Subject: Protonation states in proteins

From: Charles Letner <[email-masked]>
Date: Tue, 5 Jul 1994 12:45:41 -0700 (PDT)

Hello all,
	I am using AMBER to run some MM and MD on proteins.  A question
that I have begun to ponder is the effect of the protonation state of the
acid and basic amino acids on the results.  I've been going back over the
papers I have on the application of MM & MD to proteins.  What I'm finding
is that most people really don't say much about which AA's are protonated
and which are not.  To a first approximation I would expect surface AA's
to be charged and interior AA's to be uncharged, though active site
residues and salt bridges could obviously be exceptions to this rule.  So I'm
wonder what those of you in the virtual world think about this?  Is it
worth going through the trouble to try and determine protonation of each
residue?  Are there any efficient means of doing this?  References and
comments of any sort are welcome.
	I'll send a summary of responses.

Thanks
Chuck  

Charles Letner
Wright State University
Department of Biochemistry
Dayton, OH 45435
e-mail: [email-masked]