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Table 1 Differentially protonated residues in catB and pKa values

From: How does heparin prevent the pH inactivation of cathepsin B? Allosteric mechanism elucidated by docking and molecular dynamics

  

Average values during 40ns MD

Residue

predicted crystal

pH 5,5

pH 8

C29

2,14

3.7 ± 1.5

7.3 +1.6

E36

5,9

5.4 ± 0.5

3.4 ± 1.2

H97

6,9

7.1 ± 0.2

7.3 ± 0.4

H110

6,6

6.6 ± 0.8

8.1 ± 0.7

E171

7,7

7.4 ± 0.2

6.5 ± 0.4

H190

7,2

7.1 ± 0.2

7.4 ± 0.7

H199

7,8

8.1 ± 2

4.5 ± 1.7

  1. pKa values predicted by PROPKA and the state of ionizable groups under different pH conditions are indicated. The protonation state of C29 at pH 8 were obtained taking into account deprotonation of H199 as previously proposed for papain. The protonation states of the catalytic residues (C29 and H199) are highlighted.