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. (January 2021)

• Record Type: Journal Article
• Authors: Dutta, Debabrata; Awon, Vivek Kumar; Gangopadhyay, Gaurab
• Is Part Of: Physiological and molecular plant pathology. Volume 113(2021)
• Publication Date: 2021-01
• Subjects: R-Protein -- NB-ARC -- Amino acid substitution -- ADP -- Docking -- H-bond interaction -- Binding affinity -- Sesame; Plant diseases -- Periodicals; Diseased plants -- Physiology -- Periodicals; Phytopathogenic microorganisms -- Host plants -- Periodicals; 632
• DOI: 10.1016/j.pmpp.2020.101588
• Languages: English
• ISSNs: 0885-5765

Abstract

Abstract: 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. Highlights: NB-ARC domain contains conserved Phosphate binding loop and GLPL motif which interacts with ADP to activate R-proteins. Substitution of second and third glycine of P -loop alters ligand binding and affinity. Amino acids substitution effects hydrogen bond and electrostatic interactions between ADP and NB-ARC domain. The expression of R-gene encoding the Hyp-R protein is correlated with Macrophomina phaseolina infection in sesame.