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PubMed2004

Effect of molecular oxygen on the variable-temperature 29Si MAS NMR spectra of zeolite-sorbate complexes.

Structure determinations of siliceous zeolite-sorbate host-guest complexes by solid-state NMR require highly resolved 29Si MAS NMR spectra. As the temperature is lowered, the 29Si MAS NMR spectra of many zeolite-sorbate complexes become broadened such that the resolution of the individual 29Si peaks is lost, limiting the application of solid-state NMR for structure determination. It is shown that the 29Si peak widths are related to the 29Si T2 relaxation times and that the source of the 29Si relaxation and the line broadening is paramagnetic molecular oxygen in the channels of the zeolite. Removal of the oxygen by purging the sample with nitrogen gas leads to a dramatic increase in the resolution of the 29Si MAS NMR spectrum of the p-dibromobenzene/ZSM-5 complex. An analysis of the individual 29Si T1 relaxation times reveals that the oxygen molecules are localized mainly in the zigzag channels of ZSM-5, suggesting that the p-dibromobenzene molecules are located in the channel intersections.

Journal Article↗
PubMed2004

Nickel(II)-phenoxyl radical complexes: structure-radical stability relationship.

Nickel(II) complexes of N3O-donor tripodal ligands, 2,4-di-tert-butyl-6-[([bis(2-pyridyl)methyl]amino)methyl]phenol (HtbuL), 2,4-di-tert-butyl-6-[([(6-methyl-2-pyridyl)methyl](2-pyridylmethyl)amino)methyl]phenol (HtbuLMepy), and 2,4-di-tert-butyl-6-[([bis(6-methyl-2-pyridyl)methyl]amino)methyl]phenol (HtbuL(Mepy)2), were prepared, and [Ni(tbuL)Cl(H2O)] (1), [Ni(tbuLMepy)Cl] (2), and [Ni(tbuL(Mepy)2)Cl] (3) were structurally characterized by the X-ray diffraction method. Complexes 1 and 3 have a mononuclear structure with a coordinated phenolate moiety, while 2 has a dinuclear structure bridged by two chloride ions. The geometry of the Ni(II) center was found to be octahedral for 1 and 2 and 5-coordinate trigonal bipyramidal for 3. Complexes 1-3 exhibited similar absorption spectra in CH3CN, indicating that they all have a mononuclear structure in solution. They were converted to the phenoxyl radicals upon oxidation with Ce(IV), giving a phenoxyl radical pi-pi transition band at 394-407 nm. ESR spectra at low temperature and resonance Raman spectra established that the radical species has a Ni(II)-phenoxyl radical bond. The cyclic voltammograms showed a quasi-reversible redox wave at E1/2=0.46-0.56 V (vs Ag/AgCl) corresponding to the formation of the phenoxyl radical, which displayed a first-order decay with a half-life of 45 min at room temperature for 1 and 26 and 5.9 min at -20 degrees C for 2 and 3, respectively. The radical stability increased with the donor ability of the N ligands.

Journal Article↗
PubMed2006

Methyl ether derivatives of p-tert-Butyl[3.1.3.1]homooxacalixarene. Formation, structure, and complexes with quaternary ammonium ions.

[structure: see text] The whole set (five compounds) of partially O-methylated products of p-tert-butyl[3.1.3.1]homooxacalixarene, currently named p-tert-butyltetrahomodioxacalix[4]arene, have been prepared. Their structure has been investigated in solution through NMR techniques and in the solid state by single-crystal X-ray diffraction. A systematic investigation, extended to the parent tetraphenol and to the tetramethyl ether derivative, has been carried out on the complexation of tetramethylammonium, acetylcholine, N-methylpyridinium, and tetraethylammonium picrate in CDCl3. The observed trends in the binding and in the selectivity of the strictly related hosts could be analyzed on the basis of the varying importance of intramolecular hydrogen bonding and its effects on the conformation of the free and of the complexed ligands. On increasing the number of methyl ether functions, the cone conformation appears to be relatively less stable but deeper, so small organic cations can be more effectively encircled.

Journal Article↗
PubMed2003

High-pressure structural trends of Group 15 elements: simple packed structures versus complex host-guest arrangements.

