Three dimensional structure prediction and ligand-protein interaction study of expansin protein ATEXPA23 from Arabidopsis thaliana L.

Basu, Anamika ; Sarkar, Anasua ; Maulik, Ujjwal ; Basak, Piyali

Abstract

Arabidopsis thaliana L. is a small flowering plant that is widely used as a model organism in plant biology. In the present study, we study the peripheral membrane protein ATEXPA23 from Arabidopsis thaliana L. using homology modelling and molecular docking. The microarray analysis shows expression of ATEXPA23 (AT5G39280) protein, which leads to loosening and extension of plant cell walls. This protein is differentially expressed during different stages of plant embryogenesis. It contains one expansin-like CBD domain and one expansin-like EG45 domain. ATEXPA23 belongs to the expansin family in expansin a subfamily. The 3D model after refinement is used to explore the xyloglucan binding characteristics of ATEXPA23 using AutoDock. The docking analysis shows that the surface exposed aromatic amino acid residues Phe 193 and Phe 265 interact with ligand xyloglucan through CH-л interaction. The binding energy values of docking reflect a stable conformation of the docked complex. The interaction of expansin protein with carbohydrate xyloglucan, present in hemicellulose structures of plant cell wall, is thoroughly analysed with cellotetrose and xyloglucan heptasaccharide using electrostatic potential calculation. This CH-л non-covalent interaction predominates on the cellulose-xyloglucan interaction in plant cell wall during cell growth.

Keyword(s)

ATEXPA23, CH-л interaction; Molecular docking; Molecular modelling

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