Bioinformatics analysis of the structure and function of enterovirus 71 VP1 gene and protein / 中华传染病杂志

ABSTRACT

Objective To understand the structures and functions of enterovirus 71 (EV71)VP1 gene and its encoded protein using bioinformatics method, so as to direct studies of its biological function. Methods VP1 gene and its encoded protein of EV71 2008-GZCH07 strain and other representative EV71 strains were analyzed by online analysis at bioinformatics websites and software packages. Multi-sequence homological alignment and phylogenetic analysis were performed.Physicochemical characteristics, secondary structure, homology modeling of tertiary structure,enzymological characteristics, antigenic epitope of VP1 gene encoded protein were predicted. Results The homology of EV71 2008-GZCH07 strain was highest (97% and 98%) with ZJ001 strain, and lowest with human coxsackievirus A16. The homology of EV71 2008-GZCH07 strain and EV71 types A,B,C was 86%-98%. Phylogenetic analysis demonstrated that 2008-GZCH07 stain was close to ZJ001 and BJ08-Z025-5 stains, which belonged to C4 subtype. In VP1 encoded proteins of EV71 types A,B,C, the relationship between 2008-GZCH07 and EV71-B, EV71-C was closer than EV71-A.The whole length of VP1 gene was 510 bp, with open reading frame (ORF) located at 116-510 bp region,and it encoded 132 amino acids with isoelectric point of 4.39.The protein was rich of a-helix and random coilon without transmembrane regions, and contained 5 high hydrophobic regions and belonged to extracellular protein. The homology modeling of tertiary structure showed that the region was on the surface of protein and formed a binding loop. There was 5 antigen epitopes. And 7 key catalytic sites were located at or close to the loop. Conclusions EV71-VP1 encoded protein contains many phosphorylation sites, with many biological function sites and antigenic epitope regions, which might be a potential target antigen for immunodiagnosis, anti-schistosome drug and vaccine development, and would be basis of further study of diagnosis, treatment and prevention of EV71 infection.