Nonambipolar Transport due to Electrons with 3D Resistive Response in the KSTAR Tokamak

A small nonaxisymmetric (3D) magnetic field can induce nonambipolar transport of the particle species confined in a tokamak and thus a significant change of plasma rotation. This process can be in a favor of instability control in the region where the tokamak plasma is sufficiently collisional and resistive, as observed in the applications of n=1 resonant magnetic perturbations to the KSTAR tokamak. The plasma rotation can be globally accelerated due to radially drifting electrons and constrained to the electron root, if the radial transport is enhanced by an amplified 3D response. This mechanism is verified by a kinetically self-consistent magnetohydrodynamic modeling for both response and transport, which offers the quantitative explanations on the internal n=1 structure detected by electron-cyclotron-emission imaging and the cocurrent plasma spinning observed in the experiments.

Integrative analysis of mutational and transcriptional profiles reveals driver mutations of metastatic breast cancers

Despite the explosion in the numbers of cancer genomic studies, metastasis is still the major cause of cancer mortality. In breast cancer, approximately one-fifth of metastatic patients survive 5 years. Therefore, detecting the patients at a high risk of developing distant metastasis at first diagnosis is critical for effective treatment strategy. We hereby present a novel systems biology approach to identify driver mutations escalating the risk of metastasis based on both exome and RNA sequencing of our collected 78 normal-paired breast cancers. Unlike driver mutations occurring commonly in cancers as reported in the literature, the mutations detected here are relatively rare mutations occurring in less than half metastatic samples. By supposing that the driver mutations should affect the metastasis gene signatures, we develop a novel computational pipeline to identify the driver mutations that affect transcription factors regulating metastasis gene signatures. We identify driver mutations in ADPGK, NUP93, PCGF6, PKP2 and SLC22A5, which are verified to enhance cancer cell migration and prompt metastasis with in vitro experiments. The discovered somatic mutations may be helpful for identifying patients who are likely to develop distant metastasis.

Are the Oxford(®) medial unicompartmental knee arthroplasty new instruments reducing the bearing dislocation risk while improving components relationships? A case control study

INTRODUCTION

The recently introduced Microplasty(®) system is an upgrade of conventional phase III instrumentation. However, little is known of its impact on the position of the implant following the Oxford(®) mobile-bearing unicompartmental knee arthroplasty (UKA). This study investigated whether the Microplasty(®) instrumentation system can improve the positioning of the implant and reduce the rate of early failure.

HYPOTHESIS

Microplasty(®) provides a better positioning and decreases the rate of dislocation.

MATERIALS AND METHODS

The medical records and radiographs of 82 consecutive Oxford(®) UKAs were reviewed retrospectively. The radiographic parameters and prevalence of early failure of 41 UKAs performed with the Microplasty(®) system and 41 UKAs using the conventional instrumentation system were compared. Both groups were comparable in terms of demographics and preoperative status.

RESULTS

The femoral components in the Microplasty(®) group were more contiguously placed and more convergent in relation to the tibial components compared to the conventional instrumentation system (P<0.01). The frequency of bearing dislocation was lower in the Microplasty(®) group (P=0.04). A wide gap and the angle between components were associated with an increased risk of bearing dislocation.

CONCLUSION

The Microplasty(®) instrumentation system consistently placed the femoral and tibial components in more contiguous and convergent positions. Such changes in position decreased the risk of bearing dislocations by reducing the space available for bearing rotation.

LEVEL OF EVIDENCE

Level III, case control study.

Evidence for the importance of trapped particle resonances for resistive wall mode stability in high beta tokamak plasmas

Active measurements of the plasma stability in tokamak plasmas reveal the importance of kinetic resonances for resistive wall mode stability. The rotation dependence of the magnetic plasma response to externally applied quasistatic n=1 magnetic fields clearly shows the signatures of an interaction between the resistive wall mode and the precession and bounce motions of trapped thermal ions, as predicted by a perturbative model of plasma stability including kinetic effects. The identification of the stabilization mechanism is an essential step towards quantitative predictions for the prospects of "passive" resistive wall mode stabilization, i.e., without the use of an "active" feedback system, in fusion-alpha heated plasmas.

