Choice Architectures in the Digital Economy: Towards a New Understanding of Digital Vulnerability.

In the digital economy, consumer vulnerability is not simply a vantage point from which to assess some consumers' lack of ability to activate their awareness of persuasion. Instead, digital vulnerability describes a universal state of defencelessness and susceptibility to (the exploitation of) power imbalances that are the result of the increasing automation of commerce, datafied consumer-seller relations, and the very architecture of digital marketplaces. Digital vulnerability, we argue, is architectural, relational, and data-driven. Based on our concept of digital vulnerability, we demonstrate how and why using digital technology to render consumers vulnerable is the epitome of an unfair digital commercial practice.

Secondary organic aerosols from anthropogenic and biogenic precursors.

Secondary organic aerosol (SOA) formation from the photooxidation of an anthropogenic (1,3,5-trimethylbenzene) and a biogenic (alpha-pinene) precursor was investigated at the new PSI smog chamber. The chemistry of the gas phase was followed by proton transfer reaction mass spectrometry, while the aerosol chemistry was investigated with aerosol mass spectrometry, ion chromatography, laser desorption ionization mass spectrometry, and infrared spectroscopy, along with volatility and hygroscopicity studies. Evidence for oligomer formation for SOA from both precursors was given by an increasing abundance of compounds with a high molecular weight (up to 1000 Da) and by an increasing thermal stability with increasing aging time. The results were compared to data obtained from ambient aerosol samples, revealing a number of similar features.

Identification of organic acids in secondary organic aerosol and the corresponding gas phase from chamber experiments.

Organic acids in the gas and aerosol phase from photooxidation of 1,3,5-trimethylbenzene in the presence of 300 ppb propene and 300 ppb NOx in smog chamber experiments were determined using a wet effluent diffusion denuder/aerosol collector coupled to ion chromatography (IC) with conductivity detection. Behind the IC, the samples were collected using a fraction collector, for identification of unresolved/unidentified organic acids with IC-mass spectrometry (MS). In total, 20 organic acids were found with MS of which 10 were identified. The organic acids identified offline by IC-MS were then further quantified based on the online IC data. The identification was additionally confirmed with gas chromatography-mass spectrometry. At the maximum aerosol concentration, organic acids comprised 20-45% of the total aerosol mass. The method has a detection limit of 10-100 ng/m3 for the identified carboxylic acids.

Identification of polymers as major components of atmospheric organic aerosols.

Results from photooxidation of aromatic compounds in a reaction chamber show that a substantial fraction of the organic aerosol mass is composed of polymers. This polymerization results from reactions of carbonyls and their hydrates. After aging for more than 20 hours, about 50% of the particle mass consists of polymers with a molecular mass up to 1000 daltons. This results in a lower volatility of this secondary organic aerosol and a higher aerosol yield than a model using vapor pressures of individual organic species would predict.

Picogram quantitation of polycyclic aromatic hydrocarbons adsorbed on aerosol particles by two-step laser mass spectrometry.

Polycyclic aromatic hydrocarbons (PAHs) are emitted into the atmosphere mostly by anthropogenic combustion sources. Because of their carcinogenic and mutagenic properties, PAHs are often analyzed in air quality measurements. Atmospheric concentrations of PAHs, typically in the nanograms-per-cubic-meter range, require significant effort for sample collection and processing when conventional methods such as gas chromatography/mass spectrometry (GC/MS) or liquid chromatography/mass spectrometry are used. In contrast, two-step laser mass spectrometry (L2MS) is highly sensitive and selective for PAHs and requires almost no sample preparation. Here, we present for the first time a method based on L2MS to quantify PAHs adsorbed on aerosol particles collected on a filter. Linear ranges for quantitation were determined for five different PAHs in the mass range of 178-276 Da (i.e., phenanthrene, pyrene, chrysene, benzo[e]pyrene, benzo[ghi]perylene) covering more than 2 orders of magnitude with detection limits between 50 and 300 pg of a single PAH on a whole filter sample. A quantitative comparison with GC/MS was performed using model aerosols consisting of benzo[e]pyrene adsorbed on inorganic salt aerosol particles. On average, 25% less benzo[e]pyrene was determined with GC/MS than with L2MS, with a variability between the two methods of +/-68%. The general lower amount measured with GC/MS is attributed to losses during the sample preparation for the GC/MS measurements.

Divergent evolution of (betaalpha)8-barrel enzymes.

The (betaalpha)8-barrel is the most versatile and most frequently encountered fold among enzymes. It is an interesting question how the contemporary (betaalpha)8-barrels are evolutionarily related and by which mechanisms they evolved from more simple precursors. Comprehensive comparisons of amino acid sequences and three-dimensional structures suggest that a large fraction of the known (betaalpha)8-barrels have divergently evolved from a common ancestor. The mutational interconversion of enzymatic activities of several (betaalpha)8-barrels further supports their common evolutionary origin. Moreover, the high structural similarity between the N- and C-terminal (betaalpha)4 units of two (betaalpha)8-barrel enzymes from histidine biosynthesis indicates that the contemporary proteins evolved by tandem duplication and fusion of the gene of an ancestral 'half-barrel' precursor. In support of this hypothesis, recombinantly produced 'half-barrels' were shown to be folded, dimeric proteins.

