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• W2051223775 abstract "Computer-assisted topology predictions are widely used to build low-resolution structural models of integral membrane proteins (IMPs). Experimental validation of these models by traditional methods is labor intensive and requires modifications that might alter the IMP native conformation. This work employs oxidative labeling coupled with mass spectrometry (MS) as a validation tool for computer-generated topology models. ⋅OH exposure introduces oxidative modifications in solvent-accessible regions, whereas buried segments (e.g., transmembrane helices) are non-oxidizable. The Escherichia coli protein WaaL (O-antigen ligase) is predicted to have 12 transmembrane helices and a large extramembrane domain (Pérez et al., Mol. Microbiol. 2008,70, 1424). Tryptic digestion and LC-MS/MS were used to map the oxidative labeling behavior of WaaL. Met and Cys exhibit high intrinsic reactivities with ⋅OH, making them sensitive probes for solvent accessibility assays. Overall, the oxidation pattern of these residues is consistent with the originally proposed WaaL topology. One residue (M151), however, undergoes partial oxidation despite being predicted to reside within a transmembrane helix. Using an improved computer algorithm, a slightly modified topology model was generated that places M151 closer to the membrane interface. On the basis of the labeling data, it is concluded that the refined model more accurately reflects the actual topology of WaaL. We propose that the combination of oxidative labeling and MS represents a useful strategy for assessing the accuracy of IMP topology predictions, supplementing data obtained in traditional biochemical assays. In the future, it might be possible to incorporate oxidative labeling data directly as constraints in topology prediction algorithms." @default.
• W2051223775 created "2016-06-24" @default.
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• W2051223775 creator A5019862287 @default.
• W2051223775 creator A5032341987 @default.
• W2051223775 creator A5041019879 @default.
• W2051223775 date "2012-03-13" @default.
• W2051223775 modified "2023-09-27" @default.
• W2051223775 title "Validation of Membrane Protein Topology Models by Oxidative Labeling and Mass Spectrometry" @default.
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• W2051223775 doi "https://doi.org/10.1007/s13361-012-0342-x" @default.
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• W2051223775 hasPublicationYear "2012" @default.
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