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At least 721 records · Page 40Linked to original sources
PubMed2006

Synthesis and properties of gold alkene complexes. Crystal structure of [Au(bipy(oXyl))(eta(2)-CH(2)=CHPh)](PF(6)) and DFT calculations on the model cation [Au(bipy)(eta(2)-CH(2)=CH(2))](+).

Unprecedented 16-electron gold(i) olefin complexes of general formula [Au(bipy(R,R'))(eta(2)-olefin)](PF(6)) and [Au(2)(bipy(R,R'))(2)(mu-eta(2):eta(2)-diolefin)](PF(6))(2) (bipy(R,R') = 6-substituted-2,2'-bipyridine) have been prepared by reaction of dinuclear gold(III) oxo complexes [Au(2)(bipy(R,R'))(2)(mu-O)(2)](PF(6))(2) with the appropriate olefin. The X-ray crystal structures of two mononuclear complexes (olefin = styrene) show in-plane coordination of the olefin and a C[double bond, length as m-dash]C bond distance considerably lengthened with respect to the free olefin. The spectroscopic properties of the complexes are discussed and compared with those of analogous d(10) metal derivatives. Both structural and spectroscopic information indicate a substantial contribution of pi-back-donation to the Au-olefin bond in the three-coordinate species. Theoretical calculations carried out at the hybrid-DFT level on the model compound [Au(bipy)(eta(2)-CH(2)[double bond, length as m-dash]CH(2))](+) show excellent agreement with the experimental findings giving in addition an estimate of a pi-back-bonding contribution higher than that of the sigma-bonding.

Journal Article↗
PubMed2005

Binding of C5-dicarboxylic substrate to aspartate aminotransferase: implications for the conformational change at the transaldimination step.

The mechanism for the reaction of aspartate aminotransferase with the C4 substrate, l-aspartate, has been well established. The binding of the C4 substrate induces conformational change in the enzyme from the open to the closed form, and the entire reaction proceeds in the closed form of the enzyme. On the contrary, little is known about the reaction with the C5 substrate, l-glutamate. In this study, we analyzed the pH-dependent binding of 2-methyl-l-glutamate to the enzyme and showed that the interaction between the amino group of 2-methyl-l-glutamate and the pyridoxal 5'-phosphate aldimine is weak compared to that between 2-methyl-l-aspartate and the aldimine. The structures of the Michaelis complexes of the enzyme with l-aspartate and l-glutamate were modeled on the basis of the maleate and glutarate complex structures of the enzyme. The result showed that l-glutamate binds to the open form of the enzyme in an extended conformation, and its alpha-amino group points in the opposite direction of the aldimine, while that of l-aspartate is close to the aldimine. These models explain the observations for 2-methyl-l-glutamate and 2-methyl-l-aspartate. The crystal structures of the complexes of aspartate aminotransferase with phosphopyridoxyl derivatives of l-glutamate, d-glutamate, and 2-methyl-l-glutamate were solved as the models for the external aldimine and ketimine complexes of l-glutamate. All the structures were in the closed form, and the two carboxylate groups and the arginine residues binding them are superimposable on the external aldimine complex with 2-methyl-l-aspartate. Taking these facts altogether, it was strongly suggested that the binding of l-glutamate to aspartate aminotransferase to form the Michaelis complex does not induce a conformational change in the enzyme, and that the conformational change to the closed form occurs during the transaldimination step. The hydrophobic residues of the entrance of the active site, including Tyr70, are considered to be important for promoting the transaldimination process and hence the recognition of the C5 substrate.

Amines↗
PubMed2002

Hydrolytically active tetranuclear nickel complexes with structural resemblance to the active site of urease.

Reaction of the new asymmetric ligand 2-(N-isopropyl-N-((1-methylimidazolyl)methyl)aminomethyl)-6-(N-carboxylmethyl-N-((1-methylimidazolyl)methyl) aminomethyl)-4-methylphenol (ICIMP) with nickel perchlorate and diphenylacetic acid leads to the formation of tetranuclear nickel complexes, whose crystal structures reveal that they consist of dimers of dimers in which each Ni(2) unit has a coordination environment that is similar to the active site of urease. One complex has been shown to coordinate urea and catalyze the hydrolysis of an organophosphate monoester.