Soft x-ray virtual diagnostics for tokamak simulations

The numerical toolset, FAR-TECH Virtual Diagnostic Utility, for generating virtual experimental data based on theoretical models and comparing it with experimental data, has been developed for soft x-ray diagnostics on DIII-D. The virtual (or synthetic) soft x-ray signals for a sample DIII-D discharge are compared with the experimental data. The plasma density and temperature radial profiles needed in the soft x-ray signal modeling are obtained from experimental data, i.e., from Thomson scattering and electron cyclotron emission. The virtual soft x-ray diagnostics for the equilibriums have a good agreement with the experimental data. The virtual diagnostics based on an ideal linear instability also agree reasonably well with the experimental data. The agreements are good enough to justify the methodology presented here for utilizing virtual diagnostics for routine comparison of experimental data. The agreements also motivate further detailed simulations with improved physical models such as the nonideal magnetohydrodynamics contributions (resistivity, viscosity, nonaxisymmetric error fields, etc.) and other nonlinear effects, which can be tested by virtual diagnostics with various stability modeling.

Patellar tendon lengthening for patella infera using the Ilizarov technique

Patella infera can cause knee pain and lead to patellofemoral osteoarthritis. Treatment is usually unsatisfactory. We describe a case of severe patella infera after operative treatment for fracture of the patella. We used Ilizarov external fixation and gradual lengthening of the patellar tendon. The patellar height was restored and the patient's symptoms were much improved.

Reduced critical rotation for resistive-wall mode stabilization in a near-axisymmetric configuration

Recent DIII-D experiments with reduced neutral beam torque and minimum nonaxisymmetric perturbations of the magnetic field show a significant reduction of the toroidal plasma rotation required for the stabilization of the resistive-wall mode (RWM) below the threshold values observed in experiments that apply nonaxisymmetric magnetic fields to slow the plasma rotation. A toroidal rotation frequency of less than 10 krad/s at the q=2 surface (measured with charge exchange recombination spectroscopy using C VI) corresponding to 0.3% of the inverse of the toroidal Alfvén time is sufficient to sustain the plasma pressure above the ideal MHD no-wall stability limit. The low-rotation threshold is found to be consistent with predictions by a kinetic model of RWM damping.

Orally active antioxidative copper(II) aspirinate: synthesis, structure characterization, superoxide scavenging activity, and in vitro and in vivo antioxidative evaluations

Ever since it was proposed that reactive oxygen species (ROS) are involved in the pathogeneses of various diseases, superoxide dismutase (SOD)-mimetic complexes have been intensively studied. We prepared copper(II) aspirinate [Cu2(asp)4] from Cu(II) and aspirin, which has been in use for many years as an antipyretic, an analgesic, and an anti-inflammatory agent. However, Cu2(asp)4 has been found to have additional activities, including anti-inflammatory, antiulcer, anti-ischemic/reperfusion agent, anticancer, antimutagenic, and antimicrobial activities. The activity of copper salicylate [Cu(sal)2] was also compared with that of Cu2(asp)4. The structure of the Cu2(asp)4 was determined using X-ray structure analysis. Its SOD-mimetic activity was determined using cytochrome c, electron spin resonance (ESR) spectroscopy, and ESR spin trap methods. The activity of Cu2(asp)4 was slightly greater than CuSO4 and copper acetate [Cu(ace)2] and slightly less than that of Cu(sal)2. The in vitro antioxidant activity, evaluated in human epithelial or transformed neoplastic keratinocyte cells, HaCaT, and normal dermal fibroblasts in terms of cell survival following ultraviolet B (UVB) irradiation, was significantly increased in the presence of Cu2(asp)4, Cu(sal)2, and CuSO4. Further, ROS generation following UVA irradiation in the skin of hairless mice following oral treatment with Cu2(asp)4 for three consecutive days was significantly suppressed compared to the vehicle- or Cu(ace)2-treated mice. On the basis of these results, Cu2(asp)4 was observed to be a potent antioxidative compound possessing antioxidative activity in biological systems. In conclusion, Cu2(asp)4 is a potent antioxidative agent that may be useful for future treatment of diseases resulting from ROS.

Conformational comparison of mu-selective endomorphin-2 with its C-terminal free acid in DMSO solution, by 1H NMR spectroscopy and molecular modeling calculation

In order to make clear the structural role of the C-terminal amide group of endomorphin-2 (EM2, H-Tyr-Pro-Phe-Phe-NH2), an endogenous mu-receptor ligand, in the biological function, the solution conformations of endomorphin-2 and its C-terminal free acid (EM2OH, H-Tyr-Pro-Phe-Phe-OH), studied using two-dimensional 1H NMR measurements and molecular modeling calculations, were compared. Both peptides were in equilibrium between the cis and trans isomers around the Tyr-Pro omega bond in a population ratio of approximately/= 1:2. The lack of significant temperature and concentration dependence of NH protons suggested that the NMR spectra reflected the conformational features of the respective molecules themselves. Fifty possible 3D structures for the each isomer were generated by the dynamical simulated annealing method under the proton-proton distance constraints derived from the ROE cross-peaks. These energy-minimized conformers, which were all in the phi torsion angles estimated from J(NHCalphaH) coupling constants within +/- 30 degrees, were then classified in groups one or two according to the folding backbone structures. All trans and cis EM2 conformers adopt an open conformation in which their extended backbone structures are twisted at the Pro2-Phe3 moiety. In contrast, the trans and cis conformers of EM2OH show conformational variation between the 'bow'-shaped extended and folded backbone structures, although the cis conformers of its zwitterionic form are refined into the folded structure of the close disposition of C- and N-terminal groups. These results indicate clearly that the substitution of carboxyl group for C-terminal amide group makes the peptide flexible. The conformational requirement for mu-receptor activation has been discussed based on the active form proposed for endomorphin-1 and by comparing conformational features of EM2 and EM2OH.

