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PubMed1985

Isolation and structural analysis of two lipid A precursors from a KDO deficient mutant of Salmonella typhimurium differing in their hexadecanoic acid content.

The extraction, purification and structural characterization of two lipid A precursors (Ia and Ib) differing only in one hexadecanoic acid are described. Both precursors were synthesized at elevated temperatures by a new mutant of Salmonella typhimurium (mutant Ts5) which is conditionally defective in synthesis of the 3-deoxy-D-manno-octulosonic acid region of lipopolysaccharides. Both precursors were purified by repeated phenol/chloroform/petroleum ether (PCP) extractions followed by thin layer chromatography. The precursor preparation was free of lipopolysaccharides and phospholipids and contained less than 0.1% protein. Structural analysis which included chemical degradation procedures as well as positive ion laser desorption (LDMS) mass spectroscopy of dephosphorylated lipid A precursors showed together that precursor Ia represents a diphosphorylated glucosamine disaccharide containing two ester, two amide-linked residues of 3-hydroxytetradecanoic acid and lacks the ester-linked dodecanoic, tetradecanoic and hexadecanoic acid as well as 3-deoxy-D-manno-octulosonic acid. Precursor Ib has the same basic structure as precursor Ia, but contains in addition one mol of hexadecanoic acid per mol disaccharide which is linked to the 3-hydroxy group of the amide-bound 3-hydroxy-tetradecanoic acid of the reducing, terminal glucosamine residue. The structure of precursor Ib supports the conclusion that hexadecanoic acid incorporation occurs at an early stage in lipid A biosynthesis prior to the attachment of 3-deoxy-D-manno-octulosonic acid and/or other polar substituents.

Chromatography, DEAE-Cellulose↗
PubMed1992

Sequence of the Kluyveromyces lactis beta-galactosidase: comparison with prokaryotic enzymes and secondary structure analysis.

The LAC4 gene encoding the beta-galactosidase (beta Gal) of the yeast, Kluyveromyces lactis, was cloned on a 7.2-kb fragment by complementation of a lacZ-deficient Escherichia coli strain. The nucleotide sequence of the structural gene, with 42 bp and 583 bp of the 5'- and 3'-flanking sequences, respectively, was determined. The deduced amino acid (aa) sequence of the K. lactis beta Gal predicts a 1025-aa polypeptide with a calculated M(r) of 117618 and reveals extended sequence homologies with all the published prokaryotic beta Gal sequences. This suggests that the eukaryotic beta Gal is closely related, evolutionarily and structurally, to the prokaryotic beta Gal's. In addition, sequence similarities were observed between the highly conserved N-terminal two-thirds of the beta Gal and the entire length of the beta-glucuronidase (beta Glu) polypeptides, which suggests that beta Glu is clearly related, structurally and evolutionarily, to the N-terminal two-thirds of the beta Gal. The structural analysis of the beta Gal alignment, performed by mean secondary structure prediction, revealed that most of the invariant residues are located in turn or loop structures. The location of the invariant residues is discussed with respect to their accessibility and their possible involvement in the catalytic process.

Amino Acid Sequence↗
PubMed1984

Discriminative structural analysis using pattern recognition techniques in the structure-taste problem of perillartines.

Pattern recognition techniques have been applied to the study of structure-taste correlations for perillartine derivatives. The structure of each compound was described by hydrophobicity (log P), logarithm of water solubility (log S), and topological descriptors relating to some positions which were assigned by superposing each compound on a "template" structure. The fragment molecular connectivities were calculated as the topological descriptors. The discriminant functions between the sweet and bitter taste classes were computed by the use of the simplex optimization technique, which correctly recognized most of the compounds under investigation. It was found that the hydrophobicity and one or two topological descriptors concerned with a specific part of the molecules contributed significantly to the discrimination. The discriminant function obtained correctly classified seven of nine compounds (which were not involved in the data set for developing the function) into the taste class to which they belonged.

Cyclohexenes↗
PubMed1995

Structural analysis of affinity maturation: the three-dimensional structures of complexes of an anti-nitrophenol antibody.

