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Sample records for backbone metal cyclization

  1. Efficient backbone cyclization of linear peptides by a recombinant asparaginyl endopeptidase

    PubMed Central

    Harris, Karen S.; Durek, Thomas; Kaas, Quentin; Poth, Aaron G.; Gilding, Edward K.; Conlan, Brendon F.; Saska, Ivana; Daly, Norelle L.; van der Weerden, Nicole L.; Craik, David J.; Anderson, Marilyn A.

    2015-01-01

    Cyclotides are diverse plant backbone cyclized peptides that have attracted interest as pharmaceutical scaffolds, but fundamentals of their biosynthetic origin remain elusive. Backbone cyclization is a key enzyme-mediated step of cyclotide biosynthesis and confers a measure of stability on the resultant cyclotide. Furthermore, cyclization would be desirable for engineered peptides. Here we report the identification of four asparaginyl endopeptidases (AEPs), proteases implicated in cyclization, from the cyclotide-producing plant Oldenlandia affinis. We recombinantly express OaAEP1b and find it functions preferably as a cyclase by coupling C-terminal cleavage of propeptide substrates with backbone cyclization. Interestingly, OaAEP1b cannot cleave at the N-terminal site of O. affinis cyclotide precursors, implicating additional proteases in cyclotide biosynthesis. Finally, we demonstrate the broad utility of this enzyme by cyclization of peptides unrelated to cyclotides. We propose that recombinant OaAEP1b is a powerful tool for use in peptide engineering applications where increased stability of peptide products is desired. PMID:26680698

  2. Understanding GFP chromophore biosynthesis: controlling backbone cyclization and modifying post-translational chemistry.

    PubMed

    Barondeau, David P; Kassmann, Carey J; Tainer, John A; Getzoff, Elizabeth D

    2005-02-15

    The Aequorea victoria green fluorescent protein (GFP) undergoes a remarkable post-translational modification to create a chromophore out of its component amino acids S65, Y66, and G67. Here, we describe mutational experiments in GFP designed to convert this chromophore into a 4-methylidene-imidazole-5-one (MIO) moiety similar to the post-translational active-site electrophile of histidine ammonia lyase (HAL). Crystallographic structures of GFP variant S65A Y66S (GFPhal) and of four additional related site-directed mutants reveal an aromatic MIO moiety and mechanistic details of GFP chromophore formation and MIO biosynthesis. Specifically, the GFP scaffold promotes backbone cyclization by (1) favoring nucleophilic attack by close proximity alignment of the G67 amide lone pair with the pi orbital of the residue 65 carbonyl and (2) removing enthalpic barriers by eliminating inhibitory main-chain hydrogen bonds in the precursor state. GFP R96 appears to induce structural rearrangements important in aligning the molecular orbitals for ring cyclization, favor G67 nitrogen deprotonation through electrostatic interactions with the Y66 carbonyl, and stabilize the reduced enolate intermediate. Our structures and analysis also highlight negative design features of the wild-type GFP architecture, which favor chromophore formation by destabilizing alternative conformations of the chromophore tripeptide. By providing a molecular basis for understanding and controlling the driving force and protein chemistry of chromophore creation, this research has implications for expansion of the genetic code through engineering of modified amino acids.

  3. Intein-mediated backbone cyclization of VP1 protein enhanced protection of CVB3-induced viral myocarditis

    PubMed Central

    Qi, Xingmei; Xiong, Sidong

    2017-01-01

    CVB3 is a common human pathogen to be highly lethal to newborns and causes viral myocarditis and pancreatitis in adults. However, there is no vaccine available for clinical use. CVB3 capsid protein VP1 is an immunodominant structural protein, containing several B- and T-cell epitopes. However, immunization of mice with VP1 protein is ineffective. Cyclization of peptide is commonly used to improve their in vivo stability and biological activity. Here, we designed and synthesizd cyclic VP1 protein by using engineered split Rma DnaB intein and the cyclization efficiency was 100% in E. coli. As a result, the cyclic VP1 was significantly more stable against irreversible aggregation upon heating and against carboxypeptidase in vitro and the degradation rate was more slowly in vivo. Compared with linear VP1, immunization mice with circular VP1 significantly increased CVB3-specific serum IgG level and augmented CVB3-specific cellular immune responses, consequently afforded better protection against CVB3-induced viral myocarditis. The cyclic VP1 may be a novel candidate protein vaccine for preventing CVB3 infection and similar approaches could be employed to a variety of protein vaccines to enhance their protection effect. PMID:28148910

  4. Green chemistry: solvent- and metal-free Prins cyclization. Application to sequential reactions.

    PubMed

    Clarisse, Damien; Pelotier, Béatrice; Piva, Olivier; Fache, Fabienne

    2012-01-04

    Prins cyclization between a homoallylic alcohol and an aldehyde, promoted by trimethylsilyl halide, afforded 4-halo-tetrahydropyrans with good to excellent yields. Thanks to the absence of the solvent and metal, the THP thus obtained have been implicated without purification in several other reactions, in a sequential way, affording in particular new indole derivatives.

  5. Selective synthesis of indazoles and indoles via triazene-alkyne cyclization switched by different metals.

    PubMed

    Fang, Yan; Wang, Chengming; Su, Shengqin; Yu, Haizhu; Huang, Yong

    2014-02-21

    We described two orthogonal heterocycle syntheses, where an arene bearing both an alkyne and a triazene functionality underwent two distinct cyclization pathways mediated by different transition metals. Starting from the same substrates, a synthesis of 2H-indazole was accomplished by a Cu(II) salt promoted oxidative cyclization, while 2-substituted indoles could be accessed via a Ag(I) salt mediated N-N bond cleavage. This method represents the first synthesis of indoles from alkynyl triazenes. Computational analysis was performed for both reaction pathways, supporting a Lewis acid role for Cu and a π-acid catalysis for Ag.

  6. Metal-induced cyclization of thiosemicarbazones derived from beta-keto amides and beta-keto esters: open-chain and cyclized ligands in zinc(II) complexes.

    PubMed

    Casas, José S; Castaño, María V; Castellano, Eduardo E; Ellena, Javier; García-Tasende, María S; Gato, Angeles; Sánchez, Agustín; Sanjuán, Luisa M; Sordo, José

    2002-03-25

    The reactions of Zn(OAc)(2) with acetoacetanilide, methyl acetoacetate, o-acetoacetanisidide, and ethyl 2-methylacetoacetate thiosemicarbazones (HTSC(1), HTSC(2), HTSC(3), and HTSC(4), respectively) were explored in methanol. With HTSC(1), HTSC(2), and HTSC(3), following isolation of the corresponding zinc(II) thiosemicarbazonates [Zn(TSC(x))(2)] (x = 1, 2, 3), the mother liquors afforded pyrazolonate complexes [ZnL(1)(2)(H(2)O)] (HL(1) = 2,5-dihydro-3-methyl-5-oxo-1H-pyrazole-1-carbothioamide) that had been formed by cyclization of the corresponding TSC(-). The reaction of HTSC(4) with zinc(II) acetate gave only the pyrazolonate complex [ZnL(2)(2)(H(2)O)] (HL(2) = 2,5-dihydro-3,4-dimethyl-5-oxo-1H-pyrazole-1-carbothioamide). All compounds were studied by IR and NMR spectroscopy, and HTSC(3), [Zn(TSC(3))(2)] x DMSO, [ZnL(1)(2)(H(2)O)] x 2DMSO, and [ZnL(2)(2)(H(2)O)] x 2DMSO were also studied by X-ray diffractometry, giving a thorough picture of the cyclization process. In preliminary tests of the effects of HL(1) and [ZnL(1)(2)(H(2)O)] on rat paw inflammatory edema induced by carrageenan, HL(1) showed antiinflammatory activity.

  7. The Construction of Metal-Organic Framework with Active Backbones by the Utilization of Reticular Chemistry

    NASA Astrophysics Data System (ADS)

    Choi, Eunwoo

    With the principles of reticular chemistry, metal-organic frameworks with ultra-high porosity, chiral-recognition unit as a chiral stationary phase, metalloporhyrins for enhanced hydrogen adsorption and an intrinsic conductivity to form porous conductors, have been prepared. This dissertation presents how the principles of reticular chemistry were utilized to achieve in the preparations of metal-organic frameworks with a large surface area and active backbones. Through the simple isoreticular (having the same framework topology) expansion from MOF-177 composed with 1,3,5-tris(4'-carboxyphenyl-)benzene (BTB3-) as the strut; MOF-200 was prepared with 4,4',4"-(benzene-1,3,5-triyl-tris(benzene-4,1-diy1))tribenzoic acid an extension from BTB3- by a phenylene unit to yield one of the most porous MOFs with a Langmuir surface area of 10,400 m2. and the lowest density of 0.22 cm3.g-1. A successful thermal polymerization reaction at 325 °C inside of the pores of highly porous MOF, MOF-177, was performed and verified the integrity of the MOF structure even after the thermal reaction. 1,4-Diphenylbutadiyne that is known to polymerize upon heating to form a conjugated backbone was impregnated via solution-diffusion into MOF-177 and then subsequently polymerized by heat to form polymer impregnated MOF-177. Characterization was carried out using powder X-ray diffraction and volumetric sorption analyzer. MOF-1020 with a linear quaterphenyl dicarboxylate-based strut was designed to contain a chiral bisbinaphthyl crown-ether moiety for alkyl ammonium resolution was precisely placed into a Zn4O(CO2)6-based cubic MOF structure. Unfortunately, the chiral resolution was not achieved due to the sensitivity and the pore environment of MOF-1020. However, an interesting phenomenon was observed, where the loss of crystallinity occurs upon solvent removal while the crystallites remain shiny and crystalline, but it readily is restored upon re-solvation of the crystallites. This rare

  8. Hydride-induced anionic cyclization: an efficient method for the synthesis of 6-H-phenanthridines via a transition-metal-free process.

    PubMed

    Chen, Wei-Lin; Chen, Chun-Yuan; Chen, Yan-Fu; Hsieh, Jen-Chieh

    2015-03-20

    A novel procedure for hydride-induced anionic cyclization has been developed. It includes the reduction of a biaryl bromo-nitrile with a nucleophilic aromatic substitution (S(N)Ar). A range of polysubstituted 6-H-phenanthridines were so obtained in moderate to good yield with good substrate tolerance. This method involves a concise transition-metal-free process and was applied to synthesize natural alkaloids.

  9. Comparative experimental investigation on the actuation mechanisms of ionic polymer–metal composites with different backbones and water contents

    SciTech Connect

    Zhu, Zicai; Chang, Longfei; Wang, Yanjie; Chen, Hualing; Asaka, Kinji; Zhao, Hongxia; Li, Dichen

    2014-03-28

    Water-based ionic polymer–metal composites (IPMCs) exhibit complex deformation properties, especially when the water content changes. To explore the general actuation mechanisms, both Nafion and Flemion membranes are used as the polymer backbones. IPMC deformation includes three stages: fast anode deformation, relaxation deformation, and slow anode deformation, which is mainly dependent on the water content and the backbone. When the water content decreases from 21 to 14 wt. %, Nafion–IPMC exhibits a large negative relaxation deformation, zero deformation, a positive relaxation deformation, and a positive steady deformation without relaxation in sequence. Despite the slow anode deformation, Flemion–IPMC also shows a slight relaxation deformation, which disappears when the water content is less than 13 wt. %. The different water states are investigated at different water contents using nuclear magnetic resonance spectroscopy. The free water, which decreases rapidly at the beginning through evaporation, is proven to be critical for relaxation deformation. For the backbone, indirect evidence from the steady current response is correlated with the slow anode deformation of Flemion-IPMC. The latter is explained by the secondary dissociation of the weak acid group –COOH. Finally, we thoroughly explain not only the three deformations by swelling but also their evolvement with decreasing water content. A fitting model is also presented based on a multi-diffusion equation to reveal the deformation processes more clearly, the results from which are in good agreement with the experimental results.

  10. A 7-Step Formal Asymmetric Total Synthesis of Strictamine via an Asymmetric Propargylation and Metal-Mediated Cyclization.

    PubMed

    Smith, Myles W; Zhou, Zhiyao; Gao, Alison X; Shimbayashi, Takuya; Snyder, Scott A

    2017-03-03

    Herein is shown how a novel catalytic asymmetric propargylation of 3,4-dihydro-β-carboline, followed by a designed Au(I)/Ag(I)-mediated 6-endo-dig cyclization, can directly deliver the indolenine-fused methanoquinolizidine core of the akuammiline alkaloid strictamine in its native oxidation state, ultimately achieving a 7-step formal asymmetric total synthesis. Also demonstrated are how the cyclization products can rearrange into vincorine-type skeletons and a further use for the developed propargylation with the first catalytic asymmetric total synthesis of decarbomethoxydihydrogambirtannine.

  11. Synthesis of 3-carboxylated indoles through a tandem process involving cyclization of 2-ethynylanilines followed by CO2 fixation in the absence of transition metal catalysts.

    PubMed

    Inamoto, Kiyofumi; Asano, Narumi; Nakamura, Yuka; Yonemoto, Misato; Kondo, Yoshinori

    2012-05-18

    In this study, a facile synthesis of 3-carboxylated indoles involving a tandem-type cyclization of 2-ethynylanilines and subsequent CO2 fixation at the 3-position of the indole ring is realized. The reaction proceeds efficiently at 65 °C under 10 atm of CO2, giving rise to variously substituted 3-carboxylated indoles, generally in high yields. An inorganic base, such as K2CO3, is the only reagent required, and the addition of transition metal catalysts is not necessary. The method provides a novel, simple, and promising strategy for CO2 fixation in the research field of heterocyclic chemistry.

  12. Differentiating between fluorescence-quenching metal ions with polyfluorophore sensors built on a DNA backbone.

    PubMed

    Tan, Samuel S; Kim, Su Jeong; Kool, Eric T

    2011-03-02

    A common problem in detecting metal ions with fluorescentchemosensors is the emission-suppressing effects of fluorescence-quenching metal ions. This quenching tendency makes it difficult to design sensors with turn-on signal, and differentiate between several metal ions that may yield a strong quenching response. To address these challenges, we investigate a new sensor design strategy, incorporating fluorophores and metal ligands as DNA base replacements in DNA-like oligomers, for generating a broader range of responses for quenching metal ions. The modular molecular design enabled rapid synthesis and discovery of sensors from libraries on PEG-polystyrene beads. Using this approach, water-soluble sensors 1-5 were identified as strong responders to a set of eight typically quenching metal ions (Co(2+), Ni(2+), Cu(2+), Hg(2+), Pb(2+), Ag(+), Cr(3+), and Fe(3+)). They were synthesized and characterized for sensing responses in solution. Cross-screening with the full set of metal ions showed that they have a wide variety of responses, including emission enhancements and red- and blue-shifts. The diversity of sensor responses allows as few as two sensors (1 and 2) to be used together to successfully differentiate these eight metals. As a test, a set of unknown metal ion solutions in blind studies were also successfully identified based on the response pattern of the sensors. The modular nature of the sensor design strategy suggests a broadly applicable approach to finding sensors for differentiating many different cations by pattern-based recognition, simply by varying the sequence and composition of ligands and fluorophores on a DNA synthesizer.

  13. Synthesis and structural characterization of one- and two-dimensional coordination polymers based on platinum-silver metallic backbones.

    PubMed

    Liu, Fenghui; Chen, Wanzhi; Wang, Daqi

    2006-06-28

    Seven Pt-Ag coordination polymers [Pt(NH3)2(NHCO(t)Bu)2Ag(H2O)](ClO4) (1), [Pt2(dap)2(NHCO(t)Bu)4Ag2(NO3)(ClO4)] (dap = 1,2-diaminopropane, 2), [Pt2(en)2(NHCO(t)Bu)4Ag2(m-C6H4(CO2)2)].3H2O (en = ethylenediamine, 3), [Pt2(NH3)2(NHCO(t)Bu)2Ag2(p-C6H4(CO2)2)].2H2O (4), [Pt3(en)3(NHCO(t)Bu)6Ag2(p-C6H4(CO2)2)(1.5)].6H2O (5), [Pt(NH3)2(NHCO(t)Bu)4Ag(4-C5H4NCO2)2].10H2O (6), and [Pt2(en)2(NHCO(t)Bu)4Ag2(4-C5H4NCO2)](ClO4) (7) were synthesized from the corresponding [Pt(RNH2)2(NHCO(t)Bu)2] and Ag salts, respectively, and their structures were determined by X-ray crystallography. The Pt and Ag units aggregate into one-dimensional chains based on Pt-Ag backbones. Compounds 1, 2, and 6 possess an extended zigzag Pt-Ag chain motif, and the metallic chains arrange in a parallel fashion into layered structures. Compounds 3-5, and 7 form 2-D brick wall sheets due to the coordination of the bifunctional anions to the Ag+ ions of the neighboring chains. These polymers are constructed based on the Pt-Ag interactions and the coordination of amidate oxygen atoms to Ag ions. There are three kinds of short Pt-Ag bonds observed in the structures of these compounds. The Pt-Ag metallic backbone is formed by the stacking unsupported Pt-Ag bonds, the amidate doubly bridged Pt-Ag bonds, and the amidate singly bridged Pt-Ag bonds. In the chains, the Pt-Ag bond distances are quite short, and appear in the range of 2.78-2.97 A, which are comparable to known Pt-Ag dative bonds.

  14. Cyclization in opioid peptides.

    PubMed

    Piekielna, Justyna; Perlikowska, Renata; Gach, Katarzyna; Janecka, Anna

    2013-06-01

    Endogenous opioid peptides have been studied extensively as potential therapeutics for the treatment of pain. The major problems of using natural opioid peptides as drug candidates are their poor receptor specificity, metabolic instability and inability to reach the brain after systemic administration. A lot of synthetic efforts have been made to opioid analogs with improved pharmacological properties. One important structural modification leading to such analogs is cyclization of linear sequences. Intramolecular cyclization has been shown to improve biological properties of various bioactive peptides. Cyclization reduces conformational freedom responsible for the simultaneous activation of two or more receptors, increases metabolic stability and lipophilicity which may result in a longer half-life and easier penetration across biological membranes. This review deals with various strategies that have been employed to synthesize cyclic analogs of opioid peptides. Discussed are such bridging bonds as amide and amine linkages, sulfur-containing bonds, including monosulfide, disulfide and dithioether bridges, bismethylene bonds, monosulfide bridges of lanthionine and, finally, carbonyl and guanidine linkages. Opioid affinities and activities of cyclic analogs are given and compared with linear opioid peptides. Analgesic activities of analogs evaluated in the in vivo pain tests are also discussed.

  15. Non-Innocent Behavior of Substrate Backbone Esters in Metal-Catalyzed Carbocyclizations and Friedel-Crafts Reactions of Enynes and Arenynes.

    PubMed

    Michelet, Bastien; Thiery, Guillaume; Bour, Christophe; Gandon, Vincent

    2015-11-06

    On the basis of DFT computations and experimental results, we show that the presence of the ester group in the backbone of organic substrates can influence the mechanism of metal-catalyzed carbocyclization reactions. The non-innocent role of the ester functionality in lowering the activation barrier of the key step of the gallium- and indium-catalyzed cycloisomerization of 1,6-enynes is revealed. In the case of the gallium-catalyzed hydroarylation of arenynes, the esters in the tether can deprotonate the Wheland intermediate, thus avoiding more energetically demanding [1,3]- or [1,2]/[1,2]-H shifts. As for the gallium-catalyzed Friedel-Crafts alkylation, an unusual concerted SEAr mechanism involving the esters has been calculated. Lastly, computations evidence that the ester group of methyl propiolates enables a divergent mechanism in the platinum-catalyzed intramolecular hydroarylation.

  16. Semienzymatic cyclization of disulfide-rich peptides using Sortase A.

    PubMed

    Jia, Xinying; Kwon, Soohyun; Wang, Ching-I Anderson; Huang, Yen-Hua; Chan, Lai Y; Tan, Chia Chia; Rosengren, K Johan; Mulvenna, Jason P; Schroeder, Christina I; Craik, David J

    2014-03-07

    Disulfide-rich cyclic peptides have generated great interest in the development of peptide-based therapeutics due to their exceptional stability toward chemical, enzymatic, or thermal attack. In particular, they have been used as scaffolds onto which bioactive epitopes can be grafted to take advantage of the favorable biophysical properties of disulfide-rich cyclic peptides. To date, the most commonly used method for the head-to-tail cyclization of peptides has been native chemical ligation. In recent years, however, enzyme-mediated cyclization has become a promising new technology due to its efficiency, safety, and cost-effectiveness. Sortase A (SrtA) is a bacterial enzyme with transpeptidase activity. It recognizes a C-terminal penta-amino acid motif, LPXTG, and cleaves the amide bond between Thr and Gly to form a thioacyl-linked intermediate. This intermediate undergoes nucleophilic attack by an N-terminal poly-Gly sequence to form an amide bond between the Thr and N-terminal Gly. Here, we demonstrate that sortase A can successfully be used to cyclize a variety of small disulfide-rich peptides, including the cyclotide kalata B1, α-conotoxin Vc1.1, and sunflower trypsin inhibitor 1. These peptides range in size from 14 to 29 amino acids and contain three, two, or one disulfide bond, respectively, within their head-to-tail cyclic backbones. Our findings provide proof of concept for the potential broad applicability of enzymatic cyclization of disulfide-rich peptides with therapeutic potential.

  17. Racemization in Prins Cyclization Reactions

    PubMed Central

    Jasti, Ramesh

    2008-01-01

    Isotopic labeling experiments were performed in order to elucidate a new mechanism for racemization in Prins cyclization reactions. The loss in optical activity for these reactions was shown to occur by 2-oxonia-Cope rearrangements by way of a (Z)-oxocarbenium ion intermediate. Reaction conditions such as solvent, temperature, and the nucleophile employed played a critical role in whether an erosion in enantiomeric excess was observed. Additionally, certain structural features of Prins cyclization precursors were also shown to be important for preserving optical purity in these reactions. PMID:17031979

  18. Semienzymatic Cyclization of Disulfide-rich Peptides Using Sortase A*

    PubMed Central

    Jia, Xinying; Kwon, Soohyun; Wang, Ching-I Anderson; Huang, Yen-Hua; Chan, Lai Y.; Tan, Chia Chia; Rosengren, K. Johan; Mulvenna, Jason P.; Schroeder, Christina I.; Craik, David J.

    2014-01-01

    Disulfide-rich cyclic peptides have generated great interest in the development of peptide-based therapeutics due to their exceptional stability toward chemical, enzymatic, or thermal attack. In particular, they have been used as scaffolds onto which bioactive epitopes can be grafted to take advantage of the favorable biophysical properties of disulfide-rich cyclic peptides. To date, the most commonly used method for the head-to-tail cyclization of peptides has been native chemical ligation. In recent years, however, enzyme-mediated cyclization has become a promising new technology due to its efficiency, safety, and cost-effectiveness. Sortase A (SrtA) is a bacterial enzyme with transpeptidase activity. It recognizes a C-terminal penta-amino acid motif, LPXTG, and cleaves the amide bond between Thr and Gly to form a thioacyl-linked intermediate. This intermediate undergoes nucleophilic attack by an N-terminal poly-Gly sequence to form an amide bond between the Thr and N-terminal Gly. Here, we demonstrate that sortase A can successfully be used to cyclize a variety of small disulfide-rich peptides, including the cyclotide kalata B1, α-conotoxin Vc1.1, and sunflower trypsin inhibitor 1. These peptides range in size from 14 to 29 amino acids and contain three, two, or one disulfide bond, respectively, within their head-to-tail cyclic backbones. Our findings provide proof of concept for the potential broad applicability of enzymatic cyclization of disulfide-rich peptides with therapeutic potential. PMID:24425873

  19. Butelase-mediated cyclization and ligation of peptides and proteins.

    PubMed

    Nguyen, Giang K T; Qiu, Yibo; Cao, Yuan; Hemu, Xinya; Liu, Chuan-Fa; Tam, James P

    2016-10-01

    Enzymes that catalyze efficient macrocyclization or site-specific ligation of peptides and proteins can enable tools for drug design and protein engineering. Here we describe a protocol to use butelase 1, a recently discovered peptide ligase, for high-efficiency cyclization and ligation of peptides and proteins ranging in size from 10 to >200 residues. Butelase 1 is the fastest known ligase and is found in pods of the common medicinal plant Clitoria ternatea (also known as butterfly pea). It has a very simple C-terminal-specific recognition motif that requires Asn/Asp (Asx) at the P1 position and a dipeptide His-Val at the P1' and P2' positions. Substrates for butelase-mediated ligation can be prepared by standard Fmoc (9-fluorenylmethyloxycarbonyl) chemistry or recombinant expression with the minimal addition of this tripeptide Asn-His-Val motif at the C terminus. Butelase 1 achieves cyclizations that are 20,000 times faster than those of sortase A, a commonly used enzyme for backbone cyclization. Unlike sortase A, butelase is traceless, and it can be used for the total synthesis of naturally occurring peptides and proteins. Furthermore, butelase 1 is also useful for intermolecular ligations and synthesis of peptide or protein thioesters, which are versatile activated intermediates necessary for and compatible with many chemical ligation methods. The protocol describes steps for isolation and purification of butelase 1 from plant extract using a four-step chromatography procedure, which takes ∼3 d. We then describe steps for intramolecular cyclization, intermolecular ligation and butelase-mediated synthesis of protein thioesters. Butelase reactions are generally completed within minutes and often achieve excellent yields.

  20. SpyRing interrogation: analyzing how enzyme resilience can be achieved with phytase and distinct cyclization chemistries

    PubMed Central

    Schoene, Christopher; Bennett, S. Paul; Howarth, Mark

    2016-01-01

    Enzymes catalyze reactions with exceptional selectivity and rate acceleration but are often limited by instability. Towards a generic route to thermo-resilience, we established the SpyRing approach, cyclizing enzymes by sandwiching between SpyTag and SpyCatcher (peptide and protein partners which lock together via a spontaneous isopeptide bond). Here we first investigated the basis for this resilience, comparing alternative reactive peptide/protein pairs we engineered from Gram-positive bacteria. Both SnoopRing and PilinRing cyclization gave dramatic enzyme resilience, but SpyRing cyclization was the best. Differential scanning calorimetry for each ring showed that cyclization did not inhibit unfolding of the inserted β-lactamase. Cyclization conferred resilience even at 100 °C, where the cyclizing domains themselves were unfolded. Phytases hydrolyze phytic acid and improve dietary absorption of phosphate and essential metal ions, important for agriculture and with potential against human malnutrition. SpyRing phytase (PhyC) resisted aggregation and retained catalytic activity even following heating at 100 °C. In addition, SpyRing cyclization made it possible to purify phytase simply by heating the cell lysate, to drive aggregation of non-cyclized proteins. Cyclization via domains forming spontaneous isopeptide bonds is a general strategy to generate resilient enzymes and may extend the range of conditions for isolation and application of enzymes. PMID:26861173

  1. Synthesis of hexahydropyrrolo[2,1-a]isoquinoline compound libraries through a Pictet-Spengler cyclization/metal-catalyzed cross coupling/amidation sequence.

    PubMed

    Petersen, Rico; Cohrt, A Emil; Petersen, Michael Åxman; Wu, Peng; Clausen, Mads H; Nielsen, Thomas E

    2015-06-01

    Molecular libraries of natural product-like and structurally diverse compounds are attractive in early drug discovery campaigns. In here, we present synthetic methodology for library production of hexahydropyrrolo[2,1-a]isoquinoline (HPIQ) compounds. Two advanced HPIQ intermediates, both incorporating two handles for diversification, were synthesized through an oxidative cleavage/Pictet-Spengler reaction sequence in high overall yields. A subsequent metal-catalyzed cross coupling/amidation protocol was developed and its utility in library synthesis was validated by construction of a 20-membered natural product-like molecular library in good overall yields.

  2. Coarctate cyclization reactions: a primer.

    PubMed

    Young, Brian S; Herges, Rainer; Haley, Michael M

    2012-10-04

    The cleavage of five-membered heterocycles possessing an exocyclic carbene or nitrene to form conjugated ene-ene-yne systems has been documented for over 40 years; however, the reverse reaction, using a conjugated "ene-ene-yne" precursor to form a heterocycle is a relatively new approach. Over the past decade, the Haley and Herges groups have studied computationally and experimentally the cyclization of the "hetero-ene-ene-yne" motif via an unusual class of concerted reactions known as coarctate reactions. This feature article details our synthetic and mechanistic work involving triazene-arene-alkynes and structurally-related systems to generate heterocycles using coarctate chemistry.

  3. Reactions of thiosemicarbazones derived from beta-keto amides and beta-keto esters with Zn(II) and Cd(II) acetates: influence of metal, substitution, reagent ratio and temperature on metal-induced cyclization.

    PubMed

    Casas, José S; Castaño, María V; García-Tasende, María S; Rodríguez-Castellón, Enrique; Sánchez, Agustín; Sanjuán, Luisa M; Sordo, José

    2004-07-07

    Zinc(II) and cadmium(II) acetates were reacted in methanol under various experimental conditions with thiosemicarbazones derived from beta-keto amides or beta-keto esters (HTSC). Some of these reactions afforded thiosemicarbazonate complexes [M(TSC)2] with IR and NMR spectra compatible with N,S-coordination, but most gave complexes [ML2], where HL is a substituted 2,5-dihydro-5-oxo-1H-pyrazole-1-carbothioamide resulting from cyclization of the HTSC. Some of these pyrazolonates and two of the HL ligands were studied by X-ray diffractometry, and their structures are discussed. Surprisingly, the reactions of zinc(II) acetate with HTSC in 1:1 mol ratio usually gave a third, previously unreported type of complex with a dideprotonated ligand, [Zn(L-H)], which was also formed when [ZnL2] and Zn(OAc)2 interacted at room temperature in 1:1 mol ratio. These L-H complexes are highly insoluble in all common solvents, which hinders their characterization but suggests that they are polymeric in nature.

  4. Protein-induced bending and DNA cyclization.

    PubMed

    Kahn, J D; Crothers, D M

    1992-07-15

    We have applied T4 ligase-mediated DNA cyclization kinetics to protein-induced bending in DNA. The presence and direction of a static bend can be inferred from J factors for cyclization of 150- to 160-base-pair minicircles, which include a catabolite activator protein binding site phased against a sequence-directed bend. We demonstrate a quasi-thermodynamic linkage between cyclization and protein binding; we find that properly phased DNAs bind catabolite activator protein approximately 200-fold more tightly as circles than as linear molecules. The results unambiguously distinguish DNA bends from isotropically flexible sites and can explain cooperative binding by proteins that need not contact each other.

  5. Chiral Bidentate NHC Ligands Based on the 1,1'-Binaphthyl Scaffold: Synthesis and Application in Transition-Metal-Catalyzed Asymmetric Reactions.

    PubMed

    Xu, Qin; Gu, Peng; Jiang, Hanchun; Wei, Yin; Shi, Min

    2016-12-01

    The use of the chiral 1,1'-binaphthyl scaffold to construct chiral ligands can be traced back for a long time. However, the development of bidentate NHC ligands based on the same backbone has only appeared recently. In this account, we describe the design and synthesis of a new family of chiral NHC ligands based on the 1,1'-binaphthyl scaffold and demonstrate the applications of these chiral NHC-metal complexes in the catalyzed oxidative kinetic resolution of secondary alcohols, asymmetric carbon-carbon bond formations, hydrosilylations, and cyclizations of 1,6-enynes. The chiral NHC ligands containing the 1,1'-binaphthyl backbone can be synthesized in good yields from enantiomerically pure 1,1'-binaphthyl-2,2'-diamine. These transition metals coordinated with chiral bidentate NHC ligands exhibit high catalytic activities and good enantioselectivities for a wide range of metal-catalyzed asymmetric reactions.

  6. Robust, Chiral, and Porous BINAP-Based Metal–Organic Frameworks for Highly Enantioselective Cyclization Reactions

    SciTech Connect

    Sawano, Takahiro; Thacker, Nathan C.; Lin, Zekai; McIsaac, Alexandra R.; Lin, Wenbin

    2016-05-06

    We report here the design of BINAP-based metal–organic frameworks and their postsynthetic metalation with Rh complexes to afford highly active and enantioselective single-site solid catalysts for the asymmetric cyclization reactions of 1,6-enynes. Robust, chiral, and porous Zr-MOFs of UiO topology, BINAP-MOF (I) or BINAP-dMOF (II), were prepared using purely BINAP-derived dicarboxylate linkers or by mixing BINAP-derived linkers with unfunctionalized dicarboxylate linkers, respectively. Upon metalation with Rh(nbd)2BF4 and [Rh(nbd)Cl]2/AgSbF6, the MOF precatalysts I·Rh(BF4) and I·Rh(SbF6) efficiently catalyzed highly enantioselective (up to 99% ee) reductive cyclization and Alder-ene cycloisomerization of 1,6-enynes, respectively. I·Rh catalysts afforded cyclization products at comparable enantiomeric excesses (ee’s) and 4–7 times higher catalytic activity than the homogeneous controls, likely a result of catalytic site isolation in the MOF which prevents bimolecular catalyst deactivation pathways. However, I·Rh is inactive in the more sterically encumbered Pauson–Khand reactions between 1,6-enynes and carbon monoxide. In contrast, with a more open structure, Rh-functionalized BINAP-dMOF, II·Rh, effectively catalyzed Pauson–Khand cyclization reactions between 1,6-enynes and carbon monoxide at 10 times higher activity than the homogeneous control. II·Rh was readily recovered and used three times in Pauson–Khand cyclization reactions without deterioration of yields or ee’s. Our work has expanded the scope of MOF-catalyzed asymmetric reactions and showed that the mixed linker strategy can effectively enlarge the open space around the catalytic active site to accommodate highly sterically demanding polycyclic metallocycle transition states/intermediates in asymmetric intramolecular cyclization reactions.

  7. Reversible Bergman cyclization by atomic manipulation

    NASA Astrophysics Data System (ADS)

    Schuler, Bruno; Fatayer, Shadi; Mohn, Fabian; Moll, Nikolaj; Pavliček, Niko; Meyer, Gerhard; Peña, Diego; Gross, Leo

    2016-03-01

    The Bergman cyclization is one of the most fascinating rearrangements in chemistry, with important implications in organic synthesis and pharmacology. Here we demonstrate a reversible Bergman cyclization for the first time. We induced the on-surface transformation of an individual aromatic diradical into a highly strained ten-membered diyne using atomic manipulation and verified the products by non-contact atomic force microscopy with atomic resolution. The diyne and diradical were stabilized by using an ultrathin NaCl film as the substrate, and the diyne could be transformed back into the diradical. Importantly, the diradical and the diyne exhibit different reactivity, electronic, magnetic and optical properties associated with the changes in the bond topology, and spin multiplicity. With this reversible, triggered Bergman cyclization we demonstrated switching on demand between the two reactive intermediates by means of selective C-C bond formation or cleavage, which opens up the field of radical chemistry for on-surface reactions by atomic manipulation.

  8. Reversible Bergman cyclization by atomic manipulation.

    PubMed

    Schuler, Bruno; Fatayer, Shadi; Mohn, Fabian; Moll, Nikolaj; Pavliček, Niko; Meyer, Gerhard; Peña, Diego; Gross, Leo

    2016-03-01

    The Bergman cyclization is one of the most fascinating rearrangements in chemistry, with important implications in organic synthesis and pharmacology. Here we demonstrate a reversible Bergman cyclization for the first time. We induced the on-surface transformation of an individual aromatic diradical into a highly strained ten-membered diyne using atomic manipulation and verified the products by non-contact atomic force microscopy with atomic resolution. The diyne and diradical were stabilized by using an ultrathin NaCl film as the substrate, and the diyne could be transformed back into the diradical. Importantly, the diradical and the diyne exhibit different reactivity, electronic, magnetic and optical properties associated with the changes in the bond topology, and spin multiplicity. With this reversible, triggered Bergman cyclization we demonstrated switching on demand between the two reactive intermediates by means of selective C-C bond formation or cleavage, which opens up the field of radical chemistry for on-surface reactions by atomic manipulation.

  9. Germacrene D Cyclization: An Ab Initio Investigation

    PubMed Central

    Setzer, William N.

    2008-01-01

    Essential oils that contain large concentrations of germacrene D are typically accompanied by cadinane sesquiterpenoids. The acid-catalyzed cyclization of germacrene D to give cadinane and selinane sesquiterpenes has been computationally investigated using both density functional (B3LYP/6-31G*) and post Hartree-Fock (MP2/6-31G* *) ab initio methods. The calculated energies are in general agreement with experimentally observed product distributions, both from acid-catalyzed cyclizations as well as distribution of the compounds in essential oils. PMID:19325722

  10. Knottin cyclization: impact on structure and dynamics

    PubMed Central

    Heitz, Annie; Avrutina, Olga; Le-Nguyen, Dung; Diederichsen, Ulf; Hernandez, Jean-François; Gracy, Jérôme; Kolmar, Harald; Chiche, Laurent

    2008-01-01

    Background Present in various species, the knottins (also referred to as inhibitor cystine knots) constitute a group of extremely stable miniproteins with a plethora of biological activities. Owing to their small size and their high stability, knottins are considered as excellent leads or scaffolds in drug design. Two knottin families contain macrocyclic compounds, namely the cyclotides and the squash inhibitors. The cyclotide family nearly exclusively contains head-to-tail cyclized members. On the other hand, the squash family predominantly contains linear members. Head-to-tail cyclization is intuitively expected to improve bioactivities by increasing stability and lowering flexibility as well as sensitivity to proteolytic attack. Results In this paper, we report data on solution structure, thermal stability, and flexibility as inferred from NMR experiments and molecular dynamics simulations of a linear squash inhibitor EETI-II, a circular squash inhibitor MCoTI-II, and a linear analog lin-MCoTI. Strikingly, the head-to-tail linker in cyclic MCoTI-II is by far the most flexible region of all three compounds. Moreover, we show that cyclic and linear squash inhibitors do not display large differences in structure or flexibility in standard conditions, raising the question as to why few squash inhibitors have evolved into cyclic compounds. The simulations revealed however that the cyclization increases resistance to high temperatures by limiting structure unfolding. Conclusion In this work, we show that, in contrast to what could have been intuitively expected, cyclization of squash inhibitors does not provide clear stability or flexibility modification. Overall, our results suggest that, for squash inhibitors in standard conditions, the circularization impact might come from incorporation of an additional loop sequence, that can contribute to the miniprotein specificity and affinity, rather than from an increase in conformational rigidity or protein stability

  11. ANSS Backbone Station Quality Assessment

    NASA Astrophysics Data System (ADS)

    Leeds, A.; McNamara, D.; Benz, H.; Gee, L.

    2006-12-01

    In this study we assess the ambient noise levels of the broadband seismic stations within the United States Geological Survey's (USGS) Advanced National Seismic System (ANSS) backbone network. The backbone consists of stations operated by the USGS as well as several regional network stations operated by universities. We also assess the improved detection capability of the network due to the installation of 13 additional backbone stations and the upgrade of 26 existing stations funded by the Earthscope initiative. This assessment makes use of probability density functions (PDF) of power spectral densities (PSD) (after McNamara and Buland, 2004) computed by a continuous noise monitoring system developed by the USGS- ANSS and the Incorporated Research Institutions in Seismology (IRIS) Data Management Center (DMC). We compute the median and mode of the PDF distribution and rank the stations relative to the Peterson Low noise model (LNM) (Peterson, 1993) for 11 different period bands. The power of the method lies in the fact that there is no need to screen the data for system transients, earthquakes or general data artifacts since they map into a background probability level. Previous studies have shown that most regional stations, instrumented with short period or extended short period instruments, have a higher noise level in all period bands while stations in the US network have lower noise levels at short periods (0.0625-8.0 seconds), high frequencies (8.0- 0.125Hz). The overall network is evaluated with respect to accomplishing the design goals set for the USArray/ANSS backbone project which were intended to increase broadband performance for the national monitoring network.

  12. Cyclization improves membrane permeation by antimicrobial peptoids

    SciTech Connect

    Andreev, Konstantin; Martynowycz, Michael W.; Ivankin, Andrey; Huang, Mia L.; Kuzmenko, Ivan; Meron, Mati; Lin, Binhua; Kirshenbaum, Kent; Gidalevitz, David

    2016-10-28

    The peptidomimetic approach has emerged as a powerful tool for overcoming the inherent limitations of natural antimicrobial peptides, where the therapeutic potential can be improved by increasing the selectivity and bioavailability. Restraining the conformational flexibility of a molecule may reduce the entropy loss upon its binding to the membrane. Experimental findings demonstrate that the cyclization of linear antimicrobial peptoids increases their bactericidal activity against Staphylococcus aureus while maintaining high hemolytic concentrations. Surface X-ray scattering shows that macrocyclic peptoids intercalate into Langmuir monolayers of anionic lipids with greater efficacy than for their linear analogues. Lastly, it is suggested that cyclization may increase peptoid activity by allowing the macrocycle to better penetrate the bacterial cell membrane.

  13. Cyclization improves membrane permeation by antimicrobial peptoids

    DOE PAGES

    Andreev, Konstantin; Martynowycz, Michael W.; Ivankin, Andrey; ...

    2016-10-28

    The peptidomimetic approach has emerged as a powerful tool for overcoming the inherent limitations of natural antimicrobial peptides, where the therapeutic potential can be improved by increasing the selectivity and bioavailability. Restraining the conformational flexibility of a molecule may reduce the entropy loss upon its binding to the membrane. Experimental findings demonstrate that the cyclization of linear antimicrobial peptoids increases their bactericidal activity against Staphylococcus aureus while maintaining high hemolytic concentrations. Surface X-ray scattering shows that macrocyclic peptoids intercalate into Langmuir monolayers of anionic lipids with greater efficacy than for their linear analogues. Lastly, it is suggested that cyclization maymore » increase peptoid activity by allowing the macrocycle to better penetrate the bacterial cell membrane.« less

  14. Silica gel-promoted tandem addition-cyclization reactions of 2-alkynylbenzenamines with isothiocyanates.

    PubMed

    Ding, Qiuping; Cao, Banpeng; Zong, Zhenzhen; Peng, Yiyuan

    2010-05-10

    Tandem addition-cyclization reactions of 2-alkynylbenzenamines with isothiocyanates promoted by silica gel are described. This reaction proceeds smoothly at 80 degrees C under metal- and solvent-free conditions, which provides an efficient and practical route for the generation of 2,4-dihydro-1H-benzo[d][1,3]thiazines. The recovered silica gel could be reused for several times.

  15. The backbone of a city

    NASA Astrophysics Data System (ADS)

    Scellato, S.; Cardillo, A.; Latora, V.; Porta, S.

    2006-03-01

    Recent studies have revealed the importance of centrality measures to analyze various spatial factors affecting human life in cities. Here we show how it is possible to extract the backbone of a city by deriving spanning trees based on edge betweenness and edge information. By using as sample cases the cities of Bologna and San Francisco, we show how the obtained trees are radically different from those based on edge lengths, and allow an extended comprehension of the “skeleton” of most important routes that so much affects pedestrian/vehicular flows, retail commerce vitality, land-use separation, urban crime and collective dynamical behaviours.

  16. Facile synthesis of cyanofurans via Michael-addition/cyclization of ene-yne-ketones with trimethylsilyl cyanide.

    PubMed

    Yu, Yue; Chen, Yang; Wu, Wanqing; Jiang, Huanfeng

    2017-01-03

    We have developed a Michael-addition/cyclization procedure between ene-yne-ketones and TMSCN under metal-free conditions. A wide range of cyanofurans was delivered in high yields, which could be further transformed to a series of furo-furanimines, furo-pyridazines or carboxamido-furans. In addition, deuterium-labeling experiments have been conducted to clarify the reaction pathway.

  17. Cyclization of farnesyl pyrophosphate to the sesquiterpene olefins humulene and caryophyllene by an enzyme system from sage (Salvia officinalis)

    SciTech Connect

    Croteau, R.; Gundy, A.

    1984-09-01

    A soluble enzyme preparation obtained from sage (Salvia officinalis) leaves was shown to catalyze the divalent metal-ion dependent cyclization of trans, trans-farnesyl pyrophosphate to the macrocyclic sesquiterpene olefins humulene and caryophyllene. The identities of the biosynthetic products were confirmed by radiochromatographic analysis and by preparation of crystalline derivatives, and the specificity of labeling in the cyclization reaction was established by chemical degradation of the olefins derived enzymatically from (1-3H2)farnesyl pyrophosphate. These results constitute the first report on the cyclization of farnesyl pyrophosphate to humulene and caryophyllene, two of the most common sesquiterpenes in nature, and the first description of a soluble sesquiterpene cyclase to be isolated from leaves of a higher plant.

  18. Dearomatizing Radical Cyclizations and Cyclization Cascades Triggered by Electron-Transfer Reduction of Amide-Type Carbonyls.

    PubMed

    Huang, Huan-Ming; Procter, David J

    2017-02-01

    Highly selective dearomatizing radical cyclizations and cyclization cascades, triggered by single electron transfer to amide-type carbonyls by SmI2-H2O-LiBr, provide efficient access to unprecedented spirocyclic scaffolds containing up to five stereocenters with high diastereocontrol. The first dearomatizing radical cyclizations involving radicals derived from amide carbonyls by single electron transfer take place under mild conditions and engage a range of aromatic and heteroaromatic systems present in the barbiturate substrates. The radical cyclizations deliver new polycyclic hemiaminals or enamines selectively, depending on the conditions employed, that are based on a medicinally proven scaffold and can be readily manipulated.

  19. A Radical Cyclization Approach to Isoindolobenzazepines. Synthesis of Lennoxamine.

    PubMed

    Rodríguez, Gema; Cid, M. Magdalena; Saá, Carlos; Castedo, Luis; Domínguez, Domingo

    1996-04-19

    The alkaloid lennoxamine (1) was synthesized by transannular cyclization of a 10-membered lactam obtained by intramolecular addition of an aryl radical to a (trimethylsilyl)acetylene. The isoindolo[1,2-b][3]benzazepine skeleton present in lennoxamine was also obtained by means of regioselective 7-endo-trig radical cyclization of methylenephthalimidines.

  20. Development of a Backbone Cyclic Peptide Library as Potential Antiparasitic Therapeutics Using Microwave Irradiation.

    PubMed

    Qvit, Nir; Kornfeld, Opher S

    2016-01-26

    Protein-protein interactions (PPIs) are intimately involved in almost all biological processes and are linked to many human diseases. Therefore, there is a major effort to target PPIs in basic research and in the pharmaceutical industry. Protein-protein interfaces are usually large, flat, and often lack pockets, complicating the discovery of small molecules that target such sites. Alternative targeting approaches using antibodies have limitations due to poor oral bioavailability, low cell-permeability, and production inefficiency. Using peptides to target PPI interfaces has several advantages. Peptides have higher conformational flexibility, increased selectivity, and are generally inexpensive. However, peptides have their own limitations including poor stability and inefficiency crossing cell membranes. To overcome such limitations, peptide cyclization can be performed. Cyclization has been demonstrated to improve peptide selectivity, metabolic stability, and bioavailability. However, predicting the bioactive conformation of a cyclic peptide is not trivial. To overcome this challenge, one attractive approach it to screen a focused library to screen in which all backbone cyclic peptides have the same primary sequence, but differ in parameters that influence their conformation, such as ring size and position. We describe a detailed protocol for synthesizing a library of backbone cyclic peptides targeting specific parasite PPIs. Using a rational design approach, we developed peptides derived from the scaffold protein Leishmania receptor for activated C-kinase (LACK). We hypothesized that sequences in LACK that are conserved in parasites, but not in the mammalian host homolog, may represent interaction sites for proteins that are critical for the parasites' viability. The cyclic peptides were synthesized using microwave irradiation to reduce reaction times and increase efficiency. Developing a library of backbone cyclic peptides with different ring sizes facilitates a

  1. Flexible backbone aromatic polyimide adhesives

    NASA Technical Reports Server (NTRS)

    Progar, Donald J.; St. Clair, Terry L.

    1989-01-01

    Continuing research at Langley Research Center on the synthesis and development of new inexpensive flexible aromatic polyimides as adhesives has resulted in a material identified as LARC-F-SO2 with similarities to polyimidesulfone, PISO2, and other flexible backbone polyimides recently reported by Progar and St. Clair. Also prepared and evaluated was an endcapped version of PISO2. These two polymers were compared with LARC-TPI and LARC-STPI, polyimides research in our laboratory and reported in the literature. The adhesive evaluation, primarily based on lap shear strength (LSS) tests at RT, 177 C and 204 C, involved preparing adhesive tapes, conducting bonding studies and exposing lap shear specimens to 204 C air for up to 1000 hrs and to a 72-hour water boil. The type of adhesive failure as well as the Tg was determined for the fractured specimens. The results indicate that LARC-TPI provides the highest LSSs. LARC-F-SO2, LARC-TPI and LARC-STPI all retain their strengths after thermal exposure for 1000 hrs and PISO2 retains greater than 80 percent of its control strengths. After a 72-hr water boil exposure, most of the four adhesive systems showed reduced strengths for all test temperatures although still retaining a high percentage of their original strength (greater than 60 percent) except for one case. The predominant failure type was cohesive with no significant change in the Tgs.

  2. Flexible backbone aromatic polyimide adhesives

    NASA Technical Reports Server (NTRS)

    Progar, Donald J.; St.clair, Terry L.

    1988-01-01

    Continuing research at Langley Research Center on the synthesis and development of new inexpensive flexible aromatic polyimides as adhesives has resulted in a material identified as LARC-F-SO2 with similarities to polyimidesulfone, PISO2, and other flexible backbone polyimides recently reported by Progar and St. Clair. Also prepared and evaluated was an endcapped version of PISO2. These two polymers were compared with LARC-TPI and LARC-STPI, polyimides research in our laboratory and reported in the literature. The adhesive evaluation, primarily based on lap shear strength (LSS) tests at RT, 177 C and 204 C, involved preparing adhesive tapes, conducting bonding studies and exposing lap shear specimens to 204 C air for up to 1000 hrs and to a 72-hour water boil. The type of adhesive failure as well as the Tg was determined for the fractured specimens. The results indicate that LARC-TPI provides the highest LSSs. LARC-F-SO2, LARC-TPI and LARC-STPI all retain their strengths after thermal exposure for 1000 hrs and PISO2 retains greater than 80 percent of its control strengths. After a 72-hr water boil exposure, most of the four adhesive systems showed reduced strengths for all test temperatures although still retaining a high percentage of their original strength (greater than 60 percent) except for one case. The predominant failure type was cohesive with no significant change in the Tgs.

  3. New modes for the osmium-catalyzed oxidative cyclization.

    PubMed

    Donohoe, Timothy J; Lindsay-Scott, Peter J; Parker, Jeremy S; Callens, Cedric K A

    2010-03-05

    The osmium-catalyzed oxidative cyclization of amino alcohol initiators formally derived from 1,4-dienes is an effective method for the construction of pyrrolidines, utilizing a novel reoxidant (4-nitropyridine N-oxide = NPNO). The cyclization of enantiopure syn- and anti-amino alcohols gives rise to enantiopure cis- and trans-2,5-disubstituted pyrrolidines, respectively. Moreover, the cyclization of bis-homoallylic amines bearing an exocyclic chelating group is shown to be a complementary method for trans-pyrrolidine formation.

  4. Transition-metal-free synthesis of imidazo[2,1-b]thiazoles and thiazolo[3,2-a]benzimidazoles via an S-propargylation/5-exo-dig cyclization/isomerization sequence using propargyl tosylates as substrates.

    PubMed

    Omar, Mohamed A; Frey, Wolfgang; Conrad, Jürgen; Beifuss, Uwe

    2014-11-07

    A transition-metal-free route for the synthesis of several N-fused heterocycles, including thiazolo[3,2-a]benzimidazoles and imidazo[2,1-b]thiazoles, is reported. The reaction between propargyl tosylates and 2-mercaptobenzimidazoles under basic conditions results in 3-substituted thiazolo[3,2-a]benzimidazoles, in yields up to 92% in a single synthesis step. With 2-mercaptoimidazoles as the substrate, the corresponding imidazo[2,1-b]thiazoles were exclusively obtained. The transformation is considered to proceed as an intermolecular S-propargylation that is followed by 5-exo-dig ring closure and double-bond isomerization.

  5. External Tank - The Structure Backbone

    NASA Technical Reports Server (NTRS)

    Welzyn, Kenneth; Pilet, Jeffrey C.; Diecidue-Conners, Dawn; Worden, Michelle; Guillot, Michelle

    2011-01-01

    The External Tank forms the structural backbone of the Space Shuttle in the launch configuration. Because the tank flies to orbital velocity with the Space Shuttle Orbiter, minimization of weight is mandatory, to maximize payload performance. Choice of lightweight materials both for structure and thermal conditioning was necessary. The tank is large, and unique manufacturing facilities, tooling, handling, and transportation operations were required. Weld processes and tooling evolved with the design as it matured through several block changes, to reduce weight. Non Destructive Evaluation methods were used to assure integrity of welds and thermal protection system materials. The aluminum-lithium alloy was used near the end of the program and weld processes and weld repair techniques had to be refined. Development and implementation of friction stir welding was a substantial technology development incorporated during the Program. Automated thermal protection system application processes were developed for the majority of the tank surface. Material obsolescence was an issue throughout the 40 year program. The final configuration and tank weight enabled international space station assembly in a high inclination orbit allowing international cooperation with the Russian Federal Space Agency. Numerous process controls were implemented to assure product quality, and innovative proof testing was accomplished prior to delivery. Process controls were implemented to assure cleanliness in the production environment, to control contaminants, and to preclude corrosion. Each tank was accepted via rigorous inspections, including non-destructive evaluation techniques, proof testing, and all systems testing. In the post STS-107 era, the project focused on ascent debris risk reduction. This was accomplished via stringent process controls, post flight assessment using substantially improved imagery, and selective redesigns. These efforts were supported with a number of test programs to

  6. Structural determinants of reductive terpene cyclization in iridoid biosynthesis

    PubMed Central

    Stevenson, Clare E. M.; Kamileen, Mohammed O.; Sherden, Nathaniel H.; Geu-Flores, Fernando; Lawson, David M.; O’Connor, Sarah E.

    2015-01-01

    The carbon skeleton of ecologically and pharmacologically important iridoid monoterpenes is formed in a reductive cyclization reaction unrelated to canonical terpene cyclization. Here we report the crystal structure of the recently discovered iridoid cyclase (Catharanthus roseus) bound to a mechanism-inspired inhibitor that illuminates substrate binding and catalytic function of the enzyme. Key features that distinguish iridoid synthase from its close homologue, progesterone 5β-reductase, are highlighted. PMID:26551396

  7. Utilizing redox-mediated Bergman cyclization toward the development of dual-action metalloenediyne therapeutics.

    PubMed

    Lindahl, Sarah E; Park, Hyunsoo; Pink, Maren; Zaleski, Jeffrey M

    2013-03-13

    Reaction of 2 equiv of 1,2-bis((diphenylphosphino)ethynyl)benzene (dppeb, 1) with Pt(cod)Cl2 followed by treatment with N2H4 yields the reduced Pt(0) metalloenediyne, Pt(dppeb)2, 2. This complex is stable to both air oxidation and metal-mediated Bergman cyclization under ambient conditions due to the nearly idealized tetrahedral geometry. Reaction of 2 with 1 equiv of I2 in the presence of excess 1,4-cyclohexadiene (1,4-CHD) radical trap rapidly and near-quantitatively generates the cis-Bergman-cyclized, diiodo product 3 ((31)P: δ = 41 ppm, J(Pt-P) = 3346 Hz) with concomitant loss of 1 equiv of uncyclized phosphine chelate ((31)P: δ = -33 ppm). In contrast, addition of 2 equiv of I2 in the absence of additional radical trap instantaneously forms a metastable Pt(dppeb)2(2+) intermediate species, 4, that is characterized by δ = 51 ppm in the (31)P NMR (J(Pt-P) = 3171 Hz) and ν(C≡C) = 2169 cm(-1) in the Raman profile, indicating that it is an uncyclized, bis-ligated complex. Over 24 h, 4 undergoes ligand exchange to form a neutral, square planar complex that spontaneously Bergman cyclizes at ambient temperature to give the crystalline product Pt(dppnap-I2)I2 (dppnap-I2 = (1,4-diiodonaphthalene-2,3-diyl)bis(diphenylphosphine)), 5, in 52% isolated yield. Computational analysis of the oxidation reaction proposes two plausible flattened tetrahedral structures for intermediate 4: one where the phosphine core has migrated to a trans-spanning chelate geometry, and a second, higher energy structure (3.3 kcal/mol) with two cis-chelating phosphine ligands (41° dihedral angle) via a restricted alkyne-terminal starting point. While the energies are disparate, the common theme in both structures is the elongated Pt-P bond lengths (>2.4 Å), indicating that nucleophilic ligand substitution by I(-) is on the reaction trajectory to the cyclized product 5. The efficiency of the redox-mediated Bergman cyclization reaction of this stable Pt(0) metalloenediyne prodrug and

  8. “Click” cyclized gallium-68 labeled peptides for molecular imaging and therapy: Synthesis and preliminary in vitro and in vivo evaluation in a melanoma model system

    PubMed Central

    Martin, Molly E.; O'Dorisio, M. Sue; Leverich, Whitney M.; Kloepping, Kyle C.; Schultz, Michael K.

    2013-01-01

    Cyclization techniques are used often to impart higher in vivo stability and binding affinity to peptide targeting vectors for molecular imaging and therapy. The two most often used techniques to impart these qualities are lactam bridge construction and disufide bond formation. While these techniques have been demonstrated to be effective, orthogonal protection/deprotection steps can limit achievable product yields. In this chapter, new α-melanocyte stimulating hormone (α-MSH) peptide analogs were synthesized and cyclized by copper-catalyzed terminal azide-alkyne cycloaddition “click” chemistry techniques. The α-MSH peptide and its cognate receptor (melanocortin receptor subtype 1, MC1R) represents a well-characterized model system to examine the effect of the triazole linkage for peptide cyclization on receptor binding in vitro and in vivo. Four new DOTA-conjugated α-MSH analogs were cyclized and evaluated by in vitro competitive binding assays, serum stability testing, and in vivo imaging by positron emission tomography (PET) of tumor bearing mice. These new DOTA-conjugated click-cyclized analogs exhibited selective high binding affinity (<2 nM) MC1R to melanoma cells in vitro, high stability in human serum, and produced high contrast PET/CT images of tumor xenografts. Gallium-68 labeled DOTA bioconjugates displayed rapid pharmacokinetics with receptor mediated tumor accumulation of up to 16±5 %ID/g. The results indicate that the triazole ring is an effective bioisosteric replacement for the standard lactam bridge assemblage for peptide cyclization. Radiolabeling results confirm that Cu catalyst is sufficiently removed prior to DOTA chelator addition to enable insertion of radiometals or stable metals for molecular imaging and therapy. Thus, these click-chemistry-cyclized variants show promise as agents for melanocortin receptor-targeted imaging and radionuclide therapy. PMID:22918759

  9. Extended weak bonding interactions in DNA: pi-stacking (base-base), base-backbone, and backbone-backbone interactions.

    PubMed

    Matta, Chérif F; Castillo, Norberto; Boyd, Russell J

    2006-01-12

    We report on several weak interactions in nucleic acids, which, collectively, can make a nonnegligible contribution to the structure and stability of these molecules. Fragments of DNA were obtained from previously determined accurate experimental geometries and their electron density distributions calculated using density functional theory (DFT). The electron densities were analyzed topologically according to the quantum theory of atoms in molecules (AIM). A web of closed-shell bonding interactions is shown to connect neighboring base pairs in base-pair duplexes and in dinuleotide steps. This bonding underlies the well-known pi-stacking interaction between adjacent nucleic acid bases and is characterized topologically for the first time. Two less widely appreciated modes of weak closed-shell interactions in nucleic acids are also described: (i) interactions between atoms in the bases and atoms belonging to the backbone (base-backbone) and (ii) interactions among atoms within the backbone itself (backbone-backbone). These interactions include hydrogen bonding, dihydrogen bonding, hydrogen-hydrogen bonding, and several other weak closed-shell X-Y interactions (X, Y = O, N, C). While each individual interaction is very weak and typically accompanied by perhaps 0.5-3 kcal/mol, the sum total of these interactions is postulated to play a role in stabilizing the structure of nucleic acids. The Watson-and-Crick hydrogen bonding is also characterized in detail at the experimental geometries as a prelude to the discussion of the modes of interactions listed in the title.

  10. Computational protein design with backbone plasticity

    PubMed Central

    MacDonald, James T.; Freemont, Paul S.

    2016-01-01

    The computational algorithms used in the design of artificial proteins have become increasingly sophisticated in recent years, producing a series of remarkable successes. The most dramatic of these is the de novo design of artificial enzymes. The majority of these designs have reused naturally occurring protein structures as ‘scaffolds’ onto which novel functionality can be grafted without having to redesign the backbone structure. The incorporation of backbone flexibility into protein design is a much more computationally challenging problem due to the greatly increased search space, but promises to remove the limitations of reusing natural protein scaffolds. In this review, we outline the principles of computational protein design methods and discuss recent efforts to consider backbone plasticity in the design process. PMID:27911735

  11. Discovery of cyclotides in the fabaceae plant family provides new insights into the cyclization, evolution, and distribution of circular proteins.

    PubMed

    Poth, Aaron G; Colgrave, Michelle L; Philip, Reynold; Kerenga, Bomai; Daly, Norelle L; Anderson, Marilyn A; Craik, David J

    2011-04-15

    Cyclotides are plant proteins whose defining structural features are a head-to-tail cyclized backbone and three interlocking disulfide bonds, which in combination are known as a cyclic cystine knot. This unique structural motif confers cyclotides with exceptional resistance to proteolysis. Their endogenous function is thought to be as plant defense agents, associated with their insecticidal and larval growth-inhibitory properties. However, in addition, an array of pharmaceutically relevant biological activities has been ascribed to cyclotides, including anti-HIV, anthelmintic, uterotonic, and antimicrobial effects. So far, >150 cyclotides have been elucidated from members of the Rubiaceae, Violaceae, and Cucurbitaceae plant families, but their wider distribution among other plant families remains unclear. Clitoria ternatea (Butterfly pea) is a member of plant family Fabaceae and through its usage in traditional medicine to aid childbirth bears similarity to Oldenlandia affinis, from which many cyclotides have been isolated. Using a combination of nanospray and matrix-assisted laser desorption ionization-time-of-flight (MALDI-TOF) analyses, we examined seed extracts of C. ternatea and discovered cyclotides in the Fabaceae, the third-largest family of flowering plants. We characterized 12 novel cyclotides, thus expanding knowledge of cyclotide distribution and evolution within the plant kingdom. The discovery of cyclotides containing novel sequence motifs near the in planta cyclization site has provided new insights into cyclotide biosynthesis. In particular, MS analyses of the novel cyclotides from C. ternatea suggest that Asn to Asp variants at the cyclization site are more common than previously recognized. Moreover, this study provides impetus for the examination of other economically and agriculturally significant species within Fabaceae, now the largest plant family from which cyclotides have been described.

  12. Brønsted acid-catalyzed Nazarov cyclization of pyrrole derivatives accelerated by microwave irradiation.

    PubMed

    Bachu, Prabhakar; Akiyama, Takahiko

    2009-07-15

    The Brønsted acid-catalyzed Nazarov cyclization of pyrrole derivatives was developed. Microwave irradiation accelerated the Nazarov cyclization significantly at 40 degrees C to give cyclopenta[b]pyrrole derivatives in excellent yields with high trans selectivity.

  13. Cyclization of conotoxins to improve their biopharmaceutical properties.

    PubMed

    Clark, Richard J; Akcan, Muharrem; Kaas, Quentin; Daly, Norelle L; Craik, David J

    2012-03-15

    Conotoxins are disulfide-rich peptides from the venoms of marine cone snails that are used in prey capture. Due to their exquisite potency and selectivity for different ion channels, receptors and transporters they have attracted much interest as leads in drug design. This article gives a brief background on conotoxins, describes their structures and highlights methods for synthetic cyclization to improve their biopharmaceutical properties. The proximity of the N and C termini of many conotoxins makes them particularly suitable for cyclization with linkers of on average five to seven amino acids. By linking the ends of conotoxins it is possible to significantly decrease their susceptibility to proteolysis without loss of their intrinsic biological activity. Here, the principles of conotoxin cyclization are illustrated with applications to the α- and χ- conotoxin classes, which have been implicated as leads for the treatment of pain and a range of other disorders including neuroprotection, schizophrenia, depression and cancer.

  14. Iridium-catalyzed reductive nitro-Mannich cyclization.

    PubMed

    Gregory, Alex W; Chambers, Alan; Hawkins, Alison; Jakubec, Pavol; Dixon, Darren J

    2015-01-02

    A new chemoselective reductive nitro-Mannich cyclization reaction sequence of nitroalkyl-tethered lactams has been developed. Relying on the rapid and chemoselective iridium(I)-catalyzed reduction of lactams to the corresponding enamine, subsequent nitro-Mannich cyclization of tethered nitroalkyl functionality provides direct access to important alkaloid natural-product-like structures in yields up to 81 % and in diastereoselectivities that are typically good to excellent. An in-depth understanding of the reaction mechanism has been gained through NMR studies and characterization of reaction intermediates. The new methodology has been applied to the total synthesis of (±)-epi-epiquinamide in four steps.

  15. The cyclization of arabinosyladenine-5-prime-phosphorimidazolide

    NASA Technical Reports Server (NTRS)

    Harada, Kazuo; Orgel, Leslie E.

    1991-01-01

    When arabinosyladenine-5-prime-phosphorimidazolide is allowed to decompose in aqueous solution at room temperature and pH 7.2, depending on the buffer, 5-24 percent is converted to the 2-prime,5-prime-cyclic phosphate (V). Although the extent of cyclization is much greater than for adenosine-5-prime-phosphorimidazolide, cyclization is less efficient than hydrolysis and so would not substantially decrease the efficiency of condensation reactions in aqueous solution. The significance of this result for prebiotic chemistry is discussed.

  16. The role of structural parameters in DNA cyclization

    DOE PAGES

    Alexandrov, Ludmil B.; Bishop, Alan R.; Rasmussen, Kim O.; ...

    2016-02-04

    The intrinsic bendability of DNA plays an important role with relevance for myriad of essential cellular mechanisms. The flexibility of a DNA fragment can be experimentally and computationally examined by its propensity for cyclization, quantified by the Jacobson-Stockmayer J factor. In this paper, we use a well-established coarse-grained three-dimensional model of DNA and seven distinct sets of experimentally and computationally derived conformational parameters of the double helix to evaluate the role of structural parameters in calculating DNA cyclization.

  17. Cyclic Graft Copolymer Unimolecular Micelles: Effects of Cyclization on Particle Morphology and Thermoresponsive Behavior

    PubMed Central

    2016-01-01

    The synthesis of cyclic amphiphilic graft copolymers with a hydrophobic polycarbonate backbone and hydrophilic poly(N-acryloylmorpholine) (PNAM) side arms via a combination of ring-opening polymerization (ROP), cyclization via copper-catalyzed azide–alkyne cycloaddition (CuAAC), and reversible addition–fragmentation chain transfer (RAFT) polymerization is reported. The ability of these cyclic graft copolymers to form unimolecular micelles in water is explored using a combination of light scattering, small-angle X-ray scattering (SAXS), and cryogenic transmission electron microscopy (cryoTEM) analyses, where particle size was found to increase with increasing PNAM arm length. Further analysis revealed differences in the solution conformations, loading capabilities, and morphologies of the cyclic graft copolymers in comparison to equivalent linear graft copolymer unimolecular micelle analogues. Furthermore, the cyclic and linear graft copolymers were found to exhibit significantly different cloud point temperatures. This study highlights how subtle changes in polymer architecture (linear graft copolymer versus cyclic graft copolymer) can dramatically influence a polymer’s nanostructure and its properties. PMID:27175037

  18. Cyclization of nucleotide analogues as an obstacle to polymerization

    NASA Technical Reports Server (NTRS)

    Hill, A. R. Jr; Nord, L. D.; Orgel, L. E.; Robins, R. K.

    1988-01-01

    Cyclization of activated nucleotide analogues by intramolecular phosphodiester-bond formation is likely to compete very effectively with template-directed condensation except in the cases of ribo- and arabinonucleotides. This could have excluded derivatives of most sugars from growing polyribonucleotide chains and thus reduced chain-termination in prebiotic polynucleotide synthesis.

  19. Catalytic enantioselective cyclization and C3-fluorination of polyenes.

    PubMed

    Cochrane, Nikki A; Nguyen, Ha; Gagne, Michel R

    2013-01-16

    (Xylyl-phanephos)Pt(2+) in combination with XeF(2) mediates the consecutive diastereoselective cation-olefin cyclization/fluorination of polyene substrates. Isolated yields were typically in the 60-69% range while enantioselectivities reached as high as 87%. The data are consistent with a stereoretentive fluorination of a P(2)Pt-alkyl cation intermediate.

  20. Structural basis for biosynthetic programming of fungal aromatic polyketide cyclization.

    PubMed

    Crawford, Jason M; Korman, Tyler P; Labonte, Jason W; Vagstad, Anna L; Hill, Eric A; Kamari-Bidkorpeh, Oliver; Tsai, Shiou-Chuan; Townsend, Craig A

    2009-10-22

    Polyketides are a class of natural products with diverse structures and biological activities. The structural variability of aromatic products of fungal nonreducing, multidomain iterative polyketide synthases (NR-PKS group of IPKSs) results from regiospecific cyclizations of reactive poly-beta-keto intermediates. How poly-beta-keto species are synthesized and stabilized, how their chain lengths are determined, and, in particular, how specific cyclization patterns are controlled have been largely inaccessible and functionally unknown until recently. A product template (PT) domain is responsible for controlling specific aldol cyclization and aromatization of these mature polyketide precursors, but the mechanistic basis is unknown. Here we present the 1.8 A crystal structure and mutational studies of a dissected PT monodomain from PksA, the NR-PKS that initiates the biosynthesis of the potent hepatocarcinogen aflatoxin B(1) in Aspergillus parasiticus. Despite having minimal sequence similarity to known enzymes, the structure displays a distinct 'double hot dog' (DHD) fold. Co-crystal structures with palmitate or a bicyclic substrate mimic illustrate that PT can bind both linear and bicyclic polyketides. Docking and mutagenesis studies reveal residues important for substrate binding and catalysis, and identify a phosphopantetheine localization channel and a deep two-part interior binding pocket and reaction chamber. Sequence similarity and extensive conservation of active site residues in PT domains suggest that the mechanistic insights gleaned from these studies will prove general for this class of IPKSs, and lay a foundation for defining the molecular rules controlling NR-PKS cyclization specificity.

  1. Constructing backbone network by using tinker algorithm

    NASA Astrophysics Data System (ADS)

    He, Zhiwei; Zhan, Meng; Wang, Jianxiong; Yao, Chenggui

    2017-01-01

    Revealing how a biological network is organized to realize its function is one of the main topics in systems biology. The functional backbone network, defined as the primary structure of the biological network, is of great importance in maintaining the main function of the biological network. We propose a new algorithm, the tinker algorithm, to determine this core structure and apply it in the cell-cycle system. With this algorithm, the backbone network of the cell-cycle network can be determined accurately and efficiently in various models such as the Boolean model, stochastic model, and ordinary differential equation model. Results show that our algorithm is more efficient than that used in the previous research. We hope this method can be put into practical use in relevant future studies.

