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1

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

PubMed Central

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 ?-amino acid backbone. Here, we examine a series of peptides with backbones that feature different repeating patterns of ?- and ?-amino acid residues but an invariant side-chain sequence. In the pure ?-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 ?/?-peptide backbones can adopt sequence-encoded quaternary structures similar to that of the ? prototype. There is a loss in helix bundle stability upon ?-residue incorporation; however, stability of the quaternary structure is not a simple function of ?-residue content. We find that cyclically constrained ?-amino acid residues can stabilize the folds of ?/?-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.

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

2008-01-01

2

Increasing sequence diversity with flexible backbone protein design: the complete redesign of a protein hydrophobic core.  

PubMed

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, 1-2 Å, were needed to entirely mutate the core. The redesigned protein, DRNN, is exceptionally stable (melting point >140°C). An NMR and X-ray crystal structure show that the side chains and backbone were accurately modeled (all-atom RMSD = 1.3 Å). PMID:22632833

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

2012-06-01

3

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

NASA Astrophysics Data System (ADS)

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.

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

2014-03-01

4

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

PubMed Central

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/.

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

2012-01-01

5

Compositional Message Sequence Charts  

Microsoft Academic Search

Message sequence charts (MSCs) is a standard notation fordescribing the interaction between communicating objects. It is popularamong the designers of communication protocols. MSCs enjoy botha visual and a textual representation. High level MSCs (HMSCs) allowspecifying infinite scenarios and different choices. Specifically, an HMSCconsists of a graph, where each node is a finite MSC with matched sendand receive events, and vice

Elsa L. Gunter; Anca Muscholl; Doron Peled

2001-01-01

6

Flexibility of the B-DNA backbone: effects of local and neighbouring sequences on pyrimidine-purine steps.  

PubMed Central

The structurally correlated dihedral angles epsilon and zeta are known for their large variability within the B-DNA backbone. We have used molecular modelling to study both energetic and mechanical features of these variations which can produce BI/BII transitions. Calculations were carried out on DNA oligomers containing either YpR or RpY dinucleotides steps within various sequence environments. The results indicate that CpA and CpG steps favour the BI/BII transition more than TpA or any RpY step. The stacking energy and its intra- and inter-strand components explain these effects. Analysis of neighbouring base pairs reveals that BI/BII transitions of CpG and CpA are easiest within (Y)n(R)n sequences. These can also induce a large vibrational amplitude for TpA steps within the BI conformation.

Bertrand, H; Ha-Duong, T; Fermandjian, S; Hartmann, B

1998-01-01

7

A Bayesian-probability-based method for assigning protein backbone dihedral angles based on chemical shifts and local sequences.  

PubMed

Chemical shifts contain substantial information about protein local conformations. We present a method to assign individual protein backbone dihedral angles into specific regions on the Ramachandran map based on the amino acid sequences and the chemical shifts of backbone atoms of tripeptide segments. The method uses a scoring function derived from the Bayesian probability for the central residue of a query tripeptide segment to have a particular conformation. The Ramachandran map is partitioned into representative regions at two levels of resolution. The lower resolution partitioning is equivalent to the conventional definitions of different secondary structure regions on the map. At the higher resolution level, the alpha and beta regions are further divided into subregions. Predictions are attempted at both levels of resolution. We compared our method with TALOS using the original TALOS database, and obtained comparable results. Although TALOS may produce the best results with currently available databases which are much enlarged, the Bayesian-probability-based approach can provide a quantitative measure for the reliability of predictions. PMID:17151953

Wang, Jun; Liu, Haiyan

2007-01-01

8

One-step peptide backbone dissociations in negative-ion free radical initiated peptide sequencing mass spectrometry.  

PubMed

Peptide dissociation behavior in TEMPO (2,2,6,6-tetramethylpiperidine-1-oxyl)-based FRIPS (free radical initiated peptide sequencing) mass spectrometry was analyzed in both positive- and negative-ion modes for a number of peptides including angiotensin II, kinetensin, glycoprotein IIb fragment (296-306), des-Pro(2)-bradykinin, and ubiquitin tryptic fragment (43-48). In the positive mode, the ·Bz-C(O)-peptide radical species was produced exclusively at the initial collisional activation of o-TEMPO-Bz-C(O)-peptides, and two consecutive applications of collisional activation were needed to observe peptide backbone fragments. In contrast, in the negative-ion mode, a single application of collisional activation to o-TEMPO-Bz-C(O)-peptides produced extensive peptide backbone fragmentations as well as ·Bz-C(O)-peptide radical species. This result indicates that the duty cycle in the TEMPO-based FRIPS mass spectrometry can be reduced by one-half in the negative-ion mode. In addition, the fragment ions observed in the negative-ion experiments were mainly of the a-, c-, x-, and z-types, indicating that radical-driven tandem mass spectrometry was mainly responsible for the TEMPO-based FRIPS even with a single application of collisional activation. Furthermore, the survival fraction analysis of o-TEMPO-Bz-C(O)-peptides was made as a function of the applied normalized collision energy (NCE). This helped us to better understand the differences in FRIPS behavior between the positive- and negative-ion modes in terms of dissociation energetics. The duty-cycle improvement made in the present study provides a cornerstone for future research aiming to achieve a single-step FRIPS in the positive-ion mode. PMID:23802150

Lee, Jihye; Park, Hyeyeon; Kwon, Hyuksu; Kwon, Gyemin; Jeon, Aeran; Kim, Hugh I; Sung, Bong June; Moon, Bongjin; Oh, Han Bin

2013-08-01

9

Composition for nucleic acid sequencing  

DOEpatents

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.

Korlach, Jonas (Ithaca, NY) [Ithaca, NY; Webb, Watt W. (Ithaca, NY) [Ithaca, NY; Levene, Michael (Ithaca, NY) [Ithaca, NY; Turner, Stephen (Ithaca, NY) [Ithaca, NY; Craighead, Harold G. (Ithaca, NY) [Ithaca, NY; Foquet, Mathieu (Ithaca, NY) [Ithaca, NY

2008-08-26

10

Carr-Purcell Sequences with Composite Pulses  

NASA Astrophysics Data System (ADS)

We present novel Carr-Purcell-like sequences using composite pulses that exhibit improved performance in strongly inhomogeneous fields. The sequences are designed to retain the intrinsic error correction of the standard Carr-Purcell-Meiboom-Gill (CPMG) sequence. This is achieved by matching the excitation pulse with the refocusing cycle such that the initial transverse magnetization lies along the axis n?B characterizing the overall rotation of the refocusing cycle. Such sequences are suitable for relaxation measurements. It is shown that in sufficiently inhomogeneous fields, the echo amplitudes have an initial transient modulation that is limited to the first few echoes and then decay with the intrinsic relaxation time of the sample. We show different examples of such sequences that are constructed from simple composite pulses. Sequences of the form 90° 0-(90° 90-?/2-? 180-?/2-90° 90-?/2) n with ??90° and 270° generate signal over a bandwidth larger than that of the conventional CPMG sequence, resulting in an improved signal-to-noise ratio in inhomogeneous fields. The new sequence 127° x,y-(127° x-127° - x) n only excites signal off-resonance with a spectrum that is bimodal, peaking at ?? 0=±? 1. Depending on the phase and exact timing of the first pulse, symmetric or antisymmetric excitation is obtained. We also demonstrate several new sequences with improved dependence on the RF field strength. The sequence (22.5° 67.5-90° -22.5)-(90° 67.5-45° 157.5-90° 67.5) n has the property that the phase of the signal depends on B1, allowing coarse B1 imaging in a one-dimensional experiment.

Hürlimann, M. D.

2001-09-01

11

Extension of a local backbone description using a structural alphabet: A new approach to the sequence-structure relationship  

Microsoft Academic Search

Protein Blocks (PBs) comprise a structural alphabet of 16 protein fragments, each 5 C long. They make it possible to approximate and correctly predict local protein three-dimensional (3D) structures. We have selected the 72 most frequent sequences of five PBs, which we call Structural Words (SWs). Analysis of four different protein data banks shows that SWs cover 92% of the

Alexandre G. de Brevern; Hélène Valadié; Serge Hazout; Catherine Etchebest

2002-01-01

12

hnCOcaNH and hncoCANH pulse sequences for rapid and unambiguous backbone assignment in ( 13C, 15N) labeled proteins  

NASA Astrophysics Data System (ADS)

Time-saving in data acquisition is a major thrust of NMR pulse sequence development in the context of structural proteomics research. The conventional HNCA and HN(CA)CO pulse sequences, routinely used for sequential backbone assignment, have the limitation that they cannot distinguish inter- and intra-residue correlations. In order to remove this ambiguity, one has to record HNCO and HN(CO)CA or sequential HNCA experiments which provide unambiguous information of sequential correlations. However, this almost doubles the experimental time. Besides, they require repeated scanning through the 15N planes to search for the matching peaks along the carbon dimension. In this background, we present here two pulse sequences, termed as hncoCANH and hnCOcaNH that lead to spectra equivalent to HNCA and HN(CA)CO spectra, respectively, but with direct distinction of inter- and intra-residue peaks; these occur with opposite signs in the new experiments. The two pulse sequences have been derived by simple modification of the previously described HN(C)N pulse sequence [Panchal et al., J. Biomol. NMR 20 (2001) 135-147] to frequency-label 13C ? or 13C' instead of 15N during the t1 period. Like HN(C)N, these spectra also exhibit special patterns of self and sequential peaks around glycines and prolines, which enable direct identification of certain triplets of residues and thus provide internal checks during the sequential assignment walk. The spectra enable rapid and unambiguous assignment of H N, 15N and 13C ? (or 13C') in a single experiment, and thus would be of great value in high-throughput structural proteomics.

Kumar, Dinesh; Reddy, Jithender G.; Hosur, Ramakrishna V.

2010-09-01

13

Extension of a local backbone description using a structural alphabet: A new approach to the sequence-structure relationship  

PubMed Central

Protein Blocks (PBs) comprise a structural alphabet of 16 protein fragments, each 5 C? long. They make it possible to approximate and correctly predict local protein three-dimensional (3D) structures. We have selected the 72 most frequent sequences of five PBs, which we call Structural Words (SWs). Analysis of four different protein data banks shows that SWs cover 92% of the amino acids in them and provide a good structural approximation for residues (i.e., sequences) 9 C? long. We present most of them in a simple network that describes 90% of the overall residues and, interestingly, includes more than 80% of the amino acids present in coils. Analysis of the network shows the specificity and quality of the 3D descriptions as well as a new type of relation between local folds and amino acid distribution. The results show that the 3D structure of these protein data banks can be easily described by a combination of subgraphs included in the network. Finally, a Bayesian probabilistic approach improved the prediction rate by 4%.

de Brevern, Alexandre G.; Valadie, Helene; Hazout, Serge; Etchebest, Catherine

2002-01-01

14

N-terminal peptide sequence repetition influences the kinetics of backbone fragmentation: a manifestation of the Jahn-Teller effect?  

PubMed

Analysis of large (>10,000 entries) databases consisting of high-resolution tandem mass spectra of peptide dications revealed with high statistical significance (P?sequences composed of the same amino acids (i.e., in general AB- and BA- bonds cleave more often than AA- and BB- bonds). This effect seems to depend upon the collisional energy, being stronger at lower energies. The phenomenon is likely to indicate the presence of the diketopiperazine structure for at least some b2 (+) ions. When consisting of two identical amino acids, these species should form through intermediates that have a symmetric geometry and, thus, must be subject to the Jahn-Teller effect that reduces the stability of such systems. PMID:23633015

Good, David M; Yang, Hongqian; Zubarev, Roman A

2013-11-01

15

Analyses of single-copy Arabidopsis T-DNA-transformed lines show that the presence of vector backbone sequences, short inverted repeats and DNA methylation is not sufficient or necessary for the induction of transgene silencing  

Microsoft Academic Search

In genetically transformed plants, transgene silen- cing has been correlated with multiple and complex insertions of foreign DNA, e.g. T-DNA and vector backbone sequences. Occasionally, single-copy transgenes also suffer transgene silencing. We have compared integration patterns and T-DNA\\/plant DNA junctions in a collection of 37 single-copy T-DNA-transformed Arabidopsis lines, of which 13 displayed silencing. Vector sequences were found integrated in

Trine J. Meza; Biljana Stangeland; Inderjit S. Mercy; Magne Skarn; Dag A. Nymoen; Anita Berg; Melinka A. Butenko; Anne-Mari Hakelien; Camilla Haslekas; Leonardo A. Meza-Zepeda; Reidunn B. Aalen

2002-01-01

16

The Completely Sequenced Plasmid pEST4011 Contains a Novel IncP1 Backbone and a Catabolic Transposon Harboring tfd Genes for 2,4-Dichlorophenoxyacetic Acid Degradation  

PubMed Central

The herbicide 2,4-dichlorophenoxyacetic acid (2,4-D)-degrading bacterium Achromobacter xylosoxidans subsp. denitrificans strain EST4002 contains plasmid pEST4011. This plasmid ensures its host a stable 2,4-D+ phenotype. We determined the complete 76,958-bp nucleotide sequence of pEST4011. This plasmid is a deletion and duplication derivative of pD2M4, the 95-kb highly unstable laboratory ancestor of pEST4011, and was self-generated during different laboratory manipulations performed to increase the stability of the 2,4-D+ phenotype of the original strain, strain D2M4(pD2M4). The 47,935-bp catabolic region of pEST4011 forms a transposon-like structure with identical copies of the hybrid insertion element IS1071::IS1471 at the two ends. The catabolic regions of pEST4011 and pJP4, the best-studied 2,4-D-degradative plasmid, both contain homologous, tfd-like genes for complete 2,4-D degradation, but they have little sequence similarity other than that. The backbone genes of pEST4011 are most similar to the corresponding genes of broad-host-range self-transmissible IncP1 plasmids. The backbones of the other three IncP1 catabolic plasmids that have been sequenced (the 2,4-D-degradative plasmid pJP4, the haloacetate-catabolic plasmid pUO1, and the atrazine-catabolic plasmid pADP-1) are nearly identical to the backbone of R751, the archetype plasmid of the IncP1 ? subgroup. We show that despite the overall similarity in plasmid organization, the pEST4011 backbone is sufficiently different (51 to 86% amino acid sequence identity between individual backbone genes) from the backbones of members of the three IncP1 subgroups (the ?, ?, and ? subgroups) that it belongs to a new IncP1subgroup, the ? subgroup. This conclusion was also supported by a phylogenetic analysis of the trfA2, korA, and traG gene products of different IncP1 plasmids.

Vedler, Eve; Vahter, Merle; Heinaru, Ain

2004-01-01

17

Fold Homology Detection Using Sequence Fragment Composition Profiles of Proteins  

PubMed Central

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 (around 15 to 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 (ROC) 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”.

Solis, Armando D.; Rackovsky, Shalom R.

2010-01-01

18

Permutation genetic algorithm for stacking sequence design of composite laminates  

Microsoft Academic Search

Stacking sequence design of a composite laminate with a given set of plies is a combinatorial problem of seeking an optimal permutation. Permutation genetic algorithms optimizing the stacking sequence of a composite laminate for maximum buckling load are studied. A new permutation GA named gene–rank GA is developed and compared with an existing Partially Mapped Permutation GA, originally developed for

Boyang Liu; Raphael T. Haftka; Mehmet A. Akgün; Akira Todoroki

2000-01-01

19

Prebiotically plausible mechanisms increase compositional diversity of nucleic acid sequences  

PubMed Central

During the origin of life, the biological information of nucleic acid polymers must have increased to encode functional molecules (the RNA world). Ribozymes tend to be compositionally unbiased, as is the vast majority of possible sequence space. However, ribonucleotides vary greatly in synthetic yield, reactivity and degradation rate, and their non-enzymatic polymerization results in compositionally biased sequences. While natural selection could lead to complex sequences, molecules with some activity are required to begin this process. Was the emergence of compositionally diverse sequences a matter of chance, or could prebiotically plausible reactions counter chemical biases to increase the probability of finding a ribozyme? Our in silico simulations using a two-letter alphabet show that template-directed ligation and high concatenation rates counter compositional bias and shift the pool toward longer sequences, permitting greater exploration of sequence space and stable folding. We verified experimentally that unbiased DNA sequences are more efficient templates for ligation, thus increasing the compositional diversity of the pool. Our work suggests that prebiotically plausible chemical mechanisms of nucleic acid polymerization and ligation could predispose toward a diverse pool of longer, potentially structured molecules. Such mechanisms could have set the stage for the appearance of functional activity very early in the emergence of life.

Derr, Julien; Manapat, Michael L.; Rajamani, Sudha; Leu, Kevin; Xulvi-Brunet, Ramon; Joseph, Isaac; Nowak, Martin A.; Chen, Irene A.

2012-01-01

20

Prebiotically plausible mechanisms increase compositional diversity of nucleic acid sequences.  

PubMed

During the origin of life, the biological information of nucleic acid polymers must have increased to encode functional molecules (the RNA world). Ribozymes tend to be compositionally unbiased, as is the vast majority of possible sequence space. However, ribonucleotides vary greatly in synthetic yield, reactivity and degradation rate, and their non-enzymatic polymerization results in compositionally biased sequences. While natural selection could lead to complex sequences, molecules with some activity are required to begin this process. Was the emergence of compositionally diverse sequences a matter of chance, or could prebiotically plausible reactions counter chemical biases to increase the probability of finding a ribozyme? Our in silico simulations using a two-letter alphabet show that template-directed ligation and high concatenation rates counter compositional bias and shift the pool toward longer sequences, permitting greater exploration of sequence space and stable folding. We verified experimentally that unbiased DNA sequences are more efficient templates for ligation, thus increasing the compositional diversity of the pool. Our work suggests that prebiotically plausible chemical mechanisms of nucleic acid polymerization and ligation could predispose toward a diverse pool of longer, potentially structured molecules. Such mechanisms could have set the stage for the appearance of functional activity very early in the emergence of life. PMID:22319215

Derr, Julien; Manapat, Michael L; Rajamani, Sudha; Leu, Kevin; Xulvi-Brunet, Ramon; Joseph, Isaac; Nowak, Martin A; Chen, Irene A

2012-05-01

21

An improved string composition method for sequence comparison  

Microsoft Academic Search

BACKGROUND: Historically, two categories of computational algorithms (alignment-based and alignment-free) have been applied to sequence comparison–one of the most fundamental issues in bioinformatics. Multiple sequence alignment, although dominantly used by biologists, possesses both fundamental as well as computational limitations. Consequently, alignment-free methods have been explored as important alternatives in estimating sequence similarity. Of the alignment-free methods, the string composition vector

Guoquing Lu; Shunpu Zhang; Xiang Fang

2008-01-01

22

Maximal Words in Sequence Comparisons Based on Subword Composition  

Microsoft Academic Search

\\u000a Measures of sequence similarity and distance based more or less explicitly on subword composition are attracting an increasing\\u000a interest driven by intensive applications such as massive document classification and genome-wide molecular taxonomy. A uniform\\u000a character of such measures is in some underlying notion of relative compressibility, whereby two similar sequences are expected\\u000a to share a larger number of common substrings

Alberto Apostolico

2010-01-01

23

Bayesian estimation of bacterial community composition from 454 sequencing data.  

PubMed

Estimating bacterial community composition from a mixed sample in different applied contexts is an important task for many microbiologists. The bacterial community composition is commonly estimated by clustering polymerase chain reaction amplified 16S rRNA gene sequences. Current taxonomy-independent clustering methods for analyzing these sequences, such as UCLUST, ESPRIT-Tree and CROP, have two limitations: (i) expert knowledge is needed, i.e. a difference cutoff between species needs to be specified; (ii) closely related species cannot be separated. The first limitation imposes a burden on the user, since considerable effort is needed to select appropriate parameters, whereas the second limitation leads to an inaccurate description of the underlying bacterial community composition. We propose a probabilistic model-based method to estimate bacterial community composition which tackles these limitations. Our method requires very little expert knowledge, where only the possible maximum number of clusters needs to be specified. Also our method demonstrates its ability to separate closely related species in two experiments, in spite of sequencing errors and individual variations. PMID:22406836

Cheng, Lu; Walker, Alan W; Corander, Jukka

2012-07-01

24

Backbone flexibility in protein design theory and experiment  

NASA Astrophysics Data System (ADS)

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?1 domain (G?1). Concerted backbone motion was introduced by varying G?1'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 (???, ???, and ??) since their combination could be used to approximate most possible backbone fold. The best structure found for the ??? motif is similar to a zinc finger, and the best structure for the ??? motif is similar to a segment of a ?-barrel. The backbone obtained for the ?? 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.

Su, Alyce

25

Backbone flexibility in protein design theory and experiment  

NASA Astrophysics Data System (ADS)

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 ?1 domain (G?1). Concerted backbone motion was introduced by varying G?1'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 (?beta/alpha,/ /beta/alpha/beta, and ?alpha) since their combination could be used to approximate most possible backbone fold. The best structure found for the ?beta/alpha motif is similar to a zinc finger, and the best structure for the ?beta/alpha motif is similar to a segment of a ?-barrel. The backbone obtained for the ?alpha 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.

Su, Alyce Yaoying

26

The Evolution of Word Composition in Metazoan Promoter Sequence  

PubMed Central

The field of molecular evolution provides many examples of the principle that molecular differences between species contain information about evolutionary history. One surprising case can be found in the frequency of short words in DNA: more closely related species have more similar word compositions. Interest in this has often focused on its utility in deducing phylogenetic relationships. However, it is also of interest because of the opportunity it provides for studying the evolution of genome function. Word-frequency differences between species change too slowly to be purely the result of random mutational drift. Rather, their slow pattern of change reflects the direct or indirect action of purifying selection and the presence of functional constraints. Many such constraints are likely to exist, and an important challenge is to distinguish them. Here we develop a method to do so by isolating the effects acting at different word sizes. We apply our method to 2-, 4-, and 8-base-pair (bp) words across several classes of noncoding sequence. Our major result is that similarities in 8-bp word frequencies scale with evolutionary time for regions immediately upstream of genes. This association is present although weaker in intronic sequence, but cannot be detected in intergenic sequence using our method. In contrast, 2-bp and 4-bp word frequencies scale with time in all classes of noncoding sequence. These results suggest that different genomic processes are involved at different word sizes. The pattern in 2-bp and 4-bp words may be due to evolutionary changes in processes such as DNA replication and repair, as has been suggested before. The pattern in 8-bp words may reflect evolutionary changes in gene-regulatory machinery, such as changes in the frequencies of transcription-factor binding sites, or in the affinity of transcription factors for particular sequences.

Bush, Eliot C; Lahn, Bruce T

2006-01-01

27

Motif-directed flexible backbone design of functional interactions  

PubMed Central

Computational protein design relies on a number of approximations to efficiently search the huge sequence space available to proteins. The fixed backbone and rotamer approximations in particular are important for formulating protein design as a discrete combinatorial optimization problem. However, the resulting coarse-grained sampling of possible side-chain terminal positions is problematic for the design of protein function, which depends on precise positioning of side-chain atoms. Although backbone flexibility can greatly increase the conformation freedom of side-chain functional groups, it is not obvious which backbone movements will generate the critical constellation of atoms responsible for protein function. Here, we report an automated method for identifying protein backbone movements that can give rise to any specified set of desired side-chain atomic placements and interactions, using protein–DNA interfaces as a model system. We use a library of previously observed protein–DNA interactions (motifs) and a rotamer-based description of side-chain conformation freedom to identify placements for the protein backbone that can give rise to a favorable side-chain interaction with DNA. We describe a tree-search algorithm for identifying those combinations of interactions from the library that can be realized with minimal perturbation of the protein backbone. We compare the efficiency of this method with the alternative approach of building and screening alternate backbone conformations.

Havranek, James J; Baker, David

2009-01-01

28

Constructing optimal backbone segments for joining fixed DNA base pairs.  

PubMed Central

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.

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

1996-01-01

29

Introns form compositional clusters in parallel with the compositional clusters of the coding sequences to which they pertain.  

PubMed

This report deals with the study of compositional properties of human gene sequences evaluating similarities and differences among functionally distinct sectors of the gene independently of the reading frame. To retrieve the compositional information of DNA, we present a neighbor base dependent coding system in which the alphabet of 64 letters (DNA triplets) is compressed to an alphabet of 14 letters here termed triplet composons. The triplets containing the same set of distinct bases in whatever order and number form a triplet composon. The reading of the DNA sequence is performed starting at any letter of the initial triplet and then moving, triplet-to-triplet, until the end of the sequence. The readings were made in an overlapping way along the length of the sequences. The analysis of the compositional content in terms of the composon usage frequencies of the gene sequences shows that: (i) the compositional content of the sequences is far from that of random sequences, even in the case of non-protein coding sequences; (ii) coding sequences can be classified as components of compositional clusters; and (iii) intron sequences in a cluster have the same composon usage frequencies, even as their base composition differs notably from that of their home coding sequences. A comparison of the composon usage frequencies between human and mouse homologous genes indicated that two clusters found in humans do not have their counterpart in mouse whereas the others clusters are stable in both species with respect to their composon usage frequencies in both coding and noncoding sequences. PMID:21132282

Fuertes, Miguel A; Pérez, José M; Zuckerkandl, Emile; Alonso, Carlos

2011-01-01

30

Simulation of Ames Backbone Network  

NASA Technical Reports Server (NTRS)

The networking demands of Ames Research Center are dramatically increasing. More and more workstations are requested to run video and audio applications on the network. These applications require a much greater bandwidth than data applications. The existing ARCLAN 2000 network bandwidth is insufficient, due to the use of FDDI as its backbone, for accommodating video applications. Operating at a maximum of 100 Mbps, FDDI can handle only a few workstations running multimedia applications. The ideal solution is to replace the current ARCLAN 2000 FDDI backbone with an ATM backbone. ATM has the capability to handle the increasing traffic loads on the ARCLAN 2000 that results from these new applications. As it can be seen from Figure 1, ARCLAN 2000 have a total of 32 routers (5 being core routers) each connected to the FDDI backbone via a 100 Mbps link. This network serves 34 different locations by using 34 hubs that are connected to secondary routers. End users are connected to the secondary routers with 10 Mbps links.

Shahnasser, Hamid

1998-01-01

31

Corporate portal as security backbone  

Microsoft Academic Search

Network topologies found in audits and reviews are not capable to fulfill the needs of security and flexibility. Specialized networks and protection systems increase the complexity and reduce the overall security. Central corporate portals can be used as IT-security backbones. Constructing the corporate portals with reverse-proxy technology and with internal firewalls will secure, that no connection to sensible data or

U. Maurer

2005-01-01

32

Modeling compositional dynamics based on GC and purine contents of protein-coding sequences  

PubMed Central

Background Understanding the compositional dynamics of genomes and their coding sequences is of great significance in gaining clues into molecular evolution and a large number of publically-available genome sequences have allowed us to quantitatively predict deviations of empirical data from their theoretical counterparts. However, the quantification of theoretical compositional variations for a wide diversity of genomes remains a major challenge. Results To model the compositional dynamics of protein-coding sequences, we propose two simple models that take into account both mutation and selection effects, which act differently at the three codon positions, and use both GC and purine contents as compositional parameters. The two models concern the theoretical composition of nucleotides, codons, and amino acids, with no prerequisite of homologous sequences or their alignments. We evaluated the two models by quantifying theoretical compositions of a large collection of protein-coding sequences (including 46 of Archaea, 686 of Bacteria, and 826 of Eukarya), yielding consistent theoretical compositions across all the collected sequences. Conclusions We show that the compositions of nucleotides, codons, and amino acids are largely determined by both GC and purine contents and suggest that deviations of the observed from the expected compositions may reflect compositional signatures that arise from a complex interplay between mutation and selection via DNA replication and repair mechanisms. Reviewers This article was reviewed by Zhaolei Zhang (nominated by Mark Gerstein), Guruprasad Ananda (nominated by Kateryna Makova), and Daniel Haft.

2010-01-01

33

A mathematical consideration of the word-composition vector method in comparison of biological sequences.  

PubMed

To measure the similarity or dissimilarity between two given biological sequences, several papers proposed metrics based on the "word-composition vector". The essence of these metrics is as follows. First, we count the appearance frequencies of all the K-tuple words throughout each of two given sequences. Then, the two given sequences are transformed into their respective word-composition vectors. Next, the distance metrics, for example the angle between the two vectors, are calculated. A significant issue is to determine the optimal word size K. With a mathematical model of mutational events (including substitutions, insertions, deletions and duplications) that occur in sequences, we analyzed how the angle between the composition vectors depends on the mutational events. We also considered the optimal word size (=resolution) from our original approach. Our results were verified by computational experiments using artificially generated sequences, amino acid sequences of hemoglobin and nucleotide sequences of 16S ribosomal RNA. PMID:21745534

Aita, Takuyo; Husimi, Yuzuru; Nishigaki, Koichi

2011-11-01

34

Nucleosome positioning based on the sequence word composition.  

PubMed

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

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

2012-01-01

35

High-Fidelity Adiabatic Passage by Composite Sequences of Chirped Pulses  

SciTech Connect

We present a method for optimization of the technique of adiabatic passage between two quantum states by composite sequences of frequency-chirped pulses with specific relative phases: composite adiabatic passage (CAP). By choosing the composite phases appropriately the nonadiabatic losses can be canceled to any desired order with sufficiently long sequences, regardless of the nonadiabatic coupling. The values of the composite phases are universal for they do not depend on the pulse shapes and the chirp. The accuracy of the CAP technique and its robustness against parameter variations make CAP suitable for high-fidelity quantum information processing.

Torosov, Boyan T. [Department of Physics, Sofia University, 5 James Bourchier Boulevard, 1164 Sofia (Bulgaria); Laboratoire Interdisciplinaire Carnot de Bourgogne, UMR CNRS 5209, BP 47870, F-21078 Dijon (France); Guerin, Stephane [Laboratoire Interdisciplinaire Carnot de Bourgogne, UMR CNRS 5209, BP 47870, F-21078 Dijon (France); Vitanov, Nikolay V. [Department of Physics, Sofia University, 5 James Bourchier Boulevard, 1164 Sofia (Bulgaria)

2011-06-10

36

Compositions and Methods for Systemic Nucleic Acid Sequence Delivery.  

National Technical Information Service (NTIS)

The present invention provides systemic nucleic acid sequence delivery without conventional systemic administration aids (SAAs). In certain embodiments, vascular permeability agents (VPAs), such as VEGF, are used in conjunction with nucleic acid viral vec...

J. M. Allen J. S. Chamberlain M. J. Blankinship P. Gregorevic

2004-01-01

37

Diverse nucleotide compositions and sequence fluctuation in Rubisco protein genes  

NASA Astrophysics Data System (ADS)

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.

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

2011-09-01

38

Diverse nucleotide compositions and sequence fluctuation in Rubisco protein genes  

NASA Astrophysics Data System (ADS)

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.

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

2011-10-01

39

Precipitation sequence in a SiC\\/Al-Mg2Si alloy composite material  

Microsoft Academic Search

The precipitation sequence of an Al-1.0mass%Mg2Si composite material having 8 vol.% SiC particles was investigated by Vickers micro hardness and specific electrical resistivity measurements, and by TEM observation. The formation of GP zones was suppressed in the composite material and its age-hardenability was reduced. Distribution of precipitates in the composite material was coarser and their size was larger than that

S. Ikeno; K. Matsuda; S. Rengakuji; Y. Uetani

2001-01-01

40

A base composition analysis of natural patterns for the preprocessing of metagenome sequences  

PubMed Central

Background On the pretext that sequence reads and contigs often exhibit the same kinds of base usage that is also observed in the sequences from which they are derived, we offer a base composition analysis tool. Our tool uses these natural patterns to determine relatedness across sequence data. We introduce spectrum sets (sets of motifs) which are permutations of bacterial restriction sites and the base composition analysis framework to measure their proportional content in sequence data. We suggest that this framework will increase the efficiency during the pre-processing stages of metagenome sequencing and assembly projects. Results Our method is able to differentiate organisms and their reads or contigs. The framework shows how to successfully determine the relatedness between these reads or contigs by comparison of base composition. In particular, we show that two types of organismal-sequence data are fundamentally different by analyzing their spectrum set motif proportions (coverage). By the application of one of the four possible spectrum sets, encompassing all known restriction sites, we provide the evidence to claim that each set has a different ability to differentiate sequence data. Furthermore, we show that the spectrum set selection having relevance to one organism, but not to the others of the data set, will greatly improve performance of sequence differentiation even if the fragment size of the read, contig or sequence is not lengthy. Conclusions We show the proof of concept of our method by its application to ten trials of two or three freshly selected sequence fragments (reads and contigs) for each experiment across the six organisms of our set. Here we describe a novel and computationally effective pre-processing step for metagenome sequencing and assembly tasks. Furthermore, our base composition method has applications in phylogeny where it can be used to infer evolutionary distances between organisms based on the notion that related organisms often have much conserved code.

2013-01-01

41

Restoration objectives for internet backbone links  

Microsoft Academic Search

As more and more critical applications, such as banking and finance, use the Internet as the information infrastructure, the Internet backbone is expected to be restored quickly in the case of network failures. The 50 millisecond restoration objective has been forced onto Internet backbones as the de facto restoration requirement although this objective was actually derived from the requirements of

Qiang Ye; Mike H. MacGregor

2008-01-01

42

Digital Silk Road Backbone Feasibility Study.  

National Technical Information Service (NTIS)

The USTDA funded a backbone feasibility study to find out if it is possible to install a fiber optic backbone network linking the major towns in Afghanistan and providing links to the neighboring countries. The study was awarded in July 2003 and expected ...

2004-01-01

43

Organization of IP backbone on technology Ethernet  

Microsoft Academic Search

The tendency of last time - transition on city and backbone networks on technology IP, with transfer of packages in the pure state on a .dark fiber. The concept of the organization of the backbone on technology Ethernet is offered. The model is developed, allowing to predict the traffic main IP networks, on the basis of the data on average

Nikolaj V. Dudin

2008-01-01

44

Optimal path planning for mobile backbone networks  

Microsoft Academic Search

Mobile Backbone Networks are heterogeneous wireless networks in which a subset of the nodes are more capable than others. The more capable nodes are referred to as Mobile Backbone Nodes (MBNs), whose primary role is to provide a mobile infrastructure in order to facilitate reli able end-to-end communication between nodes in the Network. In this paper, we consider the problem

Anand Srinivas; Eytan Modiano

2008-01-01

45

Utilisation of cod backbone by biochemical fractionation  

Microsoft Academic Search

The backbone fraction obtained from industrial processing of Atlantic cod (Gadus morhua) yields about 15% of the whole fish weight. Due to a high content of muscle and bone proteins, it is a valuable raw material for further processing. In the present work minced backbones were subjected to gentle hydrolysis by proteinases to solubilize muscle proteins before the pure bone

Asbjørn Gildberg; Jan A Arnesen; Mats Carlehög

2002-01-01

46

A novel approach to extracting features from motif content and protein composition for protein sequence classification.  

