Incomplete-fusion-fragmentation model: Multifragmentation data from 600A MeV heavy-ion collisions.
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Results for “data fragmentation”
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Unknown peptide sequencing using matrix-assisted laser desorption/ionization and in-source decay.
The results of a study to determine the utility of in-source decay fragmentation of matrix-assisted laser-desorbed ions for obtaining useful sequence information on unknown peptides are presented. Six peptides were purified by high-performance liquid chromatography and submitted as single blind unknowns. The in-source decay fragment ion data were collected on a linear time-of-flight mass spectrometer equipped with delayed extraction. These fragment ion data were manually interpreted on the basis of known fragmentation pathways to determine a proposed sequence. The proposed sequences for three of the unknowns were essentially correct, with a few minor errors. A fourth unknown had significant errors associated with its proposed sequence due to misinterpretation of the fragmentation data. Two unknowns were found to have undergone significant sample degradation prior to analysis, which compromised the results for these samples. An example of the use of protein database searching of a partial peptide sequence to aid in a sequence determination is also presented.
Amino Acid Sequence↗
[Ca2+-dependent ATPases of the sarcoplasmic reticulum of skeletal and cardiac muscles and their ion-transporting fragments].
The data are presented on fractionation of cardiac and skeletal muscle Ca2+-ATPase fragments obtained by trypsin and cyanobromide hydrolysis. Amino acid composition of Ca2+-ATPases isolated from the heart and skeletal muscles and of enzyme fragments is determined. The ionophoric properties of the intact enzyme and its fragments are studied. The low-molecular weight enzyme fragment decreases velocity and the level of Ca2+-accumulation by the vesicles of sarcoplasmic reticulum. It is suggested that an "ionphoric" fragment of muscle ATPase is able to form transmembrane Ca2+-selective channel in model lipid membranes.
Amino Acids↗
Hyaluronan fragments induce the synthesis of MCP-1 and IL-8 in cultured human peritoneal mesothelial cells.
Human peritoneal mesothelial cells (HMC) play an important role in inflammatory processes by their ability to produce various cytokines and chemokines, such as monocyte chemoattractant protein 1 (MCP-1) and interleukin 8 (IL-8). In this study we investigated the effect of experimentally generated hyaluronan (HA) fragments, degradation products of the extracellular matrix component hyaluronan, which accumulate at inflammatory sites, on the expression of MCP-1 and IL-8 in cultured HMC. MCP-1 and IL-8 mRNA expression was determined by RNase protection assays, and protein levels in the supernatants were measured by enzyme-linked immunosorbent assays. HA fragments with a molecular mass of approximately 1-7x10(5) daltons upregulate MCP-1 and IL-8 synthesis in HMC dose and time dependently. The effect of HA fragments could be blocked by Ro31-8220, a specific protein kinase C inhibitor, and by PD98059, an inhibitor of the mitogen-activated protein kinase/extracellular signal-regulated kinase pathway. Upregulation of chemokine synthesis was preceded by an increase in NF-kappaB and AP-1 DNA-binding activity, suggesting that these transcription factors are activated to increase MCP-1 and IL-8 expression by HA fragments. These data demonstrate that HA fragments markedly enhance the mRNA expression and protein synthesis of MCP-1 and IL-8 in HMC. In concert with previous findings, our observations indicate that enhanced levels of HA, which are present in the peritoneal cavity of peritoneal dialysis patients, may account for a locally increased chemokine production.
Adjuvants, Immunologic↗
Inhibition of the phosphatidylinositol-specific phospholipase C from Bacillus cereus by a monoclonal antibody binding to a region with sequence similarity to eukaryotic phospholipases.
Bacterial phosphatidylinositol-specific phospholipases C (PI-PLC) display similar substrate specificity as their eukaryotic counterparts involved in signal transduction of insulin and Ca2(+)-mobilizing hormones, and are used in the study of the novel glycosylphosphatidylinositol-protein anchors (GPI-anchors). For the investigation of structure-function aspects of the PI-PLC secreted from Bacillus cereus cells, a panel of murine monoclonal antibodies was generated and shown to be specific for the PI-PLC polypeptide in enzyme-linked immunosorbent assays and Western blots. Two of the monoclonals inhibited reactions catalyzed by the bacterial enzyme in vitro: hydrolysis of phosphatidylinositol and the release of bovine erythrocyte acetylcholinesterase from its GPI-anchor. At saturating concentrations of inhibitory antibody only a few percent of the enzyme activity remained. The epitope recognized by one of the inhibitory antibodies, A72-24, was mapped by proteolytic digestion, protein sequencing, and Western blotting of the generated fragments. The data indicate that at least part of the epitope resides within an 8 kDa-stretch of the bacterial PI-PLC (Gln-45 - Lys-122). Essentially the same segment of the bacterial polypeptide has previously been shown to display limited amino acid sequence similarity with several eukaryotic PI-specific phospholipases C (Kuppe, A., Evans, L.M., McMillen, D.A. and Griffith, O.H. (1989) J. Bacteriol. 171, 6077-6083). The results reported here suggest that the conserved peptide of these enzymes may contain functionally important residues.
