糖心原创

Structural and Molecular Docking Analysis of Gibberellin Insensitive Dwarf1 (Gid1) Receptors of Abaca

Rhosener Bhea L. Koh | Vermando M. Aquino

 

Abstract:

The abaca is an economically important fiber crop; however, knowledge of the molecular mechanisms behind fiber development is limited. Gibberellins or gibberellic acids (GA) are plant growth regulators known to regulate fiber cell development in various fiber crops. GA perception in land plants is mediated by the GA receptor, GIBBERELLIN INSENSITIVE DWARF1 (GID1). GA binds to GID1 via the GA binding pocket and activates the GA-response pathway through the association of the GA-GID1 complex with the DELLA inhibitor protein. The degradation of the DELLA protein activates the transcription of GA-response genes. Recently, three abaca GID1 (MtGID1) genes were cloned and sequence analysis revealed them to be GA receptors. The study, therefore, aims to predict the 3D protein structures of the three MtGID1 proteins (MtGID1-1, MtGID1-2, and MtGID1-3) through homology modeling and to conduct protein docking analysis with DELLA protein and GA ligands. Homology modeling revealed the top structural analogs to be Arabidopsis thaliana GID1 (AtGID1a) receptor with the conservation of GID1 core domain structure and N-terminal extension lid structure. Superimposing the three MtGID1 structures showed the location of the loop variable region that connects the N-terminal lid to the GID1 core domain with MtGID1-3 having the shortest loop region among the MtGID1 proteins. Docking of MtGID1 proteins with AtDELLA showed interaction of the N-terminal lid of the three MtGID1 proteins to the DELLA motifs and resulted in negative binding affinity values indicating the spontaneous formation of the MtGID1-AtDELLA complex. Protein-ligand docking analysis of MtGID1 proteins with bioactive GA molecules showed the residues that are canonically determined to be involved in GA-binding pocket and N-terminal lid closure. These findings suggest that the identified GID1 proteins are bona fide GA receptors of abaca and are capable of activating the GA-GID1-DELLA signaling pathway in abaca.