Search PubMed⌕ Search

Biomedical subjects

D J Pappin

Publications and source records attributed to D J Pappin.

At least 37 records · Page 2Linked to original sources
PubMed1995

The myristoylated alanine-rich C-kinase substrate (MARCKS) is sequentially phosphorylated by conventional, novel and atypical isotypes of protein kinase C.

The myristoylated alanine-rich C-kinase substrate (MARCKS) is the major protein kinase C (PKC) substrate in many cell types including fibroblasts and brain cells. Here we describe the phosphorylation of MARCKS and the site specificity for different PKC isotypes. Conventional (c)PKC beta 1, novel (n)PKC delta and nPKC epsilon efficiently phosphorylated the MARCKS protein in vitro. The Km values were extremely low, reflecting a high affinity between kinases and substrate. The apparent affinity of nPKC delta (Km = 0.06 microM) was higher than that of nPKC epsilon and cPKC beta 1 (Km = 0.32 microM). The rate of substrate phosphorylation was inversely correlated with affinity and decreased in the order nPKC epsilon > cPKC beta 1 > nPKC delta. Atypical (a)PKC zeta did not phosphorylate the intact MARCKS protein. However, a 25-amino-acid peptide deduced from the MARCKS phosphorylation domain, was efficiently phosphorylated by aPKC zeta as well as by the other three PKC. Site analysis revealed that only serine residues S152, S156 and S163 were phosphorylated, with S163 phosphorylated highest, followed by S156 and S152; in contrast, S160 and S167 were not phosphorylated. No further PKC phosphorylation sites could be detected in MARCKS. The phosphorylation pattern was independent of the type of PKC isotype used. Kinetic analysis showed, that MARCKS is sequentially phosphorylated in the order S156 > S163 > S152 by cPKC, nPKC and aPKC. There was no dramatic difference in the sequential phosphorylation of MARCKS detectable when comparing the four PKC isotypes. The results are discussed in the context of the functional significance of MARCKS phosphorylation.

Intracellular Signaling Peptides and Proteins↗
PubMed1995

Identification of myocardial proteins from two-dimensional gels by peptide mass fingerprinting.

Two-dimensional gels offer a powerful method for separating complex protein mixtures, but subsequent methods for analysing individual components, such as protein sequencing and Western immunoblotting, are laborious and slow. The identification of proteins can be accelerated by using a combination of protease digestion and matrix assisted laser desorption-mass spectrometry (MALDI-MS). The peptide mass spectrum of a protein represents a unique fingerprint determined by the amino acid sequence and the cleavage properties of the protease. Software has been developed so that peptide masses can be used to search a mass-based peptide database generated from established protein sequence databases. A list of the closest matching proteins is produced to allow identification of the sample. The strategy was applied to 52 protein spots from human myocardial tissue separated by two-dimensional electrophoresis (2-DE) gels and analysed blind. Conditions for optimal trypsin digestion of proteins electroblotted onto polyvinylidene difluoride (PVDF) membranes are described. Mass data were generated from both Coomassie Brilliant Blue and sulforhodamine B-stained proteins, though the former required destaining prior to digestion. Alkylation of cysteine and oxidation of methionine were significant modifications that influenced the successful identification of a protein spot. Examples are presented to illustrate the advantages and disadvantages of this approach.

Electrophoresis, Gel, Two-Dimensional↗
PubMed1995

Identification of phosphorylation sites in the mouse oestrogen receptor.

Phosphorylation sites in the mouse oestrogen receptor, expressed in COS-1 cells in the presence of 17 beta-oestradiol, have been mapped by solid phase microsequencing. The receptor was first radio-labelled with [32P]orthophosphate and a number of 3H- or 14C-labelled amino acids, immunopurified and then tryptic peptides were separated by thin layer chromatography or high performance liquid chromatography. Amino acid sequence analysis indicated that Ser-122, Ser-156, Ser-158 and Ser-298 were phosphorylated. The substitution of Ser-122 and Ser-298 with alanine had a negligible effect on the transcriptional activity of the receptor in transfected cells. However, a reduction of transcriptional activity was observed when Ser-122 was mutated in the context of mutations in a putative amphipathic alpha-helix involved in AF-2 activity. Thus a region of AF-1 that encompasses Ser-122 appears to interact with AF-2 in the full-length receptor.

3T3 Cells↗
PubMed1995

Molecular cloning and expression of human cDNAs encoding a novel DNA ligase IV and DNA ligase III, an enzyme active in DNA repair and recombination.

