bluuebunny/crossref_metadata_2025 huggingface dataset:
GTP Promotes the Formation of Early-Import Intermediates But Is Not Required during the Translocation Step of Protein Import into Chloroplasts
Authors: Young Michael E. , Keegstra Kenneth , Froehlich John E.
Published: July 2002

Protein import into chloroplasts is an energy-requiring process mediated by a proteinaceous import apparatus. Although previous work has shown that low levels of ATP or GTP can support precursor binding, the role of GTP during the import process remains unclear. Specifically, it is unknown whether GTP plays a separate role from ATP during the early stages of protein import and whether GTP has any role in the later stages of transport. We investigated the role of GTP during the various stages of protein import into chloroplasts by using purified GTP analogs and an in vitro import assay. GTP, GDP, the nonhydrolyzable analog GMP-PNP, and the slowly hydrolyzable analogs guanosine 5′-O-(2-thiodiphosphate) and guanosine 5′-O-(3-thiotriphosphate) were used in this study. Chromatographically purified 5′-guanylyl-imido-diphosphate and guanosine 5′-O-(3-thiotriphosphate) were found to inhibit the formation of early-import intermediates, even in the presence of ATP. We also observed that GTP does not play a role during the translocation of precursors from the intermediate state. We conclude that GTP hydrolysis influences events leading to the formation of early-import intermediates, but not subsequent steps such as precursor translocation.
Water Deficit Effects on Raffinose Family Oligosaccharide Metabolism in Coleus
Authors: Pattanagul Wattana , Madore Monica A.
Published: July 2002

Variegated coleus (Coleus blumei Benth.) plants were exposed to a restricted water supply for 21 d. The relative water content in leaf tissues was reduced from 80% (control) to 60% (drought-stressed). Under drought conditions, the stomatal conductance and leaf photosynthetic rate were reduced. In green leaf tissues, drought stress also greatly decreased the diurnal light-period levels of the raffinose family oligosaccharides (RFOs) stachyose and raffinose, as well as those of other non-structural carbohydrates (galactinol, sucrose, hexoses, and starch). However, drought had little effect on soluble carbohydrate content of white, non-photosynthetic leaf tissues. In green tissues, galactinol synthase activity was depressed by drought stress. An accumulation of O-methyl-inositol was also observed, which is consistent with the induction of myoinositol-6-O-methyltransferase activity seen in the stressed green tissues. In source tissues, RFO metabolism is apparently reduced by drought stress through a combined effect of decreased photosynthesis and reduced galactinol synthase activity. Moreover, a further reduction in RFO biosynthesis may have been due to a switch in carbon partitioning to O-methyl-inositol biosynthesis, creating competition for myoinositol, a metabolite shared by both biochemical pathways.
The PsbY Protein Is Not Essential for Oxygenic Photosynthesis in the Cyanobacterium Synechocystis sp. PCC 6803
Authors: Meetam Metha , Keren Nir , Ohad Itzhak , Pakrasi Himadri B.
Published: July 2002

A tetra-manganese cluster in the photosystem II (PSII) pigment-protein complex plays a critical role in the photosynthetic oxygen evolution process. PsbY, a small membrane-spanning polypeptide, has recently been suggested to provide a ligand for manganese in PSII (A.E. Gau, H.H. Thole, A. Sokolenko, L. Altschmied, R.G. Herrmann, E.K. Pistorius [1998] Mol Gen Genet 260: 56–68). We have constructed a mutant strain of the cyanobacteriumSynechocystis sp. PCC 6803 with an inactivatedpsbY gene (sml0007). Southern-blot and polymerase chain reaction analysis showed that the mutant had completely segregated. However, the ΔpsbY mutant cells grew normally under photoautotrophic conditions. Moreover, growth of the wild-type and mutant cells were similar under high-light photoinhibition conditions, as well as in media without any added manganese, calcium, or chloride, three required inorganic cofactors for the oxygen-evolving complex of PSII. Analysis of steady-state and flash-induced oxygen evolution, fluorescence induction, and decay kinetics, and thermoluminescence profiles demonstrated that the ΔpsbY mutant cells have normal photosynthetic activities. We conclude that the PsbY protein inSynechocystis 6803 is not essential for oxygenic photosynthesis and does not provide an important binding site for manganese in the oxygen-evolving complex of PSII.
CO2-Responsive Transcriptional Regulation ofCAH1 Encoding Carbonic Anhydrase Is Mediated by Enhancer and Silencer Regions in Chlamydomonas reinhardtii
Authors: Kucho Ken-ichi , Ohyama Kanji , Fukuzawa Hideya
Published: July 2002

Chlamydomonas reinhardtii adapts to the stress of CO2-limiting conditions through the induction of a set of genes includingCAH1, which encodes a periplasmic carbonic anhydrase.CAH1 is up-regulated under low-CO2conditions (air containing 0.04% [v/v] CO2) in the presence of light, whereas it is down-regulated under high-CO2 conditions (5% [v/v] CO2) or in the dark. In an effort to identify cis-elements involved in the transcriptional regulation of CAH1, a series of 5′-nested deletions of the region upstream of CAH1 were fused to a promoterless arylsulfatase reporter gene (ARS). The upstream region from −651 to +41 relative to the transcription start site was sufficient to regulate the expression of ARS with kinetics similar to those of endogenousCAH1. Deletion of the region between −651 and −294 resulted in a significant decrease in the level of arylsulfatase activity expressed under low-CO2 conditions. The 543-bp upstream region from −651 to −109, without any promoter elements, CAAT-box, or TATA-box, could confer CO2 and light responsiveness on the β2-tubulin minimal promoter. This 543-bp region was divided into two parts: a 358-bp silencer region from −651 to −294, which represses the minimal promoter activity under high-CO2 conditions, and a 185-bp enhancer region from −293 to −109, which activates the promoter under low-CO2conditions in the presence of light.
The Regulation of 1-Aminocyclopropane-1-Carboxylic Acid Synthase Gene Expression during the Transition from System-1 to System-2 Ethylene Synthesis in Tomato
Authors: Barry Cornelius S. , Llop-Tous M. Immaculada , Grierson Donald
Published: July 2002