The Group 15 elements P, As, Sb, and Bi all have layered structures consisting of six-membered rings under ambient conditions and attain the body-centered cubic (bcc) structure at the highest pressures applied. In the intermediate pressure region, however, phosphorus and its heavier congeners behave profoundly differently. In this region P first attains the open packed simple cubic (sc) structure for a wide range of pressures and then transforms into the rarely observed simple hexagonal (sh) structure. For the heavier congeners complex, incommensurately modulated host-guest structures emerge as intermediate pressure structures. We investigated the high-pressure behavior of P and As by ab initio density functional calculations in which pseudopotentials and a plane wave basis set were employed. The incommensurately modulated high-pressure structure of As was approximated by a supercell. Our calculations reproduced the experimentally established pressure stability ranges of the sc and sh structures for P and the host-guest structure for As very well. We found that the sc and especially the sh structure are decisively stabilized by the admixture of d states in the occupied levels of the electronic structure. This admixture releases s-s antibonding states above the Fermi level (s-d mixing). With pressure, s-d mixing increases rapidly for P, whereas it remains at a low level for As. As a consequence, the band energy contribution to the total energy determines the structural stability for P in the intermediate pressure region, giving rise to simple packed structures. On the other hand, in the intermediate pressure region of the heavier Group 15 elements, a delicate interplay between the electrostatic Madelung energy and the band energy leads to the formation of complex structures.

Journal Article↗
PubMed1980

HMG proteins (1 + 2) form beaded structures when complexed with closed circular DNA.

Structures bearing a resemblance to nucleosomes can be assembled by incubating calf thymus High Mobility Group proteins (1 + 2) with closed circular DNA. These HMG proteins are capable of forming beads and inducing superhelicity when bound to DNA. However, they do not protect from nuclease digestion the discrete DNA fragments characteristic of nucleosomes. The relationship between HMGs (1 + 2) and the "primitive" histone-like DNA-packaging proteins from prokaryotes and mitochondria is discussed.

Animals↗
PubMed2004

Hydrogenation of carbon dioxide and aryl isocyanates by a tetranuclear tetrahydrido yttrium complex. Isolation, structures, and CO2 insertion reactions of methylene diolate and mu3-oxo yttrium complexes.

The reaction of carbon dioxide with a tetranuclear tetrahydrido yttrium complex [(C5Me4SiMe3)Y(mu-H)]4(L) (L = Me3SiCC(H)C(H)CSiMe3) (1) rapidly afforded the corresponding bis(methylene diolate) complex [(C5Me4SiMe3)Y]4(mu-O2CH2)2(L) (2), while the reactions of an aryl isocyanate with 1 led to selective formation of the mu3-oxo complex [(C5Me4SiMe3)Y]4(mu-O)( mu-H)2(L) (5) or [(C5Me4SiMe3)Y]4(mu-O)2(L) (7), depending on the substrate ratio. Both the methylene diolate and the oxo complexes can undergo CO2 insertion reactions to give the corresponding carbonate complexes. These reactions not only yield a new series of polynuclear yttrium complexes having novel structures but also shed new light on the mechanistic aspects of the heterogeneous hydrogenation of COmicron2. The high reactivity of the polynuclear mu3-oxo yttrium complexes 5 and 7 could also make them novel molecular models for study of metal oxide-supported catalysts.

Journal Article↗
PubMed2005

Structures of complexes between echinomycin and duplex DNA.

The structure of the bis-intercalation complex of the depsipeptide antibiotic echinomycin with (CGTACG)2 has been redetermined at a higher resolution (1.4 A) and new high-resolution structures (1.1-1.5 A) are reported for the complexes of echinomycin with (GCGTACGC)2 (at both low and high ionic strengths) and (ACGTACGT)2. The structures show the expected Hoogsteen pairing for the base pairs flanking the intercalating chromophores on the outside and Watson-Crick pairing for both base pairs enclosed by the echinomycin. In the octamer complexes but not the hexamer complex, the echinomycin molecule, which would possess a molecular twofold axis were it not for the thioacetal bridge, shows twofold disorder. In all the structures the stacking of the base pairs and chromophores is extended by intermolecular stacking. The structures provide more precise details of the hydrogen bonding and other interactions between the bis-intercalating antibiotics and the duplex DNA than were previously available.

