Mapping of dynamic allostery within p38 alpha kinase via network analyses and NMR spectroscopy
TL;DR
Dynamical network analysis is used to identify key residues involved in a dynamic allostery between the N- and C-lobes that connects the major functional units of the MAP kinase p38α, providing mechanistic insight into p38α allostery and suggesting viable opportunities for the rational design of allosteric modulators of MAP kinases.
Abstract
Kinases are major drug targets especially in cancer therapy. However, the high degree of conservation of their active sites hinders the development of selective inhibitors, motivating a deeper understanding of kinase conformational ensembles and allosteric communication pathways. Here, we use dynamical network analysis to identify key residues involved in a dynamic allostery between the N- and C-lobes that connects the major functional units of the MAP kinase p38α. By combining NMR spectroscopy, activity assays, and in silico analysis of wildtype protein and mutants in the presence or absence of an active-site inhibitor, we experimentally validate the obtained architecture with respect to global protein motion and long-range allosteric modulation. Notably, the identified network highlights communication pathways across several functional sites, prominently involving the allosteric site, the activation loop, and even the lipid-binding domain with its embedded cryptic pocket in the C-lobe. These findings provide mechanistic insight into p38α allostery and suggest viable opportunities for the rational design of allosteric modulators of MAP kinases. Here, the authors apply dynamic network analysis, alongside a set of experimental validations, to probe correlated motions within p38α kinase. The data corroborate communication between its N- and C-lobes, including in particular the lipid pocket.