Molecular docking and dynamics simulation studies uncover the host-pathogen proteinprotein interactions in Penaeus vannamei and Vibrio parahaemolyticus

Rosilan, Nur Fathiah and Mohamad Jamali, Muhamad Arif and Sufira, Siti Aishah and Waiho, Khor and Ismail, Noraznawati and Fazhan, Hanafiah and Sung, Yeong Yik and Mohamed Hussein, Zeti Azura and Abdul Hamid, Azzmer Azzar and Aleng, NorAfiqah (2024) Molecular docking and dynamics simulation studies uncover the host-pathogen proteinprotein interactions in Penaeus vannamei and Vibrio parahaemolyticus. PLOS ONE, 19 (1). ISSN 1932-6203 E-ISSN 1932-6203

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Abstract

Shrimp aquaculture contributes significantly to global economic growth, and the whiteleg shrimp, Penaeus vannamei, is a leading species in this industry. However, Vibrio parahaemolyticus infection poses a major challenge in ensuring the success of P. vannamei aquaculture. Despite its significance in this industry, the biological knowledge of its pathogenesis remains unclear. Hence, this study was conducted to identify the interaction sites and binding affinity between several immune-related proteins of P. vannamei with V. parahaemolyticus proteins associated with virulence factors. Potential interaction sites and the binding affinity between host and pathogen proteins were identified using molecular docking and dynamics (MD) simulation. The P. vannamei-V. parahaemolyticus proteinprotein interaction of Complex 1 (Ferritin-HrpE/YscL family type III secretion apparatus protein), Complex 2 (Protein kinase domain-containing protein-Chemotaxis CheY protein), and Complex 3 (GPCR-Chemotaxis CheY protein) was found to interact with -4319.76,-5271.39, and -4725.57 of the docked score and the formation of intermolecular bonds at several interacting residues. The docked scores of Complex 1, Complex 2, and Complex 3 were validated using MD simulation analysis, which revealed these complexes greatly contribute to the interactions between P. vannamei and V. parahaemolyticus proteins, with binding free energies of -22.50 kJ/mol, -30.20 kJ/mol, and -26.27 kJ/mol, respectively. This finding illustrates the capability of computational approaches to search for molecular binding sites between host and pathogen, which could increase the knowledge of Vibrio spp. infection on shrimps, which then can be used to assist in the development of effective treatment

Item Type:	Article (Journal)
Subjects:	Q Science > QR Microbiology
Kulliyyahs/Centres/Divisions/Institutes (Can select more than one option. Press CONTROL button):	Kulliyyah of Science Kulliyyah of Science > Department of Biotechnology
Depositing User:	AP. Dr. Azzmer Azzar Abdul Hamid
Date Deposited:	10 Sep 2024 08:31
Last Modified:	10 Sep 2024 08:41
URI:	http://irep.iium.edu.my/id/eprint/114333

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