Base Pairing↗
PubMed2000

Forest Canopy Stratification-Is It Useful?

It has long been recognized that the forest canopy has a complex structure that is significant for environmental interactions, regeneration, growth, and biotic habitat. Not only is the structure variously complex, but also there are many ways to conceptualize that complexity. Yet the persistent theme when considering the structure of canopies continues to be that of stratification: whether structural units are arranged in layers above the ground. We examined the use of the terms "stratification," "layering," and others in connection with canopy structure and found they had various meanings (often only implied) that were difficult to reconcile and to measure. We applied the definitions to the structure of a single, well-studied canopy located in Virginia, U.S.A., and found they failed to define consistently and clearly the presence, number, or location of strata. Additionally, we found the concept had limitations related to scale dependence, point of reference, and spatial averaging. Thus, asserting that a forest is stratified or naming the number of layers generally provided no guide to its structure. We propose alternative ways of conceptualizing and studying the forest canopy that avoid most of the problems associated with stratification. Among these are direct measurement and mapping of structural and environmental variables that have clear potential connections with canopy functions and viewing the distribution of structures or environmental conditions within the canopy as ecological gradients.

canopy↗
PubMed2006

The three-dimensional structure of complex I from Yarrowia lipolytica: a highly dynamic enzyme.

The structure of complex I from Yarrowia lipolytica was determined by three-dimensional electron microscopy. A random conical data set was collected from deep stain embedded particles. More than 14000 image pairs were analyzed. Through extensive classification combined with three-dimensional reconstruction, it was possible for the first time to show a much more detailed substructure of the complex. The peripheral arm is subdivided in at least six domains. The membrane arm shows two major protrusions on its matrix facing side and exhibits a channel like feature on the side facing the cytoplasm. Structures resembling a tether connecting the subunits near the catalytic center with the protrusions of the membrane arm provide a second connection between matrix and membrane domain.

Cell Membrane↗
PubMed1999

Crystal structure of anti-Hen egg white lysozyme antibody (HyHEL-10) Fv-antigen complex. Local structural changes in the protein antigen and water-mediated interactions of Fv-antigen and light chain-heavy chain interfaces.

In order to address the recognition mechanism of the fragments of antibody variable regions, termed Fv, toward their target antigen, an x-ray crystal structure of an anti-hen egg white lysozyme antibody (HyHEL-10) Fv fragment complexed with its cognate antigen, hen egg white lysozyme (HEL), was solved at 2.3 A. The overall structure of the complex is similar to that reported in a previous article dealing with the Fab fragment-HEL complex (PDB ID code,). However, the areas of Fv covered by HEL upon complex formation increased by about 100 A(2) in comparison with the Fab-HEL complex, and two local structural differences were observed in the heavy chain of the variable region (VH). In addition, small but significant local structural changes were observed in the antigen, HEL. The x-ray data permitted the identification of two water molecules between the VH and HEL and six water molecules retained in the interface between the antigen and the light chain complementarity determining regions (CDRs) 2 and 3 (CDR-L2 and CDR-L3). These water molecules bridge the antigen-antibody interface through hydrogen bond formation in the VL-HEL interface. Eleven water molecules were found to complete the imperfect VH-VL interface, suggesting that solvent molecules mediate the stabilization of interaction between variable regions. These results suggest that the unfavorable effect of deletion of constant regions on the antigen-antibody interaction is compensated by an increase in favorable interactions, including structural changes in the antigen-antibody interface and solvent-mediated hydrogen bond formation upon complex formation, which may lead to a minimum decreased affinity of the antibody Fv fragment toward its antigen.

Amino Acid Sequence↗
PubMed1992

A 1H NMR database computer program for the analysis of the primary structure of complex carbohydrates.

