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.

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.

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 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.

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.

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.

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 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.

Catalytic centers in the thiamin diphosphate dependent enzyme pyruvate decarboxylase at 2.4-A resolution

The crystal structure of brewers' yeast pyruvate decarboxylase, a thiamin diphosphate dependent alpha-keto acid decarboxylase, has been determined to 2.4-A resolution. The homotetrameric assembly contains two dimers, exhibiting strong intermonomer interactions within each dimer but more limited ones between dimers. Each monomeric subunit is partitioned into three structural domains, all folding according to a mixed alpha/beta motif. Two of these domains are associated with cofactor binding, while the other is associated with substrate activation. The catalytic centers containing both thiamin diphosphate and Mg(II) are located deep in the intermonomer interface within each dimer. Amino acids important in cofactor binding and likely to participate in catalysis and substrate activation are identified.

Comparative cost-effectiveness analysis of theophylline and ipratropium bromide in chronic obstructive pulmonary disease. A three-center study

The charts of 311 patients receiving theophylline (T) and 289 patients receiving ipratropium bromide (IB) for COPD were reviewed to determine the total costs and cost-effectiveness of these 2 agents in 3 different health-care settings. A direct cost-accounting method assessed cost, and a Markov decision-analysis model calculated cost-effectiveness. Costs to treat toxic effects were greater for T versus IB. The types and incidences of toxic effects, by drug, were similar among the three centers. Overall costs for T were $121.40 per patient per therapy-month versus $84.56 per patient per therapy-month for IB, as determined by the cost-accounting method. The marginal cost was $366 for T over IB when extrapolated over 1 year using the Markov model. The Markov model also predicted that patients receiving IB had a greater number of complication-free therapy-months (measurement of effectiveness) than patients receiving T. We conclude that treatment with IB was less costly and more cost-effective than T.

Crystal structure of staphylococcal enterotoxin B, a superantigen

The three-dimensional structure of staphylococcal enterotoxin B, which is both a toxin and a super-antigen, has been determined to a resolution of 2.5 A. The unusual main-chain fold containing two domains may represent a general motif adopted by all staphylococcal enterotoxins. The T-cell receptor binding site encompasses a shallow cavity formed by both domains. The MHCII molecule binds to an adjacent site. Another cavity with possible biological activity was also identified.

Refined structure of rat Clara cell 17 kDa protein at 3.0 A resolution

The rat Clara cell 17 kDa protein (previously referred to as the rat Clara cell 10 kDa protein) has been reported to inhibit phospholipase A2 and papain, and to also bind progesterone. It has been isolated from rat lung lavage fluid and crystallized in the space group P6(5)22. The structure has been determined to 3.0 A resolution using the molecular replacement method. Uteroglobin, whose amino acid sequence is 55.7% identical, was used as the search model. The structure was then refined using restrained least-squares and simulated annealing methods. The R-factor is 22.5%. The protein is a covalently bound dimer. Two disulfide bonds join the monomers together in an antiparallel manner such that the dimer encloses a large internal hydrophobic cavity. The hydrophobic cavity is large enough to serve as the progesterone binding site, but access to the cavity is limited. Each monomer is composed of four alpha-helices. The main-chain structure of the Clara cell protein closely resembles that of uteroglobin, but the nature of many of the exposed side-chains differ. This is true, particularly in a hypervariable region between residues 23 and 36, and in the H1H4 pocket.

Crystal structure of a bovine neurophysin II dipeptide complex at 2.8 A determined from the single-wavelength anomalous scattering signal of an incorporated iodine atom

The crystal structure of a dipeptide complex of bovine neurophysin II has been solved at 2.8 A resolution solely by using single-wavelength anomalous scattering data from a single iodinated derivative. The asymmetric unit is an elongated tetramer of dimensions 110 x 40 x 30 A, composed of two dimers related by pseudo twofold symmetry. Each monomer consists of two homologous layers, each with four antiparallel beta-strands. The two regions are connected by a helix followed by a long loop. Monomer-monomer contacts involve antiparallel beta-sheet interactions, which form a dimer with two layers of eight beta-strands. One peptide per monomer occupies the principal hormone-binding pocket formed by part of the amino-terminal region and parts of the connecting helix and loop, with binding to protein consistent with conclusions drawn from solution studies. Dimer-dimer contacts involve the Tyr49 region adjacent to this site. A fifth dipeptide, of unknown biological significance, helps to stabilize one of the monomer-monomer interfaces and the tetramer-tetramer network in the crystal.