Structure of staphylococcal enterotoxin C2 at various pH levels.

The three-dimensional structure of staphylococcal enterotoxin C2 (SEC2), a toxin as well as a superantigen, has been determined at various pH levels from two different crystal forms, tetragonal (pH 5.0, 5.5, 6.0 and 6.5) and monoclinic (pH 8.0) at 100 and 293 K, respectively, by the molecular-replacement method. Tetragonal crystals belong to space group P4(3)2(1)2, with unit-cell parameters a = b = 42.68, c = 289.15 A (at pH 5.0), and monoclinic crystals to space group P2(1), with unit-cell parameters a = 43.3, b = 70.6, c = 42.2 A, beta = 90.3 degrees. SEC2 contains a zinc-binding motif, D+HExxH, and accordingly a Zn atom has been identified. The coordination of the zinc ion suggests that it may be catalytic zinc rather than structural, but there is so far no biological evidence that it possesses catalytic activity. However, superantigen staphylococcal exfoliative toxins A and B have been shown to have enzymatic activity after their fold was identified to be similar to that of serine protease. The structure and its conformation are similar to the previously reported structures of SEC2. Though it was expected that the zinc ion may be leached out, as the histidines coordinating the zinc ion are expected to be protonated below pH 6.0, zinc is present at all pH values. The coordination distances to zinc increase with decreasing pH, with the distances being the least at pH 8.0. The results of automated model building using the ARP/wARP program for different data sets collected at various pH values are discussed.

Structural evidence for evolution of the beta/alpha barrel scaffold by gene duplication and fusion.

The atomic structures of two proteins in the histidine biosynthesis pathway consist of beta/alpha barrels with a twofold repeat pattern. It is likely that these proteins evolved by twofold gene duplication and gene fusion from a common half-barrel ancestor. These ancestral domains are not visible as independent domains in the extant proteins but can be inferred from a combination of sequence and structural analysis. The detection of subdomain structures may be useful in efforts to search genome sequences for functionally and structurally related proteins.

Crystallization and preliminary X-ray analysis of tetanus neurotoxin C fragment.

Two crystal forms of recombinant tetanus neurotoxin C fragment have been obtained. The C fragment corresponds to the C-terminal 451 amino-acid residues of tetanus neurotoxin and is the subunit responsible for receptor binding by the toxin. Both forms belong to space group P212121. Form I has unit-cell dimensions of a = 71.3, b = 79.7, c = 94.0 A and produces thin plate crystals. Form II has unit-cell dimensions of a = 67.4, b = 79.7, c = 91.1 A and produces thick rod-shaped crystals. Diffraction data to 2.6 A have been collected from form II crystals.

Structure-function relationships and flexible tetramer assembly in pyruvate decarboxylase revealed by analysis of crystal structures.

The crystal structures of pyruvate decarboxylase from the yeast Saccharomyces uvarum and Saccharomyces cerevisiae have been determined at 2.4 and 2.3 A resolution, respectively. These structures provide details about the protein fold and domain assembly within subunits, about subunit assembly to form dimers and about dimer assembly to form tetramers. They also provide a clear picture of the active site centered on the thiamin diphosphate cofactor, and have allowed amino acids critical for catalysis and involved in stabilization of the unusual cofactor conformation to be identified. The structural information has enabled identification of the site of allosteric activation to be centered on Cys-221, and suggests that a six residue segment leading from the regulatory site to the catalytic site may be involved in transmission of a binding signal. The importance of several amino acids within this segment in the regulatory process, as well as some involved in stabilizing and activating the cofactor has been confirmed by analyzing the behavior of recombinant enzymes with single point mutations introduced at these sites. Additional structures have been determined for pyruvate decarboxylase in multiple crystal forms, some of which were obtained from crystals grown with known allosteric activators present in the media. Currently four distinct types of tetramers have been observed, with each showing a different mode of association of dimers to form the tetramers. In some of the cases involving the presence of allosteric activators drastic changes in the mode of dimer assembly to form tetramers is seen.

Accuracy of secondary structure and solvent accessibility predictions for a clostridial neurotoxin C-fragment.