Three distinct DNA ligases, I to III, have been found previously in mammalian cells, but a cloned cDNA has been identified only for DNA ligase I, an essential enzyme active in DNA replication. A short peptide sequence conserved close to the C terminus of all known eukaryotic DNA ligases was used to search for additional homologous sequences in human cDNA libraries. Two different incomplete cDNA clones that showed partial homology to the conserved peptide were identified. Full-length cDNAs were obtained and expressed by in vitro transcription and translation. The 103-kDa product of one cDNA clone formed a characteristic complex with the XRCC1 DNA repair protein and was identical with the previously described DNA ligase III. DNA ligase III appears closely related to the smaller DNA ligase II. The 96-kDa in vitro translation product of the second cDNA clone was also shown to be an ATP-dependent DNA ligase. A fourth DNA ligase (DNA ligase IV) has been purified from human cells and shown to be identical to the 96-kDa DNA ligase by unique agreement between mass spectrometry data on tryptic peptides from the purified enzyme and the predicted open reading frame of the cloned cDNA. The amino acid sequences of DNA ligases III and IV share a related active-site motif and several short regions of homology with DNA ligase I, other DNA ligases, and RNA capping enzymes. DNA ligases III and IV are encoded by distinct genes located on human chromosomes 17q11.2-12 and 13q33-34, respectively.

Amino Acid Sequence↗
PubMed1995

Identification of an 80kD protein associated with the alpha 3 beta 1 integrin as a proteolytic fragment of the alpha 3 subunit: studies with human keratinocytes.

We have characterised a protein of approximately 80kD previously observed to co-immunoprecipitate with the alpha 3 beta 1 integrin in lysates of surface labelled human epidermalkeratinocytes. The 80kD protein only appeared when keratinocytes were harvested with trypsin/EDTA prior to lysis and a protein of similar molecular mass could be immunoprecipitated from human dermal fibroblasts following treatment of the cells with trypsin/EDTA. N terminal sequencing established that the 80kD protein had homology with the alpha 3 integrin subunit. Peptide-mass fingerprinting was used to confirm that the protein comprised the amino terminus of alpha 3 and established that the site of cleavage was after amino acid 629. The 80kD fragment could be coimmunoprecipitated with alpha 3 beta 1 using an antibody to the cytoplasmic domain of the alpha 3 subunit, showing that the fragment remained complexed with intact alpha 3 beta 1. When antibodies to the cytoplasmic and extracellular domains of alpha 3 were used to label human epidermis by immunofluorescence, the staining patterns were indistinguishable and there is therefore no evidence that proteolysis of alpha 3 plays a role in keratinocyte detachment from the basement membrane during terminal differentiation. Whether the 80kD fragment has any effects, positive or negative, on alpha 3 beta 1-mediated adhesion remains to be determined.

Amino Acid Sequence↗
PubMed1994

Structural and functional homology between mammalian DNase IV and the 5'-nuclease domain of Escherichia coli DNA polymerase I.

A nuclear 42-kDa 5'-->3'-exonuclease, DNase IV, was found previously in animal tissues. The enzyme has been purified from HeLa cells and shown to possess two catalytic properties characteristic of the 5'-nuclease function of Escherichia coli DNA polymerase I,-DNase IV removes single-stranded 5' regions from splayed-arm DNA structures by endonucleolytic incision at the bifurcation point and possesses RNase H activity. Determination of the molecular masses of tryptic and V8 peptides of DNase IV by mass spectrometry identified the enzyme as the human homolog of the Schizosaccharomyces pombe Rad2 protein. The protein sequence retains conserved residues and shows significant homology to the sequences of the 5'-nuclease domain of E. coli DNA polymerase I and related microbial enzymes.

Amino Acid Sequence↗
PubMed1994

Tyrosine phosphorylation of alpha tubulin in human T lymphocytes.

N-terminal sequencing of the 55- and 50-kDa polypeptides affinity purified on a phosphotyrosine monoclonal antibody column from activated Jurkat T cells identified alpha and beta tubulin. Two-dimensional gel analysis indicated that alpha tubulin was directly phosphorylated on tyrosine. beta Tubulin was not detectably tyrosine phosphorylated but was precipitated by anti-phosphotyrosine (PTyr) antibody by virtue of its association with the alpha subunit as a heterodimer. Phosphotyrosyl alpha tubulin was not incorporated into intact microtubules and was all in the unpolymerized soluble fraction. These results suggest that tyrosine phosphorylation of alpha tubulin may inhibit the ability of this subunit to polymerize into microtubules. Stimulation of Jurkat T cells via T cell receptor increased the amount of tubulin precipitated by the anti-PTyr antibody. These data raise the possibility that the polymerization of tubulin heterodimers may be regulated by phosphorylation on tyrosine during T cell activation.

