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PubMed2005

Equilibrium partitioning model applied to RDX-halide adduct formation in electrospray ionization mass spectrometry.

An equilibrium partitioning model is applied for the first time to the sequential formation of 1:1 and then 2:1 adducts between the high explosive cyclo-1,3,5-trimethylene-2,4,6-trinitramine (RDX) and halide anions fluoride, chloride, bromide, and iodide in electrospray ionization interface (ESI) mass spectrometry. The equilibrium partitioning model is developed and model calculations are presented to demonstrate the generic behavior of the system, which is in qualitative agreement with the observed changes in 1:1 (RDX-halide) and 2:1 (RDX-halide) responses in ESI-MS. The model is successfully applied to the experimental data with the use of octanol-water partitioning coefficients to predict interior-to-surface partitioning behavior of the complexes in droplets formed in the ESI. The data and model suggest that the significantly more hydrophobic 2:1 complexes are readily observed in ESI-MS, even though their formation constants may be several orders of magnitude less than that of the 1:1 complex. Structures for RDX-halide 1:1 and 2:1 complexes are proposed based on ion-dipole attractions and destabilizing dipole-dipole interactions.

Journal Article↗
PubMed2003

Synthesis and characterization of two polymorphic crystalline phases and an amorphous powder of nickel(II) bisimidazolate.

Nickel(II) bisimidazolate is polymorphic. Depending on the synthetic strategy adopted, two crystalline phases (alpha- and beta-Ni(im)(2)) or an amorphous material of the same composition can be prepared. The thermodynamically stable alpha-Ni(im)(2) phase, which can be prepared in water at elevated temperatures, contains a two-dimensional polymer (of nearly square meshes) with square-planar NiN(4) chromophores and exo-bidentate imidazolate ligands bridging nickel atoms that are ca. 5.73 A apart. The beta-Ni(im)(2) phase can be kinetically stabilized at lower temperatures, but the structural complexity and the lack of single crystals prevented its full structural characterization, even in the presence of an indexed powder diffraction pattern. The spectroscopic features of these crystalline phases are compared with those of the amorphous material.

Journal Article↗
PubMed2005

A solid-state NMR method for solution of zeolite crystal structures.

Since zeolites are notoriously difficult to prepare as large single crystals, structure determination usually relies on powder X-ray diffraction (XRD). However, structure solution (i.e., deriving an initial structural model) directly from powder XRD data is often very difficult due to the diffraction phase problem and the high degree of overlap between the individual reflections, particularly for materials with the structural complexity of most zeolites. Here, we report a method for structure determination of zeolite crystal structures that combines powder XRD and nuclear magnetic resonance (NMR) spectroscopy in which the crucial step of structure solution is achieved using solid-state (29)Si double-quantum dipolar recoupling NMR, which probes the distance-dependent dipolar interactions between naturally abundant (29)Si nuclei in the zeolite framework. For two purely siliceous zeolite blind test samples, we demonstrate that the NMR data can be combined with the unit cell parameters and space group to solve structural models that refine successfully against the powder XRD data.

Journal Article↗
PubMed2001

Preparation and structural properties of 7,8-dioxa[6]helicenes and 7a,14c-dihydro-7,8-dioxa[6]helicenes.

The potentially chiral 7,8-dioxa[6]helicenes 1-1c have been prepared by oxidation of their precursors the 7a,14c-dihydro-7,8-dioxa[6]helicenes 3. The crystal structure determination of 3b cis-7a,14c-dihydro-3,12-dibromo-7,8-dioxa[6]helicene unambiguously confirms the cis configuration of the 7a,-14c hydrogens in compounds 3 as previously implied from NMR measurements and also shows that 3b crystallizes in a chiral conformation in the solid state. Selective deuteration of the sterically crowded 1,14 positions of 7,8-dioxa[6]helicene 1 influenced the crystal structure. The deuterium labeled compound D2-1 exhibits a disordered structure, whereas 1 had been found to crystallize in a complex structure which can be described as an analogous partly ordered modulated superstructure. When dehydrogenation of compound 3 to obtain compound 1 was attempted, harsh synthetic conditions gave the unexpected halogenated compounds 5-chloro-7,8-dioxa[6]helicene 1c and cis-7a,14c-dibromo-7,8-dioxa[6]helicene 3c. Compounds 1d and 3b were identified by solving their crystal structure.

