Structural Information (structural + information)

Distribution by Scientific Domains
Distribution within Chemistry

Kinds of Structural Information

  • detailed structural information


  • Selected Abstracts


    A Computational Framework for Patient-Specific Analysis of Articular Cartilage Incorporating Structural Information from DT-MRI

    GAMM - MITTEILUNGEN, Issue 2 2009
    David M. Pierce
    Abstract Accurate techniques for simulating sof t biological tissue deformation are an increasingly valuable tool in many areas of biomechanical analysis and medical image computing. To model the morphology and the material response of human articular cartilage a phenomenological and patient-specific simulation approach incorporating the collagen fibre fabric is proposed. We then demonstrate a unique combination of ultra-high field Diffusion Tensor Magnetic Resonance Imaging (17.6T DT-MRI) and a novel numerical approach incorporating the empirical data to predict the collagen fibre fabric deformation for an indentation experiment (© 2009 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim) [source]


    Structural Information on the Transition Moments in Poly(ethylene-2,6-naphthalene) by Polarization FT-IR Spectroscopy

    MACROMOLECULAR SYMPOSIA, Issue 1 2005
    Alex Scott
    Abstract Oriented poly(ethylene-2,6-naphthalate) (PEN) has been characterised by polarised FT-IR spectroscopy to determine the structural angles of the transition moments to the molecular chain axis. The bands at 1130 cm,1, 1142 cm,1 and 1602 cm,1, which have been previously assigned as having their transition dipole moments parallel to the chain axis, are confirmed as parallel bands. Bands at 767 cm,1 and 831 cm,1 are confirmed as perpendicular bands. However the band at 1708 cm,1 which has previously been assigned as a perpendicular band, is shown here to have its transition moment at 72° to the molecular axis. [source]


    Structural information from quadrupolar nuclei in solid state NMR

    CONCEPTS IN MAGNETIC RESONANCE, Issue 3 2006
    Sharon E. Ashbrook
    Abstract Solid-state NMR has become the method of choice for determining details of molecular-level structure in heterogeneous systems. Though spin-1/2 nuclei still form the core of most such studies, quadrupolar nuclei are increasingly being used. This review assesses what is currently possible, from achieving high-resolution spectra for quadrupolar nuclei (a prerequisite for most structure determination work), to forming correlation spectra which give qualitative details of spatial proximity of nuclei and the determination of internuclear distances, between quadrupolar spins and quadrupolar and spin-1/2 nuclei. Examples are given of each method discussed, and the advantages and disadvantages of the various experiments for different possible applications are assessed. © 2006 Wiley Periodicals, Inc. Concepts Magn Reson Part A 28A: 183,248, 2006. [source]


    Improving thermostability and catalytic activity of pyranose 2-oxidase from Trametes multicolor by rational and semi-rational design

    FEBS JOURNAL, Issue 3 2009
    Oliver Spadiut
    The fungal homotetrameric flavoprotein pyranose 2-oxidase (P2Ox; EC 1.1.3.10) catalyses the oxidation of various sugars at position C2, while, concomitantly, electrons are transferred to oxygen as well as to alternative electron acceptors (e.g. oxidized ferrocenes). These properties make P2Ox an interesting enzyme for various biotechnological applications. Random mutagenesis has previously been used to identify variant E542K, which shows increased thermostability. In the present study, we selected position Leu537 for saturation mutagenesis, and identified variants L537G and L537W, which are characterized by a higher stability and improved catalytic properties. We report detailed studies on both thermodynamic and kinetic stability, as well as the kinetic properties of the mutational variants E542K, E542R, L537G and L537W, and the respective double mutants (L537G/E542K, L537G/E542R, L537W/E542K and L537W/E542R). The selected substitutions at positions Leu537 and Glu542 increase the melting temperature by approximately 10 and 14 °C, respectively, relative to the wild-type enzyme. Although both wild-type and single mutants showed first-order inactivation kinetics, thermal unfolding and inactivation was more complex for the double mutants, showing two distinct phases, as revealed by microcalorimetry and CD spectroscopy. Structural information on the variants does not provide a definitive answer with respect to the stabilizing effects or the alteration of the unfolding process. Distinct differences, however, are observed for the P2Ox Leu537 variants at the interfaces between the subunits, which results in tighter association. [source]


    Advanced glycation end products: a highly complex set of biologically relevant compounds detected by mass spectrometry,

    JOURNAL OF MASS SPECTROMETRY (INCORP BIOLOGICAL MASS SPECTROMETRY), Issue 4 2001
    Annunziata Lapolla
    Abstract Structural information on ,AGE-peptides,' a class of substances belonging to advanced glycation end products (AGE) and originating by proteolysis of glycated proteins, was gained through various analytical approaches on the mixture produced by proteinase K digestion of in vitro glycated bovine serum albumin. Both matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) and high-performance liquid chromatography/electrospray ionization mass spectrometry (HPLC/ESI-MS) were employed, and the results were compared with those from conventional spectroscopic methods (UV, fluorescence, gel permeation). The data acquired by the various techniques all depict the digestion mixtures as highly complex, with components exhibiting molecular mass in the range 300,3500 Da. In the analysis of HPLC/ESI-MS data, identification of AGE-peptides was facilitated by 3D mapping. Structural information was gained by means of multiple mass spectrometric experiments. Copyright © 2001 John Wiley & Sons, Ltd. [source]


