Flexibility revealed by the 1.85 angstrom crystal structure of the beta sliding-clamp subunit of Escherichia coli DNA polymerase III

The beta subunit of the Escherichia coli replicative DNA polymerase III holoenzyme is the sliding clamp that interacts with the alpha (polymerase) subunit to maintain the high processivity of the enzyme. The beta protein is a ring-shaped dimer of 40.6 kDa subunits whose structure has previously been determined at a resolution of 2.5 Angstrom [Kong et al. (1992), Cell, 69, 425-437]. Here, the construction of a new plasmid that directs overproduction of beta to very high levels and a simple procedure for large-scale purification of the protein are described. Crystals grown under slightly modified conditions diffracted to beyond 1.9 Angstrom at 100 K at a synchrotron source. The structure of the beta dimer solved at 1.85 Angstrom resolution shows some differences from that reported previously. In particular, it was possible at this resolution to identify residues that differed in position between the two subunits in the unit cell; side chains of these and some other residues were found to occupy alternate conformations. This suggests that these residues are likely to be relatively mobile in solution. Some implications of this flexibility for the function of beta are discussed.

Expression, purification, crystallization, and NMR studies of the helicase interaction domain of Escherichia coli DnaG primase

in Escherichia coli, the DnaG primase is the RNA polymerase that synthesizes RNA primers at replication forks. It is composed of three domains, a small N-terminal zinc-binding domain, a larger central domain responsible for RNA synthesis, and a C-terminal domain comprising residues 434-581 [DnaG(434-581)] that interact with the hexameric DnaB helicase. Presumably because of this interaction, it had not been possible previously to express the C-terminal domain in a stably transformed E coli strain. This problem was overcome by expression of DnaG(434-581) under control of tandem bacteriophage gimel-promoters, and the protein was purified in yields of 4-6 mg/L of culture and studied by NMR. A TOCSY spectrum of a 2 mM solution of the protein at pH 7.0, indicated that its structured core comprises residues 444-579. This was consistent with sequence conservation among most-closely related primases. Linewidths in a NOESY spectrum of a 0.5 mM sample in 10 mM phosphate, pH 6.05, 0.1 M NaCl, recorded at 36 degreesC, indicated the protein to be monomeric. Crystals of selenomethionine-substituted DnaG(434-581) obtained by the hanging-drop vapor-diffusion method were body-centered tetragonal, space group I4(1)22, with unit cell parameters a = b 142.2 Angstrom, c = 192.1 Angstrom, and diffracted beyond 2.7 Angstrom resolution with synchrotron radiation. (C) 2003 Elsevier Inc. All rights reserved.

Surface modification of metals by calcium carbonate thin films on a layer-by-layer polyelectrolyte matrix

A multilayer organic film containing poly(acrylic acid) and chitosan was fabricated on a metallic support by means of the layer-by-layer technique. This film was used as a template for calcium carbonate crystallization and presents two possible binding sites where the nucleation may be initiated, either calcium ions acting as counterions of the polyelectrolyte or those trapped in the template gel network formed by the polyelectrolyte chains. Calcium carbonate formation was carried out by carbon dioxide diffusion, where CO, was generated from ammonium carbonate decomposition. The CaCO3 nanocrystals obtained, formed a dense, homogeneous, and continuous film. Vaterite and calcite CaCO3 crystalline forms were detected. (c) 2007 Elsevier B.V All rights reserved.

Modeling of columnar-to-equiaxed transition in solidified Al-Si alloys

A Cellular-Automaton Finite-Volume-Method (CAFVM) algorithm has been developed, coupling with macroscopic model for heat transfer calculation and microscopic models for nucleation and growth. The solution equations have been solved to determine the time-dependent constitutional undercooling and interface retardation during solidification. The constitutional undercooling is then coupled into the CAFVM algorithm to investigate both the effects of thermal and constitutional undercooling on columnar growth and crystal selection in the columnar zone, and formation of equiaxed crystals in the bulk liquid. The model cannot only simulate microstructures of alloys but also investigates nucleation mechanisms and growth kinetics of alloys solidified with various solute concentrations and solidification morphologies.

