Microbiology, Metabolites and Biotechnology

Microbiology, Metabolites and Biotechnology

In silico prediction of the three-dimensional structure of the antimicrobial peptide Fa-AMP1 using a multi-tool approach and peptide-ligand docking

Document Type : Research Paper

Authors
Sahba Toosi 1
Farhad Shokouhifar 2
Saeid Malekzadeh Shafaroudi 1
Mojtaba Mamarabadi 2
Nasrin Moshtaghi 1
1 Department of Biotechnology and Plant Breeding, Faculty of Agriculture, Ferdowsi University of Mashhad. Mashhad. Iran.
2 Department of Plant Protection, Faculty of Agriculture, Ferdowsi University of Mashhad. Mashhad. Iran.
10.22104/mmb.2025.7898.1186
Abstract
The Fa-AMP1 peptide from buckwheat (Fagopyrum esculentum Moench) seed germ and 40 amino acid long has previously been reported to exhibit potent antifungal and antibacterial effects. The availability of the three-dimensional structure of this peptide could be very useful in investigating its antimicrobial function, but crystallographic information of this peptide is not available so far. The aim of the present study was to determine the three-dimensional structure of the Fa-AMP1 peptide using a comprehensive approach so that advanced modeling tools such as AlphaFold, SwissModel, and D-I-TASSER were predicted and evaluated. The predicted models were compared using validation tools QMEAN, Verify3D, WHATCHEC. The geometric position of amino acids in all three models was examined by drawing Ramachandran plots. The distance of all three models from each other was compared using the RMSD index, and the number and position of alpha-beta-coil folds were also compared as well as the position of disulfide bonds. Overall, the results showed that, the models presented by the AlphaFold and SwissModel tools have high convergence with each other, and the model presented by the D-I-TASSER tool also showed high similarity with the other two models, but did not show the necessary accuracy in the configuration of cysteine amino acids and the formation of expected disulfide bonds. In the second part of the article, the Swiss docking tool was used to investigate the interaction between the model predicted by alpha-fold and chitin as a target ligand which sourced from fungal cell wall. The docking results were analyzed based on the position of amino acids involved in binding to the ligand in the five complexes runs with the peptide model. The docking results showed that the model presented by AlphaFold in the fourth run of the results presented by Swiss docking can be placed at an appropriate distance from each other with the amino acids related to the binding site in the Fa-AMP1 peptide and the four amino acids form hydrogen bonds with the NAG1 and 2 monomers. In future studies, this prediction can be investigated by conducting additional molecular dynamics (MD) simulations.
Keywords
AlphaFold
AutoDock Vina
D-I-TASSER
Molecular Docking
SwissModel
Subjects
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Microbiology, Metabolites and Biotechnology
Volume 8, Issue 2
November 2025
Pages 106-120