Fig. 2: Substantial oxidation near trapped O2 molecules within protein cavities.
From: Hidden route of protein damage through oxygen-confined photooxidation
a Volcano plot obtained from LC-MS/MS analysis. The volcano plot shows oxidized residues of maltose-binding protein (MBP) under blue light irradiation, which are statistically significant compared to no-light condition (p value (p) < 0.05, fold change (FC) > 1.5). p values were calculated using Student’s one-tailed t test. The amino acid residues are denoted as 3-letter code. The residue numbers indicate those following the signal peptide sequence. b Structural distribution of the oxidized residues. c Barcode plot showing the binding events between MBP and O2 molecules from molecular dynamics (MD) simulations. The blue-colored regions indicate the bindings between the protein and O2, sustained within 3.5 Å for longer than 10 ns. d All distributed positions of trapped O2 molecules in simulation #1. Only the O2 molecules trapped for a specific time range (t) are represented. e All distributed center positions of protein cavities with Dcavity > Do in simulation #1. The Dcavity and Do represent the diameter of cavities and the kinetic diameter of O2 (3.46 Å), respectively.
