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Biomedical subjects

S Pongor

Publications and source records attributed to S Pongor.

At least 55 records · Page 3Linked to original sources
PubMed1996

Correlation of intrinsic DNA curvature with DNA property periodicity.

Twelve di- and trinucleotide parameter sets representing various structural, thermodynamic or bendability-related properties of DNA were tested in the prediction of DNA curvature applying Fourier analysis on curved and straight, A/T-type or G/C-type DNA sequence motifs. The best predictions were obtained with a new consensus bendability scale created by combining a nucleosome-based and a deoxyribonuclease I-based parameter set. Geometry calculations on the same sequences showed that the helical parameters derived from NMR structures can correctly predict curvature, as distinct from the parameters derived from X-ray crystallographic analysis.

Crystallography, X-Ray↗
PubMed1996

The SBASE protein domain library, Release 4.0: a collection of annotated protein sequence segments.

SBASE 4.0 is the fourth release of SBASE, a collection of annotated protein domain sequences that represent various structural, functional, ligand binding and topogenic segments of proteins. SBASE was designed to facilitate the detection of functional homologies and can be searched with standard database search tools, such as FASTA and BLAST3. The present release contains 61 137 entries provided with standardized names and cross-referenced to all major protein, nucleic acid and sequence pattern collections. The entries are clustered into 13 155 groups in order to facilitate detection of distant similarities. SBASE 4.0 is freely available by anonymous ftp file transfer from ftp.icgeb.trieste.it. Individual records can be retrieved with the gopher server at icgeb.trieste.it and with a World Wide Web server at http://www.icgeb.trieste.it. Automated searching of SBASE with BLAST can be carried out with the electronic mail server sbase@icgeb.trieste.it, which now also provides a graphic representation of the homologies. A related mail server, domain@hubi.abc.hu, assigns SBASE domain homologies on the basis of SWISS-PROT searches.

Amino Acid Sequence↗
PubMed1996

Different pathways of the release of cytotoxic proteins in LAK cells.

Human LAK cells were shown to release cytotoxic proteins by both Ca(2+)-dependent and Ca(2+)-independent mechanisms. CD3+ CD8+ CD16- and CD16+ CD8+ CD3- LAK cells were co-incubated with target cells in the presence of 4 mM EGTA. Although EGTA inhibited the exocytosis of cytolytic granules, supernatants obtained were cytotoxic for target cells. Cytotoxicity of CD3+ LAK cells and CD16+ LAK cells was due to cytotoxic proteins with MW 75 (p75), 35 (p35) and 22 (p22) kDa. LAK cells were also shown to release cytotoxic proteins by way of continuous secretion. After co-incubation in the absence of target cells LAK cells can secrete cytotoxic proteins with MW 75 (p75), 55 (p55), 38 (p38), 35 (p35), 25 (p25), 22 (p22) and 17 (p17) kDa.

CD3 Complex↗
PubMed1995

Human DNA helicase IV is nucleolin, an RNA helicase modulated by phosphorylation.

The cDNA encoding human DNA helicase IV (HDH IV), a 100-kDa protein which unwinds DNA in the 5' to 3' direction with respect to the bound strand, was cloned and sequenced. It was found to be identical to the human cDNA encoding nucleolin, a ubiquitous eukaryotic protein essential for pre-ribosome assembly. HDH IV/nucleolin can unwind RNA-RNA duplexes, as well as DNA-DNA and DNA-RNA duplexes. Phosphorylation of HDH IV/nucleolin by cdc2 kinase and casein kinase II enhanced its unwinding activity in an additive way. The Gly-rich C-terminal domain possesses a limited ATP-dependent duplex-unwinding activity which contributes to the helicase activity of HDH IV/nucleolin.

Adenosine Triphosphatases↗
PubMed1995

Rationally designed helix-turn-helix proteins and their conformational changes upon DNA binding.

Circular dichroism and electrophoretic mobility shift studies were performed to confirm that dimerized N-terminal domains of bacterial repressors containing helix-turn-helix motifs are capable of high-affinity and specific DNA recognition as opposed to the monomeric N-terminal domains. Specific, high-affinity DNA binding proteins were designed and produced in which two copies of the N-terminal 1-62 domain of the bacteriophage 434 repressor are connected either in a dyad-symmetric fashion, with a synthetic linker attached to the C-termini, or as direct sequence repeats. Both molecules bound to their presumptive cognate nearly as tightly as does the natural (full-length and non-covalently dimerized) 434 repressor, showing that covalent dimerization can be used to greatly enhance the binding activity of individual protein segments. Circular dichroism spectroscopy showed a pronounced increase in the alpha-helix content when these new proteins interacted with their cognate DNA and a similar, although 30% lower, increase was also seen upon their interaction with non-cognate DNA. These results imply that a gradual conformational change may occur when helix-turn-helix motifs bind to DNA, and that a scanning mechanism is just as plausible for this motif class as that which is proposed for the more flexible basic-leucine zipper and basic-helix-loop-helix motifs.