Affinity maturation of the immune response to nitrophenol-containing antigens has been extensively investigated. Significant strides made during the past several years with the advent of PCR technology have provided a wealth of biochemical knowledge. Structural investigations of the phenomena have however been limited. We have determined the three-dimensional structure of the Fab fragment of 88C6/12, an anti-4-hydroxy-3-nitrophenyl acetic acid antibody complexed with the immunizing hapten and with a heteroclitic iodinated hapten. The crystallographic structure of the complexes reveals that the binding is stabilized by a number of hydrogen bonds and extensive van der Waals interactions between the hapten and the antibody. In addition, the Fab binding pocket contains a region of positive electrostatic potential well suited for interaction with the predominant resonance form of the nitrophenyl ring system. The observed heteroclicity towards the iodinated hapten is not a direct result of iodine-protein interactions, but results from the enhanced stability in the iodinated ring of the resonance form that binds the antibody. In addition this investigation provides a rationale for the strong preference for the substitution in the heavy chain from the germ-line gene encoded Trp 33 to Leu 33 in the mature anti-nitrophenol response.

Amino Acid Sequence↗
PubMed1993

Structural analysis of hydroxy fatty acids by thermospray liquid chromatography/tandem mass spectrometry.

Thermospray liquid chromatography/tandem mass spectrometry provides a sensitive and convenient technique for the structural analysis of oxygenated polyunsaturates. Analysis of pentafluorobenzyl derivatives in the negative ion mode under the filament- or discharge-on condition generated abundant [M - PFB]- ions. These ions were further fragmented by collision with argon and detected in the negative ion mode. The negative ion fragmentation pattern was examined for various oxygenated polyunsaturated fatty acid standards as well as their deuterated and/or hydrogenated forms. Characteristic fragmentation occurs at the oxygenated C-C bonds, allowing unambiguous determination of the sites of oxygenation. The sample amount required is typically in the low tens of nanogram range. Using this method the structures of epoxy, hydroxy derivatives of 4,7,10,13,16,19-docosahexaenoic acid (22:6w3) formed by soybean lipoxygenase were determined. They were 13-hydroxy-16,17-epoxy-22:5w3 and 15-hydroxy-16,17-epoxy-22:5w3.

12-Hydroxy-5,8,10,14-eicosatetraenoic Acid↗
PubMed1995

Skeletal keratan sulphate structural analysis using keratanase II digestion followed by high-performance anion-exchange chromatography.

A semi-quantitative fingerprinting method has been developed for the structural analysis of skeletal keratan sulphates. This involves the digestion of the parent keratan sulphate chains with the enzyme keratanase II (Bacillus sp.), followed by reduction of the resulting oligosaccharides with sodium borohydride and chromatography on a Dionex AS4A-SC column. This column has been calibrated for the elution positions of 26 previously characterized oligosaccharides (Brown et al., Biochemistry, 33, 4836-4846, 1994; Brown et al., Eur. J. Biochem., 224, 281-308, 1994). The technique permits sample analysis with pulsed electrochemical detection (sensitive to approximately 5 ng of oligosaccharide) or by monitoring [3H] or [35S] radiolabel (potentially sensitive to approximately 1 pg or less of an oligosaccharide); thus permitting the study of sub-microgram amounts of keratan sulphates. Skeletal keratan sulphates from a number of sources have been examined in this chromatographic system and their structural features are discussed.

Acetylglucosaminidase↗
PubMed1995

Self-analysis: structure, extension, and computerization.

In this article, a structure for self-analysis is described and the expanded applicability of self-analysis implied by the suggested structure is examined. Also, the stage of computer psychotherapy programs is reviewed, and an overview of a plan for merging self-analysis and computer psychotherapy is presented.

Affect↗
PubMed1992

Structural analysis and comparison of cobrotoxin and cardiotoxins by near-IR Fourier transform Raman spectroscopy.

