Skip to main content
. 2020 Apr 15;7:50. doi: 10.3389/fmolb.2020.00050

Table 2.

Computational alanine scanning for PARP-1 and PARP-2 with the MM/GBSA_IE method.

PARP-1
Mutation ΔΔEvdw ΔΔEele ΔΔGgb ΔΔGnp ΔΔH −TΔΔS ΔΔG
Y907A 6.41 ± 0.15 −0.09 ± 0.19 −0.25 ± 0.24 0.27 ± 0.04 6.33 ± 0.15 −0.73 ± 0.13 5.60 ± 0.26
Y889A 4.05 ± 0.14 0.09 ± 0.30 −0.04 ± 0.26 0.24 ± 0.02 4.35 ± 0.18 −0.66 ± 0.23 3.69 ± 0.24
Y896A 3.33 ± 0.09 0.90 ± 0.05 −0.86 ± 0.04 0.13 ± 0.01 3.51 ± 0.09 −0.41 ± 0.05 3.10 ± 0.13
H862A 1.53 ± 0.16 −0.44 ± 0.12 0.67 ± 0.12 0.06 ± 0.00 1.81 ± 0.16 −0.17 ± 0.04 1.64 ± 0.19
E988A 1.04 ± 0.13 4.94 ± 0.11 −4.43 ± 0.10 0.09 ± 0.02 1.65 ± 0.14 −0.28 ± 0.11 1.37 ± 0.25
E763A 1.20 ± 0.21 4.90 ± 0.28 −4.43 ± 0.27 0.16 ± 0.04 1.83 ± 0.25 −0.87 ± 0.29 0.96 ± 0.23
K903A 1.38 ± 0.21 −3.59 ± 0.23 3.15 ± 0.20 0.07 ± 0.02 1.00 ± 0.17 −0.13 ± 0.05 0.87 ± 0.16
D766A 0.19 ± 0.08 4.00 ± 0.21 −3.54 ± 0.20 0.01 ± 0.01 0.67 ± 0.10 −0.15 ± 0.08 0.52 ± 0.03
V762A 0.56 ± 0.03 −0.19 ± 0.02 0.19 ± 0.02 0.03 ± 0.01 0.60 ± 0.03 −0.11 ± 0.03 0.49 ± 0.05
Q759A 0.84 ± 0.05 0.35 ± 0.26 −0.41 ± 0.23 0.05 ± 0.02 0.83 ± 0.04 −0.39 ± 0.31 0.44 ± 0.30
F897A 0.23 ± 0.01 0.24 ± 0.02 −0.18 ± 0.03 0.00 ± 0.00 0.30 ± 0.02 −0.02 ± 0.01 0.28 ± 0.02
S904A −0.55 ± 0.29 1.87 ± 0.29 −0.58 ± 0.14 0.00 ± 0.00 0.74 ± 0.13 −0.46 ± 0.14 0.28 ± 0.21
W861A 0.06 ± 0.00 −0.01 ± 0.02 0.12 ± 0.01 0.00 ± 0.00 0.17 ± 0.01 0.00 ± 0.00 0.17 ± 0.01
T887A 0.16 ± 0.06 0.12 ± 0.15 −0.09 ± 0.13 0.01 ± 0.00 0.20 ± 0.09 −0.03 ± 0.04 0.17 ± 0.10
Y989A 0.07 ± 0.01 −0.02 ± 0.01 0.05 ± 0.01 0.00 ± 0.00 0.10 ± 0.01 0.00 ± 0.00 0.10 ± 0.01
P885A 0.04 ± 0.02 0.09 ± 0.02 −0.08 ± 0.02 0.00 ± 0.00 0.05 ± 0.02 −0.01 ± 0.01 0.04 ± 0.02
N987A 0.01 ± 0.00 0.02 ± 0.02 −0.02 ± 0.02 0.00 ± 0.00 0.01 ± 0.00 0.00 ± 0.00 0.01 ± 0.00
S864A 0.03 ± 0.01 −0.05 ± 0.12 0.03 ± 0.12 0.00 ± 0.00 0.02 ± 0.01 −0.02 ± 0.02 0.00 ± 0.02
