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PubMed2005

CLPM: a cross-linked peptide mapping algorithm for mass spectrometric analysis.

BACKGROUND: Protein-protein, protein-DNA and protein-RNA interactions are of central importance in biological systems. Quadrapole Time-of-flight (Q-TOF) mass spectrometry is a sensitive, promising tool for studying these interactions. Combining this technique with chemical crosslinking, it is possible to identify the sites of interactions within these complexes. Due to the complexities of the mass spectrometric data of crosslinked proteins, new software is required to analyze the resulting products of these studies. RESULT: We designed a Cross-Linked Peptide Mapping (CLPM) algorithm which takes advantage of all of the information available in the experiment including the amino acid sequence from each protein, the identity of the crosslinker, the identity of the digesting enzyme, the level of missed cleavage, and possible chemical modifications. The algorithm does in silico digestion and crosslinking, calculates all possible mass values and matches the theoretical data to the actual experimental data provided by the mass spectrometry analysis to identify the crosslinked peptides. CONCLUSION: Identifying peptides by their masses can be an efficient starting point for direct sequence confirmation. The CLPM algorithm provides a powerful tool in identifying these potential interaction sites in combination with chemical crosslinking and mass spectrometry. Through this cost-effective approach, subsequent efforts can quickly focus attention on investigating these specific interaction sites.

Algorithms↗
PubMed1990

Peptide mapping of the four subunits of the mouse DNA polymerase alpha-primase complex.

We report a simple, two-step method (phosphocellulose and immunoaffinity column chromatographies) for purification of the mouse DNA polymerase alpha-primase complex. The advantages of this method over other procedures are its simplicity and rapidity, with little loss by proteolysis. Sedimentation analysis in a glycerol density gradient of the immunoaffinity-purified fraction revealed that four polypeptides with molecular weights of 180,000, 68,000, 54,000 and 46,000 in the enzyme fraction form a physical complex. Peptide mapping by reversed phase-high performance liquid chromatography demonstrated unequivocally that these four polypeptides constituting the complex are different entities.

Animals↗
PubMed1986

Differences of nucleoproteins of human and avian influenza A virus strains shown by polyacrylamide gel electrophoresis and by the peptide mapping technique.

Electrophoretic mobility differences in polyacrylamide gels were detected between (35S)-methionine-labelled nucleoproteins (NPs) induced in monolayer cells by 15 human and 4 avian reference strains of influenza viruses. The (35S)-methionine-labelled tryptic peptides of nucleoproteins of these strains were also analyzed by peptide mapping technique. Based on several detectable hydrophilic peptides the NPs could be arranged in 7 clearly differentiable groups. After radioiodination of NPs from 4 human and 3 avian reference strains the tryptic peptide patterns showed one clear difference between human and avian strains.

Electrophoresis, Polyacrylamide Gel↗
PubMed1991

Processing of the precursor of protamine P2 in mouse. Peptide mapping and N-terminal sequence analysis of intermediates.

Protamine P2, the major basic chromosomal protein of mouse spermatozoa, is synthesized as a precursor almost twice as long as the mature protein, its extra length arising from an N-terminal extension of 44 amino acid residues. This precursor is integrated into chromatin of spermatids, and the extension is processed during chromatin condensation in the haploid cells. We have studied processing in the mouse and have identified two intermediates generated by proteolytic cleavage of the precursor. H.p.l.c. separated protamine P2 from four other spermatid proteins, including the precursor and three proteins known to possess physiological characteristics expected of processing intermediates. Peptide mapping indicated that all of these proteins were structurally similar. Two major proteins were further purified by PAGE, transferred to poly(vinylidene difluoride) membranes and submitted to automated N-terminal sequence analysis. Both sequences were found within the deduced sequence of the precursor extension. The N-terminus of the larger intermediate, PP2C, was Gly-12, whereas the N-terminus of the smaller, PP2D, was His-21. Both processing sites involved a peptide bond in which the carbonyl function was contributed by an acidic amino acid.

Amino Acid Sequence↗
PubMed2000

Two-step fast protein liquid chromatographic purification of the Serratia marcescens hemolysin and peptide mapping with mass spectrometry.

