From owner-comp-bio@hgmp.mrc.ac.uk Mon Apr 30 21:26:04 2001 Return-Path: Received: from localhost (localhost [127.0.0.1]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id C1BE817B80 for ; Mon, 30 Apr 2001 21:26:02 +0100 (BST) Received: from localhost (localhost [127.0.0.1]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 0539117B6A for ; Mon, 30 Apr 2001 21:25:56 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6023) id 15DB417AD8; Mon, 30 Apr 2001 21:25:46 +0100 (BST) Received: from localhost (localhost [127.0.0.1]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id C640817AB3 for ; Sat, 28 Apr 2001 14:03:02 +0100 (BST) Received: from sjc3-1.relay.mail.uu.net (sjc3-1.relay.mail.uu.net [199.171.54.122]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 4853417A93 for ; Sat, 28 Apr 2001 14:02:58 +0100 (BST) Received: from smtp1.chorus.net by sjc3sosrv11.alter.net with ESMTP (peer crosschecked as: smtp1.chorus.net [216.165.129.132]) id QQkmsa23797 for ; Sat, 28 Apr 2001 13:02:56 GMT Received: from news.chorus.net (news.chorus.net [216.165.129.148]) by smtp1.chorus.net (8.9.3+Sun/8.9.3/Chorus Networks) with ESMTP id IAA29878 for ; Sat, 28 Apr 2001 08:02:56 -0500 (CDT) Received: (from news@localhost) by news.chorus.net (8.9.3+Sun/8.9.1) id IAA26304 for bionet-biology-computational@moderators.isc.org; Sat, 28 Apr 2001 08:02:55 -0500 (CDT) To: bionet-biology-computational@moderators.isc.org From: Petr Kuzmic Newsgroups: bionet.biology.computational Subject: Re: modeling a multiple ligands - fudge factor? Organization: BioKin Ltd. Message-ID: <3AEABF88.2BA0A04B@biokin.com> References: Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Trace: news.chorus.net 988462973 26295 63.161.30.172 (28 Apr 2001 13:02:53 GMT) X-Complaints-To: abuse@chorus.net NNTP-Posting-Date: 28 Apr 2001 13:02:53 GMT X-Mailer: Mozilla 4.72 [en] (WinNT; U) X-Accept-Language: en Date: Mon, 30 Apr 2001 21:25:46 +0100 (BST) Sender: owner-comp-bio@hgmp.mrc.ac.uk Precedence: bulk Dominic-Luc Webb molmed wrote: > ... I have > therefore implemented two fudge factor equations (one for forward and > one for reverse) in which the ratio of the fudged forward and > reverse rates yields the correct ka for the enzyme. I did this to > solve the numerical integration for a multiple ligand binding site > problem of general form... > > kx > Lx + R <=====> LxR > k-x > > D(LxR)/dt = kx[Lx][R] - k-x[LxR] > > I need to enter a value for kx and k-x in each iteration and > this is why the fudge factor equations were used. > > I have scanned a (neatly, I'd like to think) written one page > description of what I have done, and would like to send this to > right person for comments. I am not sure this is most intelligent > way to model an enzyme. I would really like to hear from > someone who knows about enzyme kinetics. Your approach to enzyme kinetic modeling based on "fudge factors", and especially the process of 'entering kx and k-x in each iteration', seem quite suspicious to me. Building a kinetic model for multiple binding sites can be accomplished very easily by using the software DynaFit: Kuzmic, P. (1996) Anal. Biochem. 237, 260-273. "Program DYNAFIT for the Analysis of Enzyme Kinetic Data: Application to HIV Proteinase" http://www.biokin.com/dynafit/ In DynaFit, you would type the following as part of your input data: [mechanism] E + L <==> EL : k1 k-1 EL + L <==> EL2 : k1 k-2 EL2 + L <==> EL3 : k3 k-3 etc. Based on this input, the machine will automatically construct the kinetic model in terms of first-order ordinary differential equations (ODE). Other types of biochemical problems can be solved, for example, multiple simultaneous _equilibria_ (no kinetic process here: just measuring the dependence of _equilibrium_ composition on the total concentration of components). Of course not all rate constants for multiple binding steps can be extracted from all types of experimental data. Some of the rate constants might have to be kept constant at reasonable values, while others would be treated as adjustable parameters. Hope this helps, - Petr Kuzmic -------------------------------------------------------- P e t r K u z m i c, Ph. D. * BioKin Ltd. 1652 S. Grand Ave. * Suite 337 * Pullman, WA 99163 509.334.4131 * 509.332.3493 fax * http://www.biokin.com .