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Structural Motif (structural + motif)
Kinds of Structural Motif Selected AbstractsArylimidovanadium(V) Complexes for a Tridendritic Centrosymmetric Structural Motif or Axial Chirality,ANGEWANDTE CHEMIE, Issue 1 2010Toshiyuki Moriuchi Dr. Wahlweise: Bei der Eintopfreaktion von Anilinderivaten mit VO(OiPr)3 in Gegenwart von NaH entsteht entweder dreikerniges Arylimidovanadium(V)-triisopropoxid mit einer tridendritischen zentrosymmetrischen Struktur (links im Bild) oder axial-chirales zweikerniges Arylimidovanadium(V)-triisopropoxid (rechts), bei dem die Selbstorganisation eine hoch geordnete Molekülanordnung im Festkörper zur Folge hat. [source] ChemInform Abstract: Infinite Gold Zig-Zag Chains as Structural Motif in Ca3Au3In , A Ternary Ordered Variant of the Ni4B3 Type.CHEMINFORM, Issue 11 2008Ihor R. Muts Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a "Full Text" option. The original article is trackable via the "References" option. [source] Predesigned Hexanuclear CuII and CuII/NiII Metallacycles Featuring Six-Node Metallacoronand Structural Motifs,ANGEWANDTE CHEMIE, Issue 38 2009Feng Li Dr. Dreimal Metall im Doppelpack: Mit einem 1,4-Aryl-verknüpften Bis(triketonato)-Liganden, der eine gebogene Konformation einnehmen kann, bilden CuII oder CuII und NiII ungewöhnliche sechskernige Cu6,nNinL3 -Metallacoronandstrukturen (siehe Bild; n=0, 3). Innerhalb der sechskernigen CuII -Spezies treten zwischen benachbarten Paaren von Metallionen starke antiferromagnetische Wechselwirkungen auf. [source] ChemInform Abstract: Competition Among fcc-Like, Double-Layered Flat, Tubular Cage, and Close-Packed Structural Motifs for Medium-Sized Aun (n = 21,28) ClustersCHEMINFORM, Issue 26 2008Dongxu Tian Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a "Full Text" option. The original article is trackable via the "References" option. [source] ChemInform Abstract: Condensed [PtIn3/3] and [PtIn6/6] Units as Structural Motifs in ScPtIn, TbPtIn, and HoPtIn.CHEMINFORM, Issue 6 2001Yaroslav V. Galadzhun Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a "Full Text" option. The original article is trackable via the "References" option. [source] Diboryl and Diboranyl Porphyrin Complexes: Synthesis, Structural Motifs, and Redox Chemistry: Diborenyl Porphyrin or Diboranyl Isophlorin?CHEMISTRY - A EUROPEAN JOURNAL, Issue 21 2007Andre Weiss Dr. Abstract The syntheses of diboryl porphyrin complexes [(BX2)2(ttp)] (ttp: dianion of tetra- p -tolylporphyrin) and the BB single-bond diboranyl complexes [(BX)2(ttp)] (X=F, Cl, Br, I) are given. The former are prepared from the reactions of BX3 (X=F, Cl) with [Li2(ttp)] and the latter from B2Cl4 (X=Cl), the reaction of SbF3 with [(BCl)2(ttp)] (for X=F), and, in the cases of X=Br or I, in a remarkable reductive coupling reaction resulting directly from the reaction of BBr3 or BI3 with [Li2(ttp)]. Density functional theory (DFT) calculations on the thermochemical parameters for the reductive coupling reactions (and those calculated for related dipyrromethene complexes) indicate that a combination of the reducing ability of bromide and iodide ions combined with the constrained environment of the porphyrin ligand contribute to the driving force. The reductive coupling is also observed in the reaction of [(BCl2)2(ttp)] with nBuLi to give [(BnBu)2(ttp)], which was characterised crystallographically. The reaction of [(BCl)2(ttp)] with catechol gives a boron catecholato porphyrin complex, [B2(O2C6H4)(ttp)]. Chloride abstraction from [(BCl)2(ttp)] gives the planar dication [B2(ttp)]2+, whereas chemical reduction of [(BCl)2(ttp)] by using magnesium anthracenide gives a neutral complex, [B2(ttp)], in which the TTP ligand has been reduced by two electrons to give an unusual example of an isophlorin complex. The cationic and neutral complexes [B2(ttp)]2+ and [B2(ttp)] were characterised through a combination of spectroscopic data that is supported by DFT calculations on the porphine analogues. [source] Structural motifs in ,-pyridyl- and ,-furylcinnamic acid assemblies, A molecular modeling studyINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 2 2001I. Pálinkó Abstract The aggregation properties of stereoisomeric 2-(3,-furyl)-3-phenylpropenoic acids (FU3E, FU3Z, ,-furylcinnamic acids) and 2-(4,-pyridyl)-3-phenylpropenoic acids (PY4E, PY4Z, ,-pyridylcinnamic acids) were studied by the PM3 semiempirical quantum chemical method. Calculations revealed that (aromatic)CH,N(O) hydrogen bonds made possible the attachment of dimer units; thus, virtually infinite chains can be built out of FU3Z, PY4E, and PY4Z. The energy-minimized structure had zig-zag configuration. PY4Z dimers allowed the