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The isolation and structural characterization of both aldehyde- and ketone-derived proline enaminones are reported and discussed. Crystal structures of 10 proline enamines provide information on stereochemical aspects, i.e., double bond configuration and syn vs. anti-positioning of the carboxylate relative to the enamine double bond. Furthermore, the obtained crystal structures are compared with the density functional theory-calculated structures of the ground and transition state and the postulated Seebach--Eschenmoser transition state. enamine catalysis | mechanism | organocatalysis doi/ 10.1073/pnas.1006509107

The longer emission wavelengths of red fluorescent proteins (RFPs) make them attractive for whole-animal imaging because cells are more transparent to red light. Although several useful RFPs have been developed using directed evolution, the quest for further red-shifted and improved RFPs continues. Herein, we report a structure-based rational design approach to red-shift the fluorescence emission of RFPs. We applied a combined computational and experimental approach that uses computational protein design as an in silico prescreen to generate focused combinatorial libraries of mCherry mutants. The computational procedure helped us identify residues that could fulfill interactions hypothesized to cause red-shifts without destabilizing the protein fold. These interactions include stabilization of the excited state through H-bonding to the acylimine oxygen atom, destabilization of the ground state by hydrophobic packing around the charged phenolate, and stabilization of the excited state by [pi]-stacking interaction. Our methodology allowed us to identify three mCherry mutants (mRojoA, mRojoB, and mRouge) that display emission wavelengths >630 nm, representing red-shifts of 20-26 nm. Moreover, our approach required the experimental screening of a total of ~5,000 clones, a number several orders of magnitude smaller than those previously used to achieve comparable red-shifts. Additionally, crystal structures of mRojoA and mRouge allowed us to verify fulfillment of the interactions hypothesized to cause red-shifts, supporting their contribution to the observed red-shifts. bathochromic shift | computational protein design |library design mCherry | crystal structures doi/ 10.1073/pnas.1013910107

The dehydration-rehydration process in gmelinite-Na [absolute value of [Na.sub.7.27] [K.sub.0.28] [Ca.sub.0.15] [([H.sub.2]O).sub.21.85]][[Al.sub.7.71][Si.sub.17.24][O.sub.48]]-GME, a natural zeolite that can be described as a parallel stacking of double six rings of tetrahedra in the AABB sequence, was studied by X-ray diffraction data. Its space group is [P6.sub.3]/mmc with a = 13.764(1) and c = 10.078(1) [Angstrom] cell parameters. Single-crystal data collections were performed at room conditions and at increasing temperatures, in a hot nitrogen stream, up to the fragmentation of the crystals, which occurs at a temperature as low as 100[degrees]C, and afterward the crystal was cooled down to room conditions. X-ray powder diffraction data showed that gmelinite-Na transforms into a new structure with an AFI-type topology at about 300[degrees]C. At room conditions, extraframework cations are located in two symmetrically independent positions, both of which are coordinated to either framework O atoms or water molecules. When the mineral is heated to 90 [degrees]C, about 40% of [H.sub.2]O is lost, and one cation site splits over two positions, which are three-coordinated to the framework O atoms. The dehydration process is completely reversible over a period of hours. X-ray single-crystal data has highlighted that gmelinite-Na when quenched at 100 K displays remarkable modifications in its extraframework content, resulting in a strong disorder in its extraframework ions. As in the case of heating, the mineral restores its structural features when brought back to room temperature. Keywords: Gmelinite, dehydration, rehydration, in situ crystal structure, low temperature DOI: 10.2138/am.2010.3419

Hydrous wadsleyite ([beta]-[Mg.sub.2]Si[O.sub.4]) with 2.8 wt% water content has been synthesized at 15 GPa and 1250[degrees]C in a multi-anvil press. The unit-cell parameters are: a = 5.6686(8), b = 11.569(1), c = 8.2449(9) [Angstrom], [beta] = 90.14(1)[degrees], and V = 540.7(1) [[Angstrom].sup.3], and the space group is I2/m. The structure was refined in space groups Imma and I2/m. The room-pressure structure differs from that of anhydrous wadsleyite principally in the increased cation distances around O1, the non-silicate oxygen. The compression of a single crystal of this wadsleyite was measured up to 61.3(7) GPa at room temperature in a diamond anvil cell with neon as pressure medium by X-ray diffraction at Sector 13 at the Advanced Photon Source, Argonne National Laboratory. The experimental pressure range was far beyond the wadsleyite-ringwoodite phase-transition pressure at 525 km depth (17.5 GPa), while a third-order Birch-Murnaghan equation of state (EoS) [[V.sub.0] = 542.7(8) [[Angstrom].sup.3], [K.sub.TO] = 137(5) GPa, K' = 4.6(3)] still fits the data well. In comparison, the second-order fit gives [V.sub.0] = 542.7(8) [[Angstrom].sup.3], [K.sub.T] = 147(2) GPa. The relation between isothermal bulk modulus of hydrous wadsleyite [K.sub.TO] and water content [MATHEMATICAL EXPRESSION NOT REPRODUCIBLE IN ASCII] is: KTO = 171 ( 1)-12(1 ) [MATHEMATICAL EXPRESSION NOT REPRODUCIBLE IN ASCII] (up to 2.8 wt% water). The axial-compressibility [[beta].sub.c] is larger than both [[beta].sub.a] and [[beta].sub.b], consistent with previous studies and analogous to the largest coefficient of thermal expansion along the c-axis. Keywords: Compressibility, hydrous wadsleyite, neon, orthorhombic DOI: 10.2138/am.2010.3533

The present paper reports a crystal-chemical study of minerals belonging to the proustite--pyrargyrite group by evaluating 32 natural samples of proustite and 27 samples of pyrargyrite from different localities that have variable chemical compositions. The unit-cell parameters were modeled as a function of the Sb contents. The a parameter is strongly influenced by the As [left and right arrow] Sb substitution, whereas the influence on the c parameter is very minor (nearly constant trend). The following equations were obtained from the linear fitting of the data: [a.sub.pred] = 10.8433(3) + 0.2019(4)Sb (apfu) [C.sub.pred] = 8.7189(6) + 0.0059(9)Sb (apfu) [V.sub.pred] = 887.77(7) + 34.0(1)Sb (apfu). The crystal structure of the members of the proustite--pyrargyrite solid solution consists of two sets of spiral chains parallel to the c-axis. Each chain contains alternating Ag and S atoms, with each chain being connected by As and Sb atoms, which are the apices of flat pyramidal As[S.sub.3]/Sb[S.sub.3] groups. Each S atom is part of a different Ag-S chain. The compositional data support the concept that proustite--pyrargyrite solid solutions re-equilibrate and exsolve to near end-member upon cooling. Examples of intermediate compositions are rare in nature and must have quenched above the solvus. Keywords: Sulfosalts, electron microprobe, proustite, pyrargyrite DOI: 10.2138/am.2010.3563

Since its first discovery in nature, natrolite has been largely known as a sodium aluminosilicate zeolite, showing very limited preference toward cation exchange. Here we show that fully K-exchanged natrolite can be prepared from natural Na-natrolite under mild aqueous conditions and used to subsequently produce Rb-and Cs-exchanged natrolites. These cation-exchanged natrolites exhibit successive volume expansions by ca. 10, 15.7, and 18.5% for K-, Rb-, and Cs-forms, respectively, compared to the original Na-natrolite. This constitutes the largest, ever-reported volume expansion via cation substitution observed in zeolites and occurs by converting the elliptical channels into progressively circular ones. The observed cation-dependent changes in the channel volume and shape thus show the flexibility limits of the natrolite framework and suggest the possible existence of compositionally altered analogues in suitable environments as well as a novel means to tailor the cation selectivity of this class of small pore zeolites toward various industrial and environmental applications. Keywords: Natrolite, ion-exchange, volume expansion, Rietveld refinement DOI: 10.2138/am.2010.3607

The crystal structures of biogenic Mn oxides produced by three fungal strains isolated from stream pebbles were determined using chemical analyses, XANES and EXAFS spectroscopy, and powder X-ray diffraction. The fungi-mediated oxidation of aqueous [Mn.Sup.2+] produces layered Mn oxides analogous to vernadite, a natural nanostructured and turbostratic variety of birnessite. The crystallites have domain dimensions of ~10 nm in the layer plane (equivalent to ~35 Mn[O.sub.6] octahedra), and ~1.5-2.2 nm perpendicularly (equivalent to ~2-3 layers), on average. The layers have hexagonal symmetry and from 22 to 30% vacant octahedral sites. This proportion likely includes edge sites, given the extremely small lateral size of the layers. The layer charge deficit, resulting from the missing layer [Mn.sup.4+] cations, is balanced mainly by interlayer [Mn.sup.3+] cations in triple-corner sharing position above and/or below vacant layer octahedra. The high surface area, defective crystal structure, and mixed Mn valence confer to these bio-minerals an extremely high chemical reactivity. They serve in the environment as sorption substrate for trace elements and possess catalytic redox properties. Keywords: Manganese oxide, birnessite, biominerals, phyllomanganate, crystal structure DOI: 10.2138/am.2010.3516