Structure and stereochemistry of epoxyserratanes from the cuticle of Piceajezoensis var. jezoensis

Three new epoxytriterpenes, 14 beta,15 beta-epoxy-21 beta-hydroxyserratan-3-one (1), 13 alpha,14 alpha-epoxy-21 alpha-methoxyserratan-3-one (2), and 13 alpha,14 alpha-epoxy-3 beta-methoxyserratan-21 beta-ol (3), were isolated together with two known triterpenoids, 21 alpha-methoxyserrat-13-en-3-one (4) and 21 beta-hydroxyserrat-14-en-3-one (5), from the cuticle of Picea jezoensis var. jezoensis. The structures of these new compounds were established on the basis of spectral data (NMR, MS) and single-crystal X-ray analyses (1 and 2) and partial synthesis (2 and 3).

Abietane diterpenoids from the cones of Larix kaempferi and their inhibitory effects on Epstein-Barr virus activation

Four known (1-3, 8) and four new abietane diterpenes, 15-hydroxy-8alpha,14alpha,12alpha,13alpha-diepoxyabietan-18-oic acid (4), 7alpha,8alpha,13beta,14beta-diepoxyabietan-18-oic acid (5), 18-nor-abieta-8,11,13-triene-4alpha,7alpha,15-triol (6), and abieta-8,11,13-triene-7alpha,15,18-triol (7) were isolated from the CHCl3 extract of the cones of Larix koempferi. A known compound, 13,14-seco-13,14-dioxoabiet-13-en-18-oic acid (8) was isolated from natural sources for the first time. Their structures were determined by chemical and spectroscopic methods including 1D and 2D NMR techniques. The absolute stereostructure of 5 was determined by X-ray crystallographic analysis. The inhibitory effects of these compounds on Epstein-Barr virus early antigen (EBV-EA) activation induced by the tumor promoter, 12-O-tetradecanoylphorbol-13-acetate (TPA), were examined as a primary screening for antitumor promotors.

Structural studies of C-amidated amino acids and peptides: crystal structures of Z-Gly-Phe-NH2, Tyr-Lys-NH2, and Asp-Phe-NH2

As part of the series investigating the structural features of C-terminal amidated amino acids and peptides, three crystal structures of Z-Gly-Phe-NH2, Tyr-Lys-NH2, and Asp-Phe-NH2 were analyzed by the X-ray diffraction method, and their molecular conformations and intermolecular interactions were investigated. Although the respective dipeptides exhibited an energetically allowable torsion angle concerning each backbone or side chain, the observed extended (Z-Gly-Phe-NH2, Asp-Phe-NH2) and folded (Tyr-Lys-NH2) conformations were considerably different from those of the corresponding unamidated peptides, due to the conformational flexibility of the respective dipeptides. The comparison between the crystal packings of the amidated and unamidated dipeptides indicated that the C-terminal amides tend to associate with the same neighboring group through hydrogen bonds, in which both the amide NH and O=C groups participate, while the unamidated peptides prefer a linear molecular connection, where both or either of the two carboxyl oxygens participate in the hydrogen bond formation. The difference in hydrogen bonding ability between the C-terminal amide and carboxyl groups has been considered to be based on the structural data of the related peptides analyzed so far.