formation of ribbonlike network; however, the number of structural units could not be increased infinitely. One of the furyl derivatives (FU3E) could not be stabilized either in the ribbon or the chain form; however, (aromatic)CH,, or (aromatic),,(aromatic), interactions contribute to the packing pattern of the two dimers. © 2001 John Wiley & Sons, Inc. Int J Quantum Chem 84: 269,275, 2001 [source] Structural motifs in the maturation process of peptide hormones.JOURNAL OF PEPTIDE SCIENCE, Issue 2 2002The somatostatin precursor. Abstract Synthetic peptides reproducing both the native domain around the dibasic cleavage site of pro-somatostatin, and mutated sequences thereof, previously assayed in site-directed mutagenesis experiments, have been studied by CD in different solvent systems, such as water, TFE/H2O, MeCN/H2O and aqueous SDS, in order to ascertain the ability of each solvent to stabilize secondary structural motifs. A combination of deconvolution methods and empirical calculations, that allow subtraction of the contributions due to unordered structures from the spectra, suggests that mainly two distinct families of ordered conformers containing ,-helix and/or structurally different ,-turns are present in solution, the relative stability of the different conformers depending on the nature of the solvent. The presence of ,-turns is in line with a previous NMR study in DMSO and DMSO/H2O. Comparison of the CD spectra in aqueous SDS of peptides undergoing processing with a sequence not processed in vivo shows that only the latter possesses a stable and detectable ,-helix population. This observation suggests that the structuration involving ,-turns but no ,-helix, which was observed by CD both in SDS and organic solvent/H2O mixtures at high water contents, might be of biological significance. The similarity of this structuration to molecular models obtained from NMR data in DMSO and DMSO/H2O is discussed. Copyright © 2002 European Peptide Society and John Wiley & Sons, Ltd. [source] Synthesis and Characterization of a Series of New Luminescent NHC-Coordinated AuI,AgI Tetra- and Polymetallic Complexes Containing Benzoate-Bridged Ag2 DimersEUROPEAN JOURNAL OF INORGANIC CHEMISTRY, Issue 13 2009Amit K. Ghosh Abstract The reaction of [Au(CH3impy)2]PF6 (2), with substituted silver benzoate salts bearing different halide substituents produced a series of new mixed-metal species having two different structural motifs. One structural motif contains discrete tetrametallic Ag2Au2 diamond cores, whereas the other motif contains the same tetrametallic diamond core interconnected by benzoate-bridged silver dimers to form polymers. All the complexes are substitution-inert and stable both in the solid state as well as in solution. We also report the synthesis of oxidative addition products of [Au(CH3impy)2]PF6, which were also obtained during our attempts to oxidize the above-mentioned multimetallic assembly with bromine and iodine. Compounds 3,7 are intensely luminescent in frozen acetonitrile solution, but surprisingly no luminescence is observed at room temperature. All the complexes were completely characterized by 1H, 13C NMR, electronic absorption, emission spectroscopy, elemental analysis and X-ray crystallography. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2009) [source] Bulky Pyrazolate-Based Compartmental Ligand Scaffolds: Encapsulation of an Edge-Sharing Cu6O2 Bitetrahedral Core,EUROPEAN JOURNAL OF INORGANIC CHEMISTRY, Issue 34 2008Anna Sachse Abstract Upon reaction with Cu(OAc)2·H2O, pyrazole-based ligands with two appended imine chelate arms in the 3- and 5-positions of the pyrazole and bulky substituents at the imine-N yield Cu6 complexes [L2Cu6(,-OAc)6(,4 -O)2] (1a,b). They feature an unusual {Cu6(,4 -O)2}-bitetrahedral core, only the second example of this structural motif. ESI mass spectrometric and UV/Vis data confirm that the Cu6 complexes stay intact in solution, and magnetic and high-field EPR measurements reveal an S = 0 ground state with the first excited triplet at ,E , 95 cm,1. Although the new hexanuclear systems are too complex for deriving all individual exchange constants from powder susceptibility data, a rough idea of the complete energy level spectrum could be obtained.(© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2008) [source] Electronic Structure of Linearly Coordinated EQ Complexes of the Type [(N3N)W(EQ)] [N3N = N(CH2CH2NSiMe3)3; E = P, As, Sb, Bi; Q = O, S, Se, Te]: A DFT StudyEUROPEAN JOURNAL OF INORGANIC CHEMISTRY, Issue 17 2007Gábor Balázs Abstract Density functional theory (DFT) calculations were carried out on the terminal EQ complexes [(N3N)W(EQ)] {N3N = N(CH2CH2NSiMe3)3; E = P, As, Sb, Bi; Q = O, S, Se Te} to clarify the bonding situation within the linear Nax,W,E,Q core. This unusual structural motif gives rise to a bonding arrangement in which the ,-electron density is delocalised over the three atoms of the W,E,Q unit. Fragment calculations and natural bond order (NBO) data indicated that the ,-bonding component of the Nax,W,E,Q unit comprises two occupied , orbitals, while the , component of bonding comprises two sets of degenerate , orbitals. In general, the , orbitals of the Nax,W,E,Q core are higher in energy compared to the , orbitals. The phosphorus monoxide (EQ = PO) complexes provide an exception to this rule, with the 1, orbitals of the W,P,O core lower in energy than the , orbitals. Generally, as the atomic number of either the pnicogen (E) or chalcogen (Q) atom increases the extent of ,-orbital delocalisation decreases, whereas the ,-orbital delocalisation increases. Fractional bond orders and Wiberg bond indices were used to establish whether localisation of the ,-electron density gives rise to a W,E or an E,Q double or triple bond. Both methods indicate a W,E as well as an E,Q double bond. The ionic nature of the complexes were analysed by inspection of the Hirschfeld charge distribution which shows only a moderate ionic character. Exceptions are the pnicogen monoxide complexes, which are more ionic. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2007) [source] A Cyclic Fc,Histidine Conjugate: Synthesis and Properties , Interactions with Alkali Metal IonsEUROPEAN JOURNAL OF INORGANIC CHEMISTRY, Issue 5 2006Somenath Chowdhury Abstract The synthesis of the novel N,N, -(ferrocenophane-1,1,-diyldicarbonyl)-bridged histidine methyl ester 1 and of the acyclicbis(histidine methyl ester) derivative 3 are reported. The structure of 1 was studied in the solid state and in solution. The single-crystal structure of 1 shows that both proximal ferrocenyl (Fc) carbonyl groups are syn with respect to each other, which is a new structural motif for Fc,amino acid conjugates. This new syn conformation allows effective binding to alkali metal cations. Binding is evaluated by cyclic voltammetry monitoring the halfwave potential of the Fc group. Cation binding causes a shift to lower potential (Na+ > Li+ > K+, Cs+). Upon binding, compound 1 shows selectivity towards Na+ ions. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2006) [source] Tuning the Magnetic Properties of a Dinuclear Copper Complex: From Ferromagnetic to Antiferromagnetic CouplingEUROPEAN JOURNAL OF INORGANIC CHEMISTRY, Issue 2 2004Simon P. Foxon Abstract A novel structural motif in oxalate bridged copper(II) complexes has been prepared namely a metallamacrocyclic compound of the dinucleating ligand 1,3-bis[bis(2-pyridylmethyl)amino]benzene (= 1,3-tpbd). It could be demonstrated that the magnetic properties of copper(II) complexes of the 1,3-tpbd ligand can be adjusted from weakly ferromagnetic (J = +9.3 cm,1) to strongly antiferromagnetic [J = ,366(9) cm,1] by variation of the additional ligands (e.g. perchlorate, azide, oxalate etc.). (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2004) [source] Synthesis, Structure, and Reactivity of Novel Intramolecularly Coordinated Organolead(II) CompoundsEUROPEAN JOURNAL OF INORGANIC CHEMISTRY, Issue 19 2003Klaus Jurkschat Abstract The intramolecularly coordinated heteroleptic organolead(II) compounds {4- tBu-2,6-[P(O)(OEt)2]2C6H2}PbX (2, X = Cl; 3, X = SPh) have been synthesized. Single-crystal X-ray analyses reveal that both compounds adopt polymeric chain structures by intermolecular Pb,X···Pb bridges, a structural motif previously unknown for organolead(II) derivatives. Compound 2 reacts with lithium diisopropylamide, iPr2NLi, and lithium bis(trimethylsilyl)methane, (Me3Si)2CHLi, respectively, to provide in situ the corresponding organolead(II) compounds {4- tBu-2,6-[P(O)(OEt)2]2C6H2}PbX (4, X = iPr2N; 5, X = (Me3Si)2CH], which were identified by NMR spectroscopy but could not be obtained as analytically pure substances. Attempts to isolate the intramolecularly coordinated organolead(II) hexafluorophosphate {4- tBu-2,6-[P(O)(OEt)2]2C6H2}Pb+PF6, from the reaction of 2 with TlPF6 also failed. Instead, the unprecedented salt [{5- tBu-1,3-[P(O)(OEt)2]2C6H3}4·(Pb2F)] [PF6]3·4THF (6) was obtained, in which the [(Pb,F,Pb)]3+ cation is stabilized by eight intermolecular P=O,Pb interactions. Compound 6 was characterized by single-crystal X-ray analysis and electrospray mass spectrometry. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2003) [source] Permanganate Oxidation Revisited: Synthesis of 3-Deoxy-2-uloses via Indium-Mediated Chain Elongation of CarbohydratesEUROPEAN JOURNAL OF ORGANIC CHEMISTRY, Issue 25 2010Christoph Schmölzer Abstract Application of the Barbier-type indium-mediated allylation method to suitable substrates offers access to carbohydrates bearing a terminal olefin moiety. The C,C bond forming reaction generates a defined stereochemistry of the new chiral center and tolerates a wide variety of starting aldehydes thus allowing modifications in the carbohydrate backbone. Further transformations of the alkene moiety via an environmentally benign and subtle controlled protocol using potassium permanganate gives rise to the structural motif of 3-deoxy-2-uloses in good yields. The final part of the reaction sequence focuses on the deprotection of the acetyl groups essential for the success of the oxidation step. The acidic and labile 3-deoxy position of the target molecule is prone to elimination applying standard deacetylation conditions and therefore demands derivatisation of the molecule. The introduction of a thioketal moiety using microwave conditions shows promising results and subsequent standard transformations are applicable leading to the desired products. [source] Synthesis and Structural Properties of New Oligodeoxynucleotide Analogues Containing a 2,,5,-Internucleotidic Squaryldiamide Linkage Capable of Formation of a Watson,Crick Base Pair with Adenine and a Wobble Base Pair with Guanine at the 3,-Downstream Junction SiteEUROPEAN JOURNAL OF ORGANIC CHEMISTRY, Issue 10 2004Kousuke Sato Abstract A TpT dimer analogue (U2,sq5,T), in which the 3,-5, phosphodiester linkage was replaced by a 2,-5, squaryldiamide linkage and the 5,-upstream T was replaced by a 3,-deoxyuridine, was synthesized in almost quantitative yield from diethyl squarate. This new dimer structural motif was designed to eliminate the squaryldiamide skeleton-induced overall strain in T3,sq5,T, previously incorporated into DNA fragments as a new TpT mimic, through the change in the connection mode from the 3,-5, linkage to a 2,-5, linkage. Spectral analyses of U2,sq5,T suggest that the overall structure of this dimer mimic is basically similar to that of TpT. A DNA 10mer 5,-d(CGCAU2,sq5,TAGCC)-3, incorporating this dimer was synthesized. From the CD analysis, it turned out that the overall structure of a DNA duplex of 5,-d(CGCAU2,sq5,TAGCC)-3,/3,-d(GCGTAATCGG)-5, is closer to that of the unmodified duplex than the DNA duplex of 5,-d(CGCAT3,sq5,TAGCC)-3,/3,-d(GCGTAATCGG)-5,. Interestingly, extensive Tm experiments suggest that d(CGCAU2,sq5,TAGCC)-3, exhibits intriguing inherent hybridization affinity not only for the completely complementary oligodeoxynucleotide 3,-d(GCGAATCGG)-5,, but also for 3,-d(GCGTAGTCGG)-5,, with a mismatched dG. The unique property of the 3,-downstream dT moiety of U2,sq5,T , the ability to recognize both dA and dG , was also supported by more detailed computational analysis of U2,sq5,T and TpT. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2004) [source] Evolutionary divergence of valosin-containing protein/cell division cycle protein 48 binding interactions among endoplasmic reticulum-associated degradation proteinsFEBS JOURNAL, Issue 5 2009Giacomo Morreale Endoplasmic reticulum (ER)-associated degradation (ERAD) is a cell-autonomous process that eliminates large quantities of misfolded, newly synthesized protein, and is thus essential for the survival of any basic eukaryotic cell. Accordingly, the proteins involved and their interaction partners are well conserved from yeast to mammals, and Saccharomyces cerevisiae is widely used as a model system with which to investigate this fundamental cellular process. For example, valosin-containing protein (VCP) and its yeast homologue cell division cycle protein 48 (Cdc48p), which help to direct polyubiquitinated proteins for proteasome-mediated degradation, interact with an equivalent group of ubiquitin ligases in mouse and in S. cerevisiae. A conserved structural motif for cofactor binding would therefore be expected. We report a VCP-binding motif (VBM) shared by mammalian ubiquitin ligase E4b (Ube4b),ubiquitin fusion degradation protein 2a (Ufd2a), hydroxymethylglutaryl reductase degradation protein 1 (Hrd1),synoviolin and ataxin 3, and a related sequence in Mr 78 000 glycoprotein,Amfr with slightly different binding properties, and show that Ube4b and Hrd1 compete for binding to the N-terminal domain of VCP. Each of these proteins is involved in ERAD, but none has an S. cerevisiae homologue containing the VBM. Some other invertebrate model organisms also lack the VBM in one or more of these proteins, in contrast to vertebrates, where the VBM is widely conserved. Thus, consistent with their importance in ERAD, evolution has developed at least two ways to bring these proteins together with VCP,Cdc48p. However, the