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At least 235 records · Page 13Linked to original sources
PubMed1983

A structural model for the interaction of haem with unsaturated fatty acids explaining its quasi-lipoxygenase activity. Quantum chemical calculations.

The quasi-lipoxygenase activity of haemoglobin differs in many respects from the well-known haemin-catalyzed lipid peroxidation (1-4), especially in its high substrate specificity for unsaturated fatty acids containing one 1,4-pentadiene system (dienoic fatty acids). In this report a structural model for the fatty acid haem interaction based on quantum-chemical calculations is presented which show that only dienoic fatty acids are bound to the haem in such a way that the initial hydrogen abstraction that is necessary for the over-all reaction, is favoured sterically and energetically.

Animals↗
PubMedDate not supplied

A proposed structural model of endothelin.

We have assessed the hydropathic nature, secondary structure, and flexibility of endothelin and report a testable model for the structure of this 21-amino acid vasoconstrictor peptide. The proposed model consists of a rigid (disulfide bonded), hydrophilic amino-terminal half of the molecule with two turns, and an extended hydrophobic sheet structure comprising the C-terminal half of the molecule. The extended structure may be stabilized by intermolecular hydrogen bonding, leading to dimers or higher order aggregates, and is hydrophobic enough to partition into an organic solvent such as ether, as long as the molecule can keep its hydrophilic amino terminus in an aqueous phase. To test this model, partitioning measurements were made on bioactive synthetic endothelin. It was found to partition at the interface of an ether/water system in a concentration- and surface area-dependent manner. A further indication as to the amphipathic nature of the molecule is that microcrystals of synthetic endothelin tend to grow at an organic-aqueous interface in a two-phase system.

Amino Acid Sequence↗
PubMed1991

A tree-structure model for analyzing laboratory test costs.

A method of costing clinical laboratory tests is described in which total laboratory costs are apportioned into 3 components: an 'organizational overhead cost' to describe the cost of running an organization; a 'cost per episode' to describe the costs incurred per request; and a 'cost per test' to describe the actual analytical costs of tests performed. A tree-like structural model is described which allows for distribution of this 'cost per test' component to the contributing tests and the calculation of the true 'cost per test'. The implementation of this model on a computer spreadsheet has been achieved. When combined with the other cost components, the true total costs of laboratory testing can be determined for any particular test. The model also allows calculation of the incremental and marginal costs of a test and permits optimization of laboratory test frequencies and work-load to minimize laboratory analytical costs.

Algorithms↗
PubMed1984

A structural model of human erythrocyte band 2.1: alignment of chemical and functional domains.

Protein 2.1 is a 210-kilodalton protein that connects erythrocyte spectrin to the NH2-terminal cytoplasmic domain of band 3 and thereby functions as the essential linkage between the membrane skeleton and the bilayer. We cleaved this protein into specific chemical domains by limited digestion with trypsin and alpha-chymotrypsin at 0 degrees C. Intermediate-sized peptides were separated by two-dimensional isoelectric focusing/NaDodSO4/polyacrylamide gel electrophoresis and characterized by high resolution peptide mapping. We have established a provisional structural model of protein 2.1 by comparing the peptide maps of these chemical domains to maps obtained from larger overlapping chymotryptic fragments as well as fragments obtained from 2-nitro-5-thiocyanobenzoic acid cleavage. In addition to providing a provisional structural map of protein 2.1, we have identified two functional domains of protein 2.1, an 83-kilodalton tryptic peptide (T-83) which binds band 3 and a 65-kilodalton tryptic peptide (T-65) which binds spectrin. We have therefore localized the functional domains along our linear map of protein 2.1.

Anion Exchange Protein 1, Erythrocyte↗
PubMed1996

Mutational analysis and secondary structure model of the RNP1-like sequence motif of transcription termination factor Rho.