The Western Alps from the Jurassic to Oligocene: spatio-temporal constraints and evolutionary reconstructions

Despite extensive research in the last 150 years, the regional tectonic reconstruction of the Western Alps has remained controversial. The curved orogenic belt consists of several ribbon-like continental terranes (Sesia/Austroalpine, Internal Crystalline Massifs, Brianconnais), which are separated by two or more ophiolitic sutures (Piemonte, Valais, Antrona?, Lanzo/ Canavese?). High-pressure (HP) metamorphism of each terrane occurred during distinct orogenic episodes: at similar to65 Ma in the Sesia/Austroalpine, at similar to45 Ma in the Piemonte zone and at similar to35 Ma in the Internal Crystalline Massifs. It is suggested that these events reflect individual accretionary episodes, which together with kinematic indicators and the speed and direction of plate motions, provide constraints for the discussed reconstruction model. The model involves a prolonged orogenic history that took place during relative convergence of Europe and Adria (here considered as a promontory of the African plate). The first accretionary event involved the Sesia/Austroalpine terrane. Final closure of the Piemonte Ocean occurred during the Eocene (similar to45 Ma) and involved ultra-high-pressure (UHP) metamorphism of the Piemonte oceanic crust. Incorporation of the Brianconnais terrane in the accretionary wedge occurred thereafter, possibly during or after subduction of the Valais Ocean in the late Eocene (45-35 Ma). This subduction was terminated at ca. 35 Ma, when the Internal Crystalline Massifs (i.e. the assumed internal parts of the Brianconnais terrane) were buried into great depths and underwent HP and UHP metamorphism. (C) 2004 Elsevier B.V. All rights reserved.

Neoformation of micas in soils surrounding an alkaline-saline lake of Pantanal wetland, Brazil

The mineralogy and origin of micas were investigated in incipient soils surrounding a modem alkaline-saline lake of Nhecolandia, a sub-region of Pantanal wetland. Soils were sampled along a toposequence and analyzed by XRD, TEM-EDS, and ICP-MS. The studied micas, mainly concentrated in a green horizon, are dioctahedral, strongly associated with Fe(3+) and Al, and interstratified with smectite layers. Classification of individual crystals shows that glauconite and Fe-illite are the dominant micas, but one crystal of illite was recognized. Si-rich amorphous materials are associated with small crystallites in the mica-enriched horizon. A recent study shows that water samples from the studied lake and the surrounding water table have high pH, negative Eh, temperatures up to 40 C. high concentration of K. and low concentration of Si(OH)(4). Experimental studies of micas synthesis reported in the literature show that similar water conditions allow for dioctahedral mica crystallization from initial precipitation of amorphous hydroxides. Therefore, water characteristics combined with presence of Si-rich amorphous materials in the mica-enriched horizon suggest that the micas of the study area are neoformed. The alternated origin of illite, glauconite, and Fe-illite mixed-layer minerals probably occurs due to seasonal variations of pH. temperature, and chemical composition of waters in microenvironments, since the changes at this scale are possibly faster and more extreme. (C) 2010 Elsevier B.V. All rights reserved.

Numerical simulation of dendrite growth during solidification

A comprehensive probabilistic model for simulating dendrite morphology and investigating dendritic growth kinetics during solidification has been developed, based on a modified Cellular Automaton (mCA) for microscopic modeling of nucleation, growth of crystals and solute diffusion. The mCA model numerically calculated solute redistribution both in the solid and liquid phases, the curvature of dendrite tips and the growth anisotropy. This modeling takes account of thermal, curvature and solute diffusion effects. Therefore, it can simulate microstructure formation both on the scale of the dendrite tip length. This model was then applied for simulating dendritic solidification of an Al-7%Si alloy. Both directional and equiaxed dendritic growth has been performed to investigate the growth anisotropy and cooling rate on dendrite morphology. Furthermore, the competitive growth and selection of dendritic crystals have also investigated.

Determination of the solution structures of conantokin-G and conantokin-T by CD and NMR spectroscopy

Conantokin-G and conantokin-T are two paralytic polypeptide toxins originally isolated from the venom of the fish-hunting cone snails of the genus Conus. Conantokin-G and conantokin-T are the only naturally occurring peptidic compounds which possess N-methyl-D-aspartate receptor antagonist activity, produced by a selective non-competitive antagonism of polyamine responses, They are also structurally unusual in that they contain a disproportionately large number of acid labile post-translational gamma-carboxyglutamic acid (Gla) residues, Although no precise structural information has previously been published for these peptides, early spectroscopic measurements have indicated that both conantokin-G and conantokin-T form alpha-helical structures, although there is some debate whether the presence of calcium ions is required for these peptides to adopt this fold, We now report a detailed structural study of synthetic conantokin-G and conantokin-T in a range of solution conditions using CD and H-1 NMR spec troscopy. The three-dimensional structures of conantokin-T and conantokin-G were calculated from H-1 NMR-derived distance and dihedral restraints. Both conantokins were found to contain a mixture of alpha- and 3(10) helix, that give rise to curved and straight helical conformers. Conantokin-G requires the presence of divalent cations (Zn2+, Ca2+, Cu2+, Or Mg2+) to form a stable iv-helix, while conantokin-T adopts a stable alpha-helical structure in aqueous conditions, in the presence or absence of divalent cations (Zn2+, Ca2+, Cu2+, Or Mg2+).

