Endogenous S-nitrosocysteine proteomic inventories identify a core of proteins in heart metabolic pathways

Figures

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  Fig. 1. A. Number of mouse heart proteins (canonical and isoforms) and peptides identified in the curated S-nitrosocysteine data sets for each independent study. B. The number of peptides per protein detected in each study. Not depicted in the graph are 3 proteins with 13 peptides identified in studies 3, and 7 proteins in study 4 with 11–26 peptides per protein respectively. C. The percentage of proteins with one, two or three cysteine residues modified in each study. The fraction of proteins with one, two or three modified cysteine residues was not statistically different among the four studies.

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  Fig. 2. A. Venn diagram depicting the overlap of the mouse heart proteins with S-nitrosocysteine residues in the four different studies. B. The distribution of peptides per protein of a combined S-nitrosocysteine proteome created by including all the unique proteins (both canonical and isoforms) and peptides identified in all four studies.

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  Fig. 3. A. Cumulative frequency of the relative abundance of 686 proteins in the combined S-nitrosocysteine proteome (blue) using the mouse heart protein abundance histogram as background (green). For the construction of the mouse heart protein abundance plot we curated data from the PAXdb: Protein Abundance Database using data from Mus musculus heart integrated from several independent mass spectrometric studies. B. The abundance of the 80 common proteins (blue dots) in the four studies among the 6301 mouse heart proteins (data file 6).

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  Fig. 4. A. The occupancy for each of the 75 peptides in the 44 proteins that were common in all four studies. Blue indicates the proteins with a single peptide. The other colors indicate different peptides in the same protein. B. The occupancy for 1071 peptides was divided into four quartiles. Most of the peptides (75%) had occupancy less than 26%.

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  Fig. 5. Functional analysis of the proteins that are S-nitrosylated in each study. Panel A depicts selected biological processes and B the cellular component considering the values for FDR and fold enrichment. The size of the circle indicates the number of genes annotated in the corresponding biological process and cellular component. The selected biological processes and cellular components were in the top 20 annotations ranked by FDR in each study.

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  Fig. 6. A. Hydropathy index for each of the 75 S-nitrosylated cysteine residues indicating distribution in hydrophilic (negative value) and hydrophobic protein regions. B. The hydropathy index for each peptide was plotted against the percent occupancy indicating no correlation between the two variables. C. Distribution of S-nitrosocysteine residues (black) within secondary elements of proteins and the corresponding non-modified cysteine residues in the same proteins (grey). D. The apparent pKa of the S-nitrosylated cysteine residues was significantly (N = 117, p < 0.01) lower than of the unmodified cysteine residues.

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  Fig. 7. Multidimensional plot of the biochemical properties and percent occupancy of S-nitrosylated cysteine residues. The pKa and hydropathy values are plotted in the x and y-axis respectively while the color of the bubble indicates the secondary element for each cysteine residue; Green indicates Helix, Red indicates Coil, and Blue indicates Strand. The size of the bubble is proportional to the percent S-nitrosylation for each residue. (For interpretation of the references to color in this figure legend, the reader is referred to the Web version of this article.)