Forsterite ([Mg.sub.2]Si[O.sub.4]) is a silicate mineral frequently studied in the Earth sciences as it has a simple crystal structure and fast dissolution kinetics (elemental release rates under typical conditions on the order of [l0.sup.-7] mol/[m.sup.2]/[s.sup.1]). During the dissolution process, spectroscopic techniques are often utilized to augment solution chemical analysis and to provide data for determining reaction mechanisms. Nuclear magnetic resonance (NMR) is able to interrogate the local bonding arrangement and coordination of a particular nuclide to obtain structural information. Although previous NMR studies have focused on the silicon and oxygen environments in forsterite, studies focusing on the two nonequivalent magnesium environments in forsterite are limited to a few single-crystal studies. In this study, we present the results of [sup.25]Mg MAS, MQMAS, and static QCPMG experiments performed on a powdered sample of a pure synthetic forsterite. We also present spectral fits obtained from simulation software packages, which directly provide quadrupolar parameters for [sup.25]Mg nuclei occupying each of the two nonequivalent magnesium sites in the forsterite structure. These results are compared to calculations of the electric field gradient tensor conducted in previous ab initio studies to make definitive assignments correlating each peak to their respective magnesium site in the forsterite structure. Althought previous NMR investigations of forsterite have focused on single-crystal samples, we have focused on powdered forsterite as the increased surface area of powdered samples makes them more amenable to laboratory-scale dissolution studies and, ultimately, the products from chemical weathering may be monitored and quantified. Keywords: Forsterite, magnesium, [sup.25]Mg, NMR, MQMAS, QCPMG DOI: 10.2138/am.2010.3403

Invertases are highly regulated enzymes with essential functions in carbohydrate partitioning, sugar signaling, and plant development. Here we present the 2.6 A crystal structure of Arabidopsis cell-wall invertase 1 (INV1) in complex with a protein inhibitor (CIF, or cell-wall inhibitor of [beta]-fructosidase) from tobacco. The structure identifies a small amino acid motif in CIF that directly targets the invertase active site. The activity of INV1 and its interaction with CIF are strictly pH-dependent with a maximum at about pH 4.5. At this pH, isothermal titration calorimetry reveals that CIF tightly binds its target with nanomolar affinity. CIF competes with sucrose (Suc) for the same binding site, suggesting that both the extracellular Suc concentration and the pH changes regulate association of the complex. A conserved glutamate residue in the complex interface was previously identified as an important quantitative trait locus affecting fruit quality, which implicates the invertase-inhibitor complex as a main regulator of carbon partitioning in plants. Comparison of the CIF/INV1 structure with the complex between the structurally CIF-related pectin methylesterase inhibitor (PMEI) and pectin methylesterase indicates a common targeting mechanism in PMEI and CIF. However, CIF and PMEI use distinct surface areas to selectively inhibit very different enzymatic scaffolds. active site | crystallography | post-translational enzyme regulation | protein complex | sugar metabolism doi/ 10.1073/pnas.1004481107

Differences between the structures of bacterial, archaeal, and eukaryotic ribosomes account for the selective action of antibiotics. Even minor variations in the structure of ribosomes of different bacterial species may lead to idiosyncratic, species-specific interactions of the drugs with their targets. Although crystallographic structures of antibiotics bound to the peptidyl transferase center or the exit tunnel of archaeal (Haloarcula marismortui) and bacterial (Deinococcus radiodurans) large ribosomal subunits have been reported, it remains unclear whether the interactions of antibiotics with these ribosomes accurately reflect those with the ribosomes of pathogenic bacteria. Here we report X-ray crystal structures of the Escherichia coli ribosome in complexes with clinically important antibiotics of four major classes, including the macrolide erythromycin, the ketolide telithromycin, the lincosamide clindamycin, and a phenicol, chloramphenicol, at resolutions of ~3.3 [Angstrom]-3.4 [Angstrom]. Binding modes of three of these antibiotics show important variations compared to the previously determined structures. Biochemical and structural evidence also indicates that interactions of telithromycin with the E. coli ribosome more closely resembles drug binding to ribosomes of bacterial pathogens. The present data further argue that the identity of nucleotides 752, 2609, and 2055 of 23S ribosomal RNA explain in part the spectrum and selectivity of antibiotic action. ribosome structure | erythromycin | telithromycin | clindamycin | chloramphenicol doi/ 10.1073/pnas.1007988107

The increasing prevalence of antibiotic-resistant pathogens reinforces the need for structures of antibiotic-ribosome complexes that are accurate enough to enable the rational design of novel ribosome-targeting therapeutics. Structures of many antibiotics in complex with both archaeal and eubacterial ribosomes have been determined, yet discrepancies between several of these models have raised the question of whether these differences arise from species-specific variations or from experimental problems. Our structure of chloramphenicol in complex with the 70S ribosome from Thermus thermophilus suggests a model for chloramphenicol bound to the large subunit of the bacterial ribosome that is radically different from the prevailing model. Further, our structures of the macrolide antibiotics erythromycin and azithromycin in complex with a bacterial ribosome are indistinguishable from those determined of complexes with the 50S subunit of Haloarcula marismortui, but differ significantly from the models that have been published for 50S subunit complexes of the eubacterium Deinococcus radiodurans. Our structure of the antibiotic telithromycin bound to the T. thermophilus ribosome reveals a lactone ring with a conformation similar to that observed in the H. marismortui and D. radiodurans complexes. However, the alkyl-aryl moiety is oriented differently in all three organisms, and the contacts observed with the T. thermophilus ribosome are consistent with biochemical studies performed on the Escherichia coli ribosome. Thus, our results support a mode of macrolide binding that is largely conserved across species, suggesting that the quality and interpretation of electron density, rather than species specificity, may be responsible for many of the discrepancies between the models. crystal structure | structure-based drug design doi/ 10.1073/pnas.1008685107

The importance of nonclassical, multistage crystallization pathways is increasingly evident from theoretical studies on colloidal systems and experimental investigations of proteins and biomineral phases. Although theoretical predictions suggest that proteins follow these pathways as a result of fluctuations that create unstable dense-liquid states, microscopic studies indicate these states are long-lived. Using in situ atomic force microscopy to follow 2D assembly of S-layer proteins on supported lipid bilayers, we have obtained a molecular-scale picture of multistage protein crystallization that reveals the importance of conformational transformations in directing the pathway of assembly. We find that monomers with an extended conformation first form a mobile adsorbed phase, from which they condense into amorphous clusters. These clusters undergo a phase transition through S-layer folding into crystalline clusters composed of compact tetramers. Growth then proceeds by formation of new tetramers exclusively at cluster edges, implying tetramer formation is autocatalytic. Analysis of the growth kinetics leads to a quantitative model in which tetramer creation is rate limiting. However, the estimated barrier is much smaller than expected for folding of isolated S-layer proteins, suggesting an energetic rationale for this multistage pathway. in situ atomic force microscopy imaging | protein crystal growth | two-step crystallization | amorphous precursors | assembly kinetics doi/ 10.1073/pnas.1008280107

Ottoite, [Pb.sub.2]Te[O.sub.5], is a new tellurate from Otto Mountain near Baker, California. Most of the mining on Otto Mountain occurred between 1940 and 1970 and is attributed to Otto Fuetterer, for whom the mountain is now named. The new mineral occurs on fracture surfaces and in small vugs in brecciated quartz veins, which intersect granitic rocks. Ottoite is directly associated with acanthite, bromine-rich chlorargyrite, gold, iodargyrite, khinite, wulfenite, and four other new tellurates: housleyite, mark-cooperite, thorneite, and timroseite. Various other secondary minerals occur in the veins, including two other new secondary tellurium minerals, paratimroseite and telluroperite. Ottoite and most other secondary minerals of the quartz veins are interpreted as having formed from the partial oxidation of primary sulfides and tellurides during or following brecciation of the veins. A later generation of quartz mineralization then recemented the breccias, effectively isolating and protecting the secondary mineralization from further alteration. Ottoite is monoclinic, space group 12/a, with the unit cell: a = 7.5353(6), b = 5.7142(5), c = 10.8981(12) [Angstrom], [beta] = 91.330(6)[degrees], V= 469.13(8) [[Angstrom].sup.3] , and Z = 4. The mineral occurs as complex spear-shaped crystals in subparallel to divergent intergrowths. It is yellow and transparent to translucent, with a pale yellow streak and adamantine luster. Mohs hardness is estimated at 3. The mineral is brittle, with an irregular fracture and two cleavages in the [100] zone at -90[degrees]--possibly on {010} and {001}. The calculated density is 8.721 g/[cm.sup.3]. Ottoite is biaxial (-), with a large 2 V, but indices of refraction are too high to be measured. The optic orientation could only partially be determined: Y [approximately equal to] a. No pleochroism was observed. Electron microprobe analyses provided the following averages: PbO 68.88 and Te[O.sub.3]28.03, total 96.95 wt%; the empirical formula (based on O = 5) is [Pb.sub.1.96][Te.sup.6+.sub.1.01][O.sub.5]. The strongest powder X-ray diffraction lines are [[d.sub.obs] in [Angstrom] (hkl) I]: 3.131 ([bar.2]02) 64, 3.055 (013) 90, 3.015 (211) 100, 2.112 (522) 29, 1.810 (006, 215) 21, 1.773 (411,402) 43, 1.686 (033, 231) 20. The crystal structure (R~ = 0.020) consists of straight chains of trans-comer-sharing [Te.sup.6+][O.sub.6] octahedra parallel to a, which are joined by bonds to Pb atoms. The Pb atom exhibit markedly lopsided 11-coordination, typical of Pb2+ with stereoactive 6s2 lone-pair electrons. The powder X-ray diffraction pattern of ottoite is very similar to that reported for girdite. Examination of girdite type material suggests that its description was based upon data obtained from at least two and possibly three different phases, one of which may correspond to ottoite. Keywords: Ottoite, girdite, new mineral, tellurate, crystal structure, stereoactive lone-pair, Otto Mountain, California DOI: 10.2138/am.2010.3510

