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Sample records for sequence backbone composition

  1. Interplay among side chain sequence, backbone composition, and residue rigidification in polypeptide folding and assembly

    PubMed Central

    Horne, W. Seth; Price, Joshua L.; Gellman, Samuel H.

    2008-01-01

    The extent to which polypeptide conformation depends on side-chain composition and sequence has been widely studied, but less is known about the importance of maintaining an α-amino acid backbone. Here, we examine a series of peptides with backbones that feature different repeating patterns of α- and β-amino acid residues but an invariant side-chain sequence. In the pure α-backbone, this sequence corresponds to the previously studied peptide GCN4-pLI, which forms a very stable four-helix bundle quaternary structure. Physical characterization in solution and crystallographic structure determination show that a variety of α/β-peptide backbones can adopt sequence-encoded quaternary structures similar to that of the α prototype. There is a loss in helix bundle stability upon β-residue incorporation; however, stability of the quaternary structure is not a simple function of β-residue content. We find that cyclically constrained β-amino acid residues can stabilize the folds of α/β-peptide GCN4-pLI analogues and restore quaternary structure formation to backbones that are predominantly unfolded in the absence of cyclic residues. Our results show a surprising degree of plasticity in terms of the backbone compositions that can manifest the structural information encoded in a sequence of amino acid side chains. These findings offer a framework for the design of nonnatural oligomers that mimic the structural and functional properties of proteins. PMID:18587049

  2. 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. PMID:26865312

  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. 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

  5. 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

  6. 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. PMID:25670500

  7. A backbone amide protecting group for overcoming difficult sequences and suppressing aspartimide formation.

    PubMed

    Abdel-Aal, Abu-Baker M; Papageorgiou, George; Raz, Richard; Quibell, Martin; Burlina, Fabienne; Offer, John

    2016-05-01

    A backbone amide bond protecting group, 2-hydroxy-4-methoxy-5-nitrobenzyl (Hmnb), improved the synthesis of aggregation and aspartimide-prone peptides. Introduction of Hmnb is automated and carried out during peptide assembly by addition of 4-methoxy-5-nitrosalicylaldehyde to the peptidyl-resin and on-resin reduction to the secondary amine. Acylation of the hindered secondary amine is aided by the formation of an internal nitrophenol ester that undergoes a favourable O,N intramolecular acyl transfer. This activated ester participates in the coupling and generally gives complete reaction with standard coupling conditions. Hmnb is easily available in a single preparative step from commercially available material. Different methods for removing the amide protecting group were explored. The protecting group is labile to acidolysis, following reduction of the nitro group to the aniline. The two main uses of backbone protection of preventing aspartimide formation and of overcoming difficult sequences are demonstrated, first with the synthesis of a challenging aspartimide-prone test sequence and then with the classic difficult sequence ACP (65-74) and a 23-mer homopolymer of polyalanine. PMID:27086749

  8. 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.

  9. Modeling backbone flexibility to achieve sequence diversity: The design of novel alpha-helical ligands for Bcl-xL

    PubMed Central

    Fu, Xiaoran; Apgar, James R.; Keating, Amy E.

    2007-01-01

    Computational protein design can be used to select sequences that are compatible with a fixed-backbone template. This strategy has been used in numerous instances to engineer novel proteins. However, the fixed-backbone assumption severely restricts the sequence space that is accessible via design. For challenging problems, such as the design of functional proteins, this may not be acceptable. In this paper, we present a method for introducing backbone flexibility into protein design calculations and apply it to the design of diverse helical BH3 ligands that bind to the anti-apoptotic protein Bcl-xL, a member of the Bcl-2 protein family. We demonstrate how normal mode analysis can be used to sample different BH3 backbones, and show that this leads to a larger and more diverse set of low-energy solutions than can be achieved using a native high-resolution Bcl-xL complex crystal structure as a template. We tested several of the designed solutions experimentally and found that this approach worked well when normal mode calculations were used to deform a native BH3 helix structure, but less well when they were used to deform an idealized helix. A subsequent round of design and testing identified a likely source of the problem as inadequate sampling of the helix pitch. In all, we tested seventeen designed BH3 peptide sequences, including several point mutants. Of these, eight bound well to Bcl-xL and four others showed weak but detectable binding. The successful designs showed a diversity of sequences that would have been difficult or impossible to achieve using only a fixed backbone. Thus, introducing backbone flexibility via normal mode analysis effectively broadened the set of sequences identified by computational design, and provided insight into positions important for binding Bcl-xL. PMID:17597151

  10. 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.

  11. TANGLE: Two-Level Support Vector Regression Approach for Protein Backbone Torsion Angle Prediction from Primary Sequences

    PubMed Central

    Song, Jiangning; Tan, Hao; Wang, Mingjun; Webb, Geoffrey I.; Akutsu, Tatsuya

    2012-01-01

    Protein backbone torsion angles (Phi) and (Psi) involve two rotation angles rotating around the C?-N bond (Phi) and the C?-C bond (Psi). Due to the planarity of the linked rigid peptide bonds, these two angles can essentially determine the backbone geometry of proteins. Accordingly, the accurate prediction of protein backbone torsion angle from sequence information can assist the prediction of protein structures. In this study, we develop a new approach called TANGLE (Torsion ANGLE predictor) to predict the protein backbone torsion angles from amino acid sequences. TANGLE uses a two-level support vector regression approach to perform real-value torsion angle prediction using a variety of features derived from amino acid sequences, including the evolutionary profiles in the form of position-specific scoring matrices, predicted secondary structure, solvent accessibility and natively disordered region as well as other global sequence features. When evaluated based on a large benchmark dataset of 1,526 non-homologous proteins, the mean absolute errors (MAEs) of the Phi and Psi angle prediction are 27.8 and 44.6, respectively, which are 1% and 3% respectively lower than that using one of the state-of-the-art prediction tools ANGLOR. Moreover, the prediction of TANGLE is significantly better than a random predictor that was built on the amino acid-specific basis, with the p-value<1.46e-147 and 7.97e-150, respectively by the Wilcoxon signed rank test. As a complementary approach to the current torsion angle prediction algorithms, TANGLE should prove useful in predicting protein structural properties and assisting protein fold recognition by applying the predicted torsion angles as useful restraints. TANGLE is freely accessible at http://sunflower.kuicr.kyoto-u.ac.jp/~sjn/TANGLE/. PMID:22319565

  12. Utilizing next-generation sequencing to resolve the backbone of the Core Goodeniaceae and inform future taxonomic and floral form studies.

    PubMed

    Gardner, Andrew G; Sessa, Emily B; Michener, Pryce; Johnson, Eden; Shepherd, Kelly A; Howarth, Dianella G; Jabaily, Rachel S

    2016-01-01

    Though considerable progress has been made in inferring phylogenetic relationships of many plant lineages, deep unresolved nodes remain a common problem that can impact downstream efforts, including taxonomic decision-making and character reconstruction. The Core Goodeniaceae is a group affected by this issue: data from the plastid regions trnL-trnF and matK have been insufficient to generate adequate support at key nodes along the backbone of the phylogeny. We performed genome skimming for 24 taxa representing major clades within Core Goodeniaceae. The plastome coding regions (CDS) and nuclear ribosomal repeats (NRR) were assembled and complemented with additional accessions sequenced for nuclear G3PDH and plastid trnL-trnF and matk. The CDS, NRR, and G3PDH alignments were analyzed independently and topology tests were used to detect the alignments' ability to reject alternative topologies. The CDS, NRR, and G3PDH alignments independently supported a Brunonia (Scaevola s.l. (Coopernookia (Goodenia s.l.))) backbone topology, but within Goodenia s.l., the strongly-supported plastome topology (Goodenia A (Goodenia B (Velleia+Goodenia C))) contrasts with the poorly supported nuclear topology ((Goodenia A+Goodenia B) (Velleia+Goodenia C)). A fully resolved and maximally supported topology for Core Goodeniaceae was recovered from the plastome CDS, and there is excellent support for most of the major clades and relationships among them in all alignments. The composition of these seven major clades renders many of the current taxonomic divisions non-monophyletic, prompting us to suggest that Goodenia may be split into several segregate genera. PMID:26463342

  13. Loss of Internal Backbone Carbonyls: Additional Evidence for Sequence-Scrambling in Collision-Induced Dissociation of y-Type Ions

    NASA Astrophysics Data System (ADS)

    Harper, Brett; Miladi, Mahsan; Solouki, Touradj

    2014-10-01

    It is shown that y-type ions, after losing C-terminal H2O or NH3, can lose an internal backbone carbonyl (CO) from different peptide positions and yield structurally different product fragment ions upon collision-induced dissociation (CID). Such CO losses from internal peptide backbones of y-fragment ions are not unique to a single peptide and were observed in four of five model peptides studied herein. Experimental details on examples of CO losses from y-type fragment ions for an isotopically labeled AAAAH AA-NH2 heptapeptide and des-acetylated-α-melanocyte-stimulating hormone (dα-MSH) (SYSMEHFRWGKPV-NH2) are reported. Results from isotope labeling, tandem mass spectrometry (MSn), and ion mobility-mass spectrometry (IM-MS) confirm that CO losses from different amino acids of m/ z-isolated y-type ions yield structurally different ions. It is shown that losses of internal backbone carbonyls (as CID products of m/ z-isolated y-type ions) are among intermediate steps towards formation of rearranged or permutated product fragment ions. Possible mechanisms for generation of the observed sequence-scrambled a-"like" ions, as intermediates in sequence-scrambling pathways of y-type ions, are proposed and discussed.

  14. Comparative experimental study of ionic polymer-metal composites with different backbone ionomers and in various cation forms

    NASA Astrophysics Data System (ADS)

    Nemat-Nasser, Sia; Wu, Yongxian

    2003-05-01

    An ionic polymer-metal composite (IPMC) consisting of a thin perfluorinated ionomer (usually, Nafion or Flemion) strip, platinum, and/or gold plated on both faces and neutralized by a certain amount of appropriate cations undergoes large bending motion when, in a hydrated state, a small electric field is applied across its thickness. When the same membrane is suddenly bent, a small voltage of the order of millivolts is produced across its surfaces. Hence IPMCs can serve as soft bending actuators and sensors. This coupled electrical-chemical-mechanical response of IPMCs depends on the structure of the backbone ionic polymer, the morphology and conductivity of the metal electrodes, the nature of the cations, and the level of hydration (or other solvent uptake). We have carried out extensive experimental studies on both Nafion- and Flemion-based IPMCs in various cation forms, seeking to understand the fundamental properties of these composites, to explore the mechanism of their actuation, and finally, to optimize their performance for various potential applications. The results of some of these tests on both Nafion- and Flemion-based IPMCs with alkali-metal or alkyl-ammonium cations are reported here. Compared with Nafion-based IPMCs, Flemion-based IPMCs with fine dendritic gold electrodes have higher ion-exchange capacity, better surface conductivity, higher hydration capacity, and higher longitudinal stiffness. They also display greater bending actuation under the same applied voltage. In addition, they do not display a reverse relaxation under a sustained dc voltage, which is typical of Nafion-based IPMCs in alkali-metal form. Flemion IPMCs thus are promising composites for application as bending actuators.

  15. Transgene sequences free of CG dinucleotides lead to high level, long-term expression in the lung independent of plasmid backbone design.

    PubMed

    Bazzani, Reto P; Pringle, Ian A; Connolly, Mary M; Davies, Lee A; Sumner-Jones, Stephanie G; Schleef, Martin; Hyde, Stephen C; Gill, Deborah R

    2016-07-01

    Non-viral aerosol gene therapy offers great potential for treating chronic lung diseases of the airways such as cystic fibrosis (CF). Early clinical trials showed that transgene expression in the airways was transient whereas maximal duration of transgene expression is essential in order to minimise the frequency of aerosol treatments. Improved vector design, such as careful selection of the promoter/enhancer, can lead to more persistent levels of transgene expression, but multiple factors affect expression in vivo. Following aerosol delivery to the lungs of mice, we measured reporter gene expression from a CpG-free luciferase transgene cassette in the context of both a plasmid and minicircle vector configuration and showed that the vector backbone had no effect on expression. Transgene activity was affected by the vector backbone however, when a similar, but sub-optimal CpG-containing transgene was used, suggesting that aspects of the plasmid backbone had a negative impact on transgene expression. Similar studies were performed in Toll-like receptor-9 (TLR9) knockout mice to investigate a potential role for the TLR9 signalling pathway in detecting CpGs in the vector sequence. Even in the absence of TLR9, persistent expression could only be achieved with a CpG-free transgene. Together, these data indicate that in order to achieve high levels of persistent expression in vivo, a CpG-free transgene cassette is required. PMID:27061267

  16. Composition for nucleic acid sequencing

    DOEpatents

    Korlach, Jonas; Webb, Watt W.; Levene, Michael; Turner, Stephen; Craighead, Harold G.; Foquet, Mathieu

    2008-08-26

    The present invention is directed to a method of sequencing a target nucleic acid molecule having a plurality of bases. In its principle, the temporal order of base additions during the polymerization reaction is measured on a molecule of nucleic acid, i.e. the activity of a nucleic acid polymerizing enzyme on the template nucleic acid molecule to be sequenced is followed in real time. The sequence is deduced by identifying which base is being incorporated into the growing complementary strand of the target nucleic acid by the catalytic activity of the nucleic acid polymerizing enzyme at each step in the sequence of base additions. A polymerase on the target nucleic acid molecule complex is provided in a position suitable to move along the target nucleic acid molecule and extend the oligonucleotide primer at an active site. A plurality of labelled types of nucleotide analogs are provided proximate to the active site, with each distinguishable type of nucleotide analog being complementary to a different nucleotide in the target nucleic acid sequence. The growing nucleic acid strand is extended by using the polymerase to add a nucleotide analog to the nucleic acid strand at the active site, where the nucleotide analog being added is complementary to the nucleotide of the target nucleic acid at the active site. The nucleotide analog added to the oligonucleotide primer as a result of the polymerizing step is identified. The steps of providing labelled nucleotide analogs, polymerizing the growing nucleic acid strand, and identifying the added nucleotide analog are repeated so that the nucleic acid strand is further extended and the sequence of the target nucleic acid is determined.

  17. Arbitrarily accurate narrowband composite pulse sequences

    SciTech Connect

    Vitanov, Nikolay V.

    2011-12-15

    Narrowband composite pulse sequences containing an arbitrary number N of identical pulses are presented. The composite phases are given by a very simple analytic formula and the transition probability is merely sin{sup 2N}(A/2), where A is the pulse area. These narrowband sequences can be made accurate to any order with respect to variations in A for sufficiently many constituent pulses, i.e., excitation can be suppressed below any desired value for any pulse area but {pi}.

  18. Comparison of design strategies for ?-helix backbone modification in a protein tertiary fold.

    PubMed

    Tavenor, Nathan A; Reinert, Zachary E; Lengyel, George A; Griffith, Brian D; Horne, W Seth

    2016-02-25

    We report here the comparison of five classes of unnatural amino acid building blocks for their ability to be accommodated into an ?-helix in a protein tertiary fold context. High-resolution structural characterization and analysis of folding thermodynamics yield new insights into the relationship between backbone composition and folding energetics in ?-helix mimetics and suggest refined design rules for engineering the backbones of natural sequences. PMID:26853882

  19. "Pinning strategy": a novel approach for predicting the backbone structure in terms of protein blocks from sequence.

    PubMed

    De Brevern, A G; Etchebest, C; Benros, C; Hazout, S

    2007-01-01

    The description of protein 3D structures can be performed through a library of 3D fragments, named a structural alphabet. Our structural alphabet is composed of 16 small protein fragments of 5 C alpha in length, called protein blocks (PBs). It allows an efficient approximation of the 3D protein structures and a correct prediction of the local structure. The 72 most frequent series of 5 consecutive PBs, called structural words (SWs)are able to cover more than 90% of the 3D structures. PBs are highly conditioned by the presence of a limited number of transitions between them. In this study, we propose a new method called "pinning strategy" that used this specific feature to predict long protein fragments. Its goal is to define highly probable successions of PBs. It starts from the most probable SW and is then extended with overlapping SWs. Starting from an initial prediction rate of 34.4%, the use of the SWs instead of the PBs allows a gain of 4.5%. The pinning strategy simply applied to the SWs increases the prediction accuracy to 39.9%. In a second step, the sequence-structure relationship is optimized, the prediction accuracy reaches 43.6%. PMID:17426380

  20. Fold homology detection using sequence fragment composition profiles of proteins.

    PubMed

    Solis, Armando D; Rackovsky, Shalom R

    2010-10-01

    The effectiveness of sequence alignment in detecting structural homology among protein sequences decreases markedly when pairwise sequence identity is low (the so-called "twilight zone" problem of sequence alignment). Alternative sequence comparison strategies able to detect structural kinship among highly divergent sequences are necessary to address this need. Among them are alignment-free methods, which use global sequence properties (such as amino acid composition) to identify structural homology in a rapid and straightforward way. We explore the viability of using tetramer sequence fragment composition profiles in finding structural relationships that lie undetected by traditional alignment. We establish a strategy to recast any given protein sequence into a tetramer sequence fragment composition profile, using a series of amino acid clustering steps that have been optimized for mutual information. Our method has the effect of compressing the set of 160,000 unique tetramers (if using the 20-letter amino acid alphabet) into a more tractable number of reduced tetramers (approximately 15-30), so that a meaningful tetramer composition profile can be constructed. We test remote homology detection at the topology and fold superfamily levels using a comprehensive set of fold homologs, culled from the CATH database that share low pairwise sequence similarity. Using the receiver-operating characteristic measure, we demonstrate potentially significant improvement in using information-optimized reduced tetramer composition, over methods relying only on the raw amino acid composition or on traditional sequence alignment, in homology detection at or below the "twilight zone". PMID:20635424

  1. Quantitative assessments of the distinct contributions of polypeptide backbone amides versus sidechain groups to chain expansion via chemical denaturation

    PubMed Central

    Holehouse, Alex S.; Garai, Kanchan; Lyle, Nicholas; Vitalis, Andreas; Pappu, Rohit V.

    2015-01-01

    In aqueous solutions with high concentrations of chemical denaturants such as urea and guanidinium chloride (GdmCl) proteins expand to populate heterogeneous conformational ensembles. These denaturing environments are thought to be good solvents for generic protein sequences because properties of conformational distributions align with those of canonical random coils. Previous studies showed that water is a poor solvent for polypeptide backbones and therefore backbones form collapsed globular structures in aqueous solvents. Here, we ask if polypeptide backbones can intrinsically undergo the requisite chain expansion in aqueous solutions with high concentrations of urea and GdmCl. We answer this question using a combination of molecular dynamics simulations and fluorescence correlation spectroscopy. We find that the degree of backbone expansion is minimal in aqueous solutions with high concentrations denaturants. Instead, polypeptide backbones sample conformations that are denaturant-specific mixtures of coils and globules, with a persistent preference for globules. Therefore, typical denaturing environments cannot be classified as good solvents for polypeptide backbones. How then do generic protein sequences expand in denaturing environments? To answer this question, we investigated the effects of sidechains using simulations of two archetypal sequences with amino acid compositions that are mixtures of charged, hydrophobic, and polar groups. We find that sidechains lower the effective concentration of backbone amides in water leading to an intrinsic expansion of polypeptide backbones in the absence of denaturants. Additional dilution of the effective concentration of backbone amides is achieved through preferential interactions with denaturants. These effects lead to conformational statistics in denaturing environments that are congruent with those of canonical random coils. Our results highlight the role of sidechain-mediated interactions as determinants of the conformational properties of unfolded states in water and in influencing chain expansion upon denaturation. PMID:25664638

  2. Sequence-specific (1)H, (13)C and (15)N backbone resonance assignments of the plakin repeat domain of human envoplakin.

    PubMed

    Jeeves, Mark; Fogl, Claudia; Al-Jassar, Caezar; Chidgey, Martyn; Overduin, Michael

    2016-04-01

    The plakin repeat domain is a distinctive hallmark of the plakin superfamily of proteins, which are found within all epithelial tissues. Plakin repeat domains mediate the interactions of these proteins with the cell cytoskeleton and are critical for the maintenance of tissue integrity. Despite their biological importance, no solution state resonance assignments are available for any homologue. Here we report the essentially complete (1)H, (13)C and (15)N backbone chemical shift assignments of the singular 22 kDa plakin repeat domain of human envoplakin, providing the means to investigate its interactions with ligands including intermediate filaments. PMID:26590577

  3. Sequence Compositional Complexity of DNA through an Entropic Segmentation Method

    NASA Astrophysics Data System (ADS)

    Román-Roldán, Ramón; Bernaola-Galván, Pedro; Oliver, José L.

    1998-02-01

    A new complexity measure, based on the entropic segmentation of DNA sequences into compositionally homogeneous domains, is proposed. Sequence compositional complexity (SCC) deals directly with the complex heterogeneity in nonstationary DNA sequences. The plot of SCC as a function of significance level provides a profile of sequence structure at different length scales. SCC is found to be higher in sequences with long-range correlation than those without, and higher in noncoding sequences than coding sequences. Furthermore, a general agreement is found between the SCC of the DNA sequence, on one hand, and the biological complexity of the organism, on the other, attributable to an increasingly complex organization of noncoding DNA over the course of evolution.

  4. Nucleotide sequence composition and method for detection of neisseria gonorrhoeae

    SciTech Connect

    Lo, A.; Yang, H.L.

    1990-02-13

    This patent describes a composition of matter that is specific for {ital Neisseria gonorrhoeae}. It comprises: at least one nucleotide sequence for which the ratio of the amount of the sequence which hybridizes to chromosomal DNA of {ital Neisseria gonorrhoeae} to the amount of the sequence which hybridizes to chromosomal DNA of {ital Neisseria meningitidis} is greater than about five. The ratio being obtained by a method described.

  5. Methods and compositions for efficient nucleic acid sequencing

    DOEpatents

    Drmanac, Radoje

    2006-07-04

    Disclosed are novel methods and compositions for rapid and highly efficient nucleic acid sequencing based upon hybridization with two sets of small oligonucleotide probes of known sequences. Extremely large nucleic acid molecules, including chromosomes and non-amplified RNA, may be sequenced without prior cloning or subcloning steps. The methods of the invention also solve various current problems associated with sequencing technology such as, for example, high noise to signal ratios and difficult discrimination, attaching many nucleic acid fragments to a surface, preparing many, longer or more complex probes and labelling more species.

  6. Methods and compositions for efficient nucleic acid sequencing

    DOEpatents

    Drmanac, Radoje

    2002-01-01

    Disclosed are novel methods and compositions for rapid and highly efficient nucleic acid sequencing based upon hybridization with two sets of small oligonucleotide probes of known sequences. Extremely large nucleic acid molecules, including chromosomes and non-amplified RNA, may be sequenced without prior cloning or subcloning steps. The methods of the invention also solve various current problems associated with sequencing technology such as, for example, high noise to signal ratios and difficult discrimination, attaching many nucleic acid fragments to a surface, preparing many, longer or more complex probes and labelling more species.

  7. Identification of base and backbone contacts used for DNA sequence recognition and high-affinity binding by LAC9, a transcription activator containing a C6 zinc finger

    SciTech Connect

    Halvorsen, Yuan-Di C.; Nandabalan, K.; Dickson, R.C. )

    1991-04-01

    The LAC9 protein of Kluyveromyces lactis is a transcriptional regulator of genes in the lactose-galactose regulon. To regulate transcription, LAC9 must bind to 17-bp upstream activator sequences (UASs) located in front of each target gene. LAC9 is homologous to the GAL4 protein of Saccharomyces cerevisiae, and the two proteins must bind DNA in a very similar manner. In this paper the authors show that high-affinity, sequence-specific binding by LAC9 dimers is mediated primarily by 3 bp at each end of the UAS. In addition, at least one half of the UAS must have a GC or CG base pair at position 1 for high-affinity binding; LAC9k binds preferentially to the half containing the GC base pair. Hydroxyl radical footprinting shows that a LAC9 dimer binds an unusually broad region on one face of the DNA helix. Because of the data, they suggest that LAC9 contacts positions 6, 7, and 8, both plus and minus, of the UAS, which are separated by more than one turn of the DNA helix, and twists part way around the DNA, thus protecting the broad region of the minor groove between the major-groove contacts.

  8. Compositional properties of coding sequences and mammalian phylogeny.

    PubMed

    Mouchiroud, D; Bernardi, G

    1993-08-01

    The compositional distributions of large DNA fragments reflect those of the isochores that make up vertebrate genomes and can provide novel phylogenetic insights in the case of mammalian genomes (see Sabeur et al. 1993). This approach has been complemented here by an analysis of the compositional patterns of coding sequences and their codon positions (which also reflect the isochore pattern) and by a comparison of the base compositions of codon positions from homologous genes in a number of pairs of species. The results obtained using these two approaches support the existence of a general compositional pattern for mammalian genomes and of a distinct pattern for Myomorpha. The other two "special" patterns identified in a megachiropteran and in pangolin could not be tested here. PMID:8411199

  9. Backbone flexibility in protein design theory and experiment

    NASA Astrophysics Data System (ADS)

    Su, Alyce Yaoying

    The role of backbone flexibility in protein design was studied. First, the effect of explicit backbone motion on the selection of amino acids in protein design was assessed in the core of the streptococcal protein G β1 domain (Gβ1). Concerted backbone motion was introduced by varying Gβ1's supersecondary structure parameter values. The stability and structural flexibility of seven of the redesigned proteins were determined experimentally. Core variants containing as many as six of ten possible mutations retained native- like properties. This result demonstrates that backbone flexibility can be combined with amino acid side-chain selection and that the selection algorithm is sufficiently robust to tolerate perturbations as large as 15% of the native parameter values. Second, a general, quantitative design method for computing de novo backbone templates was developed. The method had to compute atomic resolution backbones compatible with the atomistic sequence selection algorithm we were using and it had to be applicable to all protein motifs. We again developed a method that uses super-secondary structure parameters to determine the orientation among secondary structural elements, given a target protein fold. Possible backbone arrangements were screened using a cost function which evaluates core packing, hydrogen bonding, loop closure, and backbone torsional geometry. Given a specified number of residues for each secondary structural element, a family of optimal configurations was found. We chose three motifs to test our method (βbeta/alpha,/ /beta/alpha/beta, and αalpha) since their combination could be used to approximate most possible backbone fold. The best structure found for the βbeta/alpha motif is similar to a zinc finger, and the best structure for the βbeta/alpha motif is similar to a segment of a β-barrel. The backbone obtained for the αalpha motif resembles minimized protein A. Last, our backbone design method was evaluated by testing the thermal stability and structural properties of the designed peptides using circular dichroism and 1D nuclear magnetic resonance. From these results, a set of heuristic rules was derived. Taken together, these studies suggest that de novo backbones assembled using our backbone design method may serve as adequate input templates for atomistic sequence selection algorithms.

  10. Backbone flexibility in protein design theory and experiment

    NASA Astrophysics Data System (ADS)

    Su, Alyce

    The role of backbone flexibility in protein design was studied. First, the effect of explicit backbone motion on the selection of amino acids in protein design was assessed in the core of the streptococcal protein Gβ1 domain (Gβ1). Concerted backbone motion was introduced by varying Gβ1's supersecondary structure parameter values. The stability and structural flexibility of seven of the redesigned proteins were determined experimentally. Core variants containing as many as six of ten possible mutations retained native-like properties. This result demonstrates that backbone flexibility can be combined with amino acid side-chain selection and that the selection algorithm is sufficiently robust to tolerate perturbations as large as 15% of the native parameter values. Second, a general, quantitative design method for computing de novo backbone templates was developed. The method had to compute atomic resolution backbones compatible with the atomistic sequence selection algorithm we were using and it had to be applicable to all protein motifs. We again developed a method that uses super-secondary structure parameters to determine the orientation among secondary structural elements, given a target protein fold. Possible backbone arrangements were screened using a cost function which evaluates core packing, hydrogen bonding, loop closure, and backbone torsional geometry. Given a specified number of residues for each secondary structural element, a family of optimal configurations was found. We chose three motifs to test our method (ββα, βαβ, and αα) since their combination could be used to approximate most possible backbone fold. The best structure found for the ββα motif is similar to a zinc finger, and the best structure for the ββα motif is similar to a segment of a β-barrel. The backbone obtained for the αα motif resembles minimized protein A. Last, our backbone design method was evaluated by testing the thermal stability and structural properties of the designed peptides using circular dichroism and 1D nuclear magnetic resonance. From these results, a set of heuristic rules was derived. Taken together, these studies suggest that de novo backbones assembled using our backbone design method may serve as adequate input templates for atomistic sequence selection algorithms.

  11. 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

  12. Backbone upgrades and DEC equipment replacement

    NASA Technical Reports Server (NTRS)

    Vancamp, Warren

    1991-01-01

    The NASA Science Internet (NSI) dual protocol backbone is outlined. It includes DECnet link upgrades to match TCP/IP link performance. It also includes the integration of backbone resources and central management. The phase 1 transition process is outlined.

  13. Plant development inhibitory genes in binary vector backbone improve quality event efficiency in soybean transformation.

    PubMed

    Ye, Xudong; Williams, Edward J; Shen, Junjiang; Esser, James A; Nichols, Amy M; Petersen, Michael W; Gilbertson, Larry A

    2008-10-01

    Conventional Agrobacterium-mediated plant transformation often produces a significant frequency of transgenic events containing vector backbone sequence, which is generally undesirable for biotechnology applications. We tested methods to reduce the frequency of transgenic plants containing vector backbone by incorporating genes into the backbone that inhibit the development of transgenic plants. Four backbone frequency reduction genes, bacterial levansucrase (sacB), maize cytokinin oxidase (CKX), Phaseolus GA 2-oxidase (GA 2-ox), and bacterial phytoene synthase (crtB), each expressed by the enhanced CaMV 35S promoter, were placed individually in a binary vector backbone near the left border (LB) of binary vectors. In transformed soybean plants, the lowest frequency of backbone presence was observed when the constitutively expressed CKX gene was used, followed by crtB. Higher backbone frequencies were found among the plants transformed with the GA 2-oxidase and sacB vectors. In some events, transfer of short backbone fragments appeared to be caused by LB readthrough and termination within the backbone reduction gene. To determine the effect of the backbone genes on transformation frequency, the crtB and CKX vectors were then compared to a control vector in soybean transformation experiments. The results revealed that there was no significant transformation frequency difference between the crtB and control vectors, but the CKX vector showed a significant transformation frequency decrease. Molecular analysis revealed that the frequency of transgenic plants containing one or two copies of the transgene and free of backbone was significantly increased by both the CKX and crtB backbone reduction vectors, indicating that there may be a correlation between transgene copy number and backbone frequency. PMID:18253857

  14. 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

    2015-06-01

    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. PMID:25843879

  15. Nucleosome positioning based on the sequence word composition.

    PubMed

    Yi, Xian-Fu; He, Zhi-Song; Chou, Kuo-Chen; Kong, Xiang-Yin

    2012-01-01

    The DNA of all eukaryotic organisms is packaged into nucleosomes (a basic repeating unit of chromatin). A nucleosome consists of histone octamer wrapped by core DNA and linker histone H1 associated with linker DNA. It has profound effects on all DNA-dependent processes by affecting sequence accessibility. Understanding the factors that influence nucleosome positioning has great help to the study of genomic control mechanism. Among many determinants, the inherent DNA sequence has been suggested to have a dominant role in nucleosome positioning in vivo. Here, we used the method of minimum redundancy maximum relevance (mRMR) feature selection and the nearest neighbor algorithm (NNA) combined with the incremental feature selection (IFS) method to identify the most important sequence features that either favor or inhibit nucleosome positioning. We analyzed the words of 53,021 nucleosome DNA sequences and 50,299 linker DNA sequences of Saccharomyces cerevisiae. 32 important features were abstracted from 5,460 features, and the overall prediction accuracy through jackknife cross-validation test was 76.5%. Our results support that sequence-dependent DNA flexibility plays an important role in positioning nucleosome core particles and that genome sequence facilitates the rapid nucleosome reassembly instead of nucleosome depletion. Besides, our results suggest that there exist some additional features playing a considerable role in discriminating nucleosome forming and inhibiting sequences. These results confirmed that the underlying DNA sequence plays a major role in nucleosome positioning. PMID:21919856

  16. A silent composite hemoglobinopathy characterized by gene sequencing.

    PubMed

    Zorai, A; Moumni, I; Benmansour, I; Chaouachi, D; Ghanem, A; Abbes, S

    2011-01-01

    We report the case of a 35-year-old Tunisian women with a chronic anemia non investigated for a long time. Laboratory analysis using advanced technology of DNA sequencing revealed a compound heterozygote for Hb O Arab and cd 39 beta degrees-thalassemia. It's the first time that such a genotype has been characterized by gene sequencing. PMID:23461145

  17. 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.

  18. 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.

  19. Data Acquisition Backbone Core DABC

    NASA Astrophysics Data System (ADS)

    Adamczewski, J.; Essel, H. G.; Kurz, N.; Linev, S.

    2008-07-01

    For the new experiments at FAIR new concepts of data acquisition systems have to be developed like the distribution of self-triggered, time stamped data streams over high performance networks for event building. The Data Acquisition Backbone Core (DABC) is a software package currently under development for FAIR detector tests, readout components test, and data flow investigations. All kinds of data channels (front-end systems) are connected by program plug-ins into functional components of DABC like data input, combiner, scheduler, event builder, analysis and storage components. After detailed simulations real tests of event building over a switched network (InfiniBand clusters with up to 110 nodes) have been performed. With the DABC software more than 900 MByte/s input and output per node can be achieved meeting the most demanding requirements. The software is ready for the implementation of various test beds needed for the final design of data acquisition systems at FAIR. The development of key components is supported by the FutureDAQ project of the European Union (FP6 I3HP JRA1).

  20. Diverse nucleotide compositions and sequence fluctuation in Rubisco protein genes

    NASA Astrophysics Data System (ADS)

    Holden, Todd; Dehipawala, S.; Cheung, E.; Bienaime, R.; Ye, J.; Tremberger, G., Jr.; Schneider, P.; Lieberman, D.; Cheung, T.

    2011-10-01

    The Rubisco protein-enzyme is arguably the most abundance protein on Earth. The biology dogma of transcription and translation necessitates the study of the Rubisco genes and Rubisco-like genes in various species. Stronger correlation of fractal dimension of the atomic number fluctuation along a DNA sequence with Shannon entropy has been observed in the studied Rubisco-like gene sequences, suggesting a more diverse evolutionary pressure and constraints in the Rubisco sequences. The strategy of using metal for structural stabilization appears to be an ancient mechanism, with data from the porphobilinogen deaminase gene in Capsaspora owczarzaki and Monosiga brevicollis. Using the chi-square distance probability, our analysis supports the conjecture that the more ancient Rubisco-like sequence in Microcystis aeruginosa would have experienced very different evolutionary pressure and bio-chemical constraint as compared to Bordetella bronchiseptica, the two microbes occupying either end of the correlation graph. Our exploratory study would indicate that high fractal dimension Rubisco sequence would support high carbon dioxide rate via the Michaelis- Menten coefficient; with implication for the control of the whooping cough pathogen Bordetella bronchiseptica, a microbe containing a high fractal dimension Rubisco-like sequence (2.07). Using the internal comparison of chi-square distance probability for 16S rRNA (~ E-22) versus radiation repair Rec-A gene (~ E-05) in high GC content Deinococcus radiodurans, our analysis supports the conjecture that high GC content microbes containing Rubisco-like sequence are likely to include an extra-terrestrial origin, relative to Deinococcus radiodurans. Similar photosynthesis process that could utilize host star radiation would not compete with radiation resistant process from the biology dogma perspective in environments such as Mars and exoplanets.

  1. Changing the topology of protein backbone: the effect of backbone cyclization on the structure and dynamics of a SH3 domain

    NASA Astrophysics Data System (ADS)

    Schumann, Frank; Varadan, Ranjani; Tayakuniyil, Praveen; Grossman, Jennifer; Camarero, Julio; Fushman, David

    2015-04-01

    Understanding of the effects of the backbone cyclization on the structure and dynamics of a protein is essential for using protein topology engineering to alter protein stability and function. Here we have determined, for the first time, the structure and dynamics of the linear and various circular constructs of the N-SH3 domain from protein c-Crk. These constructs differ in the length and amino acid composition of the cyclization region. The backbone cyclization was carried out using intein-mediated intramolecular chemical ligation between the juxtaposed N- and the C-termini. The structure and backbone dynamics studies were performed using solution NMR. Our data suggest that the backbone cyclization has little effect on the overall three-dimensional structure of the SH3 domain: besides the termini, only minor structural changes were found in the proximity of the cyclization region. In contrast to the structure, backbone dynamics are significantly affected by the cyclization. On the subnanosecond time scale, the backbone of all circular constructs on average appears more rigid than that of the linear SH3 domain; this effect is observed over the entire backbone and is not limited to the cyclization site. The backbone mobility of the circular constructs becomes less restricted with increasing length of the circularization loop. In addition, significant conformational exchange motions (on the sub-millisecond time scale) were found in the N-Src loop and in the adjacent β-strands in all circular constructs studied in this work. These effects of backbone cyclization on protein dynamics have potential implications for the stability of the protein fold and for ligand binding.

  2. Changing the topology of protein backbone: the effect of backbone cyclization on the structure and dynamics of a SH3 domain

    PubMed Central

    Schumann, Frank H.; Varadan, Ranjani; Tayakuniyil, Praveen P.; Grossman, Jennifer H.; Camarero, Julio A.; Fushman, David

    2015-01-01

    Understanding of the effects of the backbone cyclization on the structure and dynamics of a protein is essential for using protein topology engineering to alter protein stability and function. Here we have determined, for the first time, the structure and dynamics of the linear and various circular constructs of the N-SH3 domain from protein c-Crk. These constructs differ in the length and amino acid composition of the cyclization region. The backbone cyclization was carried out using intein-mediated intramolecular chemical ligation between the juxtaposed N- and the C-termini. The structure and backbone dynamics studies were performed using solution NMR. Our data suggest that the backbone cyclization has little effect on the overall three-dimensional structure of the SH3 domain: besides the termini, only minor structural changes were found in the proximity of the cyclization region. In contrast to the structure, backbone dynamics are significantly affected by the cyclization. On the subnanosecond time scale, the backbone of all circular constructs on average appears more rigid than that of the linear SH3 domain; this effect is observed over the entire backbone and is not limited to the cyclization site. The backbone mobility of the circular constructs becomes less restricted with increasing length of the circularization loop. In addition, significant conformational exchange motions (on the sub-millisecond time scale) were found in the N-Src loop and in the adjacent β-strands in all circular constructs studied in this work. These effects of backbone cyclization on protein dynamics have potential implications for the stability of the protein fold and for ligand binding. PMID:25905098

  3. 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 simulate combined environments. Processing improvements included development and use of low spray guns for foam application, additional human factors considerations for production, use of high fidelity mockups during hardware processing with video review, improved tank access, extensive use of non destructive evaluation, and producibility enhancements. Design improvements included redesigned bipod fittings, a bellows heater, a feedline camera active during ascent flight, removal of the protuberance airload ramps, redesigned ice frost ramps, and titanium brackets replaced aluminum brackets on the liquid oxygen feedline. Post flight assessment improved due to significant addition of imagery assets, greatly improving situational awareness. The debris risk was reduced by two orders of magnitude. During this time a major natural disaster was overcome when Katrina damaged the manufacturing facility. Numerous lessons from these efforts are documented within the paper.

  4. Detecting composition and monomer sequence distribution in random copolymers with interaction chromatography

    NASA Astrophysics Data System (ADS)

    Han, Junwon; Ryu, Chang Y.; Semler, James J.; Genzer, Jan

    2006-03-01

    We demonstrate that interaction chromatography (IC) is capable of discriminating among both the chemical composition and monomer sequence distribution in random copolymers. By fine-tuning the separation conditions in the IC (solvent type and stationary phase type), we were able to delineate the effect of both their chemical composition and the monomer sequence distribution of partially brominated polystyrenes on chromatographic retention. The degree of bromination and the 4-BrS sequencing was controlled by varying the bromine concentration in the reaction vessel, bromination reaction time, and solvent temperature. Our experiments suggest that 1) the blockiness of 4-BrS adsorption segments can further enhance the surface affinity of the copolymer chains at a fixed copolymer chemical composition, and 2) the adsorption-based molecular recognition of copolymer chains occurs by cooperative and synergistic adsorption of segments on surfaces along with neighboring adsorptive segments.

  5. Conformational Entropy of the RNA Phosphate Backbone and Its Contribution to the Folding Free Energy

    PubMed Central

    Mak, Chi H.; Matossian, Tyler; Chung, Wen-Yeuan

    2014-01-01

    While major contributors to the free energy of RNA tertiary structures such as basepairing, base-stacking, and charge and counterion interactions have been studied extensively, little is known about the intrinsic free energy of the backbone. To assess the magnitude of the entropic strains along the phosphate backbone and their impact on the folding free energy, we have formulated a mathematical treatment for computing the volume of the main-chain torsion-angle conformation space between every pair of nucleobases along any sequence to compute the corresponding backbone entropy. To validate this method, we have compared the computed conformational entropies against a statistical free energy analysis of structures in the crystallographic database from several-thousand backbone conformations between nearest-neighbor nucleobases as well as against extensive computer simulations. Using this calculation, we analyzed the backbone entropy of several ribozymes and riboswitches and found that their entropic strains are highly localized along their sequences. The total entropic penalty due to steric congestions in the backbone for the native fold can be as high as 2.4 cal/K/mol per nucleotide for these medium and large RNAs, producing a contribution to the overall free energy of up to 0.72 kcal/mol per nucleotide. For these RNAs, we found that low-entropy high-strain residues are predominantly located at loops with tight turns and at tertiary interaction platforms with unusual structural motifs. PMID:24703311

  6. Polyolefin backbone substitution in binders for low temperature powder injection moulding feedstocks.

    PubMed

    Hausnerova, Berenika; Kuritka, Ivo; Bleyan, Davit

    2014-01-01

    This paper reports the substitution of polyolefin backbone binder components with low melting temperature carnauba wax for powder injection moulding applications. The effect of various binder compositions of Al₂O₃ feedstock on thermal degradation parameters is investigated by thermogravimetric analysis. Within the experimental framework 29 original feedstock compositions were prepared and the superiority of carnauba wax over the polyethylene binder backbone was demonstrated in compositions containing polyethylene glycol as the initial opening agent and governing the proper mechanism of the degradation process. Moreover, the replacement of synthetic polymer by the natural wax contributes to an increase of environmental sustainability of modern industrial technologies. PMID:24583880

  7. Isolation of the protein backbone of an arabinogalactan-protein from the styles of Nicotiana alata and characterization of a corresponding cDNA.

    PubMed Central

    Du, H; Simpson, R J; Moritz, R L; Clarke, A E; Bacic, A

    1994-01-01

    Arabinogalactan-proteins (AGPs) from the styles of Nicotiana alata were isolated by ion exchange and gel filtration chromatography. After deglycosylation by anhydrous hydrogen fluoride, the protein backbones were fractionated by reversed-phase HPLC. One of the protein backbones, containing mainly hydroxyproline, alanine, and serine residues (53% of total residues), was digested with proteases, and the peptides were isolated and sequenced. This sequence information allowed the cloning of a 712-bp cDNA, AGPNa1. AGPNa1 encodes a 132-amino acid protein with three domains: an N-terminal secretion signal sequence, which is cleaved from the mature protein; a central sequence, which contains most of the hydroxyproline/proline residues; and a C-terminal hydrophobic region. AGPNa1 is expressed in many tissues of N. alata and related species. The arrangement of domains and amino acid composition of the AGP encoded by AGPNa1 are similar to that of an AGP from pear cell suspension culture filtrate, although the only sequence identity is at the N termini of the mature proteins. PMID:7827496

  8. Enzymes/non-enzymes classification model complexity based on composition, sequence, 3D and topological indices.

    PubMed

    Munteanu, Cristian Robert; González-Díaz, Humberto; Magalhães, Alexandre L

    2008-09-21

    The huge amount of new proteins that need a fast enzymatic activity characterization creates demands of protein QSAR theoretical models. The protein parameters that can be used for an enzyme/non-enzyme classification includes the simpler indices such as composition, sequence and connectivity, also called topological indices (TIs) and the computationally expensive 3D descriptors. A comparison of the 3D versus lower dimension indices has not been reported with respect to the power of discrimination of proteins according to enzyme action. A set of 966 proteins (enzymes and non-enzymes) whose structural characteristics are provided by PDB/DSSP files was analyzed with Python/Biopython scripts, STATISTICA and Weka. The list of indices includes, but it is not restricted to pure composition indices (residue fractions), DSSP secondary structure protein composition and 3D indices (surface and access). We also used mixed indices such as composition-sequence indices (Chou's pseudo-amino acid compositions or coupling numbers), 3D-composition (surface fractions) and DSSP secondary structure amino acid composition/propensities (obtained with our Prot-2S Web tool). In addition, we extend and test for the first time several classic TIs for the Randic's protein sequence Star graphs using our Sequence to Star Graph (S2SG) Python application. All the indices were processed with general discriminant analysis models (GDA), neural networks (NN) and machine learning (ML) methods and the results are presented versus complexity, average of Shannon's information entropy (Sh) and data/method type. This study compares for the first time all these classes of indices to assess the ratios between model accuracy and indices/model complexity in enzyme/non-enzyme discrimination. The use of different methods and complexity of data shows that one cannot establish a direct relation between the complexity and the accuracy of the model. PMID:18606172

  9. Protein location prediction using atomic composition and global features of the amino acid sequence

    SciTech Connect

    Cherian, Betsy Sheena; Nair, Achuthsankar S.

    2010-01-22

    Subcellular location of protein is constructive information in determining its function, screening for drug candidates, vaccine design, annotation of gene products and in selecting relevant proteins for further studies. Computational prediction of subcellular localization deals with predicting the location of a protein from its amino acid sequence. For a computational localization prediction method to be more accurate, it should exploit all possible relevant biological features that contribute to the subcellular localization. In this work, we extracted the biological features from the full length protein sequence to incorporate more biological information. A new biological feature, distribution of atomic composition is effectively used with, multiple physiochemical properties, amino acid composition, three part amino acid composition, and sequence similarity for predicting the subcellular location of the protein. Support Vector Machines are designed for four modules and prediction is made by a weighted voting system. Our system makes prediction with an accuracy of 100, 82.47, 88.81 for self-consistency test, jackknife test and independent data test respectively. Our results provide evidence that the prediction based on the biological features derived from the full length amino acid sequence gives better accuracy than those derived from N-terminal alone. Considering the features as a distribution within the entire sequence will bring out underlying property distribution to a greater detail to enhance the prediction accuracy.

  10. Influence of processing sequence on the tribological properties of VGCF-X/PA6/SEBS composites

    NASA Astrophysics Data System (ADS)

    Osada, Yu; Nishitani, Yosuke; Kitano, Takeshi

    2016-03-01

    In order to develop the new tribomaterials for mechanical sliding parts with sufficient balance of mechanical and tribological properties, we investigated the influence of processing sequence on the tribological properties of the ternary nanocomposites: the polymer blends of polyamide 6 (PA6) and styrene-ethylene/butylene-styrene copolymer (SEBS) filled with vapor grown carbon fiber (VGCF-X), which is one of carbon nanofiber (CNF) and has 15nm diameter and 3μm length. Five different processing sequences: (1) VGCF-X, PA6 and SEBS were mixed simultaneously (Process A), (2) Re-mixing (Second compounding) of the materials prepared by Process A (Process AR),(3) SEBS was blended with PA6 (PA6/SEBS blends) and then these blends were mixed with VGCF-X (Process B), (4) VGCF-X was mixed with PA6 (VGCF-X/PA6 composites) and then these composites were blended with SEBS (Process C), and (5) VGCF-X were mixed with SEBS (VGCF-X/SEBS composites) and then these composites were blended with PA6 (Process D) were attempted for preparing of the ternary nanocomposites (VGCF-X/PA6/SEBS composites). These ternary polymer nanocomposites were extruded by a twin screw extruder and injection-molded. Their tribological properties were evaluated by using a ring-on-plate type sliding wear tester under dry condition. The tribological properties such as the frictional coefficient and the specific wear rate were influenced by the processing sequence. These results may be attributed to the change of internal structure formation, which is a dispersibility of SEBS particle and VGCF-X in ternary nanocomposites (VGCF-X/PA6/SEBS) by different processing sequences. In particular, the processing sequences of AR, B and D, which are those of re-mixing of VGCF-X, have a good dispersibility of VGCF-X for the improvement of tribological properties.

  11. Optimum stacking sequence design of composite sandwich panel using genetic algorithms

    NASA Astrophysics Data System (ADS)

    Bir, Amarpreet Singh

    Composite sandwich structures recently gained preference for various structural components over conventional metals and simple composite laminates in the aerospace industries. For most widely used composite sandwich structures, the optimization problems only requires the determination of the best stacking sequence and the number of laminae with different fiber orientations. Genetic algorithm optimization technique based on Darwin's theory of survival of the fittest and evolution is most suitable for solving such optimization problems. The present research work focuses on the stacking sequence optimization of composite sandwich panels with laminated face-sheets for both critical buckling load maximization and thickness minimization problems, subjected to bi-axial compressive loading. In the previous studies, only balanced and even-numbered simple composite laminate panels have been investigated ignoring the effects of bending-twisting coupling terms. The current work broadens the application of genetic algorithms to more complex composite sandwich panels with balanced, unbalanced, even and odd-numbered face-sheet laminates including the effects of bending-twisting coupling terms.

  12. Early Folding Events, Local Interactions, and Conservation of Protein Backbone Rigidity.

    PubMed

    Pancsa, Rita; Raimondi, Daniele; Cilia, Elisa; Vranken, Wim F

    2016-02-01

    Protein folding is in its early stages largely determined by the protein sequence and complex local interactions between amino acids, resulting in lower energy conformations that provide the context for further folding into the native state. We compiled a comprehensive data set of early folding residues based on pulsed labeling hydrogen deuterium exchange experiments. These early folding residues have corresponding higher backbone rigidity as predicted by DynaMine from sequence, an effect also present when accounting for the secondary structures in the folded protein. We then show that the amino acids involved in early folding events are not more conserved than others, but rather, early folding fragments and the secondary structure elements they are part of show a clear trend toward conserving a rigid backbone. We therefore propose that backbone rigidity is a fundamental physical feature conserved by proteins that can provide important insights into their folding mechanisms and stability. PMID:26840723

  13. Pyrrolidinyl PNA with ?/?-Dipeptide Backbone: From Development to Applications.

    PubMed

    Vilaivan, Tirayut

    2015-06-16

    The specific pairing between two complementary nucleobases (AT, CG) according to the Watson-Crick rules is by no means unique to natural nucleic acids. During the past few decades a number of nucleic acid analogues or mimics have been developed, and peptide nucleic acid (PNA) is one of the most intriguing examples. In addition to forming hybrids with natural DNA/RNA as well as itself with high affinity and specificity, the uncharged peptide-like backbone of PNA confers several unique properties not observed in other classes of nucleic acid analogues. PNA is therefore suited to applications currently performed by conventional oligonucleotides/analogues and others potentially beyond this. In addition, PNA is also interesting in its own right as a new class of oligonucleotide mimics. Unlimited opportunities exist to modify the PNA structure, stimulating the search for new systems with improved properties or additional functionality not present in the original PNA, driving future research and applications of these in nanotechnology and beyond. Although many structural variations of PNA exist, significant improvements to date have been limited to a few constrained derivatives of the privileged N-2-aminoethylglycine PNA scaffold. In this Account, we summarize our contributions in this field: the development of a new family of conformationally constrained pyrrolidinyl PNA having a nonchimeric ?/?-dipeptide backbone derived from nucleobase-modified proline and cyclic ?-amino acids. The conformational constraints dictated by the pyrrolidine ring and the ?-amino acid are essential requirements determining the binding efficiency, as the structure and stereochemistry of the PNA backbone significantly affect its ability to interact with DNA, RNA, and in self-pairing. The modular nature of the dipeptide backbone simplifies the synthesis and allows for rapid structural optimization. Pyrrolidinyl PNA having a (2'R,4'R)-proline/(1S,2S)-2-aminocyclopentanecarboxylic backbone (acpcPNA) binds to DNA with outstanding affinity and sequence specificity. It also binds to RNA in a highly sequence-specific fashion, albeit with lower affinity than to DNA. Additional characteristics include exclusive antiparallel/parallel selectivity and a low tendency for self-hybridization. Modification of the nucleobase or backbone allowing site-specific incorporation of labels and other functions to acpcPNA via click and other conjugation chemistries is possible, generating functional PNAs that are suitable for various applications. DNA sensing and biological applications of acpcPNA have been demonstrated, but these are still in their infancy and the full potential of pyrrolidinyl PNA is yet to be realized. With properties competitive with, and in some aspects superior to, the best PNA technology available to date, pyrrolidinyl PNA offers great promise as a platform system for future elaboration for the fabrication of new functional materials, nanodevices, and next-generation analytical tools. PMID:26022340

  14. Determination of load sequence effects on the degradation and failure of composite materials. [Graphite-epoxy composites

    NASA Technical Reports Server (NTRS)

    Yang, J. N.; Jones, D. L.

    1981-01-01

    A theoretical model was established to predict the fatigue behavior of composite materials, with emphasis placed on predictions of the degradation of residual strength and residual stiffness during fatigue cycling. The model parameters were evaluated from three test series including static strength fatigue life and residual strength tests. The tests were applied to two graphite/epoxy laminates. Load sequence effects were emphasized for both laminates and the predicted results agreed quite well with subsequent verification tests. Dynamic as well as static stiffness reduction data were collected by use of a PDP11-03 computer, which performed quite satisfactorily and permitted the recording of a substantial amount of dynamic stiffness reduction data.

  15. Sequence composition of disordered regions fine-tunes protein half-life

    PubMed Central

    Fishbain, Susan; Inobe, Tomonao; Israeli, Eitan; Chavali, Sreenivas; Yu, Houqing; Kago, Grace; Babu, M. Madan; Matouschek, Andreas

    2015-01-01

    The proteasome controls the concentrations of most proteins in eukaryotic cells. It recognizes its protein substrates through ubiquitin tags and initiates degradation at disordered regions within the substrate. Here we find that the proteasome has pronounced preferences for the amino acid sequence composition of the regions at which it initiates degradation. Specifically, proteins where the initiation regions have biased amino acid compositions show longer half-lives in yeast. The relationship is also observed on a genomic scale in mouse cells. These preferences affect the degradation rates of proteins in vitro, can explain the unexpected stability of natural proteins in yeast, and may affect the accumulation of toxic proteins in disease. We propose that the proteasome’s sequence preferences provide a second component to the degradation code and may fine-tune protein half-life in cells. PMID:25643324

  16. Initial transcribed region sequences influence the composition and functional properties of the bacterial elongation complex.

    PubMed

    Deighan, Padraig; Pukhrambam, Chirangini; Nickels, Bryce E; Hochschild, Ann

    2011-01-01

    The bacterial RNA polymerase (RNAP) holoenzyme consists of a catalytic core enzyme (α(2)ββ'ω) in complex with a σ factor that is essential for promoter recognition and transcription initiation. During early elongation, the stability of interactions between σ and the remainder of the transcription complex decreases. Nevertheless, there is no mechanistic requirement for release of σ upon the transition to elongation. Furthermore, σ can remain associated with RNAP during transcription elongation and influence regulatory events that occur during transcription elongation. Here we demonstrate that promoter-like DNA sequence elements within the initial transcribed region that are known to induce early elongation pausing through sequence-specific interactions with σ also function to increase the σ content of downstream elongation complexes. Our findings establish σ-dependent pausing as a mechanism by which initial transcribed region sequences can influence the composition and functional properties of the transcription elongation complex over distances of at least 700 base pairs. PMID:21205867

  17. Nucleotide composition of CO1 sequences in Chelicerata (Arthropoda): detecting new mitogenomic rearrangements.

    PubMed

    Arabi, Juliette; Judson, Mark L I; Deharveng, Louis; Lourenço, Wilson R; Cruaud, Corinne; Hassanin, Alexandre

    2012-02-01

    Here we study the evolution of nucleotide composition in third codon-positions of CO1 sequences of Chelicerata, using a phylogenetic framework, based on 180 taxa and three markers (CO1, 18S, and 28S rRNA; 5,218 nt). The analyses of nucleotide composition were also extended to all CO1 sequences of Chelicerata found in GenBank (1,701 taxa). The results show that most species of Chelicerata have a positive strand bias in CO1, i.e., in favor of C nucleotides, including all Amblypygi, Palpigradi, Ricinulei, Solifugae, Uropygi, and Xiphosura. However, several taxa show a negative strand bias, i.e., in favor of G nucleotides: all Scorpiones, Opisthothelae spiders and several taxa within Acari, Opiliones, Pseudoscorpiones, and Pycnogonida. Several reversals of strand-specific bias can be attributed to either a rearrangement of the control region or an inversion of a fragment containing the CO1 gene. Key taxa for which sequencing of complete mitochondrial genomes will be necessary to determine the origin and nature of mtDNA rearrangements involved in the reversals are identified. Acari, Opiliones, Pseudoscorpiones, and Pycnogonida were found to show a strong variability in nucleotide composition. In addition, both mitochondrial and nuclear genomes have been affected by higher substitution rates in Acari and Pseudoscorpiones. The results therefore indicate that these two orders are more liable to fix mutations of all types, including base substitutions, indels, and genomic rearrangements. PMID:22362465

  18. Miniaturized proteins: the backbone cyclic proteinomimetic approach.

    PubMed

    Kasher, R; Oren, D A; Barda, Y; Gilon, C

    1999-09-17

    The field of proteinomimetics utilizes peptide-based molecules to mimic native protein functions. We describe a novel general method for mimicking proteins by small cyclic peptides for the purpose of drug design, and demonstrate its applicability on bovine pancreatic trypsin inhibitor (BPTI). These unique cyclic peptides, which both embody discontinuous residues of proteins in their bio-active conformation and ensure an induced fit, may overcome some of the pharmacological drawbacks attributed to proteins and peptides. This method, which we call the backbone cyclic (BC) proteinomimetic approach, combines backbone cyclization of peptides with a suitable selection method, cycloscan. Following this procedure, we have prepared a bicyclic nonapeptide, which mimics the binding region of BPTI. The X-ray crystal structure of the complex trypsin:mimetic, as well as kinetic studies, show that the BPTI mimetic binds to the specificity pocket of trypsin in a similar manner to BPTI. Inhibition measurements of various constructs revealed that backbone cyclization imposed the conformation crucial to binding. PMID:10493885

  19. Composite Sequences for Triple-dot Qubits that Compensate for Miscalibration and Hyperfine Gradients

    NASA Astrophysics Data System (ADS)

    Ladd, Thaddeus

    2014-03-01

    Exchange-only qubits defined in triple quantum dots form a promising means for all-electrical semiconductor quantum control, but they suffer from both charge noise and random magnetic field gradients. Low-frequency noise sources can be compensated using composite sequences, but the development of such sequences is constrained by the fact that exchange energies are always positive and the control axes are non-orthogonal. Here, we present the results of both analytical approaches and computational searches for composite pulse sequences, which compensate for simultaneous low-frequency miscalibration (due to fixed random electric fields) and hyperfine effects (due to nuclear magnetic fields) in a single triple-dot qubit. We also present compensation sequences for multi-qubit gates. These results can substantially improve the working fidelity of quantum operations in semiconductor quantum dot devices. Sponsored by United States Department of Defense. The views and conclusions contained in this document are those of the authors and should not be interpreted as representing the official policies, either expressly or implied, of the United States Department of Defense or the U.S. Government.

  20. A new decoupling method for accurate quantification of polyethylene copolymer composition and triad sequence distribution with 13C NMR.

    PubMed

    Zhou, Zhe; Kümmerle, Rainer; Qiu, Xiaohua; Redwine, David; Cong, Rongjuan; Taha, Angela; Baugh, Dan; Winniford, Bill

    2007-08-01

    (13)C NMR is a powerful analytical tool for characterizing polyethylene copolymer composition and sequence distribution. Accurate characterization of the composition and sequence distribution is critical for researchers in industry and academia. Some common composite pulse decoupling (CPD) sequences used in polyethylene copolymer (13)C NMR can lead to artifacts such as modulations of the decoupled (13)C NMR signals (decoupling sidebands) resulting in systematic errors in quantitative analysis. A new CPD method was developed, which suppresses decoupling sidebands below the limit of detection (less than 1:40,000 compared to the intensity of the decoupled signal). This new CPD sequence consists of an improved Waltz-16 CPD, implemented as a bilevel method. Compared with other conventional CPD programs this new decoupling method produced the cleanest (13)C NMR spectra for polyethylene copolymer composition and triad sequence distribution analyses. PMID:17524686

  1. Gene ontology-based protein function prediction by using sequence composition information.

    PubMed

    Dong, Qiwen; Zhou, Shuigeng; Deng, Lei; Guan, Jihong

    2010-06-01

    The prediction of protein function is a difficult and important problem in computational biology. In this study, an efficient method is presented to predict protein function with sequence composition information. Four kinds of basic building blocks of protein sequences are investigated, including N-grams, binary profiles, PFAM domains and InterPro domains. The protein sequences are mapped into high-dimensional vectors by using the occurrence frequencies of each kind of building blocks. The resulting vectors are then taken as input to support vector machine to predict their function based on gene ontology. Experiments are conducted over the subset of GOA database. The experimental results show that the protein function can be predicted from primary sequence information. The method based on InterPro domains outperforms the other building blocks, and gets an overall accuracy of 0.87 and ROC score is 0.93. We also demonstrate that the use of feature extraction algorithms such as latent semantic analysis and nonnegative matrix factorization, can efficiently remove noise and improve the prediction efficiency without significantly degrading the performance. The results obtained here are helpful for the prediction of protein function by using only sequence information. PMID:19995340

  2. Automated real-space refinement of protein structures using a realistic backbone move set.

    PubMed

    Haddadian, Esmael J; Gong, Haipeng; Jha, Abhishek K; Yang, Xiaojing; Debartolo, Joe; Hinshaw, James R; Rice, Phoebe A; Sosnick, Tobin R; Freed, Karl F

    2011-08-17

    Crystals of many important biological macromolecules diffract to limited resolution, rendering accurate model building and refinement difficult and time-consuming. We present a torsional optimization protocol that is applicable to many such situations and combines Protein Data Bank-based torsional optimization with real-space refinement against the electron density derived from crystallography or cryo-electron microscopy. Our method converts moderate- to low-resolution structures at initial (e.g., backbone trace only) or late stages of refinement to structures with increased numbers of hydrogen bonds, improved crystallographic R-factors, and superior backbone geometry. This automated method is applicable to DNA-binding and membrane proteins of any size and will aid studies of structural biology by improving model quality and saving considerable effort. The method can be extended to improve NMR and other structures. Our backbone score and its sequence profile provide an additional standard tool for evaluating structural quality. PMID:21843481

  3. Design and synthesis of backbone cyclic phosphorylated peptides: The IkappaB model.

    PubMed

    Qvit, Nir; Hatzubai, Ada; Shalev, Deborah E; Friedler, Assaf; Ben-Neriah, Yinon; Gilon, Chaim

    2009-02-01

    Phosphopeptides have been used to study phosphorylation and dephosphorylation, which are key events in protein expression. Backbone cyclization has been shown to increase the stability and selectivity of peptides. Backbone cyclic peptides with conformational diversity have produced bioactive peptides with improved pharmaceutical properties, metabolic stability, and enhanced intestinal permeability. We demonstrate a successful methodology for incorporating phospho-amino acids into backbone cyclic peptides. The nuclear factor-kappa B (NF-kappaB) is a latent mammalian protein prototype of dimeric transcription factors that exists in all cell types and plays a pivotal role in a huge number of genes, such as those responsible for chronic and acute inflammatory diseases. To inhibit NF-kappaB, backbone cyclic phosphopeptides were designed and synthesized based on the conserved sequence of the Inhibitor kappa B (IkappaB). The peptides were screened for inhibiting IkappaB ubiquitylation. The best compound showed 90% inhibition at a concentration of 3 microM, and its solution structure showed similarity to a related beta-catenin protein. This general methodology can be use for synthesizing cyclic phosphorylated, as well as backbone cyclic phosphorylated peptides for various biological targets. PMID:19025995

  4. 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.

  5. Backbone Solution Structures of Proteins Using Residual Dipolar Couplings: Application to a Novel Structural Genomics Target

    PubMed Central

    Valafar, H.; Mayer, K. L.; Bougault, C. M.; LeBlond, P. D.; Jenney, F. E.; Brereton, P. S.; Adams, M.W.W.; Prestegard, J.H.

    2006-01-01

    Structural genomics (or proteomics) activities are critically dependent on the availability of high-throughput structure determination methodology. Development of such methodology has been a particular challenge for NMR based structure determination because of the demands for isotopic labeling of proteins and the requirements for very long data acquisition times. We present here a methodology that gains efficiency from a focus on determination of backbone structures of proteins as opposed to full structures with all side chains in place. This focus is appropriate given the presumption that many protein structures in the future will be built using computational methods that start from representative fold family structures and replace as many as 70% of the side chains in the course of structure determination. The methodology we present is based primarily on residual dipolar couplings (RDCs), readily accessible NMR observables that constrain the orientation of backbone fragments irrespective of separation in space. A new software tool is described for the assembly of backbone fragments under RDC constraints and an application to a structural genomics target is presented. The target is an 8.7 kDa protein from Pyrococcus furiosus, PF1061, that was previously not well annotated, and had a nearest structurally characterized neighbor with only 33% sequence identity. The structure produced shows structural similarity to this sequence homologue, but also shows similarity to other proteins that suggests a functional role in sulfur transfer. Given the backbone structure and a possible functional link this should be an ideal target for development of modeling methods. PMID:15704012

  6. Postglacial climate-change record in biomarker lipid compositions of the Hani peat sequence, Northeastern China

    NASA Astrophysics Data System (ADS)

    Zhou, Weijian; Zheng, Yanhong; Meyers, Philip A.; Jull, A. J. Timothy; Xie, Shucheng

    2010-05-01

    The peat sequence at Hani in northeastern China accumulated over the past 16 cal kyr in a percolation mire in which rain water and ground water seeped through the peat system. The molecular compositions of n-alkanes, n-alkanols, and n-alkanoic acids extracted from the Hani peat sequence reveal different responses to the progressive evolution of climate and changes in the nature of the peat-forming vegetation. Long chain length components that originate from the waxy coatings of subaerial vascular plants dominate the n-alkane distributions throughout the Hani peat sequence. The paleoclimate integrity of these biomarker molecules appears to be well preserved. Most of the n-alkanol distributions are similarly dominated by long chain components that indicate their origins from subaerial plants. In contrast, n-alkanoic acid distributions are dominated by secondary components that record the importance of post-depositional microbial activity in this peat sequence, which evidently can be extensive in a percolation mire. Elevated n-alkane Paq values and C 23/C 29 ratios, which are both molecular proxies for water-loving plants, record an especially moist local climate in the Blling-Allerd (14.5 to 12.9 ka), Younger Dryas (12.9 to 11.5 ka), and Pre-Boreal (11.5 to 10.5 ka) portions of the Hani peat sequence. Depressed Paq values and C 23/C 29 ratios and larger n-alkane average chain length values indicate that the Holocene Climatic Optimum (10.5 to 6 ka) was a period of warmer climate with lower effective precipitation, which contrasts with evidence of wetter climates in most of East Asia.

