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Table 2 Global MM-PBSA energy calculations

From: Mechanism of PhosphoThreonine/Serine Recognition and Specificity for Modular Domains from All-atom Molecular Dynamics

domain mutated site mutation ΔΔUVDW ΔΔUCoul ΔΔWPB ΔΔEele ΔΔEtot-np ΔΔWnp ΔΔEtot
Rad53-FHA1 1 pTpS 2.50 -34.34 37.83 3.49 5.99 0.75 6.74
Rad53-FHA1 1 pTpS 0.44 -13.74 16.08 2.33 2.77 0.72 3.49
Dun1-FHA 1 pTpS -2.63 -13.70 18.84 5.15 2.52 2.34 4.86
Ki67-FHA 1 pTpS 4.30 -8.77 7.79 -0.98 3.32 -0.84 2.48
Dun1-FHA 2 pTpS -2.54 -59.30 63.39 4.09 1.55 1.95 3.50
Ki67-FHA 2 pSpT 0.94 19.77 -20.15 -0.38 0.55 0.36 0.91
BRCT 1 pSpT -3.33 28.77 -23.67 5.10 1.77 0.84 2.61
WW 1 pSpT -1.03 -39.75 36.78 -2.96 -3.99 -0.01 -4.00
  1. ΔΔUCoul and ΔΔUvdw are the electrostatic and van der Waals interactions, respectively, between the wild-type and mutants; ΔΔWPB and ΔΔWnp are the polar and non-polar contributions from the solvation energy. ΔΔEele represents the sum of ΔΔUCoul and ΔΔWPB. ΔΔ indicates the changes between two calculations of the mutated and non-mutated state. For example, ΔΔUVDW = ΔUVDW,pSer-ΔUVDW,pThr, where ΔUVDW is the interaction energy between the phosphopeptide and the domain.