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Pka of residues in an active site of protein

by johndude222
Tags: active, protein, residues
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Nov6-10, 10:07 AM
P: 1
Here is a little concept I have difficulty reasoning it out and I was hoping if someone can guide me through it.

pKa of amino acid residues in a protein active site. Take histidine for example, below pH of 6.0 it stays positively charged but above pH of 6.0 it becomes neutral with the removal of a hydrogen on its side chain.

Now if we make the its surrounding negative (i.e. all the nearby residues are negatively charged), the pKa of histidine side chain increases because histidine itself likes to remain positively charged in this negatively charged environment. That makes sense.

However, given that the hydrogen ion been removed is positive, doesn't other negatively charged residues want that hydrogen from the histidine (as opposite charges attract) and therefore it should be easier to remove that hydrogen (therefore pKa decreases).

I don't understand why the pKa increases in this context.
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Nov7-10, 02:39 PM
P: 9
Remember that pKa is measuring a thermodynamic quantity (the equilibrium constant of the acid dissociation reaction). If we add negative charges to the histidine environment we stabilize the protonated form relative to the deprotonated form and so the pKa increases (the equilibrium favours the reactant side more than it did).

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