[phenixbb] monomer-dimer

Maia Cherney chern at ualberta.ca
Mon Aug 9 08:52:44 PDT 2010

To determine the oligomeric state of a protein (monomer or dimer in your 
case), it's useful to use the PISA server. You upload your pdb file from 
the crystal structure.The server calculates the areas of interfaces 
(buried area) and  deltaG (change in Gibbs energy) upon oligomer 
dissociation. (E. Krissinel and K. Henrick (2007). /Inference of 
macromolecular assemblies from crystalline state/. J. Mol. Biol. *372*, 
774--797 . E. Krissinel and K. Henrick (2005). /Detection of Protein 
Assemblies in Crystals/. In: M.R. Berthold /et.al./ (Eds.): CompLife 
2005, LNBI 3695, pp. 163--174 <http://dx.doi.org/10.1007/11560500_15>. 
E. Krissinel (2009). /Crystal contacts as nature's docking solutions/. 
J. Comp. Chem., in press; published on-line 6 May 2009; DOI 
If the interface area (divided by 2 per one protomer) is greater than 
1000 A^2 and delta G is more than 5kcal/mol (the higher the better), 
it's a dimer. However, don't forget that most dimers can dissociate into 
monomers upon dilution. There is a dynamic equilibrium between dimers 
(oligomers) and monomers that depends on their concentration and the Kdiss.
Separating them in any method will disturb this equilibrium. If the 
re-equilibration time is greater than the separation time, you can see 
both monomers and dimers. You can even roughly calculate the 
dissociation constant:

Kdiss=[monomer]^2/[dimer] where brackets mean concentrations. To give 
you an estimate, at Kdiss=10(-3)M, you have roughly equal concentration 
of dimers and monomers at 10-3 M and only 10% dimers at 10-4 M. 
Sometimes, protein needs to dissociate easily for the biological function.


intekhab alam wrote:
> Hi everyone
> Sorry for some non specific query!!!!!
> i am working with a protein that shows a dimer in the crystal 
> structure but when i tried to figure out that with standard molecular 
> markers in gel filteration (superdex-200, 24ml column) it turned out 
> to be a monnomer. Native gel analysis after incubating the protein at 
> 20 degree, 37 degree showed more dimer at 20 degree celcius as 
> compared to 37. I tried similar strategy in gel filteration by 
> incubating my protein at various temperature,where a lot of 
> precipitation was observed at 37 degree celcius and after removing the 
> precipitates i run the gel filteration that has 0.5 ml higher elution 
> volume as compared to samples incubated at 20 degree celcius and 4 
> degree celcius.( Is this significant)
> Furthermore i have done some experiments in cold room (4 degree) where 
> the elution volume is stuck at a point irrespective of the conditions 
> (as Flow rate, concentration of protein etc) and that is higher than 
> that of the room temperature by 1 ml.
> Standard moleculr weight markers also show higher elution volume  in 
> cold room in comparison to the room temperature by 1 ml.
> I will be highly obliged if someone suggest some literature  or any 
> otherway to do gel filtrtaion so that i can clearly resolve this 
> issue. Also let me know if there is some literature available on 
> effect of temperature on the elution volume of proteins.
> Thanks in advance
> -- 
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