    1,1,1-Trichloro-3-(1-phenethylamino-ethylidene)- pentane-2,4-dione,synthesis, spectroscopic, theoretical and structural elucidation

    JOURNAL OF PHYSICAL ORGANIC CHEMISTRY, Issue 12 2007
    Tsonko M. Kolev
    Abstract 1,1,1-Trichloro-3-(1-phenethylamino-ethylidene)-pentane-2,4-dione is spectroscopically and structurally elucidated by means of linear-polarized IR spectroscopy (IR-LD) of oriented solids as a colloidal suspension in nematic liquid crystal. Structural information and IR-spectroscopic assignment are supported by quantum chemical calculations at MP2 and B3LYP level of theory and 6-311++G** basis set. The geometry is characterized with an inramolecular hydrogen bond of NH,OC with length of 2.526,Ĺ and a NHO angle of 140.5(1)°. The NHC(CH3)CCCO(CH3) fragment is nearly flat with a maximal deviation of total planarity of 10.4°. Copyright © 2007 John Wiley & Sons, Ltd. [source]


    Crystallization and preliminary crystallographic analysis of the recombinant N-terminal domain of riboflavin synthase

    ACTA CRYSTALLOGRAPHICA SECTION D, Issue 9 2001
    Winfried Meining
    Riboflavin synthase catalyzes the final step in the biosynthesis of riboflavin. Animals and humans lack this enzyme, whereas many bacteria and certain yeasts are absolutely dependent on endogenous riboflavin synthesis. Riboflavin synthase is therefore an attractive target for chemotherapy. The N-terminal domain of riboflavin synthase forms a dimer in solution and is capable of strongly binding riboflavin. It can serve as a model for the binding site of the native enzyme. Structural information obtained from this domain at high resolution will be helpful in the determination of the binding mode of riboflavin and thus for the development of antimicrobial drugs. Here, the crystallization and preliminary crystallographic analysis of the N-­terminal domain of riboflavin synthase are reported. The crystals belong to the space group C2221, with unit-cell parameters a = 50.3, b = 104.7, c = 85.3,Ĺ, , = , = , = 90°, and diffract to 2.6,Ĺ resolution. [source]


    Preliminary X-ray crystallographic analysis of the d -xylulose 5-phosphate phosphoketolase from Lactococcus lactis

    ACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 7 2010
    Georgiana Petrareanu
    Phosphoketolases are thiamine diphosphate-dependent enzymes which play a central role in the pentose-phosphate pathway of heterofermentative lactic acid bacteria. They belong to the family of aldehyde-lyases and in the presence of phosphate ion cleave the carbon,carbon bond of the specific substrate d -xylulose 5-phosphate (or d -fructose 6-phosphate) to give acetyl phosphate and d -glyceraldehyde 3-phosphate (or d -erythrose 4-phosphate). Structural information about phosphoketolases is particularly important in order to fully understand their mechanism as well as the steric course of phosphoketolase-catalyzed reactions. Here, the purification, preliminary crystallization and crystallographic characterization of d -xylulose 5-phosphate phosphoketolase from Lactococcus lactis are reported. The presence of thiamine diphosphate during purification was essential for the enzymatic activity of the purified protein. The crystals belonged to the monoclinic space group P21. Diffraction data were obtained to a resolution of 2.2,Ĺ. [source]


    Purification, crystallization and preliminary X-ray diffraction of wild-type and mutant recombinant human transforming growth factor ,-induced protein (TGFBIp)

    ACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 3 2009
    Kasper Runager
    Transforming growth factor ,-induced protein (TGFBIp) has been linked to several corneal dystrophies as certain point mutations in the protein may give rise to a progressive accumulation of insoluble protein material in the human cornea. Little is known about the biological functions of this extracellular protein, which is expressed in various tissues throughout the human body. However, it has been found to interact with a number of extracellular matrix macromolecules such as collagens and proteoglycans. Structural information about TGFBIp might prove to be a valuable tool in the elucidation of its function and its role in corneal dystrophies caused by mutations in the TGFBI gene. A simple method for the purification of wild-type and mutant forms of recombinant human TGFBIp from human cells under native conditions is presented here. Moreover, the crystallization and preliminary X-ray analysis of TGFBIp are reported. [source]


    Structural and thermodynamic encoding in the sequence of rat microsomal cytochrome b5,

    BIOPOLYMERS, Issue 5 2008
    Juliette T. J. Lecomte
    Abstract The water-soluble domain of rat microsomal cytochrome b5 is a convenient protein with which to inspect the connection between amino acid sequence and thermodynamic properties. In the absence of its single heme cofactor, cytochrome b5 contains a partially folded stretch of ,30 residues. This region is recognized as prone to disorder by programs that analyze primary structures for such intrinsic features. The cytochrome was subjected to amino acid replacements in the folded core (I12A), in the portion that refolds only when in contact with the heme group (N57P), and in both (F35H/H39A/L46Y). Despite the difficulties associated with measuring thermodynamic quantities for the heme-bound species, it was possible to rationalize the energetic consequences of both types of replacements and test a simple equation relating apoprotein and holoprotein stability. In addition, a phenomenological relationship between the change in Tm (the temperature at the midpoint of the thermal transition) and the change in thermodynamic stability determined by chemical denaturation was observed that could be used to extend the interpretation of incomplete holoprotein stability data. Structural information was obtained by nuclear magnetic resonance spectroscopy toward an atomic-level analysis of the effects. © 2007 Wiley Periodicals, Inc. Biopolymers 89: 428,442, 2008. This article was originally published online as an accepted preprint. The "Published Online" date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com [source]


