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Third Example (third + example)

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Chemistry83%

Selected Abstracts

Efficient recognition of protein fold at low sequence identity by conservative application of Psi-BLAST: application,

JOURNAL OF MOLECULAR RECOGNITION, Issue 2 2005
F. J. Stevens
Abstract Based on a study involving structural comparisons of proteins sharing 25% or less sequence identity, three rounds of Psi-BLAST appear capable of identifying remote evolutionary homologs with greater than 95% confidence provided that more than 50% of the query sequence can be aligned with the target sequence. Since it seems that more than 80% of all homologous protein pairs may be characterized by a lack of significant sequence similarity, the experimental biologist is often confronted with a lack of guidance from conventional homology searches involving pair-wise sequence comparisons. The ability to disregard levels of sequence identity and expect value in Psi-BLAST if at least 50% of the query sequence has been aligned allows for generation of new hypotheses by consideration of matches that are conventionally disregarded. In one example, we suggest a possible evolutionary linkage between the cupredoxin and immunoglobulin fold families. A thermostable hypothetical protein of unknown function may be a circularly permuted homolog to phosphotriesterase, an enzyme capable of detoxifying organophosphate nerve agents. In a third example, the amino acid sequence of another hypothetical protein of unknown function reveals the ATP binding-site, metal binding site, and catalytic sidechain consistent with kinase activity of unknown specificity. This approach significantly expands the utility of existing sequence data to define the primary structure degeneracy of binding sites for substrates, cofactors and other proteins. Copyright © 2004 John Wiley & Sons, Ltd. [source]

Debt Neutrality and the Infinite,Lived Representative Consumer

JOURNAL OF PUBLIC ECONOMIC THEORY, Issue 4 2002
Bertrand Crettez
In this paper, we study the intertemporal equilibria of an infinite,lived representative agent model with public debt. We show that for a given path of government expenditures, there generally exists a continuum of equilibria depending on various debt policies. These equilibria are characterized by different paths of consumption and leisure. Two examples illustrate the results: in the first one consumption and leisure may converge to zero, in the second one consumption goes to infinity while leisure goes to its maximum value. In a third example with externalities à la Romer, the standard intertemporal equilibrium with zero public debt may be dominated by other intertemporal equilibria. [source]

Silica-supported biomimetic membranes

THE CHEMICAL RECORD, Issue 6 2004
Katsuhiko Ariga
Abstract The hybridization of lipid membranes with inorganic silica-based framework results in mechanically stable biomembrane mimics. This account describes three types of silica-based biomimetic membranes. As the first example, a Langmuir monolayer of dialkylalkoxysilane was polymerized and immobilized onto a porous glass plate. Permeability through the monolayer-immobilized glass was regulated by phase transition of the immobilized monolayer. In the second example, spherical vesicles covalently attached to a silica cover layer (Cerasome) were prepared. The Cerasome was stable enough to be assembled into layer-by-layer films without destruction of its vesicular structure. This material could be an example of the multicellular assembly. Mesoporous silica films densely filling peptide assemblies (Proteosilica) are introduced as the third example. The Proteosilica was synthesized as a transparent film through template sol-gel reaction using amphiphilic peptides. © 2004 The Japan Chemical Journal Forum and Wiley Periodicals, Inc. Chem Rec 3: 297,307; 2004: Published online in Wiley InterScience (www.interscience.wiley.com) DOI 10.1002/tcr.10071 [source]

Unusual hydrate stabilization in the two-dimensional layered structure of quinacrinium bis(2-carboxy-4,5-dichlorobenzoate) tetrahydrate, a proton-transfer compound of the drug quinacrine