Amino Acid Sequence↗
PubMed1994

Peptide ladder sequencing by mass spectrometry using a novel, volatile degradation reagent.

A conceptually novel approach to protein sequencing involves the generation of ragged-end polypeptide chains followed by mass spectroscopic analysis of the resulting nested set of fragments. We report here on the synthesis and development of a volatile isothiocyanate (trifluoroethylisothiocyanate) that allows the identification of several consecutive residues starting with a few picomoles of peptide. The nested set of peptides is generated simply by adding equal aliquots of starting peptide each cycle and driving both the coupling and cleavage reactions to completion. No additional reagents are required to act as chain terminators and retention of the peptide terminal amine allows for subsequent modification with quaternary ammonium alkyl NHS esters to improve sensitivity. Complex washing procedures are not required each cycle, as reagents and by-products are efficiently removed under vacuum, eliminating extractive loss. Multiple peptide samples can be processed simultaneously, with each degradation cycle completed in 35-40 min. The inherent simplicity of the process should allow for easy automation and permit rapid processing of samples in parallel.

Amino Acid Sequence↗
PubMed1993

Rapid identification of proteins by peptide-mass fingerprinting.

BACKGROUND: Developments in 'soft' ionisation techniques have revolutionized mass-spectro-metric approaches for the analysis of protein structure. For more than a decade, such techniques have been used, in conjuction with digestion b specific proteases, to produce accurate peptide molecular weight 'fingerprints' of proteins. These fingerprints have commonly been used to screen known proteins, in order to detect errors of translation, to characterize post-translational modifications and to assign diulphide bonds. However, the extent to which peptide-mass information can be used alone to identify unknown sample proteins, independent of other analytical methods such as protein sequence analysis, has remained largely unexplored. RESULTS: We report here on the development of the molecular weight search (MOWSE) peptide-mass database at the SERC Daresbury Laboratory. Practical experience has shown that sample proteins can be uniquely identified from a few as three or four experimentally determined peptide masses when these are screened against a fragment database that is derived from over 50 000 proteins. Experimental errors of a few Daltons are tolerated by the scoring algorithms, thus permitting the use of inexpensive time-of-flight mass spectrometers. As with other types of physical data, such as amino-acid composition or linear sequence, peptide masses provide a set of determinants that are sufficiently discriminating to identify or match unknown sample proteins. CONCLUSION: Peptide-mass fingerprints can prove as discriminating as linear peptide sequences, but can be obtained in a fraction of the time using less protein. In many cases, this allows for a rapid identification of a sample protein before committing it to protein sequence analysis. Fragment masses also provide information, at the protein level, that is complementary to the information provided by large-scale DNA sequencing or mapping projects.

Journal Article↗
PubMed1993

Identification and preliminary characterization of a protein motif related to the zinc finger.

We have identified a protein motif, related to the zinc finger, which defines a newly discovered family of proteins. The motif was found in the sequence of the human RING1 gene, which is proximal to the major histocompatibility complex region on chromosome six. We propose naming this motif the "RING finger" and it is found in 27 proteins, all of which have putative DNA binding functions. We have synthesized a peptide corresponding to the RING1 motif and examined a number of properties, including metal and DNA binding. We provide evidence to support the suggestion that the RING finger motif is the DNA binding domain of this newly defined family of proteins.

Amino Acid Sequence↗
PubMed1992

A homologue of the Drosophila female sterile homeotic (fsh) gene in the class II region of the human MHC.

The RING3 gene maps in the class II region of the human major histocompatibility complex, at a CpG island distal of the HLA-DNA gene. RING3 cDNAs were obtained from a T cell cDNA library and the longest (4 kb) was sequenced. The sequence contained an open reading frame encoding a protein of 754 amino acids. A screen of protein databases revealed striking homology between the RING3 protein and the Drosophila female sterile homeotic gene (fsh) which is implicated in the establishment of segments in the early embryo. Partial sequence homology was also observed with some other proteins involved in cell cycle control (CCG1), cell division (ftsA) and regulation of cell growth (gamma interferons). This highly conserved gene may play an important role in human development. In addition, its location in the MHC class II region may be related to some HLA-associated diseases.