1-Aminocyclopropane-1-carboxylic acid synthase (ACS) is one of the key regulatory enzymes involved in the synthesis of the hormone ethylene and is encoded by a multigene family containing at least eight members in tomato (Lycopersicon esculentum). Increased ethylene production accompanies ripening in tomato, and this coincides with a change in the regulation of ethylene synthesis from auto-inhibitory to autostimulatory. The signaling pathways that operate to bring about this transition from so-called system-1 to system-2 ethylene production are unknown, and we have begun to address these by investigating the regulation of ACS expression during ripening. Transcripts corresponding to four ACS genes,LEACS1A, LEACS2, LEACS4, and LEACS6, were detected in tomato fruit, and expression analysis using the ripening inhibitor(rin) mutant in combination with ethylene treatments and the Never-ripe (Nr) mutant has demonstrated that each is regulated in a unique way. A proposed model suggests that system-1 ethylene is regulated by the expression ofLEACS1A and LEACS6. In fruit a transition period occurs in which the RIN gene plays a pivotal role leading to increased expression of LEACS1A and induction of LEACS4. System-2 ethylene synthesis is subsequently initiated and maintained by ethylene-dependent induction ofLEACS2.
A Minimal Serine/Threonine Protein Kinase Circadianly Regulates Phosphoenolpyruvate Carboxylase Activity in Crassulacean Acid Metabolism-Induced Leaves of the Common Ice Plant
Authors: Taybi Tahar , Patil Shameekumar , Chollet Raymond , Cushman John C.
Published: July 2002

Plant phosphoenolpyruvate carboxylase (PEPc) activity and allosteric properties are regulated by PEPc kinase (PPcK) through reversible phosphorylation of a specific serine (Ser) residue near the N terminus. We report the molecular cloning of PPcK from the facultative Crassulacean acid metabolism (CAM) common ice plant (Mesembryanthemum crystallinum), using a protein-kinase-targeted differential display reverse transcriptase-polymerase chain reaction approach. M. crystallinum PPcK encodes a minimal, Ca2+-independent Ser/threonine protein kinase that is most closely related to calcium-dependent protein kinases, yet lacks both the calmodulin-like and auto-inhibitory domains typical of plant calcium-dependent protein kinase. In the common ice plant PPcK belongs to a small gene family containing two members. McPPcK transcript accumulation is controlled by a circadian oscillator in a light-dependent manner. McPPcK encodes a 31.8-kD polypeptide (279 amino acids), making it among the smallest protein kinases characterized to date. Initial biochemical analysis of the purified, recombinant McPPcK gene product documented that this protein kinase specifically phosphorylates PEPc from CAM and C4 species at a single, N-terminal Ser (threonine) residue but fails to phosphorylate mutated forms of C4 PEPc in which this specific site has been changed to tyrosine or aspartate. McPPcK activity was specific for PEPc, Ca2+-insensitive, and displayed an alkaline pH optimum. Furthermore, recombinant McPPcK was shown to reverse the sensitivity of PEPc activity to l-malate inhibition in CAM-leaf extracts prepared during the day, but not at night, documenting that PPcK contributes to the circadian regulation of photosynthetic carbon flux in CAM plants.
Trivalent Ions Activate Abscisic Acid-Inducible Promoters through an ABI1-Dependent Pathway in Rice Protoplasts
Authors: Hagenbeek Dik , Quatrano Ralph S. , Rock Christopher D.
Published: July 2002

The plant hormone abscisic acid (ABA) mediates many vital processes in plant growth and development, including seed dormancy, cell division, water use efficiency, and adaptation to drought, salinity, chilling, pathogen attack, and UV light. Our understanding of ABA signal transduction is fragmentary and would benefit from specific and facile probes of the process. Protoplasts from rice (Oryza sativa L. cv IR54) embryonic suspension cultures cotransformed with effector plasmids encoding the maize (Zea mays)VIVIPAROUS1 cDNA and/or the Arabidopsis dominant negative mutant (abi1-1) ABA-insensitive cDNA demonstrated genetic interactions of VIVIPAROUS1 andabi1-1 in transactivation of the ABA-inducibleHVA1 promoter from barley (Hordeum vulgare), suggesting the mechanisms of these effectors are conserved among monocots and dicots. Trivalent ions have been shown to act as an effector of gene expression in plants and animals, although the mechanism of action is unknown. We show in two complementary transient ABA-inducible gene expression assays (β-glucuronidase and luciferase enzymatic activities and quantitative flow cytometry of green fluorescent protein) that trivalent ions specifically interact with an ABI1-dependent ABA-signaling pathway leading to gene expression. Trivalent ions mimic ABA effects on gene expression and may be a useful tool to study ABA signaling.
Molecular Evolution of Receptor-Like Kinase Genes in Hexaploid Wheat. Independent Evolution of Orthologs after Polyploidization and Mechanisms of Local Rearrangements at Paralogous Loci
Authors: Feuillet Catherine , Penger Anja , Gellner Klaus , Mast Austin , Keller Beat
Published: July 2002