Acetylcholinesterase↗
Domain structure and conformation of histidine-proline-rich glycoprotein.
The complete primary structure of rabbit plasma histidine-proline-rich glycoprotein (HPRG), also known as histidine-rich glycoprotein, was determined by a combination of cDNA and peptide sequencing. Limited proteolysis with plasmin yielded three disulfide-linked fragments that were further purified. Reduction of the disulfide bonds with dithiothreitol under nondenaturing conditions releases the central, histidine-proline-rich domain, which contains 15 tandem repeats of the pentapeptide [H/P]-[H/P]PHG. The N-terminal fragment (295 amino acids), consisting of two cystatin-like modules, is bound to the proline-rich C-terminal fragment (105 amino acids) via a buried disulfide bond whose reduction requires prior denaturation. Far-UV circular dichroism spectra revealed beta-sheet with some alpha-helix, polyproline-II helix, and random coil in the secondary structure of the N-terminal, central, and C-terminal domains, respectively. The modular architecture of HPRG suggests that it may have several independent binding sites and that its biological role may be to bring two or more ligands together. The histidine-proline-rich domain, which contains 34 of the 53 histidine residues of HPRG, binds heparin and has an isoelectric point of 7.15 and a relatively high apparent pKa (7.0) of its histidine residues, and thus it probably mediates the interaction between HPRG and heparin, which is strikingly sensitive to pH in the range 7.0-7.4 [Peterson et al. (1987) J. Biol. Chem. 262, 7567-7574]. Solvent perturbation and second-derivative UV spectroscopy of HPRG revealed changes in the environment of tryptophan residues upon lowering the pH. This transition had a midpoint at pH 6.0 and required the disulfide bond bridging the histidine-proline-rich domain to the N/C fragment. The data are consistent with the mutual repulsion of protonated histidine residues in the histidine-proline-rich region causing a conformational change transmitted to the rest of the molecule via the disulfide bond.
Amino Acid Sequence↗
Mass spectrometry assisted assignment of NMR resonances in 15N labeled proteins.
Application of nuclear magnetic resonance (NMR) methods for the structural characterization to larger and more complex protein systems can be facilitated through the development of new methods for resonance assignment. Here, a novel approach that relies on integration of NMR and mass spectrometry (MS) methods is explored. The approach relies on the fact that both NMR and MS are able to monitor rates of exchange of amide protons for water deuterons. Correlating the rates can connect cross-peak positions from NMR data with fragment masses from MS data to support sequential assignment. The example provided is for a small model protein, ubiquitin, but the potential for application to large, more difficult to express proteins is clear.
Amino Acid Sequence↗
Human keratinocytes adhere to and spread on synthetic peptide FN-C/H-V derived from fibronectin.
In a previous study, we reported that two synthetic peptides derived from the 33-kD carboxyl terminal cell/heparin-binding fragment of fibronectin A chain promoted keratinocyte adhesion but not spreading. Because keratinocytes are capable of spreading on the 33/66-kD fragments, we focused on identifying additional chemically synthesized peptides from the cell/heparin-binding fragments of fibronectin that might promote cell spreading. When plastic substrata were coated with peptide FN-C/H-V (WQPPRARI), which is derived from the carboxyl-terminal heparin-binding domain of all plasma fibronectin isoforms, keratinocytes adhered and displayed a spread morphology. In solution, soluble peptide FN-C/H-V inhibited cell spreading on intact fibronectin and on the 33/66-kD fragments. Furthermore, polyclonal antibodies raised against peptide FN-C/H-V also inhibited keratinocyte spreading on fibronectin and the 33/66-kD fragments. These data support the hypothesis that keratinocyte cell adhesion and cell spreading on fibronectin are mediated by multiple distinct domains and different regulatory processes.