The function of transcription termination factor Rho from Escherichia coli is dependent upon its ability to bind to specific sites on nascent RNA molecules. The roles of 19 individual amino acid residues (Ile49 to Ser67) in and near a phylogenetically conserved sequence segment of Rho that is similar to the RNP1 motif found in many RNA-binding proteins were examined by testing the phenotypic consequences of mutational changes that were introduced into rho by a random-sequence cassette mutagenesis procedure. The tests of each mutant included the ability of the cells to survive at 42 degrees C in the absence of wild-type rho, the efficiency of termination at a Rho-dependent terminator (lambdatR1) in vivo, the relative level of expression of the mutant protein, and the ability of some of the mutant proteins to bind RNA. The results revealed that residues in the RNP1-like sequence of DGFGFLR (residues 60 to 66) were more important than residues 49 to 59 for termination function and RNA binding, and identified three residues that were particularly sensitive to mutation: Asp60, Phe62 and Arg66. The properties of the mutants are consistent with a secondary structure model, derived from phylogenetic analysis, that has the RNP1-like sequence on one of the three beta-strands of an antiparallel beta-sheet with Asp60 and Gly61 in a turn and the side-chains of Phe62, Phe64 and Arg66 accessible on the same face of the beta-structure for interaction with RNA.

Amino Acid Sequence↗
PubMed1998

N-linked glycosylation of the thyroid Na+/I- symporter (NIS). Implications for its secondary structure model.

The Na+/I- symporter (NIS), a 618-amino acid membrane glycoprotein that catalyzes the active accumulation of I- into thyroid cells, was identified and characterized at the molecular level in our laboratory (Dai, G., Levy, O., and Carrasco, N. (1996) Nature 379, 458-460). Because mature NIS is highly glycosylated, it migrates in SDS-polyacrylamide gel electrophoresis as a broad polypeptide of higher molecular mass (approximately 90-110 kDa) than nonglycosylated NIS (approximately 50 kDa). Using site-directed mutagenesis, we substituted both separately and simultaneously the asparagine residues in all three putative N-linked glycosylation consensus sequences of NIS with glutamine and assessed the effects of the mutations on function and stability of NIS in COS cells. All mutants were active and displayed 50-90% of wild-type NIS activity, including the completely nonglycosylated triple mutant. This demonstrates that to a considerable extent, function and stability of NIS are preserved in the partial or even total absence of N-linked glycosylation. We also found that Asn225 is glycosylated, thus proving that the hydrophilic loop that contains this amino acid residue faces the extracellular milieu rather than the cytosol as previously suggested. We demonstrated that the NH2 terminus faces extracellularly as well. A new secondary structure model consistent with these findings is proposed.

Amino Acid Sequence↗
PubMed1995

A structural model for the mechanisms of elicitor release from fungal cell walls by plant beta-1,3-endoglucanase.

The release of elicitor-active carbohydrates from fungal cell walls by beta-1,3-endoglucanase contained in host tissues has been implicated as one of the earliest processes in the interaction between soybean (Glycine max) and the fungal pathogen Phytophthora megasperma f. sp. glycinea leading to host defense responses such as phytoalexin production. The present study was conducted to evaluate the primary structure of the glucanase-released elicitor (RE). Gel-filtration chromatography of carbohydrates released from mycelial walls by purified soybean beta-1,3-endoglucanase resolved them into the four fractions (elicitor-active RE-I, -II, and -III and elicitor-inactive RE-IV). Sugar composition analysis indicated that all of the fractions were composed almost entirely of glucose. 1H- and 13C-nuclear magnetic resonance analysis indicated the presence of both beta-1,3- and beta-1,6-linkages for the elicitor-active RE-I, -II, and -III fractions and only beta-1,3 linkage for the elicitor-inactive RE-IV fraction. Methylation analysis and degradation studies employing beta-1,3-endo- and beta-1,3-exoglucanase further suggested that the basic structure of elicitor-active RE consists of beta-1,6-linked glucan backbone chains of various lengths with frequent side branches composed of beta-1,3-linked one or two glucose moieties. From these structural analyses of RE, a structural model of how RE is originally present in fungal cell walls and released by host beta-1,3-endoglucanase is also proposed.

Carbohydrate Sequence↗
PubMed1996

Trimeric assembly and three-dimensional structure model of the FACIT collagen COL1-NC1 junction from CD and NMR analysis.

