to complement the very nice description by jeremy, you may wish to try
and decompose the vibrational modes to get this sense by focussing on
the origins of the "red shift" in the vibrational spectrum and this
accounts largely for the increased vibrational entropies upon
complexation. This paper may be used as a guide
(Dissecting the vibrational entropy change on protein/ligand binding:
burial of a water molecule in bovine pancreatic trypsin inhibitor J
Phys Chem B 2001 105 8050-8055)
&

There is some very nice work by Olano & Rick in

JACS 2004 126:7991 on Hydration free energies and entropies for water
in protein interiors.

and by carol post on how the increased entropies upon complexation are
the origin of the mechanism of some drugs. (for example Influence of
an Antiviral Compound on the Temperature Dependence of Viral Protein
Flexibility and Packing: a Molecular Dynamics Study J. Mol. Biol.
(1998) 276: 331-337)



Quoting Jeremy Tame <[log in to unmask]>:

> Different proteins do different things. Some adopt fewer
> conformations and a more rigid structure after binding
> a ligand, and others do the opposite. Haemoglobin is a nice example
> of a protein that becomes a lot more flexible
> after picking up ligands. For any reaction of the kind P + L -> PL
> there is an entropy cost of making one molecule
> from two. For the protein to activate low frequency modes in the
> complex is one way to compensate for this by
> increasing the entropy of the bound form. The paper by Sturtevant
> (PNAS 74, 2236, 1977) is worth a read, as is
> Cooper and Dryden (Eur Biophys J, 11, 103, 1984), if you are
> interested in relating fluctuations to thermodynamics.
> All too often people attempt direct comparisons of structural models
> and affinities without realising that the so-called
> "angstroms to calories" problem often frames the question in a form
> that cannot be answered sensibly. For
> example, imagine a protease which is produced as a zymogen. Both
> forms may have essentially identical crystal
> structures even though the zymogen is more flexible. The protease
> can be activated by loss of vibrational modes
> in the unbound state which are re-awakened in the complex with
> substrate; hence the zymogen will have lower
> substrate binding and activity. You might be interested in a review
> by Homans (ChemBioChem 6, 1585, 2005) which
> discusses the use of NMR to look at entropy changes in
> protein-ligand binding reactions. It is by no means unusual
> for a residue's entropy to increase in the bound state, although in
> your case it seems to be the whole protein!
>
> On Dec 9, 2012, at 1:05 PM, anita p wrote:
>
>> Hi All,
>> I am trying to understand the mechanism of protein-peptide
>> interaction in two complexes (protein-pepA and protein-pepB).
>> While trying to perform some simulation experiments, I find that
>> the root mean square fluctuation (RMSF) by residues of protein in
>> the complex is higher than that of the protein alone.
>> Please refer the figure attached to this email. pepA binds with
>> higher affinity (in uM-range) than pepB according to invitro studies.
>>
>> Does this happen normally?? Please advice.
>> Thanks in advance
>> Anita
>> <RMSF.png>