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The Epstein-Barr virus (EBV) is a [gamma]-herpesvirus that infects B cells and epithelial cells and that has been linked to malignancies in both cell types in vivo. EBV, like other herpesviruses, has three glycoproteins, glycoprotein B (gB), gH, and gL, that form the core membrane fusion machinery mediating viral penetration into the cell. The gH and gL proteins associate to form a heterodimeric complex, which is necessary for efficient membrane fusion and also implicated in direct binding to epithelial cell receptors required for viral entry. To gain insight into the mechanistic role of gH/gL, we determined the crystal structure of the EBV gH/gL complex. The structure is comprised of four domains organized along the longest axis of the molecule. Comparisons with homologous HSV-2 gH/gL and partial pseudorabies virus gH structures support the domain boundaries determined for the EBV gH/gL structure and illustrate significant differences in interdomain packing angles. The gL subunit and N-terminal residues of gH form a globular domain at one end of the structure, implicated in interactions with gB and activation of membrane fusion. The C-terminal domain of gH, proximal to the viral membrane, is also implicated in membrane fusion. The gH/gL structure locates an integrin binding motif, implicated in epithelial cell entry, on a prominent loop in the central region of the structure. Multiple regions of gH/gL, including its two extreme ends, are functionally important, consistent with the multiple roles of gH/gL in EBV entry. doi/ 10.1073/pnas.1011806108

Nitric oxide reductase (NOR) is an iron-containing enzyme that catalyzes the reduction of nitric oxide (NO) to generate a major greenhouse gas, nitrous oxide ([N.sub.2]O). Here, we report the crystal structure of NOR from Pseudomonas aeruginosa at 2.7 angstrom resolution. The structure reveals details of the catalytic binuclear center. The non-heme iron ([Fe.sub.B]) is coordinated by three His and one Glu ligands, but a His-Tyr covalent linkage common in cytochrome oxidases (COX) is absent. This structural characteristic is crucial for NOR reaction. Although the overall structure of NOR is closely related to COX, neither the D- nor K-proton pathway, which connect the COX active center to the intracellular space, was observed. Protons required for the NOR reaction are probably provided from the extracellular side. 10.1126/science.1195591

Glucansucrases are large enzymes belonging to glycoside hydrolase family 70, which catalyze the cleavage of sucrose into fructose and glucose, with the concomitant transfer of the glucose residue to a growing [alpha]-glucan polymer. Among others, plaque-forming oral bacteria secrete these enzymes to produce [alpha]-glucans, which facilitate the adhesion of the bacteria to the tooth enamel. We determined the crystal structure of a fully active, 1,031-residue fragment encompassing the catalytic and C-terminal domains of GTF180 from Lactobacillus reuteri 180, both in the native state, and in complexes with sucrose and maltose. These structures show that the enzyme has an [alpha]-amylase-like [([beta]/[alpha]).sub.8]-barrel catalytic domain that is circularly permuted compared to the catalytic domains of members of glycoside hydrolase families 13 and 77, which belong to the same GH-H superfamily. In contrast to previous suggestions, the enzyme has only one active site and one nucleophilic residue. Surprisingly, in GTF180 the peptide chain follows a 'U'-path, such that four of the five domains are made up from discontiguous N- and C-terminal stretches of the peptide chain. Finally, the structures give insight into the factors that determine the different linkage types in the polymeric product. crystal structure complexes | exopolysaccharide | Lactobacillus reuteri | dental caries doi/ 10.1073/pnas.1007531107

Numerous 2'-deoxynucleoside triphosphates (dNTPs) that are functionalized with spacious modifications such as dyes and affinity tags like biotin are substrates for DNA polymerases. They are widely employed in many cutting-edge technologies like advanced DNA sequencing approaches, microarrays, and single molecule techniques. Modifications attached to the nucleobase are accepted by many DNA polymerases, and thus, dNTPs bearing nucleobase modifications are predominantly employed. When pyrimidines are used the modifications are almost exclusively at the C5 position to avoid disturbing of Watson-Crick base pairing ability. However, the detailed molecular mechanism by which C5 modifications are processed by a DNA polymerase is poorly understood. Here, we present the first crystal structures of a DNA polymerase from Thermus aquaticus processing two C5 modified substrates that are accepted by the enzyme with different efficiencies. The structures were obtained as ternary complex of the enzyme bound to primer/template duplex with the respective modified dNTP in position poised for catalysis leading to incorporation. Thus, the study provides insights into the incorporation mechanism of the modified nucleotides elucidating how bulky modifications are accepted by the enzyme. The structures show a varied degree of perturbation of the enzyme substrate complexes depending on the nature of the modifications suggesting design principles for future developments of modified substrates for DNA polymerases. modified nucleotide | nucleobase modification | functional DNA | X-ray structure | PCR doi/ 10.1073/pnas.1013804107

Chitinases are a group of enzymes capable of hydrolysing the [beta]-(1,4)-glycosidic bonds of chitin, an essential component of the fungal cell wall, the shells of nematode eggs, and arthropod exoskeletons. Chitinases from pathogenic fungi have been shown to be putative virulence factors and can play important roles in infecting hosts. However, very limited information is available on the structure of chitinases from nematophagous fungi. Here, we present the 1.8 [Angstrom] resolution of the first structure of a Family 18 chitinase from this group of fungi, that of Clonostachys rosea CrChi1, and the 1.6 [Angstrom], resolution of CrChi1 in complex with a potent inhibitor, caffeine. Like other Family 18 chitinases, CrChi1 has the DXDXE motif at the end of strand [beta]5, with Glu174 as the catalytic residue in the middle of the open end of the [([beta]/[alpha]).sub.8] barrel. Two caffeine molecules were shown to bind to CrChi1 in subsites -1 to + 1 in the substrate-binding domain. Moreover, site-directed mutagenesis of the amino acid residues forming hydrogen bonds with caffeine molecules suggests that these residues are important for substrate binding and the hydrolytic process. Our results provide a foundation for elucidating the catalytic mechanism of chitinases from nematophagous fungi and for improving the pathogenicity of nematophagous fungi against agricultural pest hosts. DOI 10.1099/mic.0.043653-0

The atomic structure of dislocation cores is decisive for the understanding of plasticity in crystalline solids. The core structure of dislocations in sapphire introduced by high-temperature plastic deformation has been investigated with the use of the negative spherical-aberration imaging technique. The ability of this technique to discriminate oxygen columns from aluminum (Al) columns, combined with reproduction of subtle contrast features by image simulation, leads to a markedly detailed atomic model of the dislocation cores. The partial dislocations are Al-terminated, with electrical neutrality being achieved because half of the Al columns are missing. These partials also undergo core spreading, which results in random occupancy of both tetrahedrally and octahedrally coordinated sites, though Al in tetrahedral coordination never occurs in a perfect crystal Unusual dislocation core structures may be present in other technologically important nonmetallic solids. 10.1126/science.1192319

Crystal structures of prokaryotic ribosomes have described in detail the universally conserved core of the translation mechanism. However, many facets of the translation process in eukaryotes are not shared with prokaryotes. The crystal structure of the yeast 80S ribosome determined at 4.15 angstrom resolution reveals the higher complexity of eukaryotic ribosomes, which are 40% larger than their bacterial counterparts. Our model shows how eukaryote-specific elements considerably expand the network of interactions within the ribosome and provides insights into eukaryote-specific features of protein synthesis. Our crystals capture the ribosome in the ratcheted state, which is essential for translocation of mRNA and transfer RNA (tRNA), and in which the small ribosomal subunit has rotated with respect to the large subunit. We describe the conformational changes in both ribosomal subunits that are involved in ratcheting and their implications in coordination between the two associated subunits and in mRNA and tRNA translocation. 10.1126/science.1194294

Bacteriophages are the most numerous organisms in the biosphere. In spite of their biological significance and the spectrum of potential applications, little high-resolution structural detail is available on their receptor-binding fibers. Here we present the crystal structure of the receptor-binding tip of the bacteriophage T4 long tail fiber, which is highly homologous to the tip of the bacteriophage lambda side tail fibers. This structure reveals an unusual elongated six-stranded antiparallel beta-strand needle domain containing seven iron ions coordinated by histidine residues arranged colinearly along the core of the biological unit. At the end of the tip, the three chains intertwine forming a broader head domain, which contains the putative receptor interaction site. The structure reveals a previously unknown beta-structured fibrous fold, provides insights into the remarkable stability of the fiber, and suggests a framework for mutations to expand or modulate receptor-binding specificity. gene product 37 | host cell attachment | octahedral coordination | viral fibers | X-ray crystallography doi/ 10.1073/pnas.1011218107

