From chemistry-request@ccl.net Sat Apr 2 22:08:46 2005 Received: from SXT-SM-1.UCIS.Dal.Ca (SXT-SM-1.UCIS.Dal.Ca [129.173.5.72]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j3338ccR010846 for ; Sat, 2 Apr 2005 22:08:38 -0500 Received: from KIL-UPT-2.UCIS.Dal.Ca (KIL-UPT-2.UCIS.Dal.Ca [129.173.1.68]) by SXT-SM-1.UCIS.Dal.Ca (8.12.11/8.12.11) with ESMTP id j331wZtr009034; Sat, 2 Apr 2005 21:58:35 -0400 Received: from KIL-UPT-2.UCIS.Dal.Ca (localhost.localdomain [127.0.0.1]) by KIL-UPT-2.UCIS.Dal.Ca (8.12.11/8.12.11) with ESMTP id j331wZli017110; Sat, 2 Apr 2005 21:58:35 -0400 Received: (from apache@localhost) by KIL-UPT-2.UCIS.Dal.Ca (8.12.11/8.12.11/Submit) id j331wZb4017108; Sat, 2 Apr 2005 21:58:35 -0400 Received: from blk-224-150-196.eastlink.ca (blk-224-150-196.eastlink.ca [24.224.150.196]) by my2.dal.ca (IMP) with HTTP for ; Sat, 2 Apr 2005 21:58:35 -0400 Message-ID: <1112493515.424f4dcb16b3e |a| my2.dal.ca> Date: Sat, 2 Apr 2005 21:58:35 -0400 From: Cherif Matta To: SANDEEP KUMAR Cc: Eric Hu , CHEMISTRY |a| ccl.net Subject: Re: CCL:desolvation energy table for amino acids References: <9bdbda531357.424ee89b |a| jhumail.jhu.edu> In-Reply-To: <9bdbda531357.424ee89b |a| jhumail.jhu.edu> MIME-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit User-Agent: Internet Messaging Program (IMP) 3.2.4 X-Originating-IP: 24.224.150.196 X-Spam-Status: No, score=0.0 required=5.0 tests=none autolearn=failed version=3.0.1 X-Spam-Checker-Version: SpamAssassin 3.0.1 (2004-10-22) on server.ccl.net Hello Eric and Sandeep, Sandeep, do you have the ref to Makhatadze paper? Also have a look at the classic papers by Wolfenden: [1] Wolfenden R, Andersson L, Cullis PM, Southgate CCB (1981). "Affinities of amino acid side chains for solvent water". Biochem.; 20: 849-855. [2] Radzicka A, Wolfenden R (1988). "Comparing the polarities of the amino acids: side-chain distribution coefficients between the vapor phase, cyclohexane, 1-octanol, and neutral aqueous solutions". Biochem.; 27: 1664-1670. Cheers, Cherif ------------------------------------------------------- Cherif F. Matta, Ph.D., MCIC * Izaak Walton Killam Post Doctoral Fellow Department of Chemistry, Dalhousie University Halifax, NS, Canada. * Adjunct Professor of Chemistry McMaster University, Hamilton, ON, Canada. ------------------------------------------------------- * Web site: http://chem.utoronto.ca/~cmatta/ Tel: (902) 494 7021 Fax: (902) 494 1310 ------------------------------------------------------- Quoting SANDEEP KUMAR : > Hi Erick , > > Please see the work of Makhatadze and co-workers. They have compiled > hydration energies/enthalpies for amino acids transfer from Octanol to > Water. > > Good luck, > Sandeep > > ------------------------------------------------------------------- > Dr. Sandeep Kumar, > Associate Research Scientist, > Johns Hopkins University Department of Biology, > 106 Mudd Hall, 3400 N. Charles Street, > Baltimore, MD 21218, USA. > Phone: 410-516-8433, > Email: kumarsan |a| jhu.edu. > URL: http://myprofile.cos.com/Kumarsan. > or https://jshare.johnshopkins.edu/skumar23/public_html/ > > > ----- Original Message ----- > From: Eric Hu > Date: Friday, April 1, 2005 6:45 pm > Subject: CCL:desolvation energy table for amino acids > > > Hi, I wonder if anyone has knowledge of availability of a desolvation > > energy table for each individual amino acid. Thanks. > > > > Eric > > > > > > -= This is automatically added to each message by the mailing > > script =- > > To send e-mail to subscribers of CCL put the string CCL: on your > > Subject: line > > > > Send your subscription/unsubscription requests to: CHEMISTRY- > > REQUEST |a| ccl.net > > HOME Page: http://www.ccl.net | Jobs Page: > > http://www.ccl.net/jobs > > > > If your is mail bouncing from ccl.net domain due to spam filters, > > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+- > > +-+-+ > > > > > > > > > > > > > -= This is automatically added to each message by the mailing script =- > To send e-mail to subscribers of CCL put the string