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Backbone Structure (backbone + structure)
Selected AbstractsBackbone structure of a small helical integral membrane protein: A unique structural characterizationPROTEIN SCIENCE, Issue 1 2009Richard C. Page Abstract The structural characterization of small integral membrane proteins pose a significant challenge for structural biology because of the multitude of molecular interactions between the protein and its heterogeneous environment. Here, the three-dimensional backbone structure of Rv1761c from Mycobacterium tuberculosis has been characterized using solution NMR spectroscopy and dodecylphosphocholine (DPC) micelles as a membrane mimetic environment. This 127 residue single transmembrane helix protein has a significant (10 kDa) C-terminal extramembranous domain. Five hundred and ninety distance, backbone dihedral, and orientational restraints were employed resulting in a 1.16 Å rmsd backbone structure with a transmembrane domain defined at 0.40 Å. The structure determination approach utilized residual dipolar coupling orientation data from partially aligned samples, long-range paramagnetic relaxation enhancement derived distances, and dihedral restraints from chemical shift indices to determine the global fold. This structural model of Rv1761c displays some influences by the membrane mimetic illustrating that the structure of these membrane proteins is dictated by a combination of the amino acid sequence and the protein's environment. These results demonstrate both the efficacy of the structural approach and the necessity to consider the biophysical properties of membrane mimetics when interpreting structural data of integral membrane proteins and, in particular, small integral membrane proteins. [source] Enhanced Electrical Switching and Electrochromic Properties of Poly(p-phenylenebenzobisthiazole) Thin Films Embedded with Nano-WO3ADVANCED FUNCTIONAL MATERIALS, Issue 18 2010Jiahua Zhu Abstract The electrical switching and electrochromic phenomena of a novel nanocomposite comprising poly(p-phenylenebenzobisthiazole) (PBZT) and tungsten oxide (WO3) nanoparticles are investigated as a function of the nanoparticle loading. Both dissolving PBZT and doping PBZT backbone structure with acid are achieved by one simple step. Chlorosulfonic acid (CSA) is used as a solvent and spontaneously transformed to sulfuric acid upon exposure to moisture. The formed sulfuric acid serves as doping agent to improve the electrical conductivity of PBZT. The most significant enhancement of electrical switching is observed in the nanocomposites with low weight fraction (5%). The electrical conductivity of 5% WO3/PBZT nanocomposite thin film is increased by about 200 times and 2 times, respectively, as compared to those of the as-received PBZT and PBZT/CSA thin films. As the nanoparticle loading increases to 20% and 30%, the nanocomposites follow an ohmic conduction mechanism. Stable electrical conductivity switching is observed before and after applying a bias on the pristine PBZT and WO3/PBZT nanocomposite thin films. Electrochromic phenomena of both PBZT and WO3/PBZT nanocomposite thin films with high contrast ratio are observed after applying a bias (3 V). The mechanisms of the nanoparticles in enhancing the electrical switching and electrochromic properties are proposed. [source] NMR-Solution Structures of Fluoro-Substituted , -Peptides: A 314 -Helix and a Hairpin Turn.HELVETICA CHIMICA ACTA, Issue 12 2007-Fluoro-Amide Group, The First Case of a 90° OCCF Dihedral Angle in an Abstract To further study the preference of the antiperiplanar (ap) conformation in , -fluoro-amide groups, two , -peptides, 1 and 2, containing a (2-F)- ,3hAla and a (2-F)- ,2hPhe residue, have been synthesized. Their NMR-solution structures in CD3OH were determined and compared with those of non-F-substituted analogs, 3 and 4a. While we have found in a previous investigation (Helv. Chim. Acta2005, 88, 266) that a stereospecifically introduced F-substituent in the central position of a , - heptapeptide is capable of ,breaking' the 314 -helical structure by enforcing the FCCO ap -conformation, we could now demonstrate that the same procedure leads to a structure with the unfavorable ca. 90° FCCO dihedral angle, enforced by the 314 -helical folding in a , - tridecapeptide (cf.1; Fig.,4). This is interpreted as a consequence of cooperative folding in the longer , -peptide. A F-substituent placed in the turn section of a , -peptidic hairpin turn was shown to be in an ap -arrangement with respect to the neighboring CO bond (cf.2; Fig.,7). Analysis of the non-F-substituted , -tetrapeptides (with helix-preventing configurations of the two central ,2/,3 -amino acid residues) provides unusually tight hairpin structural clusters (cf.3 and 4a; Figs.,8 and 9). The skeleton of the , -tetrapeptide H-(R),3hVal-(R),2hVal-(R),3hAla-(S),3hPhe-OH (4a) is proposed as a novel, very simple backbone structure for mimicking , -peptidic hairpin turns. [source] Functional syndiotactic poly(,-hydroxyalkanoate)s via stereoselective ring-opening copolymerization of rac -,-butyrolactone and rac -allyl-,-butyrolactoneJOURNAL OF POLYMER SCIENCE (IN TWO SECTIONS), Issue 12 2009Noureddine Ajellal Abstract The copolymerization of racemic ,-butyrolactone (rac -BLMe) with racemic "allyl-,-butyrolactone" (rac -BLallyl) in toluene, catalyzed by the discrete amino-alkoxy-bis(phenolate) yttrium-amido complex 1, gave new poly(,-hydroxyalkanoate)s with unsaturated side chains. The poly(BLMe - co -BLallyl) copolymers produced have a highly syndiotactic backbone structure (Pr = 0.80,0.84) with a random enchainment of monomer units, as evidenced by 13C NMR, and high molecular weight (Mn up to 58,000 g mol,1) with a narrow polydispersity (Mw/Mn = 1.07,1.37), as determined by GPC. The comonomer incorporation (5,50 mol % rac -BLallyl) was a linear function of the feed ratio. The pendant vinyl bond of the side-chains in those poly(BLMe - co -BLallyl) copolymers allowed the effective introduction of hydroxy or epoxy groups via dihydroxylation, hydroboration-oxidation or epoxidation reactions. NMR studies indicated that all of these transformations proceed in an essentially quantitative conversion and do not affect the macromolecular architecture. Some thermal properties (Tm, ,Hm, Tg) of the prepared polymers have been also evaluated. © 2009 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 47: 3177,3189, 2009 [source] Soluble dithienothiophene polymers: Effect of link patternJOURNAL OF POLYMER SCIENCE (IN TWO SECTIONS), Issue 11 2009Shiming Zhang Abstract Soluble conjugated polymers based on 3,5-didecanyldithieno[3,2- b:2,,3,- d]thiophene,single-bond (1), double-bond (2), and triple-bond linked (3),were synthesized by palladium(0)-catalyzed Stille coupling reaction and oxidation polymerization. The thermal, absorption, emission, and electrochemical properties of these polymers were examined; the effect of the link pattern was studied. All polymers exhibit decomposition temperatures over 295 °C and glass-transition temperatures in the range of 137,202 °C. The absorption spectra of 1, 2, and 3 in thin films exhibit absorption maxima at 381, 584, and 444 nm, respectively. Polymer 1 exhibits intense green emission located at 510 nm in film, whereas polymers 2 and 3 are nonemissive both in solution and in film due to H-aggregate. Cyclic voltammograms of polymers 1, 2, and 3 display irreversible oxidation waves with onset oxidation potentials at 1.73, 0.78, and 1.03 V versus Ag+/Ag, respectively. Theory calculation on model compounds suggests that the dihedral angle decreases in the order of 1 > 3 > 2. On reducing the dihedral angle, the polymer exhibits a longer absorption maximum, a smaller bandgap, a less oxidizing potential and fluorescence quench, due to more coplanar and more ,-electron delocalized backbone structure. Polymer solar cells were fabricated based on the blend of polymer 2 and methanofullerene [6,6]-phenyl C61-butyric acid methyl ester (PCBM). The power conversion efficiency of 0.45% was achieved under AM 1.5, 100 mW cm,2 using polymer 2:PCBM (1:2, w/w) as active layer. © 2009 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 47: 2843,2852, 2009 [source] Hyperbranched copolymer containing triphenylamine and divinyl bipyridyl units for fluorescent chemosensorsJOURNAL OF POLYMER SCIENCE (IN TWO SECTIONS), Issue 1 2009Jichang Feng Abstract A fluorescent hyperbranched copolymer (HTP) and a linear copolymer (PTP) as a reference sample to HTP both containing triphenylamine and divinyl bipyridyl units were synthesized via Heck coupling reaction from 5,5,-Divinyl-2,2,-bipyridyl with tris(4-bromophenyl)amine and with 4,4,-dibromotriphenylamie, respectively. The chemical structure of HTP was confirmed by FTIR, 1H NMR, and 13C NMR. The polymer HTP had a number-average molecular weight of 1895 and a weight-average molecular weight of 2315, and good solubility in conventional organic solvents, such as THF, DMF, and chloroform, and exhibited good thermal stability. The UV,vis absorption and photoluminescence (PL) spectra exhibited absorption maximum at 428 nm and emissive maximum at 531 nm for