A simpler and more cost-effective peptide biosynthetic method using the truncated GST as carrier for epitope mapping.

There is a need to develop better methods for epitope mapping and/or identification of antibody-recognizing motifs. Here, we describe improved biosynthetic peptide (BSP) method using a newly developed plasmid pXXGST-3 as vector, which has a viral E7 gene in the cloning sites of pXXGST-1. It is crucial to employ pXXGST-3 instead of pXXGST-1, since it makes use of the BSP method simpler and easier to perform, and more cost-effective for epitope mapping. These merits are embodied in two aspects: i) convenient recovery of double enzyme-digested product due to the existence of 315 bp inserted between BamH I and Sal I sites, and thus greatly reducing the production of self-ligation clones, and ii) no longer requiring control protein when screening recombinant (r-) clones expressing 8/18mer peptides by running polyacrylamide gel electrophoresis. The protocol involves the following core steps: (i) design of plus and minus strands of DNA fragments encoding overlapping 8/18mer peptides; (ii) chemical synthesis of the designed DNA fragments; (iii) development of r-clones using pXXGST-3 vector expressing each 8/18mer peptide fused with truncated GST188 protein; (iv) screening r-clones by running the cell pellets from each induced clone on SDS-PAGE gel followed by sequencing of inserted DNA fragments for each verified r-clone; and (v) Western blotting with either monoclonal antibodies or polyclonal antibodies. This improved GST188-BSP method provides a powerful alternative tool for epitope mapping.

Epitomics: IgG-epitome decoding of E6, E7 and L1 proteins from oncogenic human papillomavirus type 58.

To enable rational multi-epitope vaccine and diagnostic antigen design, it is imperative to delineate complete IgG-epitome of the protein. Here, we describe results of IgG-epitome decoding of three proteins from high-risk (HR-) oncogenic human papillomavirus type 58 (HPV58). To reveal their entire epitomes, employing peptide biosynthetic approach, 30 precise linear B-cell epitopes (BCEs) were mapped on E6, E7 and L1 proteins using rabbits antisera to the respective recombinant proteins. Using sequence alignment based on BCE minimal motif, the specificity and conservativeness of each mapped BCE were delineated mainly among known HR-HPVs, including finding 3 broadly antibody cross-reactive BCEs of L1 that each covers almost all HR-HPVs. Western blots revealed that 13 of the 18 BCEs within L1-epitome were recognized by murine antisera to HPV58 virus-like particles, suggesting that these are antibody accessible BCEs. Also, a highly conserved epitope (YGD/XTL) of E6 was found to exist only in known common HR-HPVs, which could be used as the first peptide reference marker for judging HR-HPVs. Altogether, this study provides systemic and exhaustive information on linear BCEs of HR-HPV58 that will facilitate development of novel multi-epitope diagnostic reagents/chips for testing viral antibodies and 'universal' preventive HPV peptide vaccine based on L1 conserved BCEs.

The structural basis of the response regulator DrRRA from Deinococcus radiodurans.

DrRRA, a vital and recently discovered gene product of Deinococcus radiodurans, is a member of the OmpR/PhoB family of response regulators that couple with the cognate histidine kinase (HK) to form a typical two component system (TCS). It is known that the DrRRA is responsible for the transcriptional levels of numerous genes mostly relating to the stress response and DNA repair. In this paper, the crystal structures of the effector domain and full-length protein of DrRRA with resolutions of 1.6 and 2.3Å, respectively, are determined. These crystal structures depicted that DrRRA has the structural features of the OmpR/PhoB subfamily and were also confirmed by SAXS investigation of the protein in solution. Our data suggest that the receiver domain blocks the binding of DNA to the DNA recognition helix of effector domain; while the interdomain interface would be unwrapped, via the phosphorylation of receiver domain and/or the inducement of DNA, in order to provide DNA binding.

Mapping of minimal motifs of B-cell epitopes on human zona pellucida glycoprotein-3.

