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Structural Features (structural + feature)
Kinds of Structural Features Selected AbstractsSTRUCTURAL FEATURES OF NUCLEAR GENES IN THE CENTRIC DIATOM THALASSIOSIRA WEISSFLOGII (BACILLARIOPHYCEAE)JOURNAL OF PHYCOLOGY, Issue 5 2000E. Virginia Armbrust Thalassiosira weissflogii (Grun.) Fryxell et Hasle is one of the more commonly studied centric diatoms, and yet molecular studies of this organism are still in their infancy. The ability to identify open reading frames and thus distinguish between introns and exons, coding and noncoding sequence is essential to move from nuclear DNA sequences to predicted amino acid sequences. To facilitate the identification of open reading frames in T. weissflogii, two newly identified nuclear genes encoding ,-tubulin and t -complex polypeptide (TCP)-,, along with six previously published nuclear DNA sequences, were examined for general structural features. The coding region of the nuclear open reading frames had a G + C content of about 49% and could readily be distinguished from noncoding sequence due to a significant difference in G + C content. The introns were uniformly small, about 100 base pairs in size. Furthermore, the 5, and 3, splice sites of introns displayed the canonical GT/AG sequence, further facilitating recognition of noncoding regions. Six of the nuclear open reading frames displayed relatively little bias in the use of synonymous codons, as exemplified by the cDNAs encoding ,-tubulin and TCP-,. Two open reading frames displayed strong bias in the use of particular codons (although the codons used were different), as exemplified by the cDNA encoding fucoxanthin chlorophyll a/c binding protein. Knowledge of codon bias should facilitate, for example, design of degenerate PCR primers and potential heterologous reporter gene constructs. [source] Self-Assembled Two-Dimensional Water-Soluble Dipicolinate Cu/Na Coordination Polymer: Structural Features and Catalytic Activity for the Mild Peroxidative Oxidation of Cycloalkanes in Acid-Free MediumEUROPEAN JOURNAL OF INORGANIC CHEMISTRY, Issue 22 2008Marina V. Kirillova Abstract The new water-soluble 2D Cu/Na coordination polymer [Cu(,-dipic)2{Na2(,-H2O)4}]n·2nH2O (1) has been synthesized by self-assembly in aqueous medium from copper(II) nitrate, dipicolinic acid (H2dipic) and sodium hydroxide in the presence of triethanolamine. It has been characterized by IR spectroscopy, FAB+ -MS, elemental and single-crystal X-ray diffraction analyses, the latter featuring a layered 2D metal,organic structure that is extended to a 3D supramolecular assembly by extensive hydrogen bonding between adjacent layers and involving crystallization water molecules. Compound 1 has been shown to act as a catalyst precursor for the peroxidative oxidation of cyclohexane and cyclopentane to the corresponding cyclic ketones and alcohols by aqueous H2O2 in MeCN solution and in the absence of acid additives.(© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2008) [source] Structural Features of the NAD-Dependent In Situ Retinoic Acid Supply System in Esophageal MucosaALCOHOLISM, Issue 2010Hirokazu Yokoyama Background:, We previously reported that an NAD-dependent in situ retinoic acid supply system, which comprises some isoforms of alcohol dehydrogenase (ADH) and aldehyde dehydrogenase (ALDH) and provides retinoic acid from retinol via a 2-step oxidation process, exists in the rat esophagus. Herein, their isoforms responsible for the pathway and its localization in the rat esophagus was examined. Methods:, The expressions of mRNAs of various isoforms of ADH and ALDH were examined in the fraction mainly comprising mucosal layer of the rat esophagus by RT-PCR. Expression levels of Class IV ADH and ALDH 1A1 were compared between the fractions and that mainly comprising muscle layer of the rat esophagus by quantitative PCR. The catalytic activities producing retinoic acid from retinal were compared between the 2 fractions and its optimum pH was also determined. Results:, Classes I, III, and IV ADHs and ALDHs 1A1 and 3A1 were predominant isoforms in the rat esophageal mucosa. The expression levels of mRNA of Class IV ADH and ALDH 3A1 were significantly higher in the mucosal than in the muscle layer. Consistently, the catalytic activities producing retinoic acid from retinal were significantly higher in the former than the latter. The optimum pH of the process was 9.0. Conclusions:, Considering the affinities for retinol and retinal of ADHs and ALDHs expressed in the rat esophagus, the NAD-dependent in situ retinoic acid supply system in the rat esophagus is thought to comprise Class IV ADH and ALDH 1A1. In the rat esophagus, the system exists predominantly in the mucosal layer. [source] Neural Network Prediction of Biomass Digestibility Based on Structural FeaturesBIOTECHNOLOGY PROGRESS, Issue 2 2008Jonathan P. O'Dwyer Plots of biomass digestibility are linear with the natural logarithm of enzyme loading; the slope and intercept characterize biomass reactivity. The feed-forward back-propagation neural networks were performed to