Primer specific solid-phase detection of PCR products.
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Base Sequence↗
Biomedical subjects
Khudyakov YuE
Publications and source records attributed to Khudyakov YuE.
Immunodominant antigenic regions in a structural protein of the hepatitis E virus.
Using a set of 11 synthetic peptides containing regions of the polypeptide encoded by open reading frame 2 (ORF2) of the hepatitis E virus (HEV) genomic RNA, two immunodominant regions were found. One region is located at position 546-580 amino acids (aa). Another very strong immunodominant region was identified at position 394-470 aa. Five peptides spanning this region were found to have antigenic reactivity. One of these 5 peptides demonstrated specific reactivity with 81% of sera obtained from HEV-infected patients. To elucidate the antigenic structure of this region in fine detail, an additional set of 35 overlapped 20-mer peptides spanning the region 388-493 aa was synthesized. Two subregions with very strong antigenic reactivity, one located around position 420-440 aa and another around 450-460 aa, were identified. Thus, in addition to the strong epitope(s) in the C-terminal region of the ORF2 protein previously identified, at least two immunodominant regions were found at positions 394-470 and 546-580 aa.
Amino Acid Sequence↗
Comparative characterization of antigenic epitopes in the immunodominant region of the protein encoded by open reading frame 3 in Burmese and Mexican strains of hepatitis E virus.
To analyse the effect of strain-specific sequence variation on the antigenic properties of the protein encoded by the open reading frame 3 (ORF 3) of hepatitis E virus (HEV), two sets of short overlapping peptides spanning amino acids 91 to 123 of this protein from Burmese and Mexican strains were synthesized and tested with sera obtained from outbreaks of enterically transmitted non-A, non-B hepatitis in three different regions of the world (Mexico, Turkmenistan and Kenya). The data suggest strain-specific variation in the antigenic reactivity of the ORF 3 protein. The C-terminal region of this protein contains several antigenic epitopes located in the most variable positions. Individual sera were found to interact with different groups of epitopes from each set of peptides. The antigenic epitopes of the Mexican strain appear to be less conformation-dependent than those of the Burmese strain. The most immunoreactive epitope of the ORF 3 protein from the Mexican strain was localized at amino acid positions 95 to 101. The ORF 3 protein of the Burmese strain contains an immunodominant epitope at amino acid positions 112 to 117. Some of these short peptides may be useful for the development of a diagnostic assay to discriminate between the Burmese and Mexican strains.
Amino Acid Sequence↗
A small open reading frame of the hepatitis delta virus antigenomic RNA encodes a protein that elicits antibodies in some infected patients.
A small open reading frame (ORF) was found in the hepatitis delta virus (HDV) antigenomic RNA encoding a short peptide that shares structural similarity with a region of the hepatitis B virus terminal protein. Analysis of all published HDV genome sequences indicates a high degree of conservation for the small ORF. This ORF is located at the 3'-terminal region of the gene encoding the hepatitis delta antigen (HDAg). We speculated that a peptide encoded by this ORF can be represented as the C-terminal domain of a new protein called HDAg'. This protein contains almost the entire sequence represented in the small form of HDAg and a peptide as an additional 'extension' sequence at the C-terminus. Two long synthetic peptides representing the two different types of peptides encoded by the small ORF were synthesized. These peptides were used for the development of an immunoassay for the detection of antibody to the HDAg' specific domain in sera of patients with HDV infection. Among 162 serum samples analyzed, 13 were found to be positive for an antibody reactive with these synthetic peptides. These antibodies were identified in patients with HDV infections and were not found in patients infected with hepatitis B virus, hepatitis C virus, or non-A,non-B,non-C virus. Thus, these data support the identification and existence of a new antigen encoded by the antigenomic RNA of the HDV.
Amino Acid Sequence↗
The effect of the structure of the terminal regions of the hepatitis B virus gene C polypeptide on the formation of core antigen (HBcAg) particles.
A series of plasmids encoding native and modified sequences of the hepatitis B virus core antigen (HBcAg) was created. Analysis of the products generated by expression of the plasmid genomes in Escherichia coli showed that a polypeptide with primary structure identical to that deduced for native HBcAg forms particles in the bacterial cells which are indistinguishable from the native nucleocapsids in morphological and antigenic properties. Removal of the thirty-nine C-terminal amino acids which form a protamine-like domain caused insignificant impairment of the particle-forming process. Modification of the N-terminal region of the polypeptide showed that at least part of the structural determinant governing particle formation is localised between amino acid residues 3 and 11. When the plasmid genes were expressed in an E. coli cell-free transcription - translation system, polypeptides devoid of ten to twenty N-terminal amino acids were formed in addition to the full-length products. From the results obtained it is proposed that a protease digestion site situated within the region containing amino acid residues 10 - 20 plays a role in the formation of the HBe antigen.
Amino Acid Sequence↗
Amino acid sequence similarity between the terminal protein of hepatitis B virus and predicted hepatitis delta virus gene product.
The comparative analysis of primary and secondary structures, and hydropathy plots of hepatitis B virus (HBV) and hepatitis delta virus (HDV) proteins was carried out. Two short regions belonging to the HBV terminal protein were shown to be homologous to two regions; one encoded by HDV ORF5, and the other encoded by small ORF of the HDV antigenomic RNA strand. We propose a new protein containing both these regions may be synthesized in HDV infected cells. Striking structural homology between the terminal protein of HBV and this predicted protein called HDAg' of HDV may indicate a possible functional similarity. We hypothesize the HDAg' may interact with and inhibit the polymerase activity of HBV.
Amino Acid Sequence↗
Prediction of terminal protein and ribonuclease H domains in the gene P product of hepadnaviruses.
By means of comparative analysis of primary and secondary structures, and hydropathy plots of hepadnavirus P proteins new functional domains were revealed additionally to the polymerase domain which had been found earlier in these proteins. The C-terminal part of P proteins was revealed to be significantly similar to ribonuclease H of E. coli. The ribonuclease H functional domain is known to be an integral entity of retrovirus reverse transcriptase as a rule. Availability of this domain indicates once more the putative reverse transcriptase properties of the P products. The proteins of hepadnaviruses were compared to terminal proteins of picornaviruses, adenoviruses and bacteriophages. The data obtained suggested that a conservative N-terminal region of P proteins functions as protein primer for DNA synthesis in hepadnaviruses.
Amino Acid Sequence↗
Effect of structure of the initiator codon on translation in E. coli.
A set of plasmids carrying different initiator codons--either AUG, or GUG, or UUG, or CUG (as a control) in the hybrid gene lacIZ--was constructed by using synthetic oligonucleotides. GUG and UUG codons were demonstrated to be 2-3 times less effective than AUG in translation initiation. Furthermore, the correlation between the efficiencies of different initiator codons in translation initiation proved to vary, depending on the phase of bacterial growth. The rarely occurring usage in nature of the initiator codons GUG and UUG is supposed to be due to the particular role played by the initiator triplets in regulation of gene expression.
Bacteriophage lambda↗