Housleyite, [Pb.sub.6]Cu[Te.sub.4][O.sub.18][(OH).sub.2], is a new tellurate from Otto Mountain near Baker, California, named in honor of Robert M. Housley. The new mineral occurs on fracture surfaces and in small vugs in brecciated quartz veins. Housleyite is directly associated with acanthite, cerussite, gold, iodargyrite, khinite-40, wulfenite, and three other new tellurates: markcooperite, ottoite, and thorneite. A variety of other secondary minerals occur in the veins, including three other new secondary tellurium minerals, paratimroseite, telluroperite, and timroseite. Housleyite is monoclinic, space group [P2.sub.1]/n, a = 7.8552(5), b = 10.4836(7), c = 11.0426(8) [Angstrom], [beta] = 95.547(2)[degrees], and Z = 2. Crystals are prismatic to bladed with elongation parallel to b and typically occur in bow tie-like aggregates, drusy balls, and irregular sprays. It is pale to medium greenish blue and transparent, with pale blue streak and adamantine luster. Mohs hardness is estimated at 3. The mineral is brittle, with an irregular fracture. Cleavage was not observed, but is likely on { 101}. The calculated density is 7.845(1 ) g/[cm.sup.3]. Housleyite is biaxial (+), with 2V= 50[degrees] to 60[degrees] and strong inclined dispersion, r > v, but indices of refraction are too high to be measured. The optic orientation is Y = b, Z and c [approximately equal to] 40[degrees] in obtuse [beta] and pleochroism is Y (medium green-blue) > Z (light green-blue) > X. Energy dispersive spectroscopy provided PbO 62.53, CuO 3.77, Te[O.sub.3] 32.85, [H.sub.2]O 0.84 (structure), total 99.99 wt%.; the empirical formula (based on O = 20) is [Pb.sub.5.99][Cu.sub.1.01][Te.sub.4.00][O.sub.18][(OH).sub.2]. The strongest powder X-ray diffraction lines are [[d.sub.obs] in [Angstrom] (hkl) I]: 3.336 ([bar.2]02, 031,122) 69, 3.292 ([bar.1]13) 50, 3.195 (130, 103) 100, 3.068 ([bar.2]21,202) 47, 3.007 (023) 49, 2.942 (032, 212) 80, 2.723 (123,[bar.2]13, 132) 29, 2.580 (230, [bar.3]01, [bar.2]31) 38. The crystal structure ([R.sub.1] = 0.028) consists of comer-sharing chains of Te[O.sub.6] octahedra along [101] linked into slabs parallel to {10[bar.1]} by sharing edges and comers with strongly Jahn-Teller (4+2) distorted and severely skewed CuO6 octahedra. Lead (Pb) atoms in lopsided nine- and elevenfold coordinations form additional links within and between the octahedral sheets. Keywords: Housleyite, new mineral, tellurate, crystal structure, Otto Mountain, California DOI: 10.2138/am.2010.3511

A new high-pressure form of topaz-OH (denoted here topaz-OH 11) was obtained at 14 GPa and 1400[degrees]C. The X-ray diffraction pattern of this phase can be indexed by an orthorhombic cell with a = 4.72318(5), b = 8.91480(9), and c = 2.77276(3) [Angstrom]. The lengths of a and b are similar, but c is approximately a third of that for a previously reported topaz-OH (denoted topaz-OH I). The structural formula of topaz-OH II can be written as ([Al.sub.0.68][Si.sub.0.32])[([O.sub.0.66][(OH).sub.0.34]).sub.2], suggesting significant cation disorder in the structure. The crystal structure of topaz-OH II is solved using powder synchrotron X-ray diffraction data, and refined with constraints provided by a separate multi-nuclear NMR study. The structure has similarities with topaz-OH I and diaspore ([alpha]-A1OOH) structures, having partially occupied double edge-shared octahedral chains, and 2 x 1 tunnels with partially occupied tetrahedral and octahedral sites. Keywords: Crystal structure, high-pressure studies, phase transition, order-disorder DOI: 10.2138/am.2010.3555

Schwertmannite is a poorly crystalline mineral that forms ochre rusts and precipitates in acid mine environments. Despite its ubiquity and its role as scavenger of important contaminants such as arsenic or selenium, its structure has not been yet determined. Here, a structure for schwertmannite is presented based on pair distribution function (PDF) data, X-ray diffraction (XRD) analyses, and density functional theory (DFT) calculations. We propose a structure formed by a deformed frame of iron octahedra similar to that of akaganeite. Simulations of X-ray diffraction patterns unveil the presence of long-range order associated with the position of the sulfate molecules, providing a useful way to discern two types of sulfate complexes in the structure. The simulations suggest that two sulfate molecules per unit cell are present in the structure forming one outer sphere and one inner sphere complex inside the channels formed by iron octahedra. Knowledge of the positions of the sulfates in the structure will help to better understand exchange processes with oxyanions of trace contaminants, such as arsenate, chromate, or selenate, that strongly influence their biogeochemical cycling in mining ecosystems. Keywords: Schwertmannite, diffraction, structure, X-ray, pair distribution function, DFT, iron, sulfate DOI: 10.2138/am.2010.3446

A new polymorph of topaz-OH (denoted as topaz-OH II) was recently discovered at higher P-T conditions than has been known thus far (denoted as topaz-OH I). High-resolution [sup.1]H, [sup.29]Si, and [sup.27]Al nuclear magnetic resonance (NMR) and micro-Raman spectroscopy are applied to shed light on the crystal chemistry of both polymorphs. Topaz-OH I, synthesized at 7 GPa and 640 [degrees]C, is stoichiometric (Si/Al = 0.5) with a largely ordered local structure. Higher P-T topaz-OH I synthesized at conditions close to the polymorphic phase transition boundary, on the other hand, shows lower Si/A1 ratios (0.44-0.45) and greater local structural disorder [including a small fraction (-3%) of octahedral Si with a unique [sup.29]Si chemical shift near-133 ppm]. The latter may be accounted for by the development of defects (Si/Al in normally vacant octahedral sites and vacancies in the tetrahedral sites) at higher P-T conditions. Topaz-OH II synthesized at 13.5~14 GPa and 1300-1400 [degrees]C similarly exhibits low Si/Al ratios (0.41-0.46). The NMR and Raman spectra for these topaz-OH II are, in general, broader and revealed a substantial fraction (33-37%) of octahedral Si with a range of [sup.29]Si chemical shifts (-130 to -190 ppm), a small fraction (2-3%) of tetrahedral Al, and a range of (and overall shorter) hydrogen-bonding distances than topaz-OH I. Therefore, the phase transition from topaz-OH I to II is characterized by both a significant increase in the occupied octahedral/tetrahedral site ratio as well as disordering of cation distribution, which is unique from the viewpoint of crystal chemistry. Keywords: NMR spectroscopy, Raman spectroscopy, high pressure, crystal structure, phase transition, vacancy, vacant site, Al-Si disorder, hydrogen bonding DOI: 10.2138/am.2010.3471

[Fe.sup.3+] and [Mn.sup.3+] distributions on octahedral M1, M2, and M3 sites in synthetic epidote/piemontite from [Ca.sub.2][Al.sub.2][Fe.sup.3+.sub.l-q][Si.sub.3][O.sub.12.5] starting material and their effects on the crystal structure were investigated using X-ray Rietveld and [sup.57]Fe Mossbauer methods. Epidote and piemontite were crystallized as almost single phases from q = 1.0, 0.75, 0.5, and 0.25 starting materials at [P.sub.fluid] of 200-400 MPa and a temperature of 500[degrees]C, using standard cold-seal pressure vessels. The [Mn.sub.2][O.sub.3]-Mn[O.sub.2] buffer was used to produce fog adequate to maintain [Fe.sup.3+] and [Mn.sup.3+]. The Rietveld refinements converged to goodness-of-fit ranges from 1.21 to 1.60. At this temperature, site preferences of [summation]([Fe.sup.3+] + [Mn.sup.3+]) for octahedral sites are M3>MI(>>M2). [K.sub.D] values of [summation]([Fe.sup.3+] + [Mn.sup.3+]), where [K.sub.D] = [([Fe.sup.3+] + [[Mn.sup.3+] )/Al].sup.M1] /[([Fe.sup.3+] + [[Mn.sup.3+])/Al].sup.M3], (0.05-0.13) are similar to those of individual [Mn.sup.3+] and [Fe.sup.3+] vs. [Al.sup.3+], respectively. However, the [K.sub.D] values of [Fe.sup.3+] and [Mn.sub.3+] for M1 and M3, where [K.sub.D] = [([Fe.sup.3+]/[Mn.sup.3+]).sup.M1]/ [([Fe.sup.3+]/[Mn.sup.3+]).sup.M3], vary with [Fe.sup.3+.sub.Total]: [Mn.sup.3+.sub.Total] ratios. In epidote with [Fe.sup.3+] content larger than 0.4 atoms per formula unit (apfu) and [Mn.sup.3+] < 0.6 apfu, [Fe.sup.3+] has a stronger preference for M1 than [Mn.sup.3+]. In piemontite with 0.12 [Fe.sup.3+] and 0.73-0.78 [Mn.sup.3+] apfu, the preference of [Mn.sup.3+] for M1 is greater than that of [Fe.sup.3+]. The site occupancies of individual [Mn.sup.3+] and [Fe.sup.3+] are governed by the individual [K.sub.D] values and the [Mn.sup.3+] and [Fe.sup.3+] concentrations in corresponding epidote and piemontite. Variations of the unit-cell parameters indicate the combined result of linear variation due to Al [left and right arrow] [Fe.sup.3+] substitution and nonlinear variation due to Al [left and right arrow] [Mn.sup.3+] substitution. Keywords: Epidote, piemontite, synthesis, Rietveld refinement, M6ssbauer spectroscopy DOI: 10.2138/am.2010.3418

