Structure and biogenesis of the capsular F1 antigen from Yersinia pestis: Preserved folding energy drives fiber formation

Most gram-negative pathogens express fibrous adhesive virulence organelles that mediate targeting to the sites of infection. The F1 capsular antigen from the plague pathogen Yersinia pestis consists of linear fibers of a single subunit (Caf1) and serves as a prototype for nonpilus organelles assembled via the chaperone/usher pathway. Genetic data together with high-resolution X-ray structures corresponding to snapshots of the assembly process reveal the structural basis of fiber formation. Comparison of chaperone bound Caf1 subunit with the subunit in the fiber reveals a novel type of conformational change involving the entire hydrophobic core of the protein. The observed conformational change suggests that the chaperone traps a high-energy folding intermediate of Caf1. A model is proposed in which release of the subunit allows folding to be completed, driving fiber formation.

Energy substitutability in transition agriculture: estimates and implications for Hungary

Subsidised energy prices in pre-transition Hungary had led to excessive energy intensity in the agricultural sector. Transition has resulted in steep input price increases. In this study, Allen and Morishima elasticities of substitution are estimated to study the effects of these price changes on energy use, chemical input use, capital formation and employment. Panel data methods, Generalised Method of Moments (GMM) and instrument exogeneity tests are used to specify and estimate technology and substitution elasticities. Results indicate that indirect price policy may be effective in controlling energy consumption. The sustained increases in energy and chemical input prices have worked together to restrict energy and chemical input use, and the substitutability between energy, capital and labour has prevented the capital shrinkage and agricultural unemployment situations from being worse. The Hungarian push towards lower energy intensity may be best pursued through sustained energy price increases rather than capital subsidies. (C) 2003 Elsevier B.V. All rights reserved.

Resolving the energy paradox of chaperone/usher-mediated fibre assembly

Periplasmic chaperone/usher machineries are used for assembly of filamentous adhesion organelles of Gram-negative pathogens in a process that has been suggested to be driven by folding energy. Structures of mutant chaperone-subunit complexes revealed a final folding transition (condensation of the subunit hydrophobic core) on the release of organelle subunit from the chaperone-subunit pre-assembly complex and incorporation into the final fibre structure. However, in view of the large interface between chaperone and subunit in the pre-assembly complex and the reported stability of this complex, it is difficult to understand how final folding could release sufficient energy to drive assembly. In the present paper, we show the X-ray structure for a native chaperone-fibre complex that, together with thermodynamic data, shows that the final folding step is indeed an essential component of the assembly process. We show that completion of the hydrophobic core and incorporation into the fibre results in an exceptionally stable module, whereas the chaperone-subunit preassembly complex is greatly destabilized by the high-energy conformation of the bound subunit. This difference in stabilities creates a free energy potential that drives fibre formation.

An investigation of the germylene addition reaction, GeH2+C2H2: Time-resolved gas-phase kinetic studies and quantum chemical calculations of the reaction energy surface

Time resolved studies of germylene, GeH2, generated by laser flash photolysis of 3,4-dimethylgermacyclopentene-3, have been carried out to obtain rate constants for its bimolecular reaction with acetylene, C2H2. The reaction was studied in the gas-phase over the pressure range 1-100 Tort, with SF6 as bath gas, at 5 temperatures in the range 297-553 K. The reaction showed a very slight pressure dependence at higher temperatures. The high pressure rate constants (obtained by extrapolation at the three higher temperatures) gave the Arrhenius equation: log(k(infinity)/cm(3) molecule(-1) s(-1)) (-10.94 +/- 0.05) + (6.10 +/- 0.36 kJ mol(-1))/RTln10. These Arrhenius parameters are consistent with a fast reaction occurring at approximately 30% of the collision rate at 298 K. Quantum chemical calculations (both DFT and ab initio G2//B3LYP and G2//QCISD) of the GeC2H4 potential energy surface (PES), show that GeH2 + C2H2 react initially to form germirene which can isomerise to vinylgermylene with a relatively low barrier. RRKM modelling, based on a loose association transition state, but assuming vinylgermylene is the end product (used in combination with a weak collisional deactivation model) predicts a strong pressure dependence using the calculated energies, in conflict with the experimental evidence. The detailed GeC2H4 PES shows considerable complexity with ten other accessible stable minima (B3LYP level), the three most stable of which are all germylenes. Routes through this complex surface were examined in detail. The only product combination which appears capable of satisfying the (P-3) + C2H4.C2H4 was confirmed as a product by GC observed lack of a strong pressure dependence is Ge(P-3) + C2H4. C2H4 was confirmed as a product by GC analysis. Although the formation of these products are shown to be possible by singlet-triplet curve crossing during dissociation of 1-germiranylidene (1-germacyclopropylidene), it seems more likely (on thermochernical grounds) that the triplet biradical, (GeCH2CH2.)-Ge-., is the immediate product precursor. Comparisons are made with the reaction of SiH2 with C2H2.