Venom toxins were isolated from Formosan cobra (Naja naja atra) by cation-exchange chromatography. The near-IR FT-Raman analytical method has been applied to the characterization and classification of the toxin components in their lyophilized forms. Structural analysis and comparison of various purified toxin fractions were made with respect to their amino acid compositions and near-IR Fourier-transform Raman spectra. The results indicate that the major secondary structure of cobra toxins including cobrotoxin and various cardiotoxins is mainly anti-parallel beta-pleated sheet as judged by the Raman signals at 1238 cm-1 (amide III) and 1671 cm-1 (amide I). It is also found that the relative Raman signal intensities of Tyr, Phe, Trp and Met residues in purified toxins correlate very well with the structural data obtained from amino acid analysis. The advantage and improvement of applying the near-IR FT-Raman spectroscopy to the unambiguous classification and comparison of venom toxins are evident and the discrepancies with previous Raman studies on these venom toxins are also revealed and discussed.

Animals↗
PubMed1997

Cloning, structural analysis, and mapping of the B30 and B7 multigenic families to the major histocompatibility complex (MHC) and other chromosomal regions.

We present the cloning, structural analysis, and mapping of new members belonging to two multigenic families, the B30-RING finger family and the B7.1-B7.2 family, as well as two genes derived by exon shuffling from members of these families. Eight new members were found and three of them map to the human major histocompatibilitiy complex (MHC) region. Phylogenic and physical mapping analysis allowed us to decipher the evolutionary story of these two multigenic families and to shed light on the evolution of the MHC region. We also show that a deductive analysis can be used to predict the existence of a given gene.

Amino Acid Sequence↗
PubMed1986

Structural analysis and immunogenicity of Pseudomonas aeruginosa immunotype 2 high molecular weight polysaccharide.

We analyzed high molecular weight polysaccharide (PS) from the Fisher immunotype 2 (IT-2) strain of Pseudomonas aeruginosa for molecular composition and structure, then determined its immunogenicity in healthy adults. The PS was composed of 2-acetamido-2,6-dideoxygalactose (N-acetyl fucosamine) and glucose in a molar ratio of 2:1. Structural analysis by carbon-13 and proton nuclear magnetic resonance confirmed that the high molecular weight PS was structurally identical to that of the O-specific side chain of the lipopolysaccharide. PS differed from this material in molecular size. Immunization of 19 adult volunteers with doses of 50-100 micrograms of PS resulted in significant rises (P less than 0.04-P less than 0.0001) in binding antibody levels and killing antibody titers 2 and 4 wk postimmunization. The only reaction to the vaccine was localized tenderness at the immunization site. Analysis of the immunoglobulin isotype response to the vaccine showed a rise in specific serum IgG and IgA antibodies. Heterologous responses to other P. aeruginosa PS antigens were not seen. The antibody levels attained by vaccination were comparable with those in acute-phase serum samples of patients who survived sepsis with IT-2 P. aeruginosa and were significantly higher (P less than 0.03) than specific antibody levels in bacteremic patients who died. These results confirm that PS is a high molecular weight, immunogenic form of the P. aeruginosa IT-2 serotype antigen, eliciting levels of type-specific antibody comparable with those seen among patients surviving an episode of P. aeruginosa sepsis.

Adult↗
PubMed1992

Structural analysis of three prokaryotic 5S rRNA species and selected 5S rRNA--ribosomal-protein complexes by means of Pb(II)-induced hydrolysis.

Lead ions have been applied to the structural analysis of 5S rRNA from Thermus thermophilus, Bacillus stearothermophilus and Escherichia coli. Based on the distribution of Pb(II)-induced cleavages, some minor modifications of the consensus secondary structure model of 5S rRNA are proposed. They include the possible base pairing between nucleotides at positions 11 and 109, as well as changes in secondary interactions within the helix B region. The 'prokaryotic arm' region is completely resistant to hydrolysis in the three RNA species, suggesting that it is a relatively stable, highly ordered structure. Hydrolysis of E. coli 5S rRNA complexed with ribosomal protein L18 shows, besides the shielding effect of the bound protein, a highly enhanced cleavage between A108 and A109. It supports the concept that the major L18-induced conformational change involves the junction of helices A, B and D.

