extfieldsofstudy:
Computer Science
Medicine

text:
(Salicylato)[tris(1-methyl-1H-benzimidazol-2-ylmethyl)amine]copper(II) perchlorate dimethylformamide disolvate

In the title complex, [Cu(C7H5O3)(C27H27N7)]ClO4·2C3H7NO, the CuII ion is five-coordinated by four N atoms from the tris(1-methyl-1H-benzimidazol-2-ylmethyl)amine ligand and an O atom of the monodentate salicylate ligand. The N4O donor set defines a coordination geometry intermediate between square-pyramidal and trigonal–bipyramidal. The crystal structure is stabilized by O—H⋯O interactions. The atoms of the aromatic ring of the salicylate ligand are disordered over two sites of equal occupancy. In addition, one of the dimethylformamide solvent molecules is partially disordered over two positions, of approximately equal occupancy.

In the title complex, [Cu(C 7 H 5 O 3 )(C 27 H 27 N 7 )]ClO 4 Á2C 3 H 7 NO, the Cu II ion is five-coordinated by four N atoms from the tris(1-methyl-1H-benzimidazol-2-ylmethyl)amine ligand and an O atom of the monodentate salicylate ligand. The N 4 O donor set defines a coordination geometry intermediate between square-pyramidal and trigonal-bipyramidal. The crystal structure is stabilized by O-HÁ Á ÁO interactions. The atoms of the aromatic ring of the salicylate ligand are disordered over two sites of equal occupancy. In addition, one of the dimethylformamide solvent molecules is partially disordered over two positions, of approximately equal occupancy.
The Cu atom is five-coordinate within a N 4 O ligand set. The Mentb ligand functions as a tetradentate N-donor, and an O atom of a monodentate salicylate anion completes the coordination environment. The coordination environment of the Cu II centre has an intermediate coordination geometry as seen in the value of τ = 0.45, cf. τ = 0 for an ideal square pyramid and τ = 1 for an ideal trigonal bipyramid (Addison et al., 1984). The Cu···O2 distance of 2.960 (2) Å indicates that the O2 atom is non-coordinating. The distances and angles in Mentb and salicylate are as expected (Allen et al., 1987). O-H···O Hydrogen-bonding interactions play an important role in the crystal packing (Table 1). The atoms of the aromatic ring of the salicylate ligand are disordered over two sites with equal occupancy and one of the lattice DMF molecules is partially disordered over two positions, of approximately equal occupancy.
A blue-green crystalline product formed rapidly. The precipitate was filtered off, washed with MeOH and absolute Et 2 O, and dried in vacuo. The dried precipitate was dissolved in DMF to yield a blue-green solution that was allowed to evaporate at room temperature. Blue-green crystals suitable for X-ray diffraction studies were obtained after two weeks. Yield, 0.12 g (67%). Analysis found: C 53.63, H 5.18, N 14.07, Cu 7.09%. C 40 H 46 ClCuN 9 O 9 requires: C 53. 45,H 5.15,N 13.95,Cu 7.41%.

Refinement
The aromatic ring of the salicylate ligand was disordered over two sites and from refinement, these were determined to be of equal occupancy. One of the lattice dimethylformamide molecules is partially disordered over two positions and from refinement, the major component was found to have an occupancy factor = 0.552 (15). All H atoms were geometrically positioned and refined using a riding-model approximation with C-H distances ranging from 0.95 to 0.99 Å and O-H = 0.83 (1) Å, and with U iso (H) = 1.2U eq (C) or U iso (H) = 0.52U eq (O).
supplementary materials sup-2 Figures Fig. 1. Molecular structure and atom numbering for the components of (I). Hydrogen atoms have been omitted for clarity and the displacement ellipsoids are shown at the 30% probability level. The salicylate anion is disordered over two positions of equal occupancy and one of the lattice dimethylformamide molecules is partially disordered over two positions, only one orientation of each is shown for reasons of clarity.


extfieldsofstudy: Chemistry Medicine

text:
4-Hydroxy-4,6a,6b,9,9,12a,14b-heptamethylperhydropicen-3-one hemihydrate isolated from Adiantum incisum

The title compound, C29H48O2·0.5H2O, is a triterpenoid isolated from the stems and rhizomes of Adiantum incisum. The basic skeleton of the molecule contains five six-membered rings, all adopting chair conformations, bearing a total of seven methyl, one hydroxyl and a keto group. There are two molecules of the triterpene and one water molecule of crystallization in the asymmetric unit. The two unique triterpenoid molecules hydrogen-bond directly via an O—H⋯O=C interaction, and are also bridged by the water molecule. The water also bridges to another pair of hydrogen-bonded triterpenoid molecules.