Hexaploid wheat is a young polyploid species and represents a good model to study mechanisms of gene evolution after polyploidization. Recent studies at the scale of the whole genome have suggested rapid genomic changes after polyploidization but so far the rearrangements that have occurred in terms of gene content and organization have not been analyzed at the microlevel in wheat. Here, we have isolated members of a receptor kinase (Lrk) gene family in hexaploid and diploid wheat, Aegilops tauschii, and barley (Hordeum vulgare). Phylogenetic analysis has allowed us to establish evolutionary relationships (orthology versus paralogy) between the different members of this gene family in wheat as well as with Lrk genes from barley. It also demonstrated that the sequences of the homoeologous Lrk genes evolved independently after polyploidization. In addition, we found evidence for gene loss during the evolution of wheat and barley. Analysis of large genomic fragments isolated from nonorthologous Lrkloci showed a high conservation of the gene content and gene organization at these loci on the homoeologous group 1 chromosomes of wheat and barley. Finally, sequence comparison of two paralogous fragments of chromosome 1B showed a large number of local events (sequence duplications, deletions, and insertions), which reveal rearrangements and mechanisms for genome enlargement at the microlevel.
Maize Non-Photosynthetic Ferredoxin Precursor Is Mis-Sorted to the Intermembrane Space of Chloroplasts in the Presence of Light
Authors: Hirohashi Toshiya , Hase Toshiharu , Nakai Masato
Published: July 2002

Preprotein translocation across the outer and inner envelope membranes of chloroplasts is an energy-dependent process requiring ATP hydrolysis. Several precursor proteins analyzed so far have been found to be imported into isolated chloroplasts equally well in the dark in the presence of ATP as in the light where ATP is supplied by photophosphorylation in the chloroplasts themselves. We demonstrate here that precursors of two maize (Zea mays L. cv Golden Cross Bantam) ferredoxin isoproteins, pFdI and pFdIII, show distinct characteristics of import into maize chloroplasts. pFdI, a photosynthetic ferredoxin precursor, was efficiently imported into the stroma of isolated maize chloroplasts both in the light and in the dark. In contrast pFdIII, a non-photosynthetic ferredoxin precursor, was mostly mis-sorted to the intermembrane space of chloroplastic envelopes as an unprocessed precursor form in the light but was efficiently imported into the stroma and processed to its mature form in the dark. The mis-sorted pFdIII, which accumulated in the intermembrane space in the light, could not undergo subsequent import into the stroma in the dark, even in the presence of ATP. However, when the mis-sorted pFdIII was recovered and used for a separate import reaction, pFdIII was capable of import into the chloroplasts in the dark. pFNRII, a ferredoxin-NADP+ reductase isoprotein precursor, showed import characteristics similar to those of pFdIII. Moreover, pFdIII exhibited similar import characteristics with chloroplasts isolated from wheat (Pennisetum americanum) and pea (Pisum sativum cv Alaska). These findings suggest that the translocation of precursor proteins across the envelope membranes of chloroplasts may involve substrate-dependent light-regulated mechanisms.
New techniques for indexing:N-TREORinEXPO
Authors: Altomare Angela , Giacovazzo Carmelo , Guagliardi Antonietta , Moliterni Anna Grazia Giuseppina , Rizzi Rosanna , Werner Per-Erik
Published: July 2002

Indexing of a powder diffraction pattern is still a critical point in procedures aiming at solving crystal structures from powder data. New code has been associated to the programTREOR90 in order to define an efficient peak search procedure, to modify the crystallographic decisions coded intoTREOR90 to make it more exhaustive, to refine the selected unit cell automatically, and to make the entire procedure user friendly,viaa graphical interface. The new program, calledN-TREOR, has been integrated into the packageEXPOto create a suite of programs able to provide a structural model from the analysis of the experimental pattern.N-TREORis also available as a stand-alone program.
A structural study of amorphous Fe4.7Co70.3Si15B10
Authors: Williams D. E. G. , Fujimori H. , Brown D. S.
Published: July 2002

X-ray diffraction data obtained by scattering Mo Kα radiation from Fe4.7Co70.3Si15B10 in an as-received and an annealed state are analysed to show that the average number of nearest neighbours in the alloy is 12.5±0.4 atoms, in both states. The alloy does not appear to contain clusters and the effect of the annealing process used is to reduce density fluctuations by a factor of about 0.7.
Crystal data for benzofuroin
Authors: Durruthy O. , Fajardo F. , Pomes R.
Published: July 2002

Benzofuroin crystal data were obtained from X-ray powder diffraction patterns. Benzofuroin, C12H10O3, is monoclinic P21/c, with unit-cell parameters a = 10.672 (3), b = 16.521 (4), c = 5.586 (1) Å and γ = 110.45 (3)°, V= 922.8 (10) Å3, Z = 4, Dx
= 1.45 Mgm−3.
Dislocations in energetic materials. 2. Characterization of the growth-induced dislocation structure of pentaerythritol tetranitrate (PETN)
Authors: Halfpenny P. J. , Roberts K. J. , Sherwood J. N.
Published: July 2002

The predominant dislocation types in crystals of pentaerythritol tetranitrate (PETN) grown from solution have been observed and characterized using transmission X-ray topography. The dislocation characterization, carried out by contrast variations, was aided and simplified by comparison of observed dislocation line directions with those calculated from the theory of preferred line directions of Klapper [Habilitationsschrift (1975). RWTH, Aachen]. With few exceptions, the dislocations observed were induced during growth. Eight different types were identified comprising all possible Burgers vectors up to and including (111). Of these, one was pure edge, the remainder being of mixed character. The relative frequency of occurrence of the dislocation types is discussed, together with factors influencing dislocation contrast and characterization.
Determination of thermal-motion parameters using energy-dispersive powder diffraction
Authors: Honkimäki V. , Suortti P.
Published: July 2002

An intrinsic Ge detector is used to analyze the energy spectrum of a well collimated X-ray beam of white radiation diffracted from powder samples of Al, Mg and Ti. Two spectra on each sample are measured at scattering angles where reflections hkl and 2h
′ 2k
′ 2l occur at the same energies. The Bragg reflections are separated by fitting a model for the different components of scattering to the total spectrum. The thermal-motion parameter B is determined from the intensity ratio of several pairs of reflections. Most of the uncertainties due to a non-ideal sample or errors in the experimental parameters cancel out in the expression for B. The values of B are 0.86 (2) Å2 for Al, Ba
= 1.29 (8) Å2 and Bc
= 1.60 (9) Å2 for Mg and Ba
= 0.63 (4) Å2 and Bc
= 0.73 (7) Å2 for Ti, where Ba
is for directions perpendicular to the c axis and Bc
for the direction of the c axis. The results are in agreement with published values of the thermal-motion parameters.
A simple device for increasing the accessibility of reciprocal space in low-temperature area-detector experiments
Authors: Pressprich M. R. , Fransen B.-J. , Darovsky A. , Coppens P.
Published: July 2002

