Structure and dynamics of the radical cation of ethane arising from the Jahn-Teller and pseudo-Jahn-Teller effects.

The pulsed-field-ionization zero-kinetic-energy photoelectron spectrum of C2H6 has been recorded in the region of the adiabatic ionization threshold. The partially rotationally resolved spectrum indicates the existence of several vibronic states of C2H6+ with less than 600 cm-1 of internal excitation. The analysis of the rotational structures assisted by ab initio calculations enabled the determination of the adiabatic ionization energy of C2H6 and the investigation of the structure and dynamics of C2H6+ at low energies. The ground state of C2H6+ is found to be a 2Ag state of diborane-like structure with strongly mixed (a1g)-1 and (eg)-1 configurations. The vibrational structure reveals the importance of large-amplitude nuclear motions involving the diborane distortion modes, the C-C stretching motion, and the internal rotation at elongated C-C distances. The spectrum is analyzed in the light of the information obtained in earlier studies of C2H6+ by ab initio quantum chemistry, EPR spectroscopy and photoelectron spectroscopy.

Tropospheric Emissions: Monitoring of Pollution (TEMPO).

TEMPO was selected in 2012 by NASA as the first Earth Venture Instrument, for launch between 2018 and 2021. It will measure atmospheric pollution for greater North America from space using ultraviolet and visible spectroscopy. TEMPO observes from Mexico City, Cuba, and the Bahamas to the Canadian oil sands, and from the Atlantic to the Pacific, hourly and at high spatial resolution (~2.1 km N/S×4.4 km E/W at 36.5°N, 100°W). TEMPO provides a tropospheric measurement suite that includes the key elements of tropospheric air pollution chemistry, as well as contributing to carbon cycle knowledge. Measurements are made hourly from geostationary (GEO) orbit, to capture the high variability present in the diurnal cycle of emissions and chemistry that are unobservable from current low-Earth orbit (LEO) satellites that measure once per day. The small product spatial footprint resolves pollution sources at sub-urban scale. Together, this temporal and spatial resolution improves emission inventories, monitors population exposure, and enables effective emission-control strategies. TEMPO takes advantage of a commercial GEO host spacecraft to provide a modest cost mission that measures the spectra required to retrieve ozone (O3), nitrogen dioxide (NO2), sulfur dioxide (SO2), formaldehyde (H2CO), glyoxal (C2H2O2), bromine monoxide (BrO), IO (iodine monoxide),water vapor, aerosols, cloud parameters, ultraviolet radiation, and foliage properties. TEMPO thus measures the major elements, directly or by proxy, in the tropospheric O3 chemistry cycle. Multi-spectral observations provide sensitivity to O3 in the lowermost troposphere, substantially reducing uncertainty in air quality predictions. TEMPO quantifies and tracks the evolution of aerosol loading. It provides these near-real-time air quality products that will be made publicly available. TEMPO will launch at a prime time to be the North American component of the global geostationary constellation of pollution monitoring together with the European Sentinel-4 (S4) and Korean Geostationary Environment Monitoring Spectrometer (GEMS) instruments.

Single-field slice-imaging with a movable repeller: photodissociation of N2O from a hot nozzle.

We present a new photo-fragment imaging spectrometer, which employs a movable repeller in a single field imaging geometry. This innovation offers two principal advantages. First, the optimal fields for velocity mapping can easily be achieved even using a large molecular beam diameter (5 mm); the velocity resolution (better than 1%) is sufficient to easily resolve photo-electron recoil in (2 + 1) resonant enhanced multiphoton ionization of N2 photoproducts from N2O or from molecular beam cooled N2. Second, rapid changes between spatial imaging, velocity mapping, and slice imaging are straightforward. We demonstrate this technique's utility in a re-investigation of the photodissociation of N2O. Using a hot nozzle, we observe slice images that strongly depend on nozzle temperature. Our data indicate that in our hot nozzle expansion, only pure bending vibrations--(0, v2, 0)--are populated, as vibrational excitation in pure stretching or bend-stretch combination modes are quenched via collisional near-resonant V-V energy transfer to the nearly degenerate bending states. We derive vibrationally state resolved absolute absorption cross-sections for (0, v2 ≤ 7, 0). These results agree well with previous work at lower values of v2, both experimental and theoretical. The dissociation energy of N2O with respect to the O((1)D) + N2¹Σ(g)⁺ asymptote was determined to be 3.65 ± 0.02 eV.

