Structures of free and inhibited human secretory phospholipase A2 from inflammatory exudate

Phospholipase A2 (PLA2) participates in a wide range of cellular processes including inflammation and transmembrane signaling. A human nonpancreatic secretory PLA2 (hnps-PLA2) has been identified that is found in high concentrations in the synovial fluid of patients with rheumatoid arthritis and in the plasma of patients with septic shock. This enzyme is secreted from certain cell types in response to the proinflammatory cytokines, tumor necrosis factor or interleukin-1. The crystal structures of the calcium-bound form of this enzyme have been determined at physiological pH both in the presence [2.1 angstrom (A) resolution] and absence (2.2 A resolution) of a transition-state analogue. Although the critical features that suggest the chemistry of catalysis are identical to those inferred from the crystal structures of other extracellular PLA2s, the shape of the hydrophobic channel of hnps-PLA2 is uniquely modulated by substrate binding.     

Surface and Bulk Charge Density Wave Structure in 1 T-TaS2

Incommensurate charge density waves (CDWs) in some materials form domains within which the CDWs may be commensurate. However, two questions have remained controversial: What is the geometrical structure of these domains, and are they or are they not identical on the surface and in the bulk? To address these issues in the triclinic (T) phase of tantalum disuffide (1T-TaS(2)) the CDW domain structure has been accurately determined for both the crystal surface and the crystal bulk. By analyzing the bulk CDW wave vectors and associated satellites by x-ray diffraction, it is found that the bulk contains three dimensionally ordered striped domains that have previously been misidentified. Scanning tunneling microscope images show that the striped domain configuration propagates unaltered to the crystal surface, and their Fourier transforms yield the same satellite positions as the x-rays. These observations demonstrate that the surface and bulk CDW domain structures in 1T-TaS(2) are identical.     

Orientational disorder in solvent-free solid c70

The high-temperature structure of solvent-free C(70) has been determined with high-resolution x-ray powder difraction and electron microscopy. Samples crystallized from solution form hexagonal close-packed crystals that retain an appreciable amount of residual toluene, even after prolonged heating. Samples prepared by sublimation, which contain no detectable solvent, are primarily face-centered cubic with some admixture of a hexagonal phase. The relative volume of the hexagonal phase can be further reduced by annealing. The structures of both phases are described by a model of complete orientational disorder. The cubic phase contains an appreciable density of stacking faults along the [111] direction.     

Dioxygen binds end-on to mononuclear copper in a precatalytic enzyme complex

Copper active sites play a major role in enzymatic activation of dioxygen. We trapped the copper-dioxygen complex in the enzyme peptidylglycine-alphahydroxylating monooxygenase (PHM) by freezing protein crystals that had been soaked with a slow substrate and ascorbate in the presence of oxygen. The x-ray crystal structure of this precatalytic complex, determined to 1.85-angstrom resolution, shows that oxygen binds to one of the coppers in the enzyme with an end-on geometry. Given this structure, it is likely that dioxygen is directly involved in the electron transfer and hydrogen abstraction steps of the PHM reaction. These insights may apply to other copper oxygen-activating enzymes, such as dopamine beta-monooxygenase, and to the design of biomimetic complexes.     

Structural features that stabilize halophilic malate dehydrogenase from an archaebacterium

The high-resolution structure of halophilic malate dehydrogenase (hMDH) from the archaebacterium Haloarcula marismortui was determined by x-ray crystallography. Comparison of the three-dimensional structures of hMDH and its nonhalophilic congeners reveals structural features that may promote the stability of hMDH at high salt concentrations. These features include an excess of acidic over basic residues distributed on the enzyme surface and more salt bridges present in hMDH compared with its nonhalophilic counterparts. Other features that contribute to the stabilization of thermophilic lactate dehydrogenase and thermophilic MDH-the incorporation of alanine into alpha helices and the introduction of negatively charged amino acids near their amino termini, both of which stabilize the alpha helix as a result of interaction with the positive part of the alpha-helix dipole-also were observed in hMDH.     

