From chemistry-request $#at#$ server.ccl.net Fri Nov 9 13:34:40 2001 Received: from server.ttpharma.com ([216.237.220.134]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fA9IYeB18975 for ; Fri, 9 Nov 2001 13:34:40 -0500 Received: from jerome ([192.168.4.31]) by server.ttpharma.com (8.11.1/8.11.1) with SMTP id fA9IkgB20646; Fri, 9 Nov 2001 12:46:42 -0600 From: "Jerome Baudry" To: "'Massimo Marchi'" , Subject: RE: How to get the solvation No. from accessible surface Date: Fri, 9 Nov 2001 13:46:40 -0500 Message-ID: <000501c1694e$df239060$1f04a8c0: at :ttpharma.com> MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook CWS, Build 9.0.2416 (9.0.2910.0) Importance: Normal X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4807.1700 In-Reply-To: Hi Massimo This number comes from a (very) crude approximation of the water/protein interaction surface. In tetrahedral H-bonded water , the H-H intramolecular is ~ 2A (very approximated) and the (O)H...O intermolecular linear H-bond distance is ~1.86 A. One water molecule would fill a 'cube' in space of a side area of (1.86+2)^2 = 14.89 A^2. If you make the assumption that you can project this surface in an orthogonal fashion on the surface of the protein (assuming it is locally planar), you would have one water per 15 A^2 of protein surface. Ciao, Jerome ***************************************** Jerome Baudry, Ph.D. Research Scientist, Computational Chemistry TransTech Pharma, Inc. 4170 Mendenhall Oaks Pwky, Suite 110 High Point, NC, 27265 http://www.ttpharma.com jbaudry ^at^ ttpharma.com tel: (336) 841-0300 #120 fax: (336) 841-0310 > -----Original Message----- > From: Computational Chemistry List > [mailto:chemistry-request -A_T- ccl.net]On > Behalf Of Massimo Marchi > Sent: Friday, November 09, 2001 12:37 PM > To: chemistry -x- at -x- ccl.net > Subject: CCL:How to get the solvation No. from accessible surface > > > Dear all, > > I have seen in literature that to get the total number of water > molecules solvating a protein, some people compute the solvent > accessible surface (in some way) in A^2 and divide by 15 A^2. Does > anybody know the origin of this "magic" number? > > Thank you beforehands > > Massimo MARCHI > > ============================================================== > =========== > = Dr. Massimo MARCHI > marchi ^%at%^ villon.saclay.cea.fr = > = > = > = Centre D'Etudes de Saclay, Section de Biophysique > = > = Gif-sur-Yvette, Paris, FRANCE > = > > >