The human zona pellucida glycoprotein-3 (hZP3) by virtue of its critical role during fertilization has been proposed as a promising candidate antigen to develop a contraceptive vaccine. In this direction, it is imperative to map minimal motifs of the B cell epitopes (BCEs) so as to avoid ZP-specific oophoritogenic T cell epitopes (TCEs) in the ZP3-based immunogens. In this study, based on known results of mapping marmoset and bonnet monkey ZP3 (mstZP3 and bmZP3), two predictable epitopes(23-30 and 301-320) on hZP3 were first confirmed and five minimal motifs within four epitopes on hZP3 were defined using serum to recombinant hZP3a(22-176) or hZP3b(177-348) as well as a biosynthetic peptide strategy. These defined minimal motifs were QPLWLL(23-28) for hZP3(23-30), MQVTDD(103-108) for hZP3(93-110), EENW(178-181) for hZP3(172-190), as well as SNSWF(306-310) and EGP(313-315) for hZP3(301-320), respectively. Furthermore, the antigenicity of two peptides for hZP3(172-187) and hZP3(301-315) and specificity of the antibody response to these peptides were also evaluated, which produced high-titer antibodies in immunized animals that were capable of reacting to ZP on human oocytes, r-hZP3b(177-348) protein, as well as r-hZP3(172-190), r-hZP3(303-310), and r-hZP3(313-320) epitope peptides fused with truncated GST188 protein.

Cdc20 mediates D-box-dependent degradation of Sp100.

Cdc20 is a co-activator of the anaphase-promoting complex/cyclosome (APC/C complex), which recruits substrates at particular phases of the cell cycle and mediates their degradation. Sp100 is a PML-NB scaffold protein, which localizes to nuclear particles during interphase and disperses from them during mitosis, participates in viral resistance, transcriptional regulation, and apoptosis. However, its metabolism during the cell cycle has not yet been fully characterized. We found a putative D-box in Sp100 using the Eukaryotic Linear Motif (ELM) predictor database. The putative D-box of Sp100 was verified by mutational analysis. Overexpression of Cdc20 resulted in decreased levels of both endogenous Sp100 protein and overexpressed Sp100 mRNA in HEK 293 cells. Only an overexpressed D-box deletion mutant of Sp100 accumulated in HEK293 cells that also overexpressed Cdc20. Cdc20 knockdown by cdc20 specific siRNA resulted in increased Sp100 protein levels in cells. Furthermore, we discovered that the Cdc20 mediated degradation of Sp100 is diminished by the proteasome inhibitor MG132, which suggests that the ubiquitination pathway is involved in this process. However, unlike the other Cdc20 substrates, which display oscillating protein levels, the level of Sp100 protein remains constant throughout the cell cycle. Additionally, both overexpression and knockdown of endogenous Sp100 had no effect on the cell cycle. Our results suggested that sp100 is a novel substrate of Cdc20 and it is degraded by the ubiquitination pathway. The intact D-box of Sp100 was necessary for this process. These findings expand our knowledge of both Sp100 and Cdc20 as well as their role in ubiquitination.

Structure of the putative dihydroorotate dehydrogenase from Streptococcus mutans.

Streptococcus mutans is one of the pathogenic species involved in dental caries, especially in the initiation and development stages. Here, the crystal structure of SMU.595, a putative dihydroorotate dehydrogenase (DHOD) from S. mutans, is reported at 2.4 Šresolution. DHOD is a flavin mononucleotide-containing enzyme which catalyzes the oxidation of L-dihydroorotate to orotate, which is the fourth step and the only redox reaction in the de novo biosynthesis of pyrimidine nucleotides. The reductive lysine-methylation procedure was applied in order to improve the diffraction qualities of the crystals. Analysis of the S. mutans DHOD crystal structure shows that this enzyme is a class 1A DHOD and also suggests potential sites that could be exploited for the design of highly specific inhibitors using the structure-based chemotherapeutic design technique.

Immunogenic comparison for two different recombinant chimeric peptides (CP12 and CP22) containing one or two copies of three linear B cell epitopes from ß-hCG subunit.

To develop a superior chimeric peptide (CP) vaccine of human chorionic gonadotropin (hCG), two CP antigens (named CP12 and CP22) encoding one or two copies of three linear B cell epitopes from the ß-hCG subunit and six foreign T cell epitopes, including two promiscuous TCEs from hepatitis B surface antigen and tetanus toxoid, were constructed and biosynthesized. The hCG CP12 and CP22 of 21 or 23 kDa, respectively, were expressed in Escherichia coli at the level of ~1% of total cell proteins when inserted into thermo-inducible pBV221 expression vector. The purified CP12 and CP22 proteins with >95% relative homogeneity are immunogenic, and elicited antibodies against the ß5, ß9 and ß8 BCEs of ß-hCG in both rabbits and three different inbred strains of mice. A mouse uterine weight study in Balb/c mice demonstrated that the CP12 and CP22 antigens with an additional ß5 neutralizing epitope enhanced the in vivo bio-neutralization capacity of the induced antibodies compared to the C-terminal immunogen of ß-hCG. We propose that the biosynthesized CP22, possessing with two copies of three BCEs, represents a novel candidate antigen for an hCG contraceptive or tumor therapeutic vaccine.