the HTP solution. The spectroscopic results of HTP and PTP indicated that hyperbranched conjugated structure increases the effective conjugation length, as compared with corresponding linear conjugated structure. The fluorescence of the polymer in solution can be quenched by various transition metal ions. The effect of backbone structure of the conjugated polymer-based chemosensors on the sensitivity and selectivity in metal ions sensing have been investigated, and the quenching effect of HTP is more sensitive toward transition metal than linear copolymer PTP. © 2008 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 47: 222,230, 2009 [source] Synthesis and properties of an ionic polyacetylene with aromatic heterocyclesJOURNAL OF POLYMER SCIENCE (IN TWO SECTIONS), Issue 23 2007Yeong-Soon Gal Abstract A new ionic polyacetylene with two aromatic heterocycles (pyridyl and thienyl) was prepared by the activation polymerization of 2-ethynylpyridine by using 3-(6-bromohexyloxy)methylthiophene without any additional initiator or catalyst. The activated acetylenic triple bond of N -substituted-2-ethynylpyridinium bromide, formed at first quaternarization process, was susceptible to linear polymerization. The instrumental analysis data on the polymer structure revealed that the polymer have the conjugated polyene backbone structure with the designed two aromatic heterocycles. The photoluminescence peak is located at 510 nm corresponding to a photon energy of 2.43eV. The electrochemical properties of this ionic polyacetylene were also measured and discussed. © 2007 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 45: 5679,5685, 2007 [source] Phenylethynyl End-Capped Fluorinated Imide Oligomer AFR-PEPA- N: Morphology and Processibility CharacteristicsMACROMOLECULAR MATERIALS & ENGINEERING, Issue 1 2007Yuntao Li Abstract Two phenylethynyl phthalic anhydride-capped imide oligomers, AFR-PEPA-2 and AFR-PEPA-8, with molecular weights of 1,601 and 4,699 g,·,mol,1, respectively, were synthesized and characterized. The AFR-PEPA- N oligomers show higher glass transition temperatures and higher thermal decomposition temperatures than phenylethynyl-terminated imide PETI-5. After curing for 1 h at 390,°C, AFR-PEPA-2 and AFR-PEPA-8 have Tgs of 370 and 358,°C, respectively. AFR-PEPA- N oligomers demonstrated lower minimum complex melt viscosities than PETI-5 due to the presence of CF3 group in the backbone structure. 1,601 g,·,mol,1 AFR-PEPA-2 imide oligomer has a complex melt viscosity of 10 Pa,·,s at 340,°C, and 4,699 g,·,mol,1 AFR-PEPA-8 imide oligomer has a complex melt viscosity of 227 Pa,·,s at 371,°C. AFR-PEPA- N film's crystal morphology was observed using polarized optical microscopy and the AFR-PEPA-8 oligomer did not show crystallinity. AFR-PEPA-2 film exhibits semicrystalline behavior and the crystallinity does not disappear until the film is cured above 375,°C. [source] Backbone structure of a small helical integral membrane protein: A unique structural characterizationPROTEIN SCIENCE, Issue 1 2009Richard C. Page Abstract The structural characterization of small integral membrane proteins pose a significant challenge for structural biology because of the multitude of molecular interactions between the protein and its heterogeneous environment. Here, the three-dimensional backbone structure of Rv1761c from Mycobacterium tuberculosis has been characterized using solution NMR spectroscopy and dodecylphosphocholine (DPC) micelles as a membrane mimetic environment. This 127 residue single transmembrane helix protein has a significant (10 kDa) C-terminal extramembranous domain. Five hundred and ninety distance, backbone dihedral, and orientational restraints were employed resulting in a 1.16 Å rmsd backbone structure with a transmembrane domain defined at 0.40 Å. The structure determination approach utilized residual dipolar coupling orientation data from partially aligned samples, long-range paramagnetic relaxation enhancement derived distances, and dihedral restraints from chemical shift indices to determine the global fold. This structural model of Rv1761c displays some influences by the membrane mimetic illustrating that the structure of these membrane proteins is dictated by a combination of the amino acid sequence and the protein's environment. These results demonstrate both the efficacy of the structural approach and the necessity to consider the biophysical properties of membrane mimetics when interpreting structural data of integral membrane proteins and, in particular, small integral membrane proteins. [source] The transmembrane