ESSENTIAL DYNAMICS FROM NMR CLUSTERS - DYNAMIC PROPERTIES OF THE MYB DNA-BINDING DOMAIN AND A HINGE-BENDING ENHANCING VARIANT

Application of the ''essential dynamics'' method to the NMR cluster of structures for the R2R3 DNA-binding domain of the mouse c-Myb transcr iptional activator is described, Using this method, large concerted fl uctuations of atoms are extracted showing a hinge-bending motion betwe en the two (R2 and R3) Myb repeats on the basis of NMR data alone. Mol ecular dynamics simulation of the same protein allowed quantitative co mparison of the large concerted motions calculated from experimental a nd theoretical data, showing a significant degree of similarity. Detai led inspection of the motions reveals a conserved proline that plays a hey role in determining hinge flexibility. The proline-to-alanine mut ation at this position, which has previously been characterized bioche mically, was subjected to molecular dynamics and subsequent essential dynamics analysis. The hinge-bending motion between the two repeats wa s found to be enhanced for the mutant. The approach described should h ave general applications, predicting the effect of mutations on protei n dynamic properties of other proteins. (C) 1998 Academic Press.