Autoradiography↗
PubMed1996

Glutaredoxin-3 from Escherichia coli. Amino acid sequence, 1H AND 15N NMR assignments, and structural analysis.

The primary and secondary structure of glutaredoxin-3 (Grx3), a glutathione-disulfide oxidoreductase from Escherichia coli, has been determined. The amino acid sequence of Grx3 consists of 82 residues and contains a redox-active motif, Cys-Pro-Tyr-Cys, typical of the glutaredoxin family. Sequence comparison reveals a homology (33% identity) to that of glutaredoxin-1 (Grx1) from E. coli as well as to other members of the thioredoxin superfamily. In addition to the active site cysteine residues, Grx3 contains one additional cysteine (Cys65) corresponding to one of the two non-active site (or structural) cysteine residues present in mammalian glutaredoxins. The sequence-specific 1H and 15N nuclear magnetic resonance assignments of reduced Grx3 have been obtained. From a combined analysis of chemical shifts, 3JHNalpha coupling constants, sequential and medium range NOEs, and amide proton exchange rates, the secondary structure of reduced Grx3 was determined and found to be very similar to that inferred from amino acid sequence comparison to homologous proteins. The consequences of the proposed structural similarity to Grx1 are that Grx3, while possessing a largely intact GSH binding cleft, would have a very different spatial distribution of charged residues, most notably surrounding the active site cysteine residues and occurring in the proposed hydrophobic protein-protein interaction area. These differences may contribute to the observed very low Kcat of Grx3 as a reductant of insulin disulfides or as a hydrogen donor for ribonucleotide reductase. Thus, despite an identical active site disulfide motif and a similar secondary structure and tertiary fold, Grx3 and Grx1 display large functional differences in in vitro protein disulfide oxido-reduction reactions.

Amino Acid Sequence↗
PubMed1980

Membrane attack complex of complement: a structural analysis of its assembly.

This study was conducted to gain insight into the process of assembly of the membrane attack complex (MAC) of complement through structural analysis. Four intermediate complexes and the MAC were examined by electron microscopy and by sucrose density-gradient ultracentrifugation. The C5b-6 complex has a sedimentation rate of 11S, an elongated, slightly curved shape and dimensions of 160 x 60 x 60 A. At protein concentrattions greater than 1 mg/ml, and physiologic ionic strength and pH, the complex forms paracrystals that have the appearance of parallel strands. Equimolar quantities of C5b-6 and C7 mixed in the absence of lipids or detergents give rise to C5b-7 protein micelles which are soluble in aqueous media and have a sedimentation rate of 36S, suggesting a tetrameric composition. Ultrastructurally, C5b-7 protein micelles consist of four half-rings, each measuring 200 x 50 A, which are connected to one another by short stalks extending from the convex side of the half-rings. C5b-7 bound to dioleoyl lecithin (DOL) vesicles has a similar ultrastructural appearance. After extraction with deoxycholate (DOC), C5b-7 has a sedimentation velocity of 36S which further suggests the occurrence of C5b-7 in the form of tetrameric protein micelles. Attachment of C8 to vesicle-bound C5b-7 results in dissociation of the protein micelles. An individual C5b-8 complex appears as a half-ring attached to the DOL-vesicle via a 100-A-long and 30-A-wide stalk. After extraction from the DOL-vesicles with DOC, C5b-8 has a sedimentation velocity of approximately 18S. Binding of C9 to DOL-vesicle bound C5b-8 induces the formation of the typical ultrastructural complement lesions. C5b-9 extracted from the vesicles with DOC has a sedimentation rate of 33S, which is characteristic of the C5b-9 dimer. It is concluded that dimerization is a function of C9. C5b-9 monomers are visualized when a single C5b-9 complex or an odd number of complexes were bound per DOL-vesicle. The C5b-9 monomer has an ultrastructural appearance that is theoretically expected of a half-dimer: a 200- x 50-A half-ring which is attached to the DOL-vesicle by a 100- x 80-A appendage. Extracted with DOC, the C5b-9 monomer has a sedimentation rate of 23S. At a higher multiplicity of MAC per DOL-vesicle, large structural defects in the lipid bilayer are seen which are attributed to direct physical destruction of membranes by the known lipid-binding capacity of the MAC. It is proposed that protein micelle formation at the C5b-7 stage of MAC assembly and dissociation of these micelles upon binding of C8 are events that facilitate dimerization of C5b-9 and thus MAC formation.

