Quantifying protein interface footprinting by hydroxyl radical oxidation and molecular dynamics simulation: application to galectin-1.

Journal of the American Society for Mass Spectrometry
Olga CharvátováRobert J Woods

Abstract

Biomolecular surface mapping methods offer an important alternative method for characterizing protein-protein and protein-ligand interactions in cases in which it is not possible to determine high-resolution three-dimensional (3D) structures of complexes. Hydroxyl radical footprinting offers a significant advance in footprint resolution compared with traditional chemical derivatization. Here we present results of footprinting performed with hydroxyl radicals generated on the nanosecond time scale by laser-induced photodissociation of hydrogen peroxide. We applied this emerging method to a carbohydrate-binding protein, galectin-1. Since galectin-1 occurs as a homodimer, footprinting was employed to characterize the interface of the monomeric subunits. Efficient analysis of the mass spectrometry data for the oxidized protein was achieved with the recently developed ByOnic (Palo Alto, CA) software that was altered to handle the large number of modifications arising from side-chain oxidation. Quantification of the level of oxidation has been achieved by employing spectral intensities for all of the observed oxidation states on a per-residue basis. The level of accuracy achievable from spectral intensities was determined by examinat...Continue Reading

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Citations

Feb 16, 2010·Analytical and Bioanalytical Chemistry·Julien RoeserHjalmar P Permentier
Apr 8, 2011·Journal of the American Society for Mass Spectrometry·Patrick D DeArmondMichael C Fitzgerald
Sep 10, 2013·Journal of the American Society for Mass Spectrometry·Xiaoyan LiJoshua S Sharp
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