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S Pongor

Publications and source records attributed to S Pongor.

At least 73 records · Page 4Linked to original sources
PubMed1993

Activity of recombinant alpha and beta subunits of casein kinase II from Xenopus laevis.

Casein kinase II (CKII) is a ubiquitous protein kinase, found predominantly in cell nuclei, which has two subunits in a tetrameric alpha 2 beta 2 or alpha alpha' beta 2 conformation. The catalytic center is present in the alpha subunit which is active by itself while beta is a regulatory subunit that can greatly enhance the activity of alpha. The cDNA genes of Xenopus laevis coding for the alpha and beta subunits of CKII have been expressed in Escherichia coli and extensively purified. The recombinant subunits reconstitute a fully active holoenzyme when incubated in stoichiometric amounts. Mutations that change serines in positions 2 and 3 of the beta subunit for glycines completely eliminate the autophosphorylation site present in this subunit but do not significantly affect the capacity of beta to activate alpha. A fusion protein composed of glutathione transferase linked to the X. laevis CKII beta subunit can also activate alpha. This fusion protein binds to glutathione-agarose beads and can mediate the binding of the alpha subunit to this matrix. Conversely, the alpha subunit was found to bind to glass fiber filters in an active form that can still be activated by beta to an extent similar to that seen in solution. Using peptides containing tyrosine and glutamic acid as inhibitors of the activity of the isolated alpha subunit and of the holoenzyme, the effect of beta on the specificity of inhibition was studied.(ABSTRACT TRUNCATED AT 250 WORDS)

Amino Acid Sequence↗
PubMed1993

Interactions of USF and Ku antigen with a human DNA region containing a replication origin.

By means of a combination of ion-exchange and sequence-specific affinity chromatography techniques, we have purified to homogeneity two protein complexes binding in a human DNA region (B48) previously recognized to contain a DNA replication origin. The DNA sequence used for the protein purification (B48 binding site) contains a binding site for basic-helix-loop-helix DNA binding proteins. The first complex is composed of two polypeptides of 42- and 44-kDa; its size, heat stability, and target DNA sequence suggest that it corresponds to transcription factor USF; furthermore, the 42-kDa polypeptide is recognized by antibodies raised against 43-kDa-USF. The second complex is represented by equimolar amounts of two proteins of 72 and 87 kDa; microsequencing of the two species indicated that they correspond to the human Ku antigen. In analogy with Ku, they produce a regular pattern of footprints without an apparent sequence-specificity, and their binding can be competed by unspecific DNA provided that it contains free ends. The potential role of B48 binding site and of these cognate proteins in origin activation is discussed.

Amino Acid Sequence↗
PubMed1993

The SBASE protein domain library, release 2.0: a collection of annotated protein sequence segments.

SBASE 2.0 is the second release of SBASE, a collection of annotated protein domain sequences. SBASE entries represent various structural, functional, ligand-binding and topogenic segments of proteins [Pongor, S. et al. (1993) Prot. Eng., in press]. This release contains 34,518 entries provided with standardized names and it is cross-referenced to the major protein and nucleic acid databanks as well as to the PROSITE catalog of protein sequence patterns [Bairoch, A. (1992) Nucl. Acids Res., 20 suppl, 2013-2018]. SBASE can be used for establishing domain homologies using different database-search tools such as FASTA [Lipman and Pearson (1985) Science, 227, 1436-1441], FASTDB [Brutlag et al. (1990) Comp. Appl. Biosci., 6, 237-245] or BLAST3 [Altschul and Lipman (1990) Proc. Natl. Acad. Sci. USA, 87, 5509-5513] which is especially useful in the case of loosely defined domain types for which efficient consensus patterns can not be established. SBASE 2.0 and a set of search and retrieval tools are freely available on request to the authors or by anonymous 'ftp' file transfer from mean value of ftp.icgeb.trieste.it.

Amino Acid Sequence↗
PubMed1993

Evidence for opposite groove-directed curvature of GGGCCC and AAAAA sequence elements.

The repetitive sequence (AGGGCCCTAGAGGGGCCC-TAG)n was previously shown to be curved by gel mobility assays. Here we show, using hydroxy radical/DNase I digestion and differential helical phasing experiments that the curvature is directed towards the major groove and is located in the GGGCCC, but not the CTAGAG segments. The effect of the GC step in the context of the GGGCCC motif is apparently about as large as that of AA/TT, i.e. enough to cancel the macroscopic curvature of helically phased A-tracts. These data are in agreement with positive roll-like curvature of the GCC/GGC motif, predicted from nucleosome packing data and the 3D structure of the GGGGCCCC octamer, but they are not in agreement with the dinucleotide-based roll angle values predicted for AG/CT, TA, GG/CC and GC steps. Our results thus indicate the importance of interactions beyond the dinucleotide steps in predictive models of DNA curvature.

