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Virologica Sinica, 18 (6) : 557-562, 2003
Research Article
Variant Analysis and Three-Dimensional Structure Prediction of the Capsid Protein ofthe Chinese Early Isolate NJ85 ofRabbithemorrhagic disease virus
College of Veterinary Medicine,Nanjing Agricultural University,Nanjing 210095,China
2.Huadong Research Institute ofMedical Biotechnics,Nanjing 210002,China
Abstract:The capsid protein gene(vp60)of Rabbit hemorrhagic disease virus(RHDV)isolate NJ85
was amplified and sequenced.vp60 gene of NJ85 was in size of 1 740nt an d encoding 579aa.
Comparison with other Chinese field isolates W X84 an d TP showed that the homology were 92.7% an d
97.2% for nucleofide sequence;96.1% an d 98.6% for amino acid sequence respectively.Alignment with
other 16 sequences of RHDV isolated from other countries registe in GenBank showed that the
homology was 83.7% ~ 97.0% for nucleotide and 90.5%~ 99.0% for amino acid sequence.The results
indicated that the sequence of vp60 in diferent RHDV isolates was highly homologous.In the all six
regions ofvp60 gene,low degree ofvariation ofvp60 was found in the regions A,B,D,F and relative
high degree of variation in the regions C and E.Based on vp60 sequence,phylogenetic an alysis showed
that the historic RHDV isolates were divided into 3 branches of the lineage of RHDV according to the
am ino acid sequences and 4 branches according to the nucleotide sequences.Th ere was no obvious
correlation between geographical region,historic period and homological degree.Three Chinese field
isolates lay in 2 diferent branches of the RHDV lineage,while EBHSV formed an other fineage.Th e
molecular weight,isoelectric point,hydrophobicity,2-dimensional an d 3-dimensional structure of NJ85
vp60 were de~rmined and predicted on the theory of bioinformatics.The major secondary structure,13
一sheet,contributed to the stability of vp60.Based on the structural model,the architecture of NJ85
capsid was 32 cup—shaped depressions.Th e capsid was composed of 90 A/B5 an d C/C2 dimers formed
by the single unit of vp60.Th e conformation of the single unit in dimer existed in thre forms of A,B
and C.Th e single unit of Vp60 had a protruding(P)domain connected by a flexible hinge to a shell(S)
domain.P domain was subdivided into two subdomains,P1 an d P2.P2 subdomain that located at the
surface of the capsid contained the determinants of strain specificity an d erythrocyte binding site.
  Published online: 25 Dec 2003
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