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Results for “Peptide Mapping”

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At least 19 recordsLinked to original sources

PubMed1999

Characterization of a solid-phase extraction device for discontinuous on-line preconcentration in capillary electrophoresis-based peptide mapping.

Peptide mapping by capillary electrophoresis (CE) with UV detection is problematic for the characterization of proteins that can only be obtained at low micromolar concentrations. Dilution of peptide fragments during digestion of the protein can further reduce the detection sensitivity in peptide mapping to the point where analysis at sub-micromolar concentrations is not possible. A remedy to this problem is preconcentration (sample enrichment) of the proteolytic digest by solid-phase extraction (SPE). To minimize non-specific adsorptive losses during sample handling, on-line SPE-CE is preferred. However, packed-inlet SPE-CE is not always feasible due to either instrument or sample limitations. We describe here a simple method of preconcentration by discontinuous on-line SPE-CE, specifically applied to peptide mapping in low-pH separation buffer after protein digestion in a solid-phase enzyme microreactor. The SPE-CE system does not require application of a low pressure during electrophoretic separation to overcome reversed electroosmotic flow because the preconcentrator device is disconnected from the separation capillary before the electric field is applied. Up to a 500-fold preconcentration factor can be achieved with this device, which can be reused for many samples. Parameters such as the volume of desorption solution, the adsorption/desorption (chromatographic) process, reproducibility of packing the SPE preconcentrator and effects of sample concentration on the peptide map are investigated.

Adsorption↗

PubMed2004

Data preprocessing by wavelets and genetic algorithms for enhanced multivariate analysis of LC peptide mapping.

Peptide mapping by means of liquid chromatography is a powerful technique used for the characterisation and analysis of the primary structure of proteins. Subtle changes in the covalent structure of the protein can be detected by means of the chromatographic profile (fingerprint). Chromatographic methods, however, display variations in the chromatographic profile even at identical instrumental settings and sample conditions. These variations may be due to changes of the chromatographic conditions, e.g. slight shifts in column temperature, and degradation or alterations of the stationary phase or small changes in the trifluoroacetic acid (TFA) concentration. Such variations may result in varying retention times and peak shapes of the analytes and differences in the chromatographic baseline, thereby having a detrimental impact on the results obtained on multivariate analysis of peptide maps. In order to reduce the non-sample-related variations and to be able to more fully extract the information in peptide mapping, approaches for achieving this objective are outlined in the present study. These methods are denoising and data compression of the chromatograms by wavelets, baseline corrections by linear interpolation, and peak shift alignments towards a target chromatogram by means of a genetic algorithm. Visual inspections of preprocessed chromatograms and principal component analysis (PCA) score plots demonstrate the efficiency of the methodology used. Furthermore, deliberately added changes, e.g. insertions of small Gaussian peaks (outliers), are more easily detected by the proposed methods than from the original chromatograms by multivariate analysis.

Algorithms↗

PubMed1996

Delayed extraction improves specificity in database searches by matrix-assisted laser desorption/ionization peptide maps.

Peptide mass maps obtained by matrix-assisted laser desorption ionization (MALDI) are an attractive means to identify proteins by searches in sequence databases. Here we demonstrate that the recently introduced delayed ion-extraction technique, when coupled to reflectron MALDI time-of-flight mass spectrometry, leads to dramatically improved search specificity. Routine resolution in the range of 6,000 to 12,000 allows assignment of monoisotopic masses throughout the peptide mass range. Database searches can be performed with high precision by use of a mass accuracy which is currently better than 30 ppm over a wide mass range and better than 5 ppm for a narrow mass range. This high performance makes it possible to identify proteins with fewer peptide masses than before. Additional low intensity peaks can be assigned after a search because of the improved signal-to-noise ratio of delayed-extraction peptide mass spectra, increasing sequence coverage of matched proteins. The improvements in database search specificity can be used to identify the components of simple protein mixtures. In combination with advanced sample preparation and automation techniques, delayed-extraction MALDI time-of-flight mass spectrometry is now an extremely powerful tool for the database identification of proteins.

Amino Acid Sequence↗

PubMed1978

[Mobility on peptide maps of peptides obtained by tryptic hydrolysis of lysozyme oxidized at the S-S-bonds].

The peptide map obtained by tryptic hydrolysis of the lysozyme oxidized at the S--S-bonds was characterized and compared with that of tryptic hydrolysis of the reduced lysozyme. It was shown that the mobility of peptides containing oxidized amino acid residues is decreased under electrophoresis and chromatographic treatment. Under a decrease in the peptide charge during oxidation, the changes in electrophoretic and chromatographic mobilities show a correlation. In case when the peptide charge remains unchanged, only chromatographic mobility may be altered. It is demonstrated that the cystein residues significantly interfere with the effects of trypsin on the adjacent bonds.

