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PubMed1980

Peptide mapping of cornea collagens from chick embryos by dodecylsulfate/polyacrylamide gel electrophoresis.

Using differential salt fractionation, different collagen types were obtained from corneas of 17-day-old chick embryos. The collagen precipitated by 1.7 M and 2.5 M NaCl consisted of type I collagen, having an alpha 1: alpha 2 ratio of 2. The collagen precipitated by 5 M NaCl contained alpha A, alpha B, alpha 1 and alpha 2 chains having an alpha A: alpha B ratio of 1 and an alpha 1: alpha 2 ratio of 10. The alpha 1 and alpha 2 chains isolated from corneas were found to have higher mobility in polyacrylamide gel electrophoresis in sodium dodecylsulfate as compared with that of their counterparts isolated from embryonic chick tendons. When the alpha 1 and alpha 2 chains isolated by polyacrylamide gel electrophoresis in sodium dodecylsulfate were subjected to limited protease degradations, the peptide maps obtained from corneal alpha chains were not identical to those of tendon alpha chains. It is suggested that the type I collagen in cornea is different from type I collagen in tendon. Also the results indicated that the alpha 1 chain present in the 5 M NaCl precipitate is a type I alpha 1 chain.

Animals↗
PubMed1977

Peptide map comparison of infectious pancreatic necrosis virus-specific polypeptides.

An investigation of virus-specific protein synthesis in infectious pancreatic necrosis virus (IPNV)-infected rainbow trout gonad cells was undertaken to find a relationship between the coding capacity of the virus genome (two segments of double-stranded RNA of 2.5 x 10(6) and 2.3 x 10(6) molecular weight) and the sizes and relative amounts of virus-specific proteins. Using polyacrylamide slabgel electrophoresis and autoradiography, eight distinct virus-specific polypeptides were detected in infected, [(35)S]methionine-labeled cells. These proteins may be grouped into three size classes on the basis of molecular weight: (i) large, alpha (90,000); (ii) medium, beta(1) (59,000), beta(2) (58,000), and beta(3) (57,000); and (iii) small, gamma(1) (29,000), gamma(1A) (28,000), gamma(2) (27,000), and gamma(3) (25,000). The combined molecular weight of these polypetides (373,000) is beyond the coding capacity of the virus genome. Purified IPNV contained polypeptides alpha, beta(3), gamma(1), and gamma(1A). Pulse-chase experiments and tryptic peptide map comparisons revealed that only four of the eight intracellular proteins were primary gene products, namely, alpha, beta(1), gamma(1), and beta(2), with a combined molecular weight of 205,000. Of these primary gene products only the alpha polypeptide was found to be stable, whereas the other three underwent intracellular proteolytic cleavage during virus morphogenesis. Polypeptide beta(1) was cleaved to generate beta(2) and beta(3); gamma(1) was trimmed to produce gamma(1A), and the only nonstructural primary gene product, gamma(2), was found to be a precursor of gamma(3). These results suggest that IPNV possesses a unique mechanism to synthesize three size classes of proteins using mRNA transcripts from two high-molecular-weight double-stranded RNA genome segments.

Animals↗
PubMed1985

Composition and peptide maps of cross-linked human choriogonadotropin-receptor complexes on porcine granulosa cells.

