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bioRxiv · 10.1101/136929

Quantitative Protein Topography Measurements By High Resolution Hydroxyl Radical Protein Footprinting Enable Accurate Molecular Model Selection

Xie, B.·Sood, A.·Woods, R. J.·Sharp, J. S.
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Abstract

We report an integrated workflow that allows mass spectrometry-based high-resolution hydroxyl radical protein footprinting (HR-HRPF) measurements to accurately measure the absolute average solvent accessible surface area ( ) of amino acid side chains. This approach is based on application of multi-point HR-HRPF, electron-transfer dissociation (ETD) tandem MS (MS/MS) acquisition, measurement of effective radical doses by radical dosimetry, and proper normalization of the inherent reactivity of the amino acids. The accuracy of the resulting measurements was tested by using well-characterized protein models. Moreover, we demonstrated the ability to use measurements from HR-HRPF to differentiate molecular models of high accuracy (< 3[A] backbone RMSD) from models of lower accuracy (> 4[A] backbone RMSD). The ability of data from HR-HRPF to differentiate molecular model quality was found to be comparable to that of data obtained from X-ray crystal structures, indicating the accuracy and utility of HR-HRPF for evaluating the accuracy of computational models.

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Xie, B., Sood, A., Woods, R. J., Sharp, J. S.. 2017-05-11. Quantitative Protein Topography Measurements By High Resolution Hydroxyl Radical Protein Footprinting Enable Accurate Molecular Model Selection. https://doi.org/10.1101/136929

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