I am working on a protein whose structure is determined from NMR and its in pentameric state.
We believe that It should exist as tetramer in real life.
Is it possible to model the tetramer from Pentameric NMR structure?
If so, please let me know how to proceed?
Thanks in advance
P. Saravanan
Could you try the Rosetta symmetry module (https://www.rosettacommons.org/manuals/rosetta3.1_user_guide/symmetry.html)? If you know what sort of symmetry the tetramer has, you could define that symmetry in the module and then include intramolecular constraints taken from pentameric structure. That way a symmetric tetramer is built to be as much like the pentameric structure as possible. Rosetta also apparently has symmetric docking (but I have not used this feature) so you could try docking the pentamer monomers into tetramer symmetry.
Similar to Rosetta, HADDOCK also has a symmetry section:
http://www.bonvinlab.org/software/haddock2.2/run/
One should be able to register and access the webserver, and select an advanced setting that permits symmetry restraints to be applied to four copies of your domain. You can then define restraints based on the observed interfaces in the pentamer and transfer the central subset to the tetramer - keeping some ambiguity so as to enable the interfaces to rearrange slightly during the docking model.
http://milou.science.uu.nl/services/HADDOCK2.2/haddock.php
Hi,
in addition to the previous answers, I would suggest to try to get experimental evidence of the oligomeric state. NMR structure suggests a pentamer... how did they come to this conclusion? Why do you think the a tetrameric state is more realistic? There are simple experiments that could help you: Size Exclusion Chromatography coupled to Static Light Scattering (SEC-MALS) comes to mind, or Small Angle X-ray Scattering (SAXS, not that simple to set up as you need a synchrotron...). SAXS data could provide you with a molecular envelope that would help you to define the structure of the oligomeric state.
In addition to Laurent's suggestions, I would first perform native SDS-PAGE or cross-linking followed by SDS-PAGE as these techniques should be available in every biochemistry lab.
The protein is in pentamer state but its ortholog in human is in tetramer state. This data is confirmed with experimental studies which I came to know from literature after I post the question.
Pardon me for not explaining it with clarity
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