3
$\begingroup$

I've come across a few different contributions to entropy in macromolecules such as proteins: configurational, conformational and vibrational. The problem is that I can't seem to find a consistent definition and there may be some overlap.

In addition, I've only really understood entropy to be made up of rotational, vibrational and translational components and I'm struggling to reconcile this with the contributions to entropy for proteins described in the literature.

$\endgroup$
3
$\begingroup$

I've only really understood entropy to be made up of rotational, vibrational and translational components

There is also electronic entropy, but it's a fun exercise to show that (at least for the hydrogen atom) the corresponding partition function $q_{\text{elec}} = 1$ at room temperature, and for all intents and purposes there is only population of a single state. So, the other 3 kinds of entropy (translational, rotational, vibrational) are those directly from a statistical mechanical derivation that are relevant for most (bio)molecules.

I've come across a few different contributions to entropy in macromolecules such as proteins: configurational, conformational and vibrational.

Hopefully you agree that vibrational entropy in the context of proteins is the same as in the context of any other system in that vibrations can't be decomposed into other kinds of excitations (translational or rotational), regardless of whether or not the vibration is localized to a bond, highly delocalized, or quaternary structure subunits moving with a regular period.

Configurational and conformational entropy are being used slightly differently. From Wikipedia,

  • Conformational entropy – is the entropy associated with the physical arrangement of a polymer chain that assumes a compact or globular state in solution.
  • Configuration entropy - is the portion of a system's entropy that is related to the position of its constituent particles rather than to their velocity or momentum.

For proteins, I think the distinction between conformation and configuration is less clear than it is for more molecular systems. In my limited experience, a configuration of a protein is similar to a macrostate in statistical mechanics, which is distinguished from other possible configurations by some criteria related to the position of a protein's primary or secondary structure. More specifically, different techniques can be used for clustering the different protein conformations together into distinct configurations.

In these cases, the greater the number of conformations a protein can take, or the number of configurations it samples based on some metric, the greater the entropy. For something like an intrinsically disordered protein, its conformational and configurational entropy are likely to be higher than for a globular protein.

$\endgroup$

Your Answer

By clicking “Post Your Answer”, you agree to our terms of service, privacy policy and cookie policy

Not the answer you're looking for? Browse other questions tagged or ask your own question.