CCL: on your Subject: > line > and send your message to: CHEMISTRY |a| ccl.net > > Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST |a| ccl.net > HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs > > If your is mail bouncing from ccl.net domain due to spam filters, please > use the Web based form from CCL Home Page > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > > > > > > From chemistry-request@ccl.net Sun Apr 3 10:45:07 2005 Received: from server.ccl.net (ccl [127.0.0.1]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j33Ej6Qt004498 for ; Sun, 3 Apr 2005 10:45:06 -0400 Received: (from apache@localhost) by server.ccl.net (8.13.1/8.13.1/Submit) id j33Ej6w5004497 for chemistry /a\ ccl.net; Sun, 3 Apr 2005 10:45:06 -0400 Date: Sun, 3 Apr 2005 10:45:06 -0400 Message-Id: <200504031445.j33Ej6w5004497 /a\ server.ccl.net> X-Authentication-Warning: server.ccl.net: apache set sender to chemistry-request /a\ ccl.net using -f From: "Victor, , Belousov" To: chemistry /a\ ccl.net X-Web-Message-Number: 050403104245-4445 Subject: W:NDDO (MNDO,AM1,...) parameters for Li-Cs, Be-Ba? X-Spam-Status: No, score=-2.8 required=5.0 tests=ALL_TRUSTED autolearn=failed version=3.0.1 X-Spam-Checker-Version: SpamAssassin 3.0.1 (2004-10-22) on server.ccl.net Dear CCLers, Maybe somebody will help me. I am looking for NDDO (MNDO, AM1, PM3) parameters for alkaline and alkiline-earth metals. I have recently found out that semiempirical parametrization was extended on these elements (James J. P. Stewart // Journal of Molecular Modeling, 2004. V. 10, N. 2, P. 155 - 164), but I can not obtain the full text of this article. Long search of parameters in the Internet has not brought results. Could someone send me parameters or to specify an accessible source for their reception. Thank you very much for your help, Victor Belousov vihtor(+at+)don.tula.net The Institute of D. Mendeleev University of Chemical Technology of Russia From chemistry-request@ccl.net Sun Apr 3 15:12:50 2005 Received: from ipex1.johnshopkins.edu (ipex1.johnshopkins.edu [162.129.8.141]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j33JCf40007714 for ; Sun, 3 Apr 2005 15:12:42 -0400 Received: from jhem1.jhmi.edu (HELO jhumail.jhu.edu) (162.129.8.22) by ipex1.johnshopkins.edu with ESMTP; 03 Apr 2005 15:12:32 -0400 X-BrightmailFiltered: true X-Brightmail-Tracker: AAAAAA== X-IronPort-AV: i="3.91,144,1110171600"; d="scan'208"; a="54414988:sNHT10549635188" Received: from [70.22.34.47] by jhumail.jhu.edu (mshttpd); Sun, 03 Apr 2005 15:12:29 -0400 From: SANDEEP KUMAR To: Cherif Matta Cc: SANDEEP KUMAR , Eric Hu , CHEMISTRY /a\ ccl.net Reply-To: kumarsan /a\ JHU.edu Message-ID: <57ffe604158f.425007dd /a\ jhumail.jhu.edu> Date: Sun, 03 Apr 2005 15:12:29 -0400 X-Mailer: Sun Java(tm) System Messenger Express 6.1 HotFix 0.11 (built Jan 28 2005) MIME-Version: 1.0 Content-Language: en Subject: Re: CCL:desolvation energy table for amino acids X-Accept-Language: en Priority: normal Content-Type: text/plain; charset=us-ascii Content-Disposition: inline Content-Transfer-Encoding: 7bit X-Spam-Status: No, score=0.6 required=5.0 tests=FORGED_RCVD_HELO, FROM_ENDS_IN_NUMS autolearn=no version=3.0.1 X-Spam-Checker-Version: SpamAssassin 3.0.1 (2004-10-22) on server.ccl.net Hi Cheriff, I am sorry, I can't recall specific references, but its there in his papers /reviews with privalov in early 1990s. I did a quick pubmed search and came up with the following: Privalov PL, Makhatadze GI. Contribution of hydration to protein folding thermodynamics. II. The entropy and Gibbs energy of hydration. J Mol Biol. 1993 Jul 20;232(2):660-79. PMID: 8393941 [PubMed - indexed for MEDLINE] Makhatadze GI, Privalov PL. Contribution of hydration to protein folding thermodynamics. I. The enthalpy of hydration. J Mol Biol. 1993 Jul 20;232(2):639-59. But I also remember reading more papers by him which deal with the effect of substituting polar/non-polar amino acids on the heat capacity of Ubiquitin. That work is more recent. He also has a big table compiled