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At least 685 records · Page 38Linked to original sources
PubMed2002

Dinitro and quinodimethane derivatives of terthiophene that can be both oxidized and reduced. Crystal structures, spectra, and a method for analyzing quinoid contributions to structure.

Two new oligothiophenes, the dinitro compound 3',4'-dibutyl-5,5' '-dinitro-2,2':5',2' '-terthiophene (1) and the quinodimethane 3',4'-dibutyl-5,5' '-bis(dicyanomethylene)-5,5' '-dihydro-2,2':5',2' '-terthiophene (2), have been synthesized and studied with electrochemistry, UV-vis-NIR-IR spectroscopy, ESR, and X-ray crystallography. These compounds, designed to be both electron and hole carriers, show redox properties that are unusual for oligothiophenes. Cyclic voltammetry and spectroelectrochemistry demonstrated that each compound could be oxidized to a cation radical and reduced to an anion radical and dianion. The spectra of 2 and its three redox partners were analyzed in terms of a limiting structure in which the neutral 2 has orbitals corresponding to those of a substituted-terthiophene dication. Compound 1 crystallizes with the thiophene rings held in an unusual nonplanar, cisoid configuration in face-to-face pi-stacks, with a spacing between molecules of 3.65 A. The C-C bond lengths of the outer nitro-substituted rings have quinoid character. Compound 2 crystallizes with the thiophene rings in a planar, transoid configuration. The molecules are held in pi-stacks formed from pi-dimers with a spacing between molecules of 3.47 and 3.63 A. The C-C bond distances of the thiophene rings of 1 and 2 and other oligomers were analyzed by a principal component analysis. The analysis found that 93% of the structural variance resided in one principal component related to the quinoid structure of the oligothiophene moiety. The analysis reliably demonstrated a quinoid contribution to the structure of 1. This method should be applicable to understanding the structure of other conjugated molecules in which quinoid structures contribute.

Journal Article↗
PubMed2005

Local atomic structure of partially ordered NiMn in NiMn/NiFe exchange coupled layers: 1. XAFS measurements and structural refinement.

The local atomic structure of the Mn in NiMn/NiFe exchange coupled films was investigated using Mn K-edge extended X-ray absorption fine structure (EXAFS) measurements to elucidate the possible correlation between the coercivity that can occur even in samples that display no signs of NiMn L1(0) ordering in diffraction patterns and such ordering on a length scale below the diffraction limit. Raising the substrate growth temperature from 3 to 200 degrees C increases the extent of L1(0) ordering in the NiMn pinning layer and the associated coercivity. A short-range order parameter (S(SRO)) was derived from EXAFS data for comparison with the long-range order parameter (S(LRO)) obtained from the X-ray diffraction measurements. Analogous to S(LRO), S(SRO) increases in tandem with the pinning layer coercivity, implying the presence of nanometer-scale ordered clusters at the beginning stages of macroscopic L1(0) phase formation that apparently foster antiferromagnetism despite their small size. The behavior of the EXAFS, especially the contributions of the more distant shells, also suggests that the overall structure in materials that are not fully L1(0)-ordered is more accurately described as locally ordered, magnetically ordered, incoherent nanodomains of the L1(0) phase separated by locally disordered, strained, interdomain regions that globally average to the fcc lattice with little or no local fcc structure present. The constraints on the sizes and other characteristics of these domains were explored by examining the diffraction patterns calculated for several two-dimensional analogue structures. These demonstrated that one of the most important structural features in the development of a two-phase diffraction pattern was the presence of dislocations in response to the elastic strain at the interfaces between domains where the accumulated expitaxial mismatch was greater than half of the bond length that rendered the domains incoherent with respect to each other.

Journal Article↗
PubMed2006

Structural phase transition of magnetic [Ni(dmit)2]- salts induced by supramolecular cation structures of (M+)([12]crown-4)2.