Amino Acid Sequence↗
PubMed1991

Identification of phosphorylated sites in the mouse glucocorticoid receptor.

Glucocorticoid receptors in vivo are phosphorylated in the absence of hormone and become hyperphosphorylated in the presence of glucocorticoid agonist but not antagonists (Ortí, E., Mendel, D.B., Smith, L.I., and Munck, A. (1989) J. Biol. Chem. 264, 9728-9731). As a preliminary step to elucidating the functional significance of receptor phosphorylation, we have identified seven phosphorylated sites on the mouse receptor. Tryptic phosphopeptides from 32P-labeled receptors were purified from glucocorticoid-treated mouse thymoma cells (WEHI-7) and from stably transfected Chinese hamster ovary cells (WCL2) that express large numbers of mouse receptors. Phosphopeptide maps of receptors from these two cell types were almost indistinguishable. Solid phase sequencing revealed phosphorylation at serines 122, 150, 212, 220, 234, and 315 and threonine 159. Serines 122, 150, 212, 220, and 234 and the sequences surrounding them are conserved in the homologous regions of the rat and human receptors, but threonine 159 and serine 315 have no homologues in the human receptor. The seven phosphorylated sites are in the amino-terminal domain of the receptor. All but serine 315 are within transactivation domains identified in the human and/or rat receptors. Serines 212, 220, and 234 are in a highly acidic region that in the mouse receptor is necessary for full transcription initiation activity and reduces nonspecific DNA binding. Serines 212, 220, and 234 and threonine 159 are in consensus sequences for proline-directed kinase and/or p34cdc2 kinase. Serine 122 is in a consensus sequence for casein kinase II whereas serines 150 and 315 do not appear to be in any known kinase consensus sequence. The location of many of these sites suggests a role of phosphorylation in transactivation.

Amino Acid Sequence↗
PubMed1991

Isolation of cDNA clones encoding an enzyme from bovine cells that repairs oxidative DNA damage in vitro: homology with bacterial repair enzymes.

Ionizing radiation and radiomimetic compounds, such as hydrogen peroxide and bleomycin, generate DNA strand breaks with fragmented deoxyribose 3' termini via the formation of oxygen-derived free radicals. These fragmented sugars require removal by enzymes with 3' phosphodiesterase activity before DNA synthesis can proceed. An enzyme that reactivates bleomycin-damaged DNA to a substrate for Klenow polymerase has been purified from calf thymus. The enzyme, which has a Mr of 38,000 on SDS-PAGE, also reactivates hydrogen peroxide-damaged DNA and has an associated apurinic/apyrimidinic (AP) endonuclease activity. The N-terminal amino acid sequence of the purified protein matches that reported previously for a calf thymus enzyme purified on the basis of AP endonuclease activity. Degenerate oligonucleotide primers based on this sequence were used in the polymerase chain reaction to generate from a bovine cDNA library a fragment specific for the 5' end of the coding sequence. Using this cDNA fragment as a probe, several clones containing 1.35 kb cDNA inserts were isolated and the complete nucleotide sequence of one of these determined. This revealed an 0.95 kb open reading frame which would encode a polypeptide of Mr 35,500 and with a N-terminal sequence matching that determined experimentally. The predicted amino acid sequence shows strong homology with the sequences of two bacterial enzymes that repair oxidative DNA damage, ExoA protein of S. pneumoniae and exonuclease III of E. coli.

Amino Acid Sequence↗
PubMed1991

Functionalized membrane supports for covalent protein microsequence analysis.

Methods were developed for high yield covalent attachment of peptides and proteins to isothiocyanate and arylamine-derivatized poly(vinylidene difluoride) membranes for solid-phase sequence analysis. Solutions of protein or peptide were dried onto 8-mm membrane disks such that the functional groups on the surface and the polypeptide were brought into close proximity. In the case of the isothiocyanate membrane, reaction between polypeptide amino groups and the surface isothiocyanate moieties was promoted by application of aqueous N-methylmorpholine. Attachment of proteins and peptides to the arylamine surface was achieved by application of water-soluble carbodiimide in a pH 5.0 buffer. Edman degradation of covalently bound polypeptides was accomplished with initial and repetitive sequence yields ranging from 33 to 75% and 88.5 to 98.5%, respectively. The yields were independent of the sample load (20 pmol to greater than 1 nmol) for either surface. Significant loss of material was not observed when attachment residues were encountered during sequence runs. Application of bovine beta-lactoglobulin A chain, staphylococcus protein A, or the peptide melittin to the isothiocyanate membrane allowed for extended N-terminal sequence identification (35 residues from 20 pmol of beta-lactoglobulin). A number of synthetic and naturally occurring peptides were sequenced to the C-terminal residue following attachment to the arylamine surface. In one example, 10 micrograms of bovine alpha-casein was digested with staphylococcal protease V8 and the peptides were separated by reverse-phase chromatography. Peptide fractions were then directly applied to arylamine membrane disks for covalent sequence analysis. From as little as 2 pmol of initial signal it was possible to determine substantial sequence information (greater than 10 residues).