Prothrombin is the zymogen precursor of the clotting enzyme thrombin, which is generated by two sequential cleavages at R271 and R320 by the prothrombinase complex. The structure of prothrombin is currently unknown. Prethrombin-1 differs from prothrombin for the absence of 155 residues in the N-terminal domain and is composed of a single polypeptide chain containing fragment 2 (residues 156-271), A chain (residues 272-320), and B chain (residues 321-579). The X-ray crystal structure of prethrombin-1 solved at 2.2-[Angstrom] resolution shows an overall conformation significantly different (rmsd = 3.6 [Angstrom]) from that of its active form meizothrombin desF1 carrying a cleavage at R320. Fragment 2 is rotated around the y axis by 29[degrees] and makes only few contacts with the B chain. In the B chain, the oxyanion hole is disrupted due to absence of the I16-D194 ion pair and the [Na.sup.+] binding site and adjacent primary specificity pocket are highly perturbed. A remarkable feature of the structure is that the autolysis loop assumes a helical conformation enabling W148 and W215, located 17 [Angstrom] apart in meizothrombin desF1, to come within 3.3 [Angstrom] of each other and completely occlude access to the active site. These findings suggest that the zymogen form of thrombin possesses conformational plasticity comparable to that of the mature enzyme and have significant implications for the mechanism of prothrombin activation and the zymogen [right arrow] protease conversion in trypsin-like proteases. X-ray crystallography | blood coagulation | [E.sup.*] form doi/ 10.1073/pnas.1010262107

Culex mosquitoes introduce the pathogens responsible for filariasis, West Nile virus, St. Louis encephalitis, and other diseases into humans. Currently, traps baited with oviposition semiochemicals play an important role in detection efforts and could provide an environmentally friendly approach to controlling their populations. The odorant binding proteins (OBPs) in the female's antenna play a crucial, if yet imperfectly understood, role in sensing oviposition cues. Here, we report the X-ray crystallography and NMR 3D structures of OBP1 for Culex quinquefasciatus (CquiOBP1) bound to an oviposition pheromone (5R,6S)-6-acetoxy-5-hexadecanolide (MOP). In both studies, CquiOBP1 had the same overall six-helix structure seen in other insect OBPs, but a detailed analysis revealed an important previously undescribed feature. There are two models for OBP-mediated signal transduction: (i) direct release of the pheromone from an internal binding pocket in a pH-dependent fashion and (ii) detection of a pheromone-induced conformational change in the OBP.pheromone complex. Although CquiOBP1 binds MOP in a pH-dependent fashion, it lacks the C terminus required for the pH-dependent release model. This study shows that CquiOBP binds MOP in an unprecedented fashion using both a small central cavity for the lactone head group and a long hydrophobic channel for its tail. AaegOBP1 | AgamOBP1 | CquiOBP1 | NMR | X-ray crystallography doi/ 10.1073/pnas.1012274107

Arginine methylation modulates diverse cellular processes and represents a molecular signature of germ-line-specific Piwi family proteins. A subset of Tudor domains recognize arginine methylation modifications, but the binding mechanism has been lacking. Here we establish that, like other germ-line Tudor proteins, the ancestral staphylococcal nuclease domain-containing 1(SND1) polypeptide is expressed and associates with PIWIL1/Miwi in germ cells. We find that human SND1 binds PlWlL1 in an arginine methylation-dependent manner with a preference for symmetrically dimethylated arginine. The entire Tudor domain and a bifurcated SN domain are required for this binding activity, whereas the canonical Tudor domain alone is insufficient for methylarginine ligand binding. Crystal structures show that the intact SND1 extended Tudor domain forms a wide and negatively charged binding groove, which can accommodate distinct symmetrically dimethylated arginine peptides from PlWlL1 in different orientations. This analysis explains how SND1 preferentially recognizes symmetrical dimethylarginine via an aromatic cage and conserved hydrogen bonds, and provides a general paradigm for the binding mechanisms of methylarginine-containing peptides by extended Tudor domains. Piwi-interacting RNA | Tudor domain-containing proteins doi/ 10.1073/pnas.1013106107

Elicitation of antibodies against targets that are immunorecessive, cryptic, or transient in their native context has been a challenge for vaccine design. Here we demonstrate the elicitation of structure-specific antibodies against the HIV-1 gp41 epitope of the broadly neutralizing antibody 2F5. This conformationally flexible region of gp41 assumes mostly helical conformations but adopts a kinked, extended structure when bound by antibody 2F5. Computational techniques were employed to transplant the 2F5 epitope into select acceptor scaffolds. The resultant '2F5-epitope scaffolds' possessed nanomolar affinity for antibody 2F5 and a range of epitope flexibilities and antigenic specificities. Crystallographic characterization of the epitope scaffold with highest affinity and antigenic discrimination confirmed good to near perfect attainment of the target conformation for the gp41 molecular graft in free and 2F5-bound states, respectively. Animals immunized with 2F5-epitope scaffolds showed levels of graft-specific immune responses that correlated with graft flexibility (p < 0.04), while antibody responses against the graft--as dissected residue-by-residue with alanine substitutions--resembled more closely those of 2F5 than sera elicited with flexible or cyclized peptides, a resemblance heightened by heterologous prime-boost. Lastly, crystal structures of a gp41 peptide in complex with monoclonal antibodies elicited by the 2F5-epitope scaffolds revealed that the elicited antibodies induce gp41 to assume its 2F5-recognized shape. Epitope scaffolds thus provide a means to elicit antibodies that recognize a predetermined target shape and sequence, even if that shape is transient in nature, and a means by which to dissect factors influencing such elicitation. computational design | epitope transplantation | structural mimicry doi/ 10.1073/pnas.1004728107

Markcooperite, [Pb.sub.2](U[O.sub.2])[Te.sup.6+][O.sub.6], is a new tellurate from Otto Mountain near Baker, California, named in honor of Mark A. Cooper of the University of Manitoba for his contributions to mineralogy. The new mineral occurs on fracture surfaces and in small vugs in brecciated quartz veins. Markcooperite is directly associated with bromian chlorargyrite, iodargyrite, khinite-4O, wulfenite, and four other new tellurates: housleyite, thorneite, ottoite, and timroseite. Various other secondary minerals occur in the veins, including two other new secondary tellurium minerals: paratimroseite and telluroperite. Markcooperite is monoclinic, space group [P2.sub.1]/c, a = 5.722(2), b = 7.7478(2), c = 7.889(2) [Angstrom], [beta] = 90.833(5)[degrees], V = 349.7(2) [[Angstrom].sup.3], and Z = 2. It occurs as pseudotetragonal prisms to 0.2 mm with the forms {100} and {011} and as botryoidal intergrowths to 0.3 mm in diameter; no twinning was observed. Markcooperite is orange and transparent, with a light orange streak and adamantine luster, and is non-fluorescent. Mohs hardness is estimated at 3. The mineral is brittle, with an irregular fracture and perfect {100} cleavage. The calculated density is 8.496 g/[cm.sup.3] based on the empirical formula. Markcooperite is biaxial (+), with indices of refraction [alpha] = 2.11, [beta] = 2.12, [gamma] = 2.29 calculated using the Gladstone-Dale relationship, measured [alpha]-[beta] birefringence of 0.01 and measured 2 V of 30(5)[degrees]. The optical orientation is X = c, Y = b, Z = a. The mineral is slightly pleochroic in shades of orange, with absorption: X > Y = Z. No dispersion was observed. Electron microprobe analysis provided PbO 50.07, Te[O.sub.3] 22.64, U[O.sub.3] 25.01, C1 0.03, O[equivalent to]Cl -0.01, total 97.74 wt%; the empirical formula (based on O+Cl = 8) is [Pb.sub.2.05][U.sub.0.80][Te.sup.6+.sub.1.18][O.sub.7.99][Cl.sub.0.01]. The strongest powder X-ray diffraction lines are [[d.sub.obs] in [Angstrom] (hkl) I]: 3.235 (120, 102, [bar.1]02) 100, 2.873 (200) 40, 2.985 ([bar.1]21, 112, 121) 37, 2.774 (022) 30, 3.501 (021, 012) 29, 2.220 (221, [bar.2]21, 212) 23, 1.990 (222, [bar.2]22) 21, and 1.715 (320) 22. The crystal structure ([R.sub.1] = 0.052) is based on sheets of comer-sharing uranyl square bipyramids and tellurate octahedra, with Pb atoms between the sheets. Markcooperite is the first compound to show [Te.sup.6+] substitution for [U.sup.6+] within the same crystallographic site. Markcooperite is structurally related to synthetic Pb(U[O.sub.2])[O.sub.2]. Keywords: Markcooperite, new mineral, tellurate, uranyl, crystal structure, Otto Mountain, California DOI: 10.2138/am.2010.3513