Sandwich-type supramolecular cation structures of (M(+))([12]crown-4)(2) complexes (M(+) = Li(+), Na(+), K(+), and Rb(+)) were introduced as countercations to the [Ni(dmit)(2)](-) anion, which bears an S = (1)/(2) spin, to form novel magnetic crystals (dmit(2-) = 2-thione-1,3-dithiole-4,5-dithiolate). The zigzag arrangement of Li(+)([12]crown-4)(2) cations in Li(+)([12]crown-4)(2)[Ni(dmit)(2)](-) salt induced weak intermolecular interactions of [Ni(dmit)(2)](-) dimers, whose magnetic spins were isolated from each other. The molecular arrangements of cations and anions in M(+)([12]crown-4)(2)[Ni(dmit)(2)](-) salts (M(+) = Na(+), K(+), and Rb(+)) were isostructural to each other. In the case of Na(+)([12]crown-4)(2)[Ni(dmit)(2)](-), the space group C2/m changed to C2/c with a lowering in temperature from 298 to 100 K. This structural change occurred at 222.5 K as a first-order phase transition. The space group C2/m (T = 298 K) in the salt K(+)([12]crown-4)(2)[Ni(dmit)(2)](-) also changed to C2/c (T = 100 K), which transition occurred at 270 K. Crystal structural analyses at 298 and 100 K revealed changes in both supramolecular cation conformation and [Ni(dmit)(2)](-) anion arrangements. The transition from C2/m to C2/c crystals generated a dipole moment in the Na(+)([12]crown-4)(2) and K(+)([12]crown-4)(2) structures, which were reconstructed to cancel the net dipole moment of the C2/c crystals. These cation transformations led to changes in intermolecular interactions between the [Ni(dmit)(2)](-) anions via structural rearrangements. The crystal structure of C2/c was stabilized in Rb(+)([12]crown-4)(2)[Ni(dmit)(2)](-) at 298 K. The [Ni(dmit)(2)](-) configuration in these salts with the C2/c space group was a one-dimensional uniform chain, which showed the temperature-dependent magnetic susceptibility of a one-dimensional linear Heisenberg antiferromagnetic chain.

Journal Article↗
PubMed2006

Viscoelastic and structural properties of a phenyl-modified polysiloxane system with a three-dimensional structure.

The relationships between the viscoelastic and structural properties of glass-forming materials with polysiloxane bonds, which serve as network formers, and phenyl groups, which act as network terminators, are examined based on shear viscoelasticity, (29)Si MAS NMR, and GPC measurements during the early stages of the network-forming process. The viscosities of the present samples do not depend on the frequency at temperatures up to 200 degrees C, suggesting that the origin of the viscous flow does not include intermolecular entanglement. According to the results of the strain dependence of the elastic modulus, the bridging-oxygen number, and molecular weight, the present polysiloxane system has a complex structure, or distribution of various-sized molecules composed of a polysiloxane network with various dimensionalities, and furthermore an elementary process of the viscosity is simple flow of these molecules. The structural factors that determine the viscosity and its temperature dependence are categorized into the molecular size and the intramolecular structure by using a theory based on the free-volume model. The relationship between the viscosity and the structure around the glass transition temperature is quantitatively examined and it is concluded that introducing larger numbers of Ph groups makes the viscosity less sensitive to structural factors.

Journal Article↗
PubMed2006

Factors governing the three-dimensional hydrogen-bond network structure of poly(m-phenylene isophthalamide) and a series of its model compounds (4): similarity in local conformation and packing structure between a complicated three-arm model compound and the linear model compounds.

Crystal structure of a three-arm model compound of poly(m-phenylene isophthalamide) (PMIA), N,N',N' '-triphenyl trimesamide Phi(CONHPhi)(3), has been analyzed by the X-ray diffraction method. The torsional angles around the bonds connecting the amide group and the central benzene ring are 24-34 degrees , almost the same as those observed for many kinds of aromatic amide compounds, reflecting mainly the intramolecular energetic balance between the amide and benzene groups. On the other hand, the torsional angles around the bonds connecting the amide group and the outer benzene ring were found to distribute over a wide range of 2-51 degrees due to the additional effect of intermolecular interactions. This is the first example to show experimentally clearly the role of intra- and intermolecular interactions in the control of torsional angle around the benzene-amide linkage. The hydrogen bonds are formed between the amide groups of the neighboring molecules, resulting in the construction of three-dimensional network structure. The local packing structure of the three-arm compound was found to be essentially the same as those observed for PMIA and the linear model compounds, indicating a characteristic structural feature of the meta-linkage-type aromatic amide compounds. The energy calculation was made using the software Polymorph Predictor to extract the energetically most stable crystal structure, which was compared successfully with the X-ray analyzed structure.

