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  • Biochemistry and Biotechnology  (15)
  • Saccharomyces cerevisiae  (10)
  • 1990-1994  (25)
  • 1
    ISSN: 0173-0835
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Chemistry and Pharmacology
    Notes: In the absence of vitamin K or in the presence of the vitamin K antagonists, abnormal nonfunctional forms of prothrombin circulate in the blood. A reliable and reproducible technique, derived from traditional crossed affinoimmunoelectrophoresis in presence of calcium lactate, was developed and optimized. The technique is based on nondenaturing polyacrylamide gel affinoelectrophoresis, with calcium lactate, of plasma samples, followed by immunoblotting with rabbit anti-human prothrombin serum and detection with an anti-rabbit immunoglobulin peroxidase conjugate. Depending on the plasmas, one or two bands were visualized and quantified by densitometry of the immunoblots. The technique was able detect abnormal des-gamma-carboxylated prothrombins at concentration of 0.1 μg/mL.
    Additional Material: 3 Ill.
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  • 2
    ISSN: 1617-4623
    Keywords: Saccharomyces cerevisiae ; Cell cycle ; Bud site selection ; Guanine exchange factor ; Ras
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Guanine Exchange Factor (GEF) activity for Ras proteins has been associated with a conserved domain in Cdc25p, Sdc25p in Saccharomyces cerevisiae and several other proteins recently found in other eukaryotes. We have assessed the structure-function relationships between three different members of this family in S. cerevisiae, Cdc25p, Sdc25p and Bud5p. Cdc25p controls the Ras pathway, whereas Bud5p controls bud site localization. We demonstrate that the GEF domain of Sdc25p is closely related to that of Cdc25p. We first constructed a thermosensitive allele of SDC25 by specifically altering amino acid positions known to be changed in the cdc25-1 mutation. Secondly, we constructed three chimeric genes from CDC25 and SDC25, the products of which are as active in the Ras pathway as are the wild-type proteins. In contrast, similar chimeras made between CDC25 and BUD5 lead to proteins that are inactive both in the Ras and budding control pathways. This difference in the ability of chimeric proteins to retain activity allows us to define two subclasses of structurally different GEFs: Cdc25p and Sdc25p are Ras-specific GEFs, and Bud5p is a putative GEF for the Rsr1/Bud1 Rap-like protein.
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  • 3
    ISSN: 1617-4623
    Keywords: Saccharomyces cerevisiae ; Translation ; Splicing ; Paromomycin
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary The MSS51 gene product has been previously shown to be involved in the splicing of the mitochondrial pre-mRNA of cytochrome oxidase subunit I (COX1). We show here that it is specifically required for the translation of the COX1 mRNA. Furthermore, the paromomycin-resistance mutation (P inf454 supR ) which affects the 15 S mitoribosomal RNA, interferes, directly or indirectly, with the action of the MSS51 gene product. Possible roles of the MSS51 protein on the excision of COX1 introns are discussed.
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  • 4
    ISSN: 1617-4623
    Keywords: Saccharomyces cerevisiae ; Cell cycle ; Proline ; DNA sequencing
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary We report here the isolation of temperature-sensitive mutants of the yeast Saccharomyces cerevisiae which exhibit cdc phenotypes. The recessive mutations defined four complementation groups, named ore1, ore2, ore3 and ore4. At the non-permissive temperature, strains bearing these mutations arrested in the G1 phase of the cell cycle. The wild-type allele of the gene altered in ore2 mutants was cloned. The nucleotide sequence of a fragment which can complement the mutation showed the presence of an open reading frame capable of encoding a protein with 286 amino acid residues. The deduced amino acid sequence showed 25% identity with that of the Escherichia coli Δ1-pyrroline-5-carboxylate reductase, an enzyme of the pathway for the biosynthesis of proline. The ore2 mutants, correspondingly, were found to be capable of growing at the non-permissive temperature on a synthetic medium supplemented with proline. In addition, the chromosomal location of the gene and its restriction map were compatible with those previously reported for the PRO3 gene which encodes the S. cerevisiae Δ1-pyrroline-5-carboxylate reductase.
