ArticleBiophysical journal2023
Assessment of models for calculating the hydrodynamic radius of intrinsically disordered proteins.
Article in Biophysical journal, 2023. 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.
- Physicochemical Principles Governing the Intrinsically Disordered Salivary Peptide Histatin 5: Ensemble Structure, Electrostatics, and Environmental Responsiveness.The journal of physical chemistry. B · 2026Review
- Toward a unified framework for determining conformational ensembles of disordered proteins.Nature methods · 2026Review
- Optimisation of Alginate Extraction and Characterisation of Polysaccharides from Brown Seaweed from the Portuguese Coast.Marine drugs · 2026Article
- Ist2 promotes lipid transfer by Osh6 via its membrane tethering and lipid scramblase activities.Science advances · 2025Article
- Mapping the Role of Monomer Conformation in the Amyloid Formation of α-Synuclein Splice Variants.Journal of the American Chemical Society · 2025Article
- The C-terminal end of PLIN1 displays structural disorder.Biochemistry and biophysics reports · 2025Article
- Small Molecules Targeting the Structural Dynamics of AR-V7 Partially Disordered Proteins Using Deep Ensemble Docking.Journal of chemical theory and computation · 2025Article
- AlphaFold prediction of structural ensembles of disordered proteins.Nature communications · 2025Article
- On the use of dioxane as reference for determination of the hydrodynamic radius by NMR spectroscopy.Biophysical journal · 2024Article
- An integrative characterization of proline cis and trans conformers in a disordered peptide.Biophysical journal · 2024Article
- Design of intrinsically disordered protein variants with diverse structural properties.Science advances · 2024Article
- Hydrodynamic Radii of Intrinsically Disordered Proteins: Fast Prediction by Minimum Dissipation Approximation and Experimental Validation.The journal of physical chemistry letters · 2024Article
- Using NMR diffusion data to validate MD models of disordered proteins: Test case of N-terminal tail of histone H4.Biophysical journal · 2024Article
- Design of intrinsically disordered protein variants with diverse structural properties.bioRxiv : the preprint server for biology · 2023Article
- Diversity of hydrodynamic radii of intrinsically disordered proteins.European biophysics journal : EBJ · 2023Article
- Phosphorylation of Schizosaccharomyces pombe Dss1 mediates direct binding to the ubiquitin-ligase Dma1 in vitro.Protein science : a publication of the Protein Society · 2023Article
- Delineating Structural Propensities of the 4E-BP2 Protein via Integrative Modeling and Clustering.The journal of physical chemistry. B · 2023Article
- Review
- The Analytical Flory Random Coil Is a Simple-to-Use Reference Model for Unfolded and Disordered Proteins.The journal of physical chemistry. B · 2023Article
- The Action of Chemical Denaturants: From Globular to Intrinsically Disordered Proteins.Biology · 2023Review
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8 authors.
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Abstract
Diffusion measurements by pulsed-field gradient NMR and fluorescence correlation spectroscopy can be used to probe the hydrodynamic radius of proteins, which contains information about the overall dimension of a protein in solution. The comparison of this value with structural models of intrinsically disordered proteins is nonetheless impaired by the uncertainty of the accuracy of the methods for computing the hydrodynamic radius from atomic coordinates. To tackle this issue, we here build conformational ensembles of 11 intrinsically disordered proteins that we ensure are in agreement with measurements of compaction by small-angle x-ray scattering. We then use these ensembles to identify the forward model that more closely fits the radii derived from pulsed-field gradient NMR diffusion experiments. Of the models we examined, we find that the Kirkwood-Riseman equation provides the best description of the hydrodynamic radius probed by pulsed-field gradient NMR experiments. While some minor discrepancies remain, our results enable better use of measurements of the hydrodynamic radius in integrative modeling and for force field benchmarking and parameterization.
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