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bioRxiv · 10.1101/2023.06.02.543514

Revisiting the use of dioxane as a reference compound for determination of the hydrodynamic radius of proteins by pulsed field gradient NMR spectroscopy

Tranchant, E. E.·Pesce, F.·Jacobsen, N. L.·Fernandes, C. B.·Kragelund, B. B.·Lindorff-Larsen, K.
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Abstract

Measuring the compaction of a protein or complex is key to understand the interactions within and between biomolecules. Experimentally, protein compaction is often probed either by estimating the radius of gyration (Rg) obtained from small-angle X-ray scattering (SAXS) experiments or the hydrodynamic radius (Rh) obtained for example by pulsed field gradient nuclear magnetic resonance (PFG NMR) spectroscopy. PFG NMR experiments generally report on the translational diffusion coefficient, which in turn can be used to estimate Rh using an internal standard. Here, we examine the use of 1,4-dioxane as an internal NMR standard to account for sample viscosity and uncertainty about the gradient strength. Specifically, we revisit the basis for the commonly used reference value for the Rh of dioxane (2.12 [A]) that is used to convert measured diffusion coefficients into a hydrodynamic radius. We follow the same approach that was used to establish the current reference value for the Rh by measuring SAXS and PFG NMR data for a set of seven different proteins and using these as standards. Our analysis shows that the current Rh reference value for 1,4-dioxane Rh (2.12 [A]) is underestimated, and we instead suggest a new value of 2.27 [A] {+/-} 0.04 [A]. Using this updated reference value results in a [~]7% increase in Rh values for proteins whose hydrodynamic radius have been measured by PFG NMR. We discuss the implications for ensemble descriptions of intrinsically disordered proteins and evaluation of effect resulting from for example ligand binding, posttranslational modifications, or changes to the environment.

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Tranchant, E. E., Pesce, F., Jacobsen, N. L., Fernandes, C. B., Kragelund, B. B., Lindorff-Larsen, K.. 2023-06-03. Revisiting the use of dioxane as a reference compound for determination of the hydrodynamic radius of proteins by pulsed field gradient NMR spectroscopy. https://doi.org/10.1101/2023.06.02.543514

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