The title compound, C 29 H 48 O 2 Á0.5H 2 O, is a triterpenoid isolated from the stems and rhizomes of Adiantum incisum. The basic skeleton of the molecule contains five six-membered rings, all adopting chair conformations, bearing a total of seven methyl, one hydroxyl and a keto group. There are two molecules of the triterpene and one water molecule of crystallization in the asymmetric unit. The two unique triterpenoid molecules hydrogen-bond directly via an O-HÁ Á ÁO C interaction, and are also bridged by the water molecule. The water also bridges to another pair of hydrogenbonded triterpenoid molecules.  Table 1 Hydrogen-bond geometry (Å , ). Data collection: COLLECT (Hooft, 1998); cell refinement: DENZO (Otwinowski & Minor, 1997) and COLLECT; data reduction: DENZO and COLLECT; program(s) used to solve structure: SHELXTL (Sheldrick, 2000); program(s) used to refine structure: SHELXTL; molecular graphics: SHELXTL; software used to prepare material for publication: SHELXTL and local programs.

Comment
Triterpenoids represent an important class of natural products characterized by highly pronounced biological activities such as analgesic, anti-mutagenic, and anti-inflammatory (Matsuda et al. 1999;Janaki et al. 1999). Adiantum incisum, a fern, generally found in the Himalayas region is well known for its antibacterial, antiviral and antifungal activities (Kshirsagar et al. 1972;Wada et al. 1987). The plant for the present work was collected from the Murree hills of Pakistan and during its phytochemical investigations, title compound (I) was isolated and its crystal structure is being reported here for the first time. (I) has also been reported as one of the constituents of Adiantum monochlamys (Ageta et al. 1966).
The molecule (I) is shown in Fig.1 and contains five six membered rings, all adopting chair conformations, fused together in a trans fashion. All the rings at their juncture bear one methyl group while ring A has two extra methyl groups. Ring E is in a slightly distorted form due to the presence of one methyl and a hydroxyl group at one carbon, C1, and a keto group on the adjacent carbon, C2.
The arrangement of molecular units suggests that the three dimensional structure is stabilized by inter molecular hydrogen bonds. Carbonyl oxygen (O4) of one triterpenoid molecule is involved in hydrogen bonding with the hydroxyl hydrogen (H1) of the other while its hydroxyl hydrogen (H3) is H-bonded with the oxygen (O5) of the water molecule. The H atoms of the water molecule are involved in inter-molecular hydrogen bonding with hydroxyl oxygen O1 (O1···O5 = 3.009 (9) Å) and carbonyl oxygen O2i (O5···O2i = 2.834 (9) Å; symmetry operator i = x + 1, y, z + 1) of the adjacent pair of molecules making an infinite chain along [1 0 1] as shown in Figs 2 & 3.

Experimental
The plant (Adiantum incisum) collected from Murree hills, Pakistan, was shade dried. The dried stems and rhizomes (2.9 kg) were dipped in ethanol for fifteen days and filtered. The filtrate was concentrated under reduced pressure to obtain the extract (51.33 g) followed by column chromatography using a gradient solvent system from hexane-chloroform-methanol.
The eluted fractions were monitored by thin layer chromatography and combined to give 38 main fractions. Fraction 9 was rechromatographed on a silica-gel column with hexane-chloroform (1:1) to afford the pure title compound (I).

