I understand that actual pKa of amino acid side chains is greatly influenced by the surrounding environment. I am trying to deeply understand the equilibrium between protonated and deprotonated form of amino acid side chain by taking Lys as an example. Lets imagine a protein having solvent exposed Lys residue. At physiological pH, theoretically this Lys residue on every protein is in largely protonated form (ofcourse some are deprotonated). Now say with some reagent I modify few of this particular Lys residue (using NHS ester etc.). Now does the remaining unmodified Lys residues undergo protonation/deprotonation to nullify the effect caused by the chemical modification and maintain the state of such equilibrium? Also, I am curious is it always impossible to achieve 100 % modification of this particular Lys residue due to the existence of equilibrium state?