Articles | Volume 1, issue 1
https://doi.org/10.5194/mr-1-1-2020
© Author(s) 2020. This work is distributed under
the Creative Commons Attribution 4.0 License.
the Creative Commons Attribution 4.0 License.
https://doi.org/10.5194/mr-1-1-2020
© Author(s) 2020. This work is distributed under
the Creative Commons Attribution 4.0 License.
the Creative Commons Attribution 4.0 License.
Research article
| 
14 Feb 2020
Research article |
| 14 Feb 2020
| 14 Feb 2020
Paramagpy: software for fitting magnetic susceptibility tensors using paramagnetic effects measured in NMR spectra
Henry William Orton
Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
Thomas Huber
Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
Gottfried Otting
CORRESPONDING AUTHOR
Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
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Cited
32 citations as recorded by crossref.
- Ligand-induced structural transitions combined with paramagnetic ions facilitate unambiguous NMR assignments of methyl groups in large proteins L. Mühlberg et al. 10.1007/s10858-022-00394-0
- Paramagnetic Chemical Probes for Studying Biological Macromolecules Q. Miao et al. 10.1021/acs.chemrev.1c00708
- Phosphoserine for the generation of lanthanide-binding sites on proteins for paramagnetic nuclear magnetic resonance spectroscopy S. Mekkattu Tharayil et al. 10.5194/mr-2-1-2021
- Site-selective generation of lanthanoid binding sites on proteins using 4-fluoro-2,6-dicyanopyridine S. Mekkattu Tharayil et al. 10.5194/mr-3-169-2022
- Sparse pseudocontact shift NMR data obtained from a non-canonical amino acid-linked lanthanide tag improves integral membrane protein structure prediction K. Ledwitch et al. 10.1007/s10858-023-00412-9
- An automated iterative approach for protein structure refinement using pseudocontact shifts S. Cucuzza et al. 10.1007/s10858-021-00376-8
- A general chemical crosslinking strategy for structural analyses of weakly interacting proteins applied to preTCR–pMHC complexes R. Mizsei et al. 10.1016/j.jbc.2021.100255
- Partial Opening of Cytochrome P450cam (CYP101A1) Is Driven by Allostery and Putidaredoxin Binding S. Skinner et al. 10.1021/acs.biochem.1c00406
- Distinct stereospecific effect of chiral tether between a tag and protein on the rigidity of paramagnetic tag J. Chen et al. 10.1007/s10858-022-00399-9
- Unexpected dynamics in femtomolar complexes of binding proteins with peptides S. Cucuzza et al. 10.1038/s41467-023-43596-2
- Ligand-Capped Cobalt(II) Multiplies the Value of the Double-Histidine Motif for PCS NMR Studies W. Zhu et al. 10.1021/jacs.2c12021
- A Chiral Lanthanide Tag for Stable and Rigid Attachment to Single Cysteine Residues in Proteins for NMR, EPR and Time‐Resolved Luminescence Studies I. Herath et al. 10.1002/chem.202101143
- Reweighting methods for elucidation of conformation ensembles of proteins R. Gama Lima Costa & D. Fushman 10.1016/j.sbi.2022.102470
- Intrinsic anisotropy parameters of a series of lanthanoid complexes deliver new insights into the structure-magnetism relationship R. Vogel et al. 10.1016/j.chempr.2021.08.011
- Assignment of Ala, Ile, LeuproS, Met, and ValproS methyl groups of the protruding domain of murine norovirus capsid protein VP1 using methyl–methyl NOEs, site directed mutagenesis, and pseudocontact shifts T. Maass et al. 10.1007/s12104-022-10066-7
- NMR analysis suggests the terminal domains of Robo1 remain extended but are rigidified in the presence of heparan sulfate R. Williams et al. 10.1038/s41598-022-18769-6
- Nanobody GPS by PCS: An Efficient New NMR Analysis Method for G Protein Coupled Receptors and Other Large Proteins F. Wu et al. 10.1021/jacs.2c09692
