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PubMedDate not supplied

Molecular characterization of surface topology in protein tertiary structures by amino-acylation and mass spectrometric peptide mapping.

Amino-acetylation and -succinylation reactions in combination with mass spectrometric peptide mapping of tryptic peptide mixtures have been employed for surface topology-probing of lysine residues in bovine ribonuclease A, lysozyme, and horse heart myoglobin as model proteins of different surface structures. Direct molecular weight determinations identifying the precise number of acyl groups in partially modified proteins were obtained by electrospray and 252Cf-plasma desorption mass spectrometry. Electrospray mass spectra of multiply protonated molecular ions and deuterium exchange experiments provided a relative conformational characterization of protein derivatives and enabled the direct determinations of intact, partially acylated heme-myoglobin derivatives. Tryptic peptide mapping analysis, using plasma desorption and fast atom bombardment mass spectrometry, ascertained by mass spectrometric characterization of HPLC-separated modified peptides, yielded the exact identification of acylation sites. Relative reactivities of the amino acylation were derived from the peptide mapping data and from quantitative estimations of modified peptides upon acetylation/trideuteroacetylation and provided direct correlations with the relative surface accessibilities of lysine-epsilon-amino groups taken from X-ray crystallographic structure data of the proteins. The reactive lysine-41 residue in ribonuclease A which is part of the substrate binding site was directly identified from the mass spectrometric data. These results indicate tertiary structure-selective acylation combined with mass spectrometric peptide mapping as an efficient approach for the molecular characterization of surface topology and reactive fundamental lysine residues in proteins.

Acylation↗
PubMed1984

Peptide mapping by polyacrylamide gel electrophoresis after cleavage at aspartyl-prolyl peptide bonds in sodium dodecyl sulfate-containing buffers.

Protein samples prepared for sodium dodecyl sulfate-polyacrylamide gel electrophoresis are preferentially cleaved at aspartyl-prolyl peptide bonds upon heating at 110 degrees C. The presence of aspartyl-prolyl peptide bonds in a protein can therefore be detected by gel electrophoresis of heated samples and the resulting peptides mapped. The method of heat cleavage also works well with proteins in bands cut from electrophoresed gels using modified stacking conditions in the second electrophoresis. An immunoblotting procedure for peptide mapping of nanogram quantities of specific proteins in complex mixtures is demonstrated. Peptide maps produced by aspartyl-prolyl peptide bond cleavage of fructose-1,6-bisphosphatases from different sources show the effectiveness of the above techniques and suggest a conservation of aspartyl-prolyl peptide bonds in pig kidney and mouse and rat liver fructose-1,6-bisphosphatases.

Animals↗
PubMed2005

A comparison of different biotinylation reagents, tryptic digestion procedures, and mass spectrometric techniques for 2-D peptide mapping of membrane proteins.

2-D peptide mapping is a novel technique for the relative quantification of membrane proteins (Scheurer S. et al., Proteomics 2005, in press). Using closely related metastatic and nonmetastatic teratocarcinoma cell lines as a model system, we have performed a comparative analysis of different biotinylation reagents, tryptic digestion procedures, and mass spectrometric techniques, with the aim to increase the number of proteins identified by 2-D peptide mapping. Our experience indicates that the LC-MALDI TOF/TOF technique is superior to LC-ESI MS/MS in terms of the number of proteins identified and confidence in protein identification. Furthermore, the best results were obtained by tryptic digestion of proteins eluted from a streptavidin column using a cleavable biotin derivative.

Animals↗
PubMed1996

Preventing the generation of artifacts during peptide map analysis of recombinant human insulin-like growth factor-I.

Peptide mapping using proteolytic enzymes is one useful technique to characterize proteins. However, developing an optimized peptide map is empirical. Some proteins are resistant to proteolysis and it is thereby difficult to obtain a good peptide map. In many cases, the protease-to-substrate ratio is the first modifier to improve the peptide map. As a consequence of increasing the amount of protease, some complications such as nonspecific cleavage, disulfide interchange, transpeptidation, and autolysis of the protease itself may occur. Recombinant human insulin-like growth factor-I (r-HuIGF-I) has been shown to generate a transpeptidation product and a nonspecifically cleaved product under the conditions reported in the literature. We describe here the completion of a peptide map using a combination of Asp-N and Glu-C (V8 strain) endoproteinases. No apparent transpeptidation, nonspecific cleavage, and disulfide exchange was observed. In situ digest of r-HuIGF-I on the probe was also analyzed by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry and proved to be a quick method to analyze the sample.