Bacillus↗
PubMed1993

Chemical probing of tDNAPhe with transition metal complexes: a structural comparison of RNA and DNA.

The three-dimensional folding of tDNAPhe has been examined and compared to native tRNAPhe using a series of shape-selective transition metal complexes as chemical probes of nucleic acid structure. Rh(phen)2 phi 3+ (phen = phenanthroline, phi = 9,10-phenanthrenequinonediimine), which targets sites of tertiary interaction in tRNAPhe, cleaves specifically at similar sites on tDNAPhe. However, this rhodium complex also targets 5'-pyr-pyr-pur-3' sites within the acceptor and anticodon stems of tDNA;Rh(phen)2 phi 3+ generally targets 5'-pyr-pyr-pur-3' sites in B-form duplex DNA. On tRNAPhe, Rh(DIP)3(3+) (DIP = 4,7-diphenyl-1,10-phenanthroline) specifically cleaves C70, which neighbors a GU mismatch, and targets psi 55 as well, within the hydrophobic region of tRNAPhe. On tDNAPhe no specific cleavage by Rh(DIP)3(3+) is observed. The cleavage studies, taken together, indicate that globally the tertiary folding of tDNAPhe resembles that of tRNAPhe. However, the double helical regions of the DNA analog differ from tRNAPhe, likely in adopting a more B-like conformation. As a consequence, the GT mismatch within the acceptor stem of tDNA does not present the same recognition elements as in tRNA, and the GT mismatch is no longer recognized by the shape-selective rhodium complex. The present work underscores the utility of applying DNA analogs to studies of RNA structure and function, since the general folding characteristics of the two polymers are likely to be similar. However, structural probing with transition metal complexes offers a valuable companion to such experiments, since the shape-selective probes, with sensitivity, may be used to delineate locally on the polymer those regions which may differ in structure.

DNA↗
PubMed2001

Complex crystal structure of cesium-III.

The structure of Cs-III, stable between 4.2 and 4.3 GPa at room temperature, has been determined from single-crystal x-ray diffraction data. Rather than the simple fcc structure previously reported [Hall et al., Science 146, 1297 (1964)], the data yield a complex new type of elemental structure which is orthorhombic (space group C222(1)) with 84 atoms in the unit cell. No evidence could be found for the fcc form reported previously, even in a further experiment, conducted under conditions close to those used by Hall et al., which also yielded the 84-atom structure.

Journal Article↗
PubMed1994

New structures in complex formation between DNA and cationic liposomes visualized by freeze-fracture electron microscopy.

Structures formed during interaction of cationic liposomes and plasmid DNA were studied by freeze-fracture electron microscopy and their morphology was found to be dependent on incubation time and DNA concentration. These structures were formed with liposomes composed of DC-Chol and DOPE after 30 min incubation at DNA:lipid concentrations encompassing maximal transfection activity. They resembled liposome complexes (meatballs) and additionally bilayer-covered DNA tubules (spaghetti), whereby the DNA-tubules were found to be connected to the liposome complexes as well as occurring free in the suspension. At later times and higher DNA-to-liposome ratios the complexes grow larger while their membranes become discontinuous, allowing the self-encapsulation of the DNA. The relative transfection potency of the various morphologically distinct structures is discussed.

Avian Sarcoma Viruses↗
PubMed2005

PROVAT: a tool for Voronoi tessellation analysis of protein structures and complexes.