The crystal structure and crystal chemistry of chromian pumpellyite from basic schist in the Osayama ultramafic body, Okayama, Japan, were investigated using electron probe microanalysis (EPMA), Fourier transform infrared spectroscopy (FTIR), and single-crystal X-ray diffraction to determine the distribution of chromium between two independent octahedral sites and structural changes caused by ionic substitutions in pumpellyite, [sup.VII][W.sub.8][sup.VI][X.sub.4][sup.VI][Y.sub.8] [sup.IV][Z.sub.12][O.sub.56-n],[(OH).sub.n], (Z = 1). Five cbromian pumpellyite crystals (ocpl211, ocp0604, ocp1028, ocpl013, and ocpl016) with 0.52, 1.65, 1.26, 1.94, and 1.43 Cr atoms per formula unit (apfu) (EPMA data), respectively, were picked from a hand specimen for X-ray diffraction analysis. The crystal structures (space group C2/m) of ocp1211 [a = 19.1129(6), b = 5.8963(5), c = 8.818(1) [Angstrom],[beta] = 97.449(2)[degrees]], ocp0604 [a = 19.0935(4), b = 5.900(1), c = 8.810(2) A, [Angstrom],[beta] = 97.540(7)[degrees]], ocp1028 [a = 19.105(2), b = 5.9021(6), c = 8.8143(7) [Angstrom], [beta] = 97.513(3)[degrees]], ocp1013 [a = 19.1558(6), b = 5.9125(9), c = 8.844(1) [Angstrom], [beta] = 97.448(4)[degrees]], and ocp1016 [a = 19.174(3), b = 5.9194(8), c = 8.830(1) [Angstrom], [beta] = 97.497(4)[degrees]] were refined using 1058, 829, 1070, 1105, and 1095 unique reflections, and calculations converged at R factors of 4.08, 5.02, 6.32, 6.92, and 7.88%, respectively. The resulting site populations at the X and Y sites are [([Mg.sub.1.88][Al.sub.1.51] [Fe.sup.2+.sub.0.38] [Cr.sub.0.16][Mn.sup.2+.sub.0.05][Ni.sub.0.02]).sup.X] [([Al.sub.7.90][Ti.sub.0.07][V.sub.0.03]).sup.Y] for ocp1211, [([Mg.sub.1.81][Al.sub.1.53][Cr.sub.0.42][Fe.sup.2+.sub.0.18] [Mn.sup.2+.sub.0.04][Ni.sub.0.01]).sup.X][([Al.sub.7.34] [Cr.sub.0.65][V.sub.0.01]).sup.Y]for ocp0604, [([Al.sub.1.62] [Mg.sub.1.60][Cr.sub.0.61][Fe.sup.2+.sub.0.13][Mn.sup.2+.sub.0.03] [Ni.sub.0.01]).sup.X][([Al.sub.7.36][Cr.sub.0.61][V.sub.0.03]).sup.Y] for ocp1028, [([Mg.sub.1.79][Al.sub.1.33][Cr.sub.0.47] [Fe.sup.2+.sub.0.33][Mn.sup.2+.sub.0.08]).sup.X] ([Al.sub.1.62][Mg.sub.1.60][Cr.sub.0.61][Fe.sup.2+.sub.0.13][Mn.sup.2+. sub.0.03][Ni.sub.0.01]).sup.X]) [([Al.sub.7.36][Cr.sub.0.61][V.sub.0.03]).sup.Y] for ocp1016. [Cr.sup.3+] ions in ocp 1211 are distributed only in the X site. The distribution coefficient of Cr and Al between the X and Y sites [[(Cr/A1).sup.x]/[(Cr/Al).sup.Y]] is 1.66, 1.79, 3.09, and 4.54 for ocp1016, ocp1013, ocp0604, and ocp1028, respectively, indicating a stronger preference of Cr for the X site than the Y site. The a and b axes increase with increasing Cr content, whereas the c axis is almost constant. The mean Y-O distances increase linearly with increased [Cr.sup.3+] content in the Y site. However, the mean X-O distances do not depend on the substitution of [Cr.sup.3+] for [Al.sup.3+] at the X site. The bond valence sums and the difference-Fourier synthesis indicate that hydroxyl groups are located at the 05, 07, O10, and O11 positions. FTIR spectrum shows main absorption bands at ca. 2911, 3220, 3397, and 3512 [cm.sup.-1] of OH-stretching vibrations, indicating the presence of OH ... O hydrogen bonds. Keywords: Pumpellyite, chromium, X-ray structural analysis, crystal chemistry, FTIR DOI: 10.2138/am.2010.3376

This paper reports the results of an in situ high-pressure synchrotron X-ray powder diffraction investigation on the natural zeolite boggsite [([K.sub.0.06][Na.sub.0.36][Sr.sub.0.01] [Ca.sub.7.00] [Mg.sub.1.20])([Al.sub.17.52][Si.sub.78.62][Fe.sub.0.05][O.sub.192]) x 82.3 [H.sub.2]O]. The study was performed using both a (16:3:1) methanol:ethanol:water mixture (m.e.w.) as a nominally 'penetrating' hydrostatic P-transmitting medium and silicon oil (s.o.) as a'non-penetrating' medium. The studied pressure ranges are: [P.sub.amb] -7.6 and [P.sub.amb] -5.9 GPa in m.e.w and s.o., respectively. No complete X-ray amorphization is observed up to the highest investigated pressures, and the original unit-cell parameters are almost completely recovered upon decompression in both media. The reductions of a, b, c, and V, within the pressure-ranges investigated, are 5.3, 4.2, 4.0, and 13.0% in s.o. and 4.1, 4.1, 3.8, and 11.5% in m.e.w. The Rietveld structural refinements of the powder patterns of the experiments in m.e.w, converged successfully up to 3.6 GPa and demonstrated the penetration of 13 additional water molecules between 0.3 and 2.9 GPa. This over-hydration occurs without any unit-cell volume expansion and can be explained by the fact that no new extraframework sites arise during compression and that water penetration is the only factor to increase the occupancy of already existing sites. Boggsite compressibility is higher in s.o. than in m.e.w. In particular, compressibility in m.e.w. is lower below 3 GPa, whereas above this pressure, the P-V trend becomes similar in the two media. This can be ascribed to the fact that, during water molecule penetration (0.3 < P < 3 GPa), the effect of the P-transmitting medium is directed to compress the system as well as to penetrate the channels. Keywords: Zeolite, boggsite, high pressure, compressibility, over-hydration, crystal structure, synchrotron XRPD data DOI: 10.2138/am.2010.3482

The V K-edge spectrum of a V-bearing grossular garnet (tsavorite) single crystal has been measured by high-energy resolution fluorescence detected X-ray absorption spectroscopy (HERFD-XAS). First-principles calculations based on the density functional theory (DFT) reproduce the experimental spectra well, including the angular dependence of the pre-edge. The latter arises from pure electric quadrupole transitions since vanadium is incorporated in a centrosymmetric site, which inhibits the electric dipole transitions. An interpretation of the spectral features is given using a monoelectronic description of the transitions involved in the X-ray absorption process. The assignment of experimental pre-edge peaks in terms of 1s-3d transitions makes it possible to determine the magnitude of the 3d-splitting, which is similar to the 10 Dq crystal-field value determined from optical absorption spectroscopy. DFT calculations also indicate a full structural relaxation around [V.sup.3+] substituting [Al.sup.3+] in the garnet structure. The angular dependence only causes weak variations of the pre-edge intensity, which supports the use of V-bearing grossular garnet as a reference compound for octahedral [V.sup.3+]. Keywords: Vanadium, garnet, HERFD-XAS, DFT calculations, K pre-edge, angular dependence, structural relaxation, crystal-field splitting DOI: 10.2138/am.2010.3432

Hepatocyte growth factor (HGF) is an activating ligand of the Met receptor tyrosine kinase, whose activity is essential for normal tissue development and organ regeneration but abnormal activation of Met has been implicated in growth, invasion, and metastasis of many types of solid tumors. HGF has two natural splice variants, NK1 and NK2, which contain the N-terminal domain (N) and the first kringle (K1) or the first two kringle domains of HGF. NK1, which is a Met agonist, forms a head-to-tail dimer complex in crystal structures and mutations in the NK1 dimer interface convert NK1 to a Met antagonist. In contrast, NK2 is a Met antagonist, capable of inhibiting HGF's activity in cell proliferation without clear mechanism. Here we report the crystal structure of NK2, which forms a 'closed' monomeric conformation through interdomain interactions between the N- domain and the second kringle domain (K2). Mutations that were designed to open up the NK2 closed conformation by disrupting the N/K2 interface convert NK2 from a Met antagonist to an agonist. Remarkably, this mutated NK2 agonist can be converted back to an antagonist by a mutation that disrupts the NK1/NK1 dimer interface. These results reveal the molecular determinants that regulate the agonist/antagonist properties of HGF NK2 and provide critical insights into the dimerization mechanism that regulates the Met receptor activation by HGF. cancer metastasis | crystal structure | HGF agonist | HGF antagonist | Met receptor tyrosine kinase doi/ 10.1073/pnas.1005183107