Investigation of the prototype silylene reaction, SiH2+H2O(and D2O): time-resolved gas-phase kinetic studies, isotope effects, RRKM calculations, and quantum chemical calculations of the reaction energy surface

Time-resolved kinetic studies of the reaction of silylene, SiH2, with H2O and with D2O have been carried out in the gas phase at 296 and at 339 K, using laser flash photolysis to generate and monitor SiH2. The reaction was studied over the pressure range 10-200 Torr with SF6 as bath gas. The second-order rate constants obtained were pressure dependent, indicating that the reaction is a third-body assisted association process. Rate constants at 339 K were about half those at 296 K. Isotope effects, k(H)/k(D), were small averaging 1.076 0.080, suggesting no involvement of H- (or D-) atom transfer in the rate determining step. RRKM modeling was undertaken based on a transition state appropriate to formation of the expected zwitterionic donoracceptor complex, H2Si...OH2. Because the reaction is close to the low pressure (third order) region, it is difficult to be definitive about the activated complex structure. Various structures were tried, both with and without the incorporation of rotational modes, leading to values for the high-pressure limiting (i.e., true secondorder) rate constant in the range 9.5 x 10(-11) to 5 x 10(-10) cm(3) molecule' s(-1). The RRKM modeling and mechanistic interpretation is supported by ab initio quantum calculations carried out at the G2 and G3 levels. The results are compared and contrasted with the previous studies.

Wormlike micelle formation and flow alignment of a pluronic block copolymer in aqueous solution

The self-assembly into wormlike micelles of a poly(ethylene oxide)-b-poly(propylene oxide)-b-poly(ethylene oxide) triblock copolymer Pluronic P84 in aqueous salt solution (2 M NaCl) has been studied by rheology, small-angle X-ray and neutron scattering (SAXS/SANS), and light scattering. Measurements of the flow curves by controlled stress rheometry indicated phase separation under flow. SAXS on solutions subjected to capillary flow showed alignment of micelles at intermediate shear rates, although loss of alignment was observed for high shear rates. For dilute solutions, SAXS and static light scattering data on unaligned samples could be superposed over three decades in scattering vector, providing unique information on the wormlike micelle structure over several length scales. SANS data provided information on even shorter length scales, in particular, concerning "blob" scattering from the micelle corona. The data could be modeled based on a system of semiflexible self-avoiding cylinders with a circular cross-section, as described by the wormlike chain model with excluded volume interactions. The micelle structure was compared at two temperatures close to the cloud point (47 degrees C). The micellar radius was found not to vary with temperature in this region, although the contour length increased with increasing temperature, whereas the Kuhn length decreased. These variations result in an increase of the low-concentration radius of gyration with increasing temperature. This was consistent with dynamic light scattering results, and, applying theoretical results from the literature, this is in agreement with an increase in endcap energy due to changes in hydration of the poly(ethylene oxide) blocks as the temperature is increased.

A case of four-coordinate silver(I) adopting a high energy planar geometry. Experiment and theory

The ligands PhL and MeL are obtained by condensing 2-formylpyridine with benzil dihydrazone and diacetyl dihydrazone, respectively, in 2: 1 molar proportion. With silver( I), PhL yields a double-stranded dinuclear cationic helicate 1 in which the metal is tetrahedral but MeL gives a cationic one-dimensional polymeric complex 2 where silver( I) is distorted square planar and the ligand backbone is nearly planar. In both complexes, metal: ligand ratio is 1: 1. Ab initio calculations on the ligands at the HF/6-31+G* level reveal that while PhL strongly prefers a helical conformation, MeL has a natural inclination to remain in a planar conformation. Density functional theory calculations on model silver( I) complexes show that formation of the linear polymer in the case of MeL is also an important factor in imposing the planar geometry of Ag(I) in 2.

Solvent influences on metastable polymorph lifetimes: real-time interconversions using energy dispersive X-ray diffractometry

Solvent influences on the crystallization of polymorph and hydrate forms of the nootropic drug piracetam (2-oxo-pyrrolidineacetamide) were investigated from water, methanol, 2-propanol, isobutanol, and nitromethane. Crystal growth profiles of piracetam polymorphs were constructed using time-resolved diffraction snapshots collected for each solvent system. Measurements were performed by in situ energy dispersive X-ray diffraction recorded in Station 16.4 at the synchrotron radiation source (SRS) at Daresbury Laboratory, CCLRC UK. Crystallizations from methanol, 2-propanol, isobutanol, and nitromethane progressed in a similar fashion with the initial formation of form I which then converted relatively quickly to form II with form III being generated upon further cooling. However, considerable differences were observed for the polymorphs lifetime and both the rate and temperature of conversion using the different solvents. The thermodynamically unstable form I was kinetically favored in isobutanol and nitromethane where traces of this polymorph were observed below 10 degrees C. In contrast, the transformation of form II and subsequent growth of form III were inhibited in 2-propanol and nitromethane solutions. Aqueous solutions produced hydrate forms of piracetam which are different from the reported monohydrate; this crystallization evolved through successive generation of transient structures which transformed upon exchange of intramolecular water between the liquid and crystalline phases. (c) 2007 Wiley-Liss, Inc. and the American Pharmacists Association J Pharm Sci 96:1069-1078, 2007.

