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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