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At least 343 records · Page 19Linked to original sources
PubMed1995

Molecular structure alteration of IgG increased anticomplementary activity of intravenous immunoglobulin.

AIM: To study the cause of anticomplementary activities (ACA) of intravenous immunoglobulins (IVIG). METHODS: ACA were determined by two assays (limit test and 100CH50 test), distributions of IgG molecular size (polymer, dimer, monomer and fragment) by HPLC, IgG subclasses and IgA contents by radial immunodiffusion, prekallikrein activator (PKA) and kallikrein (KK) activities by chromogenic assay, potency of antibody against hepatitis B surface antigen (Anti-HBs) by enzyme-linked immunosorbent assay (ELISA). RESULTS: The two ACA assays showed good correlation. However, ACA levels were not associated with distributions of IgG molecular size, IgG subclasses and IgA contents, PKA and KK activities. After heating incubation, ACA levels increased markedly and Anti-HBs decreased notably, distributions of IgG molecular size remained relatively constant. CONCLUSION: Molecular structure alteration of IgG increased spontaneous complement activation of IVIG.

Complement Activation↗
PubMedDate not supplied

[Evolutionary conservatism of the molecular structure of gamma-crystallins of vertebrates].

Homology of 18 amino acid sequences of lens gamma-crystallins of several vertebrates: frog, mouse, rat, calf and human being--has been considered. Pair sequence homology varies in the range from 57 to 100%, the mean value is equal to 74%. The spatial structures have been determined only for two calf gamma-crystallins. The protein molecule consists of four-fold repeated "motifs" (patterns) which are joint in two domains. After comparison of 18 gamma-crystallin sequences it was found that "motifs" domains and whole protein molecules have about 10, 30 and 58% conservative residues, respectively, that seem to be related to the evolution of these structural units. Structure analysis shows that almost all the conservative residues have an important structural meaning and play a basic role in the domain and molecular structure organization. This result allows us to make a conclusion about the homology of spatial structures of all considered gamma-crystallins of vertebrates.

Amino Acid Sequence↗
PubMed1984

Molecular structure of anti-3,4-dihydroxy-1,2,3,4-tetrahydronaphthalene 1,2-oxide.

The molecular structure and conformation of anti-3,4-dihydroxy-1,2,3,4-tetrahydronaphthalene 1,2-oxide have been determined by X-ray crystallographic techniques. This compound has been identified as a urinary metabolite of naphthalene and also mimics various metabolites of carcinogenic polyaromatic hydrocarbons. The compound crystallizes in space group Pca2(1) with cell dimensions a = 8.120(3), b = 8.656(2), and c = 23.729(5) A. There are two unique molecules in the asymmetrical unit with similar conformations. The major difference between the two molecules is in the epoxide ring. One molecule shows symmetrical C--O bond lengths and the other shows unsymmetrical C--O bond lengths, due to steric variations in the environments of the epoxide oxygen atoms. Both molecules show a "twist-boat" conformation in the saturated portion of the carbon skeleton. Packing of the molecules in the unit cell results in alternate layers of hydrophobic and hydrophilic regions and an extensive intermolecular hydrogen bond network.

Carcinogens↗
PubMed1998

Molecular structure of a barley alpha-amylase-inhibitor complex: implications for starch binding and catalysis.