predict biomass digestibility by simulating the 1-, 6-, and 72-h slopes and intercepts of glucan, xylan, and total sugar hydrolyses of 147 poplar wood model samples with a variety of lignin contents, acetyl contents, and crystallinity indices. Regression analysis of the neural network models indicates that they performed satisfactorily. Increasing the dimensionality of the neural network input matrix allowed investigation of the influence glucan and xylan enzymatic hydrolyses have on each other. Glucan hydrolysis affected the last stage of xylan digestion, and xylan hydrolysis had no influence on glucan digestibility. This study has demonstrated that neural networks have good potential for predicting biomass digestibility over a wide range of enzyme loadings, thus providing the potential to design cost-effective pretreatment and saccharification processes. [source] Ion-Electron Transport in Strontium Ferrites: Relationships with Structural Features and Stability.CHEMINFORM, Issue 44 2004M. V. Patrakeev Abstract For Abstract see ChemInform Abstract in Full Text. [source] ChemInform Abstract: Synthesis and Analysis of Structural Features of Phenoxazine Analogues Needed to Reverse Vinblastine Resistance in Multidrug Resistant (MDR) Cancer Cells.CHEMINFORM, Issue 2 2001G. B. Eregowda Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a "Full Text" option. The original article is trackable via the "References" option. [source] New Structural Features in Heavy Alkaline Earth-Metal Chemistry , Molecular Heterobimetallic Group,1, Ba ComplexesCHEMISTRY - A EUROPEAN JOURNAL, Issue 7 2007Felisa Zuniga, Maria Abstract The preparation of heterobimetallic complexes consisting of alkali and heavy alkaline earth metals remains a challenge due to limited available synthetic strategies. Here we present a new class of group,1, Ba compounds of the type [Mn{Ba(Odpp)2+n}] (M=Na(n=1) (1), K(n=1) (2), Cs(n=1) (3), Li(n=2) (4); HOdpp=2,6-diphenylphenol) and the Lewis base adducts [Li2(thf)2{Ba(Odpp)4}],PhMe (5) and [K{Ba(Odpp)3(diglyme)}] (6) (diglyme=[bis(2-methoxy)ethyl ether]) as the first representatives of heterobimetallic group,1, Ba species of low nuclearity. The compounds display a significant degree of metal,arene interaction, believed to be a key factor in stabilizing these highly reactive species. Obtained by solid-state direct metalation, the target compounds are available without further work-up. [source] Structural Features of Interacting Complementary Liposomes Promoting Formation of Multicompartment StructuresCHEMPHYSCHEM, Issue 17 2009Zili Sideratou Dr. Abstract The structural features of complementary liposomes and factors favoring formation of multicompartment systems are investigated. Specifically, liposomal formulations consisting of PEGylated unilamellar liposomes with guanidinium moieties located at the distal end of polyethylene glycol (PEG) chains interact with complementary multilamellar liposomes bearing phosphate moieties. Furthermore, the number of PEG chains attached to the unilamellar interface of the liposomes is enhanced by incorporating PEGylated cholesterol in their bilayer. While molecular recognition of the liposomes is the driving force for initiating multicompartmentalization, it is the enhanced PEGylation at the liposomal interface that synergistically promotes fusion resulting in large and well-formed multicompartment systems. A mechanism is proposed according to which initial adhesion of the liposomes, followed by reorganization of their membrane lipids, leads to giant bilayer aggregates incorporating large liposomes. [source] Xenoestrogenic gene exression: Structural features of active polycyclic aromatic hydrocarbonsENVIRONMENTAL TOXICOLOGY & CHEMISTRY, Issue 4 2002T. Wayne Schultz Abstract Estrogenicity was assessed using the Saccharomyces cerevisiae -based Lac-Z reporter assay and was reported as the logarithm of the inverse of the 50% molar ,-galactosidase activity (log[EC50,1]). In an effort to quantify the relationship between molecular structure of polycyclic aromatic hydrocarbons (PAHs) and estrogenic gene expression, a series of PAHs were evaluated. With noted exceptions, the results of these studies indicate that the initial two-dimensional structural warning for estrogenicity, the superpositioning of a hydroxylated aromatic system on the phenolic A-ring of 17-,-estradiol, can be extended to the PAHs. This two-dimensional-alignment criterion correctly identified estrogenicity of 22 of the 29 PAHs evaluated. Moreover, the estrogenic potency of these compounds was directly related to the size of the hydrophobic backbone. The seven compounds classified incorrectly by this structural feature were either dihydroxylated naphthalenes or aromatic nitrogen-heterocyclic compounds; all such compounds were false positives. Results with dihydroxylated naphthalenes reveal derivatives that were nonestrogenic when superimposed on the phenolic A-ring of 17-,-estradiol had the second hydroxyl group in the position of the C-ring or were catechol-like in structure. Structural alerts for nitrogen-heterocyclic compounds must take into