Journal Article↗
PubMed2005

Colloidal nanocrystal synthesis and the organic-inorganic interface.

Colloidal nanocrystals are solution-grown, nanometre-sized, inorganic particles that are stabilized by a layer of surfactants attached to their surface. The inorganic cores possess useful properties that are controlled by their composition, size and shape, and the surfactant coating ensures that these structures are easy to fabricate and process further into more complex structures. This combination of features makes colloidal nanocrystals attractive and promising building blocks for advanced materials and devices. Chemists are achieving ever more exquisite control over the composition, size, shape, crystal structure and surface properties of nanocrystals, thus setting the stage for fully exploiting the potential of these remarkable materials.

Journal Article↗
PubMed1998

Correlation between requirement for SecA during export and folding properties of precursor polypeptides.

The structural complexity of a ligand in association with the molecular chaperones SecB and SecA was investigated using three species of precursor maltose-binding protein, which differ in their stability as a result of an amino acid substitution in each that affects the rate of folding of the polypeptide. In the presence of high concentrations of both SecB and SecA, the precursors were translocated in vitro with indistinguishable kinetics. However, when SecA was limiting, the translocation was more rapid for precursor species, which had lower stability in the native state relative to the stability of the wild-type precursor. We propose that, when in complex with SecB, precursors can form an element of tertiary structure and that these tertiary contacts are blocked when SecA is bound.

Adenosine Triphosphatases↗
PubMed2005

From nonpeptide toward noncarbon protease inhibitors: metallacarboranes as specific and potent inhibitors of HIV protease.

HIV protease (PR) represents a prime target for rational drug design, and protease inhibitors (PI) are powerful antiviral drugs. Most of the current PIs are pseudopeptide compounds with limited bioavailability and stability, and their use is compromised by high costs, side effects, and development of resistant strains. In our search for novel PI structures, we have identified a group of inorganic compounds, icosahedral metallacarboranes, as candidates for a novel class of nonpeptidic PIs. Here, we report the potent, specific, and selective competitive inhibition of HIV PR by substituted metallacarboranes. The most active compound, sodium hydrogen butylimino bis-8,8-[5-(3-oxa-pentoxy)-3-cobalt bis(1,2-dicarbollide)]di-ate, exhibited a K(i) value of 2.2 nM and a submicromolar EC(50) in antiviral tests, showed no toxicity in tissue culture, weakly inhibited human cathepsin D and pepsin, and was inactive against trypsin, papain, and amylase. The structure of the parent cobalt bis(1,2-dicarbollide) in complex with HIV PR was determined at 2.15 A resolution by protein crystallography and represents the first carborane-protein complex structure determined. It shows the following mode of PR inhibition: two molecules of the parent compound bind to the hydrophobic pockets in the flap-proximal region of the S3 and S3' subsites of PR. We suggest, therefore, that these compounds block flap closure in addition to filling the corresponding binding pockets as conventional PIs. This type of binding and inhibition, chemical and biological stability, low toxicity, and the possibility to introduce various modifications make boron clusters attractive pharmacophores for potent and specific enzyme inhibition.

Aspartic Acid Endopeptidases↗
PubMed1992

Predicting antisense oligonucleotide inhibitory efficacy: a computational approach using histograms and thermodynamic indices.