alpha-Amylases are widely occurring, multidomain proteins with a catalytic (beta/alpha)8-barrel. In barley alpha-amylase, insight into the catalytic mechanism is gained from the X-ray crystal structure of its molecular complex with acarbose, a pseudotetrasaccharide that acts like a transition-state analogue and which is shown to bind at two specific regions of the enzyme. The structure of the complex has been refined to an R-factor of 15.1% for all observations with Fo>sigma(Fo) between 10 and 2.8 A resolution. A difference Fourier map produced after refinement of the native structure against the data of the acarbose complex clearly revealed density corresponding to two oligosaccharide-binding sites. One of these is defined as the surface-located starch granule-binding site characteristic of cereal alpha-amylases. It involves stacking of two acarbose rings on Trp276 and Trp277. The other binding region is the active site covering subsites -1, +1 and +2. Here, Glu204 is positioned to act in general acid/base catalysis protonating the glucosidic oxygen atom assisted by Asp289. A water molecule that bridges Glu204 and Asp289 is found at the entrance cavity containing a total of five water molecules. This water molecule is proposed to reprotonate Glu204 and supply the hydroxyl ion for nucleophilic attack on the glucosyl C1 atom. Asp 179 acts as the nucleophile that can bind covalently to the substrate intermediate after bond cleavage. The present complex structure together with the conservation of active-site residues among alpha-amylases and related enzymes, are consistent with a common catalytic mechanism for this class of retaining carbohydrases.

Acarbose↗
PubMed1995

The 'Iceman': molecular structure of 5200-year-old skin characterised by Raman spectroscopy and electron microscopy.

The molecular state of about 5200-year-old skin from the so-called 'Iceman' (Similaun man or Otzi) has been characterised using Fourier transform Raman spectroscopy, and has been compared with that of contemporary man. Contemporary skin was also freeze-dried (to mimic the conditions under which the ancient skin was preserved) and its molecular structure was compared with that of Iceman skin. The results showed that the proteinaceous moiety of the ancient skin had degraded considerably and, although olefinic bonds had probably oxidised, the lipoidal component was largely unaltered. Electron microscopical comparisons of Iceman and contemporary skin showed that the gross structure of Iceman skin had survived essentially intact for five millennia.

Animals↗
PubMed1990

Integrins of normal human epidermis: differential expression, synthesis and molecular structure.

The expression of integrin cell surface receptors in normal skin and their synthesis and molecular structure in keratinocyte cultures was investigated. The reactivity of four different polypeptides of the integrin family (alpha 2-, alpha 3-, alpha 6- and beta 1-chains) was demonstrated in the basal cell layer of normal epidermis. Studies of labelled keratinocyte cell lines showed that the polypeptides were expressed as alpha 2 beta 1, alpha 3 beta 1 and alpha 6 beta 4 integrins. Only the alpha 6 beta 4 integrin showed polarization towards the basement membrane attachment site of basal layer keratinocytes, and was preferentially expressed at microvillous projections. In contrast, alpha 2 beta 1 and alpha 3 beta 1 integrins were equally expressed throughout the basal cell plasma membrane.

Basement Membrane↗
PubMedDate not supplied

Prediction of IC50 values for ACAT inhibitors from molecular structure.

A quantitative structure-activity study is performed on several series of compounds derived from N-chlorosulfonyl isocyanate to develop models that relate their structures to IC50 activity for inhibition of acyl-CoA:cholesterol O-acyltransferase (ACAT). Numerical descriptors are used to encode topological, electronic, and geometric information from the molecular structures of the inhibitors. A data set of 157 compounds showing triglyceride- and cholesterol-lowering activity is used to develop successful linear regression models and nonlinear computational neural network models. The models are validated using an external prediction set.

Enzyme Inhibitors↗
PubMed1999

Prediction of acute mammalian toxicity of organophosphorus pesticide compounds from molecular structure.

A quantitative structure-activity relationship (QSAR) investigation was done for the acute oral mammalian toxicity (LD50) of a set of 54 organophosphorus pesticide compounds. The compounds were represented with calculated molecular structure descriptors, which encoded their topological, electronic, and geometrical features. Feature selection was done with a genetic algorithm to find subsets of descriptors that would support a high quality computational neural network (CNN) model to link the structural descriptors to the -log(mmol/kg) values for the compounds. The best seven-descriptor non-linear CNN model found had an rms error of 0.22 log units for the training set compounds and 0.25 log units for the prediction set compounds.

Animals↗
PubMed2002

Molecular structures of viruses from Raman optical activity.