Amino Acid Sequence↗
Synthesis and solubility properties of peptide fragments of human hemoglobin alpha-chain (123-136).
The solubility prediction method for protected peptides was successfully applied to relatively small peptide fragments of human hemoglobin alpha-chain (123-136) which contained various polar amino acid residues such as Asp(OBzl), Glu(OBzl), Lys(Z), Ser(Bzl), and Thr(Bzl). As reported previously for hydrophobic peptides and human proinsulin C-peptide fragments, solubility data indicated that the insolubility of protected peptides having a mean value of Pc value below 0.90 appeared to begin at the octa- or nonapeptide sequence level and that beta-sheet structure played an important role in the insolubility of peptides. When a peptide has a beta-sheet structure in the solid state, we can clearly determine the critical chain length for peptide insolubility, the solubility dependence on solvent properties, and the solubility independence of amino acid compositions of peptides.
Amino Acid Sequence↗
Crossreactions and sequence homologies between recombinant polypeptides from Leishmania aethiopica and human IgG and IgM.
Recombinant DNA fragments M (154 bp) and G (206 bp), coding for recombinant polypeptides that crossreact with human IgM and IgG, have been isolated from a genomic library of Leishmania aethiopica. Epitope scanning of the two recombinant polypeptides, using overlapping octapeptides, revealed several crossreactive epitopes present in both recombinant proteins. By comparing amino acid sequences, similar sequences in human mu and gamma immunoglobulin heavy chains were identified. One of the parasite octapeptides is identical to an octapeptide in gamma1 covering the Gm(a) allotypic marker. Expression of both the M and G fragments was detected in the parasites by RT-PCR of total mRNA, using primers specific for these fragments. Preliminary data showed that the presence of autoimmune anti-IgG antibodies was more pronounced in sera from patients with diffuse cutaneous leishmaniasis than in sera from patients with localised cutaneous leishmaniasis. We suggest that these immunoglobulin-crossreacting epitopes potentially might contribute to the induction of rheumatoid factors and be involved in the interplay between the parasite and the host immune system.
Amino Acid Sequence↗
Identification of the gene lon (capR) product as a 94-kilodalton polypeptide by cloning and deletion analysis.
A mutation in the lon (capR) gene of Escherichia coli K-12 effects several phenotypic alterations in the mutant cell, such as overproduction of capsular polysaccharide and sensitivity to ultraviolet or ionizing radiation. A previously cloned 9.2-megadalton (Md) EcoRI fragment contained the capR+ gene and specified two polypeptides, 94 kilodaltons (K) and 67K. To provide evidence that the 94K polypeptide is the capR+ gene product, we constructed a capR+ plasmid pJMC40, having a 2.0-Md EcoRI-PstI fragment which codes only for the 94K polypeptide. Plasmids pJMC22 and pJMC30, having deletions of 0.7 and 0.8 Md, respectively, from one end of the 2.0-Md fragment, were also constructed. Each codes for a shortened stable polypeptide (from the 94K). Neither plasmid can confer the capR+ phenotype to capR mutants, confirming that the unaltered 94K polypeptide is the capR+ gene product. Plasmids pJMC51 and pJMC52 each have a deletion of 0.7 Md from the other end of the 2.0-Md fragment, differing only in the orientation of the remaining 1.3-Md fragment with respect to the cloning vehicle. They are nonfunctional with respect to capR+ and do not code for a common polypeptide from the 1.3-Md fragment. These data indicate that the fragments in pJMC22 and pJMC30, which both code for shortened 94K polypeptides, contain the promoter-operator region of the capR gene. The deletion plasmids were also used to map chromosomal capR mutations.
Bacterial Proteins↗
Function and Identification of a Novel Silencer in 5' Flanking Distal Region of Human beta Globin Gene.
In order to inquire into the possible function of the sequence in the 5' flanking distal region and/or delta-beta intergene of human beta-globin gene several recombinant retrovirus vectors containing beta-globin gene with different length of 5' flanking sequences were constructed and transfected into Hela cells. The levels of beta-globin gene expression determined quantitatively by Northern blotting and RT-cPCR revealed that there is a strong silencer activity in a DNA sequence(723 bp) between-2282 bp and -1559 bp upstream from the cap site of beta-globin gene. The silencer activity was further identified to be possibly located mainly on a 310bp DNA restriction fragment by using the competitive gel retardation assay(cGRA) and many known regulatory elements were found present in it as well. Luciferase reporter gene expression system was adopted to study the function of this 310bp fragment and data showed that the fragment exhibited significant inhibitory effect on each of the recombinant vectors with alpha,beta or delta gene promoters. The above results suggest that this silencer may be involved in a potential regulatory network between delta and beta globin genes and may play an important role in the regulation of globin gene expression.