Crystal structure analysis of deamino-oxytocin: conformational flexibility and receptor binding

Two crystal structures of deamino-oxytocin have been determined at better than 1.1A resolution from isomorphous replacement and anomalous scattering x-ray measurements. In each of two crystal forms there are two closely related conformers with disulfide bridges of different chirality, which may be important in receptor recognition and activation.     

Crystal Structure of Hexaazaoctadecahydrocoronene Dication [HAOC]2+, a Singlet Benzene Dication

The structures of hexaazaoctadecahydrocoronene, [HAOC](n) (n = O, + 2), have been determined by single-crystal x-ray diffraction. Although HAOC is aromatic, its dication has a localized structure that is based upon Jahn-Teller-distorted cyanine/p-phenylenediammonium fragments. The structure is consistent with the singlet ground state as determined by magnetic susceptibility and contrasts with the simplest Hückel expectation of a triplet ground state.     

High-pressure chemistry of hydrogen in metals: in situ study of iron hydride

Optical observations and x-ray diffraction measurements of the reaction between iron and hydrogen at high pressure to form iron hydride are described. The reaction is associated with a sudden pressure-induced expansion at 3.5 gigapascals of iron samples immersed in fluid hydrogen. Synchrotron x-ray diffraction measurements carried out to 62 gigapascals demonstrate that iron hydride has a double hexagonal close-packed structure, a cell volume up to 17% larger than pure iron, and a stoichiometry close to FeH. These results greatly extend the pressure range over which the technologically important iron-hydrogen phase diagram has been characterized and have implications for problems ranging from hydrogen degradation and embrittlement of ferrous metals to the presence of hydrogen in Earth's metallic core.     

Crystal structures of Fe2+ dioxygenase superoxo, alkylperoxo, and bound product intermediates

We report the structures of three intermediates in the O2 activation and insertion reactions of an extradiol ring-cleaving dioxygenase. A crystal of Fe2+-containing homoprotocatechuate 2,3-dioxygenase was soaked in the slow substrate 4-nitrocatechol in a low O2 atmosphere. The x-ray crystal structure shows that three different intermediates reside in different subunits of a single homotetrameric enzyme molecule. One of these is the key substrate-alkylperoxo-Fe2+ intermediate, which has been predicted, but not structurally characterized, in an oxygenase. The intermediates define the major chemical steps of the dioxygenase mechanism and point to a general mechanistic strategy for the diverse 2-His-1-carboxylate enzyme family.     

Crystal and molecular structure of a phospholipid component: L-alpha-glycerophosphorylcholine cadmium chloride trihydrate

The structure of L-alpha-glycerophosphorylcholine cadmium chloride trihydrate has been determined by the conventional, single-crystal, x-ray diffraction technique. The phospholipid component displays the characteristic gauche conformation for the choline residue and the gauche-gauche conformation for the glycerol moiety. Therefore, a possible model for the structures of phospholipids is similar to that proposed by Finean.     

Studying enzyme mechanism by 13C nuclear magnetic resonance

High-resolution carbon-13 nuclear magnetic resonance (NMR) spectra of enzyme-inhibitor and enzyme-substrate complexes provide detailed structural and stereochemical information on the mechanism of enzyme action. The proteases trypsin and papain are shown to form tetrahedrally coordinated complexes and acyl derivatives with a variety of compounds artificially enriched at the site or sites of interest. These results are compared with the structural information derived from x-ray diffraction. Detailed NMR studies have provided a clearer picture of the ionization state of the residues participating in enzyme-catalyzed processes than other more classical techniques. The dynamics of enzymic catalysis can be observed at sub-zero temperatures by a combination of cryoenzymology and carbon-13 NMR spectroscopy. With these powerful techniques, transient, covalently bound intermediates in enzyme-catalyzed reactions can be detected and their structures rigorously assigned.     

A hexagonal (wurtzite) form of silicon

The existence of a hexagonal (wurtzite) form of silicon, similar to that form of diamond (carbon) observed in meteorites and in the laboratory, has been identified by x-ray diffraction in reaction-bonded silicon nitride containing unreacted silicon. The presence of this phase is due to stresses created in the silicon by the nitridation reaction.     