We report a previously unknown recognition motif between the [alpha]-face of the steroid hydrocarbon backbone and [pi]-electron-rich aromatic substrates. Our study is based on a systematic and comparative analysis of the solid-state complexation of four steroids with 24 aromatic molecules. By using the solid state as a medium for complexation, we circumvent solubility and solvent competition problems that are inherent to the liquid phase. Characterization is performed using powder and single crystal X-ray diffraction, infrared solid-state spectroscopy and is complemented by a comprehensive cocrystal structure prediction methodology that surpasses earlier computational approaches in terms of realism and complexity. Our combined experimental and theoretical approach reveals that the [alpha] ... [pi] stacking is of electrostatic origin and is highly dependent on the steroid backbone's unsaturated and conjugated character. We demonstrate that the [alpha] ... [pi] stacking interaction can drive the assembly of molecules, in particular progesterone, into solid-state complexes without the need for additional strong interactions. It results in a marked difference in the solid-state complexation propensities of different steroids with aromatic molecules, suggesting a strong dependence of the steroid-binding affinity and even physicochemical properties on the steroid's A-ring structure. Hence, the hydrocarbon part of the steroid is a potentially important variable in structure-activity relationships for establishing the binding and signaling properties of steroids, and in the manufacture of pharmaceutical cocrystals. steroids | molecular recognition | mechanosynthesis | crystal structure prediction doi/ 10.1073/pnas.0915142107

Crystalline solids with extended non-interpenetrating three-dimensional crystal structures were synthesized that support well-defined pores with internal diameters of up to 48 angstroms. The [Zn.sub.4]O[(C[O.sub.2]).sub.6] unit was joined with either one or two kinds of organic link, 4,4',4'-[benzene-1,3,5-triyl-tris (ethyne-2,1-diyl)]tribenzoate (BTE), 4,4',44'-[benzene-1,3,5-triyl-tris(benzene-4,1-diyl)]tribenzoate (BBC), 4,4',44'-benzene-1,3,5-triyl-tribenzoate (BTB)/2,6-naphthalenedicarboxylate (NDC), and BTE/biphenyl-4,4'-dicarboxylate (BPDC), to give four metal-organic frameworks (MOFs), MOF-180, -200, -205, and -210, respectively. Members of this series of MOFs show exceptional porosities and gas (hydrogen, methane, and carbon dioxide) uptake capacities. For example, MOF-210 has Brunauer-Emmett-Teller and Langmuir surface areas of 6240 and 10,400 square meters per gram, respectively, and a total carbon dioxide storage capacity of 2870 milligrams per gram. The volume-specific internal surface area of MOF-210 (2060 square meters per cubic centimeter) is equivalent to the outer surface of nanoparticles (3-nanometer cubes) and near the ultimate adsorption limit for solid materials. 10.1126/science.1192160

Mtr4 is a conserved RNA helicase that functions together with the nuclear exosome. It participates in the processing of structured RNAs, including the maturation of 5.8S ribosomal RNA (rRNA). It also interacts with the polyadenylating Trf4-Air2 heterodimer to form the so-called TRAMP (Trf4-Air2-Mtr4 Polyadenylation) complex. TRAMP is involved in exosome-mediated degradation of aberrant RNAs in nuclear surveillance pathways. We report the 2.9-[Angstrom] resolution crystal structure of Saccharomyces cerevisiae Mtr4 in complex with ADP and RNA. The structure shows a central ATPase core similar to that of other DExH helicases. Inserted in the DExH core is a region characteristic of Mtr4 orthologues that folds into an elongated stalk connected to a [beta]-barrel domain. This domain shows unexpected similarity to the KOW domain of L24, a ribosomal protein that binds 23S rRNA. We find that indeed the KOW domain of Mtr4 is able to bind in vitro transcribed [tRNA.sup.iMet], suggesting it might assist in presenting RNA substrates to the helicase core. The interaction of Mtr4 with Trf4-Air2 is mediated not by the stalk/KOW insertion but by the DExH core. We find that in the context of the TRAMP complex, the DExH core functions independently in vitro as an RNA helicase and a protein-binding platform. Mtr4 has thus evolved specific structural and surface features to perform its multiple functions. doi/10.1073/pnas.1004953107

The recently elucidated Get proteins are responsible for the targeted delivery of the majority of tail-anchored (TA) proteins to the endoplasmic reticulum. Get4 and Get5 have been identified in the early steps of the pathway mediating TA substrate delivery to the cytoplasmic targeting factor Get3. Here we report a crystal structure of Get4 and an N-terminal fragment of Get5 from Saccharomyces cerevisae. We show Get4 and Get5 (Get4/5) form an intimate complex that exists as a dimer (two copies of Get4/ 5) mediated by the C-terminus of Get5. We further demonstrate that Get3 specifically binds to a conserved surface on Get4 in a nucleotide dependent manner. This work provides further evidence for a model in which Get4/5 operates upstream of Get3 and mediates the specific delivery of a TA substrate. crystallography | Get pathway | Mdy2 | Ubl4|a I tail-anchor doi/10.1073/pnas.1006036107

Problem statement: The studied dihydropyridone was synthesized for the first time via the microwave assisted reaction of curcumin and methylamine and it is important to support the mechanism by the crystal structure. Approach: The crystal structure of the title compound was determined using high resolution x-ray diffraction. PowderSolve program was used to solve the structure while the refinement was done in material studio Reflex module. Results: The findings obtained with high-resolution x-ray powder diffraction and molecular location methods based on simulated annealing algorithm after Rietveld refinement showed that the monoclinic unit cell was a = 13.4925 [Angstrom], b = 12.8162 [Angstrom], c = 11.5231 [Angstrom], [alpha] = 90.000[degrees], [beta] = 99.0401[degrees], [gamma] = 90.000[degrees]; cell volume = 1967.85 [[Angstrom].sup.3] and space group P 21/a with 4 molecules in a unit cell. Conclusion/Recommendations: Powder diffractometry could be a powerful tool for determining crystal structures for organic molecules. Key words: Dihydropyridone, x-ray powder diffraction, rietveld refinement, PowderSolve, treor, INTRODUCTION Dihydropyridones are important intermediates for synthesis of natural products, particularly alkaloids and many approaches to their synthesis have been developed (Donohoe et al., 2009; Comins and Ollinger, 2001; Song [...]

Platelet-derived growth factors (PDGFs) and their receptors (PDGFRs) are prototypic growth factors and receptor tyrosine kinases which have critical functions in development. We show that PDGFs share a conserved region in their prodomain sequences which can remain noncovalently associated with the mature cystine-knot growth factor domain after processing. The structure of the PDGF-A/propeptide complex reveals this conserved, hydrophobic association mode. We also present the structure of the complex between PDGF-B and the first three Ig domains of PDGFR[beta], showing that two PDGF-B protomers clamp PDGFR[beta] at their dimerization seam. The PDGF-B:PDGFR[beta] interface is predominantly hydrophobic, and PDGFRs and the PDGF propeptides occupy overlapping positions on mature PDGFs, rationalizing the need of propeptides by PDGFs to cover functionally important hydrophobic surfaces during secretion. A large-scale structural organization and rearrangement is observed for PDGF-B upon receptor binding, in which the PDGF-B L1 loop, disordered in the structure of the free form, adopts a highly specific conformation to form hydrophobic interactions with the third Ig domain of PDGFR[beta]. Calorimetric data also shows that the membrane-proximal homotypic PDGFR[alpha] interaction, albeit required for activation, contributes negatively to ligand binding. The structural and biochemical data together offer insights into PDGF-PDGFR signaling, as well as strategies for PDGF-antagonism. crystallography | receptor tyrosine kinase | signal transduction doi/ 10.1073/pnas.1000806107

Flagella are the bacterial organelles of motility and can play important roles in pathogenesis. Flagella biosynthesis requires the coordinated export of huge protein amounts from the cytosol to the nascent flagellar structure at the cell surface and employs a type III secretion system (T3SS). Here we show that the integral membrane protein FlhA from the gram-positive bacterium Bacillus subtilis acts as an adaptor for late export substrates at the T3SS. The maior filament protein (flagellin) and the filament-cap protein (FliD) bind to the FlhA cytoplasmic domain (FlhA-C) only in complex with their cognate chaperones (FliS and FliT). To understand the molecular details of these interactions we determined the FlhA-C crystal structure at 2.3 [Angstrom] resolution. FlhA-C consists of an N-terminal linker region, three subdomains with a novel fold, and a disordered region essential for the adaptor function. We show that the export protein FliJ associates with the linker region and modulates the binding properties of FlhA-C. While the interaction of FliD/FliT is enhanced, flagellin/FliS is not affected. FliJ also keeps FliT associated with FlhA-C and excess of FliT inhibits binding of FliD/FliT, suggesting that empty FliT chaperones stay associated with FliJ after export of FliD. Taken together, these results allow to propose a model that explains how the T3SS may switch from the stoichiometric export of FliD to the high-throughput secretion of flagellin. chaperone | flagella biosynthesis | motility | protein transport doi/ 10.1073/pnas.1001383107