Chromatography, Paper↗

PubMed1974

The selective isolation of an active-site histidine peptide from chymotrypsin-alpha by diagonal peptide 'mapping'. An N-tau-carboxymethylhistidine diagonal peptide "mapping.".

1. The selective isolation of an ;active' histidine peptide from reduced and cyanoethylated chymotrypsin-alpha inhibited with Tos-Phe-CH(2)Cl (l-1-tosylamido-2-phenylethyl chloromethyl ketone) was obtained with a His(tauCm) (N(tau)-carboxymethylhistidine) diagonal peptide-;mapping' technique. Performic acid vapours, used between the first and second dimensions of the diagonal peptide ;map', resulted in a peracid rearrangement of the alkylated (Tos-Phe-CH(2))-histidine-57 residue into an N(tau)-carboxymethylhistidine residue. The consequent change in electrophoretic mobility allowed isolation of peptides that contained the ;active' histidine. 2. Peptides containing methionine or S-cyanoethylcysteine were oxidized to their sulphones during the treatment. Peptides in which these residues were N-terminal were selectively isolated on the basis of the change in electrophoretic mobility at pH6.5 which was due to the depression of the pK of the terminal amino group by the inductive effect of the sulphonyl group. 3. An attempt to apply the method to subtilisin BPN' inhibited with l-1-benzyloxycarbonylamido-2-phenylethyl bromomethyl ketone failed to yield a peptide containing N(tau)-carboxymethylhistidine, although peptides containing N-terminal methionine were isolated by the procedure.

Amino Acid Sequence↗

PubMed1994

High resolution 2-D peptide mapping with subsequent analysis of peptides by microsequencing or lectin binding directly from PVDF membrane blots.

Peptide mapping is a technique that is frequently used to characterize proteins. Typically, the method involves the cleavage of proteins in solution or in a gel with the subsequent separation of the peptide fragments on a 1-D SDS PAGE gel. Electrophoretic peptide maps are often used to compare homologous proteins from related organisms to derive evolutionary relationships. Other applications of peptide mapping include immunoblotting studies of selected proteins. Two-dimensional peptide mapping, a less common technique, has traditionally involved a combination of thin layer or paper chromatography and electrophoresis. Amino acid sequencing of peptides that were separated using this method and then subsequently blotted to PVDF membrane was reported recently. However, the resolution achieved with these methods is far below that which can be achieved with conventional 2-D electrophoresis of proteins in polyacrylamide gels. This report describes an electrophoretic system for the high resolution 2-D separation of peptides in gels with subsequent blotting to a novel cationic PVDF membrane, Immobilon-CD, and microsequencing directly from the 2-D blot. In addition, the high resolution peptide maps can be further analyzed by techniques such as lectin probing to determine post-translational modifications.

Amino Acid Sequence↗

PubMed1992

Identification of sites of degradation in a therapeutic monoclonal antibody by peptide mapping.

A peptide mapping procedure was developed to locate regions of a monoclonal antibody, OKT3, that undergo chemical modification as the molecule degrades upon storage. The structures of these peptide degradation products were investigated. Deamidation at specific asparagine residues and oxidation of a cysteine and several methionines were found to be major routes of OKT3 degradation. A unique chain cross-linked degradation product was also observed and characterized. Changing the storage conditions of the antibody affected the relative distribution of degradation products. These results were useful in the development of more stable formulations for OKT3, and the methods can be used in the characterization of other monoclonal antibodies intended for therapeutic use.

Amino Acid Sequence↗

PubMed1982

Peptide mapping of multiple forms of cyclic nucleotide phosphodiesterase.

Purified multiple forms of 3':5'-cyclic-nucleotide phosphodiesterase (EC 3.1.4.17) were analyzed using two-dimensional tryptic pep]tide mapping of radioiodinated peptides. Comparisons of peptide maps of rat liver insulin-sensitive phosphodiesterase (PDE) with rat brain calmodulin-sensitive PDE suggest that some peptides co-migrate (31-43% co-migration). However, except for a single peptide, bovine retinal rod outer segment PDE, peptide maps appear unrelated to the other two forms (7-12% co-migration). In contrast, peptide maps of a 36,000-dalton proteolysis product of calmodulin-sensitive PDE are highly related to the peptide maps of a rat brain calmodulin-sensitive holoenzyme (73% co-migration). These results suggest that the multiple PDE forms are distinct molecular entities.

