Integrated Structural and Dynamic Analysis Reveals Destabilizing Effects of KRAS Missense Variants Associated with...

Given the established oncogenic role of KRAS in lung cancer and its predicted regulation by hsa-miR-134 and transcription factors (NCOA4, NR3C2, ETS2), we systematically catalogued genetic variation across the KRAS gene. In this study, we identified 21,598 SNPs, of which 475 were missense (2.19%), 580 were synonymous (2.68%), and 18,093 were intronic (83.77%). In silico prioritization combined with cross-validation in TCGA-LUAD and MSK-IMPACT cohorts identified four high-confidence deleterious variants (G13C, G13D, G60S, G60V), confirming the recurrence of G13C/G13D and highlighting the fully conserved switch II residue G60 as a structurally distinctive candidate. In MD simulations, G60S showed the largest conformational displacement (RMSD ≈ 8-9 Å), elevated per-residue flexibility (residues 28-37: 1.90 → 2.99 Å), increased terminal Rg, and reduced hydrogen-bond occupancy, suggesting localized, mutation-specific perturbations within the G-domain. In contrast, G13D maintained near-wild-type dynamics, indicating that functional impairment may not require global structural destabilization. Consistent ensemble analyses (PCA, DCCM, FEL) revealed a dominant single-mode rearrangement for G60S (PC1 ≈ 50.8%), a heterogeneous multi-state landscape for G60V, and a restricted low-energy ensemble for G13D, supporting distinct, position-specific mechanisms. Gene-gene and protein-protein interaction analyses linked KRAS to multiple signaling partners, GO and KEGG enrichment analyses associated KRAS with GTPase activity, Rac protein signaling, and the RAS-MAPK and PI3K-AKT pathways implicated in lung cancer progression. Overall, these findings identify G13C, G13D, G60S, and G60V as high-priority candidates for experimental validation and may inform future strategies for genomic risk assessment and mutation-specific therapeutic intervention in lung cancer.