Radioiodinated human choriogonadotropin was affinity-cross-linked with a cleavable (nondisulfide) homobifunctional reagent to the hormone receptor on porcine granulosa cells and the solubilized sample was electrophoresed. Cross-linked samples revealed four additional bands of slower electrophoretic mobility in addition to the hormone alpha, beta, and alpha beta dimer bands. The four bands corresponded to masses of 68, 74, 102, and 136 kDa whereas the alpha beta dimer band corresponded to 50 kDa. Formation of the four bands requires the 125I-hormone to bind specifically to the receptor with subsequent cross-linking. Binding can be prevented by excess of native hormone but not by follitropin. A monofunctional analog of the cross-linking reagent failed to produce the four bands. They were also produced by cross-linking Triton X-100-solubilized hormone-receptor complexes. Reagent concentration-dependent cross-linking revealed that their formation was sequential; smaller complexes formed first and then larger ones. When gels of the cross-linked sample were treated with reagents that cleave covalent cross-links and then electrophoresed in a second dimension gel, 18-, 24-, 28-, and 34-kDa components were released, in addition to the alpha and beta subunits of the native hormone. Simultaneous peptide mapping of the cross-linked complexes in the gel matrix with Staphylococcus V8 protease or papain revealed progressive proteolysis to generate terminal fragments of 30 or 27 kDa, respectively. These fragments were unique to and commonly present in the 74-, 102-, and 136-kDa hormone-receptor complexes but were not produced by proteolysis of the cross-linked human choriogonadotropin (hCG) alpha beta dimer or the hCG alpha subunit. Apparently, the radioactively labeled segment(s) of the alpha subunit of 125I-hCG was cross-linked to the 24-kDa component. The results demonstrate the protein nature of the receptor and suggest that 125I-hCG was initially cross-linked to the 24-kDa component to generate the 74-kDa complex, then the 28- and 34-kDa components were sequentially cross-linked to the 24-kDa component in the 74-kDa complex to generate the 102- and 134-kDa complexes.

Animals↗
PubMedDate not supplied

Identification of transformation sensitive proteins recorded in human two-dimensional gel protein databases by mass spectrometric peptide mapping alone and in combination with microsequencing.

A comprehensive human keratinocyte two-dimensional (2-D) gel protein database has been established to study the expression levels and properties of the thousands of proteins that orchestrate various keratinocyte functions both in health and disease, cancer included. A major task in establishing such a database is to identify known proteins in the 2-D gel patterns as well as to reveal hitherto unknown proteins. To date, protein identification has been performed by one or a combination of the following methods: (i) comigration with known proteins, (ii) Western blotting using specific antibodies, (iii) microsequencing and (iv) vaccinia virus expression of full length cDNAs. Recently, the systematic identification of proteins has gained a new dimension with the advent of computer programs for searching peptide molecular mass databases with experimentally obtained peptide mass maps. Here we investigate this approach to identify proteins that are highly up- or down-regulated in simian virus SV40 transformed human keratinocytes (K14). Peptide mass maps of several proteins, including keratins 7, 8, 18 and 19 were obtained either by plasma desorption mass spectrometry (PDMS) analysis of high performance liquid chromatography (HPLC) purified peptides or by matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) of total digests. The results demonstrated that peptide mass maps can be used for a rapid and sensitive protein identification allowing fast screening of proteins recorded in 2-D gel databases. The mass spectrometric approach when combined with microsequencing strengthened identification, and added the possibility of full characterization of post-translational modifications and sequence variations.

Amino Acid Sequence↗
PubMed1988

Peptide mapping of polypeptides separated by two-dimensional electrophoresis: protease digestion directly on the two-dimensional gel followed by electrophoresis in reverse direction.

A method is described which allows to reveal simultaneously the proteolytic patterns of numerous polypeptides separated by two-dimensional electrophoresis. After two-dimensional electrophoresis, the gels were dipped successively in buffers for preequilibration, protease digestion, and reequilibration. They were then returned to the electrophoresis tank, and electrophoresis was continued for a short time. After silver staining, digestion products appeared, lined up behind the original polypeptide spots. The method allows proteolytic patterns of numerous polypeptides to be visualized simply and quickly. Among proteins of wheat leaves, 31 groups of related polypeptides were found according to the similarity of their proteolytic patterns.

Electrophoresis, Gel, Two-Dimensional↗
PubMed1990

Molecular epitope identification by limited proteolysis of an immobilized antigen-antibody complex and mass spectrometric peptide mapping.