Calcium aluminate glasses are important materials where Al[O.sup.-.sub.4/2] is the only network former. Aluminum in crystals or glasses between CaO and [Al.sub.2][O.sub.3] can have different environments as a function of the CaO/[Al.sub.2][O.sub.3] ratio. Using X-ray absorption at the Al K- and L-edges, Raman and [sup.27]Al NMR spectroscopies, we have determined the structural surroundings of Al in glasses, crystals, and melts in this binary system. Aluminum is in octahedral coordination at high-[Al.sub.2][O.sub.3] content (>80 mol%) and essentially in fourfold coordination with 4 bridging O atoms (BOs) at [Al.sub.2][O.sub.3] contents between 30 and 75 mol%. At around 25 mol% [Al.sub.2][O.sub.3]. Al is in tetrahedral coordination with two BOs. The presence of higher-coordinated species at high-[Al.sub.2][O.sub.3] contents and their absence at low [Al.sub.2][O.sub.3] imply different viscous flow mechanisms for high- and low-concentration [Al.sub.2][O.sub.3] networks. Keywords: Aluminate, crystal, glasses, melts, Raman, NMR, XANES DOI: 10.2138/am.2010.3465

Thorneite, [Pb.sub.6]([Te.sup.6+.sub.2][O.sub.10])(C[O.sub.3])[Cl.sub.2] ([H.sub.2]O), is a new tellurate from Otto Mountain near Baker, California, named in honor of Brent Thorne. The new mineral occurs on fracture surfaces and in small vugs in hrecciated quartz veins. Thorneite is directly associated with acanthite, cerussite, gold, hessite, iodargyrite, khinite, wulfenite, and three other new tellurates: housleyite, markcooperite, and ottoite. Various other secondary minerals occur in the veins, including three other new secondary tellurium minerals: paratimroseite, telluroperite, and timroseite. Thomeite is monoclinic, space group C2/c, a = 21.305(1), b = 11.059(1), c = 7.564(1) [Angstrom] [beta] = 101.112(4)[degrees], V = 1748.8(4) [[Angstrom].sup.3], and Z= 4. Crystals are prismatic to bladed with elongation and striations parallel to c and typically occur in parallel and random aggregates. It is yellow and transparent, with pale yellow streak and adamantine luster. Mohs hardness is estimated at 2. The mineral is brittle, with an irregular to splintery fracture and good {100} cleavage. The calculated density is 6.828 g/[cm.sup.3]. Thorneite is biaxial (+), with large 2V, but indices of refraction are too high to he measured. The optic orientation is Y = b, Z [conjunction] a = 29[degrees] in obtuse [beta]. No pleochroism was observed. Electron microprobe analysis provided PbO 73.90, ZnO 0.03, Te[O.sub.3] 20.35, Cl 2.29, [H.sub.2]O 1.28 (structure), C[O.sub.2] 2.29 (structure), O[equivalent to]Cl -0.52, total 99.62 wt%; the empirical formula (based on O+Cl = 16) is ([Pb.sub.5.94][Zn.sub.0.01])([Te.sup.6+.sub.2.08][O.sub.10])([C.sub.1.00] [O.sub.3])[[Cl.sub.1.16][O.sub.0.34][(OH).sub. 0.50]]([H.sub.2]O) The strongest powder X-ray diffraction lines are [[d.sub.obs] in [Angstrom] (hkl) I]: 10.43 (200) 35, 3.733 ([bar.5]11, [bar.2]02, 002) 27, 3.595 ([bar.4]21) 33, 3.351 (112) 66, 3.224 (51l, 131) 100, 3.093 ([bar.2]22, [bar.3]31) 30, 2.900 ([bar.6]21) 44, 2.133 (821, 622, 223, 731, 242) 38. The crystal structure ([R.sub.1] = 0.028) contains edge-sharing octahedral tellurate dimers, [[[Te.sup.6+.sub.2][O.sub.10]].sup.8-] that bond to Pb atoms, which in turn are linked via bonds to Cl atoms, C[O.sub.3] triangles, and [H.sub.2]O molecules. Keywords: Thorneite, new mineral, tellurate, crystal structure, Otto Mountain, California DOI: 10.2138/am.2010.3512

A mineral assemblage involving grandidierite, ominelite, boralsilite, werdingite, dumortierite (locally Sb,Ti-rich), tourmaline, and corundum, along with the matrix minerals K-feldspar, quartz, and plagioclase, was found in a veinlet cutting leucocratic granulite at Horni Bory, Bory Granulite Massif, Moldanubian Zone of the Bohemian Massif. Zoned crystals of primary grandidierite to ominelite enclosed in quartz are locally overgrown by prismatic crystals of boralsilite and Fe-rich werdingite. Boralsilite also occurs as separate cross-shaped plumose aggregates with Fe-rich werdingite in quartz. Grandidierite is commonly rimmed by a narrow zone of secondary tourmaline or is partially replaced by the assemblage tourmaline + corundum [+ or -] hercynite. Grandidierite ([X.sub.Fe] = 0.34-0.71) exhibits dominant Fe[Mg.sub.-1] substitution and elevated contents of Li (120-1890 ppm). Boralsilite formula ranges from [Al.sub.15.97][B.sub.6.20][Si.sub.1.80][O.sub.37] to [Al.sub.15.65][B.sub.5.29][Si.sub.2.71][O.sub.37] and the formula of werdingite ranges from [(Fe,Mg).sub.1.44][Al.sub.14.61][B.sub.4.00][Si.sub.3.80][O.sub.37] to [(Fe,Mg).sub.1.22][Al.sub.14.86][B.sub.4.25][Si.sub.3.55][O.sub.37]. Dumortierite and Sb,Ti-rich dumortierite occur as zoned crystals with zones poor in minor elements ([less than or equal to]0.12 apfu Fe+Mg) and zones enriched in Sb ([less than or equal to]0.46 apfu) and Ti ([less than or equal to]0.25 apfu). Secondary tourmaline ([X.sub.Fe] = 0.44-0.75) of the schorlmagnesiofotite-foitite-olenite solid solution occurs as a replacement product of grandidierite, rarely boralsilite. Other accessory minerals in the veinlet include monazite-(Ce), ilmenite, rutile, ferberite, srilankite, lollingite, arsenopyrite, and apatite. Formation of the borosilicate-bearing veinlet post-dates the development of foliation in the host granulite and is related to the decompressional process. The assemblage most probably originated from a [H.sub.2]O-poor system at T ~ 750[degrees]C and P ~ 6-8 kbar. Textural relations as well as geological position of the borosilicate veinlet suggest that it represents the earliest intrusion related to pegmatites in the Bory Granulite Massif. Younger granitic pegmatites in the area are characterized by high contents of B, Al, P, Fe, and minor concentrations of W, Ti, Zr, Sc, and Sb. All pegmatite types probably formed within a short time period of ~5 Ma. Keywords: Boron, grandidierite, ominelite, werdingite, boralsilite, granulite, partial melting, Moldanubicum, Bohemian Massif DOI: 10.2138/am.2010.3480

The crystal chemistry of londonite, a rare Cs-bearing mineral [ideal chemical formula: (Cs,K) [Al.sub.4][Be.sub.4][(B,Be).sub.12][O.sub.28]; a = 7.3098(2) [Angstrom] at 300 K, space group P[bar.4]3m] from the granitic pegmatites of the Antsongombato Gem Mine, Betafo district, Madagascar, has been reinvestigated by means of wavelength dispersive X-ray spectroscopy, laser ablation-inductively coupled plasma-mass spectroscopy, inductively coupled plasma-atomic emission spectroscopy, X-ray powder diffraction, and single-crystal neutron diffraction at 300 and 20 K. Single-crystal anisotropic structural refinement at 300 K gave a final agreement index [R.sub.1] = 0.0479 for 32 refined parameters and 416 unique reflections with [F.sub.o] > 4[sigma]([F.sub.o]). The analysis of the difference-Fourier maps of the nuclear density discounts the presence of hydroxyl groups, as wrongly reported in some of the previous studies. The structural refinements and the chemical analyses suggested that: the tetrahedral 4e site (at x ~ 0.258) is mainly occupied by Be, but a low amount of B (~3%) likely occurs; the tetrahedral 12h site (at x ~ 0.248) is mainly occupied by B, but a significant fraction of Be (~12%) is present; the octahedral 4e site (at x ~0.361) is fully occupied by Al; and the 1a site (at x = 0, with CN = 12) is mainly occupied by Cs, with Rb and K. The significantly high amount of [B.sub.2][O.sub.3] (~50 wt%) and Cs+Rb(Cs[O.sub.2]+Rb[O.sub.2] [greater than or equal to] 8 wt%) makes the synthetic counterpart of londonite of interest as a potential neutron absorber or a potential host for nuclear waste. Keywords: Londonite, crystal chemistry, crystal structure, single-crystal neutron diffraction, low temperature DOI: 10.2138/am.2010.3554