Antisense oligonucleotides (ASOs) are designed to bind to a specific mRNA and selectively suppress its translation. To facilitate selection of optimal ASO targets, we have developed three thermodynamic indices to evaluate putative structural complexes important in ASO action. These indices are: a secondary structure score (Sscore), which estimates the strength of local mRNA secondary structures at the ASO target site; a duplex score (Dscore), which estimates the delta Gformation for the ASO:mRNA target sequence duplex; and a competition score (Cscore), which is the difference between the Dscore and the Sscore. We also present two histograms to graphically display these indices from different regions of the mRNA. The indices are compared to the inhibition reported in five studies of ASO-mediated suppression of gene expression. The Dscore is the most consistent predictor of ASO efficacy in four of the five studies (r2 from 0.44 to 0.99), while the results of the fifth study could not be predicted by any thermodynamic or physical index. Thus the Dscores and their histogram may prove useful in selection of ASO targets.

Algorithms↗
PubMed2003

Evolutionary transformations of myoseptal tendons in gnathostomes.

Axial undulations in fishes are powered by a series of three-dimensionally folded myomeres separated by sheets of connective tissue, the myosepta. Myosepta have been hypothesized to function as transmitters of muscular forces to axial structures during swimming, but the difficulty of studying these delicate complex structures has precluded a more complete understanding of myoseptal mechanics. We have developed a new combination of techniques for visualizing the three-dimensional morphology of myosepta, and here we present their collagen-fibre architecture based on examination of 62 species representing all of the major clades of notochordates. In all gnathostome fishes, each myoseptum bears a set of six specifically arranged tendons. Because these tendons are not present outside the gnathostomes (i.e. they are absent from lampreys, hagfishes and lancelets), they represent evolutionary novelties of the gnathostome ancestor. This arrangement has remained unchanged throughout 400 Myr of gnathostome evolution, changing only on the transition to land. The high uniformity of myoseptal architecture in gnathostome fishes indicates functional significance and may be a key to understanding general principles of fish swimming mechanics. In the design of future experiments or biomechanical models, myosepta have to be regarded as tendons that can distribute forces in specific directions.

Animals↗
PubMed2006

Comparative analysis reveals no consistent association between the secondary structure of the 3'-untranslated region of dengue viruses and disease syndrome.

A comparative analysis was performed of the 3'-untranslated region (UTR) of Dengue virus (DENV) sampled from Bangkok, Thailand, over a 30 year period and representing all four serotypes. Considerable genetic variation was observed both within and among serotypes. Notably, a full-length version of the critical 3'-long stable hairpin structure was absent from some isolates, suggesting the occurrence of complex structural interactions within the 3'-UTR, including the influence of upstream mutations. The Thai sequences were then combined with 61 globally sampled isolates of DENV taken from patients with either dengue fever or severe dengue disease. No consistent association was found between 3'-UTR secondary structure and the clinical outcome of DENV infection, although some evidence for a trend in this direction was observed in DENV-2. It was concluded that the 3'-UTR is not the sole determinant of DENV virulence in nature, although variation in secondary structure may greatly influence viral fitness.

3' Untranslated Regions↗
PubMed1983

The behavioral effects of lesions of the corpus striatum: a review.

Many investigators have examined the behavioral effects of lesions and/or stimulation of the corpus striatum, in a variety of species. This paper is a review of the work seeking the possible links that exist between overt behaviors and physiological structures in the brain. The corpus striatum is a very complex structure, and many of the nuclei associated with it have currently remained enigmatic with regard to function. The studies cited reflect the attempts of many individuals in finding explanations of striatal functioning.

Animals↗
PubMed1990

The effective learning of spatio temporal concepts of human structure.

The recent availability of increasingly powerful and user friendly computers is making a noticeable impact in the field of medical education. Over the past year, the power of the computer is being harnessed here in the field of anatomy to enable medical and dental students to learn the subject more effectively. Machines with excellent graphics, text and animation capabilities have made it possible to allow students to comprehend structural complexity as seen in gross anatomy or, temporal alterations of structure as seen in embryology by the use of computer based, tutorial style or self paced interactive style of learning. Positive student response to sample learning packages has encouraged the undertaking of courseware development for future use at computer workstations.

Anatomy↗
PubMed2006

[Synthetic study of nucleoside antibiotics].

