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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↗
PubMed1995

Classification of colorectal adenomas with quantitative pathology. Evaluation of morphometry, stereology, mitotic counts and syntactic structure analysis.

In search for an objective classification rule for the morphologic changes in colorectal adenomas, the results of nuclear morphometry for assessing geometric characteristics of tumour nuclei, syntactic structure analysis for assessing the arrangement of nuclei in the epithelium, stereological assessment of glandular changes, and area weighted mitotic counts were evaluated in a multivariate analysis. The H&E stained tissue sections of 59 colorectal adenomas were studied, of which 20 showed mild, 20 moderate and 19 severe dysplasia, according to blind duplicate assessments by two pathologists. In a stepwise jackknifed discriminant analysis, the combination of variables was selected that could best discriminate the cases into the previously assessed grade of dysplasia. With the combination of two variables (minimum line length and inner gland surface density), 71% of the cases could be correctly classified according to the previously assessed grade. No cases with mild dysplasia were classified as severe dysplasia and vice versa. However, since the reproduction of subjectively assessed grade was not the ultimate goal, we aimed to discriminate the cases into two groups on the basis of measurements results alone, by means of a cluster analysis. These two groups would merely reflect the cases with major versus minor morphologic changes. The results of the cluster analysis showed that all mild dysplasia cases were allocated into the low grade cluster, and that the moderate dysplasia cases were divided over both the low grade and high grade cluster. Two severe dysplasia cases with borderline morphometric results were allocated into the low grade cluster, and the remaining 16 into the high grade cluster. It is concluded that objective evaluation of dysplasia in colorectal adenomas is possible by a combination of morphometric techniques. The results of the morphometric analyses seem to favor a two-grade classification system rather than a three-grade system.

Adenoma↗
PubMed1989

Structural analysis of the carbohydrate chains of a mouse monoclonal IgM antibody.

A mouse monoclonal IgM antibody, directed against human blood group B determinant, was isolated from hybridoma culture growth medium. Chemical analysis indicated presence of N- and O-linked oligosaccharides. The N- and O-linked carbohydrate chains were liberated using two different conditions of reductive alkaline degradation. Structural analysis was carried out on the isolated chains using chemical analysis, 500-MHz 1H-NMR spectroscopy and fast-atom-bombardment mass spectrometry. The following composite structures of the N-linked chains were found: (formula; see text) where R = OH for biantennary structures and R = Neu5Ac alpha 2-3Gal beta 1-4 GlcNAc beta 1- or Neu5Ac alpha 2-3Gal beta 1-3[Neu5Ac alpha 2-6]GlcNAc beta 1- for triantennary structures. The O-linked oligosaccharides, found in the light chains, were shown to have the structure Neu5Ac alpha 2-3Gal beta 1-3GalNAc. The native IgM antibody could be separated on a concanavalin-A-Sepharose column into two subfractions, differing in the presence of a high-mannose-type oligosaccharide.

ABO Blood-Group System↗
PubMed1999

Cloning and secondary structure analysis of caleosin, a unique calcium-binding protein in oil bodies of plant seeds.

Plant seed oil bodies comprise a matrix of triacylglycerols surrounded by a monolayer of phospholipids embedded with abundant oleosins and some minor proteins. Three minor proteins, temporarily termed Sops 1-3, have been identified in sesame oil bodies. A cDNA sequence of Sop1 was obtained by PCR cloning using degenerate primers derived from two partial amino acid sequences, and subsequently confirmed via immunological recognition of its over-expressed protein in Escherichia coli. Alignment with four published homologous sequences suggests Sop1 as a putative calcium-binding protein. Immunological cross-recognition implies that this protein, tentatively named caleosin, exists in diverse seed oil bodies. Caleosin migrated faster in SDS-PAGE when incubated with Ca2+. A single copy of caleosin gene was found in sesame genome based on Southern hybridization. Northern hybridization revealed that both caleosin and oleosin genes were concurrently transcribed in maturing seeds where oil bodies are actively assembled. Hydropathy plot and secondary structure analysis suggest that caleosin comprises three structural domains, i.e., an N-terminal hydrophilic calcium-binding domain, a central hydrophobic anchoring domain, and a C-terminal hydrophilic phosphorylation domain. Compared with oleosin, a conserved proline knot-like motif is located in the central hydrophobic domain of caleosin and assumed to involve in protein assembly onto oil bodies.

Adaptor Proteins, Signal Transducing↗
PubMed1992

[Modeling in biology. Structured analysis of intracellular calcium oscillations in electrically non-excitable cells].

