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In the second basic photocycle step, the chromophore is protonated and structural changes take place in the protein.
All aspartic acid and glutamic acid residues as well as C-terminal groups were deprotonated; arginine, lysine, and N-terminal groups were protonated .
Ionizable groups were protonated to represent pH = 7.0.
The rate constants of protonation of these reactants had been measured previously by manual analysis and their pK values are directly measured.
Once all contacts are established and the ligand is protonated , the interaction is quite strong and the dissociation reaction is much slower than with similar amidine compounds.
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