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B T Chait

Publications and source records attributed to B T Chait.

At least 55 records · Page 3Linked to original sources
PubMed1998

Protein identification using mass spectrometric information.

In an effort to gain an understanding of the value of the information in different mass spectrometric measurements for protein identification, the genome of Saccharomyces cerevisiae was studied in silico. We calculate how constraining the knowledge of the mass of a proteolytic peptide is as a function of mass and mass accuracy. We also assess the value for protein identification of additional information concerning a proteolytic peptide, including the presence or absence of a given amino acid, the number of exchangeable hydrogens, the N-terminal sequence, and the masses of mass spectrometrically produced fragment ions. Knowledge of the relative value of these different constraints is useful in the design of efficient protein identification experiments. Finally, we describe a software tool, PepFrag, for searching protein and DNA sequence databases that can use different types of mass spectrometric information to restrict the search.

Amino Acid Sequence↗
PubMed1998

Direct comparison of infrared and ultraviolet wavelength matrix-assisted laser desorption/ionization mass spectrometry of proteins.

In an effort to gain an understanding of the processes governing matrix-assisted laser desorption/ionization (MALDI), we made a direct comparison of ultraviolet (UV)- and infrared (IR)-MALDI linear time-of-flight mass spectra of proteins obtained from the same samples and matrices (on the same sample surface), using two different lasers, each having short duration (< 10-ns) pulses, i.e., a tunable wavelength Nd:yttrium aluminum garnet (YAG) pumped optical parametric oscillator laser operating at 2.94 microns and a Nd:YAG laser operating at 355 nm. We observed that (1) the IR-MALDI and UV-MALDI spectra of a given protein from the same matrix were strikingly similar; (2) protein ions produced by IR-MALDI experienced less fragmentation than those produced by UV-MALDI; and (3) photochemical adducts produced during UV-MALDI were absent in IR-MALDI. These results lead us to speculate on the mechanisms for the ionization process in UV- and IR-MALDI. Because photons with a wavelength of approximately 3 microns are unlikely to effect electronic excitation of the matrix at the irradiance used for MALDI we propose that ionization in IR-MALDI occurs as a natural consequence of the solid-to-gas phase transition induced by the IR irradiation, and involves proton transfer reactions in the intermediate phase between solid and gas. The strikingly similar UV- and IR-MALDI mass spectra leads us to the additional proposal that ionization in UV-MALDI may also be a natural consequence of the phase transition and that electronic excitation may not play a primary role in the ionization process.

Animals↗
PubMed1998

Exploring infrared wavelength matrix-assisted laser desorption/ionization of proteins with delayed-extraction time-of-flight mass spectrometry.

We report a study of the application of delayed extraction (DE) to infrared-wavelength matrix-assisted time-of-flight mass spectrometry (IR-MALDI-TOF-MS) of proteins. The shapes of the spectral peaks obtained with DE-IR-MALDI-MS are compared with those obtained from the same samples and matrix using continuous extraction (CE) IR-MALDI-MS. Application of DE results in significant improvements in the peak resolution, revealing spectral features (in proteins with molecular masses < 12 kDa) that were not resolved in the corresponding CE-IR-Maldi mass spectra. Particularly significant is a series of peaks on the high mass side of the protonated protein peaks that arise through replacement of protons by adventitious sodium ions in the sample. We deduced that these sodium replacement species are a significant contributor to the broad tails (and resulting peak asymmetries) that are a feature of the DE-IR-MALDI mass spectra of proteins with molecular masses > or = 17 kDa. The peak width reduction observed in IR-MALDI by DE suggests that, as in UV-MALDI, the initial velocity distribution for ions produced in the MALDI process contributes to the peak broadness in the CE mass spectra. In a systematic comparison between DE UV-MALDI and DE IR-MALDI, we determined that photochemical matrix adduction is present in UV-MALDI but absent in IR-MALDI. In addition, we find that protein ions produced by IR irradiation are less internally excited (i.e., cooler), exhibiting less fragmentation, more Na+ replacement and/or unspecified noncovalent adduction, and more heme adduction with apomyoglobin. Thus, IR-MALDI appears to be a softer means for producing gas-phase protein ions than is UV-MALDI. It will be of considerable practical interest to determine whether large protein ions produced by IR-MALDI are sufficiently cool to survive transport through reflecting TOF mass spectrometers (without loss of small neutral species such as H2O, NH3, and CO2) and the extended time periods required for detection by quadrupole ion trap and Fourier transform ion cyclotron resonance mass analyzers.