The 3D structure of the COL1-NC1 junction of FACIT type XIV collagen was investigated using GYCDPSSCAG and (GPP*)3GYCDPSSCAG synthetic peptides, circular dichroism, and NMR. At -20 degrees C and under air oxidation catalyzed by Cu2+, the peptide (GPP*)3GYCDPSSCAG is able to self-associated with high yield into a stable triple disulfide bonded trimer. The presence of a triple helical conformation was confirmed by circular dichroism. The analysis of the trimer by 2D NMR provided a set of distance constraints for the noncollagenous part. Molecular models for the 3D structure of COL1-NC1 junction were calculated, using the NMR distance constraints in combination with the 3D structural data recently established by X-ray crystallography [Bella, J., Eaton, M., Brodsky, B., & Berman, H. M. (1994) Science 266, 75-81] for a collagenous triple helix. From the eight theoretically possible arrangements for the three interchain disulfide bonds, only two close disulfide conformers are compatible with the experimental data. The main feature of the trimer structure is the asymmetry of the molecule due to the disulfide bond pattern that induces a particular folding of one chain. This chain forms a turn-like structure locked by two disulfide bonds with the two other chains. The turn-like folding is close to that observed for the cyclized oxidized monomeric peptide. This is the first report of the 3D structure model for a junction between a collagenous triple helical domain and a noncollagenous domain.

Amino Acid Sequence↗
PubMed1990

How wide is the widening scope of psychoanalysis and how solid is its structural model? Some concerns and observations.

The author advances the thesis that in the past 35 years there has been a relatively silent but nonetheless significant movement within the mainstream of American psychoanalysis toward a more "modest" position. This movement has been stimulated from different sources, sometimes with diverse goals and different programs. One determinant was the reaction to the post-World War II euphoria in regard to psychoanalysis and its possible therapeutic powers. Another element has been the ongoing consolidation of our knowledge and understanding of the ego-psychological, structural-model approach to analytic theory and technique, an approach which emphasizes both intrapsychic conflict and compromise formations. A consequence of this more modest position has been a greater appreciation of the limitations of psychoanalysis as well as the significance of those limitations. This more realistic appraisal of psychoanalysis may not have encouraged the widening scope of the indications for analysis, but the enhanced understanding of its limitations offers the promise of more effective psychoanalytic work in areas that have not been considered ideal for the so-called "traditional" analysis. It is suggested that more sophisticated approaches in the analysis of resistance and character, of "conflict" (in distinction to "diagnoses"), together with a more applicable understanding of the psychoanalytic process, can all contribute to a deepening, if not necessarily widening, of our psychoanalytic endeavors.

Humans↗
PubMed1992

Structure model of core proteins in photosystem I inferred from the comparison with those in photosystem II and bacteria; an application of principal component analysis to detect the similar regions between distantly related families of proteins.

A principal component analysis based on the physico-chemical properties of amino acid residues is developed to assign similar regions between distantly related families of proteins, taking account of the species diversities in respective families. The most important advantage of this analysis should be that it reflects different physico-chemical properties and thus can predict more detailed structural properties, including the transmembrane helices, than the hydropathy analysis. Its first application reconfirms the similarity between the core proteins of photosynthetic reaction center in purple bacteria and those of photosystem II, indicating that the low percentage of identical amino acid residues estimated previously between them is due to much allowance for amino acid substitutions in purple bacteria. The application of this analysis to the core proteins of photosystem I reveals that any of these proteins includes two domains, each showing high similarity to the amino acid sequences of core proteins in photosystem II and purple bacteria. A core structure model of A1 and A2 proteins folded into four layers of sheets of transmembrane helices is proposed to provide a molecular basis for the electron pathway suggested by spectroscopic experiments as well as for the interaction sites with plastocyanin, 9 kDa protein and LHC proteins.

Amino Acid Sequence↗
PubMed1997

Structural model of cytochrome b559 in photosystem II based on a mutant with genetically fused subunits.

Photosystem II is a reaction center protein complex located in photosynthetic membranes of plants, algae, and cyanobacteria. Using light energy, photosystem II catalyzes the oxidation of water and the reduction of plastoquinone, resulting in the release of molecular oxygen. A key component of photosystem II is cytochrome b559, a membrane-embedded heme protein with an unknown function. The cytochrome is unusual in that a heme links two separate polypeptide subunits, alpha and beta, either as a heterodimer (alphabeta) or as two homodimers (alpha2 and beta2). To determine the structural organization of cytochrome b559 in the membrane, we used site-directed mutagenesis to fuse the coding regions of the two respective genes in the cyanobacterium Synechocystis sp. PCC 6803. In this construction, the C terminus of the alpha subunit (9 kDa) is attached to the N terminus of the beta subunit (5 kDa) to form a 14-kDa alphabeta fusion protein that is predicted to have two membrane-spanning alpha-helices with antiparallel orientations. Cells containing the alphabeta fusion protein grow photoautotrophically and assemble functional photosystem II complexes. Optical spectroscopy shows that the alphabeta fusion protein binds heme and is incorporated into photosystem II. These data support a structural model of cytochrome b559 in which one heme is coordinated to an alpha2 homodimer and a second heme is coordinated to a beta2 homodimer. In this model, each photosystem II complex contains two cytochrome b559 hemes, with the alpha2 heme located near the stromal side of the membrane and the beta2 heme located near the lumenal side.

