PMID- 30547672
OWN - NLM
STAT- MEDLINE
DCOM- 20200422
LR  - 20200422
IS  - 1557-8666 (Electronic)
IS  - 1066-5277 (Linking)
VI  - 26
IP  - 2
DP  - 2019 Feb
TI  - In Silico Characterization of B Cell and T Cell Epitopes for Subunit Vaccine 
      Design of Salmonella typhi PgtE: A Molecular Dynamics Simulation Approach.
PG  - 105-116
LID - 10.1089/cmb.2018.0010 [doi]
AB  - Typhoid fever is an acute illness in humans, caused by Salmonella typhi, a 
      gram-negative bacterium. Outer membrane proteins of S. typhi have strong 
      potential for its use in the development of subunit vaccine against typhoid. In 
      the current study, peptide-based subunit vaccine was constructed from outer 
      membrane protease E (PgtE) against S. typhi. B cell and T cell epitopes were 
      identified at fold level with a validated three-dimensional modeled structure. T 
      cell epitopes from PgtE (IHPDTSANY) have 99.5% binding to a maximum number of 
      major histocompatibility complex class I and class II alleles. They also bind to 
      the typhoid-resistant human leukocyte antigen (HLA) alleles DRB1*0401. PgtE 
      epitopes were docked with HLA-DR4 (PDB ID: 1D5M) and a contact map was 
      constructed. A simulation search for the binding site for full flexibility of the 
      peptide from CABS- (C(alpha), C(beta), side-chain)-dock shows stable interactions. 
      Molecular dynamics simulation studies revealed that the PgtE-epitope complex 
      structure was more stable throughout the simulation (20 ns) and interaction did 
      not change the radius of gyration. In conclusion, computational analysis, 
      molecular docking, and molecular dynamics (MD) simulation of PgtE-epitope complex 
      were used to elucidate the binding mode, and the dynamical changes of epitopes 
      were more suitable for vaccine development against typhoid.
FAU - Samykannu, Gopinath
AU  - Samykannu G
AD  - 1 Structural Biology Laboratory, Department of Bioinformatics, Bharathiar 
      University , Coimbatore, India .
FAU - Vijayababu, Princy
AU  - Vijayababu P
AD  - 1 Structural Biology Laboratory, Department of Bioinformatics, Bharathiar 
      University , Coimbatore, India .
FAU - Antonyraj, Christian Bharathi
AU  - Antonyraj CB
AD  - 2 Centre for Bioinformatics, Pondicherry University , Pondicherry, India .
FAU - Perumal, Perumal
AU  - Perumal P
AD  - 3 Membrane Protein Biology Group, International Centre for Genetic Engineering 
      and Biotechnology , New Delhi, India .
FAU - Narayanan, Sundarabaalaji
AU  - Narayanan S
AD  - 1 Structural Biology Laboratory, Department of Bioinformatics, Bharathiar 
      University , Coimbatore, India .
FAU - Basheer Ahamed, Syed Ibrahim
AU  - Basheer Ahamed SI
AD  - 2 Centre for Bioinformatics, Pondicherry University , Pondicherry, India .
FAU - Natarajan, Jeyakumar
AU  - Natarajan J
AD  - 4 Data Mining and Text Mining Laboratory, Department of Bioinformatics, 
      Bharathiar University , Coimbatore, India .
LA  - eng
PT  - Journal Article
DEP - 20181214
PL  - United States
TA  - J Comput Biol
JT  - Journal of computational biology : a journal of computational molecular cell 
      biology
JID - 9433358
RN  - 0 (Bacterial Outer Membrane Proteins)
RN  - 0 (Epitopes)
RN  - 0 (HLA-DR4 Antigen)
RN  - 0 (Salmonella Vaccines)
RN  - 0 (Vaccines, Subunit)
SB  - IM
MH  - B-Lymphocytes/immunology
MH  - Bacterial Outer Membrane Proteins/chemistry/immunology
MH  - Epitopes/*chemistry/immunology
MH  - HLA-DR4 Antigen/*chemistry/immunology
MH  - Humans
MH  - *Molecular Docking Simulation
MH  - Salmonella Vaccines/chemistry/*immunology
MH  - Salmonella typhi/immunology
MH  - Software
MH  - T-Lymphocytes/immunology
MH  - Vaccines, Subunit
OTO - NOTNLM
OT  - CABS-dock
OT  - PgtE
OT  - Salmonella typhi
OT  - epitope
OT  - peptide-docking
EDAT- 2018/12/15 06:00
MHDA- 2020/04/23 06:00
CRDT- 2018/12/15 06:00
PHST- 2018/12/15 06:00 [pubmed]
PHST- 2020/04/23 06:00 [medline]
PHST- 2018/12/15 06:00 [entrez]
AID - 10.1089/cmb.2018.0010 [doi]
PST - ppublish
SO  - J Comput Biol. 2019 Feb;26(2):105-116. doi: 10.1089/cmb.2018.0010. Epub 2018 Dec 
      14.