[phenixbb] monomer-dimer

intekhab alam faisaldbg at gmail.com
Mon Aug 9 18:49:05 PDT 2010

Thanks for the suggestion and your time. I will check the refrences

On Tue, Aug 10, 2010 at 12:52 AM, Maia Cherney <chern at ualberta.ca> wrote:

> 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 10.1002/jcc.21303}
> 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.
> Maia
> 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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