  7. Initial transcribed region sequences influence the composition and functional properties of the bacterial elongation complex

    PubMed Central

    Deighan, Padraig; Pukhrambam, Chirangini; Nickels, Bryce E.; Hochschild, Ann

    2011-01-01

    The bacterial RNA polymerase (RNAP) holoenzyme consists of a catalytic core enzyme (α2ββ′ω) in complex with a σ factor that is essential for promoter recognition and transcription initiation. During early elongation, the stability of interactions between σ and the remainder of the transcription complex decreases. Nevertheless, there is no mechanistic requirement for release of σ upon the transition to elongation. Furthermore, σ can remain associated with RNAP during transcription elongation and influence regulatory events that occur during transcription elongation. Here we demonstrate that promoter-like DNA sequence elements within the initial transcribed region that are known to induce early elongation pausing through sequence-specific interactions with σ also function to increase the σ content of downstream elongation complexes. Our findings establish σ-dependent pausing as a mechanism by which initial transcribed region sequences can influence the composition and functional properties of the transcription elongation complex over distances of at least 700 base pairs. PMID:21205867

  8. Chou's pseudo amino acid composition improves sequence-based antifreeze protein prediction.

    PubMed

    Mondal, Sukanta; Pai, Priyadarshini P

    2014-09-01

    Antifreeze proteins (AFP) in living organisms play a key role in their tolerance to extremely cold temperatures and have a wide range of biotechnological applications. But on account of diversity, their identification has been challenging to biologists. Earlier work explored in this area has yet to cover introduction of sequence order information which is known to represent important properties of various proteins and protein systems for prediction purposes. In this study, the effect of Chou's pseudo amino acid composition that presents sequence order of proteins was systematically explored using support vector machines for AFP prediction. Our findings suggest that introduction of sequence order information helps identify AFPs with an accuracy of 84.75% on independent test dataset, outperforming approaches such as AFP-Pred and iAFP. The relative performance calculated using Youden's Index (Sensitivity+Specificity-1) was found to be 0.71 for our predictor (AFP-PseAAC), 0.48 for AFP-Pred and 0.05 for iAFP. We hope this novel prediction approach will aid in AFP based research for biotechnological applications. PMID:24732262

  9. Targeted Sequencing Reveals Large-Scale Sequence Polymorphism in Maize Candidate Genes for Biomass Production and Composition

    PubMed Central

    Ulpinnis, Chris; Scholz, Uwe; Altmann, Thomas

    2015-01-01

    A major goal of maize genomic research is to identify sequence polymorphisms responsible for phenotypic variation in traits of economic importance. Large-scale detection of sequence variation is critical for linking genes, or genomic regions, to phenotypes. However, due to its size and complexity, it remains expensive to generate whole genome sequences of sufficient coverage for divergent maize lines, even with access to next generation sequencing (NGS) technology. Because methods involving reduction of genome complexity, such as genotyping-by-sequencing (GBS), assess only a limited fraction of sequence variation, targeted sequencing of selected genomic loci offers an attractive alternative. We therefore designed a sequence capture assay to target 29 Mb genomic regions and surveyed a total of 4,648 genes possibly affecting biomass production in 21 diverse inbred maize lines (7 flints, 14 dents). Captured and enriched genomic DNA was sequenced using the 454 NGS platform to 19.6-fold average depth coverage, and a broad evaluation of read alignment and variant calling methods was performed to select optimal procedures for variant discovery. Sequence alignment with the B73 reference and de novo assembly identified 383,145 putative single nucleotide polymorphisms (SNPs), of which 42,685 were non-synonymous alterations and 7,139 caused frameshifts. Presence/absence variation (PAV) of genes was also detected. We found that substantial sequence variation exists among genomic regions targeted in this study, which was particularly evident within coding regions. This diversification has the potential to broaden functional diversity and generate phenotypic variation that may lead to new adaptations and the modification of important agronomic traits. Further, annotated SNPs identified here will serve as useful genetic tools and as candidates in searches for phenotype-altering DNA variation. In summary, we demonstrated that sequencing of captured DNA is a powerful approach for variant discovery in maize genes. PMID:26151830

  10. Targeted Sequencing Reveals Large-Scale Sequence Polymorphism in Maize Candidate Genes for Biomass Production and Composition.

    PubMed

    Muraya, Moses M; Schmutzer, Thomas; Ulpinnis, Chris; Scholz, Uwe; Altmann, Thomas

    2015-01-01

    A major goal of maize genomic research is to identify sequence polymorphisms responsible for phenotypic variation in traits of economic importance. Large-scale detection of sequence variation is critical for linking genes, or genomic regions, to phenotypes. However, due to its size and complexity, it remains expensive to generate whole genome sequences of sufficient coverage for divergent maize lines, even with access to next generation sequencing (NGS) technology. Because methods involving reduction of genome complexity, such as genotyping-by-sequencing (GBS), assess only a limited fraction of sequence variation, targeted sequencing of selected genomic loci offers an attractive alternative. We therefore designed a sequence capture assay to target 29 Mb genomic regions and surveyed a total of 4,648 genes possibly affecting biomass production in 21 diverse inbred maize lines (7 flints, 14 dents). Captured and enriched genomic DNA was sequenced using the 454 NGS platform to 19.6-fold average depth coverage, and a broad evaluation of read alignment and variant calling methods was performed to select optimal procedures for variant discovery. Sequence alignment with the B73 reference and de novo assembly identified 383,145 putative single nucleotide polymorphisms (SNPs), of which 42,685 were non-synonymous alterations and 7,139 caused frameshifts. Presence/absence variation (PAV) of genes was also detected. We found that substantial sequence variation exists among genomic regions targeted in this study, which was particularly evident within coding regions. This diversification has the potential to broaden functional diversity and generate phenotypic variation that may lead to new adaptations and the modification of important agronomic traits. Further, annotated SNPs identified here will serve as useful genetic tools and as candidates in searches for phenotype-altering DNA variation. In summary, we demonstrated that sequencing of captured DNA is a powerful approach for variant discovery in maize genes. PMID:26151830

  11. Backbone hydration determines the folding signature of amino acid residues.

    PubMed

    Bignucolo, Olivier; Leung, Hoi Tik Alvin; Grzesiek, Stephan; Bernèche, Simon

    2015-04-01

    The relation between the sequence of a protein and its three-dimensional structure remains largely unknown. A lasting dream is to elucidate the side-chain-dependent driving forces that govern the folding process. Different structural data suggest that aromatic amino acids play a particular role in the stabilization of protein structures. To better understand the underlying mechanism, we studied peptides of the sequence EGAAXAASS (X = Gly, Ile, Tyr, Trp) through comparison of molecular dynamics (MD) trajectories and NMR residual dipolar coupling (RDC) measurements. The RDC data for aromatic substitutions provide evidence for a kink in the peptide backbone. Analysis of the MD simulations shows that the formation of internal hydrogen bonds underlying a helical turn is key to reproduce the experimental RDC values. The simulations further reveal that the driving force leading to such helical-turn conformations arises from the lack of hydration of the peptide chain on either side of the bulky aromatic side chain, which can potentially act as a nucleation point initiating the folding process. PMID:25794270

  12. Exploring the Gastrointestinal "Nemabiome": Deep Amplicon Sequencing to Quantify the Species Composition of Parasitic Nematode Communities.

    PubMed

    Avramenko, Russell W; Redman, Elizabeth M; Lewis, Roy; Yazwinski, Thomas A; Wasmuth, James D; Gilleard, John S

    2015-01-01

    Parasitic helminth infections have a considerable impact on global human health as well as animal welfare and production. Although co-infection with multiple parasite species within a host is common, there is a dearth of tools with which to study the composition of these complex parasite communities. Helminth species vary in their pathogenicity, epidemiology and drug sensitivity and the interactions that occur between co-infecting species and their hosts are poorly understood. We describe the first application of deep amplicon sequencing to study parasitic nematode communities as well as introduce the concept of the gastro-intestinal "nemabiome". The approach is analogous to 16S rDNA deep sequencing used to explore microbial communities, but utilizes the nematode ITS-2 rDNA locus instead. Gastro-intestinal parasites of cattle were used to develop the concept, as this host has many well-defined gastro-intestinal nematode species that commonly occur as complex co-infections. Further, the availability of pure mono-parasite populations from experimentally infected cattle allowed us to prepare mock parasite communities to determine, and correct for, species representation biases in the sequence data. We demonstrate that, once these biases have been corrected, accurate relative quantitation of gastro-intestinal parasitic nematode communities in cattle fecal samples can be achieved. We have validated the accuracy of the method applied to field-samples by comparing the results of detailed morphological examination of L3 larvae populations with those of the sequencing assay. The results illustrate the insights that can be gained into the species composition of parasite communities, using grazing cattle in the mid-west USA as an example. However, both the technical approach and the concept of the 'nemabiome' have a wide range of potential applications in human and veterinary medicine. These include investigations of host-parasite and parasite-parasite interactions during co-infection, parasite epidemiology, parasite ecology and the response of parasite populations to both drug treatments and control programs. PMID:26630572

  13. Prokaryote phylogeny without sequence alignment: from avoidance signature to composition distance.

    PubMed

    Hao, Bailin; Qi, Ji

    2003-01-01

    A new and essentially simple method to reconstruct prokaryotic phylogenetic trees from their complete genome data without using sequence alignment is proposed. It is based on the appearance frequency of oligopeptides of a fixed length (up to K = 6) in their proteomes. This is a method without fine adjustment and choice of genes. It can incorporate the effect of lateral gene transfer to some extent and leads to results comparable with the bacteriologists' systematics as reflected in the latest 2001 edition of the Bergey's Manual of Systematic Bacteriology [1, 2]. A key point in our approach is subtraction of a random background by using a Markovian model of order K - 1 from the composition vectors to highlight the shaping role of natural selection. PMID:16452813

  14. Enumeration search method for optimisation of stacking sequence of laminated composite plates subjected to buckling

    NASA Astrophysics Data System (ADS)

    Sedyono, Joko; Hadavinia, Homayoun; Venetsanos, Demetrios; Marchant, Denis R.

    2015-04-01

    Enumeration search method (ESM) checks all possible combinations of design variables in a bottom-up approach until it finds the global optimum solution for the design conditions. In this paper an optimum design of a multilayered laminated plate made of unidirectional fibre reinforced polymer (FRP) composite subject to uniaxial compression is sought.ESMtogether with classical laminated plate theory (CLPT) has been used to find the lightest laminate for maximizing the buckling load capable of providing structural stability for a set target uniaxial compression load. The choice of the design variables is limited to 4 possible fibres orientation angles (0,90,-45,+45) and the sequence of the laminate, making the problem an integer programming. Experimental and finite element analyses were used to verify the optimum solution. It has been shown that the exhaustive enumeration search method is a powerful tool for finding the global optimum design.

  15. Side chain chemistry mediates backbone fragmentation in hydrogen deficient peptide radicals.

    PubMed

    Sun, Qingyu; Nelson, Hosea; Ly, Tony; Stoltz, Brian M; Julian, Ryan R

    2009-02-01

    A crown ether based, photolabile radical precursor which forms noncovalent complexes with peptides has been prepared. The peptide/precursor complexes can be electrosprayed, isolated in an ion trap, and then subjected to laser photolysis and collision induced dissociation to generate hydrogen deficient peptide radicals. It is demonstrated that these peptide radicals behave very differently from the hydrogen rich peptide radicals generated by electron capture methods. In fact, it is shown that side chain chemistry dictates both the occurrence and relative abundance of backbone fragments that are observed. Fragmentation at aromatic residues occurs preferentially over most other amino acids. The origin of this selectivity relates to the mechanism by which backbone dissociation is initiated. The first step is abstraction of a beta-hydrogen from the side chain, followed by beta-elimination to yield primarily a-type fragment ions. Calculations reveal that those side chains which can easily lose a beta-hydrogen correlate well with experimentally favored sites for backbone fragmentation. In addition, radical mediated side chain losses from the parent peptide are frequently observed. Eleven amino acids exhibit unique mass losses from side chains which positively identify that particular amino acid as part of the parent peptide. Therefore, side chain losses allow one to unambiguously narrow the possible sequences for a parent peptide, which when combined with predictable backbone fragmentation should lead to greatly increased confidence in peptide identification. PMID:19113886

  16. Reconstruction of protein backbones from the BriX collection of canonical protein fragments.

    PubMed

    Baeten, Lies; Reumers, Joke; Tur, Vicente; Stricher, François; Lenaerts, Tom; Serrano, Luis; Rousseau, Frederic; Schymkowitz, Joost

    2008-05-01

    As modeling of changes in backbone conformation still lacks a computationally efficient solution, we developed a discretisation of the conformational states accessible to the protein backbone similar to the successful rotamer approach in side chains. The BriX fragment database, consisting of fragments from 4 to 14 residues long, was realized through identification of recurrent backbone fragments from a non-redundant set of high-resolution protein structures. BriX contains an alphabet of more than 1,000 frequently observed conformations per peptide length for 6 different variation levels. Analysis of the performance of BriX revealed an average structural coverage of protein structures of more than 99% within a root mean square distance (RMSD) of 1 Angstrom. Globally, we are able to reconstruct protein structures with an average accuracy of 0.48 Angstrom RMSD. As expected, regular structures are well covered, but, interestingly, many loop regions that appear irregular at first glance are also found to form a recurrent structural motif, albeit with lower frequency of occurrence than regular secondary structures. Larger loop regions could be completely reconstructed from smaller recurrent elements, between 4 and 8 residues long. Finally, we observed that a significant amount of short sequences tend to display strong structural ambiguity between alpha helix and extended conformations. When the sequence length increases, this so-called sequence plasticity is no longer observed, illustrating the context dependency of polypeptide structures. PMID:18483555

  17. Metagenomic sequencing reveals the relationship between microbiota composition and quality of Chinese Rice Wine.

    PubMed

    Hong, Xutao; Chen, Jing; Liu, Lin; Wu, Huan; Tan, Haiqin; Xie, Guangfa; Xu, Qian; Zou, Huijun; Yu, Wenjing; Wang, Lan; Qin, Nan

    2016-01-01

    Chinese Rice Wine (CRW) is a common alcoholic beverage in China. To investigate the influence of microbial composition on the quality of CRW, high throughput sequencing was performed for 110 wine samples on bacterial 16S rRNA gene and fungal Internal Transcribed Spacer II (ITS2). Bioinformatic analyses demonstrated that the quality of yeast starter and final wine correlated with microbial taxonomic composition, which was exemplified by our finding that wine spoilage resulted from a high proportion of genus Lactobacillus. Subsequently, based on Lactobacillus abundance of an early stage, a model was constructed to predict final wine quality. In addition, three batches of 20 representative wine samples selected from a pool of 110 samples were further analyzed in metagenomics. The results revealed that wine spoilage was due to rapid growth of Lactobacillus brevis at the early stage of fermentation. Gene functional analysis indicated the importance of some pathways such as synthesis of biotin, malolactic fermentation and production of short-chain fatty acid. These results led to a conclusion that metabolisms of microbes influence the wine quality. Thus, nurturing of beneficial microbes and inhibition of undesired ones are both important for the mechanized brewery. PMID:27241862

  18. Extracting the Information Backbone in Online System

    PubMed Central

    Zhang, Qian-Ming; Zeng, An; Shang, Ming-Sheng

    2013-01-01

    Information overload is a serious problem in modern society and many solutions such as recommender system have been proposed to filter out irrelevant information. In the literature, researchers have been mainly dedicated to improving the recommendation performance (accuracy and diversity) of the algorithms while they have overlooked the influence of topology of the online user-object bipartite networks. In this paper, we find that some information provided by the bipartite networks is not only redundant but also misleading. With such “less can be more” feature, we design some algorithms to improve the recommendation performance by eliminating some links from the original networks. Moreover, we propose a hybrid method combining the time-aware and topology-aware link removal algorithms to extract the backbone which contains the essential information for the recommender systems. From the practical point of view, our method can improve the performance and reduce the computational time of the recommendation system, thus improving both of their effectiveness and efficiency. PMID:23690946

  19. NET amyloidogenic backbone in human activated neutrophils.

    PubMed

    Pulze, L; Bassani, B; Gini, E; D'Antona, P; Grimaldi, A; Luini, A; Marino, F; Noonan, D M; Tettamanti, G; Valvassori, R; de Eguileor, M

    2016-03-01

    Activated human neutrophils produce a fibrillar DNA network [neutrophil extracellular traps (NETs)] for entrapping and killing bacteria, fungi, protozoa and viruses. Our results suggest that the neutrophil extracellular traps show a resistant amyloidogenic backbone utilized for addressing reputed proteins and DNA against the non-self. The formation of amyloid fibrils in neutrophils is regulated by the imbalance of reactive oxygen species (ROS) in the cytoplasm. The intensity and source of the ROS signal is determinant for promoting stress-associated responses such as amyloidogenesis and closely related events: autophagy, exosome release, activation of the adrenocorticotrophin hormone/α-melanocyte-stimulating hormone (ACTH/α-MSH) loop and synthesis of specific cytokines. These interconnected responses in human activated neutrophils, that have been evaluated from a morphofunctional and quantitative viewpoint, represent primitive, but potent, innate defence mechanisms. In invertebrates, circulating phagocytic immune cells, when activated, show responses similar to those described previously for activated human neutrophils. Invertebrate cells within endoplasmic reticulum cisternae produce a fibrillar material which is then assembled into an amyloidogenic scaffold utilized to convey melanin close to the invader. These findings, in consideration to the critical role played by NET in the development of several pathologies, could explain the structural resistance of these scaffolds and could provide the basis for developing new diagnostic and therapeutic approaches in immunomediated diseases in which the innate branch of the immune system has a pivotal role. PMID:26462606

  20. Manipulating the backbone structure of semiconducting polymers

    NASA Astrophysics Data System (ADS)

    Luscombe, Christine

    2015-03-01

    Pi-Conjugated polymers are being used in the fabrication of a wide variety of organic electronic devices such as organic field-effect transistors (OFETs), organic photovoltaic (OPV) devices, and organic light-emitting diodes (OLEDs). The advances made in organic electronics have been driven by the syntheses of pi-conjugated polymers with increasingly complex structures but have heavily relied on an Edisonian approach. Despite these advances, there are many contradictory reports in the literature about our understanding of the performance of π-conjugated polymers in many applications. Our group has been studying and developing techniques to grow semiconducting polymers using a living polymerization method. This has allowed us to synthesize polymer architectures that we haven't been able to access till now including polythiophene brushes, star-shaped P3HT, as well as hyperbranched P3HT. It also allows us to accurately control the molecular weights of P3HT and produce materials with a narrow molecular weight distribution. In this presentation, our work towards creating brush polymers will be presented where a series of fully conjugated graft copolymers containing poly(3-hexylthiophene) (P3HT) side chains and a p-type carbazole-diketopyrrolopyrrole donor-acceptor backbone were synthesized via a graft through Suzuki polymerization.

  1. Toward future IP optical backbone networks

    NASA Astrophysics Data System (ADS)

    Urushidani, Shigeo

    2005-11-01

    The rapid and aggressive penetration of broadband access services such as fiber to the home (FTTH) has been accelerating the increase in IP traffic volume and new networking technologies are required in order to accommodate future traffic in a cost-effective manner. This paper overviews the advanced IP optical network architecture and technologies for very-large-scale IP backbone networks. These technologies are the key to accommodate the huge volumes of IP traffic expected and control network resources in an effective and dynamic manner. We describe advanced IP optical networking technologies which accommodate multiple service networks using multi-instance technologies, and enable multi-layer traffic engineering using virtual network topology technologies. The migration scenario is described from the existing networks to GMPLS networks; reference is made to the advanced Path Computation Element (PCE) which enables multi-layer traffic engineering and MPLS/GMPLS migration. New network concepts such as Layer 1 Virtual Private Network (L1VPN) and GMPLS interoperability issues, which are being discussed in IETF, are also described.

  2. RNA-Redesign: a web server for fixed-backbone 3D design of RNA

    PubMed Central

    Yesselman, Joseph D.; Das, Rhiju

    2015-01-01

    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. PMID:25964298

  3. 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. PMID:25964298

  4. Local backbone structure prediction of proteins.

    PubMed

    de Brevern, Alexandre G; Benros, Cristina; Gautier, Romain; Valadié, Héléne; Hazout, Serge; Etchebest, Catherine

    2004-01-01

    A statistical analysis of the PDB structures has led us to define a new set of small 3D structural prototypes called Protein Blocks (PBs). This structural alphabet includes 16 PBs, each one is defined by the (phi, psi) dihedral angles of 5 consecutive residues. The amino acid distributions observed in sequence windows encompassing these PBs are used to predict by a Bayesian approach the local 3D structure of proteins from the sole knowledge of their sequences. LocPred is a software which allows the users to submit a protein sequence and performs a prediction in terms of PBs. The prediction results are given both textually and graphically. PMID:15724288

  5. Backbones of evolutionary history test biodiversity theory for microbes

    PubMed Central

    O’Dwyer, James P.; Kembel, Steven W.; Sharpton, Thomas J.

    2015-01-01

    Identifying the ecological and evolutionary mechanisms that determine biological diversity is a central question in ecology. In microbial ecology, phylogenetic diversity is an increasingly common and relevant means of quantifying community diversity, particularly given the challenges in defining unambiguous species units from environmental sequence data. We explore patterns of phylogenetic diversity across multiple bacterial communities drawn from different habitats and compare these data to evolutionary trees generated using theoretical models of biodiversity. We have two central findings. First, although on finer scales the empirical trees are highly idiosyncratic, on coarse scales the backbone of these trees is simple and robust, consistent across habitats, and displays bursts of diversification dotted throughout. Second, we find that these data demonstrate a clear departure from the predictions of standard neutral theories of biodiversity and that an alternative family of generalized models provides a qualitatively better description. Together, these results lay the groundwork for a theoretical framework to connect ecological mechanisms to observed phylogenetic patterns in microbial communities. PMID:26106159

  6. 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.

  7. 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.

  8. 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.}

  9. 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.

  10. Mapping Fusarium wilt race 1 resistance genes in cotton by inheritance, QTL and sequencing composition.

    PubMed

    Ulloa, Mauricio; Wang, Congli; Hutmacher, Robert B; Wright, Steven D; Davis, R Michael; Saski, Christopher A; Roberts, Philip A

    2011-07-01

    Knowledge of the inheritance of disease resistance and genomic regions housing resistance (R) genes is essential to prevent expanding pathogen threats such as Fusarium wilt [Fusarium oxysporum f.sp. vasinfectum (FOV) Atk. Sny & Hans] in cotton (Gossypium spp.). We conducted a comprehensive study combining conventional inheritance, genetic and quantitative trait loci (QTL) mapping, QTL marker-sequence composition, and genome sequencing to examine the distribution, structure and organization of disease R genes to race 1 of FOV in the cotton genome. Molecular markers were applied to F(2) and recombinant inbred line (RIL) interspecific mapping populations from the crosses Pima-S7 (G. barbadense L.) × 'Acala NemX' (G. hirsutum L.) and Upland TM-1 (G. hirsutum) × Pima 3-79 (G. barbadense), respectively. Three greenhouse tests and one field test were used to obtain sequential estimates of severity index (DSI) of leaves, and vascular stem and root staining (VRS). A single resistance gene model was observed for the F(2) population based on inheritance of phenotypes. However, additional inheritance analyses and QTL mapping indicated gene interactions and inheritance from nine cotton chromosomes, with major QTLs detected on five chromosomes [Fov1-C06, Fov1-C08, (Fov1-C11 ( 1 ) and Fov1-C11 ( 2)) , Fov1-C16 and Fov1-C19 loci], explaining 8-31% of the DSI or VRS variation. The Fov1-C16 QTL locus identified in the F(2) and in the RIL populations had a significant role in conferring FOV race 1 resistance in different cotton backgrounds. Identified molecular markers may have important potential for breeding effective FOV race 1 resistance into elite cultivars by marker-assisted selection. Reconciliation between genetic and physical mapping of gene annotations from marker-DNA and new DNA sequences of BAC clones tagged with the resistance-associated QTLs revealed defenses genes induced upon pathogen infection and gene regions rich in disease-response elements, respectively. These offer candidate gene targets for Fusarium wilt resistance response in cotton and other host plants. PMID:21533837

  11. Nano-Scale Alignment of Proteins on a Flexible DNA Backbone

    PubMed Central

    Nojima, Tatsuya; Konno, Hiroki; Kodera, Noriyuki; Seio, Kohji; Taguchi, Hideki; Yoshida, Masasuke

    2012-01-01

    Nano-scale alignment of several proteins with freedom of motion is equivalent to an enormous increase in effective local concentration of proteins and will enable otherwise impossible weak and/or cooperative associations between them or with their ligands. For this purpose, a DNA backbone made of six oligodeoxynucleotide (ODN) chains is designed in which five double-stranded segments are connected by four single-stranded flexible linkers. A desired protein with an introduced cysteine is connected covalently to the 5′-end of azido-ODN by catalyst-free click chemistry. Then, six protein-ODN conjugates are assembled with their complementary nucleotide sequences into a single multi-protein-DNA complex, and six proteins are aligned along the DNA backbone. Flexible alignment of proteins is directly observed by high-speed AFM imaging, and association of proteins with weak interaction is demonstrated by fluorescence resonance energy transfer between aligned proteins. PMID:23300700

  12. Algorithm for finding two-dimensional site percolation backbones

    NASA Astrophysics Data System (ADS)

    Yin, Wei-Guo; Tao, Ruibao

    2000-04-01

    We present an efficient algorithm for finding the current-carrying backbone in the planar site percolation model. It finds the backbone in speed to be almost four times as high as that of the old-fashioned Tarjan's depth-first-search algorithm. The scaling exponent (q/ν) (β/ν) of the probability that a site belongs to the backbone (the infinite cluster) is found to be 0.3647±0.0039 (0.1068±0.0013) and satisfy Chayes’ exponent inequality: 2 β⩽ q.

  13. On the satisfaction of backbone-carbonyl lone pairs of electrons in protein structures.

    PubMed

    Bartlett, Gail J; Woolfson, Derek N

    2016-04-01

    Protein structures are stabilized by a variety of noncovalent interactions (NCIs), including the hydrophobic effect, hydrogen bonds, electrostatic forces and van der Waals' interactions. Our knowledge of the contributions of NCIs, and the interplay between them remains incomplete. This has implications for computational modeling of NCIs, and our ability to understand and predict protein structure, stability, and function. One consideration is the satisfaction of the full potential for NCIs made by backbone atoms. Most commonly, backbone-carbonyl oxygen atoms located within α-helices and β-sheets are depicted as making a single hydrogen bond. However, there are two lone pairs of electrons to be satisfied for each of these atoms. To explore this, we used operational geometric definitions to generate an inventory of NCIs for backbone-carbonyl oxygen atoms from a set of high-resolution protein structures and associated molecular-dynamics simulations in water. We included more-recently appreciated, but weaker NCIs in our analysis, such as n→π* interactions, Cα-H bonds and methyl-H bonds. The data demonstrate balanced, dynamic systems for all proteins, with most backbone-carbonyl oxygen atoms being satisfied by two NCIs most of the time. Combinations of NCIs made may correlate with secondary structure type, though in subtly different ways from traditional models of α- and β-structure. In addition, we find examples of under- and over-satisfied carbonyl-oxygen atoms, and we identify both sequence-dependent and sequence-independent secondary-structural motifs in which these reside. Our analysis provides a more-detailed understanding of these contributors to protein structure and stability, which will be of use in protein modeling, engineering and design. PMID:26833776

  14. Site-specific oligodeoxynucleotide backbone modification for the covalent incorporation of reporter groups

    SciTech Connect

    Fidanza, J.A.

    1992-01-01

    A protocol has been developed to enable the site-specific incorporation of reporter groups to the oligodeoxynucleotide backbone. The introduction of a reactive center within the oligonucleotide sequence was accomplished using relatively standard procedures and was compatible with automated DNA synthesis techniques. The site-specific introduction of a phosphorothioate diester was achieved by substitution of a nonbridging oxygen in an internucleotidic phosphodiester by sulfur. Phosphorothioate diester-containing oligodeoxynucleotides were amenable to alkylation with reporter groups containing haloacetamides, aziridine sulfonamides, or [gamma]-bromo-[alpha], [beta]-unsaturated carbonyls. Labeling reactions proceeded most efficiently after incubation for 24 h at 50[degrees]C in the pH range of 5-8. A thiol tether has been incorporated into the oligodeoxynucleotide backbone by oxidizing a specifically placed internucleotidic hydrogen-phosphonate in the presence of cystamine. The thiol is deprotected by treatment with dithiothreitol. The tethered sulfhydryl reacts with a large variety of functional groups, and may be used to extend reporter groups at a distance from the backbone. The phosphoramidate linkage is stable over a very large range of pH. The alkylation of oligodeoxynucleotides occurred solely at the phosphorothioate diester or at the tethered sulfhydryl. Duplex structures containing either a labeled phosphorothioate or thiol tether had thermal stabilities generally similar to those of the unlabeled sequence. Labeling of an internucleotidic phosphorothioate diester or a tethered thiol provides a rapid and simple method for the site-specific covalent attachment of fluorophores, spin labels, drug derivatives or prosthetic groups to the oligonucleotide backbone. The introduction of more than one reactive center may be accomplished without necessarily increasing the complexity of the overall procedure.

  15. Species-specific shifts in centromere sequence composition are coincident with breakpoint reuse in karyotypically divergent lineages

    PubMed Central

    Bulazel, Kira V; Ferreri, Gianni C; Eldridge, Mark DB; O'Neill, Rachel J

    2007-01-01

    Background It has been hypothesized that rapid divergence in centromere sequences accompanies rapid karyotypic change during speciation. However, the reuse of breakpoints coincident with centromeres in the evolution of divergent karyotypes poses a potential paradox. In distantly related species where the same centromere breakpoints are used in the independent derivation of karyotypes, centromere-specific sequences may undergo convergent evolution rather than rapid sequence divergence. To determine whether centromere sequence composition follows the phylogenetic history of species evolution or patterns of convergent breakpoint reuse through chromosome evolution, we examined the phylogenetic trajectory of centromere sequences within a group of karyotypically diverse mammals, macropodine marsupials (wallabies, wallaroos and kangaroos). Results The evolution of three classes of centromere sequences across nine species within the genus Macropus (including Wallabia) were compared with the phylogenetic history of a mitochondrial gene, Cytochrome b (Cyt b), a nuclear gene, selenocysteine tRNA (TRSP), and the chromosomal histories of the syntenic blocks that define the different karyotype arrangements. Convergent contraction or expansion of predominant satellites is found to accompany specific karyotype rearrangements. The phylogenetic history of these centromere sequences includes the convergence of centromere composition in divergent species through convergent breakpoint reuse between syntenic blocks. Conclusion These data support the 'library hypothesis' of centromere evolution within this genus as each species possesses all three satellites yet each species has experienced differential expansion and contraction of individual classes. Thus, we have identified a correlation between the evolution of centromere satellite sequences, the reuse of syntenic breakpoints, and karyotype convergence in the context of a gene-based phylogeny. PMID:17708770

  16. Solution structure and backbone dynamics of component IV Glycera dibranchiata monomeric hemoglobin-CO.

    PubMed

    Volkman, B F; Alam, S L; Satterlee, J D; Markley, J L

    1998-08-01

    The solution structure and backbone dynamics of the recombinant, ferrous CO-ligated form of component IV monomeric hemoglobin from Glycera dibranchiata (GMH4CO) have been characterized by NMR spectroscopy. Distance geometry and simulated annealing calculations utilizing a total of 2550 distance and torsion angle constraints yielded an ensemble of 29 structures with an overall average backbone rmsd of 0.48 A from the average structure. Differences between the solution structure and a related crystal structure are confined to regions of lower precision in either the NMR or X-ray structure, or in regions where the amino acid sequences differ. 15N relaxation measurements at 76.0 and 60.8 MHz were analyzed with an extended model-free approach, and revealed low-frequency motions in the vicinity of the heme, concentrated in the F helix. Amide proton protection factors were obtained from H-D amide exchange measurements on 15N-labeled protein. Patterns in the backbone dynamics and protection factors were shown to correlate with regions of heterogeneity and disorder in the ensemble of NMR structures and with large crystallographic B-factors in the X-ray structures. Surprisingly, while the backbone atoms of the F helix have higher rmsds and larger measures of dynamics on the microsecond to millisecond time scale than the other helices, amide protection factors for residues in the F helix were observed to be similar to those of the other helices. This contrasts with H-D amide exchange measurements on sperm whale myoglobin which indicated low protection for the F helix (S. N. Loh and B. F. Volkman, unpublished results). These results for GMH4 suggest a model in which the F helix undergoes collective motions as a relatively rigid hydrogen-bonded unit, possibly pivoting about a central position near residue Val87. PMID:9692983

  17. Resonant magnetoelectric response of composite cantilevers: Theory of short vs. open circuit operation and layer sequence effects

    NASA Astrophysics Data System (ADS)

    Krantz, Matthias C.; Gugat, Jascha L.; Gerken, Martina

    2015-11-01

    The magnetoelectric effect in layered composite cantilevers consisting of strain coupled layers of magnetostrictive (MS), piezoelectric (PE), and substrate materials is investigated for magnetic field excitation at bending resonance. Analytic theories are derived for the transverse magnetoelectric (ME) response in short and open circuit operation for three different layer sequences and results presented and discussed for the FeCoBSi-AlN-Si and the FeCoBSi-PZT-Si composite systems. Response optimized PE-MS layer thickness ratios are found to greatly change with operation mode shifting from near equal MS and PE layer thicknesses in the open circuit mode to near vanishing PE layer thicknesses in short circuit operation for all layer sequences. In addition the substrate layer thickness is found to differently affect the open and short circuit ME response producing shifts and reversal between ME response maxima depending on layer sequence. The observed rich ME response behavior for different layer thicknesses, sequences, operating modes, and PE materials can be explained by common neutral plane effects and different elastic compliance effects in short and open circuit operation.

  18. A mapping of an ensemble of mitochondrial sequences for various organisms into 3D space based on the word composition.

    PubMed

    Aita, Takuyo; Nishigaki, Koichi

    2012-11-01

    To visualize a bird's-eye view of an ensemble of mitochondrial genome sequences for various species, we recently developed a novel method of mapping a biological sequence ensemble into Three-Dimensional (3D) vector space. First, we represented a biological sequence of a species s by a word-composition vector x(s), where its length [absolute value]x(s)[absolute value] represents the sequence length, and its unit vector x(s)/[absolute value]x(s)[absolute value] represents the relative composition of the K-tuple words through the sequence and the size of the dimension, N=4(K), is the number of all possible words with the length of K. Second, we mapped the vector x(s) to the 3D position vector y(s), based on the two following simple principles: (1) [absolute value]y(s)[absolute value]=[absolute value]x(s)[absolute value] and (2) the angle between y(s) and y(t) maximally correlates with the angle between x(s) and x(t). The mitochondrial genome sequences for 311 species, including 177 Animalia, 85 Fungi and 49 Green plants, were mapped into 3D space by using K=7. The mapping was successful because the angles between vectors before and after the mapping highly correlated with each other (correlation coefficients were 0.92-0.97). Interestingly, the Animalia kingdom is distributed along a single arc belt (just like the Milky Way on a Celestial Globe), and the Fungi and Green plant kingdoms are distributed in a similar arc belt. These two arc belts intersect at their respective middle regions and form a cross structure just like a jet aircraft fuselage and its wings. This new mapping method will allow researchers to intuitively interpret the visual information presented in the maps in a highly effective manner. PMID:22776549

  19. Backbone-driven collapse in unfolded protein chains.

    PubMed

    Teufel, Daniel P; Johnson, Christopher M; Lum, Jenifer K; Neuweiler, Hannes

    2011-06-01

    Collapse of unfolded protein chains is an early event in folding. It affects structural properties of intrinsically disordered proteins, which take a considerable fraction of the human proteome. Collapse is generally believed to be driven by hydrophobic forces imposed by the presence of nonpolar amino acid side chains. Contributions from backbone hydrogen bonds to protein folding and stability, however, are controversial. To date, the experimental dissection of side-chain and backbone contributions has not yet been achieved because both types of interactions are integral parts of protein structure. Here, we realized this goal by applying mutagenesis and chemical modification on a set of disordered peptides and proteins. We measured the protein dimensions and kinetics of intra-chain diffusion of modified polypeptides at the level of individual molecules using fluorescence correlation spectroscopy, thereby avoiding artifacts commonly caused by aggregation of unfolded protein material in bulk. We found no contributions from side chains to collapse but, instead, identified backbone interactions as a source sufficient to form globules of native-like dimensions. The presence of backbone hydrogen bonds decreased polypeptide water solubility dramatically and accelerated the nanosecond kinetics of loop closure, in agreement with recent predictions from computer simulation. The presence of side chains, instead, slowed loop closure and modulated the dimensions of intrinsically disordered domains. It appeared that the transient formation of backbone interactions facilitates the diffusive search for productive conformations at the early stage of folding and within intrinsically disordered proteins. PMID:21497607

  20. A Consistent Phylogenetic Backbone for the Fungi

    PubMed Central

    Ebersberger, Ingo; de Matos Simoes, Ricardo; Kupczok, Anne; Gube, Matthias; Kothe, Erika; Voigt, Kerstin; von Haeseler, Arndt

    2012-01-01

    The kingdom of fungi provides model organisms for biotechnology, cell biology, genetics, and life sciences in general. Only when their phylogenetic relationships are stably resolved, can individual results from fungal research be integrated into a holistic picture of biology. However, and despite recent progress, many deep relationships within the fungi remain unclear. Here, we present the first phylogenomic study of an entire eukaryotic kingdom that uses a consistency criterion to strengthen phylogenetic conclusions. We reason that branches (splits) recovered with independent data and different tree reconstruction methods are likely to reflect true evolutionary relationships. Two complementary phylogenomic data sets based on 99 fungal genomes and 109 fungal expressed sequence tag (EST) sets analyzed with four different tree reconstruction methods shed light from different angles on the fungal tree of life. Eleven additional data sets address specifically the phylogenetic position of Blastocladiomycota, Ustilaginomycotina, and Dothideomycetes, respectively. The combined evidence from the resulting trees supports the deep-level stability of the fungal groups toward a comprehensive natural system of the fungi. In addition, our analysis reveals methodologically interesting aspects. Enrichment for EST encoded data—a common practice in phylogenomic analyses—introduces a strong bias toward slowly evolving and functionally correlated genes. Consequently, the generalization of phylogenomic data sets as collections of randomly selected genes cannot be taken for granted. A thorough characterization of the data to assess possible influences on the tree reconstruction should therefore become a standard in phylogenomic analyses. PMID:22114356

  1. A consistent phylogenetic backbone for the fungi.

    PubMed

    Ebersberger, Ingo; de Matos Simoes, Ricardo; Kupczok, Anne; Gube, Matthias; Kothe, Erika; Voigt, Kerstin; von Haeseler, Arndt

    2012-05-01

    The kingdom of fungi provides model organisms for biotechnology, cell biology, genetics, and life sciences in general. Only when their phylogenetic relationships are stably resolved, can individual results from fungal research be integrated into a holistic picture of biology. However, and despite recent progress, many deep relationships within the fungi remain unclear. Here, we present the first phylogenomic study of an entire eukaryotic kingdom that uses a consistency criterion to strengthen phylogenetic conclusions. We reason that branches (splits) recovered with independent data and different tree reconstruction methods are likely to reflect true evolutionary relationships. Two complementary phylogenomic data sets based on 99 fungal genomes and 109 fungal expressed sequence tag (EST) sets analyzed with four different tree reconstruction methods shed light from different angles on the fungal tree of life. Eleven additional data sets address specifically the phylogenetic position of Blastocladiomycota, Ustilaginomycotina, and Dothideomycetes, respectively. The combined evidence from the resulting trees supports the deep-level stability of the fungal groups toward a comprehensive natural system of the fungi. In addition, our analysis reveals methodologically interesting aspects. Enrichment for EST encoded data-a common practice in phylogenomic analyses-introduces a strong bias toward slowly evolving and functionally correlated genes. Consequently, the generalization of phylogenomic data sets as collections of randomly selected genes cannot be taken for granted. A thorough characterization of the data to assess possible influences on the tree reconstruction should therefore become a standard in phylogenomic analyses. PMID:22114356

  2. Grid-Assembly: An oligonucleotide composition-based partitioning strategy to aid metagenomic sequence assembly.

    PubMed

    Ghosh, Tarini Shankar; Mehra, Varun; Mande, Sharmila S

    2015-06-01

    Metagenomics approach involves extraction, sequencing and characterization of the genomic content of entire community of microbes present in a given environment. In contrast to genomic data, accurate assembly of metagenomic sequences is a challenging task. Given the huge volume and the diverse taxonomic origin of metagenomic sequences, direct application of single genome assembly methods on metagenomes are likely to not only lead to an immense increase in requirements of computational infrastructure, but also result in the formation of chimeric contigs. A strategy to address the above challenge would be to partition metagenomic sequence datasets into clusters and assemble separately the sequences in individual clusters using any single-genome assembly method. The current study presents such an approach that uses tetranucleotide usage patterns to first represent sequences as points in a three dimensional (3D) space. The 3D space is subsequently partitioned into "Grids". Sequences within overlapping grids are then progressively assembled using any available assembler. We demonstrate the applicability of the current Grid-Assembly method using various categories of assemblers as well as different simulated metagenomic datasets. Validation results indicate that the Grid-Assembly approach helps in improving the overall quality of assembly, in terms of the purity and volume of the assembled contigs. PMID:25790784

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

    PubMed

    Qvit, Nir; Kornfeld, Opher S

    2016-01-01

    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 systematic screen for the most biological active conformation. This method provides a general, fast, and facile way to synthesize cyclic peptides. PMID:26863382

  4. Next generation sequencing shows high variation of the intestinal microbial species composition in Atlantic cod caught at a single location

    PubMed Central

    2013-01-01

    Background The observation that specific members of the microbial intestinal community can be shared among vertebrate hosts has promoted the concept of a core microbiota whose composition is determined by host-specific selection. Most studies investigating this concept in individual hosts have focused on mammals, yet the diversity of fish lineages provides unique comparative opportunities from an evolutionary, immunological and environmental perspective. Here we describe microbial intestinal communities of eleven individual Atlantic cod (Gadus morhua) caught at a single location based on an extensively 454 sequenced 16S rRNA library of the V3 region. Results We obtained a total of 280447 sequences and identify 573 Operational Taxonomic Units (OTUs) at 97% sequence similarity level, ranging from 40 to 228 OTUs per individual. We find that ten OTUs are shared, though the number of reads of these OTUs is highly variable. This variation is further illustrated by community diversity estimates that fluctuate several orders of magnitude among specimens. The shared OTUs belong to the orders of Vibrionales, which quantitatively dominate the Atlantic cod intestinal microbiota, followed by variable numbers of Bacteroidales, Erysipelotrichales, Clostridiales, Alteromonadales and Deferribacterales. Conclusions The microbial intestinal community composition varies significantly in individual Atlantic cod specimens caught at a single location. This high variation among specimens suggests that a complex combination of factors influence the species distribution of these intestinal communities. PMID:24206635

  5. Sequence-based Association Analysis Reveals an MGST1 eQTL with Pleiotropic Effects on Bovine Milk Composition

    PubMed Central

    Littlejohn, Mathew D.; Tiplady, Kathryn; Fink, Tania A.; Lehnert, Klaus; Lopdell, Thomas; Johnson, Thomas; Couldrey, Christine; Keehan, Mike; Sherlock, Richard G.; Harland, Chad; Scott, Andrew; Snell, Russell G.; Davis, Stephen R.; Spelman, Richard J.

    2016-01-01

    The mammary gland is a prolific lipogenic organ, synthesising copious amounts of triglycerides for secretion into milk. The fat content of milk varies widely both between and within species, and recent independent genome-wide association studies have highlighted a milk fat percentage quantitative trait locus (QTL) of large effect on bovine chromosome 5. Although both EPS8 and MGST1 have been proposed to underlie these signals, the causative status of these genes has not been functionally confirmed. To investigate this QTL in detail, we report genome sequence-based imputation and association mapping in a population of 64,244 taurine cattle. This analysis reveals a cluster of 17 non-coding variants spanning MGST1 that are highly associated with milk fat percentage, and a range of other milk composition traits. Further, we exploit a high-depth mammary RNA sequence dataset to conduct expression QTL (eQTL) mapping in 375 lactating cows, revealing a strong MGST1 eQTL underpinning these effects. These data demonstrate the utility of DNA and RNA sequence-based association mapping, and implicate MGST1, a gene with no obvious mechanistic relationship to milk composition regulation, as causally involved in these processes. PMID:27146958

  6. Sequence-based Association Analysis Reveals an MGST1 eQTL with Pleiotropic Effects on Bovine Milk Composition.

    PubMed

    Littlejohn, Mathew D; Tiplady, Kathryn; Fink, Tania A; Lehnert, Klaus; Lopdell, Thomas; Johnson, Thomas; Couldrey, Christine; Keehan, Mike; Sherlock, Richard G; Harland, Chad; Scott, Andrew; Snell, Russell G; Davis, Stephen R; Spelman, Richard J

    2016-01-01

    The mammary gland is a prolific lipogenic organ, synthesising copious amounts of triglycerides for secretion into milk. The fat content of milk varies widely both between and within species, and recent independent genome-wide association studies have highlighted a milk fat percentage quantitative trait locus (QTL) of large effect on bovine chromosome 5. Although both EPS8 and MGST1 have been proposed to underlie these signals, the causative status of these genes has not been functionally confirmed. To investigate this QTL in detail, we report genome sequence-based imputation and association mapping in a population of 64,244 taurine cattle. This analysis reveals a cluster of 17 non-coding variants spanning MGST1 that are highly associated with milk fat percentage, and a range of other milk composition traits. Further, we exploit a high-depth mammary RNA sequence dataset to conduct expression QTL (eQTL) mapping in 375 lactating cows, revealing a strong MGST1 eQTL underpinning these effects. These data demonstrate the utility of DNA and RNA sequence-based association mapping, and implicate MGST1, a gene with no obvious mechanistic relationship to milk composition regulation, as causally involved in these processes. PMID:27146958

  7. Static magnetoelectric and magnetoelastic response of composite cantilevers: Theory of short vs. open circuit operation and layer sequence effects

    NASA Astrophysics Data System (ADS)

    Krantz, Matthias C.; Gugat, Jascha L.; Gerken, Martina

    2015-11-01

    The static bending-mode transverse magnetoelectric effect and the magnetic field-induced bending response of composite cantilevers with thin magnetostrictive (MS), piezoelectric (PE), and substrate (Sub) layers is investigated for the PE layer subjected to open and short circuit conditions. Analytic theories are presented for strain-coupled three layer composites of PE, MS, and Sub layers in all layer sequences. We use constitutive equations with linear coupling of stress, strain, H, E, and D fields and present results for the open and short circuit magnetoelectric and bending responses for arbitrary layer thickness ratios for the FeCoBSi-AlN-Si materials system. Besides a rich sequence dependent behavior the theory predicts great and systematic differences between the open and short circuit magnetoelectric response yielding maxima at similar MS and PE layer thicknesses in the open circuit and near vanishing PE layer thicknesses in the short circuit cases. In contrast, the open vs. short circuit bending response differences are pronounced but much smaller. Layer sequence systematics and implications for static H-field sensors will be discussed.

  8. Polyarylether composition and membrane

    SciTech Connect

    Hung, Joyce; Brunelle, Daniel Joseph; Harmon, Marianne Elisabeth; Moore, David Roger; Stone, Joshua James; Zhou, Hongyi; Suriano, Joseph Anthony

    2010-11-09

    A composition including a polyarylether copolymer is provided. The copolymer includes a polyarylether backbone; and a sulfonated oligomeric group bonded to the polyarylether suitable for use as a cation conducting membrane. Method of bonding a sulfonated oligomeric group to the polyarylether backbone to form a polyarylether copolymer. The membrane may be formed from the polyarylether copolymer composition. The chain length of the sulfonated oligomeric group may be controlled to affect or control the ion conductivity of the membrane.

  9. BAC-end sequences analysis provides first insights into coffee (Coffea canephora P.) genome composition and evolution.

    PubMed

    Dereeper, Alexis; Guyot, Romain; Tranchant-Dubreuil, Christine; Anthony, François; Argout, Xavier; de Bellis, Fabien; Combes, Marie-Christine; Gavory, Frederick; de Kochko, Alexandre; Kudrna, Dave; Leroy, Thierry; Poulain, Julie; Rondeau, Myriam; Song, Xiang; Wing, Rod; Lashermes, Philippe

    2013-10-01

    Coffee is one of the world's most important agricultural commodities. Coffee belongs to the Rubiaceae family in the euasterid I clade of dicotyledonous plants, to which the Solanaceae family also belongs. Two bacterial artificial chromosome (BAC) libraries of a homozygous doubled haploid plant of Coffea canephora were constructed using two enzymes, HindIII and BstYI. A total of 134,827 high quality BAC-end sequences (BESs) were generated from the 73,728 clones of the two libraries, and 131,412 BESs were conserved for further analysis after elimination of chloroplast and mitochondrial sequences. This corresponded to almost 13 % of the estimated size of the C. canephora genome. 6.7 % of BESs contained simple sequence repeats, the most abundant (47.8 %) being mononucleotide motifs. These sequences allow the development of numerous useful marker sites. Potential transposable elements (TEs) represented 11.9 % of the full length BESs. A difference was observed between the BstYI and HindIII libraries (14.9 vs. 8.8 %). Analysis of BESs against known coding sequences of TEs indicated that 11.9 % of the genome corresponded to known repeat sequences, like for other flowering plants. The number of genes in the coffee genome was estimated at 41,973 which is probably overestimated. Comparative genome mapping revealed that microsynteny was higher between coffee and grapevine than between coffee and tomato or Arabidopsis. BESs constitute valuable resources for the first genome wide survey of coffee and provide new insights into the composition and evolution of the coffee genome. PMID:23708951

  10. Apollo 17 petrology and experimental determination of differentiation sequences in model moon compositions

    NASA Technical Reports Server (NTRS)

    Hodges, F. N.; Kushiro, I.

    1974-01-01

    Experimental studies of model moon compositions are discussed, taking into account questions related to the differentiation of the outer layer of the moon. Phase relations for a series of proposed lunar compositions have been determined and a petrographic and electron microprobe study was conducted on four Apollo 17 samples. Two of the samples consist of high-titanium mare basalts, one includes crushed anorthosite and gabbro, and another contains blue-gray breccia.

  11. The venom composition of the parasitic wasp Chelonus inanitus resolved by combined expressed sequence tags analysis and proteomic approach

    PubMed Central

    2010-01-01

    Background Parasitic wasps constitute one of the largest group of venomous animals. Although some physiological effects of their venoms are well documented, relatively little is known at the molecular level on the protein composition of these secretions. To identify the majority of the venom proteins of the endoparasitoid wasp Chelonus inanitus (Hymenoptera: Braconidae), we have randomly sequenced 2111 expressed sequence tags (ESTs) from a cDNA library of venom gland. In parallel, proteins from pure venom were separated by gel electrophoresis and individually submitted to a nano-LC-MS/MS analysis allowing comparison of peptides and ESTs sequences. Results About 60% of sequenced ESTs encoded proteins whose presence in venom was attested by mass spectrometry. Most of the remaining ESTs corresponded to gene products likely involved in the transcriptional and translational machinery of venom gland cells. In addition, a small number of transcripts were found to encode proteins that share sequence similarity with well-known venom constituents of social hymenopteran species, such as hyaluronidase-like proteins and an Allergen-5 protein. An overall number of 29 venom proteins could be identified through the combination of ESTs sequencing and proteomic analyses. The most highly redundant set of ESTs encoded a protein that shared sequence similarity with a venom protein of unknown function potentially specific of the Chelonus lineage. Venom components specific to C. inanitus included a C-type lectin domain containing protein, a chemosensory protein-like protein, a protein related to yellow-e3 and ten new proteins which shared no significant sequence similarity with known sequences. In addition, several venom proteins potentially able to interact with chitin were also identified including a chitinase, an imaginal disc growth factor-like protein and two putative mucin-like peritrophins. Conclusions The use of the combined approaches has allowed to discriminate between cellular and truly venom proteins. The venom of C. inanitus appears as a mixture of conserved venom components and of potentially lineage-specific proteins. These new molecular data enrich our knowledge on parasitoid venoms and more generally, might contribute to a better understanding of the evolution and functional diversity of venom proteins within Hymenoptera. PMID:21138570

  12. Cooperative UAV-Based Communications Backbone for Sensor Networks

    SciTech Connect

    Roberts, R S

    2001-10-07

    The objective of this project is to investigate the use of unmanned air vehicles (UAVs) as mobile, adaptive communications backbones for ground-based sensor networks. In this type of network, the UAVs provide communication connectivity to sensors that cannot communicate with each other because of terrain, distance, or other geographical constraints. In these situations, UAVs provide a vertical communication path for the sensors, thereby mitigating geographic obstacles often imposed on networks. With the proper use of UAVs, connectivity to a widely disbursed sensor network in rugged terrain is readily achieved. Our investigation has focused on networks where multiple cooperating UAVs are used to form a network backbone. The advantage of using multiple UAVs to form the network backbone is parallelization of sensor connectivity. Many widely spaced or isolated sensors can be connected to the network at once using this approach. In these networks, the UAVs logically partition the sensor network into sub-networks (subnets), with one UAV assigned per subnet. Partitioning the network into subnets allows the UAVs to service sensors in parallel thereby decreasing the sensor-to-network connectivity. A UAV services sensors in its subnet by flying a route (path) through the subnet, uplinking data collected by the sensors, and forwarding the data to a ground station. An additional advantage of using multiple UAVs in the network is that they provide redundancy in the communications backbone, so that the failure of a single UAV does not necessarily imply the loss of the network.

  13. Determination of protein backbone structures from residual dipolar couplings.

    PubMed

    Prestegard, J H; Mayer, K L; Valafar, H; Benison, G C

    2005-01-01

    There are a number of circumstances in which a focus on determination of the backbone structure of a protein, as opposed to a complete all-atom structure, may be appropriate. This is particularly the case for structures determined as a part of a structural genomics initiative in which computational modeling of many sequentially related structures from the backbone of a single family representative is anticipated. It is, however, also the case when the backbone may be a stepping-stone to more targeted studies of ligand interaction or protein-protein interaction. Here an NMR protocol is described that can produce a backbone structure of a protein without the need for extensive experiments directed at side chain resonance assignment or the collection of structural information on side chains. The procedure relies primarily on orientational constraints from residual dipolar couplings as opposed to distance constraints from NOEs. Procedures for sample preparation, data acquisition, and data analysis are described, along with examples from application to small target proteins of a structural genomics project. PMID:15808221

  14. Impact of template backbone heterogeneity on RNA polymerase II transcription

    PubMed Central

    Xu, Liang; Wang, Wei; Zhang, Lu; Chong, Jenny; Huang, Xuhui; Wang, Dong

    2015-01-01

    Variations in the sugar component (ribose or deoxyribose) and the nature of the phosphodiester linkage (3?-5? or 2?-5? orientation) have been a challenge for genetic information transfer from the very beginning of evolution. RNA polymerase II (pol II) governs the transcription of DNA into precursor mRNA in all eukaryotic cells. How pol II recognizes DNA template backbone (phosphodiester linkage and sugar) and whether it tolerates the backbone heterogeneity remain elusive. Such knowledge is not only important for elucidating the chemical basis of transcriptional fidelity but also provides new insights into molecular evolution. In this study, we systematically and quantitatively investigated pol II transcriptional behaviors through different template backbone variants. We revealed that pol II can well tolerate and bypass sugar heterogeneity sites at the template but stalls at phosphodiester linkage heterogeneity sites. The distinct impacts of these two backbone components on pol II transcription reveal the molecular basis of template recognition during pol II transcription and provide the evolutionary insight from the RNA world to the contemporary imperfect DNA world. In addition, our results also reveal the transcriptional consequences from ribose-containing genomic DNA. PMID:25662224

  15. 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.

  16. Increasing protein production by directed vector backbone evolution

    PubMed Central

    2013-01-01

    Recombinant protein production in prokaryotic and eukaryotic organisms was a key enabling technology for the rapid development of industrial and molecular biotechnology. However, despite all progress the improvement of protein production is an ongoing challenge and of high importance for cost-effective enzyme production. With the epMEGAWHOP mutagenesis protocol for vector backbone optimization we report a novel directed evolution based approach to increase protein production levels by randomly introducing mutations in the vector backbone. In the current study we validate the epMEGAWHOP mutagenesis protocol for three different expression systems. The latter demonstrated the general applicability of the epMEGAWHOP method. Cellulase and lipase production was doubled in one round of directed evolution by random mutagenesis of pET28a(+) and pET22b(+) vector backbones. Protease production using the vector pHY300PLK was increased ~4-times with an average of ~1.25 mutations per kb vector backbone. The epMEGAWHOP does not require any rational understanding of the expression machinery and can generally be applied to enzymes, expression vectors and related hosts. epMEGAWHOP is therefore from our point of view a robust, rapid and straight forward alternative for increasing protein production in general and for biotechnological applications. PMID:23890095

  17. Palynological composition of a Lower Cretaceous South American tropical sequence: Climatic implications and diversity comparisons with other latitudes.

    USGS Publications Warehouse

    Mejia-Velasquez, Paula J.; Dilcher, David L.; Jaramillo, Carlos A.; Fortini, Lucas B.; Manchester, Steven R.

    2012-01-01

    Premise of the study: Reconstruction of floristic patterns during the early diversification of angiosperms is impeded by the scarce fossil record, especially in tropical latitudes. Here we collected quantitative palynological data from a stratigraphic sequence in tropical South America to provide floristic and climatic insights into such tropical environments during the Early Cretaceous. Methods: We reconstructed the floristic composition of an Aptian-Albian tropical sequence from central Colombia using quantitative palynology (rarefied species richness and abundance) and used it to infer its predominant climatic conditions. Additionally, we compared our results with available quantitative data from three other sequences encompassing 70 floristic assemblages to determine latitudinal diversity patterns. Key results: Abundance of humidity indicators was higher than that of aridity indicators (61% vs. 10%). Additionally, we found an angiosperm latitudinal diversity gradient (LDG) for the Aptian, but not for the Albian, and an inverted LDG of the overall diversity for the Albian. Angiosperm species turnover during the Albian, however, was higher in humid tropics. Conclusions: There were humid climates in northwestern South America during the Aptian-Albian interval contrary to the widespread aridity expected for the tropical belt. The Albian inverted overall LDG is produced by a faster increase in per-sample angiosperm and pteridophyte diversity in temperate latitudes. However, humid tropical sequences had higher rates of floristic turnover suggesting a higher degree of morphological variation than in temperate regions.

  18. Assignment of protein backbone resonances using connectivity, torsion angles and 13Calpha chemical shifts.

    PubMed

    Morris, Laura C; Valafar, Homayoun; Prestegard, James H

    2004-05-01

    A program is presented which will return the most probable sequence location for a short connected set of residues in a protein given just (13)C(alpha) chemical shifts (delta((13)C(alpha))) and data restricting the phi and psi backbone angles. Data taken from both the BioMagResBank and the Protein Data Bank were used to create a probability density function (PDF) using a multivariate normal distribution in delta((13)C(alpha)), phi, and psi space for each amino acid residue. Extracting and combining probabilities for particular amino acid residues in a short proposed sequence yields a score indicative of the correctness of the proposed assignment. The program is illustrated using several proteins for which structure and (13)C(alpha) chemical shift data are available. PMID:15017135

  19. 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 well-defined architectures based solely on DNA. While backbone branched DNAs are useful for nanotechnological applications, backbone branches in RNA occur in nature and are involved in the distinct but related processes of splicing, debranching and RNAi. Therefore we have developed protocols for the synthesis of backbone branched nucleic acids in the solid-phase using photoprotecting groups. Using the synthesized backbone branched RNAs we have uncovered a specific substrate requirement of debranching enzyme which distinguishes it from other homologous proteins with alternative functions. Finally, through the marriage of click chemistry and backbone branches, we have produced useful progeny in the synthesis of lariat RNAs. We investigated the potential of these lariats as therapeutic agents by synthesizing siRNA sequences as lariats. We showed that these lariats are efficiently debranched by debranching enzyme and are able to induce an RNAi response in vivo. Altogether, the development of click chemistry and backbone branched nucleic acids represents a significant advantage in the ability to modify nucleic acid structure and affect its function. I envision that these methods can become generally useful to probe nucleic acid systems, useful nanomaterials and functional effectors in nucleic acid based therapies.

  20. Elevated nutrients change bacterial community composition and connectivity: high throughput sequencing of young marine biofilms.

    PubMed

    Lawes, Jasmin C; Neilan, Brett A; Brown, Mark V; Clark, Graeme F; Johnston, Emma L

    2016-01-01

    Biofilms are integral to many marine processes but their formation and function may be affected by anthropogenic inputs that alter environmental conditions, including fertilisers that increase nutrients. Density composition and connectivity of biofilms developed in situ (under ambient and elevated nutrients) were compared using 454-pyrosequencing of the 16S gene. Elevated nutrients shifted community composition from bacteria involved in higher processes (eg Pseudoalteromonas spp. invertebrate recruitment) towards more nutrient-tolerant bacterial species (eg Terendinibacter sp.). This may enable the persistence of biofilm communities by increasing resistance to nutrient inputs. A core biofilm microbiome was identified (predominantly Alteromonadales and Oceanospirillales) and revealed shifts in abundances of core microbes that could indicate enrichment by fertilisers. Fertiliser decreased density and connectivity within biofilms indicating that associations were disrupted perhaps via changes to energetic allocations within the core microbiome. Density composition and connectivity changes suggest nutrients can affect the stability and function of these important marine communities. PMID:26751559

  1. CodonExplorer: An Interactive Online Database for the Analysis of Codon Usage and Sequence Composition

    PubMed Central

    Zaneveld, Jesse; Hamady, Micah; Sueoka, Noboru; Knight, Rob

    2010-01-01

    The analysis of DNA composition and codon usage reveals many factors that influence the evolution of genes and genomes. In this chapter, we show how to use CodonExplorer, a web tool and interactive database that contains millions of genes, to better understand the principles governing evolution at the single gene and whole-genome level. We present principles and practical procedures for using analyses of GC content and codon usage frequency to identify highly expressed or horizontally transferred genes and to study the relative contribution of different types of mutation to gene and genome composition. CodonExplorer’s combination of a user-friendly web interface and a comprehensive genomic database makes these diverse analyses fast and straightforward to perform. CodonExplorer is thus a powerful tool that facilitates and automates a wide range of compositional analyses. PMID:19378146

  2. Fragmentation Characteristics of Deprotonated N-linked Glycopeptides: Influences of Amino Acid Composition and Sequence

    NASA Astrophysics Data System (ADS)

    Nishikaze, Takashi; Kawabata, Shin-ichirou; Tanaka, Koichi

    2014-06-01

    Glycopeptide structural analysis using tandem mass spectrometry is becoming a common approach for elucidating site-specific N-glycosylation. The analysis is generally performed in positive-ion mode. Therefore, fragmentation of protonated glycopeptides has been extensively investigated; however, few studies are available on deprotonated glycopeptides, despite the usefulness of negative-ion mode analysis in detecting glycopeptide signals. Here, large sets of glycopeptides derived from well-characterized glycoproteins were investigated to understand the fragmentation behavior of deprotonated N-linked glycopeptides under low-energy collision-induced dissociation (CID) conditions. The fragment ion species were found to be significantly variable depending on their amino acid sequence and could be classified into three types: (i) glycan fragment ions, (ii) glycan-lost fragment ions and their secondary cleavage products, and (iii) fragment ions with intact glycan moiety. The CID spectra of glycopeptides having a short peptide sequence were dominated by type (i) glycan fragments (e.g., 2,4AR, 2,4AR-1, D, and E ions). These fragments define detailed structural features of the glycan moiety such as branching. For glycopeptides with medium or long peptide sequences, the major fragments were type (ii) ions (e.g., [peptide + 0,2X0-H]- and [peptide-NH3-H]-). The appearance of type (iii) ions strongly depended on the peptide sequence, and especially on the presence of Asp, Asn, and Glu. When a glycosylated Asn is located on the C-terminus, an interesting fragment having an Asn residue with intact glycan moiety, [glycan + Asn-36]-, was abundantly formed. Observed fragments are reasonably explained by a combination of existing fragmentation rules suggested for N-glycans and peptides.

  3. Evaluation of bifidobacterial community composition in the human gut by means of a targeted amplicon sequencing (ITS) protocol.