Grb10 interacts with Bim L and inhibits apoptosis.

Bim is a proapoptotic member of the Bcl-2 family and is primarily involved in the regulation of the intrinsic apoptotic pathway. However, the detail of regulation of Bim's proapoptotic activity has not been clarified yet. Using Bim L as bait, we screened a human fetal cDNA library for interacting proteins and identified Grb10 as an interactor. This interaction was verified by co-immunoprecipitation and intracellular co-localization studies. The potential segment of Bim L that binds Grb10 was identified via a yeast mating test. Grb10 interacted with the DBD (dynein binding domain) of Bim and inhibited apoptosis triggered by overexpression of DBD containing Bim isoforms. The putative phosphorylation sites on DBD of Bim play a role for the anti-proapoptotic activity of Grb10. Our results suggest that Grb10 interacts with Bim L and inhibits its proapoptotic activity in a phosphorylation-dependant manner.

Minimal motif mapping of a known epitope on human zona pellucida protein-4 using a peptide biosynthesis strategy.

An important step in the development of a human zona pellucida (huZP) peptide vaccine is to define the minimal amino acid motif for a mapped B cell epitope peptide within huZP4. Identification of this minimal motif is necessary to remove an overlapping T cell epitope that induces a pathogenic T cell response. Here we describe motif (PLTLEL(314-319)) mapping of an 18mer B cell epitope peptide(308-325) on huZP4 protein (previously known as huZP1/ZPB protein), achieved using a set of 22 biosynthetic 8mer peptides fused with truncated glutathione S-transferase (GST) or truncated streptavidin protein, and detected using rabbit anti-porcine zona pellucida (pZP) IgG. The immunogenicity of the B cell epitope peptide was evaluated in rabbits using expressed B cell epitope peptide fused with truncated streptavidin as the antigen. This construct elicited high titer antibody to the 18mer B cell epitope peptide, with reactivity to native human ZP, the biosynthetic 18mer peptide and the 18mer peptide GST fusion protein.

[Preparation and characterization of monoclonal antibodies against RalB].

OBJECTIVE: In order to explore the expression of RalB (ras related; GTP binding protein B) in mammal eucaryotic cell, we prepared and characterized monoclonal antibodies against RalB. METHODS: Hybridomas were generated by the fusion with Sp2/0 myelomas and spleen cells, which were from mice immunized with RalB recombinant proteins. The monoclonal antibodies against RalB were then used to identify the expression of RalB in mammal eucaryotic cell, including normal hepatic cell and hepatoma carcinoma cells, by Western blot and Immunohistochemistry. RESULTS: Two hybridoma cell lines, F001, F002, had been produced, each of which stably secrets antibodies against RalB. Subclass of IgG are both belonged to IgG1. Immunohistochemistry demonstrated that RalB was presented in plasma membrane of hepatoma tissue. Western-blot showed that RalB was expressed in all concerned cell. CONCLUSION: The monoclonal antibodies against RalB protein have been successfully prepared, which should provide useful reagent for further investigation into the biological function of RalB.

Molecular cloning and characterization of a novel splice variant of human ZNF300 gene, which expressed highly in testis.

Zinc finger protein, one of the most important transcription factors, plays an essential role in regulating gene expression. C(2)H(2) type zinc protein with KRAB domain contains two parts, one is C(2)H(2) zinc finger motif which is use to binding to the DNA, while the other is KRAB associated box which mostly performs as a transcription repressor. In this study, we report the cloning and characterization of a novel splice variant of the human ZNF300 gene (ZNF300-B). The ZNF300-B gene cDNA is 2293 bp in length, encoding a putative protein with 619 amino acid residues. ZNF300-B gene is mapped to chromosome 5q32-5q33 with seven exons. Reverse transcription polymerase chain reaction (RT-PCR) analysis showed that ZNF300-B and ZNF-300 were expressed highly in human testis.

DAXX interacts with phage PhiC31 integrase and inhibits recombination.