Journal Article↗
PubMed2006

Dependence of DNA electronic structure on environmental and structural variations.

We present experimental and theoretical evidence that varying the local environment and physical structure of dried DNA has a direct impact on its electronic structure. By preparing samples of DNA in various solutions, it was possible to alter the type of ions present during the production of the DNA samples. These variations resulted in differences in the local chemical environment of the dried DNA molecules. X-ray absorption spectroscopy (XAS) and X-ray emission spectroscopy (XES) were used to probe the variations in the electronic structure of DNA samples. DFT calculations of a stack of 10 adenine (A)-thymine (T) nucleobase pairs show that slight structural variations in stacking height have a direct influence on the electronic structure and result in changes to the HOMO-LUMO gap. The effects of these differences in the local environment on the electronic structure are discussed and are related to the results of conductivity measurements of DNA.

DNA↗
PubMed2004

Structural Basis of Redox Signaling in Photosynthesis: Structure and Function of Ferredoxin:thioredoxin Reductase and Target Enzymes.

The role of the ferredoxin:thioredoxin system in the reversible light activation of chloroplast enzymes by thiol-disulfide interchange with thioredoxins is now well established. Recent fruitful collaboration between biochemists and structural biologists, reflected by the shared authorship of the paper, allowed to solve the structures of all of the components of the system, including several target enzymes, thus providing a structural basis for the elucidation of the activation mechanism at a molecular level. In the present Review, these structural data are analyzed in conjunction with the information that was obtained previously through biochemical and site-directed mutagenesis approaches. The unique 4Fe-4S cluster enzyme ferredoxin:thioredoxin reductase (FTR) uses photosynthetically reduced ferredoxin as an electron donor to reduce the disulfide bridge of different thioredoxin isoforms. Thioredoxins in turn reduce regulatory disulfides of various target enzymes. This process triggers conformational changes on these enzymes, allowing them to reach optimal activity. No common activation mechanism can be put forward for these enzymes, as every thioredoxin-regulated protein undergoes specific structural modifications. It is thus important to solve the structures of the individual target enzymes in order to fully understand the molecular mechanism of the redox regulation of each of them.

Journal Article↗
PubMedDate not supplied

Gene and protein structure of a beta-crystallin polypeptide in murine lens: relationship of exons and structural motifs.

A 23,000 molecular weight beta-crystallin (beta 23) of the murine eye lens is encoded in a 4.1 +/- 0.3-kilobase gene containing three introns. Each of the four exons seems to code for a separate structural motif of the protein, whose tertiary structure was predicted by an interactive computer graphics technique based on the crystallographic structure of bovine gamma II-crystallin. The first exon also encodes a hydrophobic N-terminal peptide resembling membrane anchor sequences of other proteins. Our results indicate structural homology among the beta- and gamma-crystallin polypeptides, and link gene structure with protein structure in this superfamily of lens proteins.

Amino Acid Sequence↗
PubMed1976

The effects of deoxyribonucleic acid secondary structure on tertiary structure.

The secondary structure of supercoiled DNA was varied by changes in ionic strength. For I = 0.075-0.4 the structure remained in the previously established branched form with only minor alterations in molecular dimensions. In 4M-NaCl, which induces linear DNA to change its secondary structure to the C structure and brings about an increase in the superhelix density of the molecule, no extra branches were observed on the molecules. The limiting factors that dictate supercoil structure seem to be the number and position of potential branch points and the proximity with which the two intertwining DNA strands can approach each other on the arms of the branches. This value is close to 10nm under the conditions described, and is 14-15nm at I = 0.2. It is suggested that such values should be borne in mind when models of chromosome structure are being constructed.