Crystal structure of Escherichia coli xanthine phosphoribosyltransferase

Xanthine phosphoribosyltransferase (XPRT; EC 2.4.2.22) from Escherichia coil is a tetrameric enzyme having 152 residues per subunit. XPRT catalyzes the transfer of the phosphoribosyl group from 5-phospho-alpha-D-ribosyl l-pyrophosphate (PRib-PP) to the 6-oxopurine bases guanine, xanthine, and hypoxanthine to form GMP, XMP, and IMP, respectively. Crystals grown in the absence of substrate or product were used to determine the structure of XPRT at a resolution of 1.8 Angstrom by multiple isomorphous replacement. The core structure of XPRT includes a five-stranded parallel B-sheet surrounded by three or-helices, which is similar to that observed in other known phosphoribosyltransferase (PRTase) structures. The XPRT structure also has several interesting features. A glutamine residue in the purine binding site may be responsible for the altered 6-oxopurine base specificity seen in this enzyme compared to other 6-oxopurine PRTases. Also, we observe both a magnesium ion and a sulfate ion bound at the PRib-PP binding site of XPRT. The sulfate ion interacts with Arg-37 which has a cis-peptide conformation, and the magnesium ion interacts with Asp-89, a highly conserved acidic residue in the PRib-PP binding site motif. The XPRT structure also incorporates a feature which has not been observed in other PRTase structures. The C-terminal 12 residues of XPRT adopt an unusual extended conformation and make interactions with a neighboring subunit. The very last residue, Arg-152, could form part of the active site of a symmetry-related subunit in the XPRT tetramer.

Electron paramagnetic resonance of Ni(II) doped tris(ethylenediamine)zinc(II) dinitrate

Variable temperature electron paramagnetic resonance spectra of tris(ethylenediamine)zinc(II) dinitrate single crystals doped with NI(II) have been measured. The host crystal undergoes a trigonal to monoclinic phase transition at 146 K. Above the transition temperature the zero field splitting tensor is axially symmetric with D = -0.831 cm(-1) and below it becomes rhombic with D = -0.785 cm(-1), E = -0.088 cm(-1). The low temperature spectrum is characterised by the pattern repeating every 60 degrees when the crystal is rotated about the high temperature c axis. The analysis shows that the Zn(II) site retains a C-2 symmetry axis and that the distortion away from the D-3 site symmetry observed for high temperatures is small, the principal axes being tilted by 2.6 degrees. This implies that the phase transition involves the flipping of the C-C backbone in one of the ethylenediamine ligands of the complex, resulting in a A delta delta delta to Lambda delta delta lambda type conformational change.

Crystal structure at 1.1 angstrom resolution of alpha-conotoxin PnIB: Comparison with alpha-conotoxins PnIA and GI

Conotoxins are small, cysteine-rich peptides isolated from the venom of Conus spp. of predatory marine snails, which selectively target specific receptors and ion channels critical to the functioning of the neuromuscular system. alpha-Conotoxins PnIA and PnIB are both 16-residue peptides (differing in sequence at only two positions) isolated from the molluscivorous snail Conus pennaceus. In contrast to the muscle-selective alpha-conotoxin GI from Conus geographus, PnIA and PnIB block the neuronal nicotinic acetylcholine receptor (nAChR). Here, we describe the crystal structure of PnIB, solved at a resolution of 1.1 Angstrom and phased using the Shake-and-Bake direct methods program. PnIB crystals are orthorhombic and belong to the space group P2(1)2(1)2(1) with the following unit cell dimensions: a = 14.6 Angstrom, b = 26.1 Angstrom, and c = 29.2 Angstrom. The final refined structure of alpha-conotoxin PnIB includes all 16 residues plus 23 solvent molecules and has an overall R-factor of 14.7% (R-free of 15.9%). The crystal structures of the alpha-conotoxins PnIB and PnIA are solved from different crystal forms, with different solvent contents. Comparison of the structures reveals them to be very similar, showing that the unique backbone and disulfide architecture is not strongly influenced by crystal lattice constraints or solvent interactions. This finding supports the notion that this structural scaffold is a rigid support for the presentation of important functional groups. The structures of PnIB and PnIA differ in their shape and surface charge distribution from that of GI.