Sequences of antigenic determinants were identified by limited proteolysis of peptide antigens bound to an immobilized monoclonal antibody and direct molecular weight determination of the monoclonal antibody-bound peptide fragments by 252Cf plasma desorption mass spectrometry. The epitope peptides to the monoclonal antibody h453 [Burger, R., Zilow, G., Bader, A., Friedlein, A. & Naser, W. (1988) J. Immunol. 141, 553-558] were isolated from immobilized antigen-antibody complexes by partial trypsin digestion. A synthetic eicosapeptide comprised of the C-terminal sequence of the human complement component polypeptide des-Arg77-C3a as well as guinea pig des-Arg78-C3a was used as an antigen. Conditions were developed under which trypsin specifically degraded the antigens without inactivation of the immobilized antibody. After proteolysis, epitope peptides were dissociated from the antibody with 4 M MgCl2. The antigenic peptides were purified by HPLC and identified by 252Cf plasma desorption mass spectrometry. The epitope recognized by h453 resides on the C-terminal tryptic peptides of human (residues 70-76) and guinea pig (residues 70-77) C3a. As an estimation of accuracy this method is able to provide, trypsin digestion of immune complexes caused cleavage of the antigen within a distance of two amino acid residues upstream from the epitope.

Amino Acid Sequence↗
PubMed2000

Specific applications of capillary electrochromatography to biopolymers, including proteins, nucleic acids, peptide mapping, antibodies, and so forth.

Separation of biopolymers is an obvious application of capillary electrochromatography (CEC) technology, since speed and resolution should increase significantly over high-performance liquid chromatography (HPLC). All too often, HPLC chromatograms of polymers show poorly resolved envelopes of overlapping peaks from oligomers. The practical limitation of column length and pressure drop has hindered development of high resolution separations of many polymers in HPLC. However, this generally applies only to packed beds of small particles, and not to continuous (or monolithic) beds, as introduced by Hjerten et al. [S. Hjerten, Ind. Eng. Chem. Res. 38 (1999) 1205; S. Hjerten, C. Ericson, Y.-M. Li, R. Zhang, Biomed. Chromatogr. 12 (1998) 120; C. Ericson, S. Hjerten, Anal. Chem. 71 (1999) 1621; J.-L. Liao, N. Chen, C. Ericson, S. Hjerten, Anal. Chem. 68 (1996) 3468; S. Hjerten, A. Vegvari, T. Srichaiyo, H.-X. Zhang, C. Ericson, D. Eaker, J. Capillary. Elec. 5 (1998) 13; C. Ericson, J.-L. Liao, K. Nakazato, S. Hjerten, J. Chromatogr. A 767 (1997) 33; S. Hjerten, D. Eaker, K. Elenbring, C. Ericson, K. Kubo, J.-L. Liao, C.-M. Zeng, P.-A. Lidstrom, C. Lindh, A. Palm, T. Srichiayo, L. Valtcheva, R. Zhang, Jpn. J. Electroph. 39 (1995) 1]. Throughout this review we will refer to such packings as monolithic or continuous beds, but they are identical type packings, formed by the in situ polymerization in the capillary or column. CEC capillaries can be much longer, and contain smaller particles than is practical for HPLC. This improves resolution significantly. CEC is able to capitalize on existing mobile phase technology developed over 30 years to improve separations. The requirement that the mobile phase simultaneously promote the separation and mobile phase mobility needs to be considered. In RPLC, this dual role is not much of a problem. It may be much more important in other modes, particularly ion-exchange (IEC). As the field develops, it is becoming clear that CEC is not just a simple extension of HPLC. Instruments, column technology and operating optima are clearly different than HPLC. CEC will develop into its own unique field. Open tubular HPLC is almost precluded by the high pressures required for forcing liquids through 10 microm or smaller capillaries. Electroosmotic pumping (EOF) avoids the pressure constraints and provides better flow profiles. Compared to HPCE, the ability to interact with the stationary phase may enable separations that would be difficult with electrophoresis alone. Since the mobile phase can be less complex than micellar electrokinetic chromatography (MEKC), CEC also avoids the problem of high background signals from the micelle forming compounds. Thus CEC-MS (mass spectrometry) is expected to be even more powerful than HPCE-MS. The fortuitous, simultaneous development of matrix assisted laser desorption-time of flight MS (MALDI-TOF-MS) technology will enable extension of the mass range to above 100 000 Da. Lack of familiarity is the perhaps the largest liability of CEC compared to other techniques. This paper critically compares the state-of-the-art of CEC with HPLC and HPCE, with a particular emphasis on separation of biopolymers. The goal is to help the reader overcome the fear of the unknown, in this case, CEC.

