I've done 15N hmqc to determine the interaction between ligand-protein.
There was no chemical shifts in amino acids after adding the ligand. However, the peak heights of almost every residue were decreased in a dose dependent manner.
Could someone tell me what it means please?
I'm not sure if this answer applies to 15N HMQC experiments, but in the past when we did 2-D NMR experiments to measure ligand binding to a protein by measuring chemical shift changes of peaks, a loss of multiple peak intensities was taken to mean that the ligand was binding in a non-specific manner, such as an aggregator or denaturant. Such compounds were discarded.
Adam B Shapiro thanks for the reply.
I've read somewhere that fast exchanges of ligand between the bound and free form results into collapse of two signals into a single peak, as the life time is too short for the observation of individual signals on the NMR time scale.
Could it be the case here?
I should mention that most of the peaks linewidths also show observable broadening.
Sorry if my question is too basic. I'm a real beginner in NMR.
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