Binding Sites↗
PubMed1998

Secondary structure analysis of individual transmembrane segments of the nicotinic acetylcholine receptor by circular dichroism and Fourier transform infrared spectroscopy.

Circular dichroism (CD) and attenuated total reflection Fourier transform infrared (ATR-FTIR) spectroscopy are used to establish the secondary structure of peptides containing one or more transmembrane segments (M1-M4) of the Torpedo californica nicotinic acetylcholine receptor (AChR). Peptides containing the M2-M3 and M1-M2-M3 transmembrane segments of the AChR beta-subunit and the M4 segment of the alpha- and gamma-subunits were isolated from proteolytic digests of receptor subunits, purified, and reconstituted into lipid vesicles. For each peptide, an amide I vibrational frequency centered between 1650 and 1656 cm-1 and negative CD absorption bands at 208 and 222 nm indicate that the peptide is largely alpha-helical. In addition, the CD spectrum of a tryptic peptide of the alpha-subunit containing the M1 segment is also consistent with a largely alpha-helical structure. However, secondary structure analysis of the alpha-M1 CD spectrum indicates the presence of other structures, suggesting that the M1 segment may represent either a distorted alpha-helix, likely the consequence of several proline residues, or may not be entirely alpha-helical. Overall, these findings are consistent with studies that indicate that the transmembrane region of the AChR comprises predominantly, if not exclusively, membrane-spanning alpha-helices.

Animals↗
PubMed1997

Protein structural analysis from solid-state NMR-derived orientational constraints.

High-resolution orientational constraints from solid-state NMR spectroscopy of uniformly aligned biological macromolecules provide a great structural analysis problem. Several approaches to this problem have been made in the past. Here a vector algebra method is developed that provides analytical solutions for the torsion angles and a concise and simple view of the structural possibilities. Numerical instabilities in this approach are easily predicted. Insight into how the structural ambiguities arise in the first place and how they can be reduced in number is demonstrated with this new approach.

Gramicidin↗
PubMed1988

Crystallographic structure analysis of lamprey hemoglobin from anomalous dispersion of synchrotron radiation.

The molecular structure of lamprey hemoglobin was previously determined and refined by conventional crystallographic analysis. In this study, the structural analysis has been repeated in the course of developing the method of multiwavelength anomalous diffraction (MAD) for phase determination. New experimental and analytical procedures that were devised to perform this determination should have general applicability. These include an experimental design to optimize signal strength and reduce systematic errors, experimental evaluation of anomalous scattering factors, and a least-squares procedure for analyzing the MAD data. MAD phases for the structure at 3 A resolution are as accurate overall as the multiple isomorphous replacement (MIR) phases determined previously.

Animals↗
PubMed1987

The corrinoid from Methanobacterium thermoautotrophicum (Marburg strain). Spectroscopic structure analysis and identification as Co beta-cyano-5'-hydroxybenzimidazolyl-cobamide (factor III).

The corrinoids from Methanobacterium thermoautotrophicum were extracted as the Co-cyano derivative, which was isolated in crystalline form. A consistent set of spectroscopic data was acquired (ultraviolet/visible, circular dichroic, infrared, fast-atom-bombardment mass, 1H-NMR and 13C-NMR spectra), which allowed the structural analysis of this complete corrinoid. It was assigned the structure of the Co beta-cyano-5'-hydroxybenzimidazolyl-cobamide and was identified with Friedrich and Bernhauer's 'factor III' by comparison with an authentic sample.

Circular Dichroism↗