Characterization of estrogen receptor-beta (ERbeta) messenger ribonucleic acid and protein expression in rat granulosa cells

We have examined estrogen-responsiveness of ovarian granulosa cells by focusing on estrogen receptor (ER) expression. Estrogen responsiveness was determined by examining the effect of 17beta-estradiol (1-10 nM) on luciferase reporter activity in rat granulosa cells transfected with an ERE-luciferase construct. The results demonstrate an estrogen-induced (approximately 3-fold) increase in luciferase reporter activity, indicating that granulosa cells contain functional estrogen response element (ERE)-binding transcriptional activators. Gel mobility shift assays in combination with ER antibodies show that ERbeta is the predominant ERE-binding protein in granulosa cells. Western blotting results show that granulosa cells contain ERbeta-immunoreactive protein(s) migrating at a size substantially larger than the recombinant protein generated from the originally proposed 485 amino acid open-reading frame. This size discrepancy is not due to granulosa cell expression of ERbeta isoforms with insertions within the coding region because RT-PCR assays revealed products with sizes expected for ERbeta, ERbetaB, and delta3 isoforms. This size discrepancy appears to be due to usage of a well-conserved, upstream in-frame translation initiation codon (ATG436) leading to a 530 amino acid open reading frame. ERbeta messenger RNA (mRNA) characterization using 5'-rapid amplification of complementary DNA ends (5'-RACE) show the presence of two different (P1- and P2-) 5'-ends of rat ERbeta mRNA encoding the full-length ERbeta protein. The generation of the P2-specific exon is likely due to initiation of transcription from an alternative promoter. Both P1- and P2-specific exon-containing ERbeta mRNAs are expressed in granulosa cells, and they are rapidly down-regulated by the cAMP-mediated intracellular signaling pathway in cultured granulosa cells. Taken together, our results show that rat granulosa cells produce two different 3',5'-cAMP-regulated ERbeta mRNA species and that these mRNA species are capable of encoding the full-length ERbeta protein.

Conformational change of ascidiacyclamide caused by asymmetric modification for an isoleucine residue: structural analyses of [Gly], [Leu], and [Phe]ascidiacyclamides by x-ray diffraction and NMR spectroscopy

Ascidiacyclamide, a cytotoxic cyclic peptide from tunicate, is composed of unusual amino acids and has a repeated sequence, c[-thiazole-D-Val-oxazoline-L-Ile-]2 ([Ile]ASC). The symmetric chemical structure has been assumed to be correlated with the cytotoxicity, and it is reasonable to consider that the disturbance of its structure from the C2 symmetry results in the changes of conformation and activity. In order to quantitatively estimate the molecular conformation-activity relationship, an isoleucine residue was substituted by Gly, Leu, or Phe to disturb the C2 symmetry. The conformations of three derivatives were examined by nmr spectroscopy and the crystal structure of [Leu]ASC was also analyzed by x-ray diffraction method. The 1H-nmr experiments and the constrained molecular dynamics simulations showed the twisted "figure 8" conformers for [Gly] and [Phe]ASCs and the "square" conformer for [Leu]ASC in the DMSO solution. The x-ray crystal analysis of [Leu]ASC also revealed the square form similar to the solution structure. On the other hand, their cytotoxic activities were measured using L1210 leukemia cells and were related with the bulkiness and/or hydrophobicity of the side chain of the substituted amino acid; [Phe] > or = [Ile] > [Leu] >> [Gly]ASCs. As an attempt to consider the correlation between the activity and conformer, the accessible surface area (ASA) was calculated for each derivative to estimate the size or bulkiness of its conformation. Although the ASAs of nmr structures were not directly related to the type of conformer (figure 8 or square form), it was an important probe to consider the cytotoxicity of each derivative.

Unique molecular conformation of aureobasidin A, a highly amide N-methylated cyclic depsipeptide with potent antifungal activity: X-ray crystal structure and molecular modeling studies

A structural feature of aureobasidins, cyclic depsipeptide antibiotics produced by Aureobasidium pullulans R106, is the N-methylation of four out of seven amide bonds. In order to investigate possible relationship between the molecular conformation and the amide N-methylation, aureobasidin A (AbA), which exhibits the potent antifungal activity, was subjected to X-ray crystal analysis. The crystal, recrystallized from ether (orthorhombic, space group P2(1)2(1)2(1), a = 21.643 (3) A, b = 49.865(10) A, c = 12.427 (1) A, z= 8), contained two independent conformers per asymmetric unit and they took on a similar arrowhead-like conformation. The conformation consisted of three secondary structures of antiparallel beta-sheet, and beta- and gamma-turns, and was stabilized by three intramolecular and transannular N-H O=C hydrogen bonds. The beta-hydroxy-N-methyl-l-valine residue, which is indispensable for its bioactivity, was located at the tip of the corner. Since a nearly identical conformation has been observed for aureobasidin E, a related cyclic depsipeptide, this arrowhead-like conformation may be energetically stable and important for biological activity. The contribution of the amide N-methylation to the conformation was investigated by model building and energy calculations. The energy-minimizations of AbA analogs, in which some (one to four) of four N-methylated amide bonds were replaced with usual amide bond, led to some conformers which are fairly different from the arrowhead form of AbA, although they are stabilized by three intramolecular N-H...O=C hydrogen bonds. This result explains the reason why four out of the seven amide bonds have to be methylated to manifest biological activity, i.e. the high N-methylation of aureobasidin is necessary to form only one well-defined conformation.