Refinement
In the absence of anomalous scatterers Friedel pairs were merged and the absolute configuration of the compound was arbitrarily set. H atoms bound to C were placed in geometric positions (C-H distance = 0.99 Å for methylene; 1.00 Å for methyl H; 0.84 Å for OH) using a riding model. H atoms on the water molecules were not located in difference maps or included in the model. U iso values were set to 1.2U eq (1.5U eq for methyl H and OH) of the carrier atom. The displacement parameters of the atoms C33 C36, C48, C51 and C53 were restrained to an isotropic behaviour.   -4,6a,6 b,9,9,12a,14b-  Refinement. Refinement of F 2 against ALL reflections. The weighted R-factor wR and goodness of fit S are based on F 2 , conventional R-factors R are based on F, with F set to zero for negative F 2 . The threshold expression of F 2 > 2sigma(F 2 ) is used only for calculating R-factors(gt) etc. and is not relevant to the choice of reflections for refinement. R-factors based on F 2 are statistically about twice as large as those based on F, and R-factors based on ALL data will be even larger. Flack gave no indication of absolute structure, so Friedels merged. Material isolated from a plant, but no clear idea of absolute structure. Most likely this is correct however.


Phase Separation of Bismuth Ferrite into Magnetite under Voltage Stressing

Micro-Raman studies show that under ~700 kV/cm of d.c. voltage stressing for a few seconds, thin-film bismuth ferrite BiFeO3 phase separates into magnetite Fe3O4. No evidence is found spectroscopically of hemite alpha-Fe2O3, maghemite gamma-Fe2O3, or of Bi2O3. This relates to the controversy regarding the magnitude of magnetization in BiFeO3.

in the thinner films [11]. This is in accord with experiments [11], which show an order of magnitude enhancement in M in the thinnest films.
In the present work we have used micro-Raman techniques described previously [12] to examine the phase separation of bismuth ferrite under d.c. voltage stressing at room temperature, in order to see if magnetic phases are separated in the process. As described below, we have found that magnetite is formed under these conditions. Since the Raman spectra of the BiFeO 3 starting material agrees very well with those recently published on virgin thin-film samples [13][14][15][16][17], these studies show that the magnetite is formed entirely by the applied d.c. voltage and does not exist in significant concentrations in the unstressed specimens. We note that although Fe 3 O 4 and Fe 2 O 3 differ by only 10% oxygen concentration, their bondings differ and this gives rise to distinguishable Raman spectra.
The bismuth ferrite film with thickness of 185 nm was made by using sol-gel spin coating techniques on a Pt/TiO 2 /SiO 2 /Si commercialized substrate. The top electrodes (Pt dots of 100 m x 100 m) were then deposited by sputtering on the films via TEM grids. Micro-Raman spectra were recorded in backscattering geometry at ambient conditions by CCD collection. Two types of Raman instruments were used in the present work: RM1000 Renishaw systems which uses a 514.5 nm laser and LabRam 300 equipped with 632.8 nm laser. The electrical measurements were conducted using a Radiant RT 6000S ferroelectric system. The crystallization property of our film has been confirmed by XRD measurements.
The film was stressed by applying a d.c. voltage with increasing magnitudes. At low voltages, the film shows high resistivity. The d.c. breakdown voltage is about 13 V (i.e. E B breakdown field ~700 kV/cm,) for 2 second endurance and is relatively repeatable. The a.c. breakdown voltage is relatively higher as expected and is about 15 V (i.e. ~800 kV/cm) evaluated by hysteresis measurements on a number of electrodes at 1 kHz frequency. Prebreakdown could be achieved after applying a d.c. voltage slightly lower than the breakdown strength. This manifests itself by an abrupt increase of leakage current and the appearance of a few degraded spots on the electrode (Fig 1, the dark spots as indicated by the arrow are used for Raman measurements shown later).
Then we carried out Raman studies on this film as described in detail previously [12].
Remarkably, the Raman spectra collected from the degraded areas are identical and are comparable with those for Fe 3 O 4 phase (called magnetite) [19][20][21][22][23], evidenced by the strong peak at ~642 cm -1 and several other characteristic peaks at ~314 cm -1 , 395 cm -1 , and 517 cm -1 , although these peaks are slightly shifted to lower wavenumbers compared with bulk Fe 3 O 4 . This may be due to the effect of strain on these Fe 3 O 4 nano-particles.
Note that -Fe 2 O 3 has an inverse spinel structure with a tetragonal sublattice distortion. regarding the magnitude of magnetization in BiFeO 3 thin films. This point becomes a particular concern, considering the high coercive field E c observed for BiFeO 3 thin films: it has been shown that the coercive field in bismuth ferrite thin films is about 300 kV/cm, twice or three times larger than that in common ferroelectric thin films (<100 kV/cm) [13]; hysteresis measurements sometimes require an electric field as large as 1~2 MV/cm [13,[36][37][38], compatible or even larger with the field we applied in this work. Under such a high field, interfacial phase separation of BiFeO 3 into magnetite is reasonably expected due to intensive charge injection from the electrode.
Note that BiFeO 3 single crystal or ceramics show space-commensurate ferroelectricity below the Curie point (1103 K) and space-incommensurate antiferromagnetism below the Neel temperature (643 K), with a superimposed cycloidal modulation with a wavelength of ~62 nm [39]. Consequently, its remanent magnetization and potential magnetoelectric effect both vanish macroscopically, leading to a weak quadratic magnetoelectric behavior rather than a strong linear magnetoelectric behavior [4,5]. It has been found that the cycloidal order can be destroyed and the non-zero remanent magnetization (and potential magnetoelectric effect) can be released by applying a sufficiently large magnetic field of 20 T in bulk BiFeO 3 [40] or by chemical substitutions in thin films [41]. In this work, we show that phase separation of BiFeO 3 into nano-regions of magnetite under a d.c. field, comparable to the applied field for switching measurement, may also lead to a possibility that electrical testing of samples might itself produce extrinsic magnetization.  presents a magnified view of the spectra from ~250 cm -1 to 800 cm -1 .