in Biophyiscal Chemistry on heat capacities of various polar and non-polar compounds. I guess the reference for that work is: Makhatadze GI. Heat capacities of amino acids, peptides and proteins. Biophys Chem. 1998 Apr 20;71(2-3):133-56. I think this is slightly off from the original question on CCL but still quite useful. Sincerely, Sandeep ------------------------------------------------------------------- Dr. Sandeep Kumar, Associate Research Scientist, Johns Hopkins University Department of Biology, 106 Mudd Hall, 3400 N. Charles Street, Baltimore, MD 21218, USA. Phone: 410-516-8433, Email: kumarsan /a\ jhu.edu. URL: http://myprofile.cos.com/Kumarsan. or https://jshare.johnshopkins.edu/skumar23/public_html/ ----- Original Message ----- From: Cherif Matta Date: Saturday, April 2, 2005 8:58 pm Subject: Re: CCL:desolvation energy table for amino acids > Hello Eric and Sandeep, > > Sandeep, do you have the ref to Makhatadze paper? > > Also have a look at the classic papers by Wolfenden: > > [1] Wolfenden R, Andersson L, Cullis PM, Southgate CCB (1981). > "Affinities of > amino acid side chains for solvent water". Biochem.; 20: 849-855. > > [2] Radzicka A, Wolfenden R (1988). "Comparing the polarities of > the amino > acids: side-chain distribution coefficients between the vapor phase, > cyclohexane, 1-octanol, and neutral aqueous solutions". Biochem.; 27: > 1664-1670. > > Cheers, > > Cherif > > ------------------------------------------------------- > Cherif F. Matta, Ph.D., MCIC > * Izaak Walton Killam Post Doctoral Fellow > Department of Chemistry, Dalhousie University > Halifax, NS, Canada. > * Adjunct Professor of Chemistry > McMaster University, Hamilton, ON, Canada. > ------------------------------------------------------- > * Web site: http://chem.utoronto.ca/~cmatta/ > Tel: (902) 494 7021 Fax: (902) 494 1310 > ------------------------------------------------------- > > > Quoting SANDEEP KUMAR : > > > Hi Erick , > > > > Please see the work of Makhatadze and co-workers. They have > compiled> hydration energies/enthalpies for amino acids transfer > from Octanol to > > Water. > > > > Good luck, > > Sandeep > > > > ------------------------------------------------------------------ > - > > Dr. Sandeep Kumar, > > Associate Research Scientist, > > Johns Hopkins University Department of Biology, > > 106 Mudd Hall, 3400 N. Charles Street, > > Baltimore, MD 21218, USA. > > Phone: 410-516-8433, > > Email: kumarsan /a\ jhu.edu. > > URL: http://myprofile.cos.com/Kumarsan. > > or https://jshare.johnshopkins.edu/skumar23/public_html/ > > > > > > ----- Original Message ----- > > From: Eric Hu > > Date: Friday, April 1, 2005 6:45 pm > > Subject: CCL:desolvation energy table for amino acids > > > > > Hi, I wonder if anyone has knowledge of availability of a > desolvation> > energy table for each individual amino acid. Thanks. > > > > > > Eric > > > > > > > > > -= This is automatically added to each message by the mailing > > > script =- > > > To send e-mail to subscribers of CCL put the string CCL: on your > > > Subject: line > > > > > > Send your subscription/unsubscription requests to: CHEMISTRY- > > > REQUEST /a\ ccl.net > > > HOME Page: http://www.ccl.net | Jobs Page: > > > http://www.ccl.net/jobs > > > > > > If your is mail bouncing from ccl.net domain due to spam filters, > > > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+- > +-+- > > > +-+-+ > > > > > > > > > > > > > > > > > > > > > -= This is automatically added to each message by the mailing > script =- > > To send e-mail to subscribers of CCL put the string CCL: on your > Subject:> line > > and send your message to: CHEMISTRY /a\ ccl.net > > > > Send your subscription/unsubscription requests to: CHEMISTRY- > REQUEST /a\ ccl.net> HOME Page: http://www.ccl.net | Jobs Page: > http://www.ccl.net/jobs> > > If your is mail bouncing from ccl.net domain due to spam filters, > please> use the Web based form from CCL Home Page > > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+- > +-+-+-+ > > > > > > > > > > > > >