The pore forming toxin of Serratia marcescens (ShlA) is secreted and activated by an outer membrane protein (ShlB). Activation of inactive ShlA (termed ShlA*) by ShlB is dependent on phosphatidylethanolamine (PE). Activation may be a covalent modification of ShlA. To test this hypothesis, the responsible activation domain (in the N-terminal 255 amino acids of ShlA) was isolated from whole bacteria with 8 M urea in an inactive form (ShlA-255*) and from the culture supernatant in an active form (ShlA-255), followed by a two-step purification by anion-exchange chromatography and gel permeation chromatography. Comparison of a tryptic peptide map of both forms with subsequent electrospray mass spectrometry (ES-MS) and sequencing by tandem ES-MS revealed no modification. These data imply that ShlB presumably imposes a conformation on ShlA-255 that triggers activity.

Amino Acid Sequence↗
PubMed1979

Peptide maps comparing subunits of maize chloroplast and type II nuclear DNA-dependent RNA polymerases.

Both one- and two-dimensional peptide mapping techniques have been used to compare the 180-kilodalton subunits from maize chloroplast and type II nuclear DNA-dependent RNA polymerases (nucleosidetriphosphate:RNA nucleotidyltransferase, EC 2.7.7.6). Despite their similar molecular mass, these 180-kilodalton subunits are not the same. Also, two-dimensional tryptic maps of the 160-, 43-, and 28-kilodalton polypeptides from maize type II nuclear RNA polymerase and of the 140-, 42-, and 27-kilodalton polypeptides from maize chloroplast RNA polymerase show that each of these six polypeptides is unique.

Chloroplasts↗
PubMed1985

Interspecies conservation of retinal guanosine 5'-triphosphatase. Characterization by photoaffinity labelling and tryptic-peptide mapping.

Light-activated hydrolysis of cyclic GMP is achieved through the photoexcitation of rhodopsin, a process which then triggers the replacement of GDP for GTP by a retinal guanosine 5'-triphosphatase referred to as 'transducin'. The transducin-GTP complex then switches on the phosphodiesterase [Fung, Hurley & Stryer (1981) Proc. Natl. Acad. Sci. U.S.A. 78, 152-156]. The bovine transducin consists of an alpha-subunit (39000 Mr), which is a GTP-binding component, together with a beta-(37000 Mr) and a gamma-subunit (10000 Mr). We have purified retinal transducin from cow, pig, chick and frog. The enzyme specific activities and sodium dodecyl sulphate/polyacrylamide-gel-electrophoretic profiles indicate that this enzyme is similar in all species except the frog. Whereas the bovine, pig and chick transducins consist of major 37000- and 39000-Mr components, that of the frog consists of a single 75000-Mr component. Labelling of the GTP-binding components with the photoaffinity label 8-azidoguanosine [gamma-32P]triphosphate demonstrated that the 37000-Mr components of the cow, pig and chick and the 75000-Mr component of the frog were major GTP-binding components. In addition, peptide maps of radioiodinated tryptic peptides indicate that the frog 75000-Mr protein is highly related to the pig transducin. These results demonstrate evolutionary conservation of retinal transducin and the presence of a higher-Mr, but nonetheless highly conserved form, of transducin in the frog. The relationship of this component to the recently reported rod-outer-segment inhibitor protein [Yamazaki, Stein, Chernoff & Bitensky (1983) J. Biol. Chem. 258, 8188-8194] is discussed.

Animals↗
PubMed1995

Differences in the glycosylation of recombinant and native human milk bile salt-stimulated lipase revealed by peptide mapping.

The milk of some mammals contains a bile salt-stimulated lipase (BSSL). Human milk BSSL is heavily glycosylated (30-40% carbohydrate) and present at a concentration of approximately 100-200 mg/l, thereby being one of the most abundant human whey proteins. BSSL has been shown to have an important role in the uptake of energy from human milk. The risk of HIV contamination has restricted the use of banked human milk for nutritional purposes. This has evoked an interest in the production of a recombinant form of the protein for supplementation of formula. We have produced BSSL in mouse C127 and hamster CHO cells, and used chromatographic methods for the characterization of the products. This study was focused on study of the glycosylation of the protein by using peptide mapping and isolation of glycosylated fragments. The results show how human BSSLs from different sources differ both in extent of glycosylation, in glycan heterogeneity, and in lectin binding.

Animals↗
PubMed2004

Peptide mapping identifies hotspot site of modification in human serum albumin by methylglyoxal involved in ligand binding and esterase activity.