Antibodies↗
PubMed1984

Conservation of molecular structure of DNA polymerase beta in vertebrates probed by tryptic peptide mapping.

DNA polymerase beta's from mouse myeloma, chick embryo, and cherry salmon testis were all composed of a single polypeptide of about 40K daltons as judged by a sodium dodecyl sulfate-polyacrylamide gel electrophoresis of extensively purified enzyme preparations. Although the enzyme from bullfrog ovary was not fully purified, its molecular weight was estimated to be the same as that of the chick enzyme by immunological detection after electrophoresis. All the enzymes tested cross-reacted immunologically with the antibody against chick DNA polymerase beta, indicating that they have a common molecular structure, at least in part. Two-dimensional maps of radioiodinated tryptic peptides directly showed the presence of highly conserved amino acid sequences among mouse, chick, and cherry salmon enzymes. This conserved structure is thought to be essential for the enzyme activity, which is very similar among all these vertebrates.

Animals↗
PubMed1988

Tubulin structure probed with antibodies to synthetic peptides. Mapping of three major types of limited proteolysis fragments.

We synthesized five peptides homologous to the potentially antigenic positions alpha(214-226), alpha(430-443), alpha(415-443), beta(241-256), and beta(412-431) of the porcine brain tubulin sequences. These peptides were successfully employed to raise tubulin-cross-reactive antibodies. The antibodies are specific of the regions of tubulin spanned by the peptides. They react specifically with the tubulin bands in immunoblots and with microtubules in immunofluorescence assays of cytoskeletons. The peptides of the C-terminal regions have also been employed to localize determinants recognized by two available monoclonal antibodies to tubulin in the positions alpha(415-430) and beta(412-431), respectively. In a first application of the anti-peptide antibodies, we have mapped the fragments of limited proteolysis of purified calf brain tubulin by trypsin, chymotrypsin, papain, thermolysin, subtilisin, and protease V8 from Staphylococcus aureus. Thirty-seven peptides have been identified, of which 32 have been unequivocally aligned into the tubulin sequences on the basis of their antigenic reactivity. There are three major, well-defined zones of preferential cleavage by the proteases: the C-termini and two internal zones in each chain. C-Terminal cleavages of both chains by subtilisin do not remove the antigenic reactivity of the zones alpha(415-430) and beta(412-431). C-Terminal cleavages by protease V8 are preferential of beta-tubulin. All six proteases tested cleave alpha- and/or beta-tubulin at one or both of the internal zones. These zones are located roughly at one-third and two-thirds of the chain length in both subunits. Therefore, a model of the tubulin monomers is proposed which consists of three major, proteolytically defined, compact regions (N-terminal, middle, and C-terminal thirds) and the cleavable zones. This model is discussed with the tubulin structural information presently available.

Amino Acid Sequence↗
PubMed2004

MALDI MS peptide mapping performance by in-gel digestion on a probe with prestructured sample supports.

Matrix-assisted laser desorption/ionization (tandem) mass spectrometry (MALDI MS) is widely used in protein chemistry and proteomics research for the identification and characterization of proteins isolated by polyacrylamide gel electrophoresis. In an effort to minimize sample handling and increase sample throughput, we have developed a novel in-gel digestion protocol where sample preparation is performed directly on a MALDI probe with prestructured sample support. The protocol consists of few sample-handling steps and has minimal consumption of reagents, making the protocol sensitive, timesaving, and cost-efficient. Performance of the on-probe sample preparation protocol was demonstrated by analysis of a set of rat liver proteins obtained from a fluorescently stained (Cy3 and SyproRuby) two-dimensional polyacrylamide gel. The success rate of protein identification by on-probe tryptic digestion and MALDI peptide mass mapping was 89%. The on-probe in-gel digestion procedure provided superior sensitivity and peptide mass mapping performance as compared to our standard in-gel digestion protocol. The on-probe digestion technique resulted in significantly improved amino acid sequence coverage of proteins, mainly due to efficient recovery and detection of large (>1.5 kDa) hydrophobic peptides. These observations indicate that numerous tryptic peptides are lost when using the standard in-gel digestion methods and sample preparation techniques for MALDI MS. This study also demonstrates that the on-probe digestion protocol combined with MALDI tandem mass spectrometry provides a robust platform for proteomics research, including protein identification and determination of posttranslational modifications.