3',5'-Cyclic-AMP Phosphodiesterases↗

PubMed1989

Multisite phosphorylation of microtubule-associated protein 2 (MAP-2) in rat brain: peptide mapping distinguishes between cyclic AMP-, calcium/calmodulin-, and calcium/phospholipid-regulated phosphorylation mechanisms.

Microtubule-associated protein 2 (MAP-2), a cytoskeletal protein of 280 kilodalton that is highly enriched in dendrites and neuronal perikarya, is subject to both cyclic AMP-, calcium/calmodulin-, and calcium/phospholipid-regulated phosphorylation when incubated with [gamma-32P]ATP in vitro. We have analyzed the different sites in MAP-2 phosphorylated by these three kinases in fresh or boiled cytosol from different regions of the rat brain, in particular the olfactory bulb, where only one form (MAP-2B) is present, and the cerebral cortex, where both forms (MAP-2A and MAP-2B) are equally enriched. Cyclic AMP-dependent protein kinase and calcium/calmodulin-dependent protein kinase II phosphorylated four common phosphorylation sites, as well as a number of distinct sites that were unique to each enzyme. Calcium/phospholipid-dependent protein kinase phosphorylated a minimum of 15 sites, only one of which appeared to be shared with the other protein kinases. Only serine residues were phosphorylated by cyclic AMP-dependent and calcium/phospholipid-dependent protein kinases, while both serine and threonine residues were phosphorylated by calcium/calmodulin-dependent protein kinase II. No differences were observed in the peptide maps of phospho-MAP-2 prepared from different brain regions. These results emphasize the complexity of the phosphorylation systems that may regulate the function of MAP-2 in situ.

Adenosine Triphosphate↗

PubMed1986

Antigenic and allergenic determinants of ovalbumin. I. Peptide mapping, cleavage at the methionyl peptide bonds and enzymic hydrolysis of native and carboxymethyl OA.

The effects of enzymic cleavage and perturbing the conformation of the allergenic and antigenic determinants of hens egg white albumin (OA) were examined. Hens egg white extract of a total protein concentration 8.43 g/l was prepared. Isoelectric focusing in sodium dodecyl sulfate and polyacrylamide gel peptide maps for the crude egg white extract showed 26 spots visualized by staining with Coomassie blue. The OA was purified using a TSK-2000 gel filtration chromatography column. The specific allergenic reactivity of the purified OA as measured by RAST inhibition and direct RAST was relatively high: 3 micrograms gave an inhibition of approximately 10%. The cleavage of OA with cyanogen bromide resulted in 4 fractions, all capable of binding specific IgE with the first peak showing the highest inhibition. Thermal denaturation of OA had no direct effect on the antigenic reactivity. RAST inhibition values for the denatured protein were similar to those of the native protein. Carboxymethylation of OA gave a product with only 20% of the inhibition reactivity. Further treatment with trypsin did not abolish the allergenic and antigenic reactivities as shown by RAST inhibition and by deflection of OA line in rocket line immunoelectrophoresis. On the other hand, limited pepsin hydrolysis destroyed the antigenic structure of the molecule. The reactivity of OA is thus relatively stable and could easily be retained making it possible to identify the allergenic determinants of enzymic hydrolysates used for elucidating the antigenic structure of the molecule.

Allergens↗

PubMed2001

Peptide mapping and disulfide bond analysis of the cytoplasmic region of an intrinsic membrane protein by mass spectrometry.

Intrinsic membrane proteins pose substantial obstacles to analysis by common analytical techniques due to their hydrophobic nature and solubilization requirements. This is the case for studies involving HPLC coupled to mass spectrometry. We have developed an HPLC/mass spectrometry approach to explore and map the peptide sequence of the SERCA1a Ca(2+)-ATPase from the sarcoplasmic reticulum an integral membrane protein of 110 kDa. After extensive proteolysis of the protein, the mass of the proteolytic fragments was analyzed by HPLC/mass spectrometry. Only part of the cytoplasmic fragments was recovered under nondenaturing conditions. On the other hand, peptide fragments obtained under denaturing conditions were found to cover nearly all the cytoplasmic region. Sarcoplasmic reticulum (SR) Ca(2+)-ATPase contains 24 cysteine residues, 18 of which are in the cytosolic or lumenal region of the protein. Peptides containing free cysteines were identified by a mass increase resulting from carboxyamidomethylation of the cysteines with iodoacetamide. Alkylation reactions were executed either before or after reduction of the peptide fragments by dithiothreitol. Analysis of the mass of the fragments indicates that no disulfide bonds exist in the cytoplasmic portion of SR Ca(2+)-ATPase.