    PubMed

    Milani, Christian; Lugli, Gabriele A; Turroni, Francesca; Mancabelli, Leonardo; Duranti, Sabrina; Viappiani, Alice; Mangifesta, Marta; Segata, Nicola; van Sinderen, Douwe; Ventura, Marco

    2014-11-01

    The precise appraisal of the composition of the human gut microbiota still represents a challenging task. The advent of next generation sequencing approaches has opened new ways to dissect the microbial biodiversity of this ecosystem through the use of 16S rRNA gene-based microbiota analysis approaches. However, the detailed representation of specific groups or members of the human gut microbiota, for example Bifidobacteria, may be skewed by the PCR primers employed in the amplification step of the 16S rRNA gene-based microbial profiling pipeline and by the limited resolution of the 16S rRNA gene variable regions. Here, we define the internal transcribed spacer (ITS) sequences of all currently known Bifidobacterium taxa, providing a Bifidobacterium-specific primer pair that targets a hypervariable region within the ITS suitable for precise taxonomic identification of all 48 so far recognized members of the Bifidobacterium genus. In addition, we present an optimized protocol for ITS-based profiling utilizing qiime software, allowing accurate and subspecies-specific compositional reconstruction of the bifidobacterial community in the human gut. PMID:25117972

  4. Complete sequence of heterogenous-composition mitochondrial genome (Brassica napus) and its exogenous source

    PubMed Central

    2012-01-01

    Background Unlike maternal inheritance of mitochondria in sexual reproduction, somatic hybrids follow no obvious pattern. The introgressed segment orf138 from the mitochondrial genome of radish (Raphanus sativus) to its counterpart in rapeseed (Brassica napus) demonstrates that this inheritance mode derives from the cytoplasm of both parents. Sequencing of the complete mitochondrial genome of five species from Brassica family allowed the prediction of other extraneous sources of the cybrids from the radish parent, and the determination of their mitochondrial rearrangement. Results We obtained the complete mitochondrial genome of Ogura-cms-cybrid (oguC) rapeseed. To date, this is the first time that a heterogeneously composed mitochondrial genome was sequenced. The 258,473 bp master circle constituted of 33 protein-coding genes, 3 rRNA sequences, and 23 tRNA sequences. This mitotype noticeably holds two copies of atp9 and is devoid of cox2-2. Relative to nap mitochondrial genome, 40 point mutations were scattered in the 23 protein-coding genes. atp6 even has an abnormal start locus whereas tatC has an abnormal end locus. The rearrangement of the 22 syntenic regions that comprised 80.11% of the genome was influenced by short repeats. A pair of large repeats (9731 bp) was responsible for the multipartite structure. Nine unique regions were detected when compared with other published Brassica mitochondrial genome sequences. We also found six homologous chloroplast segments (Brassica napus). Conclusions The mitochondrial genome of oguC is quite divergent from nap and pol, which are more similar with each other. We analyzed the unique regions of every genome of the Brassica family, and found that very few segments were specific for these six mitotypes, especially cam, jun, and ole, which have no specific segments at all. Therefore, we conclude that the most specific regions of oguC possibly came from radish. Compared with the chloroplast genome, six identical regions were found in the seven mitochondrial genomes, which show that the Brassica family has a stable chloroplast-derived source. PMID:23190559

  5. 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. PMID:24002904

  6. Hydrophobic core packing and backbone flexibility in coiled coils

    NASA Astrophysics Data System (ADS)

    Plecs, Joseph John

    1999-11-01

    An understanding of the structure and function of protein molecules requires an understanding of how their hydrophobic cores are assembled, including how the peptide backbone can adjust to accommodate different packing arrangements. Using coiled-coil molecules as a model of protein structures, we studied several cases in which the arrangement of packing groups in the hydrophobic core controls the structure of a folded molecule. First, we consider an example of a prosthetic packing group, where the addition of a hydrophobic ligand permits a new packing arrangement that incorporates the ligand, leading to a new overall structure. Second, the crystal structures of two peptides designed to adopt a novel fold, the right-handed coiled coils, reveal how a small change in core packing can discriminate between two different folds. And last, the design of heterodimers based on core-packing complementarity establishes that core packing can convey specificity of association between different molecules, as well as determining the molecular structure. The heterodimer designs also demonstrate the importance of a combination of backbone freedom and restriction in predicting the energetics of folded molecules. In this case, a parametrized coiled- coil backbone with appropriate parameters and restrictions was required to predict stabilities. We conclude that core packing can exert a great deal of control over the structure of proteins, and that many of its effects can be accurately predicted by modeling the molecular interactions in the context of a flexible overall structure.

  7. Reconstruction of clonal trees and tumor composition from multi-sample sequencing data

    PubMed Central

    El-Kebir, Mohammed; Oesper, Layla; Acheson-Field, Hannah; Raphael, Benjamin J.

    2015-01-01

    Motivation: DNA sequencing of multiple samples from the same tumor provides data to analyze the process of clonal evolution in the population of cells that give rise to a tumor. Results: We formalize the problem of reconstructing the clonal evolution of a tumor using single-nucleotide mutations as the variant allele frequency (VAF) factorization problem. We derive a combinatorial characterization of the solutions to this problem and show that the problem is NP-complete. We derive an integer linear programming solution to the VAF factorization problem in the case of error-free data and extend this solution to real data with a probabilistic model for errors. The resulting AncesTree algorithm is better able to identify ancestral relationships between individual mutations than existing approaches, particularly in ultra-deep sequencing data when high read counts for mutations yield high confidence VAFs. Availability and implementation: An implementation of AncesTree is available at: http://compbio.cs.brown.edu/software. Contact: braphael@brown.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:26072510

  8. Prokaryote phylogeny without sequence alignment: from avoidance signature to composition distance.

    PubMed

    Hao, Bailin; Qi, Ji

    2004-03-01

    This is a review of a new and essentially simple method of inferring phylogenetic relationships from complete genome data without using sequence alignment. The method is based on counting the appearance frequency of oligopeptides of a fixed length (up to K = 6) in the collection of protein sequences of a species. It is a method without fine adjustment and choice of genes. Applied to prokaryotic genomes it has led to results comparable with the bacteriologists' systematics as reflected in the latest 2002 outline of the Bergey's Manual of Systematic Bacteriology. The method has also been used to compare chloroplast genomes and to the phylogeny of Coronaviruses including human SARS-CoV. A key point in our approach is subtraction of a random background from the original counts by using a Markov model of order K-2 in order to highlight the shaping role of natural selection. The implications of the subtraction procedure is specially analyzed and further development of the new approach is indicated. PMID:15272430

  9. Sequence-based analysis of the microbial composition of water kefir from multiple sources.

    PubMed

    Marsh, Alan J; O'Sullivan, Orla; Hill, Colin; Ross, R Paul; Cotter, Paul D

    2013-11-01

    Water kefir is a water-sucrose-based beverage, fermented by a symbiosis of bacteria and yeast to produce a final product that is lightly carbonated, acidic and that has a low alcohol percentage. The microorganisms present in water kefir are introduced via water kefir grains, which consist of a polysaccharide matrix in which the microorganisms are embedded. We aimed to provide a comprehensive sequencing-based analysis of the bacterial population of water kefir beverages and grains, while providing an initial insight into the corresponding fungal population. To facilitate this objective, four water kefirs were sourced from the UK, Canada and the United States. Culture-independent, high-throughput, sequencing-based analyses revealed that the bacterial fraction of each water kefir and grain was dominated by Zymomonas, an ethanol-producing bacterium, which has not previously been detected at such a scale. The other genera detected were representatives of the lactic acid bacteria and acetic acid bacteria. Our analysis of the fungal component established that it was comprised of the genera Dekkera, Hanseniaspora, Saccharomyces, Zygosaccharomyces, Torulaspora and Lachancea. This information will assist in the ultimate identification of the microorganisms responsible for the potentially health-promoting attributes of these beverages. PMID:24004255

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

    PubMed Central

    Mo, Kai‐For; Daily, Michael D.

    2016-01-01

    Abstract 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. PMID:26865312

  11. Exploring the Gastrointestinal “Nemabiome”: Deep Amplicon Sequencing to Quantify the Species Composition of Parasitic Nematode Communities

    PubMed Central

    Avramenko, Russell W.; Redman, Elizabeth M.; Lewis, Roy; Yazwinski, Thomas A.; Wasmuth, James D.; Gilleard, John S.

    2015-01-01

    Parasitic helminth infections have a considerable impact on global human health as well as animal welfare and production. Although co-infection with multiple parasite species within a host is common, there is a dearth of tools with which to study the composition of these complex parasite communities. Helminth species vary in their pathogenicity, epidemiology and drug sensitivity and the interactions that occur between co-infecting species and their hosts are poorly understood. We describe the first application of deep amplicon sequencing to study parasitic nematode communities as well as introduce the concept of the gastro-intestinal “nemabiome”. The approach is analogous to 16S rDNA deep sequencing used to explore microbial communities, but utilizes the nematode ITS-2 rDNA locus instead. Gastro-intestinal parasites of cattle were used to develop the concept, as this host has many well-defined gastro-intestinal nematode species that commonly occur as complex co-infections. Further, the availability of pure mono-parasite populations from experimentally infected cattle allowed us to prepare mock parasite communities to determine, and correct for, species representation biases in the sequence data. We demonstrate that, once these biases have been corrected, accurate relative quantitation of gastro-intestinal parasitic nematode communities in cattle fecal samples can be achieved. We have validated the accuracy of the method applied to field-samples by comparing the results of detailed morphological examination of L3 larvae populations with those of the sequencing assay. The results illustrate the insights that can be gained into the species composition of parasite communities, using grazing cattle in the mid-west USA as an example. However, both the technical approach and the concept of the ‘nemabiome’ have a wide range of potential applications in human and veterinary medicine. These include investigations of host-parasite and parasite-parasite interactions during co-infection, parasite epidemiology, parasite ecology and the response of parasite populations to both drug treatments and control programs. PMID:26630572

  12. Bioinformatical parsing of folding-on-binding proteins reveals their compositional and evolutionary sequence design.

    PubMed

    Narasumani, Mohanalakshmi; Harrison, Paul M

    2015-01-01

    Intrinsic disorder occurs when (part of) a protein remains unfolded during normal functioning. Intrinsically-disordered regions can contain segments that 'fold on binding' to another molecule. Here, we perform bioinformatical parsing of human 'folding-on-binding' (FB) proteins, into four subsets: Ordered regions, FB regions, Disordered regions that surround FB regions ('Disordered-around-FB'), and Other-Disordered regions. We examined the composition and evolutionary behaviour (across vertebrate orthologs) of these subsets. From a convergence of three separate analyses, we find that for hydrophobicity, Ordered regions segregate from the other subsets, but the Ordered and FB regions group together as highly conserved, and the Disordered-around-FB and Other-Disordered regions as less conserved (with a lesser significant difference between Ordered and FB regions). FB regions are highly-conserved with net positive charge, whereas Disordered-around-FB have net negative charge and are relatively less hydrophobic than FB regions. Indeed, these Disordered-around-FB regions are excessively hydrophilic compared to other disordered regions generally. We describe how our results point towards a possible compositionally-based steering mechanism of folding-on-binding. PMID:26678310

  13. Bioinformatical parsing of folding-on-binding proteins reveals their compositional and evolutionary sequence design

    PubMed Central

    Narasumani, Mohanalakshmi; Harrison, Paul M

    2015-01-01

    Intrinsic disorder occurs when (part of) a protein remains unfolded during normal functioning. Intrinsically-disordered regions can contain segments that fold on binding to another molecule. Here, we perform bioinformatical parsing of human folding-on-binding (FB) proteins, into four subsets: Ordered regions, FB regions, Disordered regions that surround FB regions (Disordered-around-FB), and Other-Disordered regions. We examined the composition and evolutionary behaviour (across vertebrate orthologs) of these subsets. From a convergence of three separate analyses, we find that for hydrophobicity, Ordered regions segregate from the other subsets, but the Ordered and FB regions group together as highly conserved, and the Disordered-around-FB and Other-Disordered regions as less conserved (with a lesser significant difference between Ordered and FB regions). FB regions are highly-conserved with net positive charge, whereas Disordered-around-FB have net negative charge and are relatively less hydrophobic than FB regions. Indeed, these Disordered-around-FB regions are excessively hydrophilic compared to other disordered regions generally. We describe how our results point towards a possible compositionally-based steering mechanism of folding-on-binding. PMID:26678310

  14. Kerogen and biomarker compositions of uranium-rich coaly shales from Miocene sequence at Kanamaru, Japan

    NASA Astrophysics Data System (ADS)

    Yamamoto, M.; Watanabe, Y.

    2005-12-01

    We obtained a continuous 40 m-long core from the Miocene sedimentary sequence and basement Cretaceous granite at Kanamaru, northeast Japan. The Miocene sequence intercalates with a uranium-rich coaly shale seam (U = 25-100 ppm; Th = 23-42 ppm). We have analyzed the kerogen macerals and biomarkers in the core to characterize the organic matter in the uranium-rich seam. Visual kerogen analysis indicated that the relative abundance of coaly and woody kerogens in total kerogen is generally high in the samples that contain high amount of uranium. The coaly and woody kerogens consist about 80 percent of total kerogen, and the rest 20 percent are herbaceous and amorphous kerogens in uranium-rich coaly shales. TMAH-pyrolysis-GC/MS analysis showed that the organic matter in pyrolysates comprises mainly alkyl-aromatic hydrocarbons (alkyl-benzenes, alkyl-indenes, alkyl-naphthalenes, etc.) and n-alkanes. Acyclic isoprenoid alkanes (mainly pristane), n-alkenes, n-fatty acids and acyclic isoprenoid acids were detected as minor components. Most of these compounds are characteristic of the type-III kerogen that derived from terrestrial higher plants. Thermal alteration index (TAI) of Pinus pollen was about 2.6, which indicates that the thermal maturation of the coaly shale reached the stage of early catagenesis. This maturity was also suggested by high abundance of diagenetically generated isomers of hopanes in TMAH pyrolysates. A good correspondence that uranium-rich samples are always rich in type-III organic matter suggests that the type-III organic matter was able to concentrate uranium by the absorption and/or reduction of uranium during deposition and/or early diagenesis.

  15. Characterization of the structure and melting of DNAs containing backbone nicks and gaps

    SciTech Connect

    Snowden-Ifft, E.A.; Wemmer, D.E. )

    1990-06-26

    A DNA molecule containing a gap (a missing phosphate) has been examined and compared to two other molecules of the same sequence, one containing a nick (a phosphorylated gap) and the other a normal duplex containing no break in the backbone. A second gapped sequence was also compared to a normal duplex of the same sequence. The molecules containing nicks or gaps were generated as dumbbell molecules, short helices closed by a loop at each end. The dumbbells were formed by the association of two hairpins with self-complementary dangling 5'-ends. Nuclear magnetic resonance was used to monitor the melting transition and to probe structural differences between molecules. Under the conditions used here no change in stability was observed upon phosphorylation of the gap. Structural changes upon phosphorylation of a gap or closure of a nick were minimal and were localized to the region immediately around the gap or nick. Two transitions can be observed as a gapped or nicked molecule melts, although the resolution of the two transitions varies with the salt concentration. At moderate to high salt (greater than or equal to 30 mM) the molecule melts essentially all at once. At low salt the two transitions occur at temperatures that differ by as much as 15 degrees C. In addition, comparison with other NMR melting studies indicates that the duplex formed by the overlap of the dangling ends of the hairpins is stabilized relative to a free duplex of the same sequence, probably by stacking onto the hairpin stem.

  16. Bacterial community compositions of coking wastewater treatment plants in steel industry revealed by Illumina high-throughput sequencing.

    PubMed

    Ma, Qiao; Qu, Yuanyuan; Shen, Wenli; Zhang, Zhaojing; Wang, Jingwei; Liu, Ziyan; Li, Duanxing; Li, Huijie; Zhou, Jiti

    2015-03-01

    In this study, Illumina high-throughput sequencing was used to reveal the community structures of nine coking wastewater treatment plants (CWWTPs) in China for the first time. The sludge systems exhibited a similar community composition at each taxonomic level. Compared to previous studies, some of the core genera in municipal wastewater treatment plants such as Zoogloea, Prosthecobacter and Gp6 were detected as minor species. Thiobacillus (20.83%), Comamonas (6.58%), Thauera (4.02%), Azoarcus (7.78%) and Rhodoplanes (1.42%) were the dominant genera shared by at least six CWWTPs. The percentages of autotrophic ammonia-oxidizing bacteria and nitrite-oxidizing bacteria were unexpectedly low, which were verified by both real-time PCR and fluorescence in situ hybridization analyses. Hierarchical clustering and canonical correspondence analysis indicated that operation mode, flow rate and temperature might be the key factors in community formation. This study provides new insights into our understanding of microbial community compositions and structures of CWWTPs. PMID:25569032

  17. Scientific Laser Market Still The Backbone Of The Industry

    NASA Astrophysics Data System (ADS)

    Tomkins, Jon

    1988-06-01

    Good morning. I would like to thank Gary Forrest and Laser Focus for giving me the opportunity to participate in this seminar. After listening to Moe Levitt's overview of the industry outlook for 1988, it is a pleasure for me to represent one of the 'hot' sectors in the market - the old research market. My mission today is to provide a perspective of this market to you as one of the healthier parts of the industry, as one of the backbones of our industry.

  18. Robust identification of backbone curves using control-based continuation

    NASA Astrophysics Data System (ADS)

    Renson, L.; Gonzalez-Buelga, A.; Barton, D. A. W.; Neild, S. A.

    2016-04-01

    Control-based continuation is a recently developed approach for testing nonlinear dynamic systems in a controlled manner and exploring their dynamic features as system parameters are varied. In this paper, control-based continuation is adapted to follow the locus where system response and excitation are in quadrature, extracting the backbone curve of the underlying conservative system. The method is applied to a single-degree-of-freedom oscillator under base excitation, and the results are compared with the standard resonant-decay method.

  19. Improving prediction of secondary structure, local backbone angles, and solvent accessible surface area of proteins by iterative deep learning.

    PubMed

    Heffernan, Rhys; Paliwal, Kuldip; Lyons, James; Dehzangi, Abdollah; Sharma, Alok; Wang, Jihua; Sattar, Abdul; Yang, Yuedong; Zhou, Yaoqi

    2015-01-01

    Direct prediction of protein structure from sequence is a challenging problem. An effective approach is to break it up into independent sub-problems. These sub-problems such as prediction of protein secondary structure can then be solved independently. In a previous study, we found that an iterative use of predicted secondary structure and backbone torsion angles can further improve secondary structure and torsion angle prediction. In this study, we expand the iterative features to include solvent accessible surface area and backbone angles and dihedrals based on Cα atoms. By using a deep learning neural network in three iterations, we achieved 82% accuracy for secondary structure prediction, 0.76 for the correlation coefficient between predicted and actual solvent accessible surface area, 19° and 30° for mean absolute errors of backbone φ and ψ angles, respectively, and 8° and 32° for mean absolute errors of Cα-based θ and τ angles, respectively, for an independent test dataset of 1199 proteins. The accuracy of the method is slightly lower for 72 CASP 11 targets but much higher than those of model structures from current state-of-the-art techniques. This suggests the potentially beneficial use of these predicted properties for model assessment and ranking. PMID:26098304

  20. Improving prediction of secondary structure, local backbone angles, and solvent accessible surface area of proteins by iterative deep learning

    PubMed Central

    Heffernan, Rhys; Paliwal, Kuldip; Lyons, James; Dehzangi, Abdollah; Sharma, Alok; Wang, Jihua; Sattar, Abdul; Yang, Yuedong; Zhou, Yaoqi

    2015-01-01

    Direct prediction of protein structure from sequence is a challenging problem. An effective approach is to break it up into independent sub-problems. These sub-problems such as prediction of protein secondary structure can then be solved independently. In a previous study, we found that an iterative use of predicted secondary structure and backbone torsion angles can further improve secondary structure and torsion angle prediction. In this study, we expand the iterative features to include solvent accessible surface area and backbone angles and dihedrals based on Cα atoms. By using a deep learning neural network in three iterations, we achieved 82% accuracy for secondary structure prediction, 0.76 for the correlation coefficient between predicted and actual solvent accessible surface area, 19° and 30° for mean absolute errors of backbone φ and ψ angles, respectively, and 8° and 32° for mean absolute errors of Cα-based θ and τ angles, respectively, for an independent test dataset of 1199 proteins. The accuracy of the method is slightly lower for 72 CASP 11 targets but much higher than those of model structures from current state-of-the-art techniques. This suggests the potentially beneficial use of these predicted properties for model assessment and ranking. PMID:26098304

  1. Effect of Backbone Design on Hybridization Thermodynamics of Oligo-nucleic Acids: A Coarse-Grained Molecular Dynamics Simulation Study

    NASA Astrophysics Data System (ADS)

    Ghobadi, Ahmadreza F.; Jayaraman, Arthi

    DNA hybridization is the basis of various bio-nano technologies, such as DNA origami and assembly of DNA-functionalized nanoparticles. A hybridized double stranded (ds) DNA is formed when complementary nucleobases on hybridizing strands exhibit specific and directional hydrogen bonds through canonical Watson-Crick base-pairing interactions. In recent years, the need for cheaper alternatives and significant synthetic advances have driven design of DNA mimics with new backbone chemistries. However, a fundamental understanding of how these backbone modifications in the oligo-nucleic acids impact the hybridization and melting behavior of the duplex is still lacking. In this talk, we present our recent findings on impact of varying backbone chemistry on hybridization of oligo-nucleic acid duplexes. We use coarse-grained molecular dynamics simulations to isolate the effect of strand flexibility, electrostatic interactions and nucleobase spacing on the melting curves for duplexes with various strand sequences and concentrations. Since conjugation of oligo-nucleic acids with polymers serve as building blocks for thermo-responsive polymer networks and gels, we also present the effect of such conjugation on hybridization thermodynamics and polymer conformation.

  2. The role of molecular structure of sugar-phosphate backbone and nucleic acid bases in the formation of single-stranded and double-stranded DNA structures.

    PubMed

    Poltev, Valeri; Anisimov, Victor M; Danilov, Victor I; Garcia, Dolores; Sanchez, Carolina; Deriabina, Alexandra; Gonzalez, Eduardo; Rivas, Francisco; Polteva, Nina

    2014-06-01

    Our previous DFT computations of deoxydinucleoside monophosphate complexes with Na(+)-ions (dDMPs) have demonstrated that the main characteristics of Watson-Crick (WC) right-handed duplex families are predefined in the local energy minima of dDMPs. In this work, we study the mechanisms of contribution of chemically monotonous sugar-phosphate backbone and the bases into the double helix irregularity. Geometry optimization of sugar-phosphate backbone produces energy minima matching the WC DNA conformations. Studying the conformational variability of dDMPs in response to sequence permutation, we found that simple replacement of bases in the previously fully optimized dDMPs, e.g. by constructing Pyr-Pur from Pur-Pyr, and Pur-Pyr from Pyr-Pur sequences, while retaining the backbone geometry, automatically produces the mutual base position characteristic of the target sequence. Based on that, we infer that the directionality and the preferable regions of the sugar-phosphate torsions, combined with the difference of purines from pyrimidines in ring shape, determines the sequence dependence of the structure of WC DNA. No such sequence dependence exists in dDMPs corresponding to other DNA conformations (e.g., Z-family and Hoogsteen duplexes). Unlike other duplexes, WC helix is unique by its ability to match the local energy minima of the free single strand to the preferable conformations of the duplex. PMID:24170251

  3. Species composition of the genus Saprolegnia in fin fish aquaculture environments, as determined by nucleotide sequence analysis of the nuclear rDNA ITS regions.

    PubMed

    de la Bastide, Paul Y; Leung, Wai Lam; Hintz, William E

    2015-01-01

    The ITS region of the rDNA gene was compared for Saprolegnia spp. in order to improve our understanding of nucleotide sequence variability within and between species of this genus, determine species composition in Canadian fin fish aquaculture facilities, and to assess the utility of ITS sequence variability in genetic marker development. From a collection of more than 400 field isolates, ITS region nucleotide sequences were studied and it was determined that there was sufficient consistent inter-specific variation to support the designation of species identity based on ITS sequence data. This non-subjective approach to species identification does not rely upon transient morphological features. Phylogenetic analyses comparing our ITS sequences and species designations with data from previous studies generally supported the clade scheme of Diéguez-Uribeondo et al. (2007) and found agreement with the molecular taxonomic cluster system of Sandoval-Sierra et al. (2014). Our Canadian ITS sequence collection will thus contribute to the public database and assist the clarification of Saprolegnia spp. taxonomy. The analysis of ITS region sequence variability facilitated genus- and species-level identification of unknown samples from aquaculture facilities and provided useful information on species composition. A unique ITS-RFLP for the identification of S. parasitica was also described. PMID:25601147

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

    PubMed Central

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

    2015-01-01

    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. PMID:25589608

  5. Backbone resonance assignments of the human p73 DNA binding domain.

    PubMed

    Cino, Elio A; Soares, Iaci N; Freitas, Mônica S; Silva, Jerson L

    2016-04-01

    p53, p63, p73 family of proteins are transcription factors with crucial roles in regulating cellular processes such apoptosis, proliferation, differentiation, and DNA damage response. The three family members have both overlapping and unique biological functions. Sequence and structural homology are greatest in the DNA binding domains (DBD), which is the site of the majority of p53 mutations. Structurally unstable p53 DBD mutants can associate with themselves or p63 and p73 DBDs, impeding tumor suppressor functions. Evidence suggests that these proteins associate to form amyloid-like oligomers and fibrils through an aggregation-prone sequence within the DBDs. Despite having high sequence and structure similarities, p63 and p73 DBDs appear to have considerably lower tendencies to be incorporated into p53 aggregates, relative to p53. The backbone resonance assignments of p73 DBD reported here complement those previously reported for p53 and p63, allowing comparisons and providing molecular insights into their biological functions and roles in aggregation and tumor development. PMID:26294377

  6. PS1-10jh: The disruption of a main-sequence star of near-solar composition

    SciTech Connect

    Guillochon, James; Manukian, Haik; Ramirez-Ruiz, Enrico

    2014-03-01

    When a star comes within a critical distance to a supermassive black hole (SMBH), immense tidal forces disrupt the star, resulting in a stream of debris that falls back onto the SMBH and powers a luminous flare. In this paper, we perform hydrodynamical simulations of the disruption of a main-sequence star by an SMBH to characterize the evolution of the debris stream after a tidal disruption. We demonstrate that this debris stream is confined by self-gravity in the two directions perpendicular to the original direction of the star's travel and as a consequence has a negligible surface area and makes almost no contribution to either the continuum or line emission. We therefore propose that any observed emission lines are not the result of photoionization in this unbound debris, but are produced in the region above and below the forming elliptical accretion disk, analogous to the broad-line region (BLR) in steadily accreting active galactic nuclei. As each line within a BLR is observationally linked to a particular location in the accretion disk, we suggest that the absence of a line indicates that the accretion disk does not yet extend to the distance required to produce that line. This model can be used to understand the spectral properties of the tidal disruption event PS1-10jh, for which He II lines are observed, but the Balmer series and He I are not. Using a maximum likelihood analysis, we show that the disruption of a main-sequence star of near-solar composition can reproduce this event.

  7. Coupling Protein Side-Chain and Backbone Flexibility Improves the Re-design of Protein-Ligand Specificity

    PubMed Central

    Ollikainen, Noah; de Jong, René M.; Kortemme, Tanja

    2015-01-01

    Interactions between small molecules and proteins play critical roles in regulating and facilitating diverse biological functions, yet our ability to accurately re-engineer the specificity of these interactions using computational approaches has been limited. One main difficulty, in addition to inaccuracies in energy functions, is the exquisite sensitivity of protein–ligand interactions to subtle conformational changes, coupled with the computational problem of sampling the large conformational search space of degrees of freedom of ligands, amino acid side chains, and the protein backbone. Here, we describe two benchmarks for evaluating the accuracy of computational approaches for re-engineering protein-ligand interactions: (i) prediction of enzyme specificity altering mutations and (ii) prediction of sequence tolerance in ligand binding sites. After finding that current state-of-the-art “fixed backbone” design methods perform poorly on these tests, we develop a new “coupled moves” design method in the program Rosetta that couples changes to protein sequence with alterations in both protein side-chain and protein backbone conformations, and allows for changes in ligand rigid-body and torsion degrees of freedom. We show significantly increased accuracy in both predicting ligand specificity altering mutations and binding site sequences. These methodological improvements should be useful for many applications of protein – ligand design. The approach also provides insights into the role of subtle conformational adjustments that enable functional changes not only in engineering applications but also in natural protein evolution. PMID:26397464

  8. Refined solution structure and backbone dynamics of HIV-1 Nef.

    PubMed Central

    Grzesiek, S.; Bax, A.; Hu, J. S.; Kaufman, J.; Palmer, I.; Stahl, S. J.; Tjandra, N.; Wingfield, P. T.

    1997-01-01

    The tendency of HIV-1 Nef to form aggregates in solution, particularly at pH values below 8, together with its large fraction of highly mobile residues seriously complicated determination of its three-dimensional structure, both for heteronuclear solution NMR (Grzesiek et al., 1996a, Nat Struct Biol 3:340-345) and for X-ray crystallography (Lee et al., 1996, Cell 85:931-942). Methods used to determine the Nef structure by NMR at pH 8 and 0.6 mM concentration are presented, together with a detailed description of Nef's secondary and tertiary structure. The described techniques have general applicability for the NMR structure determination of proteins that are aggregating and/or have limited stability at low pH values. Extensive chemical shift assignments are reported for backbone and side chain 1H, 13C, and 15N resonances of the HIV-1 Nef deletion mutants NEF delta 2-39, NEF delta 2-39, delta 159-173, and of NEF delta 2-39, delta 159-173 in complex with the SH3 domain of the Hck tyrosine protein kinase. Besides a type II polyproline helix, Nef's structure consists of three alpha-helices, a 3(10) helix, and a five-stranded anti-parallel beta-sheet. The analysis of 15N relaxation parameters of the backbone amide sites reveals that all the secondary structure elements are non-mobile on the picosecond to nanosecond and on the millisecond time scale. A large number of slowly exchanging amide protons provides evidence for the stability of the Nef core even on the time scale of hours. Significant internal motions on the ps to ns time scale are detected for residues 60 to 71 and for residues 149 to 180, which form solvent-exposed loops. The residues of the HIV-1 protease cleavage site (W57/L58) do not exhibit large amplitude motions on the sub-nanosecond time scale, and their side chains insert themselves into a hydrophobic crevice formed between the C-terminus of helix 1 and the N-terminus of helix 2. A refined structure has been determined based on additional constraints for side-chain and backbone dihedral angles derived from a large number of three-bond J-coupling and ROE data. PMID:9194185

  9. Backbone dynamics of barstar: a (15)N NMR relaxation study.

    PubMed

    Sahu, S C; Bhuyan, A K; Majumdar, A; Udgaonkar, J B

    2000-12-01

    Backbone dynamics of uniformly (15)N-labeled barstar have been studied at 32 degrees C, pH 6.7, by using (15)N relaxation data obtained from proton-detected 2D (1)H-(15)N NMR spectroscopy. (15)N spin-lattice relaxation rate constants (R(1)), spin-spin relaxation rate constants (R(2)), and steady-state heteronuclear (1)H-(15)N NOEs have been determined for 69 of the 86 (excluding two prolines and the N-terminal residue) backbone amide (15)N at a magnetic field strength of 14.1 Tesla. The primary relaxation data have been analyzed by using the model-free formalism of molecular dynamics, using both isotropic and axially symmetric diffusion of the molecule, to determine the overall rotational correlation time (tau(m)), the generalized order parameter (S(2)), the effective correlation time for internal motions (tau(e)), and NH exchange broadening contributions (R(ex)) for each residue. As per the axially symmetric diffusion, the ratio of diffusion rates about the unique and perpendicular axes (D( parallel)/D( perpendicular)) is 0.82 +/- 0.03. The two results have only marginal differences. The relaxation data have also been used to map reduced spectral densities for the NH vectors of these residues at three frequencies: 0, omega(H), and omega(N), where omega(H),(N) are proton and nitrogen Larmor frequencies. The value of tau(m) obtained from model-free analysis of the relaxation data is 5.2 ns. The reduced spectral density analysis, however, yields a value of 5.7 ns. The tau(m) determined here is different from that calculated previously from time-resolved fluorescence data (4.1 ns). The order parameter ranges from 0.68 to 0.98, with an average value of 0.85 +/- 0.02. A comparison of the order parameters with the X-ray B-factors for the backbone nitrogens of wild-type barstar does not show any considerable correlation. Model-free analysis of the relaxation data for seven residues required the inclusion of an exchange broadening term, the magnitude of which ranges from 2 to 9.1 s(-1), indicating the presence of conformational averaging motions only for a small subset of residues. PMID:11056034

  10. Direct effects of phosphorylation on the preferred backbone conformation of peptides: a nuclear magnetic resonance study.

    PubMed Central

    Tholey, A; Lindemann, A; Kinzel, V; Reed, J

    1999-01-01

    Control of protein activity by phosphorylation appears to work principally by inducing conformational change, but the mechanisms so far reported are dependent on the structural context in which phosphorylation occurs. As the activity of many small peptides is also regulated by phosphorylation, we decided to investigate possible direct consequences of this on the preferred backbone conformation. We have performed 1H nuclear magnetic resonance (NMR) experiments with short model peptides of the pattern Gly-Ser-Xaa-Ser, where Xaa represents Ser, Thr, or Tyr in either phosphorylated or unphosphorylated form and with either free or blocked amino and carboxy termini. The chemical shifts of amide protons and the 3JNH-Halpha coupling constants were estimated from one-dimensional and two-dimensional scalar correlated spectroscopy (COSY) spectra at different pH values. The results clearly indicate a direct structural effect of serine and threonine phosphorylation on the preferred backbone dihedrals independent of the presence of charged groups in the surrounding sequence. Tyrosine phosphorylation does not induce such a charge-independent effect. Additionally, experiments with p-fluoro- and p-nitro-phenylalanine-containing peptides showed that the mere presence of an electronegative group on the aromatic ring of tyrosine does not produce direct structural effects. In the case of serine and threonine phosphorylation a strong dependence of the conformational shift on the protonation level of the phosphoryl group could be observed, showing that phosphorylation induces the strongest effect in its dianionic, i.e., physiological, form. The data reveal a hitherto unknown mechanism that may be added to the repertoire of conformational control of peptides and proteins by phosphorylation. PMID:9876124

  11. Transforming plastic surfaces with electrophilic backbones from hydrophobic to hydrophilic.

    PubMed

    Kim, Samuel; Bowen, Raffick A R; Zare, Richard N

    2015-01-28

    We demonstrate a simple nonaqueous reaction scheme for transforming the surface of plastics from hydrophobic to hydrophilic. The chemical modification is achieved by base-catalyzed trans-esterification with polyols. It is permanent, does not release contaminants, and causes no optical or mechanical distortion of the plastic. We present contact angle measurements to show successful modification of several types of plastics including poly(ethylene terephthalate) (PET) and polycarbonate (PC). Its applicability to blood analysis is explored using chemically modified PET blood collection tubes and found to be quite satisfactory. We expect this approach will reduce the cost of manufacturing plastic devices with optimized wettability and can be generalized to other types of plastic materials having an electrophilic linkage as its backbone. PMID:25565370

  12. A Native to Amyloidogenic Transition Regulated by a Backbone Trigger

    SciTech Connect

    Eakin,C.; Berman, A.; Miranker, A.

    2006-01-01

    Many polypeptides can self-associate into linear, aggregated assemblies termed amyloid fibers. High-resolution structural insights into the mechanism of fibrillogenesis are elusive owing to the transient and mixed oligomeric nature of assembly intermediates. Here, we report the conformational changes that initiate fiber formation by beta-2-microglobulin (beta2m) in dialysis-related amyloidosis. Access of beta2m to amyloidogenic conformations is catalyzed by selective binding of divalent cations. The chemical basis of this process was determined to be backbone isomerization of a conserved proline. On the basis of this finding, we designed a beta2m variant that closely adopts this intermediate state. The variant has kinetic, thermodynamic and catalytic properties consistent with its being a fibrillogenic intermediate of wild-type beta2m. Furthermore, it is stable and folded, enabling us to unambiguously determine the initiating conformational changes for amyloid assembly at atomic resolution.

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

    NASA Astrophysics Data System (ADS)

    Svalgaard, Leif; Schatten, Kenneth H.

    2016-02-01

    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.

  14. Effects of phosphorylation on the intrinsic propensity of backbone conformations of serine/threonine.

    PubMed

    He, Erbin; Yan, Guanghui; Zhang, Jian; Wang, Jun; Li, Wenfei

    2016-03-01

    Each amino acid has its intrinsic propensity for certain local backbone conformations, which can be further modulated by the physicochemical environment and post-translational modifications. In this work, we study the effects of phosphorylation on the intrinsic propensity for different local backbone conformations of serine/threonine by molecular dynamics simulations. We showed that phosphorylation has very different effects on the intrinsic propensity for certain local backbone conformations for the serine and threonine. The phosphorylation of serine increases the propensity of forming polyproline II, whereas that of threonine has the opposite effect. Detailed analysis showed that such different responses to phosphorylation mainly arise from their different perturbations to the backbone hydration and the geometrical constraints by forming side-chain-backbone hydrogen bonds due to phosphorylation. Such an effect of phosphorylation on backbone conformations can be crucial for understanding the molecular mechanism of phosphorylation-regulated protein structures/dynamics and functions. PMID:26759163

  15. Rapid Algorithm for Identifying Backbones in the Two-Dimensional Percolation Model

    NASA Astrophysics Data System (ADS)

    Yin, Wei-Guo; Tao, Ruibao

    We present a rapid algorithm for identifying the current-carrying backbone in the two-dimensional percolation model. Taking advantage of the modified Hoshen-Kopelman cluster labeling algorithm, our algorithm identifies dangling parts using their local properties. For planar graphs, it finds the backbone almost four times as fast as the commonly-used Tarjan's depth-first-search algorithm. Comparison with other algorithms for backbone identification is also addressed.

  16. Water proton spin saturation affects measured protein backbone 15 N spin relaxation rates

    NASA Astrophysics Data System (ADS)

    Chen, Kang; Tjandra, Nico

    2011-12-01

    Protein backbone 15N NMR spin relaxation rates are useful in characterizing the protein dynamics and structures. To observe the protein nuclear-spin resonances a pulse sequence has to include a water suppression scheme. There are two commonly employed methods, saturating or dephasing the water spins with pulse field gradients and keeping them unperturbed with flip-back pulses. Here different water suppression methods were incorporated into pulse sequences to measure 15N longitudinal T1 and transversal rotating-frame T1ρ spin relaxation. Unexpectedly the 15N T1 relaxation time constants varied significantly with the choice of water suppression method. For a 25-kDa Escherichiacoli. glutamine binding protein (GlnBP) the T1 values acquired with the pulse sequence containing a water dephasing gradient are on average 20% longer than the ones obtained using a pulse sequence containing the water flip-back pulse. In contrast the two T1ρ data sets are correlated without an apparent offset. The average T1 difference was reduced to 12% when the experimental recycle delay was doubled, while the average T1 values from the flip-back measurements were nearly unchanged. Analysis of spectral signal to noise ratios ( s/ n) showed the apparent slower 15N relaxation obtained with the water dephasing experiment originated from the differences in 1H N recovery for each relaxation time point. This in turn offset signal reduction from 15N relaxation decay. The artifact becomes noticeable when the measured 15N relaxation time constant is comparable to recycle delay, e.g., the 15N T1 of medium to large proteins. The 15N relaxation rates measured with either water suppression schemes yield reasonable fits to the structure. However, data from the saturated scheme results in significantly lower Model-Free order parameters (< S2> = 0.81) than the non-saturated ones (< S2> = 0.88), indicating such order parameters may be previously underestimated.

  17. Sequences of Regressions Distinguish Nonmechanical from Mechanical Associations between Metabolic Factors, Body Composition, and Bone in Healthy Postmenopausal Women123

    PubMed Central

    Goldberg, Gail R; Prentice, Ann

    2016-01-01

    Background: There is increasing recognition of complex interrelations between the endocrine functions of bone and fat tissues or organs. Objective: The objective was to describe nonmechanical and mechanical links between metabolic factors, body composition, and bone with the use of graphical Markov models. Methods: Seventy postmenopausal women with a mean ± SD age of 62.3 ± 3.7 y and body mass index (in kg/m2) of 24.9 ± 3.8 were recruited. Bone outcomes were peripheral quantitative computed tomography measures of the distal and diaphyseal tibia, cross-sectional area (CSA), volumetric bone mineral density (vBMD), and cortical CSA. Biomarkers of osteoblast and adipocyte function were plasma concentrations of leptin, adiponectin, osteocalcin, undercarboxylated osteocalcin (UCOC), and phylloquinone. Body composition measurements were lean and percent fat mass, which were derived with the use of a 4-compartment model. Sequences of Regressions, a subclass of graphical Markov models, were used to describe the direct (nonmechanical) and indirect (mechanical) interrelations between metabolic factors and bone by simultaneously modeling multiple bone outcomes and their relation with biomarker outcomes with lean mass, percent fat mass, and height as intermediate explanatory variables. Results: The graphical Markov models showed both direct and indirect associations linking plasma leptin and adiponectin concentrations with CSA and vBMD. At the distal tibia, lean mass, height, and adiponectin-UCOC interaction were directly explanatory of CSA (R2 = 0.45); at the diaphysis, lean mass, percent fat mass, leptin, osteocalcin, and age-adiponectin interaction were directly explanatory of CSA (R2 = 0.49). The regression models exploring direct associations for vBMD were much weaker, with R2 = 0.15 and 0.18 at the distal and diaphyseal sites, respectively. Lean mass and UCOC were associated, and the global Markov property of the graph indicated that this association was explained by osteocalcin. Conclusions: This study, to our knowledge, offers a novel approach to the description of the complex physiological interrelations between adiponectin, leptin, and osteocalcin and the musculoskeletal system. There may be benefits to jointly targeting both systems to improve bone health. PMID:26962186

  18. Live-attenuated influenza A virus vaccines using a B virus backbone

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The currently FDA-licensed live attenuated influenza virus vaccine contains a trivalent mixture of types A (H1N1 and H3N2) and B vaccine viruses. The two A virus vaccines have the backbone of a cold-adapted influenza A virus and the B virus vaccine has the six backbone segments derived from a cold-...

  19. 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).

  20. Abundances of Triacylglycerol Positional Isomers and Enantiomers Comprised of a Dipalmitoylglycerol Backbone and Short- or Medium-chain Fatty Acids in Bovine Milk Fat.

    PubMed

    Nagai, Toshiharu; Watanabe, Natsuko; Yoshinaga, Kazuaki; Mizobe, Hoyo; Kojima, Koichi; Kuroda, Ikuma; Odanaka, Yuki; Saito, Tadao; Beppu, Fumiaki; Gotoh, Naohiro

    2015-01-01

    Bovine milk fat (BMF) is composed of triacylglycerols (TAG) rich in palmitic acid (P), oleic acid (O), and short-chain or medium-chain fatty acids (SCFAs or MCFAs). The composition and binding positions of the fatty acids on the glycerol backbone determine their physical and nutritional properties. SCFAs and MCFAs are known to characteristically bind to the sn-3 position of the TAGs in BMF; however, there are very few non-destructive analyses of TAG enantiomers binding the fatty acids at this position. We previously reported a method to resolve the enantiomers of TAGs, binding both long-chain saturated fatty acid and unsaturated fatty acid at the sn-1 and 3 positions, in palm oil, fish oil, and marine mammal oil using chiral HPLC. Here, we further developed a method to resolve several TAG enantiomers containing a dipalmitoyl (PP) glycerol backbone and one SCFA (or MCFA) in BMF. We revealed that the predominant TAG structure in BMF was homochiral, such as 1,2-dipalmitoyl-3-butyroyl-sn-glycerol. This is the first quantitative determination of many TAG enantiomers, which bind to a SCFA or MCFA, in BMF was evaluated simultaneously. Furthermore, the results indicated that the amount ratios of the positional isomers and enantiomers of TAGs consisting of a dipalmitoyl (PP) glycerol backbone and SCFA (or MCFA), resembled the whole TAG structures containing the other diacylglycerol backbones consisting of P, O, myristic acid, and/or stearic acid in BMF. PMID:26329769

  1. Strong liquid-crystalline polymeric compositions

    DOEpatents

    Dowell, F.

    1993-12-07

    Strong liquid-crystalline polymeric (LCP) compositions of matter are described. LCP backbones are combined with liquid crystalline (LC) side chains in a manner which maximizes molecular ordering through interdigitation of the side chains, thereby yielding materials which are predicted to have superior mechanical properties over existing LCPs. The theoretical design of LCPs having such characteristics includes consideration of the spacing distance between side chains along the backbone, the need for rigid sections in the backbone and in the side chains, the degree of polymerization, the length of the side chains, the regularity of the spacing of the side chains along the backbone, the interdigitation of side chains in sub-molecular strips, the packing of the side chains on one or two sides of the backbone to which they are attached, the symmetry of the side chains, the points of attachment of the side chains to the backbone, the flexibility and size of the chemical group connecting each side chain to the backbone, the effect of semiflexible sections in the backbone and the side chains, and the choice of types of dipolar and/or hydrogen bonding forces in the backbones and the side chains for easy alignment. 27 figures.

  2. Strong liquid-crystalline polymeric compositions

    DOEpatents

    Dowell, Flonnie (Los Alamos, NM)

    1993-01-01

    Strong liquid-crystalline polymeric (LCP) compositions of matter. LCP backbones are combined with liquid crystalline (LC) side chains in a manner which maximizes molecular ordering through interdigitation of the side chains, thereby yielding materials which are predicted to have superior mechanical properties over existing LCPs. The theoretical design of LCPs having such characteristics includes consideration of the spacing distance between side chains along the backbone, the need for rigid sections in the backbone and in the side chains, the degree of polymerization, the length of the side chains, the regularity of the spacing of the side chains along the backbone, the interdigitation of side chains in sub-molecular strips, the packing of the side chains on one or two sides of the backbone to which they are attached, the symmetry of the side chains, the points of attachment of the side chains to the backbone, the flexibility and size of the chemical group connecting each side chain to the backbone, the effect of semiflexible sections in the backbone and the side chains, and the choice of types of dipolar and/or hydrogen bonding forces in the backbones and the side chains for easy alignment.

  3. Bond distances in polypeptide backbones depend on the local conformation.

    PubMed

    Improta, Roberto; Vitagliano, Luigi; Esposito, Luciana

    2015-06-01

    By combining quantum-mechanical analysis of small model peptides and statistical surveys of high-resolution protein structures, a systematic conformational dependence of bond lengths in polypeptide backbones has been unveiled which involves both the peptide bond (C-O and C-N) and those bonds centred on the C(α) atom. All of these bond lengths indeed display a systematic variability in the ψ angle according to both calculations and surveys of protein structures. The overall agreement between the computed and the statistical data suggests that these trends are essentially driven by local effects. The dependence of C(α) distances on ψ is governed by interactions between the σ system of the C(α) moiety and the C-O π system of the peptide bond. Maximum and minimum values for each bond distance are found for conformations with the specific bond perpendicular and parallel to the adjacent CONH peptide plane, respectively. On the other hand, the variability of the C-O and C-N distances is related to the strength of the interactions between the lone pair of the N atom and the C-O π* system, which is modulated by the ψ angle. The C-O and C-N distances are related but their trends are not strictly connected to peptide-bond planarity, although a correlation amongst all of these parameters is expected on the basis of the classical resonance model. PMID:26057667

  4. Quantitative Analysis of PMLA Nanoconjugate Components after Backbone Cleavage

    PubMed Central

    Ding, Hui; Patil, Rameshwar; Portilla-Arias, Jose; Black, Keith L.; Ljubimova, Julia Y.; Holler, Eggehard

    2015-01-01

    Multifunctional polymer nanoconjugates containing multiple components show great promise in cancer therapy, but in most cases complete analysis of each component is difficult. Polymalic acid (PMLA) based nanoconjugates have demonstrated successful brain and breast cancer treatment. They consist of multiple components including targeting antibodies, Morpholino antisense oligonucleotides (AONs), and endosome escape moieties. The component analysis of PMLA nanoconjugates is extremely difficult using conventional spectrometry and HPLC method. Taking advantage of the nature of polyester of PMLA, which can be cleaved by ammonium hydroxide, we describe a method to analyze the content of antibody and AON within nanoconjugates simultaneously using SEC-HPLC by selectively cleaving the PMLA backbone. The selected cleavage conditions only degrade PMLA without affecting the integrity and biological activity of the antibody. Although the amount of antibody could also be determined using the bicinchoninic acid (BCA) method, our selective cleavage method gives more reliable results and is more powerful. Our approach provides a new direction for the component analysis of polymer nanoconjugates and nanoparticles. PMID:25894227

  5. A New Secondary Structure Assignment Algorithm Using Cα Backbone Fragments.

    PubMed

    Cao, Chen; Wang, Guishen; Liu, An; Xu, Shutan; Wang, Lincong; Zou, Shuxue

    2016-01-01

    The assignment of secondary structure elements in proteins is a key step in the analysis of their structures and functions. We have developed an algorithm, SACF (secondary structure assignment based on Cα fragments), for secondary structure element (SSE) assignment based on the alignment of Cα backbone fragments with central poses derived by clustering known SSE fragments. The assignment algorithm consists of three steps: First, the outlier fragments on known SSEs are detected. Next, the remaining fragments are clustered to obtain the central fragments for each cluster. Finally, the central fragments are used as a template to make assignments. Following a large-scale comparison of 11 secondary structure assignment methods, SACF, KAKSI and PROSS are found to have similar agreement with DSSP, while PCASSO agrees with DSSP best. SACF and PCASSO show preference to reducing residues in N and C cap regions, whereas KAKSI, P-SEA and SEGNO tend to add residues to the terminals when DSSP assignment is taken as standard. Moreover, our algorithm is able to assign subtle helices (310-helix, π-helix and left-handed helix) and make uniform assignments, as well as to detect rare SSEs in β-sheets or long helices as outlier fragments from other programs. The structural uniformity should be useful for protein structure classification and prediction, while outlier fragments underlie the structure-function relationship. PMID:26978354

  6. 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 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. 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.

  8. 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

  9. A New Secondary Structure Assignment Algorithm Using Cα Backbone Fragments

    PubMed Central

    Cao, Chen; Wang, Guishen; Liu, An; Xu, Shutan; Wang, Lincong; Zou, Shuxue

    2016-01-01

    The assignment of secondary structure elements in proteins is a key step in the analysis of their structures and functions. We have developed an algorithm, SACF (secondary structure assignment based on Cα fragments), for secondary structure element (SSE) assignment based on the alignment of Cα backbone fragments with central poses derived by clustering known SSE fragments. The assignment algorithm consists of three steps: First, the outlier fragments on known SSEs are detected. Next, the remaining fragments are clustered to obtain the central fragments for each cluster. Finally, the central fragments are used as a template to make assignments. Following a large-scale comparison of 11 secondary structure assignment methods, SACF, KAKSI and PROSS are found to have similar agreement with DSSP, while PCASSO agrees with DSSP best. SACF and PCASSO show preference to reducing residues in N and C cap regions, whereas KAKSI, P-SEA and SEGNO tend to add residues to the terminals when DSSP assignment is taken as standard. Moreover, our algorithm is able to assign subtle helices (310-helix, π-helix and left-handed helix) and make uniform assignments, as well as to detect rare SSEs in β-sheets or long helices as outlier fragments from other programs. The structural uniformity should be useful for protein structure classification and prediction, while outlier fragments underlie the structure–function relationship. PMID:26978354

  10. 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.

  11. Analysis of BAC end sequences in oak, a keystone forest tree species, providing insight into the composition of its genome

    PubMed Central

    2011-01-01

    Background One of the key goals of oak genomics research is to identify genes of adaptive significance. This information may help to improve the conservation of adaptive genetic variation and the management of forests to increase their health and productivity. Deep-coverage large-insert genomic libraries are a crucial tool for attaining this objective. We report herein the construction of a BAC library for Quercus robur, its characterization and an analysis of BAC end sequences. Results The EcoRI library generated consisted of 92,160 clones, 7% of which had no insert. Levels of chloroplast and mitochondrial contamination were below 3% and 1%, respectively. Mean clone insert size was estimated at 135 kb. The library represents 12 haploid genome equivalents and, the likelihood of finding a particular oak sequence of interest is greater than 99%. Genome coverage was confirmed by PCR screening of the library with 60 unique genetic loci sampled from the genetic linkage map. In total, about 20,000 high-quality BAC end sequences (BESs) were generated by sequencing 15,000 clones. Roughly 5.88% of the combined BAC end sequence length corresponded to known retroelements while ab initio repeat detection methods identified 41 additional repeats. Collectively, characterized and novel repeats account for roughly 8.94% of the genome. Further analysis of the BESs revealed 1,823 putative genes suggesting at least 29,340 genes in the oak genome. BESs were aligned with the genome sequences of Arabidopsis thaliana, Vitis vinifera and Populus trichocarpa. One putative collinear microsyntenic region encoding an alcohol acyl transferase protein was observed between oak and chromosome 2 of V. vinifera. Conclusions This BAC library provides a new resource for genomic studies, including SSR marker development, physical mapping, comparative genomics and genome sequencing. BES analysis provided insight into the structure of the oak genome. These sequences will be used in the assembly of a future genome sequence for oak. PMID:21645357

  12. Glucuronic acid directly linked to galacturonic acid in the rhamnogalacturonan backbone of beet pectins.

    PubMed

    Renard, C M; Crépeau, M J; Thibault, J F

    1999-12-01

    Sugar-beet pulp was de-esterified and submitted to 72 h hydrolysis by 0.1 M HCl at 80 degrees C. Oligomers containing a single glucuronic acid (GlcA) moiety in addition to n(>/= 2) repeats of the dimer -->4)-alpha-D-GalpA-(1-->2)-alpha-L-Rhap-(1--> were isolated from the hydrolysate by ion-exchange and gel-permeation. Glycosyl linkage composition analysis and 1H NMR studies indicated that the GlcA was attached to O-3 of a galacturonic acid (GalA) residue, as shown for the two pentamers beta-D-GlcpA-(1-->3)-alpha-D-GalpA-(1-->2)-alpha-L-Rhap-(1-->4)-alpha-D-GalpA-(1-->2)-L-Rhap and alpha-D-GalpA-(1-->2)-alpha-L-Rhap-(1-->4)-[beta-D-GlcpA-(1-->3)]-alpha-D-GalpA-(1-->2)-L-Rhap. Substitution by GlcA was estimated as occurring on one GalA residue out of 72 in the rhamnogalacturonan fraction of the backbone of beet pectins. PMID:10561599

  13. Typing of core and backbone domains of mucin-type oligosaccharides from human ovarian-cyst glycoproteins by 500-MHz 1H-NMR spectroscopy.

    PubMed

    Mutsaers, J H; van Halbeek, H; Vliegenthart, J F; Wu, A M; Kabat, E A

    1986-05-15

    Human blood-group A active glycoproteins from ovarian-cyst fluid were subjected to Smith degradation and subsequent beta-elimination. The resulting oligosaccharide-alditols represent the core and backbone domains of the O-linked carbohydrate chains. Nine of these, ranging in size from disaccharides to hexasaccharides, were investigated by 1H-NMR spectroscopy. Their primary structures could be adequately characterized. In particular, the core types, i.e. the substitution patterns of N-acetylgalactosaminitol (GalNAc-ol) as well as the types of backbone, i.e. the linkage types of alternating Gal-GlcNAc sequences, were unambiguously identified. The core type GlcNAc beta(1-3)GalNAc-ol is described for the first time as occurring in ovarian-cyst glycoprotein. PMID:3709529

  14. Backbone and side-chain resonance assignment of the A147T polymorph of mouse TSPO in complex with a high-affinity radioligand.

    PubMed

    Jaremko, Mariusz; Jaremko, Łukasz; Giller, Karin; Becker, Stefan; Zweckstetter, Markus

    2016-04-01

    The integral polytopic membrane protein TSPO is the target for numerous endogenous and synthetic ligands. However, the affinity of many ligands is influenced by a common polymorphism in TSPO, in which an alanine at position 147 is replaced by threonine, thereby complicating the use of several radioligands for clinical diagnosis. In contrast, the best-characterized TSPO ligand (R)-PK11195 binds with similar affinity to both variants of mitochondrial TSPO (wild-type and A147T variant). Here we report the (1)H, (13)C, (15)N backbone and side-chain resonance assignment of the A147T polymorph of TSPO from Mus Musculus in complex with (R)-PK11195 in DPC detergent micelles. More than 90 % of all resonances were sequence-specifically assigned, demonstrating the ability to obtain high-quality spectral data for both the backbone and the side-chains of medically relevant integral membrane proteins. PMID:26364056

  15. 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.

  16. Attosecond Electron Delocalization in the Conduction Band through the Phosphate Backbone of Genomic DNA

    SciTech Connect

    Ikeura-Sekiguchi, Hiromi; Sekiguchi, Tetsuhiro

    2007-11-30

    Partial density of states in the empty conduction band of the phosphate backbone sites in DNA was probed using energy-dependent resonant Auger spectroscopy. Results show that genomic DNA with periodic backbones exhibits an extended state despite separation of each phosphate group by an insulating sugar group. In antisense DNA with an aperiodic backbone, the equivalent state is localized. Remarkably rapid electron delocalization occurs at ca. 740 attoseconds for wet DNA, as estimated using the core-hole clock method. Such delocalization is comparable to the Fermi velocity of carbon nanotubes.

  17. A Synthetic HIV-1 Subtype C Backbone Generates Comparable PR and RT Resistance Profiles to a Subtype B Backbone in a Recombinant Virus Assay

    PubMed Central

    Nauwelaers, David; Van Houtte, Margriet; Winters, Bart; Steegen, Kim; Van Baelen, Kurt; Chi, Ellen; Zhou, Mimi; Steiner, Derek; Bonesteel, Rachelle; Aston, Colin; Stuyver, Lieven J.

    2011-01-01

    In order to determine phenotypic protease and reverse transcriptase inhibitor-associated resistance in HIV subtype C virus, we have synthetically constructed an HIV-1 subtype C (HIV-1-C) viral backbone for use in a recombinant virus assay. The in silico designed viral genome was divided into 4 fragments, which were chemically synthesized and joined together by conventional subcloning. Subsequently, gag-protease-reverse-transcriptase (GPRT) fragments from 8 HIV-1 subtype C-infected patient samples were RT-PCR-amplified and cloned into the HIV-1-C backbone (deleted for GPRT) using In-Fusion reagents. Recombinant viruses (1 to 5 per patient sample) were produced in MT4-eGFP cells where cyto-pathogenic effect (CPE), p24 and Viral Load (VL) were monitored. The resulting HIV-1-C recombinant virus stocks (RVS) were added to MT4-eGFP cells in the presence of serial dilutions of antiretroviral drugs (PI, NNRTI, NRTI) to determine the fold-change in IC50 compared to the IC50 of wild-type HIV-1 virus. Additionally, viral RNA was extracted from the HIV-1-C RVS and the amplified GPRT products were used to generate recombinant virus in a subtype B backbone. Phenotypic resistance profiles in a subtype B and subtype C backbone were compared. The following observations were made: i) functional, infectious HIV-1 subtype C viruses were generated, confirmed by VL and p24 measurements; ii) their rate of infection was slower than viruses generated in the subtype B backbone; iii) they did not produce clear CPE in MT4 cells; and iv) drug resistance profiles generated in both backbones were very similar, including re-sensitizing effects like M184V on AZT. PMID:21629677

  18. Animal Protection and Structural Studies of a Consensus Sequence Vaccine Targeting the Receptor Binding Domain of the Type IV Pilus of Pseudomonas aeruginosa

    SciTech Connect

    Kao, Daniel J.; Churchill, Mair E.A.; Irvin, Randall T.; Hodges, Robert S.

    2008-09-23

    One of the main obstacles in the development of a vaccine against Pseudomonas aeruginosa is the requirement that it is protective against a wide range of virulent strains. We have developed a synthetic-peptide consensus-sequence vaccine (Cs1) that targets the host receptor-binding domain (RBD) of the type IV pilus of P. aeruginosa. Here, we show that this vaccine provides increased protection against challenge by the four piliated strains that we have examined (PAK, PAO, KB7 and P1) in the A.BY/SnJ mouse model of acute P. aeruginosa infection. To further characterize the consensus sequence, we engineered Cs1 into the PAK monomeric pilin protein and determined the crystal structure of the chimeric Cs1 pilin to 1.35 {angstrom} resolution. The substitutions (T130K and E135P) used to create Cs1 do not disrupt the conserved backbone conformation of the pilin RBD. In fact, based on the Cs1 pilin structure, we hypothesize that the E135P substitution bolsters the conserved backbone conformation and may partially explain the immunological activity of Cs1. Structural analysis of Cs1, PAK and K122-4 pilins reveal substitutions of non-conserved residues in the RBD are compensated for by complementary changes in the rest of the pilin monomer. Thus, the interactions between the RBD and the rest of the pilin can either be mediated by polar interactions of a hydrogen bond network in some strains or by hydrophobic interactions in others. Both configurations maintain a conserved backbone conformation of the RBD. Thus, the backbone conformation is critical in our consensus-sequence vaccine design and that cross-reactivity of the antibody response may be modulated by the composition of exposed side-chains on the surface of the RBD. This structure will guide our future vaccine design by focusing our investigation on the four variable residue positions that are exposed on the RBD surface.

  19. Animal protection and structural studies of a consensus sequence vaccine targeting the receptor binding domain of the type IV pilus of Pseudomonas aeruginosa.

    PubMed

    Kao, Daniel J; Churchill, Mair E A; Irvin, Randall T; Hodges, Robert S

    2007-11-23

    One of the main obstacles in the development of a vaccine against Pseudomonas aeruginosa is the requirement that it is protective against a wide range of virulent strains. We have developed a synthetic-peptide consensus-sequence vaccine (Cs1) that targets the host receptor-binding domain (RBD) of the type IV pilus of P. aeruginosa. Here, we show that this vaccine provides increased protection against challenge by the four piliated strains that we have examined (PAK, PAO, KB7 and P1) in the A.BY/SnJ mouse model of acute P. aeruginosa infection. To further characterize the consensus sequence, we engineered Cs1 into the PAK monomeric pilin protein and determined the crystal structure of the chimeric Cs1 pilin to 1.35 A resolution. The substitutions (T130K and E135P) used to create Cs1 do not disrupt the conserved backbone conformation of the pilin RBD. In fact, based on the Cs1 pilin structure, we hypothesize that the E135P substitution bolsters the conserved backbone conformation and may partially explain the immunological activity of Cs1. Structural analysis of Cs1, PAK and K122-4 pilins reveal substitutions of non-conserved residues in the RBD are compensated for by complementary changes in the rest of the pilin monomer. Thus, the interactions between the RBD and the rest of the pilin can either be mediated by polar interactions of a hydrogen bond network in some strains or by hydrophobic interactions in others. Both configurations maintain a conserved backbone conformation of the RBD. Thus, the backbone conformation is critical in our consensus-sequence vaccine design and that cross-reactivity of the antibody response may be modulated by the composition of exposed side-chains on the surface of the RBD. This structure will guide our future vaccine design by focusing our investigation on the four variable residue positions that are exposed on the RBD surface. PMID:17936788

  20. Analysis of microbial composition in acid whey for dairy fan making in Yunnan by conventional method and 16S rRNA sequencing.

    PubMed

    Liu, Wenjun; Sun, Zhihong; Zhang, Jiachao; Gao, Wa; Wang, Weihong; Wu, Lan; Sun, Tiansong; Chen, Wei; Liu, Xiaoming; Zhang, Heping

    2009-08-01

    Dairy fan is a traditional milk product made by adding 'acid juice' and heating up. It has been consumed by people of minority ethnic region in Yunnan Province of China for over 1,000 years. In order to improve the quality of dairy fan for further industrial-scale production, we investigated the microbial composition, especially Lactic Acid Bacteria (LAB), by conventional method and 16S rRNA sequences analysis in acid whey, which was the starter culture for traditional dairy fan making. Twenty samples of acid whey were collected from Yunnan. Ninety-one phylotypes of LAB were isolated from these samples and identified by conventional method and 16S rRNA sequencing analysis. The results showed that all isolates belonged to three genera and nine different species. Moreover, Lactobacillus helveticus was the predominant population among these samples, mesophilic and thermophilic LAB could be considered as the major microbial composition of acid whey in the Yunnan Province of China. This paper systematically studied the LAB composition of acid whey, which may be valuable for designing starter culture for dairy fan production. PMID:19459001

  1. Toward quantification of protein backbone–backbone hydrogen bonding energies: An energetic analysis of an amide-to-ester mutation in an α-helix within a protein

    PubMed Central

    Gao, Jianmin; Kelly, Jeffery W.

    2008-01-01

    Amide-to-ester backbone mutagenesis enables a specific backbone–backbone hydrogen bond (H-bond) in a protein to be eliminated in order to quantify its energetic contribution to protein folding. To extract a H-bonding free energy from an amide-to-ester perturbation free energy (ΔG folding,wt − ΔG folding,mut), it is necessary to correct for the putative introduction of a lone pair–lone pair electrostatic repulsion, as well as for the transfer free energy differences that may arise between the all amide sequence and the predominantly amide sequence harboring an ester bond. Mutation of the 9–10 amide bond within the V9F variant of the predominantly helical villin headpiece subdomain (HP35) to an ester or an E-olefin backbone bond results in a less stable but defined wild-type fold, an attribute required for this study. Comparing the folding free energies of the ester and E-olefin mutants, with correction for the desolvation free energy differences (ester and E-olefin) and the loss of an n-to-π* interaction (E-olefin), yields an experimentally based estimate of +0.4 kcal/mol for the O–O repulsion energy in an α-helical context, analogous to our previous experimentally based estimate of the O–O repulsion free energy in the context of a β-sheet. The small O–O repulsion energy indicates that amide-to-ester perturbation free energies can largely be attributed to the deletion of the backbone H-bonds after correction for desolvation differences. Quantitative evaluation of H-bonding in an α-helix should now be possible, an important step toward deciphering the balance of forces that enable spontaneous protein folding. PMID:18434500

  2. Chlorobenzoate catabolic transposon Tn5271 is a composite class I element with flanking class II insertion sequences.

    PubMed Central

    Nakatsu, C; Ng, J; Singh, R; Straus, N; Wyndham, C

    1991-01-01

    The structure of a transposon specifying the biodegradation of chlorobenzoate contaminants is described. Tn5271 is a 17-kilobase (kb) transposon that resides in the plasmid or chromosome of Alcaligenes sp. strain BR60 and allows this organism to grow on 3- and 4-chlorobenzoate. The transposon is flanked by a directly repeated sequence of 3201 base pairs (bp), which in turn is flanked by 110-bp inverted repeats. The 3.2-kb repeated sequence, designated IS1071, exists in multiple copies in the genome of Alcaligenes sp. strain BR60 and is involved in recombination of the catabolic genes into the chromosome of this strain. Sequence analysis revealed that the inverted repeat of IS1071 and the derived amino acid sequence of the single open reading frame within IS1071 are related to the inverted repeats and transposase (TnpA) proteins of the class II (Tn3 family) transposable elements. The absence of a resolvase gene within IS1071 suggests that this element is capable of determining the first step in class II transposition only. This was confirmed by observations on the IS1071-dependent formation of stable cointegrates in a recombination-deficient Escherichia coli. These results support an evolutionary scheme in which the class II transposable elements descended from simple insertion sequences. PMID:1656436

  3. Composite-180 Pulse-Based Symmetry Sequences to Recouple Proton Chemical Shift Anisotropy Tensors under Ultrafast MAS Solid-State NMR Spectroscopy

    PubMed Central

    Pandey, Manoj Kumar; Malon, Michal; Ramamoorthy, Ayyalusamy; Nishiyama, Yusuke

    2015-01-01

    There is considerable interest in the measurement of proton (1H) chemical shift anisotropy (CSA) tensors to obtain deeper insights into H-bonding interactions which find numerous applications in chemical and biological systems. However, the presence of strong 1H/1H dipolar interaction makes it difficult to determine small size 1H CSAs from the homogeneously broadened NMR spectra. Previously reported pulse sequences for 1H CSA recoupling are prone to the effects of radio frequency field (B1) inhomogeneity. In the present work we have carried out a systematic study using both numerical and experimental approaches to evaluate ?-encoded radio frequency (RF) pulse sequences based on R-symmetries that recouple 1H CSA in the indirect dimension of a 2D 1H/1H anisotropic/isotropic chemical shift correlation experiment under ultrafast magic angle spinning (MAS) frequencies. The spectral resolution and sensitivity can be significantly improved in both frequency dimensions of the 2D 1H/1H correlation spectrum without decoupling 1H/1H dipolar couplings but by using ultrafast MAS rates up to 70 kHz. We successfully demonstrate that with a reasonable RF field requirement (< 200 kHz) a set of symmetry-based recoupling sequences, with a series of phase-alternating 2700-90180 composite-180 pulses, are more robust in combating B1 inhomogeneity effects. In addition, our results show that the new pulse sequences render remarkable 1H CSA recoupling efficiency and undistorted CSA lineshapes. Experimental results on citric acid and malonic acid comparing the efficiencies of these newly developed pulse sequences with that of previously reported CSA recoupling pulse sequences are also reported under ultrafast MAS conditions. PMID:25497846

  4. Composite-180° pulse-based symmetry sequences to recouple proton chemical shift anisotropy tensors under ultrafast MAS solid-state NMR spectroscopy.

