Citation: WANG Yong—shan 一, LU Cheng—ping, ZHOU Zong—an. Variant Analysis and Three-Dimensional Structure Prediction of the Capsid Protein ofthe Chinese Early Isolate NJ85 ofRabbithemorrhagic disease virus .VIROLOGICA SINICA, 2003, 18(6) : 557-562.

Variant Analysis and Three-Dimensional Structure Prediction of the Capsid Protein ofthe Chinese Early Isolate NJ85 ofRabbithemorrhagic disease virus

  • Available online: 25 December 2003
  • 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.

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    Variant Analysis and Three-Dimensional Structure Prediction of the Capsid Protein ofthe Chinese Early Isolate NJ85 ofRabbithemorrhagic disease virus

    • 1. College of Veterinary Medicine,Nanjing Agricultural University,Nanjing 210095,China
    • 2. Huadong Research Institute ofMedical Biotechnics,Nanjing 210002,China

    Abstract: 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.

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