Effect of mRNA cap structure on eIF-4E phosphorylation and cap binding analyses using Ser209-mutated eIF-4Es

The in vitro phosphorylation of human recombinant eIF-4E by protein kinase C was most effective in the absence of m7GTP, supporting a 'performed complex model' as the mRNA binding step of initiation, i. e., eIF-4E first forms an initiation complex eIF-4F and is phosphorylated before interacting with mRNA. On the other hand, the comparison of m7GTP-binding ability of wild-type eIF-4E with those of four Ser209-mutated ones (S209A, S209D, S209E and S209K) showed that the addition of anionic charge on Ser209 increases the cap affinity of eIF-4E by repressing the release of the cap from the complex, not by increasing the complex formation, suggesting the importance of a retractable ionic bridge between Ser209 and Lys159 in controlling the cap binding by eIF-4E phosphorylation.

Synthesis, structure and quantitative structure-activity relationships of sigma receptor ligands, 1-[2-(3,4-dimethoxyphenyl)ethyl]-4-(3-phenylpropyl) piperazines

A set of the title compounds having different substituents (R1, R2) on their phenyl groups was synthesized to find sigma receptor binding affinity. Among the compounds, 2b (R1 = R2 = Cl) has the most potent sigma 1-binding activity, while 2a (R1 = R2 = H, SA4503) was most selective to sigma 1 over sigma 2 receptor. The crystal structures of 2a and 2b were shown, by X-ray crystallography, to be similar except for the one torsional angle of their propylene parts. Quantitative structure-activity relationship study suggested the affinity of the compounds to the sigma 1 receptor was dependent on the electronic feature, Swain-Lupton's R or Sz that was derived by molecular orbital method, of R1 and R2.

Structural properties of synthetic ionophore GL 2 E 4 diastereomers, 18-membered cyclic lactone tetraepoxides, by X-ray crystal analyses: possible relation between crystal structure and Ca2+-transportation ability. Addendum

Structure factors, anisotropic displacement parameters, H-atom coordinates and complete geometry for the paper by Doi, In Nishino, Ishida, Inoue, Shibuya, Ohashi, Narita & Kitagawa [Acta Cryst. (1995), B51, 1045–1050] have been deposited with the IUCr (Reference: AS0697). Copies may be obtained through The Mangaging Editor, International Union of Crystallography, 5 Abbey Square, Chester CH1 2HU, England.

Structure of ascidiacyclamide as the ethanol water solvate, a cytotoxic cyclic peptide from Ascidian

The X-ray crystal structure determination of the C2H5OH.H2O solvate of ascidiacyclamide (C36H52N8O6S2), a cytotoxic cyclic peptide from marine tunicate Ascidian, revealed a C2-symmetric saddle-shaped rectangular conformation of the molecule. The water and ethanol molecules are located on the crystallographic diad axis and are held by hydrogen bonds and van der Waals contacts with the polar ring N atoms and nonpolar D-Val side-chain atoms, respectively. The molecular conformation and the interaction with solvent molecules are nearly the same as those of the compound with C2H5OH.2H2O [Ishida, In, Doi, Inoue, Hamada & Shioiri (1992). Biopolymers, 32, 131-143].

Characteristic molecular packing in the crystal structure of tert-butoxycarbonyl-L-phenylalanyl-L-methionine methyl ester

The molecular conformation and association of the peptide Boc-L-Phe-L-Met-OMe have been studied in the solid state by X-ray diffraction. The peptide crystallizes in the orthorhombic system, space group P2(1)2(1)2(1), with cell parameters of a = 9.821(2), b = 25.394(6), c = 28.714(8) A, V = 7161(3) A3. The structure has been solved by direct methods and refined to a final R of 0.079 for 5464 independent reflections with Fo > or = sigma(Fo). The crystal consists of three independent molecular conformations per asymmetric unit. Respective peptide backbones adopt an extended conformation with the side-chains of Phe and Met residues being arranged below and above the backbone chains. Contrary to the sheet structure most frequently observed in the crystal packing of the extended peptide conformations, three independent molecules lie spirally along the c-axis and form a pin-wheel-like crystal packing. The sheet structures formed by two of three independent molecules are almost at right angles to the backbone of the remaining molecule. This molecular packing mode would provide a possible interaction model between the intersecting beta-sheet structure and single-strand structure of polypeptide.