The heptameric coatomer complex forms the protein shell of membrane-bound vesicles that are involved in transport from the Golgi to the endoplasmatic reticulum and in intraGolgi trafficking. The heptamer can be dissected into a heterotetrameric F-subcomplex, which displays similarities to the adapter complex of the 'inner' coat in clathrin-coated vesicles, and a heterotrimeric B-subcomplex, which is believed to form an 'outer' coat with a morphology distinct from that of clathrin-coated vesicles. We have determined the crystal structure of the complex between the c-terminal domain (CTD) of [alpha]-COP and full-length c-COP, two components of the B-subcomplex, at a 2.9 [Angstrom] resolution. The [alpha]-[COP.sup.CTD] * c-COP heterodimer forms a rod-shaped structure, in which c-COP adopts a tetratricopeptide repeat (TPR) fold that deviates substantially from the canonical superhelical conformation. The [alpha]-COP CTD adopts a U-shaped architecture that complements the TPR fold of c-COR The c-COP TPRs form a circular bracelet that wraps around a protruding [beta]-hairpin of the [alpha]-COP CTD, thus interlocking the two proteins. The [alpha]-[COP.sup.CTD] * c-COP complex forms heterodimers in solution, and we demonstrate biochemically that the heterodimer directly interacts with the Dsll tethering complex. These data suggest that the heterodimer is exposed on COPI vesicles, while the remaining part of the B-subcomplex oligomerizes underneath into a cage. coatomer | interaction studies | membrane coat | U-shaped [alpha]-helical solenoid | tetratricopeptide repeat (TPR) doi/ 10.1073/pnas.1006297107

Resistance nodulation cell division (RND)-based efflux complexes mediate multidrug and heavy-metal resistance in many Gramnegative bacteria. Efflux of toxic compounds is driven by membrane proton/substrate antiporters (RND protein) in the plasma membrane, linked by a membrane fusion protein (MFP) to an outer-membrane protein. The three-component complex forms an efflux system that spans the entire cell envelope. The MFP is required for the assembly of this complex and is proposed to play an important active role in substrate efflux. To better understand the role of MFPs in RND-driven efflux systems, we chose ZneB, the MFP component of the ZneCAB heavy-metal efflux system from Cupriavidus metallidurans CH34. ZneB is shown to be highly specific for [Zn.sup.2+] alone. The crystal structure of ZneB to 2.8 [Angstrom] resolution defines the basis for metal ion binding in the coordination site at a flexible interface between the [beta]-barrel and membrane proximal domains. The conformational differences observed between the crystal structures of metal-bound and apo forms are monitored in solution by spectroscopy and chromatography. The structural rearrangements between the two states suggest an active role in substrate efflux through metal binding and release. Cupriavidus metallidurans CH34 | heavy-metal resistance resistance nodulation cell division | periplasmic adaptor protein doi/ 10.1073/pnas.1003908107

Lipopolysaccharide (LPS) of Gram-negative bacteria is a common pathogen-associated molecular pattern (PAMP) that induces potent innate immune responses. The host immune response against LPS is triggered by myeloid differentiation factor 2 (MD-2) in association with Toll-like receptor 4 (TLR4) on the cell surface. The MD-2/ TLR4-mediated LPS response is regulated by the evolutionarily related complex of MD-1 and Toll-like receptor homoIog RP105. Here, we report crystallographic and biophysical data that demonstrate a previously unidentified direct interaction of MD-1 with LPS. The crystal structure of chicken MD-1 (cMD-1) at 2.0 A resolution exhibits a [beta]-cup-like fold, similar to M D-2, that encloses a hydrophobic cavity between the two [beta]-sheets. A lipid-like moiety was observed inside the cavity, suggesting the possibility of a direct MD-1/ LPS interaction. LPS was subsequently identified as an MD-1 ligand by native gel electrophoresis and gel filtration analyses. The crystal structure of CMD-1 with lipid IVa, an LPS precursor, at 2.4 A resolution revealed that the lipid inserts into the deep hydrophobic cavity of the [beta]-cup-like structure, but with some important differences compared with MD-2. These findings suggest that soluble MD-1 alone, in addition to its complex with RP105, can regulate host LPS sensitivity. lipopolysaccharide | MD-2 | RP105 | TLR4 | innate immunity doi/ 10.1073/pnas.1004153107

The RNA-dependent RNA polymerase core complex formed upon infection of Escherichia coli by the bacteriophage Q[beta] is composed of the viral catalytic [beta]-subunit as well as the host translation elongation factors EF-Tu and EF-Ts, which are required for initiation of RNA replication. We have determined the crystal structure of the complex between the [beta]-subunit and the two host proteins to 2.5-[Angstrom] resolution. Whereas the basic catalytic machinery in the viral subunit appears similar to other RNA-dependent RNA polymerases, a unique C-terminal region of the [beta]-subunit engages in extensive interactions with EF-Tu and may contribute to the separation of the transient duplex formed between the template and the nascent product to allow exponential amplification of the phage genome. The evolution of resistance by the host appears to be impaired because of the interactions of the [beta]-subunit with parts of EF-Tu essential in recognition of aminoacyl-tRNA. protein biosynthesis | virus doi/ 10.1073/pnas.1003015107

Regulation of endosomal trafficking by Rab GTPases depends on selective interactions with multivalent effectors, including EEA1 and Rabenosyn-5, which facilitate endosome tethering, sorting, and fusion. Both EEA1 and Rabenosyn-5 contain a distinctive N-terminal [C.sub.2][H.sub.2] zinc finger that binds Rab5. How these [C.sub.2][H.sub.2] zinc fingers recognize Rab GTPases remains unknown. Here, we report the crystal structure of Rab5A in complex with the EEA1 [C.sub.2][H.sub.2] zinc finger. The binding interface involves all elements of the zinc finger as well as a short N-terminal extension but is restricted to the switch and interswitch regions of Rab5. High selectivity for Rab5 and, to a lesser extent Rab22, is observed in quantitative profiles of binding to Rab family GTPases. Although critical determinants are identified in both switch regions, Rab4-to-Rab5 conversion-of-specificity mutants reveal an essential requirement for additional substitutions in the proximal protein core that are predicted to indirectly influence recognition through affects on the structure and conformational stability of the switch regions. Rab5 | effector | Rabenosyn-5 | endosome | structure doi/ 10.1073/pnas.1000843107

Inositol phosphates (InsPs) are signaling molecules with multiple roles in cells. In particular Ins(1,2,3,4,5,6)[P.sub.6] ([InsP.sub.6]) is involved in mRNA export and editing or chromatin remodeling among other events. [InsP.sub.6] accumulates as mixed salts (phytate) in storage tissues of plants and plays a key role in their physiology. Human diets that are exclusively grain-based provide an excess of [InsP.sub.6] that, through chelation of metal ions, may have a detrimental effect on human health. Ins (1,3,4,5,6)[P.sub.5] 2-kinase ([InsP.sub.5] 2-kinase or Ipk1) catalyses the synthesis of [InsP.sub.6] from [InsP.sub.5] and ATP, and is the only enzyme that transfers a phosphate group to the axial 2-OH of the myo-inositide. We present the first structure for an [InsP.sub.5] 2-kinase in complex with both substrates and products. This enzyme presents a singular structural region for inositide binding that encompasses almost half of the protein. The key residues in substrate binding are identified, with Asp368 being responsible for recognition of the axial 2-OH. This study sheds light on the unique molecular mechanism for the synthesis of the precursor of inositol pyrophosphates. [InsP.sub.5] 2-kinase | IP5 | IP6 | ipkl | crystal structure www.pnas.org/cgi/doi/10.1073/pnas.0912979107

Members of the Bin/amphiphysin/Rvs (BAR) domain protein super-family are involved in membrane remodeling in various cellular pathways ranging from endocytic vesicle and T-tubule formation to cell migration and neuromorphogenesis. Membrane curvature induction and stabilization are encoded within the BAR or Fer-CIP4 homology-BAR (F-BAR) domains, a-helical coiled coils that dimerize into membrane-binding modules. BAR/F-BAR domain proteins often contain an SH3 domain, which recruits binding partners such as the oligomeric membrane-fissioning GTPase dynamin. How precisely BAR/F-BAR domain-mediated membrane deformation is regulated at the cellular level is unknown. Here we present the crystal structures of full-length syndapin 1 and its F-BAR domain. Our data show that syndapin 1 F-BAR-mediated membrane deformation is subject to autoinhibition by its SH3 domain. Release from the clamped conformation is driven by association of syndapin I SH3 with the proline-rich domain of dynamin 1, thereby unlocking its potent membrane-bending activity. We hypothesize that this mechanism might be commonly used to regulate BAR/F-BAR domain-induced membrane deformation and to potentially couple this process to dynamin-mediated fission. Our data thus suggest a structure-based model for SH3-mediated regulation of BAR/F-BAR domain function. dynamin | endocytosis | membrane bending | syndapin doi/ 10.1073/pnas.1003478107