Phage PhiC31 integrase has potential as a means of inserting therapeutic genes into specific sites in the human genome. However, the possible interactions between PhiC31 integrase and cellular proteins have never been investigated. Using pLexA-PhiC31 integrase as bait, we screened a pB42AD-human fetal brain cDNA library for potential interacting cellular proteins. Among 61 positives isolated from 10(6) independent clones, 51 contained DAXX C-terminal fragments. The strong interaction between DAXX and PhiC31 was further confirmed by co-immunoprecipitation. Deletion analysis revealed that the fas-binding domain of DAXX is also the region for PhiC31 binding. Hybridization between a PhiC31 integrase peptide array and an HEK293 cell extract revealed that a tetramer, 451RFGK454, in the C-terminus of PhiC31 is responsible for the interaction with DAXX. This tetramer is also necessary for PhiC31 integrase activity as removal of this tetramer resulted in a complete loss of integrase activity. Co-expression of DAXX with PhiC31 integrase in a HEK293-derived PhiC31 integrase activity reporter cell line significantly reduced the PhiC31-mediated recombination rate. Knocking down DAXX with a DAXX-specific duplex RNA resulted in increased recombination efficiency. Therefore, endogenous DAXX may interact with PhiC31 causing a mild inhibition in the integration efficiency. This is the first time that PhiC31 was shown to interact with an important cellular protein and the potential effect of this interaction should be further studied.

Expression pattern and preliminary functional analysis of human CREB4 gene.

cAMP response element-binding (CREB) proteins are a family of mammalian transcription activators that mediate cAMP and calcium-dependent gene expression through the cAMP response element (CRE). CREB4 is a novel member of the human CREB family. RT-PCR showed CREB4 transcripts were found in lung carcinoma LX-1, colon adenocarcinoma CX-1, prastatic adenocarcinoma PC-3, colon carcinoma G1-112, and pancreatic adenocarcinoma G1-103. Constructing CREB4 and CREB(215-395aa) fusion protein with the entire prokaryotic LexA protein respectively disclosed that CREB4 protein functioned as a transcription activator and its N-terminal accounted for the activation ability. Furthermore,a fusion protein of GFP and full-length CREB4 was localized in cytoplasm,whereas the fusion protein of GFP and a deletion mutant lacking the C-terminal putative transmembrane domain was translocated in nucleus. Our results suggested that putative transmembrane domain of CREB4 protein was associated with modulation of its function for the transcriptional activation.

Identification, expression pattern, and subcellular location of human RIP isoforms.

XRIP alpha was identified as an adapter protein involved in RAP nuclear import. Several homologs were reported in mammal EST analysis, but the expression pattern and genomic organization of hRIP isoforms were not clarified yet. We isolated nine isoforms of hRIP from a premade human fetal brain library. hRIP alpha is the longest isoform with 219 residues, containing a N-terminal arginine-rich basic region, followed by an acidic region and two C-terminal Zn finger-like structures. hRIP beta deletes one Zn-finger-like structure. Three hRIP alpha isoforms and four hRIP sigma isoforms express truncated proteins due to frame shift. hRIP gamma isoforms lost the C-terminal Zn-finger-like structure. hRIP delta isoforms only contain the N-terminal arginine-rich basic region and the core sequence of the acidic region. The genomic organization of hRIP was identified by bioinformatic analysis. hRIP, containing seven exons, is located at human chromosome 17p13. hRIP was expressed in all 16 detected human tissues with a similar pattern. All EGFP-hRIP fusion proteins were located at the nucleus in the HEK293 cell. The two-polar molecular structure of hRIP might be involved in the basic cell function, and plays a role in the alternative nuclear ingress.

Over-expression of Bim alpha3, a novel isoform of human Bim, result in cell apoptosis.

Bim proteins are essential factors of apoptosis. Nine isoforms of Bim have been submitted to GenBank database. In order to improve the understanding of the regulation of Bims' proapoptotic activity, we screened a multiple tissue cDNA panels for Bim isoforms and tested their proapoptotic activity by over-expression. Two novel cDNA isoforms of Bim family are generated by alternative splicing. One isoform encodes a 79 residue putative protein with a BH3 domain, named Bim alpha3. There is not any significant ORF found in another isoform, named Bim beta5. Subcellular localized analysis of EGFP-Bim fusion protein suggests Bim alpha3 distributed to both plasma and nucleus of HEK 293 cell. HEK 293 cells transfected with pcDNA-Bim alpha3 presented a similar proapoptotic activity (32.05 +/- 6.42%) with Bim alpha2 (30.14 +/- 2.66%). The proapoptotic activity of Bim alpha3 was obviously weaker than that of Bim S (46.52 +/- 5.07%) and Bim L (55.53 +/- 1.99%). Anti-sense over-expression of Bim in HEK 293 cells results in a weak down-regulated proapoptotic level. Expression pattern analysis reveals that both the novel cDNAs are expressed widely in normal tissue just like the other reported isoforms. The expression pattern of Bim isoforms shows tissue specific obviously. The results suggest that BH3 domain is sufficiency for proapoptotic activity of Bim proteins. The functional state of Bims might be regulated both in the transcript and post transcript process.

