Phosphorylation and Structural Adaptability of EphA1 SAM Domain

Abstract

Background: Ephrin type-A receptor 1 (EphA1) receptor tyrosine kinase plays a pivotal role in disease development by orchestrating cell-cell communication. Although phosphorylation regulates Eph receptor signaling, its dynamic impact on sterile alpha motif (SAM) domain conformation and function remains poorly understood. This study integrates molecular dynamics simulations with biophysical analyses to explore how phosphorylation reprograms structural landscape of EphA1 SAM domain. Methods: The wild-type SAM domain phosphorylation sites were computationally predicted, and molecular dynamics simulations were performed for both phosphorylated and non-phosphorylated states. Trajectory analyses were performed to characterize conformational stability and dynamics. Results: Simulations reveal that phosphorylation at conserved residues destabilizes the domain, disrupts helical architecture, and elevates structural flexibility. Phosphorylated structures showed significantly higher atomic deviations and lower TM-scores compared to non-phosphorylated structures, along with increased residual fluctuations and solvent accessibility. Principal component and clustering analyses confirmed that phosphorylation expands the conformational space sampled by domain. These conformational shifts expose cryptic interaction surfaces, enabling recruitment of non-canonical effectors. Comparative analyses highlight divergence from related Eph receptors, with EphA1 prioritizing conformational heterogeneity over binary state switching, reflecting evolutionary adaptation to context-dependent signaling. Conclusion: This work advances beyond static structural models, capturing phosphorylation-induced states thereby redefining SAM domains as dynamic allosteric hubs. These insights not only elucidate EphA1 regulation but also establish a framework to study dynamic post-translational modifications in other signaling systems and bridge computational predictions with therapeutic innovation.