homotrimer of ADAM 1 in model lipid bilayersPROTEIN SCIENCE, Issue 2 2007Siok Wan Gan Abstract Fertilin is a transmembrane protein heterodimer formed by the two subunits fertilin , and fertilin , that plays an important role in sperm,egg fusion. Fertilin , and , are members of the ADAM family, and contain each one transmembrane ,-helix, and are termed ADAM 1 and ADAM 2, respectively. ADAM 1 is the subunit that contains a putative fusion peptide, and we have explored the possibility that the transmembrane ,-helical domain of ADAM 1 forms homotrimers, in common with other viral fusion proteins. Although this peptide was found to form various homooligomers in SDS, the infrared dichroic data obtained with the isotopically labeled peptide at specific positions is consistent with the presence of only one species in DMPC or POPC lipid bilayers. Comparison of the experimental orientational data with molecular dynamics simulations performed with sequence homologues of ADAM 1 show that the species present in lipid bilayers is only consistent with an evolutionarily conserved homotrimeric model for which we provide a backbone structure. These results support a model where ADAM 1 forms homotrimers as a step to create a fusion active intermediate. [source] Gas-phase fragmentation study of novel synthetic 1,5-benzodiazepine derivatives using electrospray ionization tandem mass spectrometryRAPID COMMUNICATIONS IN MASS SPECTROMETRY, Issue 14 2008Mohamed Rida The fragmentation patterns of a series of three novel synthesized 3-hydroxy-4-phenyl-tetrahydro-1,5-benzodiazepin-2-ones (1,3), possessing the same backbone structure, were investigated using electrospray ionization mass spectrometry (ESI-MS) and tandem mass spectrometry (MS/MS) techniques. A simple methodology, based on the use of ESI (positive ion mode) and by increasing the declustering potential in the atmospheric pressure/vacuum interface, collision-induced dissociation (CID), was used to enhance the formation of the fragment ions. In general, the novel synthetic 1,5-benzodiazepine derivatives afforded, in the gas phase, both protonated and sodiated molecules. This led to the confirmation of the molecular masses and chemical structures of the studied compounds. Exact accurate masses were measured using a high-resolution ESI-quadrupole orthogonal time-of-flight (QqToF)-MS/MS hybrid mass spectrometer instrument. The breakdown routes of the protonated molecules were rationalized by conducting low-energy collision CID-MS/MS analyses (product ion- and precursor ion scans) using a conventional quadrupole-hexapole-quadrupole (QhQ) tandem mass spectrometer. All the observed major fragmentations for the 1,5-benzodiazepines occurred in the saturated seven-membered ring containing the nitrogen atoms. These formed a multitude of product ions by different breakdown routes. All the major fragmentations involved cleavages of the N -1,C -2 andC -3,C -4 bonds. These occurred with concomitant eliminations of glyoxal, benzene and ethyl formate, forming the product ion at m/z 119, which was observed in all the studied compounds. In addition, an unique simultaneous CID-MS/MS fragmentation was noticed for the 1,5-benzodiazepines 1 and 3, which occurred by a pathway dictated by the substituent located on the N -1-position. It was evident that the aromatic ring portion of the 1,5-benzodiazepines was resistant to CID-MS/MS fragmentation. Re-confirmation of the various geneses of the product ions was achieved by conducting a series of precursor ion scans. ESI-MS and CID-MS/MS analyses have thus proven to be a specific and very sensitive method for the structural identification of these novel 1,5-benzodiazepine derivatives. Copyright © 2008 John Wiley & Sons, Ltd. [source] Matrix-assisted laser desorption/ionisation mass spectrometry for the direct analysis of enzymatically digested kappa - iota - and hybrid iota/nu -carrageenans,RAPID COMMUNICATIONS IN MASS SPECTROMETRY, Issue 16 2005Aristotelis Antonopoulos Enzymatically digested oligosaccharides of kappa -, iota - and hybrid iota/nu -carrageenans were analysed using matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry in the negative-ion mode. nor -Harmane was used as matrix. Depending on the stock concentration and the laser intensity applied, the oligosaccharides exhibited losses of sulphate units (neutralised by the Na+ ion, and thus non-stable), leaving the primary backbone structure in most cases with only the deprotonated sulphate groups (carrying the negative charge, stable). This meant that kappa - and iota -oligosaccharides could not be easily