Free-solution isoelectric focusing for the purification of Staphylococcus aureus enterotoxin C1

A free-solution isoelectric focusing protocol was developed for the preparative purification of Staphylococcus aureus enterotoxin C1 (SEC1). A toxin consisting of a single isoelectric species, pI 8.8, was purified. Thirty-nine milligrams of SEC1 was recovered from 3 liters of culture supernatant. This significantly improved purification scheme utilized ammonium sulfate precipitation and the Bio-Rad Rotofor isoelectric cell to complete isolation in 2 days, thereby avoiding the protein degradation prevalent when published procedures are used. The purification protocol developed here for SEC1 is used to illustrate the utility of Rotofor fractionation in the general purification of bacterial exotoxins.

Preliminary crystallographic data for the thiamin diphosphate-dependent enzyme pyruvate decarboxylase from brewers' yeast

Single crystals of the thiamin diphosphate (the vitamin B1 coenzyme)-dependent enzyme pyruvate decarboxylase (EC 4.1.1.1) from brewers' yeast have been grown using polyethylene glycol as a precipitating agent. Crystals of the homotetrameric version alpha 4 of the holoenzyme are triclinic, space group P1, with cell constants a = 81.0, b = 82.4, c = 116.6 A, alpha = 69.5 beta = 72.6, gamma = 62.4 degrees. The crystals are reasonably stable in a rotating anode x-ray beam and diffract to at least 2.5 A resolution. The Vm value of 2.55 A/dalton is consistent with a unit cell containing four subunits with mass of approximately 60 kDa each. Rotation function results with native data indicate strong non-crystallographic 222 symmetry relating the four identical subunits, thus density averaging methods are likely to play a role in the structure determination.

Direct methods with single isomorphous replacement data. I. Reduction of systematic errors

The direct-methods procedure for single isomorphous replacement (SIR) data [Hauptman (1982). Acta Cryst. A38, 289-294], as modified by Fortier, Moore & Fraser [Acta Cryst. (1985), A41, 571-577] has been implemented and tested with a large number of known structures. It was found that the modified procedure greatly reduces the bias toward 'unresolved' SIR invariant values associated with estimates of 0 or pi, but does not remove it entirely. If the heavy atoms are not in a centrosymmetric array the centroid of the distribution of invariant estimates is not centered on true protein values, but is biased toward conventional SIR values by up to 15 degrees, thus errors in the estimates are not random but systematic. When the heavy atoms are in a centrosymmetric array (or single heavy-atom site in space group P21), the distribution of estimates is often sharply bimodal, with peaks centered at both true invariant values and pure 'unresolved' SIR values. Simple procedures are given which can be applied in both situations to reduce significantly the bias with no overall loss of accuracy. An additional correction factor is then described which can be used to remove nearly all of the bias, and improve the accuracy as well. The result is that errors in the corrected invariant estimates are small in magnitude, but are now also random instead of systematic. Since the number of estimates greatly exceeds the number of phases, the remaining random errors should have little impact in phasing processes.

Crystallization and preliminary X-ray study of rat Clara cell 10,000 Mr protein

Single crystals of Clara cell 10,000 Mr protein have been grown by vapour diffusion in the presence of ammonium sulphate. The space group is P4(1)32 or P4(3)32 with unit cell dimension a = 156.9 A. Crystals diffract to about 3.8 A resolution.

A new crystal form of ricin-OR

Ricin-OR, an antitumor toxin, has been crystallized in space group P2 with cell parameters a = 8.77 nm, b = 4.64 nm, c = 7.64 nm and beta = 101 degrees. There is one molecule in the asymmetric unit and the solvent content is estimated to be 48% by volume. The crystals diffract to 0.25 nm resolution which is higher than that of the previously reported C2 crystal form which had a solvent content of 65%.

