Demystifying the implications of disease-susceptible missense SNPs within CTLA-4 ligand binding domain and its...

Alteration of a nucleotide within a triplet codon results in substitution of a different amino acid in the protein sequence, collectively termed as missense or non-synonymous Single-Nucleotide Polymorphisms (nsSNPs). Cytoplasmic T Lymphocytes Antigen-4 (CTLA-4) gene encodes a transmembrane protein expressed on activated T cells. CTLA-4 receptor acts as an immunoregulatory molecule that prompts immunological self-tolerance by rapidly inhibiting T cell-mediated immune responses, via inactivation and elimination of T cells. Polymorphism within CTLA-4 coding region could efficiently disrupt trans-endocytosis process by decreasing its interaction towards B7 ligands (B7-1: CD80 and B7-2: CD86) molecules expressed on Antigen Presenting Cells (APCs). In the present study, we utilized several computational techniques to predict the highly disease-susceptible nsSNPs that potentially impact on structure and function of CTLA-4 protein. Followed by computational docking and Molecular Dynamics (MD) simulations for CTLA-4/CD80 protein complex were conducted. Our research findings reveal that seventeen nsSNPs were found to be highly pathogenic and structurally destabilizing CTLA-4 protein. Subsequently, an evolutionary ConSurf profile reveals that nine nsSNPs were highly conserved and also affect bio-physicochemical properties, three-dimensional RNA structure, post-translational modification sites, secondary and tertiary structure of CTLA-4 protein. Molecular docking of CTLA-4/CD80 protein complex indicates that rs1553657429-P137L and rs1356678649-N145H nsSNPs have efficiently decreased the binding affinity towards B7-1 protein. The MD simulation also reveal CTLA-4 P137L, located within ligand-binding domain (MYPPPY motif) and N145H at N-glycosylation site, were significantly considered to be high-risk nsSNPs that interfere association with B7-1 protein by decreasing structural stability and flexibility of CTLA-4 protein.