A 1H NMR database computer program has been developed to determine the primary structure of complex carbohydrates. The database contains carbohydrate structures, their corresponding 1H NMR data, and literature references. From an input list of chemical shift values, the program generates an output list of partially or completely matching carbohydrate structures. In order to facilitate the recognition of the matching part of the selected carbohydrate structures, these structures are displayed with the matching structural elements highlighted. This new 1H NMR database, together with the search program described, now provides a fast access to the published 1H NMR data of complex carbohydrates and furnishes easy links to carbohydrate structures. The performance of the program is demonstrated by the analysis of five carbohydrate fractions prepared from a pool of horse serum glycoproteins.

Carbohydrate Conformation↗
PubMed2005

Molecular orbital investigation of the protonated H2X2AlNHn(CH3)3-n+ (X = F, Cl, and Br; n = 0-3) complexes.

Structures of protonated alane-Lewis base donor-acceptor complexes H2X2AlNHn(CH3)(3-n)+ (X = F, Cl, and Br; n = 0-3) as well as their neutral parents were investigated. All the monocations H2X2AlNHn(CH3)(3-n)+ are Al-H protonated involving hypercoordinated alane with a three-center two-electron bond and adopt the C(s) symmetry arrangement. The energetic results show that the protonated alane-Lewis complexes are more stable than the neutral ones. They also show that this stability decreases on descending in the corresponding periodic table column from fluorine to bromine atoms. The calculated protonation energies of HX2AlNHn(CH3)(3-n) to form H2X2AlNHn(CH3)(3-n)+ were found to be highly exothermic. The possible dissociation of the cations H2X2AlNHn(CH3)(3-n)+ into X2AlNHn(CH3)(3-n)+ and molecular H2 is calculated to be endothermic.

Journal Article↗
PubMed2004

Structural basis of leukotriene B4 12-hydroxydehydrogenase/15-Oxo-prostaglandin 13-reductase catalytic mechanism and a possible Src homology 3 domain binding loop.

The bifunctional leukotriene B(4) 12-hydroxydehydrogenase/15-oxo-prostaglandin 13-reductase (LTB(4) 12-HD/PGR) is an essential enzyme for eicosanoid inactivation. It is involved in the metabolism of the E and F series of 15-oxo-prostaglandins (15-oxo-PGs), leukotriene B(4) (LTB(4)), and 15-oxo-lipoxin A(4) (15-oxo-LXA(4)). Some nonsteroidal anti-inflammatory drugs (NSAIDs), which primarily act as cyclooxygenase inhibitors also inhibit LTB(4) 12-HD/PGR activity. Here we report the crystal structure of the LTB(4) 12-HD/PGR, the binary complex structure with NADP(+), and the ternary complex structure with NADP(+) and 15-oxo-PGE(2). In the ternary complex, both in the crystalline form and in solution, the enolate anion intermediate accumulates as a brown chromophore. PGE(2) contains two chains, but only the omega-chain of 15-oxo-PGE(2) was defined in the electron density map in the ternary complex structure. The omega-chain was identified at the hydrophobic pore on the dimer interface. The structure showed that the 15-oxo group forms hydrogen bonds with the 2'-hydroxyl group of nicotine amide ribose of NADP(+) and a bound water molecule to stabilize the enolate intermediate during the reductase reaction. The electron-deficient C13 atom of the conjugated enolate may be directly attacked by a hydride from the NADPH nicotine amide in a stereospecific manner. The moderate recognition of 15-oxo-PGE(2) is consistent with a broad substrate specificity of LTB(4) 12-HD/PGR. The structure also implies that a Src homology domain 3 may interact with the left-handed proline-rich helix at the dimer interface and regulate LTB(4) 12-HD/PGR activity by disruption of the substrate binding pore to accommodate the omega-chain.

15-Oxoprostaglandin 13-Reductase↗
PubMed1993

Refined 1.6 A resolution crystal structure of the complex formed between porcine beta-trypsin and MCTI-A, a trypsin inhibitor of the squash family. Detailed comparison with bovine beta-trypsin and its complex.