The crystal chemistry of six natural datolites from different localities was investigated by electron microprobe analysis in the wavelength dispersive mode and single-crystal X-ray diffraction. The chemical analyses show no significant site substitution. The single-crystal structure refinements confirm the structural model of datolite previously reported (with a ~ 4.83, b ~ 7.61, c ~ 9.63 [Angstrom], and [beta] ~ 90.15[degrees], space group [P2.sub.1]/c). Intra-polyhedral bond distances and angles show common features in all samples at room T: (1) the Si-tetrahedron is strongly deformed, with Si-O distances ranging between ~1.57 and ~1.66 [Angstrom] and O-Si-O angles ranging between ~105.4 and ~115.3[degrees]; (2) the B-tetrahedron is almost regular; (3) the Ca-polyhedron is significantly distorted, with bond distances ranging between ~2.28 and ~2.67 [Angstrom]; (4) only one independent H-site occurs and its refined position suggests a bifurcated hydrogen bonding scheme with O5 as donor and O4 and O2 as acceptors [with O5-H ~ 0.8 [Angstrom] and (1) O5 ... O4 ~ 2.99 [Angstrom], H ... O4 ~ 2.33 [Angstrom], and O5-H ... O4 ~ 140[degrees], and (2) O5 ... O2 ~ 2.96 [Angstrom], H ... O2 ~ 2.36 [Angstrom], and O5-H ... O2 ~ 131[degrees]]. Low-temperature diffraction measurements between 300 and 100 K show that the thermal expansion of datolite is mainly governed by the axial response along [100] and [010], whereas the c-axis length is almost unchanged in this temperature interval. The volume thermal expansion coefficient ([[alpha].sub.v] = [V.sup.-1][partial derivative]V/[partial derivative]T) between 100 and 280 K is [[alpha].sub.v] = 1.5(2) x [10.sup.-5] [K.sup.-1]. The higher thermal expansion of the a-axis is due to the layered nature of the structure of datolite: the Ca-O bond distances are the most compressible and expandable, and govern the contraction, upon cooling, along the direction perpendicular to the polyhedral layers. The tetrahedral layer is significantly more rigid and no changes of the tetrahedral tilts are observed from 300 to 100 K. Keywords: Datolite, crystal structure, crystal chemistry, low temperature, single-crystal X-ray diffraction DOI: 10.2138/am.2010.3536

Sizes of cavities and their packing schemes in selected zeolites and clathrasils were studied by means of least squares fitting of circumscribed spheres to them. Resulting packing of spheres of different diameters was analyzed by the coordinates of their centers, their volumes and sphericity, and interpreted by comparison with analogous packings of atoms in inorganic compounds and alloys. The topology is described qualitatively as 'negative' structures formed by the cavities. Melanophlogite and dodecasils 3C and 1H are all clathrasils with isolated cavities. They all have pentagonal dodecahedral [[5.sup.12]] cages, associated with other cavity types. The packing of cavities in melanophlogite is analogous to the packing of atoms in the structure of [Cr.sub.3]Si, where the Cr atoms form icosahedra around the Si sites. Dodecasil 3C has a cubic arrangement of [[5.sup.12]] cavities, which is described as ABC stacking of kagome nets and its cavity packing is an analog to the packing scheme of atoms in the cubic Laves phase Mg[Cu.sub.2]. Dodecasil 1H has an arrangement of [[5.sup.12]] cavities in an AA stacking of kagome nets and is analogous to the alloy structure type Ca[Zn.sub.5]. Edingtonite and natrolite are built from two types of cavities, tetragonal scalenohedra and [[8.sup.6]] cavities. The [[8.sup.6]] cavities have different shape and packing in the two structures. In paulingite, the largest cavity, a large rhombicuboctahedron [[4.sup.12][6.sup.8][8.sup.6]] with a diameter of 11.02 [Angstrom] is in a body centered configuration. It is interspaced by six other types of cavities with diameters from 5.10 to 8.20 [Angstrom], arranged in a complex pattern. In this structure, there are three non-intersecting channel systems. Their cavity arrangements mimic sodalite and a modified Re[O.sub.3] structure. The cubic structure of sodalite has only one type of cavity, a truncated octahedron [[4.sup.6][6.sup.8]] with a diameter of 6.41 [Angstrom], arranged in a body-centered packing analogous to [alpha]-Fe. Chabasite has a rhombohedral packing of elongate cavities [[4.sup.12][6.sup.2][8.sup.6]], whereas Linde Type A has [[4.sup.6][6.sup.8]] and [[4.sup.12][6.sup.8][8.sup.6]] cavities in a CsCl-type arrangement. The cavity representation used here gives a clear picture of cavities and interconnections even for complicated cases. Keywords: Clathrates, zeolites, functional cavities, cavity packing, alloys DOI: 10.2138/am.2010.3426

The synthesis of the salt [4,4'-[H.sub.2]bipy][Co[Br.sub.4] 3 and metallo-organic framework (MOF) [[{(4,4'-bipy)Co[Br.sub.2]}.sub.n] 4 by a range of solid state (mechanochemical and thermochemical) and solution methods is reported; they are isostructural with their respective chloride analogues 1 and 2. 3 and 4 can be interconverted by means of HBr elimination and absorption. Single phases of controlled composition and general formula [4,4'-[H.sub.2]bipy][Co[Br.sub.4.x][CI.sub.x] [5.sub.x ]may be prepared from 2 and 4 by solid--gas reactions involving HBr or HCI respectively. Crystalline single phase samples of [5.sub.x] and [[{(4,4'-bipy)Co[Br.sub.2-x][CI.sub.x]}.sub.n] [6.sub.x] were prepared by solid-state mechanochemical routes, allowing fine control over the composition and unit cell volume of the product. Collectively these methods enable continuous variation of the unit cell dimensions of the salts [4,4'-[H.sub.2]bipy][Co[Br.sub.4-x][CI.sub.x] ([5.sub.x]) and the MOFs [[{/4,4'-bipy)Co[Br.sub.2-x][Cl.sub.x}.sub.n] ([6.sub.x]) by varying the bromide to chloride ratio and establish a means of controlling MOF composition and the lattice metrics, and so the physical and chemical properties that derive from it. metric engineering I solid-state reactivity www.pnas.org/cgi/doi/10.1073/pnas.0910146107

Heterotrimeric GTP-binding proteins (G proteins) transmit extracellular stimuli perceived by G protein-coupled receptors (GPCRs) to intracellular signaling cascades. Hundreds of GPCRs exist in humans and are the targets of a large percentage of the pharmaceutical drugs used today. Because G proteins are regulated by GPCRs, small molecules that directly modulate G proteins have the potential to become therapeutic agents. However, strategies to develop modulators have been hampered by a lack of structural knowledge of targeting sites for specific modulator binding. Here we present the mechanism of action of the cyclic depsipeptide YM-254890, which is a recently discovered [G.sub.q]-selective inhibitor. YM-254890 specifically inhibits the GDP/GTP exchange reaction of [alpha] subunit of [G.sub.q] protein (G[[alpha].sub.q]) by inhibiting the GDP release from G[[alpha].sub.q]. X-ray crystal structure analysis of the G[[alpha].sub.q][beta][gamma]-YM-254890 complex shows that YM-254890 binds the hydrophobic cleft between two interdomain linkers connecting the GTPase and helical domains of the G[[alpha].sub.q]. The binding stabilizes an inactive GDP-bound form through direct interactions with switch I and impairs the linker flexibility. Our studies provide a novel targeting site for the development of small molecules that selectively inhibit each G[alpha] subunit and an insight into the molecular mechanism of G protein activation. G protein | crystal structure | specific inhibitor doi/ 10.1073/pnas.1003553107

This paper presents a new method in designing the core layer of adaptive sandwich structures. The proposed design formulation treats the core layer as a compliant unit cell network while the unit cell network is synthesized by repeatedly linked identical compliant unit cells. Each unit cell is designed to possess shape adaptive functions independently and through the accumulation of the number of cells within the network, the global adaptive functions are accumulated also. Therefore, the network is capable of achieving large scale shape adaptations of complex profile with high fidelity. Topology optimization is used to design the compliant unit cell. Depending on the problem formulation, topology optimization can perform the simultaneous design of both the host material and the actuation material in the defined environment. This research includes a numerical case study to illustrate the technical aspects of this design philosophy. This is followed by the rapid prototyping of two scaled models and experimental validation. [DOI: 10.1115/1.4002201] Keywords: topology optimization, compliant structures, unit cell networks

A real-valued random field {[Z.sub.i,j]} with piecewise constant samples and defined on a lattice L in [R.sup.2] is developed to characterize two-dimensional metallic polycrystals. The subsets defined by constant values of {[Z.sub.i,j]} are virtual grains and the values of {[Z.sub.i,j]} give Euler angles at the nodes of L. The field {[Z.sub.i,j]} is completely defined by its marginal distribution and conditional probabilities associated with the nearest neighbor model. The defining probabilities of {[Z.sub.i,j]} need to be estimated from measurements of atomic lattice orientation. Random fields {[Z.sub.i,j]} calibrated to the measurements of crystallographic texture in two AA7075 aluminum plates have been used to generate virtual polycrystals. Virtual and actual polycrystals are similar. DOI: 10.1061/(ASCE)EM.1943-7889.0000163 CE Database subject headings: Monte Carlo method; Lattices; Probability; Aluminum; Measurement. Author keywords: Conditional/joint probabilities; Metallic.