Animals↗
PubMed1983

Assignment of a polymorphic polypeptide to the human mitochondrial DNA unidentified reading frame 3 gene by a new peptide mapping strategy.

A new method of peptide analysis is presented which allows assignment of unknown proteins to coding regions of genomes which have been sequenced. This approach involves comparison of the molecular weights of peptides generated by partial proteolytic digestion with those predicted for a protein whose primary amino acid sequence is deduced from a corresponding nucleotide sequence. The proteolytic digestions are accomplished in situ in the stacking gel of a two-dimensional polyacrylamide gel system. We have used this system to show that two variant proteins of the human mitochondrial DNA, MV-1 and MV-2, are allelic and encoded by the unidentified reading frame 3 (URF 3) gene. This assignment was supported by sequence analysis of a clone of this mtDNA region from a HeLa cell line which expresses the uncommon variant MV-2. Four nucleotide changes were found in HeLa URF 3, relative to the reported sequence from human placenta. Two of these changes alter the primary amino acid sequence of the encoded protein. It is proposed that one of those amino acid changes may account for the observed molecular weight variation in MV-1 and MV-2 by proteolytic cleavage, conformational change, or secondary modification. We have used this method to also assign a mitochondrially translated protein to URF 6. These are the first assignments of mitochondrially synthesized polypeptides to human URF genes and prove conclusively that at least some of these genes are expressed in human cells.

Amino Acid Sequence↗
PubMed2004

Peptide mapping by capillary electrophoresis with Pluronic F127.

Separation of peptides and proteins by capillary zone electrophoresis suffers from the interaction of these solutes with the capillary wall which results in the formation of broad peaks and low resolution. To minimize the protein/peptide-capillary wall interaction we tried to use Pluronic F127, a triblock copolymer of the general formula (polyethylene oxide)(x)(polypropylene oxide)(y)(polyethylene oxide)(z) when x=106, y=70 and z=106 which can be considered a surfactant capable of self-association both into isotropic and anisotropic gels. The analytes studied were enzymatic digests (obtained by trypsin or pepsin treatment) of insoluble matrix proteins from avian eggshell. The best separations were obtained by a system exploiting 10% Pluronic F127 in 20 mmol/l phosphate buffer, pH 2.5. Electrophoretic peptide profiles obtained were very complex owing to the complicated nature of the samples (the exact composition of the proteinous insoluble part of the eggshell is still unknown). The separation in phosphate buffer only offered complex maps of incompletely resolved peaks. The use of Pluronic F127 distinctly improved the separation with a considerably better resolution regarding both the number of peaks obtained and the quality of the separation.

Buffers↗
PubMedDate not supplied

[The peptide mapping of the E2-2 and E2-6 sites of the E2 glycoprotein in the Venezuelan equine encephalomyelitis virus].

Nine peptides were synthesized for detailed mapping of VEE virus E2-2 and E2-6 sites responsible for the formation of protective antibodies that neutralize the virus and block hemagglutination. The sequence of the peptides over-lapped the regions of amino acid residues 30-75 and 202-250 of VEE virus E2 protein in which antigenic mutations caused by monoclonal antibodies to E2-2 and E2-6 sites had been mapped. None of the synthesized peptides reacted in the enzyme immunoassay with a panel of 17 Mabs to VEE virus E2 protein. However, eight peptides reacted with polyclonal antiviral serum and two of them elicited antiviral antibody production. The E2-2 site might be associated with amino acid residues 30-45, and the region of E2 residues 57-62 in which antigenic mutations are observed is not a linear type antigenic determinant, but participates in the formation of antigenic determinants of the conformational type. The mapping of residues 202-250 demonstrated that all the peptides in this region were well recognized by polyclonal antiviral serum. The residues 235-240 were shown to form a linear epitope which provided a crossover between VEE and EEE viruses and was not recognized by 19 types of monoclonal antibodies cross-reacting with VEE and EEE viruses.