PubMed

This paper presents a novel approach to extracting features from motif content and protein composition for protein sequence classification. First, we formulate a protein sequence as a fixed-dimensional vector using the motif content and protein composition. Then, we further project the vectors into a low-dimensional space by the Principal Component Analysis (PCA) so that they can be represented by a combination of the eigenvectors of the covariance matrix of these vectors. Subsequently, the Genetic Algorithm (GA) is used to extract a subset of biological and functional sequence features from the eigen-space and to optimize the regularization parameter of the Support Vector Machine (SVM) simultaneously. Finally, we utilize the SVM classifiers to classify protein sequences into corresponding families based on the selected feature subsets. In comparison with the existing PSI-BLAST and SVM-pairwise methods, the experiments show the promising results of our approach. PMID:16153801

Zhao, Xing-Ming; Cheung, Yiu-Ming; Huang, De-Shuang

2005-10-01

47

Sequence composition similarities with the 7SL RNA are highly predictive of functional genomic features  

PubMed Central

Transposable elements derived from the 7SL RNA gene, such as Alu elements in primates, have had remarkable success in several mammalian lineages. The results presented here show a broad spectrum of functions for genomic segments that display sequence composition similarities with the 7SL RNA gene. Using thoroughly documented loci, we report that DNaseI-hypersensitive sites can be singled out in large genomic sequences by an assessment of sequence composition similarities with the 7SL RNA gene. We apply a root word frequency approach to illustrate a distinctive relationship between the sequence of the 7SL RNA gene and several classes of functional genomic features that are not presumed to be of transposable origin. Transposable elements that show noticeable similarities with the 7SL sequence include Alu sequences, as expected, but also long terminal repeats and the 5?-untranslated regions of long interspersed repetitive elements. In sequences masked for repeated elements, we find, when using the 7SL RNA gene as query sequence, distinctive similarities with promoters, exons and distal gene regulatory regions. The latter being the most notoriously difficult to detect, this approach may be useful for finding genomic segments that have regulatory functions and that may have escaped detection by existing methods.

Paquet, Yanick; Anderson, Alan

2010-01-01

48

Flexible backbone aromatic polyimide adhesives  

NASA Technical Reports Server (NTRS)

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.

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

1988-01-01

49

Flexible backbone aromatic polyimide adhesives  

NASA Technical Reports Server (NTRS)

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.

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

1989-01-01

50

SARP: A Novel Algorithm to Assess Compositional Biases in Protein Sequences  

PubMed Central

The composition of a defined set of subunits (nucleotides, amino acids) is one of the key features of biological sequences. Compositional biases are local shifts in amino acid or nucleotide frequencies that can occur as an adaptation of an organism to an extreme ecological niche, or as the signature of a specific function or localization of the corresponding protein. The calculation of probability is a method for annotating compositional bias and providing accurate detection of biased subsequences. Here, we present a Sequence Analysis based on the Ranking of Probabilities (SARP), a novel algorithm for the annotation of compositional biases based on ranking subsequences by their probabilities. SARP provides the same accuracy as the previously published Lower Probability Subsequences (LPS) algorithm but performs at an approximately 230-fold faster rate. It can be recommended for use when working with large datasets to reduce the time and resources required.

Antonets, Kirill S.; Nizhnikov, Anton A.

2013-01-01

51

Compositional segmentation and long-range fractal correlations in DNA sequences  

NASA Astrophysics Data System (ADS)

A segmentation algorithm based on the Jensen-Shannon entropic divergence is used to decompose long-range correlated DNA sequences into statistically significant, compositionally homogeneous patches. By adequately setting the significance level for segmenting the sequence, the underlying power-law distribution of patch lengths can be revealed. Some of the identified DNA domains were uncorrelated, but most of them continued to display long-range correlations even after several steps of recursive segmentation, thus indicating a complex multi-length-scaled structure for the sequence. On the other hand, by separately shuffling each segment, or by randomly rearranging the order in which the different segments occur in the sequence, shuffled sequences preserving the original statistical distribution of patch lengths were generated. Both types of random sequences displayed the same correlation scaling exponents as the original DNA sequence, thus demonstrating that neither the internal structure of patches nor the order in which these are arranged in the sequence is critical; therefore, long-range correlations in nucleotide sequences seem to rely only on the power-law distribution of patch lengths.

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

1996-05-01

52

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

PubMed

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

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

2008-09-21

53

A scatter search algorithm for stacking sequence optimisation of laminate composites  

Microsoft Academic Search

This paper explores the metaheuristic approach called scatter search for lay-up sequence optimisation of laminate composite panels. Scatter search is an evolutionary method that has recently been found to be promising for solving combinatorial optimisation problems. The scatter search framework is flexible and allows the development of alternative implementations with varying degree of sophistication. The main objective of this paper

A. Rama Mohan Rao; N. Arvind

2005-01-01

54

Epoxy\\/Polyurethane\\/Clay Ternary Nanocomposites – Effect of Components Mixing Sequence on the Composites Properties  

Microsoft Academic Search

The present work investigates the mixing sequence of montmorillonite (MMT) and polyurethane (PUR) on epoxy resin (EP) properties. Mechanical properties were evaluated and structures analyzed by means of infrared spectroscopy (FTIR), X-ray diffraction (XRD) and transmission electron microscopy (TEM). The measured properties of all tested compositions were improved in comparison with unmodified epoxy resin. The best mechanical properties were exhibited

M. Bakar; M. Lavorgna; J. Szyma?ska; A. D?tkowska

2012-01-01

55

Classification of scorpion toxins according to amino acid composition and sequence.  

PubMed

Scorpion venom toxins were systematically classified according to amino acid composition, insertion/deletion events and sequence. The significance of each comparison method and its outcome is discussed in relation to known immunological and structural properties. A general classification of the toxins is proposed that accounts for both the immunological groupings and the differences in mode of action. PMID:6433030

Dufton, M J; Rochat, H

1984-01-01

56

Sequence Composition and Gene Content of the Short Arm of Rye (Secale cereale) Chromosome 1  

PubMed Central

Background The purpose of the study is to elucidate the sequence composition of the short arm of rye chromosome 1 (Secale cereale) with special focus on its gene content, because this portion of the rye genome is an integrated part of several hundreds of bread wheat varieties worldwide. Methodology/Principal Findings Multiple Displacement Amplification of 1RS DNA, obtained from flow sorted 1RS chromosomes, using 1RS ditelosomic wheat-rye addition line, and subsequent Roche 454FLX sequencing of this DNA yielded 195,313,589 bp sequence information. This quantity of sequence information resulted in 0.43× sequence coverage of the 1RS chromosome arm, permitting the identification of genes with estimated probability of 95%. A detailed analysis revealed that more than 5% of the 1RS sequence consisted of gene space, identifying at least 3,121 gene loci representing 1,882 different gene functions. Repetitive elements comprised about 72% of the 1RS sequence, Gypsy/Sabrina (13.3%) being the most abundant. More than four thousand simple sequence repeat (SSR) sites mostly located in gene related sequence reads were identified for possible marker development. The existence of chloroplast insertions in 1RS has been verified by identifying chimeric chloroplast-genomic sequence reads. Synteny analysis of 1RS to the full genomes of Oryza sativa and Brachypodium distachyon revealed that about half of the genes of 1RS correspond to the distal end of the short arm of rice chromosome 5 and the proximal region of the long arm of Brachypodium distachyon chromosome 2. Comparison of the gene content of 1RS to 1HS barley chromosome arm revealed high conservation of genes related to chromosome 5 of rice. Conclusions The present study revealed the gene content and potential gene functions on this chromosome arm and demonstrated numerous sequence elements like SSRs and gene-related sequences, which can be utilised for future research as well as in breeding of wheat and rye.

Fluch, Silvia; Kopecky, Dieter; Burg, Kornel; Simkova, Hana; Taudien, Stefan; Petzold, Andreas; Kubalakova, Marie; Platzer, Matthias; Berenyi, Maria; Krainer, Siegfried; Dolezel, Jaroslav; Lelley, Tamas

2012-01-01

57

External Tank - The Structure Backbone  

NASA Technical Reports Server (NTRS)

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.

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

2011-01-01

58

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

PubMed

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 Al?O? 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

Hausnerova, Berenika; Kuritka, Ivo; Bleyan, Davit

2014-01-01

59

Optimum stacking sequence design of composite sandwich panel using genetic algorithms  

NASA Astrophysics Data System (ADS)

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.

Bir, Amarpreet Singh

60

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

NASA Technical Reports Server (NTRS)

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.

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

1981-01-01

61

A view of an elemental naturalist at the DNA world (Base composition, sequences, methylation)  

Microsoft Academic Search

The pioneering data on base composition and pyrimidine sequences in DNA of pro-and eukaryotes are considered, and their significance\\u000a for the origin of genosystematics is discussed. The modern views on specificity and functional role of enzymatic DNA methylation\\u000a in eukaryotes are described. DNA methylation controls all genetic functions and is a mechanism of cellular differentiation\\u000a and gene silencing. A model

B. F. Vanyushin

2007-01-01

62

Diversity of Ligularia kanaitzensis in sesquiterpenoid composition and neutral DNA sequences  

Microsoft Academic Search

Twenty-six eremophilane-type sesquiterpenoids, including six new compounds, were isolated from the title species. One of the new compounds, kanaitzensol, suggested the presence of an enzyme for the conversion of eremophil-7(11)-en-8-one derivative to furanoeremophilanes. The plant was collected at 15 locations in Yunnan Province of China and found to be diverse with respect to its sesquiterpenoid composition. DNA sequencing also revealed

Motoo Tori; Aki Watanabe; Sachie Matsuo; Yasuko Okamoto; Kana Tachikawa; Shigeru Takaoka; Xun Gong; Chiaki Kuroda; Ryo Hanai

2008-01-01

63

31P NMR Investigation of Backbone Dynamics in DNA Binding Sites  

PubMed Central

The backbone conformation of DNA plays an important role in the indirect readout mechanisms for protein-DNA recognition events. Thus, investigating the backbone dynamics of each step in DNA binding sequences provides useful information necessary for the characterization of these interactions. Here we use 31P Dynamic NMR to characterize the backbone conformation and dynamics in the Dickerson Dodecamer, a sequence containing the EcoRI binding site, and confirm solid-state 2H-NMR results showing that the C3pG4 and C9pG10 steps experience unique dynamics and that these dynamics are quenched upon cytosine methylation. In addition, we show that cytosine methylation affects the conformation and dynamics of neighboring nucleotide steps but this effect is localized to only near neighbors and base pairing partners. Lastly, we have been able to characterize the %BII in each backbone step and illustrate that the C3pG4 and C9pG10 favor the non-canonical BII conformation, even at low temperatures. Our results demonstrate that 31P Dynamic NMR provides a robust and efficient method for characterizing the backbone dynamics in DNA. This allows simple, rapid determination of sequence-dependent dynamical information, providing a useful method for studying trends in protein-DNA recognition events.

Tian, Ye; Kayatta, Michael; Shultis, Katharine; Gonzalez, Alejandro; Mueller, Leonard J.; Hatcher, Mary E.

2009-01-01

64

Coding sequence composition flanking either signal element alters V(D)J recombination efficiency.  

PubMed Central

Lymphoid V(D)J rearrangement is targeted by recombination signal sequences (RSS) bordering V, D or J exons. We demonstrate that the DNA composition of flanking coding positions, particularly poly(A) or poly(T) stretches at one or both RSS, diminishes V(D)J recombination up to 100-fold. Positionally correct cleavages occur in the inhibited reactions, since the junctions formed show the same frequency of precision as uninhibited reactions. Open/shut cleavage/rejoining is not increased at a normal RSS in substrates containing inhibitory A/T homopolymers versus random sequence at a second RSS. Thus recombinase action at both cleavage sites is severely disrupted by modified coding sequences.

Boubnov, N V; Wills, Z P; Weaver, D T

1995-01-01

65

Ribosomal synthesis of backbone macrocyclic peptides.  

PubMed

A wealth of knowledge has been accumulated on ribosomal synthesis of macrocyclic peptides in the past decade. In nature, backbone cyclization of the translated linear peptides is generally catalyzed by specific enzymes, giving them peptidase resistance, thermodynamic stability and various other physiological activities. Due to these biochemical traits, backbone cyclic peptides have become an attractive resource for the discovery of drug leads. Recently, various new methodologies have also been established to generate man-made cyclic peptides. Here, we describe the biosynthetic mechanisms of naturally occurring backbone macrocyclic peptides focusing on cyclotides, sunflower trypsin inhibitors (SFTIs) and cyanobactins as well as several new emerging methodologies, such as sortase mediated ligation, protein splicing method and genetic code reprogramming. PMID:21766105

Katoh, Takayuki; Goto, Yuki; Reza, Md Shamim; Suga, Hiroaki

2011-09-28

66

Securing IP backbones in building automation networks  

Microsoft Academic Search

The use of IP networks as common backbone is becoming of increased interest in today's building automation systems (BAS). With the use of IP also new attack scenarios that threaten the overall security of BAS are introduced. Due to the absence of native security mechanisms in IP and because of its long standing and pervasive use in the IT world,

Wolfgang Granzer; Daniel Lechner; Fritz Praus; Wolfgang Kastner

2009-01-01

67

Sequencer  

NSDL National Science Digital Library

In this activity, you will learn about number patterns in sequences and recursions. You will have the opportunity to choose a starting number, a multiplier, and an add-on. When the graph is made, the numbers in the sequence are displayed on a graph, and they are also listed below the graph.

2010-01-01

68

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

NASA Astrophysics Data System (ADS)

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 Bølling-Allerød (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.

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

2010-05-01

69

Sequence composition and environment effects on residue fluctuations in protein structures  

NASA Astrophysics Data System (ADS)

Structure fluctuations in proteins affect a broad range of cell phenomena, including stability of proteins and their fragments, allosteric transitions, and energy transfer. This study presents a statistical-thermodynamic analysis of relationship between the sequence composition and the distribution of residue fluctuations in protein-protein complexes. A one-node-per-residue elastic network model accounting for the nonhomogeneous protein mass distribution and the interatomic interactions through the renormalized inter-residue potential is developed. Two factors, a protein mass distribution and a residue environment, were found to determine the scale of residue fluctuations. Surface residues undergo larger fluctuations than core residues in agreement with experimental observations. Ranking residues over the normalized scale of fluctuations yields a distinct classification of amino acids into three groups: (i) highly fluctuating-Gly, Ala, Ser, Pro, and Asp, (ii) moderately fluctuating-Thr, Asn, Gln, Lys, Glu, Arg, Val, and Cys, and (iii) weakly fluctuating-Ile, Leu, Met, Phe, Tyr, Trp, and His. The structural instability in proteins possibly relates to the high content of the highly fluctuating residues and a deficiency of the weakly fluctuating residues in irregular secondary structure elements (loops), chameleon sequences, and disordered proteins. Strong correlation between residue fluctuations and the sequence composition of protein loops supports this hypothesis. Comparing fluctuations of binding site residues (interface residues) with other surface residues shows that, on average, the interface is more rigid than the rest of the protein surface and Gly, Ala, Ser, Cys, Leu, and Trp have a propensity to form more stable docking patches on the interface. The findings have broad implications for understanding mechanisms of protein association and stability of protein structures.

Ruvinsky, Anatoly M.; Vakser, Ilya A.

2010-10-01

70

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

PubMed

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

Mondal, Sukanta; Pai, Priyadarshini P

2014-09-01

71

Unifying the analysis of high-throughput sequencing datasets: characterizing RNA-seq, 16S rRNA gene sequencing and selective growth experiments by compositional data analysis  

PubMed Central

Background Experimental designs that take advantage of high-throughput sequencing to generate datasets include RNA sequencing (RNA-seq), chromatin immunoprecipitation sequencing (ChIP-seq), sequencing of 16S rRNA gene fragments, metagenomic analysis and selective growth experiments. In each case the underlying data are similar and are composed of counts of sequencing reads mapped to a large number of features in each sample. Despite this underlying similarity, the data analysis methods used for these experimental designs are all different, and do not translate across experiments. Alternative methods have been developed in the physical and geological sciences that treat similar data as compositions. Compositional data analysis methods transform the data to relative abundances with the result that the analyses are more robust and reproducible. Results Data from an in vitro selective growth experiment, an RNA-seq experiment and the Human Microbiome Project 16S rRNA gene abundance dataset were examined by ALDEx2, a compositional data analysis tool that uses Bayesian methods to infer technical and statistical error. The ALDEx2 approach is shown to be suitable for all three types of data: it correctly identifies both the direction and differential abundance of features in the differential growth experiment, it identifies a substantially similar set of differentially expressed genes in the RNA-seq dataset as the leading tools and it identifies as differential the taxa that distinguish the tongue dorsum and buccal mucosa in the Human Microbiome Project dataset. The design of ALDEx2 reduces the number of false positive identifications that result from datasets composed of many features in few samples. Conclusion Statistical analysis of high-throughput sequencing datasets composed of per feature counts showed that the ALDEx2 R package is a simple and robust tool, which can be applied to RNA-seq, 16S rRNA gene sequencing and differential growth datasets, and by extension to other techniques that use a similar approach.

2014-01-01

72

Role of sequence and membrane composition in structure of transmembrane domain of Amyloid Precursor Protein  

NASA Astrophysics Data System (ADS)

Aggregation of proteins of known sequence is linked to a variety of neurodegenerative disorders. The amyloid ? (A?) protein associated with Alzheimer's Disease (AD) is derived from cleavage of the 99 amino acid C-terminal fragment of Amyloid Precursor Protein (APP-C99) by ?-secretase. Certain familial mutations of APP-C99 have been shown to lead to altered production of A? protein and the early onset of AD. We describe simulation studies exploring the structure of APP-C99 in micelle and membrane environments. Our studies explore how changes in sequence and membrane composition influence (1) the structure of monomeric APP-C99 and (2) APP-C99 homodimer structure and stability. Comparison of simulation results with recent NMR studies of APP-C99 monomers and dimers in micelle and bicelle environments provide insight into how critical aspects of APP-C99 structure and dimerization correlate with secretase processing, an essential component of the A? protein aggregation pathway and AD.

Straub, John

2013-03-01

73

Dead-End Elimination with Perturbations ("DEEPer"): A provable protein design algorithm with continuous sidechain and backbone flexibility  

PubMed Central

Computational protein and drug design generally require accurate modeling of protein conformations. This modeling typically starts with an experimentally-determined protein structure and considers possible conformational changes due to mutations or new ligands. The DEE/A* algorithm provably finds the GMEC (global minimum-energy conformation) of a protein assuming the backbone does not move and the sidechains take on conformations from a set of discrete, experimentally-observed conformations called rotamers. DEE/A* can efficiently find the overall GMEC for exponentially many mutant sequences. Previous improvements to DEE/A* include modeling ensembles of sidechain conformations and either continuous sidechain or backbone flexibility. We present a new algorithm, DEEPer (Dead-End Elimination with Perturbations), that combines these advantages and can also handle much more extensive backbone flexibility and backbone ensembles. DEEPer provably finds the GMEC or, if desired by the user, all conformations and sequences within a specified energy window of the GMEC. It includes the new abilities to handle arbitrarily large backbone perturbations and to generate ensembles of backbone conformations. It also incorporates the shear, an experimentally-observed local backbone motion never before used in design. Additionally, we derive a new method to accelerate DEE/A*-based calculations, indirect pruning, that is particularly useful for DEEPer. In 67 benchmark tests on 64 proteins, DEEPer consistently identified lower-energy conformations than previous methods did, indicating more accurate modeling. Additional tests demonstrated its ability to incorporate larger, experimentally-observed backbone conformational changes and to model realistic conformational ensembles. These capabilities provide significant advantages for modeling protein mutations and protein-ligand interactions.

Hallen, Mark A.; Keedy, Daniel A.; Donald, Bruce R.

2012-01-01

74

Oligonucleotides with novel, cationic backbone substituents: aminoethylphosphonates.  

PubMed Central

Oligonucleotide (2-aminoethyl)phosphonates in which the backbone consisted of isomerically pure, alternating (2-aminoethyl)-phosphonate and phosphodiester linkages have been prepared and characterized. One of these single isomer oligonucleotides (Rp) formed a more stable duplex with DNA or RNA than its corresponding natural counterpart. Hybrid stability was more pH-dependent, but less salt-dependent than a natural duplex. The specificity of hybridization was examined by hybridization of an oligonucleotide containing one (2-aminoethyl)phosphonate to oligonucleotides possessing mismatches in the region opposite to the aminoethyl group. In contrast to oligonucleotides containing (aminomethyl)-phosphonate linkages, oligonucleotide (2-aminoethyl)phosphonates were completely stable to hydrolysis in aqueous solution. These oligonucleotides were resistant to nuclease activity but did not induce RNase H mediated cleavage of a complementary RNA strand. Incubation in a serum-containing medium resulted in minimal degradation over 24 hours. Studies of cell uptake by flow cytometry and confocal microscopy demonstrated temperature dependent uptake and intracellular localization. (2-Aminoethyl)phosphonates represent a novel approach to the introduction of positive charges into the backbone of oligonucleotides. Images

Fathi, R; Huang, Q; Coppola, G; Delaney, W; Teasdale, R; Krieg, A M; Cook, A F

1994-01-01

75

Backbone Dynamics Of Intracellular Lipid Binding Proteins  

NASA Astrophysics Data System (ADS)

The family of intracellular lipid binding proteins (iLBPs) comprises a group of homologous 14-15 kDa proteins that specifically bind and facilitate the transport of fatty acids, bile acids, retinoids or eicosanoids. Members of this family include several types of fatty acid binding proteins (FABPs), ileal lipid binding protein, cellular retinoic acid binding proteins and cellular retinoid binding proteins. As a contribution to understanding the structure-function relationship in this protein family, the solution structure and backbone dynamics of human epidermal-type FABP (E-FABP) determined by NMR spectroscopy are reported. Moreover, hydrogen/deuterium exchange experiments indicated a direct correlation between the stability of the hydrogen-bonding network in the ?-sheet structure and the conformational exchange in the millisecond-to-microsecond time range. The features of E-FABP backbone dynamics discussed in the present study are compared with those obtained for other phylogenetically related proteins. A strong interdependence with the overall protein stability and possibly also with the ligand-binding affinity for members of the lipid-binding protein family is shown.

Gutiérrez-González, Luis H.

2005-04-01

76

Influence of fibre orientation and stacking sequence on petalling of glass\\/polyester composite cylindrical shells under axial compression  

Microsoft Academic Search

The energy absorbing capability of FRP composite cylindrical tubes used as energy absorbers, by destroying itself progressively, depends on the way in which the tube material is crushed i.e., trend of petalling. This paper investigates the influence of fibre orientation and stacking sequence on the petal formation and specific energy absorption (SEA) of four and six-ply, 0°\\/90° glass\\/polyester composite cylindrical

S. Solaimurugan; R. Velmurugan

2007-01-01

77

Improving the accuracy of protein stability predictions with multistate design using a variety of backbone ensembles.  

PubMed

Multistate computational protein design (MSD) with backbone ensembles approximating conformational flexibility can predict higher quality sequences than single-state design with a single fixed backbone. However, it is currently unclear what characteristics of backbone ensembles are required for the accurate prediction of protein sequence stability. In this study, we aimed to improve the accuracy of protein stability predictions made with MSD by using a variety of backbone ensembles to recapitulate the experimentally measured stability of 85 Streptococcal protein G domain ?1 sequences. Ensembles tested here include an NMR ensemble as well as those generated by molecular dynamics (MD) simulations, by Backrub motions, and by PertMin, a new method that we developed involving the perturbation of atomic coordinates followed by energy minimization. MSD with the PertMin ensembles resulted in the most accurate predictions by providing the highest number of stable sequences in the top 25, and by correctly binning sequences as stable or unstable with the highest success rate (?90%) and the lowest number of false positives. The performance of PertMin ensembles is due to the fact that their members closely resemble the input crystal structure and have low potential energy. Conversely, the NMR ensemble as well as those generated by MD simulations at 500 or 1000 K reduced prediction accuracy due to their low structural similarity to the crystal structure. The ensembles tested herein thus represent on- or off-target models of the native protein fold and could be used in future studies to design for desired properties other than stability. PMID:24174277

Davey, James A; Chica, Roberto A

2014-05-01

78

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

PubMed

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

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

2011-07-01

79

Functionalized gold nanoparticles as additive to form polymer/metal composite matrix for improved DNA sequencing by capillary electrophoresis.  

PubMed

A new matrix additive, poly (N,N-dimethylacrylamide)-functionalized gold nanoparticle (GNP-PDMA), was prepared by "grafting-to" approach, and then incorporated into quasi-interpenetrating network (quasi-IPN) composed of linear polyacrylamide (LPA, 3.3 MDa) and PDMA to form novel polymer/metal composite sieving matrix (quasi-IPN/GNP-PDMA) for DNA sequencing by capillary electrophoresis. Without complete optimization, quasi-IPN/GNP-PDMA yielded a readlength of 801 bases at 98% accuracy in about 64 min by using the ABI 310 Genetic Analyzer at 50 degrees C and 150 V/cm. Compared with previous quasi-IPN/GNPs, quasi-IPN/GNP-PDMA can further improve DNA sequencing performances. This is because the presence of GNP-PDMA can improve the compatibility of GNPs with the whole sequencing system, enhance the entanglement degree of networks, and increase the GNP concentration in system, which consequently lead to higher restriction and stability, higher apparent molecular weight (MW), and smaller pore size of the total sieving networks. Furthermore, the composite matrix was also compared with quasi-IPN containing higher-MW LPA and commercial POP-6. The results indicate that the composite matrix is a promising one for DNA sequencing to achieve full automation due to the separation provided with high resolution, speediness, excellent reproducibility, and easy loading in the presence of GNP-PDMA. PMID:19782213

Zhou, Dan; Yang, Liping; Yang, Runmiao; Song, Weihua; Peng, Shuhua; Wang, Yanmei

2009-11-15

80

Reverse transcriptase backbone can alter the polymerization and RNase activities of non-nucleoside reverse transcriptase mutants K101E+G190S.  

PubMed

Previous work by our group showed that human immunodeficiency virus type 1 (HIV-1) reverse transcriptase (RT) containing non-nucleoside RT inhibitor (NNRTI) drug resistance mutations has defects in RNase H activity as well as reduced amounts of RT protein in virions. These deficits correlate with replication fitness in the absence of NNRTIs. Viruses with the mutant combination K101E+G190S replicated better in the presence of NNRTIs than in the absence of drug. Stimulation of virus growth by NNRTIs occurred during the early steps of the virus life cycle and was modulated by the RT backbone sequence in which the resistance mutations arose. We wanted to determine what effects RT backbone sequence would have on RT content and polymerization and RNase H activities in the absence of NNRTIs. We compared a NL4-3 RT with K101E+G190S to a patient-isolate RT sequence D10 with K101E+G190S. We show here that, unlike the NL4-3 backbone, the D10 backbone sequence decreased the RNA-dependent DNA polymerization activity of purified recombinant RT compared to WT. In contrast, RTs with the D10 backbone had increased RNase H activity compared to WT and K101E+G190S in the NL4-3 backbone. D10 virions also had increased amounts of RT compared to K101E+G190S in the NL4-3 backbone. We conclude that the backbone sequence of RT can alter the activities of the NNRTI drug-resistant mutant K101E+G190S, and that identification of the amino acids responsible will aid in understanding the mechanism by which NNRTI drug-resistant mutants alter fitness and NNRTIs stimulate HIV-1 virus replication. PMID:23804564

Wang, Jiong; Li, Dongge; Bambara, Robert A; Dykes, Carrie

2013-10-01

81

BACKBONE MECHANICS OF THE BLUE MARLIN MAKAIRA NIGRICANS (PISCES, ISTIOPHORIDAE)  

Microsoft Academic Search

Summary Over most of its length, the backbone of the blue marlin, like that of all other istiophorids, contains enlarged and flattened neural and hemal spines and zygapophyses, all of which span the intervertebral joints. These plates of bone restrict dorso-ventral bending of the backbone but their arrangement permits a high degree of lateral flexion. The spines and zygapophyses also

JOHN H. HEBRANK; MARY R. HEBRANK; JOHN H. LONG; BARBARA A. BLOCK; STEPHEN A. WAIN WRIGHT

1990-01-01

82

Evaluation of a wireless enterprise backbone network architecture  

Microsoft Academic Search

IEEE 802.11 wireless LAN technology is mainly used as an access network within corporate enterprises. All the WLAN access points are eventually connected to a wired backbone to reach the Internet or enterprise computing resources. We aim to expand WLAN into an enterprise-scale backbone network technology by developing a multichannel wireless mesh network architecture called Hyacinth. Hyacinth equips each node

Ashish Raniwala; Tzi-cker Chiueh

2004-01-01

83

Extracting the information backbone in online system.  

PubMed

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

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

2013-01-01

84

Structure of HLA Antigens: AminoAcid and Carbohydrate Compositions and NH2Terminal Sequences of Four Antigen Preparations  

Microsoft Academic Search

Amino-acid and carbohydrate compositions in addition to limited NH2-terminal sequence data of four preparations of HLA antigens, including products of both of the major histocompatibility loci (HLA-A and HLA-B), show that the antigens have great homology in the primary structure. A striking observation is that HLA antigens also have a considerable structure homology with mouse H-2 antigens. HLA antigens appear

Cox Terhorst; Peter Parham; Dean L. Mann; Jack L. Strominger

1976-01-01

85

Nano-Scale Alignment of Proteins on a Flexible DNA Backbone  

PubMed Central

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.

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

2012-01-01

86

Protein backbone and sidechain torsion angles predicted from NMR chemical shifts using artificial neural networks.  

PubMed

A new program, TALOS-N, is introduced for predicting protein backbone torsion angles from NMR chemical shifts. The program relies far more extensively on the use of trained artificial neural networks than its predecessor, TALOS+. Validation on an independent set of proteins indicates that backbone torsion angles can be predicted for a larger, ?90 % fraction of the residues, with an error rate smaller than ca 3.5 %, using an acceptance criterion that is nearly two-fold tighter than that used previously, and a root mean square difference between predicted and crystallographically observed (?, ?) torsion angles of ca 12º. TALOS-N also reports sidechain ?(1) rotameric states for about 50 % of the residues, and a consistency with reference structures of 89 %. The program includes a neural network trained to identify secondary structure from residue sequence and chemical shifts. PMID:23728592

Shen, Yang; Bax, Ad

2013-07-01

87

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

NASA Astrophysics Data System (ADS)

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.

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

1998-12-01

88

Graphical Representation of the Digital Astronaut Physiology Backbone.  

National Technical Information Service (NTIS)

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 oper...

D. Briers

2010-01-01

89

End-to-End Performance of Simplified ADF Backbone Infrastructure.  

National Technical Information Service (NTIS)

Main objective of this report is to develop models for the current ADF backbone infrastructure, to improve understanding of ADF network functionality as well as the capability of available network analysis tools. Preliminary results show that the smaller ...

J. Choi E. Sydow C. Fuchs

1998-01-01

90

Exploiting Backbone Routing Redundancy in Industrial Wireless Systems  

Microsoft Academic Search

Industrial wireless applications must interoperate with backbone infrastructure for operation and monitoring by control systems. Most of these systems are designed with multiple backbone routers (BbRs) to enhance reliability. Multiple BbRs have a significant impact on wireless systems as the redundancy of multiple BbRs offers a number of benefits, such as spatial diversity and load balancing. Here, we investigate the

Yosuke Ishii

2009-01-01

91

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

Microsoft Academic Search

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

M. Yamamoto; Y. Watanabe

2005-01-01

92

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

PubMed Central

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.

2013-01-01

93

Polyarylether composition and membrane  

DOEpatents

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.

Hung, Joyce (Auburn, AL); Brunelle, Daniel Joseph (Burnt Hills, NY); Harmon, Marianne Elisabeth (Redondo Beach, CA); Moore, David Roger (Albany, NY); Stone, Joshua James (Worcester, NY); Zhou, Hongyi (Niskayuna, NY); Suriano, Joseph Anthony (Clifton Park, NY)

2010-11-09

94

Backbone structure of a small helical integral membrane protein: A unique structural characterization.  

PubMed

The structural characterization of small integral membrane proteins pose a significant challenge for structural biology because of the multitude of molecular interactions between the protein and its heterogeneous environment. Here, the three-dimensional backbone structure of Rv1761c from Mycobacterium tuberculosis has been characterized using solution NMR spectroscopy and dodecylphosphocholine (DPC) micelles as a membrane mimetic environment. This 127 residue single transmembrane helix protein has a significant (10 kDa) C-terminal extramembranous domain. Five hundred and ninety distance, backbone dihedral, and orientational restraints were employed resulting in a 1.16 A rmsd backbone structure with a transmembrane domain defined at 0.40 A. The structure determination approach utilized residual dipolar coupling orientation data from partially aligned samples, long-range paramagnetic relaxation enhancement derived distances, and dihedral restraints from chemical shift indices to determine the global fold. This structural model of Rv1761c displays some influences by the membrane mimetic illustrating that the structure of these membrane proteins is dictated by a combination of the amino acid sequence and the protein's environment. These results demonstrate both the efficacy of the structural approach and the necessity to consider the biophysical properties of membrane mimetics when interpreting structural data of integral membrane proteins and, in particular, small integral membrane proteins. PMID:19177358

Page, Richard C; Lee, Sangwon; Moore, Jacob D; Opella, Stanley J; Cross, Timothy A

2009-01-01

95

Using Chou's pseudo amino acid composition to predict protein quaternary structure: a sequence-segmented PseAAC approach.  

PubMed

In the protein universe, many proteins are composed of two or more polypeptide chains, generally referred to as subunits, which associate through noncovalent interactions and, occasionally, disulfide bonds to form protein quaternary structures. It has long been known that the functions of proteins are closely related to their quaternary structures; some examples include enzymes, hemoglobin, DNA polymerase, and ion channels. However, it is extremely labor-expensive and even impossible to quickly determine the structures of hundreds of thousands of protein sequences solely from experiments. Since the number of protein sequences entering databanks is increasing rapidly, it is highly desirable to develop computational methods for classifying the quaternary structures of proteins from their primary sequences. Since the concept of Chou's pseudo amino acid composition (PseAAC) was introduced, a variety of approaches, such as residue conservation scores, von Neumann entropy, multiscale energy, autocorrelation function, moment descriptors, and cellular automata, have been utilized to formulate the PseAAC for predicting different attributes of proteins. Here, in a different approach, a sequence-segmented PseAAC is introduced to represent protein samples. Meanwhile, multiclass SVM classifier modules were adopted to classify protein quaternary structures. As a demonstration, the dataset constructed by Chou and Cai [(2003) Proteins 53:282-289] was adopted as a benchmark dataset. The overall jackknife success rates thus obtained were 88.2-89.1%, indicating that the new approach is quite promising for predicting protein quaternary structure. PMID:18427713

Zhang, Shao-Wu; Chen, Wei; Yang, Feng; Pan, Quan

2008-10-01

96

Utilizing sequence intrinsic composition to classify protein-coding and long non-coding transcripts  

PubMed Central

It is a challenge to classify protein-coding or non-coding transcripts, especially those re-constructed from high-throughput sequencing data of poorly annotated species. This study developed and evaluated a powerful signature tool, Coding-Non-Coding Index (CNCI), by profiling adjoining nucleotide triplets to effectively distinguish protein-coding and non-coding sequences independent of known annotations. CNCI is effective for classifying incomplete transcripts and sense–antisense pairs. The implementation of CNCI offered highly accurate classification of transcripts assembled from whole-transcriptome sequencing data in a cross-species manner, that demonstrated gene evolutionary divergence between vertebrates, and invertebrates, or between plants, and provided a long non-coding RNA catalog of orangutan. CNCI software is available at http://www.bioinfo.org/software/cnci.

