Bioinformatic analysis of the VacA protein of helicobacter pylori
Objective To understand the structure and function of vacuolating cytotoxin A(VacA)of helicobacter pylori,and to analyze its epitopes.Methods The bioinformatics software ORF Finder,Protpapram,ProtScale,Cell-PLoc 2.0,SignalP-6.0,TMHMM-2.0,NetNGlyc-1.0,NetPhos and B-3.1.SOPMA,SWISSMODEL,IEDB,SYFPEITHI and STRING were used to predict the physical and chemical properties,hydrophobic,subcellular localization,signal peptide,transmembrane region structure,glycosylation and phosphorylation sites,structure,antigen determination cluster,B cells,Th cell epitopes and interacting proteins.Results VacA protein consisted of 747 amino acids with the formula C3549H5597N1009O1111S9 and a total of 11 275,encoding 3 867 bp,isoelectric point 9.33,instability index 18.53,aliphatic amino acid index 82.40,and an average hydrophobicity of-0.342.The protein had a transmembrane region without a signal peptide,with 12 glycosylation sites and 71 phosphorylation sites.The protein was mainly unregularly coiled(44.03％)and belongs to a stable hydrophilic protein.The VacA protein contained nine B cell epitopes and multiple T cell epitopes.The interacting proteins were cyss and murj.Conclusions VacA can be phosphorylated,which can phosphorylate and interact with multiple proteins,and it can be used as a candidate protein against helicobacter pylori vaccine.
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