Hydrogen bond-induced pair formation of glycine on the chiral Cu{531} surface

Enantio-specific interactions on intrinsically chiral or chirally modified surfaces can be identified experimentally via comparison of the adsorption geometries of similar nonchiral and chiral molecules. Information about the effects of substrate-related and in interactions on the adsorption geometry of glycine, the only natural nonchiral amino acid, is therefore important for identifying enantio-specific interactions of larger chiral amino acids. We have studied the long- and short-range adsorption geometry and bonding properties of glycine on the intrinsically chiral Cu{531} surface with low-energy electron diffraction, near-edge X-ray absorption One structure spectroscopy, X-ray photoelectron spectroscopy, and temperature-programmed desorption. For coverages between 0.15 and 0.33 ML (saturated chemisorbed layer) and temperatures between 300 and 430 K, glycine molecules adsorb in two different azimuthal orientations, which are associated with adsorption sites on the {110} and {311} microfacets of Cu{531}. Both types of adsorption sites allow a triangular footprint with surface bonds through the two oxygen atoms and the nitrogen atom. The occupation of the two adsorption sites is equal for all coverages, which can be explained by pair formation due to similar site-specific adsorption energies and the possibility of forming hydrogen bonds between molecules on adjacent {110} and {311} sites. This is not the ease for alanine and points toward higher site specificity in the case of alanine, which is eventually responsible for the enantiomeric differences observed for the alanine system.

Kinetic energy analysis of the response of the Atlantic meridional overturning circulation to CO2-forced climate change

Atmosphere–ocean general circulation models (AOGCMs) predict a weakening of the Atlantic meridional overturning circulation (AMOC) in response to anthropogenic forcing of climate, but there is a large model uncertainty in the magnitude of the predicted change. The weakening of the AMOC is generally understood to be the result of increased buoyancy input to the north Atlantic in a warmer climate, leading to reduced convection and deep water formation. Consistent with this idea, model analyses have shown empirical relationships between the AMOC and the meridional density gradient, but this link is not direct because the large-scale ocean circulation is essentially geostrophic, making currents and pressure gradients orthogonal. Analysis of the budget of kinetic energy (KE) instead of momentum has the advantage of excluding the dominant geostrophic balance. Diagnosis of the KE balance of the HadCM3 AOGCM and its low-resolution version FAMOUS shows that KE is supplied to the ocean by the wind and dissipated by viscous forces in the global mean of the steady-state control climate, and the circulation does work against the pressure-gradient force, mainly in the Southern Ocean. In the Atlantic Ocean, however, the pressure-gradient force does work on the circulation, especially in the high-latitude regions of deep water formation. During CO2-forced climate change, we demonstrate a very good temporal correlation between the AMOC strength and the rate of KE generation by the pressure-gradient force in 50–70°N of the Atlantic Ocean in each of nine contemporary AOGCMs, supporting a buoyancy-driven interpretation of AMOC changes. To account for this, we describe a conceptual model, which offers an explanation of why AOGCMs with stronger overturning in the control climate tend to have a larger weakening under CO2 increase.

A data framework for measuring the energy consumption of the non-domestic building stock

The transition to a low-carbon economy urgently demands better information on the drivers of energy consumption. UK government policy has prioritized energy efficiency in the built stock as a means of carbon reduction, but the sector is historically information poor, particularly the non-domestic building stock. This paper presents the results of a pilot study that investigated whether and how property and energy consumption data might be combined for non-domestic energy analysis. These data were combined in a ‘Non-Domestic Energy Efficiency Database’ to describe the location and physical attributes of each property and its energy consumption. The aim was to support the generation of a range of energy-efficiency statistics for the industrial, commercial and institutional sectors of the non-domestic building stock, and to provide robust evidence for national energy-efficiency and carbon-reduction policy development and monitoring. The work has brought together non-domestic energy data, property data and mapping in a ‘data framework’ for the first time. The results show what is possible when these data are integrated and the associated difficulties. A data framework offers the potential to inform energy-efficiency policy formation and to support its monitoring at a level of detail not previously possible.