Amino Acid Sequence↗
PubMed1998

The flow of excitation energy in LHCII monomers: implications for the structural model of the major plant antenna.

Spectral and kinetic information on energy transfer within the light-harvesting complex II (LHCII) monomer was obtained from this subpicosecond transient absorption study, by using selective excitation (663, 669, 672, 678, and 682 nm) of various Chl a absorption bands and detecting the induced changes over the entire Qy region (650-700 nm). It is shown that transfer from the pigment(s) absorbing around 663 nm to the low energy ones occurs in 5 +/- 1 ps, whereas the 670-nm excitation is delivered to the same "destination" in two phases (0.30 +/- 0.05 ps, and 12 +/- 2 ps), and a fast equilibration (lifetime 0.45 +/- 0.05 ps) takes place within the main absorption band (675-680 nm). From comparison with results from similar time-resolved measurements on trimeric samples, it can be concluded that the intramonomeric energy transfer completely determines the spectral equilibration observed in native LHCII complexes. To correlate the measured lifetimes and their associated spectra with the pigment organization within the available structural model of LHCII (. Nature. 367:614-621), extensive but straightforward theoretical modeling was used. Thus it is demonstrated that the pigment assignment (Chl a or Chl b) given by Kuhlbrandt and co-workers cannot simultaneously describe the dichroic spectra and the transient absorption results for the rather homologous LHCII and CP29 proteins. A more recent assignment for CP29, in which a Chl b molecule ("Chl b5") is identified as a Chl a (Dr. R. Bassi, personal communication), leads to a much better description of both CP29 and LHCII. Furthermore, the orientations of the transition dipole moments, which have not been obtained in the crystal structure, are now assigned for most of the Chl's.

Biophysical Phenomena↗
PubMed1997

Inclusion of conserved buried water molecules in the model structure of rat submaxillary kallikrein.

A new approach to the molecular modelling of homologous serine proteases is adopted, by including a set of 21 buried waters known to be preserved in enzymes sharing the primary specificity of trypsin, in the homology modelling of rat submaxillary gland kallikrein. Buried waters--water molecules sequestered from bulk solvent within a protein matrix--appear to be integral conserved components of all serine proteases of known structure and should be incorporated into serine protease models built on the basis of sequence/structural homology to this family. The absence of such waters might induce errors in a force field simulation, favouring the formation of nonexistent hydrogen bonds and locally inaccurate structure. The kallikrein model refinement has led to the conclusion that an additional buried water should be added to the original rigid matrix of 21 conserved water molecules. The structurally preserved protein cavities of such waters validate the modelled structure.

Amino Acid Sequence↗
PubMed1993

A structural model for the GroEL chaperonin.

Individual particle analysis of end views from negatively stained specimens of purified GroEL from Escherichia coli showed the presence of two different particle populations, those with a six-fold symmetry and those with a seven-fold symmetry, when studied at pH 7.7 and 5.0. Image processing of particles from frozen-hydrated specimens revealed at both pH values a homogeneous population of particles with a strong seven-fold symmetry component and an average image with seven asymmetric units. Biochemical analysis of purified GroEL showed unequivocally the presence of a single polypeptide with the N-terminal sequence identical to that of GroEL. These results are compatible with a structural model of GroEL as an asymmetric aggregate built up by two rings of seven-fold and six-fold symmetries, respectively.

Amino Acid Sequence↗
PubMed1987

Drosophila mitochondrial DNA: conserved sequences in the A + T-rich region and supporting evidence for a secondary structure model of the small ribosomal RNA.

