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Biomedical subjects

B Dasmahapatra

Publications and source records attributed to B Dasmahapatra.

At least 19 recordsLinked to original sources
PubMed2000

Hepatitis C NS3 protease: restoration of NS4A cofactor activity by N-biotinylation of mutated NS4A using synthetic peptides.

The NS3 serine protase of Hepatitis C virus (HCV) requires NS4A protein as a cofactor for efficient cleavage at four sites in the nonstructural region. The cofactor activity has been mapped to the central hydrophobic region (aa 22-34) of this 54-amino-acid NS4A protein, and site-directed mutagenesis has identified alternating hydrophobic amino acids, particularly Ile25 and Ile29, as critically important. A double mutant of NS4A cofactor peptide, I25A/I29A, completely abolished the cofactor activity. We now report that the cofactor peptide activity in the I25A/I29A double mutant can be restored specifically by introducing a biotin-aminohexanoic acid fusion at the N-terminus. In addition, a similar N-terminal fusion of biotin-aminohexanoic acid with the wild-type 4A peptide significantly enhanced cofactor activity. Our data corroborate the crystal structure-based hypothesis of hydrophobic interaction between the N-terminus of NS4A and the N-terminal alpha(0) helix of NS3 protease.

Amino Acid Sequence↗
PubMed1996

Enhancement of hepatitis C virus NS3 proteinase activity by association with NS4A-specific synthetic peptides: identification of sequence and critical residues of NS4A for the cofactor activity.

The NS3 proteinase of hepatitis C virus utilizes NS4A as a cofactor for cleavages at four sites (3/4A, 4A/4B, 4B/5A, and 5A/5B) in the nonstructural region of the viral polyprotein. To characterize NS4A for its role in modulating the NS3 proteinase activity at various cleavage sites, synthetic peptides spanning various parts of NS4A were synthesized and tested in a cell-free trans-cleavage reaction using purified NS3 proteinase domain and polyprotein substrates. The NS3 proteinase domain was expressed in Escherichia coli, purified, denatured, and refolded to an enzymatically active form. We found that a 12-amino-acid peptide containing amino acid residues 22 to 33 in NS4A (CVVIVGRIVLSG) was sufficient for cofactor activity in NS3-mediated proteolysis. The peptide enhanced the cleavage at the NS5A/5B site and was necessary for NS3-mediated cleavage at NS4A/4B and NS4B/5A. Sequential amino acid substitution within the designated peptide identified residues I29 and I25 as critical for potential cofactor activity. We provide evidence that the NS4A peptide and the NS3 catalytic domain form an enzymatically active complex. These data suggest that the central 12-amino-acid peptide (aa 22-33) of NS4A is primarily important for the cofactor activity through complex formation with NS3, and the interaction may represent a new target for antiviral drug development.

Amino Acid Sequence↗
PubMed1994

The synthesis of novel HIV-protease inhibitors.

The syntheses, enzyme inhibition and antiviral activity of potent HIV-protease inhibitors containing novel beta-hydroxy ether and thioethers based on the transition state mimetic concept are discussed.

Amino Acid Sequence↗
PubMed1992

A genetic system for studying the activity of a proteolytic enzyme.

We describe a genetic system for monitoring the activity of a specific proteolytic enzyme by taking advantage of the properties of the yeast transcriptional activator GAL4. The GAL4 protein contains two separable and functionally essential domains: the amino-terminal DNA binding domain and the carboxyl-terminal transcriptional activating domain. We constructed two hybrid proteins by inserting between the DNA binding domain and the activation domain of GAL4 either (i) a self-cleaving protease (3C protease of a picornavirus, coxsackievirus B3) or (ii) a mutant form of the protease that is unable to cleave. We show that, although the hybrid protein containing the mutant protease activates transcription of GAL1-lacZ reporter gene, the hybrid protein bearing the wild-type protease is proteolytically cleaved and fails to activate transcription. Our approach to monitor the proteolytic activity could be used to develop simple genetic systems to study other proteases.

Amino Acid Sequence↗
PubMed1991

Expression of functional beta-galactosidase containing the coxsackievirus 3C protease as an internal fusion.

