In a ligand-protein binding 2D NMR study, what does it mean when there is no chemical shifts but there's a decrease in peak intensities and an increase in linewidths?
It could be an indication of binding where the interaction is of intermediate rate or where the binding is non-specific from the ligand perspective. The following two papers report a similar phenomenon.
https://www.nature.com/articles/nsmb.2045#Sec15
https://portlandpress.com/biochemj/article-abstract/474/22/3849/49560/
Jani Rahkila thanks for the reply.
Do you think it's somehow related to fast exchanges of ligand between the bound and free form which resulted into collapse of two signals into a single peak and therefore no chemical shift is observed?
I should mention that my protein is an intrinsically disorderd.
Sorry, I just realized my question was probably wrong because of the line broadening of the peaks.
Jani Rahkila I've got another question.
Almost all peak intensities of residues decreased in a dose dependent manner in the presence of different concentration of the ligand. But, only some of the linewidths broadened, specifically in a specific concentration of the ligand.
Could you please tell me what it means?
We have seen such phenomena if a protein binds to high MW "objects" (e.g. a mAB, or a Aggregate of the Protein under investigation). The part which is substantially immobilized broadens (and may even disappear) whereas other parts of the protein remain "floppy" and free in solution. I would try to measure DOSY in absence and presence of the ligand...
How big is your ligand?
Could you have a look at it with STD-NMR or tr-NOESY?
Jani Rahkila one of them is 975 g/mol and the other one is 328 g/mol.
No, I don't have access to the NMR machine at the moment.
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