Table S2.
Human SOD1 limited proteolytic digest peptides identified by MS
| Form of SOD | Observed | Mr(expt) | Mr(calc) | Peptide | Mascot assignment | Notes |
| V8 (100 mM phosphate, pH 4.0, t = 1 min) | ||||||
| Monomer | No matches | First peptide identified at t = 5 min | ||||
| Dimer | No matches | No peptides out to t = 10 min | ||||
| Trimer | 1,459.0857 | 1,458.0784 | 1,457.7514 | D.GPVQGIINFEQKE.S | SOD1 G12-E24 | |
| 2,396.6919 | 2,395.6846 | 2,395.1616 | E.ERHVGDLGNVTADKDGVADVSIE.D | SOD1 E78-E100 | ||
| Chymotrypsin (100 mM Tris 50 mM CaCl2, pH 7.8, t = 2 min) | ||||||
| Monomer | No matches | First peptide identified at t = 10 min | ||||
| Dimer | No matches | No peptides out to t = 10 min | ||||
| Trimer | 1,400.4094 | 1,399.4021 | 1,399.7096 | F.EQKESNGPVKVW.G | SOD1 E21-W32 | |
| 3,580.9929 | 3,579.9856 | 3,580.7904 | L.VVHEKADDLGKGGNEESTKTGNAGSRLACGVIGIAQ.- | SOD1 V118-Q153 | ||
| Pepsin (100 mM acetate, pH 3.5, t = 1 min) | ||||||
| Monomer | 1,244.4987 | 1,243.4914 | 1,243.6561 | L.KGDGPVQGIINF.E | SOD1 K9-F20 | |
| 2,696.9983 | 2,695.9910 | 2,696.3922 | F.EQKESNGPVKVWGSIKGLTEGLHGF.H | SOD1 E21-F45 | ||
| Dimer | 1,244.7208 | 1,243.7135 | 1,243.6561 | L.KGDGPVQGIINF.E | SOD1 K9-F20 | |
| 2,697.4995 | 2,696.4922 | 2,696.3922 | F.EQKESNGPVKVWGSIKGLTEGLHGF.H | SOD1 E21-F45 | ||
| Trimer | 1,244.6426 | 1,243.6353 | 1,243.6561 | L.KGDGPVQGIINF.E | SOD1 K9-F20 | |
We used three proteases with different specificity: V8 cuts after D and E; chymotrypsin cuts after F, W, Y, H, M, and L (unless followed by P); and pepsin cuts before L, F, W, and Y (unless preceded by P). Buffer, pH, and digest time are listed for each limited proteolytic reaction with the purified SOD1 monomer, dimer, or trimer. SOD1 monomer and dimer required longer digest times with V8 or chymotrypsin to observe proteolytic cleavage products; we collected time points of proteolytic cleavage reactions out to t = 10 min. Notably, we did not observe proteolytic cleavage of the SOD1 dimer with V8 or chymotrypsin even after 10 min of incubation, in agreement with the known highly stable structure of the native SOD1 dimer. Mr(calc) is the calculated molecular mass from the matched peptide sequence, Mr(expt) is the experimental m/z transformed to a relative molecular mass, and Observed is the experimental m/z from the mass spectrometer. Definitions are from Matrix Science (www.matrixscience.com/help/pmf_summaries_help.html#PROTSUM).