Amino Acid Sequence↗
PubMed1995

Sequence-dependent bending propensity of DNA as revealed by DNase I: parameters for trinucleotides.

Structural parameters characterizing the bending propensity of trinucleotides were deduced from DNase I digestion data using simple probabilistic models. In contrast to dinucleotide-based models of DNA bending and/or bendability, the trinucleotide parameters are in good agreement with X-ray crystallographic data on bent DNA. This improvement may be due to the fact that the trinucleotide model incorporates more sequence context information than do dinucleotide-based descriptions.

Base Sequence↗
PubMed1995

Trinucleotide models for DNA bending propensity: comparison of models based on DNaseI digestion and nucleosome packaging data.

DNaseI digestion studies (Brukner et al, EMBO J 14, 1812-1818 1995) and nucleosomebinding data (Satchwell et al, J. Mol. Biol. 191, 639-659 1986, Goodsell and Dickerson, Nucleic trinucleotides. A detailed comparison of the two models suggests that while both of them represent improvements with respect to dinucleotide based descriptions, the individual trinucleotide parameters are not highly correlated (linear correlation coefficient is 0.53), and a number of motifs such as TA-elements and CCA/TGG motifs are more realistically described in the DNaseI-based model. This may be due to the fact that the DNaseI-based model does not rely on a static geometry but rather captures a dynamic ability of ds DNA to bend towards the major grove. Future refinement of both models of both models on larger experimental data sets is expected to further improve the prediction of macroscopic DNA-curvature.

DNA↗
PubMed1994

A novel alpha-amylase inhibitor from amaranth (Amaranthus hypocondriacus) seeds.

The major alpha-amylase inhibitor (AAI) present in the seeds of Amaranthus hypocondriacus, a variety of the Mexican crop plant amaranth, is a 32-residue-long polypeptide with three disulfide bridges. Purified AAI strongly inhibits the alpha-amylase activity of insect larvae (Tribolium castaneum and Prostephanus truncatus) and does not inhibit proteases and mammalian alpha-amylases. AAI was sequenced with the automated Edman method, and the disulfide bridges were localized using enzymatic and chemical fragmentation methods combined with N-terminal sequencing. AAI is the shortest alpha-amylase inhibitor described so far which has no known close homologs in the sequence data bases. Its residue conservation patterns and disulfide connectivity are related to the squash family of proteinase inhibitors, to the cellulose binding domain of cellobiohydrolase, and to omega-conotoxin, i.e. a group of small proteins termed "knottins" by Nguyen, D. L., Heitz, A., Chiche, L., Castro, B., Boigegrain, R., Favel, A., and Coletti-Previero, M. ((1990) (Biochimie 72, 431-435) The three-dimensional model of AAI was built according to the common structural features of this group of proteins using side-chain replacement and molecular dynamics refinement techniques.

Amino Acid Sequence↗
PubMed1994

Predicted conformation of poly(dehydroalanine): a preference for turns.

Repetitive conformations of poly(dehydroalanine) were studied using molecular mechanics. An exhaustive search of the conformational space was carried out on a delta Ala octapeptide model, using the AMBER force field and the delta Ala parameters of Alagona et al [26], under three dielectric conditions, epsilon = 1 (vacuum), epsilon = r and epsilon = 4r (solvent). In all cases, two major groups of low-energy conformers were found, one corresponding to a regular 3/10 helix or type III turn, the other to an irregular conformation, phi = -157 to -170 degrees, psi = -1 to 15 degrees which however can be found in the i + 2 position of gamma-turns. The data confirm that delta Ala may induce turn-like structures in peptides and also indicate that it may confer flexibility to the peptide chain.

Hydrogen Bonding↗
PubMed1994

Physiological concentration of magnesium ions induces a strong macroscopic curvature in GGGCCC-containing DNA.

