Fig. 5: Positional correlation between Trp and oxidized residues in CA II.
From: Hidden route of protein damage through oxygen-confined photooxidation
a Structural distribution of oxidized residues, tryptophan (Trp) residues, protein cavities, and trapped O2 molecules in human carbonic anhydrase II (CA II). Only the O2 molecules trapped for a specific time range (t) are represented. The Dcavity and Do represent the diameter of cavities and the kinetic diameter of O2 (3.46 Å), respectively. b Close-up views of the regions surrounding the oxidized residues. c Proportion of oxidized residues’ side-chain atoms located in the protein core and surface regions. d Minimum distances from oxidized residues to trapped O2 molecules or Trp residues. e Maximum end-to-end distances of trapped O2 molecules within the protein obtained from molecular dynamics (MD) simulations. f, g Monte Carlo analysis for the proximity between Trp and oxidized residues (see “Methods”). The f shows the probability density functions of average distance from oxidized residues to each residue type (PDFavg). The data for other residue types in f are distinguishably presented in Supplementary Fig. 21b. Trp* represents a subset of Trp residues (Trp97, Trp192, Trp209, and Trp245), which are responsible for the leftmost peak in the PDFavg for Trp (see the main text for more details). The PDFavg shown in blue is constructed from the sampling of Trp*. The g shows the occurrence probabilities of the proximity by chance for all residue types, which have a larger number of residues than the number of benchmark Trp* residues.
