Comparative in silico study of the differences in the structure and ligand interaction properties of three alpha-expansin proteins from Fragaria chiloensis fruit

Abstract

Expansins are cell wall proteins associated with several processes, including changes in the cell wall during ripening of fruit, which matches softening of the fruit. We have previously reported an increase in expression of specific expansins transcripts during softening of Fragaria chiloensis fruit. Here, we characterized three α-expansins. Their full-length sequences were obtained, and through qRT-PCR (real-time PCR) analyses, their transcript accumulation during softening of F. chiloensis fruit was confirmed. Interestingly, differential but overlapping expression patterns were observed. With the aim of elucidating their roles, 3D protein models were built using comparative modeling methodology. The models obtained were similar and displayed cellulose binding module(CBM ) with a β-sandwich structure, and a catalytic domain comparable to the catalytic core of protein of the family 45 glycosyl hydrolase. An open groove located at the central part of each expansin was described; however, the shape and size are different. Their protein–ligand interactions were evaluated, showing favorable binding affinity energies with xyloglucan, homogalacturonan, and cellulose, cellulose being the best ligand. However, small differences were observed between the protein–ligand conformations. Molecular mechanics-generalized Born-surface area (MM-GBSA) analyses indicate the major contribution of van der Waals forces and non-polar interactions. The data provide a dynamic view of interaction between expansins and cellulose as putative cell wall ligands at the molecular scale.

Communicated by Ramaswamy H. Sarma

Keywords:

• plant cell wall
• molecular modeling
• molecular dynamics simulations
• fruit ripening
• RT-qPCR

Acknowledgements

We thank Dr. Andrew Allan ([email protected]) from the Plant & Food Research from New Zealand for critical reading of the manuscript. F.V-R and R.L. acknowledges Universidad de Talca for a doctoral scholarship. We acknowledge the helpful comments and suggestions made by the anonymous reviewers and the editor of this manuscript.

Disclosure statement

No potential conflict of interest was reported by the authors.

Additional information

Funding

This work was supported by FONDECYT [grants number 11150543, 1171530], CONICYT Anillo [grant number ACT-1110]. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.