Amino acid substitution in the conserved motifs of a hypothetical R-protein in sesame imparts a significant effect on ADP binding position and hydrogen bond interaction

The Resistant (R) proteins play a fundamental role in the innate immunity of plants. Most of these R-proteins have centrally located NB-ARC domain which regulates the R-protein by NTPase activity. Though the effect of amino acid substitution in RNBS, MHD motifs of the NB-ARC domain has been studied in detail, the P-loop motif remains still less explored. With the help of in-silico analysis of a hypothetical R-protein (Hyp-R) in sesame, we tested the hypothesis that how amino acid substitution in the conserved P-loop motif can affect the interaction between ligand and NB-ARC domain. We report I188G, I188V, T192P substitution in P-loop motif and V356S adjacent to GLPL motif in three different sesame genotypes. Docking results and atomic interaction analysis revealed a cumulative effect of these substitutions on the hydrogen bond interactions, which in turn impart effects on ligand binding affinity in Sesamum indicum (−6.6 kcal/mol), Sesamum mulayanum (−7.3 kcal/mol) and recombinant line (−7.5 kcal/mol). We correlated expression of the R-gene encoding Hyp-R protein in sesame after inoculating with Macrophomina phaseolina. This study suggests that amino acid substitution in P-loop and adjacent to GLPL motif have an immense effect on ligand binding affinity.