    PubMed

    Pandey, Manoj Kumar; Malon, Michal; Ramamoorthy, Ayyalusamy; Nishiyama, Yusuke

    2015-01-01

    There is considerable interest in the measurement of proton ((1)H) chemical shift anisotropy (CSA) tensors to obtain deeper insights into H-bonding interactions which find numerous applications in chemical and biological systems. However, the presence of strong (1)H/(1)H dipolar interaction makes it difficult to determine small size (1)H CSAs from the homogeneously broadened NMR spectra. Previously reported pulse sequences for (1)H CSA recoupling are prone to the effects of radio frequency field (B1) inhomogeneity. In the present work we have carried out a systematic study using both numerical and experimental approaches to evaluate γ-encoded radio frequency (RF) pulse sequences based on R-symmetries that recouple (1)H CSA in the indirect dimension of a 2D (1)H/(1)H anisotropic/isotropic chemical shift correlation experiment under ultrafast magic angle spinning (MAS) frequencies. The spectral resolution and sensitivity can be significantly improved in both frequency dimensions of the 2D (1)H/(1)H correlation spectrum without decoupling (1)H/(1)H dipolar couplings but by using ultrafast MAS rates up to 70 kHz. We successfully demonstrate that with a reasonable RF field requirement (<200 kHz) a set of symmetry-based recoupling sequences, with a series of phase-alternating 270°0-90°180 composite-180° pulses, are more robust in combating B1 inhomogeneity effects. In addition, our results show that the new pulse sequences render remarkable (1)H CSA recoupling efficiency and undistorted CSA lineshapes. Experimental results on citric acid and malonic acid comparing the efficiencies of these newly developed pulse sequences with that of previously reported CSA recoupling pulse sequences are also reported under ultrafast MAS conditions. PMID:25497846

  5. DNA extraction protocols cause differences in 16S rRNA amplicon sequencing efficiency but not in community profile composition or structure.

    PubMed

    Rubin, Benjamin E R; Sanders, Jon G; Hampton-Marcell, Jarrad; Owens, Sarah M; Gilbert, Jack A; Moreau, Corrie S

    2014-12-01

    The recent development of methods applying next-generation sequencing to microbial community characterization has led to the proliferation of these studies in a wide variety of sample types. Yet, variation in the physical properties of environmental samples demands that optimal DNA extraction techniques be explored for each new environment. The microbiota associated with many species of insects offer an extraction challenge as they are frequently surrounded by an armored exoskeleton, inhibiting disruption of the tissues within. In this study, we examine the efficacy of several commonly used protocols for extracting bacterial DNA from ants. While bacterial community composition recovered using Illumina 16S rRNA amplicon sequencing was not detectably biased by any method, the quantity of bacterial DNA varied drastically, reducing the number of samples that could be amplified and sequenced. These results indicate that the concentration necessary for dependable sequencing is around 10,000 copies of target DNA per microliter. Exoskeletal pulverization and tissue digestion increased the reliability of extractions, suggesting that these steps should be included in any study of insect-associated microorganisms that relies on obtaining microbial DNA from intact body segments. Although laboratory and analysis techniques should be standardized across diverse sample types as much as possible, minimal modifications such as these will increase the number of environments in which bacterial communities can be successfully studied. PMID:25257543

  6. DNA extraction protocols cause differences in 16S rRNA amplicon sequencing efficiency but not in community profile composition or structure

    SciTech Connect

    2014-12-01

    The recent development of methods applying next-generation sequencing to microbial community characterization has led to the proliferation of these studies in a wide variety of sample types. Yet, variation in the physical properties of environmental samples demands that optimal DNA extraction techniques be explored for each new environment. The microbiota associated with many species of insects offer an extraction challenge as they are frequently surrounded by an armored exoskeleton, inhibiting disruption of the tissues within. In this study, we examine the efficacy of several commonly used protocols for extracting bacterial DNA from ants. While bacterial community composition recovered using Illumina 16S rRNA amplicon sequencing was not detectably biased by any method, the quantity of bacterial DNA varied drastically, reducing the number of samples that could be amplified and sequenced. These results indicate that the concentration necessary for dependable sequencing is around 10,000 copies of target DNA per microliter. Exoskeletal pulverization and tissue digestion increased the reliability of extractions, suggesting that these steps should be included in any study of insect-associated microorganisms that relies on obtaining microbial DNA from intact body segments. Although laboratory and analysis techniques should be standardized across diverse sample types as much as possible, minimal modifications such as these will increase the number of environments in which bacterial communities can be successfully studied.

  7. DNA extraction protocols cause differences in 16S rRNA amplicon sequencing efficiency but not in community profile composition or structure

    DOE PAGESBeta

    None

    2014-12-01

    The recent development of methods applying next-generation sequencing to microbial community characterization has led to the proliferation of these studies in a wide variety of sample types. Yet, variation in the physical properties of environmental samples demands that optimal DNA extraction techniques be explored for each new environment. The microbiota associated with many species of insects offer an extraction challenge as they are frequently surrounded by an armored exoskeleton, inhibiting disruption of the tissues within. In this study, we examine the efficacy of several commonly used protocols for extracting bacterial DNA from ants. While bacterial community composition recovered using Illuminamore » 16S rRNA amplicon sequencing was not detectably biased by any method, the quantity of bacterial DNA varied drastically, reducing the number of samples that could be amplified and sequenced. These results indicate that the concentration necessary for dependable sequencing is around 10,000 copies of target DNA per microliter. Exoskeletal pulverization and tissue digestion increased the reliability of extractions, suggesting that these steps should be included in any study of insect-associated microorganisms that relies on obtaining microbial DNA from intact body segments. Although laboratory and analysis techniques should be standardized across diverse sample types as much as possible, minimal modifications such as these will increase the number of environments in which bacterial communities can be successfully studied.« less

  8. DNA extraction protocols cause differences in 16S rRNA amplicon sequencing efficiency but not in community profile composition or structure

    PubMed Central

    Rubin, Benjamin E R; Sanders, Jon G; Hampton-Marcell, Jarrad; Owens, Sarah M; Gilbert, Jack A; Moreau, Corrie S

    2014-01-01

    The recent development of methods applying next-generation sequencing to microbial community characterization has led to the proliferation of these studies in a wide variety of sample types. Yet, variation in the physical properties of environmental samples demands that optimal DNA extraction techniques be explored for each new environment. The microbiota associated with many species of insects offer an extraction challenge as they are frequently surrounded by an armored exoskeleton, inhibiting disruption of the tissues within. In this study, we examine the efficacy of several commonly used protocols for extracting bacterial DNA from ants. While bacterial community composition recovered using Illumina 16S rRNA amplicon sequencing was not detectably biased by any method, the quantity of bacterial DNA varied drastically, reducing the number of samples that could be amplified and sequenced. These results indicate that the concentration necessary for dependable sequencing is around 10,000 copies of target DNA per microliter. Exoskeletal pulverization and tissue digestion increased the reliability of extractions, suggesting that these steps should be included in any study of insect-associated microorganisms that relies on obtaining microbial DNA from intact body segments. Although laboratory and analysis techniques should be standardized across diverse sample types as much as possible, minimal modifications such as these will increase the number of environments in which bacterial communities can be successfully studied. PMID:25257543

  9. Bacillus mojavensis sp. nov., distinguishable from Bacillus subtilis by sexual isolation, divergence in DNA sequence, and differences in fatty acid composition.

    PubMed

    Roberts, M S; Nakamura, L K; Cohan, F M

    1994-04-01

    A number of Bacillus strains isolated from desert soil samples were shown to belong to a previously unidentified species, for which we propose the name Bacillus mojavensis. The type strain is RO-H-1 (= NRRL B-14698). On the basis of restriction digest data, B. mojavensis is most closely related to Bacillus amyloliquefaciens, Bacillus atrophaeus, and Bacillus subtilis. So far, B. mojavensis can be distinguished from B. subtilis only by differences in whole-cell fatty acid composition, divergence in DNA sequence, and resistance to genetic transformation between taxa (in addition to reduced genome relatedness values). Sequence divergence and sexual isolation may prove to be more useful than metabolic characteristics for delimiting cryptic Bacillus species. PMID:8186089

  10. Composite Sequence-Structure Stability Models as Screening Tools for Identifying Vulnerable Targets for HIV Drug and Vaccine Development.

    PubMed

    Manocheewa, Siriphan; Mittler, John E; Samudrala, Ram; Mullins, James I

    2015-11-01

    Rapid evolution and high sequence diversity enable Human Immunodeficiency Virus (HIV) populations to acquire mutations to escape antiretroviral drugs and host immune responses, and thus are major obstacles for the control of the pandemic. One strategy to overcome this problem is to focus drugs and vaccines on regions of the viral genome in which mutations are likely to cripple function through destabilization of viral proteins. Studies relying on sequence conservation alone have had only limited success in determining critically important regions. We tested the ability of two structure-based computational models to assign sites in the HIV-1 capsid protein (CA) that would be refractory to mutational change. The destabilizing mutations predicted by these models were rarely found in a database of 5811 HIV-1 CA coding sequences, with none being present at a frequency greater than 2%. Furthermore, 90% of variants with the low predicted stability (from a set of 184 CA variants whose replication fitness or infectivity has been studied in vitro) had aberrant capsid structures and reduced viral infectivity. Based on the predicted stability, we identified 45 CA sites prone to destabilizing mutations. More than half of these sites are targets of one or more known CA inhibitors. The CA regions enriched with these sites also overlap with peptides shown to induce cellular immune responses associated with lower viral loads in infected individuals. Lastly, a joint scoring metric that takes into account both sequence conservation and protein structure stability performed better at identifying deleterious mutations than sequence conservation or structure stability information alone. The computational sequence-structure stability approach proposed here might therefore be useful for identifying immutable sites in a protein for experimental validation as potential targets for drug and vaccine development. PMID:26556362

  11. High-throughput sequencing of 16S rDNA amplicons characterizes bacterial composition in cerebrospinal fluid samples from patients with purulent meningitis

    PubMed Central

    Liu, Aicui; Wang, Chao; Liang, Zhijuan; Zhou, Zhi-Wei; Wang, Lin; Ma, Qiaoli; Wang, Guowei; Zhou, Shu-Feng; Wang, Zhenhai

    2015-01-01

    Purulent meningitis (PM) is a severe infectious disease that is associated with high rates of morbidity and mortality. It has been recognized that bacterial infection is a major contributing factor to the pathogenesis of PM. However, there is a lack of information on the bacterial composition in PM, due to the low positive rate of cerebrospinal fluid bacterial culture. Herein, we aimed to discriminate and identify the main pathogens and bacterial composition in cerebrospinal fluid sample from PM patients using high-throughput sequencing approach. The cerebrospinal fluid samples were collected from 26 PM patients, and were determined as culture-negative samples. The polymerase chain reaction products of the hypervariable regions of 16S rDNA gene in these 26 samples of PM were sequenced using the 454 GS FLX system. The results showed that there were 71,440 pyrosequencing reads, of which, the predominant phyla were Proteobacteria and Firmicutes; and the predominant genera were Streptococcus, Acinetobacter, Pseudomonas, and Neisseria. The bacterial species in the cerebrospinal fluid were complex, with 61.5% of the samples presenting with mixed pathogens. A significant number of bacteria belonging to a known pathogenic potential was observed. The number of operational taxonomic units for individual samples ranged from six to 75 and there was a comparable difference in the species diversity that was calculated through alpha and beta diversity analysis. Collectively, the data show that high-throughput sequencing approach facilitates the characterization of the pathogens in cerebrospinal fluid and determine the abundance and the composition of bacteria in the cerebrospinal fluid samples of the PM patients, which may provide a better understanding of pathogens in PM and assist clinicians to make rational and effective therapeutic decisions. PMID:26300628

  12. Composites

    NASA Astrophysics Data System (ADS)

    Taylor, John G.

    The Composites market is arguably the most challenging and profitable market for phenolic resins aside from electronics. The variety of products and processes encountered creates the challenges, and the demand for high performance in critical operations brings value. Phenolic composite materials are rendered into a wide range of components to supply a diverse and fragmented commercial base that includes customers in aerospace (Space Shuttle), aircraft (interiors and brakes), mass transit (interiors), defense (blast protection), marine, mine ducting, off-shore (ducts and grating) and infrastructure (architectural) to name a few. For example, phenolic resin is a critical adhesive in the manufacture of honeycomb sandwich panels. Various solvent and water based resins are described along with resin characteristics and the role of metal ions for enhanced thermal stability of the resin used to coat the honeycomb. Featured new developments include pultrusion of phenolic grating, success in RTM/VARTM fabricated parts, new ballistic developments for military vehicles and high char yield carbon-carbon composites along with many others. Additionally, global regional market resin volumes and sales are presented and compared with other thermosetting resin systems.

  13. A highly selective and sensitive electrochemical CS-MWCNTs/Au-NPs composite DNA biosensor for Staphylococcus aureus gene sequence detection.

    PubMed

    Sun, Yange; He, Xingxing; Ji, Jian; Jia, Min; Wang, Zhouping; Sun, Xiulan

    2015-08-15

    This paper presents a new electrochemical DNA biosensor constructed using a substrate electrode composed of a novel nanocomposite material prepared using gold nanoparticles (Au-NPs) and multiwalled carbon nanotubes (MWCNTs) and further modified with an Au electrode (AuE), which was used as the substrate electrode. A single-stranded DNA (ssDNA) probe was immobilized on the Au-NPs/CS-MWCNTs/AuE electrode by means of facile gold-thiol affinity, which resulted in hybridization with the target ssDNA sequence. Hybridization reactions were assessed by using the reduction peak current of methylene blue (MB) as an electrochemical indicator. The advantages of the nanomaterials were found to include high surface area, favorable electronic properties, and strong electrocatalytic activity. The amount of ssDNA adsorbed on the electrode surface was increased and the electrochemical response of MB accelerated. The differential pulse voltammetric responses of MB were in line with the specific target ssDNA sequence within the concentration range 1.0×10(-15)-1.0×10(-8)M with the detection limit 3.3×10(-16)M (3σ). In the colony forming unit (CFU) we were able to detect 10CFU mL(-1)of Staphylococcus aureus in the tap water, achieving good discrimination ability between one- and three-base mismatched ssDNA sequences. The polymerase chain reaction (PCR) amplification products of S. aureus nuc gene sequence were also detected with satisfactory results. PMID:25966418

  14. Bacterial pathogens and community composition in advanced sewage treatment systems revealed by metagenomics analysis based on high-throughput sequencing.

    PubMed

    Lu, Xin; Zhang, Xu-Xiang; Wang, Zhu; Huang, Kailong; Wang, Yuan; Liang, Weigang; Tan, Yunfei; Liu, Bo; Tang, Junying

    2015-01-01

    This study used 454 pyrosequencing, Illumina high-throughput sequencing and metagenomic analysis to investigate bacterial pathogens and their potential virulence in a sewage treatment plant (STP) applying both conventional and advanced treatment processes. Pyrosequencing and Illumina sequencing consistently demonstrated that Arcobacter genus occupied over 43.42% of total abundance of potential pathogens in the STP. At species level, potential pathogens Arcobacter butzleri, Aeromonas hydrophila and Klebsiella pneumonia dominated in raw sewage, which was also confirmed by quantitative real time PCR. Illumina sequencing also revealed prevalence of various types of pathogenicity islands and virulence proteins in the STP. Most of the potential pathogens and virulence factors were eliminated in the STP, and the removal efficiency mainly depended on oxidation ditch. Compared with sand filtration, magnetic resin seemed to have higher removals in most of the potential pathogens and virulence factors. However, presence of the residual A. butzleri in the final effluent still deserves more concerns. The findings indicate that sewage acts as an important source of environmental pathogens, but STPs can effectively control their spread in the environment. Joint use of the high-throughput sequencing technologies is considered a reliable method for deep and comprehensive overview of environmental bacterial virulence. PMID:25938416

  15. Bacterial Pathogens and Community Composition in Advanced Sewage Treatment Systems Revealed by Metagenomics Analysis Based on High-Throughput Sequencing

    PubMed Central

    Lu, Xin; Zhang, Xu-Xiang; Wang, Zhu; Huang, Kailong; Wang, Yuan; Liang, Weigang; Tan, Yunfei; Liu, Bo; Tang, Junying

    2015-01-01

    This study used 454 pyrosequencing, Illumina high-throughput sequencing and metagenomic analysis to investigate bacterial pathogens and their potential virulence in a sewage treatment plant (STP) applying both conventional and advanced treatment processes. Pyrosequencing and Illumina sequencing consistently demonstrated that Arcobacter genus occupied over 43.42% of total abundance of potential pathogens in the STP. At species level, potential pathogens Arcobacter butzleri, Aeromonas hydrophila and Klebsiella pneumonia dominated in raw sewage, which was also confirmed by quantitative real time PCR. Illumina sequencing also revealed prevalence of various types of pathogenicity islands and virulence proteins in the STP. Most of the potential pathogens and virulence factors were eliminated in the STP, and the removal efficiency mainly depended on oxidation ditch. Compared with sand filtration, magnetic resin seemed to have higher removals in most of the potential pathogens and virulence factors. However, presence of the residual A. butzleri in the final effluent still deserves more concerns. The findings indicate that sewage acts as an important source of environmental pathogens, but STPs can effectively control their spread in the environment. Joint use of the high-throughput sequencing technologies is considered a reliable method for deep and comprehensive overview of environmental bacterial virulence. PMID:25938416

  16. Paleoproterozoic sequences and magmatic complexes of the Losevo suture zone of the Voronezh crystalline massif: Geological position, material composition, geochemistry, and paleogeodynamics

    NASA Astrophysics Data System (ADS)

    Terentiev, R. A.

    2014-03-01

    In order to resolve the contradictions associated with uncertainty in the identification of the material composition, subdivision, and conditions of formation of the Paleoproterozoic intrusive, metavolcanogenic, and metasedimentary sequences of the Losevo suture zone of the Voronezh crystalline massif, this work presents geological, petrographic, petrochemical, and geochemical features of these sequences. The stratigraphic and magmatic scheme of the central part of the Losevo suture zone is clarified. In particular, the Paleoproterozoic Losevo Series is divided into two sequences: Strelitsa (marginal sea) and Podgornoe (island arc). A new hypabyssal Novo-Voronezh metagabbro-diabase complex, comagmatic to metatholeiites of the Podgornoe sequence, is distinguished. The isotope age of the Strelitsa sequence is assumed to be 2172 ± 17 Ma on the basis of the results of age dating of zircon cores from the Usman plagiogranites, intruding this sequence. The upper age boundary of the Strelitsa sequence corresponds to the age of premetamorphic gabbro of the Rozhdestvenskoe complex, comagmatic to metavolcanites (2120 ± 11-2158 ± 43 Ma). The age of the Usman plagiogranite complex is clarified. On the basis of geological-structural and petrographic-mineralogical analyses of metavolcanogenic rocks, lithological analysis of metasedimentary formations, and new geochemical data obtained from metavolcanites and metamorphosed deposits, the pattern of paleogeodynamic evolution of the Losevo suture zone in the first half of the Paleoproterozoic is proposed. The next stages are distinguished: (1) intrusion of tholeiites of transition T-MORB type in spreading zones and deposition of terrigenous strata in the marginal sea basins; (2) intrusion of Nb-depleted tholeiites and plagiorhyolites, the geochemical characteristics indicating their formation in the subduction setting; (3) intrusion of gabbroids of the Rozhdestvenskoe complex; (4) formation of an island arc synchronously with stage 2, tholeiitic and calc-alkaline (Podgornoe sequence) volcanism; (5) intrusions of gabbro-diabases, subsynchronous to volcanism, of the Novovoronezh complex and diorite-granitoides, crystallization of granitoides of the Usman complex; (6) a break in sedimentation and formation of molasses of the Voronezh (Somovo) Formation.

  17. Using self-consistent fields to bias Monte Carlo methods with applications to designing and sampling protein sequences

    NASA Astrophysics Data System (ADS)

    Zou, Jinming; Saven, Jeffery G.

    2003-02-01

    For complex multidimensional systems, Monte Carlo methods are useful for sampling probable regions of a configuration space and, in the context of annealing, for determining "low energy" or "high scoring" configurations. Such methods have been used in protein design as means to identify amino acid sequences that are energetically compatible with a particular backbone structure. As with many other applications of Monte Carlo methods, such searches can be inefficient if trial configurations (protein sequences) in the Markov chain are chosen randomly. Here a mean-field biased Monte Carlo method (MFBMC) is presented and applied to designing and sampling protein sequences. The MFBMC method uses predetermined sequence identity probabilities wi(α) to bias the sequence selection. The wi(α) are calculated using a self-consistent, mean-field theory that can estimate the number and composition of sequences having predetermined values of energetically related foldability criteria. The MFBMC method is applied to both a simple protein model, the 27-mer lattice model, and an all-atom protein model. Compared to conventional Monte Carlo (MC) and configurational bias Monte Carlo (BMC), the MFBMC method converges faster to low energy sequences and samples such sequences more efficiently. The MFBMC method also tolerates faster cooling rates than the MC and BMC methods. The MFBMC method can be applied not only to protein sequence search, but also to a wide variety of polymeric and condensed phase systems.

  18. Optical Characterization of Semiconducting Natural Rubber Nanoparticles and its Composites

    NASA Astrophysics Data System (ADS)

    Neena, P.; Mathew, Anisha Mary

    2011-10-01

    The present work explains optical properties of semiconducting natural rubber nanoparticles from pristine natural rubber by doping. The studies give evidence that the SbCl5 is an efficient dopant for natural rubber. The mechanism of conduction predominantly involves the formation of conjugated sequence of unsaturated double bond in the polymer backbone. Examination of the UV/Vis study reveals the formation of charge transfer complexes in the polymer back bone. Particle filled elastomeric composites have become attractive owing to their low cost and widespread industrial applications. The arrival of nanometer fillers to polymer materials is a promising channel for their property modification. Natural rubber composite is prepared by mixing the pristine natural rubber with semiconducting natural rubber powder.

  19. Composites

    NASA Astrophysics Data System (ADS)

    Chmielewski, M.; Nosewicz, S.; Pietrzak, K.; Rojek, J.; Strojny-Nędza, A.; Mackiewicz, S.; Dutkiewicz, J.

    2014-11-01

    It is commonly known that the properties of sintered materials are strongly related to technological conditions of the densification process. This paper shows the sintering behavior of a NiAl-Al2O3 composite, and its individual components sintered separately. Each kind of material was processed via the powder metallurgy route (hot pressing). The progress of sintering at different stages of the process was tested. Changes in the microstructure were examined using scanning and transmission electron microscopy. Metal-ceramics interface was clean and no additional phases were detected. Correlation between the microstructure, density, and mechanical properties of the sintered materials was analyzed. The values of elastic constants of NiAl/Al2O3 were close to intermetallic ones due to the volume content of the NiAl phase particularly at low densities, where small alumina particles had no impact on the composite's stiffness. The influence of the external pressure of 30 MPa seemed crucial for obtaining satisfactory stiffness for three kinds of the studied materials which were characterized by a high dense microstructure with a low number of isolated spherical pores.

  20. Backbone NMR reveals allosteric signal transduction networks in the β1-adrenergic receptor.

    PubMed

    Isogai, Shin; Deupi, Xavier; Opitz, Christian; Heydenreich, Franziska M; Tsai, Ching-Ju; Brueckner, Florian; Schertler, Gebhard F X; Veprintsev, Dmitry B; Grzesiek, Stephan

    2016-02-11

    G protein-coupled receptors (GPCRs) are physiologically important transmembrane signalling proteins that trigger intracellular responses upon binding of extracellular ligands. Despite recent breakthroughs in GPCR crystallography, the details of ligand-induced signal transduction are not well understood owing to missing dynamical information. In principle, such information can be provided by NMR, but so far only limited data of functional relevance on few side-chain sites of eukaryotic GPCRs have been obtained. Here we show that receptor motions can be followed at virtually any backbone site in a thermostabilized mutant of the turkey β1-adrenergic receptor (β1AR). Labelling with [(15)N]valine in a eukaryotic expression system provides over twenty resolved resonances that report on structure and dynamics in six ligand complexes and the apo form. The response to the various ligands is heterogeneous in the vicinity of the binding pocket, but gets transformed into a homogeneous readout at the intracellular side of helix 5 (TM5), which correlates linearly with ligand efficacy for the G protein pathway. The effect of several pertinent, thermostabilizing point mutations was assessed by reverting them to the native sequence. Whereas the response to ligands remains largely unchanged, binding of the G protein mimetic nanobody NB80 and G protein activation are only observed when two conserved tyrosines (Y227 and Y343) are restored. Binding of NB80 leads to very strong spectral changes throughout the receptor, including the extracellular ligand entrance pocket. This indicates that even the fully thermostabilized receptor undergoes activating motions in TM5, but that the fully active state is only reached in presence of Y227 and Y343 by stabilization with a G protein-like partner. The combined analysis of chemical shift changes from the point mutations and ligand responses identifies crucial connections in the allosteric activation pathway, and presents a general experimental method to delineate signal transmission networks at high resolution in GPCRs. PMID:26840483

  1. 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. PMID:25843303

  2. Backbone resonance assignments for G protein ?(i3) subunit in the GDP-bound state.

    PubMed

    Mase, Yoko; Yokogawa, Mariko; Osawa, Masanori; Shimada, Ichio

    2014-10-01

    Guanine-nucleotide binding proteins (G proteins) serve as molecular switches in signaling pathways, by coupling the activation of G protein-coupled receptors (GPCRs) at the cell surface to intracellular responses. In the resting state, G protein forms a heterotrimer, consisting of the G protein ? subunit with GDP (G?GDP) and the G protein ?? subunit (G??). Ligand binding to GPCRs promotes the GDP-GTP exchange on G?, leading to the dissociation of the GTP-bound form of G? (G?GTP) and G??. Then, G?GTP and G?? bind to their downstream effector enzymes or ion channels and regulate their activities, leading to a variety of cellular responses. Finally, G? hydrolyzes the bound GTP to GDP and returns to the resting state by re-associating with G??. The G proteins are classified with four major families based on the amino acid sequences of G?: i/o, s, q/11, and 12/13. Here, we established the backbone resonance assignments of human G?i3, a member of the i/o family with a molecular weight of 41 K, in complex with GDP. The chemical shifts were compared with those of G?(i3) in complex with a GTP-analogue, GTP?S, which we recently reported, indicating that the residues with significant chemical shift differences are mostly consistent with the regions with the structural differences between the GDP- and GTP?S-bound states, as indicated in the crystal structures. The assignments of G?(i3)GDP would be useful for the analyses of the dynamics of G?(i3) and its interactions with various target molecules. PMID:23771857

  3. iTIS-PseTNC: a sequence-based predictor for identifying translation initiation site in human genes using pseudo trinucleotide composition.

    PubMed

    Chen, Wei; Feng, Peng-Mian; Deng, En-Ze; Lin, Hao; Chou, Kuo-Chen

    2014-10-01

    Translation is a key process for gene expression. Timely identification of the translation initiation site (TIS) is very important for conducting in-depth genome analysis. With the avalanche of genome sequences generated in the postgenomic age, it is highly desirable to develop automated methods for rapidly and effectively identifying TIS. Although some computational methods were proposed in this regard, none of them considered the global or long-range sequence-order effects of DNA, and hence their prediction quality was limited. To count this kind of effects, a new predictor, called "iTIS-PseTNC," was developed by incorporating the physicochemical properties into the pseudo trinucleotide composition, quite similar to the PseAAC (pseudo amino acid composition) approach widely used in computational proteomics. It was observed by the rigorous cross-validation test on the benchmark dataset that the overall success rate achieved by the new predictor in identifying TIS locations was over 97%. As a web server, iTIS-PseTNC is freely accessible at http://lin.uestc.edu.cn/server/iTIS-PseTNC. To maximize the convenience of the vast majority of experimental scientists, a step-by-step guide is provided on how to use the web server to obtain the desired results without the need to go through detailed mathematical equations, which are presented in this paper just for the integrity of the new prection method. PMID:25016190

  4. Native sequence determines sidechain packing in a protein, but does optimal sidechain packing determine the native sequence?

    SciTech Connect

    Koehl, P.; Delarue, M.

    1996-12-31

    Globular proteins have highly compact structures and the corresponding packing interactions are widely considered as the principal determinant of the native structure. It is therefore important that theoretical approaches to protein design explicitly take packing into account, which requires that a full atomic representation of the designed protein is maintained. As a first step towards this goal, we have developed in this report an inverse folding algorithm with the aim of specifically designing amino acid sequences which optimize sidechain packing for a given protein fold. The design is performed by a global Monte Carlo optimization in sequence space, with constant amino acid composition and a full-atom representation of the various protein models. Packing is defined by a Lennard-Jones potential. The program was tested by designing stable sequence variants for the chymotrypsin inhibitor fold. The final protein models showed an increase in intramolecular atomic contacts and a decrease in the overall volume compared to the native structure. Starting from the backbone only of the target structure, the algorithm did gradually retrieve reliable though limited sequence information. Higher compatibility might be achieved by improving the potential, however our results suggest that packing interactions are an essential element of a yet-to-be-defined successful energy function for protein design. 44 refs., 5 figs.

  5. Deriving High-Resolution Protein Backbone Structure Propensities from All Crystal Data Using the Information Maximization Device

    PubMed Central

    Solis, Armando D.

    2014-01-01

    The most informative probability distribution functions (PDFs) describing the Ramachandran phi-psi dihedral angle pair, a fundamental descriptor of backbone conformation of protein molecules, are derived from high-resolution X-ray crystal structures using an information-theoretic approach. The Information Maximization Device (IMD) is established, based on fundamental information-theoretic concepts, and then applied specifically to derive highly resolved phi-psi maps for all 20 single amino acid and all 8000 triplet sequences at an optimal resolution determined by the volume of current data. The paper shows that utilizing the latent information contained in all viable high-resolution crystal structures found in the Protein Data Bank (PDB), totaling more than 77,000 chains, permits the derivation of a large number of optimized sequence-dependent PDFs. This work demonstrates the effectiveness of the IMD and the superiority of the resulting PDFs by extensive fold recognition experiments and rigorous comparisons with previously published triplet PDFs. Because it automatically optimizes PDFs, IMD results in improved performance of knowledge-based potentials, which rely on such PDFs. Furthermore, it provides an easy computational recipe for empirically deriving other kinds of sequence-dependent structural PDFs with greater detail and precision. The high-resolution phi-psi maps derived in this work are available for download. PMID:24896099

  6. Whole-rock geochemistry and Sr-Nd isotopic composition of the pre-rift sequence of the Camamu Basin, northeastern Brazil

    NASA Astrophysics Data System (ADS)

    Silva, D. R. A.; Mizusaki, A. M. P.; Milani, E. J.; Pimentel, M.; Kawashita, K.

    2012-11-01

    Whole-rock geochemistry, combined with Sr-Nd isotopic composition of pelitic sedimentary rocks, have been considered to be useful parameters to estimate not only their provenance but also to make inferences about their depositional environment as well as the weathering processes they have been through. The basal sedimentary units of the basins of the northeastern Brazilian continental margin, particularly those of the pre-rift sequence, have been subject of interest of studies based on chemical and isotopic data, since they lack fossil content to establish their age and, therefore, stratigraphic correlations are difficult. The major and trace element contents as well as Sr-Nd isotopic compositions of whole-rock shale samples from five outcrops attributed to the pre-rift supersequence of the Camamu Basin were analyzed with the purpose of characterizing and obtaining further information that would allow a better correlation between the sites studied. The geochemical data suggest that the rocks exposed in the studied outcrops are part of the same sedimentary unit and that they might be correlated to the Capianga Member of the Aliana Formation of the Recncavo Basin, exposed to the north of the Camamu Basin. The chemical index of alteration (CIA) suggests conditions associated with a humid tropical/subtropical climate at the time of deposition. Nd isotopic compositions indicate provenance from the Paleoproterozoic rocks of the Sao Francisco craton. The results presented here, therefore, show that the combined use of chemical and isotopic analyses may be of great interest to characterize and correlate lithologically homogeneous clastic sedimentary sequences.

  7. The role of detrital composition and climate on the diagenetic evolution of continental molasses: evidence from the Cambro—Ordovician guaritas sequence, southern Brazil

    NASA Astrophysics Data System (ADS)

    De Ros, Luiz F.; Morad, S.; Paim, Paulo S. G.

    1994-09-01

    The Cambro-Ordovician molassic Guaritas Sequence (Camaquã Basin, southern Brazil) comprises alluvial-fan and braided fluvial sandstones and conglomerates with intercalated aeolian and lacustrine-deltaic deposits and andesitic lava flows. The sediments display a complex detrital composition derived from plutonic/gneissic, acidic volcanic and low-grade metamorphic source rocks. This detrital assemblage was strongly modified by semi-arid continental near-surface diagenesis. Early cementation by hematite, smectite, quartz and calcite, and the relatively limited burial prevented strong compaction and preserved some primary macroporosity in most of the sandstones, whereas the absence of early cements and/or abundance of ductile grains promoted substantial porosity destruction by compaction and the inhibition of further diagenetic modifications. The diagenetic dissolution and replacement of volcanic rock fragments and detrital feldspars by clays and albite changed the original framework composition, as well as the tectonic provenance classification of the sandstones. Detailed quantitative petrographic study allowed the reconstruction of the original detrital compositions and the distinction of six different pathways of diagenetic evolution of the sandstones, attesting to the efficiency of this method for diagenetic modelling and provenance analyses of ancient sandstones.

  8. Emergence of Sequence Type 779 Methicillin-Resistant Staphylococcus aureus Harboring a Novel Pseudo Staphylococcal Cassette Chromosome mec (SCCmec)-SCC-SCCCRISPR Composite Element in Irish Hospitals

    PubMed Central

    Kinnevey, Peter M.; Shore, Anna C.; Brennan, Grainne I.; Sullivan, Derek J.; Ehricht, Ralf; Monecke, Stefan; Slickers, Peter

    2013-01-01

    Methicillin-resistant Staphylococcus aureus (MRSA) has been a major cause of nosocomial infection in Irish hospitals for 4 decades, and replacement of predominant MRSA clones has occurred several times. An MRSA isolate recovered in 2006 as part of a larger study of sporadic MRSA exhibited a rare spa (t878) and multilocus sequence (ST779) type and was nontypeable by PCR- and DNA microarray-based staphylococcal cassette chromosome mec (SCCmec) element typing. Whole-genome sequencing revealed the presence of a novel 51-kb composite island (CI) element with three distinct domains, each flanked by direct repeat and inverted repeat sequences, including (i) a pseudo SCCmec element (16.3 kb) carrying mecA with a novel mec class region, a fusidic acid resistance gene (fusC), and two copper resistance genes (copB and copC) but lacking ccr genes; (ii) an SCC element (17.5 kb) carrying a novel ccrAB4 allele; and (iii) an SCC element (17.4 kb) carrying a novel ccrC allele and a clustered regularly interspaced short palindromic repeat (CRISPR) region. The novel CI was subsequently identified by PCR in an additional 13 t878/ST779 MRSA isolates, six from bloodstream infections, recovered between 2006 and 2011 in 11 hospitals. Analysis of open reading frames (ORFs) carried by the CI showed amino acid sequence similarity of 44 to 100% to ORFs from S. aureus and coagulase-negative staphylococci (CoNS). These findings provide further evidence of genetic transfer between S. aureus and CoNS and show how this contributes to the emergence of novel SCCmec elements and MRSA strains. Ongoing surveillance of this MRSA strain is warranted and will require updating of currently used SCCmec typing methods. PMID:23147725

  9. Incorporating substrate sequence motifs and spatial amino acid composition to identify kinase-specific phosphorylation sites on protein three-dimensional structures

    PubMed Central

    2013-01-01

    Background Protein phosphorylation catalyzed by kinases plays crucial regulatory roles in cellular processes. Given the high-throughput mass spectrometry-based experiments, the desire to annotate the catalytic kinases for in vivo phosphorylation sites has motivated. Thus, a variety of computational methods have been developed for performing a large-scale prediction of kinase-specific phosphorylation sites. However, most of the proposed methods solely rely on the local amino acid sequences surrounding the phosphorylation sites. An increasing number of three-dimensional structures make it possible to physically investigate the structural environment of phosphorylation sites. Results In this work, all of the experimental phosphorylation sites are mapped to the protein entries of Protein Data Bank by sequence identity. It resulted in a total of 4508 phosphorylation sites containing the protein three-dimensional (3D) structures. To identify phosphorylation sites on protein 3D structures, this work incorporates support vector machines (SVMs) with the information of linear motifs and spatial amino acid composition, which is determined for each kinase group by calculating the relative frequencies of 20 amino acid types within a specific radial distance from central phosphorylated amino acid residue. After the cross-validation evaluation, most of the kinase-specific models trained with the consideration of structural information outperform the models considering only the sequence information. Furthermore, the independent testing set which is not included in training set has demonstrated that the proposed method could provide a comparable performance to other popular tools. Conclusion The proposed method is shown to be capable of predicting kinase-specific phosphorylation sites on 3D structures and has been implemented as a web server which is freely accessible at http://csb.cse.yzu.edu.tw/PhosK3D/. Due to the difficulty of identifying the kinase-specific phosphorylation sites with similar sequenced motifs, this work also integrates the 3D structural information to improve the cross classifying specificity. PMID:24564522

  10. Purifying selection, sequence composition, and context-specific indel mutations shape intraspecific variation in a bacterial endosymbiont.

    PubMed

    Williams, Laura E; Wernegreen, Jennifer J

    2012-01-01

    Comparative genomics of closely related bacterial strains can clarify mutational processes and selective forces that impact genetic variation. Among primary bacterial endosymbionts of insects, such analyses have revealed ongoing genome reduction, raising questions about the ultimate evolutionary fate of these partnerships. Here, we explored genomic variation within Blochmannia vafer, an obligate mutualist of the ant Camponotus vafer. Polymorphism analysis of the Illumina data set used previously for de novo assembly revealed a second Bl. vafer genotype. To determine why a single ant colony contained two symbiont genotypes, we examined polymorphisms in 12 C. vafer mitochondrial sequences assembled from the Illumina data; the spectrum of variants suggests that the colony contained two maternal lineages, each harboring a distinct Bl. vafer genotype. Comparing the two Bl. vafer genotypes revealed that purifying selection purged most indels and nonsynonymous differences from protein-coding genes. We also discovered that indels occur frequently in multimeric simple sequence repeats, which are relatively abundant in Bl. vafer and may play a more substantial role in generating variation in this ant mutualist than in the aphid endosymbiont Buchnera. Finally, we explored how an apparent relocation of the origin of replication in Bl. vafer and the resulting shift in strand-associated mutational pressures may have caused accelerated gene loss and an elevated rate of indel polymorphisms in the region spanning the origin relocation. Combined, these results point to significant impacts of purifying selection on genomic polymorphisms as well as distinct patterns of indels associated with unusual genomic features of Blochmannia. PMID:22117087

  11. Fast Bayesian identification of a class of elastic weakly nonlinear systems using backbone curves

    NASA Astrophysics Data System (ADS)

    Hill, T. L.; Green, P. L.; Cammarano, A.; Neild, S. A.

    2016-01-01

    This paper introduces a method for the identification of the parameters of nonlinear structures using a probabilistic Bayesian framework, employing a Markov chain Monte Carlo algorithm. This approach uses analytical models to describe the unforced, undamped dynamic responses of structures in the frequency-amplitude domain, known as the backbone curves. The analytical models describing these backbone curves are then fitted to measured responses, found using the resonant-decay method. To investigate the proposed identification method, a nonlinear two-degree-of-freedom example structure is simulated numerically and analytical expressions describing the backbone curves are found. These expressions are then used, in conjunction with the backbone curve data found through simulated experiment, to estimate the system parameters. It is shown that the use of these computationally-cheap analytical expressions allows for an extremely efficient method for modelling the dynamic behaviour, providing an identification procedure that is both fast and accurate. Furthermore, for the example structure, it is shown that the estimated parameters may be used to accurately predict the existence of dynamic behaviours that are well-away from the backbone curve data provided; specifically the existence of an isola is predicted.

  12. Liquid crystall elastomers as artificial muscles: role of side-chain-backbone coupling

    NASA Astrophysics Data System (ADS)

    Ratna, Banahalli R.; Thomsen, D. Laurence, III; Keller, Patrick

    2001-07-01

    Ordered liquid crystal elastomer films exhibit anisotropic deformations on macroscopic length scales on changing the orientational order of the liquid crystal group by external stimuli such as temperature and electric field. We have developed laterally attached side-chain nematic elastomers with mechanical properties approaching stress, strain and time scale of skeletal muscle activation. The mechanical and structural characterization has led to the ability to improve desired physical properties such as backbone extension and coupling between the backbone and liquid crystal side chain. We have studied the effect of the coupling length on the change in the conformational entropy of the backbone and the viscoelastic behavior. In this paper we discuss the results of our stress relaxation tests.

  13. Protein Geometry Database: a flexible engine to explore backbone conformations and their relationships to covalent geometry

    PubMed Central

    Berkholz, Donald S.; Krenesky, Peter B.; Davidson, John R.; Karplus, P. Andrew

    2010-01-01

    The backbone bond lengths, bond angles, and planarity of a protein are influenced by the backbone conformation (φ,Ψ), but no tool exists to explore these relationships, leaving this area as a reservoir of untapped information about protein structure and function. The Protein Geometry Database (PGD) enables biologists to easily and flexibly query information about the conformation alone, the backbone geometry alone, and the relationships between them. The capabilities the PGD provides are valuable for assessing the uniqueness of observed conformational or geometric features in protein structure as well as discovering novel features and principles of protein structure. The PGD server is available at http://pgd.science.oregonstate.edu/ and the data and code underlying it are freely available to use and extend. PMID:19906726

  14. Side-Chain-Induced Rigid Backbone Organization of Polymer Semiconductors through Semifluoroalkyl Side Chains.

    PubMed

    Kang, Boseok; Kim, Ran; Lee, Seon Baek; Kwon, Soon-Ki; Kim, Yun-Hi; Cho, Kilwon

    2016-03-23

    While high-mobility p-type conjugated polymers have been widely reported, high-mobility n-type conjugated polymers are still rare. In the present work, we designed semifluorinated alkyl side chains and introduced them into naphthalene diimide-based polymers (PNDIF-T2 and PNDIF-TVT). We found that the strong self-organization of these side chains induced a high degree of order in the attached polymer backbones by forming a superstructure composed of "backbone crystals" and "side-chain crystals". This phenomenon was shown to greatly enhance the ordering along the backbone direction, and the resulting polymers thus exhibited unipolar n-channel transport in field-effect transistors with remarkably high electron mobility values of up to 6.50 cm(2) V(-1) s(-1) and with a high on-off current ratio of 10(5). PMID:26653799

  15. Cross-backbone templating; ribodinucleotides made on poly(C)

    PubMed Central

    Majerfeld, Irene; Puthenvedu, Deepa; Yarus, Michael

    2016-01-01

    G5′pp5′G synthesis from pG and chemically activated 2MeImpG is accelerated by the addition of complementary poly(C), but affected only slightly by poly(G) and not at all by poly(U) and poly(A). This suggests that 3′–5′ poly(C) is a template for uncatalyzed synthesis of 5′–5′ GppG, as was poly(U) for AppA synthesis, previously. The reaction occurs at 50 mM mono- and divalent ion concentrations, at moderate temperatures, and near pH 7. The reactive complex at the site of enhanced synthesis of 5′–5′ GppG seems to contain a single pG, a single phosphate-activated nucleotide 2MeImpG, and a single strand of poly(C). Most likely this structure is base-paired, as the poly(C)-enhanced reaction is completely disrupted between 30 and 37°C, whereas slower, untemplated synthesis of GppG accelerates. More specifically, the reactive center acts as would be expected for short, isolated G nucleotide stacks expanded and ordered by added poly(C). For example, poly(C)-mediated GppG production is very nonlinear in overall nucleotide concentration. Uncatalyzed NppN synthesis is now known for two polymers and their complementary free nucleotides. These data suggest that varied, simple, primordial 3′–5′ RNA sequences could express a specific chemical phenotype by encoding synthesis of complementary, reactive, coenzyme-like 5′–5′ ribodinucleotides. PMID:26759450

  16. 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.

  17. Lactobacillus rhamnosus Accelerates Zebrafish Backbone Calcification and Gonadal Differentiation through Effects on the GnRH and IGF Systems

    PubMed Central

    Avella, Matteo A.; Place, Allen; Du, Shao-Jun; Williams, Ernest; Silvi, Stefania; Zohar, Yonathan; Carnevali, Oliana

    2012-01-01

    Endogenous microbiota play essential roles in the host’s immune system, physiology, reproduction and nutrient metabolism. We hypothesized that a continuous administration of an exogenous probiotic might also influence the host’s development. Thus, we treated zebrafish from birth to sexual maturation (2-months treatment) with Lactobacillus rhamnosus, a probiotic species intended for human use. We monitored for the presence of L. rhamnosus during the entire treatment. Zebrafish at 6 days post fertilization (dpf) exhibited elevated gene expression levels for Insulin-like growth factors -I and -II, Peroxisome proliferator activated receptors -α and -β, VDR-α and RAR-γ when compared to untreated-10 days old zebrafish. Using a gonadotropin-releasing hormone 3 GFP transgenic zebrafish (GnRH3-GFP), higher GnRH3 expression was found at 6, 8 and 10 dpf upon L. rhamnosus treatment. The same larvae exhibited earlier backbone calcification and gonad maturation. Noteworthy in the gonad development was the presence of first testes differentiation at 3 weeks post fertilization in the treated zebrafish population -which normally occurs at 8 weeks- and a dramatic sex ratio modulation (93% females, 7% males in control vs. 55% females, 45% males in the treated group). We infer that administration of L. rhamnosus stimulated the IGF system, leading to a faster backbone calcification. Moreover we hypothesize a role for administration of L. rhamnosus on GnRH3 modulation during early larval development, which in turn affects gonadal development and sex differentiation. These findings suggest a significant role of the microbiota composition on the host organism development profile and open new perspectives in the study of probiotics usage and application. PMID:23029107

  18. Lactobacillus rhamnosus accelerates zebrafish backbone calcification and gonadal differentiation through effects on the GnRH and IGF systems.

    PubMed

    Avella, Matteo A; Place, Allen; Du, Shao-Jun; Williams, Ernest; Silvi, Stefania; Zohar, Yonathan; Carnevali, Oliana

    2012-01-01

    Endogenous microbiota play essential roles in the host's immune system, physiology, reproduction and nutrient metabolism. We hypothesized that a continuous administration of an exogenous probiotic might also influence the host's development. Thus, we treated zebrafish from birth to sexual maturation (2-months treatment) with Lactobacillus rhamnosus, a probiotic species intended for human use. We monitored for the presence of L. rhamnosus during the entire treatment. Zebrafish at 6 days post fertilization (dpf) exhibited elevated gene expression levels for Insulin-like growth factors -I and -II, Peroxisome proliferator activated receptors -α and -β, VDR-α and RAR-γ when compared to untreated-10 days old zebrafish. Using a gonadotropin-releasing hormone 3 GFP transgenic zebrafish (GnRH3-GFP), higher GnRH3 expression was found at 6, 8 and 10 dpf upon L. rhamnosus treatment. The same larvae exhibited earlier backbone calcification and gonad maturation. Noteworthy in the gonad development was the presence of first testes differentiation at 3 weeks post fertilization in the treated zebrafish population -which normally occurs at 8 weeks- and a dramatic sex ratio modulation (93% females, 7% males in control vs. 55% females, 45% males in the treated group). We infer that administration of L. rhamnosus stimulated the IGF system, leading to a faster backbone calcification. Moreover we hypothesize a role for administration of L. rhamnosus on GnRH3 modulation during early larval development, which in turn affects gonadal development and sex differentiation. These findings suggest a significant role of the microbiota composition on the host organism development profile and open new perspectives in the study of probiotics usage and application. PMID:23029107

  19. Evaluation of composition and individual variability of rumen microbiota in yaks by 16S rRNA high-throughput sequencing technology.

    PubMed

    Guo, Wei; Li, Ying; Wang, Lizhi; Wang, Jiwen; Xu, Qin; Yan, Tianhai; Xue, Bai

    2015-08-01

    The Yak (Bos grunniens) is a unique species of ruminant animals that is important to agriculture of the Tibetan plateau, and has a complex intestinal microbial community. The objective of the present study was to characterize the composition and individual variability of microbiota in the rumen of yaks using 16S rRNA gene high-throughput sequencing technique. Rumen samples used in the present study were obtained from grazing adult male yaks (n = 6) in a commercial farm in Ganzi Autonomous Prefecture of Sichuan Province, China. Universal prokaryote primers were used to target the V4-V5 hypervariable region of 16S rRNA gene. A total of 7200 operational taxonomic units (OTUs) were obtained after sequence filtering and chimera removal. Within these OTUs, 0.56% belonged to Archaea (40 OTUs), 7.19% to unassigned species (518 OTUs), and the remaining OTUs (6642) in all samples were of bacterial origin. When examining the community structure of bacteria, we identified 23 phyla within 159 families after taxonomic summarization. Bacteroidetes and Firmicutes were the predominant phyla accounting for 39.68% (SD = 0.05) and 45.90% (SD = 0.06), respectively. Moreover, 3764 OTUs were identified as shared OTUs (i.e. represented in all yaks) and belonged to 35 genera, exhibiting highly variable abundance across individual samples. Phylogenetic placement of these genera across individual samples was examined. In addition, we evaluated the distance among the 6 rumen samples by adding taxon phylogeny using UniFrac, representing 24.1% of average distance. In summary, the current study reveals a shared rumen microbiome and phylogenetic lineage and presents novel information on composition and individual variability of the bacterial community in the rumen of yaks. PMID:25911445

  20. Electric field induced localization phenomena in a ladder network with superlattice configuration: Effect of backbone environment

    SciTech Connect

    Dutta, Paramita; Karmakar, S. N.; Maiti, Santanu K.

    2014-09-15

    Electric field induced localization properties of a tight-binding ladder network in presence of backbone sites are investigated. Based on Green's function formalism we numerically calculate two-terminal transport together with density of states for different arrangements of atomic sites in the ladder and its backbone. Our results lead to a possibility of getting multiple mobility edges which essentially plays a switching action between a completely opaque to fully or partly conducting region upon the variation of system Fermi energy, and thus, support in fabricating mesoscopic or DNA-based switching devices.

  1. 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 chain cavities in bulk water, in agreement with earlier work in the literature on analysis of cavity fluctuations at nonpolar molecular surfaces. The cavity and dispersion interaction contributions correlate quite well with the solvent accessible surface area of the nonpolar side chains attached to the backbone. This correlation however is weak for the overall solvation free energies owing to the fact that the cavity and dispersion free energy contributions are almost exactly cancelling each other.

  2. Polyboramines for Hydrogen Release: Polymers Containing Lewis Pairs in their Backbone.

    PubMed

    Ledoux, Audrey; Larini, Paolo; Boisson, Christophe; Monteil, Vincent; Raynaud, Jean; Lacôte, Emmanuel

    2015-12-21

    The one-step polycondensation of diamines and diboranes triggered by the in situ deprotonation of the diammonium salts and concomitant reduction of bisboronic acids leads to the assembly of polymer chains through multiple Lewis pairing in their backbone. These new polyboramines are dihydrogen reservoirs that can be used for the hydrogenation of imines and carbonyl compounds. They also display a unique dihydrogen thermal release profile that is a direct consequence of the insertion of the amine-borane linkages in the polymeric backbone. PMID:26563914

  3. TargetFreeze: Identifying Antifreeze Proteins via a Combination of Weights using Sequence Evolutionary Information and Pseudo Amino Acid Composition.

    PubMed

    He, Xue; Han, Ke; Hu, Jun; Yan, Hui; Yang, Jing-Yu; Shen, Hong-Bin; Yu, Dong-Jun

    2015-12-01

    Antifreeze proteins (AFPs) are indispensable for living organisms to survive in an extremely cold environment and have a variety of potential biotechnological applications. The accurate prediction of antifreeze proteins has become an important issue and is urgently needed. Although considerable progress has been made, AFP prediction is still a challenging problem due to the diversity of species. In this study, we proposed a new sequence-based AFP predictor, called TargetFreeze. TargetFreeze utilizes an enhanced feature representation method that weightedly combines multiple protein features and takes the powerful support vector machine as the prediction engine. Computer experiments on benchmark datasets demonstrate the superiority of the proposed TargetFreeze over most recently released AFP predictors. We also implemented a user-friendly web server, which is openly accessible for academic use and is available at http://csbio.njust.edu.cn/bioinf/TargetFreeze. TargetFreeze supplements existing AFP predictors and will have potential applications in AFP-related biotechnology fields. PMID:26058944

  4. Chicken skin virome analyzed by high-throughput sequencing shows a composition highly different from human skin.

    PubMed

    Denesvre, Caroline; Dumarest, Marine; Rémy, Sylvie; Gourichon, David; Eloit, Marc

    2015-10-01

    Recent studies show that human skin at homeostasis is a complex ecosystem whose virome include circular DNA viruses, especially papillomaviruses and polyomaviruses. To determine the chicken skin virome in comparison with human skin virome, a chicken swabs pool sample from fifteen indoor healthy chickens of five genetic backgrounds was examined for the presence of DNA viruses by high-throughput sequencing (HTS). The results indicate a predominance of herpesviruses from the Mardivirus genus, coming from either vaccinal origin or presumably asymptomatic infection. Despite the high sensitivity of the HTS method used herein to detect small circular DNA viruses, we did not detect any papillomaviruses, polyomaviruses, or circoviruses, indicating that these viruses may not be resident of the chicken skin. The results suggest that the turkey herpesvirus is a resident of chicken skin in vaccinated chickens. This study indicates major differences between the skin viromes of chickens and humans. The origin of this difference remains to be further studied in relation with skin physiology, environment, or virus population dynamics. PMID:26223320

  5. Concordance of HIV Type 1 Tropism Phenotype to Predictions Using Web-Based Analysis of V3 Sequences: Composite Algorithms May Be Needed to Properly Assess Viral Tropism

    PubMed Central

    Cabral, Gabriela Bastos; Ferreira, João Leandro de Paula; Coelho, Luana Portes Osório; Fonsi, Mylva; Estevam, Denise Lotufo; Cavalcanti, Jaqueline Souza

    2012-01-01

    Abstract Genotypic prediction of HIV-1 tropism has been considered a practical surrogate for phenotypic tests and recently an European Consensus has set up recommendations for its use in clinical practice. Twenty-five antiretroviral-experienced patients, all heavily treated cases with a median of 16 years of antiretroviral therapy, had viral tropism determined by the Trofile assay and predicted by HIV-1 sequencing of partial env, followed by interpretation using web-based tools. Trofile determined 17/24 (71%) as X4 tropic or dual/mixed viruses, with one nonreportable result. The use of European consensus recommendations for single sequences (geno2pheno false-positive rates 20% cutoff) would lead to 4/24 (16.7%) misclassifications, whereas a composite algorithm misclassified 1/24 (4%). The use of the geno2pheno clinical option using CD4 T cell counts at collection was useful in resolving some discrepancies. Applying the European recommendations followed by additional web-based tools for cases around the recommended cutoff would resolve most misclassifications. PMID:21919801

  6. The sequence of intermetallic formation and solidification pathway of an Al–13Mg–7Si–2Cu in-situ composite

    SciTech Connect

    Farahany, Saeed; Nordin, Nur Azmah; Ourdjini, Ali; Abu Bakar, TutyAsma; Hamzah, Esah; Idris, Mohd Hasbullah; Hekmat-Ardakan, Alireza

    2014-12-15

    The phase transformation sequence and solidification behaviour of an Al–13Mg–7Si–2Cu in-situ composite was examined using a combination of computer-aided cooling curve thermal analysis and interrupted quenching techniques. Five different phases were identified by analysing the derivative cooling curves, the X-ray diffraction profile, optical and scanning electron microscopy images and the corresponding energy dispersive spectroscopy. It has been found that the solidification of this alloy begins with primary Mg{sub 2}Si precipitation and continues with the formation of eutectic Al–Mg{sub 2}Si, followed by Al{sub 5}FeSi and simultaneous precipitation of Al{sub 5}Cu{sub 2}Mg{sub 8}Si{sub 6} and Al{sub 2}Cu complex intermetallic phases. The formation of the last three intermetallic compounds changes the solidification behaviour of these composites remarkably due to their complex eutectic formation reactions. The solidification of the alloy, calculated using the Factsage thermochemical analysis software, has demonstrated a good agreement with the experiments in terms of compound prediction, their weight fractions and reaction temperatures. - Highlights: • Solidification path of a commercial Al-13Mg-7Si-2Cu composite was characterized. • Five different phases were identified and then confirmed with EDS and XRD results. • Mg{sub 2}Si, Al-Mg{sub 2}Si,Al{sub 5}FeSi (β),Al{sub 5}Cu{sub 2}Mg{sub 8}Si{sub 6} (Q) and Al{sub 2}Cu(θ) precipitated respectively. • Solidification was predicted using the Factsage thermochemical analysis software.

  7. Improved knockdown from artificial microRNAs in an enhanced miR-155 backbone: a designer's guide to potent multi-target RNAi.

    PubMed

    Fowler, Daniel K; Williams, Carly; Gerritsen, Alida T; Washbourne, Philip

    2016-03-18

    Artificial microRNA (amiRNA) sequences embedded in natural microRNA (miRNA) backbones have proven to be useful tools for RNA interference (RNAi). amiRNAs have reduced off-target and toxic effects compared to other RNAi-based methods such as short-hairpin RNAs (shRNA). amiRNAs are often less effective for knockdown, however, compared to their shRNA counterparts. We screened a large empirically-designed amiRNA set in the synthetic inhibitory BIC/miR-155 RNA (SIBR) scaffold and show common structural and sequence-specific features associated with effective amiRNAs. We then introduced exogenous motifs into the basal stem region which increase amiRNA biogenesis and knockdown potency. We call this modified backbone the enhanced SIBR (eSIBR) scaffold. Using chained amiRNAs for multi-gene knockdown, we show that concatenation of miRNAs targeting different genes is itself sufficient for increased knockdown efficacy. Further, we show that eSIBR outperforms wild-type SIBR (wtSIBR) when amiRNAs are chained. Finally, we use a lentiviral expression system in cultured neurons, where we again find that eSIBR amiRNAs are more potent for multi-target knockdown of endogenous genes. eSIBR will be a valuable tool for RNAi approaches, especially for studies where knockdown of multiple targets is desired. PMID:26582923

  8. Improved knockdown from artificial microRNAs in an enhanced miR-155 backbone: a designer's guide to potent multi-target RNAi

    PubMed Central

    Fowler, Daniel K.; Williams, Carly; Gerritsen, Alida T.; Washbourne, Philip

    2016-01-01

    Artificial microRNA (amiRNA) sequences embedded in natural microRNA (miRNA) backbones have proven to be useful tools for RNA interference (RNAi). amiRNAs have reduced off-target and toxic effects compared to other RNAi-based methods such as short-hairpin RNAs (shRNA). amiRNAs are often less effective for knockdown, however, compared to their shRNA counterparts. We screened a large empirically-designed amiRNA set in the synthetic inhibitory BIC/miR-155 RNA (SIBR) scaffold and show common structural and sequence-specific features associated with effective amiRNAs. We then introduced exogenous motifs into the basal stem region which increase amiRNA biogenesis and knockdown potency. We call this modified backbone the enhanced SIBR (eSIBR) scaffold. Using chained amiRNAs for multi-gene knockdown, we show that concatenation of miRNAs targeting different genes is itself sufficient for increased knockdown efficacy. Further, we show that eSIBR outperforms wild-type SIBR (wtSIBR) when amiRNAs are chained. Finally, we use a lentiviral expression system in cultured neurons, where we again find that eSIBR amiRNAs are more potent for multi-target knockdown of endogenous genes. eSIBR will be a valuable tool for RNAi approaches, especially for studies where knockdown of multiple targets is desired. PMID:26582923

  9. Synthesis and evaluation of backbone/amide-modified analogs of leualacin.

    PubMed

    Hu, M K; Yang, F C; Chou, C C; Yen, M H

    1999-02-22

    Leualacin (1), a cyclic depsi-pentapeptide, and its backbone/amide-modified analogs 2-4 were synthesized. Amide analogue 3 exhibited stronger vasodilatory effects. It also strongly inhibited collagen- and arachidonic acid (AA)-induced platelet aggregations with IC50s of 0.6 microM and 2.0 microM, respectively. PMID:10098664

  10. Graduate Education in Kinesiology: Are We Part of "America's Backbone for Competitiveness and Innovation"?

    ERIC Educational Resources Information Center

    DePauw, Karen P.

    2008-01-01

    Graduate education in the United States has been identified as being the backbone of American competitiveness and innovation in a recent report by the Council of Graduate Schools. The report provides a framework for examining the role of graduate education in partnership with business and government to advance an action agenda for achieving…

  11. Graduate Education in Kinesiology: Are We Part of "America's Backbone for Competitiveness and Innovation"?

    ERIC Educational Resources Information Center

    DePauw, Karen P.

    2008-01-01

    Graduate education in the United States has been identified as being the backbone of American competitiveness and innovation in a recent report by the Council of Graduate Schools. The report provides a framework for examining the role of graduate education in partnership with business and government to advance an action agenda for achieving

  12. 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…

  13. Inferring the Evolutionary History of IncP-1 Plasmids Despite Incongruence among Backbone Gene Trees

    PubMed Central

    Sen, Diya; Brown, Celeste J.; Top, Eva M.; Sullivan, Jack

    2013-01-01

    Plasmids of the incompatibility group IncP-1 can transfer and replicate in many genera of the Proteobacteria. They are composed of backbone genes that encode a variety of essential functions and accessory genes that have implications for human health and environmental remediation. Although it is well understood that the accessory genes are transferred horizontally between plasmids, recent studies have also provided examples of recombination in the backbone genes of IncP-1 plasmids. As a consequence, phylogeny estimation based on backbone genes is expected to produce conflicting gene tree topologies. The main goal of this study was therefore to infer the evolutionary history of IncP-1 plasmids in the presence of both vertical and horizontal gene transfer. This was achieved by quantifying the incongruence among gene trees and attributing it to known causes such as 1) phylogenetic uncertainty, 2) coalescent stochasticity, and 3) horizontal inheritance. Topologies of gene trees exhibited more incongruence than could be attributed to phylogenetic uncertainty alone. Species-tree estimation using a Bayesian framework that takes coalescent stochasticity into account was well supported, but it differed slightly from the maximum-likelihood tree estimated by concatenation of backbone genes. After removal of the gene that demonstrated a signal of intergroup recombination, the concatenated tree was congruent with the species-tree estimate, which itself was robust to inclusion/exclusion of the recombinant gene. Thus, in spite of horizontal gene exchange both within and among IncP-1 subgroups, the backbone genome of these IncP-1 plasmids retains a detectable vertical evolutionary history. PMID:22936717

  14. Analysis of Polygala tenuifolia Transcriptome and Description of Secondary Metabolite Biosynthetic Pathways by Illumina Sequencing

    PubMed Central

    Tian, Hongling; Xu, Xiaoshuang; Zhang, Fusheng; Wang, Yaoqin; Guo, Shuhong; Qin, Xuemei; Du, Guanhua

    2015-01-01

    Radix polygalae, the dried roots of Polygala tenuifolia and P. sibirica, is one of the most well-known traditional Chinese medicinal plants. Radix polygalae contains various saponins, xanthones, and oligosaccharide esters and these compounds are responsible for several pharmacological properties. To provide basic breeding information, enhance molecular biological analysis, and determine secondary metabolite biosynthetic pathways of P. tenuifolia, we applied Illumina sequencing technology and de novo assembly. We also applied this technique to gain an overview of P. tenuifolia transcriptome from samples with different years. Using Illumina sequencing, approximately 67.2% of unique sequences were annotated by basic local alignment search tool similarity searches against public sequence databases. We classified the annotated unigenes by using Nr, Nt, GO, COG, and KEGG databases compared with NCBI. We also obtained many candidates CYP450s and UGTs by the analysis of genes in the secondary metabolite biosynthetic pathways, including putative terpenoid backbone and phenylpropanoid biosynthesis pathway. With this transcriptome sequencing, future genetic and genomics studies related to the molecular mechanisms associated with the chemical composition of P. tenuifolia may be improved. Genes involved in the enrichment of secondary metabolite biosynthesis-related pathways could enhance the potential applications of P. tenuifolia in pharmaceutical industries. PMID:26543847

  15. Phase behaviour of two-component bottle-brush polymers with flexible backbones under poor solvent conditions

    NASA Astrophysics Data System (ADS)

    Fytas, Nikolaos G.; Theodorakis, Panagiotis E.

    2014-03-01

    The phase behaviour of two-component bottle-brush polymers with fully flexible backbones under poor solvent conditions is studied via molecular-dynamics simulations, using a coarse-grained bead-spring model and side chains of up to N = 40 effective monomers. We consider a symmetric model where side chains of type A and B are grafted alternately onto a flexible backbone. The aim of this study is to explore the phase behaviour of two-component bottle-brushes depending on parameters, such as as the grafting density \\sigma , the backbone length {{N}_{b}}, the side-chain length N, and the temperature T. Based on a cluster analysis, we identify for our range of parameters the regimes of fully phase separated systems, i.e., A-type side chains form one cluster and B-type chains another, while the interface that separates these two clusters contains the backbone monomers. We find that pearl-necklace or Janus-like structures, which normally occur for bottle-brush polymers with rigid backbones under poor solvent conditions, are fully attributed to the backbone rigidity, and, therefore, such structures are unlikely in the case of bottle brushes with fully flexible backbones. Also, a comparative discussion with earlier work on the phase behaviour of single-component bottle-brush polymers with flexible backbones is performed.

