Folding, mathematically or random?

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Folding, mathematically or random?

Postby Theodore » Mon Feb 18, 2019 10:40 pm

I always wondered, if protein folding happens strictly mathematically, or if there is a random aspect in the equation?

I presume that the proteins we fold on our hardware, emulate an environment in which protein chains often find themselves in; without external influence of say, radiation or impacts of small particles?
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Re: Folding, mathematically or random?

Postby bruce » Tue Feb 19, 2019 12:45 am

Atomic motions all involve some thermal statistical motions (except simulated at absolute zero, which would be meaningless for proteins). That's part of the math that's included in the GROMACS code or the OpenMM code.

Look up "Brownian motion."
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Re: Folding, mathematically or random?

Postby Theodore » Tue Feb 19, 2019 1:13 am

Thanks Bruce!
I presume the brownian motion you mention is the movement of atoms of the cluster being emulated, and no outside interference.

Is there any relation found, to the development of cancer and temperature (temperature being one of the forms of radiation)?
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Re: Folding, mathematically or random?

Postby bruce » Tue Feb 19, 2019 6:50 pm

Most simulations are run at body temperatures. That value is set by the scientist and when appropriate, it's adjusted to nearby temperatures when it's considered experimentally appropriate.

All simulations consider the solvent, so if that's included in your "outside interference" category, then that's significant. In the early days of FAH (and occasionally, today) the solvent is simulated as an equation of a uniform field of atoms. Now that the hardware being used is more powerful than early x86 CPUs, a simulation box surrounding the protein(s) is filled with a lot of discrete H2O molecules plus a few other atoms of whatever "contaminants" are appropriate. This gives each H and each O atoms the appropriate polar torsional effects. That simulation box is mathematically replicated in adjacent blocks of an infinite 3D field so mathematically speaking, there are multiple molecules of protein in a vast space filled with them in a vast solvent (though all protein molecules re-shape themselves in unison.

I don't know the specifics of past or future cancer studies, but I'd guess that since there is a known relationship with tumor heating, that temperature would be an important variable. Go to the "papers" page and read whatever studies that have been published. Maybe you'll find the information you're seeking.
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