Base Sequence↗
PubMed1993

The SBASE domain library: a collection of annotated protein segments.

SBASE is a database of annotated protein domain sequences representing various structural, functional, ligand binding and topogenic segments of proteins. The current release of SBASE contains 27,211 entries which are provided with standardized names in order to facilitate retrieval. SBASE is cross-referenced to the major protein and nucleic acid databanks as well as to the PROSITE catalog of protein sequence patterns [Bairoch, A. (1992) Nucleic Acids Res., 20, Suppl., 2013-2118]. SBASE can be used to establish domain homologies through database search using programs such as FASTA [Lipman and Pearson (1985) Science, 227, 1436-1441], FASTDB [Brutlag et al. (1990) Comp. Appl. Biosci., 6, 237-245] or BLAST3 [Altschul and Lipman (1990) Proc. Natl. Acad. Sci. USA, 87, 5509-5513], which is especially useful in the case of loosely defined domain types for which efficient consensus patterns cannot be established. The use of SBASE is illustrated on the DNA binding protein Brain-4. The database and a set of search and retrieval tools are freely available on request to the authors or by anonymous 'ftp' file transfer from < ftp.icgeb.trieste.it >.

Amino Acid Sequence↗
PubMed1993

Is an amphiphilic region responsible for the haemolytic activity of Bacillus thuringiensis toxin?

The amino acid sequence of the 27 kDa protein responsible for the haemolytic activity of Bacillus thuringiensis subsp. israelensis toxin has been analysed by secondary structure prediction, helical wheel/net diagrams and molecular mechanics calculations. We found that segment 116-126 presumably forms a strongly amphiphilic alpha-helix. This is supported by the findings that the synthesized segment 116-126 (a) has a significant alpha-helical content in water, and (b) displays an in vitro haemolytic activity comparable to that of bee venom peptide melittin. As segment 116-126 is present in the haemolyzing, but not present in the non-haemolyzing proteins from B. thuringiensis toxins, we suggest that this segment is responsible for the lytic potential of the B. thuringiensis subsp. israelensis protein.

Amino Acid Sequence↗
PubMed1992

Spectral and sequence similarity between vasoactive intestinal peptide and the second conserved region of human immunodeficiency virus type 1 envelope glycoprotein (gp120): possible consequences on prevention and therapy of AIDS.

Recently, in sera of HIV infected individuals, antibodies recognizing nonimmunogenic C-terminal domain of the second conserved region of HIV-1 gp120 were identified (1). These antibodies are significantly more prevalent in asymptomatic carriers than in AIDS patients (1). Here we reported striking spectral and sequence homologies between human vasoactive intestinal peptide (VIP) and the conserved peptide derived from HIV-1 gp120 which binds these antibodies. The possible consequences of these findings on therapy and prevention of AIDS are discussed.

Acquired Immunodeficiency Syndrome↗
PubMed1992

Improved detection of homology in distantly related proteins: similarity of adducin with actin-binding proteins.

A novel and generally applicable method is described for the detection of homology in distantly related proteins using a new domain sequence database that contains over 20,000 protein sequence segments of known function. The use of the method is illustrated on distantly related domains shared by complement components C1S and C1R, calcium-dependent serine proteinase and bone morphogenetic protein 1. New homologies are shown between human adducin and the actin-binding domains of alfa-actinin and dystrophin.

Actinin↗
PubMed1991

Protein and DNA-sequence homologies between the V3-loop of human immunodeficiency virus type I envelope protein gp120 and immunoglobulin variable regions.

We found that a common amino acid sequence motif exists between the V3-loop region of the human immunodeficiency virus type I envelope protein HIV gp120 and the human immunoglobulin heavy chain variable regions of subclass III (Ig VH-III). In the Ig VH-III sequences, the common motif overlaps with framework-1, complementarity-determining-region-1 and framework-2. In the homologous regions, the two groups of sequences also have a similar distribution of residue variability. On the DNA sequence level, the homology includes the conserved rearrangement signals of the VH-III genes, which lends support to the speculation that the V3 region of gp120 also may be involved in rearrangement processes.

Amino Acid Sequence↗
PubMed1991

Molecular cloning of an adducin-like protein: evidence of a polymorphism in the normotensive and hypertensive rats of the Milan strain.

