A description of the structural and functional impacts of the SCID- and OS-associated variants on RAG1 through MD simulations.

UNLABELLED: The immune system is the body's defense mechanism that uses cells and organs to protect against foreign substances called pathogens. The absence or dysfunction of elements within immune system lead to immune diseases such as severe combined immunodeficiency (SCID). SCIDs are hereditary disorders that are characterized and sub-classified by an impaired number and function of T and B cells as T-B + SCID and T-B-SCID. The association between varied SCID phenotypes, including Omenn Syndrome, in clinics has been revealed with the presence of missense mutatinos in RAG1 gene. Here, we aim to understand the structural impacts of varied SCID phenotypes associated variants in RAG1 by utilizing in silico tools, molecular dynamics simulations and docking studies. Along 100 ns, classical MD simulations are run with mutant RAG1 complexes, including Arg396Leu(rs104894291), Arg396His(rs104894291), Val433Met(rs199474679), Met435Val(rs141524540), Arg474His(rs199474686), Arg474Cys(rs199474678), Trp522Cys(rs193922461), Glu722Lys(rs28933392), Arg778Gln(rs121918569), and Arg975Trp(rs121918570). Any structural alterations experienced in RAG1 due to presence of these missense variants were studied together with the change in RAG1-RAG2 protein-protein binding dynamics and 12-RSS heptamer/23-RSS nanomer bindings to RAG1 to understand the functional impacts of these missense variants on RAG1. These calculations have suggested that Arg396Leu(rs104894291), Arg474His(rs199474686), Arg474Cys(rs199474678), and Glu722Lys(rs28933392) have resulted in more drastic alterations in RAG1's structure and function compared to others. We ended up with the theoretical background constituted by molecular dynamics simulations and docking calculations for each SCID or atypic SCID (Omenn Syndrome). Our calculations would be further utilized to design a novel molecule or to run drug repurposing to ensure the proper functioning of mutant RAG1. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at https://doi.org/10.1007/s40203-026-00725-1.