Table 4.
Amino acid usage varies between UniAbs and H2L2 antibodies.
| V3-23 | V4-39 | |||
|---|---|---|---|---|
| CDR_category | % Difference: UniRat vs. H2L2 | p-value | % Difference: UniRat vs. H2L2 | p-value |
| CDR1: hydrophobic | −0.2 | −0.7 | ||
| CDR1: special cases | −0.3 | 0.0 | ||
| CDR1: charged | −1.1 | −0.4 | ||
| CDR1: polar uncharged | +1.6 | +1.1 | ||
| CDR2: hydrophobic | −1.5 | −1.9 | ||
| CDR2: special cases | −0.6 | −0.3 | ||
| CDR2: charged | +0.4 | +2.4 | 1.0E−24 | |
| CDR2: polar uncharged | +1.7 | −0.2 | ||
| CDR3: hydrophobic | −8.7 | 1.3E−223 | −7.4 | 1.4E−101 |
| CDR3: special cases | +0.1 | −1.9 | ||
| CDR3: charged | +5.0 | 2.7E−87 | +3.4 | 1.6E−29 |
| CDR3: polar uncharged | +3.6 | 1.4E−44 | +5.8 | 1.2E−65 |
| Categories | Amino Acids | |||
| Hydrophobic | A, V, I, L, M, F, Y, W | |||
| Special cases | C, G, P | |||
| Charged | R, H, K, D, E | |||
| Polar uncharged | S, T, N, Q | |||
Amino acids were categorized into one of four classes as indicated. The frequency of each category in the CDR1, CDR2, and CDR3 was determined for a large set of UniAbs and fixed-light chain H2L2 antibodies that use either IGHV3-23 or IGHV4-39. The differences in frequencies for each category were then compared between UniAbs and H2L2 antibodies, revealing that UniAbs contain more charged and polar uncharged amino acids and fewer hydrophobic residues. These trends were particularly notable in the CDR3 region. Differences of more than 2% are highlighted in the table below and were found to be statistically significant using a Mann-Whitney test. Usage frequencies and standard deviations are included in Supplemental Table 2.