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Table 2 Estimated binding free energiesG bind ) using MM-GB/PBSA methods

From: Molecular basis of HHQ biosynthesis: molecular dynamics simulations, enzyme kinetic and surface plasmon resonance studies

MD code GBSA
  E_GAS EGB ΔGbind STD
C1 PqsD + ACoA ( chain B )
−308 196 111 14
C2 PqsD + ACoA ( chain A )
−32 −50 82 8
PqsD + ACoA ( chain B )
25 −88 63 7
E1 PqsD- CSJ + single β K, primary funnel ( chain A )
−44 17 27 2.5
E2a PqsD- CSJ + single β K, secondary channel ( chain A )
15 −42 27 6
E2b PqsD- CSJ + β K in secondary channel ( chain A )
−7 −37 44 5
PqsD- CSJ + β K in secondary channel ( chain B )
  6 −32 26 6
F PqsD + HHQ ( chain B )
  −54 14 40 3
  1. STD. - standard deviation; E_GAS - binding energy in vacuum, EGB - binding energy in implicit solvent computed with GB method.
  2. ΔGbind (kcal/mol) are computed for ACoA, βK and HHQ in the different PqsD complexes describing the kinetic cycle: C1 – PqsD with ACoA in chain B, C2 – PqsD with ACoA in the primary funnel of chain A and B, D – PqsD with Cys112-bound anthranilate (PqsD-CSJ), E1 - PqsD-CSJ with βK in the primary funnel of chain B, E2a - PqsD-CSJ with βK in the secondary channel of chain A, E2b - PqsD-CSJ with βK in the secondary funnel of chain A and B, F – PqsD with HHQ in the primary funnel of chain B.