[Protein-analysis] Re: Enthalpy of protein

Raoul Fleckman via proteins%40net.bio.net (by raoulnonspam.fleckman from gmail.com)
Wed Mar 28 17:24:55 EST 2007


On 2007-03-27, Protenger <yellowish from gmail.com> wrote:
> On Mar 26, 10:37 am, Frank Küster <f... from kuesterei.ch> wrote:
>> "Protenger" <yellow... 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]
>
> Tanks for your reply
> I ask my question in another format.
> Suppose we have a native protein with its own intristic (absolute)
> enthalpy, then by protein engineering we introduce a pair
> of opposide charged residues on its surface so its stability
> increases.
> Does absolut (and not delta H) enthalpy of mutant decrease?
>
> regards
> rahim
>

one wonders if this question has a finite number of microstates [wink]

without a doubt a quantum-thermodynamic-lawyer will find seven flaws in
this reply, however consider that perhaps the main effect of your
gedanken experiment is to reduce the local entropy?  that is, perhaps
the change in enthalpy is relatively small.  as for "absolute" values
for any of these matters, you'll have to consult a guru on a mountain
higher than any i've discovered, (that is, regard with caution anyone
that says they can calculate absolute enthalpies based on molecular
models)

good luck
-- 
angue prune



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