Bacteriophages↗
PubMed2004

Analysis and simulation of the structure of nanoparticles that undergo a surface-driven structural transformation.

A room temperature solid-state structural transformation was observed in 3 nm ZnS nanoparticles in methanol following the addition of water (Zhang et al., Nature 424, 1025, 2003). Experimental wide angle x-ray scattering (WAXS), x-ray absorption near edge structure (XANES) and extended x-ray absorption fine structure (EXAFS) spectroscopy measurements show a large increase in crystallinity associated with water addition, in agreement with molecular dynamics (MD) predictions. Here we perform first-shell EXAFS and pair distribution function analysis and whole-nanoparticle calculations of WAXS, EXAFS and XANES to compare structural data with the MD predictions. The predicted WAXS patterns give excellent agreement with data, while the predicted EXAFS and XANES spectra give poor agreement. Relative to WAXS, XANES and EXAFS spectra contain additional structural information related to the distribution of disorder. The discrepancy between the x-ray diffraction and x-ray absorption results indicates that structural disorder is partitioned between interior and surface regions more strongly than predicted in the MD simulations.

Journal Article↗
PubMed2006

Structure and stability of Co(n)(pyridine)(m)- clusters: absence of metal inserted structures.

A synergistic approach combining the experimental photoelectron spectroscopy and theoretical electronic structure studies is used to probe the geometrical structure and the spin magnetic moment of Co(n)(pyridine)(m) (-) clusters. It is predicted that the ground state of Co(pyridine)(-) is a structure where the Co atom is inserted in a CH bond. However, the insertion is marked by a barrier of 0.33 eV that is not overcome under the existing experimental conditions resulting in the formation of a structure where Co occupies a site above the pyridine plane. For Co(2)(pyridine)(-), a ground-state structure is predicted in which the Co(2) diametric moiety is inserted in one of the CH bonds, but again because of a barrier, the structure which matches the photoelectron spectrum is a higher-energy isomer in which the Co(2) moiety is bonded directly to nitrogen on the pyridine ring. In all cases, the Co sites have finite magnetic moments suggesting that the complexes may provide ways of making cluster-based magnetic materials.

Journal Article↗
PubMed1985

Repeating modular structure of the fibronectin gene: relationship to protein structure and subunit variation.

Analysis of the exon-intron structure of the rat fibronectin gene shows that exons correspond precisely with repeating structural units in the protein and that alternative use of some exons produces fibronectin subunits that differ by the presence or absence of certain structural modules. Secondary structure predictions suggest that the repeating structure of the protein is further subdivided into smaller structural units and that these also correspond with exons in the gene.

Animals↗
PubMed1987

Molecular structure of mammalian neuropeptide Y: analysis by molecular cloning and computer-aided comparison with crystal structure of avian homologue.

Identification and characterization of the cDNA encoding rat neuropeptide Y revealed the nucleotide sequence coding for a 98-amino acid precursor. The deduced amino acid sequence for rat neuropeptide Y is identical to the human peptide and is highly homologous to avian pancreatic polypeptide. The tertiary structure of avian pancreatic polypeptide has been previously derived from crystallographic data by Blundell and coworkers. The homology between neuropeptide Y and avian pancreatic polypeptide preserves all of the residues essential for the maintenance of the tertiary structure. Thus, it has been possible to compute a three-dimensional model of the mammalian neuropeptide, neuropeptide Y, based on the known structure of the avian homologue. This model suggest that neuropeptide preserves a compact tertiary structure characterized by extensive hydrophobic interactions between an N-terminal polyproline-II-like helix and a C-terminal alpha-helix. The model has been used to identify amino acids residing in key positions within this structure and, thereby, to direct future analysis of neuropeptide Y structure-function relationships.

Amino Acid Sequence↗
PubMed1994

Crystal structure of peanut lectin, a protein with an unusual quaternary structure.