  2. ANSS Backbone Station Installation and Site Characterization

    NASA Astrophysics Data System (ADS)

    Meremonte, M.; Leeds, A.; Overturf, D.; McMillian, J.; Allen, J.; McNamara, D.

    2004-12-01

    During 2004 several new broadband seismic stations have been deployed as a part of the USGS's Advanced National Seismic System (ANSS) backbone and regional networks. New stations include: ERPA, MNTX, OGLA, AMTX, NATX, KCCO, BMO, MARC, TZTN, LAO, DGMT, REDW, KSU1, MOOW, TPAW, LOHW, RAMW. Permanent station locations were chosen to minimize the local noise conditions by recording continuous data and using a quantitative analysis of the statistical distribution of noise power estimates. For each one-hour segment of continuous data, a power spectral density (PSD) is estimated and smoothed in full octave averages at 1/8 octave intervals. Powers for each 1/8 period interval were then accumulated in one dB power bins. A statistical analysis of power bins yields probability density functions (PDFs) as a function of noise power for each of the octave bands at each station and component. Examination of earthquake signal, artifacts related to station operation and episodic cultural noise in the PDFs allow us to estimate both the overall station quality and the level of earth noise at each potential backbone site. The main function of a seismic network, such as the ANSS, is to provide high quality data for earthquake monitoring, source studies, and Earth structure research. The utility of seismic data is greatly increased when noise levels are reduced. A good quantification and understanding of seismic noise is a first step at reducing noise levels in seismic data and improving overall data quality from the ANSS backbone network.

  3. Backbone cyclised peptides from plants show molluscicidal activity against the rice pest Pomacea canaliculata (golden apple snail).

    PubMed

    Plan, Manuel Rey R; Saska, Ivana; Cagauan, Arsenia G; Craik, David J

    2008-07-09

    Golden apple snails ( Pomacea canaliculata) are serious pests of rice in South East Asia. Cyclotides are backbone cyclized peptides produced by plants from Rubiaceae and Violaceae. In this study, we investigated the molluscicidal activity of cyclotides against golden apple snails. Crude cyclotide extracts from both Oldenlandia affinis and Viola odorata plants showed molluscicidal activity comparable to the synthetic molluscicide metaldehyde. Individual cyclotides from each extract demonstrated a range of molluscicidal activities. The cyclotides cycloviolacin O1, kalata B1, and kalata B2 were more toxic to golden apple snails than metaldehyde, while kalata B7 and kalata B8 did not cause significant mortality. The toxicity of the cyclotide kalata B2 on a nontarget species, the Nile tilapia ( Oreochromis niloticus), was three times lower than the common piscicide rotenone. Our findings suggest that the existing diversity of cyclotides in plants could be used to develop natural molluscicides.

  4. Mechanical Manipulation of Chemical Reactions: Reactivity Switching of Bergman Cyclizations.

    PubMed

    Krupička, Martin; Sander, Wolfram; Marx, Dominik

    2014-03-06

    Photoswitches incorporated into molecular frameworks have been used since a long time to trigger chemical processes on demand. Here, it is shown how mechanophores can be used as switches in order to drastically change the reactivity of a neighboring functional group as a function of external stress. The reactivities of cyclic enediynes, which are highly toxic agents when undergoing Bergman cyclization, roughly correlate with the distance between the bond-forming carbons in many cases. It is demonstrated how this distance, and thus enediyne reactivity, can be tuned upon applying mechanical stress. Depending on suitable substitution patterns, chemically inert species can be turned into highly reactive ones and vice versa, thus extending the concept of photoswitching to mechanoswitching. Moreover, depending on the derivative, it is found that C1-C5 cyclization becomes energetically preferred over the Bergman (C1-C6) pathway at nano-Newton forces, thus leading to a force-induced switch in selectivity in such cases.

  5. Telephone wire is backbone of security system

    SciTech Connect

    Brede, K.; Rackson, L.T.

    1995-09-01

    Video provides a variety of low-cost, high-quality solutions in today`s security environment. Cost-conscious managers of power generation stations, casinos, prison facilities, military bases and office buildings are considering using regular telephone wire (unshielded twisted pair-UTP) within their existing systems as the backbone of a video to the PC, personal and video-conferencing and training are other areas where phone wire in a building can save money and provide an alternative to coax or fiber for video. More and more, businesses and government agencies are meeting their needs efficiently by using telephone wires for more than just telephones.

  6. Survey of 2,11-cyclized cembranoids from Caribbean sources.

    PubMed

    Cóbar, Oscar M

    2009-01-01

    This review covers the literature published since the report of the first compound to December 2006, for marine natural 2,11-cyclized cembranoids isolated from Caribbean sources, with 30 citations, most of them from 2000 to 2006, referring to compounds isolated from the Caribbean gorgonian octocorals Briareum asbestinum, Briareum polyanthes, and Erithropodiun caribaeorum. The emphasis is on all of these natural compounds isolated to date, with an overview of their biogenetic pathway and relevant biological activity.

  7. Rational reprogramming of fungal polyketide first-ring cyclization

    PubMed Central

    Xu, Yuquan; Zhou, Tong; Zhou, Zhengfu; Su, Shiyou; Roberts, Sue A.; Montfort, William R.; Zeng, Jia; Chen, Ming; Zhang, Wei; Lin, Min; Zhan, Jixun; Molnár, István

    2013-01-01

    Resorcylic acid lactones and dihydroxyphenylacetic acid lactones represent important pharmacophores with heat shock response and immune system modulatory activities. The biosynthesis of these fungal polyketides involves a pair of collaborating iterative polyketide synthases (iPKSs): a highly reducing iPKS with product that is further elaborated by a nonreducing iPKS (nrPKS) to yield a 1,3-benzenediol moiety bridged by a macrolactone. Biosynthesis of unreduced polyketides requires the sequestration and programmed cyclization of highly reactive poly-β-ketoacyl intermediates to channel these uncommitted, pluripotent substrates to defined subsets of the polyketide structural space. Catalyzed by product template (PT) domains of the fungal nrPKSs and discrete aromatase/cyclase enzymes in bacteria, regiospecific first-ring aldol cyclizations result in characteristically different polyketide folding modes. However, a few fungal polyketides, including the dihydroxyphenylacetic acid lactone dehydrocurvularin, derive from a folding event that is analogous to the bacterial folding mode. The structural basis of such a drastic difference in the way a PT domain acts has not been investigated until now. We report here that the fungal vs. bacterial folding mode difference is portable on creating hybrid enzymes, and we structurally characterize the resulting unnatural products. Using structure-guided active site engineering, we unravel structural contributions to regiospecific aldol condensations and show that reshaping the cyclization chamber of a PT domain by only three selected point mutations is sufficient to reprogram the dehydrocurvularin nrPKS to produce polyketides with a fungal fold. Such rational control of first-ring cyclizations will facilitate efforts to the engineered biosynthesis of novel chemical diversity from natural unreduced polyketides. PMID:23509261

  8. Advanced routing in interplanetary backbone network

    NASA Astrophysics Data System (ADS)

    Xu, Ge; Sheng, Min; Wu, Chengke

    2007-11-01

    Interplanetary (IPN) Internet is a communication infrastructure providing communication services for scientific data delivery and navigation services for the explorer spacecrafts and orbiters of the future deep space missions. The interplanetary backbone network has the unique characteristics hence routing through the backbone network present many challenges that are not presented in traditional networks. Some routing algorithms have been proposed, in which, LPDB integrates the shortest path algorithm and the directional broadcast method to guarantee fast and reliable message delivery. Through this mutipath routing strategy, unpredictable link failures is addressed, but additional network overhead is introduced. In this paper, we propose an improvement of the LPDB named ALPDB in which the source could adaptively decide the next-hop nodes according to the link condition, hence reduce the network overhead. We model this algorithm on the network simulation platform of OPNET and compare it with other applicable algorithms in data passing ratio, data delay and network overhead. The result indicates that the ALPDB algorithm could not only guarantee reliable message delivery, but also decrease the cost significantly.

  9. Nonlinear backbone torsional pair correlations in proteins

    NASA Astrophysics Data System (ADS)

    Long, Shiyang; Tian, Pu

    2016-10-01

    Protein allostery requires dynamical structural correlations. Physical origin of which, however, remain elusive despite intensive studies during last two and half decades. Based on analysis of molecular dynamics (MD) simulation trajectories for ten proteins with different sizes and folds, we found that nonlinear backbone torsional pair (BTP) correlations, which are mainly spatially long-ranged and are dominantly executed by loop residues, exist extensively in most analyzed proteins. Examination of torsional motion for correlated BTPs suggested that such nonlinear correlations are mainly associated aharmonic torsional state transitions and in some cases strongly anisotropic local torsional motion of participating torsions, and occur on widely different and relatively longer time scales. In contrast, correlations between backbone torsions in stable α helices and β strands are mainly linear and spatially short-ranged, and are more likely to associate with harmonic local torsional motion. Further analysis revealed that the direct cause of nonlinear contributions are heterogeneous linear correlations. These findings implicate a general search strategy for novel allosteric modulation sites of protein activities.

  10. Nonlinear backbone torsional pair correlations in proteins

    PubMed Central

    Long, Shiyang; Tian, Pu

    2016-01-01

    Protein allostery requires dynamical structural correlations. Physical origin of which, however, remain elusive despite intensive studies during last two and half decades. Based on analysis of molecular dynamics (MD) simulation trajectories for ten proteins with different sizes and folds, we found that nonlinear backbone torsional pair (BTP) correlations, which are mainly spatially long-ranged and are dominantly executed by loop residues, exist extensively in most analyzed proteins. Examination of torsional motion for correlated BTPs suggested that such nonlinear correlations are mainly associated aharmonic torsional state transitions and in some cases strongly anisotropic local torsional motion of participating torsions, and occur on widely different and relatively longer time scales. In contrast, correlations between backbone torsions in stable α helices and β strands are mainly linear and spatially short-ranged, and are more likely to associate with harmonic local torsional motion. Further analysis revealed that the direct cause of nonlinear contributions are heterogeneous linear correlations. These findings implicate a general search strategy for novel allosteric modulation sites of protein activities. PMID:27708342

  11. Synthesis of 1,2,4-Triazolo[4,3-a]pyridines and Related Heterocycles by Sequential Condensation and Iodine-Mediated Oxidative Cyclization.

    PubMed

    Li, Ertong; Hu, Zhiyuan; Song, Lina; Yu, Wenquan; Chang, Junbiao

    2016-07-25

    A facile and efficient approach to access 1,2,4-triazolo[4,3-a]pyridines and related heterocycles has been accomplished through condensation of readily available aryl hydrazines with corresponding aldehydes followed by iodine-mediated oxidative cyclization. This transition-metal-free synthetic process is broadly applicable to a variety of aromatic, aliphatic, and α,β-unsaturated aldehydes, and can be conveniently conducted on the gram scale.

  12. Synthesis of oxazolidine-2,4-diones by a tandem phosphorus-mediated carboxylative condensation-cyclization reaction using atmospheric carbon dioxide.

    PubMed

    Zhang, Wen-Zhen; Xia, Tian; Yang, Xu-Tong; Lu, Xiao-Bing

    2015-04-11

    The oxazolidine-2,4-dione motif is found frequently in biologically important compounds. A tandem phosphorus-mediated carboxylative condensation of primary amines and α-ketoesters/base-catalyzed cyclization reaction have been developed. These processes provide a novel and convenient access to various oxazolidine-2,4-diones in a one-pot fashion using atmospheric carbon dioxide and readily available substrates under very mild and transition-metal-free conditions.

  13. Cyclization and N-iodosuccinimide-induced electrophilic iodocyclization of 3-aza-1,5-enynes to synthesize 1,2-dihydropyridines and 3-iodo-1,2-dihydropyridines.

    PubMed

    Xin, Xiaoyi; Wang, Dongping; Wu, Fan; Li, Xincheng; Wan, Boshun

    2013-04-19

    Metal-free cyclization and N-iodosuccinimide-induced electrophilic iodocyclization of readily available 3-aza-1,5-enynes have been developed. The reactions selectively give 1,2-dihydropyridines and 3-iodo-1,2-dihydropyridines involving an aza-Claisen rearrangement and a 6π-electrocyclization step. Furthermore, the reaction could be carried out in 10 g scale for the synthesis of 1,2-dihydropyridines.

  14. Cyclization strategies to polyenes using Pd(II)-catalyzed couplings of pinacol vinylboronates.

    PubMed

    Iafe, Robert G; Chan, Daniel G; Kuo, Jonathan L; Boon, Byron A; Faizi, Darius J; Saga, Tomomi; Turner, Jonathan W; Merlic, Craig A

    2012-08-17

    As a complement to Pd(0)-catalyzed cyclizations, seven Pd(II)-catalyzed cyclization strategies are reported. α,ω-Diynes are selectively hydroborated to bis(boronate esters), which cyclize under Pd(II)-catalysis producing a diverse array of small, medium, and macrocyclic polyenes with controlled E,E, Z,Z, or E,Z stereochemistry. Various functional groups are tolerated including aryl bromides, and applications are illustrated.

  15. Gas-Phase Intramolecular Cyclization of Argentinated N-Allylbenzamides

    NASA Astrophysics Data System (ADS)

    Sun, Hezhi; Chai, Yunfeng; Jin, Zhe; Sun, Cuirong; Pan, Yuanjiang

    2015-05-01

    The fragmentations of argentinated N-allylbenzamides have been exhaustively studied through collision-induced dissociation and through deuterium labeling. The intriguing elimination of AgOH is certified as the consequence of intramolecular cyclization between terminal olefin and carbonyl carbon following proton transfer to carbonyl oxygen, rather than simple enolization of amide. Linear free energy correlations and density functional theory (DFT) calculations were performed to understand the competitive relationship between AgOH loss and AgH loss, which results from the 1,2-elimination of α-hydrogen (to the amido nitrogen) with the silver.

  16. Cyclization cascade of allenyl azides: A dual mechanism

    PubMed Central

    López, Carlos Silva; Faza, Olalla Nieto; Feldman, Ken S.; Iyer, Malliga R.; Hester, D. Keith

    2008-01-01

    A density functional theory based computational approach to describing the mechanistic course of the allene azide cycloaddition cascade sequence has been developed. The results of these calculations permit characterization of key reactive intermediates (diradicals and/or indolidenes), and explain the different behaviour observed in the experimental studies between conjugated and non-conjugated species. Furthermore, computational analysis of certain intermediates offer insight into issues of regioselectivity and stereoselectivity in cases where different reaction channels are in competition, suggesting suitable substitutions to achieve a single regioisomer in the indole synthesis via azide-allene cyclization. PMID:17530848

  17. Structural Studies of Geosmin Synthase, a Bifunctional Sesquiterpene Synthase with αα Domain Architecture That Catalyzes a Unique Cyclization-Fragmentation Reaction Sequence.

    PubMed

    Harris, Golda G; Lombardi, Patrick M; Pemberton, Travis A; Matsui, Tsutomu; Weiss, Thomas M; Cole, Kathryn E; Köksal, Mustafa; Murphy, Frank V; Vedula, L Sangeetha; Chou, Wayne K W; Cane, David E; Christianson, David W

    2015-12-08

    Geosmin synthase from Streptomyces coelicolor (ScGS) catalyzes an unusual, metal-dependent terpenoid cyclization and fragmentation reaction sequence. Two distinct active sites are required for catalysis: the N-terminal domain catalyzes the ionization and cyclization of farnesyl diphosphate to form germacradienol and inorganic pyrophosphate (PPi), and the C-terminal domain catalyzes the protonation, cyclization, and fragmentation of germacradienol to form geosmin and acetone through a retro-Prins reaction. A unique αα domain architecture is predicted for ScGS based on amino acid sequence: each domain contains the metal-binding motifs typical of a class I terpenoid cyclase, and each domain requires Mg(2+) for catalysis. Here, we report the X-ray crystal structure of the unliganded N-terminal domain of ScGS and the structure of its complex with three Mg(2+) ions and alendronate. These structures highlight conformational changes required for active site closure and catalysis. Although neither full-length ScGS nor constructs of the C-terminal domain could be crystallized, homology models of the C-terminal domain were constructed on the basis of ∼36% sequence identity with the N-terminal domain. Small-angle X-ray scattering experiments yield low-resolution molecular envelopes into which the N-terminal domain crystal structure and the C-terminal domain homology model were fit, suggesting possible αα domain architectures as frameworks for bifunctional catalysis.

  18. Structural Studies of Geosmin Synthase, a Bifunctional Sesquiterpene Synthase with Alpha-Alpha Domain Architecture that Catalyzes a Unique Cyclization-Fragmentation Reaction Sequence

    PubMed Central

    Harris, Golda G.; Lombardi, Patrick M.; Pemberton, Travis A.; Matsui, Tsutomu; Weiss, Thomas M.; Cole, Kathryn E.; Köksal, Mustafa; Murphy, Frank V.; Vedula, L. Sangeetha; Chou, Wayne K.W.; Cane, David E.; Christianson, David W.

    2015-01-01

    Geosmin synthase from Streptomyces coelicolor (ScGS) catalyzes an unusual, metal-dependent terpenoid cyclization and fragmentation reaction sequence. Two distinct active sites are required for catalysis: the N-terminal domain catalyzes the ionization and cyclization of farnesyl diphosphate to form germacradienol and inorganic pyrophosphate (PPi), and the C-terminal domain catalyzes the protonation, cyclization, and fragmentation of germacradienol to form geosmin and acetone through a retro-Prins reaction. A unique αα domain architecture is predicted for ScGS based on amino acid sequence: each domain contains the metal-binding motifs typical of a class I terpenoid cyclase, and each domain requires Mg2+ for catalysis. Here, we report the X-ray crystal structure of the unliganded N-terminal domain of ScGS and the structure of its complex with 3 Mg2+ ions and alendronate. These structures highlight conformational changes required for active site closure and catalysis. Although neither full-length ScGS nor constructs of the C-terminal domain could be crystallized, homology models of the C-terminal domain were constructed based on ~36% sequence identity with the N-terminal domain. Small-angle X-ray scattering experiments yield low resolution molecular envelopes into which the N-terminal domain crystal structure and the C-terminal domain homology model were fit, suggesting possible αα domain architectures as frameworks for bifunctional catalysis. PMID:26598179

  19. Enantioselective Synthesis of 4- and 6-Azaindolines by a Cation-Directed Cyclization

    PubMed Central

    2016-01-01

    Functionalized 4- and 6-azaindolines are accessible with high levels of enantioselectivity by the cation-directed cyclization of aminopyridine-derived imines via phase-transfer catalysis. The extension of this methodology to diastereoselective cyclizations is also described. PMID:27709963

  20. Ultrasonic-assisted synthesis of flavones by oxidative cyclization of 2'-hydroxychalcones using iodine monochloride.

    PubMed

    Lahyani, Achraf; Trabelsi, Mahmoud

    2016-07-01

    This paper presents an efficient methodology for the synthesis of flavones via the oxidative cyclization of 2'-hydroxychalcones in the presence of iodine monochloride with DMSO under ultrasound irradiation. Ultrasonic irradiation enhances the cyclization reaction and leads to reduced reaction time at lower reaction temperatures while generating flavones with high yields.

  1. Strategies to control alkoxy radical-initiated relay cyclizations for the synthesis of oxygenated tetrahydrofuran motifs.

    PubMed

    Zhu, Hai; Leung, Joe C T; Sammis, Glenn M

    2015-01-16

    Radical relay cyclizations initiated by alkoxy radicals are a powerful tool for the rapid construction of substituted tetrahydrofurans. The scope of these relay cyclizations has been dramatically increased with the development of two strategies that utilize an oxygen atom in the substrate to accelerate the desired hydrogen atom transfer (HAT) over competing pathways. This has enabled a chemoselective 1,6-HAT over a competing 1,5-HAT. Furthermore, this allows for a chemoselective 1,5-HAT over competing direct cyclizations and β-fragmentations. Oxygen atom incorporation leads to a general increase in cyclization diastereoselectivity over carbon analogues. This chemoselective relay cyclization strategy was utilized in the improved synthesis of the tetrahydrofuran fragment in (−)-amphidinolide K.

  2. 40 CFR 721.990 - 1,4-Benzedicarboxylic acid, dimethyl ester, polymer with 1,4 - butanediol, cyclized.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... ester, polymer with 1,4 - butanediol, cyclized. 721.990 Section 721.990 Protection of Environment..., dimethyl ester, polymer with 1,4 - butanediol, cyclized. (a) Chemical substance and significant new uses..., polymer with 1,4 - butanediol, cyclized (PMN P-00-0789; CAS No. 263244-54-8) is subject to reporting...

  3. 40 CFR 721.990 - 1,4-Benzedicarboxylic acid, dimethyl ester, polymer with 1,4 - butanediol, cyclized.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... ester, polymer with 1,4 - butanediol, cyclized. 721.990 Section 721.990 Protection of Environment..., dimethyl ester, polymer with 1,4 - butanediol, cyclized. (a) Chemical substance and significant new uses..., polymer with 1,4 - butanediol, cyclized (PMN P-00-0789; CAS No. 263244-54-8) is subject to reporting...

  4. 40 CFR 721.990 - 1,4-Benzedicarboxylic acid, dimethyl ester, polymer with 1,4 - butanediol, cyclized.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... ester, polymer with 1,4 - butanediol, cyclized. 721.990 Section 721.990 Protection of Environment..., dimethyl ester, polymer with 1,4 - butanediol, cyclized. (a) Chemical substance and significant new uses..., polymer with 1,4 - butanediol, cyclized (PMN P-00-0789; CAS No. 263244-54-8) is subject to reporting...

  5. 40 CFR 721.990 - 1,4-Benzedicarboxylic acid, dimethyl ester, polymer with 1,4 - butanediol, cyclized.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... ester, polymer with 1,4 - butanediol, cyclized. 721.990 Section 721.990 Protection of Environment..., dimethyl ester, polymer with 1,4 - butanediol, cyclized. (a) Chemical substance and significant new uses..., polymer with 1,4 - butanediol, cyclized (PMN P-00-0789; CAS No. 263244-54-8) is subject to reporting...

  6. 40 CFR 721.990 - 1,4-Benzedicarboxylic acid, dimethyl ester, polymer with 1,4 - butanediol, cyclized.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... ester, polymer with 1,4 - butanediol, cyclized. 721.990 Section 721.990 Protection of Environment..., dimethyl ester, polymer with 1,4 - butanediol, cyclized. (a) Chemical substance and significant new uses..., polymer with 1,4 - butanediol, cyclized (PMN P-00-0789; CAS No. 263244-54-8) is subject to reporting...

  7. A Dioxane Template for Highly Selective Epoxy Alcohol Cyclizations

    PubMed Central

    Mousseau, James J.; Morten, Christopher J.

    2013-01-01

    Ladder polyether natural products are a class of natural products denoted by their high functional group density and large number of well-defined stereocenters. They comprise the toxic component of harmful algal blooms (HABs), having significant negative economic and environmental ramifications. However, their mode of action, namely blocking various cellular ion channels, also denotes their promise as potential anticancer agents. Understanding their potential mode of biosynthesis will not only help with developing ways to limit the damage of HABs, but would also facilitate the synthesis of a range of analogues with interesting biological activity. 1,3-Dioxan-5-ol substrates display remarkable ‘enhanced template effects’ in water-promoted epoxide cyclization processes en route to the synthesis of these ladder polyether natural products. In many cases they provide near complete endo to exo selectivity in the cyclization of epoxy alcohols, thereby strongly favouring the formation of tetrahydropyran (THP) over tetrahydrofuran (THF) rings. The effects of various Brønsted and Lewis acidic and basic conditions are explored to demonstrate the superior selectivity of the template over the previously reported THP-based epoxy alcohols. In addition, the consideration of other synthetic routes are also considered with the goal of gaining rapid access to a plethora of potential starting materials applicable towards the synthesis of ladder polyethers. Finally, cascade sequences with polyepoxides are investigated, further demonstrating the versatility of this new reaction template. PMID:23775936

  8. Free backbone carbonyls mediate rhodopsin activation

    PubMed Central

    Kimata, Naoki; Pope, Andreyah; Sanchez-Reyes, Omar B.; Eilers, Markus; Opefi, Chikwado A.; Ziliox, Martine; Reeves, Philip J.; Smith, Steven O.

    2016-01-01

    Conserved prolines in the transmembrane helices of G protein-coupled receptors (GPCRs) are often considered to function as hinges that divide the helix into two segments capable of independent motion. Depending on their potential to hydrogen-bond, the free C=O groups associated with these prolines can facilitate conformational flexibility, conformational switching or stabilize receptor structure. To address the role of conserved prolines in family A GPCRs, we focus on bovine rhodopsin, a GPCR in the visual receptor subfamily, using solid-state NMR spectroscopy. The free backbone C=O groups on helices H5 and H7 are found to stabilize the inactive rhodopsin structure through hydrogen-bonds to residues on adjacent helices. In response to light-induced isomerization of the retinal chromophore, hydrogen-bonding interactions involving these C=O groups are released facilitating H5 and H7 repacking onto the transmembrane core of the receptor. These results provide insights into the multiple structural and functional roles prolines play in membrane proteins. PMID:27376589

  9. The Backbone of the Climate Networks

    NASA Astrophysics Data System (ADS)

    Zou, Y.; Donges, J. F.; Marwan, N.; Kurths, J.

    2009-12-01

    We propose a method to reconstruct and analyze a complex network from data generated by a spatio-temporal dynamical system, relying on the nonlinear mutual information of time series analysis and betweenness centrality of complex network theory. We show, that this approach reveals a rich internal structure in complex climate networks constructed from reanalysis and model surface air temperature data. Our novel method uncovers peculiar wave-like structures of high energy flow, that we relate to global surface ocean currents. This points to a major role of the oceanic surface circulation in coupling and stabilizing the global temperature field in the long term mean (140 years for the model run and 60 years for reanalysis data). We find that these results cannot be obtained using classical linear methods of multivariate data analysis. Furthermore, we introduce significance tests to quantify the robustness of measured network properties to uncertainties. References: [1] J.F. Donges, Y. Zou, N. Marwan, and J. Kurths. Complex networks in climate dynamics -- -- Comparing linear and nonlinear network construction methods. European Physical Journal -- Special Topics, 174, 157-179, 2009. [2] J.F. Donges, Y. Zou, N. Marwan, and J. Kurths. Backbone of the climate network. Europhysics Letters, in press, 2009.

  10. High Speed Fibre Optic Backbone LAN

    NASA Astrophysics Data System (ADS)

    Tanimoto, Masaaki; Hara, Shingo; Kajita, Yuji; Kashu, Fumitoshi; Ikeuchi, Masaru; Hagihara, Satoshi; Tsuzuki, Shinji

    1987-09-01

    Our firm has developed the SUMINET-4100 series, a fibre optic local area network (LAN), to serve the communications system trunk line needs for facilities, such as steel refineries, automobile plants and university campuses, that require large transmission capacity, and for the backbone networks used in intelligent building systems. The SUMINET-4100 series is already in service in various fields of application. Of the networks available in this series, the SUMINET-4150 has a trunk line speed of 128 Mbps and the multiplexer used for time division multiplexing (TDM) was enabled by designing an ECL-TTL gate array (3000 gates) based custom LSI. The synchronous, full-duplex V.24 and V.3.5 interfaces (SUMINET-2100) are provided for use with general purpose lines. And the IBM token ring network, the SUMINET-3200, designed for heterogeneous PCs and the Ethernet can all be connected to sub loops. Further, the IBM 3270 TCA and 5080 CADAM can be connected in the local mode. Interfaces are also provided for the NTT high-speed digital service, the digital PBX systems, and the Video CODEC system. The built-in loop monitor (LM) and network supervisory processor (NSP) provide management of loop utilization and send loop status signals to the host CPU's network configuration and control facility (NCCF). These built-in functions allow both the computer system and LAN to be managed from a single source at the host. This paper outlines features of the SUMINET-4150 and provides an example of its installation.

  11. Detecting the Significant Flux Backbone of Escherichia coli metabolism.

    PubMed

    Güell, Oriol; Sagués, Francesc; Serrano, M Ángeles

    2017-04-09

    The heterogeneity of computationally predicted reaction fluxes in metabolic networks within a single flux state can be exploited to detect their significant flux backbone. Here, we disclose the backbone of Escherichia coli, and compare it with the backbones of other bacteria. We find that, in general, the core of the backbones is mainly composed of reactions in energy metabolism corresponding to ancient pathways. In E. coli, the synthesis of nucleotides and the metabolism of lipids form smaller cores which rely critically on energy metabolism. Moreover, the consideration of different media leads to the identification of pathways sensitive to environmental changes. The metabolic backbone of an organism is thus useful for tracing, simultaneously, both its evolution and adaptation fingerprints. This article is protected by copyright. All rights reserved.

  12. Oxidative cyclizations in orthosomycin biosynthesis expand the known chemistry of an oxygenase superfamily

    SciTech Connect

    McCulloch, Kathryn M.; McCranie, Emilianne K.; Smith, Jarrod A.; Sarwar, Maruf; Mathieu, Jeannette L.; Gitschlag, Bryan L.; Du, Yu; Bachmann, Brian O.; Iverson, T. M.

    2015-08-03

    Orthosomycins are oligosaccharide antibiotics that include avilamycin, everninomicin, and hygromycin B and are hallmarked by a rigidifying interglycosidic spirocyclic ortho-δ-lactone (orthoester) linkage between at least one pair of carbohydrates. A subset of orthosomycins additionally contain a carbohydrate capped by a methylenedioxy bridge. The orthoester linkage is necessary for antibiotic activity but rarely observed in natural products. Orthoester linkage and methylenedioxy bridge biosynthesis require similar oxidative cyclizations adjacent to a sugar ring. In this paper, we have identified a conserved group of nonheme iron, α-ketoglutarate–dependent oxygenases likely responsible for this chemistry. High-resolution crystal structures of the EvdO1 and EvdO2 oxygenases of everninomicin biosynthesis, the AviO1 oxygenase of avilamycin biosynthesis, and HygX of hygromycin B biosynthesis show how these enzymes accommodate large substrates, a challenge that requires a variation in metal coordination in HygX. Excitingly, the ternary complex of HygX with cosubstrate α-ketoglutarate and putative product hygromycin B identified an orientation of one glycosidic linkage of hygromycin B consistent with metal-catalyzed hydrogen atom abstraction from substrate. These structural results are complemented by gene disruption of the oxygenases evdO1 and evdMO1 from the everninomicin biosynthetic cluster, which demonstrate that functional oxygenase activity is critical for antibiotic production. Finally, our data therefore support a role for these enzymes in the production of key features of the orthosomycin antibiotics.

  13. Oxidative cyclizations in orthosomycin biosynthesis expand the known chemistry of an oxygenase superfamily

    PubMed Central

    McCulloch, Kathryn M.; McCranie, Emilianne K.; Smith, Jarrod A.; Sarwar, Maruf; Mathieu, Jeannette L.; Gitschlag, Bryan L.; Du, Yu; Bachmann, Brian O.; Iverson, T. M.

    2015-01-01

    Orthosomycins are oligosaccharide antibiotics that include avilamycin, everninomicin, and hygromycin B and are hallmarked by a rigidifying interglycosidic spirocyclic ortho-δ-lactone (orthoester) linkage between at least one pair of carbohydrates. A subset of orthosomycins additionally contain a carbohydrate capped by a methylenedioxy bridge. The orthoester linkage is necessary for antibiotic activity but rarely observed in natural products. Orthoester linkage and methylenedioxy bridge biosynthesis require similar oxidative cyclizations adjacent to a sugar ring. We have identified a conserved group of nonheme iron, α-ketoglutarate–dependent oxygenases likely responsible for this chemistry. High-resolution crystal structures of the EvdO1 and EvdO2 oxygenases of everninomicin biosynthesis, the AviO1 oxygenase of avilamycin biosynthesis, and HygX of hygromycin B biosynthesis show how these enzymes accommodate large substrates, a challenge that requires a variation in metal coordination in HygX. Excitingly, the ternary complex of HygX with cosubstrate α-ketoglutarate and putative product hygromycin B identified an orientation of one glycosidic linkage of hygromycin B consistent with metal-catalyzed hydrogen atom abstraction from substrate. These structural results are complemented by gene disruption of the oxygenases evdO1 and evdMO1 from the everninomicin biosynthetic cluster, which demonstrate that functional oxygenase activity is critical for antibiotic production. Our data therefore support a role for these enzymes in the production of key features of the orthosomycin antibiotics. PMID:26240321

  14. Oxidative cyclizations in orthosomycin biosynthesis expand the known chemistry of an oxygenase superfamily

    DOE PAGES

    McCulloch, Kathryn M.; McCranie, Emilianne K.; Smith, Jarrod A.; ...

    2015-08-03

    Orthosomycins are oligosaccharide antibiotics that include avilamycin, everninomicin, and hygromycin B and are hallmarked by a rigidifying interglycosidic spirocyclic ortho-δ-lactone (orthoester) linkage between at least one pair of carbohydrates. A subset of orthosomycins additionally contain a carbohydrate capped by a methylenedioxy bridge. The orthoester linkage is necessary for antibiotic activity but rarely observed in natural products. Orthoester linkage and methylenedioxy bridge biosynthesis require similar oxidative cyclizations adjacent to a sugar ring. In this paper, we have identified a conserved group of nonheme iron, α-ketoglutarate–dependent oxygenases likely responsible for this chemistry. High-resolution crystal structures of the EvdO1 and EvdO2 oxygenases ofmore » everninomicin biosynthesis, the AviO1 oxygenase of avilamycin biosynthesis, and HygX of hygromycin B biosynthesis show how these enzymes accommodate large substrates, a challenge that requires a variation in metal coordination in HygX. Excitingly, the ternary complex of HygX with cosubstrate α-ketoglutarate and putative product hygromycin B identified an orientation of one glycosidic linkage of hygromycin B consistent with metal-catalyzed hydrogen atom abstraction from substrate. These structural results are complemented by gene disruption of the oxygenases evdO1 and evdMO1 from the everninomicin biosynthetic cluster, which demonstrate that functional oxygenase activity is critical for antibiotic production. Finally, our data therefore support a role for these enzymes in the production of key features of the orthosomycin antibiotics.« less

  15. Identical repeated backbone of the human genome

    PubMed Central

    2010-01-01

    Background Identical sequences with a minimal length of about 300 base pairs (bp) have been involved in the generation of various meiotic/mitotic genomic rearrangements through non-allelic homologous recombination (NAHR) events. Genomic disorders and structural variation, together with gene remodelling processes have been associated with many of these rearrangements. Based on these observations, we identified and integrated all the 100% identical repeats of at least 300 bp in the NCBI version 36.2 human genome reference assembly into non-overlapping regions, thus defining the Identical Repeated Backbone (IRB) of the reference human genome. Results The IRB sequences are distributed all over the genome in 66,600 regions, which correspond to ~2% of the total NCBI human genome reference assembly. Important structural and functional elements such as common repeats, segmental duplications, and genes are contained in the IRB. About 80% of the IRB bp overlap with known copy-number variants (CNVs). By analyzing the genes embedded in the IRB, we were able to detect some identical genes not previously included in the Ensembl release 50 annotation of human genes. In addition, we found evidence of IRB gene copy-number polymorphisms in raw sequence reads of two diploid sequenced genomes. Conclusions In general, the IRB offers new insight into the complex organization of the identical repeated sequences of the human genome. It provides an accurate map of potential NAHR sites which could be used in targeting the study of novel CNVs, predicting DNA copy-number variation in newly sequenced genomes, and improve genome annotation. PMID:20096123

  16. Inter- versus intra-molecular cyclization of tripeptides containing tetrahydrofuran amino acids: a density functional theory study on kinetic control.

    PubMed

    Kumar, N V Suresh; Priyakumar, U Deva; Singh, Harjinder; Roy, Saumya; Chakraborty, Tushar Kanti

    2012-07-01

    Density functional B3LYP method was used to investigate the preference of intra- and inter-molecular cyclizations of linear tripeptides containing tetrahydrofuran amino acids. Two distinct model pathways were conceived for the cyclization reaction, and all possible transition states and intermediates were located. Analysis of the energetics indicate intermolecular cyclization being favored by both thermodynamic and kinetic control. Geometric and NBO analyses were performed to explain the trends obtained along both the reaction pathways. Conceptual density functional theory-based reactive indices also show that reaction pathways leading to intermolecular cyclization of the tripeptides are relatively more facile compared to intramolecular cyclization.

  17. Radiation safety system (RSS) backbones: Design, engineering, fabrication and installation

    SciTech Connect

    Wilmarth, J.E.; Sturrock, J.C.; Gallegos, F.R.

    1998-12-01

    The Radiation Safety System (RSS) Backbones are part of an electrical/electronic/mechanical system insuring safe access and exclusion of personnel to areas at the Los Alamos Neutron Science Center (LANSCE) accelerator. The RSS Backbones control the safety fusible beam plugs which terminate transmission of accelerated ion beams in response to predefined conditions. Any beam or access fault of the backbone inputs will cause insertion of the beam plugs in the low energy beam transport. The Backbones serve the function of tying the beam plugs to the access control systems, beam spill monitoring systems and current-level limiting systems. In some ways the Backbones may be thought of as a spinal column with beam plugs at the head and nerve centers along the spinal column. The two Linac Backbone segments and experimental area segments form a continuous cable plant over 3,500 feet from beam plugs to the tip on the longest tail. The Backbones were installed in compliance with current safety standards, such as installation of the two segments in separate conduits or tray. Monitoring for ground-faults and input wiring verification was an added enhancement to the system. The system has the capability to be tested remotely.

  18. Radiation Safety System (RSS) backbones: Design, engineering, fabrication, and installation

    SciTech Connect

    Wilmarth, J. E.; Sturrock, J. C.; Gallegos, F. R.

    1998-12-10

    The Radiation Safety System (RSS) backbones are part of an electrical/electronic/mechanical system ensuring safe access and exclusion of personnel to areas at the Los Alamos Neutron Science Center (LANSCE) accelerator. The RSS backbones control the safety-fusible beam plugs which terminate transmission of accelerated ion beams in response to predefined conditions. Any beam or access fault of the backbone inputs will cause insertion of the beam plugs in the low-energy beam transport. The backbones serve the function of tying the beam plugs to the access control systems, beam spill monitoring systems and current-level limiting systems. In some ways the backbones may be thought of as a spinal column with beam plugs at the head and nerve centers along the spinal column. The two linac backbone segments and the experimental area segments form a continuous cable plant over 3500 feet from the beam plugs to the tip on the longest tail. The backbones were installed in compliance with current safety standards, such as installation of the two segments in separate conduits or tray. Monitoring for ground-faults and input wiring verification was an added enhancement to the system. The system has the capability to be tested remotely.

  19. Radiation Safety System (RSS) backbones: Design, engineering, fabrication, and installation

    SciTech Connect

    Wilmarth, J.E.; Sturrock, J.C.; Gallegos, F.R.

    1998-12-01

    The Radiation Safety System (RSS) backbones are part of an electrical/electronic/mechanical system ensuring safe access and exclusion of personnel to areas at the Los Alamos Neutron Science Center (LANSCE) accelerator. The RSS backbones control the safety-fusible beam plugs which terminate transmission of accelerated ion beams in response to predefined conditions. Any beam or access fault of the backbone inputs will cause insertion of the beam plugs in the low-energy beam transport. The backbones serve the function of tying the beam plugs to the access control systems, beam spill monitoring systems and current-level limiting systems. In some ways the backbones may be thought of as a spinal column with beam plugs at the head and nerve centers along the spinal column. The two linac backbone segments and the experimental area segments form a continuous cable plant over 3500 feet from the beam plugs to the tip on the longest tail. The backbones were installed in compliance with current safety standards, such as installation of the two segments in separate conduits or tray. Monitoring for ground-faults and input wiring verification was an added enhancement to the system. The system has the capability to be tested remotely. {copyright} {ital 1998 American Institute of Physics.}

  20. Radiation Safety System (RSS) backbones: Design, engineering, fabrication, and installation

    NASA Astrophysics Data System (ADS)

    Wilmarth, J. E.; Sturrock, J. C.; Gallegos, F. R.

    1998-12-01

    The Radiation Safety System (RSS) backbones are part of an electrical/electronic/mechanical system ensuring safe access and exclusion of personnel to areas at the Los Alamos Neutron Science Center (LANSCE) accelerator. The RSS backbones control the safety-fusible beam plugs which terminate transmission of accelerated ion beams in response to predefined conditions. Any beam or access fault of the backbone inputs will cause insertion of the beam plugs in the low-energy beam transport. The backbones serve the function of tying the beam plugs to the access control systems, beam spill monitoring systems and current-level limiting systems. In some ways the backbones may be thought of as a spinal column with beam plugs at the head and nerve centers along the spinal column. The two linac backbone segments and the experimental area segments form a continuous cable plant over 3500 feet from the beam plugs to the tip on the longest tail. The backbones were installed in compliance with current safety standards, such as installation of the two segments in separate conduits or tray. Monitoring for ground-faults and input wiring verification was an added enhancement to the system. The system has the capability to be tested remotely.

  1. Sequential Norrish type II photoelimination and intramolecular aldol cyclization of α-diketones: synthesis of polyhydroxylated cyclopentitols by ring contraction of hexopyranose carbohydrate derivatives.

    PubMed

    Alvarez-Dorta, Dimitri; León, Elisa I; Kennedy, Alan R; Martín, Angeles; Pérez-Martín, Inés; Riesco-Fagundo, Concepción; Suárez, Ernesto

    2013-07-29

    The excitation of the innermost carbonyl of nono-2,3-diulose derivatives by irradiation with visible-light initiates a sequential Norrish type II photoelimination and aldol cyclization process that finally gives polyfunctionalized cyclopentitols. The rearrangement has been confirmed by the isolation of stable acyclic photoenol intermediates that can be independently cyclized by a thermal 5-(enolexo)-exo-trig uncatalyzed aldol reaction with high diastereoselectivity. In this last step, the large deuterium kinetic isotope effect found for the 1,5-hydrogen atom transfer seems to indicate that the aldol reaction runs through a concerted pericyclic mechanism. Owing to the ready availability of pyranose sugars of various configurations, this protocol has been used to study the influence of pyranose ring-substituents on the diastereoselectivity of the aldol cyclization reaction. In contrast with other pyranose ring contraction methodologies no transition-metal reagents are needed and the sequential rearrangement occurs simply by using visible light and moderate heating (0 to 60 °C).

  2. A Pd(0)-Mediated Indole (Macro)cyclization Reaction

    PubMed Central

    Breazzano, Steven P.; Poudel, Yam B.; Boger, Dale L.

    2013-01-01

    Herein, we report a systematic study of the Larock indole annulation designed to explore the scope and define the generality of its use in macrocyclization reactions, its use in directly accessing the chloropeptin I versus II DEF ring system as well as key unnatural isomers, its utility for both peptide-derived and more conventional carbon-chain based macrocycles, and its extension to intramolecular cyclizations with formation of common ring sizes. The studies define a powerful method complementary to the Stille or Suzuki cross-coupling reactions for the synthesis of cyclic or macrocyclic ring systems containing an embedded indole, tolerating numerous functional groups and incorporating various (up to 28-membered) ring sizes. As a result of the efforts to expand the usefulness and scope of the reaction, we also disclose a catalytic variant of the reaction along with a powerful Pd2(dba)3 derived catalyst system, and an examination of the factors impacting reactivity and catalysis. PMID:23298368

  3. Autocatalytic cyclization of an excised intervening sequence RNA is a cleavage-ligation reaction.

    PubMed

    Zaug, A J; Grabowski, P J; Cech, T R

    The intervening sequence (IVS) of the Tetrahymena ribosomal RNA precursor is excised as a linear RNA molecule which subsequently cyclizes itself in a protein-independent reaction. Cyclization involves cleavage of the linear IVS RNA 15 nucleotides from its 5' end and formation of a phosphodiester bond between the new 5' phosphate and the original 3'-hydroxyl terminus of the IVS. This recombination mechanism is analogous to that by which splicing of the precursor RNA is achieved. The circular molecules appear to have no direct function in RNA splicing, and we propose the cyclization serves to prevent unwanted RNA from driving the splicing reactions backwards.

  4. Branching Reaction in Melanogenesis: The Effect of Intramolecular Cyclization on Thiol Binding

    NASA Astrophysics Data System (ADS)

    Kishida, Ryo; Kasai, Hideaki; Aspera, Susan Meñez; Arevalo, Ryan Lacdao; Nakanishi, Hiroshi

    2017-01-01

    With the aid of density functional theory-based first principles calculations, we investigated energetics and electronic structure changes in reactions involving dopaquinone to give insights into the branching behaviors in melanogenesis. The reactions we investigated are the intramolecular cyclization and thiol binding, which are competing with each other. It was found that, in order to accomplish thiol binding, charge transfer of around one electron from thiol to dopaquinone occurs. Furthermore, intramolecular cyclization of dopaquinone increases the lowest unnoccupied molecular orbital level substantially. This result clearly shows prevention of the binding of thiol by intramolecular cyclization.

  5. A backbone lever-arm effect enhances polymer mechanochemistry.

    PubMed

    Klukovich, Hope M; Kouznetsova, Tatiana B; Kean, Zachary S; Lenhardt, Jeremy M; Craig, Stephen L

    2013-02-01

    Mechanical forces along a polymer backbone can be used to bring about remarkable reactivity in embedded mechanically active functional groups, but little attention has been paid to how a given polymer backbone delivers that force to the reactant. Here, single-molecule force spectroscopy was used to directly quantify and compare the forces associated with the ring opening of gem-dibromo and gem-dichlorocyclopropanes affixed along the backbone of cis-polynorbornene and cis-polybutadiene. The critical force for isomerization drops by about one-third in the polynorbornene scaffold relative to polybutadiene. The root of the effect lies in more efficient chemomechanical coupling through the polynorbornene backbone, which acts as a phenomenological lever with greater mechanical advantage than polybutadiene. The experimental results are supported computationally and provide the foundation for a new strategy by which to engineer mechanochemical reactivity.

  6. A backbone lever-arm effect enhances polymer mechanochemistry

    NASA Astrophysics Data System (ADS)

    Klukovich, Hope M.; Kouznetsova, Tatiana B.; Kean, Zachary S.; Lenhardt, Jeremy M.; Craig, Stephen L.

    2013-02-01

    Mechanical forces along a polymer backbone can be used to bring about remarkable reactivity in embedded mechanically active functional groups, but little attention has been paid to how a given polymer backbone delivers that force to the reactant. Here, single-molecule force spectroscopy was used to directly quantify and compare the forces associated with the ring opening of gem-dibromo and gem-dichlorocyclopropanes affixed along the backbone of cis-polynorbornene and cis-polybutadiene. The critical force for isomerization drops by about one-third in the polynorbornene scaffold relative to polybutadiene. The root of the effect lies in more efficient chemomechanical coupling through the polynorbornene backbone, which acts as a phenomenological lever with greater mechanical advantage than polybutadiene. The experimental results are supported computationally and provide the foundation for a new strategy by which to engineer mechanochemical reactivity.

  7. Large-scale measurement and modeling of backbone Internet traffic

    NASA Astrophysics Data System (ADS)

    Roughan, Matthew; Gottlieb, Joel

    2002-07-01

    There is a brewing controversy in the traffic modeling community concerning how to model backbone traffic. The fundamental work on self-similarity in data traffic appears to be contradicted by recent findings that suggest that backbone traffic is smooth. The traffic analysis work to date has focused on high-quality but limited-scope packet trace measurements; this limits its applicability to high-speed backbone traffic. This paper uses more than one year's worth of SNMP traffic data covering an entire Tier 1 ISP backbone to address the question of how backbone network traffic should be modeled. Although the limitations of SNMP measurements do not permit us to comment on the fine timescale behavior of the traffic, careful analysis of the data suggests that irrespective of the variation at fine timescales, we can construct a simple traffic model that captures key features of the observed traffic. Furthermore, the model's parameters are measurable using existing network infrastructure, making this model practical in a present-day operational network. In addition to its practicality, the model verifies basic statistical multiplexing results, and thus sheds deep insight into how smooth backbone traffic really is.

  8. Constructing optimal backbone segments for joining fixed DNA base pairs.

    PubMed Central

    Mazur, J; Jernigan, R L; Sarai, A

    1996-01-01

    A method is presented to link a sequence of space-fixed base pairs by the sugar-phosphate segments of single nucleotides and to evaluate the effects in the backbone caused by this positioning of the bases. The entire computational unit comprises several nucleotides that are energy-minimized, subject to constraints imposed by the sugar-phosphate backbone segments being anchored to space-fixed base pairs. The minimization schemes are based on two stages, a conjugate gradient method followed by a Newton-Raphson algorithm. Because our purpose is to examine the response, or relaxation, of an artificially stressed backbone, it is essential to be able to obtain, as closely as possible, a lowest minimum energy conformation of the backbone segment in conformational space. For this purpose, an algorithm is developed that leads to the generation of an assembly of many local energy minima. From these sets of local minima, one conformation corresponding to the one with the lowest minimum is then selected and designated to represent the backbone segment at its minimum. The effective electrostatic potential of mean force is expressed in terms of adjustable parameters that incorporate solvent screening action in the Coulombic interactions between charged backbone atoms; these parameters are adjusted to obtain the best fit of the nearest-neighbor phosphorous atoms in an x-ray structure. PMID:8874023

  9. SpyTag/SpyCatcher Cyclization Enhances the Thermostability of Firefly Luciferase

    PubMed Central

    Si, Meng; Xu, Qing

    2016-01-01

    SpyTag can spontaneously form a covalent isopeptide bond with its protein partner SpyCatcher. Firefly luciferase from Photinus pyralis was cyclized in vivo by fusing SpyCatcher at the N terminus and SpyTag at the C terminus. Circular LUC was more thermostable and alkali-tolerant than the wild type, without compromising the specific activity. Structural analysis indicated that the cyclized LUC increased the thermodynamic stability of the structure and remained more properly folded at high temperatures when compared with the wild type. We also prepared an N-terminally and C-terminally shortened form of the SpyCatcher protein and cyclization using this truncated form led to even more thermostability than the original form. Our findings suggest that cyclization with SpyTag and SpyCatcher is a promising and effective strategy to enhance thermostability of enzymes. PMID:27658030

  10. Triazine-Based Sequence-Defined Polymers with Side-Chain Diversity and Backbone-Backbone Interaction Motifs.

    PubMed

    Grate, Jay W; Mo, Kai-For; Daily, Michael D

    2016-03-14

    Sequence control in polymers, well-known in nature, encodes structure and functionality. Here we introduce a new architecture, based on the nucleophilic aromatic substitution chemistry of cyanuric chloride, that creates a new class of sequence-defined polymers dubbed TZPs. Proof of concept is demonstrated with two synthesized hexamers, having neutral and ionizable side chains. Molecular dynamics simulations show backbone-backbone interactions, including H-bonding motifs and pi-pi interactions. This architecture is arguably biomimetic while differing from sequence-defined polymers having peptide bonds. The synthetic methodology supports the structural diversity of side chains known in peptides, as well as backbone-backbone hydrogen-bonding motifs, and will thus enable new macromolecules and materials with useful functions.

  11. Syntheses, thermal reactivities, and computational studies of aryl-fused quinoxalenediynes: effect of extended benzannelation on Bergman cyclization energetics.

    PubMed

    Spence, John D; Rios, Andro C; Frost, Megan A; McCutcheon, Claire M; Cox, Christopher D; Chavez, Sonia; Fernandez, Ramiro; Gherman, Benjamin F

    2012-11-16

    A series of [b]-fused 6,7-diethynylquinoxaline derivatives have been synthesized through an imine condensation strategy to examine the effect of extended benzannelation on the thermal reactivity of enediynes. Absorption and emission spectra of the highly conjugated quinoxalenediynes were red-shifted approximately 100-200 nm relative to those of 1,2-diethynylbenzene. Strong exotherms indicative of enediyne cyclization were observed by differential scanning calorimetry, while solution cyclizations in the presence of 1,4-cyclohexadiene confirmed C(1)-C(6) Bergman cyclization. To provide further insight into Bergman cyclization energetics, computational studies were performed to compare changes in the cyclization enthalpy barrier, reaction enthalpy, and barrier of retro-Bergman ring-opening. Extension of benzannelation from 1,2-diethynylbenzene to either 2,3-diethynylnaphthalene or the 6,7-diethynylquinoxalines had a minimal effect on the cyclization barrier. In comparison, the enthalpies of cyclization were increased upon linearly extended benzannelation, which resulted in reduced barriers to retro-Bergman ring-opening. In addition, the orientation of extended benzannelation was found to have a significant effect on the cyclization endothermicity. In particular, 5,6-diethynylquinoxaline exhibited a 6.9 kcal/mol decrease in cyclization enthalpy compared to 6,7-diethynylquinoxaline due to increased aromatic stabilization energy in the respective angularly versus linearly fused azaacene cyclized products.

  12. Organic Photocatalytic Cyclization of Polyenes: A Visible-Light-Mediated Radical Cascade Approach.

    PubMed

    Yang, Zhongbo; Li, Han; Zhang, Long; Zhang, Ming-Tian; Cheng, Jin-Pei; Luo, Sanzhong

    2015-10-12

    A visible-light-mediated, organic photocatalytic stereoselective radical cascade cyclization of polyprenoids is described. The desired cascade cyclization products are achieved in good yields and high stereoselectivities with eosin Y as photocatalyst in hexafluoro-2-propanol. The catalyst system is also suitable for 1,3-dicarbonyl compounds, which require only catalytic amounts of LiBr to promote the formation of the corresponding enols.

  13. Microwave-accelerated spiro-cyclizations of o-halobenzyl cyclohexenyl ethers by palladium(0) catalysis.

    PubMed

    Svennebring, Andreas; Nilsson, Peter; Larhed, Mats

    2007-07-20

    A number of new spiro[cyclohexane-1,1'-isobenzofuran]-based compounds was synthesized by palladium(0)-catalyzed 5-exo cyclization of a series of cyclohexenyl o-halobenzyl ethers. Controlled microwave heating was found to promote both product yield and reaction rate without compromising the selectivity. Heck cyclization of aryl iodide 6, 2-(2-iodobenzyloxy)cyclohex-2-enyl acetate, proceeded selectively without involvement of the allylic acetate functionality.

  14. A Raney Cobalt Mediated Reductive Cyclization Route to the Uleine Alkaloid Gilbertine.

    PubMed

    Tang, Fei; Banwell, Martin G; Willis, Anthony C

    2016-11-04

    Reductive cyclization of the 2,4,5-trisubstituted cyclohexenone 16 using dihydogen in the presence of Raney cobalt afforded compound 17 (60%) that could be elaborated over a further five steps, including one involving a cationic cyclization process, into the racemic modification of the unusual uleine alkaloid gilbertine. Single-crystal X-ray analyses of compounds (±)-1, 16, and a derivative of 17 are reported.

  15. Synthesis of tyrocidine A and its analogues by spontaneous cyclization in aqueous solution.

    PubMed

    Bu, Xianzhang; Wu, Xiaoming; Xie, Guiyang; Guo, Zhihong

    2002-08-22

    [reaction: see text] Head-to-tail cyclization of peptides is a multistep process involving tedious C-terminal activation and side chain protection. Here we report a facile, quantitative cyclization method in aqueous ammonia solution for the total syntheses of the cyclic decapeptide antibiotic Tyrocidine A and its analogues from their fully deprotected linear thioester precursors on a solid support. This novel aqueous method is conformation-dependent and may be applicable to syntheses of other natural cyclic peptides.

  16. Powdered KOH in DMSO: an efficient base for asymmetric cyclization via memory of chirality at ambient temperature.

    PubMed

    Kawabata, Takeo; Moriyama, Katsuhiko; Kawakami, Shimpei; Tsubaki, Kazunori

    2008-03-26

    Enolate chemistry has been extensively used for stereoselective C-C bond formation, in which metal amide bases are frequently employed in strictly anhydrous solvents at low temperatures. However, we found that asymmetric intramolecular C-C bond formation via axially chiral enolate intermediates proceeded in up to 99% ee at 20 degrees C using powdered KOH in dry or wet DMSO as a base. The enantioselectivity was even higher than that of the corresponding reactions with potassium hexamethyldisilazide in DMF at -60 degrees C. The racemization barrier of the axially chiral enolate intermediate was estimated to be approximately 15.5 kcal/mol. On the basis of the barrier, the chiral enolate intermediate was supposed to undergo cyclization within approximately 10(-3) sec at 20 degrees C after it is generated to give the product in >or=99% ee. Thus, enolates generated with powdered KOH in DMSO were expected to be extremely reactive.

  17. SpyTag/SpyCatcher cyclization confers resilience to boiling on a mesophilic enzyme.

    PubMed

    Schoene, Christopher; Fierer, Jacob O; Bennett, S Paul; Howarth, Mark

    2014-06-10

    SpyTag is a peptide that spontaneously forms an amide bond with its protein partner SpyCatcher. SpyTag was fused at the N terminus of β-lactamase and SpyCatcher at the C terminus so that the partners could react to lock together the termini of the enzyme. The wild-type enzyme aggregates above 37 °C, with irreversible loss of activity. Cyclized β-lactamase was soluble even after heating at 100 °C; after cooling, the catalytic activity was restored. SpyTag/SpyCatcher cyclization led to a much larger increase in stability than that achieved through point mutation or alternative approaches to cyclization. Cyclized dihydrofolate reductase was similarly resilient. Analyzing unfolding through calorimetry indicated that cyclization did not increase the unfolding temperature but rather facilitated refolding after thermal stress. SpyTag/SpyCatcher sandwiching represents a simple and efficient route to enzyme cyclization, with potential to greatly enhance the robustness of biocatalysts.

  18. Structural studies of intermediates along the cyclization pathway of Aplysia ADP-ribosyl cyclase.

    PubMed

    Kotaka, Masayo; Graeff, Richard; Chen, Zhe; Zhang, Li He; Lee, Hon Cheung; Hao, Quan

    2012-01-20

    Cyclic ADP-ribose (cADPR) is a calcium messenger that can mobilize intracellular Ca²⁺ stores and activate Ca²⁺ influx to regulate a wide range of physiological processes. Aplysia cyclase is the first member of the ADP-ribosyl cyclases identified to catalyze the cyclization of NAD⁺ into cADPR. The catalysis involves a two-step reaction, the elimination of the nicotinamide ring and the cyclization of the intermediate resulting in the covalent attachment of the purine ring to the terminal ribose. Aplysia cyclase exhibits a high degree of leniency towards the purine base of its substrate, and the cyclization reaction takes place at either the N1- or the N7-position of the purine ring. To decipher the mechanism of cyclization in Aplysia cyclase, we used a crystallization setup with multiple Aplysia cyclase molecules present in the asymmetric unit. With the use of natural substrates and analogs, not only were we able to capture multiple snapshots during enzyme catalysis resulting in either N1 or N7 linkage of the purine ring to the terminal ribose, we were also able to observe, for the first time, the cyclized products of both N1 and N7 cyclization bound in the active site of Aplysia cyclase.

  19. Cyclization strategies of meditopes: affinity and diffraction studies of meditope–Fab complexes

    SciTech Connect

    Bzymek, Krzysztof P.; Ma, Yuelong; Avery, Kendra A.; Horne, David A.; Williams, John C.

    2016-05-23

    An overview of cyclization strategies of a Fab-binding peptide to maximize affinity. Recently, a unique binding site for a cyclic 12-residue peptide was discovered within a cavity formed by the light and heavy chains of the cetuximab Fab domain. In order to better understand the interactions that drive this unique complex, a number of variants including the residues within the meditope peptide and the antibody, as well as the cyclization region of the meditope peptide, were created. Here, multiple crystal structures of meditope peptides incorporating different cyclization strategies bound to the central cavity of the cetuximab Fab domain are presented. The affinity of each cyclic derivative for the Fab was determined by surface plasmon resonance and correlated to structural differences. Overall, it was observed that the disulfide bond used to cyclize the peptide favorably packs against a hydrophobic ‘pocket’ and that amidation and acetylation of the original disulfide meditope increased the overall affinity ∼2.3-fold. Conversely, replacing the terminal cysteines with serines and thus creating a linear peptide reduced the affinity over 50-fold, with much of this difference being reflected in a decrease in the on-rate. Other cyclization methods, including the formation of a lactam, reduced the affinity but not to the extent of the linear peptide. Collectively, the structural and kinetic data presented here indicate that small perturbations introduced by different cyclization strategies can significantly affect the affinity of the meditope–Fab complex.

  20. T4 DNA ligase is more than an effective trap of cyclized dsDNA.

    PubMed

    Yuan, Chongli; Lou, Xiong Wen; Rhoades, Elizabeth; Chen, Huimin; Archer, Lynden A

    2007-01-01

    T4 DNA ligase is used in standard cyclization assays to trap double-stranded DNA (dsDNA) in low-probability, cyclic or highly bent conformations. The cyclization probability, deduced from the relative yield of cyclized product, can be used in conjunction with statistical mechanical models to extract the bending stiffness of dsDNA. By inserting the base analog 2-aminopurine (2-AP) at designated positions in 89 bp and 94 bp dsDNA fragments, we find that T4 DNA ligase can have a previously unknown effect. Specifically, we observe that addition of T4 ligase to dsDNA in proportions comparable to what is used in the cyclization assay leads to a significant increase in fluorescence from 2-AP. This effect is believed to originate from stabilization of local base-pair opening by formation of transient DNA-ligase complexes. Non-specific binding of T4 ligase to dsDNA is also confirmed using fluorescence correlation spectroscopy (FCS) experiments, which reveal a systematic reduction of dsDNA diffusivity in the presence of ligase. ATP competes with regular DNA for non-covalent binding to the T4 ligase and is found to significantly reduce DNA-ligase complexation. For short dsDNA fragments, however, the population of DNA-ligase complexes at typical ATP concentrations used in DNA cyclization studies is determined to be large enough to dominate the cyclization reaction.

  1. Photomodulation of conformational states. I. Mono- and bicyclic peptides with (4-amino)phenylazobenzoic acid as backbone constituent.

    PubMed

    Renner, C; Behrendt, R; Spörlein, S; Wachtveitl, J; Moroder, L

    2000-12-01

    The thioredoxin reductase active-site fragment H-Ala-Cys-Ala-Thr-Cys-Asp-Gly-Phe-OH [134-141], which is known for its high tendency to assume an almost identical conformation as in the intact enzyme, was backbone cyclized with the photoresponsive (4-amino)phenylazobenzoic acid (APB) to produce a monocyclic and disulfide-bridged bicyclic APB-peptide. Light-induced reversible cis/trans isomerization occurs at identical extents in both the linear and the two cyclic forms. Nuclear magnetic resonance conformational analysis clearly revealed that in the bicyclic APB-peptide both as a trans- and cis-azo-isomer the constraints imparted by the bicyclic structure do not allow the molecule to relax into a defined low energy conformation, thus making the molecule a frustrated system that flip-flops between multiple conformational states. Conversely, the monocyclic APB peptide folds into a well-defined lowest energy structure as a trans-azo-isomer, which upon photoisomerization to the cis-azo configuration relaxes into a less restricted conformational space. First femtosecond spectroscopic analysis of the dynamics of the photoreaction confirm a fast first phase on the femtosecond time scale related to the cis/trans isomerization of the azobenzene moiety followed by a slower phase in the picosecond time scale that involves an adjustment of the peptide backbone. Due to the well- defined photoresponsive two-state transition of this monocyclic peptide molecule, it represents a model system well suited for studying the ultrafast dynamics of conformational transitions by time-resolved spectroscopy.

  2. Degradation of Hole Transport Materials via Exciton-Driven Cyclization.

    PubMed

    Bell, Bruce M; Clark, Michael B; Devore, David D; De Vries, Timothy S; Froese, Robert D; Gray, Kaitlyn C; Jackson, David H K; Kuech, T F; Na, Hong-Yeop; Kearns, Kenneth L; Lee, Kyung-Joo; Mukhopadhyay, Sukrit; Rachford, Aaron A; Spencer, Liam P; Woodward, W H Hunter

    2017-04-06

    Organic light-emitting diode (OLED) displays have been an active and intense area of research for well over a decade and have now reached commercial success for displays from cell phones to large format televisions. A more thorough understanding of the many different potential degradation modes which cause OLED device failure will be necessary to develop the next generation of OLED materials, improve device lifetime, and to ultimately improve the cost vs performance ratio. Each of the different organic layers in an OLED device can be susceptible to unique decomposition pathways, however stability toward excitons is critical for emissive layer (EML) materials as well as any layer near the recombination zone. This study will specifically focus on degradation modes within the hole transport layer (HTL) with the goal being to identify the general decomposition paths occurring in an operating device and use this information to design new derivatives which can block these pathways. Through post-mortem analyses of several aged OLED devices, an apparently common intramolecular cyclization pathway has been identified that was not previously reported for arylamine-containing HTL materials and that operates parallel to but faster than the previously described fragmentation pathways.

  3. Gold-Catalyzed Cyclization Processes: Pivotal Avenues for Organic Synthesis.

    PubMed

    Kumar, Amit; Singh, Sukhdev; Sharma, Sunil K; Parmar, Virinder S; Van der Eycken, Erik V

    2016-02-01

    Over the years, gold catalysis has materialized as an incredible synthetic approach among the scientific community. Due to the trivial reaction conditions and great functional compatibility, these progressions are synthetically expedient, because practitioners can implement them to build intricate architectures from readily amassed building blocks with high bond forming indices. The incendiary growth of gold catalysts in organic synthesis has been demonstrated as one of the most prevailing soft Lewis acids for electrophilic activation of carbon-carbon multiple bonds towards a great assortment of nucleophiles. Nowadays, organic chemists consistently employ gold catalysts to carry out a diverse array of organic transformations to build unprecedented molecular architectures. Despite all these achievements and a plethora of reports, many vital challenges remain. In this account, we describe the reactivity of various gold catalysts towards cyclization processes developed over the years. These protocols give access to a wide scope of polyheterocyclic structures, containing different medium-sized ring skeletons. This is interesting, as the quest for highly selective reactions to assemble diversely functionalized products has attracted much attention. We envisage that these newly developed chemo-, regio-, and diastereoselective protocols could provide an expedient route to architecturally cumbersome heterocycles of importance for the pharmaceutical industry.

  4. Aminoacyl-tRNA Substrate and Enzyme Backbone Atoms Contribute to Translational Quality Control by YbaK

    PubMed Central

    Kumar, Sandeep; Das, Mom; Hadad, Christopher M.; Musier-Forsyth, Karin

    2012-01-01

    Amino acids are covalently attached to their corresponding tRNAs by aminoacyl-tRNA synthetases. Proofreading mechanisms exist to ensure that high fidelity is maintained in this key step in protein synthesis. Prolyl-tRNA synthetase (ProRS) can misacylate cognate tRNAPro with Ala and Cys. The cis-editing domain of ProRS (INS) hydrolyzes Ala-tRNAPro, whereas Cys-tRNAPro is hydrolyzed by a single domain editing protein, YbaK, in trans. Previous studies have proposed a model of substrate-binding by bacterial YbaK and elucidated a substrate-assisted mechanism of catalysis. However, the microscopic steps in this mechanism have not been investigated. In this work, we carried out biochemical experiments together with a detailed hybrid quantum mechanics/molecular mechanics study to investigate the mechanism of catalysis by Escherichia coli YbaK. The results support a mechanism wherein cyclization of the substrate Cys results in cleavage of the Cys-tRNA ester bond. Protein side chains do not play a significant role in YbaK catalysis. Instead, protein backbone atoms play crucial roles in stabilizing the transition state, while the product is stabilized by the 2'-OH of the tRNA. PMID:23185990

  5. Theoretical studies of chromophore maturation in the wild-type green fluorescent protein: ONIOM(DFT:MM) investigation of the mechanism of cyclization.

    PubMed

    Ma, Yingying; Sun, Qiao; Li, Zhen; Yu, Jian-Guo; Smith, Sean C

    2012-02-02

    The availability of a gene encoding green fluorescence immediately stimulates interest in the puzzle of autocatalytic formation of the green fluorescent protein (GFP) chromophore. Numerous experimental and theoretical studies have indicated that cyclization is the first and most important step in the maturation process of the GFP. In our previous paper based on cluster models [J. Phys. Chem. B2010, 114, 9698-9705], two possible mechanisms have been investigated with the conclusion that the backbone condensation initiated by deprotonation of the Gly67 amide nitrogen is easier than deprotonation of the Tyr66 α-carbon. However, the impact of the protein environment on the reaction mechanism remains to be explored. In this paper, we investigated the two possible mechanisms with inclusion of protein environmental effects by using molecular dynamics (MD) and combined quantum mechanics/molecular mechanics (QM/MM) calculations. Our calculations reveal no hydrogen bonding network that would facilitate deprotonation of the amide nitrogen of Gly67, although it is the lower energy pathway in the cluster model system. Contrastingly, there is a hydrogen bonding network between Tyr66 α-carbon and Glu222, which is in good agreement with X-ray data. The ONIOM studies show that proton transfer from Tyr66 α-carbon to Glu222 is a long-distance charge transfer process. The charge distribution of the MM region has a significant perturbation to the wave function for the QM region, with the QM energy for the proton transfer product being increased under the influence of the electrostatic protein environment. The barrier for the rate-limiting step in cyclization is quite high, about 40.0 kcal/mol in the case of ONIOM-EE.

  6. Structural dependencies of protein backbone 2JNC' couplings.

    PubMed

    Juranić, Nenad; Dannenberg, J J; Cornilescu, Gabriel; Salvador, Pedro; Atanasova, Elena; Ahn, Hee-Chul; Macura, Slobodan; Markley, John L; Prendergast, Franklyn G

    2008-04-01

    Protein folding can introduce strain in peptide covalent geometry, including deviations from planarity that are difficult to detect, especially for a protein in solution. We have found dependencies in protein backbone (2)J(NC') couplings on the planarity and the relative orientation of the sequential peptide planes. These dependences were observed in experimental (2)J(NC') couplings from seven proteins, and also were supported by DFT calculations for a model tripeptide. Findings indicate that elevated (2)J(NC') couplings may serve as reporters of structural strain in the protein backbone imposed by protein folds. Such information, supplemented with the H-bond strengths derived from (h3)J(NC') couplings, provides useful insight into the overall energy profile of the protein backbone in solution.

  7. Structural dependencies of protein backbone 2JNC′ couplings

    PubMed Central

    Juranić, Nenad; Dannenberg, J.J.; Cornilescu, Gabriel; Salvador, Pedro; Atanasova, Elena; Ahn, Hee-Chul; Macura, Slobodan; Markley, John L.; Prendergast, Franklyn G.

    2008-01-01

    Protein folding can introduce strain in peptide covalent geometry, including deviations from planarity that are difficult to detect, especially for a protein in solution. We have found dependencies in protein backbone 2JNC′ couplings on the planarity and the relative orientation of the sequential peptide planes. These dependences were observed in experimental 2JNC′ couplings from seven proteins, and also were supported by DFT calculations for a model tripeptide. Findings indicate that elevated 2JNC′ couplings may serve as reporters of structural strain in the protein backbone imposed by protein folds. Such information, supplemented with the H-bond strengths derived from h3JNC′ couplings, provides useful insight into the overall energy profile of the protein backbone in solution. PMID:18305196

  8. Cyclization strategies of meditopes: affinity and diffraction studies of meditope–Fab complexes

    PubMed Central

    Bzymek, Krzysztof P.; Ma, Yuelong; Avery, Kendra A.; Horne, David A.; Williams, John C.