differing molecular architecture of VCP,Cdc48p complexes indicates a key point of divergence in the molecular details of ERAD mechanisms. [source] Mutation of residues in the coenzyme binding pocket of Dopa decarboxylaseFEBS JOURNAL, Issue 10 2001Effects on catalytic properties Residues D271, H192, H302 and N300 of l -3,4-dihydroxyphenylalanine decarboxylase (DDC), a homodimeric pyridoxal 5,-phosphate (PLP) enzyme, were mutated in order to acquire information on the catalytic mechanism. These residues are potential participants in catalysis because they belong to the common PLP-binding structural motif of group I, II and III decarboxylases and other PLP enzymes, and because they are among the putative active-site residues of structural modelled rat liver DDC. The spectroscopic features of the D271E, H192Q, H302Q and N300A mutants as well as their dissociation constants for PLP suggest that substitution of each of these residues causes alteration of the state of the bound coenzyme molecule and of the conformation of aromatic amino acids, possibly in the vicinity of the active site. This supports, but does not prove, the possibility that these residues are located in the coenzyme-binding cleft. Interestingly, mutation of each residue generates an oxidative decarboxylase activity towards l -3,4-dihydroxyphenylalanine (l -Dopa), not inherent in the wild-type in aerobiosis, and reduces the nonoxidative decarboxylase activity of l -Dopa from 3- to 390-fold. The partition ratio between oxidative and nonoxidative decarboxylation ranges from 5.7 × 10,4 for N300A mutant to 946 × 10,4 for H302Q mutant. Unlike wild-type enzyme, the mutants catalyse these two reactions to the same extent either in the presence or absence of O2. In addition, all four mutants exhibit an extremely low level of the oxidative deaminase activity towards serotonin with respect to wild-type. All these findings demonstrate that although D271, H192, H302 and N300 are not essential for catalysis, mutation of these residues alters the nature of catalysis. A possible relationship among the integrity of the PLP cleft, the productive binding of O2 and the transition to a closed conformational state of DDC is discussed. [source] Catalytic Asymmetric Synthesis of Oxindoles Bearing a Tetrasubstituted Stereocenter at the C-3 PositionADVANCED SYNTHESIS & CATALYSIS (PREVIOUSLY: JOURNAL FUER PRAKTISCHE CHEMIE), Issue 9 2010Feng Zhou Abstract The 3,3,-disubstituted oxindole structural motif is a prominent feature in many alkaloid natural products, which include all kinds of tetrasubstituted carbon stereocenters, spirocyclic or not, all-carbon or heteroatom-containing. The catalytic asymmetric synthesis of the tetrasubstituted carbon stereocenter at the C-3 position of the oxindole framework integrates new synthetic methods and chiral catalysts, reflects the latest achievements in asymmetric catalysis, and facilitates the synthesis of sufficient quantities of related compounds as potential medicinal agents and biological probes. This review summarizes the recent progress in this area, and applications in the total synthesis of related bioactive compounds. [source] Identification of single photoswitchable molecules in nanopores of silica xerogels using powder diffractionJOURNAL OF APPLIED CRYSTALLOGRAPHY, Issue 5-1 2010Antonio Cervellino Single photoswitchable molecules of (CN3H6)2[Fe(CN)5NO] (GuNP) are embedded into nanopores of an SiO2 xerogel. It is shown that it is possible to identify the structural motif (`fingerprint') of the embedded complex by analyzing neutron powder diffraction data in a limited Q range (Q < 37,nm,1) using the Debye approach. The structural study reveals that the pores are occupied by GuNP monomers with a fill factor of 60,80%. The mutual arrangement of the anion and cations in the GuNP monomer is slightly changed (,1% elongation), while the bond lengths within the anion and cation are changed by less than 0.2% with respect to the single-crystalline form of GuNP. [source] Structure, function, property, and role in neurologic diseases and other diseases of the sHsp22JOURNAL OF NEUROSCIENCE RESEARCH, Issue 10 2007Zhiping Hu Abstract Small heat shock proteins are members of the heat shock proteins family. They share important identical features: 1) they form the conserved structure ,,-crystallin domain' with about 80,100 residues in the C-terminal part of the proteins; 2) they have monomeric molecular masses ranging in 12,43 kDa; 3) they associate into large oligomers consisting in many cases of subunits; 4) they increase expression under stress conditions; 5) they exhibit a highly dynamic structure; and 6) they play a chaperone-like role. Hsp22 (also known as HspB8, H11, and