Protein Folding

Simulations of the villin headpiece

The villin headpiece is a small, 36-residue alpha helical protein. It has been heavily studied experimentally and by simulation since is perhaps one of the smallest, fastest folding proteins. It has a hydrophobic core made of 3 phenylalanines, but also has two groups (a tryptophan and another phenylalanine) which are hydrophobic, but are solvent exposed (for functional reasons). Duan and Kollman simulated 1 microsecond of MD time, in a ground breaking simulation.

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[BillyJack7]

I think there was s light error at 0:53.

[mlcarrol]

What do you think it was?

[sagun111]

How long does it take a protein to fold?

[blacklinen99]

A MICROSECOND of MD? Christ, NASA and Google want their computers back.

[JesseVictors]

@sagun111 some as fast as a millionth of a second. Simulating this takes a long time on a computer. In fact, it takes about a day to simulate a nanosecond (1/1,000,000,000 of a second). Unfortunately, proteins fold on the tens of microsecond timescale (10,000 nanoseconds), and some on the millisecond scale. Look up Folding@home

[iamvillainmo]

@sagun111 Less than 1 ms in many cases. It is astonishing when you consider how many different arrangements of the primary structure are possible.

[duguder]

Are they saying all these dancing take only 1 microsecond?

[spencertron88]

That's only 1 microsecond? That really makes me appreciate life. One can't even begin to imagine all those proteins in every cell in your body, folding at 1 million times that speed.

[hieronumos]

1 microsecond

[slimxdi]

and which nanosecond?

[r0galik]

good point