    2016-01-01

    Recently, a unique binding site for a cyclic 12-residue peptide was discovered within a cavity formed by the light and heavy chains of the cetuximab Fab domain. In order to better understand the interactions that drive this unique complex, a number of variants including the residues within the meditope peptide and the antibody, as well as the cyclization region of the meditope peptide, were created. Here, multiple crystal structures of meditope peptides incorporating different cyclization strategies bound to the central cavity of the cetuximab Fab domain are presented. The affinity of each cyclic derivative for the Fab was determined by surface plasmon resonance and correlated to structural differences. Overall, it was observed that the disulfide bond used to cyclize the peptide favorably packs against a hydrophobic ‘pocket’ and that amidation and acetylation of the original disulfide meditope increased the overall affinity ∼2.3-fold. Conversely, replacing the terminal cysteines with serines and thus creating a linear peptide reduced the affinity over 50-fold, with much of this difference being reflected in a decrease in the on-rate. Other cyclization methods, including the formation of a lactam, reduced the affinity but not to the extent of the linear peptide. Collectively, the structural and kinetic data presented here indicate that small perturbations introduced by different cyclization strategies can significantly affect the affinity of the meditope–Fab complex. PMID:27303895

  9. The Graphical Representation of the Digital Astronaut Physiology Backbone

    NASA Technical Reports Server (NTRS)

    Briers, Demarcus

    2010-01-01

    This report summarizes my internship project with the NASA Digital Astronaut Project to analyze the Digital Astronaut (DA) physiology backbone model. The Digital Astronaut Project (DAP) applies integrated physiology models to support space biomedical operations, and to assist NASA researchers in closing knowledge gaps related to human physiologic responses to space flight. The DA physiology backbone is a set of integrated physiological equations and functions that model the interacting systems of the human body. The current release of the model is HumMod (Human Model) version 1.5 and was developed over forty years at the University of Mississippi Medical Center (UMMC). The physiology equations and functions are scripted in an XML schema specifically designed for physiology modeling by Dr. Thomas G. Coleman at UMMC. Currently it is difficult to examine the physiology backbone without being knowledgeable of the XML schema. While investigating and documenting the tags and algorithms used in the XML schema, I proposed a standard methodology for a graphical representation. This standard methodology may be used to transcribe graphical representations from the DA physiology backbone. In turn, the graphical representations can allow examination of the physiological functions and equations without the need to be familiar with the computer programming languages or markup languages used by DA modeling software.

  10. Backbone fractal dimension and fractal hybrid orbital of protein structure

    NASA Astrophysics Data System (ADS)

    Peng, Xin; Qi, Wei; Wang, Mengfan; Su, Rongxin; He, Zhimin

    2013-12-01

    Fractal geometry analysis provides a useful and desirable tool to characterize the configuration and structure of proteins. In this paper we examined the fractal properties of 750 folded proteins from four different structural classes, namely (1) the α-class (dominated by α-helices), (2) the β-class (dominated by β-pleated sheets), (3) the (α/β)-class (α-helices and β-sheets alternately mixed) and (4) the (α + β)-class (α-helices and β-sheets largely segregated) by using two fractal dimension methods, i.e. "the local fractal dimension" and "the backbone fractal dimension" (a new and useful quantitative parameter). The results showed that the protein molecules exhibit a fractal behavior in the range of 1 ⩽ N ⩽ 15 (N is the number of the interval between two adjacent amino acid residues), and the value of backbone fractal dimension is distinctly greater than that of local fractal dimension for the same protein. The average value of two fractal dimensions decreased in order of α > α/β > α + β > β. Moreover, the mathematical formula for the hybrid orbital model of protein based on the concept of backbone fractal dimension is in good coincidence with that of the similarity dimension. So it is a very accurate and simple method to analyze the hybrid orbital model of protein by using the backbone fractal dimension.

  11. Total Synthesis of (+)-Sieboldine A: Evolution of A Pinacol-Terminated Cyclization Strategy

    PubMed Central

    Canham, Stephen M.; France, David J.; Overman, Larry E.

    2013-01-01

    This article describes synthetic studies that culminated in the first total synthesis of the Lycopodium alkaloid sieboldine A. During this study a number of pinacol-terminated cationic cyclizations were examined to form the cis-hydrindanone core of sieboldine A. Of these, a mild Au(I)-promoted 1,6-enyne cyclization that was terminated by a semipinacol rearrangement proved to be most efficient. Fashioning the unprecedented N-hydroxyazacyclononane ring embedded within the bicyclo[5.2.1]decane-N,O-acetal moiety of sieboldine A was a formidable challenge. Ultimately, the enantioselective total synthesis of (+)-sieboldine A was completed by forming this ring in good yield by cyclization of a protected-hydroxylamine thioglycoside precursor. PMID:22734821

  12. Silyl Enol Ether Prins Cyclization: Diastereoselective Formation of Substituted Tetrahydropyran-4-ones

    PubMed Central

    2015-01-01

    A diastereoselective synthesis of cis-2,6-disubstituted tetrahydropyran-4-ones was developed. The key step of this methodology, a silyl enol ether Prins cyclization, was promoted by a condensation reaction between a hydroxy silyl enol ether and an aldehyde to afford substituted tetrahydropyran-4-ones. The cyclization was tolerant of many functional groups, and the modular synthesis of the hydroxy silyl enol ether allowed for the formation of more than 30 new tetrahydropyran-4-ones with up to 97% yield and >95:5 dr. The cyclization step forms new carbon–carbon and carbon–oxygen bonds, as well as a quaternary center with good diastereoselectivity. The method provides a versatile route for the synthesis of substituted tetrahydropyrans. PMID:25200563

  13. Fates of imine intermediates in radical cyclizations of N-sulfonylindoles and ene-sulfonamides.

    PubMed

    Zhang, Hanmo; Hay, E Ben; Geib, Stephen J; Curran, Dennis P

    2015-01-01

    Two new fates of imine intermediates formed on radical cyclizations of ene-sulfonamides have been identified, reduction and hydration/fragmentation. Tin hydride-mediated cyclizations of 2-halo-N-(3-methyl-N-sulfonylindole)anilines provide spiro[indoline-3,3'-indolones] or spiro-3,3'-biindolines (derived from imine reduction), depending on the indole C2 substituent. Cyclizations of 2-haloanilide derivatives of 3-carboxy-N-sulfonyl-2,3-dihydropyrroles also presumably form spiro-imines as primary products. However, the lactam carbonyl group facilitates the ring-opening of these cyclic imines by a new pathway of hydration and retro-Claisen-type reaction, providing rearranged 2-(2'-formamidoethyl)oxindoles.

  14. Fates of imine intermediates in radical cyclizations of N-sulfonylindoles and ene-sulfonamides

    PubMed Central

    Zhang, Hanmo; Hay, E Ben; Geib, Stephen J

    2015-01-01

    Summary Two new fates of imine intermediates formed on radical cyclizations of ene-sulfonamides have been identified, reduction and hydration/fragmentation. Tin hydride-mediated cyclizations of 2-halo-N-(3-methyl-N-sulfonylindole)anilines provide spiro[indoline-3,3'-indolones] or spiro-3,3'-biindolines (derived from imine reduction), depending on the indole C2 substituent. Cyclizations of 2-haloanilide derivatives of 3-carboxy-N-sulfonyl-2,3-dihydropyrroles also presumably form spiro-imines as primary products. However, the lactam carbonyl group facilitates the ring-opening of these cyclic imines by a new pathway of hydration and retro-Claisen-type reaction, providing rearranged 2-(2'-formamidoethyl)oxindoles. PMID:26664585

  15. Reagent based DOS: a "Click, Click, Cyclize" strategy to probe chemical space.

    PubMed

    Rolfe, Alan; Lushington, Gerald H; Hanson, Paul R

    2010-05-07

    The synthesis of small organic molecules as probes for discovering new therapeutic agents has been an important aspect of chemical-biology. Herein we report a reagent-based, diversity-oriented synthetic (DOS) strategy to probe chemical and biological space via a "Click, Click, Cyclize" protocol. In this DOS approach, three sulfonamide linchpins underwent cyclization protocols with a variety of reagents to yield a collection of structurally diverse S-heterocycles. In silico analysis is utilized to evaluate the diversity of the compound collection against chemical space (PC analysis), shape space (PMI) and polar surface area (PSA) calculations.

  16. Drawing from a pool of radicals for the design of selective enyne cyclizations.

    PubMed

    Mondal, Sayantan; Mohamed, Rana K; Manoharan, Mariappan; Phan, Hoa; Alabugin, Igor V

    2013-11-15

    Despite the possibility of intermolecular attack at four different locations, the Bu3Sn-mediated radical cyclization of aromatic enynes is surprisingly selective. The observed reaction path originates from the least stable of the equilibrating pool of isomeric radicals produced by intermolecular Bu3Sn attack at the π-bonds of substrates. The radical pool components are kinetically self-sorted via 5-exo-trig closure, the fastest of the four possible cyclizations. The resulting Sn-substituted indenes are capable of further transformations in reactions with electrophiles.

  17. Conversion of Substrate Analogs Suggests a Michael Cyclization in Iridoid Biosynthesis

    PubMed Central

    Lindner, Stephanie; Geu-Flores, Fernando; Bräse, Stefan; Sherden, Nathaniel H.; O’Connor, Sarah E.

    2014-01-01

    Summary The core structure of the iridoid monoterpenes is formed by a unique cyclization reaction. The enzyme that catalyzes this reaction, iridoid synthase, is mechanistically distinct from other terpene cyclases. Here we describe the synthesis of two substrate analogs to probe the mechanism of iridoid synthase. Enzymatic assay of these substrate analogs along with clues from the product profile of the native substrate strongly suggest that iridoid synthase utilizes a Michael reaction to achieve cyclization. This improved mechanistic understanding will facilitate the exploitation of the potential of iridoid synthase to synthesize new cyclic compounds from nonnatural substrates. PMID:25444551

  18. Total synthesis of (±)-sacidumlignans D and A through Ueno-Stork radical cyclization reaction.

    PubMed

    Zhang, Jian-Jian; Yan, Chang-Song; Peng, Yu; Luo, Zhen-Biao; Xu, Xiao-Bo; Wang, Ya-Wen

    2013-04-21

    Efficient synthesis of (±)-sacidumlignan D (4) has been successfully achieved employing Ueno-Stork radical cyclization of α-bromo acetal 21 as a key step. Two synthetic approaches for the symmetrical diaryl ketone 19 have been discussed in detail. Notably, sacidumlignan A (1) can be also efficiently synthesized in only 7 steps with 25% overall yield, where acid triggered tandem reaction starting from analogous Ueno-Stork cyclization product 27 played an important role. Moreover, potentially biomimetic conversion from (±)-sacidumlignan D (4) to sacidumlignan A (1) could be realized.

  19. On-surface formation of one-dimensional polyphenylene through Bergman cyclization.

    PubMed

    Sun, Qiang; Zhang, Chi; Li, Zhiwen; Kong, Huihui; Tan, Qinggang; Hu, Aiguo; Xu, Wei

    2013-06-12

    On-surface fabrication of covalently interlinked conjugated nanostructures has attracted significant attention, mainly because of the high stability and efficient electron transport ability of these structures. Here, from the interplay of scanning tunneling microscopy imaging and density functional theory calculations, we report for the first time on-surface formation of one-dimensional polyphenylene chains through Bergman cyclization followed by radical polymerization on Cu(110). The formed surface nanostructures were further corroborated by the results for the ex situ-synthesized molecular product after Bergman cyclization. These findings are of particular interest and importance for the construction of molecular electronic nanodevices on surfaces.

  20. A novel C,D-spirodioxene taxoid synthesized through an unexpected Pd-mediated ring cyclization.

    PubMed

    Wang, Shao-Rong; Sánchez-Murcia, Pedro A; Gago, Federico; Fang, Wei-Shuo

    2016-01-07

    A novel C,D-spirodioxene taxoid (6) was prepared from paclitaxel (1a), with the key steps including an unexpected Pd-mediated ring cyclization. The anti-tubulin activity of 6 was decreased relative to that of 1a and a previously reported C,D-spirolactone taxane (5). These observations could be rationalized on the basis of molecular modeling results. To the best of our knowledge, this is the first example indicating that 1,4-dioxenes can be synthesized from a mono-allyl vicinal diol through a Wacker-type cyclization. This strategy may be applicable to the synthesis of other C,D-spiro taxoids.

  1. Triaryl-Substituted Divinyl Ketones Cyclization: Nazarov Reaction versus Friedel-Crafts Electrophilic Substitution.

    PubMed

    Shirinian, Valerii Z; Lvov, Andrey G; Yadykov, Anton V; Yaminova, Liana V; Kachala, Vadim V; Markosyan, Ashot I

    2016-12-16

    The acid-catalyzed cyclization of a wide range of triaryl-substituted divinyl ketones has been studied. It was found that the reaction pathway strongly depends on the nature of the aryl substituent at the α-position to the carbonyl group. An electron-rich aromatic substituent promotes the reaction to proceed through the intramolecular Friedel-Crafts electrophilic substitution giving dihydronaphthalene derivatives. In contrast, the presence of an electron-deficient substituent is favorable for the Nazarov 4π-conrotatory cyclization yielding triaryl-substituted cyclopentenones. The electrophilic substitution reaction was applied to thiophene and thiazole derivatives.

  2. How do analogous alpha-chloroenamides and alpha-iodoenamides give different product distributions in 5-endo radical cyclizations?

    PubMed

    Curran, Dennis P; Guthrie, David B; Geib, Steven J

    2008-07-02

    5-Endo cyclizations of N-alkenyl carbamoylmethyl radicals provide gamma-lactam radicals, which in turn evolve to reduced or non-reduced (alkene) products depending on reagents and reaction conditions. Several groups have made surprising observations that chlorides are better radical precursors than iodides in such cyclizations. Here is described a detailed study of tin and silicon hydride-mediated radical cyclizations of N-benzyl-2-halo-N-cyclohex-1-enylacetamides. The ratios of directly reduced, cyclized/reduced, and cyclized/non-reduced products depend not only on the reaction conditions and reducing reagent but also on the precursor. Prior explanations for the precursor-dependent product ratios based on amide rotamer effects are ruled out. The precursor-dependent behavior is further dissected into two different effects: (1) the ratio of cyclized/reduced products to cyclized/non-reduced products depends on the ability of the radical precursor to react with the product gamma-lactam radical in competition with tin hydride (iodides can compete, chlorides cannot), and (2) the occurrence of large amounts of directly reduced (noncyclized) products in the case of iodides is attributed to a competing ionic chain reaction by which the precursor is reductively deiodinated with HI. This side reaction is not available to chlorides, thereby explaining why the chlorides are better precursors in such reactions. The ability of the iodides to provide cyclized products can be largely restored by adding base. The chlorides and iodides then become complementary precursors, with chlorides giving largely cyclized/reduced products and iodides giving largely cyclized/non-reduced products.

  3. Identification of systems containing nonlinear stiffnesses using backbone curves

    NASA Astrophysics Data System (ADS)

    Londoño, Julián M.; Cooper, Jonathan E.; Neild, Simon A.

    2017-02-01

    This paper presents a method for the dynamic identification of structures containing discrete nonlinear stiffnesses. The approach requires the structure to be excited at a single resonant frequency, enabling measurements to be made in regimes of large displacements where nonlinearities are more likely to be significant. Measured resonant decay data is used to estimate the system backbone curves. Linear natural frequencies and nonlinear parameters are identified using these backbone curves assuming a form for the nonlinear behaviour. Numerical and experimental examples, inspired by an aerospace industry test case study, are considered to illustrate how the method can be applied. Results from these models demonstrate that the method can successfully deliver nonlinear models able to predict the response of the test structure nonlinear dynamics.

  4. Geometry motivated alternative view on local protein backbone structures.

    PubMed

    Zacharias, Jan; Knapp, Ernst Walter

    2013-11-01

    We present an alternative to the classical Ramachandran plot (R-plot) to display local protein backbone structure. Instead of the (φ, ψ)-backbone angles relating to the chemical architecture of polypeptides generic helical parameters are used. These are the rotation or twist angle ϑ and the helical rise parameter d. Plots with these parameters provide a different view on the nature of local protein backbone structures. It allows to display the local structures in polar (d, ϑ)-coordinates, which is not possible for an R-plot, where structural regimes connected by periodicity appear disconnected. But there are other advantages, like a clear discrimination of the handedness of a local structure, a larger spread of the different local structure domains--the latter can yield a better separation of different local secondary structure motives--and many more. Compared to the R-plot we are not aware of any major disadvantage to classify local polypeptide structures with the (d, ϑ)-plot, except that it requires some elementary computations. To facilitate usage of the new (d, ϑ)-plot for protein structures we provide a web application (http://agknapp.chemie.fu-berlin.de/secsass), which shows the (d, ϑ)-plot side-by-side with the R-plot.

  5. Viral RNA switch mediates the dynamic control of flavivirus replicase recruitment by genome cyclization

    PubMed Central

    Liu, Zhong-Yu; Li, Xiao-Feng; Jiang, Tao; Deng, Yong-Qiang; Ye, Qing; Zhao, Hui; Yu, Jiu-Yang; Qin, Cheng-Feng

    2016-01-01

    Viral replicase recruitment and long-range RNA interactions are essential for RNA virus replication, yet the mechanism of their interplay remains elusive. Flaviviruses include numerous important human pathogens, e.g., dengue virus (DENV) and Zika virus (ZIKV). Here, we revealed a highly conserved, conformation-tunable cis-acting element named 5′-UAR-flanking stem (UFS) in the flavivirus genomic 5′ terminus. We demonstrated that the UFS was critical for efficient NS5 recruitment and viral RNA synthesis in different flaviviruses. Interestingly, stabilization of the DENV UFS impaired both genome cyclization and vRNA replication. Moreover, the UFS unwound in response to genome cyclization, leading to the decreased affinity of NS5 for the viral 5′ end. Thus, we propose that the UFS is switched by genome cyclization to regulate dynamic RdRp binding for vRNA replication. This study demonstrates that the UFS enables communication between flavivirus genome cyclization and RdRp recruitment, highlighting the presence of switch-like mechanisms among RNA viruses. DOI: http://dx.doi.org/10.7554/eLife.17636.001 PMID:27692070

  6. Highly Functionalized Cyclopentane Derivatives by Tandem Michael Addition/Radical Cyclization/Oxygenation Reactions.

    PubMed

    Holan, Martin; Pohl, Radek; Císařová, Ivana; Klepetářová, Blanka; Jones, Peter G; Jahn, Ullrich

    2015-06-26

    Densely functionalized cyclopentane derivatives with up to four consecutive stereocenters are assembled by a tandem Michael addition/single-electron transfer oxidation/radical cyclization/oxygenation strategy mediated by ferrocenium hexafluorophosphate, a recyclable, less toxic single-electron transfer oxidant. Ester enolates were coupled with α-benzylidene and α-alkylidene β-dicarbonyl compounds with switchable diastereoselectivity. This pivotal steering element subsequently controls the diastereoselectivity of the radical cyclization step. The substitution pattern of the radical cyclization acceptor enables a switch of the cyclization mode from a 5-exo pattern for terminally substituted olefin units to a 6-endo mode for internally substituted acceptors. The oxidative anionic/radical strategy also allows efficient termination by oxygenation with the free radical 2,2,6,6-tetramethyl-1-piperidinoxyl, and two C-C bonds and one C-O bond are thus formed in the sequence. A stereochemical model is proposed that accounts for all of the experimental results and allows the prediction of the stereochemical outcome. Further transformations of the synthesized cyclopentanes are reported.

  7. Enantioselective Cascade Cyclization/Protodemetalation of Polyenes with N3Pt(2+) Catalysts.

    PubMed

    Nguyen, Ha; Gagné, Michel R

    2014-03-07

    The combination of the N-based pincer ligand PyBOX with Pt(2+) leads to new catalysts for the enantioselective cycloisomerization of dienyl- and trienyl-ols. The mechanistic combination of electrophilic cyclization followed by rapid protodemetalation is surprising and leads to a powerful construct for developing new reactions.

  8. Enantioselective Michael addition/iminium ion cyclization cascades of tryptamine-derived ureas.

    PubMed

    Aillaud, Isabelle; Barber, David M; Thompson, Amber L; Dixon, Darren J

    2013-06-21

    A Michael addition/iminium ion cyclization cascade of enones with tryptamine-derived ureas under BINOL phosphoric acid (BPA) catalysis is reported. The cascade reaction tolerates a wide variety of easily synthesized tryptamine-derived ureas, including those bearing substituents on the distal nitrogen atom of the urea moiety, affording polyheterocyclic products in good yields and good to excellent enantioselectivities.

  9. Leveraging the micellar effect: gold-catalyzed dehydrative cyclizations in water at room temperature.

    PubMed

    Minkler, Stefan R K; Isley, Nicholas A; Lippincott, Daniel J; Krause, Norbert; Lipshutz, Bruce H

    2014-02-07

    The first examples of gold-catalyzed cyclizations of diols and triols to the corresponding hetero- or spirocycles in an aqueous medium are presented. These reactions take place within nanomicelles, where the hydrophobic effect is operating, thereby driving the dehydrations, notwithstanding the surrounding water. By the addition of simple salts such as sodium chloride, reaction times and catalyst loadings can be significantly decreased.

  10. Solvent-free cyclization of linear dienes using olefin metathesis and the Thorpe-Ingold effect

    SciTech Connect

    Forbees, M.D.E.; Myers, T.L.; Maynard, H.D.; Schulz, G.R. ); Patton, J.T.; Smith, D.W. Jr.; Wagener, K.B. )

    1992-12-30

    The olefin metathesis reaction is of great synthetic utility in polymer chemistry. The recent development of ring-opening (ROMP) and acyclic diene (ADMET) metathesis polymerization reactions has opened new avenues for the synthesis of novel polymeric materials. Recently the authors used ADMET to synthesize several photochemically active poly(keto olefins) using the catalyst Mo(CHCMe[sub 2]Ph)(NAr)(OCMe(CF[sub 3])[sub 2])[sub 2] (Ar = 2,6-diisopropylphenyl) (1) developed by Schrock and co-workers in 1990. In the course of that work, they discovered that neat samples of highly substituted dienes will cyclize quantitatively via metathesis to give difunctional five- and seven-membered rings instead of the expected linear polymer. Examples of substituted diene cyclizations by metathesis even in the presence of a solvent are rare. Their systematic exploitation in organic synthesis has therefore been limited to two recent studies by Fu and Grubbs, who cyclized several substituted diene ethers, amines, and amides to unsaturated oxygen and nitrogen heterocycles. Cyclization of unsubstituted dienes in various solvents has been reported, but complete conversion occurred in only a few cases. Formation of cyclic alkene oligomers from back-biting during the ROMP reaction is also known. The reactions reported here are unusual in that they are intermolecular between catalyst and substrate, yet can give 100% yield of product solely from the monomer in the absence of solvent. 13 refs.

  11. Enantioselective Total Synthesis of (−)-Nardoaristolone B via a Gold(I)-Catalyzed Oxidative Cyclization

    PubMed Central

    2015-01-01

    The first enantioselective total synthesis of (−)-nardoaristolone B is accomplished by the implementation of an enantio- and diastereoselective copper(I)-catalyzed conjugate addition/enolate trapping sequence and a gold(I)-catalyzed oxidative cyclization (intermolecular oxidant), employed for the first time in total synthesis. PMID:25563976

  12. Construction of a Spirooxindole Amide Library through Nitrile Hydrozirconation-Acylation-Cyclization Cascade

    PubMed Central

    LaPorte, Matthew G.; Tsegay, Sammi; Hong, Ki Bum; Lu, Chunliang; Fang, Cheng; Wang, Lirong; Xie, Xiang-Qun; Floreancig, Paul E.

    2013-01-01

    A library of spirooxindoles containing varied elements of structural and stereochemical diversity has been constructed via a three step, one pot nitrile hydrozirconation-acylation-cyclization reaction sequence from common acyclic indole intermediates. The resulting library was evaluated for novelty through comparison with MLSMR and Maybridge compound collections. PMID:23731121

  13. Synthesis of multiply substituted 1,6-dihydropyridines through Cu(I)-catalyzed 6-endo cyclization.

    PubMed

    Mizoguchi, Haruki; Watanabe, Ryo; Minami, Shintaro; Oikawa, Hideaki; Oguri, Hiroki

    2015-06-07

    Copper-catalyzed 6-endo cyclization of N-propargylic β-enaminocarbonyls was developed for the synthesis of oxidation-labile 1,6-dihydropyridines. This synthetic method allows flexible and regio-defined assembly of various substituents at the N1, C2, C3, C4, and C6 positions of 1,6-dihydropyridines under mild conditions.

  14. Spirocyclic dihydropyridines by electrophile-induced dearomatizing cyclization of N-alkenyl pyridinecarboxamides.

    PubMed

    Senczyszyn, Jemma; Brice, Heloise; Clayden, Jonathan

    2013-04-19

    On treatment with acylating or sulfonylating agents, N-alkenyl pyridine carboxamides (N-pyridinecarbonyl enamines) undergo a dearomatizing cyclization initiated by pyridine acylation and followed by intramolecular trapping of the resulting pyridinium cation. The products are spirocyclic dihydropyridines which may be further elaborated to spirocyclic heterocycles with drug-like features.

  15. Retrieving Backbone String Neighbors Provides Insights Into Structural Modeling of Membrane Proteins*

    PubMed Central

    Sun, Jiang-Ming; Li, Tong-Hua; Cong, Pei-Sheng; Tang, Sheng-Nan; Xiong, Wen-Wei

    2012-01-01

    Identification of protein structural neighbors to a query is fundamental in structure and function prediction. Here we present BS-align, a systematic method to retrieve backbone string neighbors from primary sequences as templates for protein modeling. The backbone conformation of a protein is represented by the backbone string, as defined in Ramachandran space. The backbone string of a query can be accurately predicted by two innovative technologies: a knowledge-driven sequence alignment and encoding of a backbone string element profile. Then, the predicted backbone string is employed to align against a backbone string database and retrieve a set of backbone string neighbors. The backbone string neighbors were shown to be close to native structures of query proteins. BS-align was successfully employed to predict models of 10 membrane proteins with lengths ranging between 229 and 595 residues, and whose high-resolution structural determinations were difficult to elucidate both by experiment and prediction. The obtained TM-scores and root mean square deviations of the models confirmed that the models based on the backbone string neighbors retrieved by the BS-align were very close to the native membrane structures although the query and the neighbor shared a very low sequence identity. The backbone string system represents a new road for the prediction of protein structure from sequence, and suggests that the similarity of the backbone string would be more informative than describing a protein as belonging to a fold. PMID:22415040

  16. SpyRings Declassified: A Blueprint for Using Isopeptide-Mediated Cyclization to Enhance Enzyme Thermal Resilience.

    PubMed

    Schoene, C; Bennett, S P; Howarth, M

    2016-01-01

    Enzymes often have marginal stability, with unfolding typically leading to irreversible denaturation. This sensitivity is a major barrier, both for de novo enzyme development and for expanding enzyme impact beyond the laboratory. Seeking an approach to enhance resilience to denaturation that could be applied to a range of different enzymes, we developed SpyRing cyclization. SpyRings contain genetically encoded SpyTag (13 amino acids) on the N-terminus and SpyCatcher (12kDa) on the C-terminus of the enzyme, so that the Spy partners spontaneously react together through an irreversible isopeptide bond. SpyRing cyclization gave major increases in thermal resilience, including on a model for enzyme evolution, β-lactamase, and an industrially important enzyme in agriculture and nutrition, phytase. We outline the SpyRing rationale, including comparison of SpyRing cyclization to other cyclization strategies. The cloning strategy is presented for the simple insertion of enzyme genes for recombinant expression. We discuss structure-based approaches to select suitable enzyme cyclization targets. Approaches to evaluate the cyclization reaction and its effect on enzyme resilience are described. We also highlight the use of differential scanning calorimetry to understand how SpyRing cyclization promotes enzyme refolding. Efficiently searching sequence space will continue to be important for enzyme improvement, but the SpyRing platform may be a valuable rational adjunct for conferring resilience.

  17. Icosahedral medium-range orders and backbone formation in an amorphous alloy

    NASA Astrophysics Data System (ADS)

    Lee, Mirim; Kim, Hong-Kyu; Lee, Jae-Chul

    2010-12-01

    Analyses of metallic amorphous solids constructed using molecular dynamics (MD) simulations have demonstrated that individual short-range orders (SROs) are linked with neighboring SROs and form various medium-range orders (MROs). These MROs have been observed to have different structural stability depending on their linking patterns. On the basis of the assessment of the structural stability of various MROs, we propose new types of structural organization, namely, icosahedral medium-range orders (I-MROs) and their extended-range order that forms the backbone of amorphous solids. We also discuss why the atomic-scale structure of an amorphous alloy can be more appropriately described in terms of I-MROs, rather than by the degree of short-range ordering as characterized by the fractions of SROs.

  18. Tandem SN2' nucleophilic substitution/oxidative radical cyclization of aryl substituted allylic alcohols with 1,3-dicarbonyl compounds.

    PubMed

    Zhang, Zhen; Li, Cheng; Wang, Shao-Hua; Zhang, Fu-Min; Han, Xue; Tu, Yong-Qiang; Zhang, Xiao-Ming

    2017-03-23

    A novel and efficient tandem SN2' nucleophilic substitution/oxidative radical cyclization reaction of aryl substituted allylic alcohols with 1,3-dicarbonyl compounds has been developed by using Mn(OAc)3 as an oxidant, which enables the expeditious synthesis of polysubstituted dihydrofuran (DHF) derivatives in moderate to high yields. The use of weakly acidic hexafluoroisopropanol (HFIP) as the solvent rather than AcOH has successfully improved the yields and expanded the substrate scope of this type of radical cyclization reactions. Mechanistic studies confirmed the cascade reaction process involving a final radical cyclization.

  19. Radical cyclizations of cyclic ene sulfonamides occur with β-elimination of sulfonyl radicals to form polycyclic imines.

    PubMed

    Zhang, Hanmo; Hay, E Ben; Geib, Steven J; Curran, Dennis P

    2013-11-06

    Radical cyclizations of cyclic ene sulfonamides provide stable bicyclic and tricyclic aldimines and ketimines in good yields. Depending on the structure of the precursor, the cyclizations occur to provide fused and spirocyclic imines with five-, six-, and seven-membered rings. The initial radical cyclization produces an α-sulfonamidoyl radical that undergoes elimination to form the imine and a phenylsulfonyl radical. In a related method, 3,4-dihydroquinolines can also be produced by radical translocation reactions of N-(2-iodophenylsulfonyl)tetrahydroiso-quinolines. In either case, very stable sulfonamides are cleaved to form imines (rather than amines) under mild reductive conditions.

  20. Radical cyclizations of cyclic ene sulfonamides occur with β-elimination of sulfonyl radicals to form polycyclic imines

    PubMed Central

    Zhang, Hanmo; Hay, E. Ben; Geib, Steven J.; Curran, Dennis P.

    2013-01-01

    Radical cyclizations of cyclic ene sulfonamides provide stable bicyclic and tricyclic aldimines and ketimines in good yields. Depending on the structure of the precursor, the cyclizations occur to provide fused and spirocyclic imines with five-, six-, and seven-membered rings. The initial radical cyclization produces an α-sulfonamidoyl radical that undergoes elimination to form the imine and a phenylsulfonyl radical. In a related method, 3,4-dihydroquinolines can also be produced by radical translocation reactions of N-(2-iodophenylsulfonyl)tetrahydroisoquinolines. In either case, very stable sulfonamides are cleaved to form imines (rather than amines) under mild reductive conditions. PMID:24111991

  1. Melanoma Therapy with Rhenium-Cyclized Alpha Melanocyte Stimulating Hormone Peptide Analogs

    SciTech Connect

    Thomas P Quinn

    2005-11-22

    Malignant melanoma is the 6th most commonly diagnosed cancer with increasing incidence in the United States. It is estimated that 54,200 cases of malignant melanoma will be newly diagnosed and 7,600 cases of death will occur in the United States in the year 2003 (1). At the present time, more than 1.3% of Americans will develop malignant melanoma during their lifetime (2). The average survival for patients with metastatic melanoma is about 6-9 months (3). Moreover, metastatic melanoma deposits are resistant to conventional chemotherapy and external beam radiation therapy (3). Systematic chemotherapy is the primary therapeutic approach to treat patients with metastatic melanoma. Dacarbazine is the only single chemotherapy agent approved by FDA for metastatic melanoma treatment (5). However, the response rate to Dacarbazine is only approximately 20% (6). Therefore, there is a great need to develop novel treatment approaches for metastatic melanoma. The global goal of this research program is the rational design, characterization and validation of melanoma imaging and therapeutic radiopharmaceuticals. Significant progress has been made in the design and characterization of metal-cyclized radiolabeled alpha-melanocyte stimulating hormone peptides. Therapy studies with {sup 188}Re-CCMSH demonstrated the therapeutic efficacy of the receptor-targeted treatment in murine and human melanoma bearing mice (previous progress report). Dosimetry calculations, based on biodistribution data, indicated that a significant dose was delivered to the tumor. However, {sup 188}Re is a very energetic beta-particle emitter. The longer-range beta-particles theoretically would be better for larger tumors. In the treatment of melanoma, the larger primary tumor is usually surgically removed leaving metastatic disease as the focus of targeted radiotherapy. Isotopes with lower beta-energies and/or shorter particle lengths should be better suited for targeting metastases. The {sup 177}Lu

  2. Electron-impact total ionization cross sections of DNA sugar-phosphate backbone and an additivity principle

    NASA Technical Reports Server (NTRS)

    Huo, Winifred M.; Dateo, Christopher E.

    2005-01-01

    The improved binary-encounter dipole (iBED) model [W.M. Huo, Phys. Rev. A64, 042719-1 (2001)l is used to study the total ionization cross sections of the DNA sugar-phosphate backbone by electron impact. Calculations using neutral fragments found that the total ionization cross sections of C3' - and C5', -deoxyribose-phospate, two conformers of the sugar-phosphate backbone, are close to each other. Furthermore, the sum of the ionization cross sections of the separate deoxyribose and phosphate fragments is in close agreement with the C3' - and C5" -deoxyribose-phospate cross sections, differing by less than 10%. The result implies that certain properties of the-DNA, like the total singly ionization cross section, are localized properties and a building-up or additivity principle may apply. This allows us to obtain accurate properties of larger molecular systems built up from the results of smaller subsystem fragments. Calculations are underway using a negatively charged sugar-phosphate backbone with a metal counter-ion.

  3. Resistance of Feynman diagrams and the percolation backbone dimension.

    PubMed

    Janssen, H K; Stenull, O; Oerding, K

    1999-06-01

    We present an alternative view of Feynman diagrams for the field theory of random resistor networks, in which the diagrams are interpreted as being resistor networks themselves. This simplifies the field theory considerably as we demonstrate by calculating the fractal dimension D(B) of the percolation backbone to three loop order. Using renormalization group methods we obtain D(B)=2+epsilon/21-172epsilon(2)/9261+2epsilon(3)[-74 639+22 680zeta(3)]/4 084 101, where epsilon=6-d with d being the spatial dimension and zeta(3)=1.202 057... .

  4. Visible light mediated cyclization of tertiary anilines with maleimides using nickel(II) oxide surface-modified titanium dioxide catalyst.

    PubMed

    Tang, Jian; Grampp, Günter; Liu, Yun; Wang, Bing-Xiang; Tao, Fei-Fei; Wang, Li-Jun; Liang, Xue-Zheng; Xiao, Hui-Quan; Shen, Yong-Miao

    2015-03-06

    Surface-modified titanium dioxides by highly dispersed NiO particles have an extended absorption in the visible light region and a reduced hole-electron pair recombination than unmodified TiO2. They have now been successfully applied as highly active heterogeneous photocatalysts in the visible light mediated direct cyclization of tertiary anilines with maleimides to give tetrahydroquinoline products in moderate to high yields at ambient temperature. In contrast with unmodified titanium dioxide catalysts that are conventionally used in a stoichiometric amount in combination with UVA light, only a catalytic amount (1 mol %) of the surface-modified TiO2 catalyst is needed along with visible light to efficiently catalyze the reaction. Compared with transition-metal complexes such as Ru(bpy)3Cl2 or Ir(ppy)2(dtbbpy)PF6, advantages of these surface-modified titanium dioxides as photocatalyst include high catalytic activity, low cost, ease of recovering, and being able to be used for at least nine times without significant decay of catalytic activity.

  5. Energetics of DNA twisting. I. Relation between twist and cyclization probability.

    PubMed

    Shore, D; Baldwin, R L

    1983-11-15

    The twisting potential of DNA has been determined directly by a method that measures the cyclization probability or j-factor of EcoRI restriction fragments as a function of DNA twist. The cyclization probability is proportional to Kc, the equilibrium constant for cyclization of the restriction fragment via its cohesive ends (Shore et al., 1981). Here we vary the twist of the DNA by making small internal additions to or deletions from a 242 bp EcoRI restriction fragment. A series of 12 DNA molecules has been studied, which range in length from 237 to 254 bp. The cyclization probability is measured from the rates of covalent closure by phage T4 DNA ligase of two systems: (1) a linear restriction fragment in equilibrium with its cyclized form and (2) half molecules (cut by a blunt-end endonuclease) in equilibrium with joined half molecules. The striking result is that, in this DNA size range, the j-factor depends strongly on the fractional twist: the difference between the total helical twist and the nearest integer. Thus j depends in an oscillatory manner on DNA length between 237 and 254 bp with a period of about 10 bp. These data give the free energy of DNA twisting as a function of twist. The curve of j versus DNA length can be fitted to a harmonic twisting potential with a torsional constant of C = 2.4 X 10(-19) erg cm. This value is in reasonable agreement with different estimates of C made by Barkley & Zimm (1979: C = 1.8 X 10(-19) to 4.1 X 10(-19) erg cm) and is somewhat larger than the value obtained resulting from the kinetics of DNA twisting measured by fluorescence depolarization of ethidium intercalated into DNA (C = 1.4 X 10(-19) erg cm; Millar et al., 1982; Thomas et al., 1980) or from spin label studies (Hurley et al., 1982). Our experiments provide a direct measurement of the torsional free energy and they show that the DNA twisting potential is symmetric. Our experiments also indicate that the DNA helix is continuous, or nearly so, in a nicked circle

  6. Radical-Radical Cyclization Cascades of Barbiturates Triggered by Electron-Transfer Reduction of Amide-Type Carbonyls.

    PubMed

    Huang, Huan-Ming; Procter, David J

    2016-06-22

    Radical-radical cyclization cascades, triggered by single-electron transfer to amide-type carbonyls by SmI2-H2O, convert simple achiral barbiturates in one step to hemiaminal- or enamine-containing tricyclic scaffolds containing up to five contiguous stereocenters (including quaternary stereocenters). Furthermore, we describe the surprising beneficial effect of LiBr on the most challenging of the radical-radical cyclization cascades. An alternative fragmentation-radical cyclization sequence of related substrates allows access to bicyclic uracil derivatives. The radical-radical cyclization process constitutes the first example of a radical cascade involving ET reduction of the amide carbonyl. Products of the cascade can be readily manipulated to give highly unusual and medicinally relevant bi- and tricyclic barbiturates.

  7. A phylogenetic backbone for Bivalvia: an RNA-seq approach.

    PubMed

    González, Vanessa L; Andrade, Sónia C S; Bieler, Rüdiger; Collins, Timothy M; Dunn, Casey W; Mikkelsen, Paula M; Taylor, John D; Giribet, Gonzalo

    2015-02-22

    Bivalves are an ancient and ubiquitous group of aquatic invertebrates with an estimated 10 000-20 000 living species. They are economically significant as a human food source, and ecologically important given their biomass and effects on communities. Their phylogenetic relationships have been studied for decades, and their unparalleled fossil record extends from the Cambrian to the Recent. Nevertheless, a robustly supported phylogeny of the deepest nodes, needed to fully exploit the bivalves as a model for testing macroevolutionary theories, is lacking. Here, we present the first phylogenomic approach for this important group of molluscs, including novel transcriptomic data for 31 bivalves obtained through an RNA-seq approach, and analyse these data with published genomes and transcriptomes of other bivalves plus outgroups. Our results provide a well-resolved, robust phylogenetic backbone for Bivalvia with all major lineages delineated, addressing long-standing questions about the monophyly of Protobranchia and Heterodonta, and resolving the position of particular groups such as Palaeoheterodonta, Archiheterodonta and Anomalodesmata. This now fully resolved backbone demonstrates that genomic approaches using hundreds of genes are feasible for resolving phylogenetic questions in bivalves and other animals.

  8. Long-term forecasting of internet backbone traffic.

    PubMed

    Papagiannaki, Konstantina; Taft, Nina; Zhang, Zhi-Li; Diot, Christophe

    2005-09-01

    We introduce a methodology to predict when and where link additions/upgrades have to take place in an Internet protocol (IP) backbone network. Using simple network management protocol (SNMP) statistics, collected continuously since 1999, we compute aggregate demand between any two adjacent points of presence (PoPs) and look at its evolution at time scales larger than 1 h. We show that IP backbone traffic exhibits visible long term trends, strong periodicities, and variability at multiple time scales. Our methodology relies on the wavelet multiresolution analysis (MRA) and linear time series models. Using wavelet MRA, we smooth the collected measurements until we identify the overall long-term trend. The fluctuations around the obtained trend are further analyzed at multiple time scales. We show that the largest amount of variability in the original signal is due to its fluctuations at the 12-h time scale. We model inter-PoP aggregate demand as a multiple linear regression model, consisting of the two identified components. We show that this model accounts for 98% of the total energy in the original signal, while explaining 90% of its variance. Weekly approximations of those components can be accurately modeled with low-order autoregressive integrated moving average (ARIMA) models. We show that forecasting the long term trend and the fluctuations of the traffic at the 12-h time scale yields accurate estimates for at least 6 months in the future.

  9. Synthesis of the Tetracyclic ABCD Ring Domain of Calyciphylline A-Type Alkaloids via Reductive Radical Cyclizations.

    PubMed

    Coussanes, Guilhem; Bonjoch, Josep

    2017-02-17

    A tetracyclic compound with the ABCD ring framework of calyciphylline A-type alkaloids was synthesized from a cis-3a-methyloctahydroindole triggered by a 5-endo radical cyclization. The synthesis required two additional ring-forming steps: the construction of a seven-membered ring by aldol cyclization and the azabicyclic fragment by a radical ring closure of a trichloroacetamide-tethered enol acetate followed by a diastereoselective α-methylation of the lactam group.

  10. Synthesis of indoles, benzofurans, and related heterocycles via an acetylene-activated SNAr/intramolecular cyclization cascade sequence in water or DMSO.

    PubMed

    Hudson, R; Bizier, N P; Esdale, K N; Katz, J L

    2015-02-28

    The synthesis of 2-substituted indoles and benzofurans was achieved by nucleophilic aromatic substitution, followed by subsequent 5-endo-dig cyclization between the nucleophile and an ortho acetylene. The acetylene serves the dual role of the electron withdrawing group to activate the substrate for SNAr, and the C1-C2 carbon scaffold for the newly formed 5-membered heteroaromatic ring. This method allows for the bond forming sequence of Ar-X-N/O-C1 to proceed in a single synthetic step, furnishing indoles and benzofurans in moderate to high yields. Since the method is not transition metal mediated, brominated and chlorinated substrates are tolerated, and benzofuran formation can be conducted using water or water-DMSO mixtures as solvent.

  11. Synthesis and characterization of cyclic polystyrene using copper-catalyzed alkyne-azide cycloaddition coupling - evaluation of physical properties and optimization of cyclization conditions

    NASA Astrophysics Data System (ADS)

    Elupula, Ravinder

    Polymers with a cyclic topology exhibit a range of unique and potentially useful physical properties, including reduced rates of degradation and increased rates of diffusion in bulk relative to linear analogs. However the synthesis of high purity cyclic polymers, and verification of their structural purity remains challenging. The copper-catalyzed azide-alkyne "click" cyclization route toward cyclic polymers has been used widely, due to its synthetic ease and its compatibility with diverse polymer backbones. Yet unoptimized click cyclization conditions have been observed to generate oligomeric byproducts. In order to optimize these cyclization conditions, and to better understand the structure of the higher molecular weight oligomers, these impurities have been isolated by size exclusion chromatography (SEC) and characterized by mass spectrometry (MS). Matrix-Assisted Laser Desorption/Ionization Time of Flight Mass Spectrometry (MALDI-ToF) MS is a particularly valuable characterization tool and was used to determine that the high molecular weight impurities are predominantly cyclic oligomers. It should also be noted that the rapid analysis and small analyte requirements of this MS technique make it particularly attractive as a general tool for elucidating polymer architecture. Ability to tailor the physical properties of polymers by changing the architecture alone has garnered a lot of attention over the past few decades. Compared to their linear analogues, these novel polymer architectures behave completely different in nanoscale regime. Cyclic polymers are especially intriguing since we can compare the differences in the physical properties with that of the linear chains. One of the major physical property changes are T g-confinement effect. Using ATRP and "click chemistry" we have produced highly pure cyclic PS (c-PS) with number-average molecular weight (MW) of 3.4 kg/mol and 9.1 kg/mol. Bulk glass transition temperatures for c-PS were weakly depended on MWs

  12. Gold-catalyzed cyclizations of alkynol-based compounds: synthesis of natural products and derivatives.

    PubMed

    Alcaide, Benito; Almendros, Pedro; Alonso, José M

    2011-09-13

    The last decade has witnessed dramatic growth in the number of reactions catalyzed by gold complexes because of their powerful soft Lewis acid nature. In particular, the gold-catalyzed activation of propargylic compounds has progressively emerged in recent years. Some of these gold-catalyzed reactions in alkynes have been optimized and show significant utility in organic synthesis. Thus, apart from significant methodology work, in the meantime gold-catalyzed cyclizations in alkynol derivatives have become an efficient tool in total synthesis. However, there is a lack of specific review articles covering the joined importance of both gold salts and alkynol-based compounds for the synthesis of natural products and derivatives. The aim of this Review is to survey the chemistry of alkynol derivatives under gold-catalyzed cyclization conditions and its utility in total synthesis, concentrating on the advances that have been made in the last decade, and in particular in the last quinquennium.

  13. An enzymatic [4+2] cyclization cascade creates the pentacyclic core of pyrroindomycins.

    PubMed

    Tian, Zhenhua; Sun, Peng; Yan, Yan; Wu, Zhuhua; Zheng, Qingfei; Zhou, Shuaixiang; Zhang, Hua; Yu, Futao; Jia, Xinying; Chen, Dandan; Mándi, Attila; Kurtán, Tibor; Liu, Wen

    2015-04-01

    The [4+2] cycloaddition remains one of the most intriguing transformations in synthetic and natural products chemistry. In nature, however, there are remarkably few enzymes known to have this activity. We herein report an unprecedented enzymatic [4+2] cyclization cascade that has a central role in the biosynthesis of pyrroindomycins, which are pentacyclic spirotetramate natural products. Beginning with a linear intermediate that contains two pairs of 1,3-diene and alkene groups, the dedicated cyclases PyrE3 and PyrI4 act in tandem to catalyze the formation of two cyclohexene rings in the dialkyldecalin system and the tetramate spiro-conjugate of the molecules. The two cyclizations are completely enzyme dependent and proceed in a regio- and stereoselective manner to establish the enantiomerically pure pentacyclic core. Analysis of a related spirotetronate pathway confirms that homologs are functionally exchangeable, establishing the generality of these findings and explaining how nature creates diverse active molecules with similar rigid scaffolds.

  14. A strategy for sequence control in vinyl polymers via iterative controlled radical cyclization

    PubMed Central

    Hibi, Yusuke; Ouchi, Makoto; Sawamoto, Mitsuo

    2016-01-01

    There is a growing interest in sequence-controlled polymers toward advanced functional materials. However, control of side-chain order for vinyl polymers has been lacking feasibility in the field of polymer synthesis because of the inherent feature of chain-growth propagation. Here we show a general and versatile strategy to control sequence in vinyl polymers through iterative radical cyclization with orthogonally cleavable and renewable bonds. The proposed methodology employs a repetitive and iterative intramolecular cyclization via a radical intermediate in a one-time template with a radical-generating site at one end and an alkene end at the other, each of which is connected to a linker via independently cleavable and renewable bonds. The unique design specifically allowed control of radical addition reaction although inherent chain-growth intermediate (radical species) was used, as well as the iterative cycle and functionalization for resultant side chains, to lead to sequence-controlled vinyl polymers (or oligomers). PMID:26996881

  15. Nucleophilic addition/double cyclization cascade processes between enynyl Fischer carbene complexes and alkynyl malonates.

    PubMed

    Álvarez-Fernández, Ana; Suárez-Rodríguez, Tatiana; Suárez-Sobrino, Ángel L

    2014-07-18

    Two new selective cascade processes for enynyl Fischer carbene complexes 1 are described in their reaction with alkynyl malonates. When carbene complexes 1 react with the sodium enolate of homopropargyl malonates 3 a consecutive Michael-type addition/cyclopentannulation/6-exo cyclization takes place leading, in a regio- and stereoselective way, to n/5/6 angular tricyclic compounds 5. Furthermore, when propargylic malonates are used, a delayed protonation of the reaction mixture allows intermediate 1,4-addition adduct Ia to evolve through a 5-exo cyclization, consisting of an intramolecular nucleophilic attack from the central carbon of the allenylmetallate over the triple C-C bond. Further spontaneous cyclopentannulation of the resulting metallatriene gives rise to bicyclic and linear polycyclic compounds 6 and 7, some of them bearing a polyquinane framework.

  16. Titanocene-catalyzed cascade cyclization of epoxypolyprenes: straightforward synthesis of terpenoids by free-radical chemistry.

    PubMed

    Justicia, José; Rosales, Antonio; Buñuel, Elena; Oller-López, Juan L; Valdivia, Mónica; Haïdour, Ali; Oltra, J Enrique; Barrero, Alejandro F; Cárdenas, Diego J; Cuerva, Juan M

    2004-04-02

    The titanocene-catalyzed cascade cyclization of epoxypolyenes, which are easily prepared from commercially available polyprenoids, has proven to be a useful procedure for the synthesis of C(10), C(15), C(20), and C(30) terpenoids, including monocyclic, bicyclic, and tricyclic natural products. Both theoretical and experimental evidence suggests that this cyclization takes place in a nonconcerted fashion via discrete carbon-centered radicals. Nevertheless, the termination step of the process seems to be subjected to a kind of water-dependent control, which is unusual in free-radical chemistry. The catalytic cycle is based on the use of the novel combination Me(3)SiCl/2,4,6-collidine to regenerate the titanocene catalyst. In practice this procedure has several advantages: it takes place at room temperature under mild conditions compatible with different functional groups, uses inexpensive reagents, and its end step can easily be controlled to give exocyclic double bonds by simply excluding water from the medium.

  17. Protein cyclization enhanced thermostability and exopeptidase-resistance of green fluorescent protein.

    PubMed

    Zhao, Zhonglin; Ma, Xin; Li, Liang; Zhang, Wei; Ping, Shuzhen; Xu, Ming-Qun; Lin, Min

    2010-03-01

    A mutant of green fluorescent protein (GFPmut3*) from the jellyfish Aequorea victoria was cyclized in vitro and in vivo by the use of a naturally split intein from the dnaE gene of Synechocystis species PCC6803 (Ssp). Cyclization of GFPmut3* was confirmed by amino acid sequencing and resulted in an increased electrophoretic mobility compared with the linear GFPmut3*. The circular GFPmut3* was 5 degrees C more thermostable than the linear form and significantly more resistant to proteolysis of exopeptidase. The circular GFPmut3* also displayed increased relative fluorescence intensity. In addition, chemical stability of GFPmut3* against GdnHCl revealed more stability of the circular form compared with the linear form.

  18. Catalytic enantioselective synthesis of indanes by a cation-directed 5-endo-trig cyclization.

    PubMed

    Johnston, Craig P; Kothari, Abhishek; Sergeieva, Tetiana; Okovytyy, Sergiy I; Jackson, Kelvin E; Paton, Robert S; Smith, Martin D

    2014-02-01

    5-Endo-trig cyclizations are generally considered to be kinetically unfavourable, as described by Baldwin's rules. Consequently, observation of this mode of reaction under kinetic control is rare. This is usually ascribed to challenges in achieving appropriate approach trajectories for orbital overlap in the transition state. Here, we describe a highly enantio- and diastereoselective route to complex indanes bearing all-carbon quaternary stereogenic centres via a 5-endo-trig cyclization catalysed by a chiral ammonium salt. Through computation, the preference for the formally disfavoured 5-endo-trig Michael reaction over the formally favoured 5-exo-trig Dieckmann reaction is shown to result from thermodynamic contributions to the innate selectivity of the nucleophilic group, which outweigh the importance of the approach trajectory as embodied by Baldwin's rules. Our experimental and theoretical findings demonstrate that geometric and stereoelectronic constraints may not be decisive in the observed outcome of irreversible ring-closing reactions.

  19. Trisubstituted 2-trifluoromethyl pyrrolidines via catalytic asymmetric Michael addition/reductive cyclization.

    PubMed

    Corbett, Michael T; Xu, Qihai; Johnson, Jeffrey S

    2014-05-02

    The stereoselective synthesis of trisubstituted 2-trifluoromethyl pyrrolidines by asymmetric Michael addition/hydrogenative cyclization is described. The direct organocatalytic addition of 1,1,1-trifluoromethylketones to nitroolefins proceeds under mild reaction conditions and low catalyst loadings to provide Michael adducts in high yield with excellent diastereo- and enantioselectivity. Catalytic hydrogenation of the Michael adducts stereoselectively generates 2-trifluoromethylated pyrrolidines bearing three contiguous stereocenters. A stereospecific route to epimeric 2-trifluoromethyl pyrrolidines from a common intermediate is described.

  20. Polyfunctionalized pyrrolidines by Ugi multicomponent reaction followed by palladium-mediated SN2' cyclizations.

    PubMed

    Banfi, Luca; Basso, Andrea; Cerulli, Valentina; Guanti, Giuseppe; Riva, Renata

    2008-02-15

    A 4-component Ugi reaction with a suitable isocyanide, followed by a novel secondary transformation involving a Pd(II)-mediated (R5 = H) or a Pd(0)-mediated (R5 = CO2Me) SN2' cyclization to give highly functionalized N-acyl-2-vinylpyrrolidines, is reported. The overall yields are usually good and in most cases the Pd(0)-catalyzed reaction gave the final product in almost quantitative yield.

  1. Hydroxyl-Substituted Ladder Polyethers via Selective Tandem Epoxidation/Cyclization Sequence

    PubMed Central

    Czabaniuk, Lara C.; Jamison, Timothy F.

    2015-01-01

    A new and highly selective method for the synthesis of hydroxyl-substituted tetrahydropyrans is described. This method utilizes titanium(IV) iso-propoxide and diethyl tartrate to perform a diastereoselective epoxidation followed by in situ epoxide activation and highly selective endo-cyclization to form the desired tetrahydropyran ring. The HIJ ring fragment of the marine ladder polyether yessotoxin was synthesized using this two-stage tactic that proceeds with high efficiency and excellent regioselectivity. PMID:25647091

  2. Synthesis of pachastrissamine from phytosphingosine: a comparison of cyclic sulfate vs an epoxide intermediate in cyclization.

    PubMed

    Lee, Taeho; Lee, Sukjin; Kwak, Young Shin; Kim, Deukjoon; Kim, Sanghee

    2007-02-01

    [reaction: see text] The syntheses of the cytotoxic natural product pachastrissamine and its unnatural 4-epi-congener were accomplished starting from a natural phytosphingosine. The relatively unstrained cyclic sulfate intermediate smoothly underwent the 5-endo cyclization to yield the 2,3,4-trisubstituted tetrahydrofuran ring system of pachastrissamine. The corresponding epoxy alcohol afforded the 4-epi-congener via a tosylate-mediated double inversion process.

  3. Enantioselective palladium-catalyzed dearomative cyclization for the efficient synthesis of terpenes and steroids.

    PubMed

    Du, Kang; Guo, Pan; Chen, Yuan; Cao, Zhen; Wang, Zheng; Tang, Wenjun

    2015-03-02

    A novel enantioselective palladium-catalyzed dearomative cyclization has been developed for the efficient construction of a series of chiral phenanthrenone derivatives bearing an all-carbon quaternary center. The effectiveness of this method in the synthesis of terpenes and steroids was demonstrated by a highly efficient synthesis of a kaurene intermediate, the facile construction of the skeleton of the anabolic steroid boldenone, and the enantioselective total synthesis of the antimicrobial diterpene natural product (-)-totaradiol.

  4. Reductive cyclizations of hydroxysulfinyl ketones: enantioselective access to tetrahydropyran and tetrahydrofuran derivatives.

    PubMed

    Carreño, M Carmen; Des Mazery, Renaud; Urbano, Antonio; Colobert, Françoise; Solladié, Guy

    2003-10-03

    The stereocontrolled formation of cis-2,5-disubstituted tetrahydrofurans and cis-2,6-disubstituted tetrahydropyrans is achieved from enantiopure ketosulfinyl esters by reduction, Weinreb's amide, and ketone formation, followed by the reductive cyclization (Et3SiH/TMSOTf) of the resulting hydroxysulfinyl ketones. The sulfoxide-bearing heterocycles were transformed into two natural products, (-)-centrolobine (1) and both enantiomers of cis-(6-methyltetrahydropyran-2-yl)acetic acid (2).

  5. A seco-catechin cyclization approach to 4→6-linked catechin dimers.

    PubMed

    Watanabe, Gen; Ohmori, Ken; Suzuki, Keisuke

    2014-11-28

    A viable route has been developed for the selective synthesis of the 4→6-linked catechin dimers, scarcely accessible from Nature and/or through synthesis. An acyclic nucleophilic catechin precursor (seco-catechin) was used for the regioselective union with an electrophilic catechin unit, and subsequent pyran cyclization gave the desired 4→6-linked dimers, i.e., procyanidin B6 and catechin-(4α→6)-gallocatechin.

  6. Palladium-catalyzed imidoylative cyclization of α-isocyanoacetamides: efficient access to C2-diversified oxazoles.

    PubMed

    Wang, Jian; Luo, Shuang; Huang, Jinbo; Mao, Tingting; Zhu, Qiang

    2014-08-25

    A novel procedure for the synthesis of C2-diversified oxazoles, through palladium-catalyzed imidoylative cyclization of α-isocyanoacetamides with aryl, vinyl, alkynyl halides, or triflates, was developed. Migratory insertion of isocyanide into a Csp3-palladium(II) intermediate in a cascade process was also realized, generating alkyl-substituted oxazoles. Therefore, oxazoles functionalized at the C2 position with sp, sp(2), and sp(3) hybridized carbon atoms are accessible by applying this method.

  7. Synthesis of oxazoles by silver catalysed oxidative decarboxylation-cyclization of α-oxocarboxylates and isocyanides.

    PubMed

    Ma, Yiyang; Yan, Zhiyuan; Bian, Changliang; Li, Ke; Zhang, Xiaowen; Wang, Mengfan; Gao, Xinlong; Zhang, Heng; Lei, Aiwen

    2015-07-04

    A silver catalysed synthesis of oxazoles by the oxidative decarboxylation-cyclization of α-oxocarboxylates and isocyanides was developed. This method provided a novel strategy to construct oxazole rings compared to traditional methods. Mechanistic investigations such as operando IR, EPR and radical inhibition experiments were carefully done and confirmed the acyl cation and Ag(II) as the intermediates in this transformation, and the involvement of a radical decarboxylative process.

  8. Hydroxyl-substituted ladder polyethers via selective tandem epoxidation/cyclization sequence.

    PubMed

    Czabaniuk, Lara C; Jamison, Timothy F

    2015-02-20

    A new and highly selective method for the synthesis of hydroxyl-substituted tetrahydropyrans is described. This method utilizes titanium(IV) isopropoxide and diethyl tartrate to perform a diastereoselective epoxidation followed by in situ epoxide activation and highly selective endo-cyclization to form the desired tetrahydropyran ring. The HIJ ring fragment of the marine ladder polyether yessotoxin was synthesized using this two-stage tactic that proceeds with high efficiency and excellent regioselectivity.

  9. Synthesis of 6'-branched locked nucleic acid by a radical TEMPO-scavanged stereoselective mercury cyclization.

    PubMed

    Enderlin, Gerald; Nielsen, Poul

    2008-09-05

    A 6'(R)-hydroxymethyl derivative of the locked nucleic acid (LNA)-thymidine monomer has been synthesized by a stereoselective mercury cyclization and subsequent use of TEMPO as a radical scavenger. This compound was converted to an azide derivative, which in a Huisgen-type [3 + 2] cycloaddition afforded a double-headed nucleoside with a triazole linking an additional thymine to the 6'-position of the LNA-nucleoside monomer.

  10. Synthesis of derivatives of indole and quinoline by the intramolecular catalytic cyclization of allylanilines

    SciTech Connect

    Abdrakmanov, I.B.; Mustafin, A.G.; Tolstikov, G.A.; Fakhretdinov, R.N.; Dzhemilev, U.M.

    1986-09-01

    An effective method for the isolation of 3-methyl-2-ethylindole and 2,4-dimethyl-quinoline by the intramolecular cyclization of N-(1-methyl-2-butenyl)- and 2-(1-methyl-2-butenyl)anilines under the action of the catalyst PdCl/sub 2/ (DMSO)/sub n/ was developed. The influence of the nature of the solvent, the temperature, and the concentration of the catalyst on the yield and the ratio of the reaction products was investigated.

  11. Backbone building from quadrilaterals: a fast and accurate algorithm for protein backbone reconstruction from alpha carbon coordinates.

    PubMed

    Gront, Dominik; Kmiecik, Sebastian; Kolinski, Andrzej

    2007-07-15

    In this contribution, we present an algorithm for protein backbone reconstruction that comprises very high computational efficiency with high accuracy. Reconstruction of the main chain atomic coordinates from the alpha carbon trace is a common task in protein modeling, including de novo structure prediction, comparative modeling, and processing experimental data. The method employed in this work follows the main idea of some earlier approaches to the problem. The details and careful design of the present approach are new and lead to the algorithm that outperforms all commonly used earlier applications. BBQ (Backbone Building from Quadrilaterals) program has been extensively tested both on native structures as well as on near-native decoy models and compared with the different available existing methods. Obtained results provide a comprehensive benchmark of existing tools and evaluate their applicability to a large scale modeling using a reduced representation of protein conformational space. The BBQ package is available for downloading from our website at http://biocomp.chem.uw.edu.pl/services/BBQ/. This webpage also provides a user manual that describes BBQ functions in detail.

  12. Synthesis of triazafluoranthenones via silver(I)-mediated nonoxidative and oxidative intramolecular palladium-catalyzed cyclizations.

    PubMed

    Koutentis, Panayiotis A; Loizou, Georgia; Lo Re, Daniele

    2011-07-15

    Silver(I) fluoride (AgF)-mediated intramolecular nonoxidative and oxidative palladium-catalyzed cyclizations of 1,3-diphenyl- and 8-iodo-1,3-diphenylbenzo[e][1,2,4]triazin-7(1H)-ones 6a (R = H) and 7a (R = I) afford a new 'alkaloid like' ring system 2-phenyl-6H-[1,2,4]triazino[5,6,1-jk]carbazol-6-one 8a (triazafluoranthenone) in 86 and 100% yields, respectively. Furthermore, these cyclization protocols were used to prepare triazafluoranthenone analogues 8b-e bearing dialkylamino, methoxy, and phenylsulfanyl substituents at C-5, which were also independently synthesized from triazafluoranthenone 8a by regioselective nucleophilic addition. Similar AgF-mediated intramolecular nonoxidative and oxidative palladium-catalyzed cyclizations of 8,10-dihydro-1-iodo-10-phenylphenazin-2(7H)-ones 13 gave the new 'alkaloid like' ring system 8H-indolo[1,2,3-mn]phenazin-8-one 14 in 80 and 18% yields, respectively.

  13. Intramolecular Cyclization of Thiophene-Based [7]Helicenes to Quasi-[8]Circulenes

    SciTech Connect

    Rajca, Andrzej; Miyasaka, Makoto; Xiao, Shuzhang; Boratynski, Przemystaw J.; Pink, Maren; Rajca, Suchada

    2009-12-08

    Intramolecular cyclization in a series of thiophene-based dibromo[7]helicenes (4-6) with different helix structures is investigated by vacuum pyrolysis, tin- and palladium-mediated C-C bond forming reactions. The product with the cyclic structure of the annelated aromatic rings, which resembles [8]circulene devoid of an atom linkage, is referred to as quasi-[8]circulene. Vacuum pyrolysis of 4 gives insoluble, unidentified products, while 5 and 6 yield the corresponding quasi-[8]circulenes under similar conditions. Thermogravimetry (TG) and differential scanning calorimetry (DSC) analyses for 4 indicate complex reaction pathways, while those for 5 and 6 show a single process corresponding to a loss of 1 equiv of Br2 at about 330 C. Pd-mediated reductive cyclization provides quasi-[8]circulenes for all three [7]helicenes, though only 4 gives a good isolated yield. Tributyltin hydride-mediated radical cyclization of 4-6 provides quasi-[8]circulenes in excellent yields, and it is practically insensitive to the helix structure. Experimental and calculated UV-vis absorption spectra for quasi-[8]circulenes and [8]circulenes are reported. The results suggest that the lack of atom linkage in quasi-[8]circulene does not significantly affect properties and conformation, compared to those for the corresponding [8]circulenes.

  14. Flow Pickering Emulsion Interfaces Enhance Catalysis Efficiency and Selectivity for Cyclization of Citronellal.

    PubMed

    Yang, Hengquan; Chen, Huan; Zou, Houbing; Hao, Yajuan

    2017-03-23

    Cyclization of citronellal is a necessary intermediate step to produce the important flavor chemical (-)-menthol. We here demonstrate a continuous flow Pickering emulsion (FPE) strategy for selective cyclization of citronellal to (-)-isopulegol, using water droplets hosting heteropolyacid catalyst (HPA) to fill a column reactor. Owing to the large liquid-liquid interface and the excellent confinement capability of droplets toward HPA, the FPE system exhibits a catalysis efficiency much higher than those of batch systems (2~5 fold) and an excellent durability (two months). Moreover, a remarkably enhanced selectivity is observed from 34.8% of batch reactions to 64% of the FPE reactions. It is found that the water droplet size and the flow rate significantly impact on the catalysis selectivity and the catalysis efficiency. This study not only represents an unprecedented and more sustainable process for the selective cyclization of citronellal but also points out a novel flow interface catalysis effect that is useful for designing innovative catalysis systems in future.

  15. Mechanics and chemistry: single molecule bond rupture forces correlate with molecular backbone structure.

    PubMed

    Frei, Michael; Aradhya, Sriharsha V; Koentopp, Max; Hybertsen, Mark S; Venkataraman, L

    2011-04-13

    We simultaneously measure conductance and force across nanoscale junctions. A new, two-dimensional histogram technique is introduced to statistically extract bond rupture forces from a large data set of individual junction elongation traces. For the case of Au point contacts, we find a rupture force of 1.4 ± 0.2 nN, which is in good agreement with previous measurements. We then study systematic trends for single gold metal-molecule-metal junctions for a series of molecules terminated with amine and pyridine linkers. For all molecules studied, single molecule junctions rupture at the Au-N bond. Selective binding of the linker group allows us to correlate the N-Au bond-rupture force to the molecular backbone. We find that the rupture force ranges from 0.8 nN for 4,4' bipyridine to 0.5 nN in 1,4 diaminobenzene. These experimental results are in excellent quantitative agreement with density functional theory based adiabatic molecular junction elongation and rupture calculations.

  16. Chemical characteristics and antithrombotic effect of chondroitin sulfates from sturgeon skull and sturgeon backbone.

    PubMed

    Gui, Meng; Song, Juyi; Zhang, Lu; Wang, Shun; Wu, Ruiyun; Ma, Changwei; Li, Pinglan

    2015-06-05

    Chondroitin sulfates (CSs) were extracted from sturgeon skull and backbone, and their chemical composition, anticoagulant, anti-platelet and thrombolysis activities were evaluated. The average molecular weights of CS from sturgeon skull and backbone were 38.5kDa and 49.2kDa, respectively. Disaccharide analysis indicated that the sturgeon backbone CS was primarily composed of disaccharide monosulfated in position four of the GalNAc (37.8%) and disaccharide monosulfated in position six of the GalNAc (59.6%) while sturgeon skull CS was primarily composed of nonsulfated disaccharide (74.2%). Sturgeon backbone CS showed stronger antithrombotic effect than sturgeon skull CS. Sturgeon backbone CS could significantly prolong activated partial thromboplastin time (APTT) and thrombin time (TT), inhibited ADP-induced platelet aggregation and dissolved platelet plasma clots in vitro. The results suggested that sturgeon backbone CS can be explored as a functional food with antithrombotic function.

  17. Reconstruction of the Sunspot Group Number: The Backbone Method

    NASA Astrophysics Data System (ADS)

    Svalgaard, Leif; Schatten, Kenneth H.

    2016-11-01

    We have reconstructed the sunspot-group count, not by comparisons with other reconstructions and correcting those where they were deemed to be deficient, but by a re-assessment of original sources. The resulting series is a pure solar index and does not rely on input from other proxies, e.g. radionuclides, auroral sightings, or geomagnetic records. "Backboning" the data sets, our chosen method, provides substance and rigidity by using long-time observers as a stiffness character. Solar activity, as defined by the Group Number, appears to reach and sustain for extended intervals of time the same level in each of the last three centuries since 1700 and the past several decades do not seem to have been exceptionally active, contrary to what is often claimed.

  18. 1H, 13C, and 15N backbone, side-chain, and heme chemical shift assignments for oxidized and reduced forms of the monoheme c-type cytochrome ApcA isolated from the acidophilic metal-reducing bacterium Acidiphilium cryptum.

    SciTech Connect

    Cort, John R.; Swenson, Michael; Magnuson, Timothy S.

    2011-03-04

    We report the 1H, 13C, and 15N chemical shift assignments of both oxidized and reduced forms of an abundant periplasmic c-type cytochrome, designated ApcA, from the acidophilic gram-negative facultatively anaerobic metal-reducing alpha-proteobacterium Acidiphilium cryptum. These resonance assignments prove that ApcA is a monoheme cytochrome c2 and the product of the Acry_2099 gene. An absence of resonance peaks in the NMR spectra for the 21 N-terminal residues suggests that a predicted N-terminal signal sequence is cleaved. We also describe the preparation and purification of the protein in labeled form from laboratory cultures of A. cryptum growing on 13C- and 15N- labeled substrates.