Infrared Rays↗
PubMed1998

Estrogen reduces neuronal generation of Alzheimer beta-amyloid peptides.

Alzheimer's disease (AD) is characterized by the accumulation of cerebral plaques composed of 40- and 42-amino acid beta-amyloid (Abeta) peptides, and autosomal dominant forms of AD appear to cause disease by promoting brain Abeta accumulation. Recent studies indicate that postmenopausal estrogen replacement therapy may prevent or delay the onset of AD. Here we present evidence that physiological levels of 17beta-estradiol reduce the generation of Abeta by neuroblastoma cells and by primary cultures of rat, mouse and human embryonic cerebrocortical neurons. These results suggest a mechanism by which estrogen replacement therapy can delay or prevent AD.

Alzheimer Disease↗
PubMed1997

Systematic enhancement of polymerization of recombinant sickle hemoglobin mutants: implications for transgenic mouse model for sickle cell anemia.

To provide quantitative information on the sites that promote polymerization of sickle hemoglobin (HbS) after formation of the initial hydrophobic bond involving Val-6(beta) [E6V(beta)] and also to provide hemoglobins with an enhanced polymerization that could be used in a mouse model for sickle cell anemia, we have expressed recombinant double, triple, and quadruple HbS mutants with substitutions on both the alpha- and beta-chains, E6V(beta)/E121R(beta), D75Y(alpha)/E6V(beta)/E121R(beta) and D6A(alpha)/D75Y(alpha)/E6V(beta)/E121R(beta). These recombinant hemoglobins were extensively characterized by high-performance liquid chromatography analysis, sodium dodecyl sulfate-polyacrylamide gel electrophoresis, isoelectric focusing, amino acid analysis, and mass spectroscopy. They retained the functional properties of the Hb tetramer and polymerized in a linear manner at progressively lower Hb concentration as a function of the degree of substitution, suggesting that these remote sites (alphaD6A, alphaD75Y, and betaE121R) on the alpha- and beta-chains exhibit additive, enhanced polymerization properties. The quadruple mutant has a polymerization concentration close to that of the purified SAD hemoglobin from transgenic mouse red blood cells consisting of HbS, Hb Antilles, and Hb D-Punjab. Normal mouse Hb increases the polymerization concentration of each mutant. Thus, the general approach of using recombinant Hbs as described here should prove useful in elucidating the quantitative aspects of the mechanism of HbS polymerization and in identifying the contribution of individual sites to the overall process. The strategy described here demonstrates the feasibility of a systematic approach to achieve future recombinant HbS mutants that could provide a new generation of the transgenic mouse model for sickle cell anemia.

Amino Acids↗
PubMed1997

A strategy for rapid, high-confidence protein identification.

A procedure is described for rapid, high-confidence identification of proteins using matrix-assisted laser desorption/ionization tandem ion trap mass spectrometry in conjunction with a genome database searching strategy. The procedure involves excision of copper-stained bands or spots from electrophoretic gels, in-gel trypsin digestion of the proteins, single-stage mass spectrometric analysis of the resultant mixture of tryptic peptides, followed by tandem ion trap mass spectrometric analysis of selected individual peptides, and database searching of the relevant genomic database using the program PepFrag. The scheme provides sensitive, real-time protein identification as well as facile identification of modifications. A single operator can unambiguously identify 5-10 proteins/day from an organism whose genome is known at a level of > 0.5 pmol of protein loaded on a gel. The utility of the technique was demonstrated by the identification and characterization of a band from a human HTLV-I preparation and 11 different proteins from a yeast RNA polymerase II C-terminal repeat domain-affinity preparation. The technology has great potential for postgenome biological science, where it promises to facilitate the dissection and anatomy of macromolecular assemblages, the definition of disease state markers, and the investigation of protein targets in biological processes such as the cell cycle and signal transduction.

Amino Acid Sequence↗
PubMed1997

Identification and characterization of posttranslational modifications of proteins by MALDI ion trap mass spectrometry.