account the position of the hydroxyl group and the in-ring nitrogen atom; compounds with the hydroxyl group and nitrogen atom involved with the same ring were observed to be nonactive. [source] Superacid-Catalyzed Dimerization/Cyclization of Isopropenyl-PAHs , Novel Pathways to PAH Dimers, Phenalenes and Their Stable CarbocationsEUROPEAN JOURNAL OF ORGANIC CHEMISTRY, Issue 21 2008Cédric Brulé Abstract The isopropenyl derivatives of representative classes of polycyclic aromatic hydrocarbons (PAHs) having four and five fused-ring systems, namely pyrene, chrysene, benzo[c]phenanthrene (BcPh), dibenzo[a,c]anthracene (benzo[f]tetraphene) and perylene, were synthesized by Wittig olefination from the corresponding acetyl-PAHs. Under the influence of triflic acid (TfOH), the isopropenyl derivatives were converted to novel PAH dimers and/or phenalenes in a simple one-pot procedure. A plausible mechanism for this process has been outlined, and the synthetic scope of this chemistry has been explored. Structural features in the PAH dimers were examined by DFT. As representative initial and final carbocation intermediates in the reaction sequence, stable carbocations derived from 3-isopropenylperylene and from 4,6,6-trimethyl-6H -dibenzo[a,kl]anthracene were generated and studied directly by NMR spectroscopy. The NMR characteristics and charge delocalization modes in the resulting benzylic carbocations are discussed. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2008) [source] It's all relative: Competition and status drive interpersonal perceptionEUROPEAN JOURNAL OF SOCIAL PSYCHOLOGY, Issue 7 2008Ann Marie T. Russell Structural features of interpersonal relationships, particularly competition and status, can cause people, respectively, to (dis)like and (dis)respect each other, although they think they are reacting to the target's personality. Two studies manipulate structural relationships between students in a 2,×,2 between-participants design. Competition and status, respectively, differentiate perceptions of the target's warmth and competence. In Study 1's pre,post design, the pre- and post-interaction warmth, but status affected only pre-interaction competence. Study 2 post-interaction-only design did replicate both of Study 1's pre-interaction results. Competing targets were judged less warm than cooperating targets; high-status targets were judged more competent than low-status targets. These experiments demonstrate the structural predictors of the intergroup stereotype content model at the interpersonal level. Copyright © 2008 John Wiley & Sons, Ltd. [source] Structural features in the C-terminal region of the Sinorhizobium meliloti RmInt1 group II intron-encoded protein contribute to its maturase and intron DNA-insertion functionFEBS JOURNAL, Issue 1 2010María D. Molina-Sánchez Group II introns are both catalytic RNAs and mobile retroelements that move through a process catalyzed by a RNP complex consisting of an intron-encoded protein and the spliced intron lariat RNA. Group II intron-encoded proteins are multifunctional and contain an N-terminal reverse transcriptase domain, followed by a putative RNA-binding domain (domain X) associated with RNA splicing or maturase activity and a C-terminal DNA binding/DNA endonuclease region. The intron-encoded protein encoded by the mobile group II intron RmInt1, which lacks the DNA binding/DNA endonuclease region, has only a short C-terminal extension (C-tail) after a typical domain X, apparently unrelated to the C-terminal regions of other group II intron-encoded proteins. Multiple sequence alignments identified features of the C-terminal portion of the RmInt1 intron-encoded protein that are conserved throughout evolution in the bacterial ORF class D, suggesting a group-specific functionally important protein region. The functional importance of these features was demonstrated by analyses of deletions and mutations affecting conserved amino acid residues. We found that the C-tail of the RmInt1 intron-encoded protein contributes to the maturase function of this reverse transcriptase protein. Furthermore, within the C-terminal region, we identified, in a predicted ,-helical region and downstream, conserved residues that are specifically required for the insertion of the intron into DNA targets in the orientation that would make it possible to use the nascent leading strand as a primer. These findings suggest that these group II intron intron-encoded proteins may have adapted to function in mobility by different mechanisms to make use of either leading or lagging-oriented targets in the absence of an endonuclease domain. [source] Assembly of cytochrome f into the cytochrome bf complex in isolated pea chloroplastsFEBS JOURNAL, Issue 3 2001Ruth M. Mould Structural features of cytochrome f necessary for assembly into the cytochrome bf complex were examined in isolated pea chloroplasts following import of 35S-labelled chimeric precursor proteins, consisting of the presequence of the small subunit of Rubisco fused to the turnip cytochrome f precursor. Assembly was detected by nondenaturing gel electrophoresis