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

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.