Matrix-assisted laser desorption/ionization (MALDI) ion trap mass spectrometry is shown to be a powerful tool for the elucidation of protein modifications. Low-energy covalent bonds that originate from certain posttranslational modifications dissociate preferentially to produce characteristic mass spectrometric signatures that prove useful for the accurate, confident identification and characterization of such modifications. Because the MALDI ion trap is an authentic tandem mass spectrometer, it proves feasible to acquire secondary information to test hypotheses as to the nature and site of the putative modifications--further increasing the reliability of the tool. The method combines the advantageous features of MALDI (i.e., the ability to measure the same sample repeatedly, to measure unfractionated complex mixtures without the need for sample cleaning, and to determine peptide mixtures with subpicomole sensitivity) with the ease and the speed of the ion trap measurement. We demonstrate how the unique properties of MALDI ion trap MS can be used to address problems involving the determination of both native posttranslational modifications of proteins (e.g., disulfide mapping, glycosylation determination, and phosphorylation determination) and non-native chemical modifications of proteins (e.g., methionine oxidation and photo-cross-linking of proteins with DNA).

Cross-Linking Reagents↗
PubMed1997

Determinants for Escherichia coli RNA polymerase assembly within the beta subunit.

We used binding assays and other approaches to identify fragments of the Escherichia coli RNAP beta subunit involved in the obligatory interaction with the alpha subunit to form the stable assembly intermediate alpha2beta as well as in the interaction to recruit the beta' subunit into the alpha2beta sub-assembly. We show that two regions of evolutionarily conserved sequence near the C terminus of beta (conserved regions H and I) are central to the assembly of RNAP and likely make subunit-subunit contacts with both alpha and beta'.

Binding Sites↗
PubMed1997

Mass spectrometry of whole proteins eluted from sodium dodecyl sulfate-polyacrylamide gel electrophoresis gels.

In this report we describe a novel approach to the mass spectrometric analysis of whole proteins from gels. The strategy consists of three components: conventional SDS-PAGE gels, reversible negative staining procedures, and passive elution of proteins from gels followed by mass spectrometric analysis. Protein bands are excised from SDS-PAGE gels, destained, and extracted. For gel loadings > or = 25 pmol of soluble protein, the proteins can be directly extracted into a solution consisting of formic acid/water/2-propanol. The recovered protein is suitable for matrix-assisted laser desorption/ionization (MALDI) or electrospray ionization mass spectrometric analysis. For gel loadings < 25 pmol protein, the mass spectrometric response, using the direct extraction procedure, drops off sharply, an outcome that is attributed to protein recovery losses. To offset the protein losses, the extraction procedure is slightly modified by performing the passive extraction of the gel with a saturated MALDI matrix solution. During the extraction period, the matrix is allowed to crystallize, forming a suspension in solution. Protein that elutes from the gel has a chance to cocrystallize with the matrix that can be retrieved for MALDI-MS analysis. This method of "capturing" eluted protein into matrix crystals is sensitive to 1 pmol of recombinant mouse leptin protein (16 kDa) loaded onto SDS-PAGE gels and can be used for proteins as large as 70 kDa. Our strategy has particular application to the characterization of endogenous forms of mature proteins from SDS-PAGE gels.

Animals↗
PubMed1997

Rapid, sensitive structure analysis of oligosaccharides.

We have developed an efficient method for the derivatization of oligosaccharides, wherein the oligosaccharide is efficiently ligated to a basic aminooxyacetyl peptide by oxime formation. The resulting glycopeptide yields much higher sensitivity in matrix-assisted laser desorption/ionization mass spectrometry than does the underivatized oligosaccharide. Digestion of the glycopeptide by a exoglycosidase array and subsequent mass spectrometric assay of the digestion products provide a sensitive and rapid way to elucidate the structure of the oligosaccharide. In addition to oligosaccharide sequencing, the ligation reaction between an oligosaccharide and an aminooxyacetyl peptide also provides a potentially very convenient and efficient way for the synthesis of glycopeptides or glycoproteins.

Carbohydrate Conformation↗
PubMed1997

A molecular redox switch on p21(ras). Structural basis for the nitric oxide-p21(ras) interaction.

We have identified the site of molecular interaction between nitric oxide (NO) and p21(ras) responsible for initiation of signal transduction. We found that p21(ras) was singly S-nitrosylated and localized this modification to a fragment of p21(ras) containing Cys118. A mutant form of p21(ras), in which Cys118 was changed to a serine residue and termed p21(ras)C118S, was not S-nitrosylated. NO-related species stimulated guanine nucleotide exchange on wild-type p21(ras), resulting in an active form, but not on p21(ras)C118S. Furthermore, in contrast to parental Jurkat T cells, NO-related species did not stimulate mitogen-activated protein kinase activity in cells transfected with p21(ras)C118S. These data indicate that Cys118 is a critical site of redox regulation of p21(ras), and S-nitrosylation of this residue triggers guanine nucleotide exchange and downstream signaling.