Amino Acid Sequence↗
PubMed2003

Peptide mapping of immunoglobulin E and immunoglobulin G immunodominant epitopes of an allergenic Blomia tropicalis paramyosin, Blo t 11.

BACKGROUND: The identification of immunodominant peptides containing the IgE and IgG epitopes on allergen molecules is an important step in understanding the interaction of the allergen with the immune system and, thus, essential for the development of effective immunotherapeutic and diagnostic reagents. The present study aimed to map the IgE and IgG immunodominant peptides of Blomia tropicalis (Bt) allergen Blo t 11, a high molecular weight allergen homologous to paramyosin, exhibiting important allergenic activity. METHODS: Eleven overlapping fragments of Blo t 11 cDNA gene were expressed as glutathione s-transferase (GST) fusion peptides, which were affinity-purified using the glutathione-Sepharose column. Human IgE and IgG immunodominant peptides were determined by dot blot immunoassay using crude Bt extract-positive sera from asthmatic patients. Evaluation of allergenicity, specific hIgG subclass analysis, and cross- and self-inhibition studies were determined by enzyme-linked immunosorbent assay. RESULTS: Blo t 11 contains multiple IgE and IgG immunodominant peptides scattered throughout the molecule. The dominant IgE and IgG peptides were mapped at amino acid positions 336-557 and 698-875, respectively. An immunodominant peptide (fD) registered a higher percentage of IgE and IgG reactivity compared to the rFL-Blo t 11. Significant serum levels of Blo t 11- and fD-specific IgG1, IgG2 and IgG4, but not IgG3 were detected in the Bt extract-positive sera tested. Cross-inhibition study revealed the rFL-Blo t 11 was significantly inhibited by fD. CONCLUSION: The IgE and IgG immunodominant peptides of Blo t 11 have been mapped. Our data suggest that utilization of Blo t 11 fragment(s) or chimeric fusion fragments containing IgE and IgG epitopes could be a better alternative in the development of diagnostic and therapeutic reagents for mite allergy.

Allergens↗
PubMedDate not supplied

Synthetic peptides mapping to epitopes of the extracellular domain of the interleukin-2 receptor beta-chain to inhibit T-cell activation.

Expression of the high-affinity IL-2 receptor (IL-2R) on the surface of activated T cells makes it an attractive target for selective inhibition of alloreactive T cells in organ transplantation. IL-2 binds to its receptor via the extracellular domain of the beta-chain. In this study we synthesized synthetic peptides that map to epitopes of this domain and tested their ability to inhibit the activation and proliferation of mitogen-stimulated peripheral-blood T cells. Solid-phase synthesis was applied to create three oligopeptides of primary structures corresponding to the epitopes M(107)-E(118), Y(178)-Q(199), and E(190)-Q(199) of the extracellular domain of the IL-2Rbeta-chain. A nonhomologous peptide served as control. Peripheral-blood mononuclear cells isolated from 16 healthy volunteers (median age 41 years, range 26 to 56 years) were cultured with various concentrations of peptides and the mitogen phytohemagglutinin (PHA). The inhibitory effect of the peptides on cell proliferation was evaluated by automated cell counting and colorimetric proliferation assays. Cell activation was assessed by immunophenotyping using antibodies directed toward CD4, CD25, or CD69. The amount of IL-2 in culture supernates was measured by enzyme-linked immunoassay. Cultures in the presence of the peptide M(107)-E(118) (500 nmol/L) inhibited PHA-induced T-cell proliferation by 38%, and IL-2 secretion by 57%. Immunophenotyping confirmed suppression of activated T cells. Peptides Y(178)-Q(199) and E(190)-Q(199) inhibited proliferation, but failed to significantly affect IL-2 secretion. The control peptide showed no effect on the activation parameters. Our data indicate that the M(107)-E(118) peptide has promise for organ transplantation therapy.

Adult↗