Crystal structure of an antifreeze polypeptide and its mechanistic implications

The X-ray crystallographic structure of an antifreeze polypeptide from the fish winter flounder, has been determined at 2.5 A by an analysis of the Patterson function. This is the first report of a polypeptide of this size that is a single alpha-helix. A proposed mechanism of antifreeze binding to ice surfaces is given which requires: first, that the dipole moment from the helical structure dictates the preferential alignment of the peptide to the c-axis of ice nuclei; second, amphiphilicity of the helix; and third, torsional freedom of the side chains to facilitate hydrogen bonding to ice surfaces.

Crystals of modified bovine neurophysin II

An enzymatically modified form of bovine neurophysin II has been crystallized in three unique crystal forms. The orthorhombic form crystallizes in space group P2(1)2(1)2 with a = 15.33 nm, b = 6.92 nm, c = 3.63 nm, with four molecules in the asymmetric unit. The monoclinic form crystallizes in space group P2(1) with a = 6.22 nm, b = 9.55 nm, c = 5.45 nm and beta = 110.2 degrees, with eight molecules in the asymmetric unit. The tetragonal form crystallizes in space group P4(1)2(1)2 or P4(3)2(1)2 with a = 14.1 nm and c = 14.2 nm, with twelve molecules in the asymmetric unit. We report here the crystallization conditions, as well as the crystal data.

Structure of a novel Bence-Jones protein (Rhe) fragment at 1.6 A resolution

The crystal structure of Rhe, a lambda-type Bence-Jones protein fragment, has been solved and refined to a resolution of 1.6 A. A model fragment consisting of the complete variable domain and the first three residues of the constant domain yields a crystallographic residual RF value of 0.149. The protein exists as a dimer both in solution and in the crystals. Although the "immunoglobulin fold" is generally preserved in the structure, there are significant differences in both the monomer conformation and in the mode of association of monomers into dimers, when compared to other known Bence-Jones proteins or Fab fragments. The variations in conformation within monomers are particularly significant as they involve non-hypervariable residues, which previously were believed to be part of a "structurally invariant" framework common to all immunoglobulin variable domains. The novel mode of dimerization is equally important, as it can result in combining site shapes and sizes unobtainable with the conventional mode of dimerization. A comparison of the structure with other variable domain dimers reveals further that the variations within monomers and between domains in the dimer are coupled. Some possible functional implications revealed by this coupling are greater variability, induced fitting of the combining site to better accommodate antigenic determinants, and a mechanism for relaying binding information from one end of the variable domain dimer to the other. In addition to providing the most accurate atomic parameters for an immunoglobulin domain yet obtained, the high resolution and extensive refinement resulted in identification of several tightly bound water molecules in key structural positions. These water molecules may be regarded as integral components of the protein. Other water molecules appear to be required to stabilize the novel conformation.

Effect of baclofen enantiomorphs on the spinal trigeminal nucleus and steric similarities of carbamazepine

The seemingly structurally different drugs, baclofen and carbamazepine, have a similar neurophysiologic effect on the cat spinal trigeminal nucleus and a similar clinical effect in the amelioration of trigeminal neuralgia pain. In this investigation, we report on the enhancement of segmental inhibition by carbamazepine and l-baclofen; d-baclofen produced no effect on segmental inhibition. Doses of l-baclofen one fifth its equivalent racemic dosage produced a much greater enhancement of segmental inhibition. d-Baclofen, when given prior to l-baclofen, blocked the effect of l-baclofen on segmental inhibition and the unconditioned response at previously effective doses. Pretreatment with d-baclofen also blocked the effect of subsequent carbamazepine on segmental inhibition, but had no effect on the unconditioned response. Crystallographic evaluation of carbamazepine and the enantiomorphs of baclofen revealed a surprisingly good fit of baclofen isomers to moieties of the carbamazepine molecule. The results suggest that the baclofen enantiomorphs and carbamazepine have a common mechanism of action in the cat spinal trigeminal nucleus, and that d-baclofen, though inactive, is capable of interfering with the effect of l-baclofen and to a lesser extent with carbamazepine.