  19. Computational design of high-affinity epitope scaffolds by backbone grafting of a linear epitope.

    PubMed

    Azoitei, Mihai L; Ban, Yih-En Andrew; Julien, Jean-Philippe; Bryson, Steve; Schroeter, Alexandria; Kalyuzhniy, Oleksandr; Porter, Justin R; Adachi, Yumiko; Baker, David; Pai, Emil F; Schief, William R

    2012-01-06

    Computational grafting of functional motifs onto scaffold proteins is a promising way to engineer novel proteins with pre-specified functionalities. Typically, protein grafting involves the transplantation of protein side chains from a functional motif onto structurally homologous regions of scaffold proteins. Using this approach, we previously transplanted the human immunodeficiency virus 2F5 and 4E10 epitopes onto heterologous proteins to design novel "epitope-scaffold" antigens. However, side-chain grafting is limited by the availability of scaffolds with compatible backbone for a given epitope structure and offers no route to modify backbone structure to improve mimicry or binding affinity. To address this, we report here a new and more aggressive computational method-backbone grafting of linear motifs-that transplants the backbone and side chains of linear functional motifs onto scaffold proteins. To test this method, we first used side-chain grafting to design new 2F5 epitope scaffolds with improved biophysical characteristics. We then independently transplanted the 2F5 epitope onto three of the same parent scaffolds using the newly developed backbone grafting procedure. Crystal structures of side-chain and backbone grafting designs showed close agreement with both the computational models and the desired epitope structure. In two cases, backbone grafting scaffolds bound antibody 2F5 with 30- and 9-fold higher affinity than corresponding side-chain grafting designs. These results demonstrate that flexible backbone methods for epitope grafting can significantly improve binding affinities over those achieved by fixed backbone methods alone. Backbone grafting of linear motifs is a general method to transplant functional motifs when backbone remodeling of the target scaffold is necessary.

  20. Oxidation and cyclization of casbene in the biosynthesis of Euphorbia factors from mature seeds of Euphorbia lathyris L.

    PubMed Central

    Luo, Dan; Callari, Roberta; Hamberger, Britta; Wubshet, Sileshi Gizachew; Nielsen, Morten T.; Andersen-Ranberg, Johan; Hallström, Björn M.; Cozzi, Federico; Lindberg Møller, Birger; Hamberger, Björn

    2016-01-01

    The seed oil of Euphorbia lathyris L. contains a series of macrocyclic diterpenoids known as Euphorbia factors. They are the current industrial source of ingenol mebutate, which is approved for the treatment of actinic keratosis, a precancerous skin condition. Here, we report an alcohol dehydrogenase-mediated cyclization step in the biosynthetic pathway of Euphorbia factors, illustrating the origin of the intramolecular carbon–carbon bonds present in lathyrane and ingenane diterpenoids. This unconventional cyclization describes the ring closure of the macrocyclic diterpene casbene. Through transcriptomic analysis of E. lathyris L. mature seeds and in planta functional characterization, we identified three enzymes involved in the cyclization route from casbene to jolkinol C, a lathyrane diterpene. These enzymes include two cytochromes P450 from the CYP71 clan and an alcohol dehydrogenase (ADH). CYP71D445 and CYP726A27 catalyze regio-specific 9-oxidation and 5-oxidation of casbene, respectively. When coupled with these P450-catalyzed monooxygenations, E. lathyris ADH1 catalyzes dehydrogenation of the hydroxyl groups, leading to the subsequent rearrangement and cyclization. The discovery of this nonconventional cyclization may provide the key link to complete elucidation of the biosynthetic pathways of ingenol mebutate and other bioactive macrocyclic diterpenoids. PMID:27506796

  1. Density Functional Theory-Based First Principles Calculations of Rhododendrol-Quinone Reactions: Preference to Thiol Binding over Cyclization

    NASA Astrophysics Data System (ADS)

    Kishida, Ryo; Kasai, Hideaki; Meñez Aspera, Susan; Lacdao Arevalo, Ryan; Nakanishi, Hiroshi

    2017-02-01

    Using density functional theory-based first principles calculations, we investigated the changes in the energetics and electronic structures of rhododendrol (RD)-quinone for the initial step of two important reactions, viz., cyclization and thiol binding, to give significant insights into the mechanism of the cause of cytotoxic effects. We found that RD-quinone in the electroneutral structure cannot undergo cyclization, indicating a slow cyclization of RD-quinone at neutral pH. Furthermore, using methane thiolate ion as a model thiol, we found that the oxidized form of the cyclized RD-quinone, namely RD-cyclic quinone, exhibited a reduced binding energy for thiols. However, this reduction of binding energy is clearly smaller than the case of dopaquinone, which is a molecule originally involved in the melanin synthesis. This study clearly shows that RD-quinone has a preference toward thiol bindings than cyclization compared to the case of dopaquinone. Considering that thiol bindings have been reported to induce cytotoxic effects in various ways, the preference toward thiol bindings is an important chemical property for the cytotoxicity caused by RD.

  2. Pendant Dynamics of Ethylene-Oxide Containing Polymers with Diverse Backbones

    NASA Astrophysics Data System (ADS)

    Bartels, Joshua; Wang, Jing-Han Helen; Chen, Quan; Runt, James; Colby, Ralph

    In the last twenty years, a wide variety of ion conducting polymers have used ether oxygens to facilitate ion conduction, and it is therefore important to understand the dynamics of ether oxygens (EOs) when attached to different polymer backbones. Four different EO-containing polymer architectures are studied by dielectric spectroscopy to understand the backbone effect on the EO dipoles. Polysiloxanes, polyphosphazenes, polymethylmethacrylates, and a polyester ether are compared, with different EO pendant lengths for the siloxane and methylmethacrylate backbones. The flexible polysiloxanes and polyphosphazene backbones impart superior segmental mobility with a glass transition temperature 15 K lower than that of the organic backbone polymers. Short EO pendants are found to impart a lower static dielectric constant at comparable EO content as compared to longer EO pendants of either inorganic or organic backbones. The long-pendant polymethylmethacrylate polymers show two relaxations corresponding to fast EOs near the pendant tail end and slow EOs close to the slower backbone, whereas the long-pendant polysiloxane shows a single relaxation due to the siloxane backbone relaxing faster than the EO pendant. Supported by the NSF Division of Materials Research Polymers Program through Grants DMR-1404586 (RHC) and DMR-1505953 (JR).

  3. Backbone of complex networks of corporations: The flow of control

    NASA Astrophysics Data System (ADS)

    Glattfelder, J. B.; Battiston, S.

    2009-09-01

    We present a methodology to extract the backbone of complex networks based on the weight and direction of links, as well as on nontopological properties of nodes. We show how the methodology can be applied in general to networks in which mass or energy is flowing along the links. In particular, the procedure enables us to address important questions in economics, namely, how control and wealth are structured and concentrated across national markets. We report on the first cross-country investigation of ownership networks, focusing on the stock markets of 48 countries around the world. On the one hand, our analysis confirms results expected on the basis of the literature on corporate control, namely, that in Anglo-Saxon countries control tends to be dispersed among numerous shareholders. On the other hand, it also reveals that in the same countries, control is found to be highly concentrated at the global level, namely, lying in the hands of very few important shareholders. Interestingly, the exact opposite is observed for European countries. These results have previously not been reported as they are not observable without the kind of network analysis developed here.

  4. Backbone Assignment of the MALT1 Paracaspase by Solution NMR.

    PubMed

    Unnerståle, Sofia; Nowakowski, Michal; Baraznenok, Vera; Stenberg, Gun; Lindberg, Jimmy; Mayzel, Maxim; Orekhov, Vladislav; Agback, Tatiana

    2016-01-01

    Mucosa-associated lymphoid tissue lymphoma translocation protein 1 (MALT1) is a unique paracaspase protein whose protease activity mediates oncogenic NF-κB signalling in activated B cell-like diffuse large B cell lymphomas (ABC-DLBCLs). ABC-DLBCLs are aggressive lymphomas with high resistance to current chemotherapies. Low survival rate among patients emphasizes the urgent need for alternative treatment options. The characterization of the MALT1 will be an essential tool for developing new target-directed drugs against MALT1 dependent disorders. As the first step in the atomic-level NMR studies of the system, here we report, the (15)N/(13)C/(1)H backbone assignment of the apo form of the MALT1 paracaspase region together with the third immunoglobulin-like (Ig3) domain, 44 kDa, by high resolution NMR. In addition, the non-uniform sampling (NUS) based targeted acquisition procedure is evaluated as a mean of decreasing acquisition and analysis time for larger proteins.

  5. Thermogelling Biodegradable Polymers with Hydrophilic Backbones: PEG-g-PLGA

    SciTech Connect

    Jeong, Byeongmoon; Kibbey, Merinda R.; Birnbaum, Jerome C.; Won, You-Yeong; Gutowska, Anna

    2000-10-31

    The aqueous solutions of poly(ethylene glycol)grafted with poly(lactic acid-co-glycolic acid) flow freely at room temperature but form gels at higher temperature. The existence of micelles in water at low polymer concentration was confirmed by Cro-transmission electron microscopy and dye solubilization studies. The micellar diameter and critical micelle concentration are about 9 nm and 0.47 wt.% respectively. The critical gel concentration, above which a gel phase appears was 16 wt.% and sol-to-gel transition temperature was slightly affected by the concentration in the range of 16 {approx} 25 wt.%. At sol-to-gel transition, viscosity increased abruptly and C-NMR showed molecular motion of hydrophilic poly(lactic acid-co-glycolic acid) side-chains increased. The hydrogel of PEG-g-PLGA with hydrophilic backbones was transparent during degradation and remained a gel for one week, suggesting a promising material for short-term drug delivery.

  6. Backbone Assignment of the MALT1 Paracaspase by Solution NMR

    PubMed Central

    Unnerståle, Sofia; Nowakowski, Michal; Baraznenok, Vera; Stenberg, Gun; Lindberg, Jimmy; Mayzel, Maxim; Orekhov, Vladislav; Agback, Tatiana

    2016-01-01

    Mucosa-associated lymphoid tissue lymphoma translocation protein 1 (MALT1) is a unique paracaspase protein whose protease activity mediates oncogenic NF-κB signalling in activated B cell-like diffuse large B cell lymphomas (ABC-DLBCLs). ABC-DLBCLs are aggressive lymphomas with high resistance to current chemotherapies. Low survival rate among patients emphasizes the urgent need for alternative treatment options. The characterization of the MALT1 will be an essential tool for developing new target-directed drugs against MALT1 dependent disorders. As the first step in the atomic-level NMR studies of the system, here we report, the 15N/13C/1H backbone assignment of the apo form of the MALT1 paracaspase region together with the third immunoglobulin-like (Ig3) domain, 44 kDa, by high resolution NMR. In addition, the non-uniform sampling (NUS) based targeted acquisition procedure is evaluated as a mean of decreasing acquisition and analysis time for larger proteins. PMID:26788853

  7. Backbone of complex networks of corporations: the flow of control.

    PubMed

    Glattfelder, J B; Battiston, S

    2009-09-01

    We present a methodology to extract the backbone of complex networks based on the weight and direction of links, as well as on nontopological properties of nodes. We show how the methodology can be applied in general to networks in which mass or energy is flowing along the links. In particular, the procedure enables us to address important questions in economics, namely, how control and wealth are structured and concentrated across national markets. We report on the first cross-country investigation of ownership networks, focusing on the stock markets of 48 countries around the world. On the one hand, our analysis confirms results expected on the basis of the literature on corporate control, namely, that in Anglo-Saxon countries control tends to be dispersed among numerous shareholders. On the other hand, it also reveals that in the same countries, control is found to be highly concentrated at the global level, namely, lying in the hands of very few important shareholders. Interestingly, the exact opposite is observed for European countries. These results have previously not been reported as they are not observable without the kind of network analysis developed here.

  8. SmI2-induced cyclizations and their applications in natural product synthesis.

    PubMed

    Nakata, Tadashi

    2010-06-01

    Since the isolation of brevetoxin-B, a red tide toxin, many bioactive marine natural products featuring synthetically challenging trans-fused polycyclic ether ring systems have been reported. We have developed SmI(2)-induced cyclization of beta-alkoxyacrylate with aldehyde, affording 2,6-syn-2,3-trans-tetrahydropyran (THP) or 2,7-syn-2,3-trans-oxepane with complete stereoselection, as a key reaction of efficient iterative and bi-directional strategies for the construction of these polycyclic ethers. This reaction is also applicable to the synthesis of 3-, 5-, and 6-methyl-THPs and 3,5-dimethyl-THP. The synthesis of 2-methyl- and 2,6-dimethyl-THPs was accomplished by means of a unique methyl insertion. Recently, the SmI(2)-induced cyclization was extended to similar reactions using beta-alkoxyvinyl sulfone and sulfoxide. Reaction of (E)- and (Z)-beta-alkoxyvinyl sulfone-aldehyde afforded 2,6-syn-2,3-trans- and 2,6-syn-2,3-cis- THPs, respectively. Reaction of (E)-beta-alkoxyvinyl (R)- and (S)-sulfoxides gave 2,6-anti-2,3-cis- and 2,6-syn-2,3-trans-THPs, respectively. Reaction of (Z)-beta-alkoxyvinyl (R)-sulfoxides gave 2,6-syn-2,3-cis-THP and an olefinic product, while that of (Z)-beta-alkoxyvinyl (S)-sulfoxide afforded a mixture of many products. These SmI(2)-induced cyclizations have been applied to the total syntheses of various natural products, including brevetoxin-B, mucocin, pyranicin, and pyragonicin. Synthetic studies on gambierol and maitotoxin are also introduced.

  9. Synthesis of anionic phosphorus-containing heterocycles by intramolecular cyclizations involving N-functionalized phosphinecarboxamides.

    PubMed

    Robinson, Thomas P; Goicoechea, Jose M

    2015-04-07

    We report that the 2-phosphaethynolate anion (PCO(-)) reacts with propargylamines in the presence of a proton source to afford novel N-derivatized phosphinecarboxamides bearing alkyne functionalities. Deprotonation of these species gives rise to novel five- and six-membered anionic heterocycles resulting from intramolecular nucleophilic attack of the resulting phosphide at the alkyne functionality (via 5-exo-dig or 6-endo-dig cyclizations, respectively). The nature of the substituents on the phosphinecarboxamide can be used to influence the outcome of these reactions. This strategy represents a unique approach to phosphorus-containing heterocylic systems that are closely related to known organic molecules with interesting bio-active properties.

  10. New strategies for cyclization and bicyclization of oligonucleotides by click chemistry assisted by microwaves.

    PubMed

    Lietard, Jory; Meyer, Albert; Vasseur, Jean-Jacques; Morvan, François

    2008-01-04

    The synthesis of cyclic, branched, and bicyclic oligonucleotides was performed by copper-catalyzed azide-alkyne cycloaddition assisted by microwaves in solution and on solid support. For that purpose, new phosphoramidite building blocks and new solid supports were designed to introduce alkyne and bromo functions into the same oligonucleotide by solid-phase synthesis on a DNA synthesizer. The bromine atom was then substituted by sodium azide to yield azide oligonucleotides. Cyclizations were found to be more efficient in solution than on solid support. This method allowed the efficient preparation of cyclic (6- to 20-mers), branched (with one or two dangling sequences), and bicyclic (2 x 10-mers) oligonucleotides.

  11. The polysiloxane cyclization equilibrium constant: a theoretical focus on small and intermediate size rings.

    PubMed

    Madeleine-Perdrillat, Claire; Delor-Jestin, Florence; de Sainte Claire, Pascal

    2014-01-09

    The nonlinear dependence of polysiloxane cyclization constants (log(K(x))) with ring size (log(x)) is explained by a thermodynamic model that treats specific torsional modes of the macromolecular chains with a classical coupled hindered rotor model. Several parameters such as the dependence of the internal rotation kinetic energy matrix with geometry, the effect of potential energy hindrance, anharmonicity, and the couplings between internal rotors were investigated. This behavior arises from the competing effects of local molecular entropy that is mainly driven by the intrinsic transformation of vibrations in small cycles into hindered rotations in larger cycles and configurational entropy.

  12. Raman spectroscopic approach to monitor the in vitro cyclization of creatine → creatinine

    NASA Astrophysics Data System (ADS)

    Gangopadhyay, Debraj; Sharma, Poornima; Singh, Sachin Kumar; Singh, Pushkar; Tarcea, Nicolae; Deckert, Volker; Popp, Jürgen; Singh, Ranjan K.

    2015-01-01

    The creatine → creatinine cyclization, an important metabolic phenomenon has been initiated in vitro at acidic pH and studied through Raman spectroscopic and DFT approach. The equilibrium composition of neutral, zwitterionic and protonated microspecies of creatine has been monitored with time as the reaction proceeds. Time series Raman spectra show clear signature of creatinine formation at pH 3 after ∼240 min at room temperature and reaction is faster at higher temperature. The spectra at pH 1 and pH 5 do not show such signature up to 270 min implying faster reaction rate at pH 3.

  13. The direct oxidative diene cyclization and related reactions in natural product synthesis

    PubMed Central

    2016-01-01

    Summary The direct oxidative cyclization of 1,5-dienes is a valuable synthetic method for the (dia)stereoselective preparation of substituted tetrahydrofurans. Closely related reactions start from 5,6-dihydroxy or 5-hydroxyalkenes to generate similar products in a mechanistically analogous manner. After a brief overview on the history of this group of transformations and a survey on mechanistic and stereochemical aspects, this review article provides a summary on applications in natural product synthesis. Moreover, current limitations and future directions in this area of chemistry are discussed. PMID:27829917

  14. Heterologous Production of Fungal Maleidrides Reveals the Cryptic Cyclization Involved in their Biosynthesis

    PubMed Central

    Szwalbe, Agnieszka J.; Mulholland, Nicholas P.; Vincent, Jason L.; Bailey, Andrew M.; Willis, Christine L.; Simpson, Thomas J.

    2016-01-01

    Abstract Fungal maleidrides are an important family of bioactive secondary metabolites that consist of 7, 8, or 9‐membered carbocycles with one or two fused maleic anhydride moieties. The biosynthesis of byssochlamic acid (a nonadride) and agnestadride A (a heptadride) was investigated through gene disruption and heterologous expression experiments. The results reveal that the precursors for cyclization are formed by an iterative highly reducing fungal polyketide synthase supported by a hydrolase, together with two citrate‐processing enzymes. The enigmatic ring formation is catalyzed by two proteins with homology to ketosteroid isomerases, and assisted by two proteins with homology to phosphatidylethanolamine‐binding proteins. PMID:27099957

  15. Stereocontrolled synthesis of rosuvastatin calcium via iodine chloride-induced intramolecular cyclization.

    PubMed

    Xiong, Fangjun; Wang, Haifeng; Yan, Lingjie; Han, Sheng; Tao, Yuan; Wu, Yan; Chen, Fener

    2016-01-28

    A novel, stereoselective approach towards rosuvastatin calcium from the known (S)-homoallylic alcohol has been developed. The synthesis is highlighted by a regio- and stereocontrolled ICl-induced intramolecular cyclization of chiral homoallylic carbonate to deliver the C6-formyl statin side chain with a syn-1,3-diol moiety. An improved synthesis of the rosuvastatin pyrimidine core moiety is also included. Moreover, this methodology is useful in the asymmetric synthesis of structural variants of statins such as pitavastatin calcium and atorvastatin calcium and their related analogs.

  16. Controlling both ground- and excited-state thermal barriers to Bergman cyclization with alkyne termini substitution.

    PubMed

    Nath, Mahendra; Pink, Maren; Zaleski, Jeffrey M

    2005-01-19

    The cross-coupling reaction of 2,3-dibromo-5,10,15,20-tetraphenylporphyrin with corresponding organostannanes in the presence of a Pd0 catalyst in THF at reflux temperature yields free base 2,3-dialkynylporphyrins 1a,c-e. The subsequent deprotection of trimethylsilyl group of 1a with TBAF in THF under aqueous conditions produces the 2,3-diethynyl-5,10,15,20-tetraphenylporphyrins 1b in 87% yield. Compounds 1a-d undergo zinc insertion upon treatment with Zn(OAc)2.2H2O in CHCl3/MeOH to give zinc(II) 2,3-dialkynyl-5,10,15,20-tetraphenylporphyrins (2a-d) in 70-92% yields. Thermal Bergman cyclization of 1a-e and 2a-d was studied in chlorobenzene and approximately 35-fold 1,4-cyclohexadiene at 120-210 degrees C. Compounds 1b and 2b with R = H react at lower temperature (120 degrees C) and produce cyclized products 3b and 4b in higher yields (65-70%) than their propyl, isopropyl, and phenyl analogues, with R = Ph being the most stable. Continuing in this trend, the -TMS derivatives 1a and 2a exhibit no reactivity even after heating at 190 degrees C in chlorobenzene/CHD for 24 h. Photolysis (at lambda >/= 395 nm) of 1b and 2b at 10 degrees C leads the formation of isolable picenoporphyrin products in 15 and 35% yields, respectively, in 72 h, whereas these compounds are stable in solution under same reaction conditions at 25 degrees C in the dark. Unlike thermolysis at 125 degrees C, which did not yield Bergman cyclized product for R = Ph, photolysis generated very small amounts of picenoporphyrin products (3c: 5%; 4c: 8% based on 1H NMR) as well as a mixture of reduced porphyrin products that were not separable. Thus, trends in the barrier to Bergman cyclization in the excited state exhibit the same trend as those observed in the ground state as a function of R-group. Finally, photolysis of 2b at 10 degrees C with lambda >/= 515 or 590 nm in benzene/iPrOH (4:1, 72 h) produces 4b in 15 and 6% isolated yields, indicating that conjugation of the enediyne unit into the

  17. Cyclization of a cell-penetrating peptide via click-chemistry increases proteolytic resistance and improves drug delivery.

    PubMed

    Reichart, Florian; Horn, Mareike; Neundorf, Ines

    2016-06-01

    In this work we report synthesis and biological evaluation of a cell-penetrating peptide (CPP), that is partly cyclized via a triazole bridge. Recently, beneficious properties have been reported for cyclized peptides concerning their metabolic stability and intracellular uptake. A CPP based on human calcitonin was used in this study, and side chain cyclization was achieved via copper catalyzed alkyne-azide click reaction. Cell viability studies in several cell-lines revealed no cytotoxic effects. Furthermore, efficient uptake in breast cancer MCF-7 cells could be determined. Moreover, preliminary studies using this novel peptide as drug transporter for daunorubicin were performed. Copyright © 2016 European Peptide Society and John Wiley & Sons, Ltd.

  18. Progress toward the syntheses of (+)-GB 13, (+)-himgaline, and himandridine. new insights into intramolecular imine/enamine aldol cyclizations.

    PubMed

    Evans, David A; Adams, Drew J; Kwan, Eugene E

    2012-05-16

    A full account of our total synthesis of the galbulimima alkaloids GB 13 and himgaline is provided. Using a strategy adapted from the proposed biosynthesis of the GB alkaloid family, a linear precursor underwent successive intramolecular Diels-Alder, Michael, and imine aldol cyclizations to form the polycyclic alkaloid core. We now show that modification of this strategy can also deliver an advanced intermediate en route to the related alkaloid himandridine. The success of the key imine aldol cyclization is acutely sensitive to substrate structure and solvent, including a case in which cyclization was spontaneous in protic solvents. A detailed computational investigation of the course of the reaction closely correlates with, and suggests a rationale for, the observed patterns of imine aldol reactivity.

  19. 7-endo radical cyclizations catalyzed by titanocene(III). Straightforward synthesis of terpenoids with seven-membered carbocycles.

    PubMed

    Justicia, José; Oller-López, Juan L; Campaña, Araceli G; Oltra, J Enrique; Cuerva, Juan M; Buñuel, Elena; Cárdenas, Diego J

    2005-10-26

    We describe a novel procedure for the straightforward synthesis of seven-membered carbocycles via free-radical chemistry, based on titanocene(III)-catalyzed 7-endo-dig and 7-endo-trig cyclizations. This procedure has proved to be useful for the chemical preparation of terpenoids with different skeletons containing cycloheptane rings, including the first total syntheses of dauca-4(11),8-diene (2), barekoxide (3), authentic laukarlaol (81), and a valparane diterpenoid (72), as well as a substantially improved synthesis of karahanaenone (1). We also provide theoretical and experimental evidence in support of a plausible mechanism, which may rationalize the preference for the unusual 7-endo cyclization mode shown by radicals with substitution patterns characteristic of the linalyl, nerolidyl, and geranyl linalyl systems. In light of these chemical findings, we discuss the potential involvement of radical cyclizations in the biosynthesis of some terpenoids containing seven-membered carbocycles.

  20. Methanesulfonic acid cataylzed cyclization of 3-arylpropanoic and 4-arylbutanoic acids to 1-indanones and 1-tetralones

    SciTech Connect

    Premasagar, V.; Palaniswamy, V.A.; Eisenbraun, E.J.

    1981-07-03

    Since methanesulfonic acid (MSA), does not cause sulfonation of aromatic rings, it was used at elevated temperatures to prepare 1-indanones and 1-tetralones through cyclization of 3-arylpropanoic and 4-arylbutanoic acids. The twelve ketones which were prepared from MSA-catalyzed cyclization of 3 and 4-aryl substituted carboxylic acids are pesented in a table, along with their yields, time and temperature. Studies under a variety of temperatures, concentrations and reaction times show that 30 min. to 3 hours is needed for cyclization depending on the reactivity of the starting material. The use of neat MSA as a substitute for Friedel-Crafts catalyst was not promising. Trial studies in which m-xylene was treated with acetic acid in the presence of anhydrous MSA at 110/sup 0/C for 3 hours gave low yields of acetylation product (ca. 30%), and gas chromatography analysis of the product showed unreacted m-xylene.

  1. Rotational isomers of N-methyl-N-arylacetamides and their derived enolates: implications for asymmetric Hartwig oxindole cyclizations

    PubMed Central

    Mandel, Jérémie; Pan, Xiaohong; Ben Hay, E.; Geib, Steven J.

    2013-01-01

    The rotational preferences of N-(2-bromo-4,6-dimethylphenyl)-N-methyl 2-phenyl-propanamide were studied as a model of precursors for Hartwig asymmetric oxindole cyclizations. The atropisomers of this compound were separated by flash chromatography, then the enantiomers were resolved and the interconversions of the stereocenter and the N–Ar axis were studied. Under thermal conditions, the axis is very stable. Under the basic conditions of the Hartwig cyclization, both the stere-ocenter and the chiral axis equilibrate via enolate formation. The N–Ar rotation barrier of a 2-phenylacetamide analog was reduced from 31 kcal mol−1 in the precursor to 17 kcal mol−1 in the enolate. Reasons for this dramatic barrier reduction and implications of both N–Ar and amide C–N rotations for Hartwig cyclizations are discussed. PMID:23534372

  2. Structure and backbone dynamics of a microcrystalline metalloprotein by solid-state NMR

    PubMed Central

    Knight, Michael J.; Pell, Andrew J.; Bertini, Ivano; Felli, Isabella C.; Gonnelli, Leonardo; Pierattelli, Roberta; Herrmann, Torsten; Emsley, Lyndon; Pintacuda, Guido

    2012-01-01

    We introduce a new approach to improve structural and dynamical determination of large metalloproteins using solid-state nuclear magnetic resonance (NMR) with 1H detection under ultrafast magic angle spinning (MAS). The approach is based on the rapid and sensitive acquisition of an extensive set of 15N and 13C nuclear relaxation rates. The system on which we demonstrate these methods is the enzyme Cu, Zn superoxide dismutase (SOD), which coordinates a Cu ion available either in Cu+ (diamagnetic) or Cu2+ (paramagnetic) form. Paramagnetic relaxation enhancements are obtained from the difference in rates measured in the two forms and are employed as structural constraints for the determination of the protein structure. When added to 1H-1H distance restraints, they are shown to yield a twofold improvement of the precision of the structure. Site-specific order parameters and timescales of motion are obtained by a Gaussian axial fluctuation (GAF) analysis of the relaxation rates of the diamagnetic molecule, and interpreted in relation to backbone structure and metal binding. Timescales for motion are found to be in the range of the overall correlation time in solution, where internal motions characterized here would not be observable. PMID:22723345

  3. Synthesis of 2,1-benzisoxazole-3(1H)-ones by base-mediated photochemical N–O bond-forming cyclization of 2-azidobenzoic acids

    PubMed Central

    Dzhons, Daria Yu

    2016-01-01

    Summary The base-mediated photochemical cyclization of 2-azidobenzoic acids with the formation of 2,1-benzisoxazole-3(1H)-ones is reported. The optimization and scope of this cyclization reaction is discussed. It is shown that an essential step of the ring closure of 2-azidobenzoic acids is the formation and photolysis of 2-azidobenzoate anions. PMID:27340478

  4. Biomimetic cationic polyannulation reaction catalyzed by Bi(OTf)3: cyclization of 1,6-dienes, 1,6,10-trienes, and aryl polyenes.

    PubMed

    Godeau, Julien; Olivero, Sandra; Antoniotti, Sylvain; Duñach, Elisabet

    2011-07-01

    Nonactivated trienes and aryltrienes were cyclized into polycyclic compounds in good to excellent yields under bismuth triflate catalysis in a biomimetic fashion. The reaction showed broad applicability and allowed for the formation of functionalized bicyclic to tetracyclic structures from simple precursors in one pot. For some specific substrates, the cyclization was followed by a methyl shift as encountered in terpenoid biosynthesis.

  5. Sesquiterpene synthases Cop4 and Cop6 from Coprinus cinereus: Catalytic promiscuity and cyclization of farnesyl pyrophosphate geometrical isomers

    PubMed Central

    Lopez-Gallego, Fernando; Agger, Sean A.; Pella, Daniel A.; Distefano, Mark D.; Schmidt-Dannert, Claudia

    2010-01-01

    Sesquiterpene synthases catalyze with different catalytic fidelity the cyclization of farnesyl pyrophosphate (FPP) into hundreds of known compounds with diverse structures and stereochemistries. Two sesquiterpene synthases, Cop4 and Cop6, were previously isolated from Coprinus cinereus as part of a fungal genome survey. This study investigates the reaction mechanism and catalytic fidelity of the two enzymes. Cyclization of all-trans-FPP ((E,E)-FPP) was compared to the cyclization of the cis-trans isomer of FPP ((Z,E)-FPP) as a surrogate for the secondary cisoid neryl cation intermediate generated by sesquiterpene synthases capable of isomerizing the C2-C3 π bond of all-trans-FPP. Cop6 is a “high-fidelity” α-cuprenene synthase that retains its fidelity under various conditions tested. Cop4 is a catalytically promiscuous enzyme that cyclizes (E,E)-FPP into multiple products, including (−)-germacrene D and cubebol. Changing the pH of the reaction drastically alters the fidelity of Cop4 and makes it a highly selective enzyme. Cyclization of (Z,E)-FPP by Cop4 and Cop6 yields products that are very different from those obtained with (E,E)-FPP. Conversion of (E,E)-FPP proceeds via a (6R)-β-bisabolyl carbocation in the case of Cop6 and an (E,E)-germacradienyl carbocation in the case of Cop4. However, (Z,E)-FPP is cyclized via a (6S)-β-bisabolene carbocation by both enzymes. Structural modeling suggests that differences in the active site and the loop that covers the active site of the two enzymes may explain their different catalytic fidelities. PMID:20419721

  6. Biosynthesis of monoterpenes: Stereochemistry of the coupled isomerization and cyclization of geranyl pyrophosphate to camphane and isocamphane monoterpenes

    SciTech Connect

    Croteau, R.; Gershenzon, J.; Wheeler, C.J.; Satterwhite, D.M. )

    1990-03-01

    The conversion of geranyl pyrophosphate to (+)-bornyl pyrophosphate and (+)-camphene is considered to proceed by the initial isomerization of the substrate to (-)-(3R)-linalyl pyrophosphate and the subsequent cyclization of this bound intermediate. In the case of (-)-bornyl pyrophosphate and (-)-camphene, isomerization of the substrate to the (+)-(3S)-linalyl intermediate precedes cyclization. The geranyl and linalyl precursors were shown to be mutually competitive substrates (inhibitors) of the relevant cyclization enzymes isolated from Salvia officinalis (sage) and Tanacetum vulgare (tansy) by the mixed substrate analysis method, demonstrating that isomerization and cyclization take place at the same active site. Incubation of partially purified enzyme preparations with (3R)-(1Z-3H)linalyl pyrophosphate plus (1-14C)geranyl pyrophosphate gave rise to double-labeled (+)-bornyl pyrophosphate and (+)-camphene, whereas incubation of enzyme preparations catalyzing the antipodal cyclizations with (3S)-(1Z-3H)-linalyl pyrophosphate plus (1-14C)geranyl pyrophosphate yielded double-labeled (-)-bornyl pyrophosphate and (-)-camphene. Each product was then transformed to the corresponding (+)- or (-)-camphor without change in the 3H:14C isotope ratio, and the location of the tritium label was deduced in each case by stereoselective, base-catalyzed exchange of the exo-alpha-hydrogen of the derived ketone. The finding that the 1Z-3H of the linalyl precursor was positioned at the endo-alpha-hydrogen of the corresponding camphor in all cases, coupled to the previously demonstrated retention of configuration at C1 of the geranyl substrate in these transformations, confirmed the syn-isomerization of geranyl pyrophosphate to linalyl pyrophosphate and the cyclization of the latter via the anti,endo- conformer.

  7. The Development of a Palladium-Catalyzed Tandem Addition/Cyclization for Direct Construction of Indole Skeletons.

    PubMed

    Yu, Shuling; Qi, Linjun; Hu, Kun; Gong, Julin; Cheng, Tianxing; Wang, Qingzong; Chen, Jiuxi; Wu, Huayue

    2017-03-13

    A palladium-catalyzed tandem addition/cyclization of 2-(2-aminoaryl)acetonitriles with arylboronic acids has been developed for the first time, achieving a new strategy for direct construction of indole skeletons. This system shows good functional group tolerance and remarkable chemoselectivity. Especially, the halogen (e.g. bromo and iodo) substituents are amenable for further synthetic elaborations thereby broadening the diversity of the products. Preliminary mechanistic experiments indicate that this transformation involves sequential nucleophilic addition followed by an intramolecular cyclization.

  8. FeCl3-Catalyzed Tandem Prins and Friedel-Crafts Cyclization: A Highly Diastereoselective Route to Polycyclic Ring Structures.

    PubMed

    Ghosh, Arun K; Keyes, Chad; Veitschegger, Anne M

    2014-07-23

    Catalytic FeCl3 in the presence of 4Å molecular sieves has been shown to effect highly diastereoselective tandem Prins and Friedel-Crafts cyclization of substituted (E/Z)-6-phenylhex-3-en-1-ol and a variety of aldehydes to provide a range of polycyclic compounds in good to excellent yields. The reaction of an enantioenriched alcohol with an aldehyde provided the cyclization product without loss of optical activity. Furthermore, a Lewis acid catalyzed ring opening resulted in functionalized tetralin derivatives with multiple chiral centers.

  9. Enzyme-Like Catalysis of the Nazarov Cyclization by Supramolecular Encapsulation

    SciTech Connect

    Hastings, Courtney; Pluth, Michael; Bergman, Robert; Raymond, Kenneth

    2010-03-29

    A primary goal in the design and synthesis of molecular hosts has been the selective recognition and binding of a variety of guests using non-covalent interactions. Supramolecular catalysis, which is the application of such hosts towards catalysis, has much in common with many enzymatic reactions, chiefly the use of both spatially appropriate binding pockets and precisely oriented functional groups to recognize and activate specific substrate molecules. Although there are now many examples which demonstrate how selective encapsulation in a host cavity can enhance the reactivity of a bound guest, all have failed to reach the degree of increased reactivity typical of enzymes. We now report the catalysis of the Nazarov cyclization by a self-assembled coordination cage, a carbon-carbon bond-forming reaction which proceeds under mild, aqueous conditions. The acceleration in this system is over a million-fold, and represents the first example of supramolecular catalysis that achieves the level of rate enhancement comparable to that observed in several enzymes. We explain the unprecedented degree of rate increase as due to the combination of (a) preorganization of the encapsulated substrate molecule, (b) stabilization of the transition state of the cyclization by constrictive binding, and (c) increase in the basicity of the complexed alcohol functionality.

  10. Stabilization of a binary protein complex by intein-mediated cyclization.

    PubMed

    Jeffries, Cy M; Graham, Stephen C; Stokes, Philippa H; Collyer, Charles A; Guss, J Mitchell; Matthews, Jacqueline M

    2006-11-01

    The study of protein-protein interactions can be hampered by the instability of one or more of the protein complex components. In this study, we showed that intein-mediated cyclization can be used to engineer an artificial intramolecular cyclic protein complex between two interacting proteins: the largely unstable LIM-only protein 4 (LMO4) and an unstructured domain of LIM domain binding protein 1 (ldb1). The X-ray structure of the cyclic complex is identical to noncyclized versions of the complex. Chemical and thermal denaturation assays using intrinsic tryptophan fluorescence and dynamic light scattering were used to compare the relative stabilities of the cyclized complex, the intermolecular (or free) complex, and two linear versions of the intramolecular complex (in which the interacting domains of LMO4 and ldb1 were fused, via a flexible linker, in either orientation). In terms of resistance to denaturation, the cyclic complex is the most stable variant and the intermolecular complex is the least stable; however, the two linear intramolecular variants show significant differences in stability. These differences appear to be related to the relative contact order (the average distance in sequence between residues that make contacts within a structure) of key binding residues at the interface of the two proteins. Thus, the restriction of the more stable component of a complex may enhance stability to a greater extent than restraining less stable components.

  11. Proteins of well-defined structures can be designed without backbone readjustment by a statistical model.

    PubMed

    Zhou, Xiaoqun; Xiong, Peng; Wang, Meng; Ma, Rongsheng; Zhang, Jiahai; Chen, Quan; Liu, Haiyan

    2016-12-01

    We report that using mainly a statistical energy model, protein sequence design for designable backbones can be carried out with high confidence without considering backbone relaxation. A recently-developed statistical energy function for backbone-based protein sequence design has been rationally revised to improve its accuracy. As a demonstrative example, this revised model is applied to design a de novo protein for a target backbone for which the previous model had relied on after-design directed evolution to produce a well-folded protein. The actual backbone structure of the newly designed protein agrees excellently with the corresponding target. Besides presenting a new protein design protocol with experimentally verifications on different backbone types, our study implies that with an energy model of an appropriate resolution, proteins of well-defined structures instead of molten globules can be designed without the explicit consideration of backbone variations due to side chain changes, even if the side chain changes correspond to complete sequence redesigns.

  12. Uganda's National Transmission Backbone Infrastructure Project: Technical Challenges and the Way Forward

    NASA Astrophysics Data System (ADS)

    Bulega, T.; Kyeyune, A.; Onek, P.; Sseguya, R.; Mbabazi, D.; Katwiremu, E.

    2011-10-01

    Several publications have identified technical challenges facing Uganda's National Transmission Backbone Infrastructure project. This research addresses the technical limitations of the National Transmission Backbone Infrastructure project, evaluates the goals of the project, and compares the results against the technical capability of the backbone. The findings of the study indicate a bandwidth deficit, which will be addressed by using dense wave division multiplexing repeaters, leasing bandwidth from private companies. Microwave links for redundancy, a Network Operation Center for operation and maintenance, and deployment of wireless interoperability for microwave access as a last-mile solution are also suggested.

  13. Computation-Guided Backbone Grafting of a Discontinuous Motif onto a Protein Scaffold

    SciTech Connect

    Azoitei, Mihai L.; Correia, Bruno E.; Ban, Yih-En Andrew; Carrico, Chris; Kalyuzhniy, Oleksandr; Chen, Lei; Schroeter, Alexandria; Huang, Po-Ssu; McLellan, Jason S.; Kwong, Peter D.; Baker, David; Strong, Roland K.; Schief, William R.

    2012-02-07

    The manipulation of protein backbone structure to control interaction and function is a challenge for protein engineering. We integrated computational design with experimental selection for grafting the backbone and side chains of a two-segment HIV gp120 epitope, targeted by the cross-neutralizing antibody b12, onto an unrelated scaffold protein. The final scaffolds bound b12 with high specificity and with affinity similar to that of gp120, and crystallographic analysis of a scaffold bound to b12 revealed high structural mimicry of the gp120-b12 complex structure. The method can be generalized to design other functional proteins through backbone grafting.

  14. Importance of cytochromes in cyclization reactions: quantum chemical study on a model reaction of proguanil to cycloguanil.

    PubMed

    Arfeen, Minhajul; Patel, Dhilon S; Abbat, Sheenu; Taxak, Nikhil; Bharatam, Prasad V

    2014-10-30

    Proguanil, an anti-malarial prodrug, undergoes cytochrome P450 catalyzed biotransformation to the pharmacologically active triazine metabolite (cycloguanil), which inhibits plasmodial dihydrofolate reductase. This cyclization is catalyzed by CYP2C19 and many anti-malarial lead compounds are being designed and synthesized to exploit this pathway. Quantum chemical calculations were performed using the model species (Cpd I for active species of cytochrome and N4-isopropyl-N6-methylbiguanide for proguanil) to elucidate the mechanism of the cyclization pathway. The overall reaction involves the loss of a water molecule, and is exothermic by approximately 55 kcal/mol, and involves a barrier of approximately 17 kcal/mol. The plausible reaction pathway involves the initial H-radical abstraction from the isopropyl group by Cpd I, followed by two alternative paths- (i) oxygen rebound to provide hydroxyl derivative and (ii) loss of additional H-radical to yield 1,3,5-triazatriene, which undergoes cyclization. This study helped in understanding the role of the active species of cytochromes in this important cyclization reaction.

  15. SYNTHESIS OF TETRAHYDROPYRAN DERIVATIVES VIA A NOVEL INDIUM TRICHLORIDE MEDIATED CROSS-CYCLIZATION BETWEEN EPOXIDES AND HOMOALLYL ALCOHOLS. (R822668)

    EPA Science Inventory

    Abstract

    A cross-cyclization between epoxides and homoallyl alcohols catalyzed by indium chloride generates tetrahydropyran derivatives in high yields.

    Graphical Abstract


    Enantioselective Nickel-Catalyzed anti-Carbometallative Cyclizations of Alkynyl Electrophiles Enabled by Reversible Alkenylnickel E/Z Isomerization

    PubMed Central

    2016-01-01

    Nickel-catalyzed additions of arylboronic acids to alkynes, followed by enantioselective cyclizations of the alkenylnickel species onto tethered ketones or enones, are reported. These reactions are reliant upon the formal anti-carbonickelation of the alkyne, which is postulated to occur by the reversible E/Z isomerization of an alkenylnickel species. PMID:27333360

  16. Catalyst-free intramolecular oxidative cyclization of N-allylbenzamides: a new route to 2,5-substituted oxazoles.

    PubMed

    Zhou, Wei; Xie, Chen; Han, Jianlin; Pan, Yi

    2012-09-21

    A catalyst-free intramolecular oxidative cyclization reaction of N-allylbenzamides has been developed to prepare 2,5-disubstituted oxazoles with good yields. This reaction gives an efficient synthetic strategy to form an oxazole nucleus directly from easily accessible substrates under temperate conditions.

  17. Pd-Catalyzed C-H activation/oxidative cyclization of acetanilide with norbornene: concise access to functionalized indolines.

    PubMed

    Gao, Yang; Huang, Yubing; Wu, Wanqing; Huang, Kefan; Jiang, Huanfeng

    2014-08-07

    An efficient Pd-catalyzed oxidative cyclization reaction for the synthesis of functionalized indolines by direct C-H activation of acetanilide has been developed. The norbornylpalladium species formed via direct ortho C-H activation of acetanilides is supposed to be a key intermediate in this transformation.

  18. Radical cation cyclization of 1,5-hexadiene to cyclohexene via the cyclohexane-2,5-diyl radical cation intermediate

    SciTech Connect

    Guo, Q.X.; Qin, X.Z.; Wang, J.T.; Williams, F.

    1988-03-16

    The classical example of a neutral carbon-centered radical cyclization reaction is the regioselective 1,5-ring closure (exocyclization) of the 5-hexenyl radical to the cyclopentylcarbinyl radical. Here the authors report the title reaction, a comparable addition process whereby an ..cap alpha.., omega-diene radical cation reacts by endocyclization and hydrogen shift(s) to produce a cycloolefin radical cation.

  19. Dearomatization-induced transannular cyclization: synthesis of electron-accepting thiophene-S,S-dioxide-fused biphenylene.

    PubMed

    Fukazawa, Aiko; Oshima, Hiroya; Shimizu, Soji; Kobayashi, Nagao; Yamaguchi, Shigehiro

    2014-06-18

    The transannular cyclization of dehydroannulenes bearing several alkyne moieties in close proximity is a powerful synthetic method for producing polycyclic aromatic hydrocarbons. We report that the reactivity can be switched by the aromaticity of the ring skeletons fused with the dehydroannulene core. Thus, while thiophene-fused bisdehydro[12]annulene 1 was handled as a stable compound in the air at room temperature, the oxidation with m-chloroperbenzoic acid from the aromatic thiophene rings to the nonaromatic thiophene-S,S-dioxides induced the transannular cyclization, even at room temperature, which was completed within 1 day to produce the formal [2 + 2] cycloadduct 3. This is in stark contrast to the fact that the thermal cyclization of 1 itself required heating at 80 °C for 9 days for completion. Experimental and theoretical studies indicate that the oxidation of even one thiophene ring in 1 sufficiently decreases the activation barrier for the transannular cyclization that proceeds through the 8π and 4π electrocyclic reaction sequence. The thiophene-S,S-dioxide-fused biphenylene 3 thus produced exhibits a set of intriguing properties, such as a higher electron affinity (E1/2 = -1.17 V vs Fc and Fc(+)) and a stronger fluorescence (ΦF = 0.20) than the other relevant biphenylene derivatives, which have electron-donating and nonfluorescent characteristics.

  1. Asymmetric Synthesis of Ramariolides A and C through Bimetallic Cascade Cyclization and Z-E Isomerization Reaction.

    PubMed

    Pal, Pratik; Nanda, Samik

    2017-03-03

    A short and flexible asymmetric synthesis of ramariolides A and C was accomplished. A bimetallic catalytic system consisting of Pd-Cu-mediated cascade cyclization, unprecedented Z-E isomerization by a Ru-based metathesis catalyst, and late-stage stereoselective epoxidation are the key steps involved in the synthesis.

  2. Modeling 15N NMR chemical shift changes in protein backbone with pressure

    NASA Astrophysics Data System (ADS)

    La Penna, Giovanni; Mori, Yoshiharu; Kitahara, Ryo; Akasaka, Kazuyuki; Okamoto, Yuko

    2016-08-01

    Nitrogen chemical shift is a useful parameter for determining the backbone three-dimensional structure of proteins. Empirical models for fast calculation of N chemical shift are improving their reliability, but there are subtle effects that cannot be easily interpreted. Among these, the effects of slight changes in hydrogen bonds, both intramolecular and with water molecules in the solvent, are particularly difficult to predict. On the other hand, these hydrogen bonds are sensitive to changes in protein environment. In this work, the change of N chemical shift with pressure for backbone segments in the protein ubiquitin is correlated with the change in the population of hydrogen bonds involving the backbone amide group. The different extent of interaction of protein backbone with the water molecules in the solvent is put in evidence.

  3. Increasing Sequence Diversity with Flexible Backbone Protein Design: The Complete Redesign of a Protein Hydrophobic Core

    SciTech Connect

    Murphy, Grant S.; Mills, Jeffrey L.; Miley, Michael J.; Machius, Mischa; Szyperski, Thomas; Kuhlman, Brian

    2015-10-15

    Protein design tests our understanding of protein stability and structure. Successful design methods should allow the exploration of sequence space not found in nature. However, when redesigning naturally occurring protein structures, most fixed backbone design algorithms return amino acid sequences that share strong sequence identity with wild-type sequences, especially in the protein core. This behavior places a restriction on functional space that can be explored and is not consistent with observations from nature, where sequences of low identity have similar structures. Here, we allow backbone flexibility during design to mutate every position in the core (38 residues) of a four-helix bundle protein. Only small perturbations to the backbone, 12 {angstrom}, were needed to entirely mutate the core. The redesigned protein, DRNN, is exceptionally stable (melting point >140C). An NMR and X-ray crystal structure show that the side chains and backbone were accurately modeled (all-atom RMSD = 1.3 {angstrom}).

  4. Modeling (15)N NMR chemical shift changes in protein backbone with pressure.

    PubMed

    La Penna, Giovanni; Mori, Yoshiharu; Kitahara, Ryo; Akasaka, Kazuyuki; Okamoto, Yuko

    2016-08-28

    Nitrogen chemical shift is a useful parameter for determining the backbone three-dimensional structure of proteins. Empirical models for fast calculation of N chemical shift are improving their reliability, but there are subtle effects that cannot be easily interpreted. Among these, the effects of slight changes in hydrogen bonds, both intramolecular and with water molecules in the solvent, are particularly difficult to predict. On the other hand, these hydrogen bonds are sensitive to changes in protein environment. In this work, the change of N chemical shift with pressure for backbone segments in the protein ubiquitin is correlated with the change in the population of hydrogen bonds involving the backbone amide group. The different extent of interaction of protein backbone with the water molecules in the solvent is put in evidence.

  5. Transition-metal-free synthesis of phenanthridinones from biaryl-2-oxamic acid under radical conditions.

    PubMed

    Yuan, Ming; Chen, Li; Wang, Junwei; Chen, Shenjie; Wang, Kongchao; Xue, Yongbo; Yao, Guangmin; Luo, Zengwei; Zhang, Yonghui

    2015-01-16

    Na2S2O8-promoted decarboxylative cyclization of biaryl-2-oxamic acid for phenanthridinones has been developed. This work illustrates the first example of intramolecular decarboxylative amidation of unactivated arene under transition-metal-free conditions. Additionally, this approach provides an efficient and economical method to access biologically interesting phenanthridinones, an important structure motif in many natural products.

  6. A simple model of backbone flexibility improves modeling of side-chain conformational variability.

    PubMed

    Friedland, Gregory D; Linares, Anthony J; Smith, Colin A; Kortemme, Tanja

    2008-07-18

    The considerable flexibility of side-chains in folded proteins is important for protein stability and function, and may have a role in mediating allosteric interactions. While sampling side-chain degrees of freedom has been an integral part of several successful computational protein design methods, the predictions of these approaches have not been directly compared to experimental measurements of side-chain motional amplitudes. In addition, protein design methods frequently keep the backbone fixed, an approximation that may substantially limit the ability to accurately model side-chain flexibility. Here, we describe a Monte Carlo approach to modeling side-chain conformational variability and validate our method against a large dataset of methyl relaxation order parameters derived from nuclear magnetic resonance (NMR) experiments (17 proteins and a total of 530 data points). We also evaluate a model of backbone flexibility based on Backrub motions, a type of conformational change frequently observed in ultra-high-resolution X-ray structures that accounts for correlated side-chain backbone movements. The fixed-backbone model performs reasonably well with an overall rmsd between computed and predicted side-chain order parameters of 0.26. Notably, including backbone flexibility leads to significant improvements in modeling side-chain order parameters for ten of the 17 proteins in the set. Greater accuracy of the flexible backbone model results from both increases and decreases in side-chain flexibility relative to the fixed-backbone model. This simple flexible-backbone model should be useful for a variety of protein design applications, including improved modeling of protein-protein interactions, design of proteins with desired flexibility or rigidity, and prediction of correlated motions within proteins.

  7. A Readily Accessible Chiral NNN Pincer Ligand with a Pyrrole Backbone and Its Ni(II) Chemistry: Syntheses, Structural Chemistry, and Bond Activations.

    PubMed

    Wenz, Jan; Kochan, Alexander; Wadepohl, Hubert; Gade, Lutz H

    2017-03-20

    A new class of chiral C2-symmetric N-donor pincer ligands, 2,5-bis(2-oxazolinyldimethylmethyl)pyrroles (PdmBox)H, was synthesized starting from the readily available ethyl 2,2-dimethyl-3-oxobutanoate (1). The synthesis of the ligand backbone was achieved by oxidative enole coupling with CuC12 followed by Paal-Knorr-type pyrrole synthesis. The corresponding protioligands ((R)PdmBox)H (R = iPr: 5a; Ph: 5b) were obtained by condensation with amino alcohols and subsequent zinc-catalyzed cyclization. Reaction of the lithiated ligands with [NiCl2(dme)] yielded the corresponding square-planar nickel(II) complexes [((R)PdmBox)NiCl] (6a/b). Salt metathesis of 6a with the corresponding alkali or cesium salts in acetone led to the formation of air- and moisture-stable [((iPr)PdmBox)NiX] (X = F (7), X = Br (8), X = I (9), X = N3 (10), X = OAc (11). Furthermore, the conversion of [((iPr)PdmBox)NiF] (7) with hydride transfer reagents such as PhSiH3 led to the stable hydrido species [((iPr)PdmBox)NiH] (27), the stoichiometric transformations of which were studied. Treatment of 6a with organometallic reagents such as ZnEt2, PhLi, PhC≡CLi, NsLi, or ((4F)Bn)2Mg(THF)2 gave the corresponding alkyl, alkynyl, or aryl complexes. The availability of the new nonisomerizable PdmBox pincer ligands allowed the comparative study of their ligation to square-planar complexes as helically twisted spectator ligands as opposed to the enforced planar rigidity of their iso-PmBox analogues and the way this influences the reactivity of the Ni complexes.

  8. Gas-Phase Nazarov Cyclization of Protonated 2-Methoxy and 2-Hydroxychalcone: An Example of Intramolecular Proton-Transport Catalysis

    PubMed Central

    George, M.; Sebastian, V. S.; Reddy, P. Nagi; Srinivas, R.; Giblin, Daryl; Gross, Michael L.

    2009-01-01

    Upon CA, ESI generated [M + H]+ ions of chalcone (benzalacetophenone) and 3-phenyl-indanone both undergo losses of H2O, CO, and the elements of benzene. CA of the [M + H]+ ions of 2-methoxy and 2-hydroxychalcone, however, prompts instead a dominant loss of ketene. In addition, CA of the [M + H]+ ions of 2-methoxy-β-methylchalcone produces an analogous loss of methylketene instead. Furthermore, the [M + D]+ ion of 2-methoxychalcone upon CA eliminates only unlabeled ketene, and the resultant product, the [M + D - ketene]+ ion, yields only the benzyl-d1 cation upon CA. We propose that the 2-methoxy and 2-hydroxy (ortho) substituents facilitate a Nazarov cyclization to the corresponding protonated 3-aryl-indanones by mediating a critical proton transfer. The resultant protonated indanones then undergo a second proton transport catalysis facilitated by the same ortho substituents producing intermediates that eliminate ketene to yield 2-methoxy- or 2-hydroxyphenyl-phenyl-methylcarbocations, respectively. The basicity of the ortho substituent is important; for example, replacement of the ortho function with a chloro substituent does not provide an efficient catalyst for the proton transports. The Nazarov cyclization must compete with an alternate cyclization, driven by the protonated carbonyl group of the chalcone that results in losses of H2O and CO. The assisted proton transfer mediated by the ortho substituent shifts the competition in favor of the Nazarov cyclization. The proposed mechanisms for cyclization and fragmentation are supported by high-mass resolving power data, tandem mass spectra, deuterium labeling, and molecular orbital calculations. PMID:19230703

  9. AbDesign: an algorithm for combinatorial backbone design guided by natural conformations and sequences

    PubMed Central

    Lapidoth, Gideon D.; Baran, Dror; Pszolla, Gabriele M.; Norn, Christoffer; Alon, Assaf; Tyka, Michael D.; Fleishman, Sarel J.

    2016-01-01

    Computational design of protein function has made substantial progress, generating new enzymes, binders, inhibitors, and nanomaterials not previously seen in nature. However, the ability to design new protein backbones for function – essential to exert control over all polypeptide degrees of freedom – remains a critical challenge. Most previous attempts to design new backbones computed the mainchain from scratch. Here, instead, we describe a combinatorial backbone and sequence optimization algorithm called AbDesign, which leverages the large number of sequences and experimentally determined molecular structures of antibodies to construct new antibody models, dock them against target surfaces and optimize their sequence and backbone conformation for high stability and binding affinity. We used the algorithm to produce antibody designs that target the same molecular surfaces as nine natural, high-affinity antibodies; in six the backbone conformation at the core of the antibody binding surface is similar to the natural antibody targets, and in several cases sequence and sidechain conformations recapitulate those seen in the natural antibodies. In the case of an anti-lysozyme antibody, designed antibody CDRs at the periphery of the interface, such as L1 and H2, show a greater backbone conformation diversity than the CDRs at the core of the interface, and increase the binding surface area compared to the natural antibody, which could enhance affinity and specificity. PMID:25670500

  10. Tuneable enhancement of the salt and thermal stability of polymeric micelles by cyclized amphiphiles

    PubMed Central

    Honda, Satoshi; Yamamoto, Takuya; Tezuka, Yasuyuki

    2013-01-01

    Cyclic molecules provide better stability for their aggregates. Typically in nature, the unique cyclic cell membrane lipids allow thermophilic archaea to inhabit extreme conditions. By mimicking the biological design, the robustness of self-assembled synthetic nanostructures is expected to be improved. Here we report topology effects by cyclized polymeric amphiphiles against their linear counterparts, demonstrating a drastic enhancement in the thermal, as well as salt stability of self-assembled micelles. Furthermore, through coassembly of the linear and cyclic amphiphiles, the stability was successfully tuned for a wide range of temperatures and salt concentrations. The enhanced thermal/salt stability was exploited in a halogen exchange reaction to stimulate the catalytic activity. The mechanism for the enhancement was also investigated. These topology effects by the cyclic amphiphiles offer unprecedented opportunities in polymer materials design unattainable by traditional means. PMID:23481382

  11. Spectral assignments and structural studies of a warfarin derivative stereoselectively formed by tandem cyclization

    NASA Astrophysics Data System (ADS)

    Velayutham Pillai, M.; Rajeswari, K.; Vidhyasagar, T.

    2015-11-01

    The structural elucidation of a Mannich condensation product of rac-Warfarin with benzaldehyde and methyl amine was carried out using IR, Mass, 1H NMR, 13C NMR, 1H-1H COSY, 1H-13C COSY, DEPT-135, HMBC, NOESY spectra and single crystal X-ray diffraction. Formation of a new pyran ring via a tandem cyclization in the presence of methyl amine was observed. The optimized geometry and HOMO-LUMO energy gap along with other important physical parameters were found by Gaussian 09 program using HF 6-31G (d, p) and B3YLP/DFT 6-31G (d, p) level of theory. The preferred conformation of the piperidine ring in solution state was found to be chair from the NMR spectra. Single crystal X-ray diffraction and optimized geometry (by theoretical study) also confirms the chair conformation in the solid state.

  12. Kinetics of hydrolysis and cyclization of ethyl 2-(aminosulfonyl)benzoate to saccharin.

    PubMed

    Di Loreto, H E; Czarnowski, J; dos Santos Afonso, M

    2002-10-01

    The cyclization of ethyl 2-(aminosulfonyl)benzoate (ASB) to give saccharin was investigated in aqueous solutions at pH between 5.2 and 9.5 and in the temperature range of 296.2-334.2 K. The initial concentration of the reactant was varied between 1.45 x 10(-5) and 3.86 x 10(-4) M. Ultraviolet spectroscopy was used to obtain the kinetic data. The reaction is acid catalyzed and follows pseudo-first-order kinetics. The experimental rate constant, k(obs), increases with temperature and pH. Its dependence on the temperature and pH is well described by: k(obs) = k1 [OH-] = [(2.52 +/- 0.9) x 10(16) exp(-20.2 +/- 1 kcalmol(-1)/RT) s(-1)][OH-] A mechanism is proposed and the half-life of ethyl ASB is calculated.

  13. A Van Leusen deprotection-cyclization strategy as a fast entry into two imidazoquinoxaline families.

    PubMed

    De Moliner, Fabio; Hulme, Christopher

    2012-10-24

    A concise synthesis of two pharmacologically relevant classes of molecules possessing the imidazoquinoxaline core is reported. The protocol involves use of 1,2-phenylenediamines and glyoxylic acid derivatives, namely ethyl glyoxylate or benzylglyoxamide, along with tosylmethylisocyanides in a microwave-assisted Van Leusen three-component condensation. Subsequent unmasking (Boc removal) of an internal amino-nucleophile promotes deprotection and cyclization that take place either spontaneously in a one-pot fashion to give 8 or upon acidic treatment under microwave irradiation after isolation of the imidazole intermediate to give 11. Of note, a tricyclic framework is hence assembled by means of a rapid and straightforward method with a high bond-forming efficiency.

  14. Palladium-catalyzed direct arylation and cyclization of o-iodobiaryls to a library of tetraphenylenes

    PubMed Central

    Zhu, Chendan; Zhao, Yue; Wang, Di; Sun, Wei-Yin; Shi, Zhuangzhi

    2016-01-01

    Aryl–aryl bond formation constitutes one of the most important subjects in organic synthesis. The recent developments in direct arylation reactions forming aryl–aryl bond have emerged as very attractive alternatives to traditional cross-coupling reactions. Here, we describe a general palladium-catalyzed direct arylation and cyclization of o-iodobiaryls to build a library of tetraphenylenes. This transformation represents one of the very few examples of C-H activation process that involves simultaneous formation of two aryl–aryl bonds. Oxygen plays a vital role by ensuring high reactivity, with air as the promoter furnished the best results. We anticipate this ligand-free and aerobic catalytic system will simplify the synthesis of tetraphenylenes as many of the reported methods involve use of preformed organometallic reagents and will lead to the discovery of highly efficient new direct arylation process. PMID:27629701

  15. Cyclization of 1,4-hydroxycarbonyls is not a homogenous gas phase process

    NASA Astrophysics Data System (ADS)

    Dibble, Theodore S.

    2007-10-01

    Previous studies of 1,4-hydroxycarbonyls derived from alkanes have suggested that they can cyclize to saturated furans, which can subsequently eliminate water to form the corresponding dihydrofurans. CBS-QB3 and G3 studies of 5-hydroxy-2-pentanone and 2-hydroxypentanal show that both steps have activation barriers far too large for these reactions to occur as homogenous gas phase reactions. Similar results were obtained in CBS-QB3 studies of the analogous process leading from 2- and 3-methyl-4-hydroxy-2-butenal (species posited to form in the degradation of isoprene) to 3-methylfuran. The latter two processes are much more favorable, thermodynamically, than the formation of dihydrofurans from the saturated 1,4-hydroxycarbonyls.

  16. Palladium-catalyzed direct arylation and cyclization of o-iodobiaryls to a library of tetraphenylenes

    NASA Astrophysics Data System (ADS)

    Zhu, Chendan; Zhao, Yue; Wang, Di; Sun, Wei-Yin; Shi, Zhuangzhi

    2016-09-01

    Aryl–aryl bond formation constitutes one of the most important subjects in organic synthesis. The recent developments in direct arylation reactions forming aryl–aryl bond have emerged as very attractive alternatives to traditional cross-coupling reactions. Here, we describe a general palladium-catalyzed direct arylation and cyclization of o-iodobiaryls to build a library of tetraphenylenes. This transformation represents one of the very few examples of C-H activation process that involves simultaneous formation of two aryl–aryl bonds. Oxygen plays a vital role by ensuring high reactivity, with air as the promoter furnished the best results. We anticipate this ligand-free and aerobic catalytic system will simplify the synthesis of tetraphenylenes as many of the reported methods involve use of preformed organometallic reagents and will lead to the discovery of highly efficient new direct arylation process.

  17. Synergistic effects between Lewis and Brønsted acids: application to the Prins cyclization.

    PubMed

    Breugst, Martin; Grée, René; Houk, K N

    2013-10-04

    Brønsted and Lewis acids can catalyze the Prins cyclization, an efficient method for the synthesis of tetrahydropyrans from homoallylic alcohols and carbonyl compounds. Synergistic effects between weak Brønsted and Lewis acids in these reactions have been analyzed by density functional theory [M06-L/def2-QZVP/IEFPCM(CH2Cl2)//M06-L/6-311+G(2df,2p)]. In order to characterize the reactivities of the employed Lewis acids, methyl anion and hydroxide affinities were determined. On the basis of our calculations, we found that the coordination of Lewis acids to carboxylic and sulfonic acids results in a significant increase in the Brønsted acidities of the latter.

  18. Titanocene(III)-catalyzed 6-exo versus 7-endo cyclizations of epoxypolyprenes: efficient control and synthesis of versatile terpenic building blocks.

    PubMed

    Justicia, José; Jiménez, Tania; Miguel, Delia; Contreras-Montoya, Rafael; Chahboun, Rachid; Alvarez-Manzaneda, Enrique; Collado-Sanz, Daniel; Cárdenas, Diego J; Cuerva, Juan M

    2013-10-18

    In this article, a complete study on the selectivity of titanocene(III) cyclization of epoxypolyprenes is presented. The requirements for the formation of six- or seven-membered rings during these cyclizations are determined, taking into account the different substitution pattern in the epoxypolyprene precursor. Thus, a complete selectivity to 6-exo or 7-endo cyclization process has been achieved, yielding mono-, bi-, and even tricyclic compounds, constituting a new and efficient access to this type of derivative. Additionally, this procedure opens the possibility to prepare excellent building blocks for the synthesis of polycyclic compounds with a trisubstituted oxygenated function, which is present in several natural terpenes.

  19. A ruthenium(II) complex as turn-on Cu(II) luminescent sensor based on oxidative cyclization mechanism and its application in vivo

    PubMed Central

    Zhang, Yunfei; Liu, Zonglun; Yang, Kui; Zhang, Yi; Xu, Yongqian; Li, Hongjuan; Wang, Chaoxia; Lu, Aiping; Sun, Shiguo

    2015-01-01

    Copper ions play a vital role in a variety of fundamental physiological processes not only in human beings and plants, but also for extensive insects and microorganisms. In this paper, a novel water-soluble ruthenium(II) complex as a turn-on copper(II) ions luminescent sensor based on o-(phenylazo)aniline was designed and synthesized. The azo group would undergo a specific oxidative cyclization reaction with copper(II) ions and turn into high luminescent benzotriazole, triggering significant luminescent increasements which were linear to the concentrations of copper(II) ions. The sensor distinguished by its high sensitivity (over 80-fold luminescent switch-on response), good selectivity (the changes of the emission intensity in the presence of other metal ions or amino acids were negligible) and low detection limit (4.42 nM) in water. Moreover, the copper(II) luminescent sensor exhibited good photostability under light irradiation. Furthermore, the applicability of the proposed sensor in biological samples assay was also studied and imaged copper(II) ions in living pea aphids successfully. PMID:25640000

  20. Bis(phosphinimino)methanide rare earth amides: synthesis, structure, and catalysis of hydroamination/cyclization, hydrosilylation, and sequential hydroamination/hydrosilylation.

    PubMed

    Rastätter, Marcus; Zulys, Agustino; Roesky, Peter W

    2007-01-01

    A series of yttrium and lanthanide amido complexes [Ln{N(SiHMe(2))2}2{CH(PPh(2)NSiMe(3))2}] (Ln=Y, La, Sm, Ho, Lu) were synthesized by three different pathways. The title compounds can be obtained either from [Ln{N(SiHMe(2))2}3(thf)2] and [CH(2)(PPh(2)NSiMe(3))2] or from KN(SiHMe(2))2 and [Ln{CH(PPh(2)NSiMe(3))2}Cl(2)]2, while in a third approach the lanthanum compound was synthesized in a one-pot reaction starting from K{CH(PPh(2)NSiMe(3))2}, LaCl3, and KN(SiHMe(2))2. All the complexes have been characterized by single-crystal X-ray diffraction. The new complexes, [Ln{N(SiHMe(2))2}2{CH(PPh(2)NSiMe(3))2}], were used as catalysts for hydroamination/cyclization and hydrosilylation reactions. A clear dependence of the reaction rate on the ionic radius of the center metal was observed, showing the lanthanum compound to be the most active one in both reactions. Furthermore, a combination of both reactions--a sequential hydroamination/hydrosilylation reaction--was also investigated.

  1. A ruthenium(II) complex as turn-on Cu(II) luminescent sensor based on oxidative cyclization mechanism and its application in vivo

    NASA Astrophysics Data System (ADS)

    Zhang, Yunfei; Liu, Zonglun; Yang, Kui; Zhang, Yi; Xu, Yongqian; Li, Hongjuan; Wang, Chaoxia; Lu, Aiping; Sun, Shiguo

    2015-02-01

    Copper ions play a vital role in a variety of fundamental physiological processes not only in human beings and plants, but also for extensive insects and microorganisms. In this paper, a novel water-soluble ruthenium(II) complex as a turn-on copper(II) ions luminescent sensor based on o-(phenylazo)aniline was designed and synthesized. The azo group would undergo a specific oxidative cyclization reaction with copper(II) ions and turn into high luminescent benzotriazole, triggering significant luminescent increasements which were linear to the concentrations of copper(II) ions. The sensor distinguished by its high sensitivity (over 80-fold luminescent switch-on response), good selectivity (the changes of the emission intensity in the presence of other metal ions or amino acids were negligible) and low detection limit (4.42 nM) in water. Moreover, the copper(II) luminescent sensor exhibited good photostability under light irradiation. Furthermore, the applicability of the proposed sensor in biological samples assay was also studied and imaged copper(II) ions in living pea aphids successfully.

  2. Domino cyclization-alkylation protocol for the synthesis of 2,3-functionalized indoles from o-alkynylanilines and allylic alcohols.

    PubMed

    Xu, Chang; Murugan, Vinod K; Pullarkat, Sumod A

    2012-05-21

    A practical and efficient protocol for the one-pot synthesis of 2,3-substituted indoles was developed via a palladacycle catalyzed domino cyclization-alkylation reaction involving 2-alkynylanilines and allylic alcohols under mild conditions without any additives.

  3. Tandem Suzuki-Miyaura coupling/acid-catalyzed cyclization between vinyl ether boronates and vinyl halides: a concise approach to polysubstituted furans.

    PubMed

    Butkevich, Alexey N; Meerpoel, Lieven; Stansfield, Ian; Angibaud, Patrick; Corbu, Andrei; Cossy, Janine

    2013-08-02

    Polysubstituted 2-(ω-hydroxyalkyl)furans were prepared by tandem Suzuki-Miyaura coupling/acid-catalyzed cyclization starting from appropriately substituted 3-haloallylic alcohols and dihydrofuran-, dihydropyran- or glycal-derived pinacol boronates.

  4. A cyclization-induced emission enhancement (CIEE)-based ratiometric fluorogenic and chromogenic probe for the facile detection of a nerve agent simulant DCP.

    PubMed

    Mahapatra, Ajit Kumar; Maiti, Kalipada; Manna, Saikat Kumar; Maji, Rajkishor; Mondal, Sanchita; Das Mukhopadhyay, Chitrangada; Sahoo, Prithidipa; Mandal, Debasish

    2015-06-14

    The first ratiometric fluorescent probe for the detection of a nerve agent simulant was developed based on tandem phosphorylation and intramolecular cyclization, by which high sensitivity as well as large emission shift could be achieved.

  5. Diastereoselective Synthesis of Highly Substituted Tetrahydrofurans by Pd-Catalyzed Tandem Oxidative Cyclization-Redox Relay Reactions Controlled by Intramolecular Hydrogen Bonding.

    PubMed

    Brooks, Joshua L; Xu, Liping; Wiest, Olaf; Tan, Derek S

    2017-01-06

    Palladium-catalyzed oxidative cyclization of alkenols provides a convenient entry into cyclic ethers but typically proceeds with little or no diastereoselectivity for cyclization of trisubstituted olefins to form tetrahydrofurans due to the similar energies of competing 5-membered transition-state conformations. Herein, a new variant of this reaction has been developed in which a PdCl2/1,4-benzoquinone catalyst system coupled with introduction of a hydrogen-bond acceptor in the substrate enhances both diastereoselectivity and reactivity. Cyclization occurs with 5-exo Markovnikov regioselectivity. Mechanistic and computational studies support an anti-oxypalladation pathway in which intramolecular hydrogen bonding increases the nucleophilicity of the alcohol and enforces conformational constraints that enhance diastereoselectivity. The cyclization is followed by a tandem redox-relay process that provides versatile side-chain functionalities for further derivatization.