Experimental studies established that calcium undergoes several counterintuitive transitions under pressure: fcc [right arrow] bcc [right arrow] simple cubic [right arrow] Ca-IV [right arrow] Ca-V, and becomes a good superconductor in the simple cubic and higher-pressure phases. Here, using ab initio evolutionary simulations, we explore the behavior of Ca under pressure and find a number of new phases. Our structural sequence differs from the traditional picture for Ca, but is similar to that for Sr. The [beta]-tin ([14.sub.1]/amd) structure, rather than simple cubic, is predicted to be the theoretical ground state at 0 K and 33-71 GPa. This structure can be represented as a large distortion of the simple cubic structure, just as the higher-pressure phases stable between 71 and 134 GPa. The structure of Ca-V, stable above 134 GPa, is a complex host-guest structure. According to our calculations, the predicted phases are superconductors with Tc increasing under pressure and reaching approximately 20 K at 120 GPa, in good agreement with experiment. evolutionary algorithms | high pressure | structure prediction | density functional theory | superconductivity doi: 10.1073/pnas.0910335107

The 2009 H1N1 swine flu is the first influenza pandemic in decades. The crystal structure of the hemagglutinin from the A/California/04/2009 H1N1 virus shows that its antigenic structure, particularly within the Sa antigenic site, is extreme[y similar to those of human H1N1 viruses circulating early in the 20th century. The cocrystal structure of the 1918 hemagglutinin with 2D1, an antibody from a survivor of the 1918 Spanish flu that neutralizes both 1918 and 2009 H1N1 viruses, reveals an epitope that is conserved in both pandemic viruses. Thus, antigenic similarity between the 2009 and 1918-like viruses provides an explanation for the age-related immunity to the current influenza pandemic. 10.1126/science.1186430

In this work, we structurally characterize defects, grain boundaries, and intergrowth phases observed in various Mo-V-O materials using aberration-corrected high-angle annular dark-field (HAADF) imaging within a scanning transmission electron microscope (STEM). Atomic-level imaging of these preparations clearly shows domains of the orthorhombic M1-type phase intergrown with the trigonal phase. Idealized models based on HAADF imaging indicate that atomic-scale registry at the domain boundaries can be seamless with several possible trigonal and Ml-type unit cell orientation relationships. The alignment of two trigonal domains separated by an M1-type domain or vice versa can be predicted by identifying the number of rows/columns of parallel symmetry operators. Intergrowths of the M1 catalyst with the M2 phase or with the [Mo.sub.5][O.sub.14]-type phase have not been observed. The resolution enhancements provided by aberration-correction have provided new insights to the understanding of phase equilibria of complex Mo-V-O materials. This study exemplifies the utility of STEM for the characterization of local structure at crystalline phase boundaries. propane | oxidation | catalyst | acrylonitrile | bronze doi/10.1073/pnas.1001239107

The use of nanoscale x-ray probes overcomes several key limitations in the study of materials up to multimegabar (>200) pressures, namely, the spatial resolution of measurements of multiple samples, stress gradients, and crystal domains in micron to submicron size samples in diamond-anvil cells. Mixtures of Fe, Pt, and W were studied up to 282 GPa with 250-600 nm size synchrotron x-ray absorption and diffraction probes. The probes readily resolve signals from individual materials, between sample and gasket, and peak pressures, in contrast to the 5-[micro]m-sized x-ray beams that are now becoming routine. The use of nanoscale x-ray beams also enables single-crystal x-ray diffraction studies in nominally polycrystalline samples at ultrahigh pressures, as demonstrated in measurements of (Mg, Fe/Si[O.sub.3] postperovskite. These capabilities have potential for driving a push toward higher maximum pressures and further miniaturization of high-pressure devices, in the process advancing studies at extreme conditions. extreme conditions | imaging | x-ray doi/10.1073/pnas.1001141107

Streptococcus mutans antigen 1/11 (AgI/II) is a cell surface-localized protein adhesin that interacts with salivary components within the salivary pellicle. AgI/II contributes to virulence and has been studied as an immunological and structural target, but a fundamental understanding of its underlying architecture has been lacking. Here we report a high-resolution (1.8 A) crystal structure of the [A.sub.3][VP.sub.1] fragment of S. mutans AgI/II that demonstrates a unique fibrillar form (155 A) through the interaction of two noncontiguous regions in the primary sequence. The [A.sub.3] repeat of the alanine-rich domain adopts an extended a-helix that intertwines with the P1 repeat polyproline type II (PPII) helix to form a highly extended stalk-like structure heretofore unseen in prokaryotic or eukaryotic protein structures. Velocity sedimentation studies indicate that full-length AgI/II that contains three A/P repeats extends over 50 nanometers in length. Isothermal titration calorimetry revealed that the high-affinity association between the [A.sub.3] and [P.sub.1] helices is enthalpically driven. Two distinct binding sites on AgI/II to the host receptor salivary agglutinin (SAG) were identified by surface plasmon resonance (SPR). The current crystal structure reveals that AgI/II family proteins are extended fibrillar structures with the number of alanine and proline-rich repeats determining their length. bacterial adhesion | dental caries | Streptococcus | x-ray crystallography | fibrous proteins doi/10.1073/pnas.0912293107

The bifunctional proline catabolic flavoenzyme, proline utilization A (PutA), catalyzes the oxidation of proline to glutamate via the sequential activities of FAD-dependent proline dehydrogenase (PRODH) and [NAD.sup.+]-dependent [[DELTA].sup.1]-pyrroline-5-carboxylate dehydrogenase (P5CDH) domains. Although structures for some of the domains of PutA are known, a structure for the full-length protein has not previously been solved. Here we report the 2.1 [Angstrom] resolution crystal structure of PutA from Bradyrhizobium japonicum, along with data from small-angle x-ray scattering, analytical ultracentrifugation, and steady-state and rapid-reaction kinetics. PutA forms a ring-shaped tetramer in solution having a diameter of 150 [Angstrom]. Within each protomer, the PRODH and P5CDH active sites face each other at a distance of 41 [Angstrom] and are connected by a large, irregularly shaped cavity. Kinetics measurements show that glutamate production occurs without a lag phase, suggesting that the intermediate, [[DELTA].sup.1]-pyrroline-5-carboxylate, is preferably transferred to the P5CDH domain rather than released into the bulk medium. The structural and kinetic data imply that the cavity serves both as a microscopic vessel for the hydrolysis of [[DELTA].sup.1]-pyrroline-5-carboxylate to glutamate semialdehyde and a protected conduit for the transport of glutamate semialdehyde to the P5CDH active site. proline catabolism | substrate channeling www.pnas.org/cgi/doi/10.1073/pnas.0906101107

Cholera is an acute intestinal infection caused by the bacterium Vibrio cholerae. In order for V. cholerae to cause disease, it must produce two virulence factors, the toxin-coregulated pilus (TCP) and cholera toxin (CT), whose expression is controlled by a transcriptional cascade culminating with the expression of the AraC-family regulator, ToxT. We have solved the 1.9 [Angstrom] resolution crystal structure of ToxT, which reveals folds in the N- and C-terminal domains that share a number of features in common with AraC, MarA, and Rob as well as the unexpected presence of a buried 16-carbon fatty acid, cis-palmitoleate. The finding that cis-palmitoleic acid reduces TCP and CT expression in V. cholerae and prevents ToxT from binding to DNA in vitro provides a direct link between the host environment of V. cholerae and regulation of virulence gene expression. AraC | crystal structure | pathogenesis | oleic acid | palmitoleic acid www.pnas.org/cgi/doi/10.1073/pnas.0915021107

We present the crystal structure of the extracytoplasmic domain of the Bacillus subtilis PhoR sensor histidine kinase, part of a two-component system involved in adaptation to low environmental phosphate concentrations. In addition to the PhoR structure, we predict that the majority of the extracytoplasmic domains of B. subtilis sensor kinases will adopt a fold similar to the ubiquitous PAS domain. doi:10.1128/JB.01508-09

