Code center > Specialization, Metabolism, Digestions and Env Grid
Built-in Enzyme Regulation
Numsgil:
Basically, any regulation of the enzyme has to be for the entire enzyme complex, not just for individual activation sites.
Remember that regulation sites deform the entire enzyme complex, not just individual parts.
So what we really need are activation sites and regulation sites, each defined similarly.
Activation site: efficiency bits - activation code - efficiency bits
Regulation sites: threshold bits - regulation code - threshold bits
shvarz:
Nah, too complicated.
Here, I'll explain on example. Let's say we want to have a potential for 4000 molecules, that is 2^12. So a glucose can be defined as 111000111000.
Then we want to allow glucose to be involved in 16 different pathways: 8 degradational, 8 generational. That is 2^4. So we say conversion to pyruvate is defined as 1010
Then the activation site for enzyme converting glucose to pyruvate is:
111000111000 1010.
This is the bare minimum to activate enzyme: 16-bit string. All enzymes working on glucose will have tha same first 12 bits, so when enzyme mutates it is very likely to turn into enzyme working on glucose. We can even have sugars designed to be similar in sequence to glucose so that the mutated enzyme will be more likely to keep working on carbohydrates than to suddenly start splitting proteins.
After the first 16 bits of activation sequence we will have regulatory bits. Say we want to define threshhold of inhibition of enzyme. Maybe make it a log scale with 8 possibilities: 0 (no inhibition), 1, 5, 25, 125, 625, 3125, 15625. This adds another three bits. And the sequence like 111000111000 1010 000 will mean "enzyme converting glucose to pyruvate with no feedback inhibition".
Then we can add more and more regulatory bits. But their order should be of decreasing importance, allowing finer and finer tuning of enzyme's functionality.
Numsgil:
I agree that coding patterns for like reactions should be very similar. That's not difficult at all to acomplish. But remember that alot of reactions aren't just A->B but A+B-> C. As far as enzymes are concerned, I think it's the actual reaction more than the substrates that define it.
Also remember that sometimes you don't want to regulate a reaction with it's direct byproduct. if A->B->C you might want to regualte A with C instead. So you need a molecule code and a threshold value.
Then, on top of that, you have which direction the threshold works. Does the protein turn on if the value is greater than or less than the threshold?
THEN, on top of all that, you need the ability to have multiple regulatory sites. If A->B->C and A->B->D then you might want to regulate A with C and D.
shvarz:
So, what is your solution? I did not quite understand the idea of regulation codes. Sounds like these bit-strings are starting to get huge.
I would solve it like this:
I will find what regulates what in nature and we just assign the regulatory molecule ourselves. Just one. And not even for all enzymes. Yes, it is not flexible. But it would be just one way to regulate them. We'll have more.
Numsgil:
Okay, here's what I think I'm saying:
Imagine your long string of bits. This is a complex. Inside this string are several activation sites or enzymes. Now, in addition to these activation sites are regulatory sites that work for all enzymes in this complex.
Liek this:
01010110101010101010101010101010101010101010100 -> complex
....|---enzyme1---|.|--enzyme 2|.....|---regulation site---|
The regulation site turns on/off both enzyme 1 and enzyme 2 depending.
Depending on what you ask?
Well, a regulatory site works like this:
3 bits for threshold value - molecule code (should be fairly long to prevent lots of regulation sites from cropping up in large complexes) - 1 bit that defines greater than or less than - 2 bits for threshold value
Threshold value works logarithmically as you suggest, with 0 being unregulated and 32 being regulated at 32000.
Maybe 20 is like ~9000.
The molecule code will need to be quite lengthy to prevent lots of regulation sites cropping up in a complex. Longer complexes, though, are increasingly likely to posses one. I haven't tried to figure out the statistical test for percentages yet.
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