Sun, Liang; Luo, Haitao; Bu, Dechao; Zhao, Guoguang; Yu, Kuntao; Zhang, Changhai; Liu, Yuanning; Chen, Runsheng; Zhao, Yi

2013-01-01

97

Three-Dimensional Solutions for Contact Area in Laminated Composite Pinned Joints with Symmetric and Non-Symmetric Stacking Sequences  

NASA Astrophysics Data System (ADS)

The aim of this study is computing and evaluating the behavior of the laminated composite plate at the contact area in single lap, mechanically fastened joints. The analyses involve three dimensional finite element models performed by ABAQUS 6.4-PR11 code to evaluate the stress distribution in contact surface, separation angle, the magnitude and location of maximum radial stress. Results are determined for composite laminates with different layer configurations and attempts are made to validate the models with previous works. For cross ply and angle ply configurations only symmetric stacking sequences are used while for quasi-isotropic laminate both symmetric and non-symmetric models are generated. In cross-ply laminate symmetric separation about bearing plane could be found while in quasi-isotropic and angle-ply laminates non-symmetric separation occurs. Also, the separation angle is less than 90° in symmetric laminates and greater than 90° in some plies of non-symmetric laminates.

Javadi, H.; Rajabi, I.; Yavari, V.; Kadivar, M. H.

98

Peptide amphiphile nanofibers with conjugated polydiacetylene backbones in their core.  

PubMed

The coupling of electronic and biological functionality through self-assembly is an interesting target in supramolecular chemistry. We report here on a set of diacetylene-derivatized peptide amphiphiles (PAs) that react to form conjugated polydiacetylene backbones following self-assembly into cylindrical nanofibers. The polymerization reaction yields highly conjugated backbones when the peptidic segment of the PAs has a linear, as opposed to a branched, architecture. Given the topotactic nature of the polymerization, these results suggest that a high degree of internal order exists in the supramolecular nanofibers formed by the linear PA. On the basis of microscopy, the formation of a polydiacetylene backbone to covalently connect the beta-sheets that help form the fibers does not disrupt the fiber shape. Interestingly, we observe the appearance of a polydiacetylene (PDA) circular dichroism band at 547 nm in linear PA nanofibers suggesting the conjugated backbone in the core of the nanostructures is twisted. We believe this CD signal is due to chiral induction by the beta-sheets, which are normally twisted in helical fashion. Heating and cooling shows simultaneous changes in beta-sheet and conjugated backbone structure, indicating they are both correlated. At the same time, poor polymerization in nanofibers formed by branched PAs indicates that less internal order exists in these nanostructures and, as expected, then a circular dichroism signal is not observed for the conjugated backbone. The general variety of materials investigated here has the obvious potential to couple electronic properties and in vitro bioactivity. Furthermore, the polymerization of monomers in peptide amphiphile assemblies by a rigid conjugated backbone also leads to mechanical robustness and insolubility, two properties that may be important for the patterning of these materials at the cellular scale. PMID:18314978

Hsu, Lorraine; Cvetanovich, Gregory L; Stupp, Samuel I

2008-03-26

99

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

PubMed Central

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.

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

2010-01-01

100

Correlations of nucleotide substitution rates and base composition of mammalian coding sequences with protein structure  

Microsoft Academic Search

We investigated the relationships between the nucleotide substitution rates and the predicted secondary structures in the three states representation (?-helix, ?-sheet, and coil). The analysis was carried out on 34 alignments, each of which comprised sequences belonging to at least four different mammalian orders. The rates of synonymous substitution were found to be significantly different in regions predicted to be

Maria Luisa Chiusano; Giuseppe D'Onofrio; Fernando Alvarez-Valin; Kamel Jabbari; Giovanni Colonna; Giorgio Bernardi

1999-01-01

101

Stacking sequence design of composite laminates for maximum strength using genetic algorithms  

Microsoft Academic Search

This paper uses genetic algorithms (GAs) for the optimal design of symmetric composite laminates subject to various loading and boundary conditions. To analyze these laminates, the finite element method based on shear deformation theory is used. The Tsai–Hill failure criterion is taken as the fitness function, and the ply orientation angles are the design variables. In the GA, tournament selection

J. H. Park; J. H. Hwang; C. S. Lee; W. Hwang

2001-01-01

102

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

PubMed

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., (2,4)AR, (2,4)AR-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 + (0,2)X0-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. PMID:24664808

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

2014-06-01

103

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

NASA Astrophysics Data System (ADS)

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.

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

2014-03-01

104

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

NASA Astrophysics Data System (ADS)

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.

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

2014-06-01

105

Structural dependencies of protein backbone 2JNC? couplings  

PubMed Central

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

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

2008-01-01

106

A Consistent Phylogenetic Backbone for the Fungi  

PubMed Central

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.

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

2012-01-01

107

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

PubMed

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

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

2013-11-01

108

LARC-IA: A flexible backbone polyimide  

NASA Technical Reports Server (NTRS)

A new linear, aromatic, thermoplastic polyimide, prepared from oxydiphthalic anhydride (ODPA) and 3,4'-oxydianiline (ODA) in diglyme and identified as LARC-IA, was synthesized and evaluated. The monomers are relatively inexpensive and physiologically safe. Molecular weight was controlled by use of a monofunctional anhydride, phthalic anhydride (PA), in order to promote controlled flow and wetting properties. The polymer is considered a safe alternative to commercially available LARC-TPI which is prepared with an expensive diamine of uncertain carcinogenicity. The evaluation was based primarily on the polymer's adhesive properties as determined by thermal and water boil exposure of lap shear specimens. Strengths were determined at room temperature, 177, 204 and 232 C before and after exposure to determine the adhesive system's durability to adverse environments over a period of time. Other properties (FWT, G(1c), film and composite properties) were examined which were determined to be typical of a high temperature polyimide. Results of the study show a favorable comparison to LARC-TPI, a commercially available polyimide.

Progar, Donald J.; Stclair, Terry L.

1990-01-01

109

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

NASA Astrophysics Data System (ADS)

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.

Yamamoto, M.; Watanabe, Y.

2005-12-01

110

Profiling internet backbone traffic: behavior models and applications  

Microsoft Academic Search

Recent spates of cyber-attacks and frequent emergence of applications affecting Internet traffic dynamics have made it imperative to develop effective techniques that can extract, and make sense of, significant communication patterns from Internet traffic data for use in network operations and security management. In this paper, we present a general methodology for building comprehensive behavior profiles of Internet backbone traffic

Kuai Xu; Zhi-Li Zhang; Supratik Bhattacharyya

2005-01-01

111

Cooperative UAV-Based Communications Backbone for Sensor Networks  

Microsoft Academic Search

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

2001-01-01

112

Cooperative UAV-Based Communications Backbone for Sensor Networks  

SciTech Connect

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.

Roberts, R S

2001-10-07

113

Provisioning IP Backbone Networks to Support Latency Sensitive Traffic  

Microsoft Academic Search

To support latency sensitive traffic such as voice, network providers can either use service differentiation to prioritize such traffic or provision their network with enough bandwidth so that all traffic meets the most stringent delay requirements. In the context of wide- area Internet backbones, two factors make overprovisioning an attractive approach. First, the high link speeds and large volumes of

Chuck Fraleigh; Fouad A. Tobagi; Christophe Diot

2003-01-01

114

Backbone additivity in the transfer model of protein solvation  

PubMed Central

The transfer model implying additivity of the peptide backbone free energy of transfer is computationally tested. Molecular dynamics simulations are used to determine the extent of change in transfer free energy (?Gtr) with increase in chain length of oligoglycine with capped end groups. Solvation free energies of oligoglycine models of varying lengths in pure water and in the osmolyte solutions, 2M urea and 2M trimethylamine N-oxide (TMAO), were calculated from simulations of all atom models, and ?Gtr values for peptide backbone transfer from water to the osmolyte solutions were determined. The results show that the transfer free energies change linearly with increasing chain length, demonstrating the principle of additivity, and provide values in reasonable agreement with experiment. The peptide backbone transfer free energy contributions arise from van der Waals interactions in the case of transfer to urea, but from electrostatics on transfer to TMAO solution. The simulations used here allow for the calculation of the solvation and transfer free energy of longer oligoglycine models to be evaluated than is currently possible through experiment. The peptide backbone unit computed transfer free energy of ?54 cal/mol/M compares quite favorably with ?43 cal/mol/M determined experimentally.

Hu, Char Y; Kokubo, Hironori; Lynch, Gillian C; Bolen, D Wayne; Pettitt, B Montgomery

2010-01-01

115

Increasing protein production by directed vector backbone evolution  

PubMed Central

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.

2013-01-01

116

The Graphical Representation of the Digital Astronaut Physiology Backbone  

NASA Technical Reports Server (NTRS)

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.

Briers, Demarcus

2010-01-01

117

Backbone Additivity in the Transfer Model of Protein Solvation  

SciTech Connect

The transfer model implying additivity of the peptide backbone free energy of transfer is computationally tested. Molecular dynamics simulations are used to determine the extent of change in transfer free energy (?Gtr) with increase in chain length of oligoglycine with capped end groups. Solvation free energies of oligoglycine models of varying lengths in pure water and in the osmolyte solutions, 2M urea and 2M trimethylamine N-oxide (TMAO), were calculated from simulations of all atom models, and ?Gtr values for peptide backbone transfer from water to the osmolyte solutions were determined. The results show that the transfer free energies change linearly with increasing chain length, demonstrating the principle of additivity, and provide values in reasonable agreement with experiment. The peptide backbone transfer free energy contributions arise from van der Waals interactions in the case of transfer to urea, but from electrostatics on transfer to TMAO solution. The simulations used here allow for the calculation of the solvation and transfer free energy of longer oligoglycine models to be evaluated than is currently possible through experiment. The peptide backbone unit computed transfer free energy of –54 cal/mol/Mcompares quite favorably with –43 cal/mol/M determined experimentally.

Hu, Char Y.; Kokubo, Hironori; Lynch, Gillian C.; Bolen, D Wayne; Pettitt, Bernard M.

2010-05-01

118

High permeability backbones and their influence on flow and transport  

NASA Astrophysics Data System (ADS)

Spatial heterogeneity of permeability field affects flow and transport. As flow tends to avoid low permeable zones and concentrate in highly permeable ones, flux field becomes also heterogeneous. Looking at Darcy flow field one can observe existence of preferential flow paths along which main flow is focused, so-called 'channels', and sluggish zones, inside which flux is slow and contaminant particles are stuck. This phenomenon causes anomalous solute transport behavior that averages out during common up-scaling procedures. The main idea of this article is to divide the permeability field on two parts: connected high permeable backbone and low permeable inclusions and to explore how they influence on flow and transport. For this we developed an algorithm to delineate the backbone and vary its geometrical size keeping its fixed topological structure. The algorithm is based on two operations of mathematical morphology: erosion and dilation, but with a little adaptation for continuous fields. The backbone can be of different topology, geometry and channel thickness, it also can occupy different percentage of the domain. Permeability inside the backbone can also be very heterogeneous itself. Inclusions represent various distributions of sizes, orientations in respect to head gradient, and permeability. We investigate influence of these parameters on flow and transport behavior for highly heterogeneous (? = 2.5) static connected and disconnected fields. Numerical experiments showed that in most cases of highly connected fields this algorithm predicts flow concentration paths precisely. Effective permeability of the field is closely related to average permeability and spatial fraction of the backbone in the field. Similar behavior is observed for advective transport: as the first-arrival time is associated with the fastest path and the fastest path passes through the backbone, peak arrival time is determined by permeability of the backbone and its structure, but not by its thickness and spatial fraction. Low-permeable inclusions, in turn, cause tailing of the BTCs, and mainly the distribution of permeability inside low-permeable inclusions controls the BTC slope. The proposed approach can be used for first approximation of the BTCs behavior.

Tyukhova, A.; Willmann, M.; Dentz, M.; Kinzelbach, W.

2013-12-01

119

RNA backbone: Consensus all-angle conformers and modular string nomenclature (an RNA Ontology Consortium contribution)  

PubMed Central

A consensus classification and nomenclature are defined for RNA backbone structure using all of the backbone torsion angles. By a consensus of several independent analysis methods, 46 discrete conformers are identified as suitably clustered in a quality-filtered, multidimensional dihedral angle distribution. Most of these conformers represent identifiable features or roles within RNA structures. The conformers are given two-character names that reflect the seven-angle ??????? combinations empirically found favorable for the sugar-to-sugar “suite” unit within which the angle correlations are strongest (e.g., 1a for A-form, 5z for the start of S-motifs). Since the half-nucleotides are specified by a number for ??? and a lowercase letter for ????, this modular system can also be parsed to describe traditional nucleotide units (e.g., a1) or the dinucleotides (e.g., a1a1) that are especially useful at the level of crystallographic map fitting. This nomenclature can also be written as a string with two-character suite names between the uppercase letters of the base sequence (N1aG1gN1aR1aA1cN1a for a GNRA tetraloop), facilitating bioinformatic comparisons. Cluster means, standard deviations, coordinates, and examples are made available, as well as the Suitename software that assigns suite conformer names and conformer match quality (suiteness) from atomic coordinates. The RNA Ontology Consortium will combine this new backbone system with others that define base pairs, base-stacking, and hydrogen-bond relationships to provide a full description of RNA structural motifs.

Richardson, Jane S.; Schneider, Bohdan; Murray, Laura W.; Kapral, Gary J.; Immormino, Robert M.; Headd, Jeffrey J.; Richardson, David C.; Ham, Daniela; Hershkovits, Eli; Williams, Loren Dean; Keating, Kevin S.; Pyle, Anna Marie; Micallef, David; Westbrook, John; Berman, Helen M.

2008-01-01

120

Sequences of Mixed Ions in Polypeptoid Surfaces  

NASA Astrophysics Data System (ADS)

Polypeptoids, a unique, sequence specific class of polymers, are used to investigate the influence of charge spacing, grouping, and chemistry on the surface properties of polymer coatings. Short peptoid oligomers composed of cationic and anionic groups, and superhydrophobic (fluorinated) functionalities were attached to a synthetic backbone to form comb-shaped molecules. These molecules display different surface chemistry as a function of side chain composition, as indicated by near edge X-ray absorption fine structure spectroscopy (NEXAFS). A 50:50 ratio of peptoid:fluorinated functionality resulted in optimal surface segregation of the comb block while preventing surface reconstruction upon immersing the polymer films in water. Antifouling experiments with the green algae Ulva showed that polymers with non-ionic peptoid functional groups resulted in superior antifouling coatings compared to polymers with charged peptoids. The effects of decreasing the peptoid charge spacing even further (zwitterionic side chains) and exploring stronger ionic moieties, such as phosphate groups, will also be discussed.

Buss, Hilda; van Zoelen, Wendy; Ellebracht, Nathan; Zuckermann, Ronald; Segalman, Rachel

2013-03-01

121

Novel variants of AbaR resistance islands with a common backbone in Acinetobacter baumannii isolates of European clone II.  

PubMed

In this study, the genetic organization of three novel genomic antibiotic resistance islands (AbaRs) in Acinetobacter baumannii isolates belonging to group of European clone II (EC II) comM integrated sequences of 18-, 21-, and 23-kb resistance islands were determined. These resistance islands carry the backbone of AbaR-type transposon structures, which are composed of the transposition module coding for potential transposition proteins and other genes coding for the intact universal stress protein (uspA), sulfate permease (sul), and proteins of unknown function. The antibiotic resistance genes strA, strB, tetB, and tetR and insertion sequence CR2 element were found to be inserted into the AbaR transposons. GenBank homology searches indicated that they are closely related to the AbaR sequences found integrated in comM in strains of EC II (A. baumannii strains 1656-2 and TCDC-AB0715) and AbaR4 integrated in another location of A. baumannii AB0057 (EC I). All of the AbaRs showed structural similarity to the previously described AbaR4 island and share a 12,008-bp backbone. AbaRs contain Tn1213, Tn2006, and the multiple fragments which could be derived from transposons Tn3, Tn10, Tn21, Tn1000, Tn5393, and Tn6020, the insertion sequences IS26, ISAba1, ISAba14, and ISCR2, and the class 1 integron. Moreover, chromosomal DNA was inserted into distinct regions of the AbaR backbone. Sequence analysis suggested that the AbaR-type transposons have evolved through insertions, deletions, and homologous recombination. AbaR islands, sharing the core structure similar to AbaR4, appeared to be distributed in isolates of EC I and EC II via integration into distinct genomic sites, i.e., pho and comM, respectively. PMID:22290980

Seputiene, Vaida; Povilonis, Justas; Suziedeliene, Edita

2012-04-01

122

Importance of backbone angles versus amino acid configurations in peptide vibrational Raman optical activity spectra  

NASA Astrophysics Data System (ADS)

In this work, we investigate whether the differential scattering of right- and left-circularly polarized light in peptide Raman optical activity spectra are uniquely dominated by the backbone conformation, or whether the configurations of the individual amino acid also play a significant role. This is achieved by calculating Raman optical activity spectra using density functional theory for four structurally related peptides with a common backbone conformation, but with different sequences of amino acid configurations. Furthermore, the ROA signals of the amide normal modes are decomposed into contributions from groups of individual atoms. It is found that the amino acid configuration has a considerable influence on the ROA peaks in the amide I, II, and III regions, although the local decomposition reveals that the side-chain atoms only contribute to those peaks directly in the case of the amide II vibrations. Furthermore, small changes in the amide normal modes may lead to large and irregular modifications in the ROA intensity differences, making it difficult to establish transferable ROA intensity differences even for structurally similar vibrations.

Herrmann, Carmen; Ruud, Kenneth; Reiher, Markus

2008-01-01

123

Photodegradation of human growth hormone: a novel backbone cleavage between Glu-88 and Pro-89.  

PubMed

The exposure of protein pharmaceuticals to light can cause loss of potency, oxidation, structural changes and aggregation. To elucidate the chemical pathways of photodegradation, we irradiated human growth hormone (hGH) at ? = 254 nm, ? ? 265-340 nm, and ? ? 295-340 nm (using the spectral cutoff of borosilicate glass) and analyzed the products by mass spectrometry. By means of LC-MS/MS analysis, we observed an unusual peptide backbone cleavage between Glu-88 and Pro-89. The crystal structure of hGH indicates that these residues are in proximity to Trp-86, which likely mediates this backbone cleavage. The two cleavage fragments observed by MS/MS analysis indicate the loss of CO from the amide bond and replacement of the Glu-C(? O)Pro bond with a Glu-H bond, accompanied by double bond formation on proline. The reaction is oxygen-independent and likely involves hydrogen transfer to the C? of Glu-88. To probe the influence of the protein fold, we irradiated hGH in its unfolded state, in 1:1 (v/v) acetonitrile/water, and also the isolated tryptic peptide Ile-78-Arg-90, which contains the Glu-88-Pro-89 sequence. In both cases, the cleavage between Glu-88 and Pro-89 was largely suppressed, while other cleavage pathways became dominant, notably between Gln-84 and Ser-85, as well as Ser-85 and Trp-86. PMID:23721578

Steinmann, Daniel; Ji, J Andrea; Wang, Y John; Schöneich, Christian

2013-07-01

124

A hydrogen-bonded electron-tunneling circuit reads base composition of unmodified DNA  

PubMed Central

Using a tunnel junction in which one electrode is guanidinium-functionalized (to trap DNA by hydrogen bonding to the backbone phosphates) and a second electrode which is functionalized with a base (to capture its complementary target on the DNA), current vs. distance curves yield an accurate measure of the base-composition of DNA oligomers. With this long tunneling path, resolution is limited to sequence blocks of about twenty bases or larger, because of the need to form a large-area tunnel junction. A shorter hydrogen-bonded path across bases will be required for DNA sequencing. Nonetheless, these measurements point the way to a new type of nanoscale sensor.

He, Jin; Lin, Lisha; Liu, Hao; Zhang, Peiming; Lee, Myeong; Sankey, O F; Lindsay, SM

2008-01-01

125

Modifications to the Peptidoglycan Backbone Help Bacteria To Establish Infection ?  

PubMed Central

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.

Davis, Kimberly M.; Weiser, Jeffrey N.

2011-01-01

126

Composites  

NSDL National Science Digital Library

In this activity, learners explore how composites work by creating and testing their own composite for an imaginary company. This activity shows learners that composites are simply materials that are made up of two or more visibly distinct substances. Use this activity to talk about how composites are everywhere in our lives.

Research, Cornell C.

2003-01-01

127

RDC derived protein backbone resonance assignment using fragment assembly  

Microsoft Academic Search

Experimental residual dipolar couplings (RDCs) in combination with structural models have the potential for accelerating the\\u000a protein backbone resonance assignment process because RDCs can be measured accurately and interpreted quantitatively. However,\\u000a this application has been limited due to the need for very high-resolution structural templates. Here, we introduce a new\\u000a approach to resonance assignment based on optimal agreement between the

Xingsheng Wang; Brian Tash; John M. Flanagan; Fang Tian

2011-01-01

128

Packet-level traffic measurements from the Sprint IP backbone  

Microsoft Academic Search

Network traffic measurements provide essential data for networking research and network management. In this article we describe a passive monitoring system designed to capture GPS synchronized packet-level traffic measurements on OC-3, OC-12, and OC-48 links. Our system is deployed in four POP in the Sprint IP backbone. Measurement data is stored on a 10 Tbyte storage area network and analyzed

Chuck Fraleigh; Sue Moon; Bryan Lyles; Chase Cotton; Mujahid Khan; Deb Moll; Rob Rockell; Ted Seely; S. C. Diot

2003-01-01

129

Extracting the globally and locally adaptive backbone of complex networks.  

PubMed

A complex network is a useful tool for representing and analyzing complex systems, such as the world-wide web and transportation systems. However, the growing size of complex networks is becoming an obstacle to the understanding of the topological structure and their characteristics. In this study, a globally and locally adaptive network backbone (GLANB) extraction method is proposed. The GLANB method uses the involvement of links in shortest paths and a statistical hypothesis to evaluate the statistical importance of the links; then it extracts the backbone, based on the statistical importance, from the network by filtering the less important links and preserving the more important links; the result is an extracted subnetwork with fewer links and nodes. The GLANB determines the importance of the links by synthetically considering the topological structure, the weights of the links and the degrees of the nodes. The links that have a small weight but are important from the view of topological structure are not belittled. The GLANB method can be applied to all types of networks regardless of whether they are weighted or unweighted and regardless of whether they are directed or undirected. The experiments on four real networks show that the link importance distribution given by the GLANB method has a bimodal shape, which gives a robust classification of the links; moreover, the GLANB method tends to put the nodes that are identified as the core of the network by the k-shell algorithm into the backbone. This method can help us to understand the structure of the networks better, to determine what links are important for transferring information, and to express the network by a backbone easily. PMID:24936975

Zhang, Xiaohang; Zhang, Zecong; Zhao, Han; Wang, Qi; Zhu, Ji

2014-01-01

130

Autonomous reconfiguration of backbones in free space optical networks  

Microsoft Academic Search

This research focuses on algorithms for autonomous reconfiguration of backbone networks utilizing the free space optical (FSO) technology. Such networks consist of high data rate and narrow beam FSO links between fixed and\\/or mobile nodes. The main challenge is to maintain the required quality and connectivity of such networks amidst changing atmospheric (obscuration\\/loss of sight\\/scintillation etc), platform (mobility\\/jitter) and traffic

Aniket Desai; Jaime Llorca; Stuart Milner

2004-01-01

131

Extracting the Globally and Locally Adaptive Backbone of Complex Networks  

PubMed Central

A complex network is a useful tool for representing and analyzing complex systems, such as the world-wide web and transportation systems. However, the growing size of complex networks is becoming an obstacle to the understanding of the topological structure and their characteristics. In this study, a globally and locally adaptive network backbone (GLANB) extraction method is proposed. The GLANB method uses the involvement of links in shortest paths and a statistical hypothesis to evaluate the statistical importance of the links; then it extracts the backbone, based on the statistical importance, from the network by filtering the less important links and preserving the more important links; the result is an extracted subnetwork with fewer links and nodes. The GLANB determines the importance of the links by synthetically considering the topological structure, the weights of the links and the degrees of the nodes. The links that have a small weight but are important from the view of topological structure are not belittled. The GLANB method can be applied to all types of networks regardless of whether they are weighted or unweighted and regardless of whether they are directed or undirected. The experiments on four real networks show that the link importance distribution given by the GLANB method has a bimodal shape, which gives a robust classification of the links; moreover, the GLANB method tends to put the nodes that are identified as the core of the network by the k-shell algorithm into the backbone. This method can help us to understand the structure of the networks better, to determine what links are important for transferring information, and to express the network by a backbone easily.

Zhang, Xiaohang; Zhang, Zecong; Zhao, Han; Wang, Qi; Zhu, Ji

2014-01-01

132

Predicting Secretory Proteins of Malaria Parasite by Incorporating Sequence Evolution Information into Pseudo Amino Acid Composition via Grey System Model  

PubMed Central

The malaria disease has become a cause of poverty and a major hindrance to economic development. The culprit of the disease is the parasite, which secretes an array of proteins within the host erythrocyte to facilitate its own survival. Accordingly, the secretory proteins of malaria parasite have become a logical target for drug design against malaria. Unfortunately, with the increasing resistance to the drugs thus developed, the situation has become more complicated. To cope with the drug resistance problem, one strategy is to timely identify the secreted proteins by malaria parasite, which can serve as potential drug targets. However, it is both expensive and time-consuming to identify the secretory proteins of malaria parasite by experiments alone. To expedite the process for developing effective drugs against malaria, a computational predictor called “iSMP-Grey” was developed that can be used to identify the secretory proteins of malaria parasite based on the protein sequence information alone. During the prediction process a protein sample was formulated with a 60D (dimensional) feature vector formed by incorporating the sequence evolution information into the general form of PseAAC (pseudo amino acid composition) via a grey system model, which is particularly useful for solving complicated problems that are lack of sufficient information or need to process uncertain information. It was observed by the jackknife test that iSMP-Grey achieved an overall success rate of 94.8%, remarkably higher than those by the existing predictors in this area. As a user-friendly web-server, iSMP-Grey is freely accessible to the public at http://www.jci-bioinfo.cn/iSMP-Grey. Moreover, for the convenience of most experimental scientists, a step-by-step guide is provided on how to use the web-server to get the desired results without the need to follow the complicated mathematical equations involved in this paper.

Lin, Wei-Zhong; Fang, Jian-An; Xiao, Xuan; Chou, Kuo-Chen

2012-01-01

133

PS1-10jh: The Disruption of a Main-sequence Star of Near-solar Composition  

NASA Astrophysics Data System (ADS)

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.

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

2014-03-01

134

Hydrophobic core packing and backbone flexibility in coiled coils  

NASA Astrophysics Data System (ADS)

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.

Plecs, Joseph John

1999-11-01

135

Extracting the multiscale backbone of complex weighted networks.  

PubMed

A large number of complex systems find a natural abstraction in the form of weighted networks whose nodes represent the elements of the system and the weighted edges identify the presence of an interaction and its relative strength. In recent years, the study of an increasing number of large-scale networks has highlighted the statistical heterogeneity of their interaction pattern, with degree and weight distributions that vary over many orders of magnitude. These features, along with the large number of elements and links, make the extraction of the truly relevant connections forming the network's backbone a very challenging problem. More specifically, coarse-graining approaches and filtering techniques come into conflict with the multiscale nature of large-scale systems. Here, we define a filtering method that offers a practical procedure to extract the relevant connection backbone in complex multiscale networks, preserving the edges that represent statistically significant deviations with respect to a null model for the local assignment of weights to edges. An important aspect of the method is that it does not belittle small-scale interactions and operates at all scales defined by the weight distribution. We apply our method to real-world network instances and compare the obtained results with alternative backbone extraction techniques. PMID:19357301

Serrano, M Angeles; Boguñá, Marián; Vespignani, Alessandro

2009-04-21

136

Extracting the multiscale backbone of complex weighted networks  

PubMed Central

A large number of complex systems find a natural abstraction in the form of weighted networks whose nodes represent the elements of the system and the weighted edges identify the presence of an interaction and its relative strength. In recent years, the study of an increasing number of large-scale networks has highlighted the statistical heterogeneity of their interaction pattern, with degree and weight distributions that vary over many orders of magnitude. These features, along with the large number of elements and links, make the extraction of the truly relevant connections forming the network's backbone a very challenging problem. More specifically, coarse-graining approaches and filtering techniques come into conflict with the multiscale nature of large-scale systems. Here, we define a filtering method that offers a practical procedure to extract the relevant connection backbone in complex multiscale networks, preserving the edges that represent statistically significant deviations with respect to a null model for the local assignment of weights to edges. An important aspect of the method is that it does not belittle small-scale interactions and operates at all scales defined by the weight distribution. We apply our method to real-world network instances and compare the obtained results with alternative backbone extraction techniques.

Serrano, M. Angeles; Boguna, Marian; Vespignani, Alessandro

2009-01-01

137

Rollout Algorithms for Integrated Topology Control and Routing in Wireless Optical Backbone Networks.  

National Technical Information Service (NTIS)

The authors consider a wireless backbone network with free space optical point-to-point links. Such a network could form a backbone for either a cellular or hierarchical ad hoc network. Each backbone node has a limited number of transceivers with which to...

A. Kashyap K. Lee M. Shayman

2003-01-01

138

Propensities for loop structures of RNA & DNA backbones.  

PubMed

RNA oligonucleotides exhibit a large tendency to bend and form a loop conformation which is a major motif contributing to their complex three-dimensional structure. This is in contrast to DNA molecules that predominantly form the double-helix structure. In this paper we investigate by molecular dynamics simulation, as well as, by its combination with the replica-exchange method, the propensity of RNA chains containing the GCUAA pentaloop to form spontaneously a hairpin conformation. The results were then compared with those of analogous hybrid oligonucleotides in which the ribose groups in the loop-region were substituted by deoxyriboses. We find that the RNA oligomers exhibit a marginal excess stability to form loop structures. The equilibrium constant for opening the loop to an extended conformation is twice as large in the hybrid than it is in the RNA chain. Analyses of the hydrogen bonds indicate that the excess stability for forming a hairpin is a result of hydrogen bonds the 2'-hydroxyls in the loop region form with other groups in the loop. Of these hydrogen bonds, the most important is the hydrogen bond donated from the 2'-OH at the first position of the loop to N7 of adenine at the forth position. RNA and DNA backbones are characterized by different backbone dihedral angles and sugar puckering that can potentially facilitate or hamper the hydrogen bonds involving the 2'-OH. Nevertheless, the sugar puckerings of all the pentaloop nucleotides were not significantly different between the two chains displaying the C3'-endo conformation characteristic to the A-form double helix. All of the other backbone dihedrals also did not show any considerable difference in the loop-region except of the ?-dihedral. In this case, the RNA loop exhibited bimodal distributions corresponding to, both, the RNA and DNA backbones, whereas the loop of the hybrid chain behaved mostly as that of a DNA backbone. Thus, it is possible that the behavior of the ?-dihedrals in the loop-region of the RNA adopts conformations that facilitate the intra-nucleotide hydrogen bondings of the 2'-hydroxyls, and consequently renders loop structures in RNA more stable. PMID:23933331

Paladino, Antonella; Zangi, Ronen

2013-01-01

139

Mapping backbone dynamics in solution with site-directed spin labeling: GCN4-58 bZip free and bound to DNA.  

PubMed

In site-directed spin labeling, a nitroxide-containing side chain is introduced at selected sites in a protein. The EPR spectrum of the labeled protein encodes information about the motion of the nitroxide on the nanosecond time scale, which has contributions from the rotary diffusion of the protein, from internal motions in the side chain, and from backbone fluctuations. In the simplest model for the motion of noninteracting (surface) side chains, the contribution from the internal motion is sequence independent, as is that from protein rotary diffusion. Hence, differences in backbone motions should be revealed by comparing the sequence-dependent motions of nitroxides at structurally homologous sites. To examine this model, nitroxide side chains were introduced, one at a time, along the GCN4-58 bZip sequence, for which NMR (15)N relaxation experiments have identified a striking gradient of backbone mobility along the DNA-binding region [Bracken et al. (1999) J. Mol. Biol. 285, 2133]. Spectral simulation techniques and a simple line width measure were used to extract dynamical parameters from the EPR spectra, and the results reveal a mobility gradient similar to that observed in NMR relaxation, indicating that side chain motions mirror backbone motions. In addition, the sequence-dependent side chain dynamics were analyzed in the DNA/protein complex, which has not been previously investigated by NMR relaxation methods. As anticipated, the backbone motions are damped in the DNA-bound state, although a gradient of motion persists with residues at the DNA-binding site being the most highly ordered, similar to those of helices on globular proteins. PMID:15182173

Columbus, Linda; Hubbell, Wayne L

2004-06-15

140

Isolation, sequencing, and structure-activity relationships of cyclotides.  

PubMed

Cyclotides are a topologically fascinating family of miniproteins discovered over the past decade that have expanded the diversity of plant-derived natural products. They are approximately 30 amino acids in size and occur in plants of the Violaceae, Rubiaceae, and Cucurbitaceae families. Despite their proteinaceous composition, cyclotides behave in much the same way as many nonpeptidic natural products in that they are resistant to degradation by enzymes or heat and can be extracted from plants using methanol. Their stability arises, in large part, due to their characteristic cyclic cystine knot (CCK) structural motif. Cystine knots are present in a variety of proteins of insect, plant, and animal origin, comprising a ring formed by two disulfide bonds and their connecting backbone segments that is threaded by a third disulfide bond. In cyclotides, the cystine knot is uniquely embedded within a head-to-tail cyclized peptide backbone, leading to the ultrastable CCK structural motif. Apart from the six absolutely conserved cysteine residues, the majority of amino acids in the six backbone loops of cyclotides are tolerant to variation. It has been predicted that the family might include up to 50,000 members; although, so far, sequences for only 140 have been reported. Cyclotides exhibit a variety of biological activities, including insecticidal, nematocidal, molluscicidal, antimicrobial, antibarnacle, anti-HIV, and antitumor activities. Due to their diverse activities and common structural core from which variable loops protrude, cyclotides can be thought of as combinatorial peptide templates capable of displaying a variety of amino acid sequences. They have thus attracted interest in drug design as well as in crop protection applications. PMID:20718473

Ireland, David C; Clark, Richard J; Daly, Norelle L; Craik, David J

2010-09-24

141

Ultradeep 16S rRNA Sequencing Analysis of Geographically Similar but Diverse Unexplored Marine Samples Reveal Varied Bacterial Community Composition  

PubMed Central

Background Bacterial community composition in the marine environment differs from one geographical location to another. Reports that delineate the bacterial diversity of different marine samples from geographically similar location are limited. The present study aims to understand whether the bacterial community compositions from different marine samples harbour similar bacterial diversity since these are geographically related to each other. Methods and Principal Findings In the present study, 16S rRNA deep sequencing analysis targeting V3 region was performed using Illumina bar coded sequencing. A total of 22.44 million paired end reads were obtained from the metagenomic DNA of Marine sediment, Rhizosphere sediment, Seawater and the epibacterial DNA of Seaweed and Seagrass. Diversity index analysis revealed that Marine sediment has the highest bacterial diversity and the least bacterial diversity was observed in Rhizosphere sediment. Proteobacteria, Actinobacteria and Bacteroidetes were the dominant taxa present in all the marine samples. Nearly 62–71% of rare species were identified in all the samples and most of these rare species were unique to a particular sample. Further taxonomic assignment at the phylum and genus level revealed that the bacterial community compositions differ among the samples. Conclusion This is the first report that supports the fact that, bacterial community composition is specific for specific samples irrespective of its similar geographical location. Existence of specific bacterial community for each sample may drive overall difference in bacterial structural composition of each sample. Further studies like whole metagenomic sequencing will throw more insights to the key stone players and its interconnecting metabolic pathways. In addition, this is one of the very few reports that depicts the unexplored bacterial diversity of marine samples (Marine sediment, Rhizosphere sediment, Seawater) and the host associated marine samples (Seaweed and Seagrass) at higher depths from uncharacterised coastal region of Palk Bay, India using next generation sequencing technology.