Kinetic energy analysis of the response of the Atlantic meridional overturning circulation to CO2-forced climate change

Atmosphere–ocean general circulation models (AOGCMs) predict a weakening of the Atlantic meridional overturning circulation (AMOC) in response to anthropogenic forcing of climate, but there is a large model uncertainty in the magnitude of the predicted change. The weakening of the AMOC is generally understood to be the result of increased buoyancy input to the north Atlantic in a warmer climate, leading to reduced convection and deep water formation. Consistent with this idea, model analyses have shown empirical relationships between the AMOC and the meridional density gradient, but this link is not direct because the large-scale ocean circulation is essentially geostrophic, making currents and pressure gradients orthogonal. Analysis of the budget of kinetic energy (KE) instead of momentum has the advantage of excluding the dominant geostrophic balance. Diagnosis of the KE balance of the HadCM3 AOGCM and its low-resolution version FAMOUS shows that KE is supplied to the ocean by the wind and dissipated by viscous forces in the global mean of the steady-state control climate, and the circulation does work against the pressure-gradient force, mainly in the Southern Ocean. In the Atlantic Ocean, however, the pressure-gradient force does work on the circulation, especially in the high-latitude regions of deep water formation. During CO2-forced climate change, we demonstrate a very good temporal correlation between the AMOC strength and the rate of KE generation by the pressure-gradient force in 50–70°N of the Atlantic Ocean in each of nine contemporary AOGCMs, supporting a buoyancy-driven interpretation of AMOC changes. To account for this, we describe a conceptual model, which offers an explanation of why AOGCMs with stronger overturning in the control climate tend to have a larger weakening under CO2 increase

Effect of a methyl group on the spontaneous resolution of a square-pyramidal coordination compound: crystal packing and conglomerate formation

Reaction of [Cu(pic)2]·2H2O (where pic stands for 2-picolinato) with 2-({[2-(dimethylamino)ethyl]amino}methyl)phenol (HL1) produces the square-pyramidal complex [CuL1(pic)] (1), which crystallizes as a conglomerate (namely a mixture of optically pure crystals) in the Sohncke space group P212121. The use of the methylated ligand at the benzylic position, i.e. (±)-2-(1-{[2-(dimethylamino)ethyl]amino}ethyl)phenol (HL2), yields the analogous five-coordinate complex [CuL2(pic)] (2) that crystallizes as a true racemate (namely the crystals contain both enantiomers) in the centrosymmetric space group P21/c. Density functional theory (DFT) calculations indicate that the presence of the methyl group indeed leads to a distinct crystallization behaviour, not only by intramolecular steric effects, but also because its involvement in non-covalent C–H···π and hydrophobic intermolecular contacts appears to be an important factor contributing to the crystal-lattice (stabilizing) energy of 2

Effect of shear rupture on aggregate scale formation in sea ice

A discrete element model is used to study shear rupture of sea ice under convergent wind stresses. The model includes compressive, tensile, and shear rupture of viscous elastic joints connecting floes that move under the action of the wind stresses. The adopted shear rupture is governed by Coulomb’s criterion. The ice pack is a 400 km long square domain consisting of 4 km size floes. In the standard case with tensile strength 10 times smaller than the compressive strength, under uniaxial compression the failure regime is mainly shear rupture with the most probable scenario corresponding to that with the minimum failure work. The orientation of cracks delineating formed aggregates is bimodal with the peaks around the angles given by the wing crack theory determining diamond-shaped blocks. The ice block (floe aggregate) size decreases as the wind stress gradient increases since the elastic strain energy grows faster leading to a higher speed of crack propagation. As the tensile strength grows, shear rupture becomes harder to attain and compressive failure becomes equally important leading to elongation of blocks perpendicular to the compression direction and the blocks grow larger. In the standard case, as the wind stress confinement ratio increases the failure mode changes at a confinement ratio within 0.2–0.4, which corresponds to the analytical critical confinement ratio of 0.32. Below this value, the cracks are bimodal delineating diamond shape aggregates, while above this value failure becomes isotropic and is determined by small-scale stress anomalies due to irregularities in floe shape.

Oppositely charged polyelectrolytes: complex formation and effects of chain asymmetry

The formation of complexes in solutions of oppositely charged polyions has been studied by Monte Carlo simulations. The amount as well as the length, and thus, the absolute charge of one of the polyions have been varied. There is an increasing tendency to form large clusters as the excess of one kind of polyion decreases. When all polyions have the same length, this tendency reaches a maximum near, but off, equivalent amounts of the two types of polyions. When one kind of polyion is made shorter, the propensity to form large clusters decreases and the fluctuations in cluster charge increases. Simple free-energy expressions have been formulated on the basis of a set of simple rules that help rationalize the observations. By calculating cluster distributions in both grand canonical and canonical ensembles, it has been possible to show the extent of finite-size effects in the simulations.