  6. Backbone dipoles generate positive potentials in all proteins: origins and implications of the effect.

    PubMed Central

    Gunner, M R; Saleh, M A; Cross, E; ud-Doula, A; Wise, M

    2000-01-01

    Asymmetry in packing the peptide amide dipole results in larger positive than negative regions in proteins of all folding motifs. The average side chain potential in 305 proteins is 109 +/- 30 mV (2. 5 +/- 0.7 kcal/mol/e). Because the backbone has zero net charge, the non-zero potential is unexpected. The larger oxygen at the negative and smaller proton at the positive end of the amide dipole yield positive potentials because: 1) at allowed phi and psi angles residues come off the backbone into the positive end of their own amide dipole, avoiding the large oxygen; and 2) amide dipoles with their carbonyl oxygen surface exposed and amine proton buried make the protein interior more positive. Twice as many amides have their oxygens exposed than their amine protons. The distribution of acidic and basic residues shows the importance of the bias toward positive backbone potentials. Thirty percent of the Asp, Glu, Lys, and Arg are buried. Sixty percent of buried residues are acids, only 40% bases. The positive backbone potential stabilizes ionization of 20% of the acids by >3 pH units (-4.1 kcal/mol). Only 6.5% of the bases are equivalently stabilized by negative regions. The backbone stabilizes bound anions such as phosphates and rarely stabilizes bound cations. PMID:10692303

  7. Subgraph "backbone" analysis of dynamic brain networks during consciousness and anesthesia.

    PubMed

    Shin, Jeongkyu; Mashour, George A; Ku, Seungwoo; Kim, Seunghwan; Lee, Uncheol

    2013-01-01

    General anesthesia significantly alters brain network connectivity. Graph-theoretical analysis has been used extensively to study static brain networks but may be limited in the study of rapidly changing brain connectivity during induction of or recovery from general anesthesia. Here we introduce a novel method to study the temporal evolution of network modules in the brain. We recorded multichannel electroencephalograms (EEG) from 18 surgical patients who underwent general anesthesia with either propofol (n = 9) or sevoflurane (n = 9). Time series data were used to reconstruct networks; each electroencephalographic channel was defined as a node and correlated activity between the channels was defined as a link. We analyzed the frequency of subgraphs in the network with a defined number of links; subgraphs with a high probability of occurrence were deemed network "backbones." We analyzed the behavior of network backbones across consciousness, anesthetic induction, anesthetic maintenance, and two points of recovery. Constitutive, variable and state-specific backbones were identified across anesthetic state transitions. Brain networks derived from neurophysiologic data can be deconstructed into network backbones that change rapidly across states of consciousness. This technique enabled a granular description of network evolution over time. The concept of network backbones may facilitate graph-theoretical analysis of dynamically changing networks.

  8. Complete backbone and DENQ side chain NMR assignments in proteins from a single experiment: implications to structure-function studies.

    PubMed

    Reddy, Jithender G; Hosur, Ramakrishna V

    2014-03-01

    Resonance assignment is the first and the most crucial step in all nuclear magnetic resonance (NMR) investigations on structure-function relationships in biological macromolecules. Often, the assignment exercise has to be repeated several times when specific interactions with ligands, substrates etc., have to be elucidated for understanding the functional mechanisms. While the protein backbone serves to provide a scaffold, the side chains interact directly with the ligands. Such investigations will be greatly facilitated, if there are rapid methods for obtaining exhaustive information with minimum of NMR experimentation. In this context, we present here a pulse sequence which exploits the recently introduced technique of parallel detection of multiple nuclei, e.g. (1)H and (13)C, and results in two 3D-data sets simultaneously. These yield complete backbone resonance assignment ((1)H(N), (15)N, (13)CO, (1)Hα/(13)Cα, and (1)Hβ/(13)Cβ chemical shifts) and side chain assignment of D, E, N and Q residues. Such an exhaustive assignment has the potential of yielding accurate 3D structures using one or more of several algorithms which calculate structures of the molecules very reliably on the basis of NMR chemical shifts alone. The side chain assignments of D, E, N, and Q will be extremely valuable for interaction studies with different ligands; D and E side chains are known to be involved in majority of catalytic activities. Utility of this experiment has been demonstrated with Ca(2+) bound M-crystallin, which contains largely D, E, N and Q residues at the metal binding sites.

  9. Metal-free oxidative hydroxyalkylarylation of activated alkenes by direct sp3 C-H functionalization of alcohols.

    PubMed

    Meng, Yuan; Guo, Li-Na; Wang, Hua; Duan, Xin-Hua

    2013-09-04

    A metal-free tandem radical addition/cyclization reaction of activated alkenes and alcohols has been developed. The process provides an efficient and atom economical access to various valuable hydroxyl-containing oxindoles through the direct sp(3) C-H functionalization of alcohols.

  10. Fast extraction of the backbone of projected bipartite networks to aid community detection

    NASA Astrophysics Data System (ADS)

    Liebig, J.; Rao, A.

    2016-01-01

    This paper introduces a computationally inexpensive method for extracting the backbone of one-mode networks projected from bipartite networks. We show that the edge weights in the one-mode projections are distributed according to a Poisson binomial distribution and that finding the expected weight distribution of a one-mode network projected from a random bipartite network only requires knowledge of the bipartite degree distributions. Being able to extract the backbone of a projection is highly beneficial in filtering out redundant information in large complex networks and narrowing down the information in the one-mode projection to the most relevant. We demonstrate that the backbone of a one-mode projection aids in the detection of communities.

  11. Wetting of nonconserved residue-backbones: A feature indicative of aggregation associated regions of proteins.

    PubMed

    Pradhan, Mohan R; Pal, Arumay; Hu, Zhongqiao; Kannan, Srinivasaraghavan; Chee Keong, Kwoh; Lane, David P; Verma, Chandra S

    2016-02-01

    Aggregation is an irreversible form of protein complexation and often toxic to cells. The process entails partial or major unfolding that is largely driven by hydration. We model the role of hydration in aggregation using "Dehydrons." "Dehydrons" are unsatisfied backbone hydrogen bonds in proteins that seek shielding from water molecules by associating with ligands or proteins. We find that the residues at aggregation interfaces have hydrated backbones, and in contrast to other forms of protein-protein interactions, are under less evolutionary pressure to be conserved. Combining evolutionary conservation of residues and extent of backbone hydration allows us to distinguish regions on proteins associated with aggregation (non-conserved dehydron-residues) from other interaction interfaces (conserved dehydron-residues). This novel feature can complement the existing strategies used to investigate protein aggregation/complexation.

  12. No-Enclave Percolation Corresponds to Holes in the Cluster Backbone

    NASA Astrophysics Data System (ADS)

    Hu, Hao; Ziff, Robert M.; Deng, Youjin

    2016-10-01

    The no-enclave percolation (NEP) model introduced recently by Sheinman et al. can be mapped to a problem of holes within a standard percolation backbone, and numerical measurements of such holes give the same size-distribution exponent τ =1.82 (1 ) as found for the NEP model. An argument is given that τ =1 +dB/2 ≈1.822 for backbone holes, where dB is the backbone dimension. On the other hand, a model of simple holes within a percolation cluster yields τ =1 +df/2 =187 /96 ≈1.948 , where df is the fractal dimension of the cluster, and this value is consistent with the experimental results of gel collapse of Sheinman et al., which give τ =1.91 (6 ). This suggests that the gel clusters are of the universality class of percolation cluster holes. Both models give a discontinuous maximum hole size at pc, signifying explosive percolation behavior.

  13. Rh(III)-Catalyzed C-H Bond Addition/Amine-Mediated Cyclization of Bis-Michael Acceptors.

    PubMed

    Potter, Tyler J; Ellman, Jonathan A

    2016-08-05

    A Rh(III)-catalyzed C-H bond addition/primary amine-promoted cyclization of bis-Michael acceptors is reported. The C-H bond addition step occurs with high chemoselectivity, and the subsequent intramolecular Michael addition, mediated by a primary amine catalyst, sets three contiguous stereocenters with high diastereoselectivity. A broad range of directing groups and both aromatic and alkenyl C-H bonds were shown to be effective in this transformation, affording functionalized piperidines, tetrahydropyrans, and cyclohexanes.

  14. Hydroxyl Radical-Mediated Novel Modification of Peptides: N-Terminal Cyclization through the Formation of α-Ketoamide.

    PubMed

    Lee, Seon Hwa; Kyung, Hyunsook; Yokota, Ryo; Goto, Takaaki; Oe, Tomoyuki

    2015-01-20

    The hydroxyl radical-mediated oxidation of peptides and proteins constitutes a large group of post-translational modifications that can result in structural and functional changes. These oxidations can lead to hydroxylation, sulfoxidation, or carbonylation of certain amino acid residues and cleavage of peptide bonds. In addition, hydroxyl radicals can convert the N-terminus of peptides to an α-ketoamide via abstraction of the N-terminal α-hydrogen and hydrolysis of the ketimine intermediate. In the present study, we identified N-terminal cyclization as a novel modification mediated by a hydroxyl radical. The reaction of angiotensin (Ang) II (DRVYIHPF) and the hydroxyl radical generated by the Cu(II)/ascorbic acid (AA) system or UV/hydrogen peroxide system produced N-terminal cyclized-Ang II (Ang C) and pyruvamide-Ang II (Ang P, CH3COCONH-RVYIHPF). The structure of Ang C was confirmed by mass spectrometry and comparison to an authentic standard. The subsequent incubation of isolated Ang P in the presence of Cu(II)/AA revealed that Ang P was the direct precursor of Ang C. The proposed mechanism involves the formation of a nitrogen-centered (aminyl) radical, which cyclizes to form a five-membered ring containing the alkoxy radical. The subsequent β-scission reaction of the alkoxyl radical results in the cleavage of the terminal CH3CO group. The initial aminyl radical can be stabilized by chelation to the Cu(II) ions. The affinity of Ang C toward the Ang II type 1 receptor was significantly lower than that of Ang II or Ang P. Ang C was not further metabolized by aminopeptidase A, which converts Ang II to Ang III. Hydroxyl radical-mediated N-terminal cyclization was also observed in other Ang peptides containing N-terminal alanine, arginine, valine, and amyloid β 1-11 (DAEFRHDSGYE).

  15. Silver(I)‐Catalyzed Intramolecular Cyclizations of Epoxide‐Propargylic Esters to 1,4‐Oxazine Derivatives

    PubMed Central

    Li, Peng‐Hua; Yang, Jin‐Ming; Wei, Yin

    2016-01-01

    Abstract An interesting silver(I)‐catalyzed, one‐pot intramolecular cyclization of epoxide‐propargylic esters is described. A variety of 1,4‐oxazine derivatives were obtained through a novel domino sequence, including three‐membered ring‐opening, 3,3‐sigmatropic rearrangement, 6‐exo‐cycloisomerization and subsequent intramolecular elimination in moderate yields under mild conditions. PMID:28168146

  16. Convergent Synthesis of Diverse Nitrogen Heterocycles via Rh(III)-Catalyzed C-H Conjugate Addition/Cyclization Reactions.

    PubMed

    Weinstein, Adam B; Ellman, Jonathan A

    2016-07-01

    The development of Rh(III)-catalyzed C-H conjugate addition/cyclization reactions that provide access to synthetically useful fused bi- and tricyclic nitrogen heterocycles is reported. A broad scope of C-H functionalization substrates and electrophilic olefin coupling partners is effective, and depending on the nature of the directing group, cyclic imide, amide, or heteroaromatic products are obtained. An efficient synthesis of a pyrrolophenanthridine alkaloid natural product, oxoassoanine, highlights the utility of this method.

  17. Intramolecular monomer-on-monomer (MoM) Mitsunobu cyclization for the synthesis of benzofused thiadiazepine-dioxides.

    PubMed

    Maity, Pradip K; Kainz, Quirin M; Faisal, Saqib; Rolfe, Alan; Samarakoon, Thiwanka B; Basha, Fatima Z; Reiser, Oliver; Hanson, Paul R

    2011-12-14

    The utilization of a monomer-on-monomer (MoM) intramolecular Mitsunobu cyclization reaction employing norbornenyl-tagged (Nb-tagged) reagents is reported for the synthesis of benzofused thiadiazepine-dioxides. Facile purification was achieved via ring-opening metathesis (ROM) polymerization initiated by one of three metathesis catalyst methods: (i) free metathesis catalyst, (ii) surface-initiated catalyst-armed silica, or (iii) surface-initiated catalyst-armed Co/C magnetic nanoparticles.

  18. Reprogramming the Chemodiversity of Terpenoid Cyclization by Remolding the Active Site Contour of epi-Isozizaene Synthase

    PubMed Central

    2015-01-01

    The class I terpenoid cyclase epi-isozizaene synthase (EIZS) utilizes the universal achiral isoprenoid substrate, farnesyl diphosphate, to generate epi-isozizaene as the predominant sesquiterpene cyclization product and at least five minor sesquiterpene products, making EIZS an ideal platform for the exploration of fidelity and promiscuity in a terpenoid cyclization reaction. The hydrophobic active site contour of EIZS serves as a template that enforces a single substrate conformation, and chaperones subsequently formed carbocation intermediates through a well-defined mechanistic sequence. Here, we have used the crystal structure of EIZS as a guide to systematically remold the hydrophobic active site contour in a library of 26 site-specific mutants. Remolded cyclization templates reprogram the reaction cascade not only by reproportioning products generated by the wild-type enzyme but also by generating completely new products of diverse structure. Specifically, we have tripled the overall number of characterized products generated by EIZS. Moreover, we have converted EIZS into six different sesquiterpene synthases: F96A EIZS is an (E)-β-farnesene synthase, F96W EIZS is a zizaene synthase, F95H EIZS is a β-curcumene synthase, F95M EIZS is a β-acoradiene synthase, F198L EIZS is a β-cedrene synthase, and F96V EIZS and W203F EIZS are (Z)-γ-bisabolene synthases. Active site aromatic residues appear to be hot spots for reprogramming the cyclization cascade by manipulating the stability and conformation of critical carbocation intermediates. A majority of mutant enzymes exhibit only relatively modest 2–100-fold losses of catalytic activity, suggesting that residues responsible for triggering substrate ionization readily tolerate mutations deeper in the active site cavity. PMID:24517311

  19. Ligand bite angle-dependent palladium-catalyzed cyclization of propargylic carbonates to 2-alkynyl azacycles or cyclic dienamides.

    PubMed

    Daniels, David S B; Jones, Alison S; Thompson, Amber L; Paton, Robert S; Anderson, Edward A

    2014-02-10

    The regioselectivity of the palladium-catalyzed cyclization of propargylic carbonates with sulfonamide nucleophiles is critically dependent on the bite angle of the bidentate phosphine ligand. Ligands with small bite angles favor attack on the central carbon atom of an allenylpalladium intermediate to afford cyclic dienamide products, whereas the use of those with large bite angles leads to alkynyl azacycles, with high stereoselectivity. A computational analysis of the reaction pathway is also presented.

  20. Copper-mediated cross-coupling-cyclization-oxidation: a one-pot reaction to construct polysubstituted pyrroles.

    PubMed

    Liu, Pei; Liu, Jin-ling; Wang, Heng-shan; Pan, Ying-ming; Liang, Hong; Chen, Zhen-Feng

    2014-05-14

    A novel and efficient procedure for the synthesis of polysubstituted pyrroles has been developed in this work. The polysubsituted pyrroles were synthesized directly from terminal alkenes, amines and β-keto esters through cross-coupling-cyclization-oxidation in the presence of a catalytic amount of cuprous chloride. This method provides a one-pot synthesis route from terminal alkenes to polysubstituted pyrroles for the first time and opens a new area in cuprous catalysis.

  1. 7-N-(mercaptoalkyl)mitomycins: implications of cyclization for drug function.

    PubMed

    Na, Younghwa; Wang, Shuang; Kohn, Harold

    2002-05-01

    The Kyowa Hakko Kogyo and Bristol-Myers Squibb companies reported that select mitomycin C(7) aminoethylene disulfides displayed improved pharmacological profiles compared with mitomycin C (1). Mechanisms have been advanced for these mitomycins that differ from 1. Central to many of these hypotheses is the intermediate generation of 7-N-(2-mercaptoethyl)mitomycin C (5). Thiol 5 has been neither isolated nor characterized. Two efficient methods were developed for mitomycin (porfiromycin) C(7)-substituted thiols. In the first method, the thiol was produced by a thiol-mediated disulfide exchange process using an activated mixed mitomycin disulfide. In the second route, the thiol was generated by base-mediated cleavage of a porfiromycin C(7)-substituted thiol ester. We selected four thiols, 7-N-(2-mercaptoethyl)mitomycin C (5), 7-N-(2-mercaptoethyl)porfiromycin (12), 7-N-(2-mercapto-2-methylpropyl)mitomycin C (13), and 7-N-(3-mercaptopropyl)porfiromycin (14), for study. Thiols 5 and 12-14 differed in the composition of the alkyl linker that bridged the thiol with the mitomycin (porfiromycin) C(7) amino substituent. Thiol generation was documented by HPLC and spectroscopic studies and by thiol-trapping experiments. The linker affected the structure of the thiol species and the stability of the thiol. We observed that thiols 5 and 12 existed largely as their cyclic isomers. Evidence is presented that cyclization predominantly occurred at the mitomycin C(7) position. Correspondingly, alkyl linker substitution (13) or extension of the linker to three carbons (14) led to enhanced thiol stability and the predominant formation of the free thiol species. The dominant reaction of thiols 5 and 12-14 or their isomers was dimerization, and we found no evidence that thiol formation led to mitosene production and aziridine ring-opening. These findings indicated that thiol generation was not sufficient for mitomycin ring activation. The potential pharmacological advantages of

  2. AbDesign: An algorithm for combinatorial backbone design guided by natural conformations and sequences.

    PubMed

    Lapidoth, Gideon D; Baran, Dror; Pszolla, Gabriele M; Norn, Christoffer; Alon, Assaf; Tyka, Michael D; Fleishman, Sarel J

    2015-08-01

    Computational design of protein function has made substantial progress, generating new enzymes, binders, inhibitors, and nanomaterials not previously seen in nature. However, the ability to design new protein backbones for function--essential to exert control over all polypeptide degrees of freedom--remains a critical challenge. Most previous attempts to design new backbones computed the mainchain from scratch. Here, instead, we describe a combinatorial backbone and sequence optimization algorithm called AbDesign, which leverages the large number of sequences and experimentally determined molecular structures of antibodies to construct new antibody models, dock them against target surfaces and optimize their sequence and backbone conformation for high stability and binding affinity. We used the algorithm to produce antibody designs that target the same molecular surfaces as nine natural, high-affinity antibodies; in five cases interface sequence identity is above 30%, and in four of those the backbone conformation at the core of the antibody binding surface is within 1 Å root-mean square deviation from the natural antibodies. Designs recapitulate polar interaction networks observed in natural complexes, and amino acid sidechain rigidity at the designed binding surface, which is likely important for affinity and specificity, is high compared to previous design studies. In designed anti-lysozyme antibodies, complementarity-determining regions (CDRs) at the periphery of the interface, such as L1 and H2, show greater backbone conformation diversity than the CDRs at the core of the interface, and increase the binding surface area compared to the natural antibody, potentially enhancing affinity and specificity.

  3. Remote Enantioselection Transmitted by an Achiral Peptide Nucleic Acid Backbone

    NASA Technical Reports Server (NTRS)

    Kozlov, Igor A.; Orgel, Leslie E.; Nielsen, Peter E.

    2000-01-01

    short homochiral segment of DNA into a PNA helix could have guaranteed that the next short segment of DNA to be incorporated would have the same handedness as the first. Once two segments of the same handedness were present, the probability that a third segment would have the same handedness would increase, and so on. Evolution could then slowly dilute out the PNA part. This scenario would ultimately allow the formation of a chiral oligonucleotide by processes that are largely resistant to enantiomeric crossinhibition. It is important to note that the ligation of homochiral dinucleotides on a nucleic acid template would probably be at least as enantiospecific as the reaction that we have studied. The disadvantage of using chiral monomers as components of a replicating system arises from the difficulty of generating a first long homochiral template from a racemic mixture of monomers, although results of experiments designed to overcome this difficulty by employing homochiral tetramers have been reported.l l The probability of obtaining a homochiral n-mer from achiral substrates is approximately 1P-I if the nontemplate-directed extension of the primer is not enantioselective. Hence, it would be very hard to get started with a homochiral 40-mer, for example. No such difficulty exists in a scenario that originates with an achiral genetic material and in which the incorporation of very few chiral monomers in this achiral background gradually progresses towards homochirality. It seems possible that some PNA sequences could act as catalysts, analogous to ribozymes, even though PNA lacks clear metal binding sites. Although such catalysts could not be enantioselective, the incorporation of as few as two chiral nucleotides could then impose chiral specificity on the system. Furthermore, such patch chimeras could help to bridge the gap in catalytic potential between PNA and RNA, while guaranteeing enantioselectivity.

  4. Ebolavirus VP35 Coats the Backbone of Double-Stranded RNA for Interferon Antagonism

    PubMed Central

    Bale, Shridhar; Julien, Jean-Philippe; Bornholdt, Zachary A.; Krois, Alexander S.; Wilson, Ian A.

    2013-01-01

    Recognition of viral double-stranded RNA (dsRNA) activates interferon production and immune signaling in host cells. Crystal structures of ebolavirus VP35 show that it caps dsRNA ends to prevent sensing by pattern recognition receptors such as RIG-I. In contrast, structures of marburgvirus VP35 show that it primarily coats the dsRNA backbone. Here, we demonstrate that ebolavirus VP35 also coats the dsRNA backbone in solution, although binding to the dsRNA ends probably constitutes the initial binding event. PMID:23824825

  5. Solvation thermodynamics of amino acid side chains on a short peptide backbone

    SciTech Connect

    Hajari, Timir; Vegt, Nico F. A. van der

    2015-04-14

    The hydration process of side chain analogue molecules differs from that of the actual amino acid side chains in peptides and proteins owing to the effects of the peptide backbone on the aqueous solvent environment. A recent molecular simulation study has provided evidence that all nonpolar side chains, attached to a short peptide backbone, are considerably less hydrophobic than the free side chain analogue molecules. In contrast to this, the hydrophilicity of the polar side chains is hardly affected by the backbone. To analyze the origin of these observations, we here present a molecular simulation study on temperature dependent solvation free energies of nonpolar and polar side chains attached to a short peptide backbone. The estimated solvation entropies and enthalpies of the various amino acid side chains are compared with existing side chain analogue data. The solvation entropies and enthalpies of the polar side chains are negative, but in absolute magnitude smaller compared with the corresponding analogue data. The observed differences are large; however, owing to a nearly perfect enthalpy-entropy compensation, the solvation free energies of polar side chains remain largely unaffected by the peptide backbone. We find that a similar compensation does not apply to the nonpolar side chains; while the backbone greatly reduces the unfavorable solvation entropies, the solvation enthalpies are either more favorable or only marginally affected. This results in a very small unfavorable free energy cost, or even free energy gain, of solvating the nonpolar side chains in strong contrast to solvation of small hydrophobic or nonpolar molecules in bulk water. The solvation free energies of nonpolar side chains have been furthermore decomposed into a repulsive cavity formation contribution and an attractive dispersion free energy contribution. We find that cavity formation next to the peptide backbone is entropically favored over formation of similar sized nonpolar side

  6. Convenient and Scalable Synthesis of Fmoc-Protected Peptide Nucleic Acid Backbone

    PubMed Central

    Feagin, Trevor A.; Shah, Nirmal I.; Heemstra, Jennifer M.

    2012-01-01

    The peptide nucleic acid backbone Fmoc-AEG-OBn has been synthesized via a scalable and cost-effective route. Ethylenediamine is mono-Boc protected, then alkylated with benzyl bromoacetate. The Boc group is removed and replaced with an Fmoc group. The synthesis was performed starting with 50 g of Boc anhydride to give 31 g of product in 32% overall yield. The Fmoc-protected PNA backbone is a key intermediate in the synthesis of nucleobase-modified PNA monomers. Thus, improved access to this molecule is anticipated to facilitate future investigations into the chemical properties and applications of nucleobase-modified PNA. PMID:22848796

  7. Using Excel To Study The Relation Between Protein Dihedral Angle Omega And Backbone Length

    NASA Astrophysics Data System (ADS)

    Shew, Christopher; Evans, Samari; Tao, Xiuping

    How to involve the uninitiated undergraduate students in computational biophysics research? We made use of Microsoft Excel to carry out calculations of bond lengths, bond angles and dihedral angles of proteins. Specifically, we studied protein backbone dihedral angle omega by examining how its distribution varies with the length of the backbone length. It turns out Excel is a respectable tool for this task. An ordinary current-day desktop or laptop can handle the calculations for midsized proteins in just seconds. Care has to be taken to enter the formulas for the spreadsheet column after column to minimize the computing load. Supported in part by NSF Grant #1238795.

  8. Time-Resolved Spectroscopic Study of the Defluorination and Cyclization Reactions of Lomefloxacin in Water.

    PubMed

    Su, Tao; Li, Ming-De; Ma, Jiani; Phillips, David Lee

    2017-03-23

    The mechanism of the defluorination reaction(s) of lomefloxacin (LF) upon light illumination was investigated by using ultrafast laser flash photolysis combined with transient resonance Raman spectroscopy in near neutral water solution. The zwitterionic configuration of LF was determined to be the main species present in the near neutral water solution and was the species that was photoexcited to initiate the photochemical reaction. Femtosecond transient absorption revealed that the first excited singlet state (S1) of LF did not appreciably undergo intersystem crossing (ISC) and instead partially decayed to the ground state via fluorescence emission and partially underwent the cleavage of the carbon-fluorine bond at position 8 to produce a singlet LF aryl cation intermediate. The transient resonance Raman results provided a direct observation and vibrational spectral characterization of the singlet LF aryl cation species. Subsequently, the transformation from the singlet LF aryl cation to a triplet carbene via an ISC process was seen in nanosecond transient absorption spectra. Finally, the triplet carbene experienced a cyclization reaction with the N-ethyl chain to form a tricyclic product.

  9. A DFT study of the ambiphilic nature of arylpalladium species in intramolecular cyclization reactions.

    PubMed

    Fernández, Israel; Solé, Daniel; Sierra, Miguel A

    2011-03-18

    The remarkable structure-dependent reactivity observed in the cyclization of (2-haloanilino)-ketones with Pd-catalysts has been studied computationally within the density functional theory framework. The experimental reaction products ratio may be explained through the formation of a common palladaaminocyclobutane intermediate which can undergo a nucleophilic addition reaction and/or an enolate α-arilation process. The evolution of this metallacycle to the final products depends on two factors, the length of the tether joining the amino and the carbonyl groups, and the electronic nature of the substituent directly attached to the nitrogen atom. Thus, shorter chains (2 CH(2)) facilitate the nucleophic addition reaction by approximating the reactive aryl and Pd-coordinated carbonyl groups whereas longer chains (3 CH(2)) favor the enolate α-arylation proccess. For electron-withdrawing groups attached to the aniline nitrogen atom, the nucleophilic addition pathway becomes slightly disfavored, mainly due to the electron-withdrawing effect of the CO(2)Me group which avoids the delocation of the LP in the π-system, thus decreasing the nucleophilicity of the reactive arylic carbon atom. In contrast, the enolate α-arylation reaction is facilitated by the CO(2)Me group. This is translated into a small computed barrier energy difference of these competitive reaction pathways which should lead to a mixture of reaction products as experimentally found.

  10. Toward a synthesis of hirsutellone B by the concept of double cyclization

    PubMed Central

    Reber, Keith P.; Tilley, S. David; Carson, Cheryl A.; Sorensen, Erik J.

    2014-01-01

    This account describes a strategy for directly forming three of the six rings found in the polyketide natural product hirsutellone B via a novel cyclization cascade. The key step in our approach comprises two transformations: a large-ring forming, nucleophilic capture of a transient acyl ketene and an intramolecular Diels–Alder reaction, both of which occur in tandem through thermolyses of appropriately functionalized, polyunsaturated dioxinones. These thermally induced “double cyclization” cascades generate three new bonds, four contiguous stereocenters, and a significant fraction of the polycyclic architecture of hirsutellone B. The advanced macrolactam and macrolactone intermediates that were synthesized by this process possess key features of the hirsutellone framework, including the stereochemically dense decahydrofluorene core and the strained para-cyclophane ring. However, attempts to complete the carbon skeleton of hirsutellone B via transannular carbon-carbon bond formation were undermined by competitive O-alkylation reactions. This account also documents how we adapted to this undesired outcome through an evaluation of several distinct strategies for synthesis, as well as our eventual achievement of a formal total synthesis of hirsutellone B. PMID:24032341

  11. BF3 x Et2O-mediated cascade cyclizations: synthesis of schweinfurthins F and G.

    PubMed

    Mente, Nolan R; Neighbors, Jeffrey D; Wiemer, David F

    2008-10-17

    The total synthesis of the natural stilbene (+)-schweinfurthin G (8) has been accomplished through a sequence based on an efficient cationic cascade cyclization. This cascade process is initiated by Lewis acid promoted ring opening of an epoxide and terminated through a novel reaction with a phenolic oxygen "protected" as its MOM ether. Several Lewis acids have been examined for their ability to induce this new reaction, and BF3 x Et2O was found to be the most effective. The only major byproduct under these conditions was one where the expected secondary alcohol was found as its MOM ether derivative (e.g., 30). While this byproduct could be converted to the original target compound through hydrolysis, it also could be employed as a protected alcohol to allow preparation of a benzylic phosphonate (43) without dehydration of the secondary alcohol. The resulting phosphonate was employed in a Horner-Wadsworth-Emmons condensation with an aldehyde representing the right half of the target compounds, an approach complementary to previous studies based on condensation of a right-half phosphonate and a left-half aldehyde.

  12. Realization of a "lockable" molecular switch via pH- and redox-modulated cyclization.

    PubMed

    Richmond, Craig J; Parenty, Alexis D C; Song, Yu-Fei; Cooke, Graeme; Cronin, Leroy

    2008-10-01

    A switchable organic system involving four distinct states that can be interconverted by use of both pH and redox chemistry as control parameters has been developed. The key molecules involved in this system are the phenanthridine-based heterocycles 1-isobutyl-1,2,3,12b-tetrahydroimidazo[1,2-f]phenanthridine (TIP) and 5-[2-(isobutylamino)ethyl]phenanthridinium (AEP). These two states are interchangeable via pH control, and in addition they can also be further manipulated by oxidation or reduction to convert them to their "pH-inert" forms: 1-isobutyl-2,3-dihydro-1H-imidazo[1,2-f]phenanthridinium (DIP) and 5-[2-(isobutylamino)ethyl]-5,6-dihydrophenanthridine (AEDP), respectively. UV and (1)H NMR experiments carried out in a biphasic dichloromethane (DCM)/water solution were used for in situ structure determination. The results showed that the pH-modulated cyclization and phase-transfer process between the TIP and AEP states was essentially quantitative and repeatable without any significant loss in activity and that reduction or oxidation could be used to lock out these states against such acid-base-induced changes.

  13. Intramolecular cyclization of aspartic acid residues assisted by three water molecules: a density functional theory study

    NASA Astrophysics Data System (ADS)

    Takahashi, Ohgi; Kirikoshi, Ryota

    2014-01-01

    Aspartic acid (Asp) residues in peptides and proteins (l-Asp) are known to undergo spontaneous nonenzymatic reactions to form l-β-Asp, d-Asp, and d-β-Asp residues. The formation of these abnormal Asp residues in proteins may affect their three-dimensional structures and hence their properties and functions. Indeed, the reactions have been thought to contribute to aging and pathologies. Most of the above reactions of the l-Asp residues proceed via a cyclic succinimide intermediate. In this paper, a novel three-water-assisted mechanism is proposed for cyclization of an Asp residue (forming a gem-diol precursor of the succinimide) by the B3LYP/6-31 + G(d,p) density functional theory calculations carried out for an Asp-containing model compound (Ace-Asp-Nme, where Ace = acetyl and Nme = NHCH3). The three water molecules act as catalysts by mediating ‘long-range’ proton transfers. In the proposed mechanism, the amide group on the C-terminal side of the Asp residue is first converted to the tautomeric iminol form (iminolization). Then, reorientation of a water molecule and a conformational change occur successively, followed by the nucleophilic attack of the iminol nitrogen on the carboxyl carbon of the Asp side chain to form the gem-diol species. A satisfactory agreement was obtained between the calculated and experimental energetics.

  14. Crystal structure study and investigation of solid-state cyclization for AMG 222, a channel hydrate.

    PubMed

    Kiang, Y-H; Nagapudi, Karthik; Liu, Jodi; Staples, Richard J; Jona, Janan

    2013-01-30

    In this study, we investigate the solid-state structure and stability of AMG 222 (5-(2-[2-(2-cyano-pyrrolidin-1-yl)-2-oxo-ethylamino]-propyl)-5-(1H-tetrazol-5-yl)-10,11-dihydro-5H-dibenzo[a,d]cycloheptene-2,8 dicarboxylic acid bisdimethylamide), a small molecule DPP-IV inhibitor. Crystal structure of AMG 222 has been solved from single crystal X-ray analysis. Crystallographic data are as follows: monoclinic, P2(1) (no. 4), a=9.0327(5)Å, b=18.6177(8)Å, c=21.4927(10)Å, β=90.126(3)°, V=3614.4(3)Å(3), Z=4. Based on single crystal structure, AMG 222 is a pentahydrate with the water molecules sitting in channels formed by the drug framework. There are three distinct crystal structures of AMG 222 between 0 and 95% relative humidity (RH), namely the anhydrate, hemihydrate, and pentahydrate forms. Solid-state stability of the GMP batch showed a high level of cyclized degradation product. It was postulated that the degradation was promoted by increased amorphous content generated as a result of excessive drying that was employed to remove residual crystallization solvent. Material produced using a modified procedure using a humidified nitrogen purge had lower amorphous content and lower levels of cyclic degradation when compared to the GMP batch.

  15. Synthesis of Bridgehead Nitrogen Heterocycles via Cyclization of alpha-Ammonio 5-Hexenyl Radicals.

    PubMed

    Della, Ernest W.; Smith, Paul A.

    1999-03-19

    Ring-closure of the 2,2-dimethyl-2-azonia-5-hexenyl radical (4) proceeds smoothly and efficiently to give the 5-exo isomer essentially quantitatively, in accordance with predictions based on MP4SDTQ/6-31G ab initio calculations on the thermodynamic stability of alpha-ammonio radicals. The corresponding 5-hexynyl radical species 15 and its 6-phenyl derivative 19 display similar behavior affording the analogous 5-exo-3-methylenepyrrolidinium salts in high yield. In none of these cases were the products of reduction were detected. All of the radical intermediates were generated conveniently by treatment of the iodomethyl and/or phenylselenomethyl salts with tributyltin hydride. Application of this procedure to monocyclic precursors such as 1-methyl-1-iodomethyl-4-methylene-1-azoniacyclohexyl iodide (31) provided an attractive entry into quaternary derivatives of the 1-azabicyclo[2.2.1]heptyl system in good yield via a three-step sequence from 1-methylpiperidone. Dequaternization of the bicyclic salts so obtained unexpectedly leads to rupture of one of the rings rather than loss of the N-methyl group. The 1-azabicyclo[2.2.1]heptane could be accessed readily via tin hydride-induced cyclization of the corresponding N-phenylethylammonium salt 54, followed by Hofmann elimination with potassium tert-butoxide.

  16. Bending and torsional flexibility of G/C-rich sequences as determined by cyclization assays.

    PubMed

    Dlakic, M; Harrington, R E

    1995-12-15

    The structural polymorphism of DNA is a vital aspect of its biological function. However, it has become increasingly apparent in recent years that DNA polymorphism is a complicated, multidimensional phenomenon that includes not only static sequence-directed structures but dynamic effects as well, including influences of counterions and sequence context. In order to address some of these additional factors that govern DNA conformation, we have used T4 ligase-mediated cyclization to investigate bending in a series of DNA sequences containing the GGGCCC.GGGCCC motif in different sequence contexts including various helical phasings with (A)5-tracts. We present evidence for curvature in GGGCCC.GGGCCC and (A)5-tract motifs in the presence of physiological levels of Mg2+ and show that these motifs curve through similar but oppositely directed bending angles under these ionic strength conditions. Although these two sequence motifs appear to bend similarly, our results suggest significant differences in stiffness and stability of curvature between them. We also show that under the same experimental conditions, the CTAG-CTAG sequence element possesses unusual torsional flexibility and that this appears to be associated with the central TA.TA dinucleotide. The results underscore the need to include sequence context and specific ion effects as well as a dynamic basis in more complete predictive models for functionally related DNA polymorphism.

  17. Effects of Protein Stabilizing Agents on Thermal Backbone Motions: A Disulfide Trapping Study†

    PubMed Central

    Butler, Scott L.; Falke, Joseph J.

    2010-01-01

    Chemical stabilizers are widely used to enhance protein stability, both in nature and in the laboratory. Here, the molecular mechanism of chemical stabilizers is studied using a disulfide trapping assay to measure the effects of stabilizers on thermal backbone dynamics in the Escherichia coli galactose/glucose binding protein. Two types of backbone fluctuations are examined: (a) relative movements of adjacent surface α-helices within the same domain and (b) interdomain twisting motions. Both types of fluctuations are significantly reduced by all six stabilizers tested (glycerol, sucrose, trehalose, l-glucose, d-glucose, and d-galactose), and in each case larger amplitude motions are inhibited more than smaller ones. Motional inhibition does not require a high-affinity stabilizer binding site, indicating that the effects of stabilizers are nonspecific. Overall, the results support the theory that effective stabilizing agents act by favoring the most compact structure of a protein, thereby reducing local backbone fluctuations away from the fully folded state. Such inhibition of protein backbone dynamics may be a general mechanism of protein stabilization in extreme thermal or chemical environments. PMID:8718847

  18. Insights on chiral, backbone modified peptide nucleic acids: Properties and biological activity

    PubMed Central

    Moccia, Maria; Adamo, Mauro F A; Saviano, Michele

    2014-01-01

    PNAs are emerging as useful synthetic devices targeting natural miRNAs. In particular 3 classes of structurally modified PNAs analogs are herein described, namely α, β and γ, which differ by their backbone modification. Their mode and binding affinity for natural nucleic acids and their use in medicinal chemistry as potential miRNA binders is discussed. PMID:26752710

  19. Animals without Backbones: The Invertebrate Story. Grade Level 5-9.

    ERIC Educational Resources Information Center

    Jerome, Brian; Fuqua, Paul

    This guide, when used in tandem with the videotape "Animals Without Backbones," helps students learn about invertebrates. These materials promote hands-on discovery and learning. The guide is composed of six curriculum-based teaching units: (1) "Getting Started"; (2) "Porifera"; (3) "Cnidarians"; (4) "Worms"; (5) "Mollusks"; (6) "Arthropods"; and…

  20. Oligonucleotides with conjugated dihydropyrroloindole tripeptides: base composition and backbone effects on hybridization.

    PubMed Central

    Kutyavin, I V; Lukhtanov, E A; Gamper, H B; Meyer, R B

    1997-01-01

    The ability of conjugated minor groove binding (MGB) residues to stabilize nucleic acid duplexes was investigated by synthesis of oligonucleotides bearing a tethered dihydropyrroloindole tripeptide (CDPI3). Duplexes bearing one or more of these conjugated MGBs were varied by base composition (AT- or GC-rich oligonucleotides), backbone modifications (phosphodiester DNA, 2'-O-methyl phosphodiester RNA or phosphorothioate DNA) and site of attachment of the MGB moiety (5'- or 3'-end of either duplex strand). Melting temperatures of the duplexes were determined. The conjugated CDPI3 residue enhanced the stability of virtually all duplexes studied. The extent of stabilization was backbone and sequence dependent and reached a maximum value of 40-49 degrees C for d(pT)8. d(pA)8. Duplexes with a phosphorothioate DNA backbone responded similarly on CDPI3 conjugation, although they were less stable than analogous phosphodiesters. Modest stabilization was obtained for duplexes with a 2'-O-methyl RNA backbone. The conjugated CDPI3 residue stabilized GC-rich DNA duplexes, albeit to a lesser extent than for AT-rich duplexes of the same length. PMID:9278496

  1. Automated extraction of backbone deuteration levels from amide H/2H mass spectrometry experiments

    PubMed Central

    Hotchko, Matthew; Anand, Ganesh S.; Komives, Elizabeth A.; Ten Eyck, Lynn F.

    2006-01-01

    A Fourier deconvolution method has been developed to explicitly determine the amount of backbone amide deuterium incorporated into protein regions or segments by hydrogen/deuterium (H/D) exchange with high-resolution mass spectrometry. Determination and analysis of the level and number of backbone amide exchanging in solution provide more information about the solvent accessibility of the protein than do previous centroid methods, which only calculate the average deuterons exchanged. After exchange, a protein is digested into peptides as a way of determining the exchange within a local area of the protein. The mass of a peptide upon deuteration is a sum of the natural isotope abundance, fast exchanging side-chain hydrogens (present in MALDI-TOF H/2H data) and backbone amide exchange. Removal of the components of the isotopic distribution due to the natural isotope abundances and the fast exchanging side-chains allows for a precise quantification of the levels of backbone amide exchange, as is shown by an example from protein kinase A. The deconvoluted results are affected by overlapping peptides or inconsistent mass envelopes, and evaluation procedures for these cases are discussed. Finally, a method for determining the back exchange corrected populations is presented, and its effect on the data is discussed under various circumstances. PMID:16501228

  2. On the relationship between NMR-derived amide order parameters and protein backbone entropy changes.

    PubMed

    Sharp, Kim A; O'Brien, Evan; Kasinath, Vignesh; Wand, A Joshua

    2015-05-01

    Molecular dynamics simulations are used to analyze the relationship between NMR-derived squared generalized order parameters of amide NH groups and backbone entropy. Amide order parameters (O(2) NH ) are largely determined by the secondary structure and average values appear unrelated to the overall flexibility of the protein. However, analysis of the more flexible subset (O(2) NH  < 0.8) shows that these report both on the local flexibility of the protein and on a different component of the conformational entropy than that reported by the side chain methyl axis order parameters, O(2) axis . A calibration curve for backbone entropy vs. O(2) NH is developed, which accounts for both correlations between amide group motions of different residues, and correlations between backbone and side chain motions. This calibration curve can be used with experimental values of O(2) NH changes obtained by NMR relaxation measurements to extract backbone entropy changes, for example, upon ligand binding. In conjunction with our previous calibration for side chain entropy derived from measured O(2) axis values this provides a prescription for determination of the total protein conformational entropy changes from NMR relaxation measurements.

  3. Linear discrete diffraction and transverse localization of light in two-dimensional backbone lattices.

    PubMed

    Qi, Yiling; Zhang, Guoquan

    2010-09-13

    We study the linear discrete diffraction characteristics of light in two-dimensional backbone lattices. It is found that, as the refractive index modulation depth of the backbone lattice increases, high-order band gaps become open and broad in sequence, and the allowed band curves of the Floquet-Bloch modes become flat gradually. As a result, the diffraction pattern at the exit face converges gradually for both the on-site and off-site excitation cases. Particularly, when the refractive index modulation depth of the backbone lattice is high enough, for example, on the order of 0.01 for a square lattice, the light wave propagating in the backbone lattice will be localized in transverse dimension for both the on-site and off-site excitation cases. This is because only the first several allowed bands with nearly flat band curves are excited in the lattice, and the transverse expansion velocities of the Floquet-Bloch modes in these flat allowed bands approach to zero. Such a linear transverse localization of light may have potential applications in navigating light propagation dynamics and optical signal processing.

  4. Peptide-functionalized semiconductor surfaces: strong surface electronic effects from minor alterations to backbone composition.

    PubMed

    Matmor, Maayan; Lengyel, George A; Horne, W Seth; Ashkenasy, Nurit

    2017-02-22

    The use of non-canonical amino acids is a powerful way to control protein structure. Here, we show that subtle changes to backbone composition affect the ability of a dipeptide to modify solid surface electronic properties. The extreme sensitivity of the interactions to the peptide structure suggests potential applications in improving the performance of electronic devices.

  5. Toward Improved Description of DNA Backbone: Revisiting Epsilon and Zeta Torsion Force Field Parameters

    PubMed Central

    Zgarbová, Marie; Luque, F. Javier; Šponer, Jiří; Cheatham, Thomas E.; Otyepka, Michal; Jurečka, Petr

    2013-01-01

    We present a refinement of the backbone torsion parameters ε and ζ of the Cornell et al. AMBER force field for DNA simulations. The new parameters, denoted as εζOL1, were derived from quantum-mechanical calculations with inclusion of conformation-dependent solvation effects according to the recently reported methodology (J. Chem. Theory Comput. 2012, 7(9), 2886-2902). The performance of the refined parameters was analyzed by means of extended molecular dynamics (MD) simulations for several representative systems. The results showed that the εζOL1 refinement improves the backbone description of B-DNA double helices and G-DNA stem. In B-DNA simulations, we observed an average increase of the helical twist and narrowing of the major groove, thus achieving better agreement with X-ray and solution NMR data. The balance between populations of BI and BII backbone substates was shifted towards the BII state, in better agreement with ensemble-refined solution experimental results. Furthermore, the refined parameters decreased the backbone RMS deviations in B-DNA MD simulations. In the antiparallel guanine quadruplex (G-DNA) the εζOL1 modification improved the description of non-canonical α/γ backbone substates, which were shown to be coupled to the ε/ζ torsion potential. Thus, the refinement is suggested as a possible alternative to the current ε/ζ torsion potential, which may enable more accurate modeling of nucleic acids. However, long-term testing is recommended before its routine application in DNA simulations. PMID:24058302

  6. A backbone design principle for covalent organic frameworks: the impact of weakly interacting units on CO2 adsorption.

    PubMed

    Zhai, Lipeng; Huang, Ning; Xu, Hong; Chen, Qiuhong; Jiang, Donglin

    2017-03-31

    Covalent organic frameworks are designed to have backbones with different yet discrete contents of triarylamine units that interact weakly with CO2. Adsorption experiments indicate that the triarylamine units dominate the CO2 adsorption process and the CO2 uptake increases monotonically with the triarylamine content. These profound collective effects reveal a principle for designing backbones targeting for CO2 capture and separation.

  7. Drawing dependent structures, mechanical properties and cyclization behaviors of polyacrylonitrile and polyacrylonitrile/carbon nanotube composite fibers prepared by plasticized spinning.

    PubMed

    Li, Xiang; Qin, Aiwen; Zhao, Xinzhen; Liu, Dapeng; Wang, Haiye; He, Chunju

    2015-09-14

    Drawing to change the structural properties and cyclization behaviors of the polyacrylonitrile (PAN) chains in crystalline and amorphous regions is carried out on PAN and PAN/carbon nanotube (CNT) composite fibers. Various characterization methods including Fourier transform infrared spectroscopy, differential scanning calorimetry, X-ray diffraction and thermal gravimetric analysis are used to monitor the structural evolution and cyclization behaviors of the fibers. With an increase of the draw ratio during the plasticized spinning process, the structural parameters of the fibers, i.e. crystallinity and planar zigzag conformation, are decreased at first, and then increased, which are associated with the heat exchange rate and the oriented-crystallization rate. A possible mechanism for plasticized spinning is proposed to explain the changing trends of crystallinity and planar zigzag conformation. PAN and PAN/CNT fibers exhibit various cyclization behaviors induced by drawing, e.g., the initiation temperature for the cyclization (Ti) of PAN fibers is increased with increasing draw ratio, while Ti of PAN/CNT fibers is decreased. Drawing also facilitates cyclization and lowers the percentage of β-amino nitrile for PAN/CNT fibers during the stabilization.

  8. Tyrosine-lipid peroxide adducts from radical termination: para coupling and intramolecular Diels-Alder cyclization.

    PubMed

    Shchepin, Roman; Möller, Matias N; Kim, Hye-young H; Hatch, Duane M; Bartesaghi, Silvina; Kalyanaraman, Balaraman; Radi, Rafael; Porter, Ned A

    2010-12-15

    Free radical co-oxidation of polyunsaturated lipids with tyrosine or phenolic analogues of tyrosine gave rise to lipid peroxide-tyrosine (phenol) adducts in both aqueous micellar and organic solutions. The novel adducts were isolated and characterized by 1D and 2D NMR spectroscopy as well as by mass spectrometry (MS). The spectral data suggest that the polyunsaturated lipid peroxyl radicals give stable peroxide coupling products exclusively at the para position of the tyrosyl (phenoxy) radicals. These adducts have characteristic (13)C chemical shifts at 185 ppm due to the cross-conjugated carbonyl of the phenol-derived cyclohexadienone. The primary peroxide adducts subsequently undergo intramolecular Diels-Alder (IMDA) cyclization, affording a number of diastereomeric tricyclic adducts that have characteristic carbonyl (13)C chemical shifts at ~198 ppm. All of the NMR HMBC and HSQC correlations support the structure assignments of the primary and Diels-Alder adducts, as does MS collision-induced dissociation data. Kinetic rate constants and activation parameters for the IMDA reaction were determined, and the primary adducts were reduced with cuprous ion to give a phenol-derived 4-hydroxycyclohexa-2,5-dienone. No products from adduction of peroxyls at the phenolic ortho position were found in either the primary or cuprous reduction product mixtures. These studies provide a framework for understanding the nature of lipid-protein adducts formed by peroxyl-tyrosyl radical-radical termination processes. Coupling of lipid peroxyl radicals with tyrosyl radicals leads to cyclohexenone and cyclohexadienone adducts, which are of interest in and of themselves since, as electrophiles, they are likely targets for protein nucleophiles. One consequence of lipid peroxyl reactions with tyrosyls may therefore be protein-protein cross-links via interprotein Michael adducts.

  9. Insights into Diterpene Cyclization from Structure of Bifunctional Abietadiene Synthase from Abies grandis

    SciTech Connect

    Zhou, Ke; Gao, Yang; Hoy, Julie A.; Mann, Francis M.; Honzatko, Richard B.; Peters, Reuben J.

    2013-09-24

    Abietadiene synthase from Abies grandis (AgAS) is a model system for diterpene synthase activity, catalyzing class I (ionization-initiated) and class II (protonation-initiated) cyclization reactions. Reported here is the crystal structure of AgAS at 2.3 {angstrom} resolution and molecular dynamics simulations of that structure with and without active site ligands. AgAS has three domains ({alpha}, {beta}, and {gamma}). The class I active site is within the C-terminal {alpha} domain, and the class II active site is between the N-terminal {gamma} and {beta} domains. The domain organization resembles that of monofunctional diterpene synthases and is consistent with proposed evolutionary origins of terpene synthases. Molecular dynamics simulations were carried out to determine the effect of substrate binding on enzymatic structure. Although such studies of the class I active site do lead to an enclosed substrate-Mg{sup 2+} complex similar to that observed in crystal structures of related plant enzymes, it does not enforce a single substrate conformation consistent with the known product stereochemistry. Simulations of the class II active site were more informative, with observation of a well ordered external loop migration. This 'loop-in' conformation not only limits solvent access but also greatly increases the number of conformational states accessible to the substrate while destabilizing the nonproductive substrate conformation present in the 'loop-out' conformation. Moreover, these conformational changes at the class II active site drive the substrate toward the proposed transition state. Docked substrate complexes were further assessed with regard to the effects of site-directed mutations on class I and II activities.

  10. Scalable, transition-metal-free direct oxime O-arylation: rapid access to O-arylhydroxylamines and substituted benzo[b]furans.

    PubMed

    Gao, Hongyin; Xu, Qing-Long; Keene, Craig; Kürti, László

    2014-07-14

    O-aryloximes, generated from readily available and inexpensive oximes through transition-metal-free O-arylation, can either be hydrolyzed to O-arylhydroxylamines or conveniently converted to structurally diverse benzo[b]furans through an environmentally benign, one-pot [3,3]-sigmatropic rearrangement/cyclization sequence.

  11. Impact of HIV-1 Backbone on Neutralization Sensitivity: Neutralization Profiles of Heterologous Envelope Glycoproteins Expressed in Native Subtype C and CRF01_AE Backbone

    PubMed Central

    Sanders-Buell, Eric; Wesberry, Maggie; Towle, Teresa; Pillis, Devin M.; Molnar, Sebastian; McLinden, Robert; Edmonds, Tara; Hirsch, Ivan; O’Connell, Robert; McCutchan, Francine E.; Montefiori, David C.; Ochsenbauer, Christina; Kappes, John C.; Kim, Jerome H.; Polonis, Victoria R.; Tovanabutra, Sodsai

    2013-01-01

    Standardized assays to assess vaccine and antiviral drug efficacy are critical for the development of protective HIV-1 vaccines and drugs. These immune assays will be advanced by the development of standardized viral stocks, such as HIV-1 infectious molecular clones (IMC), that i) express a reporter gene, ii) are representative of globally diverse subtypes and iii) are engineered to easily exchange envelope (env) genes for expression of sequences of interest. Thus far, a subtype B IMC backbone expressing Renilla luciferase (LucR), and into which the ectodomain of heterologous env coding sequences can be expressed has been successfully developed but as execution of HIV-1 vaccine efficacy trials shifts increasingly to non-subtype B epidemics (Southern African and Southeast Asia), non-subtype B HIV-1 reagents are needed to support vaccine development. Here we describe two IMCs derived from subtypes C and CRF01_AE HIV-1 primary isolates expressing LucR (IMC.LucR) that were engineered to express heterologous gp160 Envs. 18 constructs expressing various subtypes C and CRF01_AE Envs, mostly acute, in subtype-matched and –unmatched HIV backbones were tested for functionality and neutralization sensitivity. Our results suggest a possible effect of non-env HIV-1 genes on the interaction of Env and neutralizing antibodies and highlight the need to generate a library of IMCs representative of the HIV-1 subtype spectrum to be used as standardized neutralization assay reagents for assessing HIV-1 vaccine efficacy. PMID:24312165

  12. Backbone chemical shift assignments for Xanthomonas campestris peroxiredoxin Q in the reduced and oxidized states: a dramatic change in backbone dynamics.

    PubMed

    Buchko, Garry W; Perkins, Arden; Parsonage, Derek; Poole, Leslie B; Karplus, P Andrew

    2016-04-01

    Peroxiredoxins (Prx) are ubiquitous enzymes that reduce peroxides as part of antioxidant defenses and redox signaling. While Prx catalytic activity and sensitivity to hyperoxidative inactivation depend on their dynamic properties, there are few examples where their dynamics has been characterized by NMR spectroscopy. Here, we provide a foundation for studies of the solution properties of peroxiredoxin Q from the plant pathogen Xanthomonas campestris (XcPrxQ) by assigning the observable (1)H(N), (15)N, (13)C(α), (13)C(β), and (13)C' chemical shifts for both the reduced (dithiol) and oxidized (disulfide) states. In the reduced state, most of the backbone amide resonances (149/152, 98 %) can be assigned in the XcPrxQ (1)H-(15)N HSQC spectrum. In contrast, a remarkable 51 % (77) of these amide resonances are not visible in the (1)H-(15)N HSQC spectrum of the disulfide state of the enzyme, indicating a substantial change in backbone dynamics associated with the formation of an intramolecular C48-C84 disulfide bond.

  13. Backbone dynamics measurements on leukemia inhibitory factor, a rigid four-helical bundle cytokine.

    PubMed Central

    Yao, S.; Smith, D. K.; Hinds, M. G.; Zhang, J. G.; Nicola, N. A.; Norton, R. S.

    2000-01-01

    The backbone dynamics of the four-helical bundle cytokine leukemia inhibitory factor (LIF) have been investigated using 15N NMR relaxation and amide proton exchange measurements on a murine-human chimera, MH35-LIF. For rapid backbone motions (on a time scale of 10 ps to 100 ns), as probed by 15N relaxation measurements, the dynamics parameters were calculated using the model-free formalism incorporating the model selection approach. The principal components of the inertia tensor of MH35-LIF, as calculated from its NMR structure, were 1:0.98:0.38. The global rotational motion of the molecule was, therefore, assumed to be axially symmetric in the analysis of its relaxation data. This yielded a diffusion anisotropy D(parallel)/D(perpendicular) of 1.31 and an effective correlation time (4D(perpendicular) + 2D(parallel))(-1) of 8.9 ns. The average values of the order parameters (S2) for the four helices, the long interhelical loops, and the N-terminus were 0.91, 0.84, and 0.65, respectively, indicating that LIF is fairly rigid in solution, except at the N-terminus. The S2 values for the long interhelical loops of MH35-LIF were higher than those of their counterparts in short-chain members of the four-helical bundle cytokine family. Residues involved in LIF receptor binding showed no consistent pattern of backbone mobilities, with S2 values ranging from 0.71 to 0.95, but residues contributing to receptor binding site III had relatively lower S2 values, implying higher amplitude motions than for the backbone of sites I and II. In the relatively slow motion regime, backbone amide exchange measurements showed that a number of amides from the helical bundle exchanged extremely slowly, persisting for several months in 2H2O at 37 degrees C. Evidence for local unfolding was considered, and correlations among various structure-related parameters and the backbone amide exchange rates were examined. Both sets of data concur in showing that LIF is one of the most rigid four

  14. Biosynthesis of monoterpenes. Stereochemistry of the enzymatic cyclizations of geranyl pyrophosphate to (+)-alpha-pinene and (-)-beta-pinene

    SciTech Connect

    Croteau, R.; Satterwhite, D.M.; Wheeler, C.J.; Felton, N.M.

    1989-02-05

    The conversion of geranyl pyrophosphate to (+)-alpha-pinene and to (-)-beta-pinene is considered to proceed by the initial isomerization of the substrate to (-)-(3R)- and to (+)-(3S)-linalyl pyrophosphate, respectively, and the subsequent cyclization of the anti, endo-conformer of these bound intermediates by mirror-image sequences which should result in the net retention of configuration at C1 of the geranyl precursor. Incubation of (1R)-(2-14C,1-3H)- and (1S)-(2-14C,1-3H)geranyl pyrophosphate with (+)-pinene cyclase and with (-)-pinene cyclase from common sage (Salvia officinalis) gave labeled (+)-alpha- and (-)-beta-pinene of unchanged 3H/14C ratio in all cases, and the (+)- and (-)-olefins were stereoselectively converted to (+)- and (-)-borneol, respectively, which were oxidized to the corresponding (+)- and (-)-isomers of camphor, again without change in isotope ratio. The location of the tritium was determined in each case by stereoselective, base-catalyzed exchange of the exo-alpha-hydrogens of these derived ketones. The results indicated that the configuration at C1 of the substrate was retained in the enzymatic transformations to the (+)- and (-)-pinenes, which is entirely consistent with the syn-isomerization of geranyl pyrophosphate to linalyl pyrophosphate, transoid to cisoid rotation, and anti, endo-cyclization of the latter. The absolute stereochemical elements of the antipodal reaction sequences were confirmed by the selective enzymatic conversions of (3R)- and (3S)-1Z-(1-3H)linalyl pyrophosphate to (+)-alpha-pinene and (-)-beta-pinene, respectively, and by the location of the tritium in the derived camphors as before. The summation of the results fully defines the overall stereochemistry of the coupled isomerization and cyclization of geranyl pyrophosphate to the antipodal pinenes.

  15. Biosynthesis of monoterpenes. Enantioselectivity in the enzymatic cyclization of (+)- and (-)-linalyl pyrophosphate to (+)- and (-)-pinene and (+)- and (-)-camphene

    SciTech Connect

    Croteau, R.; Satterwhite, D.M.; Cane, D.E.; Chang, C.C.

    1988-07-25

    Cyclase I from Salvia officinalis leaf catalyzes the conversion of geranyl pyrophosphate to the stereo-chemically related bicyclic monoterpenes (+)-alpha-pinene and (+)-camphene and to lesser quantities of monocyclic and acyclic olefins, whereas cyclase II from this plant tissue converts the same acyclic precursor to (-)-alpha-pinene, (-)-beta-pinene and (-)-camphene as well as to lesser amounts of monocyclics and acyclics. These antipodal cyclizations are considered to proceed by the initial isomerization of the substrate to the respective bound tertiary allylic intermediates (-)-(3R)- and (+)-(3S)-linalyl pyrophosphate. ((3R)-8,9-14C,(3RS)-1E-3H)Linalyl pyrophosphate (3H:14C = 5.14) was tested as a substrate with both cyclases to determine the configuration of the cyclizing intermediate. This substrate with cyclase I yielded alpha-pinene and camphene with 3H:14C ratios of 3.1 and 4.2, respectively, indicating preferential, but not exclusive, utilization of the (3R)-enantiomer. With cyclase II, the doubly labeled substrate gave bicyclic olefins with 3H:14C ratios of from 13 to 20, indicating preferential, but not exclusive, utilization of the (3S)-enantiomer in this case. (3R)- and (3S)-(1Z-3H)linalyl pyrophosphate were separately compared to the achiral precursors (1-3H)geranyl pyrophosphate and (1-3H)neryl pyrophosphate (cis-isomer) as substrates for the cyclizations. With cyclase I, geranyl, neryl, and (3R)-linalyl pyrophosphate gave rise exclusively to (+)-alpha-pinene and (+)-camphene, whereas (3S)-linayl pyrophosphate produced, at relatively low rates, the (-)-isomers. With cyclase II, geranyl, neryl, and (3S)-linalyl pyrophosphate yielded exclusively the (-)-isomer series, whereas (3R)-linalyl pyrophosphate afforded the (+)-isomers at low rates.

  16. Solid polymer battery electrolyte and reactive metal-water battery

    DOEpatents

    Harrup, Mason K.; Peterson, Eric S.; Stewart, Frederick F.

    2000-01-01

    In one implementation, a reactive metal-water battery includes an anode comprising a metal in atomic or alloy form selected from the group consisting of periodic table Group 1A metals, periodic table Group 2A metals and mixtures thereof. The battery includes a cathode comprising water. Such also includes a solid polymer electrolyte comprising a polyphosphazene comprising ligands bonded with a phosphazene polymer backbone. The ligands comprise an aromatic ring containing hydrophobic portion and a metal ion carrier portion. The metal ion carrier portion is bonded at one location with the polymer backbone and at another location with the aromatic ring containing hydrophobic portion. The invention also contemplates such solid polymer electrolytes use in reactive metal/water batteries, and in any other battery.

  17. Synthesis of 2,4,5-trisubstituted thiazoles via Lawesson's reagent-mediated chemoselective thionation-cyclization of functionalized enamides.

    PubMed

    Kumar, S Vijay; Parameshwarappa, G; Ila, H

    2013-07-19

    An efficient route to 2-phenyl/(2-thienyl)-5-(het)aryl/(methylthio)-4-functionalized thiazoles via one-step chemoselective thionation-cyclization of highly functionalized enamides mediated by Lawesson's reagent is reported. These enamide precursors are obtained by nucleophilic ring-opening of 2-phenyl/(2-thienyl)-4-[bis(methylthio)/(methylthio)(het)arylmethylene]-5-oxazolones with alkoxides and a variety of primary aromatic/aliphatic amines or amino acid esters, leading to the introduction of an ester, an N-substituted carboxamide, or a peptide functionality in the 4-position of the product thiazoles.

  18. Preparation of the Core Structure of Aspidosperma and Strychnos Alkaloids from Aryl Azides by a Cascade Radical Cyclization.

    PubMed

    Wyler, Benjamin; Brucelle, François; Renaud, Philippe

    2016-03-18

    A novel approach to prepare the core structure of Aspidosperma and Strychnos alkaloids is described. The strategy is based on a cyclization cascade involving the formation of quaternary carbon center followed by trapping of the radical intermediate by an aryl azide to build the 5-membered ring of the pyrrolocarbazole system. This reaction is run with triethylborane without the need for any hydrogen atom donor such as a tin hydride or tris(trimethylsilyl)silane, and it furnishes the tetracyclic framework as a single diastereomer. The influence of different N-protecting groups on the starting iodoacetamide has been examined.

  19. Intracellular Delivery of Peptidyl Ligands by Reversible Cyclization: Discovery of a PDZ Domain Inhibitor that Rescues CFTR Activity**

    PubMed Central

    Qian, Ziqing; Xu, Xiaohua; Amacher, Jeanine F.; Madden, Dean R.; Cormet-Boyaka, Estelle

    2015-01-01

    We report a general strategy for intracellular delivery of linear peptidyl ligands by fusing them with a cell-penetrating peptide and cyclizing the fusion peptides through a disulfide bond. The resulting cyclic peptides are cell permeable and have improved proteolytic stability. Once inside the cell, the disulfide bond is reduced to produce linear, biologically active peptides. This strategy was applied to generate a cell-permeable peptide substrate for real-time detection of intracellular caspase activities during apoptosis and a CAL-PDZ domain inhibitor for potential treatment of cystic fibrosis. PMID:25785567

  20. Tryptophan 232 within oxidosqualene-lanosterol cyclase from Saccharomyces cerevisiae influences rearrangement and deprotonation but not cyclization reactions.

    PubMed

    Wu, Tung-Kung; Yu, Mei-Ting; Liu, Yuan-Ting; Chang, Cheng-Hsian; Wang, Hsing-Ju; Diau, Eric Wei-Guang

    2006-03-30

    [reaction: see text] Oxidosqualene-lanosterol cyclases convert oxidosqualene to lanosterol in yeast and mammals. Site-saturated mutants' construction of Saccharomyces cerevisiae oxidosqualene-lanosterol cyclase, at Trp232 exchanges against proteinogenic amino acids, and product profiles are shown. All mutants, except Lys and Arg, produced protosta-12,24-dien-3beta-ol, lanosterol, and parkeol. Overall, Trp232 plays a catalytic role in the influence of rearrangement process and determination of deprotonation position but does not involve intervention in the cyclization steps.

  1. Facile Access to Cyclooctanoid Ring Systems via Microwave-Assisted Tandem 6-exo dig Cyclization-Rearrangement Sequence

    PubMed Central

    Feldman, Aaron W.; Ovaska, Sami I.; Ovaska, Timo V.

    2014-01-01

    Appropriately substituted 5-alkyn-1-ol systems bearing a nitrile moiety at the triple bond serve as versatile precursors to a variety of cyclooctenone derivatives via a “one-pot” base-catalyzed oxyanionic 6-exo dig cyclization/Claisen rearrangement sequence under microwave irradiation. It was found that the initially formed cyclic intermediate consists of a mixture of endo and exocyclic isomers, which appear to be in equilibrium under the reaction conditions. However, the only observed products from these reactions are α-cyano substituted cyclooctenones, derived from the exocyclic dihydrofuran intermediates. PMID:24994941

  2. Unexpected Formation of Highly Functionalized Dihydropyrans via Addition-Cyclization Reactions Between Dimethyl Oxoglutaconate and α,β-Unsaturated Hydrazones.

    PubMed

    Mullins, Jason E; Etoga, Jean-Louis G; Gajewski, Mariusz; Degraw, Joseph I; Thompson, Charles M

    2009-05-20

    The condensation between dienophiles and α,β-unsaturated hydrazone azadienes was previously reported to afford piperidines. During an attempt to adapt this reaction to the preparation of piperidine-based conformationally-restricted analogs of glutamate, it was discovered that the electrophile, dimethyl oxoglutaconate (DOG) led to highly substituted dihydropyrans in 20-50% yield. The unexpected pyran product likely results from an initial 1,4-addition of the hydrazone to the oxoglutaconate followed by intramolecular cyclization of the resultant enolate oxygen to the α,β-unsaturated iminium ion. Further manipulations afford substituted tetrahydropyran 6-methamino-2,4-dicarboxylic acids.

  3. Unexpected Formation of Highly Functionalized Dihydropyrans via Addition-Cyclization Reactions Between Dimethyl Oxoglutaconate and α,β-Unsaturated Hydrazones

    PubMed Central

    Mullins, Jason E.; Etoga, Jean-Louis G.; Gajewski, Mariusz; DeGraw, Joseph I.; Thompson, Charles M.

    2009-01-01

    The condensation between dienophiles and α,β-unsaturated hydrazone azadienes was previously reported to afford piperidines. During an attempt to adapt this reaction to the preparation of piperidine-based conformationally-restricted analogs of glutamate, it was discovered that the electrophile, dimethyl oxoglutaconate (DOG) led to highly substituted dihydropyrans in 20–50% yield. The unexpected pyran product likely results from an initial 1,4-addition of the hydrazone to the oxoglutaconate followed by intramolecular cyclization of the resultant enolate oxygen to the α,β-unsaturated iminium ion. Further manipulations afford substituted tetrahydropyran 6-methamino-2,4-dicarboxylic acids. PMID:20161237

  4. Oxidative cyclization, 1,4-benzothiazine formation and dimerization of 2-bromo-3-(glutathion-S-yl)hydroquinone.

    PubMed

    Monks, T J; Highet, R J; Lau, S S

    1990-07-01

    Several lines of evidence suggest that the renal-specific toxicity of quinol-linked GSH conjugates is probably a result of their metabolism by gamma-glutamyl transpeptidase and selective accumulation by proximal tubular cells. Transport of the resultant quinol-cysteine and/or cystein-S-ylglycine conjugate followed by oxidation to the quinone may be important steps in the mechanism of toxicity of these compounds. Factors modulating the intracellular and/or intralumenal concentration of the cystein-S-yl and cystein-S-ylglycine conjugate will, therefore, be important determinants of toxicity. We have now studied the gamma-glutamyl transpeptidase-mediated metabolism of 2-bromo-3-(glutathion-S-yl)hydroquinone. The product of this reaction, 2-bromo-3-(cystein-S-ylglycyl)hydroquinone, undergoes an intramolecular cyclization to yield a 1,4-benzothiazine derivative that retains the glycine residue. A similar cyclization reaction occurs with 2-bromo-3-(cystein-S-yl)hydroquinone, which is unstable in aqueous solutions and undergoes a pH-dependent rearrangement that requires initial oxidation to the quinone. UV spectroscopy revealed that, at neutral pH, further reaction results in the formation of a chromophore, consistent with 1,4-benzothiazine formation. This product arises via cyclization of the cysteine residue via an intramolecular 1,4 Michael addition. Further reaction results in the precipitation of a pigment that exhibits properties of a pH indicator. The pigment undergoes a marked pH-dependent bathochromic shift (approximately 100 nm); it is red in alkali (lambda max, 480 nm) and violet in acid (lambda max, 578 nm). These properties are similar to those of the trichochrome polymers that are formed during melanin biosynthesis from S-(3,4-dihydroxyphenylalanine)-L-cysteine. Because the intramolecular cyclization reactions remove the reactive quinone moiety from the molecules, they may be regarded as detoxication reactions. 1,4-Benzothiazine formation represents a novel

  5. Mechanistic study of hemicucurbit[6]uril formation by step-growth oligomerization and end-to-end cyclization

    NASA Astrophysics Data System (ADS)

    Yoo, In Kee; Kang, Young Kee

    2017-02-01

    The formation of hemicucurbit[6]uril (hCB[6]) from ethyleneurea with formaldehyde in acidic aqueous solution was explored using density functional methods and the implicit solvation model in water. The oligomerization and cyclization barriers were approximately half lower than that of the iminium formation. Thus, the initial iminium formation is the rate-determining step, and the formation of hCB[6] is kinetically and thermodynamically favored in acidic aqueous solution. In particular, the 'alternate' conformation of hCB[6] is enthalpically and entropically preferred over the 'cone' conformation, which is consistent with the crystal structure of hCB[6].

