Unlocking the Conformational Secrets of DYRK1A Kinase With Computational Microscope: Exploring Phosphorylation-Driven Structural Dynamics

Abstract

The intricate world of cellular processes relies significantly on the dual-specificity tyrosine-phosphorylation-regulated kinase (DYRK) family of kinases, governing vital functions like brain development, splicing regulation, and apoptosis. DYRK1A, in particular, stands at the center of attention due to its pivotal role. Disruptions in its activity, whether through upregulation or downregulation, have profound implications, notably in neurological disorders and cancer progression. Understanding the impact of phosphorylation, a fundamental post-translational modification, on DYRK1A is paramount. In this study, we delved into the complex interplay of phosphorylation and the effects of the abemaciclib inhibitor on DYRK1A conformational dynamics. We employed advanced techniques such as molecular dynamics simulations and the molecular mechanics Poisson-Boltzmann surface area (MM/PBSA) scheme and deciphered the intricate dance of DYRK1A's structural elements during phosphorylation. Our exploration revealed intriguing details: the αC-helix undergoing outward movement, a distorted αC-helix, a wide-open P-loop, extended A-loop, and role of electrostatic interactions shaping A-loop dynamics. Notably, the interaction of specific residues, particularly Lys188, forming robust salt bridges with Asp307 and Glu203, plays a pivotal role in shaping the structure of the protein. Diving deeper, we conducted principal component analysis and conformational free energy sampling to uncover crucial structural intermediates. Moreover, our dynamic cross-correlation map sheds light on the influence of phosphorylation by enhancing coordinated movements while dampening anti-correlated motions across various domains. This nuanced understanding of DYRK1A kinase activation, driven by phosphorylation, not only enriches our knowledge but also holds promise in the development of targeted therapies for associated diseases. © 2025 Wiley Periodicals LLC.