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Posts: 102
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August 2004
 Re: stoichiometries of modifiers 26 Apr '05 10:27 I will give you an example of vague. This example is located in most classic textbooks on enzyme kinetics. There is a substrate S, an enzyme E, an inhibitor I, and a product P. Consider the three classic types of inhibition: competitive, non-competitive, and uncompetitive. Competitive: E + S --r> E:S --> E + P E + I --r> E:I Uncompetitive: E + S --r> E:S --> E + P E:S + I --r> E:S:I Non-competitive: E + S --r> E:S --> E + P E + I --r> E:I E:S + I --r> E:S:I If you want to use the steady state approximation on these reactions, the total balance is S --> P with some rate law (Michaelis Menten like). In your definition of modifier, for the total balance on these reactions (which is S --> P), the inhibitor and enzyme are both modifiers. However, the rate laws of all three of these types of inhibition are different. They all depend on the numbers of molecules of inhibitor and enzyme differently. To correctly calculate the rates of these reactions, you then need to know how the modifier affects the rate. The information for the reaction then needs data for not only the reactants and products, but also for the 'modifiers'. This is the simplest of examples. What happens when something more realistic comes along? Also, the rate law I gave as a power law is dependent on only the reactants of the reaction and rightly does not distinguish between reactants whose stoichiometry is zero or non-zero. Species whose stoichiometries may be zero for the total balance of the reaction may still be a variable within the rate law. And that is why the term 'modifier' is vague: it doesn't say how the numbers of molecules of the species affects the rate of the reaction. -Howard Salis Pedro Mendes wrote: >On Monday 25 April 2005 10:14 pm, Howard Salis wrote: > > >>I think the idea of 'modifiers' is too vague to be useful. >> >> > >I think the discussions in this list are starting to convince me that anyone >who wants to be doing any modeling of biochemical systems should first have >to pass an "Enzyme Kinetics" course. The concept of modifier is not vague >at all, it is quite well defined. It seems to me that there are a number of >people out there that want to define this concept according to whatever >their software thinks a modifier is. > >Power-law models do not distinguish between substrates, products or >modifiers. For power laws everything is an effector (hey, there's another >word that I expect will have a long discussion too). > >As someone else already stated in this thread, a modifier is not changed by >the reaction therefore the only number that could be attributed to its >stoichiometry is zero. > >Also, reactions do not need any modifier (eg activator) to proceed. If you >put NADH in contact with oxygen, it is only a matter of time that you end >up with NADP+ and water - no enzymes required. > >Anyway, I am one of the defenders that software should be sufficiently >user-friendly to allow non-speciallists to carry out simulation. But this >has always meant to me that they do not need to be speciallists in >mathematics, numerical analysis, or software engineering. They DO need to >know biochemistry if they want to model biochemical systems - I'm sorry for >this lengthy rant, but I am strongly opposed that we should bastardize >terms that are objective and quite specific (and old) just because some >software happens to use them in some wrong way. > >

SubjectPosterDate
stoichiometries of modifiers Hiroyuki Kuwahara25 Apr '05 09:56
Re: stoichiometries of modifiers Pedro Mendes25 Apr '05 13:39
Re: stoichiometries of modifiers emek25 Apr '05 14:26
Re: stoichiometries of modifiers Hiroyuki Kuwahara25 Apr '05 18:08
Re: stoichiometries of modifiers emek26 Apr '05 01:14
Re: stoichiometries of modifiers Hiroyuki Kuwahara26 Apr '05 08:52
Re: stoichiometries of modifiers emek26 Apr '05 11:24
RE: stoichiometries of modifiers Herbert Sauro25 Apr '05 14:40
Re: stoichiometries of modifiers zucker25 Apr '05 16:27
RE: stoichiometries of modifiers Hiroyuki Kuwahara25 Apr '05 18:09
Re: stoichiometries of modifiers Howard25 Apr '05 19:14
Re: stoichiometries of modifiers Pedro Mendes26 Apr '05 05:30
Re: stoichiometries of modifiers  Howard26 Apr '05 10:27
Re: stoichiometries of modifiers Stefan Hoops26 Apr '05 15:16