There is great interest in the exploration of hydrogen-rich compounds upon strong compression where they can become superconductors. Stannane (Sn[H.sub.4]) has been proposed to be a potential high-temperature superconductor under pressure, but its high-pressure crystal structures, fundamental for the understanding of superconductivity, remain unsolved. Using an ab initio evolutionary algorithm for crystal structure prediction, we propose the existence of two unique high-pressure metallic phases having space groups Ama2 and [P6.sub.3]/mmc, which both contain hexagonal layers of Sn atoms and semimolecular (perhydride) [H.sub.2] units. Enthalpy calculations reveal that the Ama2 and [P6.sub.3]/mmc structures are stable at 96-180 GPa and above 180 GPa, respectively, while below 96 GPa Sn[H.sub.4] is unstable with respect to elemental decomposition. The application of the Allen-Dynes modified McMillan equation reveals high superconducting temperatures of 15-22 K for the Area2 phase at 120 GPa and 52-62 K for the [P6.sub.3]/mmc phase at 200 GPa. hydrogen-rich compounds | metallization | electron-phonon coupling doi/ 10.1073/pnas.0908342107

Peapods present a model system for studying the properties of dimensionally constrained crystal structures, whose dynamical properties are very important. We have recently studied the rotational dynamics of [C.sub.60] molecules confined inside single walled carbon nanotube (SWNT) by analyzing the intermediate frequency mode lattice vibrations using near-infrared Raman spectroscopy. The rotation of [C.sub.60] was tuned to a known state by applying high pressure, at which condition [C.sub.60] first forms dimers at low pressure and then forms a single-chain, nonrotating, polymer structure at high pressure. In the latter state the molecules form chains with a 2-fold symmetry. We propose that the [C.sub.60] molecules in SWNT exhibit an unusual type of ratcheted rotation due to the interaction between [C.sub.60] and SWNT in the 'hexagon orientation,' and the characteristic vibrations of ratcheted rotation becomes more obvious with decreasing temperature. molecular rotation | peapods doi/10.1073/pnas.0911963106

Primordial organisms of the putative RNA world would have required polymerase ribozymes able to replicate RNA. Known ribozymes with polymerase activity best approximating that needed for RNA replication contain at their catalytic core the class I RNA ligase, an artificial ribozyme with a catalytic rate among the fastest of known ribozymes. Here we present the 3.0 angstrom crystal structure of this ligase. The architecture resembles a tripod, its three legs converging near the ligation junction. Interacting with this tripod scaffold through a series of 10 minor-groove interactions (including two A-minor triads) is the unpaired segment that contributes to and organizes the active site. A cytosine nucleobase and two backbone phosphates abut the ligation junction; their location suggests a model for catalysis resembling that of proteinaceous polymerases. 10.1126/science.1174676

The microstructural evolution of CaSi[O.sub.3] wollastonite subjected to carbonation reactions at T = 90[degrees]C and pC[O.sub.2]= 25 MPa was studied at three different starting conditions: (1) pure water; (2) aqueous alkaline solution (0.44 MNaOH); and (3) supercritical C[O.sub.2]. Scanning and transmission electron microscopy on reacted grains prepared in cross-section always revealed unaltered wollastonite cores surrounded by micrometer-thick pseudomorphic silica rims that were amorphous, highly porous, and fractured. The fractures were occasionally filled with nanometer-sized crystals of calcite and Ca-phyllosilicates. Nanoscale chemical profiles measured across the wollastonite-silica interfacial region always revealed sharp, step-like decreases in Ca concentration. Comparison of the Ca profiles with diffusion modeling suggests that the silica rims were not formed by preferential cation leaching (leached layer), but rather by interfacial dissolution-precipitation. Extents of carbonation as a function of time were determined by quantitative Rietveld refinement of X-ray diffractograms performed on the reacted powders. Comparing the measured extents of carbonation in water (condition 1) with kinetic modeling suggests that carbonation was rate-controlled by chemical reactions at the wollastonite interface, and not by transport limitations within the silica layers. However, at conditions 2 and 3, calcite crystals occurred as a uniform surface coating covering the silica layers, and also within pores and cracks, thereby blocking the connectivity of the originally open nanoscale porosity. These crystals ultimately may have been responsible for controlling transport of solutes through the silica layers. Therefore, this study suggests that pure silica layers were intrinsically non-passivating, whereas silica layers became partially passivating due to the presence of calcite crystallites. Keywords: C[O.sub.2] sequestration, wollastonite, carbonation, dissolution-reprecipitation, diffusion modeling, leached layers, FIB-TEM, Rietveld refinement DOI: 10.2138/am.2009.3294

The structure of argentopyrite, Ag[Fe.sub.2][S.sub.3], was determined for the first time with single-crystal X-ray diffraction. In contrast to the previously reported orthorhombic symmetry, our data show that argentopyrite is monoclinic with space group [P112.sub.1]/n (non-standard setting) and unit-cell parameters a = 6.6902(2), b = 11.4497(4), c = 6.4525(2) [angstrom], [gamma] = 90-2420(8), and V = 494.26(3) [[angstrom].sup.3]. Similar to cubanite (Cu[Fe.sub.2][S.sub.3]), the structure of argentopyrite is also based on approximately hexagonal closepacked S atoms, with cations ordered over one half of the tetrahedral sites, forming corner-shared Ag[S.sub.4] and Fe[S.sub.4] tetrahedral sheets parallel to (001). The two structures differ chiefly in the linkage between the two adjacent tetrahedral sheets and the ordering patterns of cations within a tetrahedral sheet. Topologically, the structure of argentopyrite can be obtained by a displacement of a tetrahedral sheet in the cubanite structure along the (a/2 + b/6) direction relative to the sheet beneath, giving rise to a cluster of four edge-shared Fe[S.sub.4] tetrahedra in argentopyrite, as compared to two in cubanite. There are two distinct Fe sites (Fel and Fe2) in argentopyrite, rather than only one, as in other M[Fe.sub.2][S.sub.3] sulfide minerals (M = monovalent cations). Together with published Mossbauer data, we suggest that there exists some degree of [Fe.sup.2+]-[Fe.sup.3+] order-disorder in argentopyrite, with [Fe.sub.2+] favoring the more distorted [Fe2 tetrahedral site. Argentopyrite appears to possess all the features proposed by Putnis (1977) for a high-temperauare ordered form of cubanite. Keywords: Argentopyrite, Ag[Fe.sub2][S.sub.3], Ag-Fe sulfides, cubanite-related mineral, sternbergite, crystal structure, single-crystal X-ray diffraction DOI: 10.2138/am.2009.3324

The crystal structure and crystal chemistry of two natural pollucite samples, from Buck field, Oxford County, Maine (sample M3), and from Kanzit Mawaie, Laghman, Nooristan, Afghanistan (sample N5), have been investigated by means of wavelength-dispersive X-ray microanalysis, thermogravimetric analysis, single-crystal X-ray and neutron diffraction, and single-crystal Fourier-transform infrared spectroscopy. The X-ray and neutron diffraction patterns of the two pollucite crystals show a metrically cubic unit cell [with [a.sub.M3] = 13.6914(6) [Angstrom]. and [a.sub.N5] - 13.6808(6) [Angstrom]. by neutron diffraction data; the deviation from isometry is 4[sigma]([F.sub.0]) for M3 and [R.sub.1] = 0.0693 for 31 refined parameters and 331 unique reflections with [F.sub.0] > 4[sigma]([F.sub.0]) for N5. The structure refinements show a disordered Si/Al-distribution in the tetrahedral framework. The analysis of the difference-Fourier maps of the nuclear density confirms the presence of extra-framework water molecules with oxygen sharing the Cs site (at I/8, 1/8, 1/8, Wyckoff-16b position). However, the minima, ascribable to the proton sites, are very weak in density. Two possible proton positions, leading to a reasonable [H.sub.2]O configuration, are given, and the possible hydrogen bonding is described. Sodium is located at 1/4, l/8, 0 (Wyckoff-24c position). The main IR absorption bands in the regions typical of [H.sub.2]0 are assigned, and the presence of hydroxyls in the studied samples is ruled out. Neutron diffraction and FTIR data agree with the presence of very weak hydrogen bonds in the structure. The detailed description of the crystal structure and crystal chemistry of pollucite (e.g., Si/Al-distribution, configuration of the extra-framework content, possible hydrogen bonding scheme) reported in this study is the key to understand the high thermo-elastic stability of pollucite, the immobility of Cs at non-ambient conditions, and the extremely low leaching rate of Cs, which make this open-framework silicate a promising material with potential use for fixation and deposition of Cs radioisotopes. Keywords: Pollucite, zeolite, crystal chemistry, single-crystal X-ray diffraction, single-crystal neutron diffraction, single-crystal FTIR DOI: 10.2138/am.2009.3237