Alpha complementation of beta-galactosidase (beta gal) is intracistronic and requires interaction between the alpha donor region (residues 3-41) and alpha acceptor fragment (produced by M15). We have constructed two plasmids which direct the synthesis of hybrid beta gal: coxsackievirus proteins in Escherichia coli. One plasmid, pBD1045, encodes an enzymatically active 3C protease of coxsackievirus B3 fused between the amino-terminal 79 amino acids of beta gal (containing the alpha donor region) and amino acids 80 to 1023 (alpha acceptor region). A second plasmid, pBD1043 encodes an inactive 3C protease and results in a fusion of 260 coxsackievirus amino acids between residues 79 and 80 of the beta gal monomer. Both hybrid proteins expressed by these constructs have beta-galactosidase activity regardless of whether the viral protease (183 amino acids) is autocatalytically cleaved out of the chimeric protein (pBD1045) or remains as part of a fusion protein (pBD1043). The implications of these results for structural flexibility of the complemented beta-galactosidase enzyme are discussed.

3C Viral Proteases↗
PubMed1991

Cell-free expression of the coxsackievirus 3C protease using the translational initiation signal of an insect virus RNA and its characterization.

We have expressed the 3C protease of coxsackievirus B3 (CVB3) in a cell-free system. This expression system employs the translational initiation signal of an insect virus RNA, black beetle virus (BBV) RNA 1, to direct CVB3-specific protein synthesis. Using this expression system, we demonstrate that a biologically active 3C protease is synthesized which possesses both cis and trans processing capabilities. This in vitro-synthesized 3C protease is analogous to the native 3C, which was obtained from cytoplasmic extracts of CVB3-infected HeLa cells, in all biological parameters that were evaluated. In addition, antibody prepared against the 3C protease purified from extracts of CVB3-infected HeLa cells cross-reacts with the 3C protease produced in this cell-free system. Using the translational initiation signal from BBV RNA 1, we also have expressed the CVB3 capsid precursor and part of the P2 region in vitro, and have shown that the capsid precursor is cleaved between 1C (VP3) and 1D (VP1) by the proteolytic activity of in vitro-synthesized 3C in trans. Evidence also is presented to implicate the 2A protein of CVB3 as having proteolytic function.

3C Viral Proteases↗
PubMed1990

Species-specific substrate interaction of picornavirus 3C proteinase suballelic exchange mutants.

The substrate recognition properties of the polio-virus type 1 and coxsackievirus B3 3C proteinases have been examined in vitro by allelic and suballelic exchange of 3C between the cloned virus genomes. The activity of the altered 3C proteinases was examined by translation of synthetic RNA in a rabbit reticulocyte lysate/HeLa cell extract translation system. Analysis of the subsequent processing of virus polyproteins by the altered 3C proteinases showed that all of the mutant proteinases maintained some catalytic activity. The disruption of polyprotein cleavages mediated by 3C followed a distinct pattern, suggesting a specific order of events in processing the polyprotein. Differences in cleavage activity of mutant proteinases when tested on coxsackievirus or poliovirus protein substrates suggest that, although structural elements throughout the proteinase play a role in efficient substrate utilization, the carboxyl-terminal region of the 3C proteinase contains elements most important in species-specific substrate recognition.

Alleles↗
PubMed1986

Infectious RNA derived by transcription from cloned cDNA copies of the genomic RNA of an insect virus.

RNA transcripts of cloned cDNA of the genomic RNAs of BBV (black beetle virus) are infectious to cultured cells of Drosophila melanogaster. Individual transcripts had approximately 10% of the infectivity of the corresponding authentic virion RNA. Progeny virus resulting from transcript infection was phenotypically indistinguishable from the progenitor virus used to generate the original cDNA forms as judged by sucrose density gradient sedimentation, specific infectivity, plaque morphology, and serology. Although the transcript RNAs used to produce this virus had 20 nonviral bases headed by a capping group at their 5' termini, these 20 bases were absent in the progeny viral RNAs. The cDNA forms, and therefore the resulting transcript RNAs, should be readily modifiable by the techniques of recombinant DNA technology both for viral studies and for the insertion of foreign genes into the viral genome and thus into the host cytoplasm.

