title: Determination of Protein Folding Intermediate Structures Consistent with Data from Oxidative Footprinting Mass Spectrometry.
abstract: The mapping of folding landscapes remains an important challenge in protein chemistry. Pulsed oxidative labeling of exposed residues and their detection via mass spectrometry provide new means of taking time-resolved "snapshots" of the structural changes that occur during protein folding. However, such experiments have been so far only interpreted qualitatively. Here, we report the detailed structural interpretation of mass spectrometry data from fast photochemical oxidation of proteins (FPOP) experiments at atomic resolution in a biased molecular dynamics approach. We are able to calculate structures of the early folding intermediate of the model system barstar that are fully consistent with FPOP data and Φ values. Furthermore, structures calculated with both FPOP data and Φ values are significantly less compact and have fewer helical residues than intermediate structures calculated with Φ values only. This improves the agreement with the experimental β-Tanford value and CD measurements. The restraints that we introduce facilitate the structural interpretation of FPOP data and provide new means for refined structure calculations of transiently sampled states on protein folding landscapes.
authors.affiliation: Centre for High-Throughput Biology, University of British Columbia, Vancouver, BC V6T 1Z4, Canada.
authors.forename: Florian
authors.initials: F
authors.lastname: Heinkel
authors.affiliation: Centre for High-Throughput Biology, University of British Columbia, Vancouver, BC V6T 1Z4, Canada. Electronic address: gsponer@chibi.ubc.ca.
authors.forename: Jörg
authors.initials: J
authors.lastname: Gsponer
mesh_terms: D013058:Mass Spectrometry / Q000379:methods*; D056004:Molecular Dynamics Simulation; D017510:Protein Folding; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism*
chemical_list: D011506:Proteins
keywords: fast photochemical oxidation of proteins; protein folding intermediate; restrained molecular dynamics simulation; solvent-accessible surface area; structure determination