  16. Novel method for the synthesis of urea backbone cyclic peptides using new Alloc-protected glycine building units.

    PubMed

    Hurevich, Mattan; Tal-Gan, Yftah; Klein, Shoshana; Barda, Yaniv; Levitzki, Alexander; Gilon, Chaim

    2010-04-01

    Cyclization of bioactive peptides, utilizing functional groups serving as natural pharmacophors, is often accompanied with loss of activity. The backbone cyclization approach was developed to overcome this limitation and enhance pharmacological properties. Backbone cyclic peptides are prepared by the incorporation of special building units, capable of forming amide, disulfide and coordinative bonds. Urea bridge is often used for the preparation of cyclic peptides by connecting two amine functionalized side chains. Here we present urea backbone cyclization as an additional method for the preparation of backbone cyclic peptide libraries. A straightforward method for the synthesis of crystalline Fmoc-N(alpha) [omega-amino(Alloc)-alkyl] glycine building units is presented. A set of urea backbone cyclic Glycogen Synthase Kinase 3 analogs was prepared and assessed for protein kinase B inhibition as anticancer leads. PMID:20196085

  17. Mapping Membrane Protein Backbone Dynamics: A Comparison of Site-Directed Spin Labeling with NMR 15N-Relaxation Measurements

    PubMed Central

    Lo, Ryan H.; Kroncke, Brett M.; Solomon, Tsega L.; Columbus, Linda

    2014-01-01

    The ability to detect nanosecond backbone dynamics with site-directed spin labeling (SDSL) in soluble proteins has been well established. However, for membrane proteins, the nitroxide appears to have more interactions with the protein surface, potentially hindering the sensitivity to backbone motions. To determine whether membrane protein backbone dynamics could be mapped with SDSL, a nitroxide was introduced at 55 independent sites in a model polytopic membrane protein, TM0026. Electron paramagnetic resonance spectral parameters were compared with NMR 15N-relaxation data. Sequential scans revealed backbone dynamics with the same trends observed for the R1 relaxation rate, suggesting that nitroxide dynamics remain coupled to the backbone on membrane proteins. PMID:25296323

  18. Acute Effects of TiO2 Nanomaterials on the Viability and Taxonomic Composition of Aquatic Bacterial Communities Assessed via High-Throughput Screening and Next Generation Sequencing

    PubMed Central

    Binh, Chu Thi Thanh; Tong, Tiezheng; Gaillard, Jean-Franois; Gray, Kimberly A.; Kelly, John J.

    2014-01-01

    The nanotechnology industry is growing rapidly, leading to concerns about the potential ecological consequences of the release of engineered nanomaterials (ENMs) to the environment. One challenge of assessing the ecological risks of ENMs is the incredible diversity of ENMs currently available and the rapid pace at which new ENMs are being developed. High-throughput screening (HTS) is a popular approach to assessing ENM cytotoxicity that offers the opportunity to rapidly test in parallel a wide range of ENMs at multiple concentrations. However, current HTS approaches generally test one cell type at a time, which limits their ability to predict responses of complex microbial communities. In this study toxicity screening via a HTS platform was used in combination with next generation sequencing (NGS) to assess responses of bacterial communities from two aquatic habitats, Lake Michigan (LM) and the Chicago River (CR), to short-term exposure in their native waters to several commercial TiO2 nanomaterials under simulated solar irradiation. Results demonstrate that bacterial communities from LM and CR differed in their sensitivity to nano-TiO2, with the community from CR being more resistant. NGS analysis revealed that the composition of the bacterial communities from LM and CR were significantly altered by exposure to nano-TiO2, including decreases in overall bacterial diversity, decreases in the relative abundance of Actinomycetales, Sphingobacteriales, Limnohabitans, and Flavobacterium, and a significant increase in Limnobacter. These results suggest that the release of nano-TiO2 to the environment has the potential to alter the composition of aquatic bacterial communities, which could have implications for the stability and function of aquatic ecosystems. The novel combination of HTS and NGS described in this study represents a major advance over current methods for assessing ENM ecotoxicity because the relative toxicities of multiple ENMs to thousands of naturally occurring bacterial species can be assessed simultaneously under environmentally relevant conditions. PMID:25162615

  19. The Impact of Different DNA Extraction Kits and Laboratories upon the Assessment of Human Gut Microbiota Composition by 16S rRNA Gene Sequencing

    PubMed Central

    Kennedy, Nicholas A.; Walker, Alan W.; Berry, Susan H.; Duncan, Sylvia H.; Farquarson, Freda M.; Louis, Petra; Thomson, John M.; Ahmad, T; Anderson, CA; Barrett, JC; Drummond, H; Edwards, C; Hart, A; Hawkey, C; Henderson, P; Khan, M; Lamb, CA; Lee, JC; Mansfield, JC; Mathew, CG; Mowat, C; Newman, WG; Prescott, NJ; Simmons, A; Simpson, P; Taylor, K; Taylor, K; Wilson, DC; Satsangi, Jack; Flint, Harry J.; Parkhill, Julian

    2014-01-01

    Introduction Determining bacterial community structure in fecal samples through DNA sequencing is an important facet of intestinal health research. The impact of different commercially available DNA extraction kits upon bacterial community structures has received relatively little attention. The aim of this study was to analyze bacterial communities in volunteer and inflammatory bowel disease (IBD) patient fecal samples extracted using widely used DNA extraction kits in established gastrointestinal research laboratories. Methods Fecal samples from two healthy volunteers (H3 and H4) and two relapsing IBD patients (I1 and I2) were investigated. DNA extraction was undertaken using MoBio Powersoil and MP Biomedicals FastDNA SPIN Kit for Soil DNA extraction kits. PCR amplification for pyrosequencing of bacterial 16S rRNA genes was performed in both laboratories on all samples. Hierarchical clustering of sequencing data was done using the Yue and Clayton similarity coefficient. Results DNA extracted using the FastDNA kit and the MoBio kit gave median DNA concentrations of 475 (interquartile range 228-561) and 22 (IQR 9-36) ng/µL respectively (p<0.0001). Hierarchical clustering of sequence data by Yue and Clayton coefficient revealed four clusters. Samples from individuals H3 and I2 clustered by patient; however, samples from patient I1 extracted with the MoBio kit clustered with samples from patient H4 rather than the other I1 samples. Linear modelling on relative abundance of common bacterial families revealed significant differences between kits; samples extracted with MoBio Powersoil showed significantly increased Bacteroidaceae, Ruminococcaceae and Porphyromonadaceae, and lower Enterobacteriaceae, Lachnospiraceae, Clostridiaceae, and Erysipelotrichaceae (p<0.05). Conclusion This study demonstrates significant differences in DNA yield and bacterial DNA composition when comparing DNA extracted from the same fecal sample with different extraction kits. This highlights the importance of ensuring that samples in a study are prepared with the same method, and the need for caution when cross-comparing studies that use different methods. PMID:24586470

  20. 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. PMID:26438558

  1. A Plasmid Bearing the bla(CTX-M-15) Gene and Phage P1-Like Sequences from a Sequence Type 11 Klebsiella pneumoniae Isolate.

    PubMed

    Shin, Juyoun; Ko, Kwan Soo

    2015-10-01

    Plasmid pKP12226 was extracted and analyzed from a CTX-M-15-producing Klebsiella pneumoniae sequence type 11 (ST11) isolate collected in South Korea. The plasmid represents chimeric characteristics consisting of a pIP1206-like backbone and lysogenized phage P1-like sequences. It bears a resistance region that includes resistance genes to several antibiotics and is different from previously characterized plasmids from South Korea bearing blaCTX-M-15. It may have resulted from recombination between an Escherichia coli plasmid backbone, a blaCTX-M-15-bearing resistance region, and lysogenized phage P1-like sequences. PMID:26195513

  2. Backbone dynamics measurements on leukemia inhibitory factor, a rigid four-helical bundle cytokine.

    PubMed

    Yao, S; Smith, D K; Hinds, M G; Zhang, J G; Nicola, N A; Norton, R S

    2000-04-01

    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-helical bundle cytokines. PMID:10794409

  3. Self-assembly of diphenylalanine backbone homologues and their combination with functionalized carbon nanotubes

    NASA Astrophysics Data System (ADS)

    Dinesh, Bhimareddy; Squillaci, Marco A.; Ménard-Moyon, Cécilia; Samorì, Paolo; Bianco, Alberto

    2015-09-01

    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.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. Electronic supplementary information (ESI) available. See DOI: 10.1039/c5nr04665c

  4. Persistence and epidemic propagation of a Pseudomonas aeruginosa sequence type 235 clone harboring an IS26 composite transposon carrying the blaIMP-1 integron in Hiroshima, Japan, 2005 to 2012.

    PubMed

    Shimizu, Wataru; Kayama, Shizuo; Kouda, Shuntaro; Ogura, Yoshitoshi; Kobayashi, Kanao; Shigemoto, Norifumi; Shimada, Norimitsu; Yano, Raita; Hisatsune, Junzo; Kato, Fuminori; Hayashi, Tetsuya; Sueda, Taijiro; Ohge, Hiroki; Sugai, Motoyuki

    2015-05-01

    A 9-year surveillance for multidrug-resistant (MDR) Pseudomonas aeruginosa in the Hiroshima region showed that the number of isolates harboring the metallo-β-lactamase gene bla(IMP-1) abruptly increased after 2004, recorded the highest peak in 2006, and showed a tendency to decline afterwards, indicating a history of an epidemic. PCR mapping of the variable regions of the integrons showed that this epidemic was caused by the clonal persistence and propagation of an MDR P. aeruginosa strain harboring the bla(IMP-1) gene and an aminoglycoside 6'-N-acetyltransferase gene, aac(6')-Iae in a class I integron (In113), whose integrase gene intl1 was disrupted by an IS26 insertion. Sequence analysis of the representative strain PA058447 resistance element containing the In113-derived gene cassette array showed that the element forms an IS26 transposon embedded in the chromosome. It has a Tn21 backbone and is composed of two segments sandwiched by three IS26s. In Japan, clonal nationwide expansion of an MDR P. aeruginosa NCGM2.S1 harboring chromosomally encoded In113 with intact intl1 is reported. Multilocus sequence typing and genomic comparison strongly suggest that PA058447 and NCGM2.S1 belong to the same clonal lineage. Moreover, the structures of the resistance element in the two strains are very similar, but the sites of insertion into the chromosome are different. Based on tagging information of the IS26 present in both resistance elements, we suggest that the MDR P. aeruginosa clone causing the epidemic in Hiroshima for the past 9 years originated from a common ancestor genome of PA058447 and NCGM2.S1 through an IS26 insertion into intl1 of In113 and through IS26-mediated genomic rearrangements. PMID:25712351

  5. Persistence and Epidemic Propagation of a Pseudomonas aeruginosa Sequence Type 235 Clone Harboring an IS26 Composite Transposon Carrying the blaIMP-1 Integron in Hiroshima, Japan, 2005 to 2012

    PubMed Central

    Shimizu, Wataru; Kayama, Shizuo; Kouda, Shuntaro; Ogura, Yoshitoshi; Kobayashi, Kanao; Shigemoto, Norifumi; Shimada, Norimitsu; Yano, Raita; Hisatsune, Junzo; Kato, Fuminori; Hayashi, Tetsuya; Sueda, Taijiro; Ohge, Hiroki

    2015-01-01

    A 9-year surveillance for multidrug-resistant (MDR) Pseudomonas aeruginosa in the Hiroshima region showed that the number of isolates harboring the metallo-β-lactamase gene blaIMP-1 abruptly increased after 2004, recorded the highest peak in 2006, and showed a tendency to decline afterwards, indicating a history of an epidemic. PCR mapping of the variable regions of the integrons showed that this epidemic was caused by the clonal persistence and propagation of an MDR P. aeruginosa strain harboring the blaIMP-1 gene and an aminoglycoside 6′-N-acetyltransferase gene, aac(6′)-Iae in a class I integron (In113), whose integrase gene intl1 was disrupted by an IS26 insertion. Sequence analysis of the representative strain PA058447 resistance element containing the In113-derived gene cassette array showed that the element forms an IS26 transposon embedded in the chromosome. It has a Tn21 backbone and is composed of two segments sandwiched by three IS26s. In Japan, clonal nationwide expansion of an MDR P. aeruginosa NCGM2.S1 harboring chromosomally encoded In113 with intact intl1 is reported. Multilocus sequence typing and genomic comparison strongly suggest that PA058447 and NCGM2.S1 belong to the same clonal lineage. Moreover, the structures of the resistance element in the two strains are very similar, but the sites of insertion into the chromosome are different. Based on tagging information of the IS26 present in both resistance elements, we suggest that the MDR P. aeruginosa clone causing the epidemic in Hiroshima for the past 9 years originated from a common ancestor genome of PA058447 and NCGM2.S1 through an IS26 insertion into intl1 of In113 and through IS26-mediated genomic rearrangements. PMID:25712351

  6. Tailored Living Block Copolymerization: Multiblock Poly(cyclohexene carbonate)s with Sequence Control

    SciTech Connect

    Kim, Jeung Gon; Cowman, Christina D.; LaPointe, Anne M.; Wiesner, Ulrich; Coates, Geoffrey W.

    2011-03-08

    In this Communication, the living block copolymerization of functionalized cyclohexene oxides and CO{sub 2} is described, yielding multiblock poly(cyclohexene carbonate)s [p(CHC)s] with a diverse range of functionality on the side chains and good control of block sequence and length. Unlike prior systems that contain stable vinyl backbones, the carbonate backbones of polymers reported herein are degradable, allowing possible applications where removable templates are required.

  7. 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

  8. Protonation-deprotonation of the glycine backbone as followed by Raman scattering and multiconformational analysis

    NASA Astrophysics Data System (ADS)

    Hernndez, Beln; Pflger, Fernando; Kruglik, Sergei G.; Ghomi, Mahmoud

    2013-11-01

    Because of the absence of the side chain in its chemical structure and its well defined Raman spectra, glycine was selected here to follow its backbone protonation-deprotonation. The scan of the recorded spectra in the 1800-300 cm-1 region led us to assign those obtained at pH 1, 6 and 12 to the cationic, zwitterionic and anionic species, respectively. These data complete well those previously published by Bykov et al. (2008) [16] devoted to the high wavenumber Raman spectra (>2500 cm-1). To reinforce our discussion, DFT calculations were carried out on the clusters of glycine + 5H2O, mimicking reasonably the first hydration shell of the amino acid. Geometry optimization of 141 initial clusters, reflecting plausible combinations of the backbone torsion angles, allowed exploration of the conformational features, as well as construction of the theoretical Raman spectra by considering the most stable clusters containing each glycine species.

  9. Graft Copolymers with Conducting Polymer Backbones: A Versatile Route to Functional Materials.

    PubMed

    Strover, Lisa T; Malmström, Jenny; Travas-Sejdic, Jadranka

    2016-02-01

    Graft copolymers with a conducting polymer backbone are a promising class of materials for diverse applications including, but not limited to, organic electronics, stimuli-responsive surfaces, sensors, and biomedical devices. These materials take advantage of the unique electrochemical and optoelectronic properties of conducting polymers, complemented by chemical and/or physical properties of the grafted sidechains. In this Personal Account, we discuss our work in designing functional surfaces based on graft copolymers with a conducting polymer backbone, in the context of broader developments in the field. We review the synthetic approaches available for the rational design of conducting-polymer-based graft copolymers, and examine the types of functional surfaces and soluble materials that may be engineered using these techniques. PMID:26785693

  10. Simulation study of chiral two dimensional ultraviolet (2DUV) spectroscopy of the protein backbone

    PubMed Central

    Abramavicius, Darius; Jiang, Jun; Bulheller, Benjamin M.; Hirst, Jonathan D.; Mukamel, Shaul

    2010-01-01

    Amide n –π* and π-π* excitations around 200 nm are prominent spectroscopic signatures of the protein backbone, which are routinely used in ultraviolet (UV) circular dichroism for structure characterization. Recently developed ultrafast laser sources may be used to extend these studies to two dimensions (2D). We apply a new algorithm for modelling protein electronic transitions to simulate two-dimensional ultraviolet (2DUV) photon echo signals in this regime and to identify signatures of protein backbone secondary (and tertiary) structure. Simulated signals for a set of globular and fibrillar proteins and their specific regions reveal characteristic patterns of helical and sheet secondary structures. We investigate how these patterns vary and converge with the size of the structural motif. Specific chiral polarization configurations of the UV pulses are found to be sensitive to aspects of the protein structure. This information significantly augments that available from linear circular dichroism. PMID:20481498

  11. Influence of Backbone Fluorination in Regioregular Poly(3-alkyl-4-fluoro)thiophenes.

    PubMed

    Fei, Zhuping; Boufflet, Pierre; Wood, Sebastian; Wade, Jessica; Moriarty, John; Gann, Eliot; Ratcliff, Erin L; McNeill, Christopher R; Sirringhaus, Henning; Kim, Ji-Seon; Heeney, Martin

    2015-06-01

    We report two strategies toward the synthesis of 3-alkyl-4-fluorothiophenes containing straight (hexyl and octyl) and branched (2-ethylhexyl) alkyl groups. We demonstrate that treatment of the dibrominated monomer with 1 equiv of alkyl Grignard reagent leads to the formation of a single regioisomer as a result of the pronounced directing effect of the fluorine group. Polymerization of the resulting species affords highly regioregular poly(3-alkyl-4-fluoro)thiophenes. Comparison of their properties to those of the analogous non-fluorinated polymers shows that backbone fluorination leads to an increase in the polymer ionization potential without a significant change in optical band gap. Fluorination also results in an enhanced tendency to aggregate in solution, which is ascribed to a more co-planar backbone on the basis of Raman and DFT calculations. Average charge carrier mobilities in field-effect transistors are found to increase by up to a factor of 5 for the fluorinated polymers. PMID:25994804

  12. Elucidating the backbone conformation of photoswitchable foldamers using vibrational circular dichroism.

    PubMed

    Domingos, Sérgio R; Roeters, Steven J; Amirjalayer, Saeed; Yu, Zhilin; Hecht, Stefan; Woutersen, Sander

    2013-10-28

    The backbone conformation of amphiphilic oligo(azobenzene) foldamers is investigated using vibrational circular dichroism (VCD) spectroscopy on a mode involving the stretching of the N=N bonds in the backbone. From denaturation experiments, we find that the VCD response in the helical conformation arises mainly from through-space interaction between the N=N-stretch transition-dipole moments, so that the coupled-oscillator model can be used to predict the VCD spectrum associated with a particular conformation. Using this approach, we elucidate the origin of the VCD signals in the folded conformation, and can assign the observed partial loss of VCD signals upon photo-induced unfolding to specific conformational changes. Our results show that the N=N-stretch VCD response provides an excellent probe of the helical conformation of the N=N bonds in this type of switchable molecular system. PMID:24018416

  13. Modifications to the Peptidoglycan Backbone Help Bacteria To Establish Infection ▿

    PubMed Central

    Davis, Kimberly M.; Weiser, Jeffrey N.

    2011-01-01

    Bacterial pathogens that colonize mucosal surfaces have acquired resistance to antimicrobials that are abundant at these sites. One of the main antimicrobials present on mucosal surfaces is lysozyme, a muramidase that hydrolyzes the peptidoglycan backbone of bacteria. Cleavage of the peptidoglycan backbone leads to bacterial cell death and lysis, which releases bacterial fragments, including peptidoglycan, at the site of infection. Peptidoglycan fragments can be recognized by host receptors and initiate an immune response that will aid in clearing infection. Many mucosal pathogens modify the peptidoglycan residues surrounding the cleavage site for lysozyme to avoid peptidoglycan degradation and the release of these proinflammatory fragments. This review will focus specifically on peptidoglycan modifications, their role in lysozyme resistance, and downstream effects on the host immune response to infection. PMID:21041496

  14. 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.

  15. 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.

  16. Nonparametric Combinatorial Sequence Models

    NASA Astrophysics Data System (ADS)

    Wauthier, Fabian L.; Jordan, Michael I.; Jojic, Nebojsa

    This work considers biological sequences that exhibit combinatorial structures in their composition: groups of positions of the aligned sequences are "linked" and covary as one unit across sequences. If multiple such groups exist, complex interactions can emerge between them. Sequences of this kind arise frequently in biology but methodologies for analyzing them are still being developed. This paper presents a nonparametric prior on sequences which allows combinatorial structures to emerge and which induces a posterior distribution over factorized sequence representations. We carry out experiments on three sequence datasets which indicate that combinatorial structures are indeed present and that combinatorial sequence models can more succinctly describe them than simpler mixture models. We conclude with an application to MHC binding prediction which highlights the utility of the posterior distribution induced by the prior. By integrating out the posterior our method compares favorably to leading binding predictors.

  17. Recognizing Sequences of Sequences

    PubMed Central

    Kiebel, Stefan J.; von Kriegstein, Katharina; Daunizeau, Jean; Friston, Karl J.

    2009-01-01

    The brain's decoding of fast sensory streams is currently impossible to emulate, even approximately, with artificial agents. For example, robust speech recognition is relatively easy for humans but exceptionally difficult for artificial speech recognition systems. In this paper, we propose that recognition can be simplified with an internal model of how sensory input is generated, when formulated in a Bayesian framework. We show that a plausible candidate for an internal or generative model is a hierarchy of stable heteroclinic channels. This model describes continuous dynamics in the environment as a hierarchy of sequences, where slower sequences cause faster sequences. Under this model, online recognition corresponds to the dynamic decoding of causal sequences, giving a representation of the environment with predictive power on several timescales. We illustrate the ensuing decoding or recognition scheme using synthetic sequences of syllables, where syllables are sequences of phonemes and phonemes are sequences of sound-wave modulations. By presenting anomalous stimuli, we find that the resulting recognition dynamics disclose inference at multiple time scales and are reminiscent of neuronal dynamics seen in the real brain. PMID:19680429

  18. Monitoring Backbone Hydrogen-Bond Formation in β-Barrel Membrane Protein Folding.

    PubMed

    Raschle, Thomas; Rios Flores, Perla; Opitz, Christian; Müller, Daniel J; Hiller, Sebastian

    2016-05-10

    β-barrel membrane proteins are key components of the outer membrane of bacteria, mitochondria and chloroplasts. Their three-dimensional structure is defined by a network of backbone hydrogen bonds between adjacent β-strands. Here, we employ hydrogen-deuterium (H/D) exchange in combination with NMR spectroscopy and mass spectrometry to monitor backbone hydrogen bond formation during folding of the outer membrane protein X (OmpX) from E. coli in detergent micelles. Residue-specific kinetics of interstrand hydrogen-bond formation were found to be uniform in the entire β-barrel and synchronized to formation of the tertiary structure. OmpX folding thus propagates via a long-lived conformational ensemble state in which all backbone amide protons exchange with the solvent and engage in hydrogen bonds only transiently. Stable formation of the entire OmpX hydrogen bond network occurs downhill of the rate-limiting transition state and thus appears cooperative on the overall folding time scale. PMID:27062600

  19. Transforming conotoxins into cyclotides: Backbone cyclization of P-superfamily conotoxins.

    PubMed

    Akcan, Muharrem; Clark, Richard J; Daly, Norelle L; Conibear, Anne C; de Faoite, Andrew; Heghinian, Mari D; Sahil, Talwar; Adams, David J; Marí, Frank; Craik, David J

    2015-11-01

    Peptide backbone cyclization is a widely used approach to improve the activity and stability of small peptides but until recently it had not been applied to peptides with multiple disulfide bonds. Conotoxins are disulfide-rich conopeptides derived from the venoms of cone snails that have applications in drug design and development. However, because of their peptidic nature, they can suffer from poor bioavailability and poor stability in vivo. In this study two P-superfamily conotoxins, gm9a and bru9a, were backbone cyclized by joining the N- and C-termini with short peptide linkers using intramolecular native chemical ligation chemistry. The cyclized derivatives had conformations similar to the native peptides showing that backbone cyclization can be applied to three disulfide-bonded peptides with cystine knot motifs. Cyclic gm9a was more potent at high voltage-activated (HVA) calcium channels than its acyclic counterpart, highlighting the value of this approach in developing active and stable conotoxins containing cyclic cystine knot motifs. © 2015 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 104: 682-692, 2015. PMID:26172377

  20. 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

  1. Probing the Backbone Function of Tumor Targeting Peptides by an Amide-to-Triazole Substitution Strategy.

    PubMed

    Valverde, Ibai E; Vomstein, Sandra; Fischer, Christiane A; Mascarin, Alba; Mindt, Thomas L

    2015-09-24

    Novel backbone-modified radiolabeled analogs based on the tumor targeting peptide bombesin were synthesized and fully evaluated in vitro and in vivo. We have recently introduced the use of 1,4-disubstituted 1,2,3-triazoles as metabolically stable trans-amide bond surrogates in radiolabeled peptides in order to improve their tumor targeting. As an extension of our approach, we now report several backbone-modified analogs of the studied bombesin peptide bearing multiple triazole substitutions. We investigated the effect of the modifications on several biological parameters including the internalization of the radiopeptidomimetics into tumor cells, their affinity toward the gastrin releasing peptide receptor (GRPr), metabolic stability in blood plasma, and biodistribution in mice bearing GRPr-expressing xenografts. The backbone-modified radiotracers exhibited a significantly increased resistance to proteolytic degradation. In addition, some of the radiopeptidomimetics retained a nanomolar affinity toward GRPr, resulting in an up to 2-fold increased tumor uptake in vivo in comparison to a (all amide bond) reference compound. PMID:26309061

  2. Methods and Compositions for Amplification and Detection of microRNAs (miRNAs) and Noncoding RNAs (ncRNAs) Using the Signature Sequence Amplification Method (SSAM)

    PubMed Central

    Ginsberg, Stephen D.; Che, Shaoli

    2015-01-01

    The signature sequence amplification method (SSAM) described herein is an approach for amplifying noncoding RNA (ncRNA), microRNA (miRNA), and small polynucleotide sequences. A key point of the SSAM technology is the generation of signature sequences. The signature sequences include target sequences (miRNA, ncRNA, and/or any small polynucleotide sequence) flanked by two DNA fragments. Target sequences can be amplified through DNA synthesis, RNA synthesis, or the combination of DNA and RNA synthesis. The amplification of signature sequences provides an efficient and reproducible mechanism to determine the presence or absence of the target miRNAs/ncRNAs, to analyze the quantities of the miRNAs in biological samples, and for miRNA/ncRNA profiling. PMID:25564022

  3. 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 on sulfation and cation effects, the present results can be applied to building models of CS polymers and as a point of comparison in studies of CS polymer backbone dynamics and thermodynamics. PMID:25906376

  4. 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 analysis of the static dielectric constant and show excellent agreement with x-ray scattering and DFT calculations, each ionomer strongly favoring the formation of quadrupoles. Finally a polysiloxane ionomer was considered and was mixed with three anion and/or cation solvating additives, tetraglyme, tetraethylene glycol, and branched poly(ethylenimine). The EP model of the dielectric response gives the conducting ion concentration and the mobility of conducting ions and shows an increase in conducting ion concentration with both anion solvating and cation solvating additives. The static dielectric constant indicates an increased preference for ion pairs when anion receptors are present. Most interestingly, the additive that best decreased the glass transition temperature and increased the static dielectric constant did not result in the best dc conductivity. The best dc conductivity resulted from tetraglyme because it solvated cations without interacting with the polymer. High ion conductivities have not been observed in polymer systems that decouple charge transport from polymer motion, and therefore low Tg ionomers are the natural path forward for commercially viable ionomers. Inorganic backbone polymers impart a low Tg without bringing any strong disadvantage to ionomers. These materials are very important for developing superior ion conductors and should be pursued in future ionomer research.

  5. Backbone (1)H, (15)N, (13)C NMR assignment of the 518-627 fragment of the androgen receptor encompassing N-terminal and DNA binding domains.

    PubMed

    Meyer, Sandra; Wang, Ying-Hui; Pérez-Escrivà, Pau; Kieffer, Bruno

    2016-04-01

    Androgen receptor (AR) belongs to the nuclear receptor superfamily that are ligand dependent transcription factors. This protein binds to steroid hormones such as dihydrotestosterone, to specific DNA sequences as well as to a number of co-regulatory factors. A number of these interactions involve the N-terminal domain (NTD), that is predicted to be intrinsically disordered. In order to provide functional information about possible cross-talk mechanisms between the AR NTD and its DNA binding domain (DBD), we have undertaken the NMR study of a fragment of human AR encompassing the last 37 residues of the NTD and the DBD (NTD-DBD518-627). The backbone (1)H, (15)N, (13)C NMR resonance assignments of this fragment indicate the presence of residual helical secondary structure within the AR NTD. PMID:26732902

  6. 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.

  7. 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

  8. Toward Atomistic Resolution Structure of Phosphatidylcholine Headgroup and Glycerol Backbone at Different Ambient Conditions.

    PubMed

    Botan, Alexandru; Favela-Rosales, Fernando; Fuchs, Patrick F J; Javanainen, Matti; Kanduč, Matej; Kulig, Waldemar; Lamberg, Antti; Loison, Claire; Lyubartsev, Alexander; Miettinen, Markus S; Monticelli, Luca; Määttä, Jukka; Ollila, O H Samuli; Retegan, Marius; Róg, Tomasz; Santuz, Hubert; Tynkkynen, Joona

    2015-12-10

    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://zenodo.org/collection/user-nmrlipids ) has become the most extensive publicly available collection of molecular dynamics simulation trajectories of lipid bilayers. PMID:26509669

  9. 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://zenodo.org/collection/user-nmrlipids) has become the most extensive publicly available collection of molecular dynamics simulation trajectories of lipid bilayers. PMID:26509669

  10. Simultaneous NMR assignment of backbone and side chain amides in large proteins with IS-TROSY.

    PubMed

    Liu, Aizhuo; Li, Yue; Yao, Lishan; Yan, Honggao

    2006-12-01

    A new strategy for the simultaneous NMR assignment of both backbone and side chain amides in large proteins with isotopomer-selective transverse-relaxation-optimized spectroscopy (IS-TROSY) is reported. The method considers aspects of both the NMR sample preparation and the experimental design. First, the protein is dissolved in a buffer with 50%H2O/50%D2O in order to promote the population of semideuterated NHD isotopomers in side chain amides of Asn/Gln residues. Second, a 13C'-coupled 2D 15N-1H IS-TROSY spectrum provides a stereospecific distinction between the geminal protons in the E and Z configurations of the carboxyamide group. Third, a suite of IS-TROSY-based triple-resonance NMR experiments, e.g. 3D IS-TROSY-HNCA and 3D IS-TROSY-HNCACB, are designed to correlate aliphatic carbon atoms with backbone amides and, for Asn/Gln residues, at the same time with side chain amides. The NMR assignment procedure is similar to that for small proteins using conventional 3D HNCA/3D HNCACB spectra, in which, however, signals from NH2 groups are often very weak or even missing due to the use of broad-band proton decoupling schemes and NOE data have to be used as a remedy. For large proteins, the use of conventional TROSY experiments makes resonances of side chain amides not observable at all. The application of IS-TROSY experiments to the 35-kDa yeast cytosine deaminase has established a complete resonance assignment for the backbone and stereospecific assignment for side chain amides, which otherwise could not be achieved with existing NMR experiments. Thus, the development of IS-TROSY-based method provides new opportunities for the NMR study of important structural and biological roles of carboxyamides and side chain moieties of arginine and lysine residues in large proteins as well as amino moieties in nucleic acids. PMID:17091334

  11. Comparison of multiple AMBER force fields and development of improved protein backbone parameters

    PubMed Central

    Hornak, Viktor; Abel, Robert; Okur, Asim; Strockbine, Bentley; Roitberg, Adrian; Simmerling, Carlos

    2016-01-01

    The ff94 force field that is commonly associated with the AMBER simulation package is one of the most widely used parameter sets for biomolecular simulation. After a decade of extensive use and testing, limitations in this force field, such as over stabilization of α-helices, were reported by us and other researchers. This led to a number of attempts to improve these parameters, resulting in a variety of “AMBER” force fields and significant difficulty in determining which should be used for a particular application. We show that several of these continue to suffer from inadequate balance between different secondary structure elements. In addition, the approach used in most of these studies neglected to account for the existence in AMBER of two sets of backbone φ/ψ dihedral terms. This led to parameter sets that provide unreasonable conformational preferences for glycine. We report here an effort to improve the φ/ψ dihedral terms in the ff99 energy function. Dihedral term parameters are based on fitting the energies of multiple conformations of glycine and alanine tetrapeptides from high level ab-initio quantum mechanical calculations. The new parameters for backbone dihedrals replace those in the existing ff99 force field. This parameter set, which we denote ff99SB, achieves a better balance of secondary structure elements as judged by improved distribution of backbone dihedrals for glycine and alanine with respect to PDB survey data. It also accomplishes improved agreement with published experimental data for conformational preferences of short alanine peptides, and better accord with experimental NMR relaxation data of test protein systems. PMID:16981200

  12. 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 that the chemistry of ALPS motifs is a key parameter for membrane curvature sensitivity, which can be further modulated by the surrounding protein backbone. PMID:26366573

  13. Exposing hidden alternative backbone conformations in X-ray crystallography using qFit

    DOE PAGESBeta

    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 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

  14. 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.

  15. 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.

  16. Integrating the university medical center. Phase one: providing an information backbone.

    PubMed Central

    Berry, S. J.; Reber, E.; Offeman, W. E.

    1991-01-01

    UCLA School of Medicine represents a diverse computing community where the creation of each individual network has been driven by applications, price/performance and functionality. Indeed, the ability to connect to other computers has had no bearing on selection. Yet, there exists a need to seamlessly connect the individual networks to other minicomputers, mainframes and remote computers. We have created a school wide backbone network that will enable an individual from a single workstation to access a wide variety of services residing on any number of machines. PMID:1807658

  17. Biohybrid Branched Copolymers of Controlled Nanostructure Based on Polyacrylamide Grafted to Dextran or Dextran Sulphate Backbone

    NASA Astrophysics Data System (ADS)

    Kutsevol, N.; Soushko, R.; Guenet, J.-M.; Melnyk, N.

    2008-08-01

    Branched polymers Dextran-graft-Polyacrylamide and Dextran Sulphate-graft-Polyacrylamide copolymers with long polysaccharide backbone and various amount and length of PAA-grafts were synthesised by radical polymerization using Ce(IV)/HNO3 redox system. It was established, that these copolymers have expanded conformation in solution and are able to intramolecular structure formation. Grafting efficiency is conditioned by amount of initiator and Dextran (or Dextran Sulphate) conformation in solution. It was shown that increase in content of copolymer Polyacrylamide component in Dextran Sulphate-graft-Polyacrylamide copolymers causes decrease in size of macromolecule due to blocking of polyion charge of main polysaccharide chain by counterions.

  18. 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; Woo Hwang, Sung; Jeon, Heonsu

    2016-03-17

    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. PMID:26935411

  19. Design of peptide standards with the same composition and minimal sequence variation (SCMSV) to monitor performance/selectivity of reversed-phase matrices

    PubMed Central

    Mant, Colin T.; Hodges, Robert S.

    2012-01-01

    The present manuscript extends our de novo peptide design approach to the synthesis and evaluation of a new generation of reversed-phase HPLC peptide standards with the same composition and minimal sequence variation (SCMSV). Thus, we have designed and synthesized four series of peptide standards with the sequences Gly-X-Leu-Gly-Leu-Ala-Leu-Gly-Gly-Leu-Lys-Lys-amide, where the N-terminal is either Nα-acetylated (Series 1) or contains a free α-amino group (Series 3); and Gly-Gly-Leu-Gly-Gly-Ala-Leu-Gly-X-Leu-Lys-Lys-amide, where the N-terminal is either Nα-acetylated (Series 2) or contains a free α-amino group (Series 4). In this initial study, the single substitution position, X, was substituted with alkyl side-chains (Ala

  20. Design of peptide standards with the same composition and minimal sequence variation to monitor performance/selectivity of reversed-phase matrices.

    PubMed

    Mant, Colin T; Hodges, Robert S

    2012-03-23

    The present manuscript extends our de novo peptide design approach to the synthesis and evaluation of a new generation of reversed-phase HPLC peptide standards with the same composition and minimal sequence variation (SCMSV). Thus, we have designed and synthesized four series of peptide standards with the sequences Gly-X-Leu-Gly-Leu-Ala-Leu-Gly-Gly-Leu-Lys-Lys-amide, where the N-terminal is either N(α)-acetylated (Series 1) or contains a free α-amino group (Series 3); and Gly-Gly-Leu-Gly-Gly-Ala-Leu-Gly-X-Leu-Lys-Lys-amide, where the N-terminal is either N(α)-acetylated (Series 2) or contains a free α-amino group (Series 4). In this initial study, the single substitution position, X, was substituted with alkyl side-chains (Ala

  1. Redox-controlled backbone dynamics of human cytochrome c revealed by {sup 15}N NMR relaxation measurements

    SciTech Connect

    Sakamoto, Koichi; Kamiya, Masakatsu; Faculty of Advanced Life Science, Hokkaido University, Sapporo 060-0810 ; Uchida, Takeshi; Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo 060-0810 ; Kawano, Keiichi; Faculty of Advanced Life Science, Hokkaido University, Sapporo 060-0810 ; Ishimori, Koichiro; Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo 060-0810

    2010-07-23

    Research highlights: {yields} The dynamic parameters for the backbone dynamics in Cyt c were determined. {yields} The backbone mobility of Cyt c is highly restricted due to the covalently bound heme. {yields} The backbone mobility of Cyt c is more restricted upon the oxidation of the heme. {yields} The redox-dependent dynamics are shown in the backbone of Cyt c. {yields} The backbone dynamics of Cyt c would regulate the electron transfer from Cyt c. -- Abstract: Redox-controlled backbone dynamics in cytochrome c (Cyt c) were revealed by 2D {sup 15}N NMR relaxation experiments. {sup 15}N T{sub 1} and T{sub 2} values and {sup 1}H-{sup 15}N NOEs of uniformly {sup 15}N-labeled reduced and oxidized Cyt c were measured, and the generalized order parameters (S{sup 2}), the effective correlation time for internal motion ({tau}{sub e}), the {sup 15}N exchange broadening contributions (R{sub ex}) for each residue, and the overall correlation time ({tau}{sub m}) were estimated by model-free dynamics formalism. These dynamic parameters clearly showed that the backbone dynamics of Cyt c are highly restricted due to the covalently bound heme that functions as the stable hydrophobic core. Upon oxidation of the heme iron in Cyt c, the average S{sup 2} value was increased from 0.88 {+-} 0.01 to 0.92 {+-} 0.01, demonstrating that the mobility of the backbone is further restricted in the oxidized form. Such increases in the S{sup 2} values were more prominent in the loop regions, including amino acid residues near the thioether bonds to the heme moiety and positively charged region around Lys87. Both of the regions are supposed to form the interaction site for cytochrome c oxidase (CcO) and the electron pathway from Cyt c to CcO. The redox-dependent mobility of the backbone in the interaction site for the electron transfer to CcO suggests an electron transfer mechanism regulated by the backbone dynamics in the Cyt c-CcO system.

  2. DNA sequences and composition from 12 BAC clones-derived MUSB SSR markers mapped to cotton (Gossypium Hirsutum L. x G. Barbadense L.)chromosomes 11 and 21

    Technology Transfer Automated Retrieval System (TEKTRAN)

    To discover resistance (R) and/or pathogen-induced (PR) genes involved in disease response, 12 bacterial artificial chromosome (BAC) clones from cv. Acala Maxxa (G. hirsutum) were sequenced at the Clemson University, Genomics Institute, Clemson, SC. These BACs derived MUSB single sequence repeat (SS...

  3. Anion-conducting polymer, composition, and membrane

    DOEpatents

    Pivovar, Bryan S.; Thorn, David L.

    2009-09-01

    Anion-conducing polymers and membranes with enhanced stability to aqueous alkali include a polymer backbone with attached sulfonium, phosphazenium, phosphazene, and guanidinium residues. Compositions also with enhanced stability to aqueous alkali include a support embedded with sulfonium, phosphazenium, and guanidinium salts.

  4. Anion-conducting polymer, composition, and membrane

    DOEpatents

    Pivovar, Bryan S.; Thorn, David L.

    2010-12-07

    Anion-conducing polymers and membranes with enhanced stability to aqueous alkali include a polymer backbone with attached sulfonium, phosphazenium, phosphazene, and guanidinium residues. Compositions also with enhanced stability to aqueous alkali include a support embedded with sulfonium, phosphazenium, and guanidinium salts.

  5. Anion-conducting polymer, composition, and membrane

    DOEpatents

    Pivovar, Bryan S.; Thorn, David L.

    2011-11-22

    Anion-conducing polymers and membranes with enhanced stability to aqueous alkali include a polymer backbone with attached sulfonium, phosphazenium, phosphazene, and guanidinium residues. Compositions also with enhanced stability to aqueous alkali include a support embedded with sulfonium, phosphazenium, and guanidinium salts.

  6. Anion-Conducting Polymer, Composition, and Membrane

    DOEpatents

    Pivovar, Bryan S.; Thorn, David L.

    2008-10-21

    Anion-conducing polymers and membranes with enhanced stability to aqueous alkali include a polymer backbone with attached sulfonium, phosphazenium, phosphazene, and guanidinium residues. Compositions also with enhanced stability to aqueous alkali include a support embedded with sulfonium, phosphazenium, and guanidinium salts.

  7. Structure and Assembly of Group B Streptococcus Pilus 2b Backbone Protein

    PubMed Central

    Cozzi, Roberta; Malito, Enrico; Lazzarin, Maddalena; Nuccitelli, Annalisa; Castagnetti, Andrea; Bottomley, Matthew J.; Margarit, Immaculada; Maione, Domenico; Rinaudo, C. Daniela

    2015-01-01

    Group B Streptococcus (GBS) is a major cause of invasive disease in infants. Like other Gram-positive bacteria, GBS uses a sortase C-catalyzed transpeptidation mechanism to generate cell surface pili from backbone and ancillary pilin precursor substrates. The three pilus types identified in GBS contain structural subunits that are highly immunogenic and are promising candidates for the development of a broadly-protective vaccine. Here we report the X-ray crystal structure of the backbone protein of pilus 2b (BP-2b) at 1.06Å resolution. The structure reveals a classical IgG-like fold typical of the pilin subunits of other Gram-positive bacteria. The crystallized portion of the protein (residues 185-468) encompasses domains D2 and D3 that together confer high stability to the protein due to the presence of an internal isopeptide bond within each domain. The D2+D3 region, lacking the N-terminal D1 domain, was as potent as the entire protein in conferring protection against GBS challenge in a well-established mouse model. By site-directed mutagenesis and complementation studies in GBS knock-out strains we identified the residues and motives essential for assembly of the BP-2b monomers into high-molecular weight complexes, thus providing new insights into pilus 2b polymerization. PMID:25942637

  8. 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.

  9. The Nanomechanical Properties of Lactococcus lactis Pili Are Conditioned by the Polymerized Backbone Pilin.

    PubMed

    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

  10. Phosphorothioate backbone modifications of nucleotide-based drugs are potent platelet activators.

    PubMed

    Flierl, Ulrike; Nero, Tracy L; Lim, Bock; Arthur, Jane F; Yao, Yu; Jung, Stephanie M; Gitz, Eelo; Pollitt, Alice Y; Zaldivia, Maria T K; Jandrot-Perrus, Martine; Schäfer, Andreas; Nieswandt, Bernhard; Andrews, Robert K; Parker, Michael W; Gardiner, Elizabeth E; Peter, Karlheinz

    2015-02-01

    Nucleotide-based drug candidates such as antisense oligonucleotides, aptamers, immunoreceptor-activating nucleotides, or (anti)microRNAs hold great therapeutic promise for many human diseases. Phosphorothioate (PS) backbone modification of nucleotide-based drugs is common practice to protect these promising drug candidates from rapid degradation by plasma and intracellular nucleases. Effects of the changes in physicochemical properties associated with PS modification on platelets have not been elucidated so far. Here we report the unexpected binding of PS-modified oligonucleotides to platelets eliciting strong platelet activation, signaling, reactive oxygen species generation, adhesion, spreading, aggregation, and thrombus formation in vitro and in vivo. Mechanistically, the platelet-specific receptor glycoprotein VI (GPVI) mediates these platelet-activating effects. Notably, platelets from GPVI function-deficient patients do not exhibit binding of PS-modified oligonucleotides, and platelet activation is fully abolished. Our data demonstrate a novel, unexpected, PS backbone-dependent, platelet-activating effect of nucleotide-based drug candidates mediated by GPVI. This unforeseen effect should be considered in the ongoing development programs for the broad range of upcoming and promising DNA/RNA therapeutics. PMID:25646267

  11. First-principles study of the effect of functional groups on polyaniline backbone

    NASA Astrophysics Data System (ADS)

    Chen, X. P.; Jiang, J. K.; Liang, Q. H.; Yang, N.; Ye, H. Y.; Cai, M.; Shen, L.; Yang, D. G.; Ren, T. L.

    2015-11-01

    We present a first-principles density functional theory study focused on how the chemical and electronic properties of polyaniline are adjusted by introducing suitable substituents on a polymer backbone. Analyses of the obtained energy barriers, reaction energies and minimum energy paths indicate that the chemical reactivity of the polyaniline derivatives is significantly enhanced by protonic acid doping of the substituted materials. Further study of the density of states at the Fermi level, band gap, HOMO and LUMO shows that both the unprotonated and protonated states of these polyanilines are altered to different degrees depending on the functional group. We also note that changes in both the chemical and electronic properties are very sensitive to the polarity and size of the functional group. It is worth noting that these changes do not substantially alter the inherent chemical and electronic properties of polyaniline. Our results demonstrate that introducing different functional groups on a polymer backbone is an effective approach to obtain tailored conductive polymers with desirable properties while retaining their intrinsic properties, such as conductivity.

  12. First-principles study of the effect of functional groups on polyaniline backbone

    PubMed Central

    Chen, X. P.; Jiang, J. K.; Liang, Q. H.; Yang, N.; Ye, H. Y.; Cai, M.; Shen, L.; Yang, D. G.; Ren, T. L.

    2015-01-01

    We present a first-principles density functional theory study focused on how the chemical and electronic properties of polyaniline are adjusted by introducing suitable substituents on a polymer backbone. Analyses of the obtained energy barriers, reaction energies and minimum energy paths indicate that the chemical reactivity of the polyaniline derivatives is significantly enhanced by protonic acid doping of the substituted materials. Further study of the density of states at the Fermi level, band gap, HOMO and LUMO shows that both the unprotonated and protonated states of these polyanilines are altered to different degrees depending on the functional group. We also note that changes in both the chemical and electronic properties are very sensitive to the polarity and size of the functional group. It is worth noting that these changes do not substantially alter the inherent chemical and electronic properties of polyaniline. Our results demonstrate that introducing different functional groups on a polymer backbone is an effective approach to obtain tailored conductive polymers with desirable properties while retaining their intrinsic properties, such as conductivity. PMID:26584671

  13. 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

    2016-05-01

    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. PMID:27077449

  14. First-principles study of the effect of functional groups on polyaniline backbone.

    PubMed

    Chen, X P; Jiang, J K; Liang, Q H; Yang, N; Ye, H Y; Cai, M; Shen, L; Yang, D G; Ren, T L

    2015-01-01

    We present a first-principles density functional theory study focused on how the chemical and electronic properties of polyaniline are adjusted by introducing suitable substituents on a polymer backbone. Analyses of the obtained energy barriers, reaction energies and minimum energy paths indicate that the chemical reactivity of the polyaniline derivatives is significantly enhanced by protonic acid doping of the substituted materials. Further study of the density of states at the Fermi level, band gap, HOMO and LUMO shows that both the unprotonated and protonated states of these polyanilines are altered to different degrees depending on the functional group. We also note that changes in both the chemical and electronic properties are very sensitive to the polarity and size of the functional group. It is worth noting that these changes do not substantially alter the inherent chemical and electronic properties of polyaniline. Our results demonstrate that introducing different functional groups on a polymer backbone is an effective approach to obtain tailored conductive polymers with desirable properties while retaining their intrinsic properties, such as conductivity. PMID:26584671

  15. Colloidal quantum dot lasers built on a passive two-dimensional photonic crystal backbone

    NASA Astrophysics Data System (ADS)

    Chang, Hojun; Min, Kyungtaek; Lee, Myungjae; Kang, Minsu; Park, Yeonsang; Cho, Kyung-Sang; Roh, Young-Geun; Woo Hwang, Sung; Jeon, Heonsu

    2016-03-01

    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.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. Electronic supplementary information (ESI) available. See DOI: 10.1039/c5nr08544f

  16. Osmolyte effects on protein stability and solubility: a balancing act between backbone and side-chains

    PubMed Central

    Auton, Matthew; Rösgen, Jörg; Sinev, Mikhail; Holthauzen, Luis Marcelo F.; Bolen, D. Wayne

    2011-01-01

    In adaptation biology the discovery of intracellular osmolyte molecules that in some cases reach molar levels, raises questions of how they influence protein thermodynamics. We’ve addressed such questions using the premise that from atomic coordinates, the transfer free energy of a native protein (ΔGtr,N) can be predicted by summing measured water-to-osmolyte transfer free energies of the protein’s solvent exposed side chain and backbone component parts. ΔGtr,D is predicted using a self avoiding random coil model for the protein, and ΔGtr,D − ΔGtr,N, predicts the m-value, a quantity that measures the osmolyte effect on the N ⇌ D transition. Using literature and newly measured m-values we show 1:1 correspondence between predicted and measured m-values covering a range of 12 kcal/mol/M in protein stability for 46 proteins and 9 different osmolytes. Osmolytes present a range of side chain and backbone effects on N and D solubility and protein stability key to their biological roles. PMID:21683504

  17. Highly stable alkaline polymer electrolyte based on a poly(ether ether ketone) backbone.

    PubMed

    Han, Juanjuan; Peng, Hanqing; Pan, Jing; Wei, Ling; Li, Guangwei; Chen, Chen; Xiao, Li; Lu, Juntao; Zhuang, Lin

    2013-12-26

    Alkaline polymer electrolyte fuel cells (APEFCs) promise the use of nonprecious metal catalysts and thus have attracted much research attention in the recent decade. Among the challenges of developing practical APEFC technology, the chemical stability of alkaline polymer electrolytes (APEs) seems to be rather difficult. Research found that, upon attachment of a cationic functional group, an originally stable polymer backbone, such as polysulfone (PSF), would degrade in an alkaline environment. In the present work, we try to employ poly(ether ether ketone) (PEEK), a very inert engineering plastic, as the backbone of APEs. The PEEK is functionalized with both a sulfonic acid (SA) group and a quaternary ammonia (QA) group, with the latter as the majority amount. Ionic cross-linking between SA and QA has rendered the thus-obtained membrane (xQAPEEK) with high mechanical strength and low swelling degree. More importantly, the xQAPEEK membrane exhibits outstanding stability in a 1 mol/L KOH solution at 80 C for a test period of 30 days: the total weight loss of xQAPEEK is only 6 wt %, in comparison to a large degradation of quaternary ammonia PSF (more than 40 wt %) under the same conditions. Our findings not only have demonstrated an effective approach to preparing PEEK-based APE but also cast a new light on the development of highly stable APEs for fuel-cell application. PMID:24229363

  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. 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

  20. 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. PMID:26493308

  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. Conformation-dependent backbone geometry restraints set a new standard for protein crystallographic refinement

    DOE PAGESBeta

    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)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

  3. Solution NMR analysis of the interaction between the actinoporin sticholysin I and DHPC micelles--correlation with backbone dynamics.

    PubMed

    Lpez-Castilla, Aracelys; Pazos, Fabiola; Schreier, Shirley; Pires, Jos Ricardo

    2014-06-01

    Sticholysin I (StI), an actinoporin expressed as a water-soluble protein by the sea anemone Stichodactyla helianthus, binds to natural and model membranes, forming oligomeric pores. It is proposed that the first event of a multistep pore formation mechanism consists of the monomeric protein attachment to the lipid bilayer. To date there is no high-resolution structure of the actinoporin pore or other membrane-bound form available. Here we evaluated StI:micelle complexes of variable lipid composition to look for a suitable model for NMR studies. Micelles of pure or mixed lysophospholipids and of dihexanoyl phosphatidylcholine (DHPC) were examined. The StI:DHPC micelle was found to be the best system, yielding a stable sample and good quality spectra. A comprehensive chemical shift perturbation analysis was performed to map the StI membrane recognition site in the presence of DHPC micelles. The region mapped (residues F(51), R(52), S(53) in loop 3; F(107), D(108), Y(109), W(111), Y(112), W(115) in loop 7; Q(129), Y(132), D(134), M(135), Y(136), Y(137), G(138) in helix-?2) is in agreement with previously reported data, but additional residues were found to interact, especially residues V(81), A(82), T(83), G(84) in loop 5, and A(85), A(87) in strand-?5. Backbone dynamics measurements of StI free in solution and bound to micelles highlighted the relevance of protein flexibility for membrane binding and suggested that a conformer selection process may take place during protein-membrane interaction. We conclude that the StI:DHPC micelles system is a suitable model for further characterization of an actinoporin membrane-bound form by solution NMR. PMID:24218049

  4. SDRL: a sequence-dependent protein side-chain rotamer library.

    PubMed

    Taghizadeh, Mohammad; Goliaei, Bahram; Madadkar-Sobhani, Armin

    2015-07-01

    Since the introduction of the first protein side-chain rotamer library (RL) almost half a century ago, RLs have been components of many programs and algorithms in structural bioinformatics. Based on the dependence of side-chain dihedral angles on the local backbone, three types of RLs have been identified: backbone-independent, secondary-structure-dependent and backbone-dependent. In all previous studies, the effect of sequence specificity on side-chain conformational preferences was neglected. In the effort to develop a new class of RLs, we considered that the side-chain conformation of the central residue in each triplet on a protein backbone depends on the sequence of the triplet; therefore, we developed a sequence-dependent rotamer library (SDRL). To accomplish this, 400 possible triplet sequences for 18 natural amino acids as the central residue, which corresponds to 7200 triplet sequences in total, were considered. Searching the set of 11 546 selected PDB entries for the 7200 triplet sequences resulted in 2 364 541 instances occurring for 18 amino acids. Our results show that Leu and Val experience minimal impact from the adjacent residues in adopting side-chain conformations. Cys, Ile, Trp, His, Asp, Met, Glu, Gln, Arg and Lys, on the other hand, adopt their side-chain conformations mostly based on the adjacent residues on the backbone. The remaining residue types were moderately dependent on the adjacent residues. Using the new library, side-chain repacking algorithms can find preferred conformations of each residue more easily than with other backbone-independent RLs. PMID:25953624

  5. Computational Design of the Sequence and Structure of a Protein-Binding Peptide

    SciTech Connect

    Sammond, Deanne W.; Bosch, Dustin E.; Butterfoss, Glenn L.; Purbeck, Carrie; Machius, Mischa; Siderovski, David P.; Kuhlman, Brian

    2012-08-10

    The de novo design of protein-binding peptides is challenging because it requires the identification of both a sequence and a backbone conformation favorable for binding. We used a computational strategy that iterates between structure and sequence optimization to redesign the C-terminal portion of the RGS14 GoLoco motif peptide so that it adopts a new conformation when bound to G{alpha}{sub i1}. An X-ray crystal structure of the redesigned complex closely matches the computational model, with a backbone root-mean-square deviation of 1.1 {angstrom}.

  6. Transcriptome Sequencing and Expression Analysis of Terpenoid Biosynthesis Genes in Litsea cubeba

    PubMed Central

    Han, Xiao-Jiao; Wang, Yang-Dong; Chen, Yi-Cun; Lin, Li-Yuan; Wu, Qing-Ke

    2013-01-01

    Background Aromatic essential oils extracted from fresh fruits of Litsea cubeba (Lour.) Pers., have diverse medical and economic values. The dominant components in these essential oils are monoterpenes and sesquiterpenes. Understanding the molecular mechanisms of terpenoid biosynthesis is essential for improving the yield and quality of terpenes. However, the 40 available L. cubeba nucleotide sequences in the public databases are insufficient for studying the molecular mechanisms. Thus, high-throughput transcriptome sequencing of L. cubeba is necessary to generate large quantities of transcript sequences for the purpose of gene discovery, especially terpenoid biosynthesis related genes. Results Using Illumina paired-end sequencing, approximately 23.5 million high-quality reads were generated. De novo assembly yielded 68,648 unigenes with an average length of 834 bp. A total of 38,439 (56%) unigenes were annotated for their functions, and 35,732 and 25,806 unigenes could be aligned to the GO and COG database, respectively. By searching against the Kyoto Encyclopedia of Genes and Genomes Pathway database (KEGG), 16,130 unigenes were assigned to 297 KEGG pathways, and 61 unigenes, which contained the mevalonate and 2-C-methyl-D-erythritol 4-phosphate pathways, could be related to terpenoid backbone biosynthesis. Of the 12,963 unigenes, 285 were annotated to the terpenoid pathways using the PlantCyc database. Additionally, 14 terpene synthase genes were identified from the transcriptome. The expression patterns of the 16 genes related to terpenoid biosynthesis were analyzed by RT-qPCR to explore their putative functions. Conclusion RNA sequencing was effective in identifying a large quantity of sequence information. To our knowledge, this study is the first exploration of the L. cubeba transcriptome, and the substantial amount of transcripts obtained will accelerate the understanding of the molecular mechanisms of essential oils biosynthesis. The results may help improve future genetic and genomics studies on the molecular mechanisms behind the chemical composition of essential oils in L. cubeba fruits. PMID:24130803

  7. Effect of backbone chemistry on hybridization thermodynamics of oligonucleic acids: a coarse-grained molecular dynamics simulation study.

    PubMed

    Ghobadi, Ahmadreza F; Jayaraman, Arthi

    2016-02-17

    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. PMID:26777980

  8. A smoothed backbone-dependent rotamer library for proteins derived from adaptive kernel density estimates and regressions

    PubMed Central

    Shapovalov, Maxim V.; Dunbrack, Roland L.

    2011-01-01

    Rotamer libraries are used in protein structure determination, structure prediction, and design. The backbone-dependent rotamer library consists of rotamer frequencies and their mean dihedral angles and variances as a function of the backbone dihedral angles ϕ and ψ. Previous versions of this rotamer library were not developed with smoothness in mind, although some structure prediction and protein design methods would strongly benefit from smoothing. A new version of the backbone-dependent rotamer library has been developed using adaptive kernel density estimates for the rotamer frequencies and adaptive kernel regression for the mean dihedral angles and variances. The formulation presented allows for evaluation of the rotamer probabilities, mean angles and variances at any ϕ, ψ point, i.e. as a continuous function of ϕ and ψ. Continuous probability density estimates for the non-rotameric degrees of freedom of amides, carboxylates, and aromatic side chains have been modeled as a function of the backbone dihedral angles and rotamers of the remaining degrees of freedom. New backbone-dependent rotamer libraries at varying levels of smoothing are available from http://dunbrack.fccc.edu. PMID:21645855

  9. 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.

  10. EMSCOPE - Electromagnetic Component of EarthScope Backbone and Transportable Array Experiments 2006-2008

    NASA Astrophysics Data System (ADS)

    Egbert, G.; Evans, R.; Ingate, S.; Livelybrooks, D.; Mickus, K.; Park, S.; Schultz, A.; Unsworth, M.; Wannamaker, P.

    2007-12-01

    USArray (http://www.iris.edu/USArray) in conjunction with EMSOC (Electromagnetic Studies of the Continents) (http://emsoc.ucr.edu/emsoc) is installing magnetotelluric (MT) stations as part of Earthscope. The MT component of Earthscope consists of permanent (Backbone) and transportable long period stations to record naturally occurring, time varying electric and magnetic fields to produce a regional lithospheric/asthensospheric electrical conductivity map of the United States. The recent arrival of 28 long period MT instruments allows for the final installation of the Backbone stations throughout the US and yearly transportable array studies. The Backbone MT survey consists of 7 stations spaced throughout the continental US with preliminary installation at Soap Creek, Oregon; Parkfield, California; Braden, Missouri and Socorro, New Mexico.Siting and permitting are underway or completed at stations in eastern Montana, northern Wisconsin and Virginia. These stations will be recording for at least five years to determine electrical conductivities at depths that extend into the mantle transition zone. The first transportable array experiment was performed in the summer and fall of 2006 in central and eastern Oregon (Oregon Pilot Project) using equipment loaned from EMSOC. Thirty-one long period MT stations were recorded with 14 to 21 day occupations. Preliminary 3D inverse models indicate several lithospheric electrical conductivity anomalies including a linear zone marked by low-high conductivity transition along the Klamath-Blue Mountain Lineament associated with a linear trend of gravity minima. High electrical conductivity values occur in the upper crust under the accreted terrains in the Blue Mountains region. The second transportable array experiment was performed in the summer and fall of 2007 and completes coverage of the Oregon, Washington, and western Idaho, targeting the Cascadia subduction zone, Precambrian boundaries, and sub-basalt lithologies. The 2008 transportable MT experiment will focus on the Snake River Plain and the Yellowstone Hot Spot. The disposition of future USArray magnetotelluric geotransects will be the subject of an upcoming NSF-supported planning workshop. Time series are available now from the IRIS data center (www.iris.edu/data), and magnetotelluric transfer functions will soon be available.

  11. Oligo(p-phenylene-ethynylene)s with backbone conformation controlled by competitive intramolecular hydrogen bonds.

    PubMed

    Hu, Wei; Yan, Qifan; Zhao, Dahui

    2011-06-14

    A series of conjugated oligo(p-phenylene-ethynylene) (OPE) molecules with backbone conformations (that is, the relative orientations of the contained phenylene units) controlled by competitive intramolecular hydrogen bonds to be either co-planar or random were synthesised and studied. In these oligomers, carboxylate and amido substituents were attached to alternate phenylene units in the OPE backbone. These functional groups were able to form intramolecular hydrogen bonds between neighbouring phenylene units. Thereby, all phenylene units in the backbone were confined in a co-planar conformation. This planarised structure featured a more extended effective conjugation length than that of regular OPEs with phenylene units adopting random orientation due to a low rotational-energy barrier. However, if a tri(ethylene glycol) (Tg) side chain was appended to the amido group, it enabled another type of intramolecular hydrogen bond, formed by the Tg chain folding back and the contained ether oxygen atom competing with the ester carbonyl group as the hydrogen-bond acceptor. The outcome of this competition was proven to depend on the length of the alkylene linker joining the ether oxygen atom to the amido group. Specifically, if the Tg chain folded back to form a five-membered cyclic structure, this hydrogen-bonding motif was sufficiently robust to overrule the hydrogen bonds between adjacent phenylene units. Consequently, the oligomers assumed non-planar conformations. However, if the side chain formed a six-membered ring by hydrogen bonding with the amido NH group, such a motif was much less stable and yielded in the competition with the ester carbonyl group from the adjacent phenylene unit. Thus, the hydrogen bonds between the phenylene units remained, and the co-planar conformation was manifested. In our system, the hydrogen bonds formed by the back-folded Tg chain and amido NH group relied on a single oxygen atom as the hydrogen-bond acceptor. The additional oxygen atoms in the Tg chain made a negligible contribution. A bifurcated hydrogen-bond motif was unimportant. From our results, in combination with the results from an independent study by Meijer et al., it is evident that intramolecular hydrogen bonds involving back-folded oligo(ethylene glycol) moieties may differ in their structural details. Absorption spectroscopy served as a convenient yet sensitive technique for analysing hydrogen-bonding motifs in our study. PMID:21557348

  12. Sequence composition of BAC clones and SSR markers mapped to Upland cotton chromosomes 11 and 21 targeting resistance to soil-borne pathogens

    PubMed Central

    Wang, Congli; Ulloa, Mauricio; Shi, Xinyi; Yuan, Xiaohui; Saski, Christopher; Yu, John Z.; Roberts, Philip A.

    2015-01-01

    Genetic and physical framework mapping in cotton (Gossypium spp.) were used to discover putative gene sequences involved in resistance to common soil-borne pathogens. Chromosome (Chr) 11 and its homoeologous Chr 21 of Upland cotton (G. hirsutum) are foci for discovery of resistance (R) or pathogen-induced R (PR) genes underlying QTLs involved in response to root-knot nematode (Meloidogyne incognita), reniform nematode (Rotylenchulus reniformis), Fusarium wilt (Fusarium oxysporum f.sp. vasinfectum), Verticillium wilt (Verticillium dahliae), and black root rot (Thielaviopsis basicola). Simple sequence repeat (SSR) markers and bacterial artificial chromosome (BAC) clones from a BAC library developed from the Upland cotton Acala Maxxa were mapped on Chr 11 and Chr 21. DNA sequence through Gene Ontology (GO) of 99 of 256 Chr 11 and 109 of 239 Chr 21 previously mapped SSRs revealed response elements to internal and external stimulus, stress, signaling process, and cell death. The reconciliation between genetic and physical mapping of gene annotations from new DNA sequences of 20 BAC clones revealed 467 (Chr 11) and 285 (Chr 21) G. hirsutum putative coding sequences, plus 146 (Chr 11) and 98 (Chr 21) predicted genes. GO functional profiling of Unigenes uncovered genes involved in different metabolic functions and stress response elements (SRE). Our results revealed that Chrs 11 and 21 harbor resistance gene rich genomic regions. Sequence comparisons with the ancestral diploid D5 (G. raimondii), A2 (G. arboreum) and domesticated tetraploid TM-1 AD1 (G. hirsutum) genomes revealed abundance of transposable elements and confirmed the richness of resistance gene motifs in these chromosomes. The sequence information of SSR markers and BAC clones and the genetic mapping of BAC clones provide enhanced genetic and physical frameworks of resistance gene-rich regions of the cotton genome, thereby aiding discovery of R and PR genes and breeding for resistance to cotton diseases. PMID:26483808

  13. Sequence composition of BAC clones and SSR markers mapped to Upland cotton chromosomes 11 and 21 targeting resistance to soil-borne pathogens.

    PubMed

    Wang, Congli; Ulloa, Mauricio; Shi, Xinyi; Yuan, Xiaohui; Saski, Christopher; Yu, John Z; Roberts, Philip A

    2015-01-01

    Genetic and physical framework mapping in cotton (Gossypium spp.) were used to discover putative gene sequences involved in resistance to common soil-borne pathogens. Chromosome (Chr) 11 and its homoeologous Chr 21 of Upland cotton (G. hirsutum) are foci for discovery of resistance (R) or pathogen-induced R (PR) genes underlying QTLs involved in response to root-knot nematode (Meloidogyne incognita), reniform nematode (Rotylenchulus reniformis), Fusarium wilt (Fusarium oxysporum f.sp. vasinfectum), Verticillium wilt (Verticillium dahliae), and black root rot (Thielaviopsis basicola). Simple sequence repeat (SSR) markers and bacterial artificial chromosome (BAC) clones from a BAC library developed from the Upland cotton Acala Maxxa were mapped on Chr 11 and Chr 21. DNA sequence through Gene Ontology (GO) of 99 of 256 Chr 11 and 109 of 239 Chr 21 previously mapped SSRs revealed response elements to internal and external stimulus, stress, signaling process, and cell death. The reconciliation between genetic and physical mapping of gene annotations from new DNA sequences of 20 BAC clones revealed 467 (Chr 11) and 285 (Chr 21) G. hirsutum putative coding sequences, plus 146 (Chr 11) and 98 (Chr 21) predicted genes. GO functional profiling of Unigenes uncovered genes involved in different metabolic functions and stress response elements (SRE). Our results revealed that Chrs 11 and 21 harbor resistance gene rich genomic regions. Sequence comparisons with the ancestral diploid D5 (G. raimondii), A2 (G. arboreum) and domesticated tetraploid TM-1 AD1 (G. hirsutum) genomes revealed abundance of transposable elements and confirmed the richness of resistance gene motifs in these chromosomes. The sequence information of SSR markers and BAC clones and the genetic mapping of BAC clones provide enhanced genetic and physical frameworks of resistance gene-rich regions of the cotton genome, thereby aiding discovery of R and PR genes and breeding for resistance to cotton diseases. PMID:26483808

  14. Maize Mu transposons are targeted to the 5' untranslated region of the gl8 gene and sequences flanking Mu target-site duplications exhibit nonrandom nucleotide composition throughout the genome.