A vibrational Raman optical activity (ROA) study of a range of different structural types of virus exemplified by filamentous bacteriophage fd, tobacco mosaic virus, satellite tobacco mosaic virus, bacteriophage MS2 and cowpea mosaic virus has revealed that, on account of its sensitivity to chirality, ROA is an incisive probe of their aqueous solution structures at the molecular level. Protein ROA bands are especially prominent from which, as we have shown by comparison with the ROA spectra of proteins with known structures and by using a pattern recognition program, the folds of the major coat protein subunits may be deduced. Information about amino acid side-chain conformations, exemplified here by the determination of the sign and magnitude of the torsion angle chi(2,1) for tryptophan in fd, may also sometimes be obtained. By subtracting the ROA spectrum of the empty protein capsid (top component) of cowpea mosaic virus from those of the intact middle and bottom-upper components separated by means of a caesium chloride density gradient, the ROA spectrum of the viral RNA was obtained, which revealed that the RNA takes up an A-type single-stranded helical conformation and that the RNA conformations in the middle and bottom-upper components are very similar. This information is not available from the X-ray crystal structure of cowpea mosaic virus since no nucleic acid is visible.

Bacteriophage M13↗
PubMed2001

Spectral studies of semicarbazones derived from 3- and 4-formylpyridine and 3- and 4-acetylpyridine: crystal and molecular structure of 3-formylpyridine semicarbazone.

Semicarbazones derived from 3- and 4-formylpyridine (H3FoPyS, H4FoPyS) and 3- and 4-acetylpyridine (H3AcPyS, H4AcPyS) were prepared and studied spectroscopically. Complete NMR assignments for these semicarbazones were made using DEPT135, as well as HMQC and HMBC heteronuclear correlation techniques. The crystal and molecular structures of H3FoPyS were determined.

Anticoagulants↗
PubMed2000

Molecular structure and evolution of an alpha satellite/non-alpha satellite junction at 16p11.

We have determined the detailed molecular structure and evolution of an alpha satellite junction from human chromosome 16p11. The analysis reveals that the alpha satellite sequence bordering the transition lacks higher-order structure and that the non-alpha satellite portion consists of a mosaic of duplicated segments of complex evolutionary origin. The 16p11 junction was formed recently (5-10 million years ago) by the duplication and transposition of genomic segments from Xq28 and 4q24. Once this mosaic structure was formed, a larger complex was spread among multiple pericentromeric regions. This resulted in the formation of large (>62 kb) paralogous segments that share a high degree ( approximately 97%) of sequence similarity. Both phylogenetic and comparative analyses indicate that these pericentromeric-directed duplications occurred around the time of the divergence of the human, gorilla and chimpanzee lineages, resulting in the subtle restructuring of the primate genome among these species. The available data suggest that such chimeric structures are a general property of several different human chromosomes near their alpha satellite junctions.

Animals↗
PubMed2005

Theoretical predictions of chemical degradation reaction mechanisms of RDX and other cyclic nitramines derived from their molecular structures.

Analysis of environmental degradation pathways of contaminants is aided by predictions of likely reaction mechanisms and intermediate products derived from computational models of molecular structure. Quantum mechanical methods and force-field molecular mechanics were used to characterize cyclic nitramines. Likely degradation mechanisms for hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) include hydroxylation utilizing addition of hydroxide ions to initiate proton abstraction via 2nd order rate elimination (E2) or via nucleophilic substitution of nitro groups, reductive chemical and biochemical degradation, and free radical oxidation. Due to structural similarities, it is predicted that, under homologous circumstances, certain RDX environmental degradation pathways should also be effective for octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine (HMX) and similar cyclic nitramines. Computational models provided a theoretical framework whereby likely transformation mechanisms and transformation products of cyclic nitramines were predicted and used to elucidate in situ degradation pathways.