Photoelectron spectroscopic study of the E ⊗ e Jahn-Teller effect in the presence of a tunable spin-orbit interaction. III. Two-state excitonic model accounting for observed trends in the X 2E ground state of CH3X+ (X=F, Cl, Br, I) and CH3Y (Y=O, S).

Open-shell molecules in doubly degenerate (2)E electronic states are subject to the E ⊗ e Jahn-Teller effect and spin-orbit interactions. The rotational structure of the ground vibrational level of the X(+) (2)E ground state of CH(3)F(+) has been observed by high-resolution photoelectron spectroscopy. In contrast to what is observed in other members of the isoelectronic families CH(3)X(+) (X=Cl, Br, I) and CH(3)Y (Y=O, S), the spin-orbit interaction does not lead to a splitting of the ground state of CH(3)F(+). Observed trends in the spectra of the X (2)E ground states of these molecules are summarized. Whereas certain trends, such as the reduction of the observable effects of the Jahn-Teller interactions and the increase of the spin-orbit splitting with increasing nuclear charge of X and Y are easily understood, other trends are more difficult to explain, such as the much reduced spin-orbit splitting in CH(3)F(+) compared to CH(3)O. A simple two-state excitonic model is used to account for the trends observed within the series of the methyl-halide radical cations and also the similarities and differences between CH(3)F(+) and the isoelectronic CH(3)O radical. Within this model, the electron hole in the (2)E ground states of CH(3)X(+) and CH(3)Y is described in terms of contributions from the halogenic (or chalcogenic) p(x, y) orbitals and the pyramidal-methylic (e) orbitals. This model enables a global, semi-quantitative description of the combined effects of the Jahn-Teller and spin-orbit interactions in these molecules and also a simple interpretation of the spin-orbit-coupling reduction factor ζ(e).

A series of Fas receptor agonist antibodies that demonstrate an inverse correlation between affinity and potency.

Receptor agonism remains poorly understood at the molecular and mechanistic level. In this study, we identified a fully human anti-Fas antibody that could efficiently trigger apoptosis and therefore function as a potent agonist. Protein engineering and crystallography were used to mechanistically understand the agonistic activity of the antibody. The crystal structure of the complex was determined at 1.9 Å resolution and provided insights into epitope recognition and comparisons with the natural ligand FasL (Fas ligand). When we affinity-matured the agonist antibody, we observed that, surprisingly, the higher-affinity antibodies demonstrated a significant reduction, rather than an increase, in agonist activity at the Fas receptor. We propose and experimentally demonstrate a model to explain this non-intuitive impact of affinity on agonist antibody signalling and explore the implications for the discovery of therapeutic agonists in general.

Photoelectron spectroscopic study of the E⊗e Jahn-Teller effect in the presence of a tunable spin-orbit interaction. I. Photoionization dynamics of methyl iodide and rotational fine structure of CH3I+ and CD3I+.

The high-resolution single-photon pulsed-field-ionization zero-kinetic-energy photoelectron spectra of the X̃(+) (2)E(3/2)←X̃(1)A(1) transition of CH(3)I and CD(3)I have been recorded. The spectral resolution of better than 0.15 cm(-1) enabled the observation of the rotational structure. CH(3)I(+) and CD(3)I(+) are subject to a weak E⊗e Jahn-Teller effect and strong spin-orbit coupling. The treatment of the rovibronic structure of the photoelectron spectra in the corresponding spin double group, C(3v)(2)(M), including the effects of the spin-orbit interaction and the vibrational angular momentum, allowed the reproduction of the experimentally observed transitions with spectroscopic accuracy. The relevant spin-orbit and linear Jahn-Teller coupling parameters of the X̃(+) ground state were derived from the analysis of the spectra of the two isotopomers, and improved values were obtained for the adiabatic ionization energies [E(I)(CH(3)I)/hc=76931.35(20) cm(-1) and E(I)(CD(3)I)/hc=76957.40(20) cm(-1)] and the rotational constants of the cations. Rovibronic photoionization selection rules were derived for transitions connecting neutral states following Hund's-case-(b)-type angular momentum coupling and ionic states following Hund's-case-(a)-type coupling. The selection rules, expressed in terms of the angular momentum projection quantum number P, account for all observed transitions and provide an explanation for the nonobservation of several rotational sub-bands in the mass-analyzed threshold-ionization spectra of CH(3)I and CD(3)I reported recently by Lee et al. [J. Chem. Phys. 128, 044310 (2008)].

