Determination of Protein Folding Intermediate Structures Consistent with Data from Oxidative Footprinting Mass Spectrometry. Issue 2 (29th January 2016)

• Record Type: Journal Article
• Authors: Heinkel, Florian; Gsponer, Jörg
• Is Part Of: Journal of molecular biology. Volume 428:Issue 2 Part A(2016:Jan. 15)
• Page Start: 365
• Page End: 371
• Publication Date: 2016-01-29
• Subjects: FPOP fast photochemical oxidation of proteins -- MD molecular dynamics -- MS mass spectrometry -- SASA solvent-accessible surface area; fast photochemical oxidation of proteins -- restrained molecular dynamics simulation -- solvent-accessible surface area -- protein folding intermediate -- structure determination; Molecular biology -- Periodicals; Biology -- Periodicals; Biochemistry -- Periodicals; Bacteriology -- Periodicals; Molecular Biology -- Periodicals; Biochemistry -- Periodicals; Biologie moléculaire -- Périodiques; Biologie -- Périodiques; Biochimie -- Périodiques; Moleculaire biologie; Biochemistry; Biology; Molecular biology; Periodicals; 572.805
• DOI: 10.1016/j.jmb.2015.10.022
• Languages: English
• ISSNs: 0022-2836

Abstract

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. Graphical abstract: Highlights: New molecular dynamics restraint for the use of FPOP data in structure calculations. Determination of the structure of the early folding intermediate of barstar. Improved structure quality compared to structures determined with phi values only.