Bioinformatics characteristics of B cell epitopes of UL140 gene of human cytomegalovirus clinical low-passage virus strain D2

Abstract

Objective To investigate the bioinformatics characteristics of B cell epitopes of UL140 gene of human cytomegalovirus(HCMV) clinical low-passage virus strain D2 (to call for short as HCMV D2) isolated from infected neonates in Guangdong Provincial Maternal and Child Health Institute. Methods The HCMV D2 isolated from 10 fresh urine samples of 10 neonates with HCMV positive from Neonatology department in Guangdong Provincial Maternal and Child Health Institute were selected as research materials. Applied bioinformatics methods, including analyzed the gene transmembrane structure by Hidden Markov Model (TMHMM); predicted gene hydrophilicity, surface accessibility, polarity, flexibility and antigenicity of UL140 gene through ExPASy online sequence analysis platform; the Garnier-Osguthorpe-Robson (GOR), hierarchical neutral network (HNN) and sawmill owners and plywood manufacturers association (SOPMA) were used to predict the secondary structure of UL140 gene. Aggregate analyzed the results above, and calculated the antigen index (AI) of the amino acid residues translated by UL140 gene, then summarized bioinformatics of B cell epitopes of UL140 gene. Results HCMV D2 UL140 gene contains 191 amino acid residues, the relative molecular mass was 21.5×103 and the isoelectric point was 5.12. The bioinformatics characteristics of B cell epitopes of UL140 gene were as follows. ①TMHMM predicted UL140 gene has a transmembrane protein amino acid sequence, and the 26-48 amino acid residues was a transmembrane region, 1-25 amino acid residues was extracellular region. ②ExPASy online sequence analysis platform for paramete prediction of UL140 gene showed that the hydrophilicity was located at 14-22, 66-72, 76-95, 113-125, 136-148, 155-160, 167-176 amino acid regions; the surface accessibility was located at 5-22, 50-60, 64-96, 132-160, 167-187 amino acid regions; the polarity was located at 5-22, 45-98, 103-128, 132-187 amino acid regions; the flexibility was located at 16-26, 75-100, 104-113, 136-160 amino acid regions; the antigenicity was located at 9-18, 53-58, 82-88, 115-124, 136-146, 164-187 amino acid regions. ③The secondary structure prediction of UL140 gene showed that the random coil and β-turn were mainly located at 1-8, 13-25, 79-95, 103-113, 153-159 amino acid regions. ④According to calculation of amino acid residues AI, regions of 5-10, 14-22 amino acid were much more higher. Conclusions The B cell epitopes of HCMV D2 UL140 gene may located at 5-10 and 14-22 amino acid regions or nearby. Key words: Cytomegalovirus; Clinical virus strain; UL140 gene; B cell epitopes; Infant, newborn