E2IG1) retains the structural motif of the ,,-crystallin' family of Hsps and is a member of the superfamily of sHsps. Hsp22 displays chaperone activity, autokinase activity, and trigger or block apoptosis activity. It differs from canonical family members existing as a monomer. A decrease in the HspB8 activity may contribute to the development of some neurologic diseases and others. © 2007 Wiley-Liss, Inc. [source] Role of side chains in collagen triple helix stabilization and partner recognition,JOURNAL OF PEPTIDE SCIENCE, Issue 3 2009Rita Berisio Abstract Collagen is a widespread protein family involved in a variety of biological processes. The complexity of collagen and its fibrous nature prevent detailed investigations on the full-length protein. Reductionist approaches conducted by dissecting the protein complexity through the use of model peptides have proved to be quite effective. There are, however, several issues regarding structure,stability relationships, aggregation in higher-order assemblies, and partner recognition that are still extensively investigated. In this review, we discuss the role that side chains play in triple helix stabilization and in partner recognition. On the basis of recent literature data, we show that collagen triple helix stability is the result of the interplay of different factors. As a general trend, interactions established by amino/imino acid side chains within the triple helix scaffold effectively modulate the intrinsic residue propensity for this common structural motif. The use of peptide models has also highlighted the role that side chains play in collagen self-association and in its interactions with receptors. Valuable examples in these fields are illustrated. Finally, future actions required to obtain more detailed information on the structure and the function of this complex protein are also delineated. Copyright © 2008 European Peptide Society and John Wiley & Sons, Ltd. [source] Biomimetic Polymer Nanostructures by Injection MoldingMACROMOLECULAR MATERIALS & ENGINEERING, Issue 1 2003Nikolaj Gadegaard Abstract The nanometer scale topography of self-assembling structural protein complexes in animals is believed to induce favorable cell responses. An important example of such nanostructured biological complexes is fibrillar collagen that possesses a cross-striation structure with a periodicity of 69 nm and a peak-to-valley distance of 4,6 nm. Bovine collagen type I was assembled into fibrillar structures in vitro and sedimented onto solid supports. Their structural motif was transferred into a nickel replica by physical vapor deposition of a small-grained metal layer followed by galvanic plating. The resulting inverted nickel structure was found to faithfully present most of the micrometer and nanometer scale topography of the biological original. This nickel replica was used as a die for the injection molding of a range of different thermoplastic polymers. Total injection molding cycle times were in the range of 30,45 seconds. One of the polymer materials investigated, polyethylene, displayed poor replication of the biological nanotopographical motif. However, the majority of the polymers showed very high replication fidelity as witnessed by their ability to replicate the cross-striation features of less than 5 nm height difference. The latter group of materials includes poly(propylene), poly(methyl methacrylate), poly(L -lactic acid), polycaprolactone, and a copolymer of cyclic and linear olefins (COC). This work suggests that the current limiting factor for the injection molding of nanometer scale topography in thermoplastic polymers lies with the grain size of the initial metal coating of the mold rather than the polymers themselves. [source] 7Li and 13C solid-state NMR spectra of lithium cuprates,MAGNETIC RESONANCE IN CHEMISTRY, Issue 10 2006Steffen Jost Abstract 7Li and 13C solid-state MAS NMR spectra of three lithium cuprates with known X-ray structures,lithium([12]crown-4)2 dimethyl and diphenyl cuprate (1,2) and lithium(thf)4 -[tris(trimethylsilyl) methyl]2 cuprate (3),have been measured and analysed with respect to the quadrupolar coupling constants of lithium-7, ,(7Li), and the asymmetry parameters of the quadrupolar interactions, ,(7Li), as well as the 6, 7Li and 13C chemical shifts. The ,(7Li) values of 23, 30, and 18 kHz for 1, 2 and 3, respectively, are in line with the high symmetry around the lithium nucleus in the solvent-separated structures and may be used as reference data for this structural motif. Calculations based on charges derived from ab initio 6-31 G* HF computations using the point charge model (PCM) and the program GAMESS support the experimental findings. Copyright © 