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  • 5
    ISSN: 0887-3585
    Keywords: lectins ; crystal structure ; lectin specificity ; mannose ; glucose ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The structure of the methyl-α-D-mannopyranoside-LOL I complex has been solved by the molecular replacement method using the refined saccharide-free LOL I coordinates as starting model. The methyl-α-D-mannopyranoside-LOL I complex was refined by simulated annealing using the program X-PLOR. The final R-factor value is 0.182 [Fo 〉 1σ(Fo)]. The isostructural methyl-α-D-glucopyranoside-LOL I complex was refined by X-Ray coupled energy minimization using the methyl-α-D-mannopyranoside-LOL I structure as a starting model to an R factor of 0.179 (all data). In both crystal forms, each dimer binds two molecules of sugar in pockets found near the calcium ions. The two saccharide moieties, which are in the C1 chair conformation, establish the same hydrogen bond pattern with the lectin. However, the van der Walls contacts are different between the O2, C2, C6, and O6 atoms of the two molecules and the backbone atoms of residues 208-211. Mannose, due to its axial C2 conformation, encloses the backbone atoms of the protein in a clamplike way. Van der Waals energy calculations suggest that this better complementarity of the mannoside molecule with the lectin could explain its higher affinity for isolectin I.
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  • 6
    ISSN: 0887-3585
    Keywords: α/β-barrels ; protein structure ; loops ; molecular modeling ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A systematic survey of seven parallel α/β barrel protein domains, based on exhaustive structural comparisons, reveals that a sizable proportion of the αβ loops in these proteins - 20 out of a total of 49 - belong to either one of two loop types previously described by Thornton and co-workers. Six loops are of the αβ1 type, with one residue between the α-helix and β-strand, and 13 are of the αβ3 type, with three residues between the helix and the strand. Protein fragments embedding the identified loops, and termed αβ connections since they contain parts of the flanking helix and strand, have been analyzed in detail revealing that each type of connection has a distinct set of conserved structural features. The orientation of the β-strand relative to the helix and loop portions is different owing to a very localized difference in backbone conformation. In αβ1 connections, the chain enters the β-strand via a residue adopting an extended conformation, while in αβ3 it does so via a residue in a near α-helical conformation. Other conserved structural features include distinct patterns of side chain orientation relative to the β-sheet surface and of main chain H-bonds in the loop and the β-strand moieties. Significant differences also occur in packing interactions of conserved hydrophobic residues situated in the last turn of the helix. Yet the α-helix surface of both types of connections adopts similar orientations relative to the barrel sheet surface. Our results suggest furthermore that conserved hydrophobic residues along the sequence of the connections, may be correlated more with specific patterns of interactions made with neighboring helices and sheet strands than with helix/strand packing within the connection itself. A number of intriguing observations are also made on the distribution of the identified αβ1 and αβ3 loops within the α/β-barrel motifs. They often occur adjacent to each other; αβ3 loops invariably involve even numbered β-strands, while αβ1 loops involve preferentially odd β-strands; all the analyzed proteins contain at least one αβ3 loop in the first half of the eightfold α/β barrel. Possible origins of all these observations, and their relevance to the stability and folding of parallel α/β barrel. Possible origins of all these observations, and their relevance to the stability and folding of parallel α/β barrel motifs are discussed.
    Additional Material: 6 Ill.
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  • 7
    ISSN: 0887-3585
    Keywords: X-ray structure ; TEM1 ; β-lactamase ; antibiotics ; bacterial resistance ; serine hydrolase ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The X-ray structure of Escherichia coli TEM1β-lactamase has been refined to a crystallorgphic R-factor of 16.4% for 22,510 reflections between 5.0 and 1.8 Å resolution; 199 water molecules and 1 sulphate ion were included in refinement. Except for the tips of a few solvent-exposed side chains, all protein atoms have clear electron density and refined to an average atomic temperature factor of 11 Å2. The estimated coordinates error is 0.17 Å. The substrate binding site is located at the interface of the two domains of the protein and contains 4 water molecules and the sulphate anion. One of these solvent molecules is found at hydrogen bond distance from S70 and E166. S70 and S130 are hydrogen bonded to K73 and K234, respectively. It was found that the E. coli TEM1 and Staphylococcus aureus PC1 β-lactamases crystal structures differ in the relative orientations of the two domains composing the enzymes, which result in a narrowed substrate binding cavity in the TEM1 enzyme. Local but significant differences in the vicinity of this site may explain the occurrence of TEM1 natural mutants with extended substrate specificities. © 1993 Wiley-Liss, Inc.
    Additional Material: 21 Ill.