Amino Acid Sequence↗
PubMed1993

Rapid high-sensitivity peptide mapping by liquid chromatography-mass spectrometry.

Toward a complete LC-MS mapping system for peptides and proteins, we have coupled a precision-flow microbore HPLC system to an electrospray single quadrupole mass spectrometer. The HPLC system allows fast separation of protein digests with UV detection at the low pmol level. A 2 microliters/min portion (1:25) of the effluent is passed into a high-sensitivity electrospray MS system. The electrospray source allows for molecular mass associated ions (MH+, MH2(2+), MH3(3+), etc.) to be generated as well as collision induced dissociation of these ions before MS analysis. After LC-MS runs, with or without partial fragmentation, the data generated are largely interpreted by identification of predicted peptides, incompletely digested peptides, unusual peptide cleavages, and so on, using appropriate integrated software (PEPMAP, PEPMATCH). Examples of peptide mapping at the low pmol level using this integrated system will be shown (e.g., of the protein human growth hormone and of the glycoprotein, tissue plasminogen activator).

Amino Acid Sequence↗
PubMedDate not supplied

[Comparative characteristics of the peptide maps of the major proteins of influenza viruses type A].

A comparative study of peptide maps of major proteins of hemagglutinin, nucleoprotein, membrane of influenza A virus strains A/WS/33, A/FM/1/47, A/Singapore/1/57, A/USSR/090/77, A/Port Chalmers/1/73 (MRC-11), was carried out. The greatest differences were observed in the peptide maps of heavy and light chains of hemagglutinin of different serotypes. The peptide maps of nucleoprotein and membrane were more similar. The A/USSR/090/77 strain by peptide maps was close to but not identical with the A/FM/1/47 strain. Structural polypeptides of the virion separated by SDS-polyacrylamide gel electrophoresis may be used satisfactorily for comparative studies of influenza virus peptide maps.

Animals↗
PubMed1985

On the recovery of Cys-containing peptides during peptide mapping by HPLC. Tryptic peptides of Trp-tRNA synthetase of E.coli.

Conditions are presented for separating the major tryptic peptides of E.coli tryptophanyl-transfer RNA synthetase by reversed-phase liquid chromatography using a water-methanol gradient in the presence of 0.1% trifluoroacetic acid. Three of the peptides contain cysteine and are recovered in good yields if alkylated, but otherwise cannot be detected. A convenient post-digestion alkylation procedure is appropriate for use with small samples of protein which can be digested under reducing conditions. These results will be of interest for studies of the labeling of sulfhydryl groups in other proteins.

Amino Acid Sequence↗
PubMed1990

Mass spectrometric peptide mapping analysis and structural characterization of dihydrodiol dehydrogenase isoenzymes.

The direct molecular weight determination and structural analysis of polypeptides and peptide mixtures have become amenable by the recent development of fast atom bombardment (FABMS) and 252Cf-plasma desorption (PDMS) mass spectrometry. FABMS and PDMS peptide mapping, i.e., the direct analysis of peptide mixtures resulting from proteolytic digestion, have been developed as powerful methods for the structural characterization of epoxide-metabolizing isoenzymes. The major advantage of this approach is provided by the selectivity of the endoproteolytic cleavage, combined with the specific and accurate molecular weight determination of complex digest mixtures containing peptides up to several thousands daltons in size. Furthermore, the mass spectrometric peptide mapping analysis can be combined with a range of protein-chemical modification reactions and with sequential degradation such as by carboxypeptidases. Both FABMS and PDMS peptide mapping have already been successfully applied to the structural differentiation of glutathione transferase and epoxide hydrolase isoenzymes in cases where references sequence data for at least one isoenzyme form was available. In the application described here, for a series of dihydrodiol dehydrogenase (DDH) isoenzymes with hitherto undetermined primary structures, a direct correlation between the structural differentiation from peptide mapping data and differences in their substrate specificities could be demonstrated. The mass spectrometric peptide mapping analysis of isoenzymes proved to be an efficient basis for the elucidation of the structure of one major DDH isoenzyme form; partial sequence data for this protein are reported.