The bending propensity of non-A/T DNA sequence elements is well known, but helical phasing/gel mobility experiments fail to reveal an intensive macroscopic curvature if A/T tracts are not present in the sequence. Recent X-ray data prove on the other hand that a GGCC element is intrinsically curved toward the major groove, which seemingly contradicts the fact that macroscopic curvature at GGGCCC elements is hardly detectable with a conventional gel mobility assay. Here we show that GGGCCC containing DNA, with no A/T tracts in the sequence context, has a detectable, strong gel mobility anomaly only in the presence of divalent ions (10 mM Mg2+ or Ca2+, 1 mM Zn2+). Metal ions increase the gel mobility anomaly in A/T tracts as well, but the effect is substantially stronger for GGGCCC than for the rigid A/T tracts. Our data suggest that metal ions change the sequence-dependent dynamic features of DNA; on the other hand, there is no evidence of twist-mediated change of the planarity of curvature in the presence of metal ions. The results show that near-physiological concentrations of divalent cations (10 mM MgCl2) have a strong and differential effect on various sequence elements, so that the current picture of sequence-dependent DNA curvature is changed not only in a quantitative, but also in a qualitative sense.

Base Composition↗
PubMed1994

Structural characterization of synthetic model peptides of the DNA-binding cI434 repressor by electrospray ionization and fast atom bombardment mass spectrometry.

The structural characterization of two synthetic model peptides of the cI434 repressor is described. Unequivocal determination of the structure was achieved by means of electrospray ionization mass spectrometry of the intact peptides and by fast atom bombardment mass spectrometric identification of complementary peptide fragments obtained by tryptic and chymotrypic digestion and partial separation by reversed-phase high-performance liquid chromatography. The results show the potential of this approach for characterizing synthetic peptides of relatively high molecular weight.

Amino Acid Sequence↗
PubMed1994

Substrate specificity of CDC2 kinase from human HeLa cells as determined with synthetic peptides and molecular modeling.

A systematic study was undertaken in order to assess the substrate specificity of cyclin-B/cell division control protein kinase (CDC2) isolated from human HeLa cells, using 13-15 residue peptides with a central histone-like KKSPKK motif as a model. Replacement of the proline residue by any of the other 19 amino acids or D-proline drastically reduces or abolishes phosphorylation by CDC2. Changing the basic residues to Ala on either side of the -SP- structure differentially reduces phosphorylation. Molecular modeling and dynamics simulation indicated that the phosphorylation site of the peptide may have to adopt a turn-like conformation that will orientate the charged and hydrophobic residues so as to allow interaction with postulated binding surfaces within the CDC2 active site. It thus appears that, of the 20 coded amino acids, only proline can provide this conformation in short peptides. This is in agreement with the finding that sarcosine can replace proline in this respect (S. Ando et al. Biochem. Biophys. Res. Commun. 195, 837-843, 1993).

Amino Acid Sequence↗
PubMed1994

Deletion mutants of human interleukin 1 beta with significantly reduced agonist properties: search for the agonist/antagonist switch in ligands to the interleukin 1 receptors.

The existence of an endogenous high affinity interleukin 1 receptor antagonist (IL-1ra) suggests that this molecule lacks some structural motif(s) which are present in the closely homologous agonist interleukin 1 beta (IL-1 beta) and which serve as the 'agonist switch' causing signal transduction by the agonist-receptor complex. The primary sequence alignment of IL-1 beta and IL-1ra sequences from different species reveals a six amino acid long motif that is quasi conserved among IL-1 beta sequences, but is missing from the IL-1ra sequences. The three-dimensional structure of human IL-1 beta was used as a template for building structural models of deletion mutants (delta SND 52-54 and delta EESNDK 50-55) using molecular graphics. These models indicated that the middle three residues SND 52-54 from the EESNDK 50-55 loop may be deleted without causing major changes in the tertiary structure of the mutant as compared to that of IL-1 beta. Residues SND 52-54 from the above loop were deleted. When compared with IL-1 beta the IL-1 beta-delta SND analog (delta SND 52-54) binds with the same affinity to type 2 IL-1 receptor but with a more than 10-fold lower affinity to type 1 IL-1 receptor. Despite of this small decrease in affinity at the type 1 receptor the delta SND 52-54 has a 1000-fold lower biological activity than IL-1 beta when tested in a thymocyte activating factor assay.(ABSTRACT TRUNCATED AT 250 WORDS)

Amino Acid Sequence↗
PubMed1994

Immunoglobulin-like domain of HIV-1 envelope glycoprotein gp120 encodes putative internal image of some common human proteins.

