From owner-metabolic-reg@net.bio.net Sun Dec 12 22:00:00 1993 Path: biosci!daresbury!bioftp.unibas.ch!embl-heidelberg.de!uni-heidelberg!rz.uni-karlsruhe.de!xlink.net!howland.reston.ans.net!cs.utexas.edu!uunet!pipex!uknet!festival!castle.ed.ac.uk!eanv20 Newsgroups: bionet.metabolic-reg Subject: Re: (none) Message-ID: From: eanv20@castle.ed.ac.uk (John Woods) Date: Mon, 13 Dec 1993 09:52:08 GMT Sender: news@festival.ed.ac.uk (remote news read deamon) References: <9312101457.AA24631@MIT.EDU> Distribution: bionet Organization: Edinburgh University Lines: 228 alberty@MIT.EDU writes: >help Maybe you'd like to see the preliminary FAQ? (snip)-----8<-----8<-----8<-----8<-----8<-----8<-----8<-----8<----- (snip) ********************************************************************** bionet.metabolic-reg/BTK-MCA FAQ --- version 0.3 930924103400 Discussion draft. Please treat this document as the straw man it is intended to be --- alterations and disccussion are urgently requested. NB: I'm half-serious about the last sentence in point four. If there are enough objections I'll remove it, but I'd really rather not get into philosophical nitpicking that might discourage future readers who are more interested in biochemistry than semantics. Not yet, anyway. ********************************************************************** Table of contents (sketchy) --- * indicates changes from previous version Section 1 --- about the newsgroup and mailing list 1.0) What is an FAQ? 1.1) Where can I get FAQs? 1.2) What is BTK-MCA/bionet.metabolic-reg for? 1.3) What is BioThermoKinetics? 1.4) What is Metabolic Control Analysis/Theory? 1.5) What should I read? 1.6) What should I ask? * 1.7) How should I format my messages and postings? * 1.8) How should I format maths in my messages and postings? Section 2 --- about MCT * 2.1) What are the fundamentals of MCA? * 2.2) What are the fundamental theorems of MCA? * 2.3) What is the importance of the theorems in 2.1? Section 3 --- about MCA 3.1) How do I make my yeast glycolize faster? Pump up the PFK? 3.2) Is rubisco rate-limiting? ********************************************************************** 1.0) What is a FAQ? An FAQ is a listing of Frequently Asked Questions. It is intended to prevent repeated discussion of certain points on the newsgroup and to give newcomers a brief introduction to the scope of the group. 1.1) Where can I get FAQs? There is a machine around called rtfm.*.* (somebody fill in the blanks please) which stocks the FAQs for most newsgroups. But the one for this group isn't ready for inclusion yet, so just watch for its sporadic posting in this group. 1.2) What is bionet.metabolig-reg for? Discussion of topics concerning Metabolic Regulation/Control, non-Equilibrium Thermodynamics, Kinetics, Biological Modelling, Quantitative Bioenergetics, Biochemical Systems Theory and Chanelling. I quote form our initial charter: `` `The International Study Group for BioThermoKinetics is an informal group devoted to the quantitative understanding of the kinetics, thermodynamics and control of biological processes at the cellular level ... BTK meetings are aimed at providing a forum for a vivid exchange of ideas between experimenters with a keen eye for quantitative aspects, theoreticians with a keen eye for the experimental practice and those in between.' (Preface, Programme for 5th BTK meeting) This mailing list [and newsgroup] is intended to provide not only some continuity between the biennial meetings but also to serve to propagate interest in the subjects covered. Informal participation is welcomed from all fields (and at all levels), and it is particularly, but not exclusively, encouraged in the domain of Metabolic Control Analysis --- the investigation of control in biological systems.'' 1.3) What is BioThermoKinetics? Hans Westerhoff writes: The International Study Group on BioThermoKinetics is a loosely organized group of scientists interested in the understanding of the energetics, kinetics, control and regulation aspects of living cells. The group started off with the application of Non Equilibrium Thermodynamics to Bioenergetics. Much of its first interests was therefore in mitochondria, chloroplasts and bacteria. The interest was one of doing more with experimental results than just plotting them, i.e., view them in the light of theories based on sound physical and chemical, and mathematical principles. Also, however, the intention is not to do theory just for theory's sake; the true challenge is felt to lie in the interface between theory and experiment. Soon it became clear that beyond equilibrium, thermodynamics and kinetics are often