Cyclic Fatigue Resistance of Rotary Nickel-Titanium Instruments Submitted to Nitrogen Ion Implantation

Introduction: The aim of this study was to assess cyclic fatigue resistance in rotary nickel-titanium instruments submitted to nitrogen ion implantation by using a custom-made cyclic fatigue testing apparatus. Methods: Thirty K3 files, size #25, taper 0.04, were divided into 3 experimental groups as follows: group A, 12 files exposed to nitrogen ion implantation at a dose of 2.5 x 10(17) ions/cm(2), accelerating voltage of 200 kV, currents of 1 mu A/cm(2), 130 degrees C temperature, and vacuum conditions of 10 x 10(-6) torr for 6 hours; group B, 12 nonimplanted files; and group C, 6 files submitted to thermal annealing for 6 hours at 130 degrees C. One extra file was used for process control. All files were submitted to a cyclic fatigue test that was performed with an apparatus that allowed the instruments to rotate freely, simulating rotary instrumentation of a curved canal (40-degree, 5-mm radius curve). An electric motor handpiece was used with a contra-angle of 16:1 at an operating speed of 300 rpm and a torque of 2 N-cm. Time to failure was recorded with a stopwatch in seconds and subsequently converted to number of cycles to fracture. Data were analyzed with the Student t test (P < .05). Results: Ion-implanted instruments reached significantly higher cycle numbers before fracture (mean, 510 cycles) when compared with annealed (mean, 428 cycles) and nonimplanted files (mean, 381 cycles). Conclusions: Our results showed that nitrogen ion implantation improves cyclic fatigue resistance in rotary nickel-titanium instruments. Industrial implementation. of this surface modification technique would produce rotary nickel-titanium instruments with a longer working life. (J Endod 2010;36:1183-1186)

Analysis of Apical Root Transportation Associated with Protaper Universal F3 and F4 Instruments by Using Digital Subtraction Radiography

Introduction: The aim of this study was to assess the occurrence of apical root transportation after the use of Pro Taper Universal rotary files sizes 3 (F3) and 4 (F4). Methods: Instruments were worked to the apex of the original canal, always by the same operator. Digital subtraction radiography images were produced in buccolingual and mesiodistal projections. A total of 25 radiographs were taken from root canals of human maxillary first molars with curvatures varying from 23-31 degrees. Quantitative data were analyzed by intraclass correlation coefficient and Wilcoxon nonparametric test (P = .05). Results: Buccolingual images revealed a significantly higher degree of apical transportation associated with F4 instruments when compared with F3 instruments in relation to the original canal (Wilcoxon test, P = .007). No significant difference was observed in mesiodistal images (P = .492). Conclusions: F3 instruments should be used with care in curved canals, and F4 instruments should be avoided in apical third preparation of curved canals. (J Endod 2010;36:1052-1055)

Immunocytochemical detection of dentine matrix protein 1 in experimentally induced reactionary and reparative dentine in rat incisors

Objective: Although the general mechanisms of dentinogenesis are understood, several aspects regarding tertiary dentine formation still deserve investigation, especially regarding the presence and distribution of some noncollagenous matrix proteins. As dentine matrix protein 1 (DMP 1) is present in primary dentine, it is possible that this protein may also be present in the dentine matrix secreted after injury, but there are no immunocytochemical studies attempting its detection in tertiary dentine. The aim of this study was to examine the ultrastructural immunolocalization of DMP 1 in the tertiary dentine after extrusion of the rat incisor. Study design: Upper incisors were extruded 3 mm and then repositioned into their sockets. After several periods, the incisors were fixed and processed for transmission electron microscopy and for immunocytochemistry for DMP 1. Results: Extrusion yielded both types of tertiary dentine, which varied in aspect and related cells. DMP 1 was found in the mineralized matrix of all types of dentine, presenting high affinity for collagen, but rare colloidal gold particles over predentine. DMP 1 was evident in the supranuclear region and inside the nucleus of some odontoblast-like cells. Conclusion: The observed association between DMP 1 and collagen seem to be essential for reactionary and reparative dentine formation. (C) 2010 Elsevier Ltd. All rights reserved.

Depth and percentage of penetration of endodontic sealers into dentinal tubules after root canal obturation using a lateral compaction technique: A confocal laser scanning microscopy study

Objective. The aim was to compare the percentage and depth of sealer penetration into dentinal tubules during obturation using Sealer 26, GuttaFlow, or Sealapex in root canals filled with the lateral compaction technique. Study design. Thirty root canals filled with the lateral compaction technique using GuttaFlow (n = 10), Sealapex (n = 10), or Sealer 26 (n = 10) were analyzed using confocal microscopy. The teeth were sectioned at 3 and 5 mm from the apex, and statistical analyses was performed using analysis of variance-Tukey test (P < .05). Results. Sealapex showed the deepest sealer penetration at both levels evaluated (P < .05). No statistically significance was found between Sealer 26 and GuttaFlow at the 3 mm and 5 mm levels. No statistical significance was found in the percentage of penetration around the root canal wall among the 3 sealers evaluated at both levels. Conclusions. Although Sealapex displayed deeper penetration into the dentinal tubules there was no difference in the percentage of adaptation to the root canal walls among the 3 sealers evaluated. (Oral Surg Oral Med Oral Pathol Oral Radiol Endod 2009; 108: 450-457)