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Gaming and crowdsourcing for your Scientific Research needs
Hello All,

Caught this very interesting article on the web mere moments ago.


In brief, a game developer was invited to put a troublesome enzyme to their gaming community in order to knead out a lowest-energy-state solution.

They did it, and in ten days (contrasted to the conventional methods used over 12 years, to no ends).

Wahoooo go gaming.
It sounds cool, but I don't have a clue what "folding" is. When I saw ERV's post about it, I was like "Yay...I guess." Smile
"The world is my country, and do good is my religion." - Thomas Paine
Skeeve - If you think about a chain of elements, which is really what a protein is, you tend to think of something like a straight line. What happens in nature though is that proteins form in environments that react with elements of the chain and that causes the chain to take shapes that aren't linear. The shapes that are formed because of these reactions actually can change the way the protein functions, which is why determining the precise way a protein is folded is so important.
"Those who cannot remember the past are condemned to repeat it." - George Santayana
Thanks for trying, but I can't get a mental picture. I'm sure more will be said about it, and I might pick up on it.
"The world is my country, and do good is my religion." - Thomas Paine
Ok Skeeve, prepare yourself for my analogies...!!!!

Imagine it this way:- You have a series of bar magnets, marked north and south ([N - S])

You have several of these attached by string (I) at the mid-point of each magnet with a small gap between.

[N - S]
[N - S]
[N - S]

While laying them on a table will allow you to arrange them in any way - say all Norths on the left as above - once you lift them clear of the table they will act to repel eachother and get to a steady state - i.e. N then S then N and so on down the left side.

[N - S]
[S - N]
[N - S]

Add more bar magnets to the setup, in series and parallel at different points, and you change the behaviour some what, it may settle into a steady state that is very complex.

When it comes to chemically bonded atoms/molecules the 'string' can become 'rigid' - a chemical bond is two atoms sharing its electrons - pushing them too close together will cause inner electrons to repel (or the positive nucleus itself) and pulling them apart will be resisted by the 'cloud' of the bonded electron:- Imagine two chubby rich Americans trying to leave a circlular swarm of youthful and thin criminals on bicylces cycling at speed.

In a complex chain of these atoms different 'branches' of the molecule will have slight variations in their magnetism. In free solution (hanging as with the bar magnet example) you may imagine these molecules would have twisted and contorted into their most comfortable state. In actuality the molecule was formed in part over an extended amount of time, but without knowing the evolution folding is how you can find the end result.

The benefits of Origami are two fold...

Imagine a 1m long wooden pole, and at 30cm, 40cm and 90cm you place strong magnets (all on the same side). A door is held closed by three iron pins down one side (opposite to the hinges), these are placed 30cm, 40cm and 90cm from the ground.

If you could put the stick alongside the door frame, in one orientation you will pull the pins from the door, opening the door-way - but in the other orientation this would not happen.

The sticks components have not changed, but its orientation and layout does alter its function.

In a similar way the twisting and folding of a protein and enzyme can create localised strong magnetic fields, these will be unreactive with some molecules, but for certain types they may cause bond-breaking or bond-making.

In the case of a HIV virus, the localised areas bond with things we dont want it to bond with, if we know the topology of this area, we can find or make an otherwise inert molecule that will fill it up, rendering the full virus inert.

So back to our stick analogy, this would be finding another stick, say 50cm long, placing a stong magnet at 10cm from one end, and then another at 20cm from the same end. Interacting with the first stick, this could bond to the 30cm and 40cm magnets, making them unable to pull the two lowest pins from the door - door remains closed all your valuables be safe.

There ya go, clear as a busy business day in Santiago.
Thanks TE, I'm at work atm so I'll have to read over it later this afternoon.

I skimmed it, but think I'll need to read it a bit slower.

And I can't resist - "Fucking magnets! How do they work?"
"The world is my country, and do good is my religion." - Thomas Paine
TE I think if you were my chemistry or physics teacher I may have been better at it. Great explanation of a number of things even though I will have to read over it several times to get the whole sense.
I am very appreciative of analogy - you encounter it quite often in the early years of school, but as time in education progresses the wealth of analogies dries up leaving the odd stale idea.

You often learn to count as a child with real things, these real things become the number concepts in your mind, you work with counters for instance later imagining them layed out before you, but once you become more adept at manipulating counters and groups of counters they fall from your minds eye to leave the number concept itself.

Some people are very hostile to analogies, they do not understand their power and accuse you of changing the subject or some such nonsense.
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