of dodecyl maltoside-solubilized thylakoid membranes. A cytochrome f polypeptide unable to bind haem because of mutagenesis of Cys21 and Cys24 to alanine residues was assembled into the complex and had similar stability to the wild-type polypeptide. This indicates that covalent haem binding to cytochrome f is not necessary for assembly of the protein into the cytochrome bf complex. A truncated protein lacking the C-terminal 33 amino acid residues, including the transmembrane span and the stroma-exposed region, was translocated across the thylakoid membrane, had a similar stability to wild-type cytochrome f but was not assembled into the complex. This indicates that the C-terminal region of cytochrome f is important for assembly into the complex. A mutant cytochrome f unable to bind haem and lacking the C-terminal region was also translocated across the thylakoid membrane but was extremely labile, indicating that, in the absence of the C-terminal membrane anchor, haem-less cytochrome f is recognized by a thylakoid proteolytic system. [source] Porous structure of NiO-based xerogelsJOURNAL OF APPLIED CRYSTALLOGRAPHY, Issue 3-1 2000H. Fischer NiO-based xerogels were prepared by sol-gel processing starting from the NiCl2 -BuOH-H2O system. Structural features associated to the porosity of xerogels were studied by small-angle X-ray scattering. Xerogels heat-treated at low temperatures (423 and 573 K) are composed of hydrated NiCl2 small crystals and exhibit an essentially single mode nanoporous structure with an average pore radius of ,75 Å. Xerogels heat-treated at 973 and 1173 K are composed of aggregates of NiO crystals which only contain intergrain mesopores with radii exceeding 200 Å. A mixture of phases is observed in xerogels heat-treated at 773 K. Xerogels with a water concentration of 2 mol/(mol NiCl2) exhibit a narrow nanopore size distribution. Water concentrations higher or lower than 2 mol promote the formation of nanoporous structures with wider size distributions. [source] How to go extinct: lessons from the lost plants of KrakatauJOURNAL OF BIOGEOGRAPHY, Issue 5 2000Robert J. Whittaker Abstract Aim Few data sets exist that allow measurement of long-term extinction and turnover rates for islands of the size of the three main islands of the Krakatau group. We test the reliability of previous estimates of plant species extinction and examine structure within the extinction data. Location The data analysed are for the three older Krakatau islands: Rakata, Sertung and Panjang in the Sunda Strait, Indonesia. Methods Our analysis is based on a comprehensive database incorporating all species records for each island since recolonization began after the 1883 sterilization, plus attributes such as distribution, phylogeny, population status and dispersal mechanism for each species. We employ a combination of univariate and multi-term analyses in analysing structure, and derive Minimal Adequate Models using binary logistic analyses of variance and covariance. We compare the 1883,1934 data set with the contemporary flora as represented by (1) 1979,83 records (as used in previous analyses) and (2) 1979,94 data (original). Results The improved data for the contemporary flora reduces the number of missing species by one-third. We show that a variety of estimates of extinction rate can be produced depending on what assumptions are made concerning the status of particular species groups. Structural features in the extinction data persist despite the reduction in overall numbers of losses. Losses relate to: (1) the number of islands on which a species originally occurred, (2) the primary dispersal mode, and (3) the original abundance of a species (e.g. whether it was known to have established a successful resident population, and whether it was in decline or increasing in c. 1930). The ,best' descriptive model employs the variables denoted under (3). A high proportion of losses comprised species introduced by people and rare or ephemeral species. Losses of ,residents' that had colonized naturally could largely be accounted for by reference to (1) successional loss of habitat and, to a lesser degree, (2) other habitat disturbance or loss. Main conclusions Previous analyses, based on a more limited data set, have significantly over-estimated extinction from the Krakatau flora. Few naturally colonizing and established species have become extinct. The findings indicate that caution is necessary in interpreting ,headline' island ecological rates, and in analysing and modelling such data. Examination of structural features of the data appear to be valuable both in providing ecological insights in their own right, and in enabling refinements to estimates of extinction and thus turnover. [source] Segmented block copolymers of poly(ethylene glycol) and poly(ethylene terephthalate)JOURNAL OF POLYMER SCIENCE (IN TWO SECTIONS), Issue 17 2004B. García-Gaitán Abstract A new series of segmented copolymers were synthesized from poly(ethylene terephthalate) (PET) oligomers and poly(ethylene glycol) (PEG) by a two-step solution polymerization reaction. PET oligomers