RE: Representation of Co-enzymatic reactions in SBML
27 Sep '04 05:54
> "Coenzymes/Cofactors have not been provided with a separate tag under SBML
> scheme. In the model files kept in SBML Model Repository, they have been
> presented as reactants and "products" under the tag- Specie.
As far as I know, the definition of a co-enzyme is quite vague, and
depends much on the person who's considering the reaction. According to
the model, it can be put as a "reactant" or a "modifier". I can't imagine
a situation where none of these are possible.
>>It is not possible to represent the co-enzymes using the existing tags
>>available in the model section. The reason is that the co-enzymes cannot
>> be represented under the tag of modifiers because Co-enzymes are not
>> modifiers in their full sense, as they do not play a vital role in
>> inhibiting or activating a process. Rather a co-enzyme induces an
>>inhibitor or activator to act upon the reaction under consideration.
The modifier can be the complex enzyme/co-enzyme. Beside, some co-enzyme
do actually react withe the substrates.
>>Secondly, since the concentration of co-enzymes remains unchanged during
>>the reactions, it cannot be represented as reactants
>>or the products.
Well, in fact the concentration of some do. It depends how you choose to
model it. For instance you can choose to explicitely model protonated and
Nicolas LE NOVÈRE, Computational Neurobiology,
EMBL-EBI, Wellcome-Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
Tel: +44(0)1223 494 521, Fax: +44(0)1223 494 468, Mob: +33(0)689218676
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