More Protein Folding Progress – What’s It Mean?

Re:More Protein Folding Progress – What’s It Mean? by dekhn on Monday July 26, 2021 @04:14PM (#27964809)

IIUC the folding and unfolding pathways of a protein are not time reversed wrt each other.

But you would still enjoy reading this: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC17732/ the work in this paper led to folding@home because vijay couldn't get enough computer time to run his simulations

if you really had a lot of computer time to waste, you could imagine doing simulations where you titired in or out some guanadinum chloride and inspected how disrupting h-bonds (versus hydrophobic collapse) contributes. Chaotropes are better than temperature for probing unfolding.

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Re:More Protein Folding Progress – What’s It Mean? by dnautics on Monday July 26, 2021 @10:12PM (#27967846)

> IIUC the folding and unfolding pathways of a protein are not time reversed wrt each other.

That's more or less correct, but in my proposal, we are not modeling the folding pathway of a protein. One way to think of it: we would be modelling the reverse unfolding pathway of a protein in a universe with different (simpler) physics than ours, physics in which (hopefully) the time reversed unfolding pathway yields the correctly folded protein in OUR universe.

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Re:More Protein Folding Progress – What’s It Mean? by d110af5ccf on Tuesday July 27, 2021 @03:15AM (#27969536)

Your description kind of reminds me of the 2018 World Models publication. Are you familiar with that work and/or am I off base? (https://worldmodels.github.io/) (https://arxiv.org/abs/1803.10122)

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Re:More Protein Folding Progress – What’s It Mean? by dnautics on Tuesday July 27, 2021 @11:24AM (#27973561)

Off base. I'm using universes as a florid description of the fact that our QM models are crap but they might be useful of the laws of physics were different.

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