per-36 forming efficient coherence selection or encoding chemical shift or diffusion information. Gradients 37 pulses are well-known ingredients of high-field pulse sequence recipes, but were only recently made 38 available on benchtop spectrometers, thanks to the introduction of gradient coils in 2015. This article 39 reviews the recent methodological advances making use of gradient pulses on benchtop spectrometers 40 and the applications stemming from these developments. Particular focus is made on solvent suppression 41 schemes, diffusion-encoded, and spatially-encoded experiments, while discussing both methodological 42 advances and subsequent applications. We eventually discuss the exciting development and application 43 perspectives that result from such advances.

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The GNAT: A new tool for processing NMR data

Cited by 72 publications

References 119 publications

NHS-Functionalized THP Derivative for Efficient Synthesis of Kit-Based Precursors for 68Ga Labeled PET Probes

NHS-Functionalized THP Derivative for Efficient Synthesis of Kit-Based Precursors for 68Ga Labeled PET Probes

The Ensemble of Conformations of Antifreeze Glycoproteins (AFGP8): A Study Using Nuclear Magnetic Resonance Spectroscopy

Gradient-based pulse sequences for benchtop NMR spectroscopy

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