    Modeling Relations in Nature and Eco-Informatics: A Practical Application of Rosennean Complexity

    CHEMISTRY & BIODIVERSITY, Issue 10 2007

    Abstract The purpose of eco-informatics is to communicate critical information about organisms and ecosystems. To accomplish this, it must reflect the complexity of natural systems. Present information systems are designed around mechanistic concepts that do not capture complexity. Robert Rosen's relational theory offers a way of representing complexity in terms of information entailments that are part of an ontologically implicit ,modeling relation'. This relation has corresponding epistemological components that can be captured empirically, the components being structure (associated with model encoding) and function (associated with model decoding). Relational complexity, thus, provides a long-awaited theoretical underpinning for these concepts that ecology has found indispensable. Structural information pertains to the material organization of a system, which can be represented by data. Functional information specifies potential change, which can be inferred from experiment and represented as models or descriptions of state transformations. Contextual dependency (of structure or function) implies meaning. Biological functions imply internalized or system-dependent laws. Complexity can be represented epistemologically by relating structure and function in two different ways. One expresses the phenomenal relation that exists in any present or past instance, and the other draws the ontology of a system into the empirical world in terms of multiple potentials subject to natural forms of selection and optimality. These act as system attractors. Implementing these components and their theoretical relations in an informatics system will provide more-complete ecological informatics than is possible from a strictly mechanistic point of view. This approach will enable many new possibilities for supporting science and decision making. [source]


    The embedded ion method: A new approach to the electrostatic description of crystal lattice effects in chemical shielding calculations

    CONCEPTS IN MAGNETIC RESONANCE, Issue 5 2006
    Dirk Stueber
    Abstract The nuclear magnetic shielding anisotropy of NMR active nuclei is highly sensitive to the nuclear electronic environment. Hence, measurements of the nuclear magnetic shielding anisotropy represent a powerful tool in the elucidation of molecular structure for a wide variety of materials. Quantum mechanical ab initio nuclear magnetic shielding calculations effectively complement the experimental NMR data by revealing additional structural information. The accuracy and capacity of these calculations has been improved considerably in recent years. However, the inherent problem of the limitation in the size of the systems that may be studied due to the relatively demanding computational requirements largely remains. Accordingly, ab initio shielding calculations have been performed predominantly on isolated molecules, neglecting the molecular environment. This approach is sufficient for neutral nonpolar systems, but leads to serious errors in the shielding calculations on polar and ionic systems. Conducting ab initio shielding calculations on clusters of molecules (i.e., including the nearest neighbor interactions) has improved the accuracy of the calculations in many cases. Other methods of simulating crystal lattice effects in shielding calculations that have been developed include the electrostatic representation of the crystal lattice using point charge arrays, full ab initio methods, ab initio methods under periodic boundary conditions, and hybrid ab initio/molecular dynamics methods. The embedded ion method (EIM) discussed here follows the electrostatic approach. The method mimics the intermolecular and interionic interactions experienced by a subject molecule or cluster in a given crystal in quantum mechanical shielding calculations with a large finite, periodic, and self-consistent array of point charges. The point charge arrays in the EIM are generated using the Ewald summation method and embed the molecule or ion of interest for which the ab initio shielding calculations are performed. The accuracy with which the EIM reproduces experimental nuclear magnetic shift tensor principal values, the sensitivity of the EIM to the parameters defining the point charge arrays, as well as the strengths and limitations of the EIM in comparison with other methods that include crystal lattice effects in chemical shielding calculations, are presented. © 2006 Wiley Periodicals, Inc. Concepts Magn Reson Part A 28A: 347,368, 2006 [source]


    Adaptive structured parallelism for distributed heterogeneous architectures: a methodological approach with pipelines and farms

    CONCURRENCY AND COMPUTATION: PRACTICE & EXPERIENCE, Issue 15 2010
    Horacio González-Vélez
    Abstract Algorithmic skeletons abstract commonly used patterns of parallel computation, communication, and interaction. Based on the algorithmic skeleton concept, structured parallelism provides a high-level parallel programming technique that allows the conceptual description of parallel programs while fostering platform independence and algorithm abstraction. This work presents a methodology to improve skeletal parallel programming in heterogeneous distributed systems by introducing adaptivity through resource awareness. As we hypothesise that a skeletal program should be able to adapt to the dynamic resource conditions over time using its structural forecasting information, we have developed adaptive structured parallelism (ASPARA). ASPARA is a generic methodology to incorporate structural information at compilation into a parallel program, which will help it to adapt at execution. ASPARA comprises four phases: programming, compilation, calibration, and execution. We illustrate the feasibility of this approach and its associated performance improvements using independent case studies based on two algorithmic skeletons,the task farm and the pipeline,evaluated in a non-dedicated heterogeneous multi-cluster system. Copyright © 2010 John Wiley & Sons, Ltd. [source]