Methylglyoxal is a potent glycating agent under physiological conditions. Human serum albumin is modified by methylglyoxal in vivo. The glycation adducts formed and structural and functional changes induced by methylglyoxal modification have not been fully disclosed. Methylglyoxal reacted with human serum albumin under physiological conditions to form mainly the hydroimidazolone N(delta)-(5-hydro-5-methyl-4-imidazolon-2-yl)-ornithine (92% of total modification) with a minor formation of argpyrimidine, N(epsilon)-(1-carboxyethyl)lysine, and methylglyoxal lysine dimer. When human serum albumin was modified minimally with methylglyoxal, tryptic peptide mapping indicated a hotspot of modification at Arg-410 located in drug-binding site II and the active site of albumin-associated esterase activity. Modification of Arg-410 by methylglyoxal was found in albumin glycated in vivo. Other sites of minor modification were: Arg-114, Arg-186, Arg-218, and Arg-428. Hydroimidazolone formation at Arg-410 inhibited ketoprofen binding and esterase activity; correspondingly, glycation in the presence of ketoprofen inhibited Arg-410 modification and loss of esterase activity. The pH dependence of esterase activity indicated a catalytic group with pK(a) = 7.9 +/- 0.1, assigned to the catalytic base Tyr-411 with the conjugate base stabilized by interaction with the guanidinium group of Arg-410. Modification by methylglyoxal destabilized Tyr-411 and increased the pK(a) to 8.8 +/- 0.1. Molecular dynamics and modeling studies indicated that hydroimidazolone formation caused structural distortion leading to disruption of arginine-directed hydrogen bonding and loss of electrostatic interactions. Methylglyoxal modification of critical arginine residues, therefore, whether experimental or physiological, is expected to disrupt protein-ligand interactions and inactivate enzyme activity by hydroimidazolone formation.

Amino Acid Sequence↗
PubMed2005

Peptide mapping of human serum albumin modified minimally by methylglyoxal in vitro and in vivo.

Methylglyoxal is a potent glycating agent and important precursor of advanced glycation end products (AGEs) in physiological systems. Unlike glucose, methylglyoxal is predominantly an arginine-directed glycating agent. Methylglyoxal reacts with proteins to form mainly the arginine-derived hydroimidazolone AGE, Ndelta-(5-hydro-5-methyl-4-imidazolon-2-yl)-ornithine (MG-H1), argpyrimidine, the lysine-derived AGEs, N(epsilon)-(1-carboxyethyl)lysine (CEL), and methylglyoxal-derived lysine dimer (MOLD). Sites within proteins susceptible to modification by methylglyoxal have not been identified. Here we show that modification of human serum albumin by methylglyoxal forms mainly hydroimidazolone MG-H1 residues. The location of MG-H1 residues was identified by mass spectrometric peptide mapping. This method identified a hot spot of hydroimidazolone formation at Arg-410, with other minor MG-H1 modifications at Arg-114, Arg-186, Arg-218, and Arg-428. Other extracellular and intracellular proteins are modified by methylglyoxal in physiological systems. Modification of arginine residues by methylglyoxal may be particularly damaging because arginine residues have a high frequency of occurrence in ligand and substrate recognition sites in receptor and enzyme active sites.

Arginine↗
PubMed1991

Immunogenicity of multiple antigen peptides (MAP) containing T and B cell epitopes of the repeat region of the P. falciparum circumsporozoite protein.

The immunogenicity of multiple antigen peptides (MAP) constructs containing T and B cell epitopes of the repeat region of the P. falciparum circumsporozoite (CS) protein was examined in vitro, using a human T cell clone, and in vivo, using four different strains of mice. All the MAP constructs that contained the T cell epitope, (DPNANPNVDPNANPNV), stimulated proliferation and interferon-gamma production by a human T cell clone specific for this epitope which is located in the 5' end of the repeat region of the P. falciparum CS protein. These human T cells did not recognize MAP that contained only the B cell epitope, (NANP)3, which is located in the 3' repeat region. Optimal antibody responses were obtained in mice immunized with MAP containing four copies of tandemly arranged T and B cell epitopes, (TB)4. The murine immune response to the MAP constructs was genetically restricted. Mice of a high responder strain, C57BL, recognized both the 5' and 3' repeat sequences in the MAP as T, as well as B, cell epitopes and developed very high anti-MAP and anti-sporozoite antibody titers. A/J and C3H mice, which were intermediate responders, developed lower antibody titers which varied according to the orientation of the T vs. the B cell epitopes within the MAP constructs. BALB/c mice were nonresponders and did not develop antibodies following immunization with any of the MAP constructs containing the 5' and 3' repeats of the P. falciparum CS protein.

Amino Acid Sequence↗
PubMed1997

Matrix-assisted laser desorption/ionization mass spectrometric peptide mapping of the neural cell adhesion protein neurolin purified by sodium dodecyl sulfate polyacrylamide gel electrophoresis or acidic precipitation.

