Hello Everyone, I am looking for the binding of ligand (D-Tyr3AA, which mimics D-tyrosine attached to the 3′-OH of the terminal adenosine (A76) of tRNA) with a protein. I have two types of ligands, 1st is D-Tyr3AA and 2nd is D-Tyr2AA (here 2 D-tyrosine attached to the 3′-OH of the terminal adenosine (A76) of tRNA).
I am trying to use NMR based techniques like HSQC (Heteronuclear Single Quantum Coherence) and STD (Saturation-Transfer Difference) to figure out the specificity of a protein with respect to D-Tyr2AA and D-Tyr3AA but i am unable to resolve it due to technical issues.
It would be great help if somebody suggest me any appropriate computational approach to discriminate binding of two closely related ligand (substrate).
thanks in advance.