    Development of a CE-MS method to analyze components of the potential biomarker vascular endothelial growth factor 165

    ELECTROPHORESIS, Issue 13 2009
    Angel Puerta
    Abstract The vascular endothelial growth factor 165 (VEGF165) is the predominant form of the complex VEGF-A family. Its angiogenic effect is involved in many physiological and pathological events. For this reason, its roles as a potential biomarker and as a therapeutic drug have been considered. Nevertheless, very little is known about the existence of different forms of VEGF165 arising from glycosylation and potentially from other PTMs. This aspect is important because different forms may differ in biological activity (therapeutic drug application) and the pattern of the different forms can vary with pathological changes (biomarker application). In this work a CE-MS method to separate up to seven peaks containing, at least, 19 isoforms of intact VEGF165 is described. Comparison between human VEGF165 expressed in a glycosylating system, i.e. insect cells, and in a non-glycosylating system, i.e. E. coli cells, has been carried out. The method developed provides structural information (mass fingerprint) about the different forms of VEGF165 and after the deconvolution and the analysis of the MS spectra, PTMs pattern of VEGF165 including glycosylation and loss of amino acids at the N- and C-terminus was identified. Glycans involved in PTMs promoting different glycoforms observed in the CE-MS fingerprint were confirmed by MALDI-MS after deglycosylation with peptide N-glycosidase F. This approach is a starting point to study the role of VEGF165 as a potential biomarker and to perform quality control of the drug during manufacturing. To our knowledge this is the first time that a CE-MS method for the analysis of VEGF165 has been developed. [source]


    Automated comparative protein structure modeling with SWISS-MODEL and Swiss-PdbViewer: A historical perspective

    ELECTROPHORESIS, Issue S1 2009
    Nicolas Guex
    Abstract SWISS-MODEL pioneered the field of automated modeling as the first protein modeling service on the Internet. In combination with the visualization tool Swiss-PdbViewer, the Internet-based Workspace and the SWISS-MODEL Repository, it provides a fully integrated sequence to structure analysis and modeling platform. This computational environment is made freely available to the scientific community with the aim to hide the computational complexity of structural bioinformatics and encourage bench scientists to make use of the ever-increasing structural information available. Indeed, over the last decade, the availability of structural information has significantly increased for many organisms as a direct consequence of the complementary nature of comparative protein modeling and experimental structure determination. This has a very positive and enabling impact on many different applications in biomedical research as described in this paper. [source]


    A novel approach for analysis of oligonucleotide,cisplatin interactions by continuous elution gel electrophoresis coupled to isotope dilution inductively coupled plasma mass spectrometry and matrix-assisted laser desorption/ionization mass spectrometry

    ELECTROPHORESIS, Issue 7 2008
    Wolfram Brüchert
    Abstract In this work we present a novel approach for in vitro studies of cisplatin interactions with 8-mer oligonucleotides. The approach is based on the recently developed coupling of continuous elution gel electrophoresis (GE) to an inductively coupled plasma-sector field mass spectrometer (ICP-SFMS) with the aim of monitoring the interaction process between this cytostatic drug and the nucleotides. In contrast to existing methods, the electrophoretic separation conditions used here allow both the determination of the reaction kinetics in more detail as well as the observation of dominant intermediates. Two different nucleotides sequences have been investigated for comparison purposes, one containing two adjacent guanines (5,-TCCGGTCC-3,) and one with a combination of thymine and guanine (5,-TCCTGTCC-3,), respectively. In order to gain further structural information, MALDI-TOF MS measurements have been performed after fraction collection. This allows for identification of the intermediates and the final products and confirms the stepwise coordination of cisplatin via monoadduct to bisadduct formation. Furthermore, the ICP-MS results were quantitatively evaluated in order to calculate the kinetics of the entire process. [source]


    Determination of bupivacaine and metabolites in rat urine using capillary electrophoresis with mass spectrometric detection

    ELECTROPHORESIS, Issue 14 2003
    Ryan M. Krisko
    Abstract A method using capillary electrophoresis-mass spectrometry (CE-MS) was developed for the structural elucidation of bupivacaine and metabolites in rat urine. Prior to CE-MS analysis, solid-phase extraction (SPE) was used for sample cleanup and preconcentration purposes. Exact mass and tandem mass spectrometric (MS/MS) experiments were performed to obtain structural information about the unknown metabolites. Two instruments with different mass analyzers were used for mass spectrometric detection. A quadrupole time-of-flight (Q-TOF) and a magnetic sector hybrid instrument were coupled to CE and used for the analysis of urine extracts. Hydroxybupivacaine as well as five other isomerically different metabolites were detected including methoxylated bupivacaine. [source]