extfieldsofstudy: Biology Medicine

text:
A Tertiary Twist to the Transglutaminase Tale

A novel structure shows tissue transglutaminase in its catalytically active form, revealing the mode of action of this crosslinking enzyme and facilitating the development of specific inhibitors for use in various diseases in which transglutaminases are implicated.

T issue transglutaminase (TG2) is one of a family of enzymes that covalently crosslink proteins by binding a glutamine in one protein with a lysine in another [1]. There is strong evidence that links the deregulated expression of TG2 to a variety of diseases, and although the exact role of TG2 in neurodegenerative diseases is unclear [2], in celiac disease (CD), TG2 catalyses the formation of immunogenic peptides that play a crucial role in disease development [3,4]. Although x-ray crystal structures of transglutaminases have been reported previously, the catalytic site was hidden due to the protein's conformation. In this issue of PLoS Biology, a structure of TG2 is shown in which the enzyme is captured in its active state [5] with the catalytic site visible. This provides new insight into the mode of action of TG2 and offers novel opportunities for the development of TG2 inhibitors, which could have therapeutic applications. The paper also raises questions about what regulates TG2 activation and how TG2 activation influences disease development.

The Role of TG2 in Celiac Disease
Patients with celiac disease are intolerant to gluten proteins in wheat and related cereals [3,4]. In healthy individuals, the small intestine is lined with villi, which create a larger surface for the uptake of nutrients from food. In approximately 1% of the population in the Western Hemisphere, gluten induces inflammatory immune responses in the small intestine that lead to the disappearance of these villi. Malabsorption, retarded growth, diarrhea, and stomach ache can result, and these are the characteristic symptoms associated with CD [3,4].
CD typically develops in human leukocyte antigen (HLA)-DQ2-and/or HLA-DQ8-positive individuals [3,4]. HLA molecules are receptors that specifically bind peptides and present these to the T cells of the immune system. When such peptides are derived from pathogens, an immune response is initiated to eradicate the pathogen. In the small intestine of patients with CD, erroneous T cell responses are made against gluten peptides bound to HLA-DQ2 and/or -DQ8 [6][7][8][9], as if they were pathogen derived, producing large amounts of interferon-gamma, which is a mediator of inflammation. However, it was previously unclear how HLA-DQ2 and HLA-DQ8 bind gluten peptides. These molecules prefer peptides containing one or more negatively charged amino acids, yet gluten proteins are essentially devoid of these amino acids [10][11][12]. This paradox was resolved when it was observed that TG2 converts the glutamine residues in gluten peptides into glutamic acid, introducing the negative charges required for binding to HLA-DQ2 or -DQ8 [13,14] (Figure 1). In fact, gluten and TG2 have a special relationship: due to the amino acid composition of glutens (~30% Q, ~17% P, rich in F and Y), the sequences QXPF and QXPY (X is any amino acid except P) are common and the Q is a target for TG2 [15]. TG2 modifies gluten at several positions, leading to the formation of a large number of gluten peptides that can bind to HLA-DQ2 and/or -DQ8 and induce T cell responses [15][16][17]. Together, these findings point to a crucial role of TG2 in the development of CD.