  6. Palladium-Catalyzed Ullmann Cross-Coupling/Tandem Reductive Cyclization Route to Key Members of the Uleine Alkaloid Family.

    PubMed

    Tang, Fei; Banwell, Martin G; Willis, Anthony C

    2016-04-01

    The trisubstituted cyclohexenone 12, generated through a palladium-catalyzed Ullmann cross-coupling reaction between o-iodonitrobenzene and a 4,5-trans-disubstituted 2-iodo-2-cyclohexen-1-one, engaged in a tandem reductive cyclization process upon exposure to hydrogen gas in the presence of Raney cobalt. As a result, the 1,5-methanoazocino[4,3-b]indole 13 was obtained and this could be readily elaborated to the racemic modifications of the alkaloids uleine, dasycarpidone, noruleine, and nordasycarpidone (1-4, respectively).

  7. Microwave-assisted cyclizations promoted by polyphosphoric acid esters: a general method for 1-aryl-2-iminoazacycloalkanes.

    PubMed

    Díaz, Jimena E; Mollo, María C; Orelli, Liliana R

    2016-01-01

    The first general procedure for the synthesis of 5 to 7-membered 1-aryl-2-iminoazacycloalkanes is presented, by microwave-assisted ring closure of ω-arylaminonitriles promoted by polyphosphoric acid (PPA) esters. 1-Aryl-2-iminopyrrolidines were easily prepared from the acyclic precursors employing a chloroformic solution of ethyl polyphosphate (PPE). The use of trimethylsilyl polyphosphate (PPSE) in solvent-free conditions allowed for the synthesis of 1-aryl-2-iminopiperidines and hitherto unreported 1-aryl-2-iminoazepanes. The cyclization reaction involves good to high yields and short reaction times, and represents a novel application of PPA esters in heterocyclic synthesis.

  8. Microwave-assisted cyclizations promoted by polyphosphoric acid esters: a general method for 1-aryl-2-iminoazacycloalkanes

    PubMed Central

    Díaz, Jimena E; Mollo, María C

    2016-01-01

    Summary The first general procedure for the synthesis of 5 to 7-membered 1-aryl-2-iminoazacycloalkanes is presented, by microwave-assisted ring closure of ω-arylaminonitriles promoted by polyphosphoric acid (PPA) esters. 1-Aryl-2-iminopyrrolidines were easily prepared from the acyclic precursors employing a chloroformic solution of ethyl polyphosphate (PPE). The use of trimethylsilyl polyphosphate (PPSE) in solvent-free conditions allowed for the synthesis of 1-aryl-2-iminopiperidines and hitherto unreported 1-aryl-2-iminoazepanes. The cyclization reaction involves good to high yields and short reaction times, and represents a novel application of PPA esters in heterocyclic synthesis. PMID:27829907

  9. Regioselective synthesis of 2H-indazoles using a mild, one-pot condensation-Cadogan reductive cyclization.

    PubMed

    Genung, Nathan E; Wei, Liuqing; Aspnes, Gary E

    2014-06-06

    An operationally simple and efficient one-pot synthesis of 2H-indazoles from commercially available reagents is reported. Ortho-imino-nitrobenzene substrates, generated via condensation, undergo reductive cyclization promoted by tri-n-butylphosophine to afford substituted 2H-indazoles under mild reaction conditions. A variety of electronically diverse ortho-nitrobenzaldehydes and anilines were examined. To further extend the scope of the transformation, aliphatic amines were also employed to form N2-alkyl indazoles selectively under the optimized reaction conditions.

  10. Rational design of a cytotoxic dinuclear Cu2 complex that binds by molecular recognition at two neighboring phosphates of the DNA backbone.

    PubMed

    Jany, Thomas; Moreth, Alexander; Gruschka, Claudia; Sischka, Andy; Spiering, Andre; Dieding, Mareike; Wang, Ying; Samo, Susan Haji; Stammler, Anja; Bögge, Hartmut; Fischer von Mollard, Gabriele; Anselmetti, Dario; Glaser, Thorsten

    2015-03-16

    The mechanism of the cytotoxic function of cisplatin and related anticancer drugs is based on their binding to the nucleobases of DNA. The development of new classes of anticancer drugs requires establishing other binding modes. Therefore, we performed a rational design for complexes that target two neighboring phosphates of the DNA backbone by molecular recognition resulting in a family of dinuclear complexes based on 2,7-disubstituted 1,8-naphthalenediol. This rigid backbone preorganizes the two metal ions for molecular recognition at the distance of two neighboring phosphates in DNA of 6-7 Å. Additionally, bulky chelating pendant arms in the 2,7-position impede nucleobase complexation by steric hindrance. We successfully synthesized the Cu(II)2 complex of the designed family of dinuclear complexes and studied its binding to dsDNA by independent ensemble and single-molecule methods like gel electrophoresis, precipitation, and titration experiments followed by UV-vis spectroscopy, atomic force microscopy (AFM), as well as optical tweezers (OT) and magnetic tweezers (MT) DNA stretching. The observed irreversible binding of our dinuclear Cu(II)2 complex to dsDNA leads to a blocking of DNA synthesis as studied by polymerase chain reactions and cytotoxicity for human cancer cells.

  11. A facile route to backbone-tethered N-heterocyclic carbene (NHC) ligands via NHC to aNHC rearrangement in NHC silicon halide adducts.

    PubMed

    Schneider, Heidi; Schmidt, David; Radius, Udo

    2015-02-09

    The reaction of 1,3-diisopropylimidazolin-2-ylidene (iPr2 Im) with diphenyldichlorosilane (Ph2 SiCl2 ) leads to the adduct (iPr2 Im)SiCl2 Ph2 1. Prolonged heating of isolated 1 at 66 °C in THF affords the backbone-tethered bis(imidazolium) salt [((a) HiPr2 Im)2 SiPh2 ](2+)  2 Cl(-) 2 ("(a) " denotes "abnormal" coordination of the NHC), which can be synthesized in high yields in one step starting from two equivalents of iPr2 Im and Ph2 SiCl2 . Imidazolium salt 2 can be deprotonated in THF at room temperature using sodium hydride as a base and catalytic amounts of sodium tert-butoxide to give the stable N-heterocyclic dicarbene ((a) iPr2 Im)2 SiPh2 3, in which two NHCs are backbone-tethered with a SiPh2 group. This easy-to-synthesize dicarbene 3 can be used as a novel ligand type in transition metal chemistry for the preparation of dinuclear NHC complexes, as exemplified by the synthesis of the homodinuclear copper(I) complex [{(a) (ClCuiPr2 Im)}2 SiPh2 ] 4.

  12. SABBAC: online Structural Alphabet-based protein BackBone reconstruction from Alpha-Carbon trace

    PubMed Central

    Maupetit, Julien; Gautier, R.; Tufféry, Pierre

    2006-01-01

    SABBAC is an on-line service devoted to protein backbone reconstruction from alpha-carbon trace. It is based on the assembly of fragments taken from a library of reduced size, selected from the encoding of the protein trace in a hidden Markov model-derived structural alphabet. The assembly of the fragments is achieved by a greedy algorithm, using an energy-based scoring. Alpha-carbon coordinates remain unaffected. SABBAC simply positions the missing backbone atoms, no further refinement is performed. From our tests, SABBAC performs equal or better than other similar on-line approach and is robust to deviations on the alpha-carbon coordinates. It can be accessed at . PMID:16844979

  13. Backbone and side chain chemical shift assignments of apolipophorin III from Galleria mellonella.

    PubMed

    Crowhurst, Karin A; Horn, James V C; Weers, Paul M M

    2016-04-01

    Apolipophorin III, a 163 residue monomeric protein from the greater wax moth Galleria mellonella (abbreviated as apoLp-IIIGM), has roles in upregulating expression of antimicrobial proteins as well as binding and deforming bacterial membranes. Due to its similarity to vertebrate apolipoproteins there is interest in performing atomic resolution analysis of apoLp-IIIGM as part of an effort to better understand its mechanism of action in innate immunity. In the first step towards structural characterization of apoLp-IIIGM, 99 % of backbone and 88 % of side chain (1)H, (13)C and (15)N chemical shifts were assigned. TALOS+ analysis of the backbone resonances has predicted that the protein is composed of five long helices, which is consistent with the reported structures of apolipophorins from other insect species. The next stage in the characterization of apoLp-III from G. mellonella will be to utilize these resonance assignments in solving the solution structure of this protein.

  14. How Sensitive Is the Amide I Vibration of the Polypeptide Backbone to Electric Field?

    PubMed Central

    Oh, Kwang-Im; Fiorin, Giacomo

    2015-01-01

    Site-selective isotopic labelling of amide carbonyls offers a non-perturbative means to introduce a localized infrared probe into proteins. While this strategy has been widely used to investigate various biological questions, the dependence of the underlying amide I vibrational frequency on electric field (or Stark tuning rate) has not been fully determined, which prevents it from being used in a quantitative manner in certain applications. Herein, through the use of experiments and molecular dynamics simulations, the Stark tuning rate of the amide I vibration of an isotopically labeled backbone carbonyl in a transmembrane α-helix is determined to be approximately 1.4 cm−1/(MV/cm). This result provides a quantitative basis for using this vibrational model to assess local electric fields in proteins, among other applications. For instance, using this value, we are able to show that the backbone region of a dipeptide has a surprisingly low dielectric constant. PMID:26419214

  15. Smart-Grid Backbone Network Real-Time Delay Reduction via Integer Programming.

    PubMed

    Pagadrai, Sasikanth; Yilmaz, Muhittin; Valluri, Pratyush

    2016-08-01

    This research investigates an optimal delay-based virtual topology design using integer linear programming (ILP), which is applied to the current backbone networks such as smart-grid real-time communication systems. A network traffic matrix is applied and the corresponding virtual topology problem is solved using the ILP formulations that include a network delay-dependent objective function and lightpath routing, wavelength assignment, wavelength continuity, flow routing, and traffic loss constraints. The proposed optimization approach provides an efficient deterministic integration of intelligent sensing and decision making, and network learning features for superior smart grid operations by adaptively responding the time-varying network traffic data as well as operational constraints to maintain optimal virtual topologies. A representative optical backbone network has been utilized to demonstrate the proposed optimization framework whose simulation results indicate that superior smart-grid network performance can be achieved using commercial networks and integer programming.

  16. Protein backbone and sidechain torsion angles predicted from NMR chemical shifts using artificial neural networks

    PubMed Central

    Shen, Yang; Bax, Ad

    2013-01-01

    A new program, TALOS-N, is introduced for predicting protein backbone torsion angles from NMR chemical shifts. The program relies far more extensively on the use of trained artificial neural networks than its predecessor, TALOS+. Validation on an independent set of proteins indicates that backbone torsion angles can be predicted for a larger, ≥ 90% fraction of the residues, with an error rate smaller than ca 3.5%, using an acceptance criterion that is nearly two-fold tighter than that used previously, and a root mean square difference between predicted and crystallographically observed (φ,ψ) torsion angles of ca 12°. TALOS-N also reports sidechain χ1 rotameric states for about 50% of the residues, and a consistency with reference structures of 89%. The program includes a neural network trained to identify secondary structure from residue sequence and chemical shifts. PMID:23728592

  17. Tuning efficiency of the 4-exo-trig cyclization by the electronic effect: ring closure of 3,3-difluoro-4-pentenyl carbon radicals and synthesis of a gem-difluorocyclobutane nucleoside.

    PubMed

    Kumamoto, Hiroki; Kawahigashi, Sachiko; Wakabayashi, Hiromi; Nakano, Tomohiko; Miyaike, Tomoko; Kitagawa, Yasuyuki; Abe, Hiroshi; Ito, Mika; Haraguchi, Kazuhiro; Balzarini, Jan; Baba, Masanori; Tanaka, Hiromichi

    2012-11-18

    4-exo-trig Cyclization reaction of a 4-pentenyl carbon radical containing the gem-difluoromethylene moiety adjacent to a radical accepting α,β-unsaturated ester was found to proceed efficiently to furnish a novel gem-difluorocyclobutane derivative. The cyclized product could be transformed into a gem-difluoromethylene analogue of oxetanocin T.

  18. Tritium containing polymers having a polymer backbone substantially void of tritium

    DOEpatents

    Jensen, George A.; Nelson, David A.; Molton, Peter M.

    1992-01-01

    A radioluminescent light source comprises a solid mixture of a phosphorescent substance and a tritiated polymer. The solid mixture forms a solid mass having length, width, and thickness dimensions, and is capable of self-support. In one aspect of the invention, the phosphorescent substance comprises solid phosphor particles supported or surrounded within a solid matrix by a tritium containing polymer. The tritium containing polymer comprises a polymer backbone which is essentially void of tritium.

  19. Tritium containing polymers having a polymer backbone substantially void of tritium

    DOEpatents

    Jensen, G.A.; Nelson, D.A.; Molton, P.M.

    1992-03-31

    A radioluminescent light source comprises a solid mixture of a phosphorescent substance and a tritiated polymer. The solid mixture forms a solid mass having length, width, and thickness dimensions, and is capable of self-support. In one aspect of the invention, the phosphorescent substance comprises solid phosphor particles supported or surrounded within a solid matrix by a tritium containing polymer. The tritium containing polymer comprises a polymer backbone which is essentially void of tritium. 2 figs.

  20. Small molecule-mediated duplex formation of nucleic acids with 'incompatible' backbones.

    PubMed

    Cafferty, Brian J; Musetti, Caterina; Kim, Keunsoo; Horowitz, Eric D; Krishnamurthy, Ramanarayanan; Hud, Nicholas V

    2016-04-07

    Proflavine, a known intercalator of DNA and RNA, promotes duplex formation by nucleic acids with natural and non-natural backbones that otherwise form duplexes with low thermal stability, and even some that show no sign of duplex formation in the absence of proflavine. These findings demonstrate the potential for intercalators to be used as cofactors for the assembly of rationally designed nucleic acid structures, and could provide fundamental insights regarding intercalation of natural nucleic acid duplexes.

  1. Improving the accuracy of protein stability predictions with multistate design using a variety of backbone ensembles.

    PubMed

    Davey, James A; Chica, Roberto A

    2014-05-01

    Multistate computational protein design (MSD) with backbone ensembles approximating conformational flexibility can predict higher quality sequences than single-state design with a single fixed backbone. However, it is currently unclear what characteristics of backbone ensembles are required for the accurate prediction of protein sequence stability. In this study, we aimed to improve the accuracy of protein stability predictions made with MSD by using a variety of backbone ensembles to recapitulate the experimentally measured stability of 85 Streptococcal protein G domain β1 sequences. Ensembles tested here include an NMR ensemble as well as those generated by molecular dynamics (MD) simulations, by Backrub motions, and by PertMin, a new method that we developed involving the perturbation of atomic coordinates followed by energy minimization. MSD with the PertMin ensembles resulted in the most accurate predictions by providing the highest number of stable sequences in the top 25, and by correctly binning sequences as stable or unstable with the highest success rate (≈90%) and the lowest number of false positives. The performance of PertMin ensembles is due to the fact that their members closely resemble the input crystal structure and have low potential energy. Conversely, the NMR ensemble as well as those generated by MD simulations at 500 or 1000 K reduced prediction accuracy due to their low structural similarity to the crystal structure. The ensembles tested herein thus represent on- or off-target models of the native protein fold and could be used in future studies to design for desired properties other than stability.

  2. Hash: a Program to Accurately Predict Protein Hα Shifts from Neighboring Backbone Shifts3

    PubMed Central

    Zeng, Jianyang; Zhou, Pei; Donald, Bruce Randall

    2012-01-01

    Chemical shifts provide not only peak identities for analyzing NMR data, but also an important source of conformational information for studying protein structures. Current structural studies requiring Hα chemical shifts suffer from the following limitations. (1) For large proteins, the Hα chemical shifts can be difficult to assign using conventional NMR triple-resonance experiments, mainly due to the fast transverse relaxation rate of Cα that restricts the signal sensitivity. (2) Previous chemical shift prediction approaches either require homologous models with high sequence similarity or rely heavily on accurate backbone and side-chain structural coordinates. When neither sequence homologues nor structural coordinates are available, we must resort to other information to predict Hα chemical shifts. Predicting accurate Hα chemical shifts using other obtainable information, such as the chemical shifts of nearby backbone atoms (i.e., adjacent atoms in the sequence), can remedy the above dilemmas, and hence advance NMR-based structural studies of proteins. By specifically exploiting the dependencies on chemical shifts of nearby backbone atoms, we propose a novel machine learning algorithm, called Hash, to predict Hα chemical shifts. Hash combines a new fragment-based chemical shift search approach with a non-parametric regression model, called the generalized additive model, to effectively solve the prediction problem. We demonstrate that the chemical shifts of nearby backbone atoms provide a reliable source of information for predicting accurate Hα chemical shifts. Our testing results on different possible combinations of input data indicate that Hash has a wide rage of potential NMR applications in structural and biological studies of proteins. PMID:23242797

  3. Effect of protein backbone folding on the stability of protein-ligand complexes.

    PubMed

    Estrada, Ernesto; Uriarte, Eugenio; Vilar, Santiago

    2006-01-01

    The role played by the degree of folding of protein backbones in explaining the binding energetics of protein-ligand interactions has been studied. We analyzed the protein/peptide interactions in the RNase-S system in which amino acids at two positions of the peptide S have been mutated. The global degree of folding of the protein S correlates in a significant way with the free energy and enthalpy of the protein-peptide interactions. A much better correlation is found with the local contribution to the degree of folding of one amino acid residue: Thr36. This residue is shown to have a destabilizing interaction with Lys41, which interacts directly with peptide S. Another system, consisting of the interactions of small organic molecules with HIV-1 protease was also studied. In this case, the global change in the degree of folding of the protease backbone does not explain the binding energetics of protein-ligand interactions. However, a significant correlation is observed between the free energy of binding and the contribution of two amino acid residues in the HVI-1 protease: Gly49 and Ile66. In general, it was observed that the changes in the degree of folding are not restricted to the binding site of the protein chain but are distributed along the whole protein backbone. This study provides a basis for further consideration of the degree of folding as a parameter for empirical structural parametrizations of the binding energetics of protein folding and binding.

  4. Self-assembly of diphenylalanine backbone homologues and their combination with functionalized carbon nanotubes.

    PubMed

    Dinesh, Bhimareddy; Squillaci, Marco A; Ménard-Moyon, Cécilia; Samorì, Paolo; Bianco, Alberto

    2015-10-14

    The integration of carbon nanotubes (CNTs) into organized nanostructures is of great interest for applications in materials science and biomedicine. In this work we studied the self-assembly of β and γ homologues of diphenylalanine peptides under different solvent and pH conditions. We aimed to investigate the role of peptide backbone in tuning the formation of different types of nanostructures alone or in combination with carbon nanotubes. In spite of having the same side chain, β and γ peptides formed distinctively different nanofibers, a clear indication of the role played by the backbone homologation on the self-assembly. The variation of the pH allowed to transform the nanofibers into spherical structures. Moreover, the co-assembly of β and γ peptides with carbon nanotubes covalently functionalized with the same peptide generated unique dendritic assemblies. This comparative study on self-assembly using diphenylalanine backbone homologues and of the co-assembly with CNT covalent conjugates is the first example exploring the capacity of β and γ peptides to adopt precise nanostructures, particularly in combination with carbon nanotubes. The dendritic organization obtained by mixing carbon nanotubes and peptides might find interesting applications in tissue engineering and neuronal interfacing.

  5. Androgen deprivation therapy as backbone therapy in the management of prostate cancer

    PubMed Central

    Merseburger, Axel S; Alcaraz, Antonio; von Klot, Christoph A

    2016-01-01

    Androgen deprivation therapy (ADT) is well established as a backbone therapy for metastatic prostate cancer (mPCa), and both European and American guidelines emphasize the importance of maintaining ADT after progression to metastatic castration-resistant prostate cancer (CRPC). However, the use of ADT varies widely in clinical practice despite these recommendations. Both research and development of increasingly precise assay technologies have improved our understanding of androgen production and signaling, and the recent data have suggested that a new serum testosterone cutoff value of <0.7 nmol/L should be employed. Most clinical trials to date have used the historical 1.7 nmol/L cutoff, but the <0.7 nmol/L cutoff has been associated with improved patient outcomes. Combining agents with different mechanisms of action to achieve intense androgen blockade may improve survival both before and after progression to CRPC. Data suggest that this intensive approach to androgen deprivation could delay the transition to CPRC and hence improve survival dramatically. Various combinations of backbone ADT with chemotherapy or radiotherapy are under investigation. Administration of ADT is established in patients with intermediate or high-risk localized prostate cancer (PCa) receiving radiotherapy with curative intent. This article reviews the current and potential role of ADT as backbone therapy in both hormone-sensitive PCa and CRPC with a focus on mPCa. PMID:27942220

  6. East vergent structure of Backbone Range: Insights from A-Lan-Yi area and sandbox modeling

    NASA Astrophysics Data System (ADS)

    Lee, C. A.; Lu, C. Y.

    2015-12-01

    Southern Taiwan, including Pingtung peninsula and Taitung, is the incipient oblique collision zone of Eurasian plate and Philippine Sea plate. The Luzon volcanic arc converged toward Taiwan Island and formed Hengchun Ridge south offshore Taiwan. Thus, Taiwan mountain belt developed from north to south as the Backbone Range, so that we can infer the incipient feature structure from the topography and outcrop study of southern Taiwan. Our field survey of this study concentrated at the southeast coastline of Taiwan, also known as A-Lan-Yi Trail. According to previous study, the deformational structures such as faults and folds are consistent with regional kinematic processes, and the preserved transpression structure is the most important evidence of incipient collision. In this study, we use the sedimentary sequences of study area to trace the regional tectonics from north to south. Discovered structures in this area show the similar kinematic history as the eastern flank of Backbone Range, so that we suggest they are at the same series of a tectonic event. To complete the regional structure mapping in this accessible area, besides the field geological data, we also applied the LiDAR-derived DTM which is a 3D visualization technology to improve our topography information. In addition, we use the sandbox modeling to demonstrate the development of structures in the eastern flank of Backbone Range. After combining the results of field observation and regional structure mapping, this study provides a strong evidence of backthrusting and backfolding deformation during the incipient oblique collision stage.

  7. No-Enclave Percolation Corresponds to Holes in the Cluster Backbone.

    PubMed

    Hu, Hao; Ziff, Robert M; Deng, Youjin

    2016-10-28

    The no-enclave percolation (NEP) model introduced recently by Sheinman et al. can be mapped to a problem of holes within a standard percolation backbone, and numerical measurements of such holes give the same size-distribution exponent τ=1.82(1) as found for the NEP model. An argument is given that τ=1+d_{B}/2≈1.822 for backbone holes, where d_{B} is the backbone dimension. On the other hand, a model of simple holes within a percolation cluster yields τ=1+d_{f}/2=187/96≈1.948, where d_{f} is the fractal dimension of the cluster, and this value is consistent with the experimental results of gel collapse of Sheinman et al., which give τ=1.91(6). This suggests that the gel clusters are of the universality class of percolation cluster holes. Both models give a discontinuous maximum hole size at p_{c}, signifying explosive percolation behavior.

  8. On the mechanism of RNA phosphodiester backbone cleavage in the absence of solvent

    PubMed Central

    Riml, Christian; Glasner, Heidelinde; Rodgers, M. T.; Micura, Ronald; Breuker, Kathrin

    2015-01-01

    Ribonucleic acid (RNA) modifications play an important role in the regulation of gene expression and the development of RNA-based therapeutics, but their identification, localization and relative quantitation by conventional biochemical methods can be quite challenging. As a promising alternative, mass spectrometry (MS) based approaches that involve RNA dissociation in ‘top-down’ strategies are currently being developed. For this purpose, it is essential to understand the dissociation mechanisms of unmodified and posttranscriptionally or synthetically modified RNA. Here, we have studied the effect of select nucleobase, ribose and backbone modifications on phosphodiester bond cleavage in collisionally activated dissociation (CAD) of positively and negatively charged RNA. We found that CAD of RNA is a stepwise reaction that is facilitated by, but does not require, the presence of positive charge. Preferred backbone cleavage next to adenosine and guanosine in CAD of (M+nH)n+ and (M−nH)n− ions, respectively, is based on hydrogen bonding between nucleobase and phosphodiester moieties. Moreover, CAD of RNA involves an intermediate that is sufficiently stable to survive extension of the RNA structure and intramolecular proton redistribution according to simple Coulombic repulsion prior to backbone cleavage into c and y ions from phosphodiester bond cleavage. PMID:25904631

  9. Catalyst-Free Three-Component Tandem CDC Cyclization: Convenient Access to Isoindolinones from Aromatic Acid, Amides, and DMSO by a Pummerer-Type Rearrangement.

    PubMed

    Wang, Peng-Min; Pu, Fan; Liu, Ke-Yan; Li, Chao-Jun; Liu, Zhong-Wen; Shi, Xian-Ying; Fan, Juan; Yang, Ming-Yu; Wei, Jun-Fa

    2016-04-25

    A catalyst-free multicomponent CDC reaction is rarely reported, especially for the intermolecular tandem CDC cyclization, which represents an important strategy for constructing cyclic compounds. Herein, a three-component tandem CDC cyclization by a Pummerer-type rearrangement to afford biologically relevant isoindolinones from aromatic acids, amides, and DMSO, is described. This intermolecular tandem reaction undergoes a C(sp(2) )-H/C(sp(3) )-H cross-dehydrogenative coupling, C-N bond formation, and intramolecular amidation. A notable feature of this novel protocol is avoiding a catalyst and additive (apart from oxidant).

  10. Doped Si nanoparticles with conformal carbon coating and cyclized-polyacrylonitrile network as high-capacity and high-rate lithium-ion battery anodes.

    PubMed

    Xie, Ming; Piper, Daniela Molina; Tian, Miao; Clancey, Joel; George, Steven M; Lee, Se-Hee; Zhou, Yun

    2015-09-11

    Doped Si nanoparticles (SiNPs) with conformal carbon coating and cyclized-polyacrylonitrile (PAN) network displayed capacities of 3500 and 3000 mAh g(-1) at C/20 and C/10, respectively. At 1 C, the electrode preserves a specific discharge capacity of ∼1500 mAh g(-1) for at least 60 cycles without decay. Al2O3 atomic layer deposition (ALD) helps improve the initial Coulombic efficiency (CE) to 85%. The dual coating of conformal carbon and cyclized-PAN help alleviate volume change and facilitate charge transfer. Ultra-thin Al2O3 ALD layers help form a stable solid electrolyte interphase interface.

  11. Doped Si nanoparticles with conformal carbon coating and cyclized-polyacrylonitrile network as high-capacity and high-rate lithium-ion battery anodes

    NASA Astrophysics Data System (ADS)

    Xie, Ming; Molina Piper, Daniela; Tian, Miao; Clancey, Joel; George, Steven M.; Lee, Se-Hee; Zhou, Yun

    2015-09-01

    Doped Si nanoparticles (SiNPs) with conformal carbon coating and cyclized-polyacrylonitrile (PAN) network displayed capacities of 3500 and 3000 mAh g-1 at C/20 and C/10, respectively. At 1 C, the electrode preserves a specific discharge capacity of ˜1500 mAh g-1 for at least 60 cycles without decay. Al2O3 atomic layer deposition (ALD) helps improve the initial Coulombic efficiency (CE) to 85%. The dual coating of conformal carbon and cyclized-PAN help alleviate volume change and facilitate charge transfer. Ultra-thin Al2O3 ALD layers help form a stable solid electrolyte interphase interface.

  12. Stereoselective Synthesis of Spiro Bis-C,C-α-arylglycosides by Tandem Heck Type C-Glycosylation and Friedel-Crafts Cyclization.

    PubMed

    Chen, Yen-Bo; Liu, Shi-Hao; Hsieh, Min-Tsang; Chang, Chih-Shiang; Lin, Chun-Hung; Chen, Chen-Yin; Chen, Po-Yen; Lin, Hui-Chang

    2016-04-01

    Spiro bis-C,C-α-arylglycosides were synthesized in three steps in 78-85% overall yields starting from exo-glycals. The initial Heck type C-aryl addition of exo-glycals with arylboronic acids afforded α-aryl-β-substituted C-glycosides with exclusive α-stereoselectivity. Among the products, β-ethanal α-aryl C-glycosides further reacted with alkylthiol in the presence of InCl3, followed by in situ Friedel-Crafts cyclization to yield the desirable final products. We proposed a mechanism to explain how the α-aryl group serves as a main determinant of the cyclization.

  13. Evidence for a Morin Type Intramolecular Cyclization of an Alkene with a Phenylsulfenic Acid Group in Neutral Aqueous Solution

    PubMed Central

    Keerthi, Kripa; Sivaramakrishnan, Santhosh; Gates, Kent S.

    2009-01-01

    Sulfenic acids (RSOH) are among the most common sulfur-centered reactive intermediates generated in biological systems. Given the biological occurrence of sulfenic acids, it is important to explore the reactivity of these intermediates under physiological conditions. The Morin rearrangement is a synthetic process developed for the conversion of penicillin derivatives into cephalosporins that proceeds via nucleophilic attack of an alkene on a sulfenic acid intermediate. In its classic form, the Morin reaction involves initial elimination of a sulfenic acid from a cyclic sulfoxide, followed by intramolecular cyclization of the resulting alkene and sulfenic acid groups to generate an episulfonium ion intermediate that undergoes further reaction to yield ring-expanded products. On the basis of the existing literature, it is difficult to assess whether the reaction between an alkene and a sulfenic group can occur under mild conditions because the conditions required to generate the sulfenic acid from the sulfoxide precursor in the Morin reaction typically involve high temperatures and strong acid. In the work described here, β-sulfinylketone precursors were used to generate a “Morin type” sulfenic acid intermediate under mild conditions. This approach made it possible to demonstrate that the intramolecular cyclization of an alkene with a phenylsulfenic acid to generate an episulfonium ion intermediate can occur in neutral aqueous solution at room temperature. PMID:18500784

  14. In Vivo Efficacy of Anuran Trypsin Inhibitory Peptides against Staphylococcal Skin Infection and the Impact of Peptide Cyclization

    PubMed Central

    Malik, U.; Silva, O. N.; Fensterseifer, I. C. M.; Chan, L. Y.; Clark, R. J.; Franco, O. L.; Daly, N. L.

    2015-01-01

    Staphylococcus aureus is a virulent pathogen that is responsible for a wide range of superficial and invasive infections. Its resistance to existing antimicrobial drugs is a global problem, and the development of novel antimicrobial agents is crucial. Antimicrobial peptides from natural resources offer potential as new treatments against staphylococcal infections. In the current study, we have examined the antimicrobial properties of peptides isolated from anuran skin secretions and cyclized synthetic analogues of these peptides. The structures of the peptides were elucidated by nuclear magnetic resonance (NMR) spectroscopy, revealing high structural and sequence similarity with each other and with sunflower trypsin inhibitor 1 (SFTI-1). SFTI-1 is an ultrastable cyclic peptide isolated from sunflower seeds that has subnanomolar trypsin inhibitory activity, and this scaffold offers pharmaceutically relevant characteristics. The five anuran peptides were nonhemolytic and noncytotoxic and had trypsin inhibitory activities similar to that of SFTI-1. They demonstrated weak in vitro inhibitory activities against S. aureus, but several had strong antibacterial activities against S. aureus in an in vivo murine wound infection model. pYR, an immunomodulatory peptide from Rana sevosa, was the most potent, with complete bacterial clearance at 3 mg · kg−1. Cyclization of the peptides improved their stability but was associated with a concomitant decrease in antimicrobial activity. In summary, these anuran peptides are promising as novel therapeutic agents for treating infections from a clinically resistant pathogen. PMID:25624332

  15. Synthesis of 2-phenyl-4,5-substituted oxazoles by copper-catalyzed intramolecular cyclization of functionalized enamides.

    PubMed

    Vijay Kumar, S; Saraiah, B; Misra, N C; Ila, H

    2012-12-07

    An efficient two-step synthesis of 2-phenyl-4,5-substituted oxazoles involving intramolecular copper-catalyzed cyclization of highly functionalized novel β-(methylthio)enamides as the key step has been reported. These enamides are obtained by nucleophilic ring-opening of newly synthesized 4-[(methylthio)hetero(aryl)methylene]-2-phenyl-5-oxazolone precursors by alkoxides, amines, amino acid esters and aryl/alkyl Grignard reagents, thus leading to the introduction of an ester, N-substituted carboxamide or acyl functionalities at 4-position of the product oxazoles. Synthesis of two naturally occurring 2,5-diaryloxazoles, i.e., texamine and uguenenazole, via two-step hydrolysis-decarboxylation of the corresponding 2,5-diaryloxazole-4-carboxylates has also been described. Similarly, three of the serine-derived oxazole-4-carboxamides were elaborated to novel trisubstituted 4,2'-bisoxazoles through DAST/DBU-mediated cyclodehydration-dehydrohalogenation sequence. The present protocol is complementary and an improvement to our previously reported silver carbonate-induced cyclization of β-bis(methylthio)enamides to 2-phenyl-5-(methylthio)-4-substituted oxazoles.

  16. A Highly Effective Ruthenium System for the Catalyzed Dehydrogenative Cyclization of Amine-Boranes to Cyclic Boranes under Mild Conditions.

    PubMed

    Wallis, Christopher J; Alcaraz, Gilles; Petit, Alban S; Poblador-Bahamonde, Amalia I; Clot, Eric; Bijani, Christian; Vendier, Laure; Sabo-Etienne, Sylviane

    2015-09-07

    We recently disclosed a new ruthenium-catalyzed dehydrogenative cyclization process (CDC) of diamine-monoboranes leading to cyclic diaminoboranes. In the present study, the CDC reaction has been successfully extended to a larger number of diamine-monoboranes (4-7) and to one amine-borane alcohol precursor (8). The corresponding NB(H)N- and NB(H)O-containing cyclic diaminoboranes (12-15) and oxazaborolidine (16) were obtained in good to high yields. Multiple substitution patterns on the starting amine-borane substrates were evaluated and the reaction was also performed with chiral substrates. Efforts have been spent to understand the mechanism of the ruthenium CDC process. In addition to a computational approach, a strategy enabling the kinetic discrimination on successive events of the catalytic process leading to the formation of the NB(H)N linkage was performed on the six-carbon chain diamine-monoborane 21 and completed with a (15) N NMR study. The long-life bis-σ-borane ruthenium intermediate 23 possessing a reactive NHMe ending was characterized in situ and proved to catalyze the dehydrogenative cyclization of 1, ascertaining that bis σ-borane ruthenium complexes are key intermediates in the CDC process.

  17. Cell-free cyclization of delta-(L-alpha-aminoadipyl)-L-cysteinyl-D-valine to isopenicillin N.

    PubMed Central

    Sawada, Y; Baldwin, J E; Singh, P D; Solomon, N A; Demain, A L

    1980-01-01

    Cell-free cyclization of delta-(L-alpha-aminoadipyl)-L-cysteinyl-D-valine to isopenicillin N by lytic enzyme extracts of Cephalosporium acremonium M-0198 was stimulated by ferrous ions. The optimum concentration of FeSO4 was 80 microM. No additional stimulation was observed with ascorbate, adenosine 5'-triphosphate, or alpha-ketoglutarate, but Triton X-100 and sonication of the extracts increased activity. ZnSO4 was very inhibitory to enzyme activity; CuSO4 was somewhat less inhibitory, and the least effective of the three was MnCl2. The dimer of the tripeptide was converted to a penicillin that has the biological spectrum of isopenicillin N, and this reaction was also stimulated by FeSO4. We found that sonication can be used directly to prepare extracts with cyclization activity from mycelia, without preparing protoplast lysates. The kinetics of cyclase appearance and disappearance during fermentation were similar to those of ring-expansion activity, i.e., enzyme appeared and peaked 13 h after growth ceased and then disappeared. PMID:7191691

  18. Evolution of cyclizing 5-aminolevulinate synthases in the biosynthesis of actinomycete secondary metabolites: outcomes for genetic screening techniques.

    PubMed

    Petříčková, Kateřina; Chroňáková, Alica; Zelenka, Tomáš; Chrudimský, Tomáš; Pospíšil, Stanislav; Petříček, Miroslav; Krištůfek, Václav

    2015-01-01

    A combined approach, comprising PCR screening and genome mining, was used to unravel the diversity and phylogeny of genes encoding 5-aminolevulinic acid synthases (ALASs, hemA gene products) in streptomycetes-related strains. In actinomycetes, these genes were believed to be directly connected with the production of secondary metabolites carrying the C5N unit, 2-amino-3-hydroxycyclopent-2-enone, with biological activities making them attractive for future use in medicine and agriculture. Unlike "classical" primary metabolism ALAS, the C5N unit-forming cyclizing ALAS (cALAS) catalyses intramolecular cyclization of nascent 5-aminolevulinate. Specific amino acid sequence changes can be traced by comparison of "classical" ALASs against cALASs. PCR screening revealed 226 hemA gene-carrying strains from 1,500 tested, with 87% putatively encoding cALAS. Phylogenetic analysis of the hemA homologs revealed strain clustering according to putative type of metabolic product, which could be used to select producers of specific C5N compound classes. Supporting information was acquired through analysis of actinomycete genomic sequence data available in GenBank and further genetic or metabolic characterization of selected strains. Comparison of 16S rRNA taxonomic identification and BOX-PCR profiles provided evidence for numerous horizontal gene transfers of biosynthetic genes or gene clusters within actinomycete populations and even from non-actinomycete organisms. Our results underline the importance of environmental and evolutionary data in the design of efficient techniques for identification of novel producers.

  19. Sulfation and cation effects on the conformational properties of the glycan backbone of chondroitin sulfate disaccharides.

    PubMed

    Faller, Christina E; Guvench, Olgun

    2015-05-21

    Chondroitin sulfate (CS) is one of several glycosaminoglycans that are major components of proteoglycans. A linear polymer consisting of repeats of the disaccharide -4GlcAβ1-3GalNAcβ1-, CS undergoes differential sulfation resulting in five unique sulfation patterns. Because of the dimer repeat, the CS glycosidic "backbone" has two distinct sets of conformational degrees of freedom defined by pairs of dihedral angles: (ϕ1, ψ1) about the β1-3 glycosidic linkage and (ϕ2, ψ2) about the β1-4 glycosidic linkage. Differential sulfation and the possibility of cation binding, combined with the conformational flexibility and biological diversity of CS, complicate experimental efforts to understand CS three-dimensional structures at atomic resolution. Therefore, all-atom explicit-solvent molecular dynamics simulations with Adaptive Biasing Force sampling of the CS backbone were applied to obtain high-resolution, high-precision free energies of CS disaccharides as a function of all possible backbone geometries. All 10 disaccharides (β1-3 vs β1-4 linkage × five different sulfation patterns) were studied; additionally, ion effects were investigated by considering each disaccharide in the presence of either neutralizing sodium or calcium cations. GlcAβ1-3GalNAc disaccharides have a single, broad, thermodynamically important free-energy minimum, whereas GalNAcβ1-4GlcA disaccharides have two such minima. Calcium cations but not sodium cations bind to the disaccharides, and binding is primarily to the GlcA -COO(-) moiety as opposed to sulfate groups. This binding alters the glycan backbone thermodynamics in instances where a calcium cation bound to -COO(-) can act to bridge and stabilize an interaction with an adjacent sulfate group, whereas, in the absence of this cation, the proximity of a sulfate group to -COO(-) results in two like charges being both desolvated and placed adjacent to each other and is found to be destabilizing. In addition to providing information

  20. Triazole linkages and backbone branches in nucleic acids for biological and extra-biological applications

    NASA Astrophysics Data System (ADS)

    Paredes, Eduardo

    The recently increasing evidence of nucleic acids' alternative roles in biology and potential as useful nanomaterials and therapeutic agents has enabled the development of useful probes, elaborate nanostructures and therapeutic effectors based on nucleic acids. The study of alternative nucleic acid structure and function, particularly RNA, hinges on the ability to introduce site-specific modifications that either provide clues to the nucleic acid structure function relationship or alter the nucleic acid's function. Although the available chemistries allow for the conjugation of useful labels and molecules, their limitations lie in their tedious conjugation conditions or the lability of the installed probes. The development and optimization of click chemistry with RNA now provides the access to a robust and orthogonal conjugation methodology while providing stable conjugates. Our ability to introduce click reactive groups enzymatically, rather than only in the solid-phase, allows for the modification of larger, more cell relevant RNAs. Additionally, ligation of modified RNAs with larger RNA constructs through click chemistry represents an improvement over traditional ligation techniques. We determined that the triazole linkage generated through click chemistry is compatible in diverse nucleic acid based biological systems. Click chemistry has also been developed for extra-biological applications, particularly with DNA. We have expanded its use to generate useful polymer-DNA conjugates which can form controllable soft nanoparticles which take advantage of DNA's properties, i.e. DNA hybridization and computing. Additionally, we have generated protein-DNA conjugates and assembled protein-polymer hybrids mediated by DNA hybridization. The use of click chemistry in these reactions allows for the facile synthesis of these unnatural conjugates. We have also developed backbone branched DNA through click chemistry and showed that these branched DNAs are useful in generating

  1. Inorganic backbone ionomers: Design and dielectric response of single-ion conducting polymers

    NASA Astrophysics Data System (ADS)

    Bartels, Joshua

    Ion-conducting polymers were studied primarily through the use of dielectric spectroscopy. The conclusions drawn from ion conduction models of the dielectric data are corroborated by additional independent experiments, including x-ray scattering, calorimetry, prism coupling, and DFT calculations. The broad concern of this dissertation is to understand and clarify a path forward in ion conducting polymer research. This is achieved by considering low-Tg ionomers and the advantages imparted by siloxane and phosphazene backbones. The most successful dielectric spectroscopy model for the materials studied is the electrode polarization model (EP), whereas other models, such as the Dyre random barrier model, fail to describe the experimental results. Seven nonionic ether oxygen (EO) containing polymers were studied in order to observe the effect that backbone chemistry has on dipole motion. Conventional carboncarbon backbone EO-containing polymers show no distinct advantage over similar EO-pendant polysiloxane or polyphosphazene systems. The mobility and effective backbone Tg imparted by the inorganic backbones are comparable. A short EO pendant results in a lower static dielectric constant due to restricted motion of dipoles close to the chain. The flexibility and chemical versatility of inorganic backbone polymers motivates further study of two ionomer systems. A polypohosphazene iodide conducting system was characterized by dielectric spectroscopy and x-ray scattering. Two end "tail" functionalization of the ammonium ion were used, a tail with two EOs and an alkyl tail of six carbons. This functional group plays an important role in ion dynamics and can wrap around the ion and self-solvate when EOs are present. The iodide-ammonium ionomers are observed to have unusually large high-frequency dielectric constants due to atomic polarization of ions. The strength of the atomic polarization scales with ion content. The aggregation state of ions is able to be determined from

  2. Direct generation of oxygen-stabilized radicals by H• transfer from transition metal hydrides.

    PubMed

    Kuo, Jonathan L; Hartung, John; Han, Arthur; Norton, Jack R

    2015-01-28

    Transition-metal hydrides generate α-alkoxy radicals by H• transfer to enol ethers. We have measured the rate constant for transfer from CpCr(CO)3H to n-butyl vinyl ether and have examined the chemistry of radicals generated by such transfers. Radicals from appropriate substrates undergo 5-exo cyclization, with higher diastereoselectivity than the analogous all-carbon radicals. From such radicals it is straightforward to make substituted tetrahydrofurans.

  3. Backbone dependency further improves side chain prediction efficiency in the Energy-based Conformer Library (bEBL).

    PubMed

    Subramaniam, Sabareesh; Senes, Alessandro

    2014-11-01

    Side chain optimization is an integral component of many protein modeling applications. In these applications, the conformational freedom of the side chains is often explored using libraries of discrete, frequently occurring conformations. Because side chain optimization can pose a computationally intensive combinatorial problem, the nature of these conformer libraries is important for ensuring efficiency and accuracy in side chain prediction. We have previously developed an innovative method to create a conformer library with enhanced performance. The Energy-based Library (EBL) was obtained by analyzing the energetic interactions between conformers and a large number of natural protein environments from crystal structures. This process guided the selection of conformers with the highest propensity to fit into spaces that should accommodate a side chain. Because the method requires a large crystallographic data-set, the EBL was created in a backbone-independent fashion. However, it is well established that side chain conformation is strongly dependent on the local backbone geometry, and that backbone-dependent libraries are more efficient in side chain optimization. Here we present the backbone-dependent EBL (bEBL), whose conformers are independently sorted for each populated region of Ramachandran space. The resulting library closely mirrors the local backbone-dependent distribution of side chain conformation. Compared to the EBL, we demonstrate that the bEBL uses fewer conformers to produce similar side chain prediction outcomes, thus further improving performance with respect to the already efficient backbone-independent version of the library.

  4. Rh(III)- and Zn(II)-Catalyzed Synthesis of Quinazoline N-Oxides via C-H Amidation-Cyclization of Oximes.

    PubMed

    Wang, Qiang; Wang, Fen; Yang, Xifa; Zhou, Xukai; Li, Xingwei

    2016-12-02

    Quinazoline N-oxides have been prepared from simple ketoximes and 1,4,2-dioxazol-5-ones via Rh(III)-catalyzed C-H activation-amidation of the ketoximes and subsequent Zn(II)-catalyzed cyclization. The substrate scope and functional group compatibility were examined. The reaction features relay catalysis by Rh(III) and Zn(II).

  5. PtCl2-catalyzed tandem enyne cyclization/1,2 ester migration reaction controlled by substituent effects of all-carbon 1,6-enynyl esters.

    PubMed

    Huo, Xing; Zhao, Changgui; Zhao, Gaoyuan; Tang, Shouchu; Li, Huilin; Xie, Xingang; She, Xuegong

    2013-05-01

    On the move: A novel PtCl2-catalyzed tandem 1,6-enyne cyclization/1,2-acyloxy migration reaction was developed, which was shown to be controlled by substitution effects. Using this method, a series of substituted enol esters containing the cyclopentenyl motif were prepared in moderate to high yields.

  6. 1,4-Hydroiodination of dienyl alcohols with TMSI to form homoallylic alcohols containing a multisubstituted Z-alkene and application to Prins cyclization.

    PubMed

    Xu, Yongjin; Yin, Zhiping; Lin, Xinglong; Gan, Zubao; He, Yanyang; Gao, Lu; Song, Zhenlei

    2015-04-17

    A regioselective 1,4-hydroiodination of dienyl alcohols has been developed using trimethylsilyl iodide as Lewis acid and iodide source. A range of homoallylic alcohols containing a multisubstituted Z-alkene was synthesized with good to excellent configurational control. The approach was applied in sequential hydroiodination/Prins cyclization to afford multisubstituted tetrahydropyrans diastereoselectively.

  7. A Torquoselective Extrusion of Isoxazoline N-Oxides. Application to the Synthesis of Aryl Vinyl and Divinyl Ketones for Nazarov Cyclization

    PubMed Central

    Canterbury, Daniel P.; Herrick, Ildiko R.; Um, Joann; Houk, K. N.; Frontier, Alison J.

    2009-01-01

    A mild, convenient reaction sequence for the synthesis of Nazarov cyclization substrates is described. The [3+2] dipolar cycloaddition of a nitrone and an electron-deficient alkyne gives an isolable isoxazoline intermediate, which upon oxidation undergoes stereoselective extrusion of nitrosomethane to give aryl vinyl or divinyl ketones. PMID:20161228

  8. Iron-catalyzed, microwave-promoted, one-pot synthesis of 9-substituted xanthenes by a cascade benzylation-cyclization process.

    PubMed

    Xu, Xiaobing; Xu, Xiaolei; Li, Hongfeng; Xie, Xin; Li, Yanzhong

    2010-01-01

    An efficient iron-catalyzed, microwave-promoted cascade benzylation-cyclization of phenols is reported. Benzyl acetates, benzyl bromides, and benzyl carbonates are suitable benzylating reagents. The reactions proceed to afford both 9-aryl and 9-alkyl xanthene derivatives in good to high yields using FeCl(3) as the catalyst under MW irradiation conditions.

  9. Regioselective synthesis of 2-amino-substituted 1,3,4-oxadiazole and 1,3,4-thiadiazole derivatives via reagent-based cyclization of thiosemicarbazide intermediate.

    PubMed

    Yang, Seung-Ju; Lee, Seok-Hyeong; Kwak, Hyun-Jung; Gong, Young-Dae

    2013-01-18

    A regioselective, reagent-based method for the cyclization reaction of 2-amino-1,3,4-oxadiazole and 2-amino-1,3,4-thiadiazole core skeletons is described. The thiosemicarbazide intermediate 3 was reacted with EDC·HCl in DMSO or p-TsCl, triethylamine in N-methyl-2-pyrrolidone to give the corresponding 2-amino-1,3,4-oxadiazoles 4 and 2-amino-1,3,4-thiadiazoles 5 through regioselcective cyclization processes. The regioselectivity was affected by both R(1) and R(2) in p-TsCl mediated cyclization. It is shown in select sets of thiosemicarbazide 3 with R(1)(benzyl) and R(2)(phenyl). 2-Amino-1,3,4-oxadiazole 4 was also shown in the reaction of p-TsCl mediated cyclization. The resulting 2-amino-1,3,4-oxadiazole and 2-amino-1,3,4-thiadiazole core skeleton are functionalized with various electrophiles such as alkyl halide, acid halides, and sulfornyl chloride in high yields.

  10. Palladium-catalyzed oxidative cyclization of aniline-tethered alkylidenecyclopropanes with O2: a facile protocol to selectively synthesize 2- and 3-vinylindoles.

    PubMed

    Cao, Bo; Simaan, Marwan; Marek, Ilan; Wei, Yin; Shi, Min

    2016-12-20

    A novel palladium-catalyzed oxidative cyclization of aniline-tethered alkylidenecyclopropanes using molecular oxygen as the terminal oxidant through β-carbon elimination of aminopalladation intermediates is disclosed. The reaction opens up an effective way to obtain a series of 2- and 3-vinylindoles which are important synthetic intermediates in many natural indole derivatives.

  11. Asymmetric synthesis of tetrahydroquinolin-3-ols via CoCl2-catalyzed reductive cyclization of nitro cyclic sulfites with NaBH4.

    PubMed

    Jagdale, Arun R; Reddy, R Santhosh; Sudalai, Arumugam

    2009-02-19

    A new method for the construction of chiral 3-substituted tetrahydroquinoline derivatives based on asymmetric dihydroxylation and CoCl(2)-catalyzed reductive cyclization of nitro cyclic sulfites with NaBH(4) has been described with high optical purities. This method has been successfully applied in the formal synthesis of PNU 95666E and anachelin H chromophore.

  12. Effect of Liquid-Crystalline Epoxy Backbone Structure on Thermal Conductivity of Epoxy-Alumina Composites

    NASA Astrophysics Data System (ADS)

    Giang, Thanhkieu; Kim, Jinhwan

    2017-01-01

    In a series of papers published recently, we clearly demonstrated that the most important factor governing the thermal conductivity of epoxy-Al2O3 composites is the backbone structure of the epoxy. In this study, three more epoxies based on diglycidyl ester-terminated liquid-crystalline epoxy (LCE) have been synthesized to draw conclusions regarding the effect of the epoxy backbone structure on the thermal conductivity of epoxy-alumina composites. The synthesized structures were characterized by proton nuclear magnetic resonance (1H-NMR) and Fourier-transform infrared (FT-IR) spectroscopy. Differential scanning calorimetry, thermogravimetric analysis, and optical microscopy were also employed to examine the thermal and optical properties of the synthesized LCEs and the cured composites. All three LCE resins exhibited typical liquid-crystalline behaviors: clear solid crystalline state below the melting temperature ( T m), sharp crystalline melting at T m, and transition to nematic phase above T m with consequent isotropic phase above the isotropic temperature ( T i). The LCE resins displayed distinct nematic liquid-crystalline phase over a wide temperature range and retained liquid-crystalline phase after curing, with high thermal conductivity of the resulting composite. The thermal conductivity values ranged from 3.09 W/m-K to 3.89 W/m-K for LCE-Al2O3 composites with 50 vol.% filler loading. The steric effect played a governing role in the difference. The neat epoxy resin thermal conductivity was obtained as 0.35 W/m-K to 0.49 W/m-K based on analysis using the Agari-Uno model. The results clearly support the objective of this study in that the thermal conductivity of the LCE-containing networks strongly depended on the epoxy backbone structure and the degree of ordering in the cured network.

  13. On the role of thermal backbone fluctuations in myoglobin ligand gate dynamics

    NASA Astrophysics Data System (ADS)

    Krokhotin, Andrey; Niemi, Antti J.; Peng, Xubiao

    2013-05-01

    We construct an energy function that describes the crystallographic structure of sperm whale myoglobin backbone. As a model in our construction, we use the Protein Data Bank entry 1ABS that has been measured at liquid helium temperature. Consequently, the thermal B-factor fluctuations are very small, which is an advantage in our construction. The energy function that we utilize resembles that of the discrete nonlinear Schrödinger equation. Likewise, ours supports topological solitons as local minimum energy configurations. We describe the 1ABS backbone in terms of topological solitons with a precision that deviates from 1ABS by an average root-mean-square distance, which is less than the experimentally observed Debye-Waller B-factor fluctuation distance. We then subject the topological multi-soliton solution to extensive numerical heating and cooling experiments, over a very wide range of temperatures. We concentrate in particular to temperatures above 300 K and below the Θ-point unfolding temperature, which is around 348 K. We confirm that the behavior of the topological multi-soliton is fully consistent with Anfinsen's thermodynamic principle, up to very high temperatures. We observe that the structure responds to an increase of temperature consistently in a very similar manner. This enables us to characterize the onset of thermally induced conformational changes in terms of three distinct backbone ligand gates. One of the gates is made of the helix F and the helix E. The two other gates are chosen similarly, when open they provide a direct access route for a ligand to reach the heme. We find that out of the three gates we investigate, the one which is formed by helices B and G is the most sensitive to thermally induced conformational changes. Our approach provides a novel perspective to the important problem of ligand entry and exit.

  14. Exposing Hidden Alternative Backbone Conformations in X-ray Crystallography Using qFit.

    PubMed

    Keedy, Daniel A; Fraser, James S; van den Bedem, Henry

    2015-10-01

    Proteins must move between different conformations of their native ensemble to perform their functions. Crystal structures obtained from high-resolution X-ray diffraction data reflect this heterogeneity as a spatial and temporal conformational average. Although movement between natively populated alternative conformations can be critical for characterizing molecular mechanisms, it is challenging to identify these conformations within electron density maps. Alternative side chain conformations are generally well separated into distinct rotameric conformations, but alternative backbone conformations can overlap at several atomic positions. Our model building program qFit uses mixed integer quadratic programming (MIQP) to evaluate an extremely large number of combinations of sidechain conformers and backbone fragments to locally explain the electron density. Here, we describe two major modeling enhancements to qFit: peptide flips and alternative glycine conformations. We find that peptide flips fall into four stereotypical clusters and are enriched in glycine residues at the n+1 position. The potential for insights uncovered by new peptide flips and glycine conformations is exemplified by HIV protease, where different inhibitors are associated with peptide flips in the "flap" regions adjacent to the inhibitor binding site. Our results paint a picture of peptide flips as conformational switches, often enabled by glycine flexibility, that result in dramatic local rearrangements. Our results furthermore demonstrate the power of large-scale computational analysis to provide new insights into conformational heterogeneity. Overall, improved modeling of backbone heterogeneity with high-resolution X-ray data will connect dynamics to the structure-function relationship and help drive new design strategies for inhibitors of biomedically important systems.

  15. Membrane Curvature Sensing by Amphipathic Helices Is Modulated by the Surrounding Protein Backbone

    PubMed Central

    Doucet, Christine M.; Esmery, Nina; de Saint-Jean, Maud; Antonny, Bruno

    2015-01-01

    Membrane curvature is involved in numerous biological pathways like vesicle trafficking, endocytosis or nuclear pore complex assembly. In addition to its topological role, membrane curvature is sensed by specific proteins, enabling the coordination of biological processes in space and time. Amongst membrane curvature sensors are the ALPS (Amphipathic Lipid Packing Sensors). ALPS motifs are short peptides with peculiar amphipathic properties. They are found in proteins targeted to distinct curved membranes, mostly in the early secretory pathway. For instance, the ALPS motif of the golgin GMAP210 binds trafficking vesicles, while the ALPS motif of Nup133 targets nuclear pores. It is not clear if, besides curvature sensitivity, ALPS motifs also provide target specificity, or if other domains in the surrounding protein backbone are involved. To elucidate this aspect, we studied the subcellular localization of ALPS motifs outside their natural protein context. The ALPS motifs of GMAP210 or Nup133 were grafted on artificial fluorescent probes. Importantly, ALPS motifs are held in different positions and these contrasting architectures were mimicked by the fluorescent probes. The resulting chimeras recapitulated the original proteins localization, indicating that ALPS motifs are sufficient to specifically localize proteins. Modulating the electrostatic or hydrophobic content of Nup133 ALPS motif modified its avidity for cellular membranes but did not change its organelle targeting properties. In contrast, the structure of the backbone surrounding the helix strongly influenced targeting. In particular, introducing an artificial coiled-coil between ALPS and the fluorescent protein increased membrane curvature sensitivity. This coiled-coil domain also provided membrane curvature sensitivity to the amphipathic helix of Sar1. The degree of curvature sensitivity within the coiled-coil context remains correlated to the natural curvature sensitivity of the helices. This suggests

  16. Exposing hidden alternative backbone conformations in X-ray crystallography using qFit

    SciTech Connect

    Keedy, Daniel A.; Fraser, James S.; van den Bedem, Henry; Shehu, Amarda

    2015-10-27

    Proteins must move between different conformations of their native ensemble to perform their functions. Crystal structures obtained from high-resolution X-ray diffraction data reflect this heterogeneity as a spatial and temporal conformational average. Although movement between natively populated alternative conformations can be critical for characterizing molecular mechanisms, it is challenging to identify these conformations within electron density maps. Alternative side chain conformations are generally well separated into distinct rotameric conformations, but alternative backbone conformations can overlap at several atomic positions. Our model building program qFit uses mixed integer quadratic programming (MIQP) to evaluate an extremely large number of combinations of sidechain conformers and backbone fragments to locally explain the electron density. Here, we describe two major modeling enhancements to qFit: peptide flips and alternative glycine conformations. We find that peptide flips fall into four stereotypical clusters and are enriched in glycine residues at the n+1 position. The potential for insights uncovered by new peptide flips and glycine conformations is exemplified by HIV protease, where different inhibitors are associated with peptide flips in the “flap” regions adjacent to the inhibitor binding site. Our results paint a picture of peptide flips as conformational switches, often enabled by glycine flexibility, that result in dramatic local rearrangements. Our results furthermore demonstrate the power of large-scale computational analysis to provide new insights into conformational heterogeneity. Furthermore, improved modeling of backbone heterogeneity with high-resolution X-ray data will connect dynamics to the structure-function relationship and help drive new design strategies for inhibitors of biomedically important systems.

  17. Exposing hidden alternative backbone conformations in X-ray crystallography using qFit

    DOE PAGES

    Keedy, Daniel A.; Fraser, James S.; van den Bedem, Henry; ...

    2015-10-27

    Proteins must move between different conformations of their native ensemble to perform their functions. Crystal structures obtained from high-resolution X-ray diffraction data reflect this heterogeneity as a spatial and temporal conformational average. Although movement between natively populated alternative conformations can be critical for characterizing molecular mechanisms, it is challenging to identify these conformations within electron density maps. Alternative side chain conformations are generally well separated into distinct rotameric conformations, but alternative backbone conformations can overlap at several atomic positions. Our model building program qFit uses mixed integer quadratic programming (MIQP) to evaluate an extremely large number of combinations of sidechainmore » conformers and backbone fragments to locally explain the electron density. Here, we describe two major modeling enhancements to qFit: peptide flips and alternative glycine conformations. We find that peptide flips fall into four stereotypical clusters and are enriched in glycine residues at the n+1 position. The potential for insights uncovered by new peptide flips and glycine conformations is exemplified by HIV protease, where different inhibitors are associated with peptide flips in the “flap” regions adjacent to the inhibitor binding site. Our results paint a picture of peptide flips as conformational switches, often enabled by glycine flexibility, that result in dramatic local rearrangements. Our results furthermore demonstrate the power of large-scale computational analysis to provide new insights into conformational heterogeneity. Furthermore, improved modeling of backbone heterogeneity with high-resolution X-ray data will connect dynamics to the structure-function relationship and help drive new design strategies for inhibitors of biomedically important systems.« less

  18. Exposing Hidden Alternative Backbone Conformations in X-ray Crystallography Using qFit

    PubMed Central

    Keedy, Daniel A.; Fraser, James S.; van den Bedem, Henry

    2015-01-01

    Proteins must move between different conformations of their native ensemble to perform their functions. Crystal structures obtained from high-resolution X-ray diffraction data reflect this heterogeneity as a spatial and temporal conformational average. Although movement between natively populated alternative conformations can be critical for characterizing molecular mechanisms, it is challenging to identify these conformations within electron density maps. Alternative side chain conformations are generally well separated into distinct rotameric conformations, but alternative backbone conformations can overlap at several atomic positions. Our model building program qFit uses mixed integer quadratic programming (MIQP) to evaluate an extremely large number of combinations of sidechain conformers and backbone fragments to locally explain the electron density. Here, we describe two major modeling enhancements to qFit: peptide flips and alternative glycine conformations. We find that peptide flips fall into four stereotypical clusters and are enriched in glycine residues at the n+1 position. The potential for insights uncovered by new peptide flips and glycine conformations is exemplified by HIV protease, where different inhibitors are associated with peptide flips in the “flap” regions adjacent to the inhibitor binding site. Our results paint a picture of peptide flips as conformational switches, often enabled by glycine flexibility, that result in dramatic local rearrangements. Our results furthermore demonstrate the power of large-scale computational analysis to provide new insights into conformational heterogeneity. Overall, improved modeling of backbone heterogeneity with high-resolution X-ray data will connect dynamics to the structure-function relationship and help drive new design strategies for inhibitors of biomedically important systems. PMID:26506617

  19. Predicting the tolerated sequences for proteins and protein interfaces using RosettaBackrub flexible backbone design.

    PubMed

    Smith, Colin A; Kortemme, Tanja

    2011-01-01

    Predicting the set of sequences that are tolerated by a protein or protein interface, while maintaining a desired function, is useful for characterizing protein interaction specificity and for computationally designing sequence libraries to engineer proteins with new functions. Here we provide a general method, a detailed set of protocols, and several benchmarks and analyses for estimating tolerated sequences using flexible backbone protein design implemented in the Rosetta molecular modeling software suite. The input to the method is at least one experimentally determined three-dimensional protein structure or high-quality model. The starting structure(s) are expanded or refined into a conformational ensemble using Monte Carlo simulations consisting of backrub backbone and side chain moves in Rosetta. The method then uses a combination of simulated annealing and genetic algorithm optimization methods to enrich for low-energy sequences for the individual members of the ensemble. To emphasize certain functional requirements (e.g. forming a binding interface), interactions between and within parts of the structure (e.g. domains) can be reweighted in the scoring function. Results from each backbone structure are merged together to create a single estimate for the tolerated sequence space. We provide an extensive description of the protocol and its parameters, all source code, example analysis scripts and three tests applying this method to finding sequences predicted to stabilize proteins or protein interfaces. The generality of this method makes many other applications possible, for example stabilizing interactions with small molecules, DNA, or RNA. Through the use of within-domain reweighting and/or multistate design, it may also be possible to use this method to find sequences that stabilize particular protein conformations or binding interactions over others.

  20. Limits on variations in protein backbone dynamics from precise measurements of scalar couplings.

    PubMed

    Vögeli, Beat; Ying, Jinfa; Grishaev, Alexander; Bax, Ad

    2007-08-01

    3JHN,Halpha, 3JHN,Cbeta, and 3JHN,C' couplings, all related to the backbone torsion angle phi, were measured for the third immunoglobulin binding domain of protein G, or GB3. Measurements were carried out using both previously published methods and novel sequences based on the multiple-quantum principle, which limit attenuation of experimental couplings caused by finite lifetimes of the spin states of passive spins. High reproducibility between the multiple-quantum and conventional approaches confirms the accuracy of the measurements. With few exceptions, close agreement between 3JHN,Halpha, 3JHN,Cbeta, and 3JHN,C' and values predicted by their respective Karplus equations is observed. For the three types of couplings, up to 20% better agreement is obtained when fitting the experimental couplings to a dynamic ensemble NMR structure, which has a phi angle root-mean-square spread of 9 +/- 4 degrees and was previously calculated on the basis of a very extensive set of residual dipolar couplings, than for any single static NMR structure. Fits of 3J couplings to a 1.1-A X-ray structure, with hydrogens added in idealized positions, are 40-90% worse. Approximately half of the improvement when fitting to the NMR structures relates to the amide proton deviating from its idealized, in-peptide-plane position, indicating that the positioning of hydrogens relative to the backbone atoms is one of the factors limiting the accuracy at which the backbone torsion angle phi can be extracted from 3J couplings. Introducing an additional, residue-specific variable for the amplitude of phi angle fluctuations does not yield a statistically significant improvement when fitting to a set of dynamic Karplus curves, pointing to a homogeneous behavior of these amplitudes.

  1. ngs_backbone: a pipeline for read cleaning, mapping and SNP calling using Next Generation Sequence

    PubMed Central

    2011-01-01

    Background The possibilities offered by next generation sequencing (NGS) platforms are revolutionizing biotechnological laboratories. Moreover, the combination of NGS sequencing and affordable high-throughput genotyping technologies is facilitating the rapid discovery and use of SNPs in non-model species. However, this abundance of sequences and polymorphisms creates new software needs. To fulfill these needs, we have developed a powerful, yet easy-to-use application. Results The ngs_backbone software is a parallel pipeline capable of analyzing Sanger, 454, Illumina and SOLiD (Sequencing by Oligonucleotide Ligation and Detection) sequence reads. Its main supported analyses are: read cleaning, transcriptome assembly and annotation, read mapping and single nucleotide polymorphism (SNP) calling and selection. In order to build a truly useful tool, the software development was paired with a laboratory experiment. All public tomato Sanger EST reads plus 14.2 million Illumina reads were employed to test the tool and predict polymorphism in tomato. The cleaned reads were mapped to the SGN tomato transcriptome obtaining a coverage of 4.2 for Sanger and 8.5 for Illumina. 23,360 single nucleotide variations (SNVs) were predicted. A total of 76 SNVs were experimentally validated, and 85% were found to be real. Conclusions ngs_backbone is a new software package capable of analyzing sequences produced by NGS technologies and predicting SNVs with great accuracy. In our tomato example, we created a highly polymorphic collection of SNVs that will be a useful resource for tomato researchers and breeders. The software developed along with its documentation is freely available under the AGPL license and can be downloaded from http://bioinf.comav.upv.es/ngs_backbone/ or http://github.com/JoseBlanca/franklin. PMID:21635747

  2. Toward Atomistic Resolution Structure of Phosphatidylcholine Headgroup and Glycerol Backbone at Different Ambient Conditions†

    PubMed Central

    2015-01-01

    Phospholipids are essential building blocks of biological membranes. Despite a vast amount of very accurate experimental data, the atomistic resolution structures sampled by the glycerol backbone and choline headgroup in phoshatidylcholine bilayers are not known. Atomistic resolution molecular dynamics simulations have the potential to resolve the structures, and to give an arrestingly intuitive interpretation of the experimental data, but only if the simulations reproduce the data within experimental accuracy. In the present work, we simulated phosphatidylcholine (PC) lipid bilayers with 13 different atomistic models, and compared simulations with NMR experiments in terms of the highly structurally sensitive C–H bond vector order parameters. Focusing on the glycerol backbone and choline headgroups, we showed that the order parameter comparison can be used to judge the atomistic resolution structural accuracy of the models. Accurate models, in turn, allow molecular dynamics simulations to be used as an interpretation tool that translates these NMR data into a dynamic three-dimensional representation of biomolecules in biologically relevant conditions. In addition to lipid bilayers in fully hydrated conditions, we reviewed previous experimental data for dehydrated bilayers and cholesterol-containing bilayers, and interpreted them with simulations. Although none of the existing models reached experimental accuracy, by critically comparing them we were able to distill relevant chemical information: (1) increase of choline order parameters indicates the P–N vector tilting more parallel to the membrane, and (2) cholesterol induces only minor changes to the PC (glycerol backbone) structure. This work has been done as a fully open collaboration, using nmrlipids.blogspot.fi as a communication platform; all the scientific contributions were made publicly on this blog. During the open research process, the repository holding our simulation trajectories and files (https

  3. Metal Preferences and Metallation*

    PubMed Central

    Foster, Andrew W.; Osman, Deenah; Robinson, Nigel J.

    2014-01-01

    The metal binding preferences of most metalloproteins do not match their metal requirements. Thus, metallation of an estimated 30% of metalloenzymes is aided by metal delivery systems, with ∼25% acquiring preassembled metal cofactors. The remaining ∼70% are presumed to compete for metals from buffered metal pools. Metallation is further aided by maintaining the relative concentrations of these pools as an inverse function of the stabilities of the respective metal complexes. For example, magnesium enzymes always prefer to bind zinc, and these metals dominate the metalloenzymes without metal delivery systems. Therefore, the buffered concentration of zinc is held at least a million-fold below magnesium inside most cells. PMID:25160626

  4. Graphene-network-backboned architectures for high-performance lithium storage.

    PubMed

    Gong, Yongji; Yang, Shubin; Liu, Zheng; Ma, Lulu; Vajtai, Robert; Ajayan, Pulickel M

    2013-08-07

    An efficient hydrothermal approach is demonstrated to fabricate a series of graphene-network-backboned hybrid architectures such as MoS₂/graphene and FeOx/graphene, showing high specific surface area, porous structure, and continuous graphene networks. Such unique architectures exhibit a high reversible capacity (about 1100 mA h g⁻¹) for lithium ion batteries. High-rate capabilities of full charge to discharge in 25-45 s with a long cycle life (1500 cycles) are achieved at different rates.

  5. Sendai virus as a backbone for vaccines against RSV and other human paramyxoviruses.

    PubMed

    Russell, Charles J; Hurwitz, Julia L

    2016-01-01

    Human paramyxoviruses are the etiological agents for life-threatening respiratory virus infections of infants and young children. These viruses, including respiratory syncytial virus (RSV), the human parainfluenza viruses (hPIV1-4) and human metapneumovirus (hMPV), are responsible for millions of serious lower respiratory tract infections each year worldwide. There are currently no standard treatments and no licensed vaccines for any of these pathogens. Here we review research with which Sendai virus, a mouse parainfluenza virus type 1, is being advanced as a Jennerian vaccine for hPIV1 and as a backbone for RSV, hMPV and other hPIV vaccines for children.

  6. Localization of strain in the RNA backbone and its functional implication

    NASA Astrophysics Data System (ADS)

    Fernández, Ariel; Rabitz, Herschel

    1992-07-01

    It is known that an RNA molecule capable of self-splicing shares a common pattern of Watson-Crick base paris with other RNA species endowed with the same capability. The aim of this work is to introduce a minimal model Hamiltonian which determines a localized strain in the RNA backbone as the search for the molecular conformation is subject to the constraint imposed by the concensus secondary structure. The site where the strain is localized is shown to coincide with the splicing site of the molecule. As justified posteriori, the level of structural complexity of the model is sufficient to account for energy localization in a nontrivial fashion.