2006 John Wiley & Sons, Ltd. [source] A solid-state NMR investigation of the structure of nanocrystalline hydroxyapatiteMAGNETIC RESONANCE IN CHEMISTRY, Issue 6 2006Christian Jäger Abstract Nanocrystalline hydroxyapatite (HAp) prepared by a precipitation route was investigated. The X-ray diffraction (XRD) powder patterns of the elongated nanocrystals with a typical diameter of about 10 nm and length of 30,50 nm (by transmission electron microscopy (TEM)) revealed the presence of HAp with significantly broadened XRD reflections. However, Ca deficiency was found, as the Ca/P ratio was 1.5 only (so-called calcium-deficient hydroxyapatite (CDHA)), and not 1.67. This Ca deficiency of nanocrystalline HAp is explained using NMR. It is shown unambiguously that (i) the nanocrystals consist of a crystalline core and a (disordered) surface region with a relative phosphate content of about 1:1, (ii) the crystalline core is HAp, and (iii) the surface region is dominated by hydrogen phosphate anions (with no hydroxyapatite-like structural motif) and structural water (hydrate). From the relative phosphate content and taking into account the crystal shape, the thickness of the surface layer along the main crystal axis could be estimated to be about 1 nm, and the average chemical composition of the surface layer has been determined. Finally, a Ca/P ratio of 1.52 was estimated from the NMR data that compares well with the value of 1.51 from chemical analysis. The important consequences are that the surface of nanocrystalline HAp has nothing in common with the bulk composition and that the chemistry of such materials (e.g. the binding of protein molecules to phosphate surfaces) must be reconsidered. Copyright © 2006 John Wiley & Sons, Ltd. [source] A statistically derived parameterization for the collagen triple-helixPROTEIN SCIENCE, Issue 11 2002Jan K. Rainey Abstract The triple-helix is a unique secondary structural motif found primarily within the collagens. In collagen, it is a homo- or hetero-tripeptide with a repeating primary sequence of (Gly-X-Y)n, displaying characteristic peptide backbone dihedral angles. Studies of bulk collagen fibrils indicate that the triple-helix must be a highly repetitive secondary structure, with very specific constraints. Primary sequence analysis shows that most collagen molecules are primarily triple-helical; however, no high-resolution structure of any entire protein is yet available. Given the drastic morphological differences in self-assembled collagen structures with subtle changes in assembly conditions, a detailed knowledge of the relative locations of charged and sterically bulky residues in collagen is desirable. Its repetitive primary sequence and highly conserved secondary structure make collagen, and the triple-helix in general, an ideal candidate for a general parameterization for prediction of residue locations and for the use of a helical wheel in the prediction of residue orientation. Herein, a statistical analysis of the currently available high-resolution X-ray crystal structures of model triple-helical peptides is performed to produce an experimentally based parameter set for predicting peptide backbone and C, atom locations for the triple-helix. Unlike existing homology models, this allows easy prediction of an entire triple-helix structure based on all existing high-resolution triple-helix structures, rather than only on a single structure or on idealized parameters. Furthermore, regional differences based on the helical propensity of residues may be readily incorporated. The parameter set is validated in terms of the predicted bond lengths, backbone dihedral angles, and interchain hydrogen bonding. [source] Transmembrane signal transduction of the ,IIb,3 integrinPROTEIN SCIENCE, Issue 7 2002Kay E. Gottschalk Abstract Integrins are composed of noncovalently bound dimers of an ,- and a ,-subunit. They play an important role in cell-matrix adhesion and signal transduction through the cell membrane. Signal transduction can be initiated by the binding of intracellular proteins to the integrin. Binding leads to a major conformational change. The change is passed on to the extracellular domain through the membrane. The affinity of the extracellular domain to certain ligands increases; thus at least two states exist, a low-affinity and a high-affinity state. The conformations and conformational changes of the transmembrane (TM) domain are the focus of our interest. We show by a global search of helix,helix interactions that the TM section of the family of integrins are capable of adopting a structure similar to the structure of the homodimeric TM protein Glycophorin A. For the ,IIb,3 integrin, this structural motif