distinguished from one another since they share the same primary backbone structure. However, for the hybrid iota/nu -oligosaccharides the primary backbone structure could be identified since the nu -carrageenan repeating unit differs from that of the kappa/iota -carrageenan unit. For all types of oligosaccharides, the results indicated cleavage of an anhydrogalactose unit from the non-reducing end. Specifically, for the hybrid oligosaccharides of iota/nu -carrageenans, this type of fragmentation means that the nu -carrageenan unit is not positioned on the non-reducing end of the hybrid oligosaccharides. Dehydration reactions, and exchange reactions of Na+ with K+ and Ca2+, were also observed. Copyright © 2005 John Wiley & Sons, Ltd. [source] Interaction of angiotensin II with the C-terminal 300,320 fragment of the rat angiotensin II receptor AT1a monitored by NMRBIOPOLYMERS, Issue 2 2003Nicola D'Amelio Abstract Interaction between angiotensin II (Ang II) and the fragment peptide 300,320 (fCT300,320) of the rat angiotensin II receptor AT1a was demonstrated by relaxation measurements, NOE effects, chemical shift variations, and CD measurements. The correlation times modulating dipolar interactions for the bound and free forms of Ang II were estimated by the ratio of the nonselective and single-selective longitudinal relaxation rates. The intermolecular NOEs observed in NOESY spectra between HN protons of 9LysfCT and 6Hisang, 10PhefCT and 8Pheang, HN proton of 3TyrfCT and H, of 4Tyrang, 5PhefCTH, and H, of 4Tyrang indicated that Ang II aromatic residues are directly involved in the interaction, as also verified by relaxation data. Some fCT300,320 backbone features were inferred by the CSI method and CD experiments revealing that the presence of Ang II enhances the existential probability of helical conformations in the fCT fragment. Restrained molecular dynamics using the simulated annealing protocol was performed with intermolecular NOEs as constraints, imposing an ,-helix backbone structure to fCT300,320 fragment. In the built model, one strongly preferred interaction was found that allows intermolecular stacking between aromatic rings and forces the peptide to wrap around the 6Leu side chain of the receptor fragment. © 2003 Wiley Periodicals, Inc. Biopolymers 70: 134,144, 2003 [source] Synthesis and characterization of novel polyurethanes based on N1,N4 -bis[(4-hydroxyphenyl)methylene]succinohydrazide hard segment,JOURNAL OF APPLIED POLYMER SCIENCE, Issue 4 2008A. V. Raghu Abstract This article deals with the synthesis and characterization of novel polyurethanes (PUs) by the reaction between two aromatic diisocyanates (4,4,-diphenylmethane diisocyanate and tolylene 2,4-diisocyanate) and two aliphatic diisocyanates (isophorone diisocyanate and hexamethylene diisocyanate) with N1,N4 -bis[(4-hydroxyphenyl)methylene]succinohydrazide, which acted as hard segment. UV,vis, FTIR, 1H NMR, 13C NMR, and DSC/TGA analytical technique has been used to determine the structural characterization and thermal properties of the hard segmented PUs. X-ray diffraction revealed that PUs contained semicrystalline and amorphous regions that varied depending upon the nature of the backbone structures. PUs were soluble in polar aprotic solvents. © 2008 Wiley Periodicals, Inc. J Appl Polym Sci, 2008 [source] Molecular Modeling Suggests Conformational Scaffolds Specifically Targeting Five Subtypes of Somatostatin ReceptorsCHEMICAL BIOLOGY & DRUG DESIGN, Issue 3 2007Gregory V. Nikiforovich Several analogs of somatostatin with conformational constraints in their peptide backbones have been modeled to determine energetically feasible conformations. Comparison of low-energy backbone structures of these peptides suggested unique conformations of the central Phe/Alai -D-Trpi+1 -Lysi+2 -Thri+3 fragment characteristic for specific interactions of somatostatin with each of the five distinct subtypes of somatostatin receptors (SSTRs). The conformations obtained were in good agreement with experimental data obtained earlier by NMR measurements and/or X-ray crystallography. The results help rationalize experimental observations on the specificity of binding of various somatostatin analogs with different subtypes of the SSTRs. They also serve as templates for the design of conformationally constrained non-peptide scaffolds that effectively and selectively interact with different subtypes of SSTRs. Such scaffolds can be convenient carriers of radiolabels and near-infrared labels in specific agents for imaging tumors expressing different SSTR subtypes. [source] | |||||||||||||