Folding of villin protein simulated on GPUs

This movie shows a possible trajectory, or path, for how the villin protein folds. A single trajectory can be generated in a few days on a graphics processing unit (GPU) or a year on a single CPU.

However, protein folding is highly stochastic, or random. To actually understand the folding mechanism, thousands of trajectories have to be simulated. The underlying data to produce this typical trajectory required about 20 days on 1000 GPUs.

It was accomplished via Folding@Home, a distributed computing project by Stanford faculty Vijay Pande where people from throughout the world download and run software to band together to make one of the largest supercomputers in the world.

Access trajectory files for villin from https://simtk.org/home/foldvillin.

Learn more about Simbios research on physics-based simulations of biological structures at http://simbios.stanford.edu.

Category:

Science & Technology

Tags:

• Protein folding
• villin

[pjsteinsongs]

I agree, that, in the immediate environment of a billiard ball, one can explain the trajectory of one ball, struck with a certain force at a certain angle, by another ball; I wanted to convey that there is a microcosm of these minute, physiochemical events, recurring trillions of times, in trillions of molecular cascades, among trillions of elemental particles, that somehow interconnect, and have a final common pathway that leads to a single, purposeful event, such as my typing this word to you.

[JesseVictors]

@pjsteinsongs These activities/movements are not random. They occur as a direct result of the interplay of all the molecular forces acting upon the elements in the protein, kind of like billiard balls don't disperse randomly when you strike them at the start of a game. The proteins need to assemble before they can do anything functional. Optimally, the proteins would exist in a "comfortable" state, where the forces are stable/limited. Hydrophobic regions want to avoid water for example.

[Puddy88]

@22biochemist They provide a hydrophilic environment for the protein and functions more in preventing bad folding that might occur in the cytoplasm. At least that's what the chaperonin complex in E.coli does. I'm not sure if every protein requires this. Probably not.

[pjsteinsongs]

Is this not anthropomorphism? The proteins are "trying" to assemble? or know what feels "right"; or a "state that's better"? The blue phenylalanine is "perfectly happy to stay in a state like this"? My reasoning: all these biochemical activities, movements, interactions, are by chance, are random, selected over hundreds of millions of years. Random connections have survived through natural selection, embedded in the genome.These are chance collisions, without consciousness, without goals...pete

[22biochemist]

How is a chaperone protein involved in protein folding? Does it create the hydrogen, ionic, sulfhydryl, etc. bonds in the tertiary structure? Or does it form the other types of structures?

[jch607123]

wow

[myfood123]

if you pause exactly at 1:10 or some where around there

the blue thing formed a penis rofl

[inventorOz84]

lovely.

[Lahmy88]

cool