Alkylation↗

PubMed1981

Analysis of HLA-DR polymorphism by two-dimensional peptide mapping.

Two-dimensional peptide mapping was used to study the polymorphism of DR antigens, membrane glycoproteins composed of two chains, alpha and beta, and encoded by the human major histocompatibility complex (MHC). Four DR antigens were purified by immunoabsorption from four human lymphoblastoid cell lines homozygous at the DR locus. After labeling with 125I, alpha and beta chains were separated by polyacrylamide gel electrophoresis in sodium dodecyl sulfate and digested with pepsin. Comparison of the peptide maps showed a marked degree of polymorphism among beta chains: only 43% of peptides were common to all four chains and 15-21% of the spots were unique to a given chain. By contrast, only a limited variability was observed among alpha chains. Homology was 75% for the four chains and the percentage of unique peptides was very low. DR7 did not possess even a single unique peptide. The limited variability among alpha chains and the lack of "private" peptides in one of them point to the conclusion that the beta chain is the unique carrier of the alloantigenic specificities. Higher homology within the known crossreactive groups was not observed, suggesting that the determinants responsible for crossreactivity are on different molecules. From a genetic point of view, because beta chains show allele-associated polymorphism, they are likely to be MHC encoded, whereas the minor differences among alpha chains do not allow a similar conclusion. The available data point to an analogy between these DR antigens and the mouse I-E/C antigens.

Alleles↗

PubMed2000

Improvement of Staphylococcus aureus-V8-protease hydrolysis of bovine haemoglobin by its adsorption on to a solid phase in the presence of SDS: peptide mapping and obtention of two haemopoietic peptides.

Hydrolysis of bovine haemoglobin by the V8 protease from Staphylococcus aureus (EC 3.4.21.19) was studied in the presence of SDS in a homogeneous-phase and in a solid-phase system. In both cases, hydrolyses were performed at 37 degrees C, in 50 mM phosphate buffer, pH 6.0, containing 0.1% SDS. Solid-phase hydrolyses were carried out with haemoglobin adsorbed on a negatively charged hydrophobic support, namely Amberlyst 15Wet (Rohm and Haas). The peptides were isolated from the hydrolysates by reverse-phase HPLC and analysed for their amino acid composition on a Waters Pico-Tag column, confirmed by second-order derivative spectrometry or by MS. A peptide map of the hydrolysates was drawn up, and numerous new cleavages in haemoglobin chains were observed, especially after Asp. This study showed that SDS permitted a dramatic improvement in the hydrolysis of whole haemoglobin by V8 protease in both homogeneous-phase and solid phase systems after adsorption of haemoglobin on to an anionic support. Moreover, in the heterogeneous phase, all the theoretical cleavage sites of V8 protease, Asp as well as Glu bonds, were hydrolysed, except for four sites which were resistant owing to strong interactions with the support. These results led to us obtain two haemopoietic peptides, namely peptide alpha (Leu(76)-Pro-Gly-Ala-Leu-Ser-Glu(82)) and peptide beta (Lys(94)-Leu-His-Val-Asp-Pro-Glu(100)). These active peptides have never before been prepared from bovine haemoglobin, and they may have great potentialities in biotechnology.

Adsorption↗

PubMed1985

Comparative studies of the neurofilament triplet protein peptide mapping by chemical cleavage.

Peptide mapping of the three neurofilament protein subunits with apparent mol. weights of 210 kDa, 160 kDa and 70 kDa was performed with two different reagents: CNBr, BNPS-Skatole leading to the cleavage of methionyl and tryptophanyl bonds respectively. With BrCN we obtained two large fragments resistant to the cleavage, with mol. wts of 85 kDa for the 160 kDa and 135 kDa for the 210 kDa neurofilament proteins respectively. These fragments were located on the C-terminal part of the proteins (the tails) and correspond to specific regions responsible for their physiological identity. On the other hand, the cleavage with BNPS-Skatole at the tryptophanyl bonds gave similar patterns. The 210 kDa and 160 kDa neurofilament proteins gave a doublet of high mol. wt resistant to the cleavage, corresponding very likely to the C-terminal part and 4 fragments of mol. wt between 30 and 40 kDa corresponding to the N-terminal part. The neurofilament triplet share a common 30.5 kDa fragment located on the N-terminal part. From these peptide mapping studies, we conclude that the two neurofilament subunit proteins with mol. wts of 160 kDa and 210 kDa are different but related structures and that the CNBr characterized cleavage fragments of mol. wt 85,000 and 135 kDa are suitable polypeptides for sequence and immunological studies of the C-terminal part of these proteins.