A device is described that allows collection of oscillation method data in two different crystal orientations, without remounting of the crystal. Because of its small size, the device can be inserted into a cryostat chamber, and used for low-temperature data collection with area detectors.
Improved Signal-to-Background Ratio in Small-Angle X-ray Scattering Experiments with Synchrotron Radiation using an Evacuated Cell for Solutions
Authors: Dubuisson J.-M. , Decamps T. , Vachette P.
Published: July 2002

An evacuated, temperature-controlled cell has been built for use on the small-angle X-ray scattering instrument D24 at the synchrotron radiation facility LURE. The sample is placed in a quartz capillary sealed in a stainless-steel holder using a vacuum-tight glue. Several O rings provide a vacuum path upstream and downstream from the cell, so that the X-ray beam only meets the capillary walls and the solution under study between the slits and the beam stop, while the sample is maintained under atmospheric pressure. The cell temperature is controlled via a water circulation through a copper sheath in tight contact with the steel holder. The use of this cell results in a marked reduction of the background, as observed in two series of parallel experiments using a conventional cell and this evacuated cell. The decrease ranges from a factor of 2 at s 1 values larger than 0.008 Å−1 to more than 15 at s = 0.00116 Å−1, where s is the modulus of the scattering vector (s = 2sin θ/λ, 2θ is the scattering angle and λ is the wavelength of the X-rays).
Synchrotron Powder Diffraction using Imaging Plates: Crystal Structure Determination and Rietveld Refinement
Authors: Norby P.
Published: July 2002

The combination of intense X-ray synchrotron radiation and an imaging-plate area detector makes it possible to extract real-time structural information using Rietveld refinement of individual time slices. Powder diffraction data from capillary samples were collected using a flat imaging plate mounted perpendicular to, or at an oblique angle to, the incoming beam. Owing to the geometry of the experiments, several factors must be taken into account when Rietveld refinement of powder diffraction data obtained using a flat imaging plate is performed: (i) nonequal step sizes are obtained when the diffraction profiles are extracted; (ii) the refined zero-point correction is different from that for conventional diffraction geometry; (iii) the sample-detector distance is not constant, requiring a modified geometric term in the Lorentz factor; (iv) the geometric contribution to the instrumental resolution function must be considered. The geometric factors have been derived and are discussed. The Rietveld program XRS-82 and the profile extraction program ALLHKL have been modified to allow flat imaging-plate powder diffraction data to be refined. The Rietveld refinement of powder diffraction data of α-quartz collected using a 30 s exposure is presented. LaB6 powder diffraction data were collected using various settings. The profile variation with angle and the resolution function are described. Data were collected up to sin θ/λ = 1.29 Å−1 (d values down to 0.39 Å) using high energy and with the imaging plate inclined at an angle to the incoming beam.
Structure of NaCd2: an alternative path to a trial structure
Authors: Bergman G.
Published: July 2002

A new derivation of a trial structure of the NaCd2 compound is described. It is based on the application of the stochastic method in a form which is particularly useful in the derivation of trial structures of intermetallic compounds of high crystal symmetry for which the radius ratios of the component metals are of the appropriate magnitudes. In this form the initial assumption is made that the structure is tetrahedrally close-packed and that the coordination polyhedra are all the usual with coordination numbers 12, 14, 15 and 16, respectively. These restrictions are first invoked in the search for the correct structural arrangements along the symmetry axes. Only those arrangements are considered which have small packing strains along these axes when calculated using the metallic radii for coordination number 12.
Neutron and X-ray diffuse scattering of calcium-stabilized zirconia
Authors: Proffen Th. , Neder R. B. , Frey F.
Published: July 2002

The defect structure of calcium-stabilized zirconia (CSZ) is described in terms of a correlated distribution of microdomains within the cubic matrix of CSZ. The defect structure consists of two types of defects: microdomains based on a single oxygen vacancy with relaxed neighbouring ions and microdomains based on a pair of oxygen vacancies separated by 3 1/2/2a along <111>. The combined evaluation of neutron and X-ray data shows that the previously published structure of the single vacancy domain has to be modified: All cations next to the oxygen vacancy are most likely zirconium. This modified model leads to good agreement between observed and calculated neutron and X-ray diffraction patterns.
Interesting conformational and substitutional disorder in the crystal structures of three homologous crowns
Authors: Böcskei Zs. , Simon K. , Németh V. , Ágai B. , Tőke L.
Published: July 2002

The structures of three members of a homologous family of diphenylamine-containing crowns, 2-chloro-6,7,9,10-tetrahydro-16H-dibenzo[b,k][1,4,7,10]monoazatrioxacyclododecine (NAI), 2-chloro-6,7,9,10,12,13-hexahydro-19H-dibenzo[b,n][1,4,7,10,13]monoazatetraoxacyclopentadecine (NAII), 2-chloro-6,7,9,10,12,13,15,16-octahydro-22H-dibenzo[b,q][1,4,7,10,13,16]monoazapentaoxacyclooctadecine] (NAIII), are reported, compared and trends are established. The largest crown (an 18-crown-6-type) presents an ability to form a molecular compound with water molecules spontaneously. The propeller-like conformational behaviour of the two phenyl rings leads to the presence of two chiral conformers in the unit cell of the crystals. Additionally, due to the conformationally non-equivalent role of the two phenyl rings, the chlorine substitution leads to two further species, resulting in four different conformers in each crystal structure. The presence of so many species in one crystal generates an interesting type of disorder in two of the three cases.
A synchrotron X-ray study of the electron density in C-type rare earth oxides
Authors: Maslen E. N. , Streltsov V. A. , Ishizawa N.
Published: July 2002