Karutha Pandian, Shunmugiah

2013-01-01

142

Sequencing-Based Analysis of the Bacterial and Fungal Composition of Kefir Grains and Milks from Multiple Sources  

PubMed Central

Kefir is a fermented milk-based beverage to which a number of health-promoting properties have been attributed. The microbes responsible for the fermentation of milk to produce kefir consist of a complex association of bacteria and yeasts, bound within a polysaccharide matrix, known as the kefir grain. The consistency of this microbial population, and that present in the resultant beverage, has been the subject of a number of previous, almost exclusively culture-based, studies which have indicated differences depending on geographical location and culture conditions. However, culture-based identification studies are limited by virtue of only detecting species with the ability to grow on the specific medium used and thus culture-independent, molecular-based techniques offer the potential for a more comprehensive analysis of such communities. Here we describe a detailed investigation of the microbial population, both bacterial and fungal, of kefir, using high-throughput sequencing to analyse 25 kefir milks and associated grains sourced from 8 geographically distinct regions. This is the first occasion that this technology has been employed to investigate the fungal component of these populations or to reveal the microbial composition of such an extensive number of kefir grains or milks. As a result several genera and species not previously identified in kefir were revealed. Our analysis shows that the bacterial populations in kefir are dominated by 2 phyla, the Firmicutes and the Proteobacteria. It was also established that the fungal populations of kefir were dominated by the genera Kazachstania, Kluyveromyces and Naumovozyma, but that a variable sub-dominant population also exists.

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

2013-01-01

143

Sequencing-based analysis of the bacterial and fungal composition of kefir grains and milks from multiple sources.  

PubMed

Kefir is a fermented milk-based beverage to which a number of health-promoting properties have been attributed. The microbes responsible for the fermentation of milk to produce kefir consist of a complex association of bacteria and yeasts, bound within a polysaccharide matrix, known as the kefir grain. The consistency of this microbial population, and that present in the resultant beverage, has been the subject of a number of previous, almost exclusively culture-based, studies which have indicated differences depending on geographical location and culture conditions. However, culture-based identification studies are limited by virtue of only detecting species with the ability to grow on the specific medium used and thus culture-independent, molecular-based techniques offer the potential for a more comprehensive analysis of such communities. Here we describe a detailed investigation of the microbial population, both bacterial and fungal, of kefir, using high-throughput sequencing to analyse 25 kefir milks and associated grains sourced from 8 geographically distinct regions. This is the first occasion that this technology has been employed to investigate the fungal component of these populations or to reveal the microbial composition of such an extensive number of kefir grains or milks. As a result several genera and species not previously identified in kefir were revealed. Our analysis shows that the bacterial populations in kefir are dominated by 2 phyla, the Firmicutes and the Proteobacteria. It was also established that the fungal populations of kefir were dominated by the genera Kazachstania, Kluyveromyces and Naumovozyma, but that a variable sub-dominant population also exists. PMID:23894461

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

2013-01-01

144

PS1-10jh: The Partial Disruption of a Main-Sequence Star of Near-Solar Composition  

NASA Astrophysics Data System (ADS)

When a star comes within a critical distance to a supermassive black hole, immense tidal forces can remove a significant fraction of the star's mass, resulting in a stream of debris that falls back onto the black hole and powers a luminous flare. I will be describing the results of hydrodynamical simulations to demonstrate that self-gravity, while unimportant along the direction parallel to the debris, provides significantly confinement across the debris. As a consequence, the stream has a negligible surface area and makes almost no contribution to either the continuum or line emission. We additionally find that the debris stream is strongly compressed and virialized when it returns to pericenter, resulting in a teardrop-shaped structure with a temperature profile similar to that of a Shakura-Sunyaev accretion disk, which grows at a speed somewhat less than the star's original speed at pericenter. We propose that any observed emission lines are not the result of collisional excitation, but are produced similarly to the broad-line regions commonly observed in active galactic nuclei. As each line within a broad-line region is kinematically 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 HeII lines are observed, but H? is not. We show that a partial disruption of a main-sequence star of near-solar composition can reproduce this event.

Guillochon, James; Ramirez-Ruiz, E.

2013-04-01

145

Influence of stacking sequence on scattering characteristics of the fundamental anti-symmetric Lamb wave at through holes in composite laminates.  

PubMed

This paper investigates the scattering characteristics of the fundamental anti-symmetric (A(0)) Lamb wave at through holes in composite laminates. Three-dimensional (3D) finite element (FE) simulations and experimental measurements are used to study the physical phenomenon. Unidirectional, bidirectional, and quasi-isotropic composite laminates are considered in the study. The influence of different hole diameter to wavelength aspect ratios and different stacking sequences on wave scattering characteristics are investigated. The results show that amplitudes and directivity distribution of the scattered Lamb wave depend on these parameters. In the case of quasi-isotropic composite laminates, the scattering directivity patterns are dominated by the fiber orientation of the outer layers and are quite different for composite laminates with the same number of laminae but different stacking sequence. The study provides improved physical insight into the scattering phenomena at through holes in composite laminates, which is essential to develop, validate, and optimize guided wave damage detection and characterization techniques. PMID:21428491

Veidt, Martin; Ng, Ching-Tai

2011-03-01

146

?-Conjugated trinuclear group-9 metalladithiolenes with a triphenylene backbone.  

PubMed

Previously, we synthesized ?-conjugated trinuclear metalladithiolene complexes based on benzenehexathiol (J. Chem. Soc., Dalton Trans.1998, 2651; Dalton Trans.2009, 1939; Inorg. Chem.2011, 50, 6856). Here we report trinuclear complexes with a triphenylene backbone. A reaction with triphenylenehexathiol and group 9 metal precursors in the presence of triethylamine gives rise to trinuclear complexes 9-11. The planar structure of 11 is determined using single crystal X-ray diffraction analysis. The ligand-to-metal charge transfer bands of 9-11 move to longer wavelengths compared with those of mononuclear 12-14. Electrochemical measurements disclose that the one-electron and two-electron reduced mixed-valent states are stabilized thermodynamically. UV-vis-NIR spectroscopy for the reduced species of 9 identifies intervalence charge transfer bands for 9(-) and 9(2-), substantiating the existence of electronic communication among the three metal nuclei. These observations prove that the triphenylene backbone transmits ?-conjugation among the three metalladithiolene units. PMID:23758171

Sakamoto, Ryota; Kambe, Tetsuya; Tsukada, Satoru; Takada, Kenji; Hoshiko, Ken; Kitagawa, Yasutaka; Okumura, Mitsutaka; Nishihara, Hiroshi

2013-07-01

147

Strong liquid-crystalline polymeric compositions  

DOEpatents

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.

Dowell, F.

1993-12-07

148

Strong liquid-crystalline polymeric compositions  

DOEpatents

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.

Dowell, Flonnie (Los Alamos, NM)

1993-01-01

149

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

PubMed Central

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.

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

1999-01-01

150

Combinatorial triple-selective labeling as a tool to assist membrane protein backbone resonance assignment  

PubMed Central

Obtaining NMR assignments for slowly tumbling molecules such as detergent-solubilized membrane proteins is often compromised by low sensitivity as well as spectral overlap. Both problems can be addressed by amino-acid specific isotope labeling in conjunction with 15N–1H correlation experiments. In this work an extended combinatorial selective in vitro labeling scheme is proposed that seeks to reduce the number of samples required for assignment. Including three different species of amino acids in each sample, 15N, 1- 13C, and fully 13C/15 N labeled, permits identification of more amino acid types and sequential pairs than would be possible with previously published combinatorial methods. The new protocol involves recording of up to five 2D triple-resonance experiments to distinguish the various isotopomeric dipeptide species. The pattern of backbone NH cross peaks in this series of spectra adds a new dimension to the combinatorial grid, which otherwise mostly relies on comparison of [15N, 1H]–HSQC and possibly 2D HN(CO) spectra of samples with different labeled amino acid compositions. Application to two ?-helical membrane proteins shows that using no more than three samples information can be accumulated such that backbone assignments can be completed solely based on 3D HNCA/ HN(CO)CA experiments. Alternatively, in the case of severe signal overlap in certain regions of the standard suite of triple-resonance spectra acquired on uniformly labeled protein, or missing signals due to a lack of efficiency of 3D experiments, the remaining gaps can be filled.

Lohr, Frank; Reckel, Sina; Karbyshev, Mikhail; Connolly, Peter J.; Abdul-Manan, Norzehan; Bernhard, Frank; Moore, Jonathan M.

2013-01-01

151

Local restoration for bandwidth guaranteed connections in mobile optical backbone networks  

Microsoft Academic Search

We consider a mobile backbone network with free space optical point-to-point links. Each backbone node moves randomly but with low mobility, and future movement is not predictable. Requests for aggregate bandwidth between pairs of backbone nodes arrive one-by-one, and a bandwidth guaranteed connection is established if there are sufficient network resources (link bandwidth and node transceivers); otherwise, the request is

Fangting Sun; Mark Shayman

2005-01-01

152

Probing backbone dynamics with hydrogen/deuterium exchange mass spectrometry.  

PubMed

Protein dynamics can be probed by the solution technique amide hydrogen/deuterium exchange. The exchange rate of hydrogen for deuterium along a peptide backbone is dependent on the extent of hydrogen bonding from secondary structure, accessibility by D2O, and protein motions. Both global and local conformational changes that alter bonding or structure will lead to changes in the amount of deuterium incorporated. The deuterium can be localized via pepsin digestion of the protein and quantified by electrospray ionization mass spectrometry through the mass shifts of the resulting peptides. The technique is emerging as an essential tool to study protein structure in solution due to the exceptional capability of examining both dynamic and structural changes related to protein function. PMID:24061917

Singh, Harsimran; Busenlehner, Laura S

2014-01-01

153

A Native to Amyloidogenic Transition Regulated by a Backbone Trigger  

SciTech Connect

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.

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

2006-01-01

154

Evolution of Robust Network Topologies: Emergence of Central Backbones  

NASA Astrophysics Data System (ADS)

We model the robustness against random failure or an intentional attack of networks with an arbitrary large-scale structure. We construct a block-based model which incorporates—in a general fashion—both connectivity and interdependence links, as well as arbitrary degree distributions and block correlations. By optimizing the percolation properties of this general class of networks, we identify a simple core-periphery structure as the topology most robust against random failure. In such networks, a distinct and small “core” of nodes with higher degree is responsible for most of the connectivity, functioning as a central “backbone” of the system. This centralized topology remains the optimal structure when other constraints are imposed, such as a given fraction of interdependence links and fixed degree distributions. This distinguishes simple centralized topologies as the most likely to emerge, when robustness against failure is the dominant evolutionary force.

Peixoto, Tiago P.; Bornholdt, Stefan

2012-09-01

155

Prediction of protein side-chain rotamers from a backbone-dependent rotamer library: a new homology modeling tool 1 1 Edited by B. Honig  

Microsoft Academic Search

Modeling by homology is the most accurate computational method for translating an amino acid sequence into a protein structure. Homology modeling can be divided into two sub-problems, placing the polypeptide backbone and adding side-chains. We present a method for rapidly predicting the conformations of protein side-chains, starting from main-chain coordinates alone. The method involves using fewer than ten rotamers per

Michael J. Bower; Fred E. Cohen; Roland L. Dunbrack

1997-01-01

156

Photopolymerization of aromatic acrylate containing phosphine oxide backbone and its application to holographic recording  

NASA Astrophysics Data System (ADS)

Photopolymer compositions for holographic recording were prepared from aromatic diacrylate having phosphine oxide backbone, a hybrid sol-gel, and photoinitiator. The physical and holographic properties of photopolymer were controlled by the ratio of precursor triethoxysilylpropyl polyethyleneglycol carbamate (TSPEG) in a hybrid sol-gel binder and the content of monomer. The photopolymerization rate and conversion of monomer were monitored by photo-differential scanning calorimetry (photo-DSC). Holographic recording was attempted by photopolymerization of the monomers in the photopolymer film using a 532 nm laser. Holographic gratings were written into the photopolymer samples by interfering two collimated plane wave beams. The temporal growth of the diffracted power was monitored in real-time at 785 nm laser. Contents of monomer and TESPEG were changed in the range of 0-60 wt% and the composition were optimized in terms of diffraction efficiency. Photopolymer film exhibited very high diffraction efficiency of 93.5% and low shrinkage (<0.5%) after the contents of monomer, binder, and TSPEG were optimized.

Chang, Yu Mi; Yoon, Sung Cheol; Han, Mijeong

2007-12-01

157

Supervised method for periodontitis phenotypes prediction based on microbial composition using 16S rRNA sequences.  

PubMed

Microbes play an important role on human health, however, little is known on microbes in the past decades for the limitation of culture-based techniques. Recently, with the development of next-generation sequencing (NGS) technologies, it is now possible to sequence millions of sequences directly from environments samples, and thus it supplies us a sight to probe the hidden world of microbial communities and detect the associations between microbes and diseases. In the present work, we proposed a supervised learning-based method to mine the relationship between microbes and periodontitis with 16S rRNA sequences. The jackknife accuracy is 94.83% and it indicated the method can effectively predict disease status. These findings not only expand our understanding of the association between microbes and diseases but also provide a potential approach for disease diagnosis and forensics. PMID:24878731

Chen, Wei; Cheng, Yong-Mei; Zhang, Shao-Wu; Pan, Quan

2014-01-01

158

Vancomycin resistance: Modeling backbone variants with d-Ala-d-Ala and d-Ala-d-Lac peptides  

PubMed Central

To seek vancomycin analogs with broader antibacterial activity, effects of backbone modifications for the agylcon 2 on binding with d-Ala-d-Ala- and d-Ala-d-Lac-containing peptides were investigated by Monte Carlo/free energy perturbation (MC/FEP) calculations. The experimental trend in binding affinities for 2 with three tripeptides was well reproduced. Possible modifications of the peptide bond between residues 4 and 5 were then considered, specifically for conversion of the O=C—NH linkage to CH2NH2+ (6), FC=CH (7), HC=CH (8), and HN—C=O(9). The MC/FEP results did not yield binding improvements for 7, 8, and 9, though the fluorovinyl replacement is relatively benign. The previously reported analog 6 remains as the only variant that exhibits improved affinity for the d-Ala-d-Lac sequence and acceptable affinity for the d-Ala-d-Ala sequence.

Leung, Siegfried S. F.; Tirado-Rives, Julian; Jorgensen, William L.

2009-01-01

159

Effective Tour Searching for TSP by Contraction of Pseudo Backbone Edges  

Microsoft Academic Search

We introduce a reduction technique for the well-known TSP. The basic idea of the approach consists of transforming a TSP instance to another one with smaller size by contracting pseudo backbone edges com- puted in a preprocessing step, where pseudo backbone edges are edges which are likely to be in an optimal tour. A tour of the small instance can

Changxing Dong; Gerold Jäger; Dirk Richter; Paul Molitor

2009-01-01

160

A Novel Local Search Algorithm for the Traveling Salesman Problem that Exploits Backbones  

Microsoft Academic Search

We present and investigate a new method for the Traveling Salesman Problem (TSP) that incorpo- rates backbone information into the well known and widely applied Lin-Kernighan (LK) local search family of algorithms for the problem. We consider how heuristic backbone information can be obtained and develop methods to make biased local pertur- bations in the LK algorithm and its variants

Weixiong Zhang; Moshe Looks

2005-01-01

161

TACN-based oligomers with aromatic backbones for efficient nucleic acid delivery.  

PubMed

Cationic oligomers with a rigid aromatic backbone were first applied as non-viral gene delivery vectors. These materials showed better DNA condensation ability than their flexible analogues. In vitro transfection experiments revealed that the materials with more rigid backbone exhibited considerably higher TE and lower cytotoxicity than 25 kDa PEI. PMID:24811979

Yi, Wen-Jing; Yu, Xing-Chi; Wang, Bing; Zhang, Ji; Yu, Qing-Ying; Zhou, Xue-Dong; Yu, Xiao-Qi

2014-06-21

162

TBONE: A mobile-backbone protocol for ad hoc wireless networks  

Microsoft Academic Search

We introduce an ad hoe wireless mobile network that employs a hierarchical networking architecture. The network uses high capacity and low capacity nodes. We present a topological synthesis algorithm that selects a subset of high capacity nodes to form. a backbone network. The latter consists of interconnected backbone nodes that intercommunicate across high power links, and also makes use of

I. Rubin; A. Behzad; Runhe Zhang; Huiyu Luo; E. Caballero

2002-01-01

163

Composite  

NASA Astrophysics Data System (ADS)

Particle distribution and hot workability of an in situ Al-TiCp composite were investigated. The composite was fabricated by an in situ casting method using the self-propagating high-temperature synthesis of an Al-Ti-C system. Hot-compression tests were carried out, and power dissipation maps were constructed using a dynamic material model. Small globular TiC particles were not themselves fractured, but the clustering and grain boundary segregation of the particles contributed to the cracking of the matrix by causing the debonding of matrix/particle interfaces and providing a crack propagation path. The efficiency of power dissipation increased with increasing temperature and strain rate, and the maximum efficiency was obtained at a temperature of 723 K (450 °C) and a strain rate of 1/s. The microstructural mechanism occurring in the maximum efficiency domain was dynamic recrystallization. The role of particles in the plastic flow and the microstructure evolution were discussed.

Kim, Su-Hyeon; Cho, Young-Hee; Lee, Jung-Moo

2014-06-01

164

The mitochondrial genome sequence of the ciliate Paramecium caudatum reveals a shift in nucleotide composition and codon usage within the genus Paramecium  

PubMed Central

Background Despite the fact that the organization of the ciliate mitochondrial genome is exceptional, only few ciliate mitochondrial genomes have been sequenced until today. All ciliate mitochondrial genomes are linear. They are 40 kb to 47 kb long and contain some 50 tightly packed genes without introns. Earlier studies documented that the mitochondrial guanine + cytosine contents are very different between Paramecium tetraurelia and all studied Tetrahymena species. This raises the question of whether the high mitochondrial G+C content observed in P. tetraurelia is a characteristic property of Paramecium mtDNA, or whether it is an exception of the ciliate mitochondrial genomes known so far. To test this question, we determined the mitochondrial genome sequence of Paramecium caudatum and compared the gene content and sequence properties to the closely related P. tetraurelia. Results The guanine + cytosine content of the P. caudatum mitochondrial genome was significantly lower than that of P. tetraurelia (22.4% vs. 41.2%). This difference in the mitochondrial nucleotide composition was accompanied by significantly different codon usage patterns in both species, i.e. within P. caudatum clearly A/T ending codons dominated, whereas for P. tetraurelia the synonymous codons were more balanced with a higher number of G/C ending codons. Further analyses indicated that the nucleotide composition of most members of the genus Paramecium resembles that of P. caudatum and that the shift observed in P. tetraurelia is restricted to the P. aurelia species complex. Conclusions Surprisingly, the codon usage bias in the P. caudatum mitochondrial genome, exemplified by the effective number of codons, is more similar to the distantly related T. pyriformis and other single-celled eukaryotes such as Chlamydomonas, than to the closely related P. tetraurelia. These differences in base composition and codon usage bias were, however, not reflected in the amino acid composition. Most probably, the observed picture is best explained by a hitherto unknown (neutral or adaptive) mechanism that increased the guanine + cytosine content in P. tetraurelia mtDNA on the one hand, and strong purifying selection on the ancestral amino acid composition on the other hand. These contradicting forces are counterbalanced by a considerably altered codon usage pattern.

2011-01-01

165

Composites  

NASA Astrophysics Data System (ADS)

Ca3Co4O9 is one of the most promising p-type thermoelectric materials because of its high dimensionless figure of merit ZT. However, polycrystalline Ca3Co4O9 ceramics shows lower ZT value than that for single crystal Ca3 Co4O9 due to its higher electrical resistivity ?. Mikami et al. have reported that the addition of Ag to Ca3Co4O9 ceramics could successfully reduce ? and enhance the power factor. On the other hand, Ohtaki et al. reported that a composite structure could be highly effective to reduce ? for ZnO dually doped with Al and Ga. In this work, we tried to enhance the power factor and reduce ? by forming Ca3Co4O9/[Ca2(Co0.65Cu0.35)2O4]0.624CoO2 composite structure. As a result, the ZT value for Ca3Co4O9/[Ca2(Co0.65Cu0.35)2O4]0.624CoO2 composites reached 0.164 at 700 °C, which was 40 % higher than the value for Ca3Co4O9.

Obata, Kohei; Chonan, Yasunori; Komiyama, Takao; Abe, Kazunori; Aoyama, Takashi; Yamaguchi, Hiroyuki; Sugiyama, Shigeaki

2014-06-01

166

Cavity-containing, backbone-rigidified foldamers and macrocycles.  

PubMed

This Feature Article gives an account for a host of readily available foldamers and macrocycles with well-defined shapes and non-deformable cavities that appeared over the last decade. Efforts to create porous molecular structures have led to the establishment of an effective strategy for enforcing the folding of unnatural aromatic oligoamide strands based on an especially robust three-center (bifurcated) hydrogen-bonding interaction. Based on such a strategy, aromatic oligoamides adopting crescent and helical conformations that contain non-collapsible cavities of tunable diameters have been created. Extending the same folding principle to the preparation of aromatic polyamides that would adopt pore-containing helical conformation instead led to the discovery of a highly efficient, one-pot macrocyclization process. Such a one-pot macrocyclization process has been successfully applied to the preparation of macrocycles with aromatic amide, hydrazide, urea and other backbones. Mechanistic study indicates that the high efficiencies observed for the formation of these macrocycles are due to the folding of the corresponding uncyclized oligomeric precursors of the corresponding macrocycles. Oligoamide macrocycles, along with their uncyclized, cavity-containing counterparts, i.e., crescent oligoamides, bind guests such as guanidinium (G) and octylguanidinium (OG) ions with tunable selectivity. Recent studies revealed that these rigid macrocycles tend to engage in extraordinarily strong, directional aggregation, leading to nanotubular assemblies containing pores of fixed sizes. Consistent with the presence of self-assembling nanopores, oligoamide macrocycles were found to assemble into transmembrane channels with high conductance. PMID:23104157

Yamato, Kazuhiro; Kline, Mark; Gong, Bing

2012-12-28

167

Data Acquisition Backbone Core DABC release v1.0  

NASA Astrophysics Data System (ADS)

The Data Acquisition Backbone Core (DABC) is a general purpose software framework designed for the implementation of a wide-range of data acquisition systems - from various small detector test beds to high performance systems. DABC consists of a compact data-flow kernel and a number of plug-ins for various functional components like data inputs, device drivers, user functional modules and applications. DABC provides configurable components for implementing event building over fast networks like InfiniBand or Gigabit Ethernet. A generic Java GUI provides the dynamic control and visualization of control parameters and commands, provided by DIM servers. A first set of application plug-ins has been implemented to use DABC as event builder for the front-end components of the GSI standard DAQ system MBS (Multi Branch System). Another application covers the connection to DAQ readout chains from detector front-end boards (N-XYTER) linked to read-out controller boards (ROC) over UDP into DABC for event building, archiving and data serving. This was applied for data taking in the September 2008 test beamtime for the CBM experiment at GSI. DABC version 1.0 is released and available from the website.

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

2010-04-01

168

Backbone of complex networks of corporations: The flow of control  

NASA Astrophysics Data System (ADS)

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.

Glattfelder, J. B.; Battiston, S.

2009-09-01

169

Sequence-Based Analysis of Structural Organization and Composition of the Cultivated Sunflower (Helianthus annuus L.) Genome.  

PubMed

Sunflower is an important oilseed crop, as well as a model system for evolutionary studies, but its 3.6 gigabase genome has proven difficult to assemble, in part because of the high repeat content of its genome. Here we report on the sequencing, assembly, and analyses of 96 randomly chosen BACs from sunflower to provide additional information on the repeat content of the sunflower genome, assess how repetitive elements in the sunflower genome are organized relative to genes, and compare the genomic distribution of these repeats to that found in other food crops and model species. We also examine the expression of transposable element-related transcripts in EST databases for sunflower to determine the representation of repeats in the transcriptome and to measure their transcriptional activity. Our data confirm previous reports in suggesting that the sunflower genome is >78% repetitive. Sunflower repeats share very little similarity to other plant repeats such as those of Arabidopsis, rice, maize and wheat; overall 28% of repeats are "novel" to sunflower. The repetitive sequences appear to be randomly distributed within the sequenced BACs. Assuming the 96 BACs are representative of the genome as a whole, then approximately 5.2% of the sunflower genome comprises non TE-related genic sequence, with an average gene density of 18kbp/gene. Expression levels of these transposable elements indicate tissue specificity and differential expression in vegetative and reproductive tissues, suggesting that expressed TEs might contribute to sunflower development. The assembled BACs will also be useful for assessing the quality of several different draft assemblies of the sunflower genome and for annotating the reference sequence. PMID:24833511

Gill, Navdeep; Buti, Matteo; Kane, Nolan; Bellec, Arnaud; Helmstetter, Nicolas; Berges, Hélène; Rieseberg, Loren H

2014-01-01

170

Sequence-Based Analysis of Structural Organization and Composition of the Cultivated Sunflower (Helianthus annuus L.) Genome  

PubMed Central

Sunflower is an important oilseed crop, as well as a model system for evolutionary studies, but its 3.6 gigabase genome has proven difficult to assemble, in part because of the high repeat content of its genome. Here we report on the sequencing, assembly, and analyses of 96 randomly chosen BACs from sunflower to provide additional information on the repeat content of the sunflower genome, assess how repetitive elements in the sunflower genome are organized relative to genes, and compare the genomic distribution of these repeats to that found in other food crops and model species. We also examine the expression of transposable element-related transcripts in EST databases for sunflower to determine the representation of repeats in the transcriptome and to measure their transcriptional activity. Our data confirm previous reports in suggesting that the sunflower genome is >78% repetitive. Sunflower repeats share very little similarity to other plant repeats such as those of Arabidopsis, rice, maize and wheat; overall 28% of repeats are “novel” to sunflower. The repetitive sequences appear to be randomly distributed within the sequenced BACs. Assuming the 96 BACs are representative of the genome as a whole, then approximately 5.2% of the sunflower genome comprises non TE-related genic sequence, with an average gene density of 18kbp/gene. Expression levels of these transposable elements indicate tissue specificity and differential expression in vegetative and reproductive tissues, suggesting that expressed TEs might contribute to sunflower development. The assembled BACs will also be useful for assessing the quality of several different draft assemblies of the sunflower genome and for annotating the reference sequence.

Gill, Navdeep; Buti, Matteo; Kane, Nolan; Bellec, Arnaud; Helmstetter, Nicolas; Berges, Helene; Rieseberg, Loren H.

2014-01-01

171

Evaluation of a novel food composition database that includes glutamine and other amino acids derived from gene sequencing data  

PubMed Central

Objectives To determine the content of glutamine in major food proteins. Subjects/Methods We used a validated 131-food item food frequency questionnaire (FFQ) to identify the foods that contributed the most to protein intake among 70 356 women in the Nurses’ Health Study (NHS, 1984). The content of glutamine and other amino acids in foods was calculated based on protein fractions generated from gene sequencing methods (Swiss Institute of Bioinformatics) and compared with data from conventional (USDA) and modified biochemical (Khun) methods. Pearson correlation coefficients were used to compare the participants’ dietary intakes of amino acids by sequencing and USDA methods. Results The glutamine content varied from 0.01 to to 9.49 g/100 g of food and contributed from 1 to to 33% of total protein for all FFQ foods with protein. When comparing the sequencing and Kuhn’s methods, the proportion of glutamine in meat was 4.8 vs 4.4%. Among NHS participants, mean glutamine intake was 6.84 (s.d.=2.19) g/day and correlation coefficients for amino acid between intakes assessed by sequencing and USDA methods ranged from 0.94 to 0.99 for absolute intake, ?0.08 to 0.90 after adjusting for 100 g of protein, and 0.88 to 0.99 after adjusting for 1000 kcal. The between-person coefficient of variation of energy-adjusted intake of glutamine was 16%. Conclusions These data suggest that (1) glutamine content can be estimated from gene sequencing methods and (2) there is a reasonably wide variation in energy-adjusted glutamine intake, allowing for exploration of glutamine consumption and disease.

Lenders, CM; Liu, S; Wilmore, DW; Sampson, L; Dougherty, LW; Spiegelman, D; Willett, WC

2011-01-01

172

Flexible backbone sampling methods to model and design protein alternative conformations.  

PubMed

Sampling alternative conformations is key to understanding how proteins work and engineering them for new functions. However, accurately characterizing and modeling protein conformational ensembles remain experimentally and computationally challenging. These challenges must be met before protein conformational heterogeneity can be exploited in protein engineering and design. Here, as a stepping stone, we describe methods to detect alternative conformations in proteins and strategies to model these near-native conformational changes based on backrub-type Monte Carlo moves in Rosetta. We illustrate how Rosetta simulations that apply backrub moves improve modeling of point mutant side-chain conformations, native side-chain conformational heterogeneity, functional conformational changes, tolerated sequence space, protein interaction specificity, and amino acid covariation across protein-protein interfaces. We include relevant Rosetta command lines and RosettaScripts to encourage the application of these types of simulations to other systems. Our work highlights that critical scoring and sampling improvements will be necessary to approximate conformational landscapes. Challenges for the future development of these methods include modeling conformational changes that propagate away from designed mutation sites and modulating backbone flexibility to predictively design functionally important conformational heterogeneity. PMID:23422426

Ollikainen, Noah; Smith, Colin A; Fraser, James S; Kortemme, Tanja

2013-01-01

173

Methods in Enzymology: "Flexible backbone sampling methods to model and design protein alternative conformations"  

PubMed Central

Sampling alternative conformations is key to understanding how proteins work and engineering them for new functions. However, accurately characterizing and modeling protein conformational ensembles remains experimentally and computationally challenging. These challenges must be met before protein conformational heterogeneity can be exploited in protein engineering and design. Here, as a stepping stone, we describe methods to detect alternative conformations in proteins and strategies to model these near-native conformational changes based on backrub-type Monte Carlo moves in Rosetta. We illustrate how Rosetta simulations that apply backrub moves improve modeling of point mutant side chain conformations, native side chain conformational heterogeneity, functional conformational changes, tolerated sequence space, protein interaction specificity, and amino acid co-variation across protein-protein interfaces. We include relevant Rosetta command lines and RosettaScripts to encourage the application of these types of simulations to other systems. Our work highlights that critical scoring and sampling improvements will be necessary to approximate conformational landscapes. Challenges for the future development of these methods include modeling conformational changes that propagate away from designed mutation sites and modulating backbone flexibility to predictively design functionally important conformational heterogeneity.

Ollikainen, Noah; Smith, Colin A.; Fraser, James S.; Kortemme, Tanja

2013-01-01

174

Optical Characterization of Semiconducting Natural Rubber Nanoparticles and its Composites  

NASA Astrophysics Data System (ADS)

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.

Neena, P.; Mathew, Anisha Mary

2011-10-01

175

Logos for amino-acid preferences in different backbone packing density regions of protein structural classes.  

PubMed

A protein sequence can be classified into one of four structural classes, namely alpha, beta, alpha + beta and alpha/beta, based on its amino-acid composition. The present study aims at understanding why a particular sequence with a given amino-acid composition should fold into a specific structural class. In order to answer this question, each amino acid in the protein sequence was classified to a particular neighbor density based on the number of spatial residues surrounding it within a distance of 6.5 A. Each of the four structural classes showed a unique preference of amino acids in each of the neighbor densities. Residues which show a high compositional bias in a structural class are also found to occur in high neighbor densities. This high compositional bias towards specific residues in the four different structural classes of proteins appears to be caused by structural and functional requirements. The distribution of amino acids in different neighbor densities is graphically presented in a novel logo form which incorporates several features such as composition, the frequency of occurrence and color code for amino acids. The spatial neighbors of the residues in different neighbor densities and their secondary structural location are also represented in the form of logos. This representation helped in the identification of specific details of the whole data which may otherwise have gone unnoticed. It is suggested that the data presented in this study may be useful in knowledge-based structure modelling and de novo protein design. PMID:10957634

Kannan, N; Schneider, T D; Vishveshwara, S

2000-09-01

176

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

NASA Astrophysics Data System (ADS)

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(?) to bias the sequence selection. The wi(?) 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.

Zou, Jinming; Saven, Jeffery G.

2003-02-01

177

Exact Solutions for Internuclear Vectors and Backbone Dihedral Angles from NH Residual Dipolar Couplings in Two Media, and their Application in a Systematic Search Algorithm for Determining Protein Backbone Structure  

Microsoft Academic Search

We have derived a quartic equation for computing the direction of an internuclear vector from residual dipolar couplings (RDCs) measured in two aligning media, and two simple trigonometric equations for computing the backbone (f,?) angles from two backbone vectors in consecutive peptide planes. These equations make it possible to compute, exactly and in constant time, the backbone (f,?) angles for

Lincong Wang; Bruce Randall Donald

2004-01-01

178

Solution structure and backbone dynamics of Mason-Pfizer monkey virus (MPMV) nucleocapsid protein.  

