AMBER Archive (2005)

Subject: Re: AMBER: a nomenclature question

From: David A. Case (case_at_scripps.edu)
Date: Thu May 12 2005 - 17:18:20 CDT

On Fri, May 06, 2005, Kenley Barrett wrote:

> I working on determining the protonation states of various histidine
> residues in my protein, and referred to the CRC handbook for pKas.
> Does anyone know what the difference is between L-1-methylhistidine
> and L-3-methylhistidine? I found these in the handbook, which does not
> appear to comply with the IUPAC nomenclature recommendations.
>

In organic nomenclature, the "1" position corresponds to N-epsilon in
IUPAC/biochemical nomenclature; the "3" position corresponds to N-delta.

Looking at the methyl-histidine values doesn't directly say anything about
histidine itself. I recommend the discussion by Jack Kyte on pp. 63-64 of
"Structure in protein chemistry" (Garland Publishing, New York, 1995). This
gives a clear discussion of both microscopic and macroscopic pKa values for
histidine.

...good luck...dac

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