    Solid-State Structures and Properties of Europium and Samarium Hydrides

    EUROPEAN JOURNAL OF INORGANIC CHEMISTRY, Issue 18 2010
    Holger Kohlmann
    Abstract The structural chemistry of europium and samarium hydrides in the solid state is very rich, ranging from typical ionic hydrides following the hydride-fluoride analogy to complex transition metal hydrides and interstitial hydrides. While crystal structure, electrical, and magnetic properties suggest that europium is divalent in all hydrides investigated so far, samarium is easily transformed to a trivalent oxidation state in its hydrides and shows similarities to other lanthanide(III) hydrides. The problem of neutron absorption of europium and samarium, hampering crystal structure solution and limiting the available structural information, is discussed in detail, and practical solutions for neutron diffraction experiments are given. [source]


    Surfactant-Assisted Synthesis and Characterization of Novel Chain-Like CoNi Alloy Assemblies

    EUROPEAN JOURNAL OF INORGANIC CHEMISTRY, Issue 25 2007
    Lu-Ping Zhu
    Abstract Novel chain-like CoNi alloy assemblies with a length of up to 6,7 ,m were successfully prepared by a surfactant-assisted hydrothermal synthetic route at 100 °C for 2 h. The individual submicrospheres built from smaller CoNi nanoparticles had a diameter of about 400,500 nm. These microspheres were then integrated to form the novel chain-like CoNi alloy assemblies. The effects of synthetic parameters such as surfactant and solvent on the formation and morphology of CoNi samples were investigated. The experimental results showed that N2H4·H2O and CTA+ play important roles in the formation of the novel chain-like CoNi alloy assemblies. Based on the structural information provided by X-ray powder diffraction, scanning electron microscopy, transmission electron microscopy, selected-area electron diffraction and energy-dispersive X-ray analysis, a growth mechanism was tentatively proposed for the formation of chain-like CoNi alloy assemblies. Magnetic hysteresis measurement revealed that the chain-like CoNi alloy assemblies display ferromagnetic behavior with a saturation magnetization of 96.15 emu/g and a coercivity of 144.75 Oe at room temperature. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2007) [source]


    N -Methylation Effects on the Coordination Chemistry of Cyclic Triamines with Divalent Transition Metals and Their CoII Dioxygen Carriers

    EUROPEAN JOURNAL OF INORGANIC CHEMISTRY, Issue 2 2006
    Silvia Del Piero
    Abstract The thermodynamics of complex formation of CoII and CdII ions with the triaza macrocyclic ligand 1,4,7-triazacyclononane (tacn) and its N -methylated derivative 1,4,7-trimethyl-1,4,7-triazacyclononane (Me3tacn) has been studied in dimethyl sulfoxide (DMSO) at 298.1 K and in an ionic medium (0.1 M Et4NClO4) by means of potentiometric, UV/Vis, calorimetric and FT-IR techniques. The results are discussed by taking into account electronic and steric effects as well as solvation of the species concerned. Computational methods based on density functional theory (DFT) have been used to obtain structural information about the ligands and their complexes in order to provide further, independent insights into the effect of N -methylation on the coordination affinity of the ligands towards the metal ions. The computational suggestions are of great help to correlate steric effects and thermodynamic results. The kinetics of dioxygen uptake for the formation of the Co(tacn)2O2 superoxo adduct has also been studied by means of UV/Vis measurements. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2006) [source]


    Soil structure and pedotransfer functions

    EUROPEAN JOURNAL OF SOIL SCIENCE, Issue 3 2003
    Y.A. Pachepsky
    Summary Accurate estimates of soil hydraulic properties from other soil characteristics using pedotransfer functions (PTFs) are in demand in many applications, and soil structural characteristics are natural candidates for improving PTFs. Soil survey provides mostly categorical data about soil structure. Many available characteristics such as bulk density, aggregate distribution, and penetration resistance reflect not only structural but also other soil properties. Our objective here is to provoke a discussion of the value of structural information in modelling water transport in soils. Two case studies are presented. Data from the US National Pedon Characterization database are used to estimate soil water retention from categorical field-determined structural and textural classes. Regression-tree estimates have the same accuracy as those from textural class as determined in the laboratory. Grade of structure appears to be a strong predictor of water retention at ,33 kPa and ,1500 kPa. Data from the UNSODA database are used to compare field and laboratory soil water retention. The field-measured retention is significantly less than that measured in the laboratory for soils with a sand content of less than 50%. This could be explained by Rieu and Sposito's theory of scaling in soil structure. Our results suggest a close relationship between structure observed at the soil horizon scale and structure at finer scales affecting water retention of soil clods. Finally we indicate research needs, including (i) quantitative characterization of the field soil structure, (ii) an across-scale modelling of soil structure to use fine-scale data for coarse-scale PTFs, (iii) the need to understand the effects of soil structure on the performance of various methods available to measure soil hydraulic properties, and (iv) further studies of ways to use soil,landscape relationships to estimate variations of soil hydraulic properties across large areas of land. [source]