were obtained by glycolysis depolymerization. Structural features were defined by infrared and nuclear magnetic resonance (NMR) spectroscopy. The copolymer composition was calculated via 1H NMR spectroscopy. The content of soft PEG segments was higher than that of hard PET segments. A single glass-transition temperature was detected for all the synthesized segmented copolymers. This observation was found to be independent of the initial PET-to-PEG molar ratio. The molar masses of the copolymers were determined by gel permeation chromatography (GPC). © 2004 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 42: 4448,4457, 2004 [source] Isolation, structural features and rheological properties of water-extractable ,-glucans from different Greek barley cultivarsJOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE, Issue 10 2004Maria Irakli Abstract ,-Glucans were isolated from six Greek barley cultivars (Persefoni, Kos, Thessaloniki, Athinaida, Dimitra and Triptolemos) by water extraction at 47 °C, enzymatic removal of starch and protein and subsequent precipitation of the water-soluble ,-glucans with 37% (w/v) ammonium sulfate saturation. The purity of barley ,-glucans was high (>93% dry basis) with some small contamination by protein (<3.84%). The molecular size of the ,-glucan isolates was determined by high-performance size-exclusion chromatography (HPSEC); the weight-average molecular weights and the intrinsic viscosities ranged between 0.45 × 106 and 1.32 × 106 and 2.77 and 4.11 dl g,1, respectively. Structural features of barley ,-glucans were revealed by 13C NMR spectroscopy and high-performance anion-exchange chromatography (HPAEC) of the oligomers released by the hydrolytic action of lichenase. Lichenase degradation showed that ,-glucans from all barley cultivars consisted of blocks of cellotriosyl and cellotetraosyl units, accounting for 90.6,92.3% of the total oligomers released, with a molar proportion of these units between 2.31 and 2.77. Rheological measurements of aqueous solutions/dispersions of ,-glucans showed the behaviour of non-interacting polysaccharides and a transition from the typical viscoelastic response to gel-like properties after a time period that depended on the molecular size of the polysaccharide. The lowest molecular size ,-glucans from the Triptolemos cultivar showed shorter gelation times than their higher molecular weight counterparts. The effect of sugar incorporation (glucose, fructose, sucrose, xylose and ribose), at a concentration of 30% (w/v), to the ,-glucans gels (6% w/v) on compression parameters seemed to be related to the type of sugar used; the pentose sugars substantially reduced gel firming. Copyright © 2004 Society of Chemical Industry [source] Structural features of arabinoxylans from Sonalika variety of wheat: comparison between whole wheat flour and wheat branJOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE, Issue 13 2003CD Nandini Abstract Arabinoxylans (AX) were extracted from Sonalika variety of wheat (whole wheat flour and wheat bran) with barium hydroxide and sodium hydroxide and purified by a combination of alcohol precipitation and glucoamylase digestion. Structural features of purified AX were elucidated by methylation analysis, 13C NMR, FT-IR, periodate oxidation and optical rotation measurements. The AX showed a backbone of xylose residues with ,(1,4) linkages and were branched mainly through O-3 of xylose residues. Completely branched xylosyl residues were also present. Copyright © 2003 Society of Chemical Industry [source] Verification of literature-derived SARs for skin irritation and corrosionMOLECULAR INFORMATICS, Issue 3 2003M. Hulzebos Abstract Structural features known to irritate and corrode skin and physical properties associated with skin absorption were used to evaluate the irritation and corrosion potential of chemicals. Chemicals that irritate and corrode skin include organic acids and bases, aldehydes, halogenated esters, and chemicals with reactive groups. The activity of the reactive group decreases when sterically hindered by adjacent substituents or when electrons of the reactive group interfere with electrons of adjacent substituents. The structural features presented are a good basis for the calculation of SAR prediction rules. Also quantitative and qualitative physical conditions are given to predict skin irritation and skin corrosion. [source] Contractile roots in succulent monocots: convergence, divergence and adaptation to limited rainfallPLANT CELL & ENVIRONMENT, Issue 8 2008GRETCHEN B. NORTH ABSTRACT Contractile roots (CRs) that pull shoots further down in the soil are a possible example of convergent evolution in two monocot families, the Agavaceae and the Asphodelaceae. The association between CRs, water uptake and habitat aridity was investigated for agaves, yuccas and aloes by assessing the occurrence of CRs and the amount of root contraction for glasshouse-grown plants with respect to mean annual rainfall of their native habitats. Structural features of CRs as well as root hydraulic conductance were compared with those of non-contractile