two sides of the same coin; kinetics of energy transducing systems (e.g., ion pumps) became part of the field of interest. Subsequently the field of metabolic control analysis began to flourish and as its players had much the same interests in many the same problems, it became an important topic of the BTK group. The groups main activity is to organize a meeting every other year, which is meant, above all, to stimulate discussion. The most recent meeting was in september 1992 near Bordeaux, the next one will be september 1994, near Innsbruck. In principle, the group also organizes workshops. One on the modelling of cell physiology is in the makings. For further information please contact the acting chairman of the BTK group: Hans V. Westerhoff: HW@NKI.NL FAX: +31 20 512 2029. 1.4) What is Metabolic Control Analysis/Theory? Metabolic Control Analysis is the investigation into the mechanism and distribution of control in metabolic, and conceivably other biochemical systems. Using certain theorems, it is possible to relate the measurable *in vitro* properties of enzymes and their effectors to the *in vivo* properties which concern us. As far as I am concerned, Metabolic Control Analysis is the activity thus described, whilst Metabolic Control Theory is the theoretical foundation on which it rests. (Very much like systems analysis is something done by people who analyse systems, and systems theory is something done by people who think more about systems analysis itself than the analysis of particular systems). Mileage differs greatly in the newsgroup about this issue, and now I've had my say, further discussion is discouraged. :-) 1.5) What should I read? Try Fell, D. (1992) Biochem J. 286:313-330 for a recent review and the references therein for more introductory material. 1.6) What should I ask? Anything related to metabolic regulation or BiothermoKinetics as described above. Give us a try! * 1.7) How should I format my messages and postings? Bear in mind that most people read news and mail items with plain-text devices, so only 7-bit ASCII in less than 80 columns is guaranteed to look the same to all people. Do not assume that other output devices will respond to tabs in the same way that yours does --- use conventional spaces, and rely on the fact that all characters are the same width. Avoid wrap-aound problems --- unless you are sure that your text-editor is putting explicit line ends in your message, put them in yourself using the return key. Do not assume a width any greater than 80 characters (70 for preference) or any more than 24 lines of text to be simulataneously visible. And what looks like a u-umlaut or e-acute to you will probably look like a Yen sign or something horrible on devices configured to other languages. (German net.convention allows ue to be used in place of u-umlaut (as in Muenchen), and a", o", u", e^, e', e` etc. are acceptable and reasonable obvious. [Hint: use two spaces after periods (.) and colons (:), and three dashes (---) to represent a long (`em') dash for extra readability. For preference use a blank line to separate paragraphs, either instead of (preferred) or in addition to first line indentation.] * 1.8) How should I format maths in my messages and postings? Anything that is readily comprehensible, for preference well spaced ASCII with any necessary explanations (such as saying that `d' stands for the partial delta, for example). So, where Jq means J-subscript-q, Ep means E-subscript-p, and d stands for the partial delta, multiple definitions of the Flux Control Coefficient for the Pth enzyme on the qth flux could be written as: Jq d ln Jq dJq Ep dJq/Jq %change in Jq C = ------- = --- -- = ------ = lim ------------- Ep d ln Ep dEp Jq dEp/Ep %-->0 %change in Ep A lot of MCA and BTK people use the LaTeX document processing system. Apart from the fact that braces ({}) group things together, all you need to now is that underscore (_) means subscript and circumflex (^) means superscript. It's a lot easier than spacing everything carefully in ascii. or more simply as: C_{E_p}^{J_q} = {{d \ln J_q} \over {d \ln E_p}} = {{dJ_q \over dE_p} {E_p \over J_q}} = {{dJ_q/J_q} \over {dE_p/E_p}} = {\lim_{\% \to 0} {{\ {\rm\;\%change\;in\;J_q}} \over {\ {\rm\;\%change\;in\;E_p}} }} Section 2 --- about MCT 2.1) What are the fundamental theorems of MCA? 2.2) What is the importance of the theorems in 2.1? Section 3 --- about MCA 3.1) How do I make my yeast glycolize faster? Pump up the PFK? 3.2) Is rubisco rate-limiting? -- " Forsan et haec olim meminisse iuvabit (Virgil) [approx] Tr: The time may come when we will look back on these days and laugh " .