Azocines↗
PubMed2005

The molecular structure of fluoromalononitrile as determined by gas-phase electron diffraction and ab initio calculations.

The molecular structure of fluoromalononitrile was studied by means of gas-phase electron diffraction and quantum mechanical methods using HF/6-31G(d), MP2/6-311++G(2df,2pd) and DFT/B3LYP/6-31G(d), B3PW91/6-31G(d), B3LYP/6-311++G(2df,2pd) and B3PW91/6-311++G(2df,2pd). The r(g) and angle(alpha) structural parameters we obtained from the present analysis are: CC=1.487(5) A, CN=1.157(3) A, CF=1.386(5) A, CH=1.096 A (ass.), angleCCC=106.7(1.0) degrees , angleCCF=108.0(0.7) degrees , angleCCN=177.6(2.0) degrees . Uncertainties in parenthesis are 3sigma.

Carbon↗
PubMed2001

Can knowledge of the molecular structure of allergens improve immunotherapy?

Conventional immunotherapy may be associated with the development of adverse reactions, including anaphylaxis, due to the use of increasing doses of allergen. Standardization of extracts is necessary in order to assess the correct amount of allergen administered. In recent years, increased knowledge on the molecular structure of allergens has allowed the development of novel alternatives for immunotherapy. Initially, allergens were cloned and expressed as recombinant proteins in eukaryotic and prokaryotic systems. Crystallization of the purified proteins led to the elucidation of the tertiary structure of the allergen. Molecular biology techniques were used to construct modified allergens whose new IgE binding properties were studied. IgE antibody mapping combined with molecular modeling has allowed the recognition of IgE binding sites on the surface of the molecule. This information has been applied to the engineering of new modified allergens, with and without adjuvants, that retain immunogenicity but with reduced allergenicity. The use of these molecules for immunotherapy should allow the administration of greater doses of allergen, without the undesired side effects characteristic of conventional immunotherapy.

Allergens↗
PubMed1983

X-ray crystallographic analysis of (+/-)-7 beta,8 alpha-dihydroxy-9 beta,10 beta-epoxy-7,8,9,10-tetrahydrobenzo[a]pyrene: molecular structure of a 'syn' diol epoxide.

X-ray crystallographic analysis has been used to define the molecular structure of the cis (syn) diol epoxide, (+/-)-7 beta,8 alpha-dihydroxy-9 beta, 10 beta-epoxy-7,8,9,10-tetrahydrobenzo[a]pyrene. The two hydroxyl groups are oriented equatorially to the tetrahydrobenzene ring, contrary to predictions and there is no intramolecular hydrogen bonding in the structure.

7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide↗
PubMed2000

Biosynthesis, molecular structure, and domain architecture of potato suberin: a (13)C NMR study using isotopically labeled precursors.

Although suberin in potato wound periderm is known to be a polyester containing long-chain fatty acids and phenolics embedded within the cell wall, many aspects of its molecular structure and polymer-polymer connectivities remain elusive. The present work combines biosynthetic incorporation of site-specifically (13)C-enriched acetates and phenylalanines with one- and two-dimensional solid-state (13)C NMR spectroscopic methods to monitor the developing suberin polymer. Exogenous acetate is found to be incorporated preferentially at the carboxyl end of the aliphatic carbon chains, suggesting addition during the later elongation steps of fatty acid synthesis. Carboxyl-labeled phenylalanine precursors provide evidence for the concurrent development of phenolic esters and of monolignols typical of lignin. Experiments with ring-labeled phenylalanine precursors demonstrate a predominance of sinapyl and guaiacyl structures among suberin's phenolic moieties. Finally, the analysis of spin-exchange (solid-state NOESY) NMR experiments in ring-labeled suberin indicates distances of no more than 0.5 nm between pairs of phenolic and oxymethine carbons, which are attributed to the aromatic-aliphatic polyester and the cell wall polysaccharide matrix, respectively. These results offer direct and detailed molecular information regarding the insoluble intermediates of suberin biosynthesis, indicate probable covalent linkages between moieties of its polyester and polysaccharide domains, and yield a clearer overall picture of this agriculturally important protective material.