Patellamide A, a cytotoxic cyclic peptide from the ascidian Lissoclinum patella

The structure of crystals of patellamide A (13-methyl-9,23-bis(1-methylethyl)-2,16-bis(1-methylpropyl)-14,-28-di oxa-7,21- dithia-3,10,17,24,29,30,31,32- octaaza-pentacyclo[24.2.1.1(5,8).1(12,15).1(19,22]dotriac onta-1(29),5,- 8(30),15(31),19,22(32)-hexaene-4,11,18,25-tetraone methanol solvate monohydrate, C35H49N8O6S2.-CH4O.H2O), a cytotoxic cyclic peptide having a non-C2-symmetric methyl group, shows the C2-symmetric and saddle-shaped rectangular conformation where the methyl group is disordered into two C2-symmetric positions. The water and methanol solvents were located on the crystallographic diad axis and were held by hydrogen bonds and van der Waals contacts with the polar ring N atoms and non-polar D-Val side-chain atoms, respectively.

Cooperative face-to-face and edge-to-face aromatic interactions of tryptophan indole ring with N7-quarternized guanine and neutral cytosine bases

In order to investigate the effect of cytosine base upon the stacking interaction of N7-quarternized guanine base with tryptophan indole ring, the X-ray crystal structure of a 1:1 complex of model compounds 1 and 2 was carried out. Contrary to the expectation of the interaction of both molecules in aqueous solution, the crystal structure showed the first example of the simultaneous recognition of the Trp indole ring by guanine and cytosine bases by the coupling of the face-to-face and edge-to-face aromatic interactions, respectively.

Molecular conformation of patellamide A, a cytotoxic cyclic peptide from the ascidian Lissoclinum patella, by X-ray crystal analysis

As part of a series of investigations into the conformational stability of a C2-symmetric or related cyclic peptide isolated from the ascidian Lissoclinum patella, the molecular conformation of patellamide A, the chemical structure of which deviates slightly for C2-symmetry, was determined by X-ray crystal analysis. Patellamide A took on a saddle-shaped rectangular form and wrapped around the water and methanol solvents. This conformation which is very similar to that of C2-symmetric ascidiacyclamide would be proposed as a possible candidate for biologically "active" conformation.

Structure of Boc-Phe-D-Leu-Thr-OMe

The X-ray crystal structure analysis shows that tert-butoxycarbonyl-L-phenylalanyl-D-leucine-L-threonine methyl ester takes an open conformation in which the tert-butoxycarbonyl group is located face-to-face with the D-leucine isobutyl side chain. In the crystal, the molecules, translated by twofold screw symmetry, form an infinite sheet structure through four independent hydrogen bonds.

Conformational difference between diastereomers of Dnp-Val-Aib-Gly-Leu-pNA studied by x-ray crystal analyses

In order to investigate the conformational change of the alpha-aminoisobutyric acid (Aib) containing peptide by the D/L replacement of an amino acid residue, single crystals of two diastereomers, Dnp-L-Val-Aib-Gly-L-Leu-pNA (L-L isomer) and Dnp-D-Val-Aib-Gly-L-Leu-pNA (D-L isomer), were prepared from aqueous methanol solutions as CH3OH and CH3OH.H2O solvates, respectively, and were analyzed by the x-ray diffraction method. Molecular conformation of L-L isomer adopts consecutive two different types of beta-turns, a type II' beta-turn bent at Aib-Gly, and a type III beta-turn bent at Gly-Leu, stabilized by two intramolecular (Leu)NH...O = C(Val) and (pNA)NH...O = C(Aib) hydrogen bonds. In contrast, these two intramolecular hydrogen bonds lead the D-L isomer to a distorted 3(10)-helix conformation consisting of consecutive two type-III beta-turn of Aib-Gly-Leu sequence. The most significant structural difference between these diastereomers is the mutual orientation between the Dnp and pNA chromophores. While the extensive stacking of both the chromophores is intramolecularly formed for the folded conformation of L-L isomer, they are oriented toward an opposite direction in the open conformation of D-L isomer and are intermolecularly stacked with each other. The large separation between these diastereomers observed in the chromatography is discussed in the relation with their conformational differences.

Conformational feature of neuroactive domoic acid: X-ray structural comparison with isodomoic acid A and alpha-kainic acid

As an aid for developing a new type of potent insecticide acting on the neuromuscular junction, conformational characteristics of domoic acid and isodomoic acid A, the naturally occurring glutamate agonists, were investigated by X-ray crystal analyses. Conformational comparison with a neuroactive alpha-kainic acid provides information concerning the stereochemical feature responsible for the biological activity.