Earlier studies used Rost and Sander's artificial neural network [(1993a), J. Mol. Biol. 232, 584-599] to predict the secondary structures [Lebeda and Olson (1994), Proteins 20, 293-300] and residue solvent accessibilities [Lebeda and Olson (1997), J. Protein Chem. 16, 607-618] of the clostridial neurotoxins. Because the X-ray crystal structure of the 50-kDa C-terminal half of the heavy chain of tetanus toxin was recently determined, this report evaluates the accuracy of these network-derived predictions. For this predominantly beta-strand-containing fragment, predictions, on a per-residue basis, for both secondary structure and solvent accessibility were about 70% accurate. A more flexible and realistic analysis based on overlapping segments yielded accuracies of over 80% for the three-state secondary structure and for the two-state accessibility predictions. Because the accuracies of these predictions are comparable to those made by Rost and Sander using a dataset of 126 nonhomologous globular proteins, our predictions provide a quantitative foundation for gauging the results when building by homology the structures of related proteins.

Structure of the receptor binding fragment HC of tetanus neurotoxin.

The 2.7 A structure of the tetanus neurotoxin receptor binding fragment Hc reveals a jelly-roll domain and a beta-trefoil domain. Hc retains the unique transport properties of the holotoxin and is capable of eliciting a protective immunological response against the full length holotoxin.

Crystal structure of the thiamin diphosphate-dependent enzyme pyruvate decarboxylase from the yeast Saccharomyces cerevisiae at 2.3 A resolution.

The crystal structure of pyruvate decarboxylase (EC 4.1.1.1), a thiamin diphosphate-dependent enzyme isolated from Saccharomyces cerevisiae, has been determined and refined to a resolution of 2.3 A. Pyruvate decarboxylase is a homotetrameric enzyme which crystallizes with two subunits in an asymmetric unit. The structure has been refined by a combination of simulated annealing and restrained least squares to an R factor of 0.165 for 46,787 reflections. As in the corresponding enzyme from Saccharomyces uvarum, the homotetrameric holoenzyme assembly has approximate 222 symmetry. In addition to providing more accurate atomic parameters and certainty in the sequence assignments, the high resolution and extensive refinement resulted in the identification of several tightly bound water molecules in key structural positions. These water molecules have low temperature factors and make several hydrogen bonds with protein residues. There are six such water molecules in each cofactor binding site, and one of them is involved in coordination with the required magnesium ion. Another may be involved in the catalytic reaction mechanism. The refined model includes 1074 amino acid residues (two subunits), two thiamin diphosphate cofactors, two magnesium ions associated with cofactor binding and 440 water molecules. From the refined model we conclude that the resting state of the enzyme-cofactor complex is such that the cofactor is already deprotonated at the N4' position of the pyrimidine ring, and is poised to accept a proton from the C2 position of the thiazolium ring.

Preliminary X-ray studies on two new crystal forms of staphylococcal enterotoxin C2.

Two new crystal forms of staphylococcal enterotoxin C2 have been obtained by vapor-diffusion methods. Form 1 crystals are monoclinic in space group P2(1) with cell dimensions a = 43.43, b = 69.92, c = 42.22 A, 8 = 90.1 degrees and diffract to at least 2.7 A resolution. Form 2 crystals are tetragonal in space group P4(1)2(1)2 or P4(3)2(1)2 with cell dimensions a = b = 42.98, c = 289.92 A and diffract to 1.9 A resolution.

Residues defining V beta specificity in staphylococcal enterotoxins.

The three-dimensional structure of staphylococcal enterotoxin C2 has been determined at 2.7 A resolution by x-ray diffraction, while the structures of enterotoxins A and E have been modelled based on their sequence homology to other staphylococcal enterotoxins. The T-cell receptor-binding sites of staphylococcal enterotoxin (SE) B and SEC2 are compared and the stereochemical interactions likely to be responsible for their differing V beta specificities are identified. A similar comparison is made between SEA and SEE.

Crystallization and preliminary analysis of two crystal forms of human clara cell 16 kDa protein (CC10).

The human Clara cell 16 kDa protein (CC10), isolated from lung lavage fluid, has been crystallized in two crystal forms. The first is in space group P1 and has cell parameters a = 43.04, b = 45.90, c = 51.29 A and alpha = 62.46, beta = 69.74, gamma = 69.43 degrees. Two molecules are present in the unit cell. The second form is in space group P222, with cell parameters a = 42.24, b = 84.06, c = 40.05 A and alpha = beta = gamma = 90 degrees, and four molecules per unit cell. Its diffraction pattern displays pseudo-body-centered symmetry. Both crystal forms diffract X-rays beyond 2.0 A.

Structure of a human Clara cell phospholipid-binding protein-ligand complex at 1.9 A resolution.

The Clara cell phospholipid-binding protein, previously referred to as CC10, is a homodimeric protein of M(r) 15,800. It is secreted into the bronchioalveolar lining layer in mammalian lung. A combination of X-ray crystallography and chemical analysis was used to determine that phosphatidylcholine and phosphatidylinositol are bound to the protein as isolated from human lung lavage. We now report the crystal structure of the protein-phospholipid complex at 1.9 A resolution. The phospholipid is bound inside the protein's large hydrophobic cavity. A model is proposed for the manner in which a channel may open to provide access to the cavity, allowing the binding or potential release of phospholipid.