TABLE 3.

Decomposition of the free energies in the triplex models and association free energies for the various substructures in the triplex

A	B	C	Ion
−849.2	−847.0	−841.4	−99.7
A-B	B-C	A-C
−1690.6	−1690.1	−1683.4
(−0.7)	(−1.7)	(+0.9)
A-ion	B-ion	C-ion
−941.5	−944.8	−938.2
(−0.3)	(+0.4)	(+1.4)
AB-ion	AC-ion	BC-ion	ABC
−1795.4	−1783.0	−1792.0	−2512.8
(−6.5)	(−1.4)	(−4.4)	(+17.6–+19.0)*
ABC-ion
−2645.3
(−34.2)

Absolute free energies, and in parentheses, the effective binding energy for each model, where relevant (interacting subsystems are separated by the dash). All the sampled structures are from the triplex model trajectory. The heading in each table entry represents the portion of the model evaluated in the free-energy analysis. For example, A represents the free energy of the isolated A-strand from the triplex simulation, and ABC-ion represents the free energy of the A-, B-, and C-strand complex including the bound ion from the triplex simulation. For the interaction energy, the dash signifies how the interaction is split; for example, A-B represents the interaction of the A-strand with the B-strand (in the triplex structure). All the energies are in kcal/mol. Note that solute entropic effects are not included; these likely span the range of ∼2–3 (for an individual ion) to ∼10–15 kcal/mol (for strands) at 300 K disfavoring association (as discussed in Methods). For the sake of comparison, the free energies of the duplex simulations dimer_AB and dimer_AD are –1694.0 and –1689.4, respectively.

^*Range of association free energies for the triplex assembly ABC for A-BC, B-AC, and C-AB association in the absence of ions.