Fig. 4: Positional correlation between Trp and oxidized residues in MBP.
From: Hidden route of protein damage through oxygen-confined photooxidation
a Structural distribution of tryptophan (Trp) residues and oxidized residues in maltose-binding protein (MBP). The residue numbers indicate those following the signal peptide sequence. b–d Monte Carlo analysis for the proximity between Trp and oxidized residues (see “Methods”). The b, c show the probability density functions of average distance from oxidized residues to each residue type (PDFavg) (b) and to arbitrary residues sampled from the entire protein (c), respectively. The data for other residue types in b are distinguishably presented in Supplementary Fig. 20. In c, the occurrence probability of the proximity between Trp and oxidized residues by chance is indicated for each case of increasing sampling numbers of arbitrary residues, up to the total number of benchmark Trp residues in MBP (n = 8). The d shows the occurrence probabilities of the proximity by chance for all residue types, which have a larger number of residues than the total number of benchmark Trp residues in MBP. The proportion of each residue in the protein is shown in Supplementary Fig. 12c. The residues are denoted as 3-letter code. e Minimum distances from oxidized residues to Trp residues. f, g Maximum end-to-end distances (f) and total travel lengths (g) of trapped O2 molecules within the protein obtained from molecular dynamics (MD) simulations.
