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Table 4 Effects of epitopic missense variants on TNFA-golimumab interaction

From: Missense variants in the TNFA epitopes and their effects on interaction with therapeutic antibodies—in silico analysis

SNP_ID Amino acid positiona Amino acid change ∆∆G (Kcal/mol)b Antibody chains MutaBindb PPcheck
mCSM-PPI2 SAAMBE-3D MutaBind ∆∆G (kcal/mol) Total stabilizing energy (kJ/mol)
WT H − 290.62
L − 55.79
rs140654183 105 T/N 0.463 0.67 0.84 H 0.58 − 294.29
L 0.98 − 56.15
rs760036765 111 A/T − 0.711 0.54 1.35 H 1.62 − 300.47
L 1.01 − 55.71
rs770509340 138 R/Q 0.075 1.47 0.49 H 0.25 − 284.33
L 0.96 − 54.37
rs141307820 138 R/W 0.668 1.03 0.72 H 0.44 − 285.08
L 1.23 − 55.81
rs370893734 140 D/N 1.279 0.96 2.4 H 0.75 − 293.72
L 1.41 − 62.05
rs370893734 140 D/Y 0.213 0.78 4 H 1.01 − 285.94
L 1.42 − 53.07
rs763621932 141 Y/S 2.219 1.34 2.45 H 2.07 − 270.91
L 1.43 − 55.23
  1. aAmino acid positions were calculated excluding the signal peptide (76 amino acids)
  2. bPositive values of ∆∆G indicate decreasing affinity