Electronic structure and catalytic behavior of tungsten carbide

Tungsten carbide has been shown to be an effective catalyst for a number of reactions that are readily catalyzed by platinum, but not at all by tungsten, and it was speculated that this behavior is due to changes in the electron distribution when carbon is added to tungsten. A test of this hypothesis, made by measuring the valence band x-ray photoelectron spectrum of tungsten carbide and comparing it with the spectra of tungsten and platinum, shows that, near the Fermi level, the electronic density of states of tungsten carbide more nearly resembles that of platinum than that of tungsten.     

Crystal structure of a complex between the catalytic and regulatory (RIalpha) subunits of PKA

The 2.0-angstrom structure of the cyclic adenosine monophosphate (cAMP)-dependent protein kinase (PKA) catalytic subunit bound to a deletion mutant of a regulatory subunit (RIalpha) defines a previously unidentified extended interface. The complex provides a molecular mechanism for inhibition of PKA and suggests how cAMP binding leads to activation. The interface defines the large lobe of the catalytic subunit as a stable scaffold where Tyr247 in the G helix and Trp196 in the phosphorylated activation loop serve as anchor points for binding RIalpha. These residues compete with cAMP for the phosphate binding cassette in RIalpha. In contrast to the catalytic subunit, RIalpha undergoes major conformational changes when the complex is compared with cAMP-bound RIalpha. The inhibitor sequence docks to the active site, whereas the linker, also disordered in free RIalpha, folds across the extended interface. The beta barrel of cAMP binding domain A, which is the docking site for cAMP, remains largely intact in the complex, whereas the helical subdomain undergoes major reorganization.     

The design and catalytic properties of a simplified ribonuclease P RNA

Ribonuclease P (RNase P) RNA is the catalytic moiety of the ribonucleoprotein enzyme that removes precursor sequences from the 5' ends of pre-transfer RNAs in eubacteria. Phylogenetic variation according to recently proposed secondary structure models was used to identify structural elements of the RNase P RNA that are dispensable for catalysis. A simplified RNase P RNA that consists only of evolutionarily conserved features was designed, synthesized, and characterized. Although the simplified RNA (Min 1 RNA) is only 263 nucleotides in length, in contrast to the 354 to 417 nucleotides of naturally occurring RNase P RNAs, its specificity of pre-tRNA cleavage is identical to that of the native enzymes. Moreover, the catalytic efficiencies of the Min 1 RNA and the native RNA enzymes are similar. These results focus the search for the catalytic elements of RNase P RNAs to their conserved structure.     

The cycle of violence

Despite widespread belief that violence begets violence, methodological problems substantially restrict knowledge of the long-term consequences of childhood victimization. Empirical evidence for this cycle of violence has been examined. Findings from a cohort study show that being abused or neglected as a child increases one's risk for delinquency, adult criminal behavior, and violent criminal behavior. However, the majority of abused and neglected children do not become delinquent, criminal, or violent. Caveats in interpreting these findings and their implications are discussed in this article.     

The sulfur cycle

Even granting our uncertainties about parts of our model of the sulfur cycle, we can draw some conclusions from it: 1) Man is now contributing about one half as much as nature to the total atmospheric burden of sulfur compounds, but by A.D. 2000 he will be contributing about as much, and in the Northern Hemisphere alone he will be more than matching nature. 2) In industrialized regions he is overwhelming natural processes, and the removal processes are slow enough (several days, at least) so that the increased concentration is marked for hundreds to thousands of kilometers downwind. 3) Our main areas of uncertainty, and ones that demand immediate attention because of their importance to the regional air pollution question, are: (i) the rates of conversion of H(2)S and SO(2) to sulfate particles in polluted as well as unpolluted atmospheres; (ii) the efficiency of removal of sulfur compounds by precipitation in polluted air. And for a better understanding of the global model we need to know: (i) the amount of biogenic H(2)S that enters the atmosphere over the continents and coastal areas; (ii) means of distinguishing man-made and biogenic contributions to excess sulfate in air and precipitation; (iii) the volcanic production of sulfur compounds, and their influence on the particle concentration in the stratosphere; (iv) the large-scale atmospheric circulation patterns that exchange air between stratosphere and troposphere (although absolute amounts of sulfate particles involved are small relative to the lower tropospheric burden); (v) the role of the oceans as sources or sinks for SO(2).     

