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Comparative Study
. 2020:2141:429-445.
doi: 10.1007/978-1-0716-0524-0_21.

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

Mustapha Carab Ahmed  1 , Ramon Crehuet  1   2 , Kresten Lindorff-Larsen  3
Affiliations
Comparative Study

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

Mustapha Carab Ahmed et al. Methods Mol Biol. 2020.

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.

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