Purification, crystallization and preliminary X-ray studies of a p-nitrophenylphosphatase from Bacillus stearothermophilus.

Thermostable p-nitrophenylphosphatase from Bacillus stearothermophilus has been expressed in Escherichia coli, purified and crystallized. The crystals belong to space group C(2), with unit-cell parameters a = 67.17 A, b = 57.84 A, c = 62.49 A and alpha = 90.0 degrees, beta = 95.4 degrees, gamma = 90.0 degrees. Diffraction data were collected to 1.40 A resolution with a completeness of 94.7% (96.6% for the last shell), an R(fac) value of 0.074 (0.341) and an I/sigma (I) value of 30.1 (2.67).

Purification, crystallization and preliminary X-ray studies of GMP reductase 2 from human.

GMP reductase 2 from human has been expressed in Escherichia coli, purified and crystallized. The crystals belong to space group P3(2)21, with unit-cell parameters a = b = 110.6, c = 209.8 A, alpha = beta = 90, gamma = 120 degrees. Diffraction data were collected to 3.0 A with a completeness of 100% (100% for the last shell), an R(merge) value of 0.089 (0.189) and an I/sigma(I) value of 7.3 (3.2).

A novel cDNA encodes a putative hRALY-like protein, hRALYL.

High throughput cDNA sequencing and 5'-rapid amplification of cDNA ends (5'RACE) isolated two cDNAs that shared the same open reading fragment (ORF). Northern blot analysis with the fetal brain mRNA blots detected two transcripts with the length of 3.2 kb and 2.2 kb respectively. The ORF encodes a 291 residues putative protein that shares great homology with hRALY and hnRNPC. So it was named hRALY like protein, hRALYL. Expression pattern was detected by multiple-issue cDNA (MTC) panel based RT-PCR. It revealed that the transcripts of hRALYL were expressed ubiquitously in human tissues with different intensities. The transcript is highest in brain. Blast analysis found the cDNA corresponding to a contig NT_008292, which revealed the gene containing at least 9 exons and located the gene on human chromosome 8q21.13-8q21.2. hRALYL might be a member of hnRNPC subfamily.

Purification, crystallization and preliminary X-ray studies of human augmenter of liver regeneration.

Human augmenter of liver regeneration has been expressed in Escherichia coli, purified and crystallized. The crystals belong to space group C222, with unit-cell parameters a=51.7 A, b=78.8 A, c=63.7 A. Diffraction data were collected to 2.80 A with a completeness of 99.9% (99.9% for the last shell), a R(sym) value of 0.092(0.236) and an I/sigma(I) value of 6.2(2.7).

Expression, Purification, Crystallization and Preliminary X-ray Diffraction Analysis of the Mutant Pro(229)Ser of Thermostable Catechol 2,3-dioxygenase.

The mutant Pro(229)Ser of thermostable catechol 2,3-dioxygenase (TC23O) was expressed and purified. Enzymatic analysis revealed that its thermostability was decreased, the temperature corresponding to 50% enzyme activity being about 10.2 degrees lower than that of the wild type TC23O. Its kinetic parameter k(cat)/K(m) value (4.89x 10(6) mol(-1).s(-1)) was lower than that of the wild type TC23O(6.97x10(6) mol(-1).s(-1)). By the hanging-drop vapor-diffusion method using polyethylene glycol 400 as a precipitant, the mutant Pro(229)Ser of TC23O crystallizedat 4 degrees. X-ray diffraction analysis revealed that the crystals belong to the orthorhombic space group I(222) with unit-cell parameters a 7.059 nm, b 7.415 nm, c 13.311 nm, and they diffracted to at least 0.24 nm resolution. Assuming the presence of 2 molecules of the mutant Pro(229)Ser in the asymmetric unit, the Matthews parameter (Vm) was calculated to be 2.49x10( 3) nm(3).D(-1), and the solventcontent was about 51%. The crystal structure determination is now in progress.