Journal Article↗
Isolation and characterization of proteolytic fragments of human factor VIIa which inhibit the tissue factor-enhanced amidolytic activity of factor VIIa.
The interaction of circulating factor VII/VIIa with tissue factor presented by cells in extravascular tissues represents the initial event in the extrinsic pathway of blood coagulation. To determine the tissue factor binding domains in human factor VIIa, we have subjected recombinant human factor VIIa to tryptic digestion and isolated two proteolytic fragments (molecular mass = 32 and 20 kDa) by a combination of immunoaffinity chromatography and reversed phase high performance liquid chromatography (HPLC) which strongly inhibits the tissue factor-enhanced amidolytic activity of factor VIIa and inhibits the activation of factor X by factor VIIa in the presence of tissue factor. The 32-kDa factor VIIa fragment consisted of residues 1-137/143 from the light chain of factor VIIa connected by a disulfide bond to residues 153-277 from the heavy chain. The 20-kDa factor VIIa fragment consisted of residues 1-137 of the light chain of factor VIIa in disulfide linkage with residues 248-266 of the heavy chain. The 32- and 20-kDa factor VIIa fragments inhibited the tissue factor apoprotein-enhanced factor VIIa amidolytic activity with Ki values of 35 and 65 nM, respectively. The Ki values for the inhibition of relipidated tissue factor apoprotein-enhanced factor VIIa amidolytic activity by the 32- and 20-kDa factor VIIa fragments were 70 and 610 nM, respectively. Factor X activation by factor VIIa-relipidated tissue factor was inhibited half-maximally by the 32- and 20-kDa factor VIIa fragments at 65 and 680 nM concentrations, respectively. Equilibrium binding studies indicated that the 32- and 20-kDa factor VIIa fragments interacted with cell surface tissue factor expressed on J82 cells in a specific and saturable manner with Kd values of 30 and 64 nM, respectively. In addition, a peptide consisting of residues 1-109 from the light chain of factor VIIa obtained by reduction and HPLC of the 20-kDa factor VIIa fragment retained inhibitory activity, but the selective removal of the gamma-carboxyglutamic acid domain from the 20-kDa factor VIIa fragment by cathepsin G cleavage resulted in the complete loss of inhibitory activity in this fragment. Our data strongly suggest that the epidermal growth factor-like domains covalently linked to the gamma-carboxyglutamic acid domain in factor VIIa constitute the high affinity tissue factor binding domain in this molecule.
Amino Acid Sequence↗
Optimization of capillary chromatography ion trap-mass spectrometry for identification of gel-separated proteins.
The current paradigm for protein identification using mass spectrometric derived peptide-mass and fragment-ion data employs computer algorithms which match uninterpreted or partially interpreted fragment-ion data to sequence databases, both protein and translated nucleotide sequence databases. Nucleotide sequence databases continue to grow at a rapid rate for some species, providing an unsurpassed resource for protein identification in those species. Ion-trap mass spectrometers with their ability to rapidly generate fragment-ion spectra in a data-dependent manner with high sensitivity and accuracy has led to their increased use for protein identification. We have investigated various parameters on a commercial ion trap-mass spectrometer to enhance our ability to identify peptides separated by capillary reversed phase-high performance liquid chromatography (RP-HPLC) coupled on-line to the mass spectrometer. By systematically evaluating the standard parameters (ion injection time and number of microscans) together with selection of multiple ions from the full mass range, improved tandem mass spectrometry (MS/MS) spectra were generated, facilitating identification of proteins at a low pmol level. Application of this technology to the identification of a standard protein and an unknown from an affinity-enriched mixture are shown.
Amino Acid Sequence↗
GELYMAC: a Macintosh application for calculating DNA fragment size from gel electrophoresis migration data.