We have performed complementary time-resolved fluorescence resonance energy transfer (TR-FRET) experiments and molecular dynamics (MD) simulations to elucidate structural changes in the phosphorylation domain (PD) of smooth muscle regulatory light chain (RLC) bound to myosin. PD is absent in crystal structures, leaving uncertainty about the mechanism of regulation. Donor-acceptor pairs of probes were attached to three site-directed di-Cys mutants of RLC, each having one Cys at position 129 in the C-terminal lobe and the other at position 2, 3, or 7 in the N-terminal PD. Labeled RLC was reconstituted onto myosin subfragment 1 (S1). TR-FRET resolved two simultaneously populated structural states of RLC, closed and open, in both unphosphorylated and phosphorylated biochemical states. All three FRET pairs show that phosphorylation shifts the equilibrium toward the open state, increasing its mol fraction by ~20%. MD simulations agree with experiments in remarkable detail, confirming the coexistence of two structural states, with phosphorylation shifting the system toward the more dynamic open structural state. This agreement between experiment and simulation validates the additional structural details provided by MD simulations: In the closed state, PD is bent onto the surface of the C-terminal lobe, stabilized by interdomain salt bridges. In the open state, PD is more helical and straight, resides farther from the C-terminal lobe, and is stabilized by an intradomain salt bridge. The result is a vivid atomic-resolution visualization of the first step in the molecular mechanism by which phosphorylation activates smooth muscle. fluorescence resonance energy transfer | FRET | molecular dynamics | molecular dynamics simulation | time-resolved fluorescence doi/ 10.1073/pnas.1001941107

Nucleosomes around the promoter region are disassembled for transcription in response to various signals, such as acetylation and methylation of histones. Although the interactions between histone-acetylation-recognizing bromodomains and factors involved in nucleosome disassembly have been reported, no structural basis connecting histone modifications and nucleosome disassembly has been obtained. Here, we determined at 3.3 [Angstrom] resolution the crystal structure of histone chaperone cell cycle gene 1 (CCG1) interacting factor A/antisilencing function 1 (CIA/ASF1) in complex with the double bromodomain in the CCG1/TAF1/TAF(II)250 subunit of transcription factor lID. Structural, biochemical, and biological studies suggested that interaction between double bromodomain and CIA/ASF1 is required for their colocalization, histone eviction, and pol II entry at active promoter regions. Furthermore, the present crystal structure has characteristics that can connect histone acetylation and CIA/ASFl-mediated histone eviction. These findings suggest that the molecular complex between CIA/ASF1 and the double bromodomain plays a key role in site-specific histone eviction at active promoter regions. The model we propose here is the initial structure-based model of the biological signaling from histone modifications to structural change of the nucleosome (hi-MOST model). chromatin | transcription | transcription factor IID | x-ray crystallography doi/10.1073/pnas.0912509107

Akaogiite, an ultra-dense polymorph of Ti[O.sub.2] was encountered in heavily shocked garnet-cordieritesillimanite gneiss in the Suevite breccia of the Ries meteorite impact crater in Germany. The chemical formula ofakaogiite is Ti[O.sub.2], containing (wt%) Ti[O.sub.2] 97.6-97.7; [Nb.sub.2][O.sub.5] 0.15-0.20, and FeO 0.11-0.14. The empirical formula is: [Ti.sub.0.998][Fe.sub.0.002][Nb.sub.0.001][O.sub.2]. Akaogiite is optically distinguishable from futile only in reflected light microscopy, through its slightly higher brightness and the intense royal blue color of its internal reflections in crossed nicols. The mineral grains consist of countless randomly oriented submicrometer particles. In situ micro-beam X-ray diffraction established akaogiite to be monoclinic with the baddeleyite-type structure. Cell parameters are a = 4.606(2) [Angstrom], b = 4.896(3) [Angstrom], c = 4.933(3) [Angstrom], and [beta] = 99.17[(6).sup.o]; space group [P2.sub.1]c; molar volume = 16.82(2) cmTmol; density = 4.72 g/[cm.sup.3]. Akaogiite coexists in the shocked gneiss with graphite-diamond phase transition assemblage, a second dense Ti[O.sub.2] polymorph with the scrutinyite-type structure (Ti[O.sub.2]-11), liquidus idiomorphic jadeite inclusions in melt pockets in garnet, and a new FeTi[O.sub.3]-polymorph with the Li-niobate structure. The high-pressure assemblage constrains the equilibrium peak-shock pressure to be [less than or equal to] 22 GPa and a post-shock temperature Keywords: Akaogiite, Ries Crater, suevite impact breccia, shock, rutile, Ti[O.sub.2]-11, graphite, diamond, Li-niobate structured FeTi[O.sub.3] DOI: 10.2138/am.2010.3425

Kapundaite, ideally [(Na,Ca).sub.2][Fe.sup.3+.sub.4][(P[O.sub.4]).sub.4] [(OH).sub.3] x 5[H.sub.2]O, is a new mineral (IMA2009-047) from Toms phosphate quarry, Kapunda, South Australia, Australia. The new mineral occurs as cavernous aggregates of fibers up to several centimeters across, associated with leucophosphite, natrodufrenite, and meurigite-Na crystals and amorphous brown, black, and/or greenish coatings. Individual kapundaite crystals are very thin flattened fibers up to a few millimeters in length, but typically no more than a few micrometers in thickness. The main form observed is {100}; other forms in the [010] zone are present, but cannot be measured. Crystals of kapundaite are pale to golden yellow, transparent to translucent, have a yellow streak and silky luster, and are non-fluorescent. Mohs hardness is estimated to be about 3; no twinning or cleavage was observed. Kapundaite is biaxial (+), with indices of refraction [alpha] = 1.717(3), [beta] = 1.737(3), and [gamma] = 1.790(3). 2V could not be measured; [2V.sub.cale] is 64.7[degrees]. The optical orientation is Z = b, Y [approximately equal to] c with weak pleochroism: X= nearly colorless, Y= light brown, Z = pale brown; absorption: Y> Z > X. No dispersion was observed. The empirical chemical formula (mean of seven electron microprobe analyses) calculated on the basis of 24 O is ([Ca.sub.1.13][Na.sub.0.95])[summation]2.08[([Fe.sup.3+.sub.3.83] [Mn.sub.0.03][Al.sub.0.02][Mg.sub.0.01]).sub.[summation]3.89] [P.sub.3.92][O.sub.16]([OH).sub.3] x 5[H.sub.2.11]O. Kapundaite is triclinic, space group P[bar.1], a = 6.317(5), b - 7.698(6), c = 9.768(7) [Angstrom], [alpha] = 105.53[(1).sup.o], [beta] = 99.24[(2).sup.o], [gamma] = 90.09[(2).sub.o], V = 451.2(6) [[Angstrom].sup.3], and Z- 1. The five strongest lines in the powder X-ray diffraction pattern are [[d.sub.obs] in [Angstrom], (I) (hkl)]: 9.338 (100) (001 ), 2.753 (64) (2[bar.1]1), 5.173 (52) (011 ), 2.417 (48) ([bar.2][bar.1]-3, 202, 0[bar.1]4), and 3.828 (45)(0[bar.2]1). The crystal structure was solved from single-crystal X-ray diffraction data using synchrotron radiation and refined to [R.sub.1] = 0.1382 on the basis of 816 unique reflections with [F.sub.o] > 4[sigma]F. The structure of kapundaite is based on a unique corrugated octahedral-tetrahedral sheet, which is composed of two types of chains parallel to a. Kapundaite is structurally related to melonjosephite. The mineral is named for the nearest town to the quarry. Keywords: Kapundaite, new mineral, phosphate, Toms phosphate quarry, crystal structure, octahedral-tetrahedral sheet, melonjosephite DOI: 10.2138/am.2010.3466

Natural kaolin, from Fujian province in China, was used as raw material to synthesize zeolite 4A powder under low-temperature hydrothermal treatment in alkali solution. Optimization studies on various reaction parameters were conducted. With the addition of an inorganic binder (montmorillonite), the as-prepared powder was shaped into spheres for desiccant application in industrial fields. Zeolite 4A powder was characterized by X-ray diffraction (XRD) and scanning electron microscopy (SEM) and the obtained powder was a cubic phase with high crystallinity. The water sorption capacity (WSC) and final compression strength (FCS) of zeolite 4A desiccant were studied. Higher crystallinity of zeolite 4A powder led to the higher WSC of zeolite desiccant. The observed WSC and FCS of 21.0% and 44.8 N, respectively, confirmed the potential application of zeolite 4A for water sorption. Keywords: Zeolite 4A, desiccant, kaolin, water sorption capacity (WSC), final compression strength (FCS) DOI: 10.2138/am.2010.3288

Coulsellite, Ca[Na.sub.3]Al[Mg.sub.3][F.sub.14], from the Cleveland tin mine at Luina, western Tasmania, has a rhombohedral distortion of the cubic pyrochlore [A.sub.2][B.sub.2][X.sub.6]Y structure, with a = 7.1756(1) [Angstrom], [alpha] = 59.867[(1).sup.o], space group R[bar.3]m, Z = 1. The corresponding hexagonal cell parameters are a = 7.1620(1) [Angstrom], c = 17.5972(3) [Angstrom]. The crystals are multiply twinned about threefold axes of the pseudocubic cell. The structure was determined using X-ray data collected on a twinned crystal and refined to Robs = 0.027 for 452 observed reflections with 1 > 2[sigma](I). The structure is possibly unique among published structures of pyrochlore-like minerals in having full 1:3 ordering of Ca:Na in the A sites and Al:Mg in the B sites. Transmission electron photomicrographs show a nanodomain structure due to twinning on a scale of ~5 nm. Keywords: Rhombohedral pyrochlore, new fluoride mineral, structure determination, 1:3 cation ordering in Ca[Na.sub.3]Al[Mg.sub.3][F.sub.14] DOI: 10.2138/am.2010.3360

