Bioinformatics Analysis of PipD Protein Structure and Epitope of Salmonella Typhimurium PipD
Objective To predict and analyze the structure and antigenic epitopes of Salmonella PipD protein by bioinformatics methods,and to provide a theoretical basis for the diagnosis and treatment of Salmonella-related diseases and the development of vaccines.Methods The nucleotide sequence of Salmonella typhimurium ATCC 14028S standard strain STM14_1240 gene and the amino acid sequence of its encoded protein PipD were obtained by NCBI database.Bioinformatics tools such as ProtParam,ProtScale,SignalP 4.1 Server,TMHMM Serverv.2.0,Netphos 3.1 Server,NetNGlyc-1.0,NCBI BLAST,SOMPA,SWISSMODEL,ABCpred,SYFPEITHI and UniProt were used to predict and analyze the physicochemical properties,hydrophilicity and hydrophobicity,signal peptide,transmembrane region,phosphorylation site,glycosylation site,domain,secondary structure,tertiary structure,B cell epitope,T cell epitope and protein homology of Salmonella typhimurium PipD protein.Results PipD was a hydrophilic protein composed of 520 amino acids,the molecular formula was C2608H3963N721O780S16,the theoretical relative molecular mass was 58.4 kDa,the theoretical isoelectric point was 7.34,the fat solubility index was 67.81,and the average hydrophilic coefficient was-0.508.PipD protein had no signal peptide sequence,and contained a transmembrane helix with a length of 23 amino acids at its 35-57 amino acid residues,which belonged to transmembrane protein.It was predicted that PipD protein contained 57 phosphorylation sites and 1 glycosylation site.The secondary structure of PipD protein was mostly random coil,accounting for 36.35％,followed by α-helix,β-sheet and β-turn,accounting for 15.77％,3.27％and 44.62％,respectively.It was predicted that PipD protein could form 22 B cell dominant epitopes,17 CTL cell dominant epitopes and 30 Th cell dominant epitopes.The homology of PipD protein with human genes BCLA3,SCRN2 and MRPL4 was 29％,24.6％and 31.8％,respectively.Conclusion PipD protein is a hydrophilic protein with good thermal stability.There are multiple B cell and T cell epitopes,which have low homology with human host proteins and are not prone to cross-immune reactions.It can be used as a candidate protein for serological diagnosis and vaccine of Salmonella typhimurium.
万方数据
维普
