Biological solid state physics

[hagopbul]

TL;DR Summary

A small question about crystalline structure in biology

Hello all:

I was wondering are we have a name for protein structure , or we consider them amorphous?

Any one did a phono propagation in protein molecules ?

Protein folding and phonons any relationship?

When peptides came together and start to form the protein dose phonons/photon propagation inside that nano structure have any relationship or effect on the folding processes?

Just a small remarks I don't know any thing about biology on a university level took it only in school

Best
Hagop

 

[TeethWhitener]

Summary:: A small question about crystalline structure in biology

There are actually several unrelated questions here. You might get more constructive responses if you separate each question (or at least each topic) into its own thread.

I was wondering are we have a name for protein structure , or we consider them amorphous?

Individual proteins are molecules. They can form crystals, like many other molecules, but I'm not sure I'd consider the categories of crystalline/amorphous to apply to individual proteins.

That said, large proteins can have crystalline and amorphous domains, just as other macromolecules can. There are quasiregular secondary structure motifs that are common to many proteins; in particular the alpha helix and the beta sheet.

https://en.wikipedia.org/wiki/Protein_structure

Protein folding and phonons any relationship?

I seriously doubt it. The timescale of protein folding is on the order of milliseconds, whereas the timescale of optical phonons is closer to nano/picoseconds.

 

[klotza]

Or in terms of energy scales, the energy difference between different conformational states in a protein is typically of order kT (25 meV), whereas phonons are associated with modes in the interatomic bonds, which are of order single eV, like 40 times greater in energy. There are important things related to quantum/electromagnetic effects in proteins, for example fluorescent proteins which are extremely important in biochemistry and biophysics. Most of the literature on phonons in proteins comes is from the '80s it seems, with this one being the most cited.

 

[Dr_Nate]

Or in terms of energy scales, the energy difference between different conformational states in a protein is typically of order kT (25 meV), whereas phonons are associated with modes in the interatomic bonds, which are of order single eV, like 40 times greater in energy.

From the literature, I've seen phonons in transition-metal oxides range from a few meV to about 150 meV. The bonding energy is still on the order of electron volts, so it seems bonding energy is not the energy scale that applies to phonons.

Simple harmonic oscillator models of phonon chains produce relations like this: $\hbar\omega\propto\sqrt{\frac{k}{m}}$, where $k$ is from Hooke's "law" and $m$ is the mass of the atom in the chain. This $k$ variable shows up in potential energy as $U=\frac{1}{2} kx^2$. So, it seems to me that the width of the energy well matters, not the depth of the energy level.

That all being said, if you lower the average mass of atoms in the chain, you can increase your phonon energy. Proteins do have lighter atoms so they could go higher. I wasn't able to find any phonon dispersion curves that were near the eV range.

 

[hagopbul]

That all being said, if you lower the average mass of atoms in the chain, you can increase your phonon energy

what about crystal / amorphous arrangement of the protein wouldn't that effect some how

 

[Dr_Nate]

what about crystal / amorphous arrangement of the protein wouldn't that effect some how

Please don't forget about the forum rules on proper punctuation and grammar. It does help with communication. A few mistake are alright, but you just can't ignore the rules.

Those sure will affect the phonons. As a condensed-matter physicist, my knowledge of proteins is quite limited but, I don't think it'll help you with protein folding. When you do XRD on protein, it is in a solid and cooled with liquid nitrogen. This is not the environment your protein works in.

 

[hagopbul]

Please don't forget about the forum rules on proper punctuation and grammar. It does help with communication. A few mistake are alright, but you just can't ignore the rules.

Writing (even in my native language) considered some how challenging to me

Those sure will affect the phonons

I was trying to look into some effects , maybe the phonons will give an answer why spike can bind more effectively to AEC2

But my university education is solid state physics, laser , nuclear and don't include biophysics so this remains general ideas

Best
Hagop

 

[TeethWhitener]

From the literature, I've seen phonons in transition-metal oxides range from a few meV to about 150 meV. The bonding energy is still on the order of electron volts, so it seems bonding energy is not the energy scale that applies to phonons.

Of course phonons and bonding energy are the same scale. How else do you think bonds break than by atomic displacement?

 

[TeethWhitener]

I was trying to look into some effects , maybe the phonons will give an answer why spike can bind more effectively to AEC2

We have an answer: the electrostatic interaction between the two proteins is very favorable to binding. Why would you think we needed to bring phonons into this?

 

[Dr_Nate]

Of course phonons and bonding energy are the same scale. How else do you think bonds break than by atomic displacement?

I don't understand. Do you doubt the numbers that I wrote? Or, perhaps, we could be disagreeing as what counts as the same scale.