Some of nucleoside antibiotics include complex structures as well as sensitive functionality, which are challenging targets for organic chemists. Among complex nucleoside antibiotics, there are also good drug candidates because they possess a variety of interesting biological properties. Herbicidin B and fully protected tunicaminyluracil, which were undecose nucleoside antibiotics, were synthesized using a samarium diiodide (SmI(2)) mediated aldol reaction with the use of alpha-phenylthioketones as enolate sources. The characteristics of the SmI(2)-mediated aldol reaction are that the enolate can be regioselectively generated and the aldol reaction proceeds under near neutral condition. This reaction is proved to be a powerful reaction for the synthesis of complex nucleoside antibiotics. The synthesis of caprazol, the core structure of caprazamycins, was conducted by the strategy including beta-selective ribosylation without using a neighboring group participation and the construction of a diazepanone by a modified reductive amination. Our synthetic route would provide a range of key analogues with partial structures to define the pharmacophore, which can be a lead for the development of more effective anti-bacterial agents.

Anti-Bacterial Agents↗
PubMed2004

Chemistry and biodiversity.

Complex structures produced by noncatalyzed multi-step chemical processes must have highly probable origins and assembly routes. Within any frame of reference, life is easily the most-complex self-assembled structure known to man. It is not possible to calculate a finite time for biogenesis by statistical mechanics, but the abundance of life makes it reasonable to propose an accelerating principle of nature that naturally shortened the time for cell formation to a billion years or less. This hypothetical principle, which I have called valence-orbital bias, is thought to be responsible for the discrepancy between statistics and observation, and carries with it, as a conditio sine qua non, multiple origins of life.The new concept resolves the differences between the predictions based on statistical mechanics and the relatively rapid appearance of life during the post-accretion period. It suggests as well that species and variants, the units of propagation, may also have been the units of evolution. Produced in profusion by chemistry, the origins are culled by natural selection, whereby failure means extinction, not adaptation. Biodiversity, thus, becomes a direct consequence of chemistry without positive feedback from the environment and without a constructive role for mutation.

Animals↗
PubMed2001

On the Complexity of Additive Clustering Models.

Additive clustering provides a conceptually simple and potentially powerful approach to modeling the similarity relationships between stimuli. The ability of additive clustering models to accommodate similarity data, however, typically arises through the incorporation of large numbers of parameterized clusters. Accordingly, for the purposes of both model generation and model comparison, it is necessary to develop quantitative evaluative measures of additive clustering models that take into account both data-fit and complexity. Using a previously developed probabilistic formulation of additive clustering, the Bayesian Information Criterion is proposed for this role, and its application demonstrated. Limitations inherent in this approach, including the assumption that model complexity is equivalent to cluster cardinality, are discussed. These limitations are addressed by applying the Laplacian approximation of a marginal probability density, from which a measure of cluster structure complexity is derived. Using this measure, a preliminary investigation is made of the various properties of cluster structures that affect additive clustering model complexity. Among other things, these investigations show that, for a fixed number of clusters, a model with a strictly nested cluster structure is the least complicated, while a model with a partitioning cluster structure is the most complicated. Copyright 2001 Academic Press.

Journal Article↗
PubMed2005

Enzymatic hydrolysis of luminal coronary glycosidic structures uncovers their role in sensing coronary flow.