PubMed Central

Retroviral nucleocapsid proteins (NCPs) are CCHC-type zinc finger proteins that mediate virion RNA binding activities associated with retrovirus assembly and genomic RNA encapsidation. Mason-Pfizer monkey virus (MPMV), a type D retrovirus, encodes a 96-amino acid nucleocapsid protein, which contains two Cys-X2-Cys-X4-His-X4-Cys (CCHC) zinc fingers connected by an unusually long 15-amino acid linker. Homonuclear, two-dimensional sensitivity-enhanced 15N-1H, three-dimensional 15N-1H, and triple resonance NMR spectroscopy have been used to determine the solution structure and residue-specific backbone dynamics of the structured core domain of MPMV NCP containing residues 21-80. Structure calculations and spectral density mapping of N-H bond vector mobility reveal that MPMV NCP 21-80 is best described as two independently folded, rotationally uncorrelated globular domains connected by a seven-residue flexible linker consisting of residues 42-48. The N-terminal CCHC zinc finger domain (residues 24-37) appears to adopt a fold like that described previously for HIV-1 NCP; however, residues within this domain and the immediately adjacent linker region (residues 38-41) are characterized by extensive conformational averaging on the micros-ms time scale at 25 degrees C. In contrast to other NCPs, residues 49-77, which includes the C-terminal CCHC zinc-finger (residues 53-66), comprise a well-folded globular domain with the Val49-Pro-Gly-Leu52 sequence and C-terminal tail residues 67-77 characterized by amide proton exchange properties and 15N R1, R2, and (1H-15N) NOE values indistinguishable to residues in the core C-terminal finger. Twelve refined structural models of MPMV NCP residues 49-80 (pairwise backbone RMSD of 0.77 A) reveal that the side chains of the conserved Pro50 and Trp62 are in van der Waals contact with one another. Residues 70-73 in the C-terminal tail adopt a reverse turn-like structure. Ile77 is involved in extensive van der Waals contact with the core finger domain, while the side chains of Ser68 and Asn75 appear to form hydrogen bonds that stabilize the overall fold of this domain. These residues outside of the core finger structure are conserved in D-type and related retroviral NCPs, e.g., MMTV NCP, suggesting that the structure of MPMV NCP may be representative of this subclass of retroviral NCPs.

Gao, Y.; Kaluarachchi, K.; Giedroc, D. P.

1998-01-01

179

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

NASA Astrophysics Data System (ADS)

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 Aliança Formation of the Recôncavo 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.

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

2012-11-01

180

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

PubMed Central

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.

2013-01-01

181

In a changing environment, network backbone upgrades emerge as a wise investment.  

PubMed

The numbers, locations and needs of users change constantly, but they'll always want more bandwidth. Many experts say that upgrading to higher-speed backbones seems to be the smart investment for unsettled times. PMID:10167513

Cupito, M C

1997-05-01

182

A Markov chain model for local path protection in mobile optical backbone networks  

Microsoft Academic Search

In this paper, we propose a protection scheme to improve quality of service in a mobile backbone network with free space optical point-to-point links. We assume that the backbone nodes are mobile and with unpredictable movements, and the traffic from an ingress node is routed to its corresponding egress nodes in a multi-hop way. The QoS demanding applications are vulnerable

Mehdi Kalantari; Fangting Sun; Mark Shayman

2005-01-01

183

Irreversible Denaturation of Proteins through Aluminum-Induced Formation of Backbone Ring Structures.  

PubMed

A combination of ab?initio calculations, circular dichroism, nuclear magnetic resonance, and X-ray photoelectron spectroscopy has shown that aluminum ions can induce the formation of backbone ring structures in a wide range of peptides, including neurodegenerative disease related motifs. These ring structures greatly destabilize the protein and result in irreversible denaturation. This behavior benefits from the ability of aluminum ions to form chemical bonds simultaneously with the amide nitrogen and carbonyl oxygen atoms on the peptide backbone. PMID:24777568

Song, Bo; Sun, Qian; Li, Haikuo; Ge, Baosheng; Pan, Ji Sheng; Wee, Andrew Thye Shen; Zhang, Yong; Huang, Shaohua; Zhou, Ruhong; Gao, Xingyu; Huang, Fang; Fang, Haiping

2014-06-16

184

Backbone dynamics of the oligomerization domain of p53 determined from 15N NMR relaxation measurements  

Microsoft Academic Search

The backbone dynamics of the tetrameric p53 oligomerization domain (residues 3 19-360) have been investigated by two-dimensional inverse detected heteronuclear 'H-I5N NMR spectroscopy at 500 and 600 MHz. I5N TI, TZ, and heteronuclear NOES were measured for 39 of 40 non-proline backbone NH vectors at both field strengths. The overall correlation time for the tetramer, calculated from the TI\\/TZ ratios,

Robert T. Clubb; James G. Omichinski; Angela M. Gronenborn; G. Marius Clore; Kazuyazu Sakaguchi; Ettore Appella

2008-01-01

185

Unified description of urea denaturation: backbone and side chains contribute equally in the transfer model.  

PubMed

After studying protein denaturation by urea for many decades, conflicting views of the role of the side chains and the backbone have emerged; many results suggest that urea denatures by enhancing the solubility of both the side chains and the backbone, but the frequently applied transfer model (TM) so far ascribes denaturation exclusively to urea's action on the backbone. We use molecular dynamics simulations to rigorously test one of the TM's key assumptions, the proportionality of a molecule's transfer free energy (TFE) and its solvent-accessible surface. The performance of the TM as it is usually implemented turns out to be unsatisfactory, but the proportionality is satisfied very well after an inconsistency in the treatment of the backbone contribution is corrected. This inconsistency has so far gone unnoticed as it was obscured by a compensating error in the side-chain group TFEs used so far. The revised "universal backbone" TM presented in this work shows excellent accuracy in the prediction of experimental m values of a set of 36 proteins. It also settles the conflicting views regarding the role of the side chains because it predicts that both the side chains and the backbone on average contribute favorably to denaturation by urea. PMID:24328141

Moeser, Beate; Horinek, Dominik

2014-01-01

186

Numerical advection of correlated tracers: preserving particle size/composition moment sequences during transport of aerosol mixtures  

NASA Astrophysics Data System (ADS)

Nonlinear transport algorithms designed to reduce numerical diffusion fail to preserve correlations between moments, isotope abundances, etc. when these scalar densities are transported in models as separate tracers. In case of the particle size/composition coordinates of an aerosol, such loss can give rise to unphysical moment sets. New statistical approaches to aerosol dynamics, which involve tracking moments directly, offer highly efficient alternatives to sectional and modal methods for representing aerosols in climate models, but it is essential that moment set integrity be preserved throughout a simulation. In this paper we review the problem and weaknesses of previous attempts at solution, including vector transport - a scheme in which the moments, as internal aerosol coordinates, are transported together with a single lead tracer such as number or mass. A non-negative least squares (NNLS) solution that finally eliminates the problem without requiring modification of the transport algorithm itself is presented. Following each transport step, new moment sets are resolved into sums of previously validated sets with non-negative coefficients using NNLS Transport errors are removed and the now guaranteed-to-be-valid moment sets are ready for passage to the aerosol dynamics module. In addition to moment set validation, the new scheme reduces numerical diffusion during transport and provides greater accuracy for the source apportionment of aerosol mixtures. The method is not limited to moment transport - similar improvements in accuracy are expected using NNLS in conjunction with modal and sectional methods.

McGraw, Robert

2007-07-01

187

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

PubMed

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

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

2013-06-15

188

pH dependence of hydrogen exchange from backbone peptide amides in apamin.  

PubMed

The kinetics of hydrogen exchange of the 11 most protected backbone amides of bee venom apamin have been measured between pH 1 and pH 8.5 by using time-resolved and saturation-transfer NMR spectroscopy. The five amides most protected from base-catalyzed exchange, those of residues 5 and 12-15, show highly correlated exchange behavior in the base-catalyzed regime. It is proposed that the intramolecular hydrogen bonds stabilizing these amides define a stable cooperative unit of secondary structure in apamin (a C-terminal helix and an N-terminal beta-turn). This conformational unit is further stabilized (by 5-6 kJ mol-1) on titration of the Glu-7 side-chain carboxyl group. The relative contributions of specific intramolecular interactions to this conformational stabilization are estimated. The pHminima in the pH-dependent single amide exchange curves are compared with values predicted by correcting for sequence-dependent contributions to amide exchange rates [Molday, R. S., Englander, S. W., & Kallen, R. G. (1972) Biochemistry 11, 150-158]. The lack of correlation suggests that the "open" conformers from which amide exchange occurs are nonrandom. This conclusion is dependent on the assumption that acid-catalyzed exchange occurs via N-protonation so that residual conformational effects on exchange rates in the open conformers will affect acid- and base-catalyzed rates in approximately equal and opposite ways. A strong correlation between the measured pHminima and the amide proton chemical shifts is observed, however, and this may be most easily accommodated if acid-catalyzed exchange occurs by the imidic acid mechanism (via amide O-protonation). PMID:3741839

Dempsey, C E

1986-07-01

189

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

PubMed Central

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.

Solis, Armando D.

2014-01-01

190

In search of true reads: A classification approach to next generation sequencing data selection  

Microsoft Academic Search

Next generation sequencing (NGS) technology has increasingly become the backbone of transcriptomics analysis, but sequencer error causes biases in the read counts. In this paper we establish a framework for predicting true sequences from NGS data. We formulate this task as a classification problem. We define several features, such as log likelihood ratio of estimated true counts, error probability and

Edward Wijaya; J.-F. Pessiot; M. C. Frith; W. Fujibuchi; K. Asai; P. Horton

2010-01-01

191

The Optical Bench: The Backbone of the Chandra Observatory  

NASA Astrophysics Data System (ADS)

The Chandra Optical Bench is the large composite structure ever flown by NASA. This structure provides the critical metering system between the High Resolution Mirror Assembly (HRMA) and the Science Instruments (SI). The Optical Bench also had to with stand the Space Shuttle launch loads while maintaining the alignment between the HRMA and the SI's. This poster will show the integration and test of the Optical Bench at ITT.

Olds, Cliff; Reese, Rob

2009-09-01

192

Different conformational families of pyrimidine.purine.pyrimidine triple helices depending on backbone composition.  

PubMed Central

Different helical conformations of DNA (D), RNA (R), and DNA.RNA (DR) hybrid double and triple helices have been detected using affinity cleavage analysis. Synthetic methods were developed to attach EDTA.Fe to a single nucleotide on RNA as well as DNA oligonucleotides. Cleavage patterns generated by a localized diffusible oxidant in the major groove on the pyrimidine strand of four purine.pyrimidine double helices consisting of all DNA, all RNA, and the corresponding hybrids reveal that the relative cleavage intensity shifts to the 5' end of the purine strand increasingly in the order: DD < DR < RD < RR. These results are consistent with models derived from structural studies. In six pyrimidine.purine.pyrimidine triple helices, the altered cleavage patterns of the Watson-Crick pyrimidine strands reveal at least two conformational families: (i) D + DD, R + DD, D + DR, and R + DR and (ii) R + RD and R + RR. Images

Han, H; Dervan, P B

1994-01-01

193

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

PubMed Central

We present a refinement of the backbone torsion parameters ? and ? of the Cornell et al. AMBER force field for DNA simulations. The new parameters, denoted as ??OL1, were derived from quantum-mechanical calculations with inclusion of conformation-dependent solvation effects according to the recently reported methodology (J. Chem. Theory Comput. 2012, 7(9), 2886-2902). The performance of the refined parameters was analyzed by means of extended molecular dynamics (MD) simulations for several representative systems. The results showed that the ??OL1 refinement improves the backbone description of B-DNA double helices and G-DNA stem. In B-DNA simulations, we observed an average increase of the helical twist and narrowing of the major groove, thus achieving better agreement with X-ray and solution NMR data. The balance between populations of BI and BII backbone substates was shifted towards the BII state, in better agreement with ensemble-refined solution experimental results. Furthermore, the refined parameters decreased the backbone RMS deviations in B-DNA MD simulations. In the antiparallel guanine quadruplex (G-DNA) the ??OL1 modification improved the description of non-canonical ?/? backbone substates, which were shown to be coupled to the ?/? torsion potential. Thus, the refinement is suggested as a possible alternative to the current ?/? torsion potential, which may enable more accurate modeling of nucleic acids. However, long-term testing is recommended before its routine application in DNA simulations.

Zgarbova, Marie; Luque, F. Javier; Sponer, Jiri; Cheatham, Thomas E.; Otyepka, Michal; Jurecka, Petr

2013-01-01

194

Subgraph "Backbone" Analysis of Dynamic Brain Networks during Consciousness and Anesthesia  

PubMed Central

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

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

2013-01-01

195

Cloud Point Depression in Dilute Solutions of HEMA/DMAEMA Copolymers with Prescribed Composition Profiles and Gradient Strengths  

NASA Astrophysics Data System (ADS)

We have synthesized a random copolymer and gradient copolymers of hydroxyethyl methacrylate and dimethylaminoethyl methacrylate whose instantaneous compositions vary linearly and according to hyperbolic tangent (Tanh) functions along the backbones, all having similar molecular weights and overall compositions. The cloud point of the dilute solution of the random copolymer is 20.0^oC; the transparent-to-turbid transition occurs over 1.0^oC. Dilute solutions of linear gradient copolymers exhibit cloud point depressions of up to 3.5^oC and transition breadths of 1-3^oC compared to that of the random copolymer. The cloud points of dilute solutions of gradient copolymers with Tanh composition profiles are further suppressed by as much as 9.0^oC compared to that of the random copolymer. Our observations demonstrate the importance of monomer sequence distribution in altering the macroscopic solution properties of copolymers.

Gallow, Keith; Jhon, Young; Genzer, Jan; Loo, Yueh-Lin

2011-03-01

196

B-lineage regulated polyadenylation occurs on weak poly(A) sites regardless of sequence composition at the cleavage and downstream regions.  

PubMed Central

Early/memory and plasma B-cell lines and fibroblasts were analyzed for their ability to use a 5' proximal (variant) versus a 3' distal (constant) poly(A) site, in the absence of a competing splice, from a set of related constructs. The proximal:distal poly(A) site use (P:D ratio) of the resulting cytoplasmic poly(A)+ mRNA is a measure of poly(A) site strength. In this context the immunoglobulin gamma2b secretory-specific poly(A) site showed a P:D ratio of 1:1 in plasma cells, 0.43:1 in early/memory B-cells and an intermediate value in fibroblasts. Meanwhile, a construct with a proximal SV40 early-like poly(A) site produced mRNA with a P:D ratio of >>50:1 in all cell types. Alterations in the region downstream of the proximal poly(A) addition site and at the site itself resulted in changes in the P:D ratio. However, these poly(A) sites, all with a P:D ratio of < or = 5:1, were used most efficiently in plasma cells. Constructs totally devoid of immunoglobulin sequences, but containing heterologous poly(A) sites producing mRNA with P:D ratios of < or = 5:1, were also used more efficiently in plasma cells. We therefore conclude that weak poly(A) sites, regardless of sequence composition, are used more efficiently in plasma cells than in the other cell types.

Matis, S A; Martincic, K; Milcarek, C

1996-01-01

197

Chiral PNAs with constrained open-chain backbones.  

PubMed

Chiral open-chain PNAs have been shown to have improved properties in terms of control of helical handedness, DNA affinity, sequence selectivity, and cellular uptake. They can be synthesized either using preformed chiral monomers or by means of a submonomeric strategy. The former is preferred when only a stereogenic center is present at C-5, whereas for PNA-bearing substituents at C-2, the submonomeric approach is preferred, since racemization, generally occurring during the solid-phase synthesis, can be minimized by this procedure. Here we describe the protocols for the synthesis of PNA oligomers containing C-2- or C-5- (or both) modified monomers and a GC method for checking the optical purity of C-2-modified PNAs. PMID:24297348

Corradini, Roberto; Tedeschi, Tullia; Sforza, Stefano; Marchelli, Rosangela

2014-01-01

198

The backbone of the post-synaptic density originated in a unicellular ancestor of choanoflagellates and metazoans  

PubMed Central

Background Comparative genomics of the early diverging metazoan lineages and of their unicellular sister-groups opens new window to reconstructing the genetic changes which preceded or accompanied the evolution of multicellular body plans. A recent analysis found that the genome of the nerve-less sponges encodes the homologues of most vertebrate post-synaptic proteins. In vertebrate excitatory synapses, these proteins assemble to form the post-synaptic density, a complex molecular platform linking membrane receptors, components of their signalling pathways, and the cytoskeleton. Newly available genomes from Monosiga brevicollis (a member of Choanoflagellata, the closest unicellular relatives of animals) and Trichoplax adhaerens (a member of Placozoa: besides sponges, the only nerve-less metazoans) offer an opportunity to refine our understanding of post-synaptic protein evolution. Results Searches for orthologous proteins and reconstruction of gene gains/losses based on the taxon phylogeny indicate that post-synaptic proteins originated in two main steps. The backbone scaffold proteins (Shank, Homer, DLG) and some of their partners were acquired in a unicellular ancestor of choanoflagellates and metazoans. A substantial additional set appeared in an exclusive ancestor of the Metazoa. The placozoan genome contains most post-synaptic genes but lacks some of them. Notably, the master-scaffold protein Shank might have been lost secondarily in the placozoan lineage. Conclusions The time of origination of most post-synaptic proteins was not concomitant with the acquisition of synapses or neural-like cells. The backbone of the scaffold emerged in a unicellular context and was probably not involved in cell-cell communication. Based on the reconstructed protein composition and potential interactions, its ancestral function could have been to link calcium signalling and cytoskeleton regulation. The complex later became integrated into the evolving synapse through the addition of novel functionalities.

2010-01-01

199

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

PubMed Central

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 -? and -?, VDR-? and RAR-? 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.

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

2012-01-01

200

Analysis of ribosyl-modified, mixed backbone analogs of a bcl-2/bcl-xL antisense oligonucleotide.  

PubMed

Progress in oligonucleotide chemistry has provided second-generation antisense oligonucleotides with increased efficacy and reduced non-antisense-related toxicity. The ability of the 2'-O-(2-methoxyethylribose) (2'-MOE)-modified phosphorothioate gapmer oligonucleotide 4625, which matches the bcl-2 mRNA and has three base-mismatches to bcl-xL, to inhibit bcl-2 and bcl-xL expression and induce tumor cell apoptosis has been described. Here we investigated the consequences of adding of 2'-MOE or 2'-Me modifications to ribonucleotides at either the two ends of the sequence, or the center region together with different combinations of phosphodiester/phosphorothioate backbones on the activity of oligonucleotide 4625. The ability of the various 4625 analogs, including the parental first-generation oligonucleotide 3005, to inhibit bcl-2 and bcl-xL expression, and diminish cell growth or induce tumor cell death was assessed in SW2 lung cancer cells using real-time PCR, Western blotting and cell viability assays. Only oligonucleotide 4625 exhibited a potent bispecific antisense activity against bcl-2 and bcl-xL, which effectively reduced tumor cell viability. The other antisense oligonucleotides were either uniquely active against bcl-2 or completely inactive. Our data suggest that the 2'-MOE modification in combination with the phophorothioate gapmer chemistry is the optimal format of the 4625 sequence in terms of antisense activity and biological efficacy. PMID:12031489

Olie, Robert A; Hall, Jonathan; Natt, Francois; Stahel, Rolf A; Zangemeister-Wittke, Uwe

2002-06-01

201

Hole-vibronic coupling in oligothiophenes: impact of backbone torsional flexibility on relaxation energies.  

PubMed

Density functional theory calculations together with highly resolved gas-phase ultraviolet photoelectron spectroscopy have been applied to oligothiophene chains with up to eight thiophene rings. One of the important parameters governing the charge transport properties in the condensed phase is the amount of energy relaxation upon ionization. Here, we investigate the impact on this parameter of the backbone flexibility present in oligothiophenes as a result of inter-ring torsional motions. With respect to oligoacenes that are characterized by a coplanar and rigid backbone, the torsional flexibility in oligothiophenes adds to the relaxation energy and leads to the broadening of the first ionization peak, making its analysis more complex. PMID:17428767

Filho, Demetrio A da Silva; Coropceanu, Veaceslav; Fichou, Denis; Gruhn, Nadine E; Bill, Tonja G; Gierschner, Johannes; Cornil, Jérôme; Brédas, Jean-Luc

2007-06-15

202

A discrete search algorithm for finding the structure of protein backbones and side chains.  

PubMed

Some information about protein structure can be obtained by using Nuclear Magnetic Resonance (NMR) techniques, but they provide only a sparse set of distances between atoms in a protein. The Molecular Distance Geometry Problem (MDGP) consists in determining the three-dimensional structure of a molecule using a set of known distances between some atoms. Recently, a Branch and Prune (BP) algorithm was proposed to calculate the backbone of a protein, based on a discrete formulation for the MDGP. We present an extension of the BP algorithm that can calculate not only the protein backbone, but the whole three-dimensional structure of proteins. PMID:23649739

Sallaume, Silas; Martins, Simone de Lima; Ochi, Luiz Satoru; Da Silva, Warley Gramacho; Lavor, Carlile; Liberti, Leo

2013-01-01

203

Nonparametric Combinatorial Sequence Models  

NASA Astrophysics Data System (ADS)

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.

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

204

Remote Enantioselection Transmitted by an Achiral Peptide Nucleic Acid Backbone  

NASA Technical Reports Server (NTRS)

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.

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

2000-01-01

205

Backbone assignment and secondary structure of Rnd1, an unusual Rho family small GTPase.  

PubMed

Rho GTPases have attracted considerable interest as signaling molecules due to their variety of functional roles in cells. Rnd1 is a relatively recently discovered Rho GTPase with no enzymatic activity against its bound GTP nucleotide, setting it apart from other family members. Research has revealed a critical role for Rnd1 not only in neurite outgrowth, dendrite development, axon guidance, but also in gastric cancer and in endothelial cells during inflammation. Structural information is crucial for understanding the mechanism that forms the basis for protein-protein interactions and functions, but until recently there were no reports of NMR studies directly on the Rnd1 protein. In this paper we report assignments for the majority of Rnd1 NMR resonances based on 2D and 3D NMR spectra. Rnd1 assignment was a challenging task, however, despite optimization strategies that have facilitated NMR studies of the protein (Cao and Buck in Small GTPase 2:295-304, 2012). Besides common triple-resonance experiments, 3D HNCA, 3D HN(CO)CA, 3D HNCO which are usually employed for sequence assignment, 3D NOESY experiments and specific labeling of 13 kinds of amino acids were also utilized to gain as many (1)H(N), (13)C, and (15)N resonances assignments as possible. For 170 cross peaks observed out of 183 possible mainchain N-H correlations in the (1)H-(15)N TROSY spectrum, backbone assignment was finally completed for 127 resonances. The secondary structure was then defined by chemical shifts and TALOS+ based on the assignments. The overall structure in solution compares well with that of Rnd1 in a crystal, except for two short segments, residues 77-83 and residues 127-131. Given that some features are shared among Rho GTPases, Rnd1 assignments are also compared with two other family members, Cdc42 and Rac1. The overall level of Rnd1 assignment is lower than for Cdc42 and Rac1, consistent with its lower stability and possibly increased internal dynamics. However, while the Rnd1 switch II region remained un-assigned, the switch I region could be more fully assigned compared to Cdc42 and Rac1. The NMR assignment and structure analysis reported here provides a robust basis for future study of the binding between Rnd1 and other proteins, as well as for further studies of the molecular function of this unusual GTPase. PMID:22618864

Cao, Shufen; Mao, Xi'an; Liu, Deli; Buck, Matthias

2013-10-01

206

Automated backbone assignment of labeled proteins using the threshold accepting algorithm  

Microsoft Academic Search

The sequential assignment of backbone resonances is the first step in the structure determination of proteins by heteronuclear NMR. For larger proteins, an assignment strategy based on proton side-chain information is no longer suitable for the use in an automated procedure. Our program PASTA (Protein ASsignment by Threshold Accepting) is therefore designed to partially or fully automate the sequential assignment

Michael Leutner; Ruth M. Gschwind; Jens Liermann; Christian Schwarz; Gerd Gemmecker; Horst Kessler

1998-01-01

207

An approach to alleviate link overload as observed on an IP backbone  

Microsoft Academic Search

Shortest path routing protocols may suffer from con- gestion due to the use of a single shortest path between a source and a destination. The goal of our work is to first understand how links become overloaded in an IP backbone, and then to explore if the routing protocol, — either in its existing form, or in some enhanced form

Sundar Iyer; Supratik Bhattacharyya; Nina Taft; Christophe Diot

2003-01-01

208

Extended Medium Observation (EMO) — A load-aware metric for routing in wireless mesh backbone networks  

Microsoft Academic Search

The main advantage of using specific routing algorithms like AODV-ST or OLSR in wireless mesh backbone networks is their optimized handling of throughput from border nodes to each other. However, currently used metrics tend to ignore load situations and thus result in overloaded clusters within the mesh network. Our work presents a novel approach for load-based routing. We developed load

Heiko Kopp; Martin Krohn; Djamshid Tavangarian

2008-01-01

209

Human somatostatin receptor specificity of backbone-cyclic analogues containing novel sulfur building units.  

PubMed

Somatostatin-14 (somatostatin) and its clinically available analogues octreotide, lanreotide, and vapreotide are potent inhibitors of growth hormone, insulin, and glucagon release. Recently, a novel backbone cyclic somatostatin analogue c(GABA-Phe-Trp-(D)Trp-Lys-Thr-Phe-GlyC3-NH(2)) (analogue 1, PTR 3173) that possesses in vivo endocrine selectivity was described. This long-acting octapeptide exhibits high affinity to human recombinant somatostatin receptors (hsst) hsst2, hsst4, and hsst5. Its novel binding profile resulted in potent in vivo inhibition of growth hormone but not of insulin release. We report the synthesis, bioactivity, and structure-activity relationship studies of compounds related to 1. In these analogues, the lactam bridge of 1 was replaced by a backbone disulfide bridge. We present a novel approach for conformational constraint of peptides by utilizing sulfur-containing building units for on-resin backbone cyclization. These disulfide backbone cyclic analogues of 1 showed significant metabolic stability as tested in various enzyme mixtures. Receptor binding assays revealed different receptor selectivity profiles for these analogues in comparison to their prototype. It was found that analogues of 1, bearing a disulfide bridge, had increased selectivity to hsst2 and hsst5; however, they exhibited weaker affinity to hsst4 as compared to 1. These studies imply that ring chemistry, ring size, and ring position of the peptide template may affect the receptor binding selectivity. PMID:11931620

Gazal, Sharon; Gelerman, Garry; Ziv, Ofer; Karpov, Olga; Litman, Pninit; Bracha, Moshe; Afargan, Michel; Gilon, Chaim

2002-04-11

210

Interconnection and Competition among Asymmetric Networks in the Internet Backbone Market  

Microsoft Academic Search

We examine the interrelation between interconnection and competition in the Internet backbone market. Networks that are asymmetric in size choose among dierent interconnection regimes and compete for end-users. We show that a direct interconnection regime, peering, softens competition as com- pared to indirect interconnection since asymmetries become less inuential when networks peer. If interconnection fees are paid, the smaller network

Eric Jahna; Jens Pr

211

Design and implementation of a bootstrapping model for free-space optical backbone networks  

Microsoft Academic Search

Establishing and initially configuring a Free Space Optical (FSO) backbone is a challenging problem, especially when nodes only have local connectivity information and a limited number of transceivers. The problem of configuring an initial connected topology or bootstrapping a directional FSO network can be formulated as a Minimum Degree Spanning Tree (MDST) problem, which is known to be NP-Complete. Recently,

Jaime Llorca; Archana Anibha; Stuart Milner

2006-01-01

212

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

PubMed Central

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

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

2006-01-01

213

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

PubMed

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

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

2006-03-01

214

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

ERIC Educational Resources Information Center

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…

Jerome, Brian; Fuqua, Paul

215

Lactobacillus plantarum possesses the capability for wall teichoic acid backbone alditol switching  

PubMed Central

Background Specific strains of Lactobacillus plantarum are marketed as health-promoting probiotics. The role and interplay of cell-wall compounds like wall- and lipo-teichoic acids (WTA and LTA) in bacterial physiology and probiotic-host interactions remain obscure. L. plantarum WCFS1 harbors the genetic potential to switch WTA backbone alditol, providing an opportunity to study the impact of WTA backbone modifications in an isogenic background. Results Through genome mining and mutagenesis we constructed derivatives that synthesize alternative WTA variants. The mutants were shown to completely lack WTA, or produce WTA and LTA that lack D-Ala substitution, or ribitol-backbone WTA instead of the wild-type glycerol-containing backbone. DNA micro-array experiments established that the tarIJKL gene cluster is required for the biosynthesis of this alternative WTA backbone, and suggest ribose and arabinose are precursors thereof. Increased tarIJKL expression was not observed in any of our previously performed DNA microarray experiments, nor in qRT-PCR analyses of L. plantarum grown on various carbon sources, leaving the natural conditions leading to WTA backbone alditol switching, if any, to be identified. Human embryonic kidney NF-?B reporter cells expressing Toll like receptor (TLR)-2/6 were exposed to purified WTAs and/or the TA mutants, indicating that WTA is not directly involved in TLR-2/6 signaling, but attenuates this signaling in a backbone independent manner, likely by affecting the release and exposure of immunomodulatory compounds such as LTA. Moreover, human dendritic cells did not secrete any cytokines when purified WTAs were applied, whereas they secreted drastically decreased levels of the pro-inflammatory cytokines IL-12p70 and TNF-? after stimulation with the WTA mutants as compared to the wild-type. Conclusions The study presented here correlates structural differences in WTA to their functional characteristics, thereby providing important information aiding to improve our understanding of molecular host-microbe interactions and probiotic functionality.

2012-01-01

216

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

PubMed Central

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.

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

2013-01-01

217

FiberDock: Flexible induced-fit backbone refinement in molecular docking.  

PubMed

Upon binding, proteins undergo conformational changes. These changes often prevent rigid-body docking methods from predicting the 3D structure of a complex from the unbound conformations of its proteins. Handling protein backbone flexibility is a major challenge for docking methodologies, as backbone flexibility adds a huge number of degrees of freedom to the search space, and therefore considerably increases the running time of docking algorithms. Normal mode analysis permits description of protein flexibility as a linear combination of discrete movements (modes). Low-frequency modes usually describe the large-scale conformational changes of the protein. Therefore, many docking methods model backbone flexibility by using only few modes, which have the lowest frequencies. However, studies show that due to molecular interactions, many proteins also undergo local and small-scale conformational changes, which are described by high-frequency normal modes. Here we present a new method, FiberDock, for docking refinement which models backbone flexibility by an unlimited number of normal modes. The method iteratively minimizes the structure of the flexible protein along the most relevant modes. The relevance of a mode is calculated according to the correlation between the chemical forces, applied on each atom, and the translation vector of each atom, according to the normal mode. The results show that the method successfully models backbone movements that occur during molecular interactions and considerably improves the accuracy and the ranking of rigid-docking models of protein-protein complexes. A web server for the FiberDock method is available at: http://bioinfo3d.cs.tau.ac.il/FiberDock. PMID:20077569

Mashiach, Efrat; Nussinov, Ruth; Wolfson, Haim J

2010-05-01

218

An Adaptive Broadband Mobile Ad-Hoc Radio Backbone System; DARPA NetCentric Demonstration - Ft. Benning, GA, January 2006  

Microsoft Academic Search

This paper describes a novel autonomously adaptive networked radio system that provides a broadband tactical mobile backbone to enable netcentric warfare. The system was successfully demonstrated to seamlessly interconnect multiple heterogeneous networked radio systems during the DARPA NetCentric (NC) demonstration at Ft. Benning, GA in January 2006, serving as the high availability terrestrial backbone link between dismount units that were

Scott Seidel; Tim Krout; Larry Stotts

2006-01-01

219

Significant role of the DNA backbone in mediating the transition origin of electronic excitations of B-DNA--implication from long range corrected TDDFT and quantified NTO analysis.  

PubMed

We systematically investigate the possible complex transition origin of electronic excitations of giant molecular systems by using the recently proposed QNTO analysis [J.-H. Li, J.-D. Chai, G. Y. Guo and M. Hayashi, Chem. Phys. Lett., 2011, 514, 362.] combined with long-range corrected TDDFT calculations. Thymine (Thy) related excitations of a B-DNA biomolecule are then studied as examples, where the model systems have been constructed by extracting from the perfect or an X-ray crystal (PDB code 3BSE) B-DNA structure with at least one Thy included. In the first part, we consider the systems composed of a core molecular segment (e.g. Thy, or di-Thy) and a surrounding physical/chemical environment of interest (e.g. backbone, adjacent stacking nucleobases) in gas phase and examine how the excitation properties of the core vary in response to the environment. We find that the orbitals contributed by the DNA backbone and surrounding nucleobases often participate in a transition of Thy-related excitations affecting their composition, absorption energy, and oscillator strength. A vast number of strongly backbone-orbital involved excitations are also found at an absorption wavelength below ?180 nm predicted by TD-?B97X. In the second part, we take into account geometrically induced variation of the excitation properties of various B-DNA segments, e.g. di-Thy, dTpdT etc., obtained from different sources (ideal and 3BSE). It is found that the transition origin of several Thy-related excitations of these segments is sensitive to slight conformational variations, suggesting that DNA with thermal motions may from time to time exhibit very different photo-induced physical and/or chemical processes. PMID:22641198

Li, Jian-Hao; Chai, Jeng-Da; Guo, Guang-Yu; Hayashi, Michitoshi

2012-07-01

220

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

NASA Astrophysics Data System (ADS)

Among the suite of commonly used backbone experiments, HNCACO presents an unresolved sensitivity limitation due to fast 13CO transverse relaxation and passive 13C ?- 13C ? coupling. Here, we present a high-sensitivity 'just-in-time' (JIT) HN(CA)CO pulse sequence that uniformly refocuses 13C ?- 13C ? 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 13C ? 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 13C ? refocusing and 13C ?- 13C ? 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.

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

2006-07-01

221

Understanding the molecular determinants driving the immunological specificity of the protective pilus 2a backbone protein of group B streptococcus.  

PubMed

The pilus 2a backbone protein (BP-2a) is one of the most structurally and functionally characterized components of a potential vaccine formulation against Group B Streptococcus. It is characterized by six main immunologically distinct allelic variants, each inducing variant-specific protection. To investigate the molecular determinants driving the variant immunogenic specificity of BP-2a, in terms of single residue contributions, we generated six monoclonal antibodies against a specific protein variant based on their capability to recognize the polymerized pili structure on the bacterial surface. Three mAbs were also able to induce complement-dependent opsonophagocytosis killing of live GBS and target the same linear epitope present in the structurally defined and immunodominant domain D3 of the protein. Molecular docking between the modelled scFv antibody sequences and the BP-2a crystal structure revealed the potential role at the binding interface of some non-conserved antigen residues. Mutagenesis analysis confirmed the necessity of a perfect balance between charges, size and polarity at the binding interface to obtain specific binding of mAbs to the protein antigen for a neutralizing response. PMID:23825940

Nuccitelli, Annalisa; Rinaudo, C Daniela; Brogioni, Barbara; Cozzi, Roberta; Ferrer-Navarro, Mario; Yero, Daniel; Telford, John L; Grandi, Guido; Daura, Xavier; Zacharias, Martin; Maione, Domenico

2013-01-01

222

Understanding the Molecular Determinants Driving the Immunological Specificity of the Protective Pilus 2a Backbone Protein of Group B Streptococcus  

PubMed Central

The pilus 2a backbone protein (BP-2a) is one of the most structurally and functionally characterized components of a potential vaccine formulation against Group B Streptococcus. It is characterized by six main immunologically distinct allelic variants, each inducing variant-specific protection. To investigate the molecular determinants driving the variant immunogenic specificity of BP-2a, in terms of single residue contributions, we generated six monoclonal antibodies against a specific protein variant based on their capability to recognize the polymerized pili structure on the bacterial surface. Three mAbs were also able to induce complement-dependent opsonophagocytosis killing of live GBS and target the same linear epitope present in the structurally defined and immunodominant domain D3 of the protein. Molecular docking between the modelled scFv antibody sequences and the BP-2a crystal structure revealed the potential role at the binding interface of some non-conserved antigen residues. Mutagenesis analysis confirmed the necessity of a perfect balance between charges, size and polarity at the binding interface to obtain specific binding of mAbs to the protein antigen for a neutralizing response.

