Mutation of a kinase allosteric node uncouples dynamics linked to phosphotransfer

Abstract

The expertise of protein kinases lies in their dynamic structure, wherein they are able to modulate cellular signaling by their phosphotransferase activity. Only a few hundreds of protein kinases regulate key processes in human cells, and protein kinases play a pivotal role in health and disease. The present study dwells on understanding the working of the protein kinase-molecular switch as an allosteric network of “communities” composed of congruently dynamic residues that make up the protein kinase core. Girvan–Newman algorithm-based community maps of the kinase domain of cAMP-dependent protein kinase A allow for a molecular explanation for the role of protein conformational entropy in its catalytic cycle. The community map of a mutant, Y204A, is analyzed vis-à-vis the wild-type protein to study the perturbations in its dynamic profile such that it interferes with transfer of the γ-phosphate to a protein substrate. Conventional biochemical measurements are used to ascertain the effect of these dynamic perturbations on the kinetic profiles of both proteins. These studies pave the way for understanding how mutations far from the kinase active site can alter its dynamic properties and catalytic function even when major structural perturbations are not obvious from static crystal structures.

A dynamic hydrophobic core orchestrates allostery in protein kinases

“…However, when both the CSPs from amide and methyl probes are combined (fig. S6), it is apparent that the conformational changes involve the enzyme globally as predicted by the molecular dynamics simulations and community map analysis ( 14 , 15 ). …”

Tuning the “violin” of protein kinases: The role of dynamics‐based allostery

“…Mathematically, as the Chladni patterns show the redistribution of vibrations on the violin plate, our “community map” analysis allows for studying the redistribution of dynamics in the protein kinase domain (Fig. ) . In this way, the violin model recapitulates the founding argument of Cooper and Dryden where vibrations/fluctuations from the entire protein would participate in allosteric communication .…”

“…In light of elusive explanations but growing importance of dynamics allostery, we introduced the “violin” model of dynamics‐based allostery with the premise that protein dynamics is robust, malleable to perturbation, and prone to remodeling/redistribution (Fig. ) . It can be argued that this phenomenon can be derived from the fundamental properties of proteins that can be viewed as a set of interacting oscillators .…”

Stability and dynamics interrelations in a Lipase: Mutational and MD simulations based investigations

“…In the case of CM2, the mutation site is near the site of altered dynamics whereas in case of CM1, CM3 and CM4 these are far away in space. Such an observation, though compelling, is not out of line with the literature (40,(51)(52)(53). Such long distance effect is speculated to be through coordinated motion in protein or through alteration of hydrogen bond networks.…”