represents the high-affinity state. A second conformation of the TM domain of ,IIb,3 is identified as the low-affinity state by known mutational and nuclear magnetic resonance (NMR) studies. A transition between these two states was determined by molecular dynamics (MD) calculations. On the basis of these calculations, we propose a three-state mechanism. [source] The 1.9 Å crystal structure of Escherichia coli MurG, a membrane-associated glycosyltransferase involved in peptidoglycan biosynthesisPROTEIN SCIENCE, Issue 6 2000Sha Ha Abstract The 1.9 Å X-ray structure of a membrane-associated glycosyltransferase involved in peptidoglycan biosynthesis is reported. This enzyme, MurG, contains two ,/, open sheet domains separated by a deep cleft. Structural analysis suggests that the C-terminal domain contains the UDP-GlcNAc binding site while the N-terminal domain contains the acceptor binding site and likely membrane association site. Combined with sequence data from other MurG homologs, this structure provides insight into the residues that are important in substrate binding and catalysis. We have also noted that a conserved region found in many UDP-sugar transferases maps to a ,/,/,/, supersecondary structural motif in the donor binding region of MurG, an observation that may be helpful in glycosyltransferase structure prediction. The identification of a conserved structural motif involved in donor binding in different UDP-sugar transferases also suggests that it may be possible to identify,and perhaps alter,the residues that help determine donor specificity. [source] Can density functional theory (DFT) be used as an aid to a deeper understanding of tandem mass spectrometric fragmentation pathways?RAPID COMMUNICATIONS IN MASS SPECTROMETRY, Issue 17 2009Alexander Alex Prediction of tandem mass spectrometric (MS/MS) fragmentation for non-peptidic molecules based on structure is of immense interest to the mass spectrometrist. If a reliable approach to MS/MS prediction could be achieved its impact within the pharmaceutical industry could be immense. Many publications have stressed that the fragmentation of a molecular ion or protonated molecule is a complex process that depends on many parameters, making prediction difficult. Commercial prediction software relies on a collection of general heuristic rules of fragmentation, which involve cleaving every bond in the structure to produce a list of ,expected' masses which can be compared with the experimental data. These approaches do not take into account the thermodynamic or molecular orbital effects that impact on the molecule at the point of protonation which could influence the potential sites of bond cleavage based on the structural motif. A series of compounds have been studied by examining the experimentally derived high-resolution MS/MS data and comparing it with the in silico modelling of the neutral and protonated structures. The effect that protonation at specific sites can have on the bond lengths has also been determined. We have calculated the thermodynamically most stable protonated species and have observed how that information can help predict the cleavage site for that ion. The data have shown that this use of in silico techniques could be a possible way to predict MS/MS spectra. Copyright © 2009 John Wiley & Sons, Ltd. [source] Two different one-dimensional structural motifs in [catena -{Cu(tacn)}2Pd(CN)4]Br2·[catena -Cu(tacn)Pd(CN)4]2·H2O (tacn is 1,4,7-triazacyclononane)ACTA CRYSTALLOGRAPHICA SECTION C, Issue 7 2009Juraj Kuchár The title compound, catena -poly[[bis[(triazacyclononane-,3N,N,,N,,)copper(II)]-di-,-cyanido-,4N:C -palladate(II)-di-,-cyanido-,4C:N] dibromide bis[[(triazacyclononane-,3N,N,,N,,)copper(II)]-,-cyanido-,2N:C -[dicyanidopalladate(II)]-,-cyanido-,2C:N] monohydrate], {[Cu2Pd(CN)4(C6H15N3)2]Br2·[Cu2Pd2(CN)8(C6H15N3)2]·H2O}n, (I), was isolated from an aqueous solution containing tacn·3HBr (tacn is 1,4,7-triazacyclononane), Cu2+ and tetracyanidopalladate(2,) anions. The crystal structure of (I) is essentially ionic and built up of 2,2-electroneutral chains, viz. [Cu(tacn)(NC),Pd(CN)2,(CN),], positively charged 2,4-ribbons exhibiting the composition {[Cu(tacn)(NC)2,Pd(CN)2,Cu(tacn)]2n+}n, bromide anions and one disordered water molecule of crystallization. The O atom of the water molecule occupies two unique crystallographic positions, one on a centre of symmetry, which is half occupied, and the other in a general position with one-quarter occupancy. One of the tacn ligands also exhibits disorder. The formation of two different types of one-dimensional structural motif within the same structure is a unique feature of this compound. [source] | |||||||||||||||||||||||||||||||||||||