Chiral amplification of oligopeptides in two-dimensional crystalline self-assemblies on water

Differences in the two-dimensional packing arrangements of racemic and enantiomeric crystalline self-assemblies on the water surface of amphiphilic activated analogs of lysine and glutamic acid have been used to prepare oligopeptides of homochiral sequence and oligopeptides of single handedness from chiral nonracemic mixtures. The crystalline structures on the water surface were determined by grazing incidence x-ray diffraction and the diastereomeric composition of the oligopeptides by matrix-assisted laser desorption time-of-flight mass spectrometry with enantio-labeling. These results suggest that reactivity of ordered clusters at interfaces might have played a role in the generation of early homochiral biopolymers.     

Regulation of an enzyme by phosphorylation at the active site

The isocitrate dehydrogenase of Escherichia coli is an example of a ubiquitous class of enzymes that are regulated by covalent modification. In the three-dimensional structure of the enzyme-substrate complex, isocitrate forms a hydrogen bond with Ser113, the site of regulatory phosphorylation. The structures of Asp113 and Glu113 mutants, which mimic the inactivation of the enzyme by phosphorylation, show minimal conformational changes from wild type, as in the phosphorylated enzyme. Calculations based on observed structures suggest that the change in electrostatic potential when a negative charge is introduced either by phosporylation or site-directed mutagenesis is sufficient to inactivate the enzyme. Thus, direct interaction at a ligand binding site is an alternative mechanism to induced conformational changes from an allosteric site in the regulation of protein activity by phosphorylation.     

Conformation of N6-methyladenine, a base involved in DNA modification: restriction processes

Crystal structures of N(6),N(9)-dimethyladenine and N(6)-methyladenine hydrochloride were determined from three-dimensional x-ray diffraction data. The bases assume a conformation in which the N(6)-methyl group blocks one of the hydrogen-bonding sites normally used by adenine to form Watson-Crick pairs with thymine in double-helical DNA. When in this conformation, N(6)-methyladenine residues might alter the secondary structure of DNA. thereby preventing the scission of modified DNA's by restriction enzymes.     

Trace metals as biomarkers for eumelanin pigment in the fossil record

Well-preserved fossils of pivotal early bird and nonavian theropod species have provided unequivocal evidence for feathers and/or downlike integuments. Recent studies have reconstructed color on the basis of melanosome structure; however, the chemistry of these proposed melanosomes has remained unknown. We applied synchrotron x-ray techniques to several fossil and extant organisms, including Confuciusornis sanctus, in order to map and characterize possible chemical residues of melanin pigments. Results show that trace metals, such as copper, are present in fossils as organometallic compounds most likely derived from original eumelanin. The distribution of these compounds provides a long-lived biomarker of melanin presence and density within a range of fossilized organisms. Metal zoning patterns may be preserved long after melanosome structures have been destroyed.     

X-ray Pulsar in the Crab Nebula

X-ray pulsations have been observed in the Crab Nebula at a frequency closely matching the radio and optical pulsations. About 5 percent of the total x-ray power of the nebula appears in the pulsed component. The x-ray pulsations have the form of a main pulse and an interpulse separated by about 12 milliseconds.     

Crystal Structures of Titanium, Zirconium, and Hafnium at High Pressures

At high pressures, as determined by x-ray analysis, titanium and zirconium metal have a distorted, body-centered-cubic structure. This phase persists on pressure release. The normal hexagonal close-packed structures are recovered when the metals are heated. An electronic shift must occur in the transition. Hafnium metal showed no such transition.     

Molecular conformation of dihydrouridine: puckered base nucleoside of transfer RNA

The crystal structure of dihydrouridine hemihydrate has been determined by x-ray diffraction. Crystals of dihydrouridine contain two independent molecules in the asymmetric unit and a molecule of water. The x-ray structure determination has shown that the conformations of both molecules differ in important respects in the saturated base and the ribose. The molecular conformation of dihydrouridine has, for the first time, provided structural evidence that the rare nucleoside can proinote "loop" formation in the sugar-phosphate chain.