    PubMed Central

    Dietrich, Charles R; Cui, Feng; Packila, Mark L; Li, Jin; Ashlock, Daniel A; Nikolau, Basil J; Schnable, Patrick S

    2002-01-01

    The widespread use of the maize Mutator (Mu) system to generate mutants exploits the preference of Mu transposons to insert into genic regions. However, little is known about the specificity of Mu insertions within genes. Analysis of 79 independently isolated Mu-induced alleles at the gl8 locus established that at least 75 contain Mu insertions. Analysis of the terminal inverted repeats (TIRs) of the inserted transposons defined three new Mu transposons: Mu10, Mu 11, and Mu12. A large percentage (>80%) of the insertions are located in the 5' untranslated region (UTR) of the gl8 gene. Ten positions within the 5' UTR experienced multiple independent Mu insertions. Analyses of the nucleotide composition of the 9-bp TSD and the sequences directly flanking the TSD reveals that the nucleotide composition of Mu insertion sites differs dramatically from that of random DNA. In particular, the frequencies at which C's and G's are observed at positions -2 and +2 (relative to the TSD) are substantially higher than expected. Insertion sites of 315 RescueMu insertions displayed the same nonrandom nucleotide composition observed for the gl8-Mu alleles. Hence, this study provides strong evidence for the involvement of sequences flanking the TSD in Mu insertion-site selection. PMID:11861572

  15. Polarization driven covalently-bonded octahedral-twinning and backbone-peripheral-helical nanoarchitectures.

    PubMed

    Han, Xiaodong; Zheng, Shanliang; Zhang, Yuefei; Zheng, Kun; Zhang, Shengbai; Zhang, Ze; Zhang, Xiaona; Liu, Xianqiang; Chen, Gang; Hao, Yajuan; Guo, Xiangyun

    2008-08-01

    We report the novel superstructural chiral polar-surface induced backbone-peripheral-helical (BPH) hierarchical architecture of zincblende SiC made possible by precise helical epitaxy. We show by direct image that this architecture has the mother-daughter relationship. The center of the BPH consists of periodic octahedral modular units with chiral sidewalls. By forming Si-C covalent bonds at the sidewalls, a daughter SiC wire spontaneously vine-grows in a peripherally helical way on the mother wire. All of the information of the mother wire, including twinning, polarity and even stacking fault, are completely copied and inherited by the daughter wire one-by-one at the atomic level. Our findings thus provide a simple growth method and the necessary atomistic mechanism for novel polar surface driven superstructural twinning and subsequent BPH growth, which should be universal for zincblende semiconductors and even could be true for other noncentral-symmetric compounds. PMID:18616328

  16. Correlation between protein secondary structure, backbone bond angles, and side-chain orientations

    NASA Astrophysics Data System (ADS)

    Lundgren, Martin; Niemi, Antti J.

    2012-08-01

    We investigate the fine structure of the sp3 hybridized covalent bond geometry that governs the tetrahedral architecture around the central Cα carbon of a protein backbone, and for this we develop new visualization techniques to analyze high-resolution x-ray structures in the Protein Data Bank. We observe that there is a correlation between the deformations of the ideal tetrahedral symmetry and the local secondary structure of the protein. We propose a universal coarse-grained energy function to describe the ensuing side-chain geometry in terms of the Cβ carbon orientations. The energy function can model the side-chain geometry with a subatomic precision. As an example we construct the Cα-Cβ structure of HP35 chicken villin headpiece. We obtain a configuration that deviates less than 0.4 Å in root-mean-square distance from the experimental x-ray structure.

  17. Monolignol ferulate transferase introduces chemically labile linkages into the lignin backbone.

    PubMed

    Wilkerson, C G; Mansfield, S D; Lu, F; Withers, S; Park, J-Y; Karlen, S D; Gonzales-Vigil, E; Padmakshan, D; Unda, F; Rencoret, J; Ralph, J

    2014-04-01

    Redesigning lignin, the aromatic polymer fortifying plant cell walls, to be more amenable to chemical depolymerization can lower the energy required for industrial processing. We have engineered poplar trees to introduce ester linkages into the lignin polymer backbone by augmenting the monomer pool with monolignol ferulate conjugates. Herein, we describe the isolation of a transferase gene capable of forming these conjugates and its xylem-specific introduction into poplar. Enzyme kinetics, in planta expression, lignin structural analysis, and improved cell wall digestibility after mild alkaline pretreatment demonstrate that these trees produce the monolignol ferulate conjugates, export them to the wall, and use them during lignification. Tailoring plants to use such conjugates during cell wall biosynthesis is a promising way to produce plants that are designed for deconstruction. PMID:24700858

  18. Gene families as soft cliques with backbones: Amborella contrasted with other flowering plants

    PubMed Central

    2014-01-01

    Background Chaining is a major problem in constructing gene families. Results We define a new kind of cluster on graphs with strong and weak edges: soft cliques with backbones (SCWiB). This differs from other definitions in how it controls the "chaining effect", by ensuring clusters satisfy a tolerant edge density criterion that takes into account cluster size. We implement algorithms for decomposing a graph of similarities into SCWiBs. We compare examples of output from SCWiB and the Markov Cluster Algorithm (MCL), and also compare some curated Arabidopsis thaliana gene families with the results of automatic clustering. We apply our method to 44 published angiosperm genomes with annotation, and discover that Amborella trichopoda is distinct from all the others in having substantially and systematically smaller proportions of moderate- and large-size gene families. Conclusions We offer several possible evolutionary explanations for this result. PMID:25572777

  19. Extensive Air Showers: from the muonic smoking guns to the hadronic backbone

    NASA Astrophysics Data System (ADS)

    Cazon, L.

    2013-06-01

    Extensive Air Showers are complex macroscopic objects initiated by single ultra-high energy particles. They are the result of millions of high energy reactions in the atmosphere and can be described as the superposition of hadronic and electromagnetic cascades. The hadronic cascade is the air shower backbone, and it is mainly made of pions. Decays of neutral pions initiate electromagnetic cascades, while the decays of charged pions produce muons which leave the hadronic core and travel many kilometers almost unaffected. Muons are smoking guns of the hadronic cascade: the energy, transverse momentum, spatial distribution and depth of production are key to reconstruct the history of the air shower. In this work, we overview the phenomenology of muons on the air shower and its relation to the hadronic cascade. We briefly review the experimental efforts to analyze muons within air showers and discuss possible paths to use this information.

  20. 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.

  1. X-shooter-backbone and UV-blue and visible spectrographs: final AIV and measured performances

    NASA Astrophysics Data System (ADS)

    Rasmussen, Per Kjrgaard; Zerbi, Filippo M.; Dekker, Hans; Vernet, Joel; Andersen, Jeppe J.; De Caprio, Vincenzo; Dimarcantonio, Paolo; D'Odorico, Sandro; Lizon, Jean-Louis; Lucuix, Christian; Michaelsen, Niels; Molinari, Emilio; Nrregaard, Preben; Riva, Alberto; Riva, Marco; Santin, Paolo; Srensen, Anton N.; Span, Paolo; Wistisen, Dennis

    2008-07-01

    X-shooter is a wide band (U to K) intermediate resolution (4000-14000) single object three-arms spectrograph for the VLT. Currently in the last phase of integration, X-shooter will see the first light at ESO Paranal as the first of the VLT second generation instruments in the last quarter of 2008. We describe in this paper the final steps in the integration and testing phase of the central Backbone with its key functions (including the active flexure compensation mirrors) and of the two UV-Blue and Visible spectroscopic arms. We report on the stability results of the preslit optics and of the spectrographs and on the remarkable efficiency which is derived from the measurements of the optical components of the instrument.

  2. Facile backbone structure determination of human membrane proteins by NMR spectroscopy

    PubMed Central

    Klammt, Christian; Maslennikov, Innokentiy; Bayrhuber, Monika; Eichmann, Cédric; Vajpai, Navratna; Chiu, Ellis Jeremy Chua; Blain, Katherine Y; Esquivies, Luis; Kwon, June Hyun Jung; Balana, Bartosz; Pieper, Ursula; Sali, Andrej; Slesinger, Paul A; Kwiatkowski, Witek; Riek, Roland; Choe, Senyon

    2013-01-01

    Although nearly half of today’s major pharmaceutical drugs target human integral membrane proteins (hIMPs), only 30 hIMP structures are currently available in the Protein Data Bank, largely owing to inefficiencies in protein production. Here we describe a strategy for the rapid structure determination of hIMPs, using solution NMR spectroscopy with systematically labeled proteins produced via cell-free expression. We report new backbone structures of six hIMPs, solved in only 18 months from 15 initial targets. Application of our protocols to an additional 135 hIMPs with molecular weight <30 kDa yielded 38 hIMPs suitable for structural characterization by solution NMR spectroscopy without additional optimization. PMID:22609626

  3. Sequential backbone resonance assignments of the E. coli dihydrofolate reductase Gly67Val mutant: folate complex.

    PubMed

    Puthenpurackal Narayanan, Sunilkumar; Maeno, Akihiro; Wada, Yuji; Tate, Shin-Ichi; Akasaka, Kazuyuki

    2016-04-01

    Occasionally, a mutation in an exposed loop region causes a significant change in protein function and/or stability. A single mutation Gly67Val of E. coli dihydrofolate reductase (DHFR) in the exposed CD loop is such an example. We have carried out the chemical shift assignments for H(N), N(H), C(α) and C(β) atoms of the Gly67Val mutant of E. coli DHFR complexed with folate at pH 7.0, 35 °C, and then evaluated the H(N), N(H), C(α) and C(β) chemical shift changes caused by the mutation. The result indicates that, while the overall secondary structure remains the same, the single mutation Gly67Val causes site-specific conformational changes of the polypeptide backbone restricted around the adenosine-binding subdomain (residues 38-88) and not in the distant catalytic domain. PMID:26482924

  4. Sendai virus as a backbone for vaccines against RSV and other human paramyxoviruses.

    PubMed

    Russell, Charles J; Hurwitz, Julia L

    2016-02-01

    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. PMID:26648515

  5. A recombinant, chimeric tetravalent dengue vaccine candidate based on a dengue virus serotype 2 backbone.

    PubMed

    Osorio, Jorge E; Wallace, Derek; Stinchcomb, Dan T

    2016-04-01

    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. PMID:26635182

  6. An avian live attenuated master backbone for potential use in epidemic and pandemic influenza vaccines.

    PubMed

    Hickman, Danielle; Hossain, Md Jaber; Song, Haichen; Araya, Yonas; Solórzano, Alicia; Perez, Daniel R

    2008-11-01

    The unprecedented emergence in Asia of multiple avian influenza virus (AIV) subtypes with a broad host range poses a major challenge in the design of vaccination strategies that are both effective and available in a timely manner. The present study focused on the protective effects of a genetically modified AIV as a source for the preparation of vaccines for epidemic and pandemic influenza. It has previously been demonstrated that a live attenuated AIV based on the internal backbone of influenza A/Guinea fowl/Hong Kong/WF10/99 (H9N2), called WF10att, is effective at protecting poultry species against low- and high-pathogenicity influenza strains. More importantly, this live attenuated virus provided effective protection when administered in ovo. In order to characterize the WF10att backbone further for use in epidemic and pandemic influenza vaccines, this study evaluated its protective effects in mice. Intranasal inoculation of modified attenuated viruses in mice provided adequate protective immunity against homologous lethal challenges with both the wild-type influenza A/WSN/33 (H1N1) and A/Vietnam/1203/04 (H5N1) viruses. Adequate heterotypic immunity was also observed in mice vaccinated with modified attenuated viruses carrying H7N2 surface proteins. The results presented in this report suggest that the internal genes of a genetically modified AIV confer similar protection in a mouse model and thus could be used as a master donor strain for the generation of live attenuated vaccines for epidemic and pandemic influenza. PMID:18931063

  7. Electrostatic screening and backbone preferences of amino acid residues in urea-denatured ubiquitin

    PubMed Central

    Avbelj, Franc; Grdadolnik, Simona Golic

    2007-01-01

    Local structures in denatured proteins may be important in guiding a polypeptide chain during the folding and misfolding processes. Existence of local structures in chemically denatured proteins is a highly controversial issue. NMR parameters [coupling constants 3 J(Hα,HN) and chemical shifts] of chemically denatured proteins in general deviate little from their values in small peptides. These peptides were presumed to be completely unstructured; therefore, it was considered that chemically denatured proteins are random coils. But recent experimental studies show that small peptides adopt relatively stable structures in aqueous solutions. Small deviations of the NMR parameters from their values in small peptides may thus actually indicate the existence of local structures in chemically denatured proteins. Using NMR data and theoretical predictions we show here that fluctuating β-strands exist in urea-denatured ubiquitin (8 M urea at pH 2). Residues in such β-strands populate more frequently the left side of the broad β region of φ–ψ space. Urea-denatured ubiquitin contains no detectable β-sheet secondary structures; nevertheless, the fluctuating β-strands in urea-denatured ubiquitin coincide to the β-strands in the native state. Formation of β-strands is in accord with the electrostatic screening model of unfolded proteins. The free energy of a residue in an unfolded protein is in this model determined by the local backbone electrostatics and its screening by backbone solvation. These energy terms introduce strong electrostatic coupling between neighboring residues, which causes cooperative formation of β-strands in denatured proteins. We propose that fluctuating β-strands in denatured proteins may serve as initiation sites to form fibrils. PMID:17242431

  8. TOAC spin labels in the backbone of alamethicin: EPR studies in lipid membranes.

    PubMed

    Marsh, Derek; Jost, Micha; Peggion, Cristina; Toniolo, Claudio

    2007-01-15

    Alamethicin is a 19-amino-acid residue hydrophobic peptide that produces voltage-dependent ion channels in membranes. Analogues of the Glu(OMe)(7,18,19) variant of alamethicin F50/5 that are rigidly spin-labeled in the peptide backbone have been synthesized by replacing residue 1, 8, or 16 with 2,2,6,6-tetramethyl-piperidine-1-oxyl-4-amino-4-carboxyl (TOAC), a helicogenic nitroxyl amino acid. Conventional electron paramagnetic resonance spectra are used to determine the insertion and orientation of the TOAC(n) alamethicins in fluid lipid bilayer membranes of dimyristoyl phosphatidylcholine. Isotropic (14)N-hyperfine couplings indicate that TOAC(8) and TOAC(16) are situated in the hydrophobic core of the membrane, whereas the TOAC(1) label resides closer to the membrane surface. Anisotropic hyperfine splittings show that alamethicin is highly ordered in the fluid membranes. Experiments with aligned membranes demonstrate that the principal diffusion axis lies close to the membrane normal, corresponding to a transmembrane orientation. Combination of data from the three spin-labeled positions yields both the dynamic order parameter of the peptide backbone and the intramolecular orientations of the TOAC groups. The latter are compared with x-ray diffraction results from alamethicin crystals. Saturation transfer electron paramagnetic resonance, which is sensitive to microsecond rotational motion, reveals that overall rotation of alamethicin is fast in fluid membranes, with effective correlation times <30 ns. Thus, alamethicin does not form large stable aggregates in fluid membranes, and ionic conductance must arise from transient or voltage-induced associations. PMID:17056731

  9. TOAC Spin Labels in the Backbone of Alamethicin: EPR Studies in Lipid Membranes

    PubMed Central

    Marsh, Derek; Jost, Micha; Peggion, Cristina; Toniolo, Claudio

    2007-01-01

    Alamethicin is a 19-amino-acid residue hydrophobic peptide that produces voltage-dependent ion channels in membranes. Analogues of the Glu(OMe)7,18,19 variant of alamethicin F50/5 that are rigidly spin-labeled in the peptide backbone have been synthesized by replacing residue 1, 8, or 16 with 2,2,6,6-tetramethyl-piperidine-1-oxyl-4-amino-4-carboxyl (TOAC), a helicogenic nitroxyl amino acid. Conventional electron paramagnetic resonance spectra are used to determine the insertion and orientation of the TOACn alamethicins in fluid lipid bilayer membranes of dimyristoyl phosphatidylcholine. Isotropic 14N-hyperfine couplings indicate that TOAC8 and TOAC16 are situated in the hydrophobic core of the membrane, whereas the TOAC1 label resides closer to the membrane surface. Anisotropic hyperfine splittings show that alamethicin is highly ordered in the fluid membranes. Experiments with aligned membranes demonstrate that the principal diffusion axis lies close to the membrane normal, corresponding to a transmembrane orientation. Combination of data from the three spin-labeled positions yields both the dynamic order parameter of the peptide backbone and the intramolecular orientations of the TOAC groups. The latter are compared with x-ray diffraction results from alamethicin crystals. Saturation transfer electron paramagnetic resonance, which is sensitive to microsecond rotational motion, reveals that overall rotation of alamethicin is fast in fluid membranes, with effective correlation times <30 ns. Thus, alamethicin does not form large stable aggregates in fluid membranes, and ionic conductance must arise from transient or voltage-induced associations. PMID:17056731

  10. Statistical mechanics of protein allostery: Roles of backbone and side-chain structural fluctuations

    NASA Astrophysics Data System (ADS)

    Itoh, Kazuhito; Sasai, Masaki

    2011-03-01

    A statistical mechanical model of allosteric transition of proteins is developed by extending the structure-based model of protein folding to cases that a protein has two different native conformations. Partition function is calculated exactly within the model and free-energy surfaces associated with allostery are derived. In this paper, the model of allosteric transition proposed in a previous paper [Proc. Natl. Acad. Sci. U.S.A 134, 7775 (2010)] is reformulated to describe both fluctuation in side-chain configurations and that in backbone structures in a balanced way. The model is applied to example proteins, Ras, calmodulin, and CheY: Ras undergoes the allosteric transition between guanosine diphosphate (GDP)-bound and guanosine triphosphate (GTP)-bound forms, and the model results show that the GDP-bound form is stabilized enough to prevent unnecessary signal transmission, but the conformation in the GTP-bound state bears large fluctuation in side-chain configurations, which may help to bind multiple target proteins for multiple pathways of signaling. The calculated results of calmodulin show the scenario of sequential ordering in Ca2 + binding and the associated allosteric conformational change, which are realized though the sequential appearing of pre-existing structural fluctuations, i.e., fluctuations to show structures suitable to bind Ca2 + before its binding. Here, the pre-existing fluctuations to accept the second and third Ca2 + ions are dominated by the side-chain fluctuation. In CheY, the calculated side-chain fluctuation of Tyr106 is coordinated with the backbone structural change in the β4-α4 loop, which explains the pre-existing Y-T coupling process in this protein. Ability of the model to explain allosteric transitions of example proteins supports the view that the large entropic effects lower the free-energy barrier of allosteric transition.

  11. An avian live attenuated master backbone for potential use in epidemic and pandemic influenza vaccines

    PubMed Central

    Hickman, Danielle; Hossain, Md Jaber; Song, Haichen; Araya, Yonas; Solórzano, Alicia; Perez, Daniel R.

    2008-01-01

    The unprecedented emergence in Asia of multiple avian influenza virus (AIV) subtypes with a broad host range poses a major challenge in the design of vaccination strategies that are both effective and available in a timely manner. The present study focused on the protective effects of a genetically modified AIV as a source for the preparation of vaccines for epidemic and pandemic influenza. It has previously been demonstrated that a live attenuated AIV based on the internal backbone of influenza A/Guinea fowl/Hong Kong/WF10/99 (H9N2), called WF10att, is effective at protecting poultry species against low- and high-pathogenicity influenza strains. More importantly, this live attenuated virus provided effective protection when administered in ovo. In order to characterize the WF10att backbone further for use in epidemic and pandemic influenza vaccines, this study evaluated its protective effects in mice. Intranasal inoculation of modified attenuated viruses in mice provided adequate protective immunity against homologous lethal challenges with both the wild-type influenza A/WSN/33 (H1N1) and A/Vietnam/1203/04 (H5N1) viruses. Adequate heterotypic immunity was also observed in mice vaccinated with modified attenuated viruses carrying H7N2 surface proteins. The results presented in this report suggest that the internal genes of a genetically modified AIV confer similar protection in a mouse model and thus could be used as a master donor strain for the generation of live attenuated vaccines for epidemic and pandemic influenza. PMID:18931063

  12. 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.

  13. An effective approach for alleviating cation-induced backbone degradation in aromatic ether-based alkaline polymer electrolytes.

    PubMed

    Han, Juanjuan; Liu, Qiong; Li, Xueqi; Pan, Jing; Wei, Ling; Wu, Ying; Peng, Hanqing; Wang, Ying; Li, Guangwei; Chen, Chen; Xiao, Li; Lu, Juntao; Zhuang, Lin

    2015-02-01

    Aromatic ether-based alkaline polymer electrolytes (APEs) are one of the most popular types of APEs being used in fuel cells. However, recent studies have demonstrated that upon being grafted by proximal cations some polar groups in the backbone of such APEs can be attacked by OH(-), leading to backbone degradation in an alkaline environment. To resolve this issue, we performed a systematic study on six APEs. We first replaced the polysulfone (PS) backbone with polyphenylsulfone (PPSU) and polyphenylether (PPO), whose molecular structures contain fewer polar groups. Although improved stability was seen after this change, cation-induced degradation was still obvious. Thus, our second move was to replace the ordinary quaternary ammonia (QA) cation, which had been closely attached to the polymer backbone, with a pendant-type QA (pQA), which was linked to the backbone through a long side chain. After a stability test in a 1 mol/L KOH solution at 80 °C for 30 days, all pQA-type APEs (pQAPS, pQAPPSU, and pQAPPO) exhibited as low as 8 wt % weight loss, which is close to the level of the bare backbone (5 wt %) and remarkably lower than those of the QA-type APEs (QAPS, QAPPSU, and QAPPO), whose weight losses under the same conditions were >30%. The pQA-type APEs also possessed clear microphase segregation morphology, which led to ionic conductivities that were higher, and water uptakes and degrees of membrane swelling that were lower, than those of the QA-type APEs. These observations unambiguously indicate that designing pendant-type cations is an effective approach to increasing the chemical stability of aromatic ether-based APEs. PMID:25594224

  14. Electron Transfer Dissociation Reveals Changes in the Cleavage Frequencies of Backbone Bonds Distant to Amide-to-Ester Substitutions in Polypeptides

    NASA Astrophysics Data System (ADS)

    Hansen, Thomas A.; Jung, Hye R.; Kjeldsen, Frank

    2011-11-01

    Interrogation of electron transfer dissociation (ETD) mass spectra of peptide amide-to-ester backbone bond substituted analogues (depsipeptides) reveals substantial differences in the entire backbone cleavage frequencies. It is suggested that the point permutation of backbone bonds leads to changes in the predominant ion structures by removal/weakening of specific hydrogen bonding. ETD responds to these changes by redistributing the cleavage frequencies of the peptide backbone bonds. In comparison, no distinction between depsi-/peptide was observed using collision-activated dissociation, which is consistent with a general unfolding and elimination of structural information of these ions. These results should encourage further exploration of depsipeptides for gas-phase structural characterization.

  15. Analysis on the sequence of formation of Ti{sub 3}SiC{sub 2} and Ti{sub 3}SiC{sub 2}/SiC composites

    SciTech Connect

    Radhakrishnan, R.; Bhaduri, S.B.; Henager, C.H. Jr.

    1995-05-01

    Ti{sub 3}SiC{sub 2}, a compound in the ternary Ti-Si-C system, is reported to be ductile. This paper reports the sequence of formation of Ti{sub 3}SiC{sub 2} and Ti{sub 3}SiC{sub 2}/SiC composites involving either combustion synthesis or by displacement reaction, respectively. Onset of exothermic reaction temperatures were determined using Differential Thermal Analysis (DTA). Phases present after the exothermic temperatures were analyzed by X-Ray diffraction. Based on these observations, a route to formation of Ti{sub 3}SiC{sub 2} and Ti{sub 3}SiC{sub 2}/SiC composites is proposed for the two`s thesis methods.

  16. Structural insights into the evolution of a sexy protein: novel topology and restricted backbone flexibility in a hypervariable pheromone from the red-legged salamander, Plethodon shermani.

    PubMed

    Wilburn, Damien B; Bowen, Kathleen E; Doty, Kari A; Arumugam, Sengodagounder; Lane, Andrew N; Feldhoff, Pamela W; Feldhoff, Richard C

    2014-01-01

    In response to pervasive sexual selection, protein sex pheromones often display rapid mutation and accelerated evolution of corresponding gene sequences. For proteins, the general dogma is that structure is maintained even as sequence or function may rapidly change. This phenomenon is well exemplified by the three-finger protein (TFP) superfamily: a diverse class of vertebrate proteins co-opted for many biological functions - such as components of snake venoms, regulators of the complement system, and coordinators of amphibian limb regeneration. All of the >200 structurally characterized TFPs adopt the namesake "three-finger" topology. In male red-legged salamanders, the TFP pheromone Plethodontid Modulating Factor (PMF) is a hypervariable protein such that, through extensive gene duplication and pervasive sexual selection, individual male salamanders express more than 30 unique isoforms. However, it remained unclear how this accelerated evolution affected the protein structure of PMF. Using LC/MS-MS and multidimensional NMR, we report the 3D structure of the most abundant PMF isoform, PMF-G. The high resolution structural ensemble revealed a highly modified TFP structure, including a unique disulfide bonding pattern and loss of secondary structure, that define a novel protein topology with greater backbone flexibility in the third peptide finger. Sequence comparison, models of molecular evolution, and homology modeling together support that this flexible third finger is the most rapidly evolving segment of PMF. Combined with PMF sequence hypervariability, this structural flexibility may enhance the plasticity of PMF as a chemical signal by permitting potentially thousands of structural conformers. We propose that the flexible third finger plays a critical role in PMF:receptor interactions. As female receptors co-evolve, this flexibility may allow PMF to still bind its receptor(s) without the immediate need for complementary mutations. Consequently, this unique adaptation may establish new paradigms for how receptor:ligand pairs co-evolve, in particular with respect to sexual conflict. PMID:24849290

  17. Structural Insights into the Evolution of a Sexy Protein: Novel Topology and Restricted Backbone Flexibility in a Hypervariable Pheromone from the Red-Legged Salamander, Plethodon shermani

    PubMed Central

    Wilburn, Damien B.; Bowen, Kathleen E.; Doty, Kari A.; Arumugam, Sengodagounder; Lane, Andrew N.; Feldhoff, Pamela W.; Feldhoff, Richard C.

    2014-01-01

    In response to pervasive sexual selection, protein sex pheromones often display rapid mutation and accelerated evolution of corresponding gene sequences. For proteins, the general dogma is that structure is maintained even as sequence or function may rapidly change. This phenomenon is well exemplified by the three-finger protein (TFP) superfamily: a diverse class of vertebrate proteins co-opted for many biological functions – such as components of snake venoms, regulators of the complement system, and coordinators of amphibian limb regeneration. All of the >200 structurally characterized TFPs adopt the namesake “three-finger” topology. In male red-legged salamanders, the TFP pheromone Plethodontid Modulating Factor (PMF) is a hypervariable protein such that, through extensive gene duplication and pervasive sexual selection, individual male salamanders express more than 30 unique isoforms. However, it remained unclear how this accelerated evolution affected the protein structure of PMF. Using LC/MS-MS and multidimensional NMR, we report the 3D structure of the most abundant PMF isoform, PMF-G. The high resolution structural ensemble revealed a highly modified TFP structure, including a unique disulfide bonding pattern and loss of secondary structure, that define a novel protein topology with greater backbone flexibility in the third peptide finger. Sequence comparison, models of molecular evolution, and homology modeling together support that this flexible third finger is the most rapidly evolving segment of PMF. Combined with PMF sequence hypervariability, this structural flexibility may enhance the plasticity of PMF as a chemical signal by permitting potentially thousands of structural conformers. We propose that the flexible third finger plays a critical role in PMF:receptor interactions. As female receptors co-evolve, this flexibility may allow PMF to still bind its receptor(s) without the immediate need for complementary mutations. Consequently, this unique adaptation may establish new paradigms for how receptor:ligand pairs co-evolve, in particular with respect to sexual conflict. PMID:24849290

  18. Sequence composition of BAC clones and SSR markers mapped to Upland cotton chromosomes 11 and 21 targeting resistance to soil-borne pathogens

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Genetic and physical framework mapping in cotton (Gossypium spp.) were used to discover putative gene sequences involved in resistance to common soil-borne pathogens. Chromosome (Chr) 11 and its homoeologous Chr 21 of Upland cotton (G. hirsutum) is a focus for discovery of resistance (R) or pathoge...

  19. Preparation of Er3+:Y3Al5O12/TiO2 composite film and influence of layer number and layer sequence on the visible-light photocatalytic activity

    NASA Astrophysics Data System (ADS)

    Zhang, L.; Ma, C. H.; Wang, J.; Li, S. G.; Li, Y.; Wang, B. X.

    2014-12-01

    In this work, the Er3+:Y3Al5O12 as up-conversion luminescence agent was mixed with TiO2 and the corresponding Er3+:Y3Al5O12/TiO2 composite films were prepared on the one-sided surface of treated sheet glass through sol-gel dip-coating method. The prepared Er3+:Y3Al5O12/TiO2 composite films were characterized by X-ray diffraction (XRD) and scanning electron microscope (SEM). Their photocatalytic activities were examined through the degradation of some organic dyes under visible-light irradiation. The degradation process of organic dyes was monitored by UV-Vis spectrophotometer. Furthermore, some main influence factors on the visible-light photocatalytic activity of Er3+:Y3Al5O12/TiO2 composite film such as heat-treatment temperature and heat-treatment time were studied. The results indicate that three layer Er3+:Y3Al5O12/TiO2 composite films with one Er3+:Y3Al5O12/TiO2 composite film (as first layer close to sheet glass) and two pure TiO2 film (as second and third layers) display a higher visible-light photocatalytic activity during photocatalytic degradation of Azo Fuchsine. In addition, the results showed that the visible-light photocatalytic activity of Er3+:Y3Al5O12/TiO2 composite film related to the layer number and layer sequence on the sheet glass. Perhaps, the research results may offer some meaningful references for developing solar energy continuous flow wastewater treatment reactor.

  20. Polarized Raman spectroscopy of double-stranded RNA from bacteriophage phi6: local Raman tensors of base and backbone vibrations.

    PubMed Central

    Benevides, J M; Tsuboi, M; Bamford, J K; Thomas, G J

    1997-01-01

    Raman tensors for localized vibrations of base (A, U, G, and C), ribose and phosphate groups of double-stranded RNA have been determined from polarized Raman measurements on oriented fibers of the genomic RNA of bacteriophage phi6. Polarized Raman intensities for which electric vectors of both the incident and scattered light are polarized either perpendicular (I[bb]) or parallel (I[cc]) to the RNA fiber axis have been obtained by Raman microspectroscopy using 514.5-nm excitation. Similarly, the polarized Raman components, I(bc) and I(cb), for which incident and scattered vectors are mutually perpendicular, have been obtained. Spectra collected from fibers maintained at constant relative humidity in both H2O and D2O environments indicate the effects of hydrogen-isotopic shifts on the Raman polarizations and tensors. Novel findings are the following: 1) the intense Raman band at 813 cm(-1), which is assigned to phosphodiester (OPO) symmetrical stretching and represents the key marker of the A conformation of double-stranded RNA, is characterized by a moderately anisotropic Raman tensor; 2) the prominent RNA band at 1101 cm(-1), which is assigned to phosphodioxy (PO2-) symmetrical stretching, also exhibits a moderately anisotropic Raman tensor. Comparison with results obtained previously on A, B, and Z DNA suggests that tensors for localized vibrations of backbone phosphodiester and phosphodioxy groups are sensitive to helix secondary structure and local phosphate group environment; and 3) highly anisotropic Raman tensors have been found for prominent and well-resolved Raman markers of all four bases of the RNA duplex. These enable the use of polarized Raman spectroscopy for the determination of purine and pyrimidine base residue orientations in ribonucleoprotein assemblies. The present determination of Raman tensors for dsRNA is comprehensive and accurate. Unambiguous tensors have been deduced for virtually all local vibrational modes of the 300-1800 cm(-1) spectral interval. The results provide a reliable basis for future evaluations of the effects of base pairing, base stacking, and sequence context on the polarized Raman spectra of nucleic acids. PMID:9168049

  1. Repetitive Sequences

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Repetitive sequences, or repeats, account for a substantial portion of the eukaryotic genomes. These sequences include very different types of DNA with respect to mode of origin, function, structure, and genomic distribution. Two large families of repetitive sequences can be readily recognized, ta...

  2. The IncP-1 plasmid backbone adapts to different host bacterial species and evolves through homologous recombination

    PubMed Central

    Norberg, Peter; Bergström, Maria; Jethava, Vinay; Dubhashi, Devdatt; Hermansson, Malte

    2011-01-01

    Plasmids are important members of the bacterial mobile gene pool, and are among the most important contributors to horizontal gene transfer between bacteria. They typically harbour a wide spectrum of host beneficial traits, such as antibiotic resistance, inserted into their backbones. Although these inserted elements have drawn considerable interest, evolutionary information about the plasmid backbones, which encode plasmid related traits, is sparse. Here we analyse 25 complete backbone genomes from the broad-host-range IncP-1 plasmid family. Phylogenetic analysis reveals seven clades, in which two plasmids that we isolated from a marine biofilm represent a novel clade. We also found that homologous recombination is a prominent feature of the plasmid backbone evolution. Analysis of genomic signatures indicates that the plasmids have adapted to different host bacterial species. Globally circulating IncP-1 plasmids hence contain mosaic structures of segments derived from several parental plasmids that have evolved in, and adapted to, different, phylogenetically very distant host bacterial species. PMID:21468020

  3. Sparsely-sampled High-resolution 4-D Experiments for Efficient Backbone Resonance Assignment of Disordered Proteins

    PubMed Central

    Wen, Jie; Wu, Jihui; Zhou, Pei

    2011-01-01

    Intrinsically disordered proteins (IDPs) play important roles in many critical cellular processes. Due to their limited chemical shift dispersion, IDPs often require four pairs of resonance connectivities (Hα, Cα, Cβ and CO) for establishing sequential backbone assignment. Because most conventional 4-D triple-resonance experiments share an overlapping Cα evolution period, combining existing 4-D experiments does not offer an optimal solution for non-redundant collection of a complete set of backbone resonances. Using alternative chemical shift evolution schemes, we propose a new pair of 4-D triple resonance experiments—HA(CA)CO(CA)NH/HA(CA)CONH—that complement the 4-D HNCACB/HN(CO)CACB experiments to provide complete backbone resonance information. Collection of high-resolution 4-D spectra with sparse sampling and FFT-CLEAN processing enables efficient acquisition and assignment of complete backbone resonances of IDPs. Importantly, because the CLEAN procedure iteratively identifies resonance signals and removes their associating aliasing artifacts, it greatly reduces the dependence of the reconstruction quality on sampling schemes and produces high-quality spectra even with less-than-optimal sampling schemes. PMID:21277815

  4. 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.

  5. Two-dimensional NMR spectroscopy reveals cation-triggered backbone degradation in polysulfone-based anion exchange membranes.

    PubMed

    Arges, Christopher G; Ramani, Vijay

    2013-02-12

    Anion exchange membranes (AEMs) find widespread applications as an electrolyte and/or electrode binder in fuel cells, electrodialysis stacks, flow and metal-air batteries, and electrolyzers. AEMs exhibit poor stability in alkaline media; their degradation is induced by the hydroxide ion, a potent nucleophile. We have used 2D NMR techniques to investigate polymer backbone stability (as opposed to cation stability) of the AEM in alkaline media. We report the mechanism behind a peculiar, often-observed phenomenon, wherein a demonstrably stable polysulfone backbone degrades rapidly in alkaline solutions upon derivatization with alkaline stable fixed cation groups. Using COSY and heteronuclear multiple quantum correlation spectroscopy (2D NMR), we unequivocally demonstrate that the added cation group triggers degradation of the polymer backbone in alkaline via quaternary carbon hydrolysis and ether hydrolysis, leading to rapid failure. This finding challenges the existing perception that having a stable cation moiety is sufficient to yield a stable AEM and emphasizes the importance of the often ignored issue of backbone stability. PMID:23335629

  6. Repeat Sequence Proteins as Matrices for Nanocomposites

    SciTech Connect

    Drummy, L.; Koerner, H; Phillips, D; McAuliffe, J; Kumar, M; Farmer, B; Vaia, R; Naik, R

    2009-01-01

    Recombinant protein-inorganic nanocomposites comprised of exfoliated Na+ montmorillonite (MMT) in a recombinant protein matrix based on silk-like and elastin-like amino acid motifs (silk elastin-like protein (SELP)) were formed via a solution blending process. Charged residues along the protein backbone are shown to dominate long-range interactions, whereas the SELP repeat sequence leads to local protein/MMT compatibility. Up to a 50% increase in room temperature modulus and a comparable decrease in high temperature coefficient of thermal expansion occur for cast films containing 2-10 wt.% MMT.

  7. Targeted imputation of sequence variants and gene expression profiling identifies twelve candidate genes associated with lactation volume, composition and calving interval in dairy cattle.

    PubMed

    Raven, Lesley-Ann; Cocks, Benjamin G; Kemper, Kathryn E; Chamberlain, Amanda J; Vander Jagt, Christy J; Goddard, Michael E; Hayes, Ben J

    2016-02-01

    Dairy cattle are an interesting model for gaining insights into the genes responsible for the large variation between and within mammalian species in the protein and fat content of their milk and their milk volume. Large numbers of phenotypes for these traits are available, as well as full genome sequence of key founders of modern dairy cattle populations. In twenty target QTL regions affecting milk production traits, we imputed full genome sequence variant genotypes into a population of 16,721 Holstein and Jersey cattle with excellent phenotypes. Association testing was used to identify variants within each target region, and gene expression data were used to identify possible gene candidates. There was statistical support for imputed sequence variants in or close to BTRC, MGST1, SLC37A1, STAT5A, STAT5B, PAEP, VDR, CSF2RB, MUC1, NCF4, and GHDC associated with milk production, and EPGN for calving interval. Of these candidates, analysis of RNA-Seq data demonstrated that PAEP, VDR, SLC37A1, GHDC, MUC1, CSF2RB, and STAT5A were highly differentially expressed in mammary gland compared to 15 other tissues. For nine of the other target regions, the most significant variants were in non-coding DNA. Genomic predictions in a third dairy breed (Australian Reds) using sequence variants in only these candidate genes were for some traits more accurate than genomic predictions from 632,003 common SNP on the Bovine HD array. The genes identified in this study are interesting candidates for improving milk production in cattle and could be investigated for novel biological mechanisms driving lactation traits in other mammals. PMID:26613780

  8. The Manufacturing Process for the NASA Composite Crew Module Demonstration Structure

    NASA Technical Reports Server (NTRS)

    Pelham, Larry; Higgins, John E.

    2008-01-01

    This paper will describe the approaches and methods selected in fabrication of a carbon composite demonstration structure for the Composite Crew Module (CCM) Program. The program is managed by the NASA Safety and Engineering Center with participants from ten NASA Centers and AFRL. Multiple aerospace contractors are participating in the design development, tooling and fabrication effort as well. The goal of the program is to develop an agency wide design team for composite habitable spacecraft. The specific goals for this development project are: a).To gain hands on experience in design, building and testing a composite crew module. b) To validate key assumptions by resolving composite spacecraft design details through fabrication and testing of hardware. This abstract is based on Preliminary Design data..The final design will continue to evolve through the fall of 2007 with fabrication mostly completed by conference date. From a structures perspective, the.CCM can be viewed as a pressure module with variable pressure time histories and a series of both impact and quasi-static, high intensity point, line, and area distributed loads. The portion of the overall space vehicle being designed and. fabricated by the CCM team is just the pressure module and primary loading points. The heaviest point loads are applied and distributed to the pressure module at.an aluminum Service Module/Alternate Launch Abort System (SM/ALAS) fittings and at Main and Drogue Chute fittings. Significant line loads with metal to metal impact is applied at.the Lids ring. These major external point and line loads as well as pressure impact loads (blast and water landing) are applied to the lobed floor though the reentry shield and crushable materials. The pressure module is divided into upper and lower. shells that mate together with a bonded belly band splice joint to create the completed structural assembly. The benefits of a split CCM far outweigh the risks of a joint. These benefits include lower tooling cost and less manufacturing risk. Assembly of the top and bottom halves of the pressure shell will allow access to the interior of the shell throughout remaining fabrication sequence and can also potentially permit extensive installation of equipment and .crew facilities prior to final assembly of the two shell halves. A Pi pre-form is a woven carbon composite material which is provided in pre-impregnated form and frozen for long term storage. The cross-section shape allows the top of the pi to be bonded to a flat or curved surface with a second flat plate composite section bonded between two upstanding legs of the Pi. One of the regions relying on the merits of the Pi pre-form is the backbone. All connections among plates of the backbone structure, including the upper flanges, and to the lobe base of the pressure shell are currently joined by Pi pre-forms. The intersection of backbone composite plates is formed by application of two Pi pre-forms, top flanges and lobed surfaces are bonded with one Pi pre-form. The process of applying the pre-impregnated pi-preform will be demonstrated to include important steps like surface preparation, forming, application of pressure dams, vacuum bagging for consolidation, and curing techniques. Chopped carbon fiber tooling was selected over other traditional metallic and carbon fiber tooling. The requirement of schedule and cost economy for a moderate reuse cure tool warranted composite tooling options. Composite tooling schedule duration of 18 weeks compared favorably against other metallic tooling including invar tooling. Composite tooling also shows significant cost savings over low CTE metallic options. The composite tooling options were divided into two groups and the final decision was based on the cost, schedule, tolerance, temperature, and reuse requirements.

  9. DNA sequence confidence estimation

    SciTech Connect

    Lipshutz, R.J. ); Taverner, F. ); Hennessy, K. ); Hartzell, G. ); Davis, R. )

    1994-02-01

    A significant bottleneck in the current DNA sequencing process is the manual editing of trace data generated by automated DNA sequencers. This step is used to correct base calls and to associate to each base call a confidence level. The confidence levels are used in the assembly process to determine overlaps and to resolve discrepancies in determining the consensus sequence. This single step may cost as much as 4 to 8 cents per finished base. The authors report an approach to automated trace editing using classification trees to detect and exploit context-based patterns in trace peak heights. Local base composition and nearby peak heights account for 80% of the variations in peak heights. Classification algorithms were developed to identify 37% of automated base calls that differ from the consensus sequence. With these algorithms, 12% of the base calls had confidence levels less than 90%. 16 refs., 7 figs., 3 tabs.

  10. Phosphorothioate backbone modifications of nucleotide-based drugs are potent platelet activators

    PubMed Central

    Flierl, Ulrike; Nero, Tracy L.; Lim, Bock; Arthur, Jane F.; Yao, Yu; Jung, Stephanie M.; Gitz, Eelo; Pollitt, Alice Y.; Zaldivia, Maria T.K.; Jandrot-Perrus, Martine; Schäfer, Andreas; Nieswandt, Bernhard; Andrews, Robert K.; Parker, Michael W.; Gardiner, Elizabeth E.

    2015-01-01

    Nucleotide-based drug candidates such as antisense oligonucleotides, aptamers, immunoreceptor-activating nucleotides, or (anti)microRNAs hold great therapeutic promise for many human diseases. Phosphorothioate (PS) backbone modification of nucleotide-based drugs is common practice to protect these promising drug candidates from rapid degradation by plasma and intracellular nucleases. Effects of the changes in physicochemical properties associated with PS modification on platelets have not been elucidated so far. Here we report the unexpected binding of PS-modified oligonucleotides to platelets eliciting strong platelet activation, signaling, reactive oxygen species generation, adhesion, spreading, aggregation, and thrombus formation in vitro and in vivo. Mechanistically, the platelet-specific receptor glycoprotein VI (GPVI) mediates these platelet-activating effects. Notably, platelets from GPVI function–deficient patients do not exhibit binding of PS-modified oligonucleotides, and platelet activation is fully abolished. Our data demonstrate a novel, unexpected, PS backbone–dependent, platelet-activating effect of nucleotide-based drug candidates mediated by GPVI. This unforeseen effect should be considered in the ongoing development programs for the broad range of upcoming and promising DNA/RNA therapeutics. PMID:25646267

  11. 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.

  12. NMR backbone dynamics studies of human PED/PEA-15 outline protein functional sites.

    PubMed

    Farina, Biancamaria; Pirone, Luciano; Russo, Luigi; Viparelli, Francesca; Doti, Nunzianna; Pedone, Carlo; Pedone, Emilia M; Fattorusso, Roberto

    2010-10-01

    PED/PEA-15 (phosphoprotein enriched in diabetes/phosphoprotein enriched in astrocytes) is a ubiquitously expressed protein and a key regulator of cell growth and glucose metabolism. PED/PEA-15 mediates both homotypic and heterotypic interactions and is constituted by an N-terminal canonical death effector domain and a C-terminal tail. In the present study, the backbone dynamics of PED/PEA-15 via (15)N R(1) and R(2) and steady-state [(1)H]-(15)N NOE measurements is reported. The dynamic parameters were analyzed using both Lipari-Szabo model-free formalism and a reduced spectral density mapping approach. The results obtained define a polar and charged surface of the death effector domain characterized by internal motions in the micro- to millisecond timescale, which is crucial for the multiple heterotypic functional protein-protein interactions in which PED/PEA-15 is involved. The present study contributes to a better understanding of the molecular basis of the PED/PEA-15 functional interactions and provides a more detailed surface for the design and development of PED/PEA-15 binders. PMID:20825483

  13. 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

  14. 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

  15. Robust Chemical Synthesis of Membrane Proteins through a General Method of Removable Backbone Modification.

    PubMed

    Zheng, Ji-Shen; He, Yao; Zuo, Chao; Cai, Xiao-Ying; Tang, Shan; Wang, Zhipeng A; Zhang, Long-Hua; Tian, Chang-Lin; Liu, Lei

    2016-03-16

    Chemical protein synthesis can provide access to proteins with post-translational modifications or site-specific labelings. Although this technology is finding increasing applications in the studies of water-soluble globular proteins, chemical synthesis of membrane proteins remains elusive. In this report, a general and robust removable backbone modification (RBM) method is developed for the chemical synthesis of membrane proteins. This method uses an activated O-to-N acyl transfer auxiliary to install in the Fmoc solid-phase peptide synthesis process a RBM group with switchable reactivity toward trifluoroacetic acid. The method can be applied to versatile membrane proteins because the RBM group can be placed at any primary amino acid. With RBM, the membrane proteins and their segments behave almost as if they were water-soluble peptides and can be easily handled in the process of ligation, purification, and mass characterizations. After the full-length protein is assembled, the RBM group can be readily removed by trifluoroacetic acid. The efficiency and usefulness of the new method has been demonstrated by the successful synthesis of a two-transmembrane-domain protein (HCV p7 ion channel) with site-specific isotopic labeling and a four-transmembrane-domain protein (multidrug resistance transporter EmrE). This method enables practical synthesis of small- to medium-sized membrane proteins or membrane protein domains for biochemical and biophysical studies. PMID:26943264

  16. 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

    2014-08-01

    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. PMID:25042592

  17. Backbone resonance assignment of N15, N30 and D10 T cell receptor β subunits.

    PubMed

    Mallis, Robert J; Reinherz, Ellis L; Wagner, Gerhard; Arthanari, Haribabu

    2016-04-01

    The αβT Cell receptor (TCR) governs T cell immunity through its interaction with peptide bound to major histocompatibility complex molecules (pMHC). Previously, soluble ectodomain constructs have been used to elucidate the binding mode of the TCR for the MHC. However, the full heterodimeric αβTCR has proven difficult to produce reproducibly in recombinant systems to the extent seen in the routine production of novel antibodies. Particularly, the route of production in E. coli, which is most convenient for isotopic labeling of proteins, is challenging for a wide range of αβTCR, including N15αβ, N30αβ, but not D10αβ. With the aim of understanding the TCR-pMHC interaction through the use of dynamic binding measurements, we set out to produce TCRβ subunits with which we could investigate binding with pMHC. The TCRβ constructs are more readily produced and refolded than their αβ counterparts and have proven to be an effective model of preTCR in pMHC binding studies. As a first step towards characterizing potential interactions with protein ligands, we have assigned the backbone resonances of three TCRβ subunits, N15β, N30β and D10β. PMID:26275917

  18. 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. PMID:25347287

  19. Insights into Peptoid Helix Folding Cooperativity from an Improved Backbone Potential.

    PubMed

    Mukherjee, Sudipto; Zhou, Guangfeng; Michel, Chris; Voelz, Vincent A

    2015-12-17

    Peptoids (N-substituted oligoglycines) are biomimetic polymers that can fold into a variety of unique structural scaffolds. Peptoid helices, which result from the incorporation of bulky chiral side chains, are a key peptoid structural motif whose formation has not yet been accurately modeled in molecular simulations. Here, we report that a simple modification of the backbone φ-angle potential in GAFF is able to produce well-folded cis-amide helices of (S)-N-(1-phenylethyl)glycine (Nspe), consistent with experiment. We validate our results against both QM calculations and NMR experiments. For this latter task, we make quantitative comparisons to sparse NOE data using the Bayesian Inference of Conformational Populations (BICePs) algorithm, a method we have recently developed for this purpose. We then performed extensive REMD simulations of Nspe oligomers as a function of chain length and temperature to probe the molecular forces driving cooperative helix formation. Analysis of simulation data by Lifson-Roig helix-coil theory show that the modified potential predicts much more cooperative folding for Nspe helices. Unlike peptides, per-residue entropy changes for helix nucleation and extension are mostly positive, suggesting that steric bulk provides the main driving force for folding. We expect these results to inform future work aimed at predicting and designing peptoid peptidomimetics and tertiary assemblies of peptoid helices. PMID:26584227

  20. Noise assisted excitation energy transfer in a linear model of a selectivity filter backbone strand

    NASA Astrophysics Data System (ADS)

    Bassereh, Hassan; Salari, Vahid; Shahbazi, Farhad

    2015-07-01

    In this paper, we investigate the effect of noise and disorder on the efficiency of excitation energy transfer (EET) in a N=5 sites linear chain with ‘static’ dipole-dipole couplings. In fact, here, the disordered chain is a toy model for one strand of the selectivity filter backbone in ion channels. It has recently been discussed that the presence of quantum coherence in the selectivity filter is possible and can play a role in mediating ion-conduction and ion-selectivity in the selectivity filter. The question is ‘how a quantum coherence can be effective in such structures while the environment of the channel is dephasing (i.e. noisy)?’ Basically, we expect that the presence of the noise should have a destructive effect in the quantum transport. In fact, we show that such expectation is valid for ordered chains. However, our results indicate that introducing the dephasing in the disordered chains leads to the weakening of the localization effects, arising from the multiple back-scatterings due to the randomness, and then increases the efficiency of quantum energy transfer. Thus, the presence of noise is crucial for the enhancement of EET efficiency in disordered chains. We also show that the contribution of both classical and quantum mechanical effects are required to improve the speed of energy transfer along the chain. Our analysis may help for better understanding of fast and efficient functioning of the selectivity filters in ion channels.

  1. Backbones versus core agents in initial ART regimens: one game, two players.

    PubMed

    Llibre, Josep M; Walmsley, Sharon; Gatell, Josep M

    2016-04-01

    The advances seen in ART during the last 30 years have been outstanding. Treatment has evolved from the initial use of single agents as monotherapy. The ability to use HIV RNA as a surrogate marker for clinical outcomes allowed the more rapid evaluation of new therapies. This led to the understanding that triple-drug regimens, including a core agent (an NNRTI or a boosted PI) and two NRTIs, are optimal. These combinations have demonstrated continued improvements in their efficacy and toxicity as initial therapy. However, the need for pharmacokinetic boosting, with potential drug-drug interactions, or residual issues of efficacy or toxicity have persisted for some agents. Most recently, integrase strand transfer inhibitors, particularly dolutegravir, have shown unparalleled safety and efficacy and are currently the core agents of choice. Regimens that included only core agents or only backbone agents have not been as successful as combined therapy in antiretroviral-naive patients. It appears that at least one NRTI is needed for optimal performance and lamivudine and emtricitabine may be the ideal candidates. Several studies are ongoing of agents with longer dosing intervals, lower cost and new NRTI-saving strategies to address unmet needs. PMID:26747092

  2. 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. PMID:26322177

  3. A Low-Dimensional Principal Manifold as the "Attractor Backbone" of a Chaotic Beam System

    NASA Astrophysics Data System (ADS)

    Bollt, Erik M.; Skufca, Joseph D.

    We model an elastic beam subject to a contact load which displaces under a chaotic external forcing, motivated by application of a ship carrying either a crane, or fluids in internal tanks. This model not only has rich dynamics and relevance in its own right, it gives rise to a Partial Differential Equation (PDE) whose solutions are chaotic, with an attractor whose points lie "near" a low-dimensional curve. This form identifies a data-driven dimensionality reduction which encapsulates a Cartesian product, approximately, of a principal manifold, corresponding to spatial regularity, against a temporal complex dynamics of the intrinsic variable of the manifold. The principal manifold element serves to translate the complex information at one site to all other sites on the beam. Although points of the attractor do not lie on the principal manifold, they lie sufficiently close that we describe that manifold as a "backbone" running through the attractor, allowing the manifold to serve as a suitable space to approximate behaviors.

  4. 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

  5. Noise assisted excitation energy transfer in a linear model of a selectivity filter backbone strand.

    PubMed

    Bassereh, Hassan; Salari, Vahid; Shahbazi, Farhad

    2015-07-15

    In this paper, we investigate the effect of noise and disorder on the efficiency of excitation energy transfer (EET) in a N = 5 sites linear chain with 'static' dipole-dipole couplings. In fact, here, the disordered chain is a toy model for one strand of the selectivity filter backbone in ion channels. It has recently been discussed that the presence of quantum coherence in the selectivity filter is possible and can play a role in mediating ion-conduction and ion-selectivity in the selectivity filter. The question is 'how a quantum coherence can be effective in such structures while the environment of the channel is dephasing (i.e. noisy)?' Basically, we expect that the presence of the noise should have a destructive effect in the quantum transport. In fact, we show that such expectation is valid for ordered chains. However, our results indicate that introducing the dephasing in the disordered chains leads to the weakening of the localization effects, arising from the multiple back-scatterings due to the randomness, and then increases the efficiency of quantum energy transfer. Thus, the presence of noise is crucial for the enhancement of EET efficiency in disordered chains. We also show that the contribution of both classical and quantum mechanical effects are required to improve the speed of energy transfer along the chain. Our analysis may help for better understanding of fast and efficient functioning of the selectivity filters in ion channels. PMID:26061758

  6. Pairing of isolated nucleic-acid bases in the absence of the DNA backbone

    NASA Astrophysics Data System (ADS)

    Nir, Eyal; Kleinermanns, Karl; de Vries, Mattanjah S.

    2000-12-01

    The two intertwined strands of DNA are held together through base pairing-the formation of hydrogen bonds between bases located opposite each other on the two strands. DNA replication and transcription involve the breaking and re-forming of these hydrogen bonds, but it is difficult to probe these processes directly. For example, conventional DNA spectroscopy is dominated by solvent interactions, crystal modes and collective modes of the DNA backbone; gas-phase studies, in contrast, can in principle measure interactions between individual molecules in the absence of external effects, but require the vaporization of the interacting species without thermal degradation. Here we report the generation of gas-phase complexes comprising paired bases, and the spectroscopic characterization of the hydrogen bonding in isolated guanine-cytosine (G-C) and guanine-guanine (G-G) base pairs. We find that the gas-phase G-C base pair adopts a single configuration, which may be Watson-Crick, whereas G-G exists in two different configurations, and we see evidence for proton transfer in the G-C pair, an important step in radiation-induced DNA damage pathways. Interactions between different bases and between bases and water molecules can also be characterized by our approach, providing stringent tests for high-level ab initio computations that aim to elucidate the fundamental aspects of nucleotide interactions.

  7. Backbone assignment and secondary structure of the PLAT domain of human polycystin-1.

    PubMed

    Xu, Yaoxian; Ong, Albert C M; Williamson, Mike P; Hounslow, Andrea M

    2015-10-01

    Polycystin-1 is a large transmembrane protein mutated in the common genetic disorder autosomal dominant polycystic kidney disease. One of the predicted intracellular domains of polycystin-1 is PLAT (Polycystin-1, Lipoxygenase and Alpha Toxin), which consists of 116 amino acids and is anchored to the membrane by linkers at both ends. It is predicted to have a large number of hydrophobic residues on the surface. Assignment of the NMR spectrum was hampered by considerable line broadening, and hence a programme of site-directed mutagenesis and searching for suitable solution conditions was undertaken. The optimum construct required fusion of the GB1 domain at the N-terminus and a His tag at the C-terminus, and proved to have several additional amino acids at both ends beyond the canonical domain boundaries, as well as mutation of W3128 to alanine. Optimum solubility required 500 mM sodium chloride, and usable spectra could only be obtained by perdeuteration. Backbone assignment was made using standard triple resonance spectra and is 88 % complete. The chemical shifts obtained suggest that a loop consisting of residues 3223-3228 is mobile in solution, and that the protein is similar in structure to a prediction produced by Swiss-Model based on the structure of a homologous protein. PMID:25943267

  8. 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

  9. Mechanics and Chemistry: Sinle Molecule Bond Rupture Forces Correlate with Molecular Backbone Structure

    SciTech Connect

    Frei, M.; Hybertsen, M.; Aradhya, S.V.; Koentopp, M.; Venkataraman, L.

    2011-03-02

    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.

  10. Toward High Performance n-Type Thermoelectric Materials by Rational Modification of BDPPV Backbones.

    PubMed

    Shi, Ke; Zhang, Fengjiao; Di, Chong-An; Yan, Tian-Wei; Zou, Ye; Zhou, Xu; Zhu, Daoben; Wang, Jie-Yu; Pei, Jian

    2015-06-10

    Three n-type polymers BDPPV, ClBDPPV, and FBDPPV which exhibit outstanding electrical conductivities when mixed with an n-type dopant, N-DMBI ((4-(1,3-dimethyl-2,3-dihydro-1H-benzoimidazol-2-yl)phenyl)dimethylamine), in solution. High electron mobility and an efficient doping process endow FBDPPV with the highest electrical conductivities of 14 S cm(-1) and power factors up to 28 μW m(-1) K(-2), which is the highest thermoelectric (TE) power factor that has been reported for solution processable n-type conjugated polymers. Our investigations reveal that introduction of halogen atoms to the polymer backbones has a dramatic influence on not only the electron mobilities but also the doping levels, both of which are critical to the electrical conductivities. This work suggests the significance of rational modification of polymer structures and opens the gate for applying the rapidly developed organic semiconductors with high carrier mobilities to thermoelectric field. PMID:25997085

  11. 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

  12. 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. PMID:22294890

  13. Biosensors for DNA sequence detection

    NASA Technical Reports Server (NTRS)

    Vercoutere, Wenonah; Akeson, Mark

    2002-01-01

    DNA biosensors are being developed as alternatives to conventional DNA microarrays. These devices couple signal transduction directly to sequence recognition. Some of the most sensitive and functional technologies use fibre optics or electrochemical sensors in combination with DNA hybridization. In a shift from sequence recognition by hybridization, two emerging single-molecule techniques read sequence composition using zero-mode waveguides or electrical impedance in nanoscale pores.

  14. Dynamic changes in the composition of photosynthetic picoeukaryotes in the northwestern Pacific Ocean revealed by high-throughput tag sequencing of plastid 16S rRNA genes.

    PubMed

    Choi, Dong H; An, Sung M; Chun, Sungjun; Yang, Eun C; Selph, Karen E; Lee, Charity M; Noh, Jae H

    2016-02-01

    Photosynthetic picoeukaryotes (PPEs) are major oceanic primary producers. However, the diversity of such communities remains poorly understood, especially in the northwestern (NW) Pacific. We investigated the abundance and diversity of PPEs, and recorded environmental variables, along a transect from the coast to the open Pacific Ocean. High-throughput tag sequencing (using the MiSeq system) revealed the diversity of plastid 16S rRNA genes. The dominant PPEs changed at the class level along the transect. Prymnesiophyceae were the only dominant PPEs in the warm pool of the NW Pacific, but Mamiellophyceae dominated in coastal waters of the East China Sea. Phylogenetically, most Prymnesiophyceae sequences could not be resolved at lower taxonomic levels because no close relatives have been cultured. Within the Mamiellophyceae, the genera Micromonas and Ostreococcus dominated in marginal coastal areas affected by open water, whereas Bathycoccus dominated in the lower euphotic depths of oligotrophic open waters. Cryptophyceae and Phaeocystis (of the Prymnesiophyceae) dominated in areas affected principally by coastal water. We also defined the biogeographical distributions of Chrysophyceae, prasinophytes, Bacillariophyceaea and Pelagophyceae. These distributions were influenced by temperature, salinity and chlorophyll a and nutrient concentrations. PMID:26712350

  15. iPro54-PseKNC: a sequence-based predictor for identifying sigma-54 promoters in prokaryote with pseudo k-tuple nucleotide composition

    PubMed Central

    Lin, Hao; Deng, En-Ze; Ding, Hui; Chen, Wei; Chou, Kuo-Chen

    2014-01-01

    The σ54 promoters are unique in prokaryotic genome and responsible for transcripting carbon and nitrogen-related genes. With the avalanche of genome sequences generated in the postgenomic age, it is highly desired to develop automated methods for rapidly and effectively identifying the σ54 promoters. Here, a predictor called ‘iPro54-PseKNC’ was developed. In the predictor, the samples of DNA sequences were formulated by a novel feature vector called ‘pseudo k-tuple nucleotide composition’, which was further optimized by the incremental feature selection procedure. The performance of iPro54-PseKNC was examined by the rigorous jackknife cross-validation tests on a stringent benchmark data set. As a user-friendly web-server, iPro54-PseKNC is freely accessible at http://lin.uestc.edu.cn/server/iPro54-PseKNC. For the convenience of the vast majority of experimental scientists, a step-by-step protocol guide was provided on how to use the web-server to get the desired results without the need to follow the complicated mathematics that were presented in this paper just for its integrity. Meanwhile, we also discovered through an in-depth statistical analysis that the distribution of distances between the transcription start sites and the translation initiation sites were governed by the gamma distribution, which may provide a fundamental physical principle for studying the σ54 promoters. PMID:25361964

  16. Nucleotide sequence composition adjacent to intronic splice sites improves splicing efficiency via its effect on pre-mRNA local folding in fungi.

    PubMed

    Zafrir, Zohar; Tuller, Tamir

    2015-10-01

    RNA splicing is the central process of intron removal in eukaryotes known to regulate various cellular functions such as growth, development, and response to external signals. The canonical sequences indicating the splicing sites needed for intronic boundary recognition are well known. However, the roles and evolution of the local folding of intronic and exonic sequence features adjacent to splice sites has yet to be thoroughly studied. Here, focusing on four fungi (Saccharomyces cerevisiae, Schizosaccharomyces pombe, Aspergillus nidulans, and Candida albicans), we performed for the first time a comprehensive high-resolution study aimed at characterizing the encoding of intronic splicing efficiency in pre-mRNA transcripts and its effect on intron evolution. Our analysis supports the conjecture that pre-mRNA local folding strength at intronic boundaries is under selective pressure, as it significantly affects splicing efficiency. Specifically, we show that in the immediate region of 12-30 nucleotides (nt) surrounding the intronic donor site there is a preference for weak pre-mRNA folding; similarly, in the region of 15-33 nt surrounding the acceptor and branch sites there is a preference for weak pre-mRNA folding. We also show that in most cases there is a preference for strong pre-mRNA folding further away from intronic splice sites. In addition, we demonstrate that these signals are not associated with gene-specific functions, and they correlate with splicing efficiency measurements (r = 0.77, P = 2.98 × 10(-21)) and with expression levels of the corresponding genes (P = 1.24 × 10(-19)). We suggest that pre-mRNA folding strength in the above-mentioned regions has a direct effect on splicing efficiency by improving the recognition of intronic boundaries. These new discoveries are contributory steps toward a broader understanding of splicing regulation and intronic/transcript evolution. PMID:26246046

  17. A novel dengue virus serotype 1 vaccine candidate based on Japanese encephalitis virus vaccine strain SA14-14-2 as the backbone.

    PubMed

    Yang, Huiqiang; Li, Zhushi; Lin, Hua; Wang, Wei; Yang, Jian; Liu, Lina; Zeng, Xianwu; Wu, Yonglin; Yu, Yongxin; Li, Yuhua

    2016-06-01

    To develop a potential dengue vaccine candidate, a full-length cDNA clone of a novel chimeric virus was constructed using recombinant DNA technology, with Japanese encephalitis virus (JEV) vaccine strain SA14-14-2 as the backbone, with its premembrane (prM) and envelope (E) genes substituted by their counterparts from dengue virus type 1 (DENV1). The chimeric virus (JEV/DENV1) was successfully recovered from primary hamster kidney (PHK) cells by transfection with the in vitro transcription products of JEV/DENV1 cDNA and was identified by complete genome sequencing and immunofluorescent staining. No neuroinvasiveness of this chimeric virus was observed in mice inoculated by the subcutaneous route (s.c.) or by the intraperitoneal route (i.p.), while some neurovirulence was displayed in mice that were inoculated directly by the intracerebral route (i.c.). The chimeric virus was able to stimulate high-titer production of antibodies against DENV1 and provided protection against lethal challenge with neuroadapted dengue virus in mice. These results suggest that the chimeric virus is a promising dengue vaccine candidate. PMID:26976137

  18. Automated NMR resonance assignment strategy for RNA via the phosphodiester backbone based on high-dimensional through-bond APSY experiments.

    PubMed

    Krähenbühl, Barbara; El Bakkali, Issam; Schmidt, Elena; Güntert, Peter; Wider, Gerhard

    2014-06-01

    A fast, robust and reliable strategy for automated sequential resonance assignment for uniformly [(13)C, (15)N]-labeled RNA via its phosphodiester backbone is presented. It is based on a series of high-dimensional through-bond APSY experiments: a 5D HCP-CCH COSY, a 4D H1'C1'CH TOCSY for ribose resonances, a 5D HCNCH for ribose-to-base connection, a 4D H6C6C5H5 TOCSY for pyrimidine resonances, and a 4D H8C8(C)C2H2 TOCSY for adenine resonances. The utilized pulse sequences are partially novel, and optimized to enable long evolution times in all dimensions. The highly precise APSY peak lists derived with these experiments could be used directly for reliable automated resonance assignment with the FLYA algorithm. This approach resulted in 98 % assignment completeness for all (13)C-(1)H, (15)N1/9 and (31)P resonances of a stem-loop with 14 nucleotides. PMID:24771326

  19. Sequential backbone assignment of uniformly 13C-labeled RNAs by a two-dimensional P(CC)H-TOCSY triple resonance NMR experiment.