Structure factors for small synthetic crystals of the C-type rare earth (RE) sesquioxides Y2O3, Dy2O3 and Ho2O3 were measured with focused λ = 0.7000 (2) Å, synchrotron X-radiation, and for Ho2O3 were re-measured with an MoKα (λ = 0.71073 Å) source. Approximate symmetry in the deformation electron density (Δρ) around a RE atom with pseudo-octahedral O coordination matches the cation geometry. Interactions between heavy metal atoms have a pronounced effect on the Δρ map. The electron-density symmetry around a second RE atom is also perturbed significantly by cation–anion interactions. The compounds magnetic properties reflect this complexity. Space group Ia{\bar 3}, cubic, Z = 16, T = 293 K: Y2O3, Mr
= 225.82, a = 10.5981 (7) Å, V = 1190.4 (2) Å3, Dx
= 5.040 Mg m−3, μ
0.7 = 37.01 mm−1, F(000) = 1632, R = 0.067, wR = 0.067, S = 9.0 (2) for 1098 unique reflections; Dy2O3, Mr
= 373.00, a = 10.6706 (7) Å, V = 1215.0 (2) Å3, Dx
= 8.156 Mg m−3, μ
0.7 = 44.84 mm−1, F(000) = 2496, R = 0.056, wR = 0.051, S = 7.5 (2) for 1113 unique reflections; Ho2O3, Mr
= 377.86, a = 10.606 (2) Å, V = 1193.0 (7) Å3, Dx
= 8.415 Mg m−3, μ
0.7 = 48.51 mm−1
F(000) = 2528, R = 0.072, wR = 0.045, S = 9.2 (2) for 1098 unique reflections of the synchrotron data set.
Cation disorder in ferroelectric PbBi2Nb2O9
Authors: Srikanth V. , Idink H. , White W. B. , Subbarao E. C. , Rajagopal H. , Sequeira A.
Published: July 2002

The ferroelectric Curie temperature, Tc
, of PbBi2Nb2O9 was found to shift from 833 K in samples slowly cooled from 1373 K to Tc
's up to 883 K when the samples were quenched from various temperatures in the range 973–1373 K. The variation of Tc
with heat treatment was fully reversible. Extra Raman modes appear and the width of some Raman bands change as a function of heat treatment. These results are interpreted in terms of cation order–disorder involving the Pb2+ and Bi3+ ions in the perovskite units and the Bi2O2 layer. Neutron Rietveld analyses of the structures (orthorhombic, A21
am, Z = 4, λ = 1.216) indicate a possible change in cationic order–disorder, with Pb2+ ions preferentially occupying the perovskite A-sites to the extent of 91 (7) and 80 (7)%, respectively, in the quenched and slowly cooled samples.
Structures of L-valyl-L-glutamine and L-glutamyl-L-valine
Authors: Görbitz C. H. , Backe P. H.
Published: July 2002

L-Val-L-Gln crystallizes in the orthorhombic space group P21212 with a = 16.419 (3), b = 15.309 (3) and c = 4.708 (1) Å. The final wR(F
o
2) is 0.100 for 2044 independent reflections, R(Fo
) = 0.050 for 1475 reflections with I > 2.0σ(I). L-Glu-L-Val crystallizes in the monoclinic space group P21 with a = 6.487 (2), b = 5.505 (2), c = 16.741 (4) Å and β = 97.22 (2)°. The final wR(F
F
o
2) is 0.111 for 1920 independent reflections, R(Fo
) = 0.047 for 1576 reflections with I > 2.0σ(I). Molecular geometries are normal, except for a unique eclipsed orientation of the charged amino group of L-Glu-L-Val. Dipeptides with a N-terminal hydrophobic residue and C-terminal hydrophilic residue are shown to have crystal packing patterns fundamentally different from those of dipeptides with the same types of residues in reversed order. Accordingly, the structure of L-Val-L-Glu [Eggleston (1984). Acta Cryst. C40, 1250 –1252] is rather similar to L-Val-L-Gln, but different from its retroanalogue L-Glu-L-Val. Nevertheless, the pairing of hydrogen-bond donors and acceptors is the same for L-Val-L-Glu and L-Glu-L-Val, indicating very distinct hydrogen-bonding preferences. This is the first demonstration of such a coincidence among dipeptide structures. The differences between L-Val-L-Glu and L-Val-L-Gln structures stem from modifications of the molecular geometry and cell parameters due to the formation of an additional hydrogen bond from the extra donor in the L-Gln side chain.
Application of Wallach's Rule in a Comparison of the X-ray Crystal Structures of the Racemate and the (S) Enantiomer of (1-Hydroxy-3-phenyl-2-propenyl) Dimethylphosphonate
Authors: Blazis V. J. , Koeller K. J. , Rath N. P. , Spilling C. D.
Published: July 2002

The crystal structures of the racemate and the (S) enantiomer of (1-hydroxy-3-phenyl-2-propenyl) dimethylphosphonate, C11H15O4P, were determined by X-ray diffraction. The crystal density of the racemate was found to be 6.2% greater than the crystal density of the (S) enantiomer. In both crystal structures the molecules form chains by hydrogen bonding between the OH of one molecule and the P=O of another. Observed differences in atomic displacement between the two structures are discussed in view of the C—H...O interactions.
Chain, Sheet and Framework Structures in the Adducts of Phenylphosphonic Acid with 4,4'-Bipyridyl (1/1), Piperazine (2/1) and 1,4-Diazabicyclo[2.2.2]octane (2/1)
Authors: Ferguson G. , Glidewell C. , Gregson R. M. , Meehan P. R.
Published: July 2002