Amines↗
PubMed1990

Solid-phase sequence analysis of proteins electroblotted or spotted onto polyvinylidene difluoride membranes.

Electroblotted proteins noncovalently bound to polyvinylidene difluoride (PVDF) membranes are typically sequenced using adsorptive sequencer protocols (gas-phase or pulsed-liquid) that do not require a covalent linkage between protein and surface. We have developed simple chemical protocols where proteins are first electroblotted onto unmodified PVDF membranes, visualized with common protein stains, and then immobilized for solid-phase sequence analysis. Adsorbed, stained proteins are first treated with phenylisothiocyanate (PITC) to modify alpha and epsilon amines. The protein is then overlayed with a solution of 1,4-phenylene di-isothiocyanate (DITC), followed by a few microliters of a basic solution containing a poly(alkylamine). As the polymer dries onto the surface both polymer and remaining protein amino groups are crosslinked by DITC. The protein is thus immobilized to the membrane surface by entrapment in a thin polymer coating. The coating is transparent to the degradation chemistry, and extensive enough to remain immobilized even in the absence of any covalent link between polymer and surface. Partial modification with PITC allows for identification of N-terminal and internal lysine residues during sequencing. The process was tested with a variety of poly(alkylamines), linear and branched, with molecular weights ranging from 600 to over 100,000. Proteins bound in this manner were successfully sequenced using covalent (solid-phase) sequencer protocols with cycle times as short as 26 min.

Absorption↗
PubMed1988

Isolation and characterization of a minor legumin and its constituent polypeptides from Pisum sativum (pea).

The purification and characterization of a minor legumin species from Pisum sativum is described. Electrophoretic data indicate that it corresponds to a legumin subunit pair previously designated L1. The beta-polypeptides of the minor legumin have a phenylalanine N-terminus. This is the first time that an amino acid other than glycine has been reported as the N-terminus of the basic polypeptides from legumin-like proteins from any plant species. Sequence analyses of the isolated alpha- and beta-polypeptides of the minor legumin show that it does not correspond to any of the three legumin gene families that have previously been defined on the basis of DNA hybridizations and genetic analyses.

Amino Acid Sequence↗
PubMed1987

Pig kidney angiotensin converting enzyme. Purification and characterization of amphipathic and hydrophilic forms of the enzyme establishes C-terminal anchorage to the plasma membrane.

Angiotensin converting enzyme from pig kidney was isolated by affinity chromatography after solubilization from the membrane by one of four different procedures. Solubilization with Triton X-100, trypsin or by an endogenous activity in microvillar membranes all generated hydrophilic forms of the enzyme as assessed by phase separation in Triton X-114 and failure to incorporate into liposomes. Only when solubilization and purification was effected by Triton X-100 in the presence of EDTA (10 mM) could an amphipathic form of the enzyme (membrane- or m-form) be generated. The m-form of angiotensin converting enzyme (ACE) appeared slightly larger (Mr approx. 180,000) than the hydrophilic forms (Mr approx. 175,000) after SDS/polyacrylamide-gel electrophoresis, and the m-form incorporated into liposomes, consistent with retention of the membrane anchor. The m-form of ACE showed an N-terminal sequence identical with that of preparations of enzyme isolated after solubilization with detergent alone (d-form), with trypsin (t-form) or by the endogenous mechanism (e-form). These data imply that ACE is anchored to the plasma membrane via its C-terminus, in contrast with the N-terminal anchorage of endopeptidase-24.11. No release of ACE from the membrane could be detected with a variety of phospholipases, including bacterial phosphatidylinositol-specific phospholipases C, although an endogenous EDTA-sensitive membrane-associated hydrolase was capable of releasing a soluble, hydrophilic, form of the enzyme.

Amino Acid Sequence↗