[MMTK] Solvation of the protein hemoglobin

Konrad Hinsen research at khinsen.fastmail.net
Tue Apr 13 06:12:22 UTC 2010


On 13 Apr 2010, at 03:05, prabhakar g wrote:

> But when I happen to check with one of the crystal structures (2HHB)  
> of hemoglobin, this pocket of hemoglobin was sparsely populated with  
> water molecules.  Sir my question are:
>
> 1.Does solvating the structure for simulations place more number of  
> water molecules  around and in the pocket of the protein molecule  
> than observed in the physiological conditions.

Yes. However, in the case of crystallographic water molecules, the  
problem is in the observation rather than in the simulation.  
Crystallography can observe only the most stable water molecules, the  
ones that are in nearly the same position in all copies of the unit  
cell. Crystallographic waters molecules thus always represent only a  
small subset of solvent molecules.

> 2.Is it possible to know probability of the  the inter subunit  
> pocket being completely filled with water molecules in physiological  
> conditions, in protein solutions.

As far as i know, no. There aren't many experimental techniques that  
are sufficiently sensitive to water molecules to provide this kind of  
detail. Perhaps some clever trick with something like neutron  
scattering on a carefully deuterated sample could do it.

> 3. What are the methods could one use to solvate the protein close  
> to the realistic physiological conditions.

That's impossible to say before someone has found a way to  
characterize the physiological conditions with more certainty. If you  
want to be realistic, you have to take into account not just waters,  
but ions and other small molecules that are present around proteins. I  
don't know of any experimental technique that would give you the  
information you need.

Konrad.
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Konrad Hinsen
Centre de Biophysique Moléculaire, CNRS Orléans
Synchrotron Soleil - Division Expériences
Saint Aubin - BP 48
91192 Gif sur Yvette Cedex, France
Tel. +33-1 69 35 97 15
E-Mail: research at  khinsen dot fastmail dot net
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