Comprehensive structural and functional analyses of RAD50 nsSNPs: from prediction to impact assessment.

Area of Science:

• Genetics and Genomics
• Molecular Biology
• Cancer Research

Background:

• The RAD50 gene is crucial for the MRN complex, which manages DNA double-strand break (DSB) responses and maintains genome stability.
• RAD50 is associated with breast cancer, highlighting the need to understand its functional variants.
• This study focuses on non-synonymous single-nucleotide polymorphisms (nsSNPs) in RAD50 and their effects on protein structure and MRN complex interactions.

Purpose of the Study:

• To analyze the functional impact of nsSNPs in the RAD50 gene.
• To assess how these nsSNPs affect RAD50 protein structure, stability, and interactions within the MRN complex.
• To explore the implications of RAD50 nsSNPs for DNA repair, genome stability, and breast cancer pathophysiology.

Main Methods:

• Computational analysis of 1,806 nsSNPs using tools like ConSurf to identify conserved and damaging variants.
• Protein structure prediction using AlphaFold, RoseTTAFold, and I-TASSER, and secondary structure prediction with GOR-IV.
• Assessment of nsSNP impact on RAD50-Mre11A interactions using HADDOCK docking and molecular dynamics simulations.

Main Results:

• Several pathogenic RAD50 nsSNPs were identified that significantly alter protein stability and interactions with Mre11A.
• Mutant profiles (e.g., A73P, V117F, L518P, L1092R, N1144S, A1209T) showed substantial changes in interaction patterns.
• These alterations suggest potential disruptions in DNA repair mechanisms and compromised genome stability.

Conclusions:

• The study elucidates the role of RAD50 mutations in breast cancer development.
• Identified nsSNPs provide insights into the molecular mechanisms underlying RAD50's contribution to cancer pathophysiology.
• Findings may inform therapeutic strategies targeting RAD50 mutation-deficient cancer cells.