PC Gamers Save The World, A Bit

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Perhaps you’re not familiar with the search for the molecular structure of a protein-cutting enzyme from an AIDS-like virus found in rhesus monkeys. But groups of scientists have been trying to fathom this mystery for years. And it’s just been cracked by PC gamers.

Why is this exciting? Because it’s believed that this information could be crucial to better figuring out how the AIDS virus works, and how it can be tackled. The findings, discovered via the game Foldit, are published online ahead of the next issue of Nature: Structural & Molecular Biology, with the authorship listing both scientists and gamers.

 

The results being discovered by this game are useful in many significant areas of research, the big three being AIDS, cancer and Alzheimer’s. All three diseases are related to proteins, the subject of Foldit’s puzzles, and the more that is known about how they behave, the more can be done to tackle the diseases they’re related to. And their behaviour is very much determined by their structure.

It’s the second paper Foldit has seen published in Nature, which is a remarkable achievement. The game involves folding proteins, attempting to manipulate three-dimensional models of proteins into the most energy-efficient structure possible. As such, it’s competitive, with players attempting to out-score others, and in the process getting closer to the unknown structure of the protein sought.

According to the paper, for years scientists have failed to uncover the crystal structure of M-PMV retroviral protease. However, Foldit players struck upon the solution. As the paper explains,

“Foldit players leverage human three-dimensional problem-solving skills to interact with protein structures using direct manipulation tools and algorithms from the Rosetta structure prediction methodology. Players collaborate with teammates while competing with other players to obtain the highest-scoring (lowest-energy) models. In proof-of-concept tests, Foldit players—most of whom have little or no background in biochemistry—were able to solve protein structure refinement problems in which backbone rearrangement was necessary to correctly bury hydrophobic residues. Here we report Foldit player successes in real-world modeling problems with more complex deviations from native structures, leading to the solution of a long-standing protein crystal structure problem.”

Got that?

Explained in the Sydney Morning Herald’s article, when looking down a microscope all you’ll see is a 2D splodge of the molecule you’re trying to understand, but to do anything useful you need to know about it in 3D. Which is where the puzzling comes in. It seems that computer models are not as capable as humans when working within spacial reasoning, hence the advantage of gamers approaching these challenges. Because, well according to the paper,

“Foldit players — most of whom have little or no background in biochemistry — were able to solve protein structure refinement problems in which backbone rearrangement was necessary to
correctly bury hydrophobic residue.”

Thankfully MSNBC explains it all rather well. According to the site, there are millions of ways for an enzyme’s atoms’ bonds to twist, and the secret to getting it right is finding the lowest-energy configuration for such a structure.

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I love it!
Years ago I worked with a scientist who studied CWD in deer/elk.
(I shared hunting information that broke the mystery as to why wild deer could get sick so young while penned deer, sheep and goats took years…..thorny forage causing cuts on the tongue, THEN licking the eyeball of their baby fawn….43 days old to 1st symptoms)

CWD is akin to v-CJD in humans, scrapie in sheep and ”mad cow disease.”
Some people even think it might be transmissible between humans and animals.

But the disease acts on perfect DNA inside a brain cell by unwinding it.
This caused little holes to form in the once-healthy brain which gave the disease another name: transmissible spongiform encephalopathy.
Here’s an artist’s depiction.
http://drugdiscoveryopinion.com/images/prion.jpg

I am so proud to hear that this type of three dimensional problem solving is being attacked by gamers.
I think that is a 1st step toward being able to reverse this and many other horrible, incurable diseases that “eat” your brain.

So… All my time in Starsiege Tribes was worth it?

I’m… confused now…