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

Table 2 Estimated binding free energies (ΔG_bind) using MM-GB/PBSA methods

MD code	GBSA
	E_GAS	EGB	ΔG_bind	STD
C1	PqsD + ACoA ( chain B )
C1	−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 )
E1	−44	17	− 27	2.5
E2a	PqsD- CSJ + single β K, secondary channel ( chain A )
E2a	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

STD. - standard deviation; E_GAS - binding energy in vacuum, EGB - binding energy in implicit solvent computed with GB method.
ΔG_bind (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.

ISSN: 2046-1682