Figure 1.
Structure of the AB and GH loops in the open and closed conformations.
The position of Asp30 and Leu130, and the distance between these residues is also shown. The open conformation is predominant at pH 7.5, while the closed structure is predominant at pH 5.5.
Table 1.
Average distances for selected characteristic interactions in the open and closed conformations of NP4.
Figure 2.
Time evolution of relevant parameters when closed NP4 is placed at a solvent pH of 7.5.
Top: Running average of distance Asp30-Leu130; Middle: Running average of distance Asp35-Asp129; Bottom: Asp30 microscopic pKa. The average values of these distances in the stable simulations of the closed (red) and the open (blue) structures are also shown.
Figure 3.
Thermodynamic cycle relating the relevant chemical species and their equilibrium constants.
Figure 4.
Mole fractions of the relevant chemical species as a function of pH.
KD = 100, KH = 6.31×10−3.
Figure 5.
Concentration of CH at pH 5.5 and Op− at pH 7.5 as a function of KD.
(CH) at pH 5.5 shown in red, while (Op−) at pH 7.5 is shown in blue. The concentrations are given as mole fractions.
Figure 6.
Calculated signal as a function of pH, and comparison to experimental results.
Black: Signal, as defined in Equation 2, as a function of pH for KD = 100, KH = 6.31×10−3, α = 0.03, β = 0.55 (α and β are obtained from ref. 11). Red: NO dissociation equilibrium constant (KdNO) vs pH and fit to the equation of a titration curve with an apparent pKa of 6.5, as obtained from ref. 11.
Figure 7.
Apparent pKa, calculated using Equation 3, as a function of KD.