In silico and structure-based assessment to classify VUS identified in the α-helical domain of BRCA2

• Published in: Journal of biomolecular structure & dynamics 2023-11, Vol.41 (19), p.9879-9889
• Main Authors: Khan, Mudassar Ali, Varma, Ashok K
• Format: Article
• Language: English
• Subjects: BRCA2; molecular dynamics simulation; PCA; VUS; α-helical domain
• ISSN: 0739-1102; 1538-0254
• DOI: 10.1080/07391102.2022.2148127

Breast cancer type 2 susceptibility (BRCA2) protein plays a crucial role in DNA double-strand breaks repair mechanism by homologous recombination. Pathogenic mutations in the BRCA2 gene confer an increased risk of hereditary breast and ovarian cancer (HBOC). Different missense mutations are identified from a larger cohort of patient populations in the BRCA2. However, most missense mutations are classified as 'Variants of Uncertain Significance' (VUS) due to a lack of data from structural, functional, and clinical assessments. Therefore, this study focused on assessing VUS identified in the α-helical domain of h-BRCA2 using different in silico tools and structure-based molecular dynamics simulation. A total of 286 identified VUS were evaluated using Align-GVGD, PROVEAN and PANTHER servers and 18 variants were predicted to be pathogenic. Further, out of 18 variants analyzed using the ConSurf server, 16 variants were found to be evolutionary conserved. These 16 conserved variants were submitted to PremPS and Dynamut server to assess the effect of the mutation at the protein structure level; 12 mutations were predicted to have a destabilizing effect on the native protein structure. Finally, molecular dynamics simulations revealed 5 variants BRCA2 Cys2646Tyr, Asp2665Val, Trp2619Arg, Trp2619Ser and Tyr2660Cys can alter the folding pattern and need further validation using in vitro, structural and in vivo studies to classify as pathogenic. Communicated by Ramaswamy H. Sarma