Markov State Models and Molecular Dynamics Simulations Reveal the Conformational Transition of the Intrinsically Disordered Hypervariable Region of K‑Ras4B to the Ordered Conformation

K-Ras4B, the most frequently mutated Ras isoform in human
tumors,
plays a vital part in cell growth, differentiation, and survival.
Its tail, the C-terminal hypervariable region (HVR), is involved in
anchoring K-Ras4B at the cellular plasma membrane and in isoform-specific
protein–protein interactions and signaling. In the inactive
guanosine diphosphate-bound state, the intrinsically disordered HVR
interacts with the catalytic domain at the effector-binding region,
rendering K-Ras4B in its autoinhibited state. Activation releases
the HVR from the catalytic domain, with its ensemble favoring an ordered
α-helical structure. The large-scale conformational transition
of the HVR from the intrinsically disordered to the ordered conformation
remains poorly understood. Here, we deploy a computational scheme
that integrates a transition path-generation algorithm, extensive
molecular dynamics simulation, and Markov state model analysis to
investigate the conformational landscape of the HVR transition pathway.
Our findings reveal a stepwise pathway for the HVR transition and
uncover several key conformational substates along the transition
pathway. Importantly, key interactions between the HVR and the catalytic
domain are unraveled, highlighting the pathogenesis of K-Ras4B mild
mutations in several congenital developmental anomaly syndromes. Together,
these findings provide a deeper understanding of the HVR transition
mechanism and the regulation of K-Ras4B activity at an atomic level.