roots (NCRs). CRs occurred in 55% of the 73 species examined, including 64% of the agaves and 85% of the yuccas, but in none of the aloes despite the occurrence of CRs in related genera. The phylogenetic distribution of CRs was consistent with multiple acquisitions or losses of the trait. The amount of root contraction showed a highly significant negative relationship with mean annual rainfall, although other environmental factors may also be important. Radial hydraulic conductance of the basal (contractile) zone exceeded that of the midroot zone for CRs; for NCRs, the opposite was true. Thus, CRs in the species examined may provide a mechanism for greater water uptake near the soil surface in regions with limited rainfall. [source] Structural features for the mechanism of antitumor action of a dimeric human pancreatic ribonuclease variantPROTEIN SCIENCE, Issue 1 2009Antonello Merlino Abstract A specialized class of RNases shows a high cytotoxicity toward tumor cell lines, which is critically dependent on their ability to reach the cytosol and to evade the action of the ribonuclease inhibitor (RI). The cytotoxicity and antitumor activity of bovine seminal ribonuclease (BSRNase), which exists in the native state as an equilibrium mixture of a swapped and an unswapped dimer, are peculiar properties of the swapped form. A dimeric variant (HHP2-RNase) of human pancreatic RNase, in which the enzyme has been engineered to reproduce the sequence of BSRNase helix-II (Gln28,Leu, Arg31,Cys, Arg32,Cys, and Asn34,Lys) and to eliminate a negative charge on the surface (Glu111,Gly), is also extremely cytotoxic. Surprisingly, this activity is associated also to the unswapped form of the protein. The crystal structure reveals that on this molecule the hinge regions, which are highly disordered in the unswapped form of BSRNase, adopt a very well-defined conformation in both subunits. The results suggest that the two hinge peptides and the two Leu28 side chains may provide an anchorage to a transient noncovalent dimer, which maintains Cys31 and Cys32 of the two subunits in proximity, thus stabilizing a quaternary structure, similar to that found for the noncovalent swapped dimer of BSRNase, that allows the molecule to escape RI and/or to enhance the formation of the interchain disulfides. [source] Slicing a protease: Structural features of the ATP-dependent Lon proteases gleaned from investigations of isolated domainsPROTEIN SCIENCE, Issue 8 2006Tatyana V. Rotanova Abstract ATP-dependent Lon proteases are multi-domain enzymes found in all living organisms. All Lon proteases contain an ATPase domain belonging to the AAA+ superfamily of molecular machines and a proteolytic domain with a serine-lysine catalytic dyad. Lon proteases can be divided into two subfamilies, LonA and LonB, exemplified by the Escherichia coli and Archaeoglobus fulgidus paralogs, respectively. The LonA subfamily is defined by the presence of a large N-terminal domain, whereas the LonB subfamily has no such domain, but has a membrane-spanning domain that anchors the protein to the cytoplasmic side of the membrane. The two subfamilies also differ in their consensus sequences. Recent crystal structures for several individual domains and sub-fragments of Lon proteases have begun to illuminate similarities and differences in structure,function relationships between the two subfamilies. Differences in orientation of the active site residues in several isolated Lon protease domains point to possible roles for the AAA+ domains and/or substrates in positioning the catalytic residues within the active site. Structures of the proteolytic domains have also indicated a possible hexameric arrangement of subunits in the native state of bacterial Lon proteases. The structure of a large segment of the N-terminal domain has revealed a folding motif present in other protein families of unknown function and should lead to new insights regarding ways in which Lon interacts with substrates or other cellular factors. These first glimpses of the structure of Lon are heralding an exciting new era of research on this ancient family of proteases. [source] Structural features of a zinc binding site in the superantigen strepococcal pyrogenic exotoxin A (SpeA1): Implications for MHC class II recognitionPROTEIN SCIENCE, Issue 6 2001Matthew Baker Abstract Streptococcal pyrogenic exotoxin A (SpeA) is produced by Streptococcus pyogenes, and has been associated with severe infections such as scarlet fever and Streptococcal Toxic Shock Syndrome (STSS). In this study, the crystal structure of SpeA1 (the product of speA allele 1) in the presence of 2.5 mM zinc was determined at 2.8 Å resolution. The protein crystallizes in the orthorhombic space group P21212, with four molecules in the crystallographic asymmetric unit. The final structure has a crystallographic R -factor of 21.4% for 7,031 protein atoms, 143 water molecules, and 4 zinc atoms (one zinc atom per molecule). Four protein ligands,Glu 33, Asp 77, His 106, and His 110,form a zinc binding site that is similar to the one observed in a related superantigen, staphylococcoal