4 years ago

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

B., R. J., Xie, Woods, J. S., Sood, Sharp, A.
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 (< 3A backbone RMSD) from models of lower accuracy (> 4A 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.

Publisher URL: http://biorxiv.org/cgi/content/short/136929v1

DOI: 10.1101/136929

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