The x-ray crystal structure of the tetrameric T-antigen-binding lectin from peanut, M(r) 110,000, has been determined by using the multiple isomorphous replacement method and refined to an R value of 0.218 for 22,155 reflections within the 10- to 2.95-A resolution range. Each subunit has essentially the same characteristic tertiary fold that is found in other legume lectins. The structure, however, exhibits an unusual quaternary arrangement of subunits. Unlike other well-characterized tetrameric proteins with identical subunits, peanut lectin has neither 222 (D2) nor fourfold (C4) symmetry. A noncrystallographic twofold axis relates two halves of the molecule. The two monomers in each half are related by a local twofold axis. The mutual disposition of the axes is such that they do not lead to a closed point group. Furthermore, the structure of peanut lectin demonstrates that differences in subunit arrangement in legume lectins could be due to factors intrinsic to the protein molecule and, contrary to earlier suggestions, are not necessarily caused by interactions involving covalently linked sugar. The structure provides a useful framework for exploring the structural basis and the functional implications of the variability in the subunit arrangement in legume lectins despite all of them having nearly the same subunit structure, and also for investigating the general problem of "open" quaternary assembly in oligomeric proteins.

Arachis↗
PubMed1998

The structures of the lipopolysaccharides from Rhizobium etli strains CE358 and CE359. The complete structure of the core region of R. etli lipopolysaccharides.

The structural arrangement of oligosaccharides comprising the core region of Rhizobium etli CE3 lipopolysaccharide (LPS) has been elucidated through the characterization of the LPSs from two R. etli mutants. One mutant, CE358, completely lacks the O-chain polysaccharide, while the second mutant, CE359, contains a truncated portion of this polysaccharide. This structural arrangement of the core oligosaccharides in these LPSs was determined using electrospray ionization mass spectrometry, tandem mass spectrometry, and methylation analysis. Mild acid hydrolysis of the CE359 LPS produces two major core oligosaccharides: a tetrasaccharide (1) with the structure alpha-D-Galp-(1-->6)-[alpha-D-GalpA-(1-->4)]-alpha-D-Manp-(1 -->5)-Kdo p (where Kdo represents 3-deoxy-D-manno-2-octulosonic acid) and a trisaccharide (2) having the structure alpha-D-GalpA-(1-->4)-[alpha-D-GalpA-(1-->5)]-Kdop. Structure 1 in CE358 LPS lacks the galacturonosyl residue. Glycosyl linkage and tandem mass spectrometry analyses show that the intact LPS core region consists of trisaccharide (2) attached to O-4 of the Kdo residue in tetrasaccharide 1, and that an additional Kdo residue is attached to O-6 of the galactosyl residue of 1. [structure: see text] The additional terminally linked Kdo residue is not in close proximity to the lipid A moiety, a unique location for a core Kdo residue. The mutant LPS preparations also contain minor LPS species, one of which lacks the Kdo linked to O-6 of the galactosyl residue, another that lacks the galacturonic acid attached to O-5 of Kdo, and a third that lacks two galacturonosyl residues and one Kdo residue. Thus, in addition to lacking both heptose and phosphate, the R. etli LPS core region differs substantially from the typical enterobacterial cores. The abundance of galacturonosyl residues in the R. etli core might serve as a suitable functional replacement for phosphate, such as would be predicted for Ca2+ binding.

Carbohydrate Sequence↗
PubMed2000

Re-engineering of human urokinase provides a system for structure-based drug design at high resolution and reveals a novel structural subsite.

