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Metabolism

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shvarz:
Look at this article: http://biology.plosjournals.org/perlserv/?...al.pbio.0030228

I did not read it very carefully, but it seems to be a perfect model system for metabolism in DBs.  The article is fairly easy to read, so go and read it!

shvarz:
Nums, did you look into this article?

Numsgil:
Oh yeah, sry, I forgot to post.  The idea of substances being defined as a collection of other substances I found interesting, and perhaps usable.  I couldn't figure out how they implemented the enzymes though.   The language is about 3 inches above my head, if you know what I mean.

shvarz:
Look in Materials and methods in section called "Enzymes".  Can't say I understand everything in there, but here are the basics:

An enzyme is an intermediate between donor of a group and an acceptor of a group.

Say you want to transfer the very first group in a chemical and your donor is: 1000001 and acceptor is 0000010

Edit by Numsgil to improve readability
The enzyme responsible for transfer of this group reacts with donor: 1000001+E=0000001+E(1)  The rate at which this happens depends on several things:
1. how much of enzyme is free E(0)
2. how much of enzyme is bound to this group already E(1)
3. how much donor and acceptor are available
4. efficiency of enzyme (k)
5. the amount of energy released (lost) during transfer (q)

Initially they set enzymes to be very non-speicific, so that all molecules that have this first group serve as donors and those that don't have this group serve as acceptors with some efficiency k.  And they allow these efficiencies to mutate (with zero-sum of total efficiency) so that after a while some molecules cannot be used as donors by an enzyme at all and others are used very well.

let me know if you have other questions.  

I need your opinion on feasbility of a model like this for our purposes - how much memory this baby's going to take up and how fast would it be to process all this data (2^7 molecules with free energies), about the same number of enzymes with each enzyme having 2^7 values for kinetic constants.

Numsgil:
I'm totally going to sit down and spend some time reading this article soon, but I need to print it out to do so...

I'll post my thoughts on it before tomorrow.

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