I am interested to work 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?
On 7/18/17 5:03 AM, Saravanan Parameswaran wrote: > Is it possible to model the tetramer from Pentameric NMR structure?
It depends what you mean. If you mean you want to build a model with four chains that correspond to four of the five chains in your template, then you don't have to do anything special - just add chain breaks to your alignment file, as per https://salilab.org/modeller/9.18/manual/node30.html
If, however, you want to model an entirely different state (for example, the pentameric structure has C5 symmetry and you want to build a model that has C4 symmetry) then Modeller won't magically do that, since by design the monomer-monomer interactions present in your template will end up in your model - you would instead need more information on the symmetry of the tetramer (e.g. a 3D EM map) and then use a monomer assembly tool, for example MultiFit in cyclic symmetry mode: https://salilab.org/multifit/
Ben Webb, Modeller Caretaker