    Molecular physiology of SLC4 anion exchangers

    EXPERIMENTAL PHYSIOLOGY, Issue 1 2006
    Seth L. Alper
    Plasmalemmal Cl,,HCO3, exchangers regulate intracellular pH and [Cl,] and cell volume. In polarized epithelial cells, they contribute also to transepithelial secretion and reabsorption of acid,base equivalents and of Cl,. Members of both the SLC4 and SLC26 mammalian gene families encode Na+ -independent Cl,,HCO3, exchangers. Human SLC4A1/AE1 mutations cause either the erythroid disorders spherocytic haemolytic anaemia or ovalocytosis, or distal renal tubular acidosis. SLC4A2/AE2 knockout mice die at weaning. Human SLC4A3/AE3 polymorphisms have been associated with seizure disorder. Although mammalian SLC4/AE polypeptides mediate only electroneutral Cl,,anion exchange, trout erythroid AE1 also promotes osmolyte transport and increased anion conductance. Mouse AE1 is required for DIDS-sensitive erythroid Cl, conductance, but definitive evidence for mediation of Cl, conductance is lacking. However, a single missense mutation allows AE1 to mediate both electrogenic SO42,,Cl, exchange or electroneutral, H+ -independent SO42,,SO42, exchange. In the Xenopus oocyte, the AE1 C-terminal cytoplasmic tail residues reported to bind carbonic anhydrase II are dispensable for Cl,,Cl, exchange, but required for Cl,,HCO3, exchange. AE2 is acutely and independently inhibited by intracellular and extracellular H+, and this regulation requires integrity of the most highly conserved sequence of the AE2 N-terminal cytoplasmic domain. Individual missense mutations within this and adjacent regions identify additional residues which acid-shift pHo sensitivity. These regions together are modelled to form contiguous surface patches on the AE2 cytoplasmic domain. In contrast, the N-terminal variant AE2c polypeptide exhibits an alkaline-shifted pHo sensitivity, as do certain transmembrane domain His mutants. AE2-mediated anion exchange is also stimulated by ammonium and by hypertonicity by a mechanism sensitive to inhibition by chelation of intracellular Ca2+ and by calmidazolium. This growing body of structure,function data, together with increased structural information, will advance mechanistic understanding of SLC4 anion exchangers. [source]


    Modeling of tRNA-assisted mechanism of Arg activation based on a structure of Arg-tRNA synthetase, tRNA, and an ATP analog (ANP)

    FEBS JOURNAL, Issue 17 2009
    Michiko Konno
    The ATP,pyrophosphate exchange reaction catalyzed by Arg-tRNA, Gln-tRNA and Glu-tRNA synthetases requires the assistance of the cognate tRNA. tRNA also assists Arg-tRNA synthetase in catalyzing the pyrophosphorolysis of synthetic Arg-AMP at low pH. The mechanism by which the 3,-end A76, and in particular its hydroxyl group, of the cognate tRNA is involved with the exchange reaction catalyzed by those enzymes has yet to be established. We determined a crystal structure of a complex of Arg-tRNA synthetase from Pyrococcus horikoshii, tRNAArgCCU and an ATP analog with Rfactor = 0.213 (Rfree = 0.253) at 2.0 Ĺ resolution. On the basis of newly obtained structural information about the position of ATP bound on the enzyme, we constructed a structural model for a mechanism in which the formation of a hydrogen bond between the 2,-OH group of A76 of tRNA and the carboxyl group of Arg induces both formation of Arg-AMP (Arg + ATP , Arg-AMP + pyrophosphate) and pyrophosphorolysis of Arg-AMP (Arg-AMP + pyrophosphate , Arg + ATP) at low pH. Furthermore, we obtained a structural model of the molecular mechanism for the Arg-tRNA synthetase-catalyzed deacylation of Arg-tRNA (Arg-tRNA + AMP , Arg-AMP + tRNA at high pH), in which the deacylation of aminoacyl-tRNA bound on Arg-tRNA synthetase and Glu-tRNA synthetase is catalyzed by a quite similar mechanism, whereby the proton-donating group (,NH,C+(NH2)2 or ,COOH) of Arg and Glu assists the aminoacyl transfer from the 2,-OH group of tRNA to the phosphate group of AMP at high pH. [source]


    Full-length prion protein aggregates to amyloid fibrils and spherical particles by distinct pathways

    FEBS JOURNAL, Issue 9 2008
    Driss El Moustaine
    As limited structural information is available on prion protein (PrP) misfolding and aggregation, a causative link between the specific (supra)molecular structure of PrP and transmissible spongiform encephalopathies remains to be elucidated. In this study, high pressure was utilized, as an approach to perturb protein structure, to characterize different morphological and structural PrP aggregates. It was shown that full-length recombinant PrP undergoes ,-sheet aggregation on high-pressure-induced destabilization. By tuning the physicochemical conditions, the assembly process evolves through two distinct pathways leading to the irreversible formation of spherical particles or amyloid fibrils, respectively. When the PrP aggregation propensity is enhanced, high pressure induces the formation of a partially unfolded aggregated protein, AggHP, which relaxes at ambient pressure to form amorphous aggregates. The latter largely retain the native secondary structure. On prolonged incubation at high pressure, followed by depressurization, AggHP transforms to a monodisperse population of spherical particles of about 20 nm in diameter, characterized by an essentially ,-sheet secondary structure. When the PrP aggregation propensity is decreased, an oligomeric reaction intermediate, IHP, is formed under high pressure. After pressure release, IHP relaxes to the original native structure. However, on prolonged incubation at high pressure and subsequent depressurization, it transforms to amyloid fibrils. Structural evaluation, using optical spectroscopic methods, demonstrates that the conformation adopted by the subfibrillar oligomeric intermediate, IHP, constitutes a necessary prerequisite for the formation of amyloids. The use of high-pressure perturbation thus provides an insight into the molecular mechanism of the first stages of PrP misfolding into amyloids. [source]