In this paper a systematic approach to the mathematical modeling of intracellular Ca2+ oscillations is introduced. After a structured analysis a stochastic model of the system is derived which is numerically tractable by means of a stochastic simulation. A critical discussion of theoretical models for Ca2+ oscillations reveals that not all of the proposed mechanisms are consistent with experimental data. In addition, a model for oscillatory calcium waves is presented. Uncovering these mechanisms facilitates the design of anti-mitotic drugs interfering with Ca2+ metabolism.

Animals↗
PubMed1996

Thermosensitive mutants of the MPTP and hPTP1B protein tyrosine phosphatases: isolation and structural analysis.

A PCR-based random mutagenesis procedure was employed to identify several thermosensitive mutants of the MPTP enzyme, the murine homologue of the human T-cell PTPase and rat PTP-S enzymes. Four mutants with varying degrees of thermosensitivity were characterized for their thermostability and refolding properties following incubation at the nonpermissive temperature. Structure analysis of these mutations based on the hPTP1B co-ordinate structure demonstrates a clear relationship between the position of each mutated amino acid relative to the catalytic cysteine residue and their thermostability. Introduction of two of these mutations in the related enzyme hPTP1B suggests that the structural defects and the resulting thermosensitivity of these mutations may represent an intrinsic property of all PTPase catalytic domains.

Amino Acid Sequence↗
PubMed1989

Structural analysis of glycosyl-phosphatidylinositol antigens of Leishmania major.

Three glycosyl-phosphatidylinositol glycolipids recognized by antibodies from patients with cutaneous leishmaniasis were extracted from Leishmania major promastigotes by hexane:isopropanol and then purified by thin layer chromatography and LH-20 gel chromatography. Structural analysis was carried out using chemical analyses, fast atom bombardment mass spectrometry, and 1H NMR. The major structures deduced can be summarized as follows: (formula: see text) where n = 0, 1, 2; R1 = (CH2)23-CH3; R2 = (CH2)14-CH3 or (CH2)16-CH3. Alkyl-acyl substitutions in the glycerol backbone showed considerable heterogeneity. These three glycolipids belong to a relatively new class of compounds and may represent sequential steps in the biosynthesis of glycosyl-phosphatidylinositols which anchor proteins or other glycoconjugates to Leishmania cell membranes.

Animals↗
PubMed1991

Structural analysis of a glycosylphosphatidylinositol glycolipid of Leishmania donovani.

A glycosylphosphatidylinositol (GPI) glycolipid antigen recognized by sera from patients with visceral leishmaniasis was isolated from Leishmania donovani promastigotes. The carbohydrate moiety was cleaved from the lipid part by digestion with specific phosphatidylinositol phospholipase C. After separation, structural analysis was carried out on the phosphorylated inositol oligosaccharide and the alkylacyl glycerol. The following major structures were found: [formula: see text] The presence of the conserved sequence Man alpha 1-2Man alpha 1-6Man alpha 1-4GlcN-PI of glycosyl phosphatidylinositol protein anchors in this antigen may be consistent with a precursor role of Leishmania glycosyl phosphatidylinositol anchored proteins for this glycolipid.

Animals↗
PubMed2000

Secondary structure analysis of the dissimilatory sulphite reductase in Desulfovibrio desulfuricans.

The complete sequences of the dsrA and dsrB genes coding for the alpha- and beta-subunits, respectively, of the sulphite reductase enzyme in Desulfovibrio desulfuricans were determined. Analyses of the amino acid sequences indicated a number of serohaem/Fe4S4 binding consensus sequences whilst predictive secondary structure analysis revealed a similar pattern of alpha-helix and beta-strand structures between the two subunits which was indicative of gene duplication.

Amino Acid Sequence↗
PubMed1995

Structural analysis of alkaline-soluble polysaccharide, P-1, from the kernels of Prunus mume Sieb. et Zucc.

A polysaccharide fraction extracted with cold 0.5 M NaOH from the kernels of Prunus mume exhibited some biological activities. A polysaccharide, P-1, was purified from the 0.5M NaOH extract by ion-exchange chromatography and gel-filtration. The results of the structural analysis of P-1 to determine the relationship between the activities and the structure are described in this paper. In the mild acid hydrolysis of P-1, the nondialyzable hydrolysate (I-3) believed to be its core portion was obtained. The yield of I-3 was 26.0% and contained 59.8% uronic acid as galacturonic acid (GalA). The neutral sugars of I-3 were composed of rhamnose, xylose and galactose in a molar ratio of 1.0:3.4:0.3 following analysis by gas-liquid chromatography. The molecular weight of I-3 was estimated to be ca. 14000 by gel-filtration on Toyopearl HW55F. I-3 exhibited the mitogenic activity toward spleen cells as well as P-1. These facts appeared to confirm that I-3 was the core part of P-1 and important for its biological activity. I-3 was successfully reduced by the Taylor and Conrad method to avoid so much repetition. Methylation analysis of the reduced hydrolysate by gas-liquid chromatography and gas chromatography-mass spectroscopy showed that the ratio of 1,4-linked galactopyranosyl and 1,3,4-linked galactopyranosyl residues were significantly increased in comparison with native I-3. These results suggested that I-3 was composed of 1,4- and 1,3,4-linked galacturonic acid residues in the main chain.

