Paramagpy: Software for Fitting Magnetic Susceptibility Tensors Using Paramagnetic Effects Measured in NMR Spectra

Orton, Henry; Huber, Thomas; Otting, Gottfried

doi:10.26434/chemrxiv.9643154.v1

Cited by 7 publications

(13 citation statements)

References 22 publications

(28 reference statements)

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“…The resonance assignments of the wild-type Zn 2 enzyme (BMRB entry 25063) were used to assign the 15 N-HSQC cross-peaks in the diamagnetic state. The program Paramagpy (Orton et al, 2020) was used to fit magnetic susceptibility anisotropy ( χ) tensors to crystal structures of IMP-1 solved in the absence and presence of the inhibitor captopril.…”

Section: ∆χ -Tensor Fitsmentioning

confidence: 99%

“…The χ -tensor parameters were determined using the program Paramagpy (Orton et al, 2020) using all available 1 H PCSs measured of backbone amides. Comparing the χtensor fits to the crystal structures 5EV6 chains A and C (Hinchliffe et al, 2016) and 1DDK (Concha et al, 2000) of the free protein, chain A of the structure 5EV6 proved to produce the smallest Q factor by a small margin (Fig.…”

Section: ∆χ -Tensor Fitsmentioning

confidence: 99%

“…In addition, uncertainties in the χ tensors were propagated by averaging over the results from 20 χ -tensor fits performed with random omission of 20 % of the backbone PCS data. In the present work, the routine for defining the localisation space was implemented as a script in the software Paramagpy (Orton et al, 2020). Figure 6 shows the resulting localisation spaces for the H ε1 and H ζ 2 atoms of Trp28 using the PCS data obtained for the three cysteine mutants A53C, N172C and S204C with the C2-Tb 3+ tag as well as the N172C mutant with the C12-Tb 3+ tag.…”

Section: Determining the Localisation Spaces Of Tryptophan Side Chainsmentioning

confidence: 99%

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Localising individual atoms of tryptophan side chains in the metallo-<i>β</i>-lactamase IMP-1 by pseudocontact shifts from paramagnetic lanthanoid tags at multiple sites

et al. 2022

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Abstract. The metallo-β-lactamase IMP-1 features a flexible loop near the active site that assumes different conformations in single crystal structures, which may assist in substrate binding and enzymatic activity. To probe the position of this loop, we labelled the tryptophan residues of IMP-1 with 7-13C-indole and the protein with lanthanoid tags at three different sites. The magnetic susceptibility anisotropy (Δχ) tensors were determined by measuring pseudocontact shifts (PCSs) of backbone amide protons. The Δχ tensors were subsequently used to identify the atomic coordinates of the tryptophan side chains in the protein. The PCSs were sufficient to determine the location of Trp28, which is in the active site loop targeted by our experiments, with high accuracy. Its average atomic coordinates showed barely significant changes in response to the inhibitor captopril. It was found that localisation spaces could be defined with better accuracy by including only the PCSs of a single paramagnetic lanthanoid ion for each tag and tagging site. The effect was attributed to the shallow angle with which PCS isosurfaces tend to intersect if generated by tags and tagging sites that are identical except for the paramagnetic lanthanoid ion.

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Section: ∆χ -Tensor Fitsmentioning

confidence: 99%

Section: ∆χ -Tensor Fitsmentioning

confidence: 99%

Section: Determining the Localisation Spaces Of Tryptophan Side Chainsmentioning

confidence: 99%

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Localising individual atoms of tryptophan side chains in the metallo-<i>β</i>-lactamase IMP-1 by pseudocontact shifts from paramagnetic lanthanoid tags at multiple sites

et al. 2022

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“…Coordinates of the metal position were fitted via a non-linear gradient descent using the Broyden-Fletcher-Goldfarb-Shanno (BFGS) algorithm (Fletcher 1988) for non-linear least-square minimisation of the cost function described in Eq. ( 4) (Orton et al 2020).…”

Section: Calculation Of γ 2 Presmentioning

confidence: 99%

“…Anisotropic magnetic susceptibility tensors Δ induced by lanthanoid ions were obtained by fitting of experimental PCS to Eq. ( 5) as described in Paramagpy software package (Orton et al 2020).…”

