The sign of NMR chemical shift difference as a determinant of the origin of binding selectivity: Elucidation of the position-dependence of phosphorylation in ligands binding to Scribble PDZ1.
The sign of NMR chemical shift difference as a determinant of the origin of binding selectivity: Elucidation of the position-dependence of phosphorylation in ligands binding to Scribble PDZ1.
Biochemistry. 2017 Nov 16;:
Authors: Sundell G, Vögeli B, Ivarsson Y, Chi C
Abstract
The use of NMR chemical shift perturbation to monitor changes taking place around the binding site of a ligand-protein interaction is a routine and widely applied methodology in the field of protein biochemistry. Shifts are often acquired by titrating various concentrations of ligand to a fixed concentration of the receptor and may serve the purposes, amongst others, to determine affinity constants, locate binding surfaces, or differentiate between binding mechanisms. Shifts are quantified by the so-called combined chemical shift difference. Although the directionality of shift changes are often used for detailed analysis of specific cases, the approach has not been adapted in standard chemical shift monitoring. This is surprising as it would not require additional efforts. Here, we demonstrate the importance of the sign of chemical shift difference induced by ligand-protein interaction. We analyze the sign of the 15N/1H shift changes of the PDZ1 domain of Scribble upon interaction with two pairs of phosphorylated and unphosphorylated peptides. We find that detailed differences in the molecular basis of this PDZ-ligand interaction can be obtained from our analysis to which the classical method of combined chemical shift perturbation analysis is insensitive. In addition, we find a correlation between affinity and millisecond motions. Application of the methodology to Cyclophilin, a cis-trans isomerase reveals molecular details of peptide recognition. We reckon our directionality-vector chemical shift analysis as a method of choice when distinguishing the molecular origin of binding specificities of a class of similar ligands as it is often done in drug discovery.
PMID: 29144123 [PubMed - as supplied by publisher]
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