Alcohol Oxidoreductases↗
PubMed1984

Differentiation of Newcastle disease virus strains by one-dimensional peptide mapping.

One-dimensional peptide mapping was used for the differentiation of Newcastle disease virus (NDV) strains. Virions were purified in one step, and digested with Staphylococcus aureus V8 protease or chymotrypsin without prior separation of their proteins. Peptides were separated by polyacrylamide gel electrophoresis and stained with Coomassie blue. This method proved to be a simple, economic and reproducible means of differentiating NDV strains.

Electrophoresis, Polyacrylamide Gel↗
PubMed1988

Isolation and comparative peptide mapping of fibrinogen subunits by reversed-phase high-performance liquid chromatography.

Comparative peptide mapping represents one approach to identification of structural defects in variant human fibrinogens. In view of the large size of this protein, we chose to generate peptide maps of fibrinogen subunits. A reversed-phase high-performance liquid chromatographic method was developed to isolate the subunits: fibrinogen was reduced with dithioerythritol and alkylated with iodoacetamide. Subunits were isolated on a Vydac TP, C4 column (25 x 1.0 cm). Eluent A was 0.1% aqueous trifluoroacetic acid (TFA); eluent B was 0.1% TFA in acetonitrile. Initial conditions were 65% A, 35% B, at 2 ml/min. The reduced-alkylated subunits were lyophilized, redissolved in 0.1% TFA plus 4-8 M guanidine-HCl, and chromatographed using a linear gradient (1%/min) to 50% B. This procedure provides homogeneous subunits in yields exceeding 90%, and is therefore superior to conventional cation-exchange chromatography. For comparative peptide mapping, the same stationary and mobile phases were used, except that the initial conditions were 90% A/10% B, and a linear gradient to 60% B (1%/min) was used. Alternatively, peptide maps were generated with a 10 x 0.46 cm Spherisorb ODS-2 column and very shallow gradients. The mapping procedure resolves 45-60 peptides with excellent reproducibility, and has been applied to the identification of an apparent polymorphism in fibrinogen Baltimore II, and the structural defect in fibrinogen Baltimore IV.

Chromatography, High Pressure Liquid↗
PubMed1992

Application and limitations of the multiple antigen peptide (MAP) system in the production and evaluation of anti-peptide and anti-protein antibodies.

The multiple antigen peptide (MAP) system has been proposed as a novel and valuable approach for eliciting antibodies to peptides and developing synthetic vaccines. The MAP system consists of a small immunogenically inert core matrix of lysine residues with alpha- and epsilon-amino groups for anchoring multiple copies of the same or different synthetic peptides. Several MAP systems, each containing eight copies of 6-15 residue-long peptides derived from the terminal and central regions of various proteins were analyzed in this study. The immunogenicity of MAPs was compared to that of the same peptides linked to carrier protein by means of conventional conjugation procedures. The various peptide antisera were tested in ELISA with homologous peptides conjugated to a carrier protein via their C terminal (as in the MAP system) or their N terminal end, or with their parent proteins. The antigenic properties of MAPs were studied with anti-peptide sera obtained by classical methods and with anti-protein sera. The results showed that the MAP system was an efficient antigen in ELISA except when the peptide corresponded to a C terminal epitope. However, the value of MAPs for raising anti-peptide antibodies cross-reactive with the cognate protein appeared much more limited. In the case of one N terminal peptide, the MAP construction was not immunogenic while the conventionally conjugated peptide induced antibodies that reacted strongly with the corresponding protein. In the case of the two C terminal peptides tested, the antibodies raised against MAP constructs reacted well with homologous MAPs but did not cross-react with the whole protein. Only in the case of a peptide from an internal domain of histone H2A did immunization with a MAP generate antibodies that cross-reacted with the protein.

Amino Acid Sequence↗
PubMed1998

Modification of cysteine residues by alkylation. A tool in peptide mapping and protein identification.

