Structural Stability and Flexibility Direct the Selection of Activating Mutations in Epidermal Growth Factor Receptor Kinase

Herein we investigate the potential of novel methods of molecular
dynamics analysis to provide information on the key,factors that
underlie the preferential localization and the effects of mutations
modulating protein activities. Epidermal growth factor receptor (EGFR)
kinases are selected as a test case. The combined,analysis of protein
energetics and internal dynamics indicates clear polarization in the
native protein, whereby a highly stable-and ordered scaffold in one
domain, namely the C-lobe, is combined to a flexible and loosely
stabilized domain, the N-lobe. The subdivision in two portions with
different properties directs the presence of point mutations mainly to
the N-lobe. This allows modulating protein flexibility so that the
protein can more efficiently sample the conformations necessary for
substrate recognition, while leaving the stability of the protein
unperturbed. In this context, comparative simulations of EGFR in the
wild type sequence and in the presence of the activating oncogenic
mutation G719S reveal flexibility changes in several key regions,
involving in particular the part of the kinase devoted to the regulation
of substrate recognition (regulatory cote) and an increase in the number
of stabilizing interactions in the N-lobe for the activated mutant. Our
approaches represent a promising and simple strategy toward
rationalizing the effects of mutations in modulating enzymatic
activities.