A program called GELYMAC takes data on the distances migrated by DNA fragments in a one-dimensional electrophoretic gel and, using a cubic-spline best-fit of marker fragment distance migrated versus molecular size, calculates the molecular sizes of the fragments. Written in the Rascal (Real-time Pascal) programming language, the program runs on the Macintosh family of microcomputers. Rapid entry of marker and experimental fragment migration data is afforded using a scroll bar system adjacent to a graphic representation of a gel. Output includes tabular listing of the data, graphic cartoons of the gel, and the fragment locations and molecular sizes for individual gel lanes, and the calibration curve used in data computations.
Calibration↗
Epidemiologic trends and costs of fragmentation.
The data that were reviewed in this article documented that in health systems, which manage behavioral health disorders independently from general medical disorders, the estimated 10% to 30% of patients with behavioral health service needs can expect (1) poor access or barriers to medical or mental health care; (2) when services are available, most provided will not meet minimum standards for expected outcome change; and (3) as a consequence of (1) and (2), medical and behavioral disorders will be more persistent with increased complications, will be associated with greater disability, and will lead to higher total health care and disability costs than will treatment of patients who do not have behavioral health disorders. This article proposes that these health system deficiencies will persist unless behavioral health services become an integral part of medical care (ie, integrated). By doing so, it creates a win-win situation for virtually all parties involved. Complex patients will receive coordinated general medical and behavioral health care that leads to improved outcomes. Clinicians and the hospitals that support integrated programs will be less encumbered by cross-disciplinary roadblocks as they deliver services that augment patient outcomes. Health plans (insurers) will be able to decrease administrative and claims costs because the complex patients who generate more than 80% of service use will have less complicated claims adjudication and better clinical outcomes. As a result, purchaser premiums, whether government programs, employers, or individuals, will decrease and the impact on national budgets will improve. Ongoing research will be important to assure that application of the best clinical and administrative practices are used to achieve these outcomes.
Behavioral Medicine↗
Ovine mitochondrial DNA: restriction enzyme analysis, mapping and sequencing data.
Restriction endonuclease fragment patterns of mitochondrial DNA (mtDNA) in sheep were analysed with 11 enzymes. Four breeds (Merinolandschaf, Rhoenschaf, Schwarzkoepfiges Fleischschaf and Skudde) of domestic sheep and European Mouflon were examined. A restriction map with 28 cleavage sites of seven enzymes was established. KpnI and PstI do not cut ovine mtDNA. Two EcoRI fragments of Merinolandschaf, Rhoenschaf and Mouflon each were cloned and partially sequenced. Intraspecific nucleotide sequence differences within 1.101 kb ranged from 0.09 to 0.27%. Hybridization analysis with a fragment of porcine mtDNA along with sequencing data from cloned fragments was used for orientation of the restriction map along the bovine sequence. Ovine mtDNA sequences encompassing parts of the Cyt.b-, ND5-, CoIII- and ATPase6 genes were compared with the corresponding sequences of the bovine mtDNA.
Adenosine Triphosphatases↗
Characterization of the HIV N-terminal fusion peptide-containing region in context of key gp41 fusion conformations.
Central to our understanding of human immunodeficiency virus-induced fusion is the high resolution structure of fragments of the gp41 fusion protein folded in a low energy core conformation. However, regions fundamental to fusion, like the fusion peptide (FP), have yet to be characterized in the context of the cognate protein regardless of its conformation. Based on conformation-specific monoclonal antibody recognition, we identified the polar region consecutive to the N36 fragment as a stabilizer of trimeric coiled-coil assembly, thereby enhancing inhibitory potency. This tertiary organization is retained in the context of the hydrophobic FP (N70 fragment). Our data indicate that the N70 fragment recapitulates the expected organization of this region in the viral fusion intermediate (N-terminal half of the pre-hairpin intermediate (N-PHI)), which happens to be the prime target for fusion inhibitors. Regarding the low energy conformation, we show for the first time core formation in the context of the FP (N70 core). The alpha-helical and coiled-coil stabilizing polar region confers substantial thermal stability to the core, whereas the hydrophobic FP does not add further stability. For the two key fusion conformations, N-PHI and N70 core, we find that the FP adopts a nonhelical structure and directs higher order assembly (assembly of coiled coils in N-PHI and assembly of bundles in the N70 core). This supra-molecular organization of coiled coils or folded cores is seen only in the context of the FP. This study is the first to characterize the FP region in the context of the folded core and provides a basic understanding of the role of the elusive FP for key gp41 fusion conformations.
Antibodies, Monoclonal↗