Specific Contribution of Current Manuscript
Previous studies revealed that the GDP-bound form of TG2, which functions as a G-proteins within cells, is in a conformation where the active site is inaccessible and so the enzyme is catalytically inactive. In the current issue of PLoS Biology, Pinkas and colleagues report the structure of the catalytically active form of TG2 [5]. To achieve this, they have captured the enzyme in complex with an inhibitor based on a gluten-derived substrate for TG2, the pentapeptide PQLPF. By replacing the Q with an electrophilic trap (6-diazo-5-oxo-L-norleucine; don), a peptide was generated that covalently links itself to the cys residue in the active site of TG2, thus stabilizing it in its active state.
The novel structure reveals that the active state is fundamentally different from the inactive state. The complete C-terminal beta1-and beta2-barrels, which cover the Nterminal core domain in the catalytically inactive form, are in an extended conformation in the active form. This involves a 120-Å shift of the C-terminal residues, exposing the active site and the bound pentapeptide. This pentapeptide occupies one side of a hydrophobic tunnel that is bordered by two tryptophan residues and contains the catalytic cys residue, whereas the other side of the tunnel can accommodate the lysine residue, which will be covalently linked to the glutamine in the transamidation reaction. Several hydrogen bonds and hydrophobic interactions exist between TG2 and the pentapeptide PdonLPF. This is, in part, due to the trans conformation of the proline preceding the phenylalanine, which places the phenylalanine in a hydrophobic pocket. These interactions thus reveal why gluten peptides containing a QLPF or QLPY sequence are such good substrates for TG2.
Importantly, a similar large conformational shift is now expected to occur in other transglutaminases, suggesting a general mechanism involved in the activation of this family of enzymes.

Perspective
As mentioned above, TG2 deamidates gluten peptides-a crucial step toward a full-blown T cell response against