Inhibition of urokinase has been shown to slow tumor growth and metastasis. To utilize structure-based drug design, human urokinase was re-engineered to provide a more optimal crystal form. The redesigned protein consists of residues Ile(16)-Lys(243) (in the chymotrypsin numbering system; for the urokinase numbering system it is Ile(159)-Lys(404)) and two point mutations, C122A and N145Q (C279A and N302Q). The protein yields crystals that diffract to ultra-high resolution at a synchrotron source. The native structure has been refined to 1.5 A resolution. This new crystal form contains an accessible active site that facilitates compound soaking, which was used to determine the co-crystal structures of urokinase in complex with the small molecule inhibitors amiloride, 4-iodo-benzo(b)thiophene-2-carboxamidine and phenylguanidine at 2. 0-2.2 A resolution. All three inhibitors bind at the primary binding pocket of urokinase. The structures of amiloride and 4-iodo-benzo(b)thiophene-2-carboxamidine also reveal that each of their halogen atoms are bound at a novel structural subsite adjacent to the primary binding pocket. This site consists of residues Gly(218), Ser(146), and Cys(191)-Cys(220) and the side chain of Lys(143). This pocket could be utilized in future drug design efforts. Crystal structures of these three inhibitors in complex with urokinase reveal strategies for the design of more potent nonpeptidic urokinase inhibitors.

Amiloride↗
PubMed1990

Secondary structure prediction for the spectrin 106-amino acid segment, and a proposed model for tertiary structure.

A collective secondary structure prediction for the human erythrocyte spectrin 106-residue repeat segment is developed, based on the sequences of nine segments that have been reported in the literature, utilizing a consensus of several secondary structure prediction methods for locating turn regions. The analysis predicts a five-fold structure, with three alpha-helices and two beta-strand regions, and differs from previous models on the lengths of the helices and the existence of beta-strand structure. We also demonstrate that this structural motif can be folded into tertiary structures that satisfy the experimental spectrin data and several general principles of protein organization.

Circular Dichroism↗
PubMed1977

The structure of postsynaptic densities isolated from dog cerebral cortex. II. Characterization and arrangement of some of the major proteins within the structure.

An attempt was made to identify some of the proteins of the postsynaptic density (PSD) fraction isolated from dog cerebral cortex. The major protein has been tentatively labeled "neurofilament" protein, on the basis of its 51,000 mol wt correspondence to a protein found in neurofilament preparations. Other proteins are akin to some dog myofibrillar proteins, on the basis if immunological crossreaction and equal sodium dodecyl sulfate (SDS)-gel electrophoretic mobilities. While a protein similar to dog muscle myosin is not present in the PSD fraction, a major protein present is actin, as evident from reactivity with antiactin serum, from SDS-gel mobility, and from amino acid composition. Only very little tubulin may be present in the PSD fraction, as determined by gel electrophoresis. Various treatments of the PSD fraction were attempted in order to extract some proteins, as revealed by gel electrophoresis, and to observe the structural changes of the PSD fraction residue after extraction of these proteins. The PSD is remarkably resistant to various extraction conditions, with only 4 M guanidine being found to extract most of the proteins, except the 51,000 mol wt protein. Disulfide reducing agents such as dithiothreitol (DTT), blocking agents such as p-chloromercuribenzoate (PCMB) (both in the presence of deoxycholate [DOC]), a Ca++ extractor, ethylene glycol-bis (beta- aminoethyl ether) N,N,N',N'-tetraacetate (EGTA), and guanidine caused an opening up of the native dense PSD structure, revealing approximately 10-nm filaments, presumably consisting of "neurofilament" protein. Both DTT-DOC and PCMB-DOC removed chiefly actin but also some other proteins. EGTA, in greatly opening up the structure, as observed in the electron microscope, revealed both 10-nm and 3- to 5-nm filaments; the later could be composed of actin, since actin was still in the residue after the treatment. EGTA removed a major 18,000 mol wt component and two minor proteins of 68,000 and 73,000 mol wt. Based on the morphological and biochemical evidence, a picture is presented of the PSD as a structure partly made up of 10-nm and 3- to 5-nm filaments, held together through Ca++ interaction and by bonds amendable to breakage by sulfhydrylblocking and disulfide-reducing reagents; either removal of Ca++ and/or rupture of these disulfide bonds opens up the structure. On the basis of the existence of filamentous proteins and the appearance of the PSD after certain treatments as a closed or open structure, a theory is presented with envisages the PSD to function as a modulator in the conduction of the nerve impulse, by movements of its protein relative.

Actins↗