Section: Fitting Of Alignment Tensors From Pcs Datamentioning

confidence: 99%

Ligand-induced structural transitions combined with paramagnetic ions facilitate unambiguous NMR assignments of methyl groups in large proteins

et al. 2022

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NMR spectroscopy allows the study of biomolecules in close-to-native conditions. Structural information can be inferred from the NMR spectra when an assignment is available. Protein assignment is usually a time-consuming task, being specially challenging in the case of large, supramolecular systems. Here, we present an extension of existing state-of-the-art strategies for methyl group assignment that partially overcomes signal overlapping and other difficulties associated to isolated methyl groups. Our approach exploits the ability of proteins to populate two or more conformational states, allowing for unique NOE restraints in each protein conformer. The method is compatible with automated assignment algorithms, granting assignments beyond the limits of a single protein state. The approach also benefits from long-range structural restraints obtained from metal-induced pseudocontact shifts (PCS) and paramagnetic relaxation enhancements (PREs). We illustrate the method with the complete assignment of the 199 methyl groups of a MILproSVproSAT methyl-labeled sample of the UDP-glucose pyrophosphorylase enzyme from Leishmania major (LmUGP). Protozoan parasites of the genus Leishmania causes Leishmaniasis, a neglected disease affecting over 12 million people worldwide. LmUGP is responsible for the de novo biosynthesis of uridine diphosphate-glucose, a precursor in the biosynthesis of the dense surface glycocalyx involved in parasite survival and infectivity. NMR experiments with LmUGP and related enzymes have the potential to unravel new insights in the host resistance mechanisms used by Leishmania major. Our efforts will help in the development of selective and efficient drugs against Leishmania.

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In-Cell Structural Biology by NMR: The Benefits of the Atomic Scale

Theillet

2022

Chem. Rev.

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In-cell structural biology aims at extracting structural information about proteins or nucleic acids in their native, cellular environment. This emerging field holds great promises and is already providing new facts and outlooks of interest at both fundamental and applied levels. NMR spectroscopy has important contributions on this stage: it brings information on a broad variety of nuclei at the atomic scale, which ensures its great versatility and uniqueness. Here, we detail the methods, the fundamental knowledge and the applications in biomedical engineering related to in-cell NMR. We finally propose a brief overview of the main other techniques in the field (EPR, smFRET, cryo-ET…) to draw some advisable developments for in-cell NMR. In the era of large-scale screenings and deep learning, both accurate and qualitative experimental evidences are as essential as ever to understand the interior life of cells. In-cell structural biology by NMR spectroscopy can generate such a knowledge, and it does so at the atomic scale. This review is meant to deliver comprehensive but accessible information, with advanced technical details and reflections on the methods, the nature of the results and the future of the field. CONTENTS 5.1.1. In-cell EPR 5.1.2. In-cell FRET microscopy 5.1.3. Mass-spectrometry 5.1.4. Cryo-ET 5.2. The specific benefits of in-cell NMR 5.3. The future technical challenges of in-cell NMR 6. Conclusion Author Information

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Paramagpy: Software for Fitting Magnetic Susceptibility Tensors Using Paramagnetic Effects Measured in NMR Spectra

Cited by 7 publications

References 22 publications

Localising individual atoms of tryptophan side chains in the metallo-<i>β</i>-lactamase IMP-1 by pseudocontact shifts from paramagnetic lanthanoid tags at multiple sites

Localising individual atoms of tryptophan side chains in the metallo-<i>β</i>-lactamase IMP-1 by pseudocontact shifts from paramagnetic lanthanoid tags at multiple sites

Ligand-induced structural transitions combined with paramagnetic ions facilitate unambiguous NMR assignments of methyl groups in large proteins

In-Cell Structural Biology by NMR: The Benefits of the Atomic Scale

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Paramagpy: Software for Fitting Magnetic Susceptibility Tensors Using Paramagnetic Effects Measured in NMR Spectra

Cited by 7 publications

References 22 publications

Localising individual atoms of tryptophan side chains in the metallo-&lt;i&gt;β&lt;/i&gt;-lactamase IMP-1 by pseudocontact shifts from paramagnetic lanthanoid tags at multiple sites

Localising individual atoms of tryptophan side chains in the metallo-&lt;i&gt;β&lt;/i&gt;-lactamase IMP-1 by pseudocontact shifts from paramagnetic lanthanoid tags at multiple sites

Ligand-induced structural transitions combined with paramagnetic ions facilitate unambiguous NMR assignments of methyl groups in large proteins

In-Cell Structural Biology by NMR: The Benefits of the Atomic Scale

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Localising individual atoms of tryptophan side chains in the metallo-<i>β</i>-lactamase IMP-1 by pseudocontact shifts from paramagnetic lanthanoid tags at multiple sites

Localising individual atoms of tryptophan side chains in the metallo-<i>β</i>-lactamase IMP-1 by pseudocontact shifts from paramagnetic lanthanoid tags at multiple sites