Atomic-scale structure and catalytic reactivity of the RuO(2)(110) surface

The structure of RuO(2)(110) and the mechanism for catalytic carbon monoxide oxidation on this surface were studied by low-energy electron diffraction, scanning tunneling microscopy, and density-functional calculations. The RuO(2)(110) surface exposes bridging oxygen atoms and ruthenium atoms not capped by oxygen. The latter act as coordinatively unsaturated sites-a hypothesis introduced long ago to account for the catalytic activity of oxide surfaces-onto which carbon monoxide can chemisorb and from where it can react with neighboring lattice-oxygen to carbon dioxide. Under steady-state conditions, the consumed lattice-oxygen is continuously restored by oxygen uptake from the gas phase. The results provide atomic-scale verification of a general mechanism originally proposed by Mars and van Krevelen in 1954 and are likely to be of general relevance for the mechanism of catalytic reactions at oxide surfaces.     

Crystal structure of the catalytic subunit of cyclic adenosine monophosphate-dependent protein kinase

The crystal structure of the catalytic subunit of cyclic adenosine monophosphate-dependent protein kinase complexed with a 20-amino acid substrate analog inhibitor has been solved and partially refined at 2.7 A resolution to an R factor of 0.212. The magnesium adenosine triphosphate (MgATP) binding site was located by difference Fourier synthesis. The enzyme structure is bilobal with a deep cleft between the lobes. The cleft is filled by MgATP and a portion of the inhibitor peptide. The smaller lobe, consisting mostly of amino-terminal sequence, is associated with nucleotide binding, and its largely antiparallel beta sheet architecture constitutes an unusual nucleotide binding motif. The larger lobe is dominated by helical structure with a single beta sheet at the domain interface. This lobe is primarily involved in peptide binding and catalysis. Residues 40 through 280 constitute a conserved catalytic core that is shared by more than 100 protein kinases. Most of the invariant amino acids in this conserved catalytic core are clustered at the sites of nucleotide binding and catalysis.     

The catalytic cross-coupling of unactivated arenes

The industrially important coupling of aromatic compounds has generally required differential prefunctionalization of the arene coupling partners with a halide and an electropositive group. Here we report that palladium, in conjunction with a copper oxidant, can catalyze the cross-coupling of N-acetylindoles and benzenes in high yield and high regioselectivity across a range of indoles without recourse to activating groups. These reactions are completely selective for arene cross-coupling, with no products arising from indole or benzene homo-coupling detected by spectroscopic analysis. This efficient reactivity should be useful in the design of other oxidative arene cross-couplings as well.     

The structure of a retinal-forming carotenoid oxygenase

Enzymes that produce retinal and related apocarotenoids constitute a sequence- and thus structure-related family, a member of which was analyzed by x-ray diffraction. This member is an oxygenase and contains an Fe2+-4-His arrangement at the axis of a seven-bladed beta-propeller chain fold covered by a dome formed by six large loops. The Fe2+ is accessible through a long nonpolar tunnel that holds a carotenoid derivative in one of the crystals. On binding, three consecutive double bonds of this carotenoid changed from a straight all-trans to a cranked cis-trans-cis conformation. The remaining trans bond is located at the dioxygen-ligated Fe2+ and cleaved by oxygen.     

The structure of a mycobacterial outer-membrane channel

Mycobacteria have low-permeability outer membranes that render them resistant to most antibiotics. Hydrophilic nutrients can enter by way of transmembrane-channel proteins called porins. An x-ray analysis of the main porin from Mycobacterium smegmatis, MspA, revealed a homooctameric goblet-like conformation with a single central channel. This is the first structure of a mycobacterial outer-membrane protein. No structure-related protein was found in the Protein Data Bank. MspA contains two consecutive beta barrels with nonpolar outer surfaces that form a ribbon around the porin, which is too narrow to fit the thickness of the mycobacterial outer membrane in contemporary models.     

