ArticleMethods (San Diego, Calif.)2018
Theory and practice of using solvent paramagnetic relaxation enhancement to characterize protein conformational dynamics.
Article in Methods (San Diego, Calif.), 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed.
- Accurate measurement of longitudinal paramagnetic relaxation enhancement through division after subtraction.Magnetic resonance letters · 2027Article
- Going high-throughput: Dynamic conformations and interactionsMagnetic resonance letters · 2027Review
- In Search of Shape in the Unshaped: Constructing Ensembles of Intrinsically Disordered Proteins.Biophysics reviews · 2026Article
- Protonated Structure of EmrE Reveals C-terminal Tail Gating Mechanism.bioRxiv : the preprint server for biology · 2026Article
- Evaluating the use of lanthanide containing dendrimers for solvent paramagnetic relaxation enhancement.Journal of biomolecular NMR · 2025Article
- Quantitative Interpretation of Transverse Spin Relaxation by Translational Diffusion in Liquids.The journal of physical chemistry. B · 2025Article
- Kinetic Resolution of the Atomic 3D Structures Formed by Ground and Excited Conformational States in an RNA Dynamic Ensemble.Journal of the American Chemical Society · 2023Article
- Biophysical and Integrative Characterization of Protein Intrinsic Disorder as a Prime Target for Drug Discovery.Biomolecules · 2023Review
- Peptidase Activation by a Leader Peptide-Bound RiPP Recognition Element.Biochemistry · 2023Article
- A toxin-deformation dependent inhibition mechanism in the T7SS toxin-antitoxin system of Gram-positive bacteria.Nature communications · 2022Article
- TAPBPR employs a ligand-independent docking mechanism to chaperone MR1 molecules.Nature chemical biology · 2022Article
- Preferential Regulation of Transient Protein-Protein Interaction by the Macromolecular Crowders.The journal of physical chemistry. B · 2022Article
- Paramagnetic Chemical Probes for Studying Biological Macromolecules.Chemical reviews · 2022Review
- Protein Electrostatics Investigated through Paramagnetic NMR for Nonpolar Groups.The journal of physical chemistry. B · 2022Article
- Atomic view of cosolute-induced protein denaturation probed by NMR solvent paramagnetic relaxation enhancement.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- NMR spectroscopy charges into protein surface electrostatics.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- Water Accessibility Refinement of the Extended Structure of KirBac1.1 in the Closed State.Frontiers in molecular biosciences · 2021Article
- Combining Experimental Data and Computational Methods for the Non-Computer Specialist.Molecules (Basel, Switzerland) · 2020Review
- Integrating NMR and simulations reveals motions in the UUCG tetraloop.Nucleic acids research · 2020Article
- Quantitative Interpretation of Solvent Paramagnetic Relaxation for Probing Protein-Cosolute Interactions.Journal of the American Chemical Society · 2020Article
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3 authors.
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Abstract
Paramagnetic relaxation enhancement (PRE) has been established as a powerful tool in NMR for investigating protein structure and dynamics. The PRE is usually measured with a paramagnetic probe covalently attached at a specific site of an otherwise diamagnetic protein. The present work provides the numerical formulation for probing protein structure and conformational dynamics based on the solvent PRE (sPRE) measurement, using two alternative approaches. An inert paramagnetic cosolute randomly collides with the protein, and the resulting sPRE manifests the relative solvent exposure of protein nuclei. To make the back-calculated sPRE values most consistent with the observed values, the protein structure is either refined against the sPRE, or an ensemble of conformers is selected from a pre-generated library using a Monte Carlo algorithm. The ensemble structure comprises either N conformers of equal occupancy, or two conformers with different relative populations. We demonstrate the sPRE method using GB1, a structurally rigid protein, and calmodulin, a protein comprising two domains and existing in open and closed states. The sPRE can be computed with a stand-alone program for rapid evaluation, or with the invocation of a module in the latest release of the structure calculation software Xplor-NIH. As a label-free method, the sPRE measurement can be readily integrated with other biophysical techniques. The current limitations of the sPRE method are also discussed, regarding accurate measurement and theoretical calculation, model selection and suitable timescale.
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