  7. Colloidal quantum dot lasers built on a passive two-dimensional photonic crystal backbone.

    PubMed

    Chang, Hojun; Min, Kyungtaek; Lee, Myungjae; Kang, Minsu; Park, Yeonsang; Cho, Kyung-Sang; Roh, Young-Geun; Hwang, Sung Woo; Jeon, Heonsu

    2016-03-28

    We report the room-temperature lasing action from two-dimensional photonic crystal (PC) structures composed of a passive Si3N4 backbone with an over-coat of CdSe/CdS/ZnS colloidal quantum dots (CQDs) for optical gain. When optically excited, devices lased in dual PC band-edge modes, with the modal dominance governed by the thickness of the CQD over-layer. The demonstrated laser platform should have an impact on future photonic integrated circuits as the on-chip coupling between active and passive components is readily achievable.

  8. An algorithm for converting a virtual-bond chain into a complete polypeptide backbone chain

    NASA Technical Reports Server (NTRS)

    Luo, N.; Shibata, M.; Rein, R.

    1991-01-01

    A systematic analysis is presented of the algorithm for converting a virtual-bond chain, defined by the coordinates of the alpha-carbons of a given protein, into a complete polypeptide backbone. An alternative algorithm, based upon the same set of geometric parameters used in the Purisima-Scheraga algorithm but with a different "linkage map" of the algorithmic procedures, is proposed. The global virtual-bond chain geometric constraints are more easily separable from the loal peptide geometric and energetic constraints derived from, for example, the Ramachandran criterion, within the framework of this approach.

  9. Backbone resonance assignments of the micro-RNA precursor binding region of human TRBP.

    PubMed

    Benoit, Matthieu P M H; Plevin, Michael J

    2013-10-01

    TAR-RNA binding protein (TRBP) is a multidomain human protein involved in micro-RNA (miRNA) biogenesis. TRBP is a component of both the Dicer complex, which processes precursor miRNAs, and the RNA-induced silencing complex-loading complex. In addition, TRBP is implicated in the human immunodeficiency virus replication cycle and interferon-protein kinase R activity. TRBP contains 3 double-stranded RNA binding domains the first two of which have been shown to interact with miRNA precursors. Here we present the backbone resonance assignments and secondary structure of residues 19-228 of human TRBP2.

  10. Photochemistry of allyloxybenzophenones: a pseudo-Paternò-Büchi rearrangement accompanied by hydrogen transfer induced 1,5-cyclization.

    PubMed

    Pérez-Ruiz, Raúl; Hinze, Olga; Neudörfl, Jörg-M; Blunk, Dirk; Görner, Helmut; Griesbeck, Axel G

    2008-07-01

    The solution photochemistry of the ortho allyloxy-substituted benzophenone has been investigated in detail. Product analysis revealed formation of a diastereomeric mixture of dihydrobenzofuran derivatives by cyclization via a short-lived intermediate 1,5-biradical and an unusual acetal by a pseudo-Paternò-Büchi rearrangement. The latter reaction pathway was supported by means of laser flash photolysis, where a long-lived intermediate with a maximum absorption band at 380 nm was observed. Besides, theoretical calculations (TD-DFT) of this UV-transient resulted in a band with maximum intensity at 390 nm showing a good correlation between experimental results and theoretical calculations. For comparison, the meta-substituent substrate was also investigated showing preferred triplet-triplet energy transfer.

  11. A new approach to cyclic hydroxamic acids: Intramolecular cyclization of N-benzyloxy carbamates with carbon nucleophiles

    PubMed Central

    Liu, Yuan; Jacobs, Hollie K.

    2011-01-01

    N-Alkyl-N-benzyloxy carbamates, 2, undergo facile intramolecular cyclization with a variety of carbon nucleophiles to give functionalized 5- and 6-membered protected cyclic hydroxamic acids, 3, in good to excellent yields. This method can be extended to prepare seven-membered cyclic hydroxamic acids in moderate yields. The sulfone intermediates 3 from this study can be alkylated while the corresponding phosphonates have been shown to undergo HWE reaction. The α,β-unsaturated synthon, 8, prepared by thermal elimination of sulfoxide 3m, undergoes Michael addition with secondary amines. The usefulness of this approach to prepare polydentate chelators has been demonstrated by the synthesis of bis cyclic hydroxamic acids 12, 14, and 15. PMID:21499514

  12. Bioorthogonal cyclization-mediated in situ self-assembly of small-molecule probes for imaging caspase activity in vivo.

    PubMed

    Ye, Deju; Shuhendler, Adam J; Cui, Lina; Tong, Ling; Tee, Sui Seng; Tikhomirov, Grigory; Felsher, Dean W; Rao, Jianghong

    2014-06-01

    Directed self-assembly of small molecules in living systems could enable a myriad of applications in biology and medicine, and already this has been used widely to synthesize supramolecules and nano/microstructures in solution and in living cells. However, controlling the self-assembly of synthetic small molecules in living animals is challenging because of the complex and dynamic in vivo physiological environment. Here we employ an optimized first-order bioorthogonal cyclization reaction to control the self-assembly of a fluorescent small molecule, and demonstrate its in vivo applicability by imaging caspase-3/7 activity in human tumour xenograft mouse models of chemotherapy. The fluorescent nanoparticles assembled in situ were imaged successfully in both apoptotic cells and tumour tissues using three-dimensional structured illumination microscopy. This strategy combines the advantages offered by small molecules with those of nanomaterials and should find widespread use for non-invasive imaging of enzyme activity in vivo.

  13. Giffonins J-P, Highly Hydroxylated Cyclized Diarylheptanoids from the Leaves of Corylus avellana Cultivar "Tonda di Giffoni".

    PubMed

    Masullo, Milena; Cantone, Vincenza; Cerulli, Antonietta; Lauro, Gianluigi; Messano, Francesco; Russo, Gian Luigi; Pizza, Cosimo; Bifulco, Giuseppe; Piacente, Sonia

    2015-12-24

    Two new diaryl ether heptanoids, giffonins J and K (1 and 2), along with five new diarylheptanoids, giffonins L-P (3-7), were isolated from a methanol extract of the leaves of Corylus avellana cultivar "Tonda di Giffoni". These compounds were identified as highly hydroxylated cyclized diarylheptanoids by 1D- and 2D-NMR experiments. The relative configurations of giffonins J-P (1-7) were established by a combined QM (quantum mechanical)/NMR approach, comparing the experimental (13)C/(1)H NMR chemical shift data and the related predicted values. The cytotoxic activities of giffonins J-P (1-7) were evaluated against the human osteosarcoma U2Os and SAOs cell lines.

  14. From adjacent activation in Escherichia coli and DNA cyclization to eukaryotic enhancers: the elements of a puzzle

    PubMed Central

    Amouyal, Michèle

    2014-01-01

    Deoxyribonucleic acid cyclization, Escherichia coli lac repressor binding to two spaced lac operators and repression enhancement can be successfully used for a better understanding of the conditions required for interaction between eukaryotic enhancers and the machinery of transcription initiation. Chronologically, the DNA looping model has first accounted for the properties initially defining enhancers, i.e., independence of action with distance or orientation with respect to the start of transcription. It has also predicted enhancer activity or its disruption at short distance (site orientation, alignment between promoter and enhancer sites), with high-order complexes of protein, or with transcription factor concentrations close or different from the wild-type situation. In another step, histones have been introduced into the model to further adapt it to eukaryotes. They in fact favor DNA cyclization in vitro. The resulting DNA compaction might explain the difference counted in base pairs in the distance of action between eukaryotic transcription enhancers and prokaryotic repression enhancers. The lac looping system provides a potential tool for analysis of this discrepancy and of chromatin state directly in situ. Furthermore, as predicted by the model, the contribution of operators O2 and O3 to repression of the lac operon clearly depends on the lac repressor level in the cell and is prevented in strains overproducing lac repressor. By extension, gene regulation especially that linked to cell fate, should also depend on transcription factor levels, providing a potential tool for cellular therapy. In parallel, a new function of the O1–O3 loop completes the picture of lac repression. The O1–O3 loop would at the same time ensure high efficiency of repression, inducibility through the low-affinity sites and limitation of the level of repressor through self-repression of the lac repressor. Last, the DNA looping model can be successfully adapted to the enhancer

  15. Evolution of cyclizing 5-aminolevulinate synthases in the biosynthesis of actinomycete secondary metabolites: outcomes for genetic screening techniques

    PubMed Central

    Petříčková, Kateřina; Chroňáková, Alica; Zelenka, Tomáš; Chrudimský, Tomáš; Pospíšil, Stanislav; Petříček, Miroslav; Krištůfek, Václav

    2015-01-01

    A combined approach, comprising PCR screening and genome mining, was used to unravel the diversity and phylogeny of genes encoding 5-aminolevulinic acid synthases (ALASs, hemA gene products) in streptomycetes-related strains. In actinomycetes, these genes were believed to be directly connected with the production of secondary metabolites carrying the C5N unit, 2-amino-3-hydroxycyclopent-2-enone, with biological activities making them attractive for future use in medicine and agriculture. Unlike “classical” primary metabolism ALAS, the C5N unit-forming cyclizing ALAS (cALAS) catalyses intramolecular cyclization of nascent 5-aminolevulinate. Specific amino acid sequence changes can be traced by comparison of “classical” ALASs against cALASs. PCR screening revealed 226 hemA gene-carrying strains from 1,500 tested, with 87% putatively encoding cALAS. Phylogenetic analysis of the hemA homologs revealed strain clustering according to putative type of metabolic product, which could be used to select producers of specific C5N compound classes. Supporting information was acquired through analysis of actinomycete genomic sequence data available in GenBank and further genetic or metabolic characterization of selected strains. Comparison of 16S rRNA taxonomic identification and BOX-PCR profiles provided evidence for numerous horizontal gene transfers of biosynthetic genes or gene clusters within actinomycete populations and even from non-actinomycete organisms. Our results underline the importance of environmental and evolutionary data in the design of efficient techniques for identification of novel producers. PMID:26300877

  16. Low Molecular Weight Oligomers with Aromatic Backbone as Efficient Nonviral Gene Vectors.

    PubMed

    Luan, Chao-Ran; Liu, Yan-Hong; Zhang, Ji; Yu, Qing-Ying; Huang, Zheng; Wang, Bing; Yu, Xiao-Qi

    2016-05-04

    A series of oligomers were synthesized via ring-opening polymerization. Although the molecular weights of these oligomers are only ∼2.5 kDa, they could efficiently bind and condense DNA into nanoparticles. These oligomers gave comparable transfection efficiency (TE) to PEI 25 kDa, while their TE could even increase with the presence of serum, and up to 65 times higher TE than PEI was obtained. The excellent serum tolerance was also confirmed by TEM, flow cytometry, and BSA adsorption assay. Moreover, structure-activity relationship studies revealed some interesting factors. First, oligomers containing aromatic rings in the backbone showed better DNA binding ability. These materials could bring more DNA cargo into the cells, leading to much better TE. Second, the isomerism of the disubstituted phenyl group on the oligomer backbone has large effect on the transfection. The ortho-disubstituted ones gave at least 1 order of magnitude higher TE than meta- or para-disubstituted oligomers. Gel electrophoresis involving DNase and heparin indicated that the difficulty to release DNA might contribute to the lower TE of the latter. Such clues may help us to design novel nonviral gene vectors with high efficiency and biocompatibility.

  17. Cellulose nanofiber backboned Prussian blue nanoparticles as powerful adsorbents for the selective elimination of radioactive cesium

    PubMed Central

    Vipin, Adavan Kiliyankil; Fugetsu, Bunshi; Sakata, Ichiro; Isogai, Akira; Endo, Morinobu; Li, Mingda; Dresselhaus, Mildred S.

    2016-01-01

    On 11 March 2011, the day of the unforgettable disaster of the 9 magnitude Tohoku earthquake and quickly followed by the devastating Tsunami, a damageable amount of radionuclides had dispersed from the Fukushima Daiichi’s damaged nuclear reactors. Decontamination of the dispersed radionuclides from seawater and soil, due to the huge amounts of coexisting ions with competitive functionalities, has been the topmost difficulty. Ferric hexacyanoferrate, also known as Prussian blue (PB), has been the most powerful material for selectively trapping the radioactive cesium ions; its high tendency to form stable colloids in water, however, has made PB to be impossible for the open-field radioactive cesium decontamination applications. A nano/nano combinatorial approach, as is described in this study, has provided an ultimate solution to this intrinsic colloid formation difficulty of PB. Cellulose nanofibers (CNF) were used to immobilize PB via the creation of CNF-backboned PB. The CNF-backboned PB (CNF/PB) was found to be highly tolerant to water and moreover, it gave a 139 mg/g capability and a million (106) order of magnitude distribution coefficient (Kd) for absorbing of the radioactive cesium ion. Field studies on soil and seawater decontaminations in Fukushima gave satisfactory results, demonstrating high capabilities of CNF/PB for practical applications. PMID:27845441

  18. Efficient delivery of RNAi prodrugs containing reversible charge-neutralizing phosphotriester backbone modifications

    PubMed Central

    Meade, Bryan R; Gogoi, Khirud; Hamil, Alexander S; Palm-Apergi, Caroline; van den Berg, Arjen; Hagopian, Jonathan C; Springer, Aaron D; Eguchi, Akiko; Kacsinta, Apollo D; Dowdy, Connor F; Presente, Asaf; Lönn, Peter; Kaulich, Manuel; Yoshioka, Naohisa; Gros, Edwige; Cui, Xian-Shu; Dowdy, Steven F

    2015-01-01

    RNA interference (RNAi) has great potential to treat human disease1–3. However, in vivo delivery of short interfering RNAs (siRNAs), which are negatively charged double-stranded RNA macromolecules, remains a major hurdle4–9. Current siRNA delivery has begun to move away from large lipid and synthetic nanoparticles to more defined molecular conjugates9. Here we address this issue by synthesis of short interfering ribonucleic neutrals (siRNNs) whose phosphate backbone contains neutral phosphotriester groups, allowing for delivery into cells. Once inside cells, siRNNs are converted by cytoplasmic thioesterases into native, charged phosphodiester-backbone siRNAs, which induce robust RNAi responses. siRNNs have favorable drug-like properties, including high synthetic yields, serum stability and absence of innate immune responses. Unlike siRNAs, siRNNs avidly bind serum albumin to positively influence pharmacokinetic properties. Systemic delivery of siRNNs conjugated to a hepatocyte-specific targeting domain induced extended dose-dependent in vivo RNAi responses in mice. We believe that siRNNs represent a technology that will open new avenues for development of RNAi therapeutics. PMID:25402614

  19. NMR Polypeptide Backbone Conformation of the E. coli Outer Membrane Protein W

    PubMed Central

    Horst, Reto; Stanczak, Pawel; Wüthrich, Kurt

    2014-01-01

    SUMMARY The outer membrane proteins (Omp) are key factors for bacterial survival and virulence. Among the Omps which have been structurally characterized either by X-ray crystallography or by NMR in solution, the crystal structure of OmpW stands out because three of its four extracellular loops are well defined, whereas long extracellular loops in other E. coli Omps are disordered in the crystals as well as in NMR structures. OmpW thus presented an opportunity for detailed comparison of the extracellular loops in a β-barrel membrane protein structure in crystals and in non-crystalline milieus. Here the polypeptide backbone conformation of OmpW in 30-Fos micelles was determined. Complete backbone NMR assignments were obtained and the loops were structurally characterized. In combination with the OmpW crystal structure, NMR line shape analyses and 15N{1H}-NOE data, these results showed that intact regular secondary structures in the loops undergo slow hinge motions at the detergent–solvent interface. PMID:25017731

  20. The Nanomechanical Properties of Lactococcus lactis Pili Are Conditioned by the Polymerized Backbone Pilin

    PubMed Central

    Castelain, Mickaël; Duviau, Marie-Pierre; Canette, Alexis; Schmitz, Philippe; Loubière, Pascal; Cocaign-Bousquet, Muriel; Piard, Jean-Christophe; Mercier-Bonin, Muriel

    2016-01-01

    Pili produced by Lactococcus lactis subsp. lactis are putative linear structures consisting of repetitive subunits of the major pilin PilB that forms the backbone, pilin PilA situated at the distal end of the pilus, and an anchoring pilin PilC that tethers the pilus to the peptidoglycan. We determined the nanomechanical properties of pili using optical-tweezers force spectroscopy. Single pili were exposed to optical forces that yielded force-versus-extension spectra fitted using the Worm-Like Chain model. Native pili subjected to a force of 0–200 pN exhibit an inextensible, but highly flexible ultrastructure, reflected by their short persistence length. We tested a panel of derived strains to understand the functional role of the different pilins. First, we found that both the major pilin PilB and sortase C organize the backbone into a full-length organelle and dictate the nanomechanical properties of the pili. Second, we found that both PilA tip pilin and PilC anchoring pilin were not essential for the nanomechanical properties of pili. However, PilC maintains the pilus on the bacterial surface and may play a crucial role in the adhesion- and biofilm-forming properties of L. lactis. PMID:27010408

  1. Conformation-dependent backbone geometry restraints set a new standard for protein crystallographic refinement

    SciTech Connect

    Moriarty, Nigel W.; Tronrud, Dale E.; Adams, Paul D.; Karplus, P. Andrew

    2014-06-17

    Ideal values of bond angles and lengths used as external restraints are crucial for the successful refinement of protein crystal structures at all but the highest of resolutions. The restraints in common usage today have been designed based on the assumption that each type of bond or angle has a single ideal value independent of context. However, recent work has shown that the ideal values are, in fact, sensitive to local conformation, and as a first step toward using such information to build more accurate models, ultra-high resolution protein crystal structures have been used to derive a conformation-dependent library (CDL) of restraints for the protein backbone (Berkholz et al. 2009. Structure. 17, 1316). Here, we report the introduction of this CDL into the Phenix package and the results of test refinements of thousands of structures across a wide range of resolutions. These tests show that use of the conformation dependent library yields models that have substantially better agreement with ideal main-chain bond angles and lengths and, on average, a slightly enhanced fit to the X-ray data. No disadvantages of using the backbone CDL are apparent. In Phenix usage of the CDL can be selected by simply specifying the cdl=True option. This successful implementation paves the way for further aspects of the context-dependence of ideal geometry to be characterized and applied to improve experimental and predictive modelling accuracy.

  2. Optimization of Protein Backbone Dihedral Angles by Means of Hamiltonian Reweighting

    PubMed Central

    2016-01-01

    Molecular dynamics simulations depend critically on the accuracy of the underlying force fields in properly representing biomolecules. Hence, it is crucial to validate the force-field parameter sets in this respect. In the context of the GROMOS force field, this is usually achieved by comparing simulation data to experimental observables for small molecules. In this study, we develop new amino acid backbone dihedral angle potential energy parameters based on the widely used 54A7 parameter set by matching to experimental J values and secondary structure propensity scales. In order to find the most appropriate backbone parameters, close to 100 000 different combinations of parameters have been screened. However, since the sheer number of combinations considered prohibits actual molecular dynamics simulations for each of them, we instead predicted the values for every combination using Hamiltonian reweighting. While the original 54A7 parameter set fails to reproduce the experimental data, we are able to provide parameters that match significantly better. However, to ensure applicability in the context of larger peptides and full proteins, further studies have to be undertaken. PMID:27559757

  3. Di-Isocyanate Crosslinked Aerogels with 1, 6-Bis (Trimethoxysilyl) Hexane Incorporated in Silica Backbone

    NASA Technical Reports Server (NTRS)

    Vivod, Stephanie L.; Meador, Mary Ann B.; Nguyen, Baochau N.; Quade, Derek; Randall, Jason; Perry, Renee

    2008-01-01

    Silica aerogels are desirable materials for many applications that take advantage of their light weight and low thermal conductivity. Addition of a conformal polymer coating which bonds with the amine decorated surface of the silica network improves the strength of the aerogels by as much as 200 times. Even with vast improvement in strength they still tend to undergo brittle failure due to the rigid silica backbone. We hope to increase the flexibility and elastic recovery of the silica based aerogel by altering the silica back-bone by incorporation of more flexible hexane links. To this end, we investigated the use of 1,6-bis(trimethoxysilyl)hexane (BTMSH), a polysilsesquioxane precursor3, as an additional co-reactant to prepare silica gels which were subsequently cross-linked with di-isocyanate. Previously, this approach of adding flexibility by BTMSH incorporation was demonstrated with styrene cross-linked aerogels. In our study, we varied silane concentration, mol % of silicon from BTMSH and di-isocyanate concentration by weight percent to attempt to optimize both the flexibility and the strength of the aerogels.

  4. Conformation-dependent backbone geometry restraints set a new standard for protein crystallographic refinement

    DOE PAGES

    Moriarty, Nigel W.; Tronrud, Dale E.; Adams, Paul D.; ...

    2014-06-17

    Ideal values of bond angles and lengths used as external restraints are crucial for the successful refinement of protein crystal structures at all but the highest of resolutions. The restraints in common usage today have been designed based on the assumption that each type of bond or angle has a single ideal value independent of context. However, recent work has shown that the ideal values are, in fact, sensitive to local conformation, and as a first step toward using such information to build more accurate models, ultra-high resolution protein crystal structures have been used to derive a conformation-dependent library (CDL)more » of restraints for the protein backbone (Berkholz et al. 2009. Structure. 17, 1316). Here, we report the introduction of this CDL into the Phenix package and the results of test refinements of thousands of structures across a wide range of resolutions. These tests show that use of the conformation dependent library yields models that have substantially better agreement with ideal main-chain bond angles and lengths and, on average, a slightly enhanced fit to the X-ray data. No disadvantages of using the backbone CDL are apparent. In Phenix usage of the CDL can be selected by simply specifying the cdl=True option. This successful implementation paves the way for further aspects of the context-dependence of ideal geometry to be characterized and applied to improve experimental and predictive modelling accuracy.« less

  5. Importance of backbone angles versus amino acid configurations in peptide vibrational Raman optical activity spectra

    NASA Astrophysics Data System (ADS)

    Herrmann, Carmen; Ruud, Kenneth; Reiher, Markus

    2008-01-01

    In this work, we investigate whether the differential scattering of right- and left-circularly polarized light in peptide Raman optical activity spectra are uniquely dominated by the backbone conformation, or whether the configurations of the individual amino acid also play a significant role. This is achieved by calculating Raman optical activity spectra using density functional theory for four structurally related peptides with a common backbone conformation, but with different sequences of amino acid configurations. Furthermore, the ROA signals of the amide normal modes are decomposed into contributions from groups of individual atoms. It is found that the amino acid configuration has a considerable influence on the ROA peaks in the amide I, II, and III regions, although the local decomposition reveals that the side-chain atoms only contribute to those peaks directly in the case of the amide II vibrations. Furthermore, small changes in the amide normal modes may lead to large and irregular modifications in the ROA intensity differences, making it difficult to establish transferable ROA intensity differences even for structurally similar vibrations.

  6. RNA-Redesign: a web server for fixed-backbone 3D design of RNA.

    PubMed

    Yesselman, Joseph D; Das, Rhiju

    2015-07-01

    RNA is rising in importance as a design medium for interrogating fundamental biology and for developing therapeutic and bioengineering applications. While there are several online servers for design of RNA secondary structure, there are no tools available for the rational design of 3D RNA structure. Here we present RNA-Redesign (http://rnaredesign.stanford.edu), an online 3D design tool for RNA. This resource utilizes fixed-backbone design to optimize the sequence identity and nucleobase conformations of an RNA to match a desired backbone, analogous to fundamental tools that underlie rational protein engineering. The resulting sequences suggest thermostabilizing mutations that can be experimentally verified. Further, sequence preferences that differ between natural and computationally designed sequences can suggest whether natural sequences possess functional constraints besides folding stability, such as cofactor binding or conformational switching. Finally, for biochemical studies, the designed sequences can suggest experimental tests of 3D models, including concomitant mutation of base triples. In addition to the designs generated, detailed graphical analysis is presented through an integrated and user-friendly environment.

  7. Backbone dynamics of the monomeric lambda repressor denatured state ensemble under nondenaturing conditions.

    PubMed

    Chugha, Preeti; Oas, Terrence G

    2007-02-06

    Oxidizing two native methionine residues predominantly populates the denatured state of monomeric lambda repressor (MetO-lambdaLS) under nondenaturing conditions. NMR was used to characterize the secondary structure and dynamics of MetO-lambdaLS in standard phosphate buffer. 13Calpha and 1Halpha chemical shift indices reveal a region of significant helicity between residues 9 and 29. This helical content is further supported by the observation of medium-range amide NOEs. The remaining residues do not exhibit significant helicity as determined by NMR. We determined 15N relaxation parameters for 64 of 85 residues at 600 and 800 MHz. There are two distinct regions of reduced flexibility, residues 8-32 in the N-terminal third and residues 50-83 in the C-terminal third. The middle third, residues 33-50, has greater flexibility. We have analyzed the amplitude of the backbone motions in terms of the physical properties of the amino acids and conclude that conformational restriction of the backbone MetO-lambdaLS is due to nascent helix formation in the region corresponding to native helix 1. The bulkiness of amino acid residues in the C-terminal third leads to the potential for hydrophobic interactions, which is suggested by chemical exchange detected by the difference in spectral density J(0) at the two static magnetic fields. The more flexible middle region is the result of a predominance of small side chains in this region.

  8. Cellulose nanofiber backboned Prussian blue nanoparticles as powerful adsorbents for the selective elimination of radioactive cesium

    NASA Astrophysics Data System (ADS)

    Vipin, Adavan Kiliyankil; Fugetsu, Bunshi; Sakata, Ichiro; Isogai, Akira; Endo, Morinobu; Li, Mingda; Dresselhaus, Mildred S.

    2016-11-01

    On 11 March 2011, the day of the unforgettable disaster of the 9 magnitude Tohoku earthquake and quickly followed by the devastating Tsunami, a damageable amount of radionuclides had dispersed from the Fukushima Daiichi’s damaged nuclear reactors. Decontamination of the dispersed radionuclides from seawater and soil, due to the huge amounts of coexisting ions with competitive functionalities, has been the topmost difficulty. Ferric hexacyanoferrate, also known as Prussian blue (PB), has been the most powerful material for selectively trapping the radioactive cesium ions; its high tendency to form stable colloids in water, however, has made PB to be impossible for the open-field radioactive cesium decontamination applications. A nano/nano combinatorial approach, as is described in this study, has provided an ultimate solution to this intrinsic colloid formation difficulty of PB. Cellulose nanofibers (CNF) were used to immobilize PB via the creation of CNF-backboned PB. The CNF-backboned PB (CNF/PB) was found to be highly tolerant to water and moreover, it gave a 139 mg/g capability and a million (106) order of magnitude distribution coefficient (Kd) for absorbing of the radioactive cesium ion. Field studies on soil and seawater decontaminations in Fukushima gave satisfactory results, demonstrating high capabilities of CNF/PB for practical applications.

  9. The structure of the carbohydrate backbone of the lipopolysaccharide of Pectinatus frisingensis strain VTT E-79104.

    PubMed

    Vinogradov, Evgeny; Li, Jianjun; Sadovskaya, Irina; Jabbouri, Said; Helander, Ilkka M

    2004-06-22

    The structure of the carbohydrate backbone of the lipopolysaccharide from Pectinatus frisingensis strain VTT E-79104 was analyzed using chemical degradations, NMR spectroscopy, mass spectrometry, and chemical methods. The LPS contains two major structural variants, differing in the presence or absence of an octasaccharide fragment. The largest structure of the carbohydrate backbone of the LPS, that could be deduced from experimental results, consists of 20 monosaccharides arranged in a nonrepetitive sequence: [carbohydrate structure: see text] where R is H or 4-O-Me-alpha-L-Fuc-(1-2)-4-O-Me-beta-Hep-(1-3)-alpha-GlcNAc-(1-2)-beta-Man-(1-3)-beta-ManNAc-(1-4)-alpha-Gal-(1-4)-beta-Hep-(1-3)-beta-GalNAc-(1- where Hep is a residue of D-glycero-D-galacto-heptose; all monosaccharides have the D-configuration except for 4-O-Me-L-Fuc and L-Ara4N. This structure is architecturally similar to the oligosaccharide system reported previously in P. frisingensis VTT E-82164 LPS, but differs from the latter in composition and also in the size of the outer region.

  10. Metal-coordination-driven dynamic heteroleptic architectures.

    PubMed

    De, Soumen; Mahata, Kingsuk; Schmittel, Michael

    2010-05-01

    Dynamic heteroleptic coordination at metal centres is quite common in Nature and often related to a specific biological function, such as in zinc finger proteins and in hemoglobin for oxygen transport. To achieve the required high heteroleptic fidelity, representative biological systems avail themselves of "intramolecular" multidentate coordination using the protein backbone as a "superligand". In contrast, dynamic heteroleptic coordination at a single metal centre in solution requires to bind different freely exchanging ligands under thermodynamic control. In this tutorial review we present the emerging principles of how to assemble dissimilar ligands at dynamically exchanging metal centres, with a particular emphasis on using the precepts for the fabrication of heteroleptic supramolecular assemblies in solution.

  11. Comb-type prepolymers consisting of a polyacrylamide backbone and poly(L-lysine) graft chains for multivalent ligands.

    PubMed

    Asayama, S; Maruyama, A; Akaike, T

    1999-01-01

    The comb-type copolymers consisting of a polyacrylamide (PAAm) backbone and poly(L-lysine) (PLL) graft chains have been prepared as the "prepolymer" for designing multivalent ligands. To regulate the length and density of the clusters of primary amino groups, the Nalpha-carboxyanhydride of Nepsilon-carbobenzoxy (CBZ)-L-lysine was first polymerized using p-vinylbenzylamine as an initiator. The resulting poly(CBZ-L-lysine) macromonomer was then radically copolymerized with AAm, followed by the deprotection of amino groups. For the model study, the reactive clusters of primary amino groups were completely converted into anion clusters by the reaction with succinic anhydride. The model multivalent ligands having the biotin label on the PAAm backbone were prepared by the terpolymerization of the macromonomer, AAm, and the biotin derivative having a vinyl group. The enzyme-linked immunosorbent assay showed that the biotin with no spacer on the PAAm backbone was recognized by the avidin-peroxidase conjugate specifically. Therefore, the highly sensitive detection of the interaction between cells and various model multivalent ligands was possible. The selective labeling onto the PAAm backbone revealed that the converted anion clusters of graft chains interacted exclusively with the cell and that the backbone was inert to the interaction with the cell. These results indicate that the various PAAm-graft-PLL comb-type copolymers with the defined length and density of the PLL-grafts are the potential prepolymers to investigate and to optimize the affinity of the multivalent ligands for receptors.

  12. Effect of backbone chemistry on hybridization thermodynamics of oligonucleic acids: a coarse-grained molecular dynamics simulation study.

    PubMed

    Ghobadi, Ahmadreza F; Jayaraman, Arthi

    2016-02-28

    In this paper we study how varying oligonucleic acid backbone chemistry affects the hybridization/melting thermodynamics of oligonucleic acids. We first describe the coarse-grained (CG) model with tunable parameters that we developed to enable the study of both naturally occurring oligonucleic acids, such as DNA, and their chemically-modified analogues, such as peptide nucleic acids (PNAs) and locked nucleic acids (LNAs). The DNA melting curves obtained using such a CG model and molecular dynamics simulations in an implicit solvent and with explicit ions match with the melting curves obtained using the empirical nearest-neighbor models. We use these CG simulations to then elucidate the effect of backbone flexibility, charge, and nucleobase spacing along the backbone on the melting curves, potential energy and conformational entropy change upon hybridization and base-pair hydrogen bond residence time. We find that increasing backbone flexibility decreases duplex thermal stability and melting temperature mainly due to increased conformational entropy loss upon hybridization. Removing charges from the backbone enhances duplex thermal stability due to the elimination of electrostatic repulsion and as a result a larger energetic gain upon hybridization. Lastly, increasing nucleobase spacing decreases duplex thermal stability due to decreasing stacking interactions that are important for duplex stability.

  13. The Inherent Conformational Preferences of Glutamine-Containing Peptides: the Role for Side-Chain Backbone Hydrogen Bonds

    NASA Astrophysics Data System (ADS)

    Walsh, Patrick S.; McBurney, Carl; Gellman, Samuel H.; Zwier, Timothy S.

    2015-06-01

    Glutamine is widely known to be found in critical regions of peptides which readily fold into amyloid fibrils, the structures commonly associated with Alzheimer's disease and glutamine repeat diseases such as Huntington's disease. Building on previous single-conformation data on Gln-containing peptides containing an aromatic cap on the N-terminus (Z-Gln-OH and Z-Gln-NHMe), we present here single-conformation UV and IR spectra of Ac-Gln-NHBn and Ac-Ala-Gln-NHBn, with its C-terminal benzyl cap. These results point towards side-chain to backbone hydrogen bonds dominating the structures observed in the cold, isolated environment of a molecular beam. We have identified and assigned three main conformers for Ac-Gln-NHBn all involving primary side-chain to backbone interactions. Ac-Ala-Gln-NHBn extends the peptide chain by one amino acid, but affords an improvement in the conformational flexibility. Despite this increase in the flexibility, only a single conformation is observed in the gas-phase: a structure which makes use of both side-chain-to-backbone and backbone-to-backbone hydrogen bonds.

  14. Polarizable Simulations with Second order Interaction Model (POSSIM) force field: Developing parameters for alanine peptides and protein backbone

    PubMed Central

    Ponomarev, Sergei Y.; Kaminski, George A.

    2011-01-01

    A previously introduced POSSIM (POlarizable Simulations with Second order Interaction Model) force field has been extended to include parameters for alanine peptides and protein backbones. New features were introduced into the fitting protocol, as compared to the previous generation of the polarizable force field for proteins. A reduced amount of quantum mechanical data was employed in fitting the electrostatic parameters. Transferability of the electrostatics between our recently developed NMA model and the protein backbone was confirmed. Binding energy and geometry for complexes of alanine dipeptide with a water molecule were estimated and found in a good agreement with high-level quantum mechanical results (for example, the intermolecular distances agreeing within ca. 0.06Å). Following the previously devised procedure, we calculated average errors in alanine di- and tetra-peptide conformational energies and backbone angles and found the agreement to be adequate (for example, the alanine tetrapeptide extended-globular conformational energy gap was calculated to be 3.09 kcal/mol quantim mechanically and 3.14 kcal/mol with the POSSIM force field). However, we have now also included simulation of a simple alpha-helix in both gas-phase and water as the ultimate test of the backbone conformational behavior. The resulting alanine and protein backbone force field is currently being employed in further development of the POSSIM fast polarizable force field for proteins. PMID:21743799

  15. Novel chimeric scaffolds to extend the exploration of receptor space: hybrid beta-D-glucose-benzoheterodiazepine structures for broad screening. Effect of amide alkylation on the course of cyclization reactions.

    PubMed

    Abrous, Leïla; Jokiel, Patrick A; Friedrich, Sarah R; Hynes, John; Smith, Amos B; Hirschmann, Ralph

    2004-01-23

    New molecular platforms which are hybrids of two scaffolds-namely, beta-d-glucose and benzodiazepine, each able to bind several proteins-were designed, synthesized and functionalized to serve as probes for broad biological screening. Herein, we describe the syntheses and chemical properties of these novel chimeric scaffolds. Attempted cyclization of the functionalized analogues (-)-96 and (-)-97 afforded the corresponding dimers (-)-98 and (-)-99, respectively, under a variety of reaction conditions, even at concentrations of only 0.001 N. Consideration of factors affecting the conformation of amide bonds and their effects on cyclization reactions led us to alkylate the amide bond. As expected, the cyclization of the N-methyl derivative (-)-110 afforded exclusively the unimolecular cyclization product (+)-111. These compounds are only now undergoing broad screening and represent therefore at present a "prospecting library."

  16. Iminoxyl radical-promoted dichotomous cyclizations: efficient oxyoximation and aminooximation of alkenes.

    PubMed

    Peng, Xie-Xue; Deng, Yun-Jing; Yang, Xiu-Long; Zhang, Lin; Yu, Wei; Han, Bing

    2014-09-05

    A novel iminoxyl radical-involved metal-free approach to vicinal oxyoximation and aminooximation of unactivated alkenes is developed. This method utilizes the dichotomous reactivity of the iminoxyl radical to furnish a general difunctionalization on alkenes using simple tert-butyl nitrite (TBN) as the iminoxyl radical initiator as well the carbon radical trap. By using this protocol, oxime featured 4,5-dihydroisoxazoles and cyclic nitrones were facilely prepared from β,γ- and γ,δ-unsaturated ketoximes, respectively.

  17. Photocaged G-Quadruplex DNAzyme and Aptamer by Post-Synthetic Modification on Phosphodiester Backbone.

    PubMed

    Feng, Mengli; Ruan, Zhiyuan; Shang, Jiachen; Xiao, Lu; Tong, Aijun; Xiang, Yu

    2017-02-15

    G-quadruplex-containing DNAzymes and aptamers are widely applied in many research fields because of their high stability and prominent activities versus the protein counterparts. In this work, G-quadruplex DNAs were equipped with photolabile groups to construct photocaged DNAzymes and aptamers. We incorporated TEEP-OH (thioether-enol phosphate, phenol substituted) into phosphodiester backbone of G-quadruplex DNA by a facile post-synthetic method to achieve efficient photocaging of their activities. Upon light irradiation, the peroxidase-mimicking activity of the caged G-quadruplex DNAzyme was activated, through the transformation of TEEP-OH into a native DNA phosphodiester without any artificial scar. Similarly, the caged G-quadruplex thrombin-binding aptamer also showed light-induced activation of thrombin inhibition activity. This method could serve as a general strategy to prepare photocaged G-quadruplex DNA with other activities for noninvasive control of their functions.

  18. Sendai Virus as a Backbone for Vaccines against RSV and other Human Paramyxoviruses

    PubMed Central

    Russell, Charles J.; Hurwitz, Julia L.

    2016-01-01

    Summary Human paramyxoviruses are the etiological agents for life-threatening respiratory virus infections of infants and young children. These viruses – including respiratory syncytial virus (RSV), the human parainfluenza viruses (hPIV1-4), and human metapneumovirus (hMPV) – are responsible for millions of serious lower respiratory tract infections each year worldwide. There are currently no standard treatments and no licensed vaccines for any of these pathogens. Here we review research with which Sendai virus, a mouse parainfluenza virus type 1, is being advanced as a Jennerian vaccine for hPIV1 and as a backbone for RSV, hMPV, and other hPIV vaccines for children. PMID:26648515

  19. Improved variation calling via an iterative backbone remapping and local assembly method for bacterial genomes

    PubMed Central

    Tae, Hongseok; Settlage, Robert E.; Shallom, Shamira; Bavarva, Jasmin H.; Preston, Dale; Hawkins, Gregory N.; Adams, L. Garry; Garner, Harold R.

    2012-01-01

    Sequencing data analysis remains limiting and problematic, especially for low complexity repeat sequences and transposon elements due to inherent sequencing errors and short sequence read lengths. We have developed a program, ReviSeq, which uses a hybrid method comprised of iterative remapping and local assembly upon a bacterial sequence backbone. Application of this method to six Brucella suis field isolates compared to the newly revised Brucella suis 1330 reference genome identified on average 13, 15, 19 and 9 more variants per sample than STAMPY/SAMtools, BWA/SAMtools, iCORN and BWA/PINDEL pipelines, and excluded on average 4, 2, 3 and 19 variants per sample, respectively. In total, using this iterative approach, we identified on average 87 variants including SNVs, short INDELs and long INDELs per strain when compared to the reference. Our program outperforms other methods especially for long INDEL calling. The program is available at http://reviseq.sourceforge.net. PMID:22967795

  20. A recombinant, chimeric tetravalent dengue vaccine candidate based on a dengue virus serotype 2 backbone.

    PubMed

    Osorio, Jorge E; Wallace, Derek; Stinchcomb, Dan T

    2016-01-01

    Dengue fever is caused by infection with one of four dengue virus (DENV) serotypes (DENV-1-4), necessitating tetravalent dengue vaccines that can induce protection against all four DENV. Takeda's live attenuated tetravalent dengue vaccine candidate (TDV) comprises an attenuated DENV-2 strain plus chimeric viruses containing the prM and E genes of DENV-1, -3 and -4 cloned into the attenuated DENV-2 'backbone'. In Phase 1 and 2 studies, TDV was well tolerated by children and adults aged 1.5-45 years, irrespective of prior dengue exposure; mild injection-site symptoms were the most common adverse events. TDV induced neutralizing antibody responses and seroconversion to all four DENV as well as cross-reactive T cell-mediated responses that may be necessary for broad protection against dengue fever.

  1. Modification of Rifamycin Polyketide Backbone Leads to Improved Drug Activity against Rifampicin-resistant Mycobacterium tuberculosis*

    PubMed Central

    Nigam, Aeshna; Almabruk, Khaled H.; Saxena, Anjali; Yang, Jongtae; Mukherjee, Udita; Kaur, Hardeep; Kohli, Puneet; Kumari, Rashmi; Singh, Priya; Zakharov, Lev N.; Singh, Yogendra; Mahmud, Taifo; Lal, Rup

    2014-01-01

    Rifamycin B, a product of Amycolatopsis mediterranei S699, is the precursor of clinically used antibiotics that are effective against tuberculosis, leprosy, and AIDS-related mycobacterial infections. However, prolonged usage of these antibiotics has resulted in the emergence of rifamycin-resistant strains of Mycobacterium tuberculosis. As part of our effort to generate better analogs of rifamycin, we substituted the acyltransferase domain of module 6 of rifamycin polyketide synthase with that of module 2 of rapamycin polyketide synthase. The resulting mutants (rifAT6::rapAT2) of A. mediterranei S699 produced new rifamycin analogs, 24-desmethylrifamycin B and 24-desmethylrifamycin SV, which contained modification in the polyketide backbone. 24-Desmethylrifamycin B was then converted to 24-desmethylrifamycin S, whose structure was confirmed by MS, NMR, and X-ray crystallography. Subsequently, 24-desmethylrifamycin S was converted to 24-desmethylrifampicin, which showed excellent antibacterial activity against several rifampicin-resistant M. tuberculosis strains. PMID:24923585

  2. Using halogen bonds to address the protein backbone: a systematic evaluation.

    PubMed

    Wilcken, Rainer; Zimmermann, Markus O; Lange, Andreas; Zahn, Stefan; Boeckler, Frank M

    2012-08-01

    Halogen bonds are specific embodiments of the sigma hole bonding paradigm. They represent directional interactions between the halogens chlorine, bromine, or iodine and an electron donor as binding partner. Using quantum chemical calculations at the MP2 level, we systematically explore how they can be used in molecular design to address the omnipresent carbonyls of the protein backbone. We characterize energetics and directionality and elucidate their spatial variability in sub-optimal geometries that are expected to occur in protein-ligand complexes featuring a multitude of concomitant interactions. By deriving simple rules, we aid medicinal chemists and chemical biologists in easily exploiting them for scaffold decoration and design. Our work shows that carbonyl-halogen bonds may be used to expand the patentable medicinal chemistry space, redefining halogens as key features. Furthermore, this data will be useful for implementing halogen bonds into pharmacophore models or scoring functions making the QM information available for automatic molecular recognition in virtual high throughput screening.

  3. Side chain and backbone contributions of Phe508 to CFTR folding

    SciTech Connect

    Thibodeau, Patrick H.; Brautigam, Chad A.; Machius, Mischa; Thomas, Philip J.

    2010-12-07

    Mutations in the cystic fibrosis transmembrane conductance regulator (CFTR), an integral membrane protein, cause cystic fibrosis (CF). The most common CF-causing mutant, deletion of Phe508, fails to properly fold. To elucidate the role Phe508 plays in the folding of CFTR, missense mutations at this position were generated. Only one missense mutation had a pronounced effect on the stability and folding of the isolated domain in vitro. In contrast, many substitutions, including those of charged and bulky residues, disrupted folding of full-length CFTR in cells. Structures of two mutant nucleotide-binding domains (NBDs) reveal only local alterations of the surface near position 508. These results suggest that the peptide backbone plays a role in the proper folding of the domain, whereas the side chain plays a role in defining a surface of NBD1 that potentially interacts with other domains during the maturation of intact CFTR.

  4. A renormalization approach to describe charge transport in quasiperiodic dangling backbone ladder (DBL)-DNA molecules

    NASA Astrophysics Data System (ADS)

    Sarmento, R. G.; Fulco, U. L.; Albuquerque, E. L.; Caetano, E. W. S.; Freire, V. N.

    2011-10-01

    We study the charge transport properties of a dangling backbone ladder (DBL)-DNA molecule focusing on a quasiperiodic arrangement of its constituent nucleotides forming a Rudin-Shapiro (RS) and Fibonacci (FB) Poly (CG) sequences, as well as a natural DNA sequence (Ch22) for the sake of comparison. Making use of a one-step renormalization process, the DBL-DNA molecule is modeled in terms of a one-dimensional tight-binding Hamiltonian to investigate its transmissivity and current-voltage (I-V) profiles. Beyond the semiconductor I-V characteristics, a striking similarity between the electronic transport properties of the RS quasiperiodic structure and the natural DNA sequence was found.

  5. Modification of rifamycin polyketide backbone leads to improved drug activity against rifampicin-resistant Mycobacterium tuberculosis.

    PubMed

    Nigam, Aeshna; Almabruk, Khaled H; Saxena, Anjali; Yang, Jongtae; Mukherjee, Udita; Kaur, Hardeep; Kohli, Puneet; Kumari, Rashmi; Singh, Priya; Zakharov, Lev N; Singh, Yogendra; Mahmud, Taifo; Lal, Rup

    2014-07-25

    Rifamycin B, a product of Amycolatopsis mediterranei S699, is the precursor of clinically used antibiotics that are effective against tuberculosis, leprosy, and AIDS-related mycobacterial infections. However, prolonged usage of these antibiotics has resulted in the emergence of rifamycin-resistant strains of Mycobacterium tuberculosis. As part of our effort to generate better analogs of rifamycin, we substituted the acyltransferase domain of module 6 of rifamycin polyketide synthase with that of module 2 of rapamycin polyketide synthase. The resulting mutants (rifAT6::rapAT2) of A. mediterranei S699 produced new rifamycin analogs, 24-desmethylrifamycin B and 24-desmethylrifamycin SV, which contained modification in the polyketide backbone. 24-Desmethylrifamycin B was then converted to 24-desmethylrifamycin S, whose structure was confirmed by MS, NMR, and X-ray crystallography. Subsequently, 24-desmethylrifamycin S was converted to 24-desmethylrifampicin, which showed excellent antibacterial activity against several rifampicin-resistant M. tuberculosis strains.

  6. Solid-phase synthesis of lidocaine and procainamide analogues using backbone amide linker (BAL) anchoring.

    PubMed

    Shannon, Simon K; Peacock, Mandy J; Kates, Steven A; Barany, George

    2003-01-01

    New solid-phase strategies have been developed for the synthesis of lidocaine (1) and procainamide (2) analogues, using backbone amide linker (BAL) anchoring. Both sets were prepared starting from a common resin-bound intermediate, followed by four general steps: (i) attachment of a primary aliphatic or aromatic amine to the solid support via reductive amination (as monitored by a novel test involving reaction of 2,4-dinitrophenylhydrazine with residual aldehyde groups); (ii) acylation of the resultant secondary amine; (iii) displacement of halide with an amine; and (iv) trifluoroacetic acid-mediated release from the support. A manual parallel strategy was followed to provide 60 novel compounds, of which two dozen have not been previously described. In most cases, initial crude purities were >80%, and overall isolated yields were in the 40-88% range.

  7. "Chameleonic" backbone hydrogen bonds in protein binding and as drug targets.

    PubMed

    Menéndez, C A; Accordino, S R; Gerbino, D C; Appignanesi, G A

    2015-10-01

    We carry out a time-averaged contact matrix study to reveal the existence of protein backbone hydrogen bonds (BHBs) whose net persistence in time differs markedly form their corresponding PDB-reported state. We term such interactions as "chameleonic" BHBs, CBHBs, precisely to account for their tendency to change the structural prescription of the PDB for the opposite bonding propensity in solution. We also find a significant enrichment of protein binding sites in CBHBs, relate them to local water exposure and analyze their behavior as ligand/drug targets. Thus, the dynamic analysis of hydrogen bond propensity might lay the foundations for new tools of interest in protein binding-site prediction and in lead optimization for drug design.

  8. The Role of Methoxy Group in the Nazarov Cyclization of 1,5-bis-(2-Methoxyphenyl)-1,4-Pentadien-3-one in the Gas Phase and Condensed Phase

    PubMed Central

    Cyriac, June; Paulose, Justin; George, Mathai; Ramesh, Marupaka; Srinivas, Ragampeta; Giblin, Daryl; Gross, Michael L.

    2014-01-01

    ESI-protonated 1,5-bis-(2-methoxyphenyl)-1,4-pentadien-3-one (1) undergoes a gas-phase Nazarov cyclization and dissociates via expulsions of ketene and anisole. The dissociations of the [M+ D]+ ions are accompanied by limited HD scrambling that supports the proposed cyclization. Solution cyclization of 1 was effected to yield the cyclic ketone, 2,3-bis-(2-methoxyphenyl)-cyclopent-2-ene-1-one, (2) on a time scale that is significantly shorter than the time for cyclization of dibenzalacetone. The dissociation characteristics of the ESI-generated [M + H]+ ion of the synthetic cyclic ketone closely resemble those of 1, suggesting that gas-phase and solution cyclization products are the same. Additional mechanistic studies by density functional theory (DFT) methods of the gas-phase reaction reveals that the initial cyclization is followed by two sequential 1,2-aryl migrations that account for the observed structure of the cyclic product in the gas phase and solution. Furthermore, the DFT calculations show that the methoxy group serves as a catalyst for the proton migrations necessary for both cyclization and fragmentation after aryl migration. An isomer formed by moving the 2-methoxy to the 4-position requires relatively higher collision energy for the elimination of anisole, as is consistent with DFT calculations. Replacement of the 2-methoxy group with an OH shows that the cyclization followed by aryl migration and elimination of phenol occurs from the [M + H]+ ion at low energy similar to that for 1. PMID:24415061

  9. Solution structure and backbone dynamics of human epidermal-type fatty acid-binding protein (E-FABP).

    PubMed Central

    Gutiérrez-González, Luis H; Ludwig, Christian; Hohoff, Carsten; Rademacher, Martin; Hanhoff, Thorsten; Rüterjans, Heinz; Spener, Friedrich; Lücke, Christian

    2002-01-01

    Human epidermal-type fatty acid-binding protein (E-FABP) belongs to a family of intracellular 14-15 kDa lipid-binding proteins, whose functions have been associated with fatty acid signalling, cell growth, regulation and differentiation. As a contribution to understanding the structure-function relationship, we report in the present study features of its solution structure and backbone dynamics determined by NMR spectroscopy. Applying multi-dimensional high-resolution NMR techniques on unlabelled and 15N-enriched recombinant human E-FABP, the 1H and 15N resonance assignments were completed. On the basis of 2008 distance restraints, the three-dimensional solution structure of human E-FABP was subsequently obtained (backbone atom root-mean-square deviation of 0.92+/-0.11 A; where 1 A=0.1 nm), consisting mainly of 10 anti-parallel beta-strands that form a beta-barrel structure. 15N relaxation experiments (T1, T2 and heteronuclear nuclear Overhauser effects) at 500, 600 and 800 MHz provided information on the internal dynamics of the protein backbone. Nearly all non-terminal backbone amide groups showed order parameters S(2)>0.8, with an average value of 0.88+/-0.04, suggesting a uniformly low backbone mobility in the nanosecond-to-picosecond time range. Moreover, hydrogen/deuterium exchange experiments indicated a direct correlation between the stability of the hydrogen-bonding network in the beta-sheet structure and the conformational exchange in the millisecond-to-microsecond time range. The features of E-FABP backbone dynamics elaborated in the present study differ markedly from those of the phylogenetically closely related heart-type FABP and the more distantly related ileal lipid-binding protein, implying a strong interdependence with the overall protein stability and possibly also with the ligand-binding affinity for members of the lipid-binding protein family. PMID:12049637

  10. Backbone-hydrazone-containing biodegradable copolymeric micelles for anticancer drug delivery

    NASA Astrophysics Data System (ADS)

    Xu, Jing; Luan, Shujuan; Qin, Benkai; Wang, Yingying; Wang, Kai; Qi, Peilan; Song, Shiyong

    2016-11-01

    Well-defined biodegradable, pH-sensitive amphiphilic block polymers, poly(ethylene glycol)-Hyd-poly(lactic acid) (mPEG-Hyd-PLA) which have acid-cleavable linkages in their backbones, were synthesized via ring-opening polymerization initiated from hydrazone-containing macroinitiators. Introducing a hydrazone bond onto the backbone of an amphiphilic copolymer will find a broad-spectrum encapsulation of hydrophobic drugs. Dynamic light scattering (DLS) and transmission electron microscopy showed that the diblock copolymers self-assembled into stable micelles with average diameters of 100 nm. The mean diameters and size distribution of the hydrazone-containing micelles changed obviously in mildly acidic pH (multiple peaks from 1 to 202 nm appeared under a pH 4.0 condition) than in neutral, while there were no changes in the case of non-sensitive ones. Doxorubicin (DOX) and paclitaxel (PTX) were loaded with drug loading content ranging from 2.4 to 3.5 %, respectively. Interestingly, the anticancer drugs released from mPEG-Hyd-PLA micelles could also be promoted by the increased acidity. An in vitro cytotoxicity study showed that the DOX-loaded mPEG-Hyd-PLA micelles have significantly enhanced cytotoxicity against HepG2 cells compared with the non-sensitive poly(ethylene glycol)-block-poly(lactic acid) (mPEG-PLA) micelles. Confocal microscopy observation indicated that more DOX were delivered into the nuclei of cells following 6 or 12 h incubation with DOX-loaded mPEG-Hyd-PLA micelles. In vivo studies on H22-bearing Swiss mice demonstrated the superior anticancer activity of DOX-loaded mPEG-Hyd-PLA micelles over free DOX and DOX-loaded mPEG-PLA micelles. These hydrazone-containing pH-responsive degradable micelles provide a useful strategy for antitumor drug delivery.

  11. Remote consultation and diagnosis in medical imaging using a global PACS backbone network

    NASA Astrophysics Data System (ADS)

    Martinez, Ralph; Sutaria, Bijal N.; Kim, Jinman; Nam, Jiseung

    1993-10-01

    A Global PACS is a national network which interconnects several PACS networks at medical and hospital complexes using a national backbone network. A Global PACS environment enables new and beneficial operations between radiologists and physicians, when they are located in different geographical locations. One operation allows the radiologist to view the same image folder at both Local and Remote sites so that a diagnosis can be performed. The paper describes the user interface, database management, and network communication software which has been developed in the Computer Engineering Research Laboratory and Radiology Research Laboratory. Specifically, a design for a file management system in a distributed environment is presented. In the remote consultation and diagnosis operation, a set of images is requested from the database archive system and sent to the Local and Remote workstation sites on the Global PACS network. Viewing the same images, the radiologists use pointing overlay commands, or frames to point out features on the images. Each workstation transfers these frames, to the other workstation, so that an interactive session for diagnosis takes place. In this phase, we use fixed frames and variable size frames, used to outline an object. The data pockets for these frames traverses the national backbone in real-time. We accomplish this feature by using TCP/IP protocol sockets for communications. The remote consultation and diagnosis operation has been tested in real-time between the University Medical Center and the Bowman Gray School of Medicine at Wake Forest University, over the Internet. In this paper, we show the feasibility of the operation in a Global PACS environment. Future improvements to the system will include real-time voice and interactive compressed video scenarios.

  12. Enhanced biosynthetically directed fractional carbon-13 enrichment of proteins for backbone NMR Assignments

    PubMed Central

    Wenrich, Broc R.; Sonstrom, Reilly E.; Gupta, Riju A.; Rovnyak, David

    2015-01-01

    Routes to carbon-13 enrichment of bacterially expressed proteins include achieving uniform or positionally selective (e.g. ILV-Me, or 13C′, etc.) enrichment. We consider the potential for biosynthetically directed fractional enrichment (e.g. carbon-13 incorporation in the protein less than 100%) for performing routine n-(D)dimensional NMR spectroscopy of proteins. First, we demonstrate an approach to fractional isotope addition where the initial growth media containing natural abundance glucose is replenished at induction with a small amount (e.g. 10%w/w u-13C-glucose) of enriched nutrient. The approach considered here is to add 10% (e.g. 200 mg for a 2 g/L culture) u-13C-glucose at the induction time (OD600=0.8), resulting in a protein with enhanced 13C incorporation that gives almost the same NMR signal levels as an exact 20% 13C sample. Second, whereas fractional enrichment is used for obtaining stereospecific methyl assignments, we find that 13C incorporation levels no greater than 20%w/w yield 13C and 13C-13C spin pair incorporation sufficient to conduct typical 3D-bioNMR backbone experiments on moderate instrumentation (600 MHz, RT probe). Typical 3D-bioNMR experiments of a fractionally enriched protein yield expected backbone connectivities, and did not show amino acid biases in this work, with one exception. When adding 10% u-13C glucose to expression media at induction, there is poor preservation of 13Cα-13Cβ spin pairs in the amino acids ILV, leading to the absence of Cβ signals in HNCACB spectra for ILV, a potentially useful editing effect. Enhanced fractional carbon-13 enrichment provides lower-cost routes to high throughput protein NMR studies, and makes modern protein NMR more cost-accessible. PMID:26256059

  13. Subpicosecond protein backbone changes detected during the green-absorbing proteorhodopsin primary photoreaction.

    PubMed

    Amsden, Jason J; Kralj, Joel M; Chieffo, Logan R; Wang, Xihua; Erramilli, Shyamsunder; Spudich, Elena N; Spudich, John L; Ziegler, Lawrence D; Rothschild, Kenneth J

    2007-10-11

    Recent studies demonstrate that photoactive proteins can react within several picoseconds to photon absorption by their chromophores. Faster subpicosecond protein responses have been suggested to occur in rhodopsin-like proteins where retinal photoisomerization may impulsively drive structural changes in nearby protein groups. Here, we test this possibility by investigating the earliest protein structural changes occurring in proteorhodopsin (PR) using ultrafast transient infrared (TIR) spectroscopy with approximately 200 fs time resolution combined with nonperturbing isotope labeling. PR is a recently discovered microbial rhodopsin similar to bacteriorhodopsin (BR) found in marine proteobacteria and functions as a proton pump. Vibrational bands in the retinal fingerprint (1175-1215 cm(-1)) and ethylenic stretching (1500-1570 cm(-1)) regions characteristic of all-trans to 13-cis chromophore isomerization and formation of a red-shifted photointermediate appear with a 500-700 fs time constant after photoexcitation. Bands characteristic of partial return to the ground state evolve with a 2.0-3.5 ps time constant. In addition, a negative band appears at 1548 cm(-1) with a time constant of 500-700 fs, which on the basis of total-15N and retinal C15D (retinal with a deuterium on carbon 15) isotope labeling is assigned to an amide II peptide backbone mode that shifts to near 1538 cm(-1) concomitantly with chromophore isomerization. Our results demonstrate that one or more peptide backbone groups in PR respond with a time constant of 500-700 fs, almost coincident with the light-driven retinylidene chromophore isomerization. The protein changes we observe on a subpicosecond time scale may be involved in storage of the absorbed photon energy subsequently utilized for proton transport.

  14. 40-Gbps optical backbone network deep packet inspection based on FPGA

    NASA Astrophysics Data System (ADS)

    Zuo, Yuan; Huang, Zhiping; Su, Shaojing

    2014-11-01

    In the era of information, the big data, which contains huge information, brings about some problems, such as high speed transmission, storage and real-time analysis and process. As the important media for data transmission, the Internet is the significant part for big data processing research. With the large-scale usage of the Internet, the data streaming of network is increasing rapidly. The speed level in the main fiber optic communication of the present has reached 40Gbps, even 100Gbps, therefore data on the optical backbone network shows some features of massive data. Generally, data services are provided via IP packets on the optical backbone network, which is constituted with SDH (Synchronous Digital Hierarchy). Hence this method that IP packets are directly mapped into SDH payload is named POS (Packet over SDH) technology. Aiming at the problems of real time process of high speed massive data, this paper designs a process system platform based on ATCA for 40Gbps POS signal data stream recognition and packet content capture, which employs the FPGA as the CPU. This platform offers pre-processing of clustering algorithms, service traffic identification and data mining for the following big data storage and analysis with high efficiency. Also, the operational procedure is proposed in this paper. Four channels of 10Gbps POS signal decomposed by the analysis module, which chooses FPGA as the kernel, are inputted to the flow classification module and the pattern matching component based on TCAM. Based on the properties of the length of payload and net flows, buffer management is added to the platform to keep the key flow information. According to data stream analysis, DPI (deep packet inspection) and flow balance distribute, the signal is transmitted to the backend machine through the giga Ethernet ports on back board. Practice shows that the proposed platform is superior to the traditional applications based on ASIC and NP.

  15. Synthesis of 3-iodoindoles by the Pd/Cu-catalyzed coupling of N,N-dialkyl-2-iodoanilines and terminal acetylenes, followed by electrophilic cyclization.

    PubMed

    Yue, Dawei; Yao, Tuanli; Larock, Richard C

    2006-01-06

    [reaction: see text] 3-Iodoindoles have been prepared in excellent yields by coupling terminal acetylenes with N,N-dialkyl-o-iodoanilines in the presence of a Pd/Cu catalyst, followed by an electrophilic cyclization of the resulting N,N-dialkyl-o-(1-alkynyl)anilines using I2 in CH2Cl2. Aryl-, vinylic-, alkyl-, and silyl-substituted terminal acetylenes undergo this process to produce excellent yields of 3-iodoindoles. The reactivity of the carbon-nitrogen bond cleavage during cyclization follows the following order: Me > n-Bu, Me > Ph, and cyclohexyl > Me. Subsequent palladium-catalyzed Sonogashira, Suzuki, and Heck reactions of the resulting 3-iodoindoles proceed smoothly in good yields.

  16. Stereoselective synthesis of 1,3-disubstituted isoindolines via Rh(III)-catalyzed tandem oxidative olefination-cyclization of 4-aryl cyclic sulfamidates.

    PubMed

    Son, Se-Mi; Seo, Yeon Ji; Lee, Hyeon-Kyu

    2016-03-21

    Rh(III)-catalyzed tandem ortho C-H olefination of cyclic 4-aryl sulfamidates (1) and subsequent intramolecular cyclization are described. This reaction serves as a method for the direct and stereoselective synthesis of 1,3-disubstituted isoindolines (3) starting with enantiomerically enriched 4-aryl cyclic sulfamidates. In this process, the configurational integrity of the stereogenic center in the starting cyclic sulfamidate is completely retained. In addition, the process generates trans-1,3-disubstituted isoindolines exclusively.

  17. Asymmetric Michael addition/intramolecular cyclization catalyzed by bifunctional tertiary amine-squaramides: construction of chiral 2-amino-4H-chromene-3-carbonitrile derivatives.

    PubMed

    Gao, Yu; Du, Da-Ming

    2014-10-01

    The efficient asymmetric Michael addition/intramolecular cyclization of malononitrile with dienones catalyzed by a chiral bifunctional tertiary amine-squaramide catalyst for the synthesis of chiral 2-amino-4H-chromene-3-carbonitrile derivatives was developed. The corresponding products were obtained in good to excellent yields (up to 99%) with excellent enantioselectivities (up to 98% ee) for most of the bisarylidenecyclopentanones.

  18. Rh(III)-catalyzed addition of alkenyl C-H bond to isocyanates and intramolecular cyclization: direct synthesis 5-ylidenepyrrol-2(5H)-ones.

    PubMed

    Hou, Wei; Zhou, Bing; Yang, Yaxi; Feng, Huijin; Li, Yuanchao

    2013-04-19

    The rhodium-catalyzed addition of an alkenyl C-H bond to isocyanates via sp(2) C-H bond activation followed by an intramolecular cyclization is described. This atom-economic and catalytic reaction affords a simple and straightforward access to biologically relevant 5-ylidene pyrrol-2(5H)-ones and can be carried out under mild and neutral conditions in the absence of any additives and environmentally hazardous waste production.

  19. Terminating Catalytic Asymmetric Heck Cyclizations by Stereoselective Intramolecular Capture of η3-Allylpalladium Intermediates: Total Synthesis of (−)-Spirotryprostatin B and Three Stereoisomers

    PubMed Central

    Overman, Larry E.; Rosen, Mark D.

    2010-01-01

    A catalytic intramolecular Heck reaction, followed by capture of the resulting η3-allylpalladium intermediate by a tethered diketopiperazine, is the central step in a concise synthetic route to (−)-spirotryprostatin B and three stereoisomers. This study demonstrates that an acyclic, chiral η3-allylpalladium fragment generated in a catalytic asymmetric Heck cyclization can be trapped by even a weakly nucleophilic diketopiperazine more rapidly than it undergoes diastereomeric equilibration. PMID:20725641

  20. Rapid pseudo five-component synthesis of intensively blue luminescent 2,5-di(hetero)arylfurans via a Sonogashira-Glaser cyclization sequence.

    PubMed

    Klukas, Fabian; Grunwald, Alexander; Menschel, Franziska; Müller, Thomas J J

    2014-01-01

    2,5-Di(hetero)arylfurans are readily accessible in a pseudo five-component reaction via a Sonogashira-Glaser coupling sequence followed by a superbase-mediated (KOH/DMSO) cyclization in a consecutive one-pot fashion. Besides the straightforward synthesis of natural products and biologically active molecules all representatives are particularly interesting due to their bright blue luminescence with remarkably high quantum yields. The electronic structure of the title compounds is additionally studied with DFT computations.

  1. Aerobic oxidative cyclization of benzamides via meta-selective C-H tert-alkylation: rapid entry to 7-alkylated isoquinolinediones.

    PubMed

    Tang, Shi; Deng, You-Lin; Li, Jie; Wang, Wen-Xin; Wang, Ying-Chun; Li, Zeng-Zeng; Yuan, Li; Chen, Shi-Lu; Sheng, Rui-Long

    2016-03-25

    A novel copper-catalyzed aerobic oxidative cyclization of benzamides via meta-selective C-H tert-alkylation using AIBN and analogues as radical precursors was described. This strategy provides an elusive and rapid means to 7-tert-alkylated isoquinolinediones, as well as the construction of tertiary alkyl-aryl C(sp(3))-C(sp(2)) bonds with positional selectivity.

  2. Copper-catalyzed difunctionalization of activated alkynes by radical oxidation-tandem cyclization/dearomatization to synthesize 3-trifluoromethyl spiro[4.5]trienones.

    PubMed

    Hua, Hui-Liang; He, Yu-Tao; Qiu, Yi-Feng; Li, Ying-Xiu; Song, Bo; Gao, Pin; Song, Xian-Rong; Guo, Dong-Hui; Liu, Xue-Yuan; Liang, Yong-Min

    2015-01-19

    A copper-catalyzed difunctionalizing trifluoromethylation of activated alkynes with the cheap reagent sodium trifluoromethanesulfinate (NaSO2CF3 or Langlois' reagent) has been developed incorporating a tandem cyclization/dearomatization process. This strategy affords a straightforward route to synthesis of 3-(trifluoromethyl)-spiro[4.5]trienones, and presents an example of difunctionalization of alkynes for simultaneous formation of two carbon-carbon single bonds and one carbon-oxygen double bond.

  3. The intramolecular cyclization of bis-2,5-dimethylene-2,5-dihydrofurans and bis-2,5-dimethylene-2,5-dihydrothiophenes: An approach to macrocycles

    SciTech Connect

    Klumpp, Doug Allen

    1994-01-11

    The first two papers of this dissertation present our work with the intramolecular cyclizations of a pair of p-quinodimethanes. The p-quinodimethanes were generated by flash vacuum pyrolysis (FVP) and were linked by a bridging chain. The third paper of this dissertation presents our work in the synthetic manipulation of the products formed from the intramolecular reactions of the p-quinodimethanes.

  4. Divergent synthetic routes for ring expansion or cyclization from 1,4-allylic diol derivatives via gold(I) catalysis or zinc(II) mediation.

    PubMed

    Zhu, Li-Li; Li, Xiao-Xiao; Zhou, Wen; Li, Xin; Chen, Zili

    2011-11-04

    A new efficient method was developed to transform cyclic alkanols into one-carbon higher homologated ketones using various esters as the leaving groups through gold-catalyzed allylic cation-promoted pinacol-type rearrangement. This reaction, coupled with oxy-Cope rearrangement, provided a new strategy to synthesize five-carbon homologated ring ketones. In addition, using ZnBr(2), 2,5-dihydrofuran products were obtained in moderate to good yields via an intramolecular cyclization process.

  5. A Raney-cobalt-mediated tandem reductive cyclization route to the 1,5-methanoazocino[4,3-b]indole framework of the uleine and Strychnos alkaloids.

    PubMed

    Reekie, Tristan A; Banwell, Martin G; Willis, Anthony C

    2012-12-07

    The readily accessible enones 8, 17, and 18 undergo 2-fold reductive cyclization reactions upon exposure to hydrogen in the presence of Raney-cobalt and thereby afford compounds 11 (72%), 19 (47%), and 20 (84%), respectively. These products embody the ABCD-ring system associated with the title alkaloids, and compound 11 can be converted, over four steps and in 33% yield, into congener 24 incorporating the ABCDE-ring system of the Strychnos alkaloids.

  6. Ruthenium-catalyzed transfer-hydrogenative cyclization of 1,6-diynes with hantzsch 1,4-dihydropyridine as a H2 surrogate.

    PubMed

    Yamamoto, Yoshihiko; Mori, Shota; Shibuya, Masatoshi

    2013-09-02

    The transfer-hydrogenative cyclization of 1,6-diynes with Hantzsch 1,4-dihydropyridine as a H2 surrogate was performed in the presence of a cationic ruthenium catalyst of the type [Cp'Ru(MeCN)3PF6]. Exocyclic 1,3-dienes or their 1,4-hydrogenation products, cycloalkenes, were selectively obtained, depending on the substrate structure and the reaction conditions.