Neurolin is a cell surface protein involved in the neural regeneration and neogenesis of the central nervous system of goldfish. Its theoretical molecular mass, based on the amino acid sequence translated from the cDNA, is 58 kDa, but in SDS-PAGE it shows an apparent MW of 86 kDa. Neurolin is stated to be a glycoprotein and it contains five potential N- and 96 potential O-glycosylation sites. The complete characterization of the primary structure and initial investigations on the postulated glycosylation of neurolin, immunopurified from goldfish brains, are described. The protein was either digested in situ in the sodium dodecyl sulfate polyacrylamide gel matrix or digested after trichloroacetic acid precipitation. Trypsin and endoprotease Glu-C were used as proteases and matrix-assisted laser desorption/ionization mass spectrometry was applied for direct peptide mapping analysis of the proteolytic mixtures. Various sample preparation techniques were performed and the mass spectra were recorded in both positive- and negative-ion modes.

Activated-Leukocyte Cell Adhesion Molecule↗
PubMed1993

Human non-secretory ribonucleases. I. Purification, peptide mapping and lectin blotting analysis of the kidney, liver and spleen enzymes.

Human non-secretory neutral ribonucleases (RNases) from kidney, liver and spleen have been purified and characterized. SDS-PAGE indicates that all three RNases are highly purified and have apparent mol. wts of 17-18 kDa. Kinetic analysis indicates that all three RNases have a broad pH optimum centred around 6.5, and all three have similar substrate specificities with significant preference for RNA and poly(U) when compared to poly(C), poly(A) and poly(G). All of the above data, as well as immunoblotting data using three polyclonal antibodies (anti-human liver RNase, anti-human pancreatic RNase, anti-human eosinophil-derived neurotoxin), indicate that the three proteins are highly purified and are non-secretory RNases (IIN). Further characterization by cyanogen bromide peptide mapping and extensive lectin blotting indicated no significant differences between the three human RNases. All three RNases appear to have very similar, if not identical, protein backbones and all three are glycoproteins which are recognized by lectins with specificity for GlcNAc, Fuc and, to a lesser extent, with specificity for Gal beta(1-4)GlcNAc. No significant tissue-specific differences were found among the three human non-secretory RNases.

Blotting, Western↗
PubMed1979

Partial N-terminal amino acid sequence analyses and comparative tryptic peptide maps of murine Ia molecules encoded by the I-A subregion.

The partial N-terminal amino acid sequences and tryptic peptide maps of I-A subregion products from the H-2b, H-2d, H-2k and H-2s haplotypes demonstrate that haplotype-associated differences are present in both alpha and beta polypeptides. The genetic and evolutionary implications of these multiple amino acid substitutions and the homology relationships among Ia molecules from human, guinea pig and the I-E subregion of the mouse are discussed.

Alleles↗
PubMed1989

Identification and characterization of the ligand binding subunit of a kainic acid receptor using monoclonal antibodies and peptide mapping.

Monoclonal antibodies (mAb) and a polyclonal antiserum were produced against a kainic acid receptor (KAR) purified from frog brain. Several of the mAb and the antiserum immunoprecipitated [3H]kainic acid binding activity from solubilized preparations of frog brain and labeled a group of proteins on immunoblots that migrated at Mr = 48,000. These results confirm that the ligand binding subunit of the frog brain KAR is contained in the Mr = 48,000 proteins. Immunoblots from different frog tissues demonstrated that the antibody reactivity was highly concentrated in the frog nervous system with no detectable immunoreactivity observed in non-neuronal tissues. The purified KAR was radioiodinated and subjected to two-dimensional gel electrophoresis and autoradiography. A series of proteins was detected at Mr = 48,000 with isoelectric points from 5.5 to 6.3. The anti-KAR mAb and the antiserum reacted with the same group of proteins from frog whole brain after separation by two-dimensional gel electrophoresis. Peptide maps of the 125I-labeled KAR separated by two-dimensional gel electrophoresis demonstrated that the group of proteins clustered at Mr = 48,000 is homologous. mAb KAR-B1 reacted on immunoblots with a protein in rat brain with a Mr = 99,000. This protein comigrated with an unreduced form of the KAR in frog brain. It was present in rat cerebral cortex, hippocampus, and cerebellum but was not detected in thalamus, globus pallidus, or brain stem, nor was it detected in rat non-neuronal tissues. The presence of the Mr = 99,000 immunoreactive polypeptide in discrete areas of rat brain suggests that this protein may be part of a mammalian KAR or a related receptor.

