Computing, Analyzing, and Comparing the Radius of Gyration and Hydrodynamic Radius in Conformational Ensembles of Intrinsically Disordered Proteins

Research output: Chapter in Book/Report/Conference proceeding › Book chapter › Research › peer-review

Standard

Computing, Analyzing, and Comparing the Radius of Gyration and Hydrodynamic Radius in Conformational Ensembles of Intrinsically Disordered Proteins. / Ahmed, Mustapha Carab; Crehuet, Ramon; Lindorff-Larsen, Kresten.

Intrinsically Disordered Proteins: Methods and Protocols. ed. / Birthe B. Kragelund; Karen Skriver. Humana Press, 2020. p. 429-445 (Methods in Molecular Biology, Vol. 2141).

Research output: Chapter in Book/Report/Conference proceeding › Book chapter › Research › peer-review

Harvard

Ahmed, MC, Crehuet, R & Lindorff-Larsen, K 2020, Computing, Analyzing, and Comparing the Radius of Gyration and Hydrodynamic Radius in Conformational Ensembles of Intrinsically Disordered Proteins. in BB Kragelund & K Skriver (eds), Intrinsically Disordered Proteins: Methods and Protocols. Humana Press, Methods in Molecular Biology, vol. 2141, pp. 429-445. https://doi.org/10.1007/978-1-0716-0524-0_21

APA

Ahmed, M. C., Crehuet, R., & Lindorff-Larsen, K. (2020). Computing, Analyzing, and Comparing the Radius of Gyration and Hydrodynamic Radius in Conformational Ensembles of Intrinsically Disordered Proteins. In B. B. Kragelund, & K. Skriver (Eds.), Intrinsically Disordered Proteins: Methods and Protocols (pp. 429-445). Humana Press. Methods in Molecular Biology Vol. 2141 https://doi.org/10.1007/978-1-0716-0524-0_21

Vancouver

Ahmed MC, Crehuet R, Lindorff-Larsen K. Computing, Analyzing, and Comparing the Radius of Gyration and Hydrodynamic Radius in Conformational Ensembles of Intrinsically Disordered Proteins. In Kragelund BB, Skriver K, editors, Intrinsically Disordered Proteins: Methods and Protocols. Humana Press. 2020. p. 429-445. (Methods in Molecular Biology, Vol. 2141). https://doi.org/10.1007/978-1-0716-0524-0_21

Author

Ahmed, Mustapha Carab ; Crehuet, Ramon ; Lindorff-Larsen, Kresten. / Computing, Analyzing, and Comparing the Radius of Gyration and Hydrodynamic Radius in Conformational Ensembles of Intrinsically Disordered Proteins. Intrinsically Disordered Proteins: Methods and Protocols. editor / Birthe B. Kragelund ; Karen Skriver. Humana Press, 2020. pp. 429-445 (Methods in Molecular Biology, Vol. 2141).

Bibtex

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title = "Computing, Analyzing, and Comparing the Radius of Gyration and Hydrodynamic Radius in Conformational Ensembles of Intrinsically Disordered Proteins",
abstract = "The level of compaction of an intrinsically disordered protein may affect both its physical and biological properties, and can be probed via different types of biophysical experiments. Small-angle X-ray scattering (SAXS) probe the radius of gyration (Rg) whereas pulsed-field-gradient nuclear magnetic resonance (NMR) diffusion, fluorescence correlation spectroscopy, and dynamic light scattering experiments can be used to determine the hydrodynamic radius (Rh). Here we show how to calculate Rg and Rh from a computationally generated conformational ensemble of an intrinsically disordered protein. We further describe how to use a Bayesian/Maximum Entropy procedure to integrate data from SAXS and NMR diffusion experiments, so as to derive conformational ensembles in agreement with those experiments.",
keywords = "Compaction, Conformational ensemble, Hydrodynamic radius, Intrinsically disordered protein, Radius of gyration",
author = "Ahmed, {Mustapha Carab} and Ramon Crehuet and Kresten Lindorff-Larsen",
year = "2020",
doi = "10.1007/978-1-0716-0524-0_21",
language = "English",
isbn = "978-1-0716-0523-3",
series = "Methods in Molecular Biology",
publisher = "Humana Press",
pages = "429--445",
editor = "Kragelund, {Birthe B.} and Karen Skriver",
booktitle = "Intrinsically Disordered Proteins",
address = "United States",

}

RIS

TY - CHAP

T1 - Computing, Analyzing, and Comparing the Radius of Gyration and Hydrodynamic Radius in Conformational Ensembles of Intrinsically Disordered Proteins

AU - Ahmed, Mustapha Carab

AU - Crehuet, Ramon

AU - Lindorff-Larsen, Kresten

PY - 2020

Y1 - 2020

N2 - The level of compaction of an intrinsically disordered protein may affect both its physical and biological properties, and can be probed via different types of biophysical experiments. Small-angle X-ray scattering (SAXS) probe the radius of gyration (Rg) whereas pulsed-field-gradient nuclear magnetic resonance (NMR) diffusion, fluorescence correlation spectroscopy, and dynamic light scattering experiments can be used to determine the hydrodynamic radius (Rh). Here we show how to calculate Rg and Rh from a computationally generated conformational ensemble of an intrinsically disordered protein. We further describe how to use a Bayesian/Maximum Entropy procedure to integrate data from SAXS and NMR diffusion experiments, so as to derive conformational ensembles in agreement with those experiments.

AB - The level of compaction of an intrinsically disordered protein may affect both its physical and biological properties, and can be probed via different types of biophysical experiments. Small-angle X-ray scattering (SAXS) probe the radius of gyration (Rg) whereas pulsed-field-gradient nuclear magnetic resonance (NMR) diffusion, fluorescence correlation spectroscopy, and dynamic light scattering experiments can be used to determine the hydrodynamic radius (Rh). Here we show how to calculate Rg and Rh from a computationally generated conformational ensemble of an intrinsically disordered protein. We further describe how to use a Bayesian/Maximum Entropy procedure to integrate data from SAXS and NMR diffusion experiments, so as to derive conformational ensembles in agreement with those experiments.

KW - Compaction

KW - Conformational ensemble

KW - Hydrodynamic radius

KW - Intrinsically disordered protein

KW - Radius of gyration

U2 - 10.1007/978-1-0716-0524-0_21

DO - 10.1007/978-1-0716-0524-0_21

M3 - Book chapter

C2 - 32696370

AN - SCOPUS:85088523610

SN - 978-1-0716-0523-3

T3 - Methods in Molecular Biology

SP - 429

EP - 445

BT - Intrinsically Disordered Proteins

A2 - Kragelund, Birthe B.

A2 - Skriver, Karen

PB - Humana Press

ER -

ID: 247337921