Amino Acid Sequence↗
PubMed1997

Structure of chain d of the gigantic hemoglobin of the earthworm.

The extracellular hemoglobin of the earthworm has four major O2-binding chains, a, b, c and d, together with additional non-heme structural chains that are required for assembly. Although the abc trimer self-associates extensively at least to (abc)10, addition of chain d results in the formation of a discrete 280 kDa complex corresponding to (abcd)4. Thus a primary function of chain d is to cap the abc association and convert an abc trimer that binds O2 with weak cooperativity to a highly cooperative (abcd)4 complex. Amino-acid sequences of the major globin chains a, b, c have been determined previously by peptide and cDNA analysis. However, the peptide sequence reported for the major chain d (Shishikura, F., Snow, J.W., Gotoh, T., Vinogradov, S.N. and Walz, D.A. (1987) J. Biol. Chem., 262. 3123-3131), has a calculated molecular mass 134-167 Da higher than masses for components of chain d determined by mass spectrometry (Owrby, D.W., Zhu, H., Schneider, K., Beavis, R.C., Chait, B.T. and Riggs, A.F. (1993) J. Biol. Chem. 268, 13539-13547). Reverse-phase HPLC confirms the presence of two distinct polypeptides, d1 and d2, together with d'1, a variant of d1, cDNA derived amino acid sequences have been determined for chains d'1 and d2 by application of the polymerase chain reaction with primers based on the NH2-terminal sequences and oligo-dT. Each of the two cDNA-derived sequences has 140 residues and they differ by 28 substitutions. The data show that the sequence originally reported had been derived from peptides generated from both polypeptides.

Amino Acid Sequence↗
PubMed1997

Dynorphin A (1-8) analog, E-2078, is stable in human and rhesus monkey blood.

E-2078 is a dynorphin A (1-8) analog, [N-methyl-Tyr1, N-methyl-Arg7-D-Leu8] Dyn A (1-8) ethylamide. Its biochemical stability against enzymatic degradation in vitro in human and rhesus monkey blood, and in vivo in rhesus monkey blood was studied using matrix-assisted laser desorption/ionization mass spectrometry. In vitro studies were carried out in freshly drawn human and rhesus monkey blood, incubated at 37 degrees C for various time periods. In vivo studies were conducted by E-2078 i.v. injection to rhesus monkeys, and blood samples were collected at various time points after the injection. It was found that E-2078 was stable against enzymatic degradation in vitro in freshly drawn human and rhesus monkey blood. Minor biotransformation products from E-2078, such as E (1-4), E (1-5) and E (3-6), were detected in vitro in some human and rhesus monkey blood, but they made up less than 5% of the total starting E-2078 peptide. No biotransformation products were detected in the blood samples from in vivo studies. The apparent half-life of elimination of E-2078 in vivo from the rhesus monkey blood was determined to be 44.0 min.

Adult↗
PubMed1997

Dynorphin A (1-8) analog, E-2078, crosses the blood-brain barrier in rhesus monkeys.

E-2078 is a dynorphin A (1-8) analog, [N-methyl-Tyr1, N-methyl-Arg7-D-Leu8] dynorphin A (1-8) ethylamide. Its ability to cross the blood-brain barrier was examined in rhesus monkeys using matrix-assisted laser desorption/ionization mass spectrometry. In vivo studies were carried out by i.v. injecting E-2078, 10 mg/kg, a dose that had been found to be antinociceptive, to rhesus monkeys. Blood and cerebrospinal fluid samples were collected at various time points after the injection. It was found that E-2078 was stable in vivo in rhesus monkey blood. No biotransformation products were detected in the blood. Mass spectrometric analysis of the cerebrospinal fluid samples collected after E-2078 injection detected the presence of E-2078, indicating that E-2078 had crossed the blood-brain barrier. These findings are consistent with the possibility that systemically administered E-2078 could produce centrally mediated behavioral and physiological effects.

Analgesics, Non-Narcotic↗
PubMed1996

Amino acid sequence of a new 2S albumin from Ricinus communis which is part of a 29-kDa precursor protein.