Nuccitelli, Annalisa; Rinaudo, C. Daniela; Brogioni, Barbara; Cozzi, Roberta; Ferrer-Navarro, Mario; Yero, Daniel; Telford, John L.; Grandi, Guido; Daura, Xavier; Zacharias, Martin; Maione, Domenico

2013-01-01

223

Predict protein structural class for low-similarity sequences by evolutionary difference information into the general form of Chou?s pseudo amino acid composition.  

PubMed

Knowledge of protein structural class plays an important role in characterizing the overall folding type of a given protein. At present, it is still a challenge to extract sequence information solely using protein sequence for protein structural class prediction with low similarity sequence in the current computational biology. In this study, a novel sequence representation method is proposed based on position specific scoring matrix for protein structural class prediction. By defined evolutionary difference formula, varying length proteins are expressed as uniform dimensional vectors, which can represent evolutionary difference information between the adjacent residues of a given protein. To perform and evaluate the proposed method, support vector machine and jackknife tests are employed on three widely used datasets, 25PDB, 1189 and 640 datasets with sequence similarity lower than 25%, 40% and 25%, respectively. Comparison of our results with the previous methods shows that our method may provide a promising method to predict protein structural class especially for low-similarity sequences. PMID:24735902

Zhang, Lichao; Zhao, Xiqiang; Kong, Liang

2014-08-21

224

Anion-Conducting Polymer, Composition, and Membrane  

DOEpatents

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.

Pivovar, Bryan S. (Los Alamos, NM) [Los Alamos, NM; Thorn, David L. (Los Alamos, NM) [Los Alamos, NM

2008-10-21

225

Anion-conducting polymer, composition, and membrane  

DOEpatents

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.

Pivovar, Bryan S. (Los Alamos, NM) [Los Alamos, NM; Thorn, David L. (Los Alamos, NM) [Los Alamos, NM

2009-09-01

226

Anion-conducting polymer, composition, and membrane  

DOEpatents

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.

Pivovar, Bryan S. (Los Alamos, NM) [Los Alamos, NM; Thorn, David L. (Los Alamos, NM) [Los Alamos, NM

2010-12-07

227

Anion-conducting polymer, composition, and membrane  

SciTech Connect

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.

Pivovar, Bryan S. (Los Alamos, NM); Thorn, David L. (Los Alamos, NM)

2011-11-22

228

Branching of the galacturonan backbone of comaruman, a pectin from the marsh cinquefoil Comarum palustre L.  

PubMed

Galacturonan, the main constituent of the backbone (core) of the comaruman macromolecule, a pectin from the marsh cinquefoil Comarum palustre L., was obtained on partial acid hydrolysis of the pectin. Using atomic force microscopy and methylation analysis of the galacturonan, the backbone of the comaruman macromolecule was shown to contain branches as side chains consisting of alpha-1,4-linked residues of D-galactopyranosyl uronic acid attached to the 2- and 3-positions of the galacturonic acid residues of the core, in addition to linear regions of alpha-1,4-D-galacturonan. A few side chains appear to attach to 2,3-positions of the D-galacturonic acid residues. PMID:16732733

Ovodova, R G; Popov, S V; Bushneva, O A; Golovchenko, V V; Chizhov, A O; Klinov, D V; Ovodov, Yu S

2006-05-01

229

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

PubMed Central

Amide n –?* and ?-?* 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.

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

2010-01-01

230

Finding Good Tours for Huge Euclidean TSP Instances by Iterative Backbone Contraction  

Microsoft Academic Search

\\u000a This paper presents an iterative, highly parallelizable approach to find good tours for very large instances of the Euclidian\\u000a version of the well-known Traveling Salesman Problem (TSP). The basic idea of the approach consists of iteratively transforming\\u000a the TSP instance to another one with smaller size by contracting pseudo backbone edges. The iteration is stopped, if the new\\u000a TSP instance

Christian Ernst; Changxing Dong; Gerold Jäger; Dirk Richter; Paul Molitor

2010-01-01

231

Heteroaromatic Moieties in the Sphingosine Backbone of ?-Galactosylceramides for Noncovalent Interactions with CD1d  

PubMed Central

A series of ?-GalCer analogues containing heterocyclic and aromatic moieties in the sphingosine backbone were synthesized to improve the selectivity in the Th1/Th2 cytokine profile via noncovalent interaction with three aromatic residues at the binding pocket of CD1d. In vitro and in vivo biological evaluations revealed the treatment of ?-GalCer analogue (6) induced the selective stimulation of natural killer T cells to facilitate the secretion of Th2 cytokines.

2012-01-01

232

Probing local backbone geometries in intrinsically disordered proteins by cross-correlated NMR relaxation.  

PubMed

An ultra-high-resolution NMR experiment for the measurement of intraresidue (1)H(i)-(15)N(i)-(13)C'(i) dipolar-chemical shift anisotropy relaxation interference is employed to extract information about local backbone geometries in intrinsically disordered proteins. The study of tumor suppressor BASP1 revealed a population shift of ?-turn geometries at low pH conditions and a compaction of the BASP1 structural ensemble. PMID:23520002

Stanek, Jan; Saxena, Saurabh; Geist, Leonhard; Konrat, Robert; Ko?mi?ski, Wiktor

2013-04-22

233

Tritium containing polymers having a polymer backbone substantially void of tritium  

DOEpatents

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.

Jensen, George A. (Richland, WA); Nelson, David A. (Richland, WA); Molton, Peter M. (Richland, WA)

1992-01-01

234

Probability distribution of the shortest path on the percolation cluster, its backbone, and skeleton  

Microsoft Academic Search

We consider the mean distribution functions Phi(r\\\\|l), PhiB(r\\\\|l), and PhiS(r\\\\|l), giving the probability that two sites on the incipient percolation cluster, on its backbone and on its skeleton, respectively, connected by a shortest path of length l are separated by an Euclidean distance r. Following a scaling argument due to de Gennes for self-avoiding walks, we derive analytical expressions for

Markus Porto; Shlomo Havlin; H. Eduardo Roman; Armin Bunde

1998-01-01

235

Lubricant Pickup of Ultra-Thin PFPE Lubricants With Different Backbone Structures  

Microsoft Academic Search

Lubricant pickups on different perfluoropolyether (PFPE)-lubricant (Z-tetraol, D-4OH, and QA-40) films were compared by using a slider surface analyzing (SSA) tester developed to observe the lubricant thickness mapping on the slider surfaces after the heads slide on the disk surfaces. These lubricants have the same four OH functional end-groups but different backbones. Z-tetraol showed the least lubricant pickup among the

H. Tani; K. Iwasaki; Y. Maruyama; I. Ota; N. Tagawa

2011-01-01

236

Lubricant pickup on ultra-thin PFPE lubricants with different backbone structure  

Microsoft Academic Search

Lubricant pickup on different PFPE lubricant (Z-tetraol, D-40H, and QA-40) film was compared by the slider surface analyzing tester (SSA tester) developed to observe the lubricant thickness mapping on the slider surfaces after the heads flying on the disk surfaces. These lubricants have same four OH functional end-groups, however, these have the different backbone. Z-tetraol showed smallest amount of lubricant

H. Tani; K. Iwasaki; M. Nakayama; Y. Maruyama; I. Ota; N. Tagawa

2010-01-01

237

Analysis of Measured Single-Hop Delay from an Operational Backbone Network  

Microsoft Academic Search

We measure and analyze the single-hop packet delay through op- erational routers in a backbone IP network. First we present our delay measurements through a single router. Then we identify step- by-step the factors contributing to single-hop delay. In addition to packet processing, transmission, and queueing delays, we iden- tify the presence of very large delays due to non-work-conserving router

Konstantina Papagiannaki; Sue B. Moon; Chuck Fraleigh; Patrick Thiran; Fouad A. Tobagi; Christophe Diot

2002-01-01

238

Tritium containing polymers having a polymer backbone substantially void of tritium  

DOEpatents

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.

Jensen, G.A.; Nelson, D.A.; Molton, P.M.

1992-03-31

239

An efficient randomized algorithm for contact-based NMR backbone resonance assignment  

Microsoft Academic Search

Motivation: Backbone resonance assignment is a critical bottleneck in studies of protein structure, dynamics and interactions by nuclear magnetic resonance (NMR) spectroscopy. A minimalist approach to assignment, which we call 'contact-based', seeks to dramatically reduce experimental time and expense by replacing the standard suite of through-bond experiments with the through-space (nuclear Overhauser enhancement spectroscopy, NOESY) experiment. In the contact-based approach,

Hetunandan Kamisetty; Chris Bailey-kellogg; Gopal Pandurangan

2006-01-01

240

Backbone dynamics of the cytotoxic Ribonuclease ?-sarcin by 15 N NMR relaxation methods  

Microsoft Academic Search

The cytotoxic ribonuclease a-sarcin is a 150-residue protein that inactivates ribosomes by selectively cleaving a single phosphodiester bond in a strictly conserved rRNA loop. In order to gain insights on the molecular basis of its highly specific activity, we have previously determined its solution structure and studied its electrostatics properties. Here, we complement those studies by analysing the backbone dynamics

José Manuel Pérez-Cañadillas; Marc Guenneugues; Ramón Campos-Olivas; Jorge Santoro; Alvaro Martínez del Pozo; José G. Gavilanes; Manuel Rico; Marta Bruix

2002-01-01

241

A new strategy for backbone resonance assignment in large proteins using a MQ-HACACO experiment  

Microsoft Academic Search

A new strategy of backbone resonance assignment is proposed based on a combination of the most sensitive TROSY-type triple resonance experiments such as TROSY-HNCA and TROSY-HNCO with a new 3D multiple-quantum HACACO experiment. The favourable relaxation properties of the multiple-quantum coherences and signal detection using the 13C' antiphase coherences optimize the performance of the proposed experiment for application to larger

Konstantin Pervushin; Alexander Eletsky

2003-01-01

242

Automated NMR determination of protein backbone dihedral angles from cross-correlated spin relaxation  

Microsoft Academic Search

The simultaneous interpretation of a suite of dipole-dipole and dipole-CSA cross-correlation rates involving the backbone nuclei 13Ca, 1Ha,13CO, 15N and 1HN can be used to resolve the ambiguities associated with each individual cross-correlation rate. The method is based on the transformation of experimental cross-correlation rates via calculated values based on standard peptide plane geometry and solid-state 13CO CSA parameters into

Karin Kloiber; Wolfgang Schüler; Robert Konrat

2002-01-01

243

Near-ultraviolet light-emitting diodes based on ?-conjugated linear silicon-backbone polymers  

Microsoft Academic Search

We report the basic device characteristics of light-emitting diodes (LEDs) based on linear silicon-backbone polymers, polysilanes, with a view to the possibility of employing them as an emissive material in a solid-state light source in the near-ultraviolet (NUV) or ultraviolet (UV) region. The LEDs we fabricated have a single-layer structure consisting of a thin film of polysilane polymer, together with

Hiroyuki Suzuki; Satoshi Hoshino; Chien-Hua Yuan; Michiya Fujiki; Seiji Toyoda; Nobuo Matsumoto

1998-01-01

244

Transit versus (Paid) Peering: Interconnection and Competition in the Internet Backbone Market  

Microsoft Academic Search

We examine the strategic interaction between interconnection and compe- tition in the Internet backbone market. Networks asymmetric in size choose among dierent interconnection regimes, IP-Transit, Bill-and-Keep Peering, and Paid Peering, and compete for end-users. We show that suciently sym- metric networks enter a Peering agreement while otherwise use an intermedi- ary network for exchanging trac. This is structurally in line

Eric Jahn; Jens Pr

245

Backbone modification of a polypeptide drug alters duration of action in vivo.  

PubMed

Systematic modification of the backbone of bioactive polypeptides through ?-amino acid residue incorporation could provide a strategy for generating molecules with improved drug properties, but such alterations can result in lower receptor affinity and potency. Using an agonist of parathyroid hormone receptor-1 (PTHR1), a G protein-coupled receptor in the B-family, we present an approach for ??? residue replacement that enables both high activity and improved pharmacokinetic properties in vivo. PMID:24929976

Cheloha, Ross W; Maeda, Akira; Dean, Thomas; Gardella, Thomas J; Gellman, Samuel H

2014-07-01

246

Small-Time Scaling Beahviors of Internet Backbone Traffic: An Empirical Study  

Microsoft Academic Search

We study the small-time (sub-seconds) scaling behaviors of Internet backbone traffic, based on traces collected from OC3\\/12\\/48 links in a tier-1 ISP. We observe that for a majority of these traces, the (second-order) scaling exponents at small time scales (1ms - 100ms) are fairly close to 0.5, indicating that traffic fluctuations at these time scales are (nearly) uncorrelated. In addition,

Zhi-li Zhang; Vinay J. Ribeiro; Sue B. Moon; Christophe Diot

2003-01-01

247

Radical Scavenging Activity of Seela ( Sphyraena barracuda) and Ribbon Fish ( Lepturacanthus savala) Backbone Protein Hydrolysates  

Microsoft Academic Search

We have investigated the antioxidant activity of protein hydrolysates prepared from backbones of two commercially important\\u000a fishes; seela (Sphyraena barracuda) and ribbon fish (Lepturacanthus savala). Pepsin and trypsin hydrolysates were found more potent to inhibit lipid peroxidation in case of ribbon and seela fish respectively\\u000a and were further purified by using fast protein liquid chromatography on anion exchange and gel

R. A. NazeerR; R. Deeptha; R. Jaiganesh; N. S. Sampathkumar; Shabeena Yousuf Naqash

2011-01-01

248

Factors Influencing the Stability of Cyclotides: Proteins with a Circular Backbone and Cystine Knot Motif  

Microsoft Academic Search

Cyclotides are a large family of mini-proteins that have the distinguishing features of a head-to-tail cyclised backbone and a cystine knot formed by six conserved cysteine residues. They are present in plants from the Rubiaceae, Violaceae and Cucurbitaceae families. The unique structural features of the cyclotides make them extremely resistant to chemical, thermal and proteolytic degradation. In this article we

Maša ?emažar; David J Craik

2006-01-01

249

Cytokinin vectors mediate marker-free and backbone-free plant transformation  

Microsoft Academic Search

Conventional Agrobacterium-mediated transformation methods rely on complex and genotype-specific tissue culture media for\\u000a selection, proliferation, and regeneration of genetically modified cells. Resulting transgenic plants may not only contain\\u000a selectable marker genes but also carry fragments of the vector backbone. Here, we describe a new method for the production\\u000a of transgenic plants that lack such foreign DNA. This method employs vectors

Craig M. Richael; Marina Kalyaeva; Robert C. Chretien; Hua Yan; Sathya Adimulam; Artesia Stivison; Caius M. Rommens

2008-01-01

250

Contribution of the peptide backbone to the action of oxytocin analogs.  

PubMed Central

This investigation was undertaken to evaluate the functional contribution of the peptide backbone of oxytocin in its interaction with receptor. Corey-Pauling-Koltun models of (Gly-7) deaminooxytocin, deaminotocinamide, and their respective retro-D-analogs built in any specific conformation (e.g., the Walter-Urry model for oxytocin) have a quai-equivalent topochemical arrangement of amino-acid side chains; however, the CO and NH elements of the peptide backbone of the retro-D-analog are reversed. The retro-D-analogs of deaminotocinamide and (Gly-7) deaminooxytocin (prepared using D-alle for L-Ile) and their respective N-formyl derivatives were assayed for uterotonic activity relative to related L-peptides. All retro-D-analogs (tested at concentrations ranging from 10-10 to 10-5 M) were devoid of angonistic (or antagonistic) activity in the isolated rat uterus, except for the retro-D-(D-alle-3, Gly-7) deaminooxytocinamine, which retains a terminal NH-2 group on the tail; the latter is a partial agonist with very low affinity. The results obtained with retro-D-analogs indicate that one or more of the elements of the peptide backbone of the tocinamide ring are essential for "occupation" and "activation" of uterine receptors. Oxytocin action may be the resultant of multiple hydrogen-bonding interactions between CO, NH, NH-2, and OH groups of the hormone with complementary groups on receptor, made possible by appropriate hydrophobic bonding.

Hechter, O; Kato, T; Nakagawa, S H; Yang, F; Flouret, G

1975-01-01

251

Conjugated backbone orientation variation in high mobility regioregular PT based copolymers  

NASA Astrophysics Data System (ADS)

The synthesis of novel solution processable conjugated polymers is an active field of study due to the potential to fabricate low cost, high though-put electronic devices such as organic field effect transistors (OFET). A regioregular copolymer based on cyclopenta[2,1-b:3,4-b']dithiophene (CDT) and pyridal[2,1,3]thiadiazole (PT) structural units has been prepared by using polymerization reactions involving reactants specifically designed to avoid random orientation of the asymmetric PT heterocycle. Compared to it's regiorandom counterpart, the regioregular polymer exhibits a two orders of magnitude increase in hole mobility from 0.005 to 0.6 cm^2V-1 s-1. A combination of X-ray scattering techniques were employed to quantitatively access the degree of orientation and crystallinity in thin films (15-20 nm) that matched device architecture. We examined the backbone orientation dependence as a function of depth via grazing incidence wide angle X-ray scattering (GIWAXS) and found significant differences in the backbone stacking orientation between the regiorandom and regioregular copolymers. These experiments suggest the backbone regularity leads to significant differences in the structural arrangement and it is another important design criteria to consider in the design of new conjugated copolymers with asymmetric structural units.

Perez, Louis; Ying, Lei; Bazan, Guillermo; Kramer, Edward

2013-03-01

252

Backbone and Side-Chain Contributions in Protein Denaturation by Urea  

PubMed Central

Urea is a commonly used protein denaturant, and it is of great interest to determine its interaction with various protein groups to elucidate the molecular basis of its effect on protein stability. Using the Trp-cage miniprotein as a model system, we report what we believe to be the first computation of changes in the preferential interaction coefficient of the protein upon urea denaturation from molecular-dynamics simulations and examine the contributions from the backbone and the side-chain groups. The preferential interaction is obtained from reversible folding/unfolding replica exchange molecular-dynamics simulations of Trp-cage in presence of urea, over a wide range of urea concentration. The increase in preferential interaction upon unfolding is dominated by the side-chain contribution, rather than the backbone. Similar trends are observed in simulations using two different force fields, Amber94 and Amber99sb, for the protein. The magnitudes of the side-chain and backbone contributions differ in the two force fields, despite containing identical protein-solvent interaction terms. The differences arise from the unfolded ensembles sampled, with Amber99sb favoring conformations with larger surface area and lower helical content. These results emphasize the importance of the side-chain interactions with urea in protein denaturation, and highlight the dependence of the computed driving forces on the unfolded ensemble sampled.

Canchi, Deepak R.; Garcia, Angel E.

2011-01-01

253

Temperature dependence of fast carbonyl backbone dynamics in chicken villin headpiece subdomain  

PubMed Central

Temperature-dependence of protein dynamics can provide information on details of the free energy landscape by probing the characteristics of the potential responsible for the fluctuations. We have investigated the temperature-dependence of picosecond to nanosecond backbone dynamics at carbonyl carbon sites in chicken villin headpiece subdomain protein using a combination of three NMR relaxation rates: 13C? longitudinal rate, and two cross-correlated rates involving dipolar and chemical shift anisotropy (CSA) relaxation mechanisms, 13C?/13C??13C? CSA/dipolar and 13C?/13C??15N CSA/dipolar. Order parameters have been extracted using the Lipari-Szabo model-free approach assuming a separation of the time scales of internal and molecular motions in the 2–16°C temperature range. There is a gradual deviation from this assumption from lower to higher temperatures, such that above 16°C the separation of the time scales is inconsistent with the experimental data and, thus, the Lipari-Szabo formalism can not be applied. While there are variations among the residues, on the average the order parameters indicate a markedly steeper temperature dependence at backbone carbonyl carbons compared to that probed at amide nitrogens in an earlier study. This strongly advocates for probing sites other than amide nitrogen for accurate characterization of the potential and other thermodynamics characteristics of protein backbone.

Vugmeyster, Liliya; Ostrovsky, Dmitry

2012-01-01

254

Populations of the three major backbone conformations in 19 amino acid dipeptides  

PubMed Central

The amide III region of the peptide infrared and Raman spectra has been used to determine the relative populations of the three major backbone conformations (PII, ?, and ?R) in 19 amino acid dipeptides. The results provide a benchmark for force field or other methods of predicting backbone conformations in flexible peptides. There are three resolvable backbone bands in the amide III region. The major population is either PII or ? for all dipeptides except Gly, whereas the ?R population is measurable but always minor (? 10%) for 18 dipeptides. (The Gly ?,? map is complex and so is the interpretation of the amide III bands of Gly.) There are substantial differences in the relative ? and PII populations among the 19 dipeptides. The band frequencies have been assigned as PII, 1,317–1,306 cm-1; ?R, 1,304–1,294 cm-1; and ?, 1,294–1,270 cm-1. The three bands were measured by both attenuated total reflection spectroscopy and by Raman spectroscopy. Consistent results, both for band frequency and relative population, were obtained by both spectroscopic methods. The ? and PII bands were assigned from the dependence of the 3J(HN,H?) coupling constant (known for all 19 dipeptides) on the relative ? population. The PII band assignment agrees with one made earlier from Raman optical activity data. The temperature dependences of the relative ? and PII populations fit the standard model with Boltzmann-weighted energies for alanine and leucine between 30 and 60?°C.

Grdadolnik, Joze; Mohacek-Grosev, Vlasta; Baldwin, Robert L.; Avbelj, Franc

2011-01-01

255

Probing the Folding Transition State Structure of the Villin Headpiece Subdomain via Sidechain and Backbone Mutagenesis  

PubMed Central

Backbone-backbone hydrogen bonds are a common feature of native protein structures, yet their thermodynamic and kinetic influence on folding has long been debated. This is reflected by the disparity between current protein folding models, which place hydrogen bond formation at different stages along the folding trajectory. For example, previous studies have suggested that the denatured-state of the villin headpiece subdomain contains residual helical structure that may provide a bias toward the folded state by confining the conformational search associated with its folding. Although helical hydrogen bonds clearly stabilize the folded state, here we show, using an amide-to-ester mutation strategy, that the formation of backbone hydrogen bonds within helices is not rate-limiting in the folding of the subdomain, thereby suggesting that such hydrogen bonds are unlikely to be formed en route from the denatured to the transition state. On the other hand, elimination of hydrogen bonds within the turn region elicits a slower folding rate, consistent with the hypothesis that these residues are involved in the formation of a folding nucleus. While illustrating a potentially conserved aspect of helix-turn-helix folding, our results further underscore the inherent importance of turns in protein supersecondary structure formation.

Bunagan, Michelle R.; Gao, Jianmin; Kelly, Jeffery W.; Gai, Feng

2009-01-01

256

NMR Studies of Localized Water and Protein Backbone Dynamics in Mechanically Strained Elastin  

PubMed Central

We report on measurements of the dynamics of localized waters of hydration and the protein backbone of elastin, a remarkable resilient protein found in vertebrate tissues, as a function of the applied external strain. Using deuterium 2D T1–T2 NMR, we separate four reservoirs in the elastin–water system characterized by water with distinguishable mobilities. The measured correlation times corresponding to random tumbling of water localized to the protein is observed to decrease with increasing strain and is interpreted as an increase in its orientational entropy. The NMR T1 and T1? relaxation times of the carbonyl and aliphatic carbons of the protein backbone are measured and indicate a reduction in the correlation time as the elastomer strain is increased. It is argued, and supported by MD simulation of a short model elastin peptide [VPGVG]3, that the observed changes in the backbone dynamics give rise to the development of an entropic elastomeric force that is responsible for elastins’ remarkable elasticity.

Sun, Cheng; Mitchell, Odingo; Huang, Jiaxin; Boutis, Gregory S.

2013-01-01

257

Linear transgene constructs lacking vector backbone sequences generate transgenic rice plants which accumulate higher levels of proteins conferring insect resistance  

Microsoft Academic Search

Biolistic transformation was used to introduce genes encoding the insecticidal proteins snowdrop lectin (Galanthus nivalis agglutinin; GNA) and cry1Ac Bt toxin (d-endotoxin from Bacillus thuringiensis) into elite rice (Oryza sativa) cultivars. Plant transformation was carried out in parallel experiments simultaneously by using either whole plasmids containing suitable gene constructs, or the corresponding minimal gene cassettes, which were linear DNA fragments

Nguyen Thi Loc; Porntip Tinjuangjun; Angharad M. R. Gatehouse; Paul Christou; John A. Gatehouse

2002-01-01

258

Next-generation transport solutions for IP backbone networks: benefits of an ASTN-based multilayer OTN network  

NASA Astrophysics Data System (ADS)

This paper concentrates on solutions for next-generation IP (Internet Protocol) backbone networks. This is a key issue for many network operators since IP will be the dominating network layer technology on which an ever increasing number of applications with growing bandwidth requirements will be based. Without new network solutions, this trend would lead to a strong increase in number and size of IP routers while already today"s requirements make it difficult to realise large-scale IP backbone networks in a stable and cost-efficient way. This paper investigates the benefits that an appropriate transport network based on ASTN (Automatic Switched Transport Network) and OTN (Optical Transport Network) technology can bring to future IP backbone networks - providing the stable basis on which next generation IP networks can be built. Network modelling is used to show that in addition to qualitative benefits a transport network based IP backbone solution can lead to a significant reduction of network equipment cost.

Spath, Jan; Bodamer, Stefan; Glingener, Christoph

2005-02-01

259

Possible Three-Dimensional Backbone Folding Around Antibody Combining Site of Immunoglobulin MOPC167. (Reannouncement with New Availability Information).  

National Technical Information Service (NTIS)

Using a recently developed method of predicting possible three dimensional foldings of immunoglobulin backbones around antibody combining sites, we have attempted to construct the structure of immunoglobulin MOPC167 which could bind phosphorylcholine. A s...

S. E. Coutre J. M. Stanford J. G. Hovis P. W. Stevens T. T. Wu

1981-01-01

260

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

PubMed Central

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.

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

2011-01-01

261

Context and Force Field Dependence of the Loss of Protein Backbone Entropy upon Folding Using Realistic Denatured and Native State Ensembles  

PubMed Central

The loss of conformational entropy is the largest unfavorable quantity affecting a protein’s stability. We calculate the reduction in the number of backbone conformations upon folding using the distribution of backbone dihedral angles (?,?) obtained from an experimentally validated denatured state model, along with all-atom simulations for both the denatured and native states. The average loss of entropy per residue is T?SBBU-N = 0.7, 0.9, or 1.1 kcal·mol?1 at T = 298 K, depending on the force field used, with a 0.6 kcal·mol?1 dispersion across the sequence. The average equates to a decrease of a factor of 3–7 in the number of conformations available per residue (f = ?Denatured/?Native) or to a total of ftot=3n–7n for an n residue protein. Our value is smaller than most previous estimates where f = 7–20, i.e., our computed T?SBBU-N is smaller by 10–100 kcal mol?1 for n=100. The differences emerge from our use of realistic native and denatured state ensembles as well as from the inclusion of accurate local sequence preferences, neighbor effects, and correlated motions (vibrations), in contrast to some previous studies that invoke gross assumptions about the entropy in either or both states. We find that the loss of entropy primarily depends on the local environment and less on properties of the native state, with the exception of ?-helical residues in some force fields.

Baxa, Michael C.; Haddadian, Esmael J.; Jha, Abhishek K.; Freed, Karl F.; Sosnick, Tobin R.

2012-01-01

262

Structure-activity relationship and metabolic stability studies of backbone cyclization and N-methylation of melanocortin peptides.  

PubMed

Backbone cyclization (BC) and N-methylation have been shown to enhance the activity and/or selectivity of biologically active peptides and improve metabolic stability and intestinal permeability. In this study, we describe the synthesis, structure-activity relationship (SAR) and intestinal metabolic stability of a backbone cyclic peptide library, BL3020, based on the linear alpha-Melanocyte stimulating hormone analog Phe-D-Phe-Arg-Trp-Gly. The drug lead, BL3020-1, selected from the BL3020 library (compound 1) has been shown to inhibit weight gain in mice following oral administration. Another member of the BL3020 library, BL3020-17, showed improved biological activity towards the mMC4R, in comparison to BL3020-1, although neither were selective for MC4R or MC5R. N-methylation, which restrains conformational freedom while increasing metabolic stability beyond that which is imparted by BC, was used to find analogs with increased selectivity. N-methylated backbone cyclic libraries were synthesized based on the BL3020 library. SAR studies showed that all the N-methylated backbone cyclic peptides demonstrated reduced biological activity and selectivity for all the analyzed receptors. N-methylation of active backbone cyclic peptides destabilized the active conformation or stabilized an inactive conformation, rendering the peptides biologically inactive. N-methylation of backbone cyclic peptides maintained stability to degradation by intestinal enzymes. PMID:18655141

Linde, Yaniv; Ovadia, Oded; Safrai, Eli; Xiang, Zhimin; Portillo, Federico P; Shalev, Deborah E; Haskell-Luevano, Carrie; Hoffman, Amnon; Gilon, Chaim

2008-01-01

263

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

PubMed

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

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

2006-12-01

264

Arabidopsis family GT43 members are xylan xylosyltransferases required for the elongation of the xylan backbone.  

PubMed

Xylan is the second most abundant polysaccharide in plant biomass targeted for biofuel production. Therefore, it is imperative to understand the biochemical mechanism underlying xylan biosynthesis. Although previous genetic studies have identified several genes implicated in xylan biosynthesis, biochemical proof of any of their encoded proteins as a xylan xylosyltransferase (XylT) responsible for xylan backbone biosynthesis is still lacking. In this study, we investigated the enzymatic activities of two Arabidopsis thaliana GT43 members, IRX9 (Irregular Xylem9) and IRX14, which have been genetically shown to be non-redundantly involved in the elongation of the xylan backbone. IRX9 and IRX14, alone or simultaneously, were heterologously expressed in tobacco BY2 cells, and microsomes isolated from the transgenic BY2 cells were tested for XylT activity using xylotetraose (Xyl(4)) as an acceptor and UDP-[(14)C]xylose as a donor. It was found that although microsomes with expression of IRX9 or IRX14 alone exhibited little incorporation of radiolabeled xylose, a high level of incorporation of radiolabeled xylose onto Xyl(4) was conferred by microsomes with co-expression of IRX9 and IRX14. Further analysis using fluorescent anthranilic acid-labeled xylotetraose (Xyl(4)-AA) as an acceptor revealed that up to five ?-(1,4)-linked xylosyl residues were able to be transferred onto Xyl(4)-AA by microsomes with co-expression of IRX9 and IRX14. Furthermore, it was shown that xylooligomers ranging from Xyl(3)-AA to Xyl(6)-AA could all be used as acceptors for the xylosyl transfer by microsomes with co-expression of IRX9 and IRX14. Together, these findings provide the first biochemical evidence that IRX9 and IRX14 are xylosyltransferases that operate cooperatively in the elongation of the xylan backbone. PMID:22080591

Lee, Chanhui; Zhong, Ruiqin; Ye, Zheng-Hua

2012-01-01

265

On the role of thermal backbone fluctuations in myoglobin ligand gate dynamics.  

PubMed

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 ?-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. PMID:23656161

Krokhotin, Andrey; Niemi, Antti J; Peng, Xubiao

2013-05-01

266

Insights on peptide backbone N-H acidity: Structure of anions, hydration effects  

NASA Astrophysics Data System (ADS)

Despite the key role played by deamidation reactions in biochemical phenomena such as aging processes, knowledge of factors determining peptide backbone N-H acidities is scarce. We report a theoretical study on this topic by means of quantum-chemical calculations. Gas-phase acidities and pKa's in water have been estimated. The results agree reasonably well with available experimental data. Further analysis suggests that the secondary peptide structure, in addition to hydration effects, is the main factor determining pKa. In particular, we predict N-H protons to be more acidic in ?-turns than in ?-helices, a finding that may have broad biological implications.

Oliva, Antoni; Henry, Bernard; Ruiz-López, Manuel F.

2013-03-01

267

Performance Behavior of Unmanned Vehicle Aided Mobile Backbone Based Wireless Ad Hoc Networks  

NSDL National Science Digital Library

Wireless communications between a mobile node and a fixed base station are adversely affected when the node moves out of range of the base station or into an area where direct transmission is fully or partially blocked; but what if the base station was also mobile? This is the question posed by two researchers from the University of California, Los Angeles. Their solution involves positioning unmanned ground or airborne vehicles in locations that maximize coverage and network connectivity. This paper formulates the Mobile Backbone Network and its underlying protocol, and shows simulation results for the system.

Rubin, Izhak; Zhang, Runhe

268

An algorithm for converting a virtual-bond chain into a complete polypeptide backbone chain  

NASA Technical Reports Server (NTRS)

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.

Luo, N.; Shibata, M.; Rein, R.

1991-01-01

269

13C solid state NMR investigation of structural relaxation of the polymer backbone in poly (ethylmethacrylate).  

PubMed

Geometry and time scale of structural relaxation of poly(n-alkylmethacrylates) above the glass transition is studied by temperature dependent one- and two-dimensional 13C-NMR spectroscopy. The geometry of the isotropization of the polymer backbone as deduced from detailed analysis of spectral line shapes is identified as random angular jumps. Analysis of echo decays confirms that at a given temperature this isotropization can adequately be described with a single correlation time. The results are discussed in terms of conformational memory and local structure recently identified in these polymeric glasses. PMID:15589734

Wind, Michael; Brombacher, Lothar; Heuer, Andreas; Graf, Robert; Spiess, Hans Wolfgang

2005-01-01

270

Solvent-induced backbone fluctuations and the collective librational dynamics of lysozyme studied by terahertz spectroscopy  

NASA Astrophysics Data System (ADS)

THz spectroscopy is used to investigate the dynamics of the globular protein hen egg white lysozyme under varying hydration and temperature conditions. An analysis of the experimental spectra has revealed that the amount of solvent in the hydration shell has a strong influence on the low-frequency protein conformational dynamics and also the arrangement of hydrogen bonds in the protein secondary structure. Furthermore at a hydration level >0.2 we identify collective backbone fluctuations in the protein secondary structure that are not present at low hydration. It is possible that these solvent induced modes are important for the biological function of the protein.

Woods, K. N.