Plexin cell surface receptors bind to semaphorin ligands and transduce signals for regulating neuronal axon guidance. The intracellular region of plexins is essential for signaling and contains a R-Ras/M-Ras GTPase activating protein (GAP) domain that is divided into two segments by a Rho GTPase-binding domain (RBD). The regulation mechanisms for plexin remain elusive, although it is known that activation requires both binding of semaphorin to the extracellular region and a Rho-family GTPase (Rac1 or Rnd1) to the RBD. Here we report the crystal structure of the plexin A3 intracellular region. The structure shows that the N- and C-terminal portions of the GAP homologous regions together form a GAP domain with an overall fold similar to other Ras GAPs. However, the plexin GAP domain adopts a closed conformation and cannot accommodate R-Ras/M-Ras in its substrate-binding site, providing a structural basis for the autoinhibited state of plexins. A comparison with the plexin B1 RBD/Rnd1 complex structure suggests that Rnd1 binding alone does not induce a conformational change in plexin, explaining the requirement of both semaphorin and a Rho GTPase for activation. The structure also identifies an N-terminal segment that is important for regulation. Both the N-terminal segment and the RBD make extensive interactions with the GAP domain, suggesting the presence of an allosteric network connecting these three domains that integrates semaphorin and Rho GTPase signals to activate the GAP. The importance of these interactions in plexin signaling is shown by both cell-based and in vivo axon guidance assays. autoinhibition | axon guidance | signaling | structure

We determined the crystal structure of 1TM-[alpha]V[beta]3, which represents the complete unconstrained ectodomain plus short C-terminal transmembrane stretches of the [alpha]V and [beta]3 subunits. 1TM-[alpha]V[beta]3 is more compact and less active in solution when compared with [DELTA]TM-[alpha]V[beta]3, which lacks the short C-terminal stretches. The structure reveals a bent conformation and defines the [alpha]-[beta] interface between IE2 (EGF-like 2) and the thigh domains. Modifying this interface by site-directed mutagenesis leads to robust integrin activation. Fluorescent life-time imaging microscopy of inactive full-length [alpha]V[beta]3 on live cells yields a donor-membrane acceptor distance, which is consistent with the bent conformation and does not change in the activated integrin. These data are the first direct demonstration of conformational coupling of the integrin leg and head domains, identify the IE2-thigh interface as a critical steric barrier in integrin activation, and suggest that inside-out activation in intact cells may involve conformational changes other than the postulated switch to a genu-linear state.

Many human diseases are caused by dysregulated gene expression. The oversupply of transcription factors may be required for the growth and metastatic behavior of human cancers. Cell permeable small molecules that can be programmed to disrupt transcription factor-DNA interfaces could silence aberrant gene expression pathways. Pyrrole-imidazole polyamides are DNA minor-groove binding molecules that are programmable for a large repertoire of DNA motifs. A high resolution X-ray crystal structure of an 8-ring cyclic Py/Im polyamide bound to the central 6 bp of the sequence d(5'-CCAGGCCTGG-3')2 reveals a 4 [Angstrom] widening of the minor groove and compression of the major groove along with a >18[degrees] bend in the helix axis toward the major groove. This allosteric perturbation of the DNA helix provides a molecular basis for disruption of transcription factor-DNA interfaces by small molecules, a minimum step in chemical control of gene networks. DNA binders I gene regulation I minor groove binders | Py-lm polyamides | crystal structure

In the formation of chiral crystals, the tendency for twist in the orientation of neighboring molecules is incompatible with ordering into a lattice: Twist is expetled from planar layers at the expense of local strain. We report the ordered state of a neat material in which a local chiral structure is expressed as twisted layers, a state made possible by spatial limitation of layering to a periodic array of nanoscale filaments. Although made of achiral molecules, the layers in these filaments are twisted and rigorously homochiral--a broken symmetry. The precise structural definition achieved in filament self-assembly enables collective organization into arrays in which an additional broken symmetry--the appearance of macroscopic coherence of the filament twist-produces a liquid crystal phase of helically precessing layers.

We introduce a concept to solve the structure of a microcrystalline material in the solid-state at natural abundance without access to distance constraints, using magic angle spinning (MAS) NMR spectroscopy in conjunction with X-ray powder diffraction and DFT calculations, The method is applied to a novel class of materials that form (semi)conductive 1D wires for supramolecular electronics and artificial light-harvesting. The zinc chlorins 3-devinyl-[3.sup.1]-hydroxymethyl-13 [sup.2]-demethoxycarbonylpheophorbide a (3',5'-bis-dodecyloxy)benzyl ester zinc complex 1 and 3-devinyl-[3.sup.1]methoxymethyl-[13.sup.2]-demethoxycarbonylpheophorbide a (3',5'-bis-dodecyloxy)benzyl ester zinc complex 2, self-assemble into extended excitonically coupled chromophore stacks. [sup.1]H-[sup.13]C heteronuclear dipolar correlation MAS NMR experiments provided the [sup.1]H resonance assignment of the chlorin rings that allowed accurate probing of ring currents related to the stacking of macrocycles. DFT ring-current shift calculations revealed that both chlorins self-assemble in antiparallel [pi]-stacks in planar layers in the solid-state. Concomitantly, X-ray powder diffraction measurements for chlorin 2 at 80 [degrees]C revealed a 3D lattice for the mesoscale packing that matches molecular mechanics optimized aggregate models. For chlorin 2 the stacks alternate with a periodicity of 0.68 nm and a 3D unit cell with an approximate volume of 6.28 [nm.sup.3] containing 4 molecules, which is consistent with space group [P2.sub.1][22.sub.1]. artificial antenna | density functional theory | microcrystafline structure | solid state NMR | X-ray diffraction

A detailed single-crystal X-ray study of conformationally flexible sulfonimide-based dendritic molecules with systematically varied molecular architectures was undertaken. Thirteen crystal structures reported in this work include 9 structures of the second-generation dendritic sulfonimides decorated with different aryl groups, 2 compounds bearing branches of both second and first generation, and 2 representatives of the first generation. Analysis of the packing patterns of 9 compounds bearing second-generation branches shows that despite their lack of strong directive functional groups there is a repeatedly reproduced intermolecular interaction mode consisting in an anchor-type packing of complementary second-generation branches of neighbouring molecules. The observed interaction tolerates a wide range of substituents in meta- and para-positions of the peripheral arylsulfonyl rings. Quantum chemical calculations of the molecule-molecule interaction energies agree at the qualitative level with the packing preferences found in the crystalline state. The calculations can therefore be used as a tool to rationalize and predict molecular structures with commensurate and non-commensurate branches for programming of different packing modes in crystal. dendrimers | single-crystal X-ray | sulfonimides | supramolecular chemistry

T-cell interaction with a target cell is a key event in the adaptive immune response and primarily driven by T-cell receptor (TCR) recognition of peptide-MHC (pMHC) complexes. TCR avidity for a given pMHC is determined by number of MHC molecules, availability of coreceptors, and TCR affinity for MHC or peptide, respectively, with peptide recognition being the most important factor to confer target specificity. Here we present high-resolution crystal structures of 2 Fab antibodies in complex with the immunodominant NY-ESO-1157-165 peptide analogue (SLLMWITQV) presented by HLA-A*0201 and compare them with a TCR recognizing the same pMHC. Binding to the central methionine-tryptophan peptide motif and orientation of binding were almost identical for Fabs and TCR. As the MW 'peg' dominates the contacts between Fab and peptide, we estimated the contributions of individual amino acids between the Fab and peptide to provide the rational basis for a peptide-focused second-generation, high-affinity antibody library. The final Fab candidate achieved better peptide binding by 2 light-chain mutations, giving a 20-fold affinity improvement to 2-4 nM, exceeding the affinity of the TCR by 1,000-fold. The high-affinity Fab when grafted as recombinant TCR on T cells conferred specific killing of HLA-A*0201/[NY-ESO-1.sub.157-165] target cells, In summary, we prove that affinity maturation of antibodies mimicking a TCR is possible and provide a strategy for engineering high-affinity antibodies that can be used in targeting specific pMHC complexes for diagnostic and therapeutic purposes. antibody engineering | crystallography | tumor immunology

