Activating mutations drive human MEK1 kinase using a gear-shifting mechanism

Abstract

There is an unmet need to classify cancer-promoting kinase mutations in a mechanistically cognizant way. The challenge is to understand mutations stabilize different kinase configurations to alter function, and how this influences pathogenic potential of the kinase and its responses to therapeutic inhibitors. This goal is made more challenging by the complexity of the mutational landscape of diseases, and is further compounded by the conformational plasticity of each variant where multiple conformations co-exist. We focus here on the human MEK1 kinase, a vital component of the RAS/MAPK pathway in which mutations cause cancers and developmental disorders called RASopathies. We sought to explore how these mutations alter the human MEK1 kinase at atomic resolution in by utilizing enhanced sampling simulations and free energy calculations. We computationally mapped the different conformational stabilities of individual mutated systems by delineating the free energy landscapes, and showed how this relates directly to experimentally quantified developmental transformation potentials of the mutations. We conclude that mutations leverage variations in the hydrogen bonding network associated with the conformational plasticity to progressively stabilize the active-like conformational state of the kinase while destabilizing the inactive-like state. The mutations alter residue-level internal molecular correlations by differentially prioritizing different conformational states, delineating the various modes of MEK1 activation reminiscent of a gear-shifting mechanism. We define the molecular basis of conversion of this kinase from its inactive to its active state, connecting structure, dynamics, and function by delineating the energy landscape and conformational plasticity, thus augmenting our understanding of MEK1 regulation.

Enhanced Sampling for Conformational Changes and Molecular Mechanisms of Human NTHL1

“…Intriguingly, our simulations also identified a stable "bundle" conformation, which was unexpected to us initially. Through the cluster domain rotation, helices in this domain collapse into the DNA-binding cleft, leading to a structure very similar to the helical "bundles" with the linker region exposed to the solvent as illustrated in 38 to demonstrate the relative stability of each conformation.…”

“…In this conformation, the values of MC10, MC9, and MC1 have drastically changed, demonstrating that the reaction coordinate identified by LINES distinguishes among the open, bundle, and closed conformations. The relative free energy difference between the three energy basins and the open conformation are also calculated by integrating the FES as Δ F E o i = k B T log true( prefix∬ normalexp ( − V b i a s k B T ) .25em normald x .25em normald y true) , to demonstrate the relative stability of each conformation.…”