From chemistry-request@ccl.net Sun Jul 18 13:25:50 2004 Received: from smtp2.es.uci.edu (smtp2.es.uci.edu [128.200.80.5]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i6IIPn33012622 for ; Sun, 18 Jul 2004 13:25:49 -0500 Received: from 192.168.0.106 (vp087184.reshsg.uci.edu [128.195.87.184]) by smtp2.es.uci.edu (8.12.8/8.12.8) with ESMTP id i6IIW4Ce006881 for ; Sun, 18 Jul 2004 11:32:09 -0700 Date: Sun, 18 Jul 2004 11:31:57 -0700 From: Qiang Lu X-Mailer: The Bat! (v1.62r) Reply-To: Qiang Lu Organization: UCI MBB X-Priority: 3 (Normal) Message-ID: <158373987.20040718113157..at..uci.edu> To: chemistry..at..ccl.net Subject: Re[2]: CCL:Question about binding energy and deprotonation energy In-Reply-To: <332c031a87.31a87332c0..at..umbi.umd.edu> References: <332c031a87.31a87332c0..at..umbi.umd.edu> MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-NACS_ES-MailScanner: No viruses found X-Spam-Status: No, hits=0.0 required=7.5 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Dear gilson and Peter, Thanks for the detailed explanation. It helps alot. In fact I am studying the zinc interface in p53. The zinc binds four ligands, HIS and 3CYS. A is the imidozole-ZN and B is three thiolate(3S) which bind to ZN. So BH here represent three thiol groups(3SH). The main function of the zinc interface is to stabilize the binding domain. Most of the zinc interface is buried in the protein. In order to get the deprotonation energy of thiol group in this structure, I calculated the energy of both structure with and without deprotonation. The ABH is about 600kcal lower than that of AB. and C-C-SH is about 300kcal lower than C-C-S. Although people used thiolate usually. I worried about which state should be in the real world. The crystal structure pH is 6.8. But the most important thing is the zinc and the around environment. -- Best regards, Qiang mailto:qiangl..at..uci.edu =================Original message text=============== Dear Qiang, The stability of AB-H relative to AB depends upon the pH. Put differently, if you want to know which species, AB-H versus AB, is preferred energetically, the answer is that this depends upon the concentration of protons. Basically, AB is a base and the relative concentrations of AB and AB-H depends upon the concentration of protons, by the law of mass action. Put differently, your statement that "the total energy of AB-H is lower than AB" is not really very meaningful, because the stability of AB-H depends upon the chemical potential of the proton. Does this help? Best regards, Mike ----- Original Message ----- From: Qiang Lu Date: Friday, July 16, 2004 4:11 pm Subject: CCL:Question about binding energy and deprotonation energy > Hi CCLERs, > > Think about the following two reaction: > > A + B-H = AB-H > A + B = AB > > The total energy of AB-H is lower than AB, but the binding energy > between A and B of AB is higher than that of AB-H. > > Then which state is prefer between AB-H and AB? In another words, > is it prefer a deprotonated state of AB-H or not in the nature? > > -- > Best regards, > Qiang Lu mailto:qiangl..at..uci.edu > ==============End of original message text===========