Animals↗
PubMedDate not supplied

Site-specific quantitative evaluation of the protein glycation product N6-(2,3-dihydroxy-5,6-dioxohexyl)-L-lysinate by LC-(ESI)MS peptide mapping: evidence for its key role in AGE formation.

Advanced glycation end products (AGEs) contribute to various pathologies associated with the general aging process and long-term complications of diabetes. Involvement of alpha-dicarbonyl intermediates in the formation of such compounds is firmly established. We now report on the first unequivocal identification of the dideoxyosone N(6)-(2,3-dihydroxy-5,6-dioxohexyl)-l-lysinate (4) on lysozyme via its quinoxaline derivative N(6)-(2,3-dihydroxy-4-quinoxalin-2-ylbutyl)-l-lysinate (6), formed by reaction of 4 with o-phenylenediamine (OPD). For accurate quantification of the total content of 6 as well as of glucosepane 5 by LC-(ESI)MS, (13)C(6)-labeled reference compounds were independently synthesized; 5 so far is the only established follow-up product of 4. With an overall lysine derivatization quota of 5%, compound 4 is shown to be a quantitatively important Maillard intermediate of which only about 8 per thousand are transformed into the cross-link 5. Hence, the major follow-up products of the highly reactive intermediate 4 are yet unknown. The site-specific quantitative evaluation of aminoketose 1 and quinoxaline 6 by LC-(ESI)MS peptide mapping shows that all lysine moieties in lysozyme are in fact modified by these compounds. If an arginine side chain is adjacent to the lysine moiety, transformation of 1 into 4 seems to be favored. The efficient formation and high reactivity of 4 clearly points to its potential as exogenous or endogenous glycotoxin.

Amino Acid Sequence↗
PubMed1987

Two distinct forms of receptors for atrial natriuretic factor in bovine adrenocortical cells. Purification, ligand binding, and peptide mapping.

The atrial natriuretic factor (ANF) receptor of bovine adrenal cortex was solubilized with Triton X-100 and purified by sequential chromatography on ANF-(99-126)-agarose, GTP-agarose, and wheat germ agglutinin-Sepharose. Two subtypes of ANF receptors were isolated, both of which showed specific ANF binding, whereas one of the ANF receptor subtypes also possessed significant cyclase activity. Both of the receptors showed high capacities (Bmax = 5.7-6.8 nmol/mg of protein) and high affinities (Kd = 54-68 pM) for ANF-(99-126). The cyclase-free receptor had high affinity (Ki = 150-220 pM) to C-terminal truncated ANF analogs, whereas the cyclase-containing receptor had a much weaker affinity (Ki = 10(6)-10(7) pM). When treated with dithiothreitol, the purified cyclase-containing and cyclase-free ANF receptors migrated as a single band at Mr 135,000 and 62,000, respectively, in sodium dodecyl sulfate-polyacrylamide gel electrophoresis. The purified cyclase-free receptor is not a product derived from the cyclase-containing receptor because (i) two proteins with Mr of 135,000 and 62,000 were specifically labeled with 4-azidobenzoyl 125I-ANF-(102-126) in nonsolubilized intact membranes; (ii) the truncated ANF analogs (10(4) pM) prevented the photolabeling of the 62,000-dalton protein but not that of the 135,000-dalton protein; and (iii) two-dimensional peptide mapping showed more than 90% difference between the profiles of the two purified ANF receptor subtypes. This study provides first direct evidence for the existence of two distinct ANF receptors which are different not only in their pharmacological properties but also in their primary structure.

Adrenal Cortex↗
PubMed1983

The periodic synthesis of tubulin in the Physarum cell cycle. Characterization of Physarum tubulins by affinity for monoclonal antibodies and by peptide mapping.

Polypeptides preferentially labeled in the G2 phase of the synchronous nuclear replication cycle of Physarum macroplasmodia were compared in electrophoretic mobility and peptide map with the tubulins enriched from Physarum myxamoebae. One major and one minor fluorographic species match the myxamoebal alpha and beta chains, respectively. Thus, tubulins are among the proteins of Physarum selectively synthesized before nuclear division. A third species P, prominently labeled in premitotic plasmodia, is distinct from the two myxamoebal tubulins even though it co-polymerizes with microtubules. The nature of P remains unknown. Two rat monoclonal antibodies directed against yeast tubulin were found to bind selectively to the alpha tubulin of porcine brain. These served to confirm the assignment of the 50,000-dalton Physarum myxamoebal tubulin as an alpha-like polypeptide.

Antibodies, Monoclonal↗