Crystals of the solid-solution series of (Ca,Sr)-lawsonite were synthesized hydrothermally at 4 GPa and 600 and 800[degrees]C in piston-cylinder experiments. Synthesis products were analyzed with SEM, EMP, and powder-XRD. Lawsonite was observed in both the orthorhombic space group Cmcm and in the monoclinic space group [P2.sub.1]/m. It is exclusively orthorhombic at low [x.sup.bulk.sub.Sr] but monoclinic at high [x.sup.bulk.sub.Sr]; in the range [x.sup.bulk.sub.Sr] = 0.18 to 0.4 both polymorphs coexist and the data suggest a two- phase field between X.sup.ortho.sub.Sr] ~0.1-0.2 and [x.sup.mono.Sr] ~0.3-0.4 at 4 GPa/600[degrees]C. Linear regression to the refined lattice parameters yields a = 0.017 X [X.sup.Sr] + 5.841 ([Angstrom]), b = 0.197 x [X.sub.Sr] + 8.787 ([Angstrom]), c = 0.263 x [x.sub.Sr] + 13.130 ([Angstrom]), and v 4.62 x [x.sub.Sr] + 101.46 ([cm.sup.3]/mol) for orthorhombic lawsonite and a = 0.119 x [x.sub.Sr] + 5.306([Angstrom]), b = 0.118 x [x.sub.Sr] + 13.160 ([Angstrom]), C = 0.025 x [x.sub.Sr] + 5.833 ([Angstrom]), [beta] = 0.38 x [x.sub.Sr] + 124.07 ([sup.o]), and v 3.20 x [x.sub.Sr] + 101.59 ([cm.sup.3]/mol) for monoclinic lawsonite. The data suggest an increasingly negative [[DELTA]v.sub.ortho-mono] with increasing [x.sub.Sr]. In monoclinic lawsonite, structural expansion due to the incorporation of Sr is primarily accomplished by tilting and rotation within the [Si.sub.2][O.sub.7]-group, whereas in orthorhombic lawsonite this tilting and rotation is prohibited by symmetry restrictions and expansion is mostly accomplished by an increase in lattice parameters. Combining the extrapolated Ca end-member volume for monoclinic lawsonite with published high-P data yields [K.sup.mono.sub.0] = 137(3) GPa (K' = 4.4). Contrary to the Ca end-member system, the Cmcm--[P2.sub.1]/m phase transition is quenchable within the Sr-bearing system. A tentative phase diagram for (Ca,Sr)-lawsonite at 600[degrees]C indicates a narrow orthorhombic-monoclinic two-phase field that shifts significantly to lower pressure with increasing Xs~. The Cmcm--[P2.sub.1]/m phase transition in the Sr end-member system is located at [less than or equal to] 1 GPa at ~400 to 600[degrees]C, 6 to 9 GPa below the transition in the Ca-system, and has a negative P-T slope. Keywords: Crystal structure, lawsonite, XRD data, experimental petrology DOI: 10.2138/am.2010.3220

In this paper, I demonstrate that the complex structure observed in natural dendritic zircon, which crystallized from a mafic magma, can be approximated by a simple model of deterministic volume-filling fractal growth. The model comprises a novel dendritic growth process that reveals a previously unrecognized underlying structure to complex dendritic crystals, and provides an ideal way of maximizing surface area at the crystal-melt interlace during dendritic crystal growth. This addresses the important kinetic effect of creating interfacial area. In turn, this relates to dissipation of the latent heat of fusion from the moving crystal-melt interlace, which, in addition to chemical diffusion, is known to be a fundamental rate-controlling process in dendritic crystal growth. A new mechanism of tip-splitting branch formation in dendritic crystals is proposed. Although both types of branch formation seem to occur simultaneously, the newly proposed mechanism operates at larger length scales and independently of classical side-branching linked with periodic perturbations caused by thermal noise. It is shown that this type of modeling potentially has applications in metallurgical engineering; and in predicting the relative lengths, orientations, and spacings of branches in mathematical modeling studies of natural and experimentally grown dendritic crystals. Keywords: Dendrite, zircon, fractal, alloy casting, crystal growth DOI: 10.2138/am.2010.3320

The response of the mesolite crystal structure ([Na.sub.16][Ca.sub.16][Al.sub.48][Si.sub.72][O.sub.240] x 64 [H.sub.2]O) to dehydration was evaluated as a function of temperature and partial pressure of water (i.e., [MATHEMATICAL EXPRESSION NOT REPRODUCIBLE IN ASCII] or relative humidity, RH) using laboratory X-ray powder diffraction (XRD; CuK[alpha] radiation) and synchrotron X-ray pair distribution function (PDF) methods. At 425[degrees]C under low-[MATHEMATICAL EXPRESSION NOT REPRODUCIBLE IN ASCII] conditions ([MATHEMATICAL EXPRESSION NOT REPRODUCIBLE IN ASCII] [less than or equal to] ~1.3 mbar), dehydrated mesolite preserved the long-range ordered aluminosilicate framework structure, which has not been previously observed. This new dehydrated phase, x-metamesolite, has unit-cell parameters [a 16.731(3) [Angstrom], b = 17.822(2) [Angstrom], c = 6.312(1) [Angstrom], V 1882.5(5) [[Angstrom].sup.3], and possible space group Fdd2] similar to those of other dehydrated natrolite phases (either [alpha]1-or [alpha]2-metanatrolite). Conversely, under high-[MATHEMATICAL EXPRESSION NOT REPRODUCIBLE IN ASCII] conditions ([MATHEMATICAL EXPRESSION NOT REPRODUCIBLE IN ASCII] > ~1.3 mbar), dehydrated mesolite became amorphous (amorphous [T.sub.5][O.sub.10]) at 425[degrees]C. The local structure of amorphous [T.sub.5][O.sub.10] was characterized by PDF analyses, which showed the formation of twisted [T.sub.5][O.sub.10] nano-fibers [with dimensions (LWH) of ~6.9 x 6.9 x 6.3 [Angstrom]] resulting from breakage of the mesolite aluminosilicate framework. The two distinct high-temperature [MATHEMATICAL EXPRESSION NOT REPRODUCIBLE IN ASCII]-dependent phase transition paths illustrate the importance of considering the combined effects of temperature and [MATHEMATICAL EXPRESSION NOT REPRODUCIBLE IN ASCII] in mesolite. In addition, the low-temperature phase transition in mesolite, involving order-disorder of the extraframework cations, also showed a [MATHEMATICAL EXPRESSION NOT REPRODUCIBLE IN ASCII]-dependent transition temperature. Although, there is no path dependence on [MATHEMATICAL EXPRESSION NOT REPRODUCIBLE IN ASCII] for this transition, the local arrangement of Na, Ca, and vacancies in disordered metamesolite (formed through the extraframework cation order-disorder phase transition) likely influences the thermal stability of the aluminosilicate framework during further heating. Keywords: Phase transition, mesolite, XRD data, crystal structure DOI: 10.2138/am.2010.3443

Esperite from Franklin, New Jersey, was first described by Moore and Ribbe (1965) as monoclinic with a well-developed 'superlattice' a = 2 x 8.814(2) [Angstrom], b = 8.270(3)[Angstrom], c = 2 x 15.26(1)[Angstrom], [beta] [approximately equal to] 90[degrees], space group [P2.sub.1]/n (subcell), and the chemical formula Pb[Ca.sub.3][(ZnSi[O.sub.4]).sub.4]. They attributed 'superlattice' reflections to the ordered distributions of Pb and Ca cations over four beryllonite-type subcells for esperite with the Ca:Pb ratio greater than 2:1. We examined two esperite fragments from the type sample using single-crystal X-ray diffraction, electron microprobe analysis, and Raman spectroscopy. Although both fragments have Ca:Pb [approximately equal to] 1.8, one exhibits the 'superlattice' reflections as observed by Moore and Ribbe (1965), whereas the other does not. The sample without 'superlattice' reflections has unit-cell parameters a = 8.7889(2), b = 8.2685(2), c = 15.254(3) [Angstrom], [beta] = 90.050[(1).sup.o], V = 1108.49(4) [[Angstrom].sup.3], and the chemical composition [Pb.sup.1.00]([Ca.sup.1.86][Fe.sup.2+.sub.0.07][Mn.sub.0.04] [Cr.sup.3+.sub.0.02]).sub.[[summation] = 1.99] [([Zn.sub.1.00][Si.sub.1.00][O.sub.4]).sub.3]. Its crystal structure was solved in space group [P2.sub.1]/n ([R.sub.1] = 0.022). Esperite is isostructural with beryllonite, NaBeP[O.sub.4], and its ideal chemical formula should, therefore, be revised to Pb[Ca.sub.2][(ZnSi[O.sub.4]).sub.3], Z = 4. The Zn[O.sub.4] and Si[O.sub.4] tetrahedra in esperite share corners to form an ordered framework, with [Pb.sup.2+] occupying the nine-coordinated site in the large channels and [Ca.sup.2+] occupying the two distinct octahedral sites in the small channels. The so-called 'superlattice' reflections are attributed to triple twins, a trilling of ~60[degrees] rotational twinning around the b axis, similar to those observed in many other beryllonite-type materials. A phase transformation from a high-temperature polymorph to the esperite structure is proposed to be responsible for the twinning formation. Keywords: Esperite, beryllonite, Pb-Zn silicates, crystal chemistry, X-ray diffraction DOI: 10.2138/am.2010.3415