The evolution and future of Earth's nitrogen cycle

Atmospheric reactions and slow geological processes controlled Earth's earliest nitrogen cycle, and by ~2.7 billion years ago, a linked suite of microbial processes evolved to form the modern nitrogen cycle with robust natural feedbacks and controls. Over the past century, however, the development of new agricultural practices to satisfy a growing global demand for food has drastically disrupted the nitrogen cycle. This has led to extensive eutrophication of fresh waters and coastal zones as well as increased inventories of the potent greenhouse gas nitrous oxide (N(2)O). Microbial processes will ultimately restore balance to the nitrogen cycle, but the damage done by humans to the nitrogen economy of the planet will persist for decades, possibly centuries, if active intervention and careful management strategies are not initiated.     

Three-dimensional structure of an oncogene protein: catalytic domain of human c-H-ras p21

The crystal structure at 2.7 A resolution of the normal human c-H-ras oncogene protein lacking a flexible carboxyl-terminal 18 residue reveals that the protein consists of a six-stranded beta sheet, four alpha helices, and nine connecting loops. Four loops are involved in interactions with bound guanosine diphosphate: one with the phosphates, another with the ribose, and two with the guanine base. Most of the transforming proteins (in vivo and in vitro) have single amino acid substitutions at one of a few key positions in three of these four loops plus one additional loop. The biological functions of the remaining five loops and other exposed regions are at present unknown. However, one loop corresponds to the binding site for a neutralizing monoclonal antibody and another to a putative "effector region"; mutations in the latter region do not alter guanine nucleotide binding or guanosine triphosphatase activity but they do reduce the transforming activity of activated proteins. The data provide a structural basis for understanding the known biochemical properties of normal as well as activated ras oncogene proteins and indicate additional regions in the molecule that may possibly participate in other cellular functions.     

The molecular structure of a DNA-triostin A complex

The molecular structure of triostin A, a cyclic octadepsipeptide antibiotic, has been solved complexed to a DNA double helical fragment with the sequence CGTACG (C, cytosine; G, guanine; T, thymine; A, adenine). The two planar quinoxaline rings of triostin A bis intercalate on the minor groove of the DNA double helix surrounding the CG base pairs at either end. The alanine residues form hydrogen bonds to the guanines. Base stacking in the DNA is perturbed, and the major binding interaction involves a large number of van der Waals contacts between the peptides and the nucleic acid. The adenine residues in the center are in the syn conformation and are paired to thymine through Hoogsteen base pairing.     

The structure of ferrihydrite, a nanocrystalline material

Despite the ubiquity of ferrihydrite in natural sediments and its importance as an industrial sorbent, the nanocrystallinity of this iron oxyhydroxide has hampered accurate structure determination by traditional methods that rely on long-range order. We uncovered the atomic arrangement by real-space modeling of the pair distribution function (PDF) derived from direct Fourier transformation of the total x-ray scattering. The PDF for ferrihydrite synthesized with the use of different routes is consistent with a single phase (hexagonal space group P6(3)mc; a = approximately 5.95 angstroms, c = approximately 9.06 angstroms). In its ideal form, this structure contains 20% tetrahedrally and 80% octahedrally coordinated iron and has a basic structural motif closely related to the Baker-Figgis delta-Keggin cluster. Real-space fitting indicates structural relaxation with decreasing particle size and also suggests that second-order effects such as internal strain, stacking faults, and particle shape contribute to the PDFs.     

The structure of a complex of recombinant hirudin and human alpha-thrombin

The crystallographic structure of a recombinant hirudin-thrombin complex has been solved at 2.3 angstrom (A) resolution. Hirudin consists of an NH2-terminal globular domain and a long (39 A) COOH-terminal extended domain. Residues Ile1 to Tyr3 of hirudin form a parallel beta-strand with Ser214 to Glu217 of thrombin with the nitrogen atom of Ile1 making a hydrogen bond with Ser195 O gamma atom of the catalytic site, but the specificity pocket of thrombin is not involved in the interaction. The COOH-terminal segment makes numerous electrostatic interactions with an anion-binding exosite of thrombin, whereas the last five residues are in a helical loop that forms many hydrophobic contacts. In all, 27 of the 65 residues of hirudin have contacts less than 4.0 A with thrombin (10 ion pairs and 23 hydrogen bonds). Such abundant interactions may account for the high affinity and specificity of hirudin.