PARP-2
Mutation ΔΔEvdw ΔΔEele ΔΔGgb ΔΔGnp ΔΔH −TΔΔS ΔΔG
Y473A 6.34 ± 0.13 0.18 ± 0.10 −0.55 ± 0.11 0.34 ± 0.01 6.31 ± 0.12 −0.91 ± 0.08 5.40 ± 0.16
Y455A 3.35 ± 0.70 0.32 ± 0.25 −0.18 ± 0.24 0.19 ± 0.08 3.67 ± 0.76 −0.53 ± 0.19 3.14 ± 0.58
Y462A 3.40 ± 0.39 0.92 ± 0.08 −0.94 ± 0.07 0.16 ± 0.05 3.54 ± 0.40 −0.43 ± 0.09 3.11 ± 0.42
E558A 1.08 ± 0.08 4.99 ± 0.11 −4.46 ± 0.11 0.11 ± 0.02 1.71 ± 0.09 −0.27 ± 0.07 1.44 ± 0.14
H428A 1.32 ± 0.21 −0.10 ± 0.31 0.29 ± 0.31 0.06 ± 0.01 1.57 ± 0.25 −0.18 ± 0.05 1.39 ± 0.28
K469A 1.10 ± 0.08 −3.41 ± 0.07 3.00 ± 0.07 0.09 ± 0.01 0.77 ± 0.08 −0.07 ± 0.02 0.69 ± 0.08
I331A 0.81 ± 0.08 −0.31 ± 0.12 0.31 ± 0.04 0.08 ± 0.05 0.88 ± 0.12 −0.38 ± 0.07 0.51 ± 0.17
L327A 0.41 ± 0.30 −0.02 ± 0.07 0.06 ± 0.07 0.04 ± 0.03 0.49 ± 0.31 −0.06 ± 0.05 0.43 ± 0.29
P451A 0.24 ± 0.15 0.03 ± 0.02 −0.01 ± 0.03 0.02 ± 0.02 0.28 ± 0.17 −0.04 ± 0.03 0.24 ± 0.15
F463A 0.22 ± 0.02 0.25 ± 0.03 −0.22 ± 0.04 0.00 ± 0.00 0.25 ± 0.04 −0.03 ± 0.01 0.23 ± 0.05
W427A 0.06 ± 0.00 −0.01 ± 0.02 0.12 ± 0.02 0.00 ± 0.00 0.17 ± 0.01 0.00 ± 0.00 0.17 ± 0.01
S470A −0.60 ± 0.26 1.83 ± 0.29 −0.61 ± 0.11 0.00 ± 0.00 0.63 ± 0.10 −0.47 ± 0.08 0.16 ± 0.14
S328A 0.38 ± 0.15 0.65 ± 0.50 −0.73 ± 0.51 0.05 ± 0.04 0.35 ± 0.16 −0.26 ± 0.29 0.09 ± 0.17
Y559A 0.06 ± 0.01 −0.03 ± 0.01 0.06 ± 0.01 0.00 ± 0.00 0.09 ± 0.01 0.00 ± 0.00 0.09 ± 0.01
N557A 0.01 ± 0.00 0.04 ± 0.01 −0.04 ± 0.01 0.00 ± 0.00 0.01 ± 0.00 0.00 ± 0.00 0.01 ± 0.00
Q332A 0.69 ± 0.56 −0.39 ± 1.11 0.26 ± 1.15 0.07 ± 0.08 0.64 ± 0.57 −0.63 ± 0.73 0.01 ± 0.29
S430A 0.03 ± 0.01 −0.02 ± 0.07 0.01 ± 0.07 0.00 ± 0.00 0.02 ± 0.01 −0.02 ± 0.00 0.00 ± 0.01

All energy values are given in kcal/mol. ΔΔEvdw, ΔΔEele, ΔΔGgb, and ΔΔGnp represent the difference of van der waals interaction, electrostatic interaction, generalize-born and nonpolar solvation free energy between WT and the mutant.