A Tertiary Twist to the Transglutaminase Tale Frits Koning
Primers provide a concise introduction into an important aspect of biology highlighted by a current PLoS Biology research article. Primer gluten [3,4]. Moreover, it is well established that TG2-specific autoantibodies are specific indicators of CD, because they are almost exclusively found in CD patients. It has been shown that TG2 can crosslink itself to gluten, and it has been speculated that if such complexes are taken up by B cells-which express surface immunoglobulin specific for TG2-the TG2 complexes would be internalized and degraded intracellularly. This would release gluten peptides that subsequently can be bound to HLA-DQ2 molecules and presented to gluten-specific T cells, which would result in B cell activation and antibody production. In this way, glutenspecific T cells would drive the production of TG2-specific antibodies [21]. In the current manuscript, Pinkas and colleagues [5] suggest an interesting alternative possibility: that the large conformational change associated with TG2 activation may expose regions of TG2 that are normally shielded and that this leads to antibody formation.
All of these ideas underscore the fact that TG2 activation is a critical step in disease development. But how is TG2 activated and which circumstances promote a broad gluten-specific T cell response? There is a large pool of extracellular TG2 in the intestine but no evidence that it is catalytically active [23]. Pinkas and colleagues [5] now speculate that in CD, this extracellular TG2 might be activated by ligands of the Toll-like receptor (TLR) receptors, which are patternrecognition receptors that alert the immune system to the presence of pathogens. However, TLR triggering is not unique to CD; it is part of the normal immune response to pathogens. So, transient TG2 activation is thus probably a natural and common phenomenon, as might be expected of an enzyme known to be involved in wound and tissue repair [1]. Similarly, evidence has been presented that indicates that certain gluten peptides might activate the innate immune system [24][25][26], which could likewise contribute to TG2 activation. But it is not clear why this would only occur in CD patients and not in healthy individuals. Further, most HLA-DQ2-and -DQ8positive individuals do not generate gluten-specific T cells or develop disease, despite the fact that they would be capable of generating deamidated gluten peptides if TG2 is active [3,4]. Thus, there must be something fundamentally different when  The function of antigen-presenting cells (APCs) is to bind peptides derived from pathogens and "present" these to the T cells of the immune system. T cells detect such HLA-peptide complexes through their T cell receptors. In celiac disease, T cells respond to gluten peptides bound to HLA-DQ2 or HLA-DQ8. Gluten-derived peptides (red diamond) bind only with low affinity to HLA-DQ2 and HLA-DQ8, but TG2 can modify such peptides, which turns them into high-affinity binders. Consequently, the HLA-gluten peptide complexes are more stable, which facilitates and enhances T cell responses to such peptides. an individual does develop CD: what is the master switch that determines disease development?
The key issue is that even though the majority of glutenreactive T cells in the intestine are specific for deamidated gluten, TG2 in the intestine is normally inactive, so no deamidated gluten peptides are generated. Then what activates TG2 and thereby initiates the deamidation of gluten? The answer may lie in the gluten-specific T cell response itself: some gluten-specific T cells respond to native gluten peptides [7,8,14], and such T cell responses could induce a low level of inflammation and the release of catalytically active TG2 from the damaged tissue [14] (Figure 1). Once this occurs, TG2 will generate a host of immunogenic gluten peptides. This may be particularly important in the early stages of disease development, because it would allow rapid epitope spreading: the diversification of a limited response to a few (native) gluten peptides to a broad response involving a multitude of peptides [8]. Obviously, the development of such a T cell response takes weeks or even months, and early in that process, no symptoms will be apparent. The sustained exposure to gluten will generate a large gluten-specific T cell compartment in the intestine that will ultimately be dominated by T cells that are specific for the most immunogenic peptides, i.e., deamidated peptides with the best HLA-DQ-binding properties.
Ultimately, the question remains as to what drives the initial gluten-specific T cell response. Immune responses in the intestine are tightly regulated to avoid deleterious responses against harmless protein antigens. Infections in the intestine, however, are common, and these will force the mucosal immune system to take appropriate steps to eradicate the pathogens. This involves the polarization of the immune system toward inflammation. And this may provide a window in which inflammatory, gluten-specific T cell responses may escape from the tight regulation that suppresses such responses. Depending on the nature, duration, and/or persistence of the infections, such responses may become uncontrollable and lead to disease, whereas under more favorable conditions, they can be ultimately suppressed. It is likely that the outcome is influenced by genetics: a recent genome-wide association study has provided compelling evidence that a gene locus containing four genes, including IL2 and IL21, contributes to the chance of developing CD [27]. Clearly, the potential involvement of these immunerelated IL2 and IL21 genes is interesting, but because the risk associated is small [27], it will be a major undertaking to understand how such gene variants influence the chance of disease development.
Finally, the structure of TG2 in its active form may allow the design of potent inhibitors for TG2. Such blockers could potentially be used for the treatment of diseases in which TG2 is thought to play a role, including neurodegenerative diseases and, of course, CD. Yet in CD, it is unclear if we would want to use them for this purpose, because a glutenfree diet is an effective and entirely safe treatment for CD. Given the overall poor understanding of the multiple functions of TG2 and its role in wound repair, there might be unwanted side effects that limit the use of such blockers for treatment of CD. Conversely, for the treatment of neurodegenerative diseases, where the role of TG2 is less clear, the severity of the diseases may warrant the use of such inhibitors, despite potential side effects.
In conclusion, the tertiary twist associated with TG2 activation opens doors that improve our understanding of the role of TG2 in disease development and may aid in the development of novel therapeutic options.