The molecular structure of the amphiphilic compound was designed in three parts: (i) a fluorinated hydrophobic tag responsible of self-assembling, (ii) a flexible and hydrophilic ethylenoxide moiety as polar head and (iii) a protonated at physiological pH primary amine responsible of binding.
A, protonated A-state of the chromophore; I, deprotonated intermediate state; B, deprotonated B-state.
The pH dependence of the spectrum permits us to evaluate a pKa of 5 6 for the equilibrium between a protonated and a deprotonated form.
The primary ph4 for the σ binding sites was defined by mapping the topographic arrangements of the phenyl ring, the N-atom, and N lone pair vector; a point was placed 2.8 Å tetrahedrally from N atoms to represent an interaction between a protonated N atom and its binding site; dummy atoms were built 3.5 Å above and below a phenyl ring to represent hydrophobic binding to a receptor.
The retinal chromophore is covalently bound, via a protonated Schiff base, to Lys216, which is located in the middle of the membrane.
The electrospray process generates dimers of purine bases that are detected in ESI MS as protonated ions, except for xanthine, for which a protonated radical dimer is detected.
The presence of salt in the vicinity of a charged (protonated) His helps to shield the charge, explaining the strong salt dependence of the p Ka of His.
Thermodynamic link and cooperative interaction are assessed demonstrating that binding of one halide ion is associated with the binding of one proton in a cooperative fashion with the formation, in the pH range 4.5 10, of a single fully protonated E2GFP·halogen complex.
The pH titrations of IAA, 2-NAA, and 2,4-D by 1H NMR spectroscopy showed the influence of solution pH on binding interactions between both protonated and anionic forms of auxin molecules and CB[7].