Animals↗
PubMed1979

Isolation and structural analysis by mass analysed ion kinetic energy spectroscopy of diverse sidechains from steroids of similar tetracyclic carbon skeletons.

The technique of mass analysed ion kinetic energy spectroscopy has been applied to the structural determination of five different substituent sidechains from five steroids of similar ring anatomy. A mass spectrometer of reversed geometry, which permits ion selection according to its mass-to-charge ratio before the ions enter the electric sector, was used to isolate the ion corresponding to the mass of each particular sidechain. Subsequent mass analysed ion kinetic energy spectra of the selected ion demonstrated daughter ions whose compositions were compatible with the structures of the model compounds. This ability to determine the structure of a specific portion of a large molecule and to permit differentiation of minor structural features in a series of compounds, whose major framework is similar, adds a new dimension to the powerful mass analysed ion kinetic energy spectroscopy technique for structural analysis of complex biological molecules.

Chemical Phenomena↗
PubMed1991

Structural analysis of proteins by laser desorption and electrospray mass spectrometry.

The development of electrospray and matrix-assisted laser desorption mass spectrometry has provided protein chemists with tools for peptide and protein structure analysis with unprecedented sensitivity and molecular weight range. The two technologies can be viewed as competitive with respect to their molecular mass determinations, but complementary with respect to their differences in instrumentation, sample preparation methods, and nature of spectra produced.

Animals↗
PubMed1997

Fabrication of stable packed capillary reversed-phase columns for protein structural analysis.

Capillary column (< or = 320-micron ID) liquid chromatography is an essential tool for the separation and concentration of low-picomole amounts of proteins and peptides for mass-spectrometric based structural analysis. We describe a detailed procedure for the fabrication of stable and efficient 50- to 180-micron ID polyimide fused-silica columns. Columns were packed by conventional slurry packing with reversed-phase silica-based supports followed by column bed consolidation with acetonitrile and sonication. PVDF membrane or internal fused-silica particles were employed for column end-frit construction. The ability of these columns to withstand high back pressures (300-400 bar) enabled their use for rapid chromatography (> 3400 cm/hr; i.e., approximately 40 microliters/min for 200-micron ID columns) and the loading of large sample volumes (up to 500 microliters). The accurate low flow rates (0.4-4.0 microliters/min) and precise gradient formation necessary to operate these columns were achieved by a simple modification of conventional HPLC systems [Moritz et al. (1992), J. Chromatogr. 599, 119-130]. Column performance was evaluated for ability to resolve low-fmol amounts of all components of a mixture of PTH-amino acids and to separate peptides for on-line LC/MS analysis of peptide mixtures derived from in situ digestion of 2-DE resolved protein spots.

Amino Acid Sequence↗
PubMed1992

Structural analysis of five new monosialylated oligosaccharides from human milk.

The total monosialylated oligosaccharide fraction from pooled human milk was isolated by gel filtration and ion-exchange chromatography. Further separation by HPLC using a mobile phase containing an ion-pairing reagent of triethylamine gave five new monosialylated oligosaccharides. Structural analysis was carried out by chemical analyses, fast atom bombardment mass spectrometry, and 500-MHz NMR spectroscopy. Combined structural data revealed the following new structures: [formula: see text]

Carbohydrate Conformation↗
PubMed1992

Medical knowledge for clinical problem solving: a structural analysis of clinical questions.

Despite technological advances that support wide-ranging access to and transfer of knowledge, practicing physicians continue to underutilize current biomedical literature. This paper explores the nature of clinically applicable medical knowledge through a structural analysis of clinical questions. The author analyzed a set of sixty questions, based on actual online search requests of practicing physicians, for stated and unstated needs, certainty levels, implicit and explicit assumptions, decision-making processes, and type of answer required. As a result, four states of information valuable in patient care were identified: prediagnostic assessment, diagnosis, treatment choice, and learning. These states are presented in frame-like structures that integrate declarative and procedural components of medical decision making. It is concluded that clinical problem solving requires a blend of declarative and procedural knowledge. The ratio depends, in part, upon the reasoning process underway at the time of the request. Procedural knowledge required for clinical problem solving may be absent from current biomedical journal literature or difficult to identify.

Decision Making↗