STRUCTURAL ANALYSIS OF PLASMID-MEDIATED VEROTOXIN GENE PRODUCING NON-O157 ESCHERICHIA COLI USING MOLECULAR DYNAMIC SIMULATIONS

Authors

  • md FAZLUL karim KHAN
  • Shah Samiur Rashid Universiti Malaysia Pahang
  • Aizi Nor Mazila Ramli Faculty of Industrial Sciences Technology, Universiti Malaysia Pahang, Gambang, 26300 Pahang, Malaysia
  • Muhammad Nomani Kabir Faculty of Computing, Universiti Malaysia Pahang, Pahang, Malaysia
  • Mohammad Nazmul Hasan Maziz Graduate School of Medicine, Perdana University, Wisma Chase Perdana, Changkat Semantan, Damansara Heights, 50490 Kuala Lumpur, Malaysia

DOI:

https://doi.org/10.15414/jmbfs.4142

Keywords:

Verotoxin gene, Molecular dynamic simulations, Gromacs, Non-O157 E. coli

Abstract

Plasmid-mediated Non-O157 VTEC is a pathogenic E. coli serotype, are responsible for many life-threatening diseases such as diarrhoea. The thermostable crystal structure has been widely sought after for industry and therapeutic applications through the structural analysis. The National Center for Biotechnology Information (NCBI) Genbank Database has been sourced to obtain plasmid-mediated Verotoxin genes producing non-O157 MN 696158 (Vtx1-1) and MN688720 (Vtx2) sequences. The tertiary structure of MN696158 (Vtx1-1) and MN688720 (Vtx2) was generated by operating MODELLER. The result exposed multiple templates during modelling processes have improved the local stereochemical quality of the produced models. The structural analysis also disclosed the similarities and differences between the models (Vtx1-1 and Vtx2). Furthermore, the thermal stability profile of plasmid-mediated non-O157 VTEC were studied. The molecular dynamics simulations of plasmid-mediated non-O157 VTEC structures (Vtx1-1 and Vtx2) illustrated the interactions between amino acids. On the other hand, Vtx1-1 and Vtx2 showed noticeable differences in their relative conformational flexibility and stability at elevated temperature. However, it is expected that the information of the thermal stable of plasmid-mediated non-O157 VTEC models can be used for potential vaccine candidate through protein engineering in future.

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Published

2021-08-01

How to Cite

KHAN, md F. karim, Shah Samiur Rashid, Aizi Nor Mazila Ramli, Muhammad Nomani Kabir, & Mohammad Nazmul Hasan Maziz. (2021). STRUCTURAL ANALYSIS OF PLASMID-MEDIATED VEROTOXIN GENE PRODUCING NON-O157 ESCHERICHIA COLI USING MOLECULAR DYNAMIC SIMULATIONS. Journal of Microbiology, Biotechnology and Food Sciences, 11(1), e4142. https://doi.org/10.15414/jmbfs.4142
Received 2020-12-28
Accepted 2021-02-24
Online Published 2021-08-01