Assessment of models for calculating the hydrodynamic radius of intrinsically disordered proteins

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Assessment of models for calculating the hydrodynamic radius of intrinsically disordered proteins. / Pesce, Francesco; Newcombe, Estella A.; Seiffert, Pernille; Tranchant, Emil E.; Olsen, Johan G.; Grace, Christy R.; Kragelund, Birthe B.; Lindorff-Larsen, Kresten.

In: Biophysical Journal, Vol. 122, No. 2, 2023, p. 310-321.

Research output: Contribution to journal › Journal article › Research › peer-review

Harvard

Pesce, F, Newcombe, EA, Seiffert, P, Tranchant, EE, Olsen, JG, Grace, CR, Kragelund, BB & Lindorff-Larsen, K 2023, 'Assessment of models for calculating the hydrodynamic radius of intrinsically disordered proteins', Biophysical Journal, vol. 122, no. 2, pp. 310-321. https://doi.org/10.1016/j.bpj.2022.12.013

APA

Pesce, F., Newcombe, E. A., Seiffert, P., Tranchant, E. E., Olsen, J. G., Grace, C. R., Kragelund, B. B., & Lindorff-Larsen, K. (2023). Assessment of models for calculating the hydrodynamic radius of intrinsically disordered proteins. Biophysical Journal, 122(2), 310-321. https://doi.org/10.1016/j.bpj.2022.12.013

Vancouver

Pesce F, Newcombe EA, Seiffert P, Tranchant EE, Olsen JG, Grace CR et al. Assessment of models for calculating the hydrodynamic radius of intrinsically disordered proteins. Biophysical Journal. 2023;122(2):310-321. https://doi.org/10.1016/j.bpj.2022.12.013

Author

Pesce, Francesco ; Newcombe, Estella A. ; Seiffert, Pernille ; Tranchant, Emil E. ; Olsen, Johan G. ; Grace, Christy R. ; Kragelund, Birthe B. ; Lindorff-Larsen, Kresten. / Assessment of models for calculating the hydrodynamic radius of intrinsically disordered proteins. In: Biophysical Journal. 2023 ; Vol. 122, No. 2. pp. 310-321.

Bibtex

@article{b3d7fa1b23bc4912a1caeb1f0b32d8d7,
title = "Assessment of models for calculating the hydrodynamic radius of intrinsically disordered proteins",
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.",
author = "Francesco Pesce and Newcombe, {Estella A.} and Pernille Seiffert and Tranchant, {Emil E.} and Olsen, {Johan G.} and Grace, {Christy R.} and Kragelund, {Birthe B.} and Kresten Lindorff-Larsen",
note = "Publisher Copyright: {\textcopyright} 2022 Biophysical Society",
year = "2023",
doi = "10.1016/j.bpj.2022.12.013",
language = "English",
volume = "122",
pages = "310--321",
journal = "Biophysical Society. Annual Meeting. Abstracts",
issn = "0523-6800",
publisher = "Biophysical Society",
number = "2",

}

RIS

TY - JOUR

T1 - Assessment of models for calculating the hydrodynamic radius of intrinsically disordered proteins

AU - Pesce, Francesco

AU - Newcombe, Estella A.

AU - Seiffert, Pernille

AU - Tranchant, Emil E.

AU - Olsen, Johan G.

AU - Grace, Christy R.

AU - Kragelund, Birthe B.

AU - Lindorff-Larsen, Kresten

N1 - Publisher Copyright: © 2022 Biophysical Society

PY - 2023

Y1 - 2023

N2 - 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.

AB - 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.

U2 - 10.1016/j.bpj.2022.12.013

DO - 10.1016/j.bpj.2022.12.013

M3 - Journal article

C2 - 36518077

AN - SCOPUS:85144936282

VL - 122

SP - 310

EP - 321

JO - Biophysical Society. Annual Meeting. Abstracts

JF - Biophysical Society. Annual Meeting. Abstracts

SN - 0523-6800

IS - 2

ER -

ID: 334258559