Free Lysine vs. Lysine in protein - The approximate pKa of free lysine is 10-11. The pKa decreases when L (Aug/18/2007 )

The approximate pKa of free lysine is 10-11. The pKa decreases when Lysine is surrounded by only hydrophobic residues in protein. What is the reason?

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When the pKa of lysine decreases that means that it is more easily deprotonated. Now, when lysine is protonated it is cationic and such a state even if unstable it can be somewhat stabilized by a hydrophilic environment. Now, if you set a protonated lysine (R-NH3+) in a hydrophobic environment (hydrophobic residues) it will not have any stabilization, therefore it will try to get rid of the extra proton as much as possible, this corresponds to a lower pKa. Hope I haven't made the explanation too confusing.

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