enterotoxin C2. Mutant toxin forms substituting Ala for each of the zinc binding residues were generated. The affinity of these mutants for zinc ion confirms the composition of this metal binding site. The implications of zinc binding to SpeA1 for MHC class II recognition are explored using a molecular modeling approach. The results indicate that, despite their common overall architecture, superantigens appear to have multiple ways of complex formation with MHC class II molecules. [source] Some Segmental Features on the Structure of the Aortic Wall of the DogANATOMIA, HISTOLOGIA, EMBRYOLOGIA, Issue 3 2004A. M. Orsi Summary Structural features of segmental parts of the aorta of the dog were studied by light microscopy (LM) and scanning electron microscopy (SEM). The variability in the wall architecture composition and vascular thickness of the ascending (T2-3 level), thoracic (T7-8 level) and abdominal (L6-7 infrarenal level) segments of the aorta was analysed. Morphological features such as presence of intimal folds, pattern of the medial myoconnective components with segmental variations in the number of elastic lamellae, whose relative number was higher in the thoracic aorta (ascending and descending parts), compared with the abdominal aorta, and a network of connective (stromal) elements formed by elastic and collagen lamellae and fibres in the adventitia were observed. The results were discussed on a histophysiological basis, because small but significant segmental differences had been characterized in the aortic wall structure of the dog. [source] 1,1-Bis(phenylsulfonyl)-1-(pyridinio)methanideACTA CRYSTALLOGRAPHICA SECTION C, Issue 7 2003Kenneth W. Muir The title disulfonyl-stabilized pyridinium ylide, C5H5N+,C,(SO2C6H5)2 or C18H15NO4S2, contains a near planar NCS2 core. The structure suggests that the formal negative charge of the ylide C atom is delocalized to the S atoms rather than the N atom. Structural features of pyridinium ylides are briefly discussed. [source] Structure and lability of archaeal dehydroquinaseACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 10 2008Natasha N. Smith Multiple sequence alignments of type I 3-dehydroquinate dehydratases (DQs; EC 4.2.1.10) show that archaeal DQs have shorter helical regions than bacterial orthologs of known structure. To investigate this feature and its relation to thermostability, the structure of the Archaeoglobus fulgidus (Af) DQ dimer was determined at 2.33,Å resolution and its denaturation temperature was measured in vitro by circular dichroism (CD) and differential scanning calorimetry (DSC). This structure, a P212121 crystal form with two 45,kDa dimers in the asymmetric unit, is the first structural representative of an archaeal DQ. Denaturation occurs at 343 ± 3,K at both low and high ionic strength and at 349,K in the presence of the substrate analog tartrate. Since the growth optimum of the organism is 356,K, this implies that the protein maintains its folded state through the participation of additional factors in vivo. The (,,)8 fold is compared with those of two previously determined type I DQ structures, both bacterial (Salmonella and Staphylococcus), which had sequence identities of ,30% with AfDQ. Although the overall folds are the same, there are many differences in secondary structure and ionic features; the archaeal protein has over twice as many salt links per residue. The archaeal DQ is smaller than its bacterial counterparts and lower in regular secondary structure, with its eight helices being an average of one turn shorter. In particular, two of the eight normally helical regions (the exterior of the barrel) are mostly nonhelical in AfDQ, each having only a single turn of 310 -helix flanked by ,-strand and coil. These `protohelices' are unique among evolutionarily close members of the (,,)8 -fold superfamily. Structural features that may contribute to stability, in particular ionic factors, are examined and the implications of having a Tm below the organism's growth temperature are considered. [source] Cross-linked agarose for separation of low molecular weight natural products in hydrophilic interaction liquid chromatographyBIOTECHNOLOGY JOURNAL, Issue 5 2010Tianwei Tan Abstract Following its market introduction in 1982, the cross-linked 12% agarose gel media Superose 12 has become widely known as a tool for size exclusion chromatography of proteins and other biological macromolecules. In this review it is shown that, when appropriate mobile phases are used, Superose possesses adsorption properties similar to that of traditional media for hydrophilic interaction liquid chromatography (HILIC). This is illustrated by the separation and purification of low molecular weight compounds such as polyphenols including active components of traditional Chinese medicinal herbs and green tea. Structural features of the cross-linked agarose that likely cause the observed adsorption effects are discussed aswell. These are identified as being primarily ether bonds acting as strong hydrogen bond acceptors as well as hydrophobic residues originating from the