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Affect of adjacent amino acids on pKa values

by James D
Tags: amino acids, pka, pkr, polypeptide
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James D
Nov19-09, 11:20 AM
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I use some standard tables of amino acids pKa values, as the one here:
and I am especially interested in the pKr (i.e. pKa of the side chains).

Correct me if I'm wrong, but pKa values listed in such tables refer to a "free" peptide, as opposed to a peptide which is a part of a polypeptide.

What I am interested in is to get some intuition as to how might pKr values change when the peptide is a part of a polypeptide. For example, if the peptide in interest is X and its "standard" pKr value is Y, do you expect this pKr value to be higher or lower when X is found in a polypeptide next to some amino acid Z?

I am not looking for exact calculation, but just some thumb rules or intuition.

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Nov19-09, 03:05 PM
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Just so you know... a peptide and an amino acid are not interchangeable. The table you referenced is for the individual amino acids. Peptides are short chains composed of amino acids and proteins (polypeptides) are longer ones.

The 3-D structure of the protein affects the pKa of the side chains as well as groups nearby (in space). Nearby groups need not be adjacent to the side chain of interest to exert their effect but I would imagine that they would be the most important. I don't believe there are any general rules of thumb for this unless you know of some rules of thumb that one could use to determine 3-D structures for given proteins.

This might help...

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