    PubMed

    Wijmenga, S S; Heus, H A; Leeuw, H A; Hoppe, H; van der Graaf, M; Hilbers, C W

    1995-01-01

    A new 1H-13C-31P triple resonance experiment is described which allows unambiguous sequential backbone assignment in 13C-labeled oligonucleotides via through-bond coherence transfer from 31P via 13C to 1H. The approach employs INEPT to transfer coherence from 31P to 13C and homonuclear TOCSY to transfer the 13C coherence through the ribose ring, followed by 13C to 1H J-cross-polarisation. The efficiencies of the various possible transfer pathways are discussed. The most efficient route involves transfer of 31Pi coherence via C4'i and C4'i-1, because of the relatively large JPC4' couplings involved. Via the homonuclear and heteronuclear mixing periods, the C4'i and C4'i-1 coherences are subsequently transferred to, amongst others, H1'i and H1'i-1, respectively, leading to a 2D 1H-31P spectrum which allows a sequential assignment in the 31P-1H1' region of the spectrum, i.e. in the region where the proton resonances overlap least. The experiment is demonstrated on a 13C-labeled RNA hairpin with the sequence 5'(GGGC-CAAA-GCCU)3'. PMID:7533569

  20. A ‘just-in-time’ HN(CA)CO experiment for the backbone assignment of large proteins with high sensitivity

    NASA Astrophysics Data System (ADS)

    Werner-Allen, Jon W.; Jiang, Ling; Zhou, Pei

    2006-07-01

    Among the suite of commonly used backbone experiments, HNCACO presents an unresolved sensitivity limitation due to fast 13CO transverse relaxation and passive 13Cα-13Cβ coupling. Here, we present a high-sensitivity 'just-in-time' (JIT) HN(CA)CO pulse sequence that uniformly refocuses 13Cα-13Cβ coupling while collecting 13CO shifts in real time. Sensitivity comparisons of the 3-D JIT HN(CA)CO, a CT-HMQC-based control, and a HSQC-based control with selective 13Cα inversion pulses were performed using a 2H/13C/15N labeled sample of the 29 kDa HCA II protein at 15 °C. The JIT experiment shows a 42% signal enhancement over the CT-HMQC-based experiment. Compared to the HSQC-based experiment, the JIT experiment is 16% less sensitive for residues experiencing proper 13Cα refocusing and 13Cα-13Cβ decoupling. However, for the remaining residues, the JIT spectrum shows a 106% average sensitivity gain over the HSQC-based experiment. The high-sensitivity JIT HNCACO experiment should be particularly beneficial for studies of large proteins to provide 13CO resonance information regardless of residue type.

  1. 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.

  2. 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

  3. The influence of the primary and secondary xanthan structure on the enzymatic hydrolysis of the xanthan backbone.

    PubMed

    Kool, Marijn M; Schols, Henk A; Delahaije, Roy J B M; Sworn, Graham; Wierenga, Peter A; Gruppen, Harry

    2013-09-12

    Differently modified xanthans, varying in degree of acetylation and/or pyruvylation were incubated with the experimental cellulase mixture C1-G1 from Myceliophthora thermophila C1. The ionic strength and/or temperature of the xanthan solutions were varied, to obtain different xanthan conformations. The exact conformation at the selected incubation conditions was determined by circular dichroism. The xanthan degradation was analyzed by size exclusion chromatography. It was shown that at a fixed xanthan conformation, the backbone degradation by cellulases is equal for each type of xanthan. Complete backbone degradation is only obtained at a fully disordered conformation, indicating that only the secondary xanthan structure influences the final degree of hydrolysis by cellulases. It is thereby shown that, independently on the degree of substitution, xanthan can be completely hydrolyzed to oligosaccharides. These oligosaccharides can be used to further investigate the primary structure of different xanthans and to correlate the molecular structure to the xanthan functionalities. PMID:23911459

  4. Functional RNAs exhibit tolerance for non-heritable 2‧-5‧ versus 3‧-5‧ backbone heterogeneity

    NASA Astrophysics Data System (ADS)

    Engelhart, Aaron E.; Powner, Matthew W.; Szostak, Jack W.

    2013-05-01

    A plausible process for non-enzymatic RNA replication would greatly simplify models of the transition from prebiotic chemistry to simple biology. However, all known conditions for the chemical copying of an RNA template result in the synthesis of a complementary strand that contains a mixture of 2‧-5‧ and 3‧-5‧ linkages, rather than the selective synthesis of only 3‧-5‧ linkages as found in contemporary RNA. Here we show that such backbone heterogeneity is compatible with RNA folding into defined three-dimensional structures that retain molecular recognition and catalytic properties and, therefore, would not prevent the evolution of functional RNAs such as ribozymes. Moreover, the same backbone heterogeneity lowers the melting temperature of RNA duplexes that would otherwise be too stable for thermal strand separation. By allowing copied strands to dissociate, this heterogeneity may have been one of the essential features that allowed RNA to emerge as the first biopolymer.

  5. 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.

  6. Fluorous Peptide Nucleic Acids: PNA Analogues with Fluorine in Backbone (γ-CF2-apg-PNA) Enhance Cellular Uptake.

    PubMed

    Ellipilli, Satheesh; Ganesh, Krishna N

    2015-09-18

    Fluorous PNA analogues possessing fluorine as inherent part of aminopropylglycine (apg) backbone (γ-CF2-apg PNA) have been synthesized and evaluated for biophysical and cell penetrating properties. These form duplexes of higher thermal stability with cRNA than cDNA, although destabilized compared to duplexes of standard aeg-PNA. Cellular uptake of the fluorinated γ-CF2-apg PNAs in NIH 3T3 and HeLa cells was 2-3-fold higher compared to that of nonfluorinated apg PNA, with NIH 3T3 cells showing better permeability compared to HeLa cells. The backbone fluorinated PNAs, which are first in this class, when combined with other chemical modifications may have potential for future PNA-based antisense agents. PMID:26322827

  7. Molecular dynamics simulations of single-component bottle-brush polymers with flexible backbones under poor solvent conditions

    NASA Astrophysics Data System (ADS)

    Fytas, Nikolaos G.; Theodorakis, Panagiotis E.

    2013-07-01

    Conformations of a single-component bottle-brush polymer with a fully flexible backbone under poor solvent conditions are studied by molecular dynamics simulations, using a coarse-grained bead-spring model with side chains of up to N = 40 effective monomers. By variation of the solvent quality and the grafting density σ with which side chains are grafted onto the flexible backbone, we study for backbone lengths of up to Nb = 100 the crossover from the brush/coil regime to the dense collapsed state. At lower temperatures, where collapsed chains with a constant monomer density are observed, the choice of the above parameters does not play any role and it is the total number of monomers that defines the dimensions of the chains. Furthermore, bottle-brush polymers with longer side chains possess higher spherical symmetry compared to polymers with lower side-chain lengths in contrast to what one may intuitively expect, as the stretching of the side chains is less important than the increase of their length. At higher temperatures, always below the Theta (Θ) temperature, coil-like configurations, similar to a single polymer chain, or brush-like configurations, similar to a homogeneous cylindrical bottle-brush polymer with a rigid backbone, are observed, depending on the choice of the particular parameters N and σ. In the crossover regime between the collapsed state (globule) and the coil/brush regime the acylindricity increases, whereas for temperatures outside of this range, bottle-brush polymers maintain a highly cylindrical symmetry in all configurational states.

  8. Predicting Protein Backbone Chemical Shifts From Cα Coordinates: Extracting High Resolution Experimental Observables from Low Resolution Models

    PubMed Central

    2015-01-01

    Given the demonstrated utility of coarse-grained modeling and simulations approaches in studying protein structure and dynamics, developing methods that allow experimental observables to be directly recovered from coarse-grained models is of great importance. In this work, we develop one such method that enables protein backbone chemical shifts (1HN, 1Hα, 13Cα, 13C, 13Cβ, and 15N) to be predicted from Cα coordinates. We show that our Cα-based method, LARMORCα, predicts backbone chemical shifts with comparable accuracy to some all-atom approaches. More importantly, we demonstrate that LARMORCα predicted chemical shifts are able to resolve native structure from decoy pools that contain both native and non-native models, and so it is sensitive to protein structure. As an application, we use LARMORCα to characterize the transient state of the fast-folding protein gpW using recently published NMR relaxation dispersion derived backbone chemical shifts. The model we obtain is consistent with the previously proposed model based on independent analysis of the chemical shift dispersion pattern of the transient state. We anticipate that LARMORCα will find utility as a tool that enables important protein conformational substates to be identified by “parsing” trajectories and ensembles generated using coarse-grained modeling and simulations. PMID:25620895

  9. 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.

  10. NAA-modified DNA oligonucleotides with zwitterionic backbones: stereoselective synthesis of A–T phosphoramidite building blocks

    PubMed Central

    Schmidtgall, Boris; Höbartner, Claudia

    2015-01-01

    Summary Modifications of the nucleic acid backbone are essential for the development of oligonucleotide-derived bioactive agents. The NAA-modification represents a novel artificial internucleotide linkage which enables the site-specific introduction of positive charges into the otherwise polyanionic backbone of DNA oligonucleotides. Following initial studies with the introduction of the NAA-linkage at T–T sites, it is now envisioned to prepare NAA-modified oligonucleotides bearing the modification at X–T motifs (X = A, C, G). We have therefore developed the efficient and stereoselective synthesis of NAA-linked 'dimeric' A–T phosphoramidite building blocks for automated DNA synthesis. Both the (S)- and the (R)-configured NAA-motifs were constructed with high diastereoselectivities to furnish two different phosphoramidite reagents, which were employed for the solid phase-supported automated synthesis of two NAA-modified DNA oligonucleotides. This represents a significant step to further establish the NAA-linkage as a useful addition to the existing 'toolbox' of backbone modifications for the design of bioactive oligonucleotide analogues. PMID:25670992

  11. Backbone Dynamics of Alamethicin Bound to Lipid Membranes: Spin-Echo Electron Paramagnetic Resonance of TOAC-Spin Labels

    PubMed Central

    Bartucci, Rosa; Guzzi, Rita; De Zotti, Marta; Toniolo, Claudio; Sportelli, Luigi; Marsh, Derek

    2008-01-01

    Alamethicin F50/5 is a hydrophobic peptide that is devoid of charged residues and that induces voltage-dependent ion channels in lipid membranes. The peptide backbone is likely to be involved in the ion conduction pathway. Electron spin-echo spectroscopy of alamethicin F50/5 analogs in which a selected Aib residue (at position n = 1, 8, or 16) is replaced by the TOAC amino-acid spin label was used to study torsional dynamics of the peptide backbone in association with phosphatidylcholine bilayer membranes. Rapid librational motions of limited angular amplitude were observed at each of the three TOAC sites by recording echo-detected spectra as a function of echo delay time, 2τ. Simulation of the time-resolved spectra, combined with conventional EPR measurements of the librational amplitude, shows that torsional fluctuations of the peptide backbone take place on the subnanosecond to nanosecond timescale, with little temperature dependence. Associated fluctuations in polar fields from the peptide could facilitate ion permeation. PMID:18096632

  12. The determinants of bond angle variability in protein/peptide backbones: A comprehensive statistical/quantum mechanics analysis.

    PubMed

    Improta, Roberto; Vitagliano, Luigi; Esposito, Luciana

    2015-11-01

    The elucidation of the mutual influence between peptide bond geometry and local conformation has important implications for protein structure refinement, validation, and prediction. To gain insights into the structural determinants and the energetic contributions associated with protein/peptide backbone plasticity, we here report an extensive analysis of the variability of the peptide bond angles by combining statistical analyses of protein structures and quantum mechanics calculations on small model peptide systems. Our analyses demonstrate that all the backbone bond angles strongly depend on the peptide conformation and unveil the existence of regular trends as function of ψ and/or φ. The excellent agreement of the quantum mechanics calculations with the statistical surveys of protein structures validates the computational scheme here employed and demonstrates that the valence geometry of protein/peptide backbone is primarily dictated by local interactions. Notably, for the first time we show that the position of the H(α) hydrogen atom, which is an important parameter in NMR structural studies, is also dependent on the local conformation. Most of the trends observed may be satisfactorily explained by invoking steric repulsive interactions; in some specific cases the valence bond variability is also influenced by hydrogen-bond like interactions. Moreover, we can provide a reliable estimate of the energies involved in the interplay between geometry and conformations. PMID:26264789

  13. The effect of junction modes between backbones and side chains of polyimides on the stability of liquid crystal vertical alignment.

    PubMed

    Che, Xinyuan; Gong, Shiming; Zhang, Heng; Liu, Bin; Wang, Yinghan

    2016-01-27

    Polyimides (PI-N9 and PI-N12) were synthesized from two kinds of functional diamines, whose junction modes between backbones and side chains were different. Side chains of PI-N9 were linked to the backbones with an ether bond spacer; and side chains of PI-N12 were directly linked to the backbones without any spacer. The PI alignment layer surfaces were investigated by atomic force microscopy, surface free energy measurements, X-ray photo-electron spectroscopy and polarized attenuated total reflection Fourier transformed infrared spectroscopy. It was found that PI-N9 lost the vertical alignment capability after high-strength rubbing, while PI-N12 could still induce liquid crystals (LCs) to align vertically under the same condition. The mechanism of the macroscopic molecular orientation of the PI surface is proposed. During the high-strength rubbing process, the side chain could rotate around the flexible ether bond which existed between the side chain and the main chain of PI-N9 and then fell over. Therefore, PI-N9 could not induce the vertical alignment of LCs anymore. But PI-N12 could keep LCs aligning vertically all the time, which proved that the stability of LC alignment induced by PI-N12 was better. PMID:26766667

  14. Screening substituent and backbone effects on the properties of bidentate P,P-donor ligands (LKB-PP(screen)).

    PubMed

    Jover, Jesús; Fey, Natalie

    2013-01-01

    We present a computational exploration of the effect of systematic variation of backbones and substituents on the properties of bidentate, cis-chelating P,P donor ligands as captured by calculated parameters. The parameters used are the same as reported for our ligand knowledge base for bidentate P,P donor ligands, LKB-PP (Organometallics 2008, 27, 1372-1383; Organometallics 2012 31, 5302-5306), but calculation protocols have been streamlined, suitable for an extensive evaluation of ligand structures. Analysis of the resulting LKB-PP(screen) database with principal component analysis (PCA) captures the effects of changing backbones and substituents on ligand properties and illustrates how these are complementary variables for these ligands. While backbone variation is routinely employed in ligand synthesis to modify catalyst properties, only a limited subset of substituents is commonly accessed and here we highlight substituents which are likely to generate new ligand properties, of interest for the design and improved sampling of bidentate ligands in homogeneous organometallic catalysis. PMID:23104510

  15. NAA-modified DNA oligonucleotides with zwitterionic backbones: stereoselective synthesis of A-T phosphoramidite building blocks.

    PubMed

    Schmidtgall, Boris; Höbartner, Claudia; Ducho, Christian

    2015-01-01

    Modifications of the nucleic acid backbone are essential for the development of oligonucleotide-derived bioactive agents. The NAA-modification represents a novel artificial internucleotide linkage which enables the site-specific introduction of positive charges into the otherwise polyanionic backbone of DNA oligonucleotides. Following initial studies with the introduction of the NAA-linkage at T-T sites, it is now envisioned to prepare NAA-modified oligonucleotides bearing the modification at X-T motifs (X = A, C, G). We have therefore developed the efficient and stereoselective synthesis of NAA-linked 'dimeric' A-T phosphoramidite building blocks for automated DNA synthesis. Both the (S)- and the (R)-configured NAA-motifs were constructed with high diastereoselectivities to furnish two different phosphoramidite reagents, which were employed for the solid phase-supported automated synthesis of two NAA-modified DNA oligonucleotides. This represents a significant step to further establish the NAA-linkage as a useful addition to the existing 'toolbox' of backbone modifications for the design of bioactive oligonucleotide analogues. PMID:25670992

  16. A model of orientational ordering in phosphatidylcholine bilayers based on conformational analysis of the glycerol backbone region.

    PubMed Central

    Strenk, L M; Westerman, P W; Doane, J W

    1985-01-01

    Molecular and conformational ordering in aqueous multilamellar suspensions of 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) have been examined by deuterium nuclear magnetic resonance (2H NMR) in the liquid crystalline (L alpha) phase. Motionally averaged quadrupolar splittings vQ from six sites in the vicinity of the glycerol backbone have been analyzed by a molecular frame and order matrix approach in which the usual assumption of a freely-rotating molecule is not invoked. By assuming a relatively rigid glycerol backbone region, the six vQ values are found to be consistent with a conformation of the glycerol backbone that is almost identical to that of one of the two structures in crystalline DMPC dihydrate (Pearson, R. H., and I. Pascher, 1979, Nature (Lond.) 281: 499-501). The orientation of the most-ordered axis of the DMPC molecule is found to be tilted at an angle of 27 +/- 2 degrees with respect to the long axis of the sn-1 chain in its extended all trans conformation. The ordering of the most ordered molecular axis with respect to the bilayer normal is expressed by an order parameter of Szz approximately equal to 0.6 +/- 0.1, consistent with values in analogous thermotropic liquid crystals. PMID:4074836

  17. Helium-abundance and other composition effects on the properties of stellar surface convection in solar-like main-sequence stars

    SciTech Connect

    Tanner, Joel D.; Basu, Sarbani; Demarque, Pierre

    2013-12-01

    We investigate the effect of helium abundance and α-element enhancement on the properties of convection in envelopes of solar-like main-sequence stars using a grid of three-dimensional radiation hydrodynamic simulations. Helium abundance increases the mean molecular weight of the gas and alters opacity by displacing hydrogen. Since the scale of the effect of helium may depend on the metallicity, the grid consists of simulations with three helium abundances (Y = 0.1, 0.2, 0.3), each with two metallicities (Z = 0.001, 0.020). We find that changing the helium mass fraction generally affects structure and convective dynamics in a way opposite to that of metallicity. Furthermore, the effect is considerably smaller than that of metallicity. The signature of helium differs from that of metallicity in the manner in which the photospheric velocity distribution is affected. We also find that helium abundance and surface gravity behave largely in similar ways, but differ in the way they affect the mean molecular weight. A simple model for spectral line formation suggests that the bisectors and absolute Doppler shifts of spectral lines depend on the helium abundance. We look at the effect of α-element enhancement and find that it has a considerably smaller effect on the convective dynamics in the superadiabatic layer compared to that of helium abundance.

  18. Identification of S-glutathionylation sites in species-specific proteins by incorporating five sequence-derived features into the general pseudo-amino acid composition.

    PubMed

    Zhao, Xiaowei; Ning, Qiao; Ai, Meiyue; Chai, Haiting; Yang, Guifu

    2016-06-01

    As a selective and reversible protein post-translational modification, S-glutathionylation generates mixed disulfides between glutathione (GSH) and cysteine residues, and plays an important role in regulating protein activity, stability, and redox regulation. To fully understand S-glutathionylation mechanisms, identification of substrates and specific S-Glutathionylated sites is crucial. Experimental identification of S-glutathionylated sites is labor-intensive and time consuming, so establishing an effective computational method is much desirable due to their convenient and fast speed. Therefore, in this study, a new bioinformatics tool named SSGlu (Species-Specific identification of Protein S-glutathionylation Sites) was developed to identify species-specific protein S-glutathionylated sites, utilizing support vector machines that combine multiple sequence-derived features with a two-step feature selection. By 5-fold cross validation, the performance of SSGlu was measured with an AUC of 0.8105 and 0.8041 for Homo sapiens and Mus musculus, respectively. Additionally, SSGlu was compared with the existing methods, and the higher MCC and AUC of SSGlu demonstrated that SSGlu was very promising to predict S-glutathionylated sites. Furthermore, a site-specific analysis showed that S-glutathionylation intimately correlated with the features derived from its surrounding sites. The conclusions derived from this study might help to understand more of the S-glutathionylation mechanism and guide the related experimental validation. For public access, SSGlu is freely accessible at http://59.73.198.144:8080/SSGlu/. PMID:27025952

  19. DNA binding to proteolytically activated TLR9 is sequence-independent and enhanced by DNA curvature

    PubMed Central

    Li, Yue; Berke, Ian C; Modis, Yorgo

    2012-01-01

    Toll-like receptor 9 (TLR9) recognizes microbial DNA in endolysosomal compartments. The ectodomain of TLR9 must be proteolytically cleaved by endosomal proteases to produce the active receptor capable of inducing an innate immune signal. We show that the cleaved TLR9 ectodomain is a monomer in solution and that DNA ligands with phosphodiester backbones induce TLR9 dimerization in a sequence-independent manner. Ligands with phosphorothioate (PS) backbones induce the formation of large TLR9–DNA aggregates, possibly due to the propensity of PS ligands to self-associate. DNA curvature-inducing proteins including high-mobility group box 1 and histones H2A and H2B significantly enhance TLR9 binding, suggesting that TLR9 preferentially recognizes curved DNA backbones. Our work sheds light on the molecular mechanism of TLR9 activation by endogenous protein–nucleic acid complexes, which are associated with autoimmune diseases including systemic lupus erythematosus. PMID:22258621

  20. Sequential HNCACB and CBCANH Protein NMR Pulse Sequences

    NASA Astrophysics Data System (ADS)

    Meissner, Axel; Sørensen, Ole Winneche

    2001-08-01

    The pulse sequences HNCACB and CBCANH correlating side chain Cβ resonances with amide resonances in the protein backbone do not distinguish between inter- and intraresidue correlations. The new pulse sequences sequential HNCACB and sequential CBCANH make this distinction by suppressing coherence transfer between 13Cα and 15N via the one-bond J(NCα) coupling so that only the sequential correlations are observed in the spectrum. The experimental results of applying sequential HNCACB in a clean-TROSY-adapted implementation to the protein Chymotrypsin Inhibitor 2 at 800 MHz are presented.

  1. Short sequence motifs, overrepresented in mammalian conservednon-coding sequences

    SciTech Connect

    Minovitsky, Simon; Stegmaier, Philip; Kel, Alexander; Kondrashov,Alexey S.; Dubchak, Inna

    2007-02-21

    Background: A substantial fraction of non-coding DNAsequences of multicellular eukaryotes is under selective constraint. Inparticular, ~;5 percent of the human genome consists of conservednon-coding sequences (CNSs). CNSs differ from other genomic sequences intheir nucleotide composition and must play important functional roles,which mostly remain obscure.Results: We investigated relative abundancesof short sequence motifs in all human CNSs present in the human/mousewhole-genome alignments vs. three background sets of sequences: (i)weakly conserved or unconserved non-coding sequences (non-CNSs); (ii)near-promoter sequences (located between nucleotides -500 and -1500,relative to a start of transcription); and (iii) random sequences withthe same nucleotide composition as that of CNSs. When compared tonon-CNSs and near-promoter sequences, CNSs possess an excess of AT-richmotifs, often containing runs of identical nucleotides. In contrast, whencompared to random sequences, CNSs contain an excess of GC-rich motifswhich, however, lack CpG dinucleotides. Thus, abundance of short sequencemotifs in human CNSs, taken as a whole, is mostly determined by theiroverall compositional properties and not by overrepresentation of anyspecific short motifs. These properties are: (i) high AT-content of CNSs,(ii) a tendency, probably due to context-dependent mutation, of A's andT's to clump, (iii) presence of short GC-rich regions, and (iv) avoidanceof CpG contexts, due to their hypermutability. Only a small number ofshort motifs, overrepresented in all human CNSs are similar to bindingsites of transcription factors from the FOX family.Conclusion: Human CNSsas a whole appear to be too broad a class of sequences to possess strongfootprints of any short sequence-specific functions. Such footprintsshould be studied at the level of functional subclasses of CNSs, such asthose which flank genes with a particular pattern of expression. Overallproperties of CNSs are affected by patterns in mutation, suggesting thatselection which causes their conservation is not always verystrong.

  2. A natural fiber composite in a pelagic limestone-chert sequence. The importance of mechanical stratigraphy for fracture type development in carbonate anticlines.

    NASA Astrophysics Data System (ADS)

    Petracchini, Lorenzo; Antonellini, Marco; Scrocca, Davide; Billi, Andrea

    2013-04-01

    Thrust fault-related folds in carbonate rocks are characterized by deformation accommodated by different kinds of structures, such as joints, faults, pressure solution seams (PSSs), and deformation bands, which may form at various stages during the folding process. Defining the distribution, orientation, and the type of fold-related structures and understanding the relationships between folding and fracturing is significant both for theoretical and practical purposes. Furthermore, as the deformation related to the folding process influences fluid flow through rocks, identifying the types of structures formed during folding is as important as predicting their geometries. To unravel the relationship between mechanical stratigraphy and folding process, the well-exposed Cingoli anticline (Northern Apennines), has been studied in detail. The Upper Cretaceous-Middle Eocene stratigraphy of the Cingoli anticline is characterized by a pelagic multilayer made up of fine-grained pelagic limestones and, marly limestones, in places alternated with thin continuous chert layers. The presence of several outcrops located in different structural positions of the anticline makes the Cingoli anticline an excellent natural laboratory to investigate relationships between folding, fracturing, and mechanical stratigraphy relative to the structural setting of the fold. The field data collected show that high angle to bedding PSSs, which formed before tilting and during the first stage of folding, are not homogeneously distributed in the pelagic limestones. Generally, high angle to bedding PSSs form in the marly pelagic limestones and they have been observed in several outcrops and in different structural positions except where the marly limestones are inter-bedded with stiffer chert layers. In order to analyse theoretically what observed in the field, we compared the deformation of limestones and chert layers with the deformation acting on fiber composites. In the mechanics of materials, composites refer to a matrix reinforced with particles, fibers, or laminae. During the early stage of folding, when the compressive stress is almost bedding parallel, chert layers act as a stiff lamina embedded in a weak limestone matrix. As a result, the stress is partitioned and the chert layers bear the greatest stress. Considering the mechanical properties (Poisson and Young's modulus) of the two materials (chert and limestone), and the estimated tectonic stress acting at the onset of the folding process, the stress magnitude in the limestone beds does not reach the expected value for the onset of pressure solution. For this reason, pelagic limestones containing chert layers are mainly characterized by joints whereas PSSs form in pelagic limestones without the stiffer phase (chert). This study suggests that within the same fold, and even within the same formation, different mechanical units can be characterized by different fractures types and fluid flow behaviour as a result of mechanical stratigraphy distribution.

  3. Dna Sequencing

    DOEpatents

    Tabor, Stanley; Richardson, Charles C.

    1995-04-25

    A method for sequencing a strand of DNA, including the steps off: providing the strand of DNA; annealing the strand with a primer able to hybridize to the strand to give an annealed mixture; incubating the mixture with four deoxyribonucleoside triphosphates, a DNA polymerase, and at least three deoxyribonucleoside triphosphates in different amounts, under conditions in favoring primer extension to form nucleic acid fragments complementory to the DNA to be sequenced; labelling the nucleic and fragments; separating them and determining the position of the deoxyribonucleoside triphosphates by differences in the intensity of the labels, thereby to determine the DNA sequence.

  4. Unconventional N-H…N Hydrogen Bonds Involving Proline Backbone Nitrogen in Protein Structures.

    PubMed

    Deepak, R N V Krishna; Sankararamakrishnan, Ramasubbu

    2016-05-10

    Contrary to DNA double-helical structures, hydrogen bonds (H-bonds) involving nitrogen as the acceptor are not common in protein structures. We systematically searched N-H…N H-bonds in two different sets of protein structures. Data set I consists of neutron diffraction and ultrahigh-resolution x-ray structures (0.9 Å resolution or better) and the hydrogen atom positions in these structures were determined experimentally. Data set II contains structures determined using x-ray diffraction (resolution ≤ 1.8 Å) and the positions of hydrogen atoms were generated using a computational method. We identified 114 and 14,347 potential N-H…N H-bonds from these two data sets, respectively, and 56-66% of these were of the Ni+1-Hi+1…Ni type, with Ni being the proline backbone nitrogen. To further understand the nature of such unusual contacts, we performed quantum chemical calculations on the model compound N-acetyl-L-proline-N-methylamide (Ace-Pro-NMe) with coordinates taken from the experimentally determined structures. A potential energy profile generated by varying the ψ dihedral angle in Ace-Pro-NMe indicates that the conformation with the N-H…N H-bond is the most stable. An analysis of H-bond-forming proline residues reveals that more than 30% of the proline carbonyl groups are also involved in n → π(∗) interactions with the carbonyl carbon of the preceding residue. Natural bond orbital analyses demonstrate that the strength of N-H…N H-bonds is less than half of that observed for a conventional H-bond. This study clearly establishes the H-bonding capability of proline nitrogen and its prevalence in protein structures. We found many proteins with multiple instances of H-bond-forming prolines. With more than 15% of all proline residues participating in N-H…N H-bonds, we suggest a new, to our knowledge, structural role for proline in providing stability to loops and capping regions of secondary structures in proteins. PMID:27166805

  5. Protein inhibitors of serine proteinases: role of backbone structure and dynamics in controlling the hydrolysis constant.

    PubMed

    Song, Jikui; Markley, John L

    2003-05-13

    Standard mechanism protein inhibitors of serine proteinases bind as substrates and are cleaved by cognate proteinases at their reactive sites. The hydrolysis constant for this cleavage reaction at the P(1)-P(1)' peptide bond (K(hyd)) is determined by the relative concentrations at equilibrium of the "intact" (uncleaved, I) and "modified" (reactive site cleaved, I*) forms of the inhibitor. The pH dependence of K(hyd) can be explained in terms of a pH-independent term, K(hyd) degrees, plus the proton dissociation constants of the newly formed amino and carboxylate groups at the cleavage site. Two protein inhibitors that differ from one another by a single residue substitution have been found to have K(hyd) degrees values that differ by a factor of 5 [Ardelt, W., and Laskowski, M., Jr. (1991) J. Mol. Biol. 220, 1041-1052]: turkey ovomucoid third domain (OMTKY3) has K(hyd) degrees = 1.0, and Indian peafowl ovomucoid third domain (OMIPF3), which differs from OMTKY3 by the substitution P(2)'-Tyr(20)His, has K(hyd) degrees = 5.15. What mechanism is responsible for this small difference? Is it structural (enthalpic) or dynamic (entropic)? Does the mutation affect the free energy of the I state, the I* state, or both? We have addressed these questions through NMR investigations of the I and I forms of OMTKY3 and OMIPF3. Information about structure was derived from measurements of NMR chemical shift changes and trans-hydrogen-bond J-couplings; information about dynamics was obtained through measurements of (15)N relaxation rates and (1)H-(15)N heteronuclear NOEs with model-free analysis of the results. Although the I forms of each variant are more dynamic than the corresponding I forms, the study revealed no appreciable difference in the backbone dynamics of either intact inhibitor (OMIPF3 vs OMTKY3) or modified inhibitor (OMIPF3* vs OMTKY3*). Instead, changes in chemical shifts and trans-hydrogen-bond J-couplings suggested that the K(hyd) degrees difference arises from differential intramolecular interactions within the intact inhibitors (OMIPF3 vs OMTKY3) in a region of each protein that becomes disordered upon reactive site cleavage (to OMIPF3* and OMTKY3*). PMID:12731859

  6. Mineralogy, composition and PGM of chromitites from Pefki, Pindos ophiolite complex (NW Greece): evidence for progressively elevated fAs conditions in the upper mantle sequence

    NASA Astrophysics Data System (ADS)

    Kapsiotis, Argirios; Grammatikopoulos, Tassos A.; Tsikouras, Basilios; Hatzipanagiotou, Konstantin; Zaccarini, Federica; Garuti, Giorgio

    2011-01-01

    The Pindos ophiolite complex, located in the northwestern part of continental Greece, hosts various chromite deposits of both metallurgical (high-Cr) and refractory (high-Al) type. The Pefki chromitites are banded and sub-concordant to the surrounding serpentinized dunites. The Cr# [Cr/(Cr + Al)] of magnesiochromite varies between 0.75 and 0.79. The total PGE grade ranges from 105.9 up to 300.0 ppb. IPGE are higher than PPGE, typical of mantle hosted ophiolitic chromitites. The PGM assemblage in chromitites comprises anduoite, ruarsite, laurite, irarsite, sperrylite, hollingworthite, Os-Ru-Ir alloys including osmium and rutheniridosmine, Ru-bearing oxides, braggite, paolovite, platarsite, cooperite, vysotskite, and palladodymite. Iridarsenite and omeiite were also observed as exsolutions in other PGM. Rare electrum and native Ag are recovered in concentrates. This PGM assemblage is of great petrogenetic importance because it is significantly different from that commonly observed in podiform mantle-hosted and banded crustal-hosted ophiolitic chromitites. PGE chalcogenides of As and S are primary, and possibly crystallized directly from a progressively enriched in As boninitic melt before or during magnesiochromite precipitation. The presence of Ru-bearing oxides implies simultaneous desulfurization and dearsenication processes. Chemically zoned laurite and composite paolovite-electrum intergrowths are indicative of the relatively high mobility of certain PGE at low temperatures under locally oxidizing conditions. The PGM assemblage and chemistry, in conjunction with geological and petrologic data of the studied chromitites, indicate that it is characteristic of chromitites found within or close to the petrologic Moho. Furthermore, the strikingly different PGM assemblages between the high-Cr chromitites within the Pindos massif is suggestive of non-homogeneous group of ores.

  7. Proteoglycan sequence

    PubMed Central

    Li, Lingyun; Ly, Mellisa

    2012-01-01

    Proteoglycans (PGs) are among the most structurally complex biomacromolecules in nature. They are present in all animal cells and frequently exert their critical biological functions through interactions with protein ligands and receptors. PGs are comprised of a core protein to which one or multiple, heterogeneous, and polydisperse glycosaminoglycan (GAG) chains are attached. Proteins, including the protein core of PGs, are now routinely sequenced either directly using proteomics or indirectly using molecular biology through their encoding DNA. The sequencing of the GAG component of PGs poses a considerably more difficult challenge because of the relatively underdeveloped state of glycomics and because the control of their biosynthesis in the endoplasmic reticulum and the Golgi is poorly understood and not believed to be template driven. Recently, the GAG chain of the simplest PG has been suggested to have a defined sequence based on its top-down Fourier transform mass spectral sequencing. This review examines the advances made over the past decade in the sequencing of GAG chains and the challenges the field face in sequencing complex PGs having critical biological functions in developmental biology and pathogenesis. PMID:22513887

  8. 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 phenomenon was studied by powder X-ray diffraction and supported by gas adsorption and thermogravimetric analysis. Layered MOFs with metalloporphyrins with Zn, Cu, Co and Fe at their +2 oxidation states as struts were prepared to facilitate non-structural metal sites and tested for hydrogen adsorption and the binding enthalpies. Steep uptakes are indeed observed, but rather due to the optimal interlayer distance of 9 A for dihydrogen, and the binding enthalpies are 6.7 -- 7.6 kJ . mo1-1 which are not ·extraordinary. Although the metals did not seem to play a large role, a trend was observed where the binding enthalpies increase as the metals in the metalloporphyrins go from late to early transition metals. With the concept of conductive metal oxides, a journey of constructing conductive MOFs was taken by attempting the formation of metal-carbon bonds by linking transition metal ions with conjugated organic struts which are 1,4-benzenediisonitrile, 1,4-benzenediethynylide and p-cyanophenylethynylide. Among the attempted systems, a reaction of Cr(III) and 1,4-benzenediethynylide yielded an amorphous material with a BET (Brunauer-Emmett-Teller) surface area of 80 m2.g-1, hydrogen uptake of 47 cm 3. g-1 and a resistance of 20 MO. Also a crystalline compound was prepared by mimicking Prussian blue by using p-cyanophenylethynylide where one end can bind metal with ethynylic carbon and the other end with the cyano nitrogen by following the similar synthesis of Prussian blue analogues. The principles of reticular chemistry are demonstrated through each chapter and show how powerful and beneficial reticular chemistry is by allowing the predetermination of the structure and function. The details of the ways to approach an ideal compound and the synthetic aspects are also described in this dissertation.

  9. Electron transfer dissociation reveals changes in the cleavage frequencies of backbone bonds distant to amide-to-ester substitutions in polypeptides.

    PubMed

    Hansen, Thomas A; Jung, Hye R; Kjeldsen, Frank

    2011-11-01

    Interrogation of electron transfer dissociation (ETD) mass spectra of peptide amide-to-ester backbone bond substituted analogues (depsipeptides) reveals substantial differences in the entire backbone cleavage frequencies. It is suggested that the point permutation of backbone bonds leads to changes in the predominant ion structures by removal/weakening of specific hydrogen bonding. ETD responds to these changes by redistributing the cleavage frequencies of the peptide backbone bonds. In comparison, no distinction between depsi-/peptide was observed using collision-activated dissociation, which is consistent with a general unfolding and elimination of structural information of these ions. These results should encourage further exploration of depsipeptides for gas-phase structural characterization. PMID:21952783

  10. The dominant role of side-chain backbone interactions in structural realization of amino acid code. ChiRotor: A side-chain prediction algorithm based on side-chain backbone interactions

    PubMed Central

    Spassov, Velin Z.; Yan, Lisa; Flook, Paul K.

    2007-01-01

    The basic differences between the 20 natural amino acid residues are due to differences in their side-chain structures. This characteristic design of protein building blocks implies that side-chain–side-chain interactions play an important, even dominant role in 3D-structural realization of amino acid codes. Here we present the results of a comparative analysis of the contributions of side-chain–side-chain (s-s) and side-chain–backbone (s-b) interactions to the stabilization of folded protein structures within the framework of the CHARMm molecular data model. Contrary to intuition, our results suggest that side-chain–backbone interactions play the major role in side-chain packing, in stabilizing the folded structures, and in differentiating the folded structures from the unfolded or misfolded structures, while the interactions between side chains have a secondary effect. An additional analysis of electrostatic energies suggests that combinatorial dominance of the interactions between opposite charges makes the electrostatic interactions act as an unspecific folding force that stabilizes not only native structure, but also compact random conformations. This observation is in agreement with experimental findings that, in the denatured state, the charge–charge interactions stabilize more compact conformations. Taking advantage of the dominant role of side-chain–backbone interactions in side-chain packing to reduce the combinatorial problem, we developed a new algorithm, ChiRotor, for rapid prediction of side-chain conformations. We present the results of a validation study of the method based on a set of high resolution X-ray structures. PMID:17242380

  11. The dominant role of side-chain backbone interactions in structural realization of amino acid code. ChiRotor: a side-chain prediction algorithm based on side-chain backbone interactions.

    PubMed

    Spassov, Velin Z; Yan, Lisa; Flook, Paul K

    2007-03-01

    The basic differences between the 20 natural amino acid residues are due to differences in their side-chain structures. This characteristic design of protein building blocks implies that side-chain-side-chain interactions play an important, even dominant role in 3D-structural realization of amino acid codes. Here we present the results of a comparative analysis of the contributions of side-chain-side-chain (s-s) and side-chain-backbone (s-b) interactions to the stabilization of folded protein structures within the framework of the CHARMm molecular data model. Contrary to intuition, our results suggest that side-chain-backbone interactions play the major role in side-chain packing, in stabilizing the folded structures, and in differentiating the folded structures from the unfolded or misfolded structures, while the interactions between side chains have a secondary effect. An additional analysis of electrostatic energies suggests that combinatorial dominance of the interactions between opposite charges makes the electrostatic interactions act as an unspecific folding force that stabilizes not only native structure, but also compact random conformations. This observation is in agreement with experimental findings that, in the denatured state, the charge-charge interactions stabilize more compact conformations. Taking advantage of the dominant role of side-chain-backbone interactions in side-chain packing to reduce the combinatorial problem, we developed a new algorithm, ChiRotor, for rapid prediction of side-chain conformations. We present the results of a validation study of the method based on a set of high resolution X-ray structures. PMID:17242380

  12. Thermoplastic copolyimides and composites therefrom

    NASA Technical Reports Server (NTRS)

    Harris, Frank (Inventor); Gabori, Patricia A. (Inventor)

    1994-01-01

    Copolyimide compositions and methods for their preparation which are melt-processible at relative low pressures, i.e. less than 1000 psi, and are suited for laminating and molding, are described. The invention additionally encompasses copolyimide precursors, reinforced polyimide composites and laminates made from said polyimides where the composite is reinforced by fibrous materials. This is achieved by reacting at least one aromatic dianhydride where each anhydride group is located on an aromatic ring with the carbonyl units in an ortho orientation relative to one another, with at least one diamine which is capable of a transmidization reaction upon incorporation into the polyimide backbone, and with at least one other diamine which is not capable of undergoing such reaction, the diamine which is capable of undergoing the transimidization reaction being present in an amount of from about 1-50 mole percent in relation to the diamine that is not susceptable to transimidization.

  13. Enhanced production of single copy backbone-free transgenic plants in multiple crop species using binary vectors with a pRi replication origin in Agrobacterium tumefaciens.

    PubMed

    Ye, Xudong; Williams, Edward J; Shen, Junjiang; Johnson, Susan; Lowe, Brenda; Radke, Sharon; Strickland, Steve; Esser, James A; Petersen, Michael W; Gilbertson, Larry A

    2011-08-01

    Single transgene copy, vector backbone-free transgenic crop plants are highly desired for functional genomics and many biotechnological applications. We demonstrate that binary vectors that use a replication origin derived from the Ri plasmid of Agrobacterium rhizogenes (oriRi) increase the frequency of single copy, backbone-free transgenic plants in Agrobacterium tumefaciens mediated transformation of soybean, canola, and corn, compared to RK2-derived binary vectors (RK2 oriV). In large scale soybean transformation experiments, the frequency of single copy, backbone-free transgenic plants was nearly doubled in two versions of the oriRi vectors compared to the RK2 oriV control vector. In canola transformation experiments, the oriRi vector produced more single copy, backbone-free transgenic plants than did the RK2 oriV vector. In corn transformation experiments, the frequency of single copy backbone-free transgenic plants was also significantly increased when using the oriRi vector, although the transformation frequency dropped. These results, derived from transformation experiments using three crops, indicate the advantage of oriRi vectors over RK2 oriV binary vectors for the production of single copy, backbone-free transgenic plants using Agrobacterium-mediated transformation. PMID:21042934

  14. DNA sequencing

    SciTech Connect

    Tabor, S.; Richardson, C.C.

    1991-02-19

    This patent describes a method for determining the nucleotide base sequence of a DNA molecule. It comprises: providing the DNA molecule annealed with a primer molecule able to hybridize to the DNA molecule; incubating the annealed molecules in a vessel containing four different deoxynucleoside triphosphates, a processive DNA polymerase, wherein the polymerase is able to remain bound for at least 500 bases to the DNA molecule in an environmental condition used in the extension reaction of a DNA sequencing reaction, the polymerase having less than 500 units of exonuclease activity per mg of the polymerase, and one of four DNA synthesis terminating agents which terminate DNA synthesis at a specific nucleotide base, wherein each the agent terminates DNA synthesis at a different nucleotide base, and separating the DNA products of the incubating reaction according to their size, whereby at least a part of the nucleotide base sequence of the DNA molecule can be determined.

  15. Hidden Markov models that use predicted local structure for fold recognition: alphabets of backbone geometry.

    PubMed

    Karchin, Rachel; Cline, Melissa; Mandel-Gutfreund, Yael; Karplus, Kevin

    2003-06-01

    An important problem in computational biology is predicting the structure of the large number of putative proteins discovered by genome sequencing projects. Fold-recognition methods attempt to solve the problem by relating the target proteins to known structures, searching for template proteins homologous to the target. Remote homologs that may have significant structural similarity are often not detectable by sequence similarities alone. To address this, we incorporated predicted local structure, a generalization of secondary structure, into two-track profile hidden Markov models (HMMs). We did not rely on a simple helix-strand-coil definition of secondary structure, but experimented with a variety of local structure descriptions, following a principled protocol to establish which descriptions are most useful for improving fold recognition and alignment quality. On a test set of 1298 nonhomologous proteins, HMMs incorporating a 3-letter STRIDE alphabet improved fold recognition accuracy by 15% over amino-acid-only HMMs and 23% over PSI-BLAST, measured by ROC-65 numbers. We compared two-track HMMs to amino-acid-only HMMs on a difficult alignment test set of 200 protein pairs (structurally similar with 3-24% sequence identity). HMMs with a 6-letter STRIDE secondary track improved alignment quality by 62%, relative to DALI structural alignments, while HMMs with an STR track (an expanded DSSP alphabet that subdivides strands into six states) improved by 40% relative to CE. PMID:12784210

  16. Bayesian probabilistic approach for predicting backbone structures in terms of protein blocks.

    PubMed

    de Brevern, A G; Etchebest, C; Hazout, S

    2000-11-15

    By using an unsupervised cluster analyzer, we have identified a local structural alphabet composed of 16 folding patterns of five consecutive C(alpha) ("protein blocks"). The dependence that exists between successive blocks is explicitly taken into account. A Bayesian approach based on the relation protein block-amino acid propensity is used for prediction and leads to a success rate close to 35%. Sharing sequence windows associated with certain blocks into "sequence families" improves the prediction accuracy by 6%. This prediction accuracy exceeds 75% when keeping the first four predicted protein blocks at each site of the protein. In addition, two different strategies are proposed: the first one defines the number of protein blocks in each site needed for respecting a user-fixed prediction accuracy, and alternatively, the second one defines the different protein sites to be predicted with a user-fixed number of blocks and a chosen accuracy. This last strategy applied to the ubiquitin conjugating enzyme (alpha/beta protein) shows that 91% of the sites may be predicted with a prediction accuracy larger than 77% considering only three blocks per site. The prediction strategies proposed improve our knowledge about sequence-structure dependence and should be very useful in ab initio protein modelling. PMID:11025540

  17. ff14SB: Improving the Accuracy of Protein Side Chain and Backbone Parameters from ff99SB.

    PubMed

    Maier, James A; Martinez, Carmenza; Kasavajhala, Koushik; Wickstrom, Lauren; Hauser, Kevin E; Simmerling, Carlos

    2015-08-11

    Molecular mechanics is powerful for its speed in atomistic simulations, but an accurate force field is required. The Amber ff99SB force field improved protein secondary structure balance and dynamics from earlier force fields like ff99, but weaknesses in side chain rotamer and backbone secondary structure preferences have been identified. Here, we performed a complete refit of all amino acid side chain dihedral parameters, which had been carried over from ff94. The training set of conformations included multidimensional dihedral scans designed to improve transferability of the parameters. Improvement in all amino acids was obtained as compared to ff99SB. Parameters were also generated for alternate protonation states of ionizable side chains. Average errors in relative energies of pairs of conformations were under 1.0 kcal/mol as compared to QM, reduced 35% from ff99SB. We also took the opportunity to make empirical adjustments to the protein backbone dihedral parameters as compared to ff99SB. Multiple small adjustments of φ and ψ parameters were tested against NMR scalar coupling data and secondary structure content for short peptides. The best results were obtained from a physically motivated adjustment to the φ rotational profile that compensates for lack of ff99SB QM training data in the β-ppII transition region. Together, these backbone and side chain modifications (hereafter called ff14SB) not only better reproduced their benchmarks, but also improved secondary structure content in small peptides and reproduction of NMR χ1 scalar coupling measurements for proteins in solution. We also discuss the Amber ff12SB parameter set, a preliminary version of ff14SB that includes most of its improvements. PMID:26574453

  18. Using protein backbone mutagenesis to dissect the link between ion occupancy and C-type inactivation in K+ channels.

    PubMed

    Matulef, Kimberly; Komarov, Alexander G; Costantino, Corey A; Valiyaveetil, Francis I

    2013-10-29

    K(+) channels distinguish K(+) from Na(+) in the selectivity filter, which consists of four ion-binding sites (S1-S4, extracellular to intracellular) that are built mainly using the carbonyl oxygens from the protein backbone. In addition to ionic discrimination, the selectivity filter regulates the flow of ions across the membrane in a gating process referred to as C-type inactivation. A characteristic of C-type inactivation is a dependence on the permeant ion, but the mechanism by which permeant ions modulate C-type inactivation is not known. To investigate, we used amide-to-ester substitutions in the protein backbone of the selectivity filter to alter ion binding at specific sites and determined the effects on inactivation. The amide-to-ester substitutions in the protein backbone were introduced using protein semisynthesis or in vivo nonsense suppression approaches. We show that an ester substitution at the S1 site in the KcsA channel does not affect inactivation whereas ester substitutions at the S2 and S3 sites dramatically reduce inactivation. We determined the structure of the KcsA S2 ester mutant and found that the ester substitution eliminates K(+) binding at the S2 site. We also show that an ester substitution at the S2 site in the KvAP channel has a similar effect of slowing inactivation. Our results link C-type inactivation to ion occupancy at the S2 site. Furthermore, they suggest that the differences in inactivation of K(+) channels in K(+) compared with Rb(+) are due to different ion occupancies at the S2 site. PMID:24128761

  19. Increased hydrophobicity and decreased backbone flexibility explain lower solubility of cataract-linked mutant of γD-crystallin

    PubMed Central

    Banerjee, Priya R.; Puttamadappa, Shadakshara S.; Pande, Ajay; Shekhtman, Alexander; Pande, Jayanti

    2011-01-01

    A number of point mutations in γD-crystallin are associated with human cataract. The Pro23Thr (P23T) mutation is perhaps the most common, geographically-widespread, and presents itself in a variety of phenotypes. It is therefore important to understand the molecular basis of lens opacity due to this mutation. In our earlier studies we noted that P23T shows retrograde and sharply lowered solubility, possibly due to the emergence of hydrophobic patches involved in protein aggregation. Binding of Bis-ANS dye, a commonly used probe of surfacehydrophobicity, competed with aggregation, suggesting that the residues involved in Bis-ANS binding are also involved in protein aggregation. Here, using NMR spectroscopy in conjunction with Bis-ANS binding, we identify three residues, Y16, D21 and Y50 in P23T, involved in binding the dye. Furthermore, using 15N NMR-relaxation experiments, we show that in the mutant protein, backbone fluctuations are restricted in picosecond to nanosecond and microsecond time-scales, relative to the wild type. Our present studies identify the residues involved in these two pivotal characteristics of the mutant protein, namely increased surface hydrophobicity and restricted mobility of the protein backbone, which can explain the nucleation and further propagation of protein aggregates. Thus we have now identified the residues in the P23T mutant that give rise to novel hydrophobic surfaces, as well as those regions of the protein backbone where fluctuations in different time-scales are restricted, providing a comprehensive understanding of how lens opacity could result from this mutation. PMID:21827768

  20. Conformation-specific spectroscopy of capped glutamine-containing peptides: role of a single glutamine residue on peptide backbone preferences.

    PubMed

    Walsh, Patrick S; Dean, Jacob C; McBurney, Carl; Kang, Hyuk; Gellman, Samuel H; Zwier, Timothy S

    2016-04-20

    The conformational preferences of a series of short, aromatic-capped, glutamine-containing peptides have been studied under jet-cooled conditions in the gas phase. This work seeks a bottom-up understanding of the role played by glutamine residues in directing peptide structures that lead to neurodegenerative diseases. Resonant ion-dip infrared (RIDIR) spectroscopy is used to record single-conformation infrared spectra in the NH stretch, amide I and amide II regions. Comparison of the experimental spectra with the predictions of calculations carried out at the DFT M05-2X/6-31+G(d) level of theory lead to firm assignments for the H-bonding architectures of a total of eight conformers of four molecules, including three in Z-Gln-OH, one in Z-Gln-NHMe, three in Ac-Gln-NHBn, and one in Ac-Ala-Gln-NHBn. The Gln side chain engages actively in forming H-bonds with nearest-neighbor amide groups, forming C8 H-bonds to the C-terminal side, C9 H-bonds to the N-terminal side, and an amide-stacked geometry, all with an extended (C5) peptide backbone about the Gln residue. The Gln side chain also stabilizes an inverse γ-turn in the peptide backbone by forming a pair of H-bonds that bridge the γ-turn and stabilize it. Finally, the entire conformer population of Ac-Ala-Gln-NHBn is funneled into a single structure that incorporates the peptide backbone in a type I β-turn, stabilized by the Gln side chain forming a C7 H-bond to the central amide group in the β-turn not otherwise involved in a hydrogen bond. This β-turn backbone structure is nearly identical to that observed in a series of X-(AQ)-Y β-turns in the protein data bank, demonstrating that the gas-phase structure is robust to perturbations imposed by the crystalline protein environment. PMID:27054830

  1. Incorporation of Heterocycles into the Backbone of Peptoids to Generate Diverse Peptoid-Inspired One Bead One Compound Libraries

    PubMed Central

    Aditya, Animesh; Kodadek, Thomas

    2012-01-01

    Combinatorial libraries of peptoids (oligo-N-substituted glycines) have proven to be useful sources of protein ligands. Each unit of the peptoid oligomer is derived from 2-haloacetic acid and a primary amine. In order to increase the chemical diversity available in peptoid libraries, we demonstrate here that heterocyclic halomethyl carboxylic acids can be employed as backbone building blocks in the synthesis of peptoid-based oligomers. Optimized conditions are reported that allow the creation of large, high quality combinatorial libraries containing these units. PMID:22320121

  2. Backbone and side-chain NMR assignments for the bromodomain of mouse BAZ1A (ACF1).

    PubMed

    Fan, Kai; Chen, Shengrong; Ge, Yifeng; Ye, Kaiqin; Yao, Qi; Jing, Jun; Zhang, Jiahai; Tu, Xiaoming; Yao, Bing

    2016-04-01

    BAZ1A, a non-catalytic subunit of the chromatin remodeler complexes ACF and CHRAC, is thought to modulate the ATPase's activity of the complexes and participate in gene transcription, DNA damage checkpoint and double-strand break repair. Recently, the essential role of BAZ1A in mouse male fertility has also been reported. BAZ1A contains one C-terminal bromodomain, which specifically recognizes acetylation of lysine. Here, we report the backbone and side chain (1)H, (13)C and (15)N resonance assignment of the mouse BAZ1A-bromodomain, as a basis for further functional studies and structure determination. PMID:26542424

  3. Intramolecular hydrogen atom migration along the backbone of cationic and neutral radical tripeptides and subsequent radical-induced dissociations.

    PubMed

    Zhao, Junfang; Song, Tao; Xu, Minjie; Quan, Quan; Siu, K W Michael; Hopkinson, Alan C; Chu, Ivan K

    2012-06-28

    Dissociation of peptide radical ions involves competition between charge-induced and radical-induced reactions that can be preceded by isomerization. The isomeric radical cations of the peptide methyl ester [G˙GR-OMe](+) and [GG˙R-OMe](+) provide very similar collision-induced dissociation (CID) spectra, suggesting that isomerization occurs prior to fragmentation. They undergo characteristic radical-induced bond cleavage of the peptide N-terminal amide bond resulting in the y2(+) ion, and of the arginine side-chain's Cα-Cβ bond giving protonated allylguanidine {[CH2[double bond, length as m-dash]CHCH2NHC(NH2)2](+), m/z 100}. The absence of a y2(+) fragment ion in the CID of the radical cationic tripeptide [ACH3G˙R](+) and of an m/z 100 ion in the spectrum of [G˙ACH3R](+) (where ACH3 is an α-aminoisobutyric acid residue, which cannot form an α-carbon-centered radical through hydrogen atom transfer) establishes the importance of hydrogen atom migration along the peptide backbone prior to specific radical-induced fragmentations. Herein we use density functional theory (DFT) at the B3LYP/6-31++G(d,p) level to evaluate the barriers for interconversion between the α-carbon-centered radicals and for dissociation. The radical cations [G˙GR](+) and [GG˙R](+) have their radicals located on the α-carbon atoms of the peptide backbone and their charge densities largely sequestered on the guanidine groups of the side-chain of arginine residues. This is in contrast to the isomeric radical cations of [GGG]˙(+), in which the charge resides necessarily on the peptide backbone. The lower charge densities on the backbones of [G˙GR](+) and [GG˙R](+) result in greater structural flexibility, decreasing the barrier for interconversion between these α-carbon-centered radicals to 36.2 kcal mol(-1) (cf. 44.7 kcal mol(-1) for [GGG]˙(+)). The total absence of charge, assessed by examining intramolecular hydrogen atom transfers among the three α-carbon centers of the isomeric neutral α-carbon-centered triglycine radicals [GGG-H]˙, leads to an additional but slight reduction in enthalpy, to approximately 34 kcal mol(-1). PMID:22614151

  4. A novel cGUUAg tetraloop structure with a conserved yYNMGg-type backbone conformation from cloverleaf 1 of bovine enterovirus 1 RNA.

    PubMed

    Ihle, Yvonne; Ohlenschläger, Oliver; Häfner, Sabine; Duchardt, Elke; Zacharias, Martin; Seitz, Simone; Zell, Roland; Ramachandran, Ramadurai; Görlach, Matthias

    2005-01-01

    The 5'-terminal cloverleaf (CL)-like RNA structures are essential for the initiation of positive- and negative-strand RNA synthesis of entero- and rhinoviruses. SLD is the cognate RNA ligand of the viral proteinase 3C (3C(pro)), which is an indispensable component of the viral replication initiation complex. The structure of an 18mer RNA representing the apical stem and the cGUUAg D-loop of SLD from the first 5'-CL of BEV1 was determined in solution to a root-mean-square deviation (r.m.s.d.) (all heavy atoms) of 0.59 A (PDB 1Z30). The first (antiG) and last (synA) nucleotide of the D-loop forms a novel 'pseudo base pair' without direct hydrogen bonds. The backbone conformation and the base-stacking pattern of the cGUUAg-loop, however, are highly similar to that of the coxsackieviral uCACGg D-loop (PDB 1RFR) and of the stable cUUCGg tetraloop (PDB 1F7Y) but surprisingly dissimilar to the structure of a cGUAAg stable tetraloop (PDB 1MSY), even though the cGUUAg BEV D-loop and the cGUAAg tetraloop differ by 1 nt only. Together with the presented binding data, these findings provide independent experimental evidence for our model [O. Ohlenschlager, J. Wohnert, E. Bucci, S. Seitz, S. Hafner, R. Ramachandran, R. Zell and M. Gorlach (2004) Structure, 12, 237-248] that the proteinase 3C(pro) recognizes structure rather than sequence. PMID:15814817

  5. {{text{C}}_{α }} - {text{C}} Bond Cleavage of the Peptide Backbone in MALDI In-Source Decay Using Salicylic Acid Derivative Matrices

    NASA Astrophysics Data System (ADS)

    Asakawa, Daiki; Takayama, Mitsuo

    2011-07-01

    The use of 5-formylsalicylic acid (5-FSA) and 5-nitrosalicylic acid (5-NSA) as novel matrices for in-source decay (ISD) of peptides in matrix-assisted laser desorption/ionization (MALDI) is described. The use of 5-FSA and 5-NSA generated a- and x-series ions accompanied by oxidized peptides [M - 2 H + H]+. The preferential formation of a- and x-series ions was found to be dependent on the hydrogen-accepting ability of matrix. The hydrogen-accepting ability estimated from the ratio of signal intensity of oxidized product [M - 2 H + H]+ to that of non-oxidized protonated molecule [M + H]+ of peptide was of the order 5-NSA > 5-FSA > 5-aminosalicylic acid (5-ASA) ≒ 2,5-dihydroxyl benzoic acid (2,5-DHB) ≒ 0. The results suggest that the hydrogen transfer reaction from peptide to 5-FSA and 5-NSA occurs during the MALDI-ISD processes. The hydrogen abstraction from peptides results in the formation of oxidized peptides containing a radical site on the amide nitrogen with subsequent radical-induced cleavage at the {{{C}}_{α }} - {{C}} bond, leading to the formation of a- and x-series ions. The most significant feature of MALDI-ISD with 5-FSA and 5-NSA is the specific cleavage of the {{{C}}_{α }} - {{C}} bond of the peptide backbone without degradation of side-chain and post-translational modifications (PTM). The matrix provides a useful complementary method to conventional MALDI-ISD for amino acid sequencing and site localization of PTMs in peptides.

  6. Evaluation of Diverse α/β Backbone Patterns for Functional α-Helix Mimicry: Analogues of the Bim BH3 Domain

    PubMed Central

    Boersma, Melissa D.; Haase, Holly S.; Peterson-Kaufman, Kimberly J.; Lee, Erinna F.; Clarke, Oliver B.; Colman, Peter M.; Smith, Brian J.; Horne, W. Seth; Fairlie, W. Douglas; Gellman, Samuel H.

    2012-01-01

    Peptidic oligomers that contain both α- and β-amino acid residues, in regular patterns throughout the backbone, are emerging as structural mimics of α-helix-forming conventional peptides (composed exclusively of α-amino acid residues). Here we describe a comprehensive evaluation of diverse α/β-peptide homologues of the Bim BH3 domain in terms of their ability to bind to the BH3-recognition sites on two partner proteins, Bcl-xL and Mcl-1. These proteins are members of the anti-apoptotic Bcl-2 family, and both bind tightly to the Bim BH3 domain itself. All α/β-peptide homologues retain the side chain sequence of the Bim BH3 domain, but each homologue contains periodic α-residue → β3-residue substitutions. Previous work has shown that the ααβαααβ pattern, which aligns the β3-residues in a 'stripe' along one side of the helix, can support functional α-helix mimicry, and the results reported here support this conclusion. The present study provides the first evaluation of functional mimicry by ααβ and αααβ patterns, which cause the β3-residues to spiral around the helix periphery. We find that the αααβ pattern can support effective mimicry of the Bim BH3 domain, as manifested by the crystal structure of an α/β-peptide bound to Bcl-xL, affinity for a variety of Bcl-2 family proteins, and induction of apoptotic signaling in mouse embryonic fibroblast extracts. The best αααβ homologue shows substantial protection from proteolytic degradation relative to the Bim BH3 α-peptide. PMID:22040025

  7. Proteomics-grade de novo sequencing approach.

    PubMed

    Savitski, Mikhail M; Nielsen, Michael L; Kjeldsen, Frank; Zubarev, Roman A

    2005-01-01

    The conventional approach in modern proteomics to identify proteins from limited information provided by molecular and fragment masses of their enzymatic degradation products carries an inherent risk of both false positive and false negative identifications. For reliable identification of even known proteins, complete de novo sequencing of their peptides is desired. The main problems of conventional sequencing based on tandem mass spectrometry are incomplete backbone fragmentation and the frequent overlap of fragment masses. In this work, the first proteomics-grade de novo approach is presented, where the above problems are alleviated by the use of complementary fragmentation techniques CAD and ECD. Implementation of a high-current, large-area dispenser cathode as a source of low-energy electrons provided efficient ECD of doubly charged peptides, the most abundant species (65-80%), in a typical trypsin-based proteomics experiment. A new linear de novo algorithm is developed combining efficiency and speed, processing on a conventional 3 GHz PC, 1000 MS/MS data sets in 60 s. More than 6% of all MS/MS data for doubly charged peptides yielded complete sequences, and another 13% gave nearly complete sequences with a maximum gap of two amino acid residues. These figures are comparable with the typical success rates (5-15%) of database identification. For peptides reliably found in the database (Mowse score > or = 34), the agreement with de novo-derived full sequences was >95%. Full sequences were derived in 67% of the cases when full sequence information was present in MS/MS spectra. Thus the new de novo sequencing approach reached the same level of efficiency and reliability as conventional database-identification strategies. PMID:16335984

  8. Composition of the summer photosynthetic pico and nanoplankton communities in the Beaufort Sea assessed by T-RFLP and sequences of the 18S rRNA gene from flow cytometry sorted samples

    PubMed Central

    Balzano, Sergio; Marie, Dominique; Gourvil, Priscillia; Vaulot, Daniel

    2012-01-01

    The composition of photosynthetic pico and nanoeukaryotes was investigated in the North East Pacific and the Arctic Ocean with special emphasis on the Beaufort Sea during the MALINA cruise in summer 2009. Photosynthetic populations were sorted using flow cytometry based on their size and pigment fluorescence. Diversity of the sorted photosynthetic eukaryotes was determined using terminal-restriction fragment length polymorphism analysis and cloning/sequencing of the 18S ribosomal RNA gene. Picoplankton was dominated by Mamiellophyceae, a class of small green algae previously included in the prasinophytes: in the North East Pacific, the contribution of an Arctic Micromonas ecotype increased steadily northward becoming the only taxon occurring at most stations throughout the Beaufort Sea. In contrast, nanoplankton was more diverse: North Pacific stations were dominated by Pseudo-nitzschia sp. whereas those in the Beaufort Sea were dominated by two distinct Chaetoceros species as well as by Chrysophyceae, Pelagophyceae and Chrysochromulina spp.. This study confirms the importance of Arctic Micromonas within picoplankton throughout the Beaufort Sea and demonstrates that the photosynthetic picoeukaryote community in the Arctic is much less diverse than at lower latitudes. Moreover, in contrast to what occurs in warmer waters, most of the key pico- and nanoplankton species found in the Beaufort Sea could be successfully established in culture. PMID:22278671

  9. MSLICE Sequencing

    NASA Technical Reports Server (NTRS)

    Crockett, Thomas M.; Joswig, Joseph C.; Shams, Khawaja S.; Norris, Jeffrey S.; Morris, John R.

    2011-01-01

    MSLICE Sequencing is a graphical tool for writing sequences and integrating them into RML files, as well as for producing SCMF files for uplink. When operated in a testbed environment, it also supports uplinking these SCMF files to the testbed via Chill. This software features a free-form textural sequence editor featuring syntax coloring, automatic content assistance (including command and argument completion proposals), complete with types, value ranges, unites, and descriptions from the command dictionary that appear as they are typed. The sequence editor also has a "field mode" that allows tabbing between arguments and displays type/range/units/description for each argument as it is edited. Color-coded error and warning annotations on problematic tokens are included, as well as indications of problems that are not visible in the current scroll range. "Quick Fix" suggestions are made for resolving problems, and all the features afforded by modern source editors are also included such as copy/cut/paste, undo/redo, and a sophisticated find-and-replace system optionally using regular expressions. The software offers a full XML editor for RML files, which features syntax coloring, content assistance and problem annotations as above. There is a form-based, "detail view" that allows structured editing of command arguments and sequence parameters when preferred. The "project view" shows the user s "workspace" as a tree of "resources" (projects, folders, and files) that can subsequently be opened in editors by double-clicking. Files can be added, deleted, dragged-dropped/copied-pasted between folders or projects, and these operations are undoable and redoable. A "problems view" contains a tabular list of all problems in the current workspace. Double-clicking on any row in the table opens an editor for the appropriate sequence, scrolling to the specific line with the problem, and highlighting the problematic characters. From there, one can invoke "quick fix" as described above to resolve the issue. Once resolved, saving the file causes the problem to be removed from the problem view.