- Characterizing conformational ensembles of multi-domain proteins using anisotropic paramagnetic NMR restraints X. Hou & H. Tochio 10.1007/s12551-021-00916-4
- Determining Local Magnetic Susceptibility Tensors in Paramagnetic Lanthanide Crystalline Powders from Solid-State NMR Chemical Shift Anisotropies R. Ince et al. 10.1021/acs.jpca.2c06955
- In-Cell Structural Biology by NMR: The Benefits of the Atomic Scale F. Theillet 10.1021/acs.chemrev.1c00937
- The Q163C/Q309C mutant of αMI-domain is an active variant suitable for NMR characterization H. Nguyen et al. 10.1371/journal.pone.0280778
- A lanthanide tag for a complementary set of pseudocontact shifts L. Topping et al. 10.1039/D4CC03007A
- 3site Multisubstrate-Bound State of Cytochrome P450cam M. Sahil et al. 10.1021/jacs.3c06144
- Localising nuclear spins by pseudocontact shifts from a single tagging site H. Orton et al. 10.5194/mr-3-65-2022
- Excellent Fe(II) Binding Tag in Protein Paramagnetic NMR Spectroscopy M. Li et al. 10.1021/acs.inorgchem.4c05233
- Pseudocontact Shifts in Biomolecular NMR Spectroscopy T. Müntener et al. 10.1021/acs.chemrev.1c00796
- Structure determination of high-energy states in a dynamic protein ensemble J. Stiller et al. 10.1038/s41586-022-04468-9
- Rational Design of Lanthanide-Binding Tags to Optimize Magnetic Anisotropy in Paramagnetic Protein NMR J. Chen et al. 10.1021/jacs.5c01192
- Incorporation of residual chemical shift anisotropy into the treatment of 15N pseudocontact shifts for structural refinement D. Nyenhuis et al. 10.1016/j.jmr.2022.107213
- Localising individual atoms of tryptophan side chains in the metallo-β-lactamase IMP-1 by pseudocontact shifts from paramagnetic lanthanoid tags at multiple sites H. Orton et al. 10.5194/mr-3-1-2022
- αMI-domain of integrin Mac-1 binds the cytokine pleiotrophin using multiple mechanisms H. Nguyen et al. 10.1016/j.str.2024.04.013
- Paramagnetic NMR in drug discovery C. Softley et al. 10.1007/s10858-020-00322-0
32 citations as recorded by crossref.
- Ligand-induced structural transitions combined with paramagnetic ions facilitate unambiguous NMR assignments of methyl groups in large proteins L. Mühlberg et al. 10.1007/s10858-022-00394-0
- Paramagnetic Chemical Probes for Studying Biological Macromolecules Q. Miao et al. 10.1021/acs.chemrev.1c00708
- Phosphoserine for the generation of lanthanide-binding sites on proteins for paramagnetic nuclear magnetic resonance spectroscopy S. Mekkattu Tharayil et al. 10.5194/mr-2-1-2021
- Site-selective generation of lanthanoid binding sites on proteins using 4-fluoro-2,6-dicyanopyridine S. Mekkattu Tharayil et al. 10.5194/mr-3-169-2022
- Sparse pseudocontact shift NMR data obtained from a non-canonical amino acid-linked lanthanide tag improves integral membrane protein structure prediction K. Ledwitch et al. 10.1007/s10858-023-00412-9
- An automated iterative approach for protein structure refinement using pseudocontact shifts S. Cucuzza et al. 10.1007/s10858-021-00376-8
- A general chemical crosslinking strategy for structural analyses of weakly interacting proteins applied to preTCR–pMHC complexes R. Mizsei et al. 10.1016/j.jbc.2021.100255
- Partial Opening of Cytochrome P450cam (CYP101A1) Is Driven by Allostery and Putidaredoxin Binding S. Skinner et al. 10.1021/acs.biochem.1c00406
- Distinct stereospecific effect of chiral tether between a tag and protein on the rigidity of paramagnetic tag J. Chen et al. 10.1007/s10858-022-00399-9
- Unexpected dynamics in femtomolar complexes of binding proteins with peptides S. Cucuzza et al. 10.1038/s41467-023-43596-2
- Ligand-Capped Cobalt(II) Multiplies the Value of the Double-Histidine Motif for PCS NMR Studies W. Zhu et al. 10.1021/jacs.2c12021
