Essential dynamics from NMR clusters: dynamic properties of the Myb DNA-binding domain and a hinge-bending enhancing variant

Abstract

Application of the "essential dynamics" method to the NMR cluster of structures for the R2R3 DNA-binding domain of the mouse c-Myb transcriptional activator is described. Using this method, large concerted fluctuations of atoms are extracted showing a hinge-bending motion between the two (R2 and R3) Myb repeats on the basis of NMR data alone. Molecular dynamics simulation of the same protein allowed quantitative comparison of the large concerted motions calculated from experimental and theoretical data, showing a significant degree of similarity. Detailed inspection of the motions reveals a conserved proline that plays a key role in determining hinge flexibility. The proline-to-alanine mutation at this position, which has previously been characterized biochemically, was subjected to molecular dynamics and subsequent essential dynamics analysis. The hinge-bending motion between the two repeats was found to be enhanced for the mutant. The approach described should have general applications, predicting the effect of mutations on protein dynamic properties of other proteins.