  10. Pemetrexed With Platinum Combination as a Backbone for Targeted Therapy in Non-Small-Cell Lung Cancer.

    PubMed

    Stinchcombe, Thomas E; Borghaei, Hossein; Barker, Scott S; Treat, Joseph Anthony; Obasaju, Coleman

    2016-01-01

    Standard platinum-based chemotherapy combinations for advanced non-small-cell lung cancer (NSCLC) have reached a plateau in terms of the survival benefit they offer for patients. In addition, the emerging clinical trend of tailored treatment based on patient characteristics has led to the development of therapeutic strategies that target specific cancer-related molecular pathways, including epidermal growth factor receptor (EGFR), angiogenesis, and anaplastic lymphoma kinase inhibitors. Current research is focused on combining targeted therapy with platinum-based chemotherapy in an endeavor to achieve an additional benefit in specific patient populations. Currently, pemetrexed is indicated for use in the first-line, maintenance, and second-line settings for the treatment of nonsquamous NSCLC. The combination of pemetrexed and cisplatin is well tolerated and is the approved standard first-line therapy. Thus, the pemetrexed-platinum backbone provides an attractive option for combination with targeted therapies. This review aims to summarize the current knowledge and future prospects of the use of pemetrexed-platinum as a backbone for combination with targeted therapies for NSCLC. PMID:26340853

  11. Improved site-specific recombinase-based method to produce selectable marker- and vector-backbone-free transgenic cells

    NASA Astrophysics Data System (ADS)

    Yu, Yuan; Tong, Qi; Li, Zhongxia; Tian, Jinhai; Wang, Yizhi; Su, Feng; Wang, Yongsheng; Liu, Jun; Zhang, Yong

    2014-02-01

    PhiC31 integrase-mediated gene delivery has been extensively used in gene therapy and animal transgenesis. However, random integration events are observed in phiC31-mediated integration in different types of mammalian cells; as a result, the efficiencies of pseudo attP site integration and evaluation of site-specific integration are compromised. To improve this system, we used an attB-TK fusion gene as a negative selection marker, thereby eliminating random integration during phiC31-mediated transfection. We also excised the selection system and plasmid bacterial backbone by using two other site-specific recombinases, Cre and Dre. Thus, we generated clean transgenic bovine fetal fibroblast cells free of selectable marker and plasmid bacterial backbone. These clean cells were used as donor nuclei for somatic cell nuclear transfer (SCNT), indicating a similar developmental competence of SCNT embryos to that of non-transgenic cells. Therefore, the present gene delivery system facilitated the development of gene therapy and agricultural biotechnology.

  12. Metal coordination architectures of triazole-based ligands: Effect of the backbone of bridging ligands on the construction of polymers

    NASA Astrophysics Data System (ADS)

    Du, Jian-Long; Hu, Tong-Liang; Bu, Xian-He

    2012-04-01

    In our efforts to investigate the influence of the backbone of different triazole-based bridging ligands on the structure of their metal complexes, four new coordination polymers, {[Cu(L1)2(H2O)2]Cl2}n (1), [Cu(L2)2Cl2]n (2), [Co(L2)2(SCN)2]n (3), and [Cu(L3)2(NO3)2]n (4), (L1 = 1,2-bis(triazol-1-ylmethyl)benzene, L2 = 1,3-bis(triazol-1-ylmethyl)benzene, L3 = 1,4-bis(triazol-1-ylmethyl)benzene), have been synthesized. All the complexes have been structurally characterized by IR, elemental analysis and single-crystal X-ray diffraction. Structural analyses show that 1 and 4 possess 2D coordination networks with (4,4) topology, and 1 shows a diagonal-diagonal inclined interpenetration. 2 and 3 are isostructural and feature 1D double chain, which further connected by C-H···Cl or π···π weak interactions to form 2D supramolecular frameworks. The results show that the structures of ligands (with different non-coordination backbone spacers) play important roles in the formation of such coordination architectures. Furthermore, EPR (Electron Paramagnetic Resonance) spectra of CuII complexes (1, 2, and 4) have been investigated in the solid state at room temperature.

  13. Localization of electrons in the sugar/phosphate backbone in DNA investigated via resonant Auger decay spectra

    SciTech Connect

    Baba, Yuji; Sekiguchi, Tetsuhiro; Shimoyama, Iwao; Hirao, Norie; Nath, Krishna G.

    2006-11-15

    In order to elucidate the localized nature of electrons in sugar/phosphate backbone in DNA molecules, resonant Auger decay spectra excited by soft x-rays around the inner-shell ionization thresholds have been measured for single-strand DNA. The systems investigated are thin films of DNA as well as related phosphorus compounds such as nucleotide (adenosine triphosphate, ATP), sodium phosphate, and indium phosphide. For ATP and DNA, it was observed that the resonant excitations from P 1s to valence unoccupied {pi}* orbitals are followed by spectator-type Auger decays where the excited electrons remain in valence orbitals during the core-hole decays. It was also found that the energy of the P KL{sub 2,3}L{sub 2,3} (2p{sup -1}{center_dot}{pi}*) spectator Auger peak shifts linearly with the photon energy due to the resonant Auger Raman scattering. Most of the decay channel at the core-to-valence resonant excitation is spectator-type Auger decay in DNA, which is quite different from the Auger decay processes in metallic and semiconducting materials. We conclude that the excited electrons in valence unoccupied states around the phosphates in DNA molecules are strongly localized, resulting in the insulating properties in a one-dimensional direction along sugar/phosphate backbone.

  14. Vanishing amplitude of backbone dynamics causes a true protein dynamical transition: H2 NMR studies on perdeuterated C-phycocyanin

    NASA Astrophysics Data System (ADS)

    Kämpf, Kerstin; Kremmling, Beke; Vogel, Michael

    2014-03-01

    Using a combination of H2 nuclear magnetic resonance (NMR) methods, we study internal rotational dynamics of the perdeuterated protein C-phycocyanin (CPC) in dry and hydrated states over broad temperature and dynamic ranges with high angular resolution. Separating H2 NMR signals from methyl deuterons, we show that basically all backbone deuterons exhibit highly restricted motion occurring on time scales faster than microseconds. The amplitude of this motion increases when a hydration shell exists, while it decreases upon cooling and vanishes near 175 K. We conclude that the vanishing of the highly restricted motion marks a dynamical transition, which is independent of the time window and of a fundamental importance. This conclusion is supported by results from experimental and computational studies of the proteins myoglobin and elastin. In particular, we argue based on findings in molecular dynamics simulations that the behavior of the highly restricted motion of proteins at the dynamical transition resembles that of a characteristic secondary relaxation of liquids at the glass transition, namely the nearly constant loss. Furthermore, H2 NMR studies on perdeuterated CPC reveal that, in addition to highly restricted motion, small fractions of backbone segments exhibit weakly restricted dynamics when temperature and hydration are sufficiently high.

  15. Solubility of polyethers in hydrocarbons at low temperatures. A model for potential genetic backbones on warm titans.

    PubMed

    McLendon, Christopher; Opalko, F Jeffrey; Illangkoon, Heshan I; Benner, Steven A

    2015-03-01

    Ethers are proposed here as the repeating backbone linking units in linear genetic biopolymers that might support Darwinian evolution in hydrocarbon oceans. Hydrocarbon oceans are found in our own solar system as methane mixtures on Titan. They may be found as mixtures of higher alkanes (propane, for example) on warmer hydrocarbon-rich planets in exosolar systems ("warm Titans"). We report studies on the solubility of several short polyethers in propane over its liquid range (from 85 to 231 K, or -188 °C to -42 °C). These show that polyethers are reasonably soluble in propane at temperatures down to ca. 200 K. However, their solubilities drop dramatically at still lower temperatures and become immeasurably low below 170 K, still well above the ∼ 95 K in Titan's oceans. Assuming that a liquid phase is essential for any living system, and genetic biopolymers must dissolve in that biosolvent to support Darwinism, these data suggest that we must look elsewhere to identify linear biopolymers that might support genetics in Titan's surface oceans. However, genetic molecules with polyether backbones may be suitable to support life in hydrocarbon oceans on warm Titans, where abundant organics and environments lacking corrosive water might make it easier for life to originate. PMID:25761113

  16. Systematic Backbone Conformational Constraints on a Cyclic Melanotropin Ligand Leads to Highly Selective Ligands for Multiple Melanocortin Receptors.

    PubMed

    Cai, Minying; Marelli, Udaya Kiran; Bao, Jennifer; Beck, Johannes G; Opperer, Florian; Rechenmacher, Florian; McLeod, Kaitlyn R; Zingsheim, Morgan R; Doedens, Lucas; Kessler, Horst; Hruby, Victor J

    2015-08-27

    Human melanocortin receptors (hMCRs) have been challenging targets to develop ligands that are explicitly selective for each of their subtypes. To modulate the conformational preferences of the melanocortin ligands and improve the biofunctional agonist/antagonist activities and selectivities, we have applied a backbone N-methylation approach on Ac-Nle-c[Asp-His-D-Nal(2')-Arg-Trp-Lys]-NH2 (Ac-Nle(4)-c[Asp(5),D-Nal(2')(7),Lys(10)]-NH2), a nonselective cyclic peptide antagonist at hMC3R and hMC4R and an agonist at hMC1R and hMC5R. Systematic N-methylated derivatives of Ac-Nle(4)-c[Asp(5),D-Nal(2')(7),Lys(10)]-NH2, with all possible backbone N-methylation combinations, have been synthesized and examined for their binding and functional activities toward melanocortin receptor subtypes 1, 3, 4, and 5 (hMCRs). Several N-methylated analogues are selective and potent agonists or antagonists for hMC1R or hMC5R or have selective antagonist activity for hMC3R. The selective hMC1R ligands show strong binding for human melanoma cells. We have also discovered the first universal antagonist (compound 19) for all subtypes of hMCRs. PMID:26218460

  17. Synthesis of graft polyrotaxane by simultaneous capping of backbone and grafting from rings of pseudo-polyrotaxane.

    PubMed

    Kato, Kazuaki; Inoue, Katsunari; Kudo, Masabumi; Ito, Kohzo

    2014-01-01

    Graft polyrotaxanes, with poly(?-caprolactone) (PCL) graft chains on the ring components were synthesized by the simultaneous ring-opening polymerization of ?-caprolactone from both ends of the backbone polymer, an end-functionalized polyethylene glycol (PEG) and the formation of inclusion complexes with ?-cyclodextrin (?-CD). PEG with multiple functional groups at each end was prepared by the condensation of PEG-amine and D-gluconic acid; the PEG derivative formed an inclusion complex with ?-CD. The polymerization of multiple hydroxy groups at the backbone ends resulted in a star-shaped end group, which served as a bulky capping group to prevent dethreading. In contrast, PEG with only one hydroxy group at each end did not produce polyrotaxanes, indicating that single PCL chains were too thin to confine ?-CDs to the complex. In addition, the grafting polymerization proceeded properly only when robust hydrogen bonds formed between ?-CDs were dissociated using a basic catalyst. Since the dissociation also induced dethreading, kinetic control of the polymerization and dissociation were crucial for producing graft polyrotaxanes. Consequently, this three-step reaction yielded graft polyrotaxanes in a good yield, demonstrating a significant simplification of the synthesis of graft polyrotaxanes. PMID:25383129

  18. Insertion Sequences

    PubMed Central

    Mahillon, Jacques; Chandler, Michael

    1998-01-01

    Insertion sequences (ISs) constitute an important component of most bacterial genomes. Over 500 individual ISs have been described in the literature to date, and many more are being discovered in the ongoing prokaryotic and eukaryotic genome-sequencing projects. The last 10 years have also seen some striking advances in our understanding of the transposition process itself. Not least of these has been the development of various in vitro transposition systems for both prokaryotic and eukaryotic elements and, for several of these, a detailed understanding of the transposition process at the chemical level. This review presents a general overview of the organization and function of insertion sequences of eubacterial, archaebacterial, and eukaryotic origins with particular emphasis on bacterial elements and on different aspects of the transposition mechanism. It also attempts to provide a framework for classification of these elements by assigning them to various families or groups. A total of 443 members of the collection have been grouped in 17 families based on combinations of the following criteria: (i) similarities in genetic organization (arrangement of open reading frames); (ii) marked identities or similarities in the enzymes which mediate the transposition reactions, the recombinases/transposases (Tpases); (iii) similar features of their ends (terminal IRs); and (iv) fate of the nucleotide sequence of their target sites (generation of a direct target duplication of determined length). A brief description of the mechanism(s) involved in the mobility of individual ISs in each family and of the structure-function relationships of the individual Tpases is included where available. PMID:9729608

  19. Polyproline II structure in a sequence of seven alanine residues

    PubMed Central

    Shi, Zhengshuang; Olson, C. Anders; Rose, George D.; Baldwin, Robert L.; Kallenbach, Neville R.

    2002-01-01

    A sequence of seven alanine residues—too short to form an α-helix and whose side chains do not interact with each other—is a particularly simple model for testing the common description of denatured proteins as structureless random coils. The 3JHNα coupling constants of individual alanine residues have been measured from 2 to 56°C by using isotopically labeled samples. The results display a thermal transition between different backbone conformations, which is confirmed by CD spectra. The NMR results suggest that polyproline II is the dominant conformation at 2°C and the content of β strand is increased by approximately 10% at 55°C relative to that at 2°C. The polyproline II conformation is consistent with recent studies of short alanine peptides, including structure prediction by ab initio quantum mechanics and solution structures for both a blocked alanine dipeptide and an alanine tripeptide. CD and other optical spectroscopies have found structure in longer “random coil” peptides and have implicated polyproline II, which is a major backbone conformation in residues within loop regions of protein structures. Our result suggests that the backbone conformational entropy in alanine peptides is considerably smaller than estimated by the random coil model. New thermodynamic data confirm this suggestion: the entropy loss on alanine helix formation is only 2.2 entropy units per residue. PMID:12091708

  20. Ultrafast clustering algorithms for metagenomic sequence analysis

    PubMed Central

    Fu, Limin; Niu, Beifang; Wu, Sitao; Wooley, John

    2012-01-01

    The rapid advances of high-throughput sequencing technologies dramatically prompted metagenomic studies of microbial communities that exist at various environments. Fundamental questions in metagenomics include the identities, composition and dynamics of microbial populations and their functions and interactions. However, the massive quantity and the comprehensive complexity of these sequence data pose tremendous challenges in data analysis. These challenges include but are not limited to ever-increasing computational demand, biased sequence sampling, sequence errors, sequence artifacts and novel sequences. Sequence clustering methods can directly answer many of the fundamental questions by grouping similar sequences into families. In addition, clustering analysis also addresses the challenges in metagenomics. Thus, a large redundant data set can be represented with a small non-redundant set, where each cluster can be represented by a single entry or a consensus. Artifacts can be rapidly detected through clustering. Errors can be identified, filtered or corrected by using consensus from sequences within clusters. PMID:22772836

  1. Original stimuli-sensitive polysaccharide derivatives/N-isopropylacrylamide hydrogels. Role of polysaccharide backbone.

    PubMed

    Hamcerencu, Mihaela; Desbrieres, Jacques; Popa, Marcel; Riess, Gérard

    2012-06-20

    This article compares the properties of a novel class of unsaturated Xanthan and Gellan derivatives/N-isopropylacrylamide stimuli-responsive hydrogels synthesized by free radical polymerization. Xanthan and Gellan Gum were partially functionalized by esterification with maleic anhydride under various conditions. By copolymerization of these maleate polysaccharides with a N-isopropylacrylamide known temperature sensitive precursor, water-swollen hydrogels with interpenetrating polymer networks (IPN) were obtained. The hydrogels were characterized for their temperature and pH-responsive behaviour by equilibrium swelling experiments and differential scanning calorimetry. The investigation of these materials also includes solid-state (13)CP/MAS NMR and elemental analysis of the nitrogen content. Morphology was visualized by scanning electron microscopy. Depending upon composition and the nature of the base-polysaccharide, the hydrogels showed different response rates to the external changes of temperature as well as pH. By changing the feed composition ratio of precursors and crosslinking agent (β-cyclodextrin acrylate or N,N'-methylenebisacrylamide respectively) the phase transition temperature (lower critical solution temperature) could also be adjusted near to the body temperature for biomedical and biotechnological applications. The role of the rigidity and the charge density of the polysaccharide chain, its ability to form hydrogen bonding on these properties are more particularly considered. PMID:24750741

  2. Radical Additions to Aromatic Residues in Peptides Facilitate Unexpected Side Chain and Backbone Losses

    NASA Astrophysics Data System (ADS)

    Zhang, Xing; Julian, Ryan R.

    2014-04-01

    Accurate identification of fragments in tandem mass spectrometry experiments is aided by knowledge of relevant fragmentation mechanisms. Herein, novel radical addition reactions that direct unexpected side-chain dissociations at tryptophan and tyrosine residues are reported. Various mechanisms that can account for the observed dissociation channels are investigated by experiment and theory. The propensity for radical addition at a particular site is found to be primarily under kinetic control, which is largely dictated by molecular structure. In certain peptides, intramolecular radical addition reactions are favored, which leads to the observation of numerous unexpected fragments. In one pathway, radical addition leads to migration of an aromatic side chain to another residue. Alternatively, radical addition followed by hydrogen atom loss leads to cyclization of the peptide and increased observation of internal sequence fragments. Radical addition reactions should be considered when assigning fragmentation spectra obtained from activation of hydrogen deficient peptides.

  3. Whole-Genome Sequence Variation among Multiple Isolates of Pseudomonas aeruginosa

    PubMed Central

    Spencer, David H.; Kas, Arnold; Smith, Eric E.; Raymond, Christopher K.; Sims, Elizabeth H.; Hastings, Michele; Burns, Jane L.; Kaul, Rajinder; Olson, Maynard V.

    2003-01-01

    Whole-genome shotgun sequencing was used to study the sequence variation of three Pseudomonas aeruginosa isolates, two from clonal infections of cystic fibrosis patients and one from an aquatic environment, relative to the genomic sequence of reference strain PAO1. The majority of the PAO1 genome is represented in these strains; however, at least three prominent islands of PAO1-specific sequence are apparent. Conversely, ∼10% of the sequencing reads derived from each isolate fail to align with the PAO1 backbone. While average sequence variation among all strains is roughly 0.5%, regions of pronounced differences were evident in whole-genome scans of nucleotide diversity. We analyzed two such divergent loci, the pyoverdine and O-antigen biosynthesis regions, by complete resequencing. A thorough analysis of isolates collected over time from one of the cystic fibrosis patients revealed independent mutations resulting in the loss of O-antigen synthesis alternating with a mucoid phenotype. Overall, we conclude that most of the PAO1 genome represents a core P. aeruginosa backbone sequence while the strains addressed in this study possess additional genetic material that accounts for at least 10% of their genomes. Approximately half of these additional sequences are novel. PMID:12562802

  4. Treatment of Gram-negative pneumonia in the critical care setting: is the beta-lactam antibiotic backbone broken beyond repair?

    PubMed

    Bassetti, Matteo; Welte, Tobias; Wunderink, Richard G

    2016-01-01

    Beta-lactam antibiotics form the backbone of treatment for Gram-negative pneumonia in mechanically ventilated patients in the intensive care unit. However, this beta-lactam antibiotic backbone is increasingly under pressure from emerging resistance across all geographical regions, and health-care professionals in many countries are rapidly running out of effective treatment options. Even in regions that currently have only low levels of resistance, the effects of globalization are likely to increase local pressures on the beta-lactam antibiotic backbone in the near future. Therefore, clinicians are increasingly faced with a difficult balancing act: the need to prescribe adequate and appropriate antibiotic therapy while reducing the emergence of resistance and the overuse of antibiotics. In this review, we explore the burden of Gram-negative pneumonia in the critical care setting and the pressure that antibiotic resistance places on current empiric therapy regimens (and the beta-lactam antibiotic backbone) in this patient population. New treatment approaches, such as systemic and inhaled antibiotic alternatives, are on the horizon and are likely to help tackle the rising levels of beta-lactam antibiotic resistance. In the meantime, it is imperative that the beta-lactam antibiotic backbone of currently available antibiotics be supported through stringent antibiotic stewardship programs. PMID:26821535

  5. Protein Side-Chain Resonance Assignment and NOE Assignment Using RDC-Defined Backbones without TOCSY Data3

    PubMed Central

    Zeng, Jianyang; Zhou, Pei; Donald, Bruce Randall

    2011-01-01

    One bottleneck in NMR structure determination lies in the laborious and time-consuming process of side-chain resonance and NOE assignments. Compared to the well-studied backbone resonance assignment problem, automated side-chain resonance and NOE assignments are relatively less explored. Most NOE assignment algorithms require nearly complete side-chain resonance assignments from a series of through-bond experiments such as HCCH-TOCSY or HCCCONH. Unfortunately, these TOCSY experiments perform poorly on large proteins. To overcome this deficiency, we present a novel algorithm, called NASCA (NOE Assignment and Side-Chain Assignment), to automate both side-chain resonance and NOE assignments and to perform high-resolution protein structure determination in the absence of any explicit through-bond experiment to facilitate side-chain resonance assignment, such as HCCH-TOCSY. After casting the assignment problem into a Markov Random Field (MRF), NASCA extends and applies combinatorial protein design algorithms to compute optimal assignments that best interpret the NMR data. The MRF captures the contact map information of the protein derived from NOESY spectra, exploits the backbone structural information determined by RDCs, and considers all possible side-chain rotamers. The complexity of the combinatorial search is reduced by using a dead-end elimination (DEE) algorithm, which prunes side-chain resonance assignments that are provably not part of the optimal solution. Then an A* search algorithm is employed to find a set of optimal side-chain resonance assignments that best fit the NMR data. These side-chain resonance assignments are then used to resolve the NOE assignment ambiguity and compute high-resolution protein structures. Tests on five proteins show that NASCA assigns resonances for more than 90% of side-chain protons, and achieves about 80% correct assignments. The final structures computed using the NOE distance restraints assigned by NASCA have backbone RMSD 0.8 – 1.5 Å from the reference structures determined by traditional NMR approaches. PMID:21706248

  6. Backbone dynamics of free barnase and its complex with barstar determined by 15N NMR relaxation study.

    PubMed

    Sahu, S C; Bhuyan, A K; Udgaonkar, J B; Hosur, R V

    2000-10-01

    Backbone dynamics of uniformly 15N-labeled free barnase and its complex with unlabelled barstar have been studied at 40 degrees C, pH 6.6, using 15N relaxation data obtained from proton-detected 2D [1H]-15N NMR spectroscopy. 15N spin-lattice relaxation rate constants (R1), spin-spin relaxation rate constants (R2), and steady-state heteronuclear [1H]-15N NOEs have been measured at a magnetic field strength of 14.1 Tesla for 91 residues of free barnase and for 90 residues out of a total of 106 in the complex (excluding three prolines and the N-terminal residue) backbone amide 15N sites of barnase. The primary relaxation data for both the cases have been analyzed in the framework of the model-free formalism using both isotropic and axially symmetric models of the rotational diffusion tensor. As per the latter, the overall rotational correlation times (tau(m)) are 5.0 and 9.5 ns for the free and complexed barnase, respectively. The average order parameter is found to be 0.80 for free barnase and 0.86 for the complex. However, the changes are not uniform along the backbone and for about 5 residues near the binding interface there is actually a significant decrease in the order parameters on complex formation. These residues are not involved in the actual binding. For the residues where the order parameter increases, the magnitudes vary significantly. It is observed that the complex has much less internal mobility, compared to free barnase. From the changes in the order parameters, the entropic contribution of NH bond vector motion to the free energy of complex formation has been calculated. It is apparent that these motion's cause significant unfavorable contributions and therefore must be compensated by many other favorable contributions to effect tight complex formation. The observed variations in the motion and their different locations with regard to the binding interface may have important implications for remote effects and regulation of the enzyme action. PMID:11101215

  7. A non-intuitive design of a cyclic decapeptide library with unique backbone structural features.

    PubMed

    Paul, P K C

    2003-12-01

    An analysis of hydrogen bonding patterns of cyclic decapeptide (CDP) beta-sheet structures has resulted in a 'non-intuitive' design of cyclic decapeptides wherein their beta-turns and residue positions can be fixed by choosing 2 of the 10 residues, i.e. positions i and i+4, to be Prolines or N-substituted residues. This sequence relationship between the two Pro or N-substituted residues is shown to uniquely define the conformation of the CDP. Furthermore, this design of the 2 beta-turn, beta-sheet CDP structure is expected to be characterised by residues disposed in an exclusive fashion in which four residues are on one side of the ring, two on the other and the four corner residues in the beta-turn are in the plane of the ring. This opens up the possibility of fine-tuning the four residues facing one way and /or the two residues facing the other way such that a library containing a myriad of chemically diverse systems could be obtained. The design process along with the molecular modelling of specific CDP-s and the building of a CDP library are discussed in detail. PMID:14683511

  8. Pentopyranosyl Oligonucleotide Systems. Part 11: Systems with Shortened Backbones: D)-beta-Ribopyranosyl-(4 yields 3 )- and (L)-alpha - Lyxopyranosyl-(4 yields 3 )-oligonucleotides

    NASA Technical Reports Server (NTRS)

    Wippo, Harald; Reck, Folkert; Kudick, Rene; Ramaseshan, Mahesh; Ceulemans, Griet; Bolli, Martin; Krishnamurthy, Ramanarayanan; Eschenmoser, Albert

    2001-01-01

    The (L)-a-lyxopyranosyl-(4'yields 3')-oligonucleotide system-a member of a pentopyranosyl oligonucleotide family containing a shortened backbone-is capable of cooperative base-pairing and of cross-pairing with DNA and RNA. In contrast, corresponding (D)-beta-ribopyransoyl-(4' yields 3')-oligonucleotides do not show base-pairing under similar conditions. We conclude that oligonucleotide systems can violate the six-bonds-per-backbone-unit rule by having five bonds instead, if their vicinally bound phosphodiester bridges can assume an antiperiplanar conformation. An additional structural feature that seems relevant to the cross-pairing capability of the (L)-a-lyxopyranosyl-(4' yields 3')-oligonucleotide system is its (small) backbone/basepair axes inclination. An inclination which is similar to that in B-DNA seems to be a prerequisite for an oligonucleotide system s capability to cross-pair with DNA.

  9. Conformationally Restricted GABA with Bicyclo[3.1.0]hexane Backbone as the First Highly Selective BGT-1 Inhibitor

    PubMed Central

    2014-01-01

    On the basis of the three-dimensional diversity-oriented conformational restriction strategy using key chiral cyclopropane units, we previously identified 3 ((2S,3R)-4-amino-3,4-methanobutyric acid) with a chiral trans-cyclopropane structure as a γ-aminobutyric acid (GABA) transporter inhibitor selective for GABA transporter (GAT) subtypes GAT-3 and BGT-1 (betaine/GABA transporter-1). Further conformational restriction of 3 with the rigid bicyclo[3.1.0]hexane backbone led to the successful development of the first highly potent and selective BGT-1 inhibitor 4 (IC50 = 0.59 μM). The bioactive conformation of 3 for BGT-1 was also identified. PMID:25147609

  10. Design and Synthesis of Peptide YY Analogues with C-terminal Backbone Amide-to-Ester Modifications

    PubMed Central

    2013-01-01

    Peptide YY (PYY) is a gut hormone that activates the G protein-coupled neuropeptide Y (NPY) receptors, and because of its appetite reducing actions, it is evaluated as an antiobesity drug candidate. The C-terminal tail of PYY is crucial for activation of the NPY receptors. Here, we describe the design and preparation of a series of PYY(3–36) depsipeptide analogues, in which backbone amide-to-ester modifications were systematically introduced in the C-terminal. Functional NPY receptor assays and circular dichroism revealed that the ψ(CONH) bonds at positions 30–31 and 33–34 are particularly important for receptor interaction and that the latter is implicated in Y2 receptor selectivity. PMID:24900634

  11. 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

    2008-07-01

    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. PMID:18557620

  12. The backbone structure of the thermophilic Thermoanaerobacter tengcongensis ribose binding protein is essentially identical to its mesophilic E. coli homolog

    SciTech Connect

    Cuneo, Matthew J.; Tian, Yaji; Allert, Malin; Hellinga, Homme W.

    2008-10-27

    We report the X-ray crystal structure of a Thermoanaerobacter tengcongensis ribose binding protein (tteRBP) determined to 1.9 {angstrom} resolution. We find that tteRBP is significantly more stable ({sup app}T{sub m} value {approx} 102 C) than the mesophilic Escherichia coli ribose binding protein (ecRBP) ({sup app}T{sub m} value {approx} 56 C). The tteRBP has essentially the identical backbone conformation (0.41 {angstrom} RMSD of 235/271 C{sub {alpha}} positions and 0.65 {angstrom} RMSD of 270/271 C{sub {alpha}} positions) as ecRBP. Classification of the amino acid substitutions as a function of structure therefore allows the identification of amino acids which potentially contribute to the observed thermal stability of tteRBP in the absence of large structural heterogeneities.

  13. Proton-detected MAS NMR experiments based on dipolar transfers for backbone assignment of highly deuterated proteins

    NASA Astrophysics Data System (ADS)

    Chevelkov, Veniamin; Habenstein, Birgit; Loquet, Antoine; Giller, Karin; Becker, Stefan; Lange, Adam

    2014-05-01

    Proton-detected solid-state NMR was applied to a highly deuterated insoluble, non-crystalline biological assembly, the Salmonella typhimurium type iii secretion system (T3SS) needle. Spectra of very high resolution and sensitivity were obtained at a low protonation level of 10-20% at exchangeable amide positions. We developed efficient experimental protocols for resonance assignment tailored for this system and the employed experimental conditions. Using exclusively dipolar-based interspin magnetization transfers, we recorded two sets of 3D spectra allowing for an almost complete backbone resonance assignment of the needle subunit PrgI. The additional information provided by the well-resolved proton dimension revealed the presence of two sets of resonances in the N-terminal helix of PrgI, while in previous studies employing 13C detection only a single set of resonances was observed.

  14. Photoleucine Survives Backbone Cleavage by Electron Transfer Dissociation. A Near-UV Photodissociation and Infrared Multiphoton Dissociation Action Spectroscopy Study

    NASA Astrophysics Data System (ADS)

    Shaffer, Christopher J.; Martens, Jonathan; Marek, Aleš; Oomens, Jos; Tureček, František

    2016-04-01

    We report a combined experimental and computational study aimed at elucidating the structure of N-terminal fragment ions of the c type produced by electron transfer dissociation of photo-leucine (L*) peptide ions GL*GGKX. The c 4 ion from GL*GGK is found to retain an intact diazirine ring that undergoes selective photodissociation at 355 nm, followed by backbone cleavage. Infrared multiphoton dissociation action spectra point to the absence in the c 4 ion of a diazoalkane group that could be produced by thermal isomerization of vibrationally hot ions. The c 4 ion from ETD of GL*GGK is assigned an amide structure by a close match of the IRMPD action spectrum and calculated IR absorption. The energetics and kinetics of c 4 ion dissociations are discussed.

  15. Pearl-necklace structures of molecular brushes with rigid backbone under poor solvent conditions: A simulation study

    NASA Astrophysics Data System (ADS)

    Theodorakis, P. E.; Paul, W.; Binder, K.

    2010-09-01

    Bottle-brush polymers, where flexible side chains containing N =20 to 50 effective monomers are grafted to a rigid backbone, are studied by molecular dynamics simulations, varying the grafting density σ and the solvent quality. Whereas for poor solvents and large enough σ the molecular brush is a cylindrical object, homogeneous in axial direction, for intermediate values of σ an axially inhomogeneous structure of "pearl-necklace" type is formed. The "pearls," however, have a strongly nonspherical ellipsoidal shape, due to the fact that several side chains cluster together in one pearl, qualitatively consistent with predictions of Sheiko et al. [Eur. Phys. J. E 13, 125 (2004)] We analyze the structure of these pearls and study both the transition to the axially uniform cylinder at high σ and to the trivial pearl-necklace structure at small σ, where each pearl contains a single collapsed chain only.

  16. Backbone and Side-chain NMR Assignments for the C-terminal Domain of Mammalian Vps28

    PubMed Central

    Peterson, Tabitha A.; Yu, Liping; Piper, Robert C.

    2015-01-01

    Vps28 is one of four cytosolic proteins comprising the Endosomal Sorting Complex Required for Transport I (ESCRT-I). ESCRT-I is involved in sorting ubiquitinated proteins to multivesicular bodies (MVB) as well as in mediating budding of retroviruses. Here, we report the backbone and side-chain assignments of the mammalian C-terminal domain of Vps28 (mVps28CTD), which is involved in interactions with other ESCRT components. We also compare the predicted secondary structures of mVps28CTDwith those of the published X-ray crystal structures of Saccharomyces cerevisiae and Xenopus laevis Vps28CTD. These NMR resonance assignments will facilitate chemical shift mapping and structural determination of mammalian Vps28 interactions with other components of the endosomal sorting machinery that sorts ubiquitinated proteins for lysosomal degradation. PMID:24366722

  17. Ultrafast vibrational dynamics of the DNA backbone at different hydration levels mapped by two-dimensional infrared spectroscopy.

    PubMed

    Guchhait, Biswajit; Liu, Yingliang; Siebert, Torsten; Elsaesser, Thomas

    2016-07-01

    DNA oligomers are studied at 0% and 92% relative humidity, corresponding to N < 2 and N > 20 water molecules per base pair. Two-dimensional (2D) infrared spectroscopy of DNA backbone modes between 920 and 1120 cm(-1) maps fluctuating interactions at the DNA surface. At both hydration levels, a frequency fluctuation correlation function with a 300 fs decay and a slow decay beyond 10 ps is derived from the 2D lineshapes. The fast component reflects motions of DNA helix, counterions, and water shell. Its higher amplitude at high hydration level reveals a significant contribution of water to the fluctuating forces. The slow component reflects disorder-induced inhomogeneous broadening. PMID:26798841

  18. (1)H, (13)C and (15)N backbone assignment of the EC-1 domain of human E-cadherin.

    PubMed

    Prasasty, Vivitri D; Krause, Mary E; Tambunan, Usman S F; Anbanandam, Asokan; Laurence, Jennifer S; Siahaan, Teruna J

    2015-04-01

    The Extracellular 1 (EC1) domain of E-cadherin has been shown to be important for cadherin-cadherin homophilic interactions. Cadherins are responsible for calcium-mediated cell-cell adhesion located at the adherens junction of the biological barriers (i.e., intestinal mucosa and the blood-brain barrier (BBB)). Cadherin peptides can modulate cadherin interactions to improve drug delivery through the BBB. However, the mechanism of modulating the E-cadherin interactions by cadherin peptides has not been fully elucidated. To provide a basis for subsequent examination of the structure and peptide-binding properties of the EC1 domain of human E-cadherin using solution NMR spectroscopy, the (1)H, (13)C and (15)N backbone resonance of the uniformly labeled-EC1 were assigned and the secondary structure was determined based on the chemical shift values. These resonance assignments are essential for assessing protein-ligand interactions and are reported here. PMID:24510398

  19. Ultrafast vibrational dynamics of the DNA backbone at different hydration levels mapped by two-dimensional infrared spectroscopy

    PubMed Central

    Guchhait, Biswajit; Liu, Yingliang; Siebert, Torsten; Elsaesser, Thomas

    2015-01-01

    DNA oligomers are studied at 0% and 92% relative humidity, corresponding to N < 2 and N > 20 water molecules per base pair. Two-dimensional (2D) infrared spectroscopy of DNA backbone modes between 920 and 1120 cm−1 maps fluctuating interactions at the DNA surface. At both hydration levels, a frequency fluctuation correlation function with a 300 fs decay and a slow decay beyond 10 ps is derived from the 2D lineshapes. The fast component reflects motions of DNA helix, counterions, and water shell. Its higher amplitude at high hydration level reveals a significant contribution of water to the fluctuating forces. The slow component reflects disorder-induced inhomogeneous broadening. PMID:26798841

  20. The polypeptide backbone of recombinant human zona pellucida glycoprotein-3 initiates acrosomal exocytosis in human spermatozoa in vitro.

    PubMed Central

    Chapman, N; Kessopoulou, E; Andrews, P; Hornby, D; Barratt, C R

    1998-01-01

    Human gamete interaction is of fundamental biological importance, yet the molecular interactions between spermatozoa and the zona pellucida are poorly understood. Surprisingly, the role of the polypeptide backbone of zona pellucida glycoprotein 3 (ZP3), the putative ligand for spermatozoa activation, has been largely overlooked. Purified recombinant human ZP3 was expressed in Escherichia coli as a C-terminal fusion to the dimeric glutathione S-transferase (GST) from Schistosoma japonicum and was shown to induce acrosomal exocytosis in live, capacitated human spermatozoa. The level of exocytosis is comparable with that obtained using purified, glycosylated, recombinant human ZP3 [van Duin, M., Polman, J.E.M., DeBreet, I.T.M., Van Ginneken, K., Bunschoten, H., Grootenhuis, A., Brindle, J. and Aitken, R.J. (1994). Biol Reprod. 51, 607-617]. These data imply that the polypeptide chain of human ZP3 contributes to recognition of spermatozoa during acrosomal exocytosis in vitro. PMID:9480899

  1. Backbone resonance assignments for the PHD-Bromo dual-domain of the human chromatin reader TRIM24.

    PubMed

    Walser, Reto; Renshaw, Jonathan; Milbradt, Alexander G

    2016-04-01

    Plant homeodomains (PHD) and Bromo domains are both chromatin reader domains that recognise histone methylation degree and acetylation state, respectively. The tripartite motif protein TRIM24 is a multidomain protein carrying a PHD-Bromo motif at its C-terminus, through which it is able to bind to histone 3 (H3) N-terminal tails with a specific modification pattern, namely unmethylated at K4 and acetylated at K23 (H3-K4me0K23ac). Here we report the [Formula: see text] and [Formula: see text] backbone resonance assignment of this 23 kDa motif, which we have obtained by heteronuclear multidimensional NMR spectroscopy. Furthermore we show that the secondary [Formula: see text] and [Formula: see text] chemical shifts are in good agreement with a previously published crystal structure. PMID:26878853

  2. Sequencing of Oligourea Foldamers by Tandem Mass Spectrometry

    NASA Astrophysics Data System (ADS)

    Bathany, Katell; Owens, Neil W.; Guichard, Gilles; Schmitter, Jean-Marie

    2013-03-01

    This study is focused on sequence analysis of peptidomimetic helical oligoureas by means of tandem mass spectrometry, to build a basis for de novo sequencing for future high-throughput combinatorial library screening of oligourea foldamers. After the evaluation of MS/MS spectra obtained for model compounds with either MALDI or ESI sources, we found that the MALDI-TOF-TOF instrument gave more satisfactory results. MS/MS spectra of oligoureas generated by decay of singly charged precursor ions show major ion series corresponding to fragmentation across both CO-NH and N'H-CO urea bonds. Oligourea backbones fragment to produce a pattern of a, x, b, and y type fragment ions. De novo decoding of spectral information is facilitated by the occurrence of low mass reporter ions, representative of constitutive monomers, in an analogous manner to the use of immonium ions for peptide sequencing.

  3. Isolation of Pristine Electronics Grade Semiconducting Carbon Nanotubes by Switching the Rigidity of the Wrapping Polymer Backbone on Demand.

    PubMed

    Joo, Yongho; Brady, Gerald J; Shea, Matthew J; Oviedo, M Belén; Kanimozhi, Catherine; Schmitt, Samantha K; Wong, Bryan M; Arnold, Michael S; Gopalan, Padma

    2015-10-27

    Conjugated polymers are among the most selective carbon nanotube sorting agents discovered and enable the isolation of ultrahigh purity semiconducting singled-walled carbon nanotubes (s-SWCNTs) from heterogeneous mixtures that contain problematic metallic nanotubes. The strong selectivity though highly desirable for sorting, also leads to irreversible adsorption of the polymer on the s-SWCNTs, limiting their electronic and optoelectronic properties. We demonstrate how changes in polymer backbone rigidity can trigger its release from the nanotube surface. To do so, we choose a model polymer, namely poly[(9,9-dioctylfluorenyl-2,7-diyl)-alt-co-(6,60-(2,20-bipyridine))] (PFO-BPy), which provides ultrahigh selectivity for s-SWCNTs, which are useful specifically for FETs, and has the chemical functionality (BPy) to alter the rigidity using mild chemistry. Upon addition of Re(CO)5Cl to the solution of PFO-BPy wrapped s-SWCNTs, selective chelation with the BPy unit in the copolymer leads to the unwrapping of PFO-BPy. UV-vis, XPS, and Raman spectroscopy studies show that binding of the metal ligand complex to BPy triggers up to 85% removal of the PFO-BPy from arc-discharge s-SWCNTs (diameter = 1.3-1.7 nm) and up to 72% from CoMoCAT s-SWCNTs (diameter = 0.7-0.8 nm). Importantly, Raman studies show that the electronic structure of the s-SWCNTs is preserved through this process. The generalizability of this method is demonstrated with two other transition metal salts. Molecular dynamics simulations support our experimental findings that the complexation of BPy with Re(CO)5Cl in the PFO-BPy backbone induces a dramatic conformational change that leads to a dynamic unwrapping of the polymer off the nanotube yielding pristine s-SWCNTs. PMID:26348205

  4. Naphthodithiophene-Based Conjugated Polymer with Linear, Planar Backbone Conformation and Strong Intermolecular Packing for Efficient Organic Solar Cells.

    PubMed

    Lee, Jaewon; Ko, Hyomin; Song, Eunjoo; Kim, Heung Gyu; Cho, Kilwon

    2015-09-30

    Two donor-acceptor copolymers, PBDT and PNDT, containing 4,8-bis(2-ethylhexyloxy)benzo[1,2-b:3,4-b']dithiophene (BDT) and 4,9-bis(2-ethylhexyloxy)naphtho[1,2-b:5,6-b']dithiophene (NDT), respectively, as an electron-rich unit and 5,6-difluoro-2,1,3-benzothiadiazole (2FBT) as an electron-deficient unit, were synthesized and compared. The introduction of the NDT core into the conjugated backbone was found to effectively improve both light harvesting and the charge carrier mobility by enhancing chain planarity and backbone linearity; the NDT copolymer has stronger noncovalent interactions and smaller bond angles than those of the BDT-based polymer. Moreover, the introduction of the NDT core brings about a drastic change in the molecular orientation into the face-on motif and results in polymer:PCBM blend films with well-mixed interpenetrating nanofibrillar bulk-heterojunction networks with small-scale phase separation, which produce solar cells with higher short-circuit current density and fill factor values. A conventional optimized device structure containing PNDT:PC71BM was found to exhibit a maximum solar efficiency of 6.35%, an open-circuit voltage of 0.84 V, a short-circuit current density of 11.92 mA cm(-2), and a fill factor of 63.5% with thermal annealing, which demonstrates that the NDT and DT2FBT moieties are a promising electron-donor/acceptor combination for high-performance photovoltaics. PMID:26360662

  5. General order parameter based correlation analysis of protein backbone motions between experimental NMR relaxation measurements and molecular dynamics simulations

    SciTech Connect

    Liu, Qing; Shi, Chaowei; Yu, Lu; Zhang, Longhua; Xiong, Ying; Tian, Changlin

    2015-02-13

    Internal backbone dynamic motions are essential for different protein functions and occur on a wide range of time scales, from femtoseconds to seconds. Molecular dynamic (MD) simulations and nuclear magnetic resonance (NMR) spin relaxation measurements are valuable tools to gain access to fast (nanosecond) internal motions. However, there exist few reports on correlation analysis between MD and NMR relaxation data. Here, backbone relaxation measurements of {sup 15}N-labeled SH3 (Src homology 3) domain proteins in aqueous buffer were used to generate general order parameters (S{sup 2}) using a model-free approach. Simultaneously, 80 ns MD simulations of SH3 domain proteins in a defined hydrated box at neutral pH were conducted and the general order parameters (S{sup 2}) were derived from the MD trajectory. Correlation analysis using the Gromos force field indicated that S{sup 2} values from NMR relaxation measurements and MD simulations were significantly different. MD simulations were performed on models with different charge states for three histidine residues, and with different water models, which were SPC (simple point charge) water model and SPC/E (extended simple point charge) water model. S{sup 2} parameters from MD simulations with charges for all three histidines and with the SPC/E water model correlated well with S{sup 2} calculated from the experimental NMR relaxation measurements, in a site-specific manner. - Highlights: • Correlation analysis between NMR relaxation measurements and MD simulations. • General order parameter (S{sup 2}) as common reference between the two methods. • Different protein dynamics with different Histidine charge states in neutral pH. • Different protein dynamics with different water models.

  6. Investigating the role of a backbone to substrate hydrogen bond in OMP decarboxylase using a site-specific amide to ester substitution

    PubMed Central

    Desai, Bijoy J.; Goto, Yuki; Cembran, Alessandro; Fedorov, Alexander A.; Almo, Steven C.; Gao, Jiali; Suga, Hiroaki; Gerlt, John A.

    2014-01-01

    Hydrogen bonds between backbone amide groups of enzymes and their substrates are often observed, but their importance in substrate binding and/or catalysis is not easy to investigate experimentally. We describe the generation and kinetic characterization of a backbone amide to ester substitution in the orotidine 5′-monophosphate (OMP) decarboxylase from Methanobacter thermoautotrophicum (MtOMPDC) to determine the importance of a backbone amide–substrate hydrogen bond. The MtOMPDC-catalyzed reaction is characterized by a rate enhancement (∼1017) that is among the largest for enzyme-catalyzed reactions. The reaction proceeds through a vinyl anion intermediate that may be stabilized by hydrogen bonding interaction between the backbone amide of a conserved active site serine residue (Ser-127) and oxygen (O4) of the pyrimidine moiety and/or electrostatic interactions with the conserved general acidic lysine (Lys-72). In vitro translation in conjunction with amber suppression using an orthogonal amber tRNA charged with l-glycerate (HOS) was used to generate the ester backbone substitution (S127HOS). With 5-fluoro OMP (FOMP) as substrate, the amide to ester substitution increased the value of Km by ∼1.5-fold and decreased the value of kcat by ∼50-fold. We conclude that (i) the hydrogen bond between the backbone amide of Ser-127 and O4 of the pyrimidine moiety contributes a modest factor (∼102) to the 1017 rate enhancement and (ii) the stabilization of the anionic intermediate is accomplished by electrostatic interactions, including its proximity of Lys-72. These conclusions are in good agreement with predictions obtained from hybrid quantum mechanical/molecular mechanical calculations. PMID:25275007

  7. Investigating the role of a backbone to substrate hydrogen bond in OMP decarboxylase using a site-specific amide to ester substitution.

    PubMed

    Desai, Bijoy J; Goto, Yuki; Cembran, Alessandro; Fedorov, Alexander A; Almo, Steven C; Gao, Jiali; Suga, Hiroaki; Gerlt, John A

    2014-10-21

    Hydrogen bonds between backbone amide groups of enzymes and their substrates are often observed, but their importance in substrate binding and/or catalysis is not easy to investigate experimentally. We describe the generation and kinetic characterization of a backbone amide to ester substitution in the orotidine 5'-monophosphate (OMP) decarboxylase from Methanobacter thermoautotrophicum (MtOMPDC) to determine the importance of a backbone amide-substrate hydrogen bond. The MtOMPDC-catalyzed reaction is characterized by a rate enhancement (∼10(17)) that is among the largest for enzyme-catalyzed reactions. The reaction proceeds through a vinyl anion intermediate that may be stabilized by hydrogen bonding interaction between the backbone amide of a conserved active site serine residue (Ser-127) and oxygen (O4) of the pyrimidine moiety and/or electrostatic interactions with the conserved general acidic lysine (Lys-72). In vitro translation in conjunction with amber suppression using an orthogonal amber tRNA charged with L-glycerate ((HO)S) was used to generate the ester backbone substitution (S127(HO)S). With 5-fluoro OMP (FOMP) as substrate, the amide to ester substitution increased the value of Km by ∼1.5-fold and decreased the value of kcat by ∼50-fold. We conclude that (i) the hydrogen bond between the backbone amide of Ser-127 and O4 of the pyrimidine moiety contributes a modest factor (∼10(2)) to the 10(17) rate enhancement and (ii) the stabilization of the anionic intermediate is accomplished by electrostatic interactions, including its proximity of Lys-72. These conclusions are in good agreement with predictions obtained from hybrid quantum mechanical/molecular mechanical calculations. PMID:25275007

  8. 31P NMR spectroscopy for quantification of moieties present in the backbone of poly(aryloxycyclotriphosphazene)

    NASA Astrophysics Data System (ADS)

    Al-Shukri, Salah Mahdi

    2015-03-01

    A new method for semi-quantification of the moieties present in the back bone of poly(aryloxycyclotriphosphazene) using 31P NMR spectroscopy was proposed based on integral values and number of phosphorus atoms of the representative resonance. Poly(m-phenylenedioxy)cyclotriphosphazenes with a different degree of crosslink were synthesized from the reaction of hexachlorocyclotriphosphazene (NPCl2)3 with 1,3-benzenediol and triethylamine in five different mole ratios, afforded structurally different products designated as PI-PV. The structures of these products and their isomeric compositions were identified based on the correlation between chemical shifts and JPP coupling constants. The data clearly demonstrated presence of a mixture contains different substitution modes and isomers. When the mole ratio of the reactants is in equal amount, the non-geminal mode is predominantly formed of about 89.03% and also geminal mode of about 10.95% has been observed. The formation of the later increased to 52.19% when the ratio of substituent was raised at the tris and tetra stage of chlorine replacement.

  9. Reconstructing of a Sequence Using Similar Sequences

    Energy Science and Technology Software Center (ESTSC)

    1995-11-28

    SIMSEQ reconstructs sequences from oligos. Similar known sequences are used as a reference. At present, simulated data are being used to develop the algorithm. SIMSEQ generates an initial random sequence, then generates a second sequence that is 60 to 90 percent similar to the first. Next, the second sequence is chopped into its appropriate oligos. All possible sequences are reconstructed to determine the most similar. Those with the highest similarity are printed as output.

  10. Paucity of moderately repetitive sequences

    SciTech Connect

    Schmid, C.W.

    1991-01-01

    We examined clones of renatured repetitive human DNA to find novel repetitive DNAs. After eliminating known repeats, the remaining clones were subjected to sequence analysis. These clones also corresponded to known repeats, but with greater sequence diversity. This indicates that either these libraries were depleted of short interspersed repeats in construction, or these repeats are much less prevalent in the human genome than is indicated by data from {und Xenopus} or sea urchin studies. We directly investigated the sequence composition of human DNA through traditional renaturation techniques with the goal of estimating the limits of abundance of repetitive sequence classes in human DNA. Our results sharply limit the maximum possible abundance to 1--2% of the human genome. Our estimate, minus the known repeats in this fraction, leaves about 1% (3 {times} 10{sup 7} nucleotides) of the human genome for novel repetitive elements. 2 refs. (MHB)

  11. Unlocking Short Read Sequencing for Metagenomics

    DOE PAGESBeta

    Rodrigue, Sébastien; Materna, Arne C.; Timberlake, Sonia C.; Blackburn, Matthew C.; Malmstrom, Rex R.; Alm, Eric J.; Chisholm, Sallie W.; Gilbert, Jack Anthony

    2010-07-28

    We describe an experimental and computational pipeline yielding millions of reads that can exceed 200 bp with quality scores approaching that of traditional Sanger sequencing. The method combines an automatable gel-less library construction step with paired-end sequencing on a short-read instrument. With appropriately sized library inserts, mate-pair sequences can overlap, and we describe the SHERA software package that joins them to form a longer composite read.

  12. Unlocking Short Read Sequencing for Metagenomics.

    SciTech Connect

    Rodrigue, S A. C.; Materna, S C; Timberlake, M C; Blacburn, R R; Malmstrom, E J. Alm; Chisholm, S W

    2010-01-01

    We describe an experimental and computational pipeline yielding millions of reads that can exceed 200 bp with quality scores approaching that of traditional Sanger sequencing. The method combines an automatable gel-less library construction step with paired-end sequencing on a short-read instrument. With appropriately sized library inserts, mate-pair sequences can overlap, and we describe the SHERA software package that joins them to form a longer composite read.

  13. Multispectral labeling of antibodies with polyfluorophores on a DNA backbone and application in cellular imaging.

    PubMed

    Guo, Jia; Wang, Shenliang; Dai, Nan; Teo, Yin Nah; Kool, Eric T

    2011-03-01

    Most current approaches to multiantigen fluorescent imaging require overlaying of multiple images taken with separate filter sets as a result of differing dye excitation requirements. This requirement for false-color composite imaging prevents the user from visualizing multiple species in real time and disallows imaging of rapidly moving specimens. To address this limitation, here we investigate the use of oligodeoxyfluoroside (ODF) fluorophores as labels for antibodies. ODFs are short DNA-like oligomers with fluorophores replacing the DNA bases and can be assembled in many colors with excitation at a single wavelength. A DNA synthesizer was used to construct several short ODFs carrying a terminal alkyne group and having emission maxima of 410-670 nm. We developed a new approach to antibody conjugation, using Huisgen-Sharpless cycloaddition, which was used to react the alkynes on ODFs with azide groups added to secondary antibodies. Multiple ODF-tagged secondary antibodies were then used to mark primary antibodies. The set of antibodies was tested for spectral characteristics in labeling tubulin in HeLa cells and revealed a wide spectrum of colors, ranging from violet-blue to red with excitation through a single filter (340-380 nm). Selected sets of the differently labeled secondary antibodies were then used to simultaneously mark four antigens in fixed cells, using a single image and filter set. We also imaged different surface tumor markers on two live cell lines. Experiments showed that all colors could be visualized simultaneously by eye under the microscope, yielding multicolor images of multiple cellular antigens in real time. PMID:21321224

  14. Organocatalytic and enantioselective Michael reaction between α-nitroesters and nitroalkenes. Syn/anti-selectivity control using catalysts with the same absolute backbone chirality

    PubMed Central

    Martínez, Jose I; Uria, Uxue; Muñiz, Maria; Reyes, Efraím

    2015-01-01

    Summary The asymmetric and catalytic Michael reaction between α-nitroesters and nitroalkenes has been studied in the presence of two bifunctional catalysts both containing the same absolute chirality at the carbon backbone. The reaction performed in similar conditions allows us to control the syn or anti selectivity of the Michael adduct obtaining good yields and high enantiocontrol in all cases. PMID:26734103

  15. Organocatalytic and enantioselective Michael reaction between α-nitroesters and nitroalkenes. Syn/anti-selectivity control using catalysts with the same absolute backbone chirality.

    PubMed

    Martínez, Jose I; Uria, Uxue; Muñiz, Maria; Reyes, Efraím; Carrillo, Luisa; Vicario, Jose L

    2015-01-01

    The asymmetric and catalytic Michael reaction between α-nitroesters and nitroalkenes has been studied in the presence of two bifunctional catalysts both containing the same absolute chirality at the carbon backbone. The reaction performed in similar conditions allows us to control the syn or anti selectivity of the Michael adduct obtaining good yields and high enantiocontrol in all cases. PMID:26734103

  16. Backbone and side-chain (1)H, (15)N, (13)C assignment and secondary structure of BPSL1445 from Burkholderia pseudomallei.

    PubMed

    Quilici, Giacomo; Berardi, Andrea; Gaudesi, Davide; Gourlay, Louise J; Bolognesi, Martino; Musco, Giovanna

    2015-10-01

    BPSL1445 is a lipoprotein produced by the Gram-negative bacterium Burkholderia pseudomallei (B. pseudomallei), the etiological agent of melioidosis. Immunodetection assays against sera patients using protein microarray suggest BPSL1445 involvement in melioidosis. Herein we report backbone, side chain NMR assignment and secondary structure for the recombinant protein. PMID:25893672

  17. An Engineered α1 Integrin-binding Collagenous Sequence

    PubMed Central

    Seo, Neungseon; Russell, Brooke H.; Rivera, Jose J.; Liang, Xiaowen; Xu, Xuejun; Afshar-Kharghan, Vahid; Höök, Magnus

    2010-01-01

    Collagen is an extracellular matrix structural component that can regulate cellular processes through its interaction with the integrins, α1β1, α2β1, α10β1, and α11β1. Collagen-like proteins have been identified in a number of bacterial species. Here, we used Scl2 from Streptococcus pyogenes serotype M28 strain MGAS6274 as a backbone for the introduction of discrete integrin-binding sequences. The introduced sequences GLPGER, GFPGER, or GFPGEN did not affect triple helix stability of the Scl (Streptococcal collagen-like) protein. Using ELISA and surface plasmon resonance, we determined that Scl2GLPGER and Scl2GFPGER bound to recombinant human α1 and α2 I-domains in a metal ion-dependent manner and without a requirement for hydroxyproline. We predicted a novel and selective integrin-binding sequence, GFPGEN, through the use of computer modeling and demonstrated that Scl2GFPGEN shows specificity toward the α1 I-domain and does not bind the α2 I-domain. Using C2C12 cells, we determined that intact integrins interact with the modified Scl2 proteins with the same selectivity as recombinant I-domains. These modified Scl2 proteins also acted as cell attachment substrates for fibroblast, endothelial, and smooth muscle cells. However, the modified Scl2 proteins were unable to aggregate platelets. These results indicate that Scl2 is a suitable backbone for the introduction of mammalian integrin-binding sequences, and these sequences may be manipulated to individually target α1β1 and α2β1. PMID:20675378

  18. Methods and compositions for chromosome-specific staining

    DOEpatents

    Gray, Joe W.; Pinkel, Daniel

    2003-07-22

    Methods and compositions for chromosome-specific staining are provided. Compositions comprise heterogenous mixtures of labeled nucleic acid fragments having substantially complementary base sequences to unique sequence regions of the chromosomal DNA for which their associated staining reagent is specific. Methods include methods for making the chromosome-specific staining compositions of the invention, and methods for applying the staining compositions to chromosomes.

  19. RNA-Binding Affinities and Crystal Structure of Oligonucleotides Containing Five-Atom Amide-Based Backbone Structures

    SciTech Connect

    Pallan, Pradeep S.; von Matt, Peter; Wilds, Christopher J.; Altmann, Karl-Heinz; Egli, Martin

    2010-03-08

    Among the hundreds of nucleic acid analogues that have been studied over the last two decades only very few exhibit backbones with linkers between residues that are either shorter or longer than the four-atom linker O3{prime}-P-O5{prime}-C5{prime} connecting sugar ring moieties in DNA and RNA. 2{prime}-Deoxyribonucleoside dimers connected by a five-atom linker O3{prime}-CH*(CH{sub 3})-CO-NH-CH{sub 2} (* designates a chiral center) were reported to lead to only a slight destabilization of RNA-DNA hybrids in which the DNA strand contained one or several of these amide-linked dimers (De Napoli, L., Iadonisi, A., Montesarchio, D., Varra, M., and Piccialli, G. (1995) Synthesis of thymidine dimers containing a new internucleosidic amide linkage and their incorporation into oligodeoxyribonucleotides, Bioorg. Med. Chem. Lett. 5, 1647-1652). To analyze the influence of various chemistries of such five-atom amide linkers on the RNA-binding affinity of modified DNA strands, we have synthesized five different amide-linked dimers, including structures with homochiral linkers of the type X3{prime}-C*H(CH{sub 3})-CO-NH-CH{sub 2} (X = O, CH{sub 2}) as well as the corresponding analogues carrying methoxy groups at the 2{prime}-position of the 3{prime}-nucleosides. We have conducted a detailed thermodynamic analysis of duplex formation between the modified DNA and RNA, with the DNA strands containing between one and seven consecutive modified dimers. Some of the five-atom-linked dimers lead to significantly higher RNA-binding affinities compared with that of native DNA. Interestingly, the linkers with opposite stereochemistry at the chiral center stabilize duplexes between the modified DNA and RNA to different degrees. CD spectroscopy in solution and a crystal structure of an RNA-DNA duplex with a single amide-linked dimer demonstrate that the longer amide backbones do not disrupt the duplex geometry. These observations provide further evidence that stable cross-pairing between two different types of nucleic acids does not require the numbers of atoms linking their individual residues to match.

  20. Broadly Neutralizing Anti-Influenza Virus Antibodies: Enhancement of Neutralizing Potency in Polyclonal Mixtures and IgA Backbones

    PubMed Central

    He, Wenqian; Mullarkey, Caitlin E.; Duty, J. Andrew; Moran, Thomas M.; Palese, Peter

    2015-01-01

    ABSTRACT Current influenza virus vaccines rely upon the accurate prediction of circulating virus strains months in advance of the actual influenza season in order to allow time for vaccine manufacture. Unfortunately, mismatches occur frequently, and even when perfect matches are achieved, suboptimal vaccine efficacy leaves several high-risk populations vulnerable to infection. However, the recent discovery of broadly neutralizing antibodies that target the hemagglutinin (HA) stalk domain has renewed hope that the development of “universal” influenza virus vaccines may be within reach. Here, we examine the functions of influenza A virus hemagglutinin stalk-binding antibodies in an endogenous setting, i.e., as polyclonal preparations isolated from human sera. Relative to monoclonal antibodies that bind to the HA head domain, the neutralization potency of monoclonal stalk-binding antibodies was vastly inferior in vitro but was enhanced by several orders of magnitude in the polyclonal context. Furthermore, we demonstrated a surprising enhancement in IgA-mediated HA stalk neutralization relative to that achieved by antibodies of IgG isotypes. Mechanistically, this could be explained in two ways. Identical variable regions consistently neutralized virus more potently when in an IgA backbone compared to an IgG backbone. In addition, HA-specific memory B cells isolated from human peripheral blood were more likely to be stalk specific when secreting antibodies of IgA isotypes compared to those secreting IgG. Taken together, our data provide strong evidence that HA stalk-binding antibodies perform optimally when in a polyclonal context and that the targeted elicitation of HA stalk-specific IgA should be an important consideration during “universal” influenza virus vaccine design. IMPORTANCE Influenza viruses remain one of the most worrisome global public health threats due to their capacity to cause pandemics. While seasonal vaccines fail to protect against the emergence of pandemic strains, a new class of broadly neutralizing antibodies has been recently discovered and may be the key to developing a “universal” influenza virus vaccine. While much has been learned about the biology of these antibodies, most studies have focused only on monoclonal antibodies of IgG subtypes. However, the study of monoclonal antibodies often fails to capture the complexity of antibody functions that occur during natural polyclonal responses. Here, we provide the first detailed analyses of the biological activity of these antibodies in polyclonal contexts, comparing both IgG and IgA isotypes isolated from human donors. The striking differences observed in the functional properties of broadly neutralizing antibodies in polyclonal contexts will be essential for guiding design of “universal” influenza virus vaccines and therapeutics. PMID:25589655

  1. Theoretical study on the torsional potential of alkyl, donor, and acceptor substituted bithiophene: the hidden role of noncovalent interaction and backbone conjugation.

    PubMed

    Lin, Tzu-Jen; Lin, Shiang-Tai

    2015-02-14

    Side chain and substituent engineering of conjugated polymers are important to their backbone design. Of particular interest here is how side chains and substituents influence the coplanarity of conjugated backbones. Steric hindrance is usually considered as the principal factor influencing the coplanarity. In this study, we used proper first-principle density functional theories to analyze the change in the torsional potentials of substituted bithiophene with substituents of varying degrees of electron donating/accepting capabilities. Besides steric hindrance, the torsional potential of substituted bithiophene is also determined by other factors such as the position of substitution, non-covalent interactions between the substituents and thiophene ring, and electron conjugation in the backbone. There is no significant change in the torsional potential unless the substituent group is located at the head position of bithiophene. The bulkiness of the substituent group increases the torsional barrier at 0 and 180 degree (planar bithiophene), while the weak noncovalent interaction (such as CH-π, NH-π, and dispersion interactions) stabilizes the transition structure and decreases the barrier at 90 degree (two thiophene rings in perpendicular). Strong electron-withdrawing substituent groups (e.g., formyl or nitro groups) are found to reduce backbone conjugation resulting in reduced internal rotation barrier at 90 degree. Any of these factors deteriorates the coplanarity of bithiophene. On the other hand, the backbone conjugation can be enhanced by introducing electron-donating groups (e.g., methoxy) resulting in an increased internal rotational barrier and stabilized planar structure. The influence of through-space interactions such as S···O, S···N and CH···O interactions are found to play a minor role in the coplanarity of substituted bithiophene. PMID:25563168

  2. Management of Adolescent Low-Risk Classical Hodgkin Lymphoma: Which Chemotherapy Backbone Gives the Best Chance of Omitting Radiotherapy Safely.

    PubMed

    Algiraigri, Ali H; Essa, Mohammed F

    2016-03-01

    Even though more than 90% of adolescents with low-risk classical Hodgkin lymphoma (LRcHL) will be cured with first-line therapy, many will suffer serious late toxic effects from radiotherapy (RT). The goals for care have shifted toward minimizing late toxic effects without compromising the outstanding cure rates by adapting a risk and response-based therapy. Recent published and ongoing randomized clinical trials, using functional imaging, may allow for better identification of those patients for whom RT may be safely omitted while maintaining excellent cure rates. To evaluate the best chemotherapy regimens with a reasonable toxicity profile and that are expected to have a high chance of omitting RT based on a response-directed therapy while maintaining high cure rates, a mini review was conducted of the recent clinical trials in pediatric and adult LRcHL. The UK RAPID trial chemotherapy backbone (3 × ABVD) followed by a response-based positron emission tomography scan offers up to a 75% chance of safely omitting RT without compromising the cure rate, which remained well above 90%. PMID:26812449

  3. Synthesis and in vitro antioxidant functions of protein hydrolysate from backbones of Rastrelliger kanagurta by proteolytic enzymes

    PubMed Central

    Sheriff, Sheik Abdulazeez; Sundaram, Balasubramanian; Ramamoorthy, Baranitharan; Ponnusamy, Ponmurugan

    2013-01-01

    Every year, a huge quantity of fishery wastes and by-products are generated by fish processing industries. These wastes are either underutilized to produce low market value products or dumped leading to environmental issues. Complete utilization of fishery wastes for recovering value added products would be beneficial to the society and individual. The fish protein hydrolysates and derived peptides of fishery resources are widely used as nutritional supplements, functional ingredients, and flavor enhancers in food, beverage and pharmaceutical industries. Antioxidants from fishery resources have attracted the attention of researchers as they are cheaper in cost, easy to derive, and do not have side effects. Thus the present investigation was designed to produce protein hydrolysate by pepsin and papain digestion from the backbones of Rastrelliger kanagurta (Indian mackerel) and evaluate its antioxidant properties through various in vitro assays. The results reveal that both hydrolysates are potent antioxidants, capable of scavenging 46% and 36% of DPPH (1,1-diphenyl-2 picrylhydrazyl) and 58.5% and 37.54% of superoxide radicals respectively. The hydrolysates exhibit significant (p < 0.05) reducing power and lipid peroxidation inhibition. Among the two hydrolysates produced, pepsin derived fraction is superior than papain derived fraction in terms of yield, DH (Degree of hydrolysis), and antioxidant activity. PMID:24596496

  4. ProCS15: a DFT-based chemical shift predictor for backbone and Cβ atoms in proteins

    PubMed Central

    Larsen, Anders S.; Bratholm, Lars A.; Christensen, Anders S.; Channir, Maher

    2015-01-01

    We present ProCS15: a program that computes the isotropic chemical shielding values of backbone and Cβ atoms given a protein structure in less than a s