Although mass spectrometric peptide mapping has become an established technique for the rapid identification of proteins isolated by polyacrylamide gel electrophoresis (PAGE), the results of the identification procedure can sometimes be ambiguous. Such ambiguities become increasingly prevalent for proteins isolated as mixtures or when only very small amounts of the proteins are isolated. The quality of the identification procedure can be improved by increasing the number of peptides that are extracted from the gel. Here we show that cysteine alkylation is required to ensure maximal coverage in matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) peptide mapping of proteins isolated by PAGE. In the described procedure, alkylation was performed prior to electrophoresis to avoid the adventitious formation of acrylamide adducts during electrophoresis. In this way, homogeneous alkylation was obtained with three different alkylating reagents (4-vinylpyridine, iodoacetamide, acrylamide). Cysteine alkylation was also used as a tool for the identification of cysteine-containing peptides. Using a 1:1 mixture of unlabeled acrylamide and deuterium-labeled acrylamide ([2,3,3'-D3]acrylamide), the proteins of interest were alkylated prior to electrophoretic separation. Peptide mixtures produced by trypsin digestion of the resulting protein bands were analyzed by MALDI-TOF MS, and the cysteine content of the peptides was inferred from the isotopic distributions. The cysteine content information was readily obtained and used to improve the protein identification process.

Acrylamide↗
PubMed2000

Statistical validation of reproducibility of HPLC peptide mapping for the identity of an investigational drug compound based on principal component analysis.

Peptide mapping is a key analytical method for studying the primary structure of proteins. The sensitivity of the peptide map to even the smallest change in the covalent structure of the protein makes it a valuable "fingerprint" for identity testing and process monitoring. We recently conducted a full method validation study of an optimized reverse-phase high-performance liquid chromatography (RP-HPLC) tryptic map of a therapeutic anti-CD4 monoclonal antibody. We have used this method routinely for over a year to test production lots for clinical trials and to support bioprocess development. One of the difficulties in the validation of the peptide mapping method is the lack of proper quantitative measures of its reproducibility. A reproducibility study may include method and system precision study, ruggedness study, and robustness study. In this paper, we discuss the use of principal component analysis (PCA) to quantitate peptide maps properly using its projected scores on the reduced dimensions. This approach allowed us not only to summarize the reproducibility study properly, but also to use the method as a diagnostic tool to investigate any troubles in the reproducibility validation process.

Antibodies, Monoclonal↗
PubMed2001

Femtomole peptide mapping by derivatization, high-performance liquid chromatography, and fluorescence detection.

A highly sensitive peptide mapping method using derivatization and fluorescence detection is described. Bovine cytochrome c was digested using a buffer compatible with the derivatization that followed. The derivatization was performed with 6-aminoquinolyl-N-hydroxysuccinimidyl carbamate. The peptide mapping of the tagged digest was conducted with both HPLC and capillary LC (CLC) systems. A capillary LC-electrospray ionization mass spectrometer (MS) was set up for measuring the molecular weights of the tagged peptides. Optimization was made of the conditions used for digestion, derivatization, and mapping. MS measurements of the tagged peptides suggested that there was only one derivatization product produced from all peptides (except one) and that all the identified peptides were fully tagged. Peptide mapping of the tagged digest reviews a larger number of peptides, covering almost the entire sequence. Peptide mapping of a 20 fmol amount of tagged digest was readily performed with the CLC system. By using derivatization and fluorescence detection, the sensitivity of peptide mapping could be improved 2000 times compared to that observed with uv detection of untagged peptides.

Amino Acid Sequence↗
PubMed1994

Peptide mapping of the subunits and deglycosylated polypeptides of human liver alpha-L-fucosidase.