ACTA CRYSTALLOGRAPHICA SECTION C, Issue 4 2009
Graham Smith
The crystal structure of the hydrated proton-transfer compound of the drug quinacrine [rac- N,-(6-chloro-2-methoxyacridin-9-yl)- N,N -diethylpentane-1,4-diamine] with 4,5-dichlorophthalic acid, C23H32ClN3O2+·2C8H3Cl2O4,·4H2O, has been determined at 200,K. The four labile water molecules of solvation in the structure form discrete ...O,H...O,H... hydrogen-bonded chains parallel to the quinacrine side chain, the two N,H groups of which act as hydrogen-bond donors for two of the water acceptor molecules. The other water molecules, as well as the acridinium H atom, also form hydrogen bonds with the two anion species and extend the structure into two-dimensional sheets. Between these sheets there are also weak cation,anion and anion,anion ,,, aromatic ring interactions. This structure represents the third example of a simple quinacrine derivative for which structural data are available but differs from the other two in that it is unstable in the X-ray beam due to efflorescence, probably associated with the destruction of the unusual four-membered water chain structures. [source]

cis,cis -Ceratospong­amide N,N -di­methyl­acet­amide hemisolvate in the presence of twinning

ACTA CRYSTALLOGRAPHICA SECTION C, Issue 6 2003
Akiko Asano
Ceratospong­amide (CS) is a potent inhibitor of secreted phospho­lipase A2, and cis,cis and trans,trans isomers, related with respect to the two proline amide bonds, are known. Crystals of cis,cis -CS were grown from N,N -di­methyl­acet­amide solution, giving the title compound, the cyclic ester of isoleucyl­oxazolinyl­phenyl­alanyl­prolyl­thia­zolyl­phenyl­alanyl­pro­line [cyclo(-Ile,Oxz,Phe,Pro,Thz,Phe,Pro-)] N,N -di­methyl­acet­amide hemisolvate, C41H49N7O6S·0.5C4H9NO. The structure is the third example of cis,cis -CS to be investigated and comprises twinned crystals, in which the a and b axes are interchanged. The ratio of co-existing twin crystals is approximately 50%. The peptide has a `saddle-like' structure and is very similar to previously reported structures of cis,cis -CS, which implies that the structure of cis,cis -CS is very stable in spite of differences in crystallization conditions. [source]

4-Fluorophenylglycine as a Label for 19F NMR Structure Analysis of Membrane-Associated Peptides

CHEMBIOCHEM, Issue 11 2003
Sergii Afonin
Abstract The non-natural amino acid 4-fluorophenylglycine (4F-Phg) was incorporated into several representative membrane-associated peptides for dual purpose. The 19F-substituted ring is directly attached to the peptide backbone, so it not only provides a well-defined label for highly sensitive 19F NMR studies but, in addition, the D and L enantiomers of the stiff side chain may serve as reporter groups on the transient peptide conformation during the biological function. Besides peptide synthesis, which is accompanied by racemisation of 4F-Phg, we also describe separation of the epimers by HPLC and removal of trifluoroacetic acid. As a first example, 18 different analogues of the fusogenic peptide "B18" were prepared and tested for induction of vesicle fusion; the results confirmed that hydrophobic sites tolerated 4F-Phg labelling. Similar fusion activities within each pair of epimers suggest that the peptide is less structured in the fusogenic transition state than in the helical ground state. In a second example, five doubly labelled analogues of the antimicrobial peptide gramicidin S were compared by using bacterial growth inhibition assays. This cyclic ,-sheet peptide could accommodate both L and D substituents on its hydrophobic face. As a third example, we tested six analogues of the antimicrobial peptide PGLa. The presence of d- 4F-Phg reduced the biological activity of the peptide by interfering with its amphiphilic ,-helical fold. Finally, to illustrate the numerous uses of l- 4F-Phg in 19F NMR spectroscopy, we characterised the interaction of labelled PGLa with uncharged and negatively charged membranes. Observing the signal of the free peptide in an aqueous suspension of unilamellar vesicles, we found a linear saturation behaviour that was dominated by electrostatic attraction of the cationic PGLa. Once the peptide is bound to the membrane, however, solid-state 19F NMR spectroscopy of macroscopically oriented samples revealed that the charge density has virtually no further influence on the structure, alignment or mobility of the peptide. [source]