Generation of human TRIM5alpha mutants with high HIV-1 restriction activity.

Rhesus macaque tripartite motif (TRIM)5alpha potently inhibits early stages of human immunodeficiency virus (HIV)-1 replication, while the human orthologue has little effect on this virus. We used PCR-based random mutagenesis to construct a large library of human TRIM5alpha variants containing mutations in the PRYSPRY domain. We then applied a functional screen to isolate human cells made resistant to HIV-1 infection by the expression of a mutated TRIM5alpha. This protocol led to the characterization of a human TRIM5alpha variant containing a mutation at arginine 335 as conferring resistance to HIV-1 infection. The level of protection stemming from expression of this mutant was comparable to that of previously described mutations at position 332. R332/R335 double mutants decreased permissiveness to HIV-1 and to other lentiviruses by 20- to 50-fold in TE671 fibroblasts and in the T-cell line SUP-T1, and prevented HIV-1 spreading infection as efficiently as the rhesus macaque TRIM5alpha orthologue did. The finding that only two substitutions in human TRIM5alpha can confer resistance to HIV-1 at levels as high as one of the most potent natural orthologues of TRIM5alpha removes a roadblock toward the use of this restriction factor in human gene therapy applications.

Studies of the molecular mechanism of caspase-8 activation by solution NMR.

Caspases are the key players of apoptosis and inflammation. They are present in the cells as latent precursors, procaspases, and are activated upon an apoptotic or inflammatory stimulus. The activation mechanism of caspases has been studied extensively by biochemical and biophysical methods. Additional structural information on active caspases with a variety of different inhibitors bound at the active site is available. In this study, we investigated the cleavage mechanism of caspase-8 from its zymogen to active caspase-8 by solution NMR and by biochemical methods. The intermolecular cleavage reaction using the catalytically inactive C285A procaspase-8 mutant is triggered by adding caspase-8 and followed by (15)N,(1)H-NMR spectroscopy. The spectrum that initially resembles the one of procaspase-8 gradually over time changes to that of caspase-8, and disappearing peaks display exponential decaying intensities. Removal of either one of the cleavage recognition motifs in the linker, or phosphorylation at Tyr380, is shown to reduce the rate of the cleavage reaction. The data suggest that dimerization repositions the linker to become suitable for intermolecular processing by the associated protomer. Furthermore, analysis of inhibitor binding to the active caspase-8 reveals an induced-fit mechanism for substrate binding.

Rovibronic analysis of the Jahn-Teller effect in CH2D2(+) at low energies.

The Jahn-Teller effect in the ground state of CH(2)D(2)(+) has been studied by pulsed-field-ionization zero-kinetic-energy photoelectron spectroscopy. The lowest three bands have been assigned to the three isomers CH([l])H([l])D(s)D(s)(+), CH([l])H(s)D([l])D(s)(+), and CH(s)H(s)D([l])D([l])(+), in which the deuterium atoms are attached to the central carbon atom by two short bonds, one short and one long bond, and two long bonds, respectively, and which have different zero-point vibrational energies. Whereas CH([l])H([l])D(s)D(s)(+) and CH(s)H(s)D([l])D([l])(+) can each be described by a single structure with C(2v) symmetry, CH([l])H(s)D([l])D(s)(+) corresponds to four equivalent C(1) structures that interconvert by tunneling. The rotational structure of these three bands is compared with predictions made on the basis of a tunneling Hamiltonian combined with a rotational Hamiltonian that incorporates the effects of the large-amplitude tunneling motion. The zero-point energies of CH([l])H(s)D([l])D(s)(+) and CH(s)H(s)D([l])D([l])(+) relative to that of CH([l])H([l])D(s)D(s)(+) are Delta = 123.6(5) cm(-1) and Delta(') = 243.2(5) cm(-1), respectively, and the tunneling matrix element sigma coupling the four C(2v) equilibrium structures of CH([l])H(s)D([l])D(s)(+) is -1.7(4) cm(-1).

