Submitted by prionprion t3_10g3kx9 in askscience
Can someone explain to me how the process in protein folding can be elaborated by quantum physics? What specific part in the process can be quantum mechanical? are there any known quantum phenomena during folding?
Any explanation with equation or article link is also appreciated
I was trying to look for more than just the bonds and forces but thank you for this!
Protein folding is not inherently quantum mechanical. Protein folding refers to the process by which a protein molecule assumes its three-dimensional structure, which is determined by the sequence of amino acids in the protein. This process is primarily determined by the laws of thermodynamics and the interactions between the various chemical groups within the protein. However, recent research has suggested that quantum mechanical effects such as quantum tunneling may play a role in certain aspects of protein dynamics, such as the formation of hydrogen bonds between the protein and its environment. However, this is still an active area of research and the exact role of quantum mechanics in protein folding is not fully understood.
Van-der-walls forces could not be more different from hydrogen bonding.
I mean, they are not the same thing but still fall under the category of intermolecular forces. And the commenter is correct that Van Der Waals forces are caused by the fluctuating polarizations of particles at a particular distance, which is understood via quantum dynamics.
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The structure of the protein is dictated by what the valence electrons do. Electrons are too light to be treated classically - their de Broglie wavelength is about 0.1nm. That means you need quantum mechanics to figure out what they're going to do (electronic structure).
good point, thanks
I think it's not extremely "quantum". Of course proteins are molecules so they ultimately obey quantum mechanics, but I think for the folding problem people are not really treating that---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. (Finding the minimal energy configuration here is already very difficult, even before starting to consider any quantum superpositions or trying to compute the pairwise interactions more exactly).
However, some people hope that quantum computers could still be helpful, e.g. this recent paper. The problem they are solving is still the classical, non-quantum setup, but there are quantum algorithms that are supposed to be good at searching for minimal-energy configurations, so it may still speed things up.
> -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
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
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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I believe protein folding can be treated with the Born-Oppenheimer approximation. Essentially, while quantum effects of the electrons in the system can be important, quantum effects of the nuclei can be neglected, and thus the nuclei are essentially treated as classical objects with definite position/momentum.
So, the quantum mechanical aspects will lie with the electronic structure; van der Waals forces, hydrogen bonds, and all that. These are all quantum phenomena.
I love this approach, thanks!
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Protein folding is quantum mechanical because it involves the movement of electrons and nuclei. The energy of the protein is determined by the quantum mechanical properties of the electron positions and the interactions between them. This means that the folding of the protein is governed by the principles of quantum mechanics.
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smnms t1_j50vf70 wrote
Quantum mechanics explains the orbitals of an atom's electrons, and also the molecular orbitals of covalent bonds between atoms. Orbitals are also important for the van-der-Waals forces, hydrogen bonds, and interactions with the molecular orbitals of surrounding water molecules, which direct protein shape.
In the end, all chemistry is applied quantum mechanics, and protein folding is chemistry.