SUMMARY: Voronoi tessellation has proved to be a useful tool in protein structure analysis. We have developed PROVAT, a versatile public domain software that enables computation and visualization of Voronoi tessellations of proteins and protein complexes. It is a set of Python scripts that integrate freely available specialized software (Qhull, Pymol etc.) into a pipeline. The calculation component of the tool computes Voronoi tessellation of a given protein system in a way described by a user-supplied XML recipe and stores resulting neighbourhood information as text files with various styles. The Python pickle file generated in the process is used by the visualization component, a Pymol plug-in, that offers a GUI to explore the tessellation visually. AVAILABILITY: PROVAT source code can be downloaded from http://raven.bioc.cam.ac.uk/~swanand/Provat1, which also provides a webserver for its calculation component, documentation and examples.

Algorithms↗
PubMed2004

Nucleoporins as components of the nuclear pore complex core structure and Tpr as the architectural element of the nuclear basket.

The vertebrate nuclear pore complex (NPC) is a macromolecular assembly of protein subcomplexes forming a structure of eightfold radial symmetry. The NPC core consists of globular subunits sandwiched between two coaxial ring-like structures of which the ring facing the nuclear interior is capped by a fibrous structure called the nuclear basket. By postembedding immunoelectron microscopy, we have mapped the positions of several human NPC proteins relative to the NPC core and its associated basket, including Nup93, Nup96, Nup98, Nup107, Nup153, Nup205, and the coiled coil-dominated 267-kDa protein Tpr. To further assess their contributions to NPC and basket architecture, the genes encoding Nup93, Nup96, Nup107, and Nup205 were posttranscriptionally silenced by RNA interference (RNAi) in HeLa cells, complementing recent RNAi experiments on Nup153 and Tpr. We show that Nup96 and Nup107 are core elements of the NPC proper that are essential for NPC assembly and docking of Nup153 and Tpr to the NPC. Nup93 and Nup205 are other NPC core elements that are important for long-term maintenance of NPCs but initially dispensable for the anchoring of Nup153 and Tpr. Immunogold-labeling for Nup98 also results in preferential labeling of NPC core regions, whereas Nup153 is shown to bind via its amino-terminal domain to the nuclear coaxial ring linking the NPC core structures and Tpr. The position of Tpr in turn is shown to coincide with that of the nuclear basket, with different Tpr protein domains corresponding to distinct basket segments. We propose a model in which Tpr constitutes the central architectural element that forms the scaffold of the nuclear basket.

HeLa Cells↗
PubMed2004

Reactivity of aqua coordinated monoporphyrinate lanthanide complexes: synthetic, structural and photoluminescent studies of lanthanide porphyrinate dimers.

Dimerization of monoporphyrinate lanthanide complexes [Yb(Por)(H(2)O)(3)]Cl, (Por = TTP(2-), TMPP(2-) and TPP(2-)) in the presence of sterically hindered tripodal ligand, zinc Schiff-base, dilute HCl, K(2)CO(3) solution, 4,4'-bipyridine (bipy), and basic 8-hydroxyquinaldine (HQ) solution was observed in CH(2)Cl(2) at room temperature. Six neutral dimeric lanthanide porphyrinate complexes, [Yb(TTP)(mu-OH)](2)(mu-THF) (1), [Yb(TMPP)(mu-OH)(H(2)O)](2) (2), [Yb(TPP)(mu-OH)(mu-H(2)O)](2) (4), [Yb(TMPP)(mu-Cl)(H(2)O)](2) (5), [Yb(TMPP)(mu-OH)](2)(THF) (6) and [Yb(TPP)](2)(mu-OH)(mu-Q) (7), were obtained. X-Ray diffraction studies showed that for the dimers, the two lanthanide ions were bridged by OH(-), Cl(-) or H(2)O. Photoluminescent studies showed that the porphyrinate dianion acted as an antenna, transferred its absorbed visible energy to the lanthanide ion and enabled the latter emitting in the near-infrared (NIR) region. In general, the NIR emission is more intense for the dimers than for the monomers, and the NIR emission intensity decreases as the number of O-H oscillators present in the molecule increases.

