Table 4A. Summary of oxidized heavy chain tryptic peptide data.
| Heavy Chain Tryptic Peptides | Detected Oxidized Residuesa | Non-normalized Rate Constant Ratioe (Dimer k:Monomer k) | Normalized Rate Constant Ratiof (Dimer k:Monomer k) | Protection Level Assignment in Dimer Relative to Monomerg |
|---|---|---|---|---|
| 1–19 |
V(12), P(14), S(17) |
2.6 |
1.0 |
No change |
|
20–38 |
Y(13), M(5), W(17) |
2.1 |
0.8 |
No change |
|
44–65 |
W(4), W(7), I(8), Y(11) |
2.0 |
0.8 |
No change |
| 68–76 |
F(3), S(8) |
4.5 |
1.7 |
Decreased |
| 77–87 |
Y(4), Q(6), M(7) |
1.3 |
0.5 |
Increased |
| 88–98 |
A(1), A(10) |
4.0 |
1.5 |
Decreased |
|
99–127b |
Y(4), H(9), W(10), Y(11), W(15) |
- |
- |
- |
| 128–139c |
F(9), P(6) |
- |
- |
No change |
| 140–153 |
L(9), V(13) |
4.0 |
1.5 |
Decreased |
| 154–216d |
Approx. Eight oxidized residues |
3.0 |
1.2 |
No change |
| 229–254 |
P(5), L(12), P(10) |
3.3 |
1.3 |
No change |
| 255–261 |
M(4) |
6.2 |
2.4 |
Decreased |
| 262–280 |
P(2), H(13), P(16) |
1.8 |
0.7 |
No change |
| 281–294 |
Y(4), V(8), H(11) |
2.6 |
1.0 |
No change |
| 299–307 |
Y(4) |
2.6 |
1.0 |
No change |
| 308–323 |
V(2), H(9), W(12) |
2.5 |
1.0 |
No change |
| 333–340 |
P(5), E(7) |
2.7 |
1.0 |
No change |
| 351–361 |
P(2), Y(5) |
2.5 |
1.0 |
No change |
| 362–366 |
M(3) |
6.3 |
2.4 |
Decreased |
| 367–376 |
S(4), T(6) |
2.0 |
0.8 |
No change |
| 377–398 |
P(4), S(13) |
2.6 |
1.0 |
No change |
| 399–415 |
T(1), P(4) |
1.8 |
0.7 |
No change |
| 423–445 |
W(1), S(8), M(12) |
6.4 |
2.5 |
Decreased |
| 446–452 | S(5) | 3.3 | 1.3 | No change |
Underlined peptides indicate CDR-containing peptides. aDenotes the detected oxidized amino acid residue, and its numerical position within the peptide. Oxidized residues confirmed by tandem MS data. bHC 99–127 non-oxidized parent peptide showed inconsistent recovery in the tryptic digests. Dose response curves were therefore not considered representative, and the peptide was excluded from structural assessment. cHC 128–139 displayed rate constants (k) of 0 in both the dimer and monomer samples (see Supplementary Files). There is therefore no difference in protection levels, though a rate constant ratio cannot be calculated. dVery large tryptic peptides (40–50 residues) with oxidized forms (+16 Da, +14 Da, +32 Da, etc.) observed by MS data. However, tandem MS data are not able to conclusively confirm the specific sites of oxidation. Based on the average number of oxidized residues observed for other peptides (approximately 2 out of 10 residues are oxidized per peptide), it is assumed that these very large peptides would have approximately 8 oxidized residues. eRate constant (k) of dimer divided by the rate constant ratio (k) of the monomer. Mean of all non-normalized ratios: 2.7. Median of all non-normalized ratios: 2.5. f Normalization factor: 2.6 (average of the mean and median of the non-normalized ratios). Mean of all normalized ratios: 1.0. Median of all normalized ratios: 1.0. gNormalized ratios from 0.6 to 1.4: No change. Normalized ratios ≤ 0.5: increased protection. Normalized ratios ≥ 1.5: decreased protection.