Phenylphosphonic acid–4,4′-bipyridyl (1/1), (1), C6H7O3P.C10H8N2, triclinic, P1¯, a = 6.9026 (8), b = 9.7086 (9), c = 12.201 (2) Å, α = 77.138 (9), β = 74.345 (10), γ = 75.477 (8)°, with Z = 2, is a salt, C10H9N2
+.[C6H5PO2(OH)]−, containing singly protonated 4,4′-bipyridyl cations: the cations and anions are linked by N—H...O and C—H...O hydrogen bonds in an R^{2}_{2}(7) motif and these aggregates are linked into centrosymmetric R^{2}_{2}(8) dimers by O—H...O hydrogen bonds; the dimer units are linked into chains by C—H...O hydrogen bonds. Phenylphosphonic acid–piperazine (2/1), (C6H7O3P)2.C4H10N2 (2), monoclinic, P21/n, a = 6.0042 (9), b = 19.746 (3), c = 8.651 (2) Å, β = 105.63 (2)°, with Z = 2, is a salt, C4H12N2
2+. [{C6H5PO2(OH)}−]2, containing doubly protonated piperazine: the anions are linked by O—H...O hydrogen bonds into centrosymmetric R^{2}_{2}(8) dimers and these dimers are linked to the centrosymmetric cations by N—H...O hydrogen bonds: each cation is hydrogen-bonded to four different anion dimers and each anion dimer is hydrogen-bonded to four different cations; the overall structure consists of two-dimensional sheets built from R^{4}_{6}(16) and R^{4}_{4}(18) rings. Phenylphosphonic acid–1,4-diazabicyclo[2.2.2]octane (2/1), (3), (C6H7O3P)2.C6H12N2, monoclinic, P21/n, a = 6.3607 (3), b = 21.8300 (11), c = 14.5965 (9) Å, β = 92.558 (6)°, with Z = 4, is a salt in which one nitrogen of the diamine is fully protonated and the other is partially protonated: the anionic components are linked into C(4) chains by O—H...O hydrogen bonds, and these chains are cross-linked via the diamines by means of N—H...O and O—H...N hydrogen bonds. The resulting sheets built from R^{8}_{8}(34) rings are linked by C—H...O hydrogen bonds into a three-dimensional framework.
Structural Analysis of Cs2HgBr4 in Normal, Incommensurate and Twinned Phases
Authors: Pinheiro C. B. , Jório A. , Pimenta M. A. , Speziali N. L.
Published: July 2002

X-ray diffraction and Raman spectroscopy experiments have been used to investigate different phases of Cs2HgBr4, dicesium mercury tetrabromide, from room temperature to 213 K. Structural analyses have shown that the crystal could be described, in the normal and in the incommensurate phases, both by ordered and disordered models, but the latter gave more consistent results. Raman results corroborate the descriptions based on X-ray analysis; the presence of an extra peak, which according to group theory should be forbidden in an ordered structure, indicates the lack of local symmetry and was associated with an orientational disorder of [HgBr4]2− tetrahedra. In the transition from the incommensurate to the commensurate phase a multi-soliton behavior was observed. The Cs2HgBr4 crystal in the low-temperature commensurate phase is composed of two types of ordered pseudomerohedral twinned domains.
Charge Density Studies Using CCD Detectors: Oxalic Acid at 100 K Revisited
Authors: Martin A. , Pinkerton A. A.
Published: July 2002

The charge density of oxalic acid dihydrate has been redetermined from 100 K X-ray diffraction data using a SMART CCD diffractometer. The quality of the data has been carefully analyzed and shown to be at least as good as that obtained using a point detector. The positional and thermal parameters obtained from least-squares refinement and the main features of difference density maps are comparable with those obtained by a number of laboratories as part of the IUCr electron density project. In particular, the comparison study has been completed by two multipole refinements carried out in parallel using both the current data set and that of a previous study [Stevens & Coppens (1980). Acta Cryst. B36, 1864–1876].
Disordered Structure of Polymeric Bismuth Tribenzoate, [Bi(C6H5COO)3]
n
Authors: Rae A. D. , Gainsford G. J. , Kemmitt T.
Published: July 2002

Bismuth tribenzoate, Bi(C6H5COO)3, was prepared by ligand exchange of bismuth triacetate with benzoic acid. A 1:1 disordered structure of P21/m symmetry, a = 7.858 (3), b = 14.442 (2), c = 16.807 (3) Å, β = 92.26 (2)°, V = 1906 (1) Å3, Z = 4, consists of polymeric chains parallel to the a axis and can be related to an ideally ordered structure of B21/a symmetry with a′ = 2a, b′ = b and c′ = 2c. This B-centred structure can itself be described as a modulation of an idealized parent structure of Pnma symmetry. The disorder is rationalized in terms of the pseudo-symmetry that relates the two formula units of Bi(C6H5COO)3 in the asymmetric unit of B21/a. In the polymeric chain each Bi atom is nominally nine-coordinate, with widely varying bond lengths arranged in a very asymmetric manner. The polymeric chain is created by each bismuth being chelated to three benzoate ligands. Each such ligand also has one of its O atoms bridging an adjacent Bi atom so that three bridging O atoms link adjacent bismuths. Apparent valences are consistent with expected values for all Bi and O atoms. A final value of 0.0454 was obtained for R(F) using the 1813 independent reflections (out of 2839) with I(h) > 3σ[I(h)] to refine 185 parameters describing 56 non-H atoms.
Disorder in the Crystal Structure of Cs2HgCl4 Studied by the Maximum Entropy Method
Authors: Bagautdinov B. , Luedecke J. , Schneider M. , van Smaalen S.
Published: July 2002