Differences genetically associated with the development of hypertension in a strain of genetically hypertensive rat (MHS) were described in ion transport across erythrocyte membranes compared to normotensive control (MNS). Antibodies against the MNS ghost proteins were raised in the MHS, producing an immunoreaction against a 105 KDa protein later identified as adducin. A clone coding for a portion of mouse adducin was isolated with these antibodies. Using this clone, overlapping cDNA clones coding for a 63 KDa adducin-like protein were isolated. A family of related mRNAs of about 3500, 3800, 4200 nt, was found to be present in spleen, kidney and heart tissues. Similar mRNAs and an additional tissue specific 8000 nt mRNA are present in brain. All mRNAs seem to be generated by alternative splicing from the transcript of a single gene. An interesting polymorphism, a Gln to Arg substitution, was detected in the carboxiterminal area of rat adducin 63.

Amino Acid Sequence↗
PubMed1985

Carbodiimide-mediated O-sulfation of hydroxy-amino acids and peptides: a reaction suitable for radiolabeling.

Carbodiimide-mediated sulfation of hydroxy-amino acids, peptides, and proteins can be accomplished in dry dimethylformamide by incubation in a 20-50 molar excess of sulfuric acid and various concentrations of dicyclohexyl carbodiimide [(1-ethyl-(3-dimethylaminopropyl)carbodiimide or 1-cyclohexyl-3-(2-morpholoethyl)carbodiimide p-toluene sulfonate)] at 4 degrees C for 2-4 h. Under these conditions, hydroxy-amino acids are quantitatively converted into O-sulfates, while cysteine yields the S-sulfonate. Other amino acids, including tryptophan, do not react and are recovered quantitatively. Porcine sodium insulin yields a product that can be separated into six bands by nondenaturing polyacrylamide gel electrophoresis. Radiolabeling of peptides by this method can be carried out with a high degree of efficiency if the added [35S]sulfuric acid is used carrier free with an acid excess provided by trifluoromethyl sulfonic acid. Under these conditions, over 60% of [35S]sulfuric acid was incorporated into insulin and bovine serum albumin. This method may prove useful in the radiolabeling of other peptides and proteins.

Amino Acids↗
PubMed1985

Prediction of homology and divergence in the secondary structure of polypeptides.

A quantitative procedure is described for the comparison of secondary structure of homologous proteins. Standard predictive methods are used to generate probability profiles from pairs of homologous amino acid sequences; correlation coefficients (R) are then computed between each pair of amino acids for alpha-helix (R alpha), extended structure (R beta), turn (R(t)), and coil (R(c)). R values are >0.2 for correctly aligned homologous sequences. Unrelated or incorrectly aligned sequences give R values near zero. Lack of correlation for a segment of otherwise well-correlated sequences is used to identify structural divergence, which is then evaluated graphically by using difference profiles. A combination of these techniques correctly predicts secondary structural differences between melittin or beta-endorphin and their respective synthetic analogs. The method is potentially useful to describe evolutionary changes in protein secondary structure as well as in the design of peptide analogs.

Amino Acid Sequence↗
PubMed1985

Microcomputer programs for prediction and comparative evaluation of protein secondary structure from nucleotide sequence data: application to ribulose-1,5-bisphosphate carboxylase sequences.

Apple II PASCAL computer programs are described for routine evaluation of protein secondary structures predicted from DNA or amino acid sequence data. The programs predict protein secondary structure using the directional information algorithm of Garnier et al. (1978), and calculate hydrophobicity (Kyte and Doolittle, 1982), hydrophilicity (Hopp and Woods, 1981), hydrophobic moment (Eisenberg et al., 1984b), and secondary structure propensity profiles. The novel feature of these programs is the application of numeric and graphic methods, designed to facilitate detection and characterization of structural similarities/divergences using the aforementioned structural parameters. The use of the programs is demonstrated on a set of sequences from the large and small subunits of ribulose-1,5-bisphosphate carboxylase.

Base Sequence↗
PubMed1984

Aging of proteins: isolation and identification of a fluorescent chromophore from the reaction of polypeptides with glucose.

Proteins exposed to glucose over long periods are known to undergo physicochemical changes including crosslinking and formation of brown fluorescent pigments of poorly characterized structure. Acid hydrolysis of both browned poly(L-lysine) and browned bovine serum albumin is found to release a major fluorescent chromophore, which after alkalinization is extractable into organic solvents and which can be purified by silica gel chromatography. The fluorescence properties of this compound very closely resemble those of the bulk browned polypeptides. By NMR, mass spectroscopy, and chemical derivatization, this compound is assigned the structure 2-(2-furoyl)-4(5)-(2-furanyl)-1H-imidazole (FFI). Confirmation was obtained by independent chemical synthesis from furylglyoxal and ammonia. The incorporation of two peptide-derived amine nitrogens and two glucose residues in FFI strongly suggests that peptide-bound FFI precursors are implicated in the crosslinking of proteins by glucose in vivo. This reaction has potential implications in the understanding of glucose-mediated protein modifications and their role in the complications of diabetes and aging.

Aging↗