Journal Article↗
PubMed1999

Charting No-Man's Land in d(0) Transition Metal Six-Coordination: Structure Predictions for the Complexes

Unusual structures between octahedral and trigonal-prismatic are found by density functional calculations for the "simple" six-coordinate d(0) title complexes. While a distorted octahedron is still slightly lower in energy than a prismatic structure for [WCl(5)CH(3)], intermediate structures start to appear for [WCl(4)(CH(3))(2)] (see picture). In the case of [WCl(3)(CH(3))(3)], prismatic arrangements are already more favorable. These and many related compounds should be accessible experimentally.

Journal Article↗
PubMed2000

Human alpha-N-acetylgalactosaminidase: site occupancy and structure of N-linked oligosaccharides.

Human alpha-N-acetylgalactosaminidase (alpha-GalNAc; also known as alpha-galactosidase B) is the lysosomal exoglycohydrolase that cleaves alpha-N-acetylgalactosaminyl moieties in glycoconjugates. Mutagenesis studies indicated that the first five (N124, N177, N201, N359, and N385) of the six potential N-glycosylation sites were occupied. Site 3 occupancy was important for enzyme function and stability. Characterization of the N-linked oligosaccharide structures on the secreted enzyme overexpressed in Chinese hamster ovary cells revealed highly heterogeneous structures consisting of complex (approximately 53%), hybrid (approximately 12%), and high mannose-type (approximately 33%) oligosaccharides. The complex structures were mono-, bi-, 2,4-tri-, 2,6-tri-, and tetraantennary, among which the biantennary structures were most predominant (approximately 53%). Approximately 80% of the complex oligo-saccharides had a core-region fucose and 50% of the complex oligosaccharides were sialylated exclusively with alpha-2,3-linked sialic acid residues. The majority of hybrid type oligo-saccharides were GalGlcNAcMan(6)GlcNAc-Fuc(0-1)GlcNAc. Approximately 54% of the hybrid oligosaccharide were phosphorylated and one-third of these structures were further sialylated, the latter representing unique phosphorylated and sialylated structures. Of the high mannose oligosaccharides, Man(5-7)GlcNAc(2) were the predominant species (approximately 90%) and about 50% of the high mannose oligosaccharides were phosphorylated, exclusively as monoesters whose positions were determined. Comparison of the oligosaccharide structures of alpha-GalNAc and alpha-galactosidase A, an evolutionary-related and highly homologous exoglycosidase, indicated that alpha-GalNAc had more completed complex chains, presumably due to differences in enzyme structure/domains, rate of biosynthesis, and/or aggregation of the overexpressed recombinant enzymes.

Animals↗
PubMed2004

A suite of 3D NMR methods for characterizing complex hydrocarbon structure fragments.

A suite of triple resonance 3D NMR experiments is presented for the complete connectivity assignment of the hydrocarbon network in complex macromolecular and supramolecular organic structures. These new 3D NMR methods rely only on the presence of a unique set of (13)C resonances (from (13)C(X)) which are separated from the rest of the (13)C NMR spectrum. These experiments take the advantage of region selective excitation and selective inversion by composite pulses to provide correlations among H(A), (13)C(A); H(B), (13)C(B) and neighboring (13)C(X) resonances along three frequency dimensions. These methods include: gHC(A)C(X), gHC(A)C(X)-HH-TOCSY and gHC(A)C(X)-CC-TOCSY experiments. The utility of this approach is illustrated with spectra of selected structure fragments in poly(ethylene-co-n-butyl acrylate-co-carbon monoxide) (polyEBC) prepared from 1,2,3-(13)C(3)-n-butyl acrylate.

Acrylates↗
PubMed1993

The multicatalytic proteinase complex (proteasome): structure and conformational changes associated with changes in proteolytic activity.

