On page 312, Nelson briefly mentions:
...in a protein uncharged and charged residues will affect each other...
meaning that the pK of amino acids within the protein can be affected by the presence of other amino acids. And this is true, in fact many enzymes work on this basis using what is known as general acid/base catalysis.
pK values of residues within the active site of an enzyme can be significantly altered relative to the outside of the protein. The pK of an acid will increase when near a non-polar group as the anionic (deprotonated) form is not stabilised. But the pK will decrease when near a positive charge as the deprotonated form is favoured. Conversely, the pK of a base decreases in a non-polar environment as the positive (protonated) form is not as stable yet the pK will increase when next to a negative charge as its protonated form is stabilised by the opposing charge.
Furthermore the dielectric constant inside a protein can be vastly different to water. Protein centres are typically described as the 'oily core', which will again affect the pK values of the amino acids present.
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