The SPRY domain of Pyrin, mutated in familial Mediterranean fever patients, interacts with inflammasome components and inhibits proIL-1beta processing.

The autoinflammatory disorders Muckle-Wells syndrome, familial cold urtecaria and chronic infantile neurological cutaneous and articular syndrome are associated with mutations in the NALP3 (Cryopyrin) gene, which is the central platform of the proinflammatory caspase-1 activating complex, named the inflammasome. In patients with another autoinflammatory disorder, familial Mediterranean fever (FMF), mutations in the SPRY domain of the Pyrin protein are frequently found. Recent evidence suggests that Pyrin associates with ASC, an inflammasome component, via its Pyrin domain, thereby halting the inflammatory response. This interaction, however, does not explain the effects of mutations of the SPRY domain found in FMF patients. Here we show that the Pyrin SPRY domain not only interacts with NALP3, but also with caspase-1 and its substrate pro-interleukin(IL)-1beta. Whereas a Pyrin knockdown results in increased caspase-1 activation and IL-1beta secretion, overexpression of the SPRY domain alone blocks these processes. Thus Pyrin binds to several inflammasome components thereby modulating their activity.

Evolution of anthropogenic aerosols in the coastal town of Salina Cruz, Mexico: part II particulate phase chemistry.

An analysis of atmospheric gases and particles during periods of land and sea breezes in a coastal city in southwest Mexico indicates limited removal of total particle mass by deposition during periods when the air resides over the ocean. The average PM(2.5) mass concentrations for land and sea breeze samples were 25+/-1.0 and 26+/-1.0 microg m(-3), respectively. The average sum of the ion concentrations (NH(4)(+), SO(4)(2-), NO(3)(-), Na(+), Cl(-)) were 10 and 11.8 microg m(-3) for the samples taken during land and sea breeze periods. The average total carbon concentrations were 6.0 and 5.3 microg m(-3) for land and sea breeze periods. The mass of sulfate in particles of ocean origin, 3.3+/-2.8 microg m(-3), is marginally higher than those originating from the land, 2.0+/-0.8 microg m(-3), presumably as a result of the conversion of SO(2) recirculated from the city. The fraction of sulfate, nitrate and ammonium ions in rainwater samples is almost a factor of two higher than the fraction measured on filtered air samples. The rainwater also contains significant concentrations of elemental and organic carbon. This study, although extending over a period of only 15 days, with limited chemical samples, suggests that recirculation of anthropogenic particles from coastal cities should be taken into consideration when diagnosing and predicting air quality in such regions.

nDsbD: a redox interaction hub in the Escherichia coli periplasm.

DsbD is a redox-active protein of the inner Escherichia coli membrane possessing an N-terminal (nDsbD) and a C-terminal (cDsbD) periplasmic domain. nDsbD interacts with four different redox proteins involved in the periplasmic disulfide isomerization and in the cytochrome c maturation systems. We review here the studies that led to the structural characterization of all soluble DsbD domains involved and, most importantly, of trapped disulfide intermediate complexes of nDsbD with three of its four redox partners. These results revealed the structural features enabling nDsbD, a 'redox hub' with an immunoglobulin-like fold, to interact efficiently with its different thioredoxin-like partners.

Evolution of anthropogenic aerosols in the coastal town of Salina Cruz, Mexico: part I particle dynamics and land-sea interactions.

Measurements of aerosol particles in a coastal city in southeast Mexico show that the concentrations and optical properties are strongly linked to land and sea breezes. Maximum concentrations of condensation nuclei (CN), black carbon (BC) and particle bound polycyclic aromatic hydrocarbons (PPAH) occur during land breeze periods and decrease with the sea breeze. The concentrations of particles in air from the ocean, however, remain significantly above background, maritime values as a result of the recirculation of anthropogenic emissions. The mass size distribution is dominated by particles larger than 5 microm when wind speeds exceed 4 m s(-1); otherwise, the uptake of water vapor onto unactivated particles is the process that dominates the growth of particles. Precipitation removes particles larger than 5 microm but CN, BC and PPAH concentrations are minimally affected.

