. Author manuscript; available in PMC: 2015 Aug 22.

Published in final edited form as: Proteins. 2012 Sep 28;81(1):93–106. doi: 10.1002/prot.24165

Table V.

Calculation of the free energy cost of moving a protonated water from solvent water to the highest point (barrier) in the proton translocation pathway (D channel) of the D132N mutant of CcO ^(a).

ΔG^np→crg

ΔΔG^w→p

Δ Δ G_{sol, L W}^{w \to p (A H, M W)}

ΔG^#=12.0+ ΔΔG^w→p

In water (ΔG^w)

−92.9

---

In protein (ΔG^p) (procedure A)

−68.9

24.0

36.0

In protein (ΔG^p) (procedure B)

−86.7

6.2

2.3

20.5

^(a)

Energy values are reported in kcal/mol. A weak constraint of 0.3 kcal/mol was used to keep the LRA/MC generated water molecules in place. The results reported were obtained from microscopic FEP calculations using two different procedures. Procedure A corresponds to using standard solvation approach while including water molecules resolved by X-ray, whereas Procedure B corresponds to using our water flooding LRA/MC screening approach. All of these molecular dynamics simulations are performed using the polarizable ENZYMIX force field [36].