The subunits of human liver alpha-L-fucosidase have been separated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis, excised, and subjected to peptide mapping after CNBr cleavage or trypsin digestion. The CNBr peptide maps of the glycosylated 56- and 51-kDa subunits were similar except that the larger subunit had several peptides with M(r)s shifted higher than those apparent for the smaller subunit. These M(r) differences were almost completely eliminated when CNBr peptide mapping was performed on the deglycosylated 48- and 45-kDa polypeptides, suggesting that the M(r) differences were due to carbohydrate differences. Minor differences not related to glycosylation were found in the CNBr peptide maps for the 48- and 45-kDa polypeptides including the presence of small amounts of three peptides in the larger polypeptide not found in the smaller polypeptide. Sequence analysis suggested that both the 48- and the 45-kDa polypeptides were blocked at their amino-termini but analysis of the largest CNBr peptide from each polypeptide indicated an identical 13-amino-acid sequence corresponding to residues 6 through 18 from the cDNA-deduced sequence of mature alpha-L-fucosidase. Tryptic peptide mapping indicated very similar HPLC peptide profiles for the deglycosylated 48- and 45-kDa polypeptides except for the presence of small amounts of six peaks present in the larger polypeptide which were not detected in the smaller polypeptide. The overall results provide the first evidence that the polypeptides of human liver fucosidase are very similar and probably encoded by the same gene. However, minor differences in the polypeptides exist, possibly due to normal allelic variation, alternative splicing, proteolytic processing, and/or posttranslational modifications other than those due to glycosylation.

Amidohydrolases↗
PubMed1999

Carbamylation of cysteine: a potential artifact in peptide mapping of hemoglobins in the presence of urea.

Peptide mapping is a useful technique for identifying posttranslational modifications. However, sometimes artifacts can be introduced during the mapping procedure which can be misleading in identifying the origin and nature of the modifications. During peptide mapping of unalkylated hemoglobins with Staphylococcus aureus V8 proteinase, we found a significant level of carbamylated cysteines. Carbamylation was not detected if recombinant human hemoglobin (rHb1.1) was alkylated prior to digestion. Our experiments indicated that this modification was an artifact of the digestion procedure in which the slightly acidic conditions promoted the reaction of cysteine sulfhydryls with residual cyanate derived from urea. Carbamylmercaptans were found to be stable under acidic conditions but were unstable in base. The extent of cysteine carbamylation can be moderated by the use of scavengers.

Alkylation↗
PubMed2002

Multiplexed on-column protein digestion and capillary electrophoresis for high-throughput comprehensive peptide mapping.

A novel scheme based on multiplexed capillary electrophoresis (CE) has been developed for high-throughput, low-cost and comprehensive peptide mapping. Orthogonal peptide maps of the protein of interest were obtained by using multiple reaction conditions with three different enzymes (trypsin, pepsin, and chymotrypsin), and multiple separation conditions with six zone electrophoresis buffers and two micellar electrokinetic chromatography (MEKC) buffers. Fifteen nanoliters of two protein samples (beta-lactoglobulin A and beta-lactoglobulin B) were separately mixed on-column and digested independently at 37 degrees C for 10 min to produce peptides in a 20-capillary system. The resulting peptides were detected simultaneously at 214 nm by a photodiode array detector. The overall analysis time from reaction to detection was about 40 min.

Buffers↗
PubMed2005

Micropreparative separation, fractionation, and peptide mapping of beta-lactoglobulin A and B variants by capillary electrophoresis.

The methodological aspects for the separation, fractionation, and peptide mapping by free zone capillary electrophoresis (CZE) of beta-lactoglobulin (beta-Lg) variants A and B were established. First, beta-Lg variants A or B were separated and fractionated by CZE. Then, the collected protein fraction was subjected to off-line tryptic digestion. Second, peptide mapping of the tryptic hydrolysates and peptide fraction collection were carried out by CZE. beta-Lg variants were separated and collected using an uncoated capillary (72 cm x 75 microm i.d.) in 0.05 M borate buffer containing 0.1% Tween 20 at pH 8.0 by applying 20 kV. By subjecting the capillary under pressure after a delay time of 15%, the protein was collected in a microvial containing digestion buffer. The most suitable conditions for the tryptic digestion of beta-Lg were established by monitoring the reaction products with CZE. A tryptic hydrolysis with an enzyme-to-substrate ratio (E/S) of 1/20 and incubation for 20 hr at 37 degrees C was found to result in the most suitable conditions. Peptides were separated and collected using an uncoated capillary (120 cm x 75 microm i.d.) in 0.15 M formic acid at pH 2.3 by applying 28 kV. Peptide maps were highly reproducible as shown by coefficients of variation of less than 0.89 and 5.42% for migration times and peak areas, respectively. Moreover, very good resolution of the peptide maps revealed the region in which the aberrant peptides of the beta-Lg variants may be located.

Chemical Fractionation↗