Zooming in on the hydrophobic ridge of H-2D(b): implications for the conformational variability of bound peptides.

Class I major histocompatibility complex (MHC) molecules, which display intracellularly processed peptides on the cell surface for scanning by T-cell receptors (TCRs), are extraordinarily polymorphic. MHC polymorphism is believed to result from natural selection, since individuals heterozygous at the corresponding loci can cope with a larger number of pathogens. Here, we present the crystal structures of the murine MHC molecule H-2D(b) in complex with the peptides gp276 and np396 from the lymphocytic choriomeningitis virus (LCMV), solved at 2.18 A and 2.20 A resolution, respectively. The most prominent feature of H-2D(b) is a hydrophobic ridge that cuts across its antigen-binding site, which is conserved in the L(d)-like family of class I MHC molecules. The comparison with previously solved crystal structures of peptide/H-2D(b) complexes shows that the hydrophobic ridge focuses the conformational variability of the bound peptides in a "hot-spot", which could allow optimal TCR interaction and discrimination. This finding suggests a functional reason for the conservation of this structural element.

Structure of the soluble domain of a membrane-anchored thioredoxin-like protein from Bradyrhizobium japonicum reveals unusual properties.

TlpA is an unusual thioredoxin-like protein present in the nitrogen-fixing soil bacterium Bradyrhizobium japonicum. A hydrophobic N-terminal transmembrane domain anchors it to the cytoplasmic membrane, whereby the hydrophilic thioredoxin domain becomes exposed to the periplasmic space. There, TlpA catalyses an essential reaction, probably a reduction, in the biogenesis of cytochrome aa(3). The soluble thioredoxin domain (TlpA(sol)), devoid of the membrane anchor, was purified and crystallized. Oxidized TlpA(sol) crystallized as a non-covalent dimer in the space group P2(1)2(1)2(1). The X-ray structure analysis was carried out by isomorphous replacement using a xenon derivative. This resulted in a high-resolution (1.6 A) three-dimensional structure that displayed all of the features of a classical thioredoxin fold. A number of peculiar structural details were uncovered: (i) Only one of the two active-site-cysteine sulphurs (Cys72, the one closer to the N terminus) is exposed on the surface, making it the likely nucleophile for the reduction of target proteins. (ii) TlpA(sol) possesses a unique structural disulphide bond, formed between Cys10 and Cys155, which connects an unprecedented N-terminal alpha helix with a beta sheet near the C terminus. (iii) An insertion of about 25 amino acid residues, not found in the thioredoxin prototype of Escherichia coli, contributes only marginally to the thioredoxin fold, but forms an extra, surface-exposed alpha helix. This region plus another surface-exposed stretch (-Ile-Gly-Arg-Ala-), which is absent even in the closest TlpA relatives, might be considered as specificity determinants for the recognition of target proteins in the periplasm. The TlpA(sol) structure paves the way towards unraveling important structure-function relationships by rational mutagenesis.

Crystal structure of neuroserpin: a neuronal serpin involved in a conformational disease.

The protease inhibitor neuroserpin regulates the development of the nervous system and its plasticity in the adult. Neuroserpins carrying the Ser53Pro or Ser56Arg mutation form polymers in neuronal cells. We describe here the structure of wild-type neuroserpin in a cleaved form. The structure provides a basis to understand the role of the mutations in the polymerization process. We propose that these mutations could delay the insertion of the reactive center loop into the central beta-sheet A, an essential step in the inhibition and possibly in the polymerization of neuroserpin.

Structural genomics: opportunities and challenges.

Following the complete genome sequencing of an increasing number of organisms, structural biology is engaging in a systematic approach of high-throughput structure determination called structural genomics to create a complete inventory of protein folds/structures that will help predict functions for all proteins. First results show that structural genomics will be highly effective in finding functional annotations for proteins of unknown function.

Caspases: key players in programmed cell death.

Research in apoptosis has established a central role for caspases. The recent determination of structures of caspase-1, caspase-3 and caspase-8, together with biochemical studies, has greatly enhanced our understanding of the structure, function and specificity of these enzymes. This provides a basis for the further elucidation of the biological role of caspases and a guide to the design of selective inhibitors to treat caspase-mediated diseases.