Endothelial luminal glycocalyx (ELG) is a multifunctional complex structure made off of a diversity of glycosilated proteins, and glycosaminoglycans (GAG). Coronary ELG may participate as a sensor of coronary flow (CF) to induce inotropic and dromotropic effects. In isolated perfused guinea pig heart we tested the role of glycosidic groups of glycans bound to proteins and GAG of the ELG on CF-induced inotropic and dromotropic effects. To study the role of saccharide related groups of certain glycans, they were removed by selective enzyme hydrolysis or bound to a selective plant lectin. CF-induced positive inotropic and positive dromotropic control curves were obtained and the effects of intracoronary infusion of enzyme or lectin determined. The analyzed groups were as follow: 1) Fucosidase enzyme and Ulex europeasus lectin; hydrolysis and binding respectively (H&Br) to alpha-linked fucosyl related groups. 2). Endoglycanase-H and Lycopersicon esculentum (H&Br to N-linked beta-1,3GlcNAc related groups). 3) O-glycanase and Arachis hypogea (H&Br to O-linked beta-Gal1, 3GalNac related groups). 4) Sialidase and Maackia amurensis (H&Br to neuraminic acid related groups). In treatments 1-3 both. lectin and corresponding enzyme, equally depressed CF-positive dromotropic effects without affecting positive inotropic effects. In treatment 4 both lectin and enzyme equally depressed CF-positive inotropic effects without dromotropic effects. The differential role of GAG hyaluran or heparan groups on CF-positive inotropism and positive dromotropism respectively was shown. Infusing hyaluranidase removed hyaluran that solely inhibited CF- inotropism while removal of heparan with heparinase solely inhibited CF-dromotropism. Only the effects of hyaluronidase were reversed infusing hyaluronidate. Our results indicate glycans of ELG are elements of complex multimolecular sensors of coronary flow.

Animals↗
PubMed2004

A structural and dynamic model for the interaction of interleukin-8 and glycosaminoglycans: support from isothermal fluorescence titrations.

Binding of interleukin-8 (IL-8) to glycosaminoglycans (GAGs) on the surface of endothelial cells is crucial for the recruitment of neutrophils to an inflammatory site. Deriving structural knowledge about this interaction from in silico docking experiments has proved difficult because of the high flexibility and the size of GAGs. Therefore, we developed a docking method that takes into account ligand and protein flexibility by running approximately 15,000 molecular dynamics simulations of the docking event with different initial orientations of the binding partners. The method was shown to successfully reproduce the residues of basic fibroblast growth factor involved in GAG binding. Docking of a heparin hexasaccharide to IL-8 gave an interaction interface involving the basic residues His18, Lys20, Arg60, Lys64, Lys67, and Arg68. By subjecting IL-8 single-site mutants, in which these amino acids were replaced by alanine, to isothermal fluorescence titrations, the affinities for heparin were determined to be wtIL-8 > IL-8(H18A) >> IL-8(R68A) > IL-8(K67A) >> IL-8(K20A) > IL-8(R60A) >> IL-8(K64A). A comparison with the binding energies calculated from the model revealed high values for wtIL-8 and the H18A mutant and significantly lower but similar energies for the remaining mutants. Connecting the two fully sulfated hexasaccharides bound to each of the two IL-8 monomers in the dimeric chemokine by an N-acetylated dodecasaccharide gave a complex structure in which the GAG molecule aligned in a parallel fashion to the N-terminal alpha-helices of IL-8 like a horseshoe. A 5-ns molecular dynamics simulation of this complex confirmed its structural stability and revealed a reorientation in both binding sites where a disaccharide became the central binding unit. Isothermal fluorescence titration experiments using differently sulfated heparin disaccharides confirmed that a single disaccharide can indeed bind IL-8 with high affinity.

Amino Acid Substitution↗
PubMed2004

Structural and functional changes in gastric epithelium in Helicobacter pylori-associated chronic gastroduodenal pathologies.

Complex structural analysis of the gastric mucosa was carried out in patients with Helicobacter pylori-associated chronic gastroduodenal ulcers, chronic gastritis, and vibration gastropathy. Microscopic examination showed stereotypical changes in the epithelium in all diseases: degeneration, focal intestinal metaplasia, dysplasia, and glandular atrophy. The severity of these changes depended on the disease entity. The most typical ultrastructural modifications of epitheliocytes were damage to the apical plasmalemma, heterogeneity of the secretory compartment of the cytoplasm, dilatation of the cytoplasmic reticulum, vacuolation, and signs of cytolysis. Plastic reactions of the gastric epithelium reflected disproportional changes in all cell metabolites caused by increased proliferative activity of the epithelium under conditions of uneven inhibition of intracellular protein synthesis.

Adolescent↗