Carbon Isotopes↗
PubMed1977

Molecular structure of the K-region cis-dihydrodiol of 7,12-dimethylbenz[a]anthracene.

The molecular structure and conformation of the cis-5,6-dihydrodiol of 7,12-dimethylbenz[a]anthracene has been determined by an X-ray crystallographic analysis. The compound crystallizes in the space group P21/a with cell dimensions a equals 17.799(6), b equals 33.211(8), c equals 5.241(1) A, beta equals 91.88(2)degrees. There are two molecules, designated A and B in the asymmetrical unit, that are not related to each other by crystallographic symmetry. Their conformations are almost identical, and there are no significant differences in their bond lengths or angles. In both molecules the 5-hydroxyl group is equatorial while the 6-hydroxyl group is axial. This conformation is probably forced by steric hindrance between the hydroxyl group, 0-6, and the hydrogen atoms of the 7-methyl group. The molecules pack in the crystal by forming hydrogen bonds between the hydroxyl groups of adjacent molecules, A with A, B, with B, and A with B. The ring system of the cis-5,6-dihydrodiol is much more buckled than is that in 7,12-dimethylbenz[a]anthracene itself. The angle between the two outermost rings is 36 degrees, the deviation from planarity being primarily a consequence of the partial saturation in the ring containing the two hydroxyl groups. Extrapolation of these results to other dihydrodiol derivatives of carcinogenic hydrocarbons permits some predictions of preferred molecular geometry. Thus, the 8,9-dihydrodiol-10,11-epoxide of 7,12-dimethylbenz]a[anthracene, analogous to the biologically active 7,8-dihydrodiol-9,10-epoxide of benzo]a[pyrene, a mutagen that is believed to be an active intermediate in carcinogenesis by benzo]a[pyrene, should probably exist preferentially in a conformation bearing the8-hydroxyl group in the axial orientation.

9,10-Dimethyl-1,2-benzanthracene↗
PubMed1993

X-ray molecular structures and theoretical conformational studies of narcotic analgesics alpha-(-)-N-cis-3-chloroallyl-normetazocine, ethylketazocine, and ketazocine.

The X-ray molecular structures of the narcotic analgesics alpha-(-)-2-cis-3-chlorallyl-2'-hydroxy-5,9-dimethyl-6,7-benzomorp han (1) and alpha-(+-)-2-cyclopropylmethyl-2'-hydroxy-5-ethyl-9-methyl-8-oxo-6,7- benzomorphan (ethylketazocine, 2) were determined. The structures and conformations in the crystal were compared and discussed with respect to that of alpha-(+-)-2-cyclopropylmethyl-2'-hydroxy-5,9-dimethyl-8- oxo-6,7-benzomorfan (ketazocine, 3) and those of 15 analogous compounds of the 2'-hydroxy-6,7-benzomorphan series whose structures were previously determined by X-ray analysis. Molecular modeling routines for 1, 2, and 3 produced configurations (N-equatorial) and conformations (distorted chair) of the piperidine ring that were in agreement with those found in the solids. Theoretical studies of the conformations and the rotational energetics of 1, 2, and 3 as cationic species were performed by both the force field (MM2) and the semiquantitative (AM1) methods. The latter method predicted three low energy conformations about N--C(12) and C(12)--C(13) bonds, one of these being more significantly populated (60-68%). The AM1 results were not reproduced by the MM2 method, which predicted four low energy conformations. An interesting common feature of 1, 2, and 3 that was noted with both methods was the restricted interconversion route from the conformational state to another through rotations about the C(12)--C(13) bond. The conformational results were discussed in terms of a working hypothesis for regulation of relative mu and kappa analgesic activities of benzomorphans.

Analgesics, Opioid↗