The first crystal structure of the neurotransmitter/sodium symporter homolog LeuT revealed an occluded binding pocket containing leucine and 2 [Na.sup.+]; later structures showed tricyclic antidepressants (TCAs) in an extracellular vestibule [approximately equal to] 11 [Angstrom]. above the bound leucine and 2 [Na.sup.+]. We recently found this region to be a second binding (S2) site and that binding of substrate to this site triggers [Na.sup.+]-coupled substrate symport. Here, we show a profound inhibitory effect of n-octyl-[beta]-D-glucopyranoside (OG), the detergent used for LeuT crystallization, on substrate binding to the S2 site. In parallel, we determined at 2.8 [Angstrom] the structure of LeuT-E290S, a mutant that, like LeuT-WT, binds 2 substrate molecules. This structure was similar to that of WT and clearly revealed an OG molecule in the S2 site. We also observed electron density at the S2 site in LeuT-WT crystals, and this also was accounted for by an OG molecule in that site. Computational analyses, based on the available crystal structures of LeuT, indicated the nature of structural arrangements in the extracellular region of LeuT that differentiate the actions of substrates from inhibitors bound in the S2 site. We conclude that the current LeuT crystal structures, all of which have been solved in OG, represent functionally blocked forms of the transporter, whereas a substrate bound in the S2 site will promote a different state that is essential for [Na.sup.+]-coupled symport. crystal | molecular dynamics simulation | neurotransmitter:sodium symport | second substrate (S2)-binding site | scintillation proximity binding assay

Proteases act in important homeostatic pathways and are tightly regulated. Here, we report an unusual structural mechanism of regulation observed by the 2.5-[Angstrom] X-ray crystal structure of the serine protease, granzyme C. Although the active-site triad residues adopt canonical conformations, the oxyanion hole is improperly formed, and access to the primary specificity (S1) pocket is blocked through a reversible rearrangement involving Phe-191. Specifically, a register shift in the 190-strand preceding the active-site serine leads to Phe-191 filling the S1 pocket. Mutation of a unique Glu--Glu motif at positions 192-193 unlocks the enzyme, which displays chymase activity, and proteomic analysis confirms that activity of the wild-type protease can be released through interactions with an appropriate substrate. The 2.5-[Angstrom] structure of the unlocked enzyme reveals unprecedented flexibility in the 190-strand preceding the active-site serine that results in Phe-191 vacating the S1 pocket. Overall, these observations describe a broadly applicable mechanism of protease regulation that cannot be predicted by template-based modeling or bioinformatic approaches alone. protease regulation | register shift | allostery

Crystal structures of potassium ([K.sup.+]) channels reveal that the selectivity filter, the narrow portion of the pore, is only ~3-[Angstrom] wide and buttressed from behind, so that its ability to expand is highly constrained, and the permeation of molecules larger than [Rb.sup.+] (2.96 [Angstrom] in diameter) is prevented. N-methyl-D-glucamine ([NMDG.sup.+]), an organic monovalent cation, is thought to be a blocker of Kv channels, as it is much larger (~7.3 [Angstrom] in mean diameter) than [K.sup.+] (2.66 [Angstrom] in diameter). However, in the absence of [K.sup.+], significant [NMDG.sup.+] currents could be recorded from human embryonic kidney cells expressing Kv3.1 or Kv3.2b channels and Kvl.5 R487Y/V, but not wild-type channels. Inward currents were much larger than outward currents due to the presence of intracellular [Mg.sup.2+] (1 mM), which blocked the outward [NMDG.sup.+] current, resulting in a strong inward rectification. The [NMDG.sup.+] current was inhibited by extracellular 4-aminopyridine (5 mM) or tetraethylammonium (10 mM), and largely eliminated in Kv3.2b by an S6 mutation that prevents the channel from opening (P468W) and by a pore helix mutation in Kvl.5 R487Y (W472F) that inactivates the channel at rest. These data indicate that [NMDG.sup.+] passes through the open ion- conducting pore and suggest a very flexible nature of the selectivity filter itself. 0.3 or 1 mM [K.sup.+] added to the external [NMDG.sup.+] solution positively shifted the reversal potential by ~16 or 31 mV, respectively, giving a permeability ratio for [K.sup.+] over [NMDG.sup.+] ([P.sub.K.sup.+]/[P.sub.NMDG.sup.+]) of ~240. Reversal potential shifts in mixtures of [K.sup.+] and [NMDG.sup.+] are in accordance with [P.sub.K.sup.+]/[P.sub.NMDG.sup.+], indicating that the ions compete for permeation and suggesting that [NMDG.sup.+] passes through the open state. Comparison of the outer pore regions of Kv3 and Kvl.5 channels identified an Arg residue in Kvl.5 that is replaced by a Tyr in Kv3 channels. Substituting R with Y or V allowed Kv1.5 channels to conduct [NMDG.sup.+], suggesting a regulation by this outer pore residue of Kv channel flexibility and, as a result, permeability.

An in-situ, high-pressure, single-crystal X-ray diffraction study has been carried out at room temperature up to 7.42 GPa on a crystal of ingersonite, ideally [Ca.sub.3][Mn.sup.2+][Sb.sup.5+.sub.4][O.sub.14], from the type material. Ingersonite is isostructural with the synthetic weberite-3T polytype and related to the pyrochlore structure-type. Owing to the P range investigated and the quality of data, a second-order Birch-Murnaghan Equation of State (EoS) is the best approximation to describe the ingersonite volume evolution with P. The refined EoS parameters are [V.sub.0] = 810.6(1) [[Angstrom].sup.3] and [K.sub.0] = 154.5(2.4) GPa. The behavior of ingersonite with pressure is almost isotropic and the decrease of the unit-cell volume is mainly due to the kinking of the polyhedra rather than their volume decrease. The overall mean distances are quite constant, indicating virtually no compressibility of both the A and B polyhedra in the P range investigated. However, some geometrical changes in the pyrochlore-like A[B.sub.3] layer can be observed and compared with those observed in synthetic pyrochlore compounds. The largest change is observed for the z atomic coordinate of the O2 atom. Using an anion-centered polyhedral description, O2 is the only O atom that is asymmetrically located in an octahedral interstice, this feature being the most remarkable difference between the structure of ingersonite (i.e., weberite-3T type, space group [P3.sub.1]21) and that of zirconolite-3T (pyrochlore structure type, space group [P3.sub.1]21), where all the O atoms occupy the tetrahedral interstices of a cubic [A.sub.2][B.sub.2] array. With the increase of pressure, the O2 atom migrates from the [A.sub.4][B.sub.2] octahedral cavity toward the adjacent [AB.sub.3] tetrahedral cavity, suggesting that a transition from weberite-3T to zirconolite-3T structure type could occur at pressures higher than 11 GPa. Keywords: Ingersonite, high pressure, compressibility, crystal structure, phase transition

The open-branched tetrahedral chain of sapphirine-group minerals contains tetrahedra with 1-3 bridging O atoms ([Q.sup.1], [Q.sup.2], and [Q.sup.3]). The topology implies that short-range order (SRO) driven by bonding enthalpies forces some long-range order (LRO). This is an ideal system to investigate the interplay between SRO, LRO, and configurational entropy. Results are presented of Monte Carlo simulations of ordering patterns involving Be, Al, and Si on the branched chain. The 'Loewenstein's Rule' enthalpy term favoring AlOSi links is insufficient to obtain the experimental LRO occupancies. Additional site-dependent potentials repelling Si from [Q.sup.1] and [Q.sup.2] and driving asymmetry between the two [Q.sup.3] sites are needed. All enthalpy terms are close to 2 RT in magnitude, so the observed LRO cannot be regarded as arising dominantly from Si-avoidance. A 'Markov Braid' method is presented of calculating configurational entropies for the simulations. The substantial SRO present is shown to reduce [S.sub.config] by only 17-18%. Khmaralite is related to sapphirine but contains ca. 1.5 Be per 12 tetrahedra and shows different LRO of {Be, Al, Si}. The minority cation Be is concentrated in [Q.sup.3] sites. If the exchange enthalpy [DELTA][H.sub.AlSi] = -2 RT, then [DELTA][H.sub.BeAl] and [DELTA][H.sub.BeSi] must be -6.5 to -7.5 RT to reproduce the observed mean Q for Be, Al, and Si. Khmaralite has a doubled chain period relative to sapphirine. This superstructure enables the formation of tetrahedral Be-octahedral [Fe.sup.2+] clusters in the structure. A small number of site-specific potentials allows the LRO of the khmaralite chain to be reproduced, but 'Be-avoidance' remains by far the dominant interaction. Site occupancies were extrapolated to Be-rich compositions. More than 1.7 Be atoms per 12 tetrahedra is predicted to drive Be into new sites and create unfavorable BeOBe links, and to drive Si from [Q.sup.3] into the [Q.sup.1] sites. This is likely to be why the related mineral welshite, which can incorporate higher Be contents, has a quite different Be ordering pattern and symmetry. Keywords: Branched tetrahedral chain, khmaralite, sapphirine, welshite, aluminum, beryllium, silicon, aluminum avoidance, beryllium avoidance, configurational entropy, long-range order, Markov braid, short-range order, silicon avoidance