By examining sequence similarity between the V3-loop of gp120 from various HIV-1 isolates and human proteins, we found that the V3 loop portion KKGIAIGPGR in strain New York 5 (HIV-1NY5) shares 70% identical residues with the collagen-like region (CLR) of human complement component C1q-A. C1q CLR was found to react with autoantibodies from several autoimmune disorders. Thus, we assumed that it would be of interest to find out the C1q reactivity with antibodies from AIDS sera. The results obtained show that the V3 loop-derived synthetic peptide KKGIAIGPGRTLY reacts both with AIDS patients sera and with antibodies purified on the V3 loop peptide-affinity column. The same affinity-purified antibodies bind also to C1q molecules. Since, according to our previous results, HIV-1 V3 loops and immunoglobulin heavy chain variable regions (Ig VH) share several common features, we suggest that the envelope of HIV-1NY5 bears a functional internal image of the C1q-A CLR epitope. Therefore, gp120 could manipulate the immune network and contribute to HIV-induced autoimmunity.

Amino Acid Sequence↗
PubMed1994

The SBASE protein domain library, release 3.0: a collection of annotated protein sequence segments.

SBASE 3.0 is the third release of SBASE, a collection of annotated protein domain sequences. SBASE entries represent various structural, functional, ligand-binding and topogenic segments of proteins as defined by their publishing authors. SBASE can be used for establishing domain homologies using different database-search tools such as FASTA [Lipman and Pearson (1985) Science, 227, 1436-1441], and 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. The present release contains 41,749 entries provided with standardized names and cross-referenced to the major protein and nucleic acid databanks as well as to the PROSITE catalogue of protein sequence patterns. The entries are clustered into 2285 groups using the BLAST algorithm for computing similarity measures. SBASE 3.0 is freely available on request to the authors or by anonymous 'ftp' file transfer from < ftp.icgeb.trieste.it >. Individual records can be retrieved with the gopher server at < icgeb.trieste.it > and with a www-server at < http:@www.icgeb.trieste.it >. Automated searching of SBASE by BLAST can be carried out with the electronic mail server < sbase@icgeb.trieste.it >. Another mail server < domain@hubi.abc.hu > assigns SBASE domain homologies on the basis of SWISS-PROT searches. A comparison of pertinent search strategies is presented.

Amino Acid Sequence↗
PubMed1993

Natural autoantibodies cross-react with a peptide derived from the second conserved region of HIV-1 envelope glycoprotein gp120.

It was recently shown that peptide NTM (RSANFTDNAKTIIVQLNESV), corresponding to residues 280-299 in the second conserved domain of HIV-1 envelope glycoprotein gp120, has spectral and sequence similarity with human vasoactive intestinal peptide, VIP (Veljkovic et al., Biochem. Biophys. Res. Commun., 189, 705-710, 1992). We found that natural autoantibodies cross-reactive with this peptide can be detected in sera from HIV-negative asthma patients and healthy blood donors. The level of these antibodies is significantly higher in asthma patients than in healthy individuals, suggesting that these antibodies can in fact be at least partly identical to natural anti-VIP antibodies previously described (Paul et al., Biochem. Biophys. Res. Commun., 130, 479-483, 1985; Paul et al., Science, 244, 158-1162, 1989). Possible origin and role of these antibodies in AIDS pathogenesis and therapy are discussed.

Adult↗
PubMed1993

Stimulation of Trypanosoma cruzi adenylyl cyclase by an alpha D-globin fragment from Triatoma hindgut: effect on differentiation of epimastigote to trypomastigote forms.

A peptide from hindguts of the Triatoma hematophagous Chagas insect vector activates adenylyl cyclase activity in Trypanosoma cruzi epimastigote membranes and stimulates the in vitro differentiation of epimastigotes to metacyclic trypomastigotes. Hindguts were obtained from insects fed 2 days earlier with chicken blood. Purification was performed by gel filtration and HPLC on C18 and C4 columns. SDS/PAGE of the purified peptide showed a single band of about 10 kDa. The following sequence was determined for the 20 amino-terminal residues of this peptide: H2N-Met-Leu-Thr-Ala-Glu-Asp-Lys-Lys-Leu-Ile-Gln- Gln-Ala-Trp-Glu-Lys-Ala-Ala-Ser-His. This sequence is identical to the amino terminus of chicken alpha D-globin. On a Western blot, the peptide immunoreacted with a polyclonal antibody against chicken globin D. A synthetic peptide corresponding to residues 1-40 of the alpha D-globin amino terminus also stimulated adenylyl cyclase activity and promoted differentiation. This 125I-labeled synthetic peptide bound specifically to T. cruzi epimastigote cells. Activation of epimastigote adenylyl cyclase by the hemoglobin-derived peptide may play an important role in T. cruzi differentiation and consequently in the transmission of Chagas disease.

Adenylyl Cyclases↗