Computational characterization and molecular dynamics simulation of the thermostable direct hemolysin-related hemolysin (TRH) amplified from Vibrio parahaemolyticus. (February 2019)

• Record Type: Journal Article
• Authors: Paria, Prasenjit; Chakraborty, Hirak Jyoti; Behera, Bijay Kumar; Das Mohapatra, Pradeep Kumar; Das, Basanta Kumar
• Is Part Of: Microbial pathogenesis. Volume 127(2019)
• Page Start: 172
• Page End: 182
• Publication Date: 2019-02
• Subjects: Vibrio parahaemolyticus -- Thermostable direct hemolysin-related hemolysin -- Comparative modelling -- Molecular dynamics simulations -- Protein pocket; Pathogenic microorganisms -- Periodicals; Pathology, Molecular -- Periodicals; Communicable Diseases -- microbiology -- Periodicals; Communicable Diseases -- parasitology -- Periodicals; Micro-organismes pathogènes -- Périodiques; Pathologie moléculaire -- Périodiques; Electronic journals; 616.9041
• DOI: 10.1016/j.micpath.2018.11.037
• Languages: English
• ISSNs: 0882-4010

Abstract

Abstract: Vibrio parahaemolyticus is a major seafood-borne pathogen that causes life-threatening gastroenteric diseases in humans through the consumption of contaminated seafoods. V. parahaemolyticus produces different kinds of toxins, including thermostable direct hemolysin (TDH), TDH-related hemolysin (TRH), and some effector proteins belonging to the Type 3 Secretion System, out of which TDH and TRH are considered to be the major factors for virulence. Although TRH is one of the major virulent proteins, there is a dearth of understanding about the structural and functional properties of this protein. This study therefore aimed to amplify the full length trh gene from V. parahaemolyticus and perform sequence-based analyses, followed by structural and functional analyses of the TRH protein using different bioinformatics tools. The TRH protein shares significant conservedness with the TDH protein. A multiple sequence alignment of TRH proteins from Vibrio and non- Vibrio species revealed that the TRH protein is highly conserved throughout evolution. The three dimensional (3D) structure of the TRH protein was constructed by comparative modelling and the quality of the predicted model was verified. Molecular dynamics simulations were performed to understand the dynamics, residual fluctuations, and the compactness of the protein. The structure of TRH was found to contain 19 pockets, of which one (pocket ID: 2) was predicted to be important from the view of drug design. Eleven residues (E138, Y140, C151, F158, C161, K162, S163, and Q164), which are reported to actively participate in the formation of the tetrameric structure, were present in this pocket. This study extends our understanding of the structural and functional dynamics of the TRH protein and as well as provides new insights for the treatment and prevention of V. parahaemolyticus infections. Graphical abstract: Image 1 Highlights: trh gene was amplified from V. parahaemolyticus, which is a virulent gene associated with gastroenteric diseases in humans. Homology driven 3D structure of TRH protein has been predicted to understand the functionality of the protein. MD simulation of TRH protein was performed to understand the dynamic nature, residual fluctuation and compactness of protein. Protein pockets were identified which could be used as a drug target site.