From watts@gwinn.medc.umn.edu Fri Jan 3 14:23:15 1997 Received: from chet.medc.umn.edu for watts@gwinn.medc.umn.edu by www.ccl.net (8.8.3/950822.1) id OAA01748; Fri, 3 Jan 1997 14:09:03 -0500 (EST) Received: from gwinn.medc.umn.edu (root@gwinn.medc.umn.edu [134.84.172.12]) by chet.medc.umn.edu (8.8.3/8.6.9) with ESMTP id NAA08140 for ; Fri, 3 Jan 1997 13:09:03 -0600 (CST) Received: from localhost (watts@localhost) by gwinn.medc.umn.edu (8.8.3/8.6.9) with SMTP id NAA00993 for ; Fri, 3 Jan 1997 13:09:01 -0600 (CST) Date: Fri, 3 Jan 1997 13:09:01 -0600 (CST) From: Chuck Watts To: The Computational Chemistry List Subject: Protein Hydration and Spectral Density Functions. Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCL: I have a small queation for you that is not completely computational in nature although it does pertain to the investigation of biomolecular dynamics using NMR and I know that many NMR spectroscopists subscribe to this list. I was recently reading the papers Otting, G.; Liepinsh, E.; Wutrich, K. (1991) "Protein Hydration in Aqueous Solution" Science 254, 974-980. and Kubinec, M. G.; Wemmer, D. E. (1992) "NMR Evidence for DNA Bound Water in Solution" JACS 114, 8739-8740. In these papers combined NOESY and ROESY experiments are used to measure the lifetimes of waters bound to BPTI and DNA as interpreted by a Random Diffusion model. The model consists of a protein molecule with a radius rp, a proton spin displaced from the protein center by pp, and a rotational correlation time of tp, a water molecule with a radius rw, a proton spin displaced from the water center by pw, and a rotational correlation time of tw, the protein and water are related to each other via the diffusion coefficient D which can then be translated into a correlation time for the interaction using the Einstein-Smoluchowski relation. The NOE and ROE rates dependency on the spectral density function are then given as k(NOE) = 6J(2wo) - J(0) k(ROE) = 3J(wo) + 2J(0) and it is stated that the spectral density is related to the rate processes that govern the modulation of the dipole-dipole coupling of the system. My question is as follows, I can easily find the generic treatment of the spectral density function that relates its dependency on a single correlation time with the assumption of isotropic tumbling, how is the spectral density function used in these studies different from this and how specifically did they generate the NOE/ROE vs. 1/D curves for this paper given the data above. Sorry, I know this pobably isn'y a short queation but I thought someone on the list might have some insight as to the solution. Best Wishes, Charles R. Watts ************************************ Department of Medicinal Chemistry * * College of Pharmacy * An appeaser is one who feeds * University of Minnesota * a crocodile, hoping it will eat * 8-101 HSUF * him last. * 308 Harvard St. SE. * * Minneapolis, MN 55455 * -Winston Churchill * Phone: (612) 624-5486 * * Fax: (612) 626-4429 * * E-Mail: watts004@128.101.118.21 ************************************