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fuzzywolf23 t1_j51uz18 wrote

Reply to comment by vilhelm_s in How is protein folding quantum mechanical? by prionprion

> -they just consider the parts of the chain as having well-defined positions in 3d-space, and add up energy from pairwise interactions between the parts that end up close to each others.

Yes, but also if you want an accurate calculation of that energy, you need to use quantum mechanics. The nuclei of the atoms have definite positions, but electrons do not

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prionprion OP t1_j52nptp wrote

this is also my point, I know the whole folding is more classical, and the folding is mainly driven by thermodynamics, but I feel like how the change in shape happen as protein jump from one conformation to another is quantum mechanical

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fuzzywolf23 t1_j52yn3z wrote

The folding is driven by thermodynamics, but in a sense, so is everything!

All of nature tends to move from higher energy to lower energy states. You can approximately calculate the energy of a protein structure, but you'll be wrong by enough that your error is bigger than the difference between candidate structures. To calculate the energy with sufficient accuracy, you need to use quantum mechanics using, e.g., density functional theory.

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