  7. Mechanism of Rh-Catalyzed Oxidative Cyclizations: Closed versus Open Shell Pathways.

    PubMed

    Park, Yoonsu; Ahn, Seihwan; Kang, Dahye; Baik, Mu-Hyun

    2016-06-21

    A conceptual theory for analyzing and understanding oxidative addition reactions that form the cornerstone of many transition metal mediated catalytic cycles that activate C-C and C-H bonds, for example, was developed. The cleavage of the σ- or π-bond in the organic substrate can be envisioned to follow a closed or an open shell formalism, which is matched by a corresponding electronic structure at the metal center of the catalyst. Whereas the assignment of one or the other mechanistic scenario appears formal and equivalent at first sight, they should be recognized as different classes of reactions, because they lead to different reaction optimization and control strategies. The closed-shell mechanism involves heterolytic bond cleavages, which give rise to highly localized charges to form at the transition state. In the open-shell pathway, bonds are broken homolytically avoiding localized charges to accumulate on molecular fragments at the transition states. As a result, functional groups with inductive effects may exert a substantial influence on the energies of the intermediate and transition states, whereas no such effect is expected if the mechanism proceeds through the open-shell mechanism. If these functional groups are placed in a way that opens an electronic communication pathway to the molecular sites where charges accumulate, for example, using hyperconjugation, electron donating groups may stabilize a positive charge at that site. An instructive example is discussed, where this stereoelectronic effect allowed for rendering the oxidative addition diastereoselective. No such control is possible, however, when the open-shell reaction pathway is followed, because the inductive effects of functional groups have little to no effect on the stabilities of radical-like substrate states that are encountered when the bonds are broken in a homolytic fashion. Whether the closed-shell or open-shell mechanism for oxidative addition is followed is determined by the

  8. Noncanonical α/γ Backbone Conformations in RNA and the Accuracy of Their Description by the AMBER Force Field.

    PubMed

    Zgarbová, Marie; Jurečka, Petr; Banáš, Pavel; Havrila, Marek; Šponer, Jiří; Otyepka, Michal

    2017-03-23

    The sugar-phosphate backbone of RNA can exist in diverse rotameric substates, giving RNA molecules enormous conformational variability. The most frequent noncanonical backbone conformation in RNA is α/γ = t/t, which is derived from the canonical backbone by a crankshaft motion and largely preserves the standard geometry of the RNA duplex. A similar conformation also exists in DNA, where it has been extensively studied and shown to be involved in DNA-protein interactions. However, the function of the α/γ = t/t conformation in RNA is poorly understood. Here, we present molecular dynamics simulations of several prototypical RNA structures obtained from X-ray and NMR experiments, including canonical and mismatched RNA duplexes, UUCG and GAGA tetraloops, Loop E, the sarcin-ricin loop, a parallel guanine quadruplex, and a viral pseudoknot. The stability of various noncanonical α/γ backbone conformations was analyzed with two AMBER force fields, ff99bsc0χOL3 and ff99bsc0χOL3 with the recent εζOL1 and βOL1 corrections for DNA. Although some α/γ substates were stable with seemingly well-described equilibria, many were unstable in our simulations. Notably, the most frequent noncanonical conformer α/γ = t/t was unstable in both tested force fields. Possible reasons for this instability are discussed. Our work reveals a potentially important artifact in RNA force fields and highlights a need for further force field refinement.

  9. Slow dynamics of a protein backbone in molecular dynamics simulation revealed by time-structure based independent component analysis

    SciTech Connect

    Naritomi, Yusuke; Fuchigami, Sotaro

    2013-12-07

    We recently proposed the method of time-structure based independent component analysis (tICA) to examine the slow dynamics involved in conformational fluctuations of a protein as estimated by molecular dynamics (MD) simulation [Y. Naritomi and S. Fuchigami, J. Chem. Phys. 134, 065101 (2011)]. Our previous study focused on domain motions of the protein and examined its dynamics by using rigid-body domain analysis and tICA. However, the protein changes its conformation not only through domain motions but also by various types of motions involving its backbone and side chains. Some of these motions might occur on a slow time scale: we hypothesize that if so, we could effectively detect and characterize them using tICA. In the present study, we investigated slow dynamics of the protein backbone using MD simulation and tICA. The selected target protein was lysine-, arginine-, ornithine-binding protein (LAO), which comprises two domains and undergoes large domain motions. MD simulation of LAO in explicit water was performed for 1 μs, and the obtained trajectory of C{sub α} atoms in the backbone was analyzed by tICA. This analysis successfully provided us with slow modes for LAO that represented either domain motions or local movements of the backbone. Further analysis elucidated the atomic details of the suggested local motions and confirmed that these motions truly occurred on the expected slow time scale.

  10. The extension of a DNA double helix by an additional Watson-Crick base pair on the same backbone.

    PubMed

    Kumar, Pawan; Sharma, Pawan K; Madsen, Charlotte S; Petersen, Michael; Nielsen, Poul

    2013-06-17

    Additional base pair: The DNA duplex can be extended with an additional Watson-Crick base pair on the same backbone by the use of double-headed nucleotides. These also work as compressed dinucleotides and form two base pairs with cognate nucleobases on the opposite strand.

  11. Slow dynamics of a protein backbone in molecular dynamics simulation revealed by time-structure based independent component analysis

    NASA Astrophysics Data System (ADS)

    Naritomi, Yusuke; Fuchigami, Sotaro

    2013-12-01

    We recently proposed the method of time-structure based independent component analysis (tICA) to examine the slow dynamics involved in conformational fluctuations of a protein as estimated by molecular dynamics (MD) simulation [Y. Naritomi and S. Fuchigami, J. Chem. Phys. 134, 065101 (2011)]. Our previous study focused on domain motions of the protein and examined its dynamics by using rigid-body domain analysis and tICA. However, the protein changes its conformation not only through domain motions but also by various types of motions involving its backbone and side chains. Some of these motions might occur on a slow time scale: we hypothesize that if so, we could effectively detect and characterize them using tICA. In the present study, we investigated slow dynamics of the protein backbone using MD simulation and tICA. The selected target protein was lysine-, arginine-, ornithine-binding protein (LAO), which comprises two domains and undergoes large domain motions. MD simulation of LAO in explicit water was performed for 1 μs, and the obtained trajectory of Cα atoms in the backbone was analyzed by tICA. This analysis successfully provided us with slow modes for LAO that represented either domain motions or local movements of the backbone. Further analysis elucidated the atomic details of the suggested local motions and confirmed that these motions truly occurred on the expected slow time scale.

  12. Oxidation Responsive Polymers with a Triggered Degradation via Arylboronate Self-Immolative Motifs on a Polyphosphazene Backbone

    PubMed Central

    2017-01-01

    Oxidation responsive polymers with triggered degradation pathways have been prepared via attachment of self-immolative moieties onto a hydrolytically unstable polyphosphazene backbone. After controlled main-chain growth, postpolymerization functionalization allows the preparation of hydrolytically stable poly(organo)phosphazenes decorated with a phenylboronic ester caging group. In oxidative environments, triggered cleavage of the caging group is followed by self-immolation, exposing the unstable glycine-substituted polyphosphazene which subsequently undergoes to backbone degradation to low-molecular weight molecules. As well as giving mechanistic insights, detailed GPC and 1H and 31P NMR analysis reveal the polymers to be stable in aqueous solutions, but show a selective, fast degradation upon exposure to hydrogen peroxide containing solutions. Since the post-polymerization functionalization route allows simple access to polymer backbones with a broad range of molecular weights, the approach of using the inorganic backbone as a platform significantly expands the toolbox of polymers capable of stimuli-responsive degradation. PMID:28251035

  13. Local Electronic and Chemical Structure of Oligo-acetylene Derivatives Formed Through Radical Cyclizations at a Surface

    PubMed Central

    2014-01-01

    Semiconducting π-conjugated polymers have attracted significant interest for applications in light-emitting diodes, field-effect transistors, photovoltaics, and nonlinear optoelectronic devices. Central to the success of these functional organic materials is the facile tunability of their electrical, optical, and magnetic properties along with easy processability and the outstanding mechanical properties associated with polymeric structures. In this work we characterize the chemical and electronic structure of individual chains of oligo-(E)-1,1′-bi(indenylidene), a polyacetylene derivative that we have obtained through cooperative C1–C5 thermal enediyne cyclizations on Au(111) surfaces followed by a step-growth polymerization of the (E)-1,1′-bi(indenylidene) diradical intermediates. We have determined the combined structural and electronic properties of this class of oligomers by characterizing the atomically precise chemical structure of individual monomer building blocks and oligomer chains (via noncontact atomic force microscopy (nc-AFM)), as well as by imaging their localized and extended molecular orbitals (via scanning tunneling microscopy and spectroscopy (STM/STS)). Our combined structural and electronic measurements reveal that the energy associated with extended π-conjugated states in these oligomers is significantly lower than the energy of the corresponding localized monomer orbitals, consistent with theoretical predictions. PMID:24387223

  14. Cobalt(III)-Catalyzed Synthesis of Indazoles and Furans by C–H Bond Functionalization/Addition/Cyclization Cascades

    PubMed Central

    2015-01-01

    The development of operationally straightforward and cost-effective routes for the assembly of heterocycles from simple inputs is important for many scientific endeavors, including pharmaceutical, agrochemical, and materials research. In this article we describe the development of a new air-stable cationic Co(III) catalyst for convergent, one-step benchtop syntheses of N-aryl-2H-indazoles and furans by C–H bond additions to aldehydes followed by in situ cyclization and aromatization. Only a substoichiometric amount of AcOH is required as an additive that is both low-cost and convenient to handle. The syntheses of these heterocycles are the first examples of Co(III)-catalyzed additions to aldehydes, and reactions are demonstrated for a variety of aromatic, heteroaromatic, and aliphatic derivatives. The syntheses of both N-aryl-2H-indazoles and furans have been performed on 20 mmol scales and should be readily applicable to larger scales. The reported heterocycle syntheses also demonstrate the use of directing groups that have not previously been applied to Co(III)-catalyzed C–H bond functionalizations. Additionally, the synthesis of furans demonstrates the first example of Co(III)-catalyzed functionalization of alkenyl C–H bonds. PMID:25494296

  15. DNA cyclization and looping in the wormlike limit: Normal modes and the validity of the harmonic approximation.

    PubMed

    Giovan, Stefan M; Hanke, Andreas; Levene, Stephen D

    2015-09-01

    For much of the last three decades, Monte Carlo-simulation methods have been the standard approach for accurately calculating the cyclization probability, J, or J factor, for DNA models having sequence-dependent bends or inhomogeneous bending flexibility. Within the last 10 years approaches based on harmonic analysis of semi-flexible polymer models have been introduced, which offer much greater computational efficiency than Monte Carlo techniques. These methods consider the ensemble of molecular conformations in terms of harmonic fluctuations about a well-defined elastic-energy minimum. However, the harmonic approximation is only applicable for small systems, because the accessible conformation space of larger systems is increasingly dominated by anharmonic contributions. In the case of computed values of the J factor, deviations of the harmonic approximation from the exact value of J as a function of DNA length have not been characterized. Using a recent, numerically exact method that accounts for both anharmonic and harmonic contributions to J for wormlike chains of arbitrary size, we report here the apparent error that results from neglecting anharmonic behavior. For wormlike chains having contour lengths less than four times the persistence length, the error in J arising from the harmonic approximation is generally small, amounting to free energies less than the thermal energy, kB T. For larger systems, however, the deviations between harmonic and exact J values increase approximately linearly with size.

  16. RAFT mediated polymerization of methyl methacrylate initiated by Bergman cyclization: access to high molecular weight narrow polydispersity polymers.

    PubMed

    Gerstel, Peter; Barner-Kowollik, Christopher

    2011-03-02

    The first RAFT mediated polymerization of methyl methacrylate initiated by diradicals derived from Bergman cyclization was performed employing 3,4-benzocyclodec-3-ene-1,5-diyne (BCDY) as diradical source and cyanoisopropyldithiobenzoate (CPDB) as RAFT agent. The polymerization was conducted in bulk at 80 °C for 3 h. The concentration of the enediyne was kept constant at 3.0 x 10⁻² mol · L⁻¹ and the RAFT agent concentration was varied between 0.0 mol · L⁻¹ and 2.4 x 10⁻¹ mol · L⁻¹. A detailed ESI-MS analysis reveals the absence of intramolecular termination reactions (ring formation) in the RAFT mediated system, which usually makes diradicalic initiation unfavorable. The presence of polymeric chains propagating at both ends could be confirmed. The conversion of the RAFT mediated polymerization was up to more than two times higher than the RAFT free polymerization at identical conditions. Thus, polymers with narrow polydispersities (1.1 ≤ PDI ≤ 1.5) even at very high molecular weights (near 400,000 Da) were obtained within modest reaction times.

  17. Elementary Flux Mode Analysis Revealed Cyclization Pathway as a Powerful Way for NADPH Regeneration of Central Carbon Metabolism.

    PubMed

    Rui, Bin; Yi, Yin; Shen, Tie; Zheng, Meijuan; Zhou, Wenwei; Du, Honglin; Fan, Yadong; Wang, Yongkang; Zhang, Zhengdong; Xu, Shengsheng; Liu, Zhijie; Wen, Han; Xie, Xiaoyao

    2015-01-01

    NADPH regeneration capacity is attracting growing research attention due to its important role in resisting oxidative stress. Besides, NADPH availability has been regarded as a limiting factor in production of industrially valuable compounds. The central carbon metabolism carries the carbon skeleton flux supporting the operation of NADPH-regenerating enzyme and offers flexibility in coping with NADPH demand for varied intracellular environment. To acquire an insightful understanding of its NADPH regeneration capacity, the elementary mode method was employed to compute all elementary flux modes (EFMs) of a network representative of central carbon metabolism. Based on the metabolic flux distributions of these modes, a cluster analysis of EFMs with high NADPH regeneration rate was conducted using the self-organizing map clustering algorithm. The clustering results were used to study the relationship between the flux of total NADPH regeneration and the flux in each NADPH producing enzyme. The results identified several reaction combinations supporting high NADPH regeneration, which are proven to be feasible in cells via thermodynamic analysis and coincident with a great deal of previous experimental report. Meanwhile, the reaction combinations showed some common characteristics: there were one or two decarboxylation oxidation reactions in the combinations that produced NADPH and the combination constitution included certain gluconeogenesis pathways. These findings suggested cyclization pathways as a powerful way for NADPH regeneration capacity of bacterial central carbon metabolism.

  18. Cobalt(III)-catalyzed synthesis of indazoles and furans by C-H bond functionalization/addition/cyclization cascades.

    PubMed

    Hummel, Joshua R; Ellman, Jonathan A

    2015-01-14

    The development of operationally straightforward and cost-effective routes for the assembly of heterocycles from simple inputs is important for many scientific endeavors, including pharmaceutical, agrochemical, and materials research. In this article we describe the development of a new air-stable cationic Co(III) catalyst for convergent, one-step benchtop syntheses of N-aryl-2H-indazoles and furans by C-H bond additions to aldehydes followed by in situ cyclization and aromatization. Only a substoichiometric amount of AcOH is required as an additive that is both low-cost and convenient to handle. The syntheses of these heterocycles are the first examples of Co(III)-catalyzed additions to aldehydes, and reactions are demonstrated for a variety of aromatic, heteroaromatic, and aliphatic derivatives. The syntheses of both N-aryl-2H-indazoles and furans have been performed on 20 mmol scales and should be readily applicable to larger scales. The reported heterocycle syntheses also demonstrate the use of directing groups that have not previously been applied to Co(III)-catalyzed C-H bond functionalizations. Additionally, the synthesis of furans demonstrates the first example of Co(III)-catalyzed functionalization of alkenyl C-H bonds.

  19. Influence of backbone rigidness on single chain conformation of thiophene-based conjugated polymers.

    PubMed

    Hu, Zhongjian; Liu, Jianhua; Simón-Bower, Lauren; Zhai, Lei; Gesquiere, Andre J

    2013-04-25

    Structural order of conjugated polymers at different length scales directs the optoelectronic properties of the corresponding materials; thus it is of critical importance to understand and control conjugated polymer morphology for successful application of these materials in organic optoelectronics. Herein, with the aim of probing the dependence of single chain folding properties on the chemical structure and rigidness of the polymer backbones, single molecule fluorescence spectroscopy was applied to four thiophene-based conjugated polymers. These include regioregular poly(3-hexylthiophene) (RR-P3HT), poly(2,5-bis(3-tetradecylthiophen-2-yl)thieno[3,2-b]thiophene) (PBTTT-14), poly(2,5-bis(3-tetradecylthiophen-2-yl)thiophene-2-yl)thiophen-2-ylthiazolo[5,4-d]thiazole) (PTzQT-12), and poly(3,3-didodecylquaterthiophene)] (PQT-12). Our previous work has shown that RR-P3HT and PBTTT-14 polymer chains fold in their nanostructures, whereas PQT-12 and PTzQT-12 do not fold in their nanostructures. At the single molecule level, it was found that RR-P3HT single chains almost exclusively fold into loosely and strongly aggregated conformations, analogous to the folding properties in nanostructures. PQT-12 displays significant chain folding as well, but only into loosely aggregated conformations, showing an absence of strongly aggregated polymer chains. PBTTT-14 exhibits a significant fraction of rigid polymer chain. The findings made for single molecules of PQT-12 and PBTTT-14 are thus in contrast with the observations made in their corresponding nanostructures. PTzQT-12 appears to be the most rigid and planar conjugated polymer of these four polymers. However, although the presumably nonfolding polymers PQT-12 and PTzQT-12 exhibit less folding than RR-P3HT, there is still a significant occurrence of chain folding for these polymers at the single molecule level. These results suggest that the folding properties of conjugated polymers can be influenced by the architecture of the

  20. Dual-functional ROMP-based betaines: effect of hydrophilicity and backbone structure on nonfouling properties.

    PubMed

    Colak, Semra; Tew, Gregory N

    2012-01-10

    Foundational materials for nonfouling coatings were designed and synthesized from a series of novel dual-functional zwitterionic polymers, Poly[NRZI], which were easily obtained via ring-opening metathesis polymerization (ROMP) followed by a single step transformation of the cationic precursor, Poly[NR(+)], to the zwitterion, Poly[NRZI]. The resulting unique dual-functional structure contained the anion and the cation within the same repeat unit but on separate side chains, enabling the hydrophilicity of the system to be tuned at the repeat unit level. These dual-functional zwitterionic polymers were specifically designed to investigate the impact of structural changes, including the backbone, hydrophilicity, and charge, on the overall nonfouling properties. To evaluate the importance of backbone structure, and as a direct comparison to previously studied methacrylate-based betaines, norbornene-based carbo- and sulfobetaines (Poly[NCarboZI] and Poly[NSulfoZI]) as well as a methacrylate-based sulfobetaine (Poly[MASulfoZI]) were synthesized. These structures contain the anion-cation pairs on the same side chain. Nonfouling coatings were prepared from copolymers, composed of the zwitterionic/cationic precursor monomer and an ethoxysilane-containing monomer. The coatings were evaluated by using protein adsorption studies, which clearly indicated that the overall hydrophilicity has a major influence on the nonfouling character of the materials. The most hydrophilic coating, from the oligoethylene glycol (OEG)-containing dual-functional betaine, Poly[NOEGZI-co-NSi], showed the best resistance to nonspecific protein adsorption (Γ(FIB) = 0.039 ng/mm(2)). Both norbornene-based polymers systems, Poly[NSulfoZI] and Poly[NCarboZI], were more hydrophilic and thus more resistant to protein adsorption than the methacrylate-based Poly[MASulfoZI]. Comparing the protein resistance of the dual-functional zwitterionic coatings, Poly[NRZI-co-NSi], to that of their cationic

  1. N-acetyl-L-aspartic acid-N'-methylamide with side-chain orientation capable of external hydrogen bonding . Backbone and side-chain folding, studied at the DFT level of quantum theory

    NASA Astrophysics Data System (ADS)

    Koo, J. C. P.; Chass, G. A.; Perczel, A.; Farkas, Ö.; Varro, A.; Torday, L. L.; Papp, J. Gy.; Csizmadia, I. G.

    2002-09-01

    In this study, we generated and analyzed the side-chain conformational potential energy hypersurfaces for each of the nine possible backbone conformers for N-acetyl-L-aspartic acid-N' methylamide. We found a total of 27 out of the 81 possible conformers optimized at the B3LYP/6-31G(d) level of theory. The relative energies, as well as the stabilization energies exerted by the side-chain on the backbone, have been calculated for each of the 27 optimized conformers at this level of theory. Various backbone-backbone (N H{\\cdot}{\\cdot}{\\cdot}O=C) and backbone-side-chain (N H{\\cdot}{\\cdot}{\\cdot}O=C; N H{\\cdot}{\\cdot}{\\cdot}OH) hydrogen bonds were analyzed. The appearance of the notoriously absent \\varepsilon_L backbone conformer may be attributed to such side-chain-backbone (SC/BB) and backbone-backbone (BB/BB) hydrogen bonds.

  2. STARD6 on steroids: solution structure, multiple timescale backbone dynamics and ligand binding mechanism

    NASA Astrophysics Data System (ADS)

    Létourneau, Danny; Bédard, Mikaël; Cabana, Jérôme; Lefebvre, Andrée; Lehoux, Jean-Guy; Lavigne, Pierre

    2016-06-01

    START domain proteins are conserved α/β helix-grip fold that play a role in the non-vesicular and intracellular transport of lipids and sterols. The mechanism and conformational changes permitting the entry of the ligand into their buried binding sites is not well understood. Moreover, their functions and the identification of cognate ligands is still an active area of research. Here, we report the solution structure of STARD6 and the characterization of its backbone dynamics on multiple time-scales through 15N spin-relaxation and amide exchange studies. We reveal for the first time the presence of concerted fluctuations in the Ω1 loop and the C-terminal helix on the microsecond-millisecond time-scale that allows for the opening of the binding site and ligand entry. We also report that STARD6 binds specifically testosterone. Our work represents a milestone for the study of ligand binding mechanism by other START domains and the elucidation of the biological function of STARD6.

  3. Enhancing backbone sampling in Monte Carlo simulations using internal coordinates normal mode analysis.

    PubMed

    Gil, Victor A; Lecina, Daniel; Grebner, Christoph; Guallar, Victor

    2016-10-15

    Normal mode methods are becoming a popular alternative to sample the conformational landscape of proteins. In this study, we describe the implementation of an internal coordinate normal mode analysis method and its application in exploring protein flexibility by using the Monte Carlo method PELE. This new method alternates two different stages, a perturbation of the backbone through the application of torsional normal modes, and a resampling of the side chains. We have evaluated the new approach using two test systems, ubiquitin and c-Src kinase, and the differences to the original ANM method are assessed by comparing both results to reference molecular dynamics simulations. The results suggest that the sampled phase space in the internal coordinate approach is closer to the molecular dynamics phase space than the one coming from a Cartesian coordinate anisotropic network model. In addition, the new method shows a great speedup (∼5-7×), making it a good candidate for future normal mode implementations in Monte Carlo methods.

  4. Dynamics of the IncW genetic backbone imply general trends in conjugative plasmid evolution.

    PubMed

    Fernández-López, Raúl; Garcillán-Barcia, M Pilar; Revilla, Carlos; Lázaro, Miguel; Vielva, Luis; de la Cruz, Fernando

    2006-11-01

    Plasmids cannot be understood as mere tools for genetic exchange: they are themselves subject to the forces of evolution. Their genomic and phylogenetic features have been less studied in this respect. Focusing on the IncW incompatibility group, which includes the smallest known conjugative plasmids, we attempt to unveil some common trends in plasmid evolution. The functional modules of IncW genetic backbone are described, with emphasis on their architecture and relationships to other plasmid groups. Some plasmid regions exhibit strong phylogenetic mosaicism, in striking contrast to others of unusual synteny conservation. The presence of genes of unknown function that are widely distributed in plasmid genomes is also emphasized, exposing the existence of ill-defined yet conserved plasmid functions. Conjugation is an essential hallmark of IncW plasmid biology and special attention is given to the organization and evolution of its transfer modules. Genetic exchange between plasmids and their hosts is analysed by following the evolution of the type IV secretion system. Adaptation of the trw conjugative machinery to pathogenicity functions in Bartonella is discussed as an example of how plasmids can change their host modus vivendi. Starting from the phage paradigm, our analysis articulates novel concepts that apply to plasmid evolution.

  5. STARD6 on steroids: solution structure, multiple timescale backbone dynamics and ligand binding mechanism

    PubMed Central

    Létourneau, Danny; Bédard, Mikaël; Cabana, Jérôme; Lefebvre, Andrée; LeHoux, Jean-Guy; Lavigne, Pierre

    2016-01-01

    START domain proteins are conserved α/β helix-grip fold that play a role in the non-vesicular and intracellular transport of lipids and sterols. The mechanism and conformational changes permitting the entry of the ligand into their buried binding sites is not well understood. Moreover, their functions and the identification of cognate ligands is still an active area of research. Here, we report the solution structure of STARD6 and the characterization of its backbone dynamics on multiple time-scales through 15N spin-relaxation and amide exchange studies. We reveal for the first time the presence of concerted fluctuations in the Ω1 loop and the C-terminal helix on the microsecond-millisecond time-scale that allows for the opening of the binding site and ligand entry. We also report that STARD6 binds specifically testosterone. Our work represents a milestone for the study of ligand binding mechanism by other START domains and the elucidation of the biological function of STARD6. PMID:27340016

  6. Is there a Climate Network - A Backbone of the Climate System? (Invited)

    NASA Astrophysics Data System (ADS)

    Kurths, J.

    2010-12-01

    We consider an inverse problem: Is there a backbone-like structure underlying the climate system? For this we propose a method to reconstruct and analyze a complex network from data generated by a spatio-temporal dynamical system. This technique is then applied to reanalysis and model surface air temperature data. Parameters of this network, as betweenness centrality, uncover relations to global circulation patterns in oceans and atmosphere. We especially study the role of hubs and of long range connections, called teleconnections, in the flows of energy and matter in the climate system. The global scale view on climate networks offers promising new perspectives for detecting dynamical structures based on nonlinear physical processes in the climate system. References Arenas, A., A. Diaz-Guilera, J. Kurths, Y. Moreno, and C. Zhou, Phys. Reports 2008, 469, 93. Donges, J., Y. Zou, N. Marwan, and J. Kurths, Europ. Phys. J. ST 2009, 174, 157-179. Donges, J., Y. Zou, N. Marwan, and J. Kurths, Europhys. Lett. 2009, 87, 48007. Nawrath, J. et al., Phys. Rev. Lett. 2010, 104, 038701. Donner, R., Y. Zou, J. Donges, N. Marwan, and J. Kurths, Phys. Rev. E 2010, 81, 015101(R ).

  7. Phylogenomics resolves a spider backbone phylogeny and rejects a prevailing paradigm for orb web evolution.

    PubMed

    Bond, Jason E; Garrison, Nicole L; Hamilton, Chris A; Godwin, Rebecca L; Hedin, Marshal; Agnarsson, Ingi

    2014-08-04

    Spiders represent an ancient predatory lineage known for their extraordinary biomaterials, including venoms and silks. These adaptations make spiders key arthropod predators in most terrestrial ecosystems. Despite ecological, biomedical, and biomaterial importance, relationships among major spider lineages remain unresolved or poorly supported. Current working hypotheses for a spider "backbone" phylogeny are largely based on morphological evidence, as most molecular markers currently employed are generally inadequate for resolving deeper-level relationships. We present here a phylogenomic analysis of spiders including taxa representing all major spider lineages. Our robust phylogenetic hypothesis recovers some fundamental and uncontroversial spider clades, but rejects the prevailing paradigm of a monophyletic Orbiculariae, the most diverse lineage, containing orb-weaving spiders. Based on our results, the orb web either evolved much earlier than previously hypothesized and is ancestral for a majority of spiders or else it has multiple independent origins, as hypothesized by precladistic authors. Cribellate deinopoid orb weavers that use mechanically adhesive silk are more closely related to a diverse clade of mostly webless spiders than to the araneoid orb-weaving spiders that use adhesive droplet silks. The fundamental shift in our understanding of spider phylogeny proposed here has broad implications for interpreting the evolution of spiders, their remarkable biomaterials, and a key extended phenotype--the spider web.

  8. Backbone, side chain and heme resonance assignments of cytochrome OmcF from Geobacter sulfurreducens.

    PubMed

    Dantas, Joana M; Silva E Sousa, Marta; Salgueiro, Carlos A; Bruix, Marta

    2015-10-01

    Gene knockout studies on Geobacter sulfurreducens (Gs) cells showed that the outer membrane cytochrome OmcF is involved in respiratory pathways leading to the extracellular reduction of Fe(III) citrate and U(VI) oxide. In addition, microarray analysis of OmcF-deficient mutant versus the wild-type strain revealed that many of the genes with decreased transcript level were those whose expression is upregulated in cells grown with a graphite electrode as electron acceptor. This suggests that OmcF also regulates the electron transfer to electrode surfaces and the concomitant electrical current production by Gs in microbial fuel cells. Extracellular electron transfer processes (EET) constitute nowadays the foundations to develop biotechnological applications in biofuel production, bioremediation and bioenergy. Therefore, the structural characterization of OmcF is a fundamental step to understand the mechanisms underlying EET. Here, we report the complete assignment of the heme proton signals together with (1)H, (13)C and (15)N backbone and side chain assignments of the OmcF, excluding the hydrophobic residues of the N-terminal predicted lipid anchor.

  9. Aggregation tendencies in the p53 family are modulated by backbone hydrogen bonds

    PubMed Central

    Cino, Elio A.; Soares, Iaci N.; Pedrote, Murilo M.; de Oliveira, Guilherme A. P.; Silva, Jerson L.

    2016-01-01

    The p53 family of proteins is comprised of p53, p63 and p73. Because the p53 DNA binding domain (DBD) is naturally unstable and possesses an amyloidogenic sequence, it is prone to form amyloid fibrils, causing loss of functions. To develop p53 therapies, it is necessary to understand the molecular basis of p53 instability and aggregation. Light scattering, thioflavin T (ThT) and high hydrostatic pressure (HHP) assays showed that p53 DBD aggregates faster and to a greater extent than p63 and p73 DBDs, and was more susceptible to denaturation. The aggregation tendencies of p53, p63, and p73 DBDs were strongly correlated with their thermal stabilities. Molecular Dynamics (MD) simulations indicated specific regions of structural heterogeneity unique to p53, which may be promoted by elevated incidence of exposed backbone hydrogen bonds (BHBs). The results indicate regions of structural vulnerability in the p53 DBD, suggesting new targetable sites for modulating p53 stability and aggregation, a potential approach to cancer therapy. PMID:27600721

  10. Antimicrobial Activity of Chitosan Derivatives Containing N-Quaternized Moieties in Its Backbone: A Review

    PubMed Central

    Martins, Alessandro F.; Facchi, Suelen P.; Follmann, Heveline D. M.; Pereira, Antonio G. B.; Rubira, Adley F.; Muniz, Edvani C.

    2014-01-01

    Chitosan, which is derived from a deacetylation reaction of chitin, has attractive antimicrobial activity. However, chitosan applications as a biocide are only effective in acidic medium due to its low solubility in neutral and basic conditions. Also, the positive charges carried by the protonated amine groups of chitosan (in acidic conditions) that are the driving force for its solubilization are also associated with its antimicrobial activity. Therefore, chemical modifications of chitosan are required to enhance its solubility and broaden the spectrum of its applications, including as biocide. Quaternization on the nitrogen atom of chitosan is the most used route to render water-soluble chitosan-derivatives, especially at physiological pH conditions. Recent reports in the literature demonstrate that such chitosan-derivatives present excellent antimicrobial activity due to permanent positive charge on nitrogen atoms side-bonded to the polymer backbone. This review presents some relevant work regarding the use of quaternized chitosan-derivatives obtained by different synthetic paths in applications as antimicrobial agents. PMID:25402643

  11. APSY-NMR for protein backbone assignment in high-throughput structural biology

    PubMed Central

    Dutta, Samit Kumar; Serrano, Pedro; Proudfoot, Andrew; Geralt, Michael; Pedrini, Bill; Herrmann, Torsten; Wüthrich, Kurt

    2014-01-01

    A standard set of three APSY-NMR experiments has been used in daily practice to obtain polypeptide backbone NMR assignments in globular proteins with sizes up to about 150 residues, which had been identified as targets for structure determination by the Joint Center for Structural Genomics (JCSG) under the auspices of the Protein Structure Initiative (PSI). In a representative sample of 30 proteins, initial fully automated data analysis with the software UNIO-MATCH-2014 yielded complete or partial assignments for over 90% of the residues. For most proteins the APSY data acquisition was completed in less than 30 hours. The results of the automated procedure provided a basis for efficient interactive validation and extension to near-completion of the assignments by reference to the same 3D heteronuclear-resolved [1H,1H]-NOESY spectra that were subsequently used for the collection of conformational constraints. High-quality structures were obtained for all 30 proteins, using the J-UNIO protocol, which includes extensive automation of NMR structure determination. PMID:25428764

  12. Dependence of crystallite formation and preferential backbone orientations on the side chain pattern in PBDTTPD polymers.

    PubMed

    El Labban, Abdulrahman; Warnan, Julien; Cabanetos, Clément; Ratel, Olivier; Tassone, Christopher; Toney, Michael F; Beaujuge, Pierre M

    2014-11-26

    Alkyl substituents appended to the π-conjugated main chain account for the solution-processability and film-forming properties of most π-conjugated polymers for organic electronic device applications, including field-effect transistors (FETs) and bulk-heterojunction (BHJ) solar cells. Beyond film-forming properties, recent work has emphasized the determining role that side-chain substituents play on polymer self-assembly and thin-film nanostructural order, and, in turn, on device performance. However, the factors that determine polymer crystallite orientation in thin-films, implying preferential backbone orientation relative to the device substrate, are a matter of some debate, and these structural changes remain difficult to anticipate. In this report, we show how systematic changes in the side-chain pattern of poly(benzo[1,2-b:4,5-b']dithiophene-alt-thieno[3,4-c]pyrrole-4,6-dione) (PBDTTPD) polymers can (i) influence the propensity of the polymer to order in the π-stacking direction, and (ii) direct the preferential orientation of the polymer crystallites in thin films (e.g., "face-on" vs "edge-on"). Oriented crystallites, specifically crystallites that are well-ordered in the π-stacking direction, are believed to be a key contributor to improved thin-film device performance in both FETs and BHJ solar cells.

  13. An Enhanced Backbone-Assisted Reliable Framework for Wireless Sensor Networks

    PubMed Central

    Tufail, Ali; Khayam, Syed Ali; Raza, Muhammad Taqi; Ali, Amna; Kim, Ki-Hyung

    2010-01-01

    An extremely reliable source to sink communication is required for most of the contemporary WSN applications especially pertaining to military, healthcare and disaster-recovery. However, due to their intrinsic energy, bandwidth and computational constraints, Wireless Sensor Networks (WSNs) encounter several challenges in reliable source to sink communication. In this paper, we present a novel reliable topology that uses reliable hotlines between sensor gateways to boost the reliability of end-to-end transmissions. This reliable and efficient routing alternative reduces the number of average hops from source to the sink. We prove, with the help of analytical evaluation, that communication using hotlines is considerably more reliable than traditional WSN routing. We use reliability theory to analyze the cost and benefit of adding gateway nodes to a backbone-assisted WSN. However, in hotline assisted routing some scenarios where source and the sink are just a couple of hops away might bring more latency, therefore, we present a Signature Based Routing (SBR) scheme. SBR enables the gateways to make intelligent routing decisions, based upon the derived signature, hence providing lesser end-to-end delay between source to the sink communication. Finally, we evaluate our proposed hotline based topology with the help of a simulation tool and show that the proposed topology provides manifold increase in end-to-end reliability. PMID:22294890

  14. Side-chain to backbone interactions dictate the conformational preferences of a cyclopentane arginine analogue

    PubMed Central

    Revilla-López, Guillem; Torras, Juan; Jiménez, Ana I.; Cativiela, Carlos; Nussinov, Ruth; Alemán, Carlos

    2009-01-01

    The intrinsic conformational preferences of the non-proteinogenic amino acids constructed by incorporating the arginine side chain in the β position of 1-aminocyclopentane-1-carboxylic acid (either in a cis or a trans orientation relative to the amino group) have been investigated using computational methods. These compounds may be considered as constrained analogues of arginine (denoted as c5Arg) in which the orientation of the side chain is fixed by the cyclopentane moiety. Specifically, the N-acetyl-N′-methylamide derivatives of cis and trans-c5Arg have been examined in the gas phase and in solution using B3LYP/6-311+G(d,p) calculations and Molecular Dynamics simulations. Results indicate that the conformational space available to these compounds is highly restricted, their conformational preferences being dictated by the ability of the guanidinium group in the side chain to establish hydrogen-bond interactions with the backbone. A comparison with the behavior previously described for the analogous phenylalanine derivatives is presented. PMID:19236034

  15. Ionization Cross Sections and Dissociation Channels of the DNA Sugar-Phosphate Backbone by Electron Collisions

    NASA Technical Reports Server (NTRS)

    Dateo, Christopher; Huo, Winifred M.; Fletcher, Graham D.

    2004-01-01

    It has been suggested that the genotoxic effects of ionizing radiation in living cells are not caused by the highly energetic incident radiation, but rather are induced by less energetic secondary species generated, the most abundant of which are free electrons.' The secondary electrons will further react to cause DNA damage via indirect and direct mechanisms. Detailed knowledge of these mechanisms is ultimately important for the development of global models of cellular radiation damage. We are studying one possible mechanism for the formation cf DNA strand breaks involving dissociative ionization of the DNA sugar-phosphate backbone induced by secondary electron co!lisions. We will present ionization cross sections at electron collision energies between threshold and 10 KeV using the improved binary encounter dipole (iBED) formulation' Preliminary results of the possible dissociative ionization pathways will be presented. It is speculated that radical fragments produced from the dissociative ionization can further react, providing a possible mechanism for double strand breaks and base damage.

  16. An enhanced backbone-assisted reliable framework for wireless sensor networks.

    PubMed

    Tufail, Ali; Khayam, Syed Ali; Raza, Muhammad Taqi; Ali, Amna; Kim, Ki-Hyung

    2010-01-01

    An extremely reliable source to sink communication is required for most of the contemporary WSN applications especially pertaining to military, healthcare and disaster-recovery. However, due to their intrinsic energy, bandwidth and computational constraints, Wireless Sensor Networks (WSNs) encounter several challenges in reliable source to sink communication. In this paper, we present a novel reliable topology that uses reliable hotlines between sensor gateways to boost the reliability of end-to-end transmissions. This reliable and efficient routing alternative reduces the number of average hops from source to the sink. We prove, with the help of analytical evaluation, that communication using hotlines is considerably more reliable than traditional WSN routing. We use reliability theory to analyze the cost and benefit of adding gateway nodes to a backbone-assisted WSN. However, in hotline assisted routing some scenarios where source and the sink are just a couple of hops away might bring more latency, therefore, we present a Signature Based Routing (SBR) scheme. SBR enables the gateways to make intelligent routing decisions, based upon the derived signature, hence providing lesser end-to-end delay between source to the sink communication. Finally, we evaluate our proposed hotline based topology with the help of a simulation tool and show that the proposed topology provides manifold increase in end-to-end reliability.

  17. Effect of Bulky Substituents in the Polymer Backbone on the Properties of Polyimide Aerogels.

    PubMed

    Viggiano, Rocco P; Williams, Jarrod C; Schiraldi, David A; Meador, Mary Ann B

    2017-03-08

    With unique advantages over inorganic aerogels including higher strengths and compressive moduli, greater toughness, and the ability to be fabricated as a flexible thin film, polymer aerogels have the potential to supplant inorganic aerogels in numerous applications. Among polymer aerogels, polyimide aerogels possess a high degree of high thermal stability as well as outstanding mechanical properties. However, while the onset of thermal decomposition for these materials is typically very high (greater than 500 °C), the polyimide aerogels undergo dramatic thermally induced shrinkage at temperatures well below their glass transition (Tg) or decomposition temperature, which limits their use. In this study, we show that shrinkage is reduced when a bulky moiety is incorporated in the polymer backbone. Twenty different formulations of polyimide aerogels were synthesized from 3,3,'4,4'-biphenyltetracarboxylic dianhydride (BPDA) and 4,4'-oxidianiline (ODA) or a combination of ODA and 9,9'-bis(4-aminophenyl)fluorene (BAPF) and cross-linked with 1,3,5-benzenetricarbonyl trichloride (BTC) in a statistically designed study. The polymer concentration, n-value, and molar concentration of ODA and BAPF were varied to demonstrate the effect of these variables on certain properties. Samples containing BAPF showed a reduction in shrinkage by as much as 50% after aging at elevated temperatures for 500 h compared to those made with ODA alone.

  18. Quantitative residue-specific protein backbone torsion angle dynamics from concerted measurement of 3J couplings.

    PubMed

    Lee, Jung Ho; Li, Fang; Grishaev, Alexander; Bax, Ad

    2015-02-04

    Three-bond (3)J(C'C') and (3)J(HNHα) couplings in peptides and proteins are functions of the intervening backbone torsion angle ϕ. In well-ordered regions, (3)J(HNHα) is tightly correlated with (3)J(C'C'), but the presence of large ϕ angle fluctuations differentially affects the two types of couplings. Assuming the ϕ angles follow a Gaussian distribution, the width of this distribution can be extracted from (3)J(C'C') and (3)J(HNHα), as demonstrated for the folded proteins ubiquitin and GB3. In intrinsically disordered proteins, slow transverse relaxation permits measurement of (3)J(C'C') and (3)J(HNH) couplings at very high precision, and impact of factors other than the intervening torsion angle on (3)J will be minimal, making these couplings exceptionally valuable structural reporters. Analysis of α-synuclein yields rather homogeneous widths of 69 ± 6° for the ϕ angle distributions and (3)J(C'C') values that agree well with those of a recent maximum entropy analysis of chemical shifts, J couplings, and (1)H-(1)H NOEs. Data are consistent with a modest (≤30%) population of the polyproline II region.

  19. Essential roles of four-carbon backbone chemicals in the control of metabolism

    PubMed Central

    Chriett, Sabrina; Pirola, Luciano

    2015-01-01

    The increasing incidence of obesity worldwide and its related cardiometabolic complications is an urgent public health problem. While weight gain results from a negative balance between the energy expenditure and calorie intake, recent research has demonstrated that several small organic molecules containing a four-carbon backbone can modulate this balance by favoring energy expenditure, and alleviating endoplasmic reticulum stress and oxidative stress. Such small molecules include the bacterially produced short chain fatty acid butyric acid, its chemically produced derivative 4-phenylbutyric acid, the main ketone body D-β-hydroxybutyrate - synthesized by the liver - and the recently discovered myokine β-aminoisobutyric acid. Conversely, another butyrate-related molecule, α-hydroxybutyrate, has been found to be an early predictor of insulin resistance and glucose intolerance. In this minireview, we summarize recent advances in the understanding of the mechanism of action of these molecules, and discuss their use as therapeutics to improve metabolic homeostasis or their detection as early biomarkers of incipient insulin resistance. PMID:26322177

  20. Essential roles of four-carbon backbone chemicals in the control of metabolism.

    PubMed

    Chriett, Sabrina; Pirola, Luciano

    2015-08-26

    The increasing incidence of obesity worldwide and its related cardiometabolic complications is an urgent public health problem. While weight gain results from a negative balance between the energy expenditure and calorie intake, recent research has demonstrated that several small organic molecules containing a four-carbon backbone can modulate this balance by favoring energy expenditure, and alleviating endoplasmic reticulum stress and oxidative stress. Such small molecules include the bacterially produced short chain fatty acid butyric acid, its chemically produced derivative 4-phenylbutyric acid, the main ketone body D-β-hydroxybutyrate - synthesized by the liver - and the recently discovered myokine β-aminoisobutyric acid. Conversely, another butyrate-related molecule, α-hydroxybutyrate, has been found to be an early predictor of insulin resistance and glucose intolerance. In this minireview, we summarize recent advances in the understanding of the mechanism of action of these molecules, and discuss their use as therapeutics to improve metabolic homeostasis or their detection as early biomarkers of incipient insulin resistance.

  1. Controlling the ambiphilic nature of σ-arylpalladium intermediates in intramolecular cyclization reactions.

    PubMed

    Solé, Daniel; Fernández, Israel

    2014-01-21

    the metal center with the carbonyl group. Second, the additive phenol exchanges the iodide ligand to give an arylpalladium(II) phenoxide complex, which has a beneficial effect on the arylation. The formation of this transient intermediate not only stabilizes the arylpalladium moiety, thus preventing the nucleophilic attack at the carbonyl group, but also assists the enolization reaction, which takes place in a more favorable intramolecular manner. The azapalladacycle intermediate is, in the words of J. R. R. Tolkien, "the one ring to bring them all and in the darkness to bind them." With this intermediate, we can easily achieve the synthesis of a variety of heterocyclic systems by selectively promoting electrophilic α-arylation or nucleophilic addition reactions from the same precursors.

  2. Chromo-fluorogenic detection of nerve-agent mimics using triggered cyclization reactions in push-pull dyes.

    PubMed

    Costero, Ana M; Parra, Margarita; Gil, Salvador; Gotor, Raúl; Mancini, Pedro M E; Martínez-Máñez, Ramón; Sancenón, Félix; Royo, Santiago

    2010-07-05

    A family of azo and stilbene derivatives (1-9) are synthesized, and their chromo-fluorogenic behavior in the presence of nerve-agent simulants, diethylchlorophosphate (DCP), diisopropylfluorophosphate (DFP), and diethylcyanophosphate (DCNP) in acetonitrile and mixed solution of water/acetonitrile (3:1 v/v) buffered at pH 5.6 with MES, is investigated. The prepared compounds contain 2-(2-N,N-dimethylaminophenyl)ethanol or 2-[(2-N,N-dimethylamino)phenoxy]ethanol reactive groups, which are part of the conjugated pi-system of the dyes and are able to give acylation reactions with phosphonate substrates followed by a rapid intramolecular N-alkylation. The nerve-agent mimic-triggered cyclization reaction transforms a dimethylamino group into a quaternary ammonium, inducing a change of the electronic properties of the delocalized systems that results in a hypsochromic shift of the absorption band of the dyes. Similar reactivity studies are also carried out with other "non-toxic" organophosphorus compounds, but no changes in the UV/Vis spectra were observed. The emission behaviour of the reagents in acetonitrile and water-acetonitrile 3:1 v/v mixtures is also studied in the presence of nerve-agent simulants and other organophosphorous derivatives. The reactivity between 1-9 and DCP, DCNP, or DFP in buffered water-acetonitrile 3:1 v/v solutions under pseudo first-order kinetic conditions, using an excess of the corresponding simulant, are studied in order to determine the rate constants (k) and the half-life times (t(1/2)=ln2/k) for the reaction. The detection limits in water/acetonitrile 3:1 v/v are also determined for 1-9 and DCP, DCNP, and DFP. Finally, the chromogenic detection of nerve agent simulants both in solution and in gas phase are tested using silica gel containing adsorbed compounds 1, 2, 3, 4, or 5 with fine results.

  3. Intein-Promoted Cyclization of Aspartic Acid Flanking the Intein Leads to Atypical N-Terminal Cleavage.

    PubMed

    Minteer, Christopher J; Siegart, Nicolle M; Colelli, Kathryn M; Liu, Xinyue; Linhardt, Robert J; Wang, Chunyu; Gomez, Alvin V; Reitter, Julie N; Mills, Kenneth V

    2017-02-28

    Protein splicing is a post-translational reaction facilitated by an intein, or intervening protein, which involves the removal of the intein and the ligation of the flanking polypeptides, or exteins. A DNA polymerase II intein from Pyrococcus abyssi (Pab PolII intein) can promote protein splicing in vitro on incubation at high temperature. Mutation of active site residues Cys1, Gln185, and Cys+1 to Ala results in an inactive intein precursor, which cannot promote the steps of splicing, including cleavage of the peptide bond linking the N-extein and intein (N-terminal cleavage). Surprisingly, coupling the inactivating mutations to a change of the residue at the C-terminus of the N-extein (N-1 residue) from the native Asn to Asp reactivates N-terminal cleavage at pH 5. Similar "aspartic acid effects" have been observed in other proteins and peptides but usually only occur at lower pH values. In this case, however, the unusual N-terminal cleavage is abolished by mutations to catalytic active site residues and unfolding of the intein, indicating that this cleavage effect is mediated by the intein active site and the intein fold. We show via mass spectrometry that the reaction proceeds through cyclization of Asp resulting in anhydride formation coupled to peptide bond cleavage. Our results add to the richness of the understanding of the mechanism of protein splicing and provide insight into the stability of proteins at moderately low pH. The results also explain, and may help practitioners avoid, a side reaction that may complicate intein applications in biotechnology.

  4. MTI-101 (cyclized HYD1) binds a CD44 containing complex and induces necrotic cell death in multiple myeloma.

    PubMed

    Gebhard, Anthony W; Jain, Priyesh; Nair, Rajesh R; Emmons, Michael F; Argilagos, Raul F; Koomen, John M; McLaughlin, Mark L; Hazlehurst, Lori A

    2013-11-01

    Our laboratory recently reported that treatment with the d-amino acid containing peptide HYD1 induces necrotic cell death in multiple myeloma cell lines. Because of the intriguing biological activity and promising in vivo activity of HYD1, we pursued strategies for increasing the therapeutic efficacy of the linear peptide. These efforts led to a cyclized peptidomimetic, MTI-101, with increased in vitro activity and robust in vivo activity as a single agent using two myeloma models that consider the bone marrow microenvironment. MTI-101 treatment similar to HYD1 induced reactive oxygen species, depleted ATP levels, and failed to activate caspase-3. Moreover, MTI-101 is cross-resistant in H929 cells selected for acquired resistance to HYD1. Here, we pursued an unbiased chemical biology approach using biotinylated peptide affinity purification and liquid chromatography/tandem mass spectrometry analysis to identify binding partners of MTI-101. Using this approach, CD44 was identified as a predominant binding partner. Reducing the expression of CD44 was sufficient to induce cell death in multiple myeloma cell lines, indicating that multiple myeloma cells require CD44 expression for survival. Ectopic expression of CD44s correlated with increased binding of the FAM-conjugated peptide. However, ectopic expression of CD44s was not sufficient to increase the sensitivity to MTI-101-induced cell death. Mechanistically, we show that MTI-101-induced cell death occurs via a Rip1-, Rip3-, or Drp1-dependent and -independent pathway. Finally, we show that MTI-101 has robust activity as a single agent in the SCID-Hu bone implant and 5TGM1 in vivo model of multiple myeloma.

  5. MTI-101 (cyclized HYD1) binds a CD44 containing complex and induces necrotic cell death in multiple myeloma

    PubMed Central

    Gebhard, Anthony W.; Jain, Priyesh; Nair, Rajesh R.; Emmons, Michael F.; Argilagos, Raul F.; Koomen, John M.; McLaughlin, Mark L.; Hazlehurst, Lori A.

    2013-01-01

    Our laboratory recently reported that treatment with the d-amino acid containing peptide HYD1 induces necrotic cell death in multiple myeloma (MM) cell lines. Due to the intriguing biological activity and promising in vivo activity of HYD1, we pursued strategies for increasing the therapeutic efficacy of the linear peptide. These efforts led to a cyclized peptidomimetic, MTI-101, with increased in vitro activity and robust in vivo activity as single agent using two myeloma models that consider the bone marrow microenvironment. MTI-101 treatment similar to HYD1 induced reactive oxygen species, depleted ATP levels and failed to activate caspase 3. Moreover, MTI-101 is cross-resistant in H929 cells selected for acquired resistance to HYD1. Here, we pursued an unbiased chemical biology approach using biotinylated peptide affinity purification and LC-MS/MS analysis to identify binding partners of MTI-101. Using this approach CD44 was identified as a predominant binding partner. Reducing the expression of CD44 was sufficient to induce cell death in MM cell lines, indicating that MM cells require CD44 expression for survival. Ectopic expression of CD44s correlated with increased binding of the FAM-conjugated peptide. However ectopic expression of CD44s was not sufficient to increase the sensitivity to MTI-101 induced cell death. Mechanistically, we show that MTI-101 induced cell death occurs via a Rip1, Rip3 or Drp1 dependent and independent pathway. Finally, we show that MTI-101 has robust activity as a single agent in the SCID-Hu bone implant and 5TGM1 in vivo model of multiple myeloma. PMID:24048737

  6. Interactions of TRIS [tris(hydroxymethyl)aminomethane] and related buffers with peptide backbone: thermodynamic characterization.

    PubMed

    Taha, Mohamed; Lee, Ming-Jer

    2010-10-21

    In a situation which is far from ideal, many buffers have been found to be quite reactive, besides maintaining their stable pH values. On the basis of apparent transfer free energies (ΔG(tr)'), through solubility measurements the interactions of zwitterionic glycine peptides: glycine (Gly), diglycine (Gly(2)), triglycine (Gly(3)), and tetraglycine (Gly(4)), with several common neutral pH, amine-based buffers have been studied. The biological buffers studied in this work, including TRIS, TES, TAPS, TAPSO, and TABS are structurally related and all contain TRIS groups. These buffers have pK(a) values ranging from 7.5-9.0, which allow them to be used in biological, biochemical or environmental studies. We observed negative values of ΔG(tr)' for Gly(3) and Gly(4) from water to buffer, indicating that the interactions are favorable. However, the ΔG(tr)' values are positive for Gly and Gly(2), revealing unfavorable interactions, which except for the latter in TRIS buffer are negative. The surprising result in our data is the unexpected extraordinarily high favorable interactions between TRIS buffer and peptides (in comparison with the effect of the most common denaturants, urea and guanidine hydrochloride). The transfer free energies (ΔG(tr)') of the peptide backbone unit (-CH(2)C=O-NH-) contributions have been estimated from ΔG(tr)' values. We have also investigated the interactions of TRIS buffer with Bovine Serum Albumin (BSA), as a globular protein, using dynamic light scattering (DLS), zeta potential, UV-Visible absorption, fluorescence and Raman spectroscopy measurements. The results indicated that TRIS buffer stabilized the BSA molecules.

  7. Nonribosomal biosynthesis of vancomycin-type antibiotics: a heptapeptide backbone and eight peptide synthetase modules.

    PubMed

    Recktenwald, Jürgen; Shawky, Riham; Puk, Oliver; Pfennig, Frank; Keller, Ulrich; Wohlleben, Wolfgang; Pelzer, Stefan

    2002-04-01

    During analysis of the recently identified gene cluster for the glycopeptide antibiotic balhimycin, produced by Amycolatopsis mediterranei DSM 5908, novel genes were identified and characterized in detail. The gene products of four of the identified genes (bpsA, bpsB, bpsC and bpsD) are nonribosomal peptide synthetases (NRPSs); one (Orf1-protein) shows similarities to small proteins associated with several NRPSs without an assigned function. BpsA and BpsB are composed of three modules each (modules 1-6), BpsC of one module (module 7) and BpsD of a minimal module (module 8). Thus, the balhimycin gene cluster encodes eight modules, whereas its biosynthetic product is a heptapeptide. Non-producing mutants were created by a gene disruption of bpsB, an in-frame deletion of bpsC and a gene replacement of bpsD. After establishment of a gene complementation system for Amycolatopsis strains, the replacement mutant of bpsD was complemented, demonstrating for the first time that BpsD, encoding the eighth module, is indeed involved in balhimycin biosynthesis. After feeding with beta-hydroxytyrosine the capability of the bpsD mutant to produce balhimycin was restored, demonstrating the participation of BpsD in the biosynthesis of this amino acid. The specificity of four of the eight adenylation domains was determined by ATP/PP(i) exchange assays: modules 4 and 5 activated L-4-hydroxyphenylglycine, module 6 activated beta-hydroxytyrosine and module 7 activated L-3,5-dihydroxyphenylglycine, which is in accordance with the sequence of the non-proteogenic amino acids 4 to 7 of the balhimycin backbone.

  8. Backbones in the parameter plane of the Hénon map

    NASA Astrophysics Data System (ADS)

    Falcolini, Corrado; Tedeschini-Lalli, Laura

    2016-01-01

    Parameter plane (b, a) of the real Hénon map has been investigated for curves of bifurcation, curves of homoclinic heteroclinic onsets, and also searching for borders of areas variously characterized. Such curves are, in general, complicated and show singularities. Pieces of two monotone curves, spanning the (b, a) parameter plane of the real Hénon map, can be detected in four quite different studies appeared along the years 1982-2008. We study the extent of their similarity to read and interpret them into the same curves. To us, these two curves are the accumulation loci of bifurcation curves of two principal families of periodic sinks of type "period-adding machine." We call them "backbones," because they are monotone; moreover, they are the borders of some important regions in the (b, a)-plane. Hamouly and Mira in 1982 [C. R. Acad. Sc. Paris1 293, 525-528 (1982)] studied the structure of bifurcation of periodic orbits and their mutual position and intersection. Gonchenko et al. [SIAM J. Appl. Dyn. Syst. 4, 407-436 (2005)] display the continuation (in parameter plane) of the first heteroclinic connection and of the first homoclinic connection between the two fixed points of the map. Alligood and Sauer [Commun. Math. Phys. 120, 105-119 (1988)] studied parameter regions characterized by the same rotation number of the "accessible" periodic saddle. Finally, Lorenz [Physica D 237, 1689-1704 (2008)] in 2008 draws areas in the parameter plane statistically characterized by a finite attractor. In this paper, we show how these criteria interact. We therefore conjecture that the wealth of curves of homoclinic onsets could be in general hierarchized by the structure of accessible saddles.

  9. Soluble and Membrane-Bound β-Glucosidases Are Involved in Trimming the Xyloglucan Backbone.

    PubMed

    Sampedro, Javier; Valdivia, Elene R; Fraga, Patricia; Iglesias, Natalia; Revilla, Gloria; Zarra, Ignacio

    2017-02-01

    In many flowering plants, xyloglucan is a major component of primary cell walls, where it plays an important role in growth regulation. Xyloglucan can be degraded by a suite of exoglycosidases that remove specific sugars. In this work, we show that the xyloglucan backbone, formed by (1→4)-linked β-d-glucopyranosyl residues, can be attacked by two different Arabidopsis (Arabidopsis thaliana) β-glucosidases from glycoside hydrolase family 3. While BGLC1 (At5g20950; for β-glucosidase active against xyloglucan 1) is responsible for all or most of the soluble activity, BGLC3 (At5g04885) is usually a membrane-anchored protein. Mutations in these two genes, whether on their own or combined with mutations in other exoglycosidase genes, resulted in the accumulation of partially digested xyloglucan subunits, such as GXXG, GXLG, or GXFG. While a mutation in BGLC1 had significant effects on its own, lack of BGLC3 had only minor effects. On the other hand, double bglc1 bglc3 mutants revealed a synergistic interaction that supports a role for membrane-bound BGLC3 in xyloglucan metabolism. In addition, bglc1 bglc3 was complemented by overexpression of either BGLC1 or BGLC3 In overexpression lines, BGLC3 activity was concentrated in a microsome-enriched fraction but also was present in soluble form. Finally, both genes were generally expressed in the same cell types, although, in some cases, BGLC3 was expressed at earlier stages than BGLC1 We propose that functional specialization could explain the separate localization of both enzymes, as a membrane-bound β-glucosidase could specifically digest soluble xyloglucan without affecting the wall-bound polymer.

  10. The multiscale backbone of the human phenotype network based on biological pathways

    PubMed Central

    2014-01-01

    Background Networks are commonly used to represent and analyze large and complex systems of interacting elements. In systems biology, human disease networks show interactions between disorders sharing common genetic background. We built pathway-based human phenotype network (PHPN) of over 800 physical attributes, diseases, and behavioral traits; based on about 2,300 genes and 1,200 biological pathways. Using GWAS phenotype-to-genes associations, and pathway data from Reactome, we connect human traits based on the common patterns of human biological pathways, detecting more pleiotropic effects, and expanding previous studies from a gene-centric approach to that of shared cell-processes. Results The resulting network has a heavily right-skewed degree distribution, placing it in the scale-free region of the network topologies spectrum. We extract the multi-scale information backbone of the PHPN based on the local densities of the network and discarding weak connection. Using a standard community detection algorithm, we construct phenotype modules of similar traits without applying expert biological knowledge. These modules can be assimilated to the disease classes. However, we are able to classify phenotypes according to shared biology, and not arbitrary disease classes. We present examples of expected clinical connections identified by PHPN as proof of principle. Conclusions We unveil a previously uncharacterized connection between phenotype modules and discuss potential mechanistic connections that are obvious only in retrospect. The PHPN shows tremendous potential to become a useful tool both in the unveiling of the diseases’ common biology, and in the elaboration of diagnosis and treatments. PMID:24460644

  11. Backbone structures in human milk oligosaccharides: trans-glycosylation by metagenomic β-N-acetylhexosaminidases.

    PubMed

    Nyffenegger, Christian; Nordvang, Rune Thorbjørn; Zeuner, Birgitte; Łężyk, Mateusz; Difilippo, Elisabetta; Logtenberg, Madelon J; Schols, Henk A; Meyer, Anne S; Mikkelsen, Jørn Dalgaard

    2015-10-01

    This paper describes the discovery and characterization of two novel β-N-acetylhexosaminidases HEX1 and HEX2, capable of catalyzing the synthesis of human milk oligosaccharides (HMO) backbone structures with fair yields using chitin oligomers as β-N-acetylglucosamine (GlcNAc) donor. The enzyme-encoding genes were identified by functional screening of a soil-derived metagenomic library. The β-N-acetylhexosaminidases were expressed in Escherichia coli with an N-terminal His6-tag and were purified by nickel affinity chromatography. The sequence similarities of the enzymes with their respective closest homologues are 59 % for HEX1 and 51 % for HEX2 on the protein level. Both β-N-acetylhexosaminidases are classified into glycosyl hydrolase family 20 (GH 20) are able to hydrolyze para-nitrophenyl-β-N-acetylglucosamine (pNP-GlcNAc) as well as para-nitrophenyl-β-N-acetylgalactosamine (pNP-GalNAc) and exhibit pH optima of 8 and 6 for HEX1 and HEX2, respectively. The enzymes are able to hydrolyze N-acetylchitooligosaccharides with a degree of polymerization of two, three, and four. The major findings were, that HEX1 and HEX2 catalyze trans-glycosylation reactions with lactose as acceptor, giving rise to the human milk oligosaccharide precursor lacto-N-triose II (LNT2) with yields of 2 and 8 % based on the donor substrate. In total, trans-glycosylation reactions were tested with the disaccharide acceptors β-lactose, sucrose, and maltose, as well as with the monosaccharides galactose and glucose resulting in the successful attachment of GlcNAc to the acceptor in all cases.

  12. Identification of high-affinity P2Y₁₂ antagonists based on a phenylpyrazole glutamic acid piperazine backbone.

    PubMed

    Zech, Gernot; Hessler, Gerhard; Evers, Andreas; Weiss, Tilo; Florian, Peter; Just, Melitta; Czech, Jörg; Czechtizky, Werngard; Görlitzer, Jochen; Ruf, Sven; Kohlmann, Markus; Nazaré, Marc

    2012-10-25

    A series of novel, highly potent P2Y₁₂ antagonists as inhibitors of platelet aggregation based on a phenylpyrazole glutamic acid piperazine backbone is described. Exploration of the structural requirements of the substituents by probing the structure-activity relationship along this backbone led to the discovery of the N-acetyl-(S)-proline cyclobutyl amide moiety as a highly privileged motif. Combining the most favorable substituents led to remarkably potent P2Y₁₂ antagonists displaying not only low nanomolar binding affinity to the P2Y₁₂ receptor but also a low nanomolar inhibition of platelet aggregation in the human platelet rich plasma assay with IC₅₀ values below 50 nM. Using a homology and a three-dimensional quantitative structure-activity relationship model, a binding hypothesis elucidating the impact of several structural features was developed.

  13. Progress in palladium-based catalytic systems for the sustainable synthesis of annulated heterocycles: a focus on indole backbones.

    PubMed

    Platon, Mélanie; Amardeil, Régine; Djakovitch, Laurent; Hierso, Jean-Cyrille

    2012-05-21

    A survey highlighting the most recent palladium catalytic systems produced and their performances for progress in direct synthesis of indole backbones by heterocarbocyclization of reactive substrates is provided. The discussion is developed in relation with the principles of sustainable chemistry concerning atom and mass economy. In this respect, the general convergent character of the syntheses is of particular interest (one-pot, domino, cascade or tandem reactions), and the substrates accessibility and reactivity, together with the final waste production, are also important. This critical review clearly indicates that the development of ligand chemistry, mainly phosphines and carbenes, in the last few decades gave a significant impetus to powerful functionalization of indoles at virtually all positions of this ubiquitous backbone (118 references).

  14. Role of monomer sequence and backbone structure in polypeptoid and polypeptide polymers for anti-fouling applications

    NASA Astrophysics Data System (ADS)

    Patterson, Anastasia; Rizis, Georgios; Wenning, Brandon; Finlay, John; Ober, Christopher; Segalman, Rachel

    Polymeric coatings rely on a fine balance of surface properties to achieve biofouling resistance. Bioinsipired polymers and oligomers provide a modular strategy for the inclusion of multiple functionalities with controlled architecture, sequence and surface properties. In this work, polypeptoid and polypeptide functionalized coatings based on PEO and PDMS block copolymers were compared with respect to surface presentation and fouling by Ulva linza. While polypeptoids and polypeptides are simple isomers of each other, the lack of backbone chirality and hydrogen bonding in polypeptoids leads to surprisingly different surface behavior. Specifically, the polypeptoids surface segregate much more strongly than analogous polypeptide functionalized polymers, which in turn affects the performance of the coating. Indeed, polypeptoid functionalized surfaces were significantly better both in terms of anti-fouling and fouling release than the corresponding polypeptide-bearing polymers. The role of specific monomer sequence and backbone chemistry will be further discussed in this poster.

  15. Free vibration analysis of a robotic fish based on a continuous and non-uniform flexible backbone with distributed masses

    NASA Astrophysics Data System (ADS)

    Coral, W.; Rossi, C.; Curet, O. M.

    2015-12-01

    This paper presents a Differential Quadrature Element Method for free transverse vibration of a robotic fish based on a continuous and non-uniform flexible backbone with distributed masses (fish ribs). The proposed method is based on the theory of a Timoshenko cantilever beam. The effects of the masses (number, magnitude and position) on the value of natural frequencies are investigated. Governing equations, compatibility and boundary conditions are formulated according to the Differential Quadrature rules. The convergence, efficiency and accuracy are compared to other analytical solution proposed in the literature. Moreover, the proposed method has been validate against the physical prototype of a flexible fish backbone. The main advantages of this method, compared to the exact solutions available in the literature are twofold: first, smaller computational cost and second, it allows analysing the free vibration in beams whose section is an arbitrary function, which is normally difficult or even impossible with other analytical methods.

  16. Large and ultrafast third-order optical nonlinearity of novel copolymers containing fluorene and tetraphenyldiaminobiphenyl units in backbones

    NASA Astrophysics Data System (ADS)

    Huang, Wentao; Wang, Shufeng; Yang, Hong; Gong, Qihuang; Zhan, Xiaowei; Liu, Yunqi; Zhu, Daoben

    2001-12-01

    A femtosecond time-resolved optical Kerr gate method, using 115 fs laser pulses at 830 nm, has been applied to investigate the third-order nonlinearity of two novel copolymers containing fluorene and tetraphenyldiaminobiphenyl units in their backbones. Ultrafast off-resonant optical Kerr responses have been observed and the magnitude of the second-order hyperpolarizability was measured as large as 10 -30 esu. The origin of the extraordinary large value was explored and compared to other organic materials.

  17. Photoinduced bending behavior of cross-linked azobenzene liquid-crystalline polymer films with a poly(oxyethylene) backbone.

    PubMed

    Lv, Jiu-an; Wang, Weiru; Xu, Jixiang; Ikeda, Tomiki; Yu, Yanlei

    2014-07-01

    Cross-linked azobenzene liquid-crystalline polymer films with a poly(oxyethylene) backbone are synthesized by photoinitiated cationic copolymerization. Azobenzene moieties in the film surface toward the light source are simultaneously photoaligned during photopolymerization with unpolarized 436 nm light and thus form a splayed alignment in the whole film. The prepared films show reversible photoinduced bending behavior with opposite bending directions when different surfaces of one film face to ultraviolet light irradiation.

  18. Assessing side-chain perturbations of the protein backbone: a knowledge-based classification of residue Ramachandran space.

    PubMed

    Dahl, David B; Bohannan, Zach; Mo, Qianxing; Vannucci, Marina; Tsai, Jerry

    2008-05-02

    Grouping the 20 residues is a classic strategy to discover ordered patterns and insights about the fundamental nature of proteins, their structure, and how they fold. Usually, this categorization is based on the biophysical and/or structural properties of a residue's side-chain group. We extend this approach to understand the effects of side chains on backbone conformation and to perform a knowledge-based classification of amino acids by comparing their backbone phi, psi distributions in different types of secondary structure. At this finer, more specific resolution, torsion angle data are often sparse and discontinuous (especially for nonhelical classes) even though a comprehensive set of protein structures is used. To ensure the precision of Ramachandran plot comparisons, we applied a rigorous Bayesian density estimation method that produces continuous estimates of the backbone phi, psi distributions. Based on this statistical modeling, a robust hierarchical clustering was performed using a divergence score to measure the similarity between plots. There were seven general groups based on the clusters from the complete Ramachandran data: nonpolar/beta-branched (Ile and Val), AsX (Asn and Asp), long (Met, Gln, Arg, Glu, Lys, and Leu), aromatic (Phe, Tyr, His, and Cys), small (Ala and Ser), bulky (Thr and Trp), and, lastly, the singletons of Gly and Pro. At the level of secondary structure (helix, sheet, turn, and coil), these groups remain somewhat consistent, although there are a few significant variations. Besides the expected uniqueness of the Gly and Pro distributions, the nonpolar/beta-branched and AsX clusters were very consistent across all types of secondary structure. Effectively, this consistency across the secondary structure classes implies that side-chain steric effects strongly influence a residue's backbone torsion angle conformation. These results help to explain the plasticity of amino acid substitutions on protein structure and should help in

  19. Generation of Marker- and/or Backbone-Free Transgenic Wheat Plants via Agrobacterium-Mediated Transformation

    PubMed Central

    Wang, Gen-Ping; Yu, Xiu-Dao; Sun, Yong-Wei; Jones, Huw D.; Xia, Lan-Qin

    2016-01-01

    Horizontal transfer of antibiotic resistance genes to animals and vertical transfer of herbicide resistance genes to the weedy relatives are perceived as major biosafety concerns in genetically modified (GM) crops. In this study, five novel vectors which used gusA and bar as a reporter gene and a selection marker gene, respectively, were constructed based on the pCLEAN dual binary vector system. Among these vectors, 1G7B and 5G7B carried two T-DNAs located on two respective plasmids with 5G7B possessing an additional virGwt gene. 5LBTG154 and 5TGTB154 carried two T-DNAs in the target plasmid with either one or double right borders, and 5BTG154 carried the selectable marker gene on the backbone outside of the T-DNA left border in the target plasmid. In addition, 5BTG154, 5LBTG154, and 5TGTB154 used pAL154 as a helper plasmid which contains Komari fragment to facilitate transformation. These five dual binary vector combinations were transformed into Agrobacterium strain AGL1 and used to transform durum wheat cv Stewart 63. Evaluation of the co-transformation efficiencies, the frequencies of marker-free transgenic plants, and integration of backbone sequences in the obtained transgenic lines indicated that two vectors (5G7B and 5TGTB154) were more efficient in generating marker-free transgenic wheat plants with no or minimal integration of backbone sequences in the wheat genome. The vector series developed in this study for generation of marker- and/or backbone-free transgenic wheat plants via Agrobacterium-mediated transformation will be useful to facilitate the creation of “clean” GM wheat containing only the foreign genes of agronomic importance. PMID:27708648

  20. P-Stereogenic bisphosphines with a hydrazine backbone: from N-N atropoisomerism to double nitrogen inversion.

    PubMed

    Prades, Amparo; Núñez-Pertíñez, Samuel; Riera, Antoni; Verdaguer, Xavier

    2017-04-10

    The synthesis of P-stereogenic bisphosphine ligands starting from a phosphinous acid chiral synthon and hydrazine is reported. The dialkylation of the hydrazine backbone yielded atropo- and nitrogen inversion isomers which are in slow exchange. The crystallization of one of the isomers allowed us to study the reaction kinetics of the equilibria. The new ligands were tested in the Rh catalysed asymmetric hydrogenation of various benchmark substrates attaining up to 99% ee.