Re: stoichiometries of modifiers Greg Blumenthal26 Apr '05 16:01
Re: stoichiometries of modifiers Nicolas Le Novere27 Apr '05 01:29
Re: stoichiometries of modifiers Mike Hucka27 Apr '05 21:07
Re: stoichiometries of modifiers Howard26 Apr '05 16:38
Re: stoichiometries of modifiers Pedro Mendes26 Apr '05 17:22
Re: stoichiometries of modifiers Howard26 Apr '05 17:36
Re: stoichiometries of modifiers Pedro Mendes26 Apr '05 19:01
Re: stoichiometries of modifiers Howard26 Apr '05 20:25
Re: stoichiometries of modifiers J.Weimar27 Apr '05 01:06
Re: stoichiometries of modifiers Howard27 Apr '05 08:43
Re: stoichiometries of modifiers Pedro Mendes27 Apr '05 10:32
Re: stoichiometries of modifiers Stefan Hoops27 Apr '05 11:02
Re: stoichiometries of modifiers Darren J Wilkinson27 Apr '05 12:55
Re: stoichiometries of modifiers Howard27 Apr '05 14:55
Re: stoichiometries of modifiers Ben Bornstein27 Apr '05 15:56
Re: stoichiometries of modifiers Tomas Radivoyevitch27 Apr '05 18:47
Re: stoichiometries of modifiers Mike Hucka27 Apr '05 20:46
Re: stoichiometries of modifiers Howard27 Apr '05 23:25
Re: stoichiometries of modifiers Howard28 Apr '05 09:12
RE: stoichiometries of modifiers Andrew Finney07 May '05 01:59
RE: stoichiometries of modifiers Andrew Finney07 May '05 01:59
Re: stoichiometries of modifiers Mike Hucka17 Jun '05 18:52
Re: stoichiometries of modifiers Mike Hucka27 Apr '05 20:52
Re: stoichiometries of modifiers Howard27 Apr '05 23:41
Re: stoichiometries of modifiers Stefan Hoops28 Apr '05 04:56
Re: stoichiometries of modifiers Stefan Hoops28 Apr '05 08:31
Re: stoichiometries of modifiers Howard28 Apr '05 10:34
Re: stoichiometries of modifiers Upinder Singh Bhalla28 Apr '05 19:34
Re: stoichiometries of modifiers Mike Hucka07 May '05 05:29
Re: stoichiometries of modifiers Upinder Singh Bhalla07 May '05 05:48
Re: stoichiometries of modifiers Mike Hucka13 May '05 18:08
RE: stoichiometries of modifiers Andrew Finney22 May '05 00:21
RE: stoichiometries of modifiers Mike Hucka17 Jun '05 18:47
Re: stoichiometries of modifiers Pedro Mendes28 Apr '05 05:34
RE: stoichiometries of modifiers Andrew Finney07 May '05 01:59
Re: stoichiometries of modifiers Ed Frank27 Apr '05 08:17
Re: stoichiometries of modifiers Mike Hucka28 Apr '05 00:40
Re: stoichiometries of modifiers Ed Frank28 Apr '05 07:45
Re: stoichiometries of modifiers Darren J Wilkinson29 Apr '05 14:31
Re: stoichiometries of modifiers emek29 Apr '05 15:15
Re: stoichiometries of modifiers Darren J Wilkinson30 Apr '05 00:47
Re: stoichiometries of modifiers Mike Hucka07 May '05 05:29
Re: stoichiometries of modifiers Pedro Mendes07 May '05 22:14
Re: stoichiometries of modifiers Stefan Hoops27 Apr '05 04:00
Re: stoichiometries of modifiers ginkel27 Apr '05 12:12
Re: stoichiometries of modifiers Hiroyuki Kuwahara26 Apr '05 11:17
Re: stoichiometries of modifiers Mike Hucka27 Apr '05 21:49
Re: stoichiometries of modifiers - is SBML too &qu... Darren J Wilkinson26 Apr '05 14:12
is SBML too"narrow"? Nicolas Le Novere26 Apr '05 14:56
Re: is SBML too"narrow"? Mike Hucka26 Apr '05 19:26
Re: is SBML too"narrow"? Sven Sahle27 Apr '05 01:23
Re: is SBML too"narrow"? Mike Hucka27 Apr '05 21:36
Re: is SBML too"narrow"? Nicolas Le Novere28 Apr '05 00:50
Re: is SBML too"narrow"? Ed Frank28 Apr '05 07:57
RE: is SBML too"narrow"? Andrew Finney07 May '05 01:59
Re: is SBML too"narrow"? Nicolas Le Novere27 Apr '05 01:35
Re: is SBML too"narrow"? Rainer Machne28 Apr '05 06:13
Re: is SBML too"narrow"? Fabien Campagne28 Apr '05 11:33
Re: stoichiometries of modifiers - is SBML too &q... Pedro Mendes26 Apr '05 15:15
Re: stoichiometries of modifiers - is SBML too &qu... Mike Hucka26 Apr '05 20:55
Re: stoichiometries of modifiers - is SBML too&quo... Tomas Radivoyevitch26 Apr '05 22:23
Re: stoichiometries of modifiers - is SBML too&quo... Mike Hucka27 Apr '05 21:59
SBML packaging Nicolas Le Novere28 Apr '05 00:59
Re: SBML packaging Mike Hucka02 May '05 00:29
Re: stoichiometries of modifiers - is SBML too &qu... Darren J Wilkinson27 Apr '05 12:47
Re: stoichiometries of modifiers - is SBML too &qu... Mike Hucka06 May '05 03:16
Re: stoichiometries of modifiers - is SBML too &q... Pedro Mendes07 May '05 21:32
RE: stoichiometries of modifiers - is SBML too&quo... Andrew Finney07 May '05 01:59
RE: stoichiometries of modifiers Andrew Finney07 May '05 01:59
RE: stoichiometries of modifiers Herbert Sauro13 May '05 18:17
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