The multicatalytic proteinase complex or proteasome is a high-molecular-mass multisubunit proteinase which is found in the nucleus and cytoplasm of eukaryotic cells. Electron microscopy of negatively stained rat liver proteinase preparations suggests that the particle has a hollow cylindrical shape (approximate width 11 nm and height 17 nm using methylamine tungstate as the negative stain) with a pseudo-helical arrangement of subunits rather than the directly stacked arrangement suggested previously. The side-on view has a 2-fold rotational symmetry, while end-on there appears to be six or seven subunits around the ring. This model is very different from that proposed by others for the proteinase from rat liver but resembles the structure of the simpler archaebacterial proteasome. The possibility of conformational changes associated with the addition of effectors of proteolytic activity has been investigated by sedimentation velocity analysis and dynamic light-scattering measurements. The results provide the first direct evidence for conformational changes associated with the observed positive co-operativity in one component of the peptidylglutamylpeptide hydrolase activity as well as with the stimulation of peptidylglutamylpeptide hydrolase activities by MnCl2. In the latter case, there appears to be a correlation between changes in the shape of the molecule and the effect on activity. KCl and low concentrations of SDS may also act by inducing conformational changes within the complex. Sedimentation-velocity measurements also provide evidence for the formation of intermediates during dissociation of the complex by urea, guanidinium chloride or sodium thiocyanate. Dissociation of the complex either by these agents or by treatment at low pH leads to inactivation of its proteolytic components. The results suggest that activation and inhibition of the various proteolytic activities may be mediated by measurable changes in size and shape of the molecules.

Animals↗
PubMed1990

Three-dimensional structures of complexes of Lathyrus ochrus isolectin I with glucose and mannose: fine specificity of the monosaccharide-binding site.

The structure of the methyl-alpha-D-mannopyranoside-LOL I complex has been solved by the molecular replacement method using the refined saccharide-free LOL I coordinates as starting model. The methyl-alpha-D-mannopyranoside-LOL I complex was refined by simulated annealing using the program X-PLOR. The final R-factor value is 0.182 [Fo greater than 1 sigma(Fo)]. The isostructural methyl-alpha-D-glucopyranoside-LOL I complex was refined by X-Ray coupled energy minimization using the methyl-alpha-D-mannopyranoside-LOL I structure as a starting model to an R factor of 0.179 (all data). In both crystal forms, each dimer binds two molecules of sugar in pockets found near the calcium ions. The two saccharide moieties, which are in the C1 chair conformation, establish the same hydrogen bond pattern with the lectin. However, the van der Waals contacts are different between the O2, C2, C6, and O6 atoms of the two molecules and the backbone atoms of residues 208-211. Mannose, due to its axial C2 conformation, encloses the backbone atoms of the protein in a clamplike way. Van der Waals energy calculations suggest that this better complementarity of the mannoside molecule with the lectin could explain its higher affinity for isolectin I.

Binding Sites↗
PubMed1979

Complementarity vs. reduction as explanation of biological complexity.

The classical structure-function relation is presented as an example of an epistemological complementarity. Complementarity implies that a satisfactory explanation requires two modes of description, neither derivable from nor reducible to the other, as well as mutual incompatibility in a formal logical sense. Complementarity arose from the difficulty in describing conditional measurement processes in the language of causal microscopic laws of physics. Biological structure is associated with description in the language of physical laws, whereas biological function is associated with description of informational processes, i.e., measurement and control, that are complementary in the above sense. An explicit incompatibility between these two modes of description is that laws are expressed as rate-dependent equations, whereas informational processes are expressed as rate-independent nonintegrable constraints. The functional mode allows a simplification of structurally complex organization that is essential, not only for explanation, but for self-description at all levels of biological organization.

Animals↗
PubMed1996

Linguistic complexity of protein sequences as compared to texts of human languages.