The disorder at room temperature in crystalline Cs2HgCl4, dicaesium mercury tetrachloride, is studied by the Maximum Entropy Method (MEM). X-ray scattering up to θ = 30° (Mo Kα radiation) revealed the orthorhombic space group Pnma, with a = 9.8136 (9), b = 7.6018 (6) and c = 13.4201 (9) Å. Refinement converged to R = 0.032 for 1046 observed unique reflections. The structure model involves unphysically short distances between Cs and Cl atoms. The MEM applied to the Bragg intensity data shows that both Cs(1) and Cl(1) exhibit strong anharmonic displacements out of the mirror plane. The relation is shown between these displacements, the soft phonons at room temperature and the static modulations at low temperatures of several A
2
BX
4 compounds. A comparision of the MEM with a refinement of anharmonic displacements parameters shows the MEM to be less affected by unwanted correlations between parameters than the refinement of anharmonic displacement parameters.
Self-assembly of NH-pyrazoles via intermolecular N—H...N hydrogen bonds
Authors: Bertolasi Valerio , Gilli Paola , Ferretti Valeria , Gilli Gastone , Fernàndez-Castaño Cristina
Published: July 2002

The crystal structures of two NH-pyrazole derivatives forming intermolecular N—H...N hydrogen bonds are reported: 5-methyl-4-(3-methylpyrazol-5-yl)pyrazol-3-ol, C8H10N4O (P1), and 3-methyl-5-dihydro-1H-naphtho[1,2-d]pyrazole hemihydrochloride, C12H12N2.-C12H13N_{2}^{+}.Cl− (P2). 26 other structures are surveyed in order to obtain a deeper insight into the ways NH-pyrazoles self-assemble by means of intermolecular N—H...N hydrogen bonds in molecular crystals. A limited number of compounds form chains or dimers via homonuclear N+—H...N positive-charge-assisted hydrogen bonds, typical of proton sponges, which can be remarkably short [e.g. N...N 2.714 (3), N—H 1.09 (3), H...N 1.63 (3) Å, N—H...N 169 (3)° in (P2)]. Most pyrazoles, however, pack via neutral N—H...N bonds which are formally assisted by resonance (resonance-assisted hydrogen bond, RAHB) through the ...N=C—C=C—NH... iminoenamine fragment, contained in the ring, giving rise to dimers, trimers, tetramers and infinite chains of pyrazole molecules. Surprisingly, the resonance does not appear to shorten the N—H...N bond with respect to the accepted mean value N...N 2.97 (10) Å for non-resonant N—H...N bonds. It is shown that this is due to the internal π-delocalization of the pyrazole ring, which can be hardly increased by the hydrogen-bond interaction, except in symmetrically 3,5-substituted pyrazoles which display N...N distances as short as 2.82 Å, identical C—C and C—N distances in the two halves of the pyrazole molecule, and typical phenomena of N—H...N dynamical proton disorder, detectable by 15N-CP/MAS solid-state NMR.
Visualization and characterization of non-covalent networks in molecular crystals: automated assignment of graph-set descriptors for asymmetric molecules
Authors: Motherwell W. D. Samuel , Shields Gregory P. , Allen Frank H.
Published: July 2002

A method of visualizing intermolecular networks (for example, hydrogen-bonded networks) in the crystalline state has been developed, based on the concept of link atoms, i.e. those atoms deemed to be in contact with each unique molecule or ion in the crystal chemical unit (CCU). Extension of a structure using each of these primary links can be achieved, enabling the generation and investigation of extended networks. Algorithms have been developed for the automatic assignment of graph-set notation for patterns up to second level, i.e. those involving one or two crystallographically independent non-covalent bonds, in the absence of internal crystallographic symmetry in the unique molecules of the CCU. The self, ring, chain and discrete motifs may be displayed by highlighting the atoms and bonds comprising the pattern. These methodologies have been implemented in the Cambridge Structural Database program PLUTO.
A simple method to calculate the expectation values of the linear momentum operator p in molecules
Authors: Roux M.
Published: July 2002

The proportionality between the expectation values (p") and the Slater effective parameters to the same power, αn
, have been used with the method of Eisenberger & Marra [Phys. Rev. Lett. ( 1971), 27, 1413-1416] in order to obtain localized expectation values of the linear momentum operator. A compilation of (p2>/2 and of (p
-1)/2 is presented for a set of AB and AH bonds, H is the hydrogen atom, while A and B vary from lithium to fluorine. A correction introducing the internuclear distances RAB
is proposed, which increases the accuracy of the results. For a given molecule it is sufficient to sum the bond terms with or without the R correction, using the Lewis localization technique. This method is useful for large molecules.
Crystallization of the catalytic domain of Clostridium cellulolyticum CeIF cellulase in the presence of a newly synthesized cellulase inhibitor
Authors: Reverbel-Leroy Corinne , Parsiegla Goetz , Moreau Vincent , Juy Michel , Tardif Chantal , Driguez Hugues , Bélaich Jean-Pierre , Haser Richard
Published: July 2002

The catalytic domain of the CeIF processive endocellulase, a family 48 glycosyl hydrolase from Clostridium cellulolyticum has been crystallized in the presence of a newly synthesized inhibitor (methyl 4-S-β-cellobiosyl-4-thio-β-cellobioside), by vapour diffusion, using PEG as a precipitant. The protein crystallizes in the orthorhombic P212121 space group and diffracts to a resolution of 2.0 Å. The unit-cell parameters are a = 61.4, b = 84.5, c = 121.9 Å.
Molecular Replacement Using DNA Helical Symmetry
Authors: Baikalov Igor , Dickerson Richard E.
Published: July 2002

The efficiency of molecular-replacement methods in the structure analysis of B-DNA is markedly increased if a knowledge of the structural properties and helical symmetry of B-DNA is incorporated into molecular-replacement procedures. The separation of the most significant or most robust parameters, such as the location of helices in the unit cell, from the less well defined parameters, such as rotation around the helix axis, further improves the reliability of molecular replacement and avoids frameshift errors in the positioning of the model. This approach has been applied successfully to solve novel structures of four B-DNA decamers in various space groups.
Structure Analysis of Two CheY Mutants: Importance of the Hydrogen-Bond Contribution to Protein Stability
Authors: Wilcock Deborah , Pisabarro María Teresa , López-Hernandez Eva , Serrano Luis , Coll Miquel
Published: July 2002