    Novel ,-carboxyglutamic acid-containing peptides from the venom of Conus textile

    FEBS JOURNAL, Issue 12 2006
    Eva Czerwiec
    The cone snail is the only invertebrate system in which the vitamin K-dependent carboxylase (or ,-carboxylase) and its product ,-carboxyglutamic acid (Gla) have been identified. It remains the sole source of structural information of invertebrate ,-carboxylase substrates. Four novel Gla-containing peptides were purified from the venom of Conus textile and characterized using biochemical methods and mass spectrometry. The peptides Gla(1),TxVI, Gla(2),TxVI/A, Gla(2),TxVI/B and Gla(3),TxVI each have six Cys residues and belong to the O -superfamily of conotoxins. All four conopeptides contain 4- trans -hydroxyproline and the unusual amino acid 6- l -bromotryptophan. Gla(2),TxVI/A and Gla(2),TxVI/B are isoforms with an amidated C-terminus that differ at positions +1 and +13. Three isoforms of Gla(3),TxVI were observed that differ at position +7: Gla(3),TxVI, Glu7,Gla(3),TxVI and Asp7-Gla(3),TxVI. The cDNAs encoding the precursors of the four peptides were cloned. The predicted signal sequences (amino acids ,46 to ,27) were nearly identical and highly hydrophobic. The predicted propeptide region (,20 to ,1) that contains the ,-carboxylation recognition site (,-CRS) is very similar in Gla(2),TxVI/A, Gla(2),TxVI/B and Gla(3),TxVI, but is more divergent for Gla(1),TxVI. Kinetic studies utilizing the Conus,-carboxylase and synthetic peptide substrates localized the ,-CRS of Gla(1),TxVI to the region ,14 to ,1 of the polypeptide precursor: the Km was reduced from 1.8 mm for Gla (1),TxVI lacking a propeptide to 24 µm when a 14-residue propeptide was attached to the substrate. Similarly, addition of an 18-residue propeptide to Gla(2),TxVI/B reduced the Km value tenfold. [source]


    Synthesis and structural characterization of a mimetic membrane-anchored prion protein

    FEBS JOURNAL, Issue 6 2006
    Matthew R. Hicks
    During pathogenesis of transmissible spongiform encephalopathies (TSEs) an abnormal form (PrPSc) of the host encoded prion protein (PrPC) accumulates in insoluble fibrils and plaques. The two forms of PrP appear to have identical covalent structures, but differ in secondary and tertiary structure. Both PrPC and PrPSc have glycosylphospatidylinositol (GPI) anchors through which the protein is tethered to cell membranes. Membrane attachment has been suggested to play a role in the conversion of PrPC to PrPSc, but the majority of in vitro studies of the function, structure, folding and stability of PrP use recombinant protein lacking the GPI anchor. In order to study the effects of membranes on the structure of PrP, we synthesized a GPI anchor mimetic (GPIm), which we have covalently coupled to a genetically engineered cysteine residue at the C-terminus of recombinant PrP. The lipid anchor places the protein at the same distance from the membrane as does the naturally occurring GPI anchor. We demonstrate that PrP coupled to GPIm (PrP,GPIm) inserts into model lipid membranes and that structural information can be obtained from this membrane-anchored PrP. We show that the structure of PrP,GPIm reconstituted in phosphatidylcholine and raft membranes resembles that of PrP, without a GPI anchor, in solution. The results provide experimental evidence in support of previous suggestions that NMR structures of soluble, anchor-free forms of PrP represent the structure of cellular, membrane-anchored PrP. The availability of a lipid-anchored construct of PrP provides a unique model to investigate the effects of different lipid environments on the structure and conversion mechanisms of PrP. [source]


    Evaluating low level sequence identities

    FEBS JOURNAL, Issue 2 2001
    AROM homologous?, Are Aspergillus QUTA
    A review published several years ago [Hawkins, A.R. & Lamb, H.K. (1995) Eur. J. Biochem. 232, 7,18] proposed that genetic, biochemical and physiological data can override sequence comparison in the determination of homology in instances where structural information is unavailable. Their lead example was the hypothesis that the transcriptional activator protein for quinate catabolism in Aspergillus nidulans, QUTA, is derived from the pentafunctional AROM protein by a gene duplication followed by cleavage [Hawkins, A.R., Lamb, H.K., Moore, J.D. & Roberts, C.F. (1993) Gene136, 49,54]. We tested this hypothesis by a sensitive combination of position-specific log-odds scoring matrix methods. The position-specific log-odds scoring matrices were derived from a large number of 3-dehydroquinate synthase and 5- enolpyruvylshikimate-3-phosphate synthase domains that were proposed to be the domains from the AROM protein that gave rise to the transcriptional activator protein for quinate metabolism. We show that the degree and pattern of similarity between these position-specific log-odds scoring matrices and the transcriptional activator protein for quinate catabolism in A. nidulans is that expected for random sequences of the same composition. This level of similarity provides no support for the suggested gene duplication and cleavage. The lack of any trace of evidence for homology following a comprehensive sequence analysis indicates that the homology hypothesis is without foundation, underlining the necessity to accept only similarity of sequence and/or structure as evidence of evolutionary relatedness. Further, QUTA is homologous throughout its entire length to an extended family of fungal transcriptional regulatory proteins, rendering the hypothesized QUTA,AROM homology even more problematic. [source]