2010-03-01

271

The Effects of NHC-Backbone Substitution on Efficiency in Ruthenium-based Olefin Metathesis  

PubMed Central

A series of ruthenium olefin metathesis catalysts bearing N-heterocyclic carbene (NHC) ligands with varying degrees of backbone and N-aryl substitution have been prepared. These complexes show greater resistance to decomposition through C–H activation of the N-aryl group, resulting in increased catalyst lifetimes. This work has utilized robotic technology to examine the activity and stability of each catalyst in metathesis, providing insights into the relationship between ligand architecture and enhanced efficiency. The development of this robotic methodology has also shown that, under optimized conditions, catalyst loadings as low as 25 ppm can lead to 100% conversion in the ring-closing metathesis of diethyl diallylmalonate.

Kuhn, Kevin M.; Bourg, Jean-Baptiste; Chung, Cheol K.; Virgil, Scott C.; Grubbs, Robert H.

2009-01-01

272

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

SciTech Connect

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.

Sakamoto, Koichi [Division of Chemistry, Graduate School of Science, Hokkaido University, Sapporo 060-0810 (Japan)] [Division of Chemistry, Graduate School of Science, Hokkaido University, Sapporo 060-0810 (Japan); Kamiya, Masakatsu [Graduate School of Life Science, Hokkaido University, Sapporo 060-0810 (Japan) [Graduate School of Life Science, Hokkaido University, Sapporo 060-0810 (Japan); Faculty of Advanced Life Science, Hokkaido University, Sapporo 060-0810 (Japan); Uchida, Takeshi [Division of Chemistry, Graduate School of Science, Hokkaido University, Sapporo 060-0810 (Japan) [Division of Chemistry, Graduate School of Science, Hokkaido University, Sapporo 060-0810 (Japan); Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo 060-0810 (Japan); Kawano, Keiichi [Graduate School of Life Science, Hokkaido University, Sapporo 060-0810 (Japan) [Graduate School of Life Science, Hokkaido University, Sapporo 060-0810 (Japan); Faculty of Advanced Life Science, Hokkaido University, Sapporo 060-0810 (Japan); Ishimori, Koichiro, E-mail: koichiro@sci.hokudai.ac.jp [Division of Chemistry, Graduate School of Science, Hokkaido University, Sapporo 060-0810 (Japan) [Division of Chemistry, Graduate School of Science, Hokkaido University, Sapporo 060-0810 (Japan); Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo 060-0810 (Japan)

2010-07-23

273

CpG-Induced IFN-? production of plasmacytoid dendritic cells: time and dosage dependence and the effect of structural modifications to the CpG backbone.  

PubMed

Plasmacytoid dendritic cells (pDCs) represent a highly specialized immune cell subset and are considered to be the main sentinels against viral infections and play an important role in the development of immune tolerance. pDCs are able to recognize cytosine-phosphate-guanosine (CpG) motifs within microbial DNA, which are unmethylated CG dinucleotides in a certain sequence context and trigger the secretion of interferon (IFN)-? and other proinflammatory cytokines. Here we used the typical class A CpG oligodeoxynucleotide (ODN) 2216, the B-class ODN 2006, and the newly synthesized CpG ODN TM64 to explore the potency and kinetics of IFN-? stimulation of pDC. TM64 CpG ODN has a hexanucleotide sequence TCGTGT that leads to an increased cellular uptake and features a CpG nucleotide within the sequence that leads to a potent specific B-cell stimulation, thus characteristics similar to a class B CpG. Our data reveals that all CpGs act as both dosage- and time-dependent stimuli of IFN-? secretion. The relationship between concentration of the stimulant and the secreted amount of IFN-? is not linear and results in a plateau formation, with saturation kinetics. Alteration to the backbone can change duration and quantity of overall IFN-? secretion. PMID:23414178

Jeske, Sabrina; Pries, Ralph; Wollenberg, Barbara

2013-04-01

274

Relative stability of major types of beta-turns as a function of amino acid composition: a study based on Ab initio energetic and natural abundance data.  

PubMed

Folding properties of small globular proteins are determined by their amino acid sequence (primary structure). This holds both for local (secondary structure) and for global conformational features of linear polypeptides and proteins composed from natural amino acid derivatives. It thus provides the rational basis of structure prediction algorithms. The shortest secondary structure element, the beta-turn, most typically adopts either a type I or a type II form, depending on the amino acid composition. Herein we investigate the sequence-dependent folding stability of both major types of beta-turns using simple dipeptide models (-Xxx-Yyy-). Gas-phase ab initio properties of 16 carefully selected and suitably protected dipeptide models (for example Val-Ser, Ala-Gly, Ser-Ser) were studied. For each backbone fold most probable side-chain conformers were considered. Fully optimized 321G RHF molecular structures were employed in medium level [B3LYP/6-311++G(d,p)//RHF/3-21G] energy calculations to estimate relative populations of the different backbone conformers. Our results show that the preference for beta-turn forms as calculated by quantum mechanics and observed in Xray determined proteins correlates significantly. PMID:12794897

Perczel, András; Jákli, Imre; McAllister, Michael A; Csizmadia, Imre G

2003-06-01

275

Genome Sequences and Photosynthesis Gene Cluster Composition of a Freshwater Aerobic Anoxygenic Phototroph, Sandarakinorhabdus sp. Strain AAP62, Isolated from the Shahu Lake in Ningxia, China  

PubMed Central

We report the first genome sequence from the recently established alpha-4 proteobacterial genus Sandarakinorhabdus. The genome of the Sandarakinorhabdus sp. strain AAP62 contains a photosynthesis gene cluster carrying major genes for bacterial reaction centers. The presence of genes related to aerobic respiratory electron transport confirms the lifestyle of this organism as an aerobic anoxygenic photoheterotroph.

Zeng, Yonghui; Feng, Fuying; Liu, Yapeng; Li, Yunxu

2013-01-01

276

The status and composition of the genus Steringophorus Odhner, 1905 (Digenea: Fellodistomidae), based on partial small subunit rRNA sequences.  

PubMed

Analysis of partial small subunit (18S) rRNA sequences shows the paraphyly of the genus Steringophorus as currently recognised. In consequence it is necessary to change the conception of the genus by the transfer of the species Steringophorus agnotus and S. sebastodis back to their original genus, Fellodistomum. PMID:8070964

Bray, R A; Soto, A; Rollinson, D

1994-05-01

277

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

PubMed

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

López-Castilla, Aracelys; Pazos, Fabiola; Schreier, Shirley; Pires, José Ricardo

2014-06-01

278

Backbone Dynamics of the Monomeric ? Repressor Denatured State Ensemble under Nondenaturing Conditions†  

PubMed Central

Oxidizing two native methionine residues predominantly populates the denatured state of monomeric ? repressor (MetO-?LS) under nondenaturing conditions. NMR was used to characterize the secondary structure and dynamics of MetO-?LS in standard phosphate buffer. 13C? and 1H? chemical shift indices reveal a region of significant helicity between residues 9 and 29. This helical content is further supported by the observation of medium-range amide NOEs. The remaining residues do not exhibit significant helicity as determined by NMR. We determined 15N relaxation parameters for 64 of 85 residues at 600 and 800 MHz. There are two distinct regions of reduced flexibility, residues 8–32 in the N-terminal third and residues 50–83 in the C-terminal third. The middle third, residues 33–50, has greater flexibility. We have analyzed the amplitude of the backbone motions in terms of the physical properties of the amino acids and conclude that conformational restriction of the backbone MetO-?LS is due to nascent helix formation in the region corresponding to native helix 1. The bulkiness of amino acid residues in the C-terminal third leads to the potential for hydrophobic interactions, which is suggested by chemical exchange detected by the difference in spectral density J(0) at the two static magnetic fields. The more flexible middle region is the result of a predominance of small side chains in this region.

Chugha, Preeti; Oas, Terrence G.

2014-01-01

279

Phosphorylation-induced changes in backbone dynamics of the dematin headpiece C-terminal domain  

PubMed Central

Dematin is an actin-binding protein abundant in red blood cells and other tissues. It contains a villin-type `headpiece' F-actin-binding domain at its extreme C-terminus. The isolated dematin headpiece domain (DHP) undergoes a significant conformational change upon phosphorylation. The mutation of Ser74 to Glu closely mimics the phosphorylation of DHP. We investigated motions in the backbone of DHP and its mutant DHPS74E using several complementary NMR relaxation techniques: laboratory frame 15N NMR relaxation, which is sensitive primarily to the ps–ns time scale, cross-correlated chemical shift modulation NMR relaxation detecting correlated ?s–ms time scale motions of neighboring 13C? and 15N nuclei, and cross-correlated relaxation of two 15N–1H dipole–dipole interactions detecting slow motions of backbone NH vectors in successive amino acid residues. The results indicate a reduction in mobility upon the mutation in several regions of the protein. The additional salt bridge formed in DHPS74E that links the N- and C-terminal subdomains is likely to be responsible for these changes.

Vugmeyster, Liliya; McKnight, C. James

2009-01-01

280

Combination cytotoxicity of backbone degradable HPMA copolymer gemcitabine and platinum conjugates toward human ovarian carcinoma cells.  

PubMed

Multiblock, backbone degradable HPMA copolymer-drug conjugates containing gemcitabine and DACH platinum (mP-GEM and mP-DACH Pt), respectively were synthesized by reversible addition-fragmentation chain transfer (RAFT) polymerization and subsequent chain extension by click chemistry. Using combination index analysis, the cytotoxicities of the two multiblock conjugates, as single agent and in combination, were evaluated in vitro in A2780 human ovarian cancer cells, with free drugs as controls. The greatest synergistic cytotoxic effect was observed when A2780 cells were sequentially exposed to mP-GEM for 24h and mP-DACH Pt for 48h. In addition, mechanistic studies support the rationale of the synergy between mP-GEM and mP-DACH Pt: mP-GEM pretreatment was able to enhance the platinum-DNA adduct accumulation and inhibit cell proliferation to a higher extent than single mP-DACH Pt treatment. These observations are useful for the development of combination macromolecular therapeutics for ovarian cancer based on the second-generation backbone degradable HPMA copolymers. PMID:24316339

Duangjai, Acharaporn; Luo, Kui; Zhou, Yan; Yang, Jiyuan; Kope?ek, Jind?ich

2014-05-01

281

TALOS+: a hybrid method for predicting protein backbone torsion angles from NMR chemical shifts.  

PubMed

NMR chemical shifts in proteins depend strongly on local structure. The program TALOS establishes an empirical relation between 13C, 15N and 1H chemical shifts and backbone torsion angles phi and psi (Cornilescu et al. J Biomol NMR 13 289-302, 1999). Extension of the original 20-protein database to 200 proteins increased the fraction of residues for which backbone angles could be predicted from 65 to 74%, while reducing the error rate from 3 to 2.5%. Addition of a two-layer neural network filter to the database fragment selection process forms the basis for a new program, TALOS+, which further enhances the prediction rate to 88.5%, without increasing the error rate. Excluding the 2.5% of residues for which TALOS+ makes predictions that strongly differ from those observed in the crystalline state, the accuracy of predicted phi and psi angles, equals +/-13 degrees . Large discrepancies between predictions and crystal structures are primarily limited to loop regions, and for the few cases where multiple X-ray structures are available such residues are often found in different states in the different structures. The TALOS+ output includes predictions for individual residues with missing chemical shifts, and the neural network component of the program also predicts secondary structure with good accuracy. PMID:19548092

Shen, Yang; Delaglio, Frank; Cornilescu, Gabriel; Bax, Ad

2009-08-01

282

Solution Structure and Backbone Dynamics of Human Liver Fatty Acid Binding Protein: Fatty Acid Binding Revisited  

PubMed Central

Liver fatty acid binding protein (L-FABP), a cytosolic protein most abundant in liver, is associated with intracellular transport of fatty acids, nuclear signaling, and regulation of intracellular lipolysis. Among the members of the intracellular lipid binding protein family, L-FABP is of particular interest as it can i), bind two fatty acid molecules simultaneously and ii), accommodate a variety of bulkier physiological ligands such as bilirubin and fatty acyl CoA. To better understand the promiscuous binding and transport properties of L-FABP, we investigated structure and dynamics of human L-FABP with and without bound ligands by means of heteronuclear NMR. The overall conformation of human L-FABP shows the typical ?-clam motif. Binding of two oleic acid (OA) molecules does not alter the protein conformation substantially, but perturbs the chemical shift of certain backbone and side-chain protons that are involved in OA binding according to the structure of the human L-FABP/OA complex. Comparison of the human apo and holo L-FABP structures revealed no evidence for an “open-cap” conformation or a “swivel-back” mechanism of the K90 side chain upon ligand binding, as proposed for rat L-FABP. Instead, we postulate that the lipid binding process in L-FABP is associated with backbone dynamics.

Cai, Jun; Lucke, Christian; Chen, Zhongjing; Qiao, Ye; Klimtchuk, Elena; Hamilton, James A.

2012-01-01

283

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

PubMed

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

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

2013-12-26

284

Di-Isocyanate Crosslinked Aerogels with 1, 6-Bis (Trimethoxysilyl) Hexane Incorporated in Silica Backbone  

NASA Technical Reports Server (NTRS)

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.

Vivod, Stephanie L.; Meador, Mary Ann B.; Nguyen, Baochau N.; Quade, Derek; Randall, Jason; Perry, Renee

2008-01-01

285

Generation of transgenic Drosophila expressing shRNAs in the miR-1 backbone.  

PubMed

In Drosophila, long-term effects of RNA interference (RNAi) must be achieved by integrating into the genome a template from which an RNAi trigger is transcribed by cellular RNA polymerases, generally RNA polymerase II or III. With encoded triggers, not only can essentially permanent silencing be achieved, but control can also be exerted over the level of trigger expression, with a resulting variation in the degree to which the target is silenced. Knockdown can also be controlled in a temporal and cell-type-dependent fashion through the use of well-established transgenic methodologies and well-tested promoters. The forms of encoded triggers vary. Long double-stranded RNAs can be expressed as extended inverted repeats. The nearest equivalent of a small interfering RNA is an artificial microRNA (miRNA) or short hairpin RNA (shRNA), where a natural miRNA backbone (also called a scaffold) is remodeled to produce a different small RNA or a small inverted repeat (<30 nucleotides) is simply expressed. This protocol describes creation of transgenic Drosophila carrying shRNA inserts in a remodeled endogenous miRNA backbone. The protocol applies to the use of miRNA-based shRNAs, but most of the vectors, principles of experimental design, and methods are also applicable to long inverted repeat transgenes. PMID:24786506

Chang, Kenneth; Marran, Krista; Valentine, Amy; Hannon, Gregory J

2014-05-01

286

Biosynthesis and antimicrobial evaluation of backbone-cyclized alpha-defensins#  

PubMed Central

Defensins are antimicrobial peptides that are important in the innate immune defense of mammals. Upon stimulation by bacterial antigens, enteric ?-defensins are secreted into the intestinal lumen where they have potent microbicidal activities. Cryptdin-4 (Crp4) is an ?-defensin expressed in Paneth cells of the mouse small intestine and the most bactericidal of the known cryptdin isoforms. The structure of Crp4 consists of a triple-stranded antiparallel ?-sheet, but lacks three amino acids between the fourth and fifth cysteine residues, making them distinct from other ?-defensins. The structure also reveals that the ?-amino and C-terminal carboxylic groups are in proximity (d ? 3 Å) in the folded structure. We present here the biosynthesis of backbone-cyclized Crp4 using a modified protein splicing unit or intein. Our data show that cyclized Crp4 can be biosynthesized by using this approach both in vitro and in vivo, although the expression yield was significantly lower when produced inside the cell. The resulting cyclic defensins retained the native ?-defensin fold and showed equivalent or better microbicidal activities against several Gram-positive and Gram-negative bacteria when compared to native Crp4. No detectable hemolytic activity against human red blood cells was observed for either the native or cyclized variants of Crp4. Moreover, both forms of Crp4 also showed high stability to degradation when incubated with human serum. Altogether, these results indicate the potential for backbone cyclized defensins in the development of novel peptide-based antimicrobial compounds.

Garcia, Angie E.; Tai, Kenneth P.; Puttamadappa, Shadakshara S.; Shekhtman, Alexander; Ouellette, Andre J.; Camarero, Julio A.

2011-01-01

287

BEST-HNN and 2D-(HN) NH experiments for rapid backbone assignment in proteins  

NASA Astrophysics Data System (ADS)

HNN has proven to be an extremely valuable experiment for rapid and unambiguous backbone (H N, 15N) assignment in ( 13C, 15N) labeled proteins. However, low sensitivity of the experiment is often a limiting factor, especially when the transverse relaxation times ( T2) are short. We show here that BEST modification Schanda et al. (2006) [2] increases the sensitivity per unit time by more than a factor of 2.0 and thus substantially increases the speed of data collection; good 3D data can be collected in 8-10 h. Next, we present a simple method for amino-acid type identification based on simple 2D versions of the HNN experiment, labeled here as 2D-(HN) NH. Each of these experiments which produce anchor points for Gly, Ala, Ser/Thr residues, can be recorded in less than an hour. These enable rapid data acquisition, rapid analysis, and consequently rapid assignment of backbone (H N, 15N) resonances. The 2D-(HN) NH experiment does not involve aliphatic/aromatic protons and hence can be applied to deuterated protein samples as well, which is an additional advantage. The experiments have been demonstrated with human ubiquitin (76 aa) and acetic-acid denatured HIV-1 protease (99 aa), as representatives of folded and unfolded protein systems, respectively.

Kumar, Dinesh; Paul, Subhradip; Hosur, Ramakrishna V.

2010-05-01

288

Sequencing Puzzle  

NSDL National Science Digital Library

The sequencing puzzle is designed to teach high school students, and perhaps even middle school, and the general public about the basics of genome sequencing. The sequencing of the tomato genome is used as the basis for this activity. It is an interactive puzzle. In addition to the puzzle, the site also contains background information on tomatoes, DNA, and various molecular terms.

289

Cycle Sequencing  

NSDL National Science Digital Library

This animation from Cold Spring Harbor Laboratory's Dolan DNA Learning Center presents the cycle sequencing. The animation contains instructions on how to sequence a piece of DNA beginning with the raw materials needed, and details on the process: "Fluorescent dyes are added to the reactions, and a laser within an automated DNA sequencing machine is used to analyze the DNA fragments produced."

2011-11-23

290

The mitochondrial genome sequence of the ciliate Paramecium caudatum reveals a shift in nucleotide composition and codon usage within the genus Paramecium  

Microsoft Academic Search

Background  Despite the fact that the organization of the ciliate mitochondrial genome is exceptional, only few ciliate mitochondrial\\u000a genomes have been sequenced until today. All ciliate mitochondrial genomes are linear. They are 40 kb to 47 kb long and contain\\u000a some 50 tightly packed genes without introns. Earlier studies documented that the mitochondrial guanine + cytosine contents\\u000a are very different between

Dana Barth; Thomas U Berendonk

2011-01-01

291

Incorporating backbone flexibility in MedusaDock improves ligand-binding pose prediction in the CSAR2011 docking benchmark.  

PubMed

Solution of the structures of ligand-receptor complexes via computational docking is an integral step in many structural modeling efforts as well as in rational drug discovery. A major challenge in ligand-receptor docking is the modeling of both receptor and ligand flexibilities in order to capture receptor conformational changes induced by ligand binding. In the molecular docking suite MedusaDock, both ligand and receptor side chain flexibilities are modeled simultaneously with sets of discrete rotamers, where the ligand rotamer library is generated "on the fly" in a stochastic manner. Here, we introduce backbone flexibility into MedusaDock by implementing ensemble docking in a sequential manner for a set of distinct receptor backbone conformations. We generate corresponding backbone ensembles to capture backbone changes upon binding to different ligands, as observed experimentally. We develop a simple clustering and ranking approach to select the top poses as blind predictions. We applied our method in the CSAR2011 benchmark exercise. In 28 out of 35 cases (80%) where the ligand-receptor complex structures were released, we were able to predict near-native poses (<2.5 Å RMSD), the highest success rate reported for CSAR2011. This result highlights the importance of modeling receptor backbone flexibility to the accurate docking of ligands to flexible targets. We expect a broad application of our fully flexible docking approach in biological studies as well as in rational drug design. PMID:23237273

Ding, Feng; Dokholyan, Nikolay V

2013-08-26

292

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

PubMed Central

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 ? and ?. 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 ?, ? point, i.e. as a continuous function of ? and ?. 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.

Shapovalov, Maxim V.; Dunbrack, Roland L.

2011-01-01

293

Comparison of multiple DNA dyes for real-time PCR: effects of dye concentration and sequence composition on DNA amplification and melting temperature  

PubMed Central

The importance of real-time polymerase chain reaction (PCR) has increased steadily in clinical applications over the last decade. Many applications utilize SYBR Green I dye to follow the accumulation of amplicons in real time. SYBR Green I has, however, a number of limitations that include the inhibition of PCR, preferential binding to GC-rich sequences and effects on melting curve analysis. Although a few alternative dyes without some of these limitations have been recently proposed, no large-scale investigation into the properties of intercalating dyes has been performed. In this study, we investigate 15 different intercalating DNA dyes for their inhibitory effects on PCR, effects on DNA melting temperature and possible preferential binding to GC-rich sequences. Our results demonstrated that in contrast to the results of SYBR Green I, two intercalating dyes SYTO-13 and SYTO-82 do not inhibit PCR, show no preferential binding to GC rich sequences and do not influence melting temperature, Tm, even at high concentrations. In addition, SYTO-82 demonstrated a 50-fold lower detection limit in a dilution series assay. In conclusion, the properties of SYTO-82 and SYTO-13 will simplify the development of multiplex assays and increase the sensitivity of real-time PCR.

Gudnason, Haukur; Dufva, Martin; Bang, D.D.; Wolff, Anders

2007-01-01

294

Comparison of multiple DNA dyes for real-time PCR: effects of dye concentration and sequence composition on DNA amplification and melting temperature.  

PubMed

The importance of real-time polymerase chain reaction (PCR) has increased steadily in clinical applications over the last decade. Many applications utilize SYBR Green I dye to follow the accumulation of amplicons in real time. SYBR Green I has, however, a number of limitations that include the inhibition of PCR, preferential binding to GC-rich sequences and effects on melting curve analysis. Although a few alternative dyes without some of these limitations have been recently proposed, no large-scale investigation into the properties of intercalating dyes has been performed. In this study, we investigate 15 different intercalating DNA dyes for their inhibitory effects on PCR, effects on DNA melting temperature and possible preferential binding to GC-rich sequences. Our results demonstrated that in contrast to the results of SYBR Green I, two intercalating dyes SYTO-13 and SYTO-82 do not inhibit PCR, show no preferential binding to GC rich sequences and do not influence melting temperature, T(m), even at high concentrations. In addition, SYTO-82 demonstrated a 50-fold lower detection limit in a dilution series assay. In conclusion, the properties of SYTO-82 and SYTO-13 will simplify the development of multiplex assays and increase the sensitivity of real-time PCR. PMID:17897966

Gudnason, Haukur; Dufva, Martin; Bang, D D; Wolff, Anders

2007-01-01

295

Sequence Recombination Improves Target Specificity in a Redesigned Collagen Peptide abc-type Heterotrimer  

PubMed Central

Stability of the collagen triple helix is largely governed by its imino acid content, namely the occurrence of proline and 4R-hydroxyproline at the X and Y positions respectively of the periodic (Gly-X-Y)n sequence. Although other amino acids at these positions reduce stability of the triple helix, this can be partially compensated by introducing intermolecular side chain salt bridges. This approach was previously used to design an abc-type heterotrimer composed of one basic, one acidic and one neutral imino acid rich chain (Gauba & Hartgerink, 2007). In this study, an abc-type heterotrimer was designed to be the most stable species using a sequence recombination strategy that preserved both the amino acid composition and the network of interchain salt-bridges of the original design. The target heterotrimer had the highest Tm of 50°C, 7°C greater than the next most stable species. Stability of the heterotrimer decreased with increasing ionic strength, consistent with the role of intermolecular salt bridges in promoting stability. Quantitative meta-analysis of these results and published stability measurements on closely related peptides was used to discriminate the contributions of backbone propensity and side chain electrostatics to collagen stability.

Giddu, Sumana; Xu, Fei; Nanda, Vikas

2012-01-01

296

The Manufacturing Process for the NASA Composite Crew Module Demonstration Structure  

NASA Technical Reports Server (NTRS)

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.

Pelham, Larry; Higgins, John E.

2008-01-01

297

1H, 13C, and 15N backbone assignment and secondary structure of the receptor-binding domain of vascular endothelial growth factor.  

PubMed Central

Nearly complete sequence-specific 1H, 13C, and 15N resonance assignments are reported for the backbone atoms of the receptor-binding domain of vascular endothelial growth factor (VEGF), a 23-kDa homodimeric protein that is a major regulator of both normal and pathological angiogenesis. The assignment strategy relied on the use of seven 3D triple-resonance experiments [HN(CO)CA, HNCA, HNCO, (HCA)CONH, HN(COCA)HA, HN(CA)HA, and CBCA-(CO)NH] and a 3D 15N-TOCSY-HSQC experiment recorded on a 0.5 mM (12 mg/mL) sample at 500 MHz, pH 7.0, 45 degrees C. Under these conditions, 15N relaxation data show that the protein has a rotational correlation time of 15.0 ns. Despite this unusually long correlation time, assignments were obtained for 94 of the 99 residues; 8 residues lack amide 1H and 15N assignments, presumably due to rapid exchange of the amide 1H with solvent under the experimental conditions used. The secondary structure of the protein was deduced from the chemical shift indices of the 1H alpha, 13C alpha, 13C beta, and 13CO nuclei, and from analysis of backbone NOEs observed in a 3D 15N-NOESY-HSQC spectrum. Two helices and a significant amount of beta-sheet structure were identified, in general agreement with the secondary structure found in a recently determined crystal structure of a similar VEGF construct [Muller YA et al., 1997, Proc Natl Acad Sci USA 94:7192-7197].

Fairbrother, W. J.; Champe, M. A.; Christinger, H. W.; Keyt, B. A.; Starovasnik, M. A.

1997-01-01

298

Megabase Level Sequencing Reveals Contrasted Organization and Evolution Patterns of the Wheat Gene and Transposable Element Spaces[W  

PubMed Central

To improve our understanding of the organization and evolution of the wheat (Triticum aestivum) genome, we sequenced and annotated 13-Mb contigs (18.2 Mb) originating from different regions of its largest chromosome, 3B (1 Gb), and produced a 2x chromosome survey by shotgun Illumina/Solexa sequencing. All regions carried genes irrespective of their chromosomal location. However, gene distribution was not random, with 75% of them clustered into small islands containing three genes on average. A twofold increase of gene density was observed toward the telomeres likely due to high tandem and interchromosomal duplication events. A total of 3222 transposable elements were identified, including 800 new families. Most of them are complete but showed a highly nested structure spread over distances as large as 200 kb. A succession of amplification waves involving different transposable element families led to contrasted sequence compositions between the proximal and distal regions. Finally, with an estimate of 50,000 genes per diploid genome, our data suggest that wheat may have a higher gene number than other cereals. Indeed, comparisons with rice (Oryza sativa) and Brachypodium revealed that a high number of additional noncollinear genes are interspersed within a highly conserved ancestral grass gene backbone, supporting the idea of an accelerated evolution in the Triticeae lineages.

Choulet, Frederic; Wicker, Thomas; Rustenholz, Camille; Paux, Etienne; Salse, Jerome; Leroy, Philippe; Schlub, Stephane; Le Paslier, Marie-Christine; Magdelenat, Ghislaine; Gonthier, Catherine; Couloux, Arnaud; Budak, Hikmet; Breen, James; Pumphrey, Michael; Liu, Sixin; Kong, Xiuying; Jia, Jizeng; Gut, Marta; Brunel, Dominique; Anderson, James A.; Gill, Bikram S.; Appels, Rudi; Keller, Beat; Feuillet, Catherine

2010-01-01

299

DNA sequence confidence estimation  

SciTech Connect

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.

Lipshutz, R.J. (Affymetrix, Santa Clara, CA (United States)); Taverner, F. (Daniel H. Wagner Associates, Sunnyvale, CA (United States)); Hennessy, K. (Applied Biosystems, Inc., Foster City, CA (United States)); Hartzell, G. (Univ. of California, Berkeley, CA (United States)); Davis, R. (Stanford Univ., CA (United States))

1994-02-01

300

Biosensors for DNA sequence detection  

NASA Technical Reports Server (NTRS)

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.

Vercoutere, Wenonah; Akeson, Mark

2002-01-01

301

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

NASA Astrophysics Data System (ADS)

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.

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

2007-12-01

302

A comparative study of the backbone dynamics of two closely related lipid binding proteins: Bovine heart fatty acid binding protein and porcine ileal lipid binding protein  

Microsoft Academic Search

The backbone dynamics of bovine heart fatty acid binding protein (H-FABP) and porcine ileal lipid binding protein (ILBP) were studied by 15N NMR relaxation (T1 and T2) and steady state heteronuclear 15N{1H} NOE measurements. The microdynamic parameters characterizing the backbone mobility were determined using the ‘model-free’ approach. For H-FABP, the non-terminal backbone amide groups display a rather compact protein structure

Christian Lücke; David Fushman; Christian Ludwig; James A. Hamilton; James C. Sacchettini; Heinz Rüterjans

1999-01-01

303

Genomic sequencing.  

PubMed Central

Unique DNA sequences can be determined directly from mouse genomic DNA. A denaturing gel separates by size mixtures of unlabeled DNA fragments from complete restriction and partial chemical cleavages of the entire genome. These lanes of DNA are transferred and UV-crosslinked to nylon membranes. Hybridization with a short 32P-labeled single-stranded probe produces the image of a DNA sequence "ladder" extending from the 3' or 5' end of one restriction site in the genome. Numerous different sequences can be obtained from a single membrane by reprobing. Each band in these sequences represents 3 fg of DNA complementary to the probe. Sequence data from mouse immunoglobulin heavy chain genes from several cell types are presented. The genomic sequencing procedures are applicable to the analysis of genetic polymorphisms, DNA methylation at deoxycytidines, and nucleic acid-protein interactions at single nucleotide resolution. Images

Church, G M; Gilbert, W

1984-01-01

304

Exact solution for a diffusive process on a backbone structure: Green function approach and external force  

NASA Astrophysics Data System (ADS)

The effects of an external force on a diffusive process subjected to a backbone structure are investigated. This analysis is performed by considering the system governed by the Fokker-Planck equation {?ial _t}? = {D_y}?ial _y^2? + {D_x}? (y)?ial _x^2? - nabla \\cdot ({?c F_? }) with ?c F = v_x + ? (y)v^prime_x,v_y. The equation is subjected to the boundary conditions ?(±?, y; t) = 0 and ?(x, ±? t) = 0 with ? (x,y;0) = hat ? (x,y), where hat ? (x,y) is normalized. Applying the Green function approach, we obtain exact solutions and analyze the relaxation process through the mean square displacement evaluated for the x and y directions. Our results show an anomalous spreading of the system characterized by one or several diffusive regimes connected to anomalous diffusion and stationary states.

Lenzi, E. K.; da Silva, L. R.; Tateishi, A. A.; Lenzi, M. K.; Ribeiro, H. V.

2014-03-01

305

Highly efficient blue electrophosphorescent polymers with fluorinated poly(arylene ether phosphine oxide) as Backbone.  

PubMed

In view of the tolerance of F atoms in FIrpic to the nucleophilic aromatic substitution polymerization, an activated fluorinated poly(arylene ether phosphine oxide) backbone is used to construct novel blue electrophosphorescent polymers containing FIrpic as the blue emitter, because they can be synthesized under a milder temperature of 120 °C. Compared with the counterparts prepared at high temperature (165 °C), unexpected bathochromic shift is successfully avoided, and a state-of-art luminous efficiency as high as 19.4 cd A(-1) is achieved. The efficiency is comparable to the corresponding physical blend system, which indicates that the fluorinated poly(arylene ether phosphine oxide) has the potential to be used as the platform for the development of high-performance all-phosphorescent white polymer based on single polymer system. PMID:22950598

Shao, Shiyang; Ding, Junqiao; Wang, Lixiang; Jing, Xiabin; Wang, Fosong

2012-09-19

306

Side chain and backbone contributions of Phe508 to CFTR folding  

SciTech Connect

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.

Thibodeau, Patrick H.; Brautigam, Chad A.; Machius, Mischa; Thomas, Philip J. (U. of Texas-SMED)

2010-12-07

307

Backbone resonance assignments of the outer membrane lipoprotein FrpD from Neisseria meningitidis.  

PubMed

The iron-regulated FrpD protein is a unique lipoprotein embedded into the outer membrane of the Gram-negative bacterium Neisseria meningitidis. The biological function of FrpD remains unknown but might consist in anchoring to the bacterial cell surface the Type I-secreted FrpC protein, which belongs to a Repeat in ToXins (RTX) protein family and binds FrpD with very high affinity (K(d) = 0.2 nM). Here, we report the backbone (1)H, (13)C, and (15)N chemical shift assignments for the FrpD(43-271) protein that allow us to characterize the intimate interaction between FrpD and the N-terminal domain of FrpC. PMID:23225222

Bumba, Ladislav; Sviridova, Ekaterina; Kutá Smatanová, Ivana; ?ezá?ová, Pavlína; Veverka, Václav

2014-04-01

308

On the photostability of peptides after selective photoexcitation of the backbone: prompt versus slow dissociation.  

PubMed

Vulnerability of biomolecules to ultraviolet radiation is intimately linked to deexcitation pathways: photostability requires fast internal conversion to the electronic ground state, but also intramolecular vibrational redistribution and cooling on a time scale faster than dissociation. Here we present a protocol to disentangle slow and non-hazardous statistical dissociation from prompt cleavage of peptide bonds by 210 nm light based on experiments on protonated peptides isolated in vacuo and tagged by 18-crown-6 ether (CE). The weakest link in the system is between the charged site and CE, which is remote from the initial site of excitation. Hence loss of CE serves as direct proof that energy has reached the charge-site end, leaving the backbone intact. Our work demonstrates that excitation of tertiary amide moieties (proline linkages) results in both prompt dissociation and statistical dissociation after energy randomisation over all vibrational degrees of freedom. PMID:24945849

Byskov, Camilla Skinnerup; Jensen, Frank; Jørgensen, Thomas J D; Nielsen, Steen Brøndsted

2014-07-01

309

Synthesis and backbone conformations of cyclic hexapeptides cyclo-(Xxx-Pro-D-Gln)2.  

PubMed

The solution syntheses of cyclo-(Xxx-Pro-D-Gln)2, where Xxx = Gly, Ala, Leu, Phe and Val are described. Several routes were examined, the most successful involving the intermediate Z-Xxx-Pro-D-Gln-O-tBu and proceeding to cyclization of H-Xxx-Pro-D-Gln-Xxx-Pro-D-Gln-OH using diphenylphosphoryl azide. The N--H regions of the proton magnetic resonance spectra of aqueous solutions of these peptides were examined, and in the Xxx = Leu and Val peptides an unsymmetrical backbone, presumably with one cis Xxx-Pro peptide bond, was found to be important. Previous reports of cyclo-(Xxx-Pro-D-Yyy)2 peptides have shown only C2-symmetric forms. PMID:6853028

Kopple, K D; Parameswaran, K N

1983-03-01

310

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

PubMed

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

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

311

Aftershock Sequences  

NSDL National Science Digital Library

In this activity, learners will look at some of the characteristic properties of aftershock sequences, and relate them to variables in two equations: the modified version of Omori's Law, and the Gutenberg-Richter relation for aftershock sequences. The database provided in this link can be searched to extract the magnitude and time-after-mainshock for selected earthquakes. From this information, users can discover the real-world meanings of various properties of aftershock sequences.