The crystal structure of the complex formed by porcine beta-trypsin with the MCTI-A inhibitor (Momordica charantia, Linn. Cucurbitaceae) has been determined at 1.6 A resolution using the molecular replacement method. The sequence of MCTI-A was determined by recognizing the electron density, and shows that MCTI-A is a member of the squash family of trypsin inhibitors. We report the first high-resolution structure of porcine beta-trypsin. Detailed comparisons have been made on the overall structure, solvent structure and active-site geometries between this complex and bovine beta-trypsin and its complexes. On the basis of our results, we discuss the interaction patterns between inhibitor and trypsin. Unlike other complex structures formed by bovine trypsin with inhibitors, no out-of-plane distortion around the inhibitor's scissible peptide was observed. The role of the trypsin catalytic triad is also discussed on the basis of this structure.

Animals↗
PubMed2001

Trigonal planar copper(I) complex: synthesis, structure, and spectra of a redox pair of novel copper(II/I) complexes of tridentate bis(benzimidazol-2'-yl) ligand framework as models for electron-transfer copper proteins.

The copper(II) and copper(I) complexes of the chelating ligands 2,6-bis(benzimidazol-2'-ylthiomethyl)pyridine (bbtmp) and N,N-bis(benzimidazol-2'-ylthioethyl)methylamine (bbtma) have been isolated and characterized by electronic and EPR spectra. The molecular structures of a redox pair of Cu(II/I) complexes, viz., [Cu(bbtmp)(NO(3))]NO(3), 1, and [Cu(bbtmp)]NO(3), 2, and of [Cu(bbtmp)Cl], 3, have been determined by single-crystal X-ray crystallography. The cation of the green complex [Cu(bbtmp)(NO(3))]NO(3) possesses an almost perfectly square planar coordination geometry in which the corners are occupied by the pyridine and two benzimidazole nitrogen atoms of the bbtmp ligand and an oxygen atom of the nitrate ion. The light-yellow complex [Cu(bbtmp)]NO(3) contains copper(I) with trigonal planar coordination geometry constituted by the pyridine and two benzimidazole nitrogen atoms of the bbtmp ligand. In the yellow chloride complex [Cu(bbtmp)Cl] the asymmetric unit consists of two complex molecules that are crystallographically independent. The coordination geometry of copper(I) in these molecules, in contrast to the nitrate, is tetrahedral, with pyridine and two benzimidazole nitrogen atoms of bbtmp ligand and the chloride ion occupying the apexes. The above coordination structures are unusual in that the thioether sulfurs are not engaged in coordination and the presence of two seven-membered chelate rings facilitates strong coordination of the benzimidazole nitrogens and discourage any distortion in Cu(II) coordination geometry. The solid-state coordination geometries are retained even in solution, as revealed by electronic, EPR, and (1)H NMR spectra. The electrochemical behavior of the present and other similar CuN(3) complexes has been examined, and the thermodynamic aspects of the electrode process are correlated to the stereochemical reorganizations accompanying the redox changes. The influence of coordinated pyridine and amine nitrogen atoms on the spectral and electrochemical properties has been discussed.

Benzimidazoles↗
PubMed2006

The recognition of local DNA conformation by the human papillomavirus type 6 E2 protein.

The E2 proteins are transcription/replication factors from papillomaviruses. Human papillomaviruses (HPVs) can be broadly divided in two groups; low-risk HPV subtypes cause benign warts while high-risk HPVs give rise to cervical cancer. Although a range of crystal structures of E2 DNA-binding domains (DBD) from both high- and low-risk HPV subtypes have been reported previously, structures of E2 DBD:DNA complexes have only been available for high-risk HPV18 and bovine papillomavirus (BPV1). In the present study we report the unliganded and DNA complex structures of the E2 DBD from the low-risk HPV6. As in the previous E2-DNA structures, complex formation results in considerable bending of the DNA, which is facilitated by sequences with A:T-rich spacers that adopt a pre-bent conformation. The low-risk HPV6 E2-DNA complex differs from the earlier structures in that minimal deformation of the protein accompanies complex formation. Stopped-flow kinetic studies confirm that both high- and low-risk E2 proteins adapt their structures on binding to DNA, although this is achieved more readily for HPV6 E2. It therefore appears that the higher selectivity of the HPV6 E2 protein may arise from its limited molecular adaptability, a property that might distinguish the behaviour of E2 proteins from high- and low-risk HPV subtypes.

Binding Sites↗