Animals↗
PubMed1985

Structure of the black beetle virus genome and its functional implications.

The black beetle virus (BBV) is an isometric insect virus whose genome consists of two messenger-active RNA molecules encapsidated in a single virion. The nucleotide sequence of BBV RNA1 (3105 bases) has been determined, and this, together with the sequence of BBV RNA2 (1399 bases) provides the complete primary structure of the BBV genome. The RNA1 sequence encompasses a 5' non-coding region of 38 nucleotides, a coding region for a protein of predicted molecular weight 101,873 (protein A, implicated in viral RNA synthesis) and a 3' proximal region encoding RNA3 (389 bases), a subgenomic messenger RNA made in infected cells but not encapsidated into virions. The RNA3 sequence starts 16 bases inside the coding region of protein A and contains two overlapping open reading frames for proteins of molecular weight 10,760 and 11,633, one of which is believed to be protein B, made in BBV-infected cells. A limited homology exists between the sequences of RNA1 and RNA2. Sequence regions have been identified that provide energetically favorable bonding between RNA2 and RNA1 possibly to facilitate their common encapsidation, and between RNA2 and negative strand RNA1 possibly to regulate the production of RNA3.

Base Sequence↗
PubMed1984

Primary and secondary structure of black beetle virus RNA2, the genomic messenger for BBV coat protein precursor.

The nucleotide sequence of black beetle virion (BBV) RNA2 has been determined. RNA2 is 1399 b long. Its 5' terminus is capped. Its 3' terminus has an unidentified moiety that renders the RNA resistent to polyadenylation and ligation. The first AUG codon at base 23 is followed by an open reading frame for a protein 407 amino acids long, the predicted size of coat protein precursor. A second open reading frame for a putative protein 72 amino acid residues long begins at base 1110. No other large open reading frames exist. The 5' half of the RNA can be folded into a long, imperfect hairpin of high predicted stability. The 3' half of the RNA can fold into a complex set of multiply bifurcated stem and loop regions.

Amino Acid Sequence↗
PubMed1984

Sequence of the black beetle virus subgenomic RNA and its location in the viral genome.

BBV (black beetle virus) RNA3, the subgenomic messenger RNA for BBV protein B and its double-stranded form (dsRNA3) were purified from cells infected with BBV and were sequenced. RNA3 is 389 bases long. The sequence is homologous to that of the 3'-terminal region of virion RNA1. RNA3 has a very limited homology to virion RNA2. RNA3 is capped at its 5' terminus and has a structural feature at its 3' terminus that renders it inert to the action of the enzymes RNA ligase and poly(A) polymerase. RNA3 has two overlapping reading frames for putative proteins of size 10,768 and 11,633 Da. The positive and negative strands of dsRNA3 are not capped and correspond in length and sequence to RNA3 itself.

Base Sequence↗
PubMed1981

Protein synthesis in yeast. I. Purification and properties of elongation factor 3 from Saccharomyces cerevisiae.

Elongation factor 3 from the yeast Saccharomyces cerevisiae was purified over 230-fold from a high speed supernatant fraction. The homogeneity of the protein was shown by gel filtration and sedimentation equilibrium analysis of the native protein and by sodium dodecyl sulfate gel electrophoresis of the denatured protein. The molecular weight of the protein was estimated to be 125,000 by the above-mentioned methods. The protein consists of a single polypeptide chain. Amino acid analysis revealed no unusual features. Antibody raised against the purified factor showed a single cross-reacting band with the characteristic hexagonal pattern in an Ouchterlony double diffusion plate. The immune serum had no reactivity against the other two elongation factors (EF). The polymerization reaction was inhibited by the anti-EF3. Addition of excess EF3 could overcome this effect. Factor 3 is absolutely required by the yeast ribosomes for polyphenylalanine synthesis. Ribosomes from other eukaryotes do not require this protein. The function of the third factor in polyphenylalanine synthesis cannot be defined at this time. The protein showed ribosome-dependent GTPase and ATPase activities. Studies of partial reactions showed that EF3 was not required for Phe-tRNA binding to ribosomes, peptide bond formation, or translocation. Nucleotide exchange by EF1 was not stimulated by EF3.

Adenosine Triphosphatases↗