Bioinformatics analysis of Muscovy duck parvovirus REP and VP1 proteins

Abstract

This article was aimed at analyzing the sequence, structure, and function of the two Muscovy duck parvovirus proteins, including REP and VP1. The antigenicity, physical and chemical properties, transmembrane regions, phosphorylation sites, glycosylation sites, three-dimensional structure, and linear epitope of VP1 and REP were predicted and analyzed through bioinformatics methods. A multi-epitope vaccine was also constructed based on the screened epitopes, and the vaccine was characterized, modeled, molecularly docked and molecularly cloned. The epitopes were screened according to the criteria of antigenicity, non-allergenicity and non-toxicity, and 12 epitope fragments were obtained. The B cell epitopes were analyzed according to four scales: β-turn, hydrophilicity, surface accessibility and antigenicity. Combined with the epitope prediction results based on structure, the final epitope prediction results were obtained. The multi-epitope vaccine used an EAAAK-linked adjuvant, a GPGPG-linked T-cell epitope, and a KK-linked B-cell epitope. The analysis showed that the vaccine was stable hydrophilic, antigenic, conserved and non-allergenic. Based on molecular docking it was shown that good interactions between the vaccine and the immune receptor were generated and were essential to generate an immune response. The final vaccine was reverse translated into cDNA and the DNA vaccine was designed by codon optimization and molecular cloning. Further trials are still needed to demonstrate the immunogenicity and other aspects of vaccine efficacy.

Communicated by Ramaswamy H. Sarma

Keywords:

• Muscovy duck parvovirus
• bioinformatics
• 3D structure
• AlphaFold2
• epitope prediction

Disclosure statement

The authors declare that they have no conflicts of interest.

Data availability statement

Databases used are from https://www.ncbi.nlm.nih.gov/, http://www.ddg-pharmfac.net/vaxijen/VaxiJen/VaxiJen.html, https://web.expasy.org/protparam/, https://npsa-prabi.ibcp.fr/cgi-bin/npsa_automat.pl?page=npsa_sopma.html, https://services.healthtech.dtu.dk/service.php?TMHMM-2.0, https://services.healthtech.dtu.dk/service.php?NetPhos-3.1, https://services.healthtech.dtu.dk/service.php?NetNGlyc-1.0, https://services.healthtech.dtu.dk/service.php?NetOGlyc-4.0, https://web.expasy.org/protscale/, https://services.healthtech.dtu.dk/service.php?NetMHCcons-1.1, https://services.healthtech.dtu.dk/service.php?NetMHCIIpan-4.0, https://services.healthtech.dtu.dk/service.php?NetCTLpan-1.1.

Additional information

Funding

This work was supported by the Natural Science Foundation of Heilongjiang Province under Grant No. LH2020C110 and Heilongjiang Provincial Education Department under Grant No. YSTSXK201881.