Molecular Dynamics Simulations of 53BP1 Structural Mechanisms in DNA Double-Strand Break Repair and Implications for Therapeutic Development

##article.abstract##

DNA double-strand breaks (DSBs) pose significant threats to genomic integrity, requiring precise repair mechanisms to maintain cellular health. 53BP1 serves as a critical regulator of DSB repair pathway choice, promoting non-homologous end joining (NHEJ) while inhibiting homologous recombination (HR). Despite extensive research on 53BP1 function, comprehensive understanding of its structural-functional relationships and dynamic regulation mechanisms remains limited. This study employed 3D computational molecular dynamics simulations using UCSF ChimeraX to elucidate the mechanistic, structural, and functional features of 53BP1 in DNA repair processes. Protein structures were obtained from the Protein Data Bank, with homology modeling applied where necessary to examine 53BP1 domain interactions with histone modifications and effector proteins. Simulations revealed stable, specific binding between the Tudor domain and dimethylated histone H4 lysine 20 (H4K20me2) with high affinity (Kd ≈ 20 nM), confirming its recruitment mechanism to damaged chromatin. The flexibility of BRCT repeats and oligomerization domains demonstrated their crucial role in forming liquid-like condensates at DSB sites, creating microenvironments that concentrate repair factors. Phosphorylation-dependent interactions with RIF1 and PTIP were validated through binding interface analysis, supporting experimental findings on regulatory mechanisms. These structural insights bridge existing knowledge gaps and provide a foundation for targeted bioengineering strategies in therapeutic development for genomic instability-related diseases, particularly cancer. The integration of computational modeling with experimental data offers new perspectives for understanding 53BP1's multifaceted role in maintaining genomic stability.