Animals↗

PubMed1994

Identification of proteins in polyacrylamide gels by mass spectrometric peptide mapping combined with database search.

Mass spectrometric peptide mapping of proteins separated by one-dimensional sodium dodecyl sulphate polyacrylamide gel electrophoresis has been investigated. The best results are obtained after blotting of the proteins onto polyvinylidene difluoride membranes followed by enzymatic digestion of the protein on the membrane. The peptide maps were investigated in terms of completeness and applicability for protein identification using a previously developed database search program as well as for the possibility for full characterization of covalent modifications in the proteins. The most complete peptide maps were obtained when the proteins were reduced and alkylated on the membrane prior to enzymatic digestion followed by separation of the resulting mixture by high performance liquid chromatography prior to mass spectrometric analysis. Such peptide maps cover up to 98% of the sequence and consequently may allow complete characterization of post-translational modifications in proteins for which the amino acid sequence is known. The fastest and most sensitive procedure to obtain peptide maps sufficient for protein identification was direct analysis of the extracted peptide mixture by matrix-assisted laser desorption ionization (MALDI) mass spectrometry. The use of external and internal calibration of MALDI spectra for database searches is evaluated as well as the possibility of including a post-calibration routine within the search program.

Alkylation↗

PubMed1986

Biochemical and immunological studies of bovine and porcine neurofilament triplet proteins by peptide mapping after cyanogen bromide cleavage.

Peptide mapping of the three bovine and porcine neurofilament protein subunits ("L", "M" and "H") with apparent mol. wts of 70, 160 and 210 kDa were performed with CNBr, leading to the cleavage of methionyl bonds. We have obtained two characteristic large fragments with molecular weights of 85 kDa for the "M" bovine subunit and 135 kDa for the "H" subunit of bovine neurofilament. A comparison of the electrophoretic patterns of CNBr generated polypeptides of "L" subunit from beef and pig showed that they are highly related structures. The peptide mappings of CNBr peptides of "M" and "H" subunits from beef and pig were significantly different. Antibodies were raised against the 85 kDa and 135 kDa CNBr fragments. Immunoblotting results with anti-85 kDa and anti-135 kDa of beef are in favour of large differences of structure between the "M" subunits from pig and beef. The "H" proteins were very similar and they also showed that the C-terminal part of bovine "H" and "M" proteins share common antigenic determinants.

Animals↗

PubMed1977

Structural polypeptides of Sendai virus: analysis by tryptic peptide mapping.

Tryptic peptide patterns identified Sendai virus polypeptides polypeptides HN, HN, P,F0, NP, and M as unique gene products, and confirmed the precursor-product relationship of polypeptides F0 and F. By the same criterion, the major nucleocapsid polypeptides, P and NP, in virions were derived from the same genes as their counterparts in nucleocapsids obtained from infected cells.

Culture Techniques↗

PubMed1980

Brush-border alpha-actinin? Comparison of two proteins of the microvillus core with alpha-actinin by two-dimensional peptide mapping.

The bundle of filaments within the intestinal microvillus contains four major polypeptides in addition to actin calmodulin, a 70-kdalton subunit and two polypeptides with molecular masses similar to that of the Z-line component alpha-actinin (95 and 105 kdaltons). Two-dimensional mapping of tryptic peptides indicates that (a) alpha-actinins from chicken skeletal, cardiac, and smooth muscle are similar but not identical proteins and that skeletal alpha-actinin in more similar to the cardiac subunit than to the alpha-actinin from gizzard; (b) the brush-border 95- and 105-kdalton subunits are closely related to each other, but the smaller subunit is not a proteolytic fragment of the 105-kdalton subunit; and (c) although there is considerable peptide overlap between the brush-border subunits and the three alpha-actinins, the peptide maps of the 95- and 105-kdalton proteins are substantially distinct from the various alpha-actinin maps, suggesting that neither brush-border subunit is a bona fide alpha-actinin. Nevertheless, on the basis of peptide mapping criteria alone, one cannot exclude the possibility that the brush-border subunits are "alpha-actinin-like." However, there is no immunological cross-reactivity between the brush-border subunits and alpha-actinins, using antibodies prepared against gizzard alpha actinin.

Actinin↗