    Global analysis of functional surfaces of core histones with comprehensive point mutants

    GENES TO CELLS, Issue 1 2007
    Kazuko Matsubara
    The core histones are essential components of the nucleosome that act as global negative regulators of DNA-mediated reactions including transcription, DNA replication and DNA repair. Modified residues in the N-terminal tails are well characterized in transcription, but not in DNA replication and DNA repair. In addition, roles of residues in the core globular domains are not yet well characterized in any DNA-mediated reactions. To comprehensively understand the functional surface(s) of a core histone, we constructed 320 yeast mutant strains, each of which has a point mutation in a core histone, and identified 42 residues responsible for the suppressor of Ty (Spt - ) phenotypes, and 8, 30 and 61 residues for sensitivities to 6-azauracil (6AU), hydroxyurea (HU) and methyl-methanesulfonate (MMS), respectively. In addition to residues that affect one specific assay, residues involved in multiple reactions were found, and surprisingly, about half of them were clustered at either the nucleosome entry site, the surface required for nucleosome,nucleosome interactions in crystal packing or their surroundings. This comprehensive mutation approach was proved to be powerful for identification of the functional surfaces of a core histone in a variety of DNA-mediated reactions and could be an effective strategy for characterizing other evolutionarily conserved hub-like factors for which surface structural information is available. [source]


    Diffraction imaging in depth

    GEOPHYSICAL PROSPECTING, Issue 5 2008
    T.J. Moser
    ABSTRACT High resolution imaging is of great value to an interpreter, for instance to enable identification of small scale faults, and to locate formation pinch-out positions. Standard approaches to obtain high-resolution information, such as coherency analysis and structure-oriented filters, derive attributes from stacked, migrated images. Since they are image-driven, these techniques are sensitive to artifacts due to an inadequate migration velocity; in fact the attribute derivation is not based on the physics of wave propagation. Diffracted waves on the other hand have been recognized as physically reliable carriers of high- or even super-resolution structural information. However, high-resolution information, encoded in diffractions, is generally lost during the conventional processing sequence, indeed migration kernels in current migration algorithms are biased against diffractions. We propose here methods for a diffraction-based, data-oriented approach to image resolution. We also demonstrate the different behaviour of diffractions compared to specular reflections and how this can be leveraged to assess characteristics of subsurface features. In this way a rough surface such as a fault plane or unconformity may be distinguishable on a diffraction image and not on a traditional reflection image. We outline some characteristic properties of diffractions and diffraction imaging, and present two novel approaches to diffraction imaging in the depth domain. The first technique is based on reflection focusing in the depth domain and subsequent filtering of reflections from prestack data. The second technique modifies the migration kernel and consists of a reverse application of stationary-phase migration to suppress contributions from specular reflections to the diffraction image. Both techniques are proposed as a complement to conventional full-wave pre-stack depth migration, and both assume the existence of an accurate migration velocity. [source]


    Internal structure of an alpine rock glacier based on crosshole georadar traveltimes and amplitudes

    GEOPHYSICAL PROSPECTING, Issue 3 2006
    Martin Musil
    ABSTRACT Rapid melting of permafrost in many alpine areas has increased the probability of catastrophic rock slides. In an attempt to provide critical structural information needed for the design and implementation of suitable mitigation procedures, we have acquired low frequency (22 MHz) cross-hole radar data from within a fast-moving rock glacier, an important form of alpine permafrost. Since the ice, rock and pockets of water and air found in the underground of high alpine areas have very different dielectric permittivities and electrical conductivities, the radar method was well-suited for investigating the structure and state of the rock glacier. Our interpretation of the radar velocities and attenuations was constrained by geomorphological observations, borehole lithological logs and the results of a surface seismic survey. The radar data revealed the existence of a discontinuous 7,11 m thick ice-rich zone distinguished by high velocities (0.14,0.17 m/ns) and low attenuations (0.04,0.09 m,1) and a thin underlying ice-free zone characterized by moderate velocities (0.11,0.12 m/ns) and low attenuations (0.04,0.09 m,1). Beneath these two zones, we observed a prominent band of high velocities (0.14,0.17 m/ns) and moderately high attenuations (0.10,0.20 m,1) associated with unconsolidated glacial sediments and numerous large air-filled voids, which in the past were probably filled with ice. At greater depths, the variably dry to water-saturated sediments were represented by generally lower velocities (0.08,0.10 m/ns) and higher attenuations (0.16,0.24 m,1). The bedrock surface was represented by an abrupt ,0.03 m/ns velocity increase. We speculate that the disappearance of ice, both laterally and with depth, occurred during the past one to two decades. [source]