Effect of the D-Phe2 residue on molecular conformation of an endogenous neuropeptide achatin-I. Comparison of X-ray crystal structures of achatin-I (H-Gly-D-Phe-Ala-Asp-OH) and achatin-II (H-Gly-Phe-Ala-Asp-OH)

The molecular conformation of achatin-II neutral form (H-Gly-Phe-Ala-Asp-OH), an endogenous peptide from the Achatina fulica ganglia, was elucidated by X-ray crystal analysis. The molecule takes an extended beta-pleated structure stabilized by 5 intermolecular hydrogen bonds with the antiparallely arranged molecules. This is in contrast with the turn conformation of a neuroactive achatin-I (H-Gly-D-Phe-Ala-Asp-OH) [(1992) FEBS Lett. 276,95-97]. The conformational comparison of both of the molecules makes clear the structural role which D-Phe residue of achatin-I plays in forming a definite active form.

Calcium binding to phospholipid: structural study of calcium glycerophosphate

To consider possible interaction of the phospholipid membrane with calcium ions, crystal structures of calcium dl-alpha- and beta-glycerophosphates (alpha- and beta-CaGs, respectively) were investigated by X-ray diffraction methods. After many attempts, relatively large single crystals of beta-CaG were prepared from the aqueous solution containing HCl, while crystals of CaHPO4.2H2O were obtained from alpha-CaG solution under the same crystallization conditions. The crystal structure of beta-CaG is orthorhombic with space group Pna2(1) and cell dimensions of a = 8.251(1), b = 13.038(3), c = 25.483 (10) A, V = 2741.5 (13) A3 and Z = 16 [four molecules (A to D) in an asymmetric unit]. Molecules of A to D took, as a whole, similar extended conformations, although A and B were different from C and D in the orientation about a glycerol C-C bond. Four independent beta-glycerophosphates commonly act as two types of bidentate ligands, where one is the coordination to the calcium ion by the glycerol O(1) and phosphate O(22) atoms, and the other by the phosphate O(22) and O(23) atoms, thus forming the calcium coordination of a distorted square plane, respectively. Each of four independent calcium ions forms the same coordination geometry of a distorted pentagonal bipyramid. Infinite double layers consisting of alternate A/B molecules and of alternative C/D ones and sandwiching calcium ions were arranged face-to-face along the b-direction and were piled up in the a-direction, thus forming the stacked bilayer unit with the thickness of d002 = 12.75 A. The elaborate networks of calcium coordinations and hydrogen bondings were formed among the layers and stabilized the crystal structure. Based on the structural parameters of the present beta-CaG crystal, a possible interaction model of phospholipid with calcium ions was proposed.

Crystal structure and molecular conformation of achatin-I (H-Gly-D-Phe-Ala-Asp-OH), an endogenous neuropeptide containing a D-amino acid residue

In order to investigate the active conformation of achatin-I (H-Gly-D-Phe-Ala-Asp-OH), an endogenous neuropeptide from the Achatina fulica ganglia, its crystal structure and molecular conformation were analysed by the X-ray diffraction method. Crystals from methanol/dioxane are monoclinic, space group P2(1) with a = 5.083(1), b = 9.125(1), c = 20.939(3) A, beta = 94.73(1) degrees. The structure was solved by direct methods and refined to R = 0.051 for 1714 independent reflections with /Fo/ greater than sigma (Fo). The molecule exists as a zwitterion with the Gly N-terminal end protonated and Asp beta-carboxyl deprotonated; the C-terminal of Asp is in a neutral state. The molecule takes a kind of beta turn structure with the D-Phe-Ala residues at the corner of the bend. This turn conformation is primarily formed by the strong intramolecular hydrogen bonds of NH(Gly)...O delta 1 (Asp) and NH(Asp)...O delta 1 (Asp) pairs, thus forming a 15-membered ring structure. Judging from the published data concerning the structure-activity relationship, this turn conformation may reflect an important feature related to the neuroexcitatory activity of achatin-I.

Molecular conformation of ascidiacyclamide, a cytotoxic cyclic peptide from Ascidian: X-ray analyses of its free form and solvate crystals

In order to investigate the conformational variation of ascidiacyclamide, a cytotoxic cyclic peptide from marine tunicate Ascidian, single crystals were prepared from ethanol and aqueous ethanol solutions as its free form (crystal I) and H2O/0.5 C2H5OH solvate (crystal II), respectively, and were determined by the x-ray diffraction method. Crystal I showed a pseudo C2-symmetric saddle-shaped rectangular conformation. Similar conformations were also observed in crystal II, where there were two crystallographically independent C2-symmetric molecules (named Mol-A and -B) per asymmetric unit. Mol-A and -B included H2O and H2O/C2H5OH solvents within their ring structures, respectively. These water and ethanol molecules were located on the crystallographic dyad axes, and were stabilized by the van der Waals contacts (including hydrogen bonds) with the polar-ring N atoms and nonpolar D-Val side-chain atoms. The conformational characteristics of ascidiacyclamide and its fluctuation/variation were discussed based on the present and previously reported x-ray results.