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  • 8
    ISSN: 0887-3585
    Keywords: serine carboxypeptidase ; protein modeling ; mutation analysis ; comparative modeling ; cathepsin A ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The deficiency of the lysosomal protective protein/carboxypeptidase L (CARB L) causes the lysosomal storage disorder, galactosialidosis, characterized by neuraminidase and β-galactosidase deficiencies in patients' cells. The three enzymes form a complex inside the lysosome, and the neuraminidase and β-galactosidase deficiencies are secondary to CARB L deficiency. Sequence similarity and common enzymological properties suggest that the protomeric tertiary structure of CARB L is conserved within a family of serine carboxypeptidases which includes the yeast carboxypeptidase Y, killer expression I gene product and several plant carboxypeptidases. We used this homology to build a model of the CARB L structure based on the recently published X-ray atomic coordinates of the wheat carboxypeptidase II (CPDW-II) which shares 32% primary structure identity with CARB L. Small insertions and deletions were accommodated into the model structure by energy minimization using the DREIDING II force field. The Cα atomic-coordinates of the final CARB L model have a RMS shift of 1.01 Å compared to the corresponding conserved residues in the CPDW-II template structure. The correct orientation of the homologous catalytic triad residues Ser150, His429 and Asp392, the potential energy calculations and the distribution of hydrophobic and hydrophillic residues in the structure all support the validity of the CARB L model. Most missense mutations identified in galactosialidosis patients were located in secondary structural elements except for the Tyr211→Asn mutation which is in a loop. The other mutant residues have their side chains deeply buried in the central β-sheet of the model structure except for the Phe412→Val mutation which is located in the dimer interface. The predicted effects of specific mutations on CARB L structural stability correlates well with recently published transient expression studies of mutant CARB L (Shimmoto, M. et al., J. Clin. Invest., 91:2393-2399, 1993). © 1994 John Wiley & Sons, Inc.
    Additional Material: 6 Ill.
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  • 9
    ISSN: 0749-503X
    Keywords: RVS161 gene ; Saccharomyces cerevisiae ; stationary phase entry ; viability loss ; Life and Medical Sciences ; Genetics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology
    Notes: In yeast, nutrient starvation leads to entry into stationary phase. Mutants that do not respond properly to starvation conditons have been isolated in Saccharomyces cerevisiae. Among them the rvs161 mutant (RVS for Reduced Viability upon Starvation) is sensitive to carbon, nitrogen and sulphur starvation. When these nutrients are depleted in the medium, mutant cells show cellular viability loss with morphological changes. The mutation rvs161-1 is very pleiotropic, and besides the defects in stationary phase entry, the mutant strain presents other alterations: sensitivity to high salt concentrations, hypersensitivity to amino acid analogs, no growth on lactate or acetate medium. The addition of salts or amino acid analogs leads to the same morphological defects observed in starved cells, suggesting that the gene could be implicated mainly in the control of cellular viability. The gene RVS161 was cloned; it codes for a 30,252 daltons protein. No homology was detected with the proteins contained in the databases. Moreover, Southern analysis revealed the presence of other sequences homologous to the RVS161 gene in the yeast genome.
    Additional Material: 6 Ill.
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  • 10
    ISSN: 0749-503X
    Keywords: Chromosome III ; Saccharomyces cerevisiae ; mating type ; HML ; BUD5 ; Life and Medical Sciences ; Genetics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology
    Notes: This paper reports the DNA sequence of a segment of 9·8 kb of the chromosome III. The sequenced DNA contains the MATα locus. The new sequence of the MATα locus differs from the previously reported sequence by six modifications in the W segment. We have found the same modifications in the HML locus. The corrected sequence contains, in HML, an open reading frame (ORF) of 190 codons which ends at the border between the W segment and the flanking DNA. In the MAT locus, this ORF extends in the flanking DNA up to 538 codons. This ORF corresponds to a gene independently identified as BUD5 (Chant et al., 1991). This gene presents homologies with the exchange factors SDC25 and CDC25. A large ORF of 1399 codons is found on the opposite side of MATα (toward the telomere). This ORF corresponds to a new gene YCR724. Next to this gene is a small ORF, YCR725, of 127 codons. The localization of this fragment on chromosome III, originally supposed to be distal from the MAT locus based on genetic distance, illustrates variation in recombination frequency along the chromosome and suggests the existence of hot spots of recombination between MAT and the THR4 locus.
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