The crystal structures of two double mutants (F14N/V21T and F14N/V86T) of the signal transduction protein CheY have been determined to a resolution of 2.4 and 2.2 Å, respectively. The structures were solved by molecular replacement and refined to final R values of 18.4 and 19.2%, respectively. Together with urea-denaturation experiments the structures have been used to analyse the effects of mutations where hydrophobic residues are replaced by residues capable of establishing hydrogen bonds. The large increase in stabilization (−12.1 kJ mol−1) of the mutation Phe14Asn arises from two factors: a reverse hydrophobic effect and the formation of a good N-cap at α-helix 1. In addition, a forward–backward hydrogen-bonding pattern, resembling an N-capping box and involving Asn14 and Arg18, has been found. The two Val to Thr mutations at the hydrophobic core have different thermodynamic effects: the mutation Val21Thr does not affect the stability of the protein while the mutation Val86Thr causes a small destabilization of 1.7 kJ mol−1. At site 21 a backward side-chain-to-backbone hydrogen bond is formed inside α-helix 1 with the carbonyl O atom of the i − 4 residue without movement of the mutated side chain. The destabilizing effect of introducing a polar group in the core is efficiently compensated for by the formation of an extra hydrogen bond. At site 86 the new Oγ atom escapes from the hydrophobic environment by a χ1 rotation into an adjacent hydrophilic cavity to form a new hydrogen bond. In this case the isosteric Val to Thr substitution is disruptive but the loss in stabilization energy is partly compensated by the formation of a hydrogen bond. The two crystal structures described in this work underline the significance of the hydrogen-bond component to protein stability.
Ab initio solution and refinement of two high-potential iron protein structures at atomic resolution
Authors: Parisini Emilio , Capozzi Francesco , Lubini Paolo , Lamzin Victor , Luchinat Claudio , Sheldrick George M.
Published: July 2002

The crystal structure of the reduced high-potential iron protein (HiPIP) from Chromatium vinosum has been redetermined in a new orthorhombic crystal modification, and the structure of its H42Q mutant has been determined in orthorhombic (H42Q-1) and cubic (H42Q-2) modifications. The first two were solved by ab initio direct methods using data collected to atomic resolution (1.20 and 0.93 Å, respectively). The recombinant wild type (rc-WT) with two HiPIP molecules in the asymmetric unit has 1264 protein atoms and 335 solvent sites, and is the second largest structure reported so far that has been solved by pure direct methods. The solutions were obtained in a fully automated way and included more than 80% of the protein atoms. Restrained anisotropic refinement for rc-WT and H42Q-1 converged to R_1=\sum\big||F_o|-|F_c|\big|\big/\sum|F_o| of 12.0 and 13.6%, respectively [data with I>2\sigma(I)], and 12.8 and 15.5% (all data). H42Q-2 contains two molecules in the asymmetric unit and diffracted only to 2.6 Å. In both molecules of rc-WT and in the single unique molecule of H42Q-1 the [Fe4S4]2+ cluster dimensions are very similar and show a characteristic tetragonal distortion with four short Fe—S bonds along four approximately parallel cube edges, and eight long Fe—S bonds. The unique protein molecules in H42Q-2 and rc-WT are also very similar in other respects, except for the hydrogen bonding around the mutated residue that is at the surface of the protein, supporting the hypothesis that the difference in redox potentials at lower pH values is caused primarily by differences in the charge distribution near the surface of the protein rather than by structural differences in the cluster region.
Cryocrystallography of a Kunitz-type serine protease inhibitor: the 90 K structure of winged bean chymotrypsin inhibitor (WCI) at 2.13 Å resolution
Authors: Ravichandran S. , Sen U. , Chakrabarti C. , Dattagupta J. K.
Published: July 2002

The crystal structure of a Kunitz-type double-headed α-chymotrypsin inhibitor from winged bean seeds has been refined at 2.13 Å resolution using data collected from cryo-cooled (90 K) crystals which belong to the hexagonal space group P6122 with unit-cell parameters a = b = 60.84, c = 207.91 Å. The volume of the unit cell is reduced by 5.3% on cooling. The refinement converged to an R value of 20.0% (R
free = 25.8%) for 11100 unique reflections and the model shows good stereochemistry, with r.m.s. deviations from ideal values for bond lengths and bond angles of 0.011 Å and 1.4°, respectively. The structural architecture of the protein consists of 12 antiparallel β-strands joined in the form of a characteristic β-trefoil fold, with the two reactive-site regions, Asn38–Leu43 and Gln63–Phe68, situated on two external loops. Although the overall protein fold is the same as that of the room-temperature model, some conformational changes are observed in the loop regions and in the side chains of a few surface residues. A total of 176 ordered water molecules and five sulfate ions are included in the model.
Optics systems for the home laboratory: caveat emptor
Authors: Yang Cheng , Courville Adam , Ferrara Joseph D.
Published: July 2002

A careful and detailed evaluation of different multilayer optics (Osmic Cross-coupled Max-Flux Optics and Osmic Confocal Max-Flux Optics) compared with MSC/Yale Total-Reflection Mirrors has been completed. This report provides a detailed comparison of usable flux, spectral purity, divergence, beam profile and data quality for these systems. The most striking results have been obtained using either the Osmic #4 or #7 Confocal Max-Flux Optic, which were designed for 0. l and 0.2 mm focal spots, respectively, in conjunction with a 0.3 mm focal spot. These optic configurations provide a 5.8-fold and 8.2-fold increase in flux through a 0.2 mm aperture, respectively, compared with the MSC/Yale Mirrors.