[Protein-analysis] Re: Enthalpy of protein

Frank Küster via proteins%40net.bio.net (by frank from kuesterei.ch)
Mon Mar 26 01:37:19 EST 2007

"Protenger" <yellowish from gmail.com> wrote:

> Hello
> I have a very simple question.
> Suppose in a protein folding pathway we have two opposite charged
> residues seperated by "d" angstrom such that there is a weak
> interaction between them. We name it state A, so its enthalpy is Ha.
> As protein conformation changes through folding pathway we suppose "d"
> decreases, so interaction between charges become stronger. Now we name
> it State B and its enthalpy as Hb.
> My simple question is: is Ha>Hb? or Hb>Ha?

Well, in vacuum or even in pure water it's easy to answer, isn't it?
(Unless you are actually asking for signing conventions for
thermodynamic quantities.)

In reality, you've got buffer ions around, which (in either of the two
states) might or might not be able to sit near one of the charges, and
sit either quite statically "bound", or just have a higher average
probability of being there.  Moreover, at least one of the states will
be partially folded and hence can only be treated as an ensemble of
structures: Then one single distance d cannot be meaningfully assigned,
it should be treated as a distribution of distances with a dynamic
exchange of substates.

Does that help to confuse you? ;-)

Regards, Frank
But this:
> For fucks sake...
is just offensive.  It should have an apostrophe(!)
[MJ Ray, nowhere]

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