X-ray crystallographic conformational study of 5'-O-[N-(L-alanyl)-sulfamoyl]adenosine, a substrate analogue for alanyl-tRNA synthetase

In order to elucidate the substrate specificity of alanyl-tRNA synthetase, 5'-O-[N-(L-alanyl)sulfamoyl]adenosine (Ala-SA), an analogue of alanyl-AMP, was chemically synthesized. Its binding ability is similar to that of the substrate based on the inhibitory activity for the aminoacylation of alanyl-tRNA synthetase. Taking advantage of the stable sulfamoyl bond of Ala-Sa, compared with the highly labile aminoacyl bond of alanyl-AMP, the molecular conformation of the former inhibitor was studied by X-ray single crystal analysis. Crystal data are as follows: C13H19N7O7S.2H2O, space group C2, a = 39.620(6), b = 5.757(1), c = 20.040(3) A, beta = 117.2(1) degrees, V = 4065(9) A3, Z = 8, and final R = 0.065 for 2785 independent reflections of F(2)0 greater than or equal to 2 sigma (F0)2. In the crystal, the molecule is in a zwitterionic state with the terminal amino group protonated and sulfamoyl group deprotonated, and takes an open conformation, where the L-alanine moiety is located far from the adenosine moiety with gauche/trans and trans orientations about the exocyclic C(4')-C(5') and C(5')-O(5') bonds, respectively. The conformation of the adenosine moiety is anti for the glycosyl bond and C(3')-endo for the ribose puckering, and alanine is in the usually observed trans region for the psi torsion angle. The molecular dimensions of the sulfamoyl group are nearly the same as those of the phosphate group. The biological significance of the observed Ala-SA conformation is discussed in relation with the molecular conformation of tyrosyl-AMP complexed with tyrosyl-tRNA synthetase.

Structural study of aldose reductase inhibitors. Ten oxazolecarbamate derivatives

(1) Benzyl 4-isopropyl-5-phenyl-2-oxazolecarbamate, C20H20N2O3, Mr = 336.39, P1, a = 19.469 (7), b = 11.270 (3), c = 8.667 (3) A, alpha = 95.48 (3), beta = 99.61 (3), gamma = 104.96 (3) degrees, V = 1792 (1) A3, Z = 4, Dm = 1.266 (2), Dx = 1.247 g cm-3, lambda (Cu K alpha) = 1.5418 A, mu = 6.49 cm-1, F(000) = 712, T = 288 K, R = 0.048 for 5244 reflections. (2) Benzyl 4-ethyl-5-phenyl-2-oxazolecarbamate, C19H18N2O3, Mr = 322.37, P2(1)/n, a = 9.131 (7), b = 18.81 (1), c = 9.680 (8) A, beta = 101.07 (3) degrees, V = 1631 (2) A3, Z = 4, Dm = 1.310 (2), Dx = 1.313 g cm-3, lambda (Cu K alpha) = 1.5418 A, mu = 6.92 cm-1, F(000) = 680, T = 288 K, R = 0.063 for 2535 reflections. (3) Benzyl 4-methyl-5-phenyl-2-oxazolecarbamate, C18H16N2O3, Mr = 308.34, P2(1)/n, a = 9.210 (7), b = 8.785 (6), c = 19.800 (9) A, beta = 99.60 (3) degrees, V = 1580 (2) A3, Z = 4, Dm = 1.299 (3), Dx = 1.300 g cm-3, lambda (Cu K alpha) = 1.5418 A, mu = 6.93 cm-1, F(000) = 648, T = 288 K, R = 0.057 for 2190 reflections.(ABSTRACT TRUNCATED AT 250 WORDS)

Molecular and crystal structures of 2-(2-pyridyl)thioacetamide derivatives and possible relationship with inhibitory activity for gastric acid secretion

As a possible method to determine the key atoms and their spatial orientation which are necessary for the gastric mucosal protective and antisecretory activity, crystal structures of sixteen 2-(2-pyridyl) thioacetamide derivatives have been analyzed by the X-ray diffraction method. The characteristics of the molecular and crystal structures of the derivatives are described in this paper. The energetic stability of the molecular conformation is also investigated by means of the molecular force field method. Using the conformational data, a possible relationship between the stereostructure and inhibitory activity for gastric acid secretion is considered by QSAR analyses. The results suggest that the activity is related to the overall molecular conformation, and that the spatial distribution of the side-chain polar atoms with respect to the fixed pyridine is especially important for the activity.