The isolation and sequence determination of a new 2S albumin storage protein from Ricinus communis seeds denoted 2S ASP-Ib are described. The fragment approach using selective enzymatic cleavage, Edman degradation, and mass spectrometry was used to demonstrate that the 11-kDa heterodimer protein linked by disulfide bridges has the following structure: short chain, GEREGSSSQQCRQEVQRKDLSSCERYLRQSSS; long chain, <QQQESQQLQQCCNQVKQVRDECQCEAIKYIAEDQIQQGQLHGEESERVAQRAGEIVSSCGVRCMR . The molecular weight of the intact protein, 11,140 +/- 2, determined by matrix-assisted laser desorption mass spectrometry was consistent with the assigned structure. The S- and L-chains are identical to residues 18-49 and 66-130 of the precursor protein predicted by S. D. Irwin, J. N. Keen, J. B. C. Findlay, and J. M. Lord [(1990) Mol. Gen. Genet. 222, 400-408], on the basis of the structure of a cDNA isolated using probes based on the sequence of another 2S albumin, described by F. S. Sharief and S. S. L. Li [(1982) J. Biol. Chem. 257, 14753-14759], which we denote 2S ASP-Ia. Three of the four termini could have been produced by posttranslational processing by endopeptidase(s) and carboxypeptidase(s) which utilized basic residues as the cleavage sites. Mass spectrometric evidence suggested that the protein presented microheterogeneity at its termini, i.e., truncated forms presumably due to processing heterogeneity. The present characterization of the 2S ASP-Ib protein, the second 2S albumin from Ricinus communis seeds, demonstrates that the 237-residue precursor protein codes for two different heterodimer proteins containing 97 and 99 residues each. This system should be useful for studying the posttranslational processing of plant storage proteins.

Amino Acid Sequence↗
PubMed1996

Domain organization of the Escherichia coli RNA polymerase sigma 70 subunit.

We used limited trypsin digestion to determine the domain organization of the Escherichia coli RNA polymerase sigma 70 subunit. Trypsin-resistant fragments containing sigma 70 conserved region 2 (sigma 70(2)), and carboxy-terminal fragments containing conserved regions 3 and 4 (sigma 70(3-4)) were identified by a combination of amino acid sequencing and mass spectrometry. The domains were studied for partial biochemical functions of sigma 70.sigma 70(2) bound core RNA polymerase competitively with intact sigma 70. In contrast to sigma 70(2) alone, the RNA polymerase holoenzyme formed with sigma 70(2) specifically bound a single-stranded DNA oligomer with a sequence corresponding to the non-template strand of the -10 promoter element (the Pribnow box). Sigma 70(2) also forms crystals that are suitable for X-ray analysis. Sigma 70(3-4) bound the T4 AsiA protein with high affinity. The epitope for T4 AsiA on sigma 70 was further localized to within sigma 70[551-608], comprising sigma conserved region 4.2.

Amino Acid Sequence↗
PubMed1996

DNA binding of in vitro activated Stat1 alpha, Stat1 beta and truncated Stat1: interaction between NH2-terminal domains stabilizes binding of two dimers to tandem DNA sites.

Stat1 alpha, Stat1 beta and a proteolytically defined truncated Stat1 (132-713, Stat1tc) have been prepared from recombinant sources. All three proteins were specifically phosphorylated on Tyr701 in vitro and the phosphoprotein purified to homogeneity. This was achieved by employing a new isolation scheme that does not include DNA affinity steps and readily allows for the isolation of tens of milligrams of activated Stat protein. The purified phosphoprotein was free of traces of unphosphorylated polypeptide as detected by mass spectrometry. The phosphorylated Stat1 preparations bound to various DNA recognition sites with the same Keq of approximately 1 x 10(-9) M; distinction between 'weak' and 'strong' binding sites is determined by the very rapid dissociation (< 30 s, t1/2) from 'weak' sites compared with 'strong' sites (approximately 3 min, t1/2). Reports of 'weak' tandem binding sites in a natural gene caused us to examine binding to tandem sites leading to the finding that the Stat1 alpha or beta (38 amino acids shorter on the C terminus) bound to two tandem sites (but not two head-to-head sites) with a higher stability than to a single recognition site. The N-terminally truncated protein Stat1tc did not show this cooperative binding, thus implicating the N-terminal domain in promoting Stat1-Stat1 dimer interaction.

Binding Sites↗