ArticleJournal of the American Society for Mass Spectrometry2012
Validation of membrane protein topology models by oxidative labeling and mass spectrometry.
Article in Journal of the American Society for Mass Spectrometry, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed.
- Optimized Digestion Conditions for Membrane Protein Footprinting and Mass Spectrometry Analysis.Membranes · 2026Article
- Mass Spectrometry-Based Protein Footprinting for Protein Structure Characterization.Accounts of chemical research · 2025Article
- Precursor Reagent Hydrophobicity Affects Membrane Protein Footprinting.Journal of the American Society for Mass Spectrometry · 2023Article
- Investigating Daptomycin-Membrane Interactions Using Native MS and Fast Photochemical Oxidation of Peptides in Nanodiscs.Analytical chemistry · 2023Article
- Review
- Investigating Antimicrobial Peptide-Membrane Interactions Using Fast Photochemical Oxidation of Peptides in Nanodiscs.Journal of the American Society for Mass Spectrometry · 2022Article
- MEMBRANE PROTEIN STRUCTURES AND INTERACTIONS FROM COVALENT LABELING COUPLED WITH MASS SPECTROMETRY.Mass spectrometry reviews · 2022Review
- Diethylpyrocarbonate Footprints a Membrane Protein in Micelles.Journal of the American Society for Mass Spectrometry · 2021Article
- Free-Radical Membrane Protein Footprinting by Photolysis of Perfluoroisopropyl Iodide Partitioned to Detergent Micelle by Sonication.Angewandte Chemie (International ed. in English) · 2021Article
- Real Time Normalization of Fast Photochemical Oxidation of Proteins Experiments by Inline Adenine Radical Dosimetry.Analytical chemistry · 2018Article
- Covalent labeling-mass spectrometry with non-specific reagents for studying protein structure and interactions.Methods (San Diego, Calif.) · 2018Review
- Topological Dissection of the Membrane Transport Protein Mhp1 Derived from Cysteine Accessibility and Mass Spectrometry.Analytical chemistry · 2017Article
- Systematic analysis of the use of amphipathic polymers for studies of outer membrane proteins using mass spectrometry.International journal of mass spectrometry · 2015Article
- Using hydroxyl radical footprinting to explore the free energy landscape of protein folding.Methods (San Diego, Calif.) · 2015Article
- Amphipols outperform dodecylmaltoside micelles in stabilizing membrane protein structure in the gas phase.Analytical chemistry · 2015Article
- Mass spec studio for integrative structural biology.Structure (London, England : 1993) · 2014Article
- Topological mapping methods for α-helical bacterial membrane proteins--an update and a guide.MicrobiologyOpen · 2013Review
- Integral membrane proteins and bilayer proteomics.Analytical chemistry · 2013Review
- Site-specific interaction between α-synuclein and membranes probed by NMR-observed methionine oxidation rates.Journal of the American Chemical Society · 2013Article
- Electrospray ionization-induced protein unfolding.Journal of the American Society for Mass Spectrometry · 2012Article
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4 authors.
Funding
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.
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