- A Chiral Lanthanide Tag for Stable and Rigid Attachment to Single Cysteine Residues in Proteins for NMR, EPR and Time‐Resolved Luminescence Studies I. Herath et al. 10.1002/chem.202101143
- Reweighting methods for elucidation of conformation ensembles of proteins R. Gama Lima Costa & D. Fushman 10.1016/j.sbi.2022.102470
- Intrinsic anisotropy parameters of a series of lanthanoid complexes deliver new insights into the structure-magnetism relationship R. Vogel et al. 10.1016/j.chempr.2021.08.011
- Assignment of Ala, Ile, LeuproS, Met, and ValproS methyl groups of the protruding domain of murine norovirus capsid protein VP1 using methyl–methyl NOEs, site directed mutagenesis, and pseudocontact shifts T. Maass et al. 10.1007/s12104-022-10066-7
- NMR analysis suggests the terminal domains of Robo1 remain extended but are rigidified in the presence of heparan sulfate R. Williams et al. 10.1038/s41598-022-18769-6
- Nanobody GPS by PCS: An Efficient New NMR Analysis Method for G Protein Coupled Receptors and Other Large Proteins F. Wu et al. 10.1021/jacs.2c09692
- Characterizing conformational ensembles of multi-domain proteins using anisotropic paramagnetic NMR restraints X. Hou & H. Tochio 10.1007/s12551-021-00916-4
- Determining Local Magnetic Susceptibility Tensors in Paramagnetic Lanthanide Crystalline Powders from Solid-State NMR Chemical Shift Anisotropies R. Ince et al. 10.1021/acs.jpca.2c06955
- In-Cell Structural Biology by NMR: The Benefits of the Atomic Scale F. Theillet 10.1021/acs.chemrev.1c00937
- The Q163C/Q309C mutant of αMI-domain is an active variant suitable for NMR characterization H. Nguyen et al. 10.1371/journal.pone.0280778
- A lanthanide tag for a complementary set of pseudocontact shifts L. Topping et al. 10.1039/D4CC03007A
- 3site Multisubstrate-Bound State of Cytochrome P450cam M. Sahil et al. 10.1021/jacs.3c06144
- Localising nuclear spins by pseudocontact shifts from a single tagging site H. Orton et al. 10.5194/mr-3-65-2022
- Excellent Fe(II) Binding Tag in Protein Paramagnetic NMR Spectroscopy M. Li et al. 10.1021/acs.inorgchem.4c05233
- Pseudocontact Shifts in Biomolecular NMR Spectroscopy T. Müntener et al. 10.1021/acs.chemrev.1c00796
- Structure determination of high-energy states in a dynamic protein ensemble J. Stiller et al. 10.1038/s41586-022-04468-9
- Rational Design of Lanthanide-Binding Tags to Optimize Magnetic Anisotropy in Paramagnetic Protein NMR J. Chen et al. 10.1021/jacs.5c01192
- Incorporation of residual chemical shift anisotropy into the treatment of 15N pseudocontact shifts for structural refinement D. Nyenhuis et al. 10.1016/j.jmr.2022.107213
- Localising individual atoms of tryptophan side chains in the metallo-β-lactamase IMP-1 by pseudocontact shifts from paramagnetic lanthanoid tags at multiple sites H. Orton et al. 10.5194/mr-3-1-2022
- αMI-domain of integrin Mac-1 binds the cytokine pleiotrophin using multiple mechanisms H. Nguyen et al. 10.1016/j.str.2024.04.013
- Paramagnetic NMR in drug discovery C. Softley et al. 10.1007/s10858-020-00322-0
Latest update: 22 May 2025
Short summary
Nuclear magnetic resonance is a technique that allows the measurement of the nanoscale distances between the atoms of a molecule. It is often relied upon for finding the structure of a molecule and how atoms are bonded, but measurements become inaccurate for large distances and therefore for large biological molecules. This research presents a new software for calculating the distances between nuclei and unpaired electrons which offers more accurate long-range distances in biological molecules.
Nuclear magnetic resonance is a technique that allows the measurement of the nanoscale distances...
