From owner-chemistry@ccl.net Thu Apr  9 02:39:00 2009
From: "alexandra.marques.|*|.fc.up.pt" <owner-chemistry|*|server.ccl.net>
To: CCL
Subject: CCL: transition states of enzymes
Message-Id: <-39041-090408185956-10380-1ClQb8qIXk3bzTxxvhHrzQ|*|server.ccl.net>
X-Original-From: alexandra.marques|fc.up.pt
Content-Disposition: inline
Content-Transfer-Encoding: 7bit
Content-Type: text/plain;
	charset=ISO-8859-1;
	DelSp="Yes";
	format="flowed"
Date: Thu, 09 Apr 2009 00:04:07 +0200
MIME-Version: 1.0


Sent to CCL by: alexandra.marques=-=fc.up.pt
Hi,

I have been read some articles about the search for transitions state  
structures in enzymatic reactions but I still have some doubts:
1) It seems that when the full enzyme is intended to be used the most  
widely used approach is to use QM/MM to model the enzyme and perform a  
relaxed PES scan along some reaction coordinate. Is this correct or  
there are better methods?
2) Imagining that an approximate transition state can be identified in  
a PES scan with the full enzyme, then, which method shall be used to  
prove that this is the correct transition state? I am asking that  
because I think a frequency calculation or even the IRC method cannot  
be applied for a large system?
Can anyone help me please.
Thanks a lot
Alexandra


-------------------------------------------------------------------------
A FCUP utiliza o sistema open source de webmail Horde/IMP (www.horde.org)
Visite: http://www.fc.up.pt/ http://info.fc.up.pt/