The sequence of a segment of the Drosophila virilis mitochondrial DNA (mtDNA) molecule that contains the A + T-rich region, the small rRNA gene, the tRNA(f-met), tRNA(gln), and tRNA(ile) genes, and portions of the ND2 and tRNA(val) genes is presented and compared with the corresponding segment of the D. yakuba mtDNA molecule. The A + T-rich regions of D. virilis and D. yakuba contain two correspondingly located sequences of 49 and 276/274 nucleotides that appear to have been conserved during evolution. In each species the replication origin of the mtDNA molecule is calculated to lie within a region that overlaps the larger conserved sequence, and within this overlap is found a potential hairpin structure. Substitutions between the larger conserved sequences of the A + T-rich regions, the small mt-rRNA genes, and the ND2 genes are biased in favor of transversions, 71-97% of which are A----T changes. There is a 13.8 times higher frequency of nucleotide differences between the 5' halves than between the 3' halves of the D. virilis and D. yakuba small mt-rRNA genes. Considerations of the effects of observed substitutions and deletion/insertions on possible nucleotide pairing within the small mt-rRNA genes of D. virilis and D. yakuba strongly support the secondary structure model for the Drosophila small mt-rRNA that we previously proposed.

Adenine↗
PubMed1982

A structural model of 5S RNA from E. coli based on intramolecular crosslinking evidence.

We describe new results obtained using the bifunctional chemical reagent phenyldiglyoxal (PDG) to study the intramolecular crosslinking of ribosomal 5S RNA from E. coli. In a previous publication (Wagner & Garrett [1]) we reported the identification of a crosslink in the stem region of 5S RNA (G2-G112) using the same reagent but were unable to obtain further information because of the presence of monofunctional adducts which confused the analyses. To overcome this problem, we have removed the monoaddition products by coupling them via their free reagent ends to a solid support bearing reactive groups. Using this system we have been able to identify a new crosslink G41-G72 in native 5S RNA which has considerable structural implications. We propose a structural model in which the proximity of both nucleotides is maintained by secondary interactions.

Base Sequence↗
PubMed1996

Structure model of a complex between the factor for inversion stimulation (FIS) and DNA: modeling protein-DNA complexes with dyad symmetry and known protein structures.

A method is presented to predict overall conformations of protein-DNA complexes on the basis of the known three-dimensional structures of the proteins. The method is restricted to proteins with a common twofold symmetry axis, which show only minor conformational changes upon binding to DNA. The method uses a numerical finite difference solution of the linearized Poisson-Boltzmann equation and subsequent energy minimization cycles. Structural parameters-the rotation angle of the DNA relative to the protein around the common symmetry axis, the protein-DNA distance, and intermolecular hydrogen-bonding contacts-are presented for two test cases, DNA bound to CAP (catabolite gene activator protein) and to the Cro-repressor of bacteriophage 434. The DNA curvature in the starting model of the docking procedure was chosen as a smoothed approximation of the conformation found in the X-ray structures of these complexes. The method is further used to predict the unknown structure of the complex between the factor for inversion stimulation (FIS) and DNA, which is bent upon binding to FIS. In contrast to the test cases, the unknown curvature of the starting model is derived from a calibration of electrostatic precalculations for different proteins according to crystallographically observed DNA bending. The results of the modeling are in good accordance with the experimentally observed overall structure of protein-DNA complexes for the two test cases; for FIS, they correspond to several of the experimentally proposed protein-DNA contacts.

DNA↗
PubMed1999

Selectivity of von Willebrand factor triplet bands towards heparin binding supports structural model.

Human plasma-derived von Willebrand factor (hp-vWF) and recombinant von Willebrand factor (r-vWF) have been fractionated by heparin affinity chromatography followed by multimer analysis using SDS-agarose gel electrophoresis. Because heparin binding sites are contained in each vWF subunit, high molecular weight multimers of r-vWF and hp-vWF, respectively, were eluted with higher salt concentration, in comparison to r-vWF and hp-vWF molecules with a low degree of multimerization. Heparin affinity chromatography did not affect the multimer composition of r-vWF. By contrast, faster migrating satellite bands and slower migrating satellite bands of hp-vWF exhibited reduced and increased heparin affinity, respectively, compared to the intermediate band of the same triplet. Because heparin binding sites are localised in the N-terminal domain of the hp-vWF subunit, this result confirms a structural model of hp-vWF (Fischer et al., Biochem. J. 1998;331:483-488) suggested recently, in which the slower migrating satellite bands have excess of one N-terminal fragment and the faster migrating satellite bands lack one N-terminal fragment, respectively, in comparison with the corresponding intermediate triplet band.

Binding Sites↗