cross-linking reagents. [source] Drug design: hiding in full viewDRUG DEVELOPMENT RESEARCH, Issue 1 2008Norman S. Radin Abstract Compounds that can produce potent biological effects in cells encompass a variety of structural motifs. Many of these compounds share a structural feature that has rarely been noted. It is an allylic cluster of atoms, a 3-carbon chain with a double bond between two of the atoms and an oxygen atom at the other end. The oxygen can be in a hydroxyl group, or in an ether or ketal or ester linkage, or simply a carbonyl form. In the latter case, the linkage is an allylic ketone (ene-one) structure. Nitrogen is often seen in equivalent forms. Inclusion of at least one allylic moiety appears to be able to turn a modestly active or inert compound into an effective drug or toxin. Some compounds lack the allylic moiety but develop one by enzymatic action, usually via cytochrome P-450 enzymes. These metabolites probably represent the active drug forms. The above concepts seem to be radically simplistic and improbable, but the evidence supporting them and the explanations for the biological activities are hidden "in plain view." Comparisons with the pleiotropic activities of the allylic sphingolipid, ceramide, indicate that many allylic drugs operate by controlling the state of protein phosphorylation, by activating proteases, by generating reactive oxygen species, by slowing mitochondrial electron transport, or by lowering cellular glutathione concentrations. Drug Dev Res 69:15,25, 2008 © 2008 Wiley-Liss, Inc. [source] Black Employment, Segregation, and the Social Organization of Metropolitan Labor MarketsECONOMIC GEOGRAPHY, Issue 3 2007Niki T. Dickerson Abstract: This broad analysis of the employment of blacks in metropolitan areas examines the role of residential segregation in comparison with four other key structural explanations for racial metropolitan inequality: industrial composition, minority concentration, immigration, and the racial disparity in skills. The goal of the analysis was to determine whether the spatial configuration of blacks relative to whites in a metropolitan area influences the employment rates of black men and black women in the context of the structural conditions of the local labor market. The study expanded the analysis of space and work beyond an emphasis on the physical distance between black communities and jobs to a broader conceptualization of residential segregation as a structural feature of the entire metropolitan labor market that is representative of its social organization with regard to race. Using a longitudinal data set of the structural characteristics of the 95 largest U.S. cities from the 1980, 1990, and 2000 decennial censuses, the study used a cross-sectional analysis of the cities in 2000 and a fixed-effects analysis to assess the impact of five dimensions of residential segregation and the four other structural factors on the employment of blacks across different labor markets and across time within each labor market. The results revealed that when the other structural characteristics are controlled, the employment rates of blacks are lower in more segregated cities and decrease as cities become more segregated over time. The clustering and evenness dimensions of residential segregation were the most determinative of black employment. [source] Xenoestrogenic gene exression: Structural features of active polycyclic aromatic hydrocarbonsENVIRONMENTAL TOXICOLOGY & CHEMISTRY, Issue 4 2002T. Wayne Schultz Abstract Estrogenicity was assessed using the Saccharomyces cerevisiae -based Lac-Z reporter assay and was reported as the logarithm of the inverse of the 50% molar ,-galactosidase activity (log[EC50,1]). In an effort to quantify the relationship between molecular structure of polycyclic aromatic hydrocarbons (PAHs) and estrogenic gene expression, a series of PAHs were evaluated. With noted exceptions, the results of these studies indicate that the initial two-dimensional structural warning for estrogenicity, the superpositioning of a hydroxylated aromatic system on the phenolic A-ring of 17-,-estradiol, can be extended to the PAHs. This two-dimensional-alignment criterion correctly identified estrogenicity of 22 of the 29 PAHs evaluated. Moreover, the estrogenic potency of these compounds was directly related to the size of the hydrophobic backbone. The seven compounds classified incorrectly by this structural feature were either dihydroxylated naphthalenes or aromatic nitrogen-heterocyclic compounds; all such compounds were false positives. Results with dihydroxylated naphthalenes reveal derivatives that were nonestrogenic when superimposed on the phenolic A-ring of 17-,-estradiol had the second hydroxyl group in the position of the C-ring or were catechol-like in structure. Structural alerts for nitrogen-heterocyclic compounds must take into account the position of the hydroxyl group and the in-ring nitrogen atom; compounds with the hydroxyl group and nitrogen atom involved with the same ring were observed to be nonactive. [source] | |||||||||||||||||||||||||||||||||||||||||||||||||