A notion and a measure of linguistic complexity introduced earlier (Trifonov, 1990) were originally used for analysis of nucleotide sequences. This measure was shown to reflect multiplicity of codes (messages) of different natures superimposed in the sequences. Unlike human language texts, genetic texts are 'read' by cellular mechanisms in several different ways, each time using a different selection of the characters of the same text while skipping others (Trifonov, 1989). Human texts are read in one way only, sequentially and involving all characters (one code). The conceptual significance and essence of the idea on the multiplicity of overlapping codes in genetic sequences, as opposed to human languages, is discussed. The linguistic complexity technique allows a calculation to be made of the structural complexity of any linear sequence of characters irrespective of whether the text is cognized or presently undeciphered. The texts (sequences) are compared exclusively from the point of view of their structural complexity with no reference to the meaning of the texts which is beyond the scope of this article. Results of such a comparison of protein sequences with various texts, written in English, Italian and Welsh are presented. The human texts are found to be structurally simpler than genetic (protein) texts, reflecting, apparently, a difference in the reading modes: single code versus many codes.

Amino Acid Sequence↗
PubMed2007

MTO Schiff-base complexes: synthesis, structures and catalytic applications in olefin epoxidation.

Several Schiff-base ligands readily form complexes with methyltrioxorhenium(VII) (MTO) by undergoing a hydrogen transfer from a ligand-bound OH group to a ligand N atom. The resulting complexes are stable at room temperature and can be handled and stored in air without problems. Due to the steric demands of the ligands they display distorted trigonal-bipyramidal structures in the solid state, as shown by X-ray crystallography, with the O(-) moiety binding to the Lewis acidic Re atom and the Re-bound methyl group being located either in cis or trans position to the Schiff base. In solution, however, the steric differences seem not to be maintained, as can be deduced from (17)O NMR spectroscopy. Furthermore, the Schiff-base ligands exchange with donor ligands. Nevertheless, the catalytic behaviour is influenced significantly by the Schiff bases coordinated to the MTO moiety, which lead either to high selectivities and good activities or to catalyst decomposition. A large excess of ligand, in contrast to the observations with aromatic N-donor ligands, is detrimental to the catalytic performance as it leads to catalyst decomposition.

Journal Article↗
PubMed2006

'Fractional recovery' analysis of a presynaptic synaptotagmin 1-anchored endocytic protein complex.

BACKGROUND: The integral synaptic vesicle protein and putative calcium sensor, synaptotagmin 1 (STG), has also been implicated in synaptic vesicle (SV) recovery. However, proteins with which STG interacts during SV endocytosis remain poorly understood. We have isolated an STG-associated endocytic complex (SAE) from presynaptic nerve terminals and have used a novel fractional recovery (FR) assay based on electrostatic dissociation to identify SAE components and map the complex structure. The location of SAE in the presynaptic terminal was determined by high-resolution quantitative immunocytochemistry at the chick ciliary ganglion giant calyx-type synapse. METHODOLOGY/PRINCIPLE FINDINGS: The first step in FR analysis was to immunoprecipitate (IP) the complex with an antibody against one protein component (the IP-protein). The immobilized complex was then exposed to a high salt (1150 mM) stress-test that caused shedding of co-immunoprecipitated proteins (co-IP-proteins). A Fractional Recovery ratio (FR: recovery after high salt/recovery with control salt as assayed by Western blot) was calculated for each co-IP-protein. These FR values reflect complex structure since an easily dissociated protein, with a low FR value, cannot be intermediary between the IP-protein and a salt-resistant protein. The structure of the complex was mapped and a blueprint generated with a pair of FR analyses generated using two different IP-proteins. The blueprint of SAE contains an AP180/X/STG/stonin 2/intersectin/epsin core (X is unknown and epsin is hypothesized), and an AP2 adaptor, H-/L-clathrin coat and dynamin scission protein perimeter. Quantitative immunocytochemistry (ICA/ICQ method) at an isolated calyx-type presynaptic terminal indicates that this complex is associated with STG at the presynaptic transmitter release face but not with STG on intracellular synaptic vesicles. CONCLUSIONS/SIGNIFICANCE: We hypothesize that the SAE serves as a recognition site and also as a seed complex for clathrin-mediated synaptic vesicle recovery. The combination of FR analysis with quantitative immunocytochemistry provides a novel and effective strategy for the identification and characterization of biologically-relevant multi-molecular complexes.

Animals↗