I read an article where an intrinsically flexible protein was crystallized using chaperon (here chaperon is a protein that helps to stabilize other protein) . i was wondering what would be the criteria of selection of chaperon for crystallizing an intrinsically disordered region.
The problem with the use of nanobodies might be that they are conformation-specific. To my knowledge, nanobodies are still only obtained by injecting the protein into live animals (lamas, typically, unless you have a pet shark). If your protein has various conformations, you'd need to stablise a particular conformation prior to injecting into the animal, to obtain the appropriate nanobody. If your protein region of interest is intrinsically disordered, then this might not work.
So you might be better off choosing a natural ligand for your flexible part, and then crystallise.
The most important question would be why you wish to obtain a crystal structure of an unstructured region? What would be the biological insights gained from such a structure? As an alternative, you could use SAXS or NMR to characterise this region in its unliganded state. If you have biological ligands, then you could add those to SAXS / NMR and analyse. And then only crystallise a relevant fragment bound to 3D ligand.
you might want to try nano-bodies (single chain antibodies) that would bind different conformations of the protein.
The problem with the use of nanobodies might be that they are conformation-specific. To my knowledge, nanobodies are still only obtained by injecting the protein into live animals (lamas, typically, unless you have a pet shark). If your protein has various conformations, you'd need to stablise a particular conformation prior to injecting into the animal, to obtain the appropriate nanobody. If your protein region of interest is intrinsically disordered, then this might not work.
So you might be better off choosing a natural ligand for your flexible part, and then crystallise.
The most important question would be why you wish to obtain a crystal structure of an unstructured region? What would be the biological insights gained from such a structure? As an alternative, you could use SAXS or NMR to characterise this region in its unliganded state. If you have biological ligands, then you could add those to SAXS / NMR and analyse. And then only crystallise a relevant fragment bound to 3D ligand.
I agree with Stefan that the use of nanobodies is not the best approach in this case. I also agree with him that the use of natural ligands to stabilize your protein in the bound form is a better way to go. However, please keep in mind that intrinsically disordered proteins (IDPs) are able to fold very differently upon binding to different partners. Also, many IDPs are known to preserve significant amount of disorder even in their bound forms. As far as the selection of a suitable chaperone for crystallizing an intrinsically disordered region is concerned, I am afraid that there is no simple answer to this question since existing literature on this subject is very limited. You always can try chaperone described in the paper you mentioned, but be prepared for a long search for a suitable partner. Again, Stefan is right and you should consider NMR.
I also agree with Stefan and Vladimir. Moreover, if you use an indifferent (means not biologically relevant to the IDP) protein which is able to help everything to crystallize, than you may end with a structure, which is completely artificial, and may mislead you when you try to analyze structure-function relationships. Use natural partner for crystallization, or NMR / SAXS as it was mentioned before, and always take into consideration what Prof Uversky said about many conformations, and fuzziness.
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