312

DNA Sequencing  

NSDL National Science Digital Library

Teachers' Domain presents this interactive, adapted from the Dolan DNA Learning Center, with reading material and animations to help students learn the basics of DNA sequencing. The lesson is divided two parts: Sanger Sequencing and Cycle Sequencing. The processes for both techniques are covered and animations help students visualize the material presented. On the site, visitors will also find a supplemental background essay, discussion questions, and standards alignment from Teachers' Domain.

2010-10-05

313

RNABC: Forward Kinematics to Reduce All-Atom Steric Clashes in RNA Backbone  

PubMed Central

Although accurate details in RNA structure are of great importance for understanding RNA function, the backbone conformation is difficult to determine, and most existing RNA structures show serious steric clashes (? 0.4Å overlap) when hydrogen atoms are taken into account. We have developed a program called RNABC (RNA Backbone Correction) that performs local perturbations to search for alternative conformations that avoid those steric clashes or other local geometry problems. Its input is an all-atom coordinate file for an RNA crystal structure (usually from the MolProbity web service), with problem areas specified. RNABC rebuilds a suite (the unit from sugar to sugar) by anchoring the phosphorus and base positions, which are clearest in crystallographic electron density, and reconstructing the other atoms using forward kinematics. Geometric parameters are constrained within user-specified tolerance of canonical or original values, and torsion angles are constrained to ranges defined through empirical database analyses. Several optimizations reduce the time required to search the many possible conformations. The output results are clustered and presented to the user, who can choose whether to accept one of the alternative conformations. Two test evaluations show the effectiveness of RNABC, first on the S-motifs from 42 RNA structures, and second on the worst problem suites (clusters of bad clashes, or serious sugar pucker outliers) in 25 unrelated RNA structures. Among the 101 S-motifs, 88 had diagnosed problems, and RNABC produced clash-free conformations with acceptable geometry for 71 of those (about 80%). For the 154 worst problem suites, RNABC proposed alternative conformations for 72. All but 8 of those were judged acceptable after examining electron density (where available) and local conformation. Thus, even for these worst cases, nearly half the time RNABC suggested corrections suitable to initiate further crystallographic refinement. The program is available from http://kinemage.biochem.duke.edu.

Wang, Xueyi; Kapral, Gary; Murray, Laura; Richardson, David; Richardson, Jane; Snoeyink, Jack

2007-01-01

314

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

PubMed

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

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

2008-11-01

315

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

PubMed Central

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.

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

2007-01-01

316

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

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

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

2014-01-01

317

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

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.

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

2014-01-01

318

Matrix and fiber influences on the cryogenic microcracking of carbon fiber\\/epoxy composites  

Microsoft Academic Search

Cryogenic cycling effects on symmetric carbon fiber\\/epoxy laminates were examined using model prepreg systems. The properties of the composite materials studied were altered through the introduction of variations in their structure and composition. The curing agent used, matrix backbone flexibility, toughening agents, and longitudinal coefficient of thermal expansion of the reinforcing fibers were changed to investigate their role in cryogenic

John F Timmerman; Matthew S Tillman; Brian S Hayes; James C Seferis

2002-01-01

319

Sequence Bracelets  

NSDL National Science Digital Library

In this craft-based activity, learners make DNA sequence bracelets that carry the code of an organism such as a human, trout, chimpanzee or butterfly. This activity reinforces the principle of complementary base pairs as learners are given one strand of the sequence and they have to match up the other strand correctly.

Institute, Wellcome T.

2012-06-26

320

Sequencing technologies and genome sequencing  

Microsoft Academic Search

The high-throughput - next generation sequencing (HT-NGS) technologies are currently the hottest topic in the field of human\\u000a and animals genomics researches, which can produce over 100 times more data compared to the most sophisticated capillary sequencers\\u000a based on the Sanger method. With the ongoing developments of high throughput sequencing machines and advancement of modern\\u000a bioinformatics tools at unprecedented pace,

Chandra Shekhar Pareek; Rafal Smoczynski; Andrzej Tretyn

321

The Deuterator: software for the determination of backbone amide deuterium levels from H/D exchange MS data  

PubMed Central

Background The combination of mass spectrometry and solution phase amide hydrogen/deuterium exchange (H/D exchange) experiments is an effective method for characterizing protein dynamics, and protein-protein or protein-ligand interactions. Despite methodological advancements and improvements in instrumentation and automation, data analysis and display remains a tedious process. The factors that contribute to this bottleneck are the large number of data points produced in a typical experiment, each requiring manual curation and validation, and then calculation of the level of backbone amide exchange. Tools have become available that address some of these issues, but lack sufficient integration, functionality, and accessibility required to address the needs of the H/D exchange community. To date there is no software for the analysis of H/D exchange data that comprehensively addresses these issues. Results We have developed an integrated software system for the automated analysis and representation of H/D exchange data that has been titled "The Deuterator". Novel approaches have been implemented that enable high throughput analysis, automated determination of deuterium incorporation, and deconvolution of overlapping peptides. This has been achieved by using methods involving iterative theoretical envelope fitting, and consideration of peak data within expected m/z ranges. Existing common file formats have been leveraged to allow compatibility with the output from the myriad of MS instrument platforms and peptide sequence database search engines. A web-based interface is used to integrate the components of The Deuterator that are able to analyze and present mass spectral data from instruments with varying resolving powers. The results, if necessary, can then be confirmed, adjusted, re-calculated and saved. Additional tools synchronize the curated calculation parameters with replicate time points, increasing throughput. Saved results can then be used to plot deuterium buildup curves and 3D structural overlays. The system has been used successfully in a production environment for over one year and is freely available as a web tool at the project home page . Conclusion The automated calculation and presentation of H/D exchange data in a user interface enables scientists to organize and analyze data efficiently. Integration of the different components of The Deuterator coupled with the flexibility of common data file formats allow this system to be accessible to the broadening H/D exchange community.

Pascal, BD; Chalmers, MJ; Busby, SA; Mader, CC; Southern, MR; Tsinoremas, NF; Griffin, PR

2007-01-01

322

A PDDA/poly(2,6-pyridinedicarboxylic acid)-CNTs composite film DNA electrochemical sensor and its application for the detection of specific sequences related to PAT gene and NOS gene.  

PubMed

2,6-Pyridinedicarboxylic acid (PDC) was electropolymerized on the glassy carbon electrode (GCE) surface combined with carboxylic group-functionalized single-walled carbon nanotubes (SWNTs) by cyclic voltammetry (CV) to form PDC-SWNTs composite film, which was rich in negatively charged carboxylic group. Then, poly(diallyldimethyl ammonium chloride) (PDDA), a linear cationic polyelectrolyte, was electrostatically adsorbed on the PDC-SWNTs/GCE surface. DNA probes with negatively charged phosphate group at the 5' end were immobilized on the PDDA/PDC-SWNTs/GCE due to the strong electrostatic attraction between PDDA and phosphate group of DNA. It has been found that modification of the electrode with PDC-SWNTs film has enhanced the effective electrode surface area and electron-transfer ability, in addition to providing negatively charged groups for the electrostatic assembly of cationic polyelectrolyte. PDDA plays a key role in the attachment of DNA probes to the PDC-SWNTs composite film and acts as a bridge to connect DNA with PDC-SWNTs film. The cathodic peak current of methylene blue (MB), an electroactive label, decreased obviously after the hybridization of DNA probe (ssDNA) with the complementary DNA (cDNA). This peak current change was used to monitor the recognition of the specific sequences related to PAT gene in the transgenic corn and the polymerase chain reaction (PCR) amplification of NOS gene from the sample of transgenic soybean with satisfactory results. Under optimal conditions, the dynamic detection range of the sensor to PAT gene target sequence was from 1.0x10(-11) to 1.0x10(-6) mol/L with the detection limit of 2.6x10(-12) mol/L. PMID:18585173

Yang, Tao; Zhang, Wei; Du, Meng; Jiao, Kui

2008-05-30

323

Backbone and sidechain 1H, 15N and 13C assignments of the KSR1 CA1 domain  

PubMed Central

The backbone and side chain resonance assignments of the murine KSR1 CA1 domain have been determined based on triple-resonance experiments using uniformly [13C, 15N]-labeled protein. This assignment is the first step towards the determination of the three-dimensional structure of the unique KSR1 CA1 domain.

Koveal, Dorothy; Pinheiro, Anderson S.; Peti, Wolfgang; Page, Rebecca

2014-01-01

324

Slow dynamics of a protein backbone in molecular dynamics simulation revealed by time-structure based independent component analysis  

NASA Astrophysics Data System (ADS)

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 ?s, and the obtained trajectory of C? 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.

Naritomi, Yusuke; Fuchigami, Sotaro

2013-12-01

325

Slow dynamics of a protein backbone in molecular dynamics simulation revealed by time-structure based independent component analysis  

SciTech Connect

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 ?s, and the obtained trajectory of C{sub ?} 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.

Naritomi, Yusuke [Department of Supramolecular Biology, Graduate School of Nanobioscience, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045 (Japan)] [Department of Supramolecular Biology, Graduate School of Nanobioscience, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045 (Japan); Fuchigami, Sotaro, E-mail: sotaro@tsurumi.yokohama-cu.ac.jp [Department of Medical Life Science, Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045 (Japan)] [Department of Medical Life Science, Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045 (Japan)

2013-12-07

326

A Polynomial-Time Algorithm for De Novo Protein Backbone Structure Determination from Nuclear Magnetic Resonance Data  

Microsoft Academic Search

We describe an efficient algorithm for protein backbone structure determination from solu- tion Nuclear Magnetic Resonance (NMR) data. A key feature of our algorithm is that it finds the conformation and orientation of secondary structure elements as well as the global fold in polynomial time. This is the first polynomial-time algorithm for de novo high-resolution biomacromolecular structure determination using experimentally

Lincong Wang; Ramgopal R. Mettu; Bruce Randall Donald

2006-01-01

327

Backbone 1H, 13C, and 15N resonance assignments of guanylyl cyclase activating protein-1, GCAP1  

PubMed Central

Guanylyl cyclase activating protein 1 (GCAP1), a member of the neuronal calcium sensor subclass of the calmodulin superfamily, confers Ca2+-dependent activation of retinal guanylyl cyclase that regulates the visual light response. GCAP1 is genetically linked to retinal degenerative diseases. We report backbone NMR chemical shift assignments of Ca2+-saturated GCAP1 (BMRB no. 18026).

Lim, Sunghyuk; Peshenko, Igor V.; Dizhoor, Alexander M.

2014-01-01

328

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

PubMed Central

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 (H?, C?, C? and CO) for establishing sequential backbone assignment. Because most conventional 4-D triple-resonance experiments share an overlapping C? 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.

Wen, Jie; Wu, Jihui; Zhou, Pei

2011-01-01

329

Automated sequence-specific protein NMR assignment using the memetic algorithm MATCH  

Microsoft Academic Search

MATCH (Memetic Algorithm and Combinatorial Optimization Heuristics) is a new memetic algorithm for automated sequence-specific polypeptide backbone NMR assignment of proteins. MATCH\\u000a employs local optimization for tracing partial sequence-specific assignments within a global, population-based search environment,\\u000a where the simultaneous application of local and global optimization heuristics guarantees high efficiency and robustness.\\u000a MATCH thus makes combined use of the two predominant

Jochen Volk; Torsten Herrmann; Kurt Wüthrich

2008-01-01

330

The reference genetic linkage map for the multinational Brassica rapa genome sequencing project  

Microsoft Academic Search

We describe the construction of a reference genetic linkage map for the Brassica A genome, which will form the backbone for anchoring sequence contigs for the Multinational Brassica rapa Genome Sequencing Project. Seventy-eight doubled haploid lines derived from anther culture of the F1 of a cross between two diverse Chinese cabbage (B.\\u000a rapa ssp. pekinensis) inbred lines, ‘Chiifu-401-42’ (C) and

Su Ryun Choi; Graham R. Teakle; Prikshit Plaha; Jeong Hee Kim; Charlotte J. Allender; Elena Beynon; Zhong Yun Piao; Pilar Soengas; Tae Ho Han; Graham J. King; Guy C. Barker; Paul Hand; Derek J. Lydiate; Jacqueline Batley; David Edwards; Dal Hoe Koo; Jae Wook Bang; Beom-Seok Park; Yong Pyo Lim

2007-01-01

331

A conserved sequence block in murine and human T cell receptor (TCR) J? region is a composite element that enhances TCR ? enhancer activity and binds multiple nuclear factors  

PubMed Central

A conserved sequence block (CSB) located in a noncoding region of the mouse and human TCR ?/? loci, showing six differences over 125 nucleotide positions (95% similar), was subjected to detailed analyses in this study. Transient transfection results showed that the CSB-containing element in conjunction with the TCR ? enhancer up-regulated the ? enhancer activity, whereas no enhancer activity was detected when CSB alone was assayed. In vitro occupancy analyses of CSB by nuclear factors reveal the existence of an unexpectedly intricate network of CSB–protein and protein–protein interactions. Lymphoid-specific as well as T-lineage-specific nuclear factors are involved to differentially form CSB-bound complexes in extracts of various tissues and cell lines. Liver was shown to contain factor(s) sequestering thymic CSB-binding factors. Furthermore, the putative binding sites for transcription factors known to be important for lymphoid-lineage development are present in CSB and are targeted by nuclear factors. On the basis of these results, we propose that the CSB element may play a role in shaping the chromatin structure by which the accessibility of TCR ?/? loci to the recombinase complex and/or to the transcriptional apparatus can be controlled.

Kuo, Chia-Lam; Chen, Mei-Ling; Wang, Kai; Chou, Chuan-Kai; Vernooij, Bernard; Seto, Donald; Koop, Ben F.; Hood, Leroy

1998-01-01

332

Dna Sequencing  

DOEpatents

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.

Tabor, Stanley (Cambridge, MA); Richardson, Charles C. (Chestnut Hill, MA)

1995-04-25

333

Influence of the backbone structure on the release of bioactive volatiles from maleic acid-based polymer conjugates.  

PubMed

Poly(maleic acid monoester)-based ?-mercapto ketones were synthesized and investigated as potential delivery systems for the controlled release of bioactive, volatile, ?,?-unsaturated enones (such as damascones and damascenones) by retro 1,4-addition. The bioconjugates were prepared in a one-pot synthesis using 2-mercaptoethanol as a linker. The thiol group of 2-mercaptoethanol adds to the double bond of the enone to form a ?-mercapto ketone, which was then grafted via nucleophilic ring-opening of the remaining alcohol function onto a series of alternating copolymers of maleic anhydride and 1-octadecene, ethylene, isobutylene, and methyl vinyl ether. The influence of copolymer backbones on the release of ?-damascone was investigated in buffered aqueous solution as a function of pH and time. In the presence of a cationic surfactant, the polymer conjugates were transferred from an aqueous medium to a cotton surface. The deposition and the release of ?-damascone from the cotton surface as a function of the polymer backbone structure were measured by fluorescence spectroscopy and dynamic headspace analysis, respectively. All polymer conjugates were found to deliver higher amounts of the volatile into the headspace than the reference consisting of unmodified ?-damascone. Polymers with a hydrophobic backbone were generally efficiently deposited on the cotton surface, but released ?-damascone only moderately in solution. Conjugates with a more hydrophilic backbone release the active compound more efficiently in water, but are deposited to a lower extent onto the target surface. A good balance of the hydrophobicity and hydrophilicity of the polymer backbone is the key factor to maximize the deposition of the conjugates on the target surface and to optimize the release of the bioactive volatiles. PMID:20936844

Berthier, Damien L; Paret, Nicolas; Trachsel, Alain; Herrmann, Andreas

2010-11-17

334

De Novo Determination of Protein Backbone Structure from Residual Dipolar Couplings Using Rosetta  

Microsoft Academic Search

Abstract: As genome-sequencing projects rapidly increase the database of protein sequences, the gap between known sequences and known structures continues to grow exponentially, increasing the demand to accelerate structure determination methods. Residual dipolar couplings (RDCs) are an attractive source of experimental restraints for NMR structure determination, particularly rapid, high-throughput methods, because they yield both local and long-range orientational information and

Carol A. Rohl; David Baker

2002-01-01

335

Applications of Recursive Segmentation to the Analysis of DNA Sequences  

Microsoft Academic Search

Recursive segmentation is a procedure that partitions a DNA sequence into domains with a homogeneous composition of the four nucleotides A, C, G and T. This procedure can also be applied to any sequence converted from a DNA sequence, such as to a binary strong(G + C)\\/weak(A+ T) sequence, to a binary sequence indicating the presence or absence of the

Wentian Li; Pedro Bernaola-galván; Fatameh Haghighi; Ivo Grosse

2002-01-01

336

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)

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.

Kapsiotis, Argirios; Grammatikopoulos, Tassos A.; Tsikouras, Basilios; Hatzipanagiotou, Konstantin; Zaccarini, Federica; Garuti, Giorgio

2011-01-01

337

Proteoglycan sequence  

PubMed Central

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.

Li, Lingyun; Ly, Mellisa

2012-01-01

338

New Generation of Plasmid Backbones Devoid of Antibiotic Resistance Marker for Gene Therapy Trials  

PubMed Central

Since it has been established that the injection of plasmid DNA can lead to an efficient expression of a specific protein in vivo, nonviral gene therapy approaches have been considerably improved, allowing clinical trials. However, the use of antibiotic resistance genes as selection markers for plasmid production raises safety concerns which are often pointed out by the regulatory authorities. Indeed, a horizontal gene transfer to patient's bacteria cannot be excluded, and residual antibiotic in the final product could provoke allergic reactions in sensitive individuals. A new generation of plasmid backbones devoid of antibiotic resistance marker has emerged to increase the safety profile of nonviral gene therapy trials. This article reviews the existing strategies for plasmid maintenance and, in particular, those that do not require the use of antibiotic resistance genes. They are based either on the complementation of auxotrophic strain, toxin–antitoxin systems, operator–repressor titration, RNA markers, or on the overexpression of a growth essential gene. Minicircles that allow removing of the antibiotic resistance gene from the initial vector will also be discussed. Furthermore, reported use of antibiotic-free plasmids in preclinical or clinical studies will be listed to provide a comprehensive view of these innovative technologies.

Vandermeulen, Gaelle; Marie, Corinne; Scherman, Daniel; Preat, Veronique

2011-01-01

339

Backbone Trace of Partitivirus Capsid Protein from Electron Cryomicroscopy and Homology Modeling  

PubMed Central

Abstract Most dsRNA viruses have a genome-enclosing capsid that comprises 120 copies of a single coat protein (CP). These 120 CP subunits are arranged as asymmetrical dimers that surround the icosahedral fivefold axes, forming pentamers of dimers that are thought to be assembly intermediates. This scheme is violated, however, in recent structures of two dsRNA viruses, a fungal virus from family Partitiviridae and a rabbit virus from family Picobirnaviridae, both of which have 120 CP subunits organized as dimers of quasisymmetrical dimers. In this study, we report the CP backbone trace of a second fungal partitivirus, determined in this case by electron cryomicroscopy and homology modeling. This virus also exhibits quasisymmetrical CP dimers that are connected by prominent surface arches and stabilized by domain swapping between the two CP subunits. The CP fold is dominated by ?-helices, although ?-strands mediate several important contacts. A dimer-of-dimers assembly intermediate is again implicated. The disordered N-terminal tail of each CP subunit protrudes into the particle interior and likely interacts with the genome during packaging and/or transcription. These results broaden our understanding of conserved and variable aspects of partitivirus structure and reflect the growing use of electron cryomicroscopy for atomic modeling of protein folds.

Tang, Jinghua; Pan, Junhua; Havens, Wendy M.; Ochoa, Wendy F.; Guu, Tom S.Y.; Ghabrial, Said A.; Nibert, Max L.; Tao, Yizhi Jane; Baker, Timothy S.

2010-01-01

340

OLIGOMERIZATION OF A RETROVIRAL MATRIX PROTEIN IS FACILITATED BY BACKBONE FLEXIBILITY ON NS TIMESCALE  

PubMed Central

Oligomerization capacity of the retroviral matrix protein is an important feature that affects assembly of immature virions and their interaction with cellular membrane. A combination of NMR relaxation measurements and advanced analysis of molecular dynamics simulation trajectory provided an unprecedentedly detailed insight into internal mobility of matrix proteins of the Mason-Pfizer monkey virus. Strong evidences have been obtained that the oligomerization capacity of the wild type matrix protein is closely related to the enhanced dynamics of several parts of its backbone on ns timescale. Increased flexibility has been observed for two regions: the loop between ?-helices ?2 and ?3 and the C-terminal half of ?-helix ?3 which accommodate amino acid residues that form the oligomerization interface. On the other hand, matrix mutant R55F that has changed structure and does not exhibit any specific oligomerization in solution was found considerably more rigid. Our results document that conformational selection mechanism together with induced fit and favorable structural pre-organization play an important role in the control of the oligomerization process.

Srb, Pavel; Vlach, Jiri; Prchal, Jan; Grocky, Marian; Ruml, Tomas; Lang, Jan; Hrabal, Richard

2011-01-01

341

Backbone resonance assignment and order tensor estimation using residual dipolar couplings  

PubMed Central

An NMR investigation of proteins with known X-ray structures is of interest in a number of endeavors. Performing these studies through nuclear magnetic resonance (NMR) requires the costly step of resonance assignment. The prevalent assignment strategy does not make use of existing structural information and requires uniform isotope labeling. Here we present a rapid and cost-effective method of assigning NMR data to an existing structure—either an X-ray or computationally modeled structure. The presented method, Exhaustively Permuted Assignment of RDCs (EPAR), utilizes unassigned residual dipolar coupling (RDC) data that can easily be obtained by NMR spectroscopy. The algorithm uses only the backbone N–H RDCs from multiple alignment media along with the amino acid type of the RDCs. It is inspired by previous work from Zweckstetter and provides several extensions. We present results on 13 synthetic and experimental datasets from 8 different structures, including two homodimers. Using just two alignment media, EPAR achieves an average assignment accuracy greater than 80%. With three media, the average accuracy is higher than 94%. The algorithm also outputs a prediction of the assignment accuracy, which has a correlation of 0.77 to the true accuracy. This prediction score can be used to establish the needed confidence in assignment accuracy.

Shealy, Paul; Liu, Yizhou; Simin, Mikhail

2014-01-01

342

Structurally diverse cyclisation linkers impose different backbone conformations in bicyclic peptides.  

PubMed

Combinatorial libraries of structurally diverse peptide macrocycles offer a rich source for the development of high-affinity ligands to targets of interest. In this work we have developed linkers for the generation of genetically encoded bicyclic peptides and tested whether the peptides cyclised by them have significant variations in their backbone conformations. Two new cyclisation reagents, each containing three thiol-reactive groups, efficiently and selectively cyclised linear peptides containing three cysteine moieties. When the mesitylene linker of the bicyclic peptide PK15, a potent inhibitor of plasma kallikrein (K(i)=2 nM), was replaced by the new linkers, its inhibitory activity dropped by a factor of more than 1000, suggesting that the linkers impose different conformations on the peptide. Indeed, structural analysis by solution-state NMR revealed different NOE constraints in the three bicyclic peptides, indicating that these relatively small linkers at the centres of bicyclic peptide structures significantly influence the conformations of the peptides. These results demonstrate the prominent structural role of linkers in peptide macrocycles and suggest that application of different cyclisation linkers in a combinatorial fashion could be an attractive means to generate topologically diverse macrocycle libraries. PMID:22492661

Chen, Shiyu; Morales-Sanfrutos, Julia; Angelini, Alessandro; Cutting, Brian; Heinis, Christian

2012-05-01

343

Ionization Cross Sections and Dissociation Channels of the DNA Sugar-Phosphate Backbone by Electron Collisions  

NASA Technical Reports Server (NTRS)

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.

Dateo, Christopher; Huo, Winifred M.; Fletcher, Graham D.

2004-01-01

344

Design and Synthesis of Efficient Fluorescent Dyes for Incorporation into DNA Backbone and Biomolecule Detection  

PubMed Central

We report here the design and synthesis of a series of ?-conjugated fluorescent dyes with D-A-D (D: donor; A: Acceptor), D-?-D, A-?-A, and D-?-A for applications as the signaling motif in biological-synthetic hybrid foldamers for DNA detection. Horner-Wadsworth-Emmons (HWE) reaction and Knoevenagel condensation were demonstrated as the optimum ways for construction of long ?-conjugated systems. Such rod-like chromophores have distinct advantages, as their fluorescence properties are not quenched by the presence of DNA. To be incorporated into the backbone of DNA, the chromophores need to be reasonably soluble in organic solvent for solid-phase synthesis, and therefore a strategy of using flexible tetra(ethylene glycol) (TEG) linkers at either end of these rod-like dyes were developed. The presence of TEG facilitates the protection of the chain-growing hydroxyl group with DMTrCl (dimethoxy trityl chloride) as well as the activation of the coupling step with phosphoramidite chemistry on an automated DNA synthesizer. To form fluorescence resonance energy transfer (FRET) pairs, six synthetic chromophores with blue to red fluorescence have been developed and those with orthogonal fluorescent emission were chosen for incorporation into DNA-chromophore hybrid foldamers.

Wang, Wei; Li, Alexander D. Q.

2008-01-01

345

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

PubMed

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

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

2014-06-01

346

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

PubMed

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

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

1995-01-01

347

Backbone dynamics of the CDK inhibitor p19(INK4d) studied by 15N NMR relaxation experiments at two field strengths.  

PubMed

The four members of the INK4 gene family, p16(INK4a), p15(INK4b), p18(INK4c) and p19(INK4d), are known to bind to and inhibit the closely related cyclin-dependent kinases CDK4 and CDK6 as part of the regulation of the G1/S transition in the cell division cycle. Loss of INK4 gene product function, and particularly that of p16(INK4a), is found in human cancer. 15N NMR relaxation rates of p19(INK4d) were analyzed using the reduced spectral density mapping method. Most of the backbone of p19(INK4d) exists in a well-defined structure of limited conformational flexibility on the nanosecond to picosecond time-scales. Introducing appropriate scaling to account for the effects of anisotropy, a considerable amount of exchange broadening was found for several residues throughout the sequence, especially residues in the second ankyrin repeat and in the beginnings and ends of loops connecting ankyrin repeats. A possible mode of binding between p19(INK4d) and CDK4 and CDK6 could therefore involve the loop segments of p19(INK4d). The average overall correlation time taumeff was determined to be 13.6 ns, reflecting the tendency of p19(INK4d) to aggregate. PMID:9761685

Renner, C; Baumgartner, R; Noegel, A A; Holak, T A

1998-01-01

348

Comparison of DNA Sequences with Protein Sequences  

Microsoft Academic Search

The FASTA package of sequence comparison programs has been expanded to include FASTX and FASTY, which compare a DNA sequence to a protein sequence database, translating the DNA sequence in three frames and aligning the translated DNA sequence to each sequence in the protein database, allowing gaps and frameshifts. Also new are TFASTX and TFASTY, which compare a protein sequence

William R. Pearson; Todd Wood; Zheng Zhang; Webb Miller

1997-01-01

349

Solution studies of staphylococcal nuclease H124L. 1. Backbone sup 1 H and sup 15 N resonances and secondary structure of the unligated enzyme as identified by three-dimensional NMR spectroscopy  

SciTech Connect

The backbone {sup 1}H and {sup 15}N resonances of unligated staphylococcal nuclease H124L (recombinant protein produced in Escherichia coli whose sequence is identical to the nuclease produced by the V8 strain of Staphylococcus aureus) have been assigned by three-dimensional (3D) {sup 1}H-{sup 15}N NOESY-HMQC NMR spectroscopy at 14.1 tesla. The protein sample used in this study was labeled uniformly with {sup 15}N to a level greater than 95% by growing the E. coli host on a medium containing (99% {sup 15}N)ammonium sulfate as the sole nitrogen source. The assignments include 82% of the backbone {sup 1}H{sup N} and {sup 1}H{sup {alpha}} resonances as well as the {sup 15}N resonances of non-proline residues. Secondary structural elements ({alpha}-helices, {beta}-sheets, reverse turns, and loops) were determined by analysis of patterns of NOE connectivities present in the 3D spectrum.

Wang, Jinfeng; Mooberry, E.S.; Walkenhorst, W.F.; Markley, J.L. (Univ. of Wisconsin, Madison (United States))

1992-01-28

350

Solution NMR structure and backbone dynamics of the major cold-shock protein (CspA) from Escherichia coli: evidence for conformational dynamics in the single-stranded RNA-binding site.  

PubMed

The major cold-shock protein (CspA) from Escherichia coli is a single-stranded nucleic acid-binding protein that is produced in response to cold stress. We have previously reported its overall chain fold as determined by NMR spectroscopy [Newkirk, K., Feng, W., Jiang, W., Tejero, R., Emerson, S. D., Inouye, M., and Montelione, G. T. (1994) Proc. Natl. Acad. Sci. U.S.A. 91, 5114-5118]. Here we describe the complete analysis of 1H, 13C, and 15N resonance assignments for CspA, together with a refined solution NMR structure based on 699 conformational constraints and an analysis of backbone dynamics based on 15N relaxation rate measurements. An extensive set of triple-resonance NMR experiments for obtaining the backbone and side chain resonance assignments were carried out on uniformly 13C- and 15N-enriched CspA. Using a subset of these triple-resonance experiments, the computer program AUTOASSIGN provided automatic analysis of sequence-specific backbone N, Calpha, C', HN, Halpha, and side chain Cbeta resonance assignments. The remaining 1H, 13C, and 15N resonance assignments for CspA were then obtained by manual analysis of additional NMR spectra. Dihedral angle constraints and stereospecific methylene Hbeta resonance assignments were determined using a new conformational grid search program, HYPER, and used together with longer-range constraints as input for three-dimensional structure calculations. The resulting solution NMR structure of CspA is a well-defined five-stranded beta-barrel with surface-exposed aromatic groups that form a single-stranded nucleic acid-binding site. Backbone dynamics of CspA have also been characterized by 15N T1, T2, and heteronuclear 15N-1H NOE measurements and analyzed using the extended Lipari-Szabo formalism. These dynamic measurements indicate a molecular rotational correlation time taum of 4.88 +/- 0.04 ns and provide evidence for fast time scale (taue < 500 ps) dynamics in surface loops and motions on the microsecond to millisecond time scale within the proposed nucleic acid-binding epitope. PMID:9692981

Feng, W; Tejero, R; Zimmerman, D E; Inouye, M; Montelione, G T

1998-08-01

351

Functional RNAs exhibit tolerance for non-heritable 2?-5? vs. 3?-5? backbone heterogeneity  

PubMed Central

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 containing 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.

Engelhart, Aaron E.; Powner, Matthew W.; Szostak, Jack W.

2014-01-01

352

Functional RNAs exhibit tolerance for non-heritable 2?-5? versus 3?-5? backbone heterogeneity  

NASA Astrophysics Data System (ADS)

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.

Engelhart, Aaron E.; Powner, Matthew W.; Szostak, Jack W.

2013-05-01

353

Surface energy and adhesion of perfluoropolyether nanofilms on carbon overcoat: The end group and backbone chain effect  

NASA Astrophysics Data System (ADS)

In this paper, we have investigated the surface energy and adhesion of one functional PFPE (Zdol) and two series of nonfunctional PFPEs (Z and D) on carbon-overcoated disk surfaces. The effects of end group functionality, backbone chain flexibility, molecular weight, and film thickness were systematically examined. Our results indicated that nonfunctional PFPEs have weak attraction with carbon overcoat. However, due to backbone chain effect, Z has slightly stronger attraction than D. Based on the surface energy analyses and bonded thickness results, schematic bonding models were proposed, which indicate strong hydrogen bonding/ordered packing structure/low mobility for functional PFPE films and weak attraction/less-ordered packing structure/high mobility for nonfunctional PFPE films.

Chen, Haigang; Li, Lei; Merzlikine, Alexei G.; Hsia, Yiao-Tee; Jhon, Myung S.

2006-04-01

354

Backbone 1H, 15N and 13C assignments for the subunit a of the E. coli ATP synthase.  

PubMed

The structure of the 30 KDa subunit a of the membrane component (F(0)) of E. coli ATP synthase is investigated in a mixture of chloroform, methanol and water, a solvent previously used for solving the structure of another integral membrane protein, subunit c. Near complete backbone chemical shift assignments were made from a set of TROSY experiments including HNCO, HNCA, HN(CA)CB, HN(CO)CACB and 4D HNCOCA and HNCACO. Secondary structure of subunit a was predicted from the backbone chemical shifts using TALOS program. The protein was found to consist of multiple elongated alpha-helical segments. This finding is generally consistent with previous predictions of multiple transmembrane alpha-helices in this polytopic protein. PMID:15213458

Dmitriev, Oleg Y; Abildgaard, Frits; Markley, John L; Fillingame, Robert H

2004-07-01

355

Comparing theoretical and experimental backbone-dependent sidechain conformational preferences for linear, branched, aromatic and polar residues  

NASA Astrophysics Data System (ADS)

An Ecepp-3 conformational study based on a ?-? grid search with sidechain minimization was carried out on the N-acetyl N'-methyl amides of four representative amino acids: Met, Phe, Ile, and Ser, and the distribution of ?1 backbone-dependent rotamer preferences was compared with the similar distribution obtained from the backbone-dependent rotamer library for proteins developed by Dunbrack and Karplus (J. Mol. Biol. 230 (1993) 543). The experimental distribution is best reproduced theoretically in the case of the linear sidechain of Met, reasonably well for the bulky sidechains of the aromatic Phe and asymmetrically ?-branched Ile, and only partially for the short polar sidechain of Ser. In the case of the Ser dipeptide the difference is accounted for by the missing H bonds.

Marcus, Emil; Keller, Donald A.; Shibata, Masayuki; Ornstein, Rick L.; Rein, Robert

1996-04-01

356

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

PubMed

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

Kool, Marijn M; Schols, Henk A; Delahaije, Roy J B M; Sworn, Graham; Wierenga, Peter A; Gruppen, Harry

2013-09-12

357

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

NASA Astrophysics Data System (ADS)

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.

Choi, Eunwoo

358

Sequencing Time  

NSDL National Science Digital Library

In this activity, students gain an understanding of relative and numerical time by placing events in sequence and assigning relative times to the events. This will familarize them with the methods used by scientists to develop the geologic time scale. This activity contains objectives, materials, procedure, and extensions.

2007-12-12

359

Conformer selection and induced fit in flexible backbone protein-protein docking using computational and NMR ensembles  

PubMed Central

Accommodating backbone flexibility continues to be the most difficult challenge in computational docking of protein-protein complexes. Towards that end, we simulate four distinct biophysical models of protein binding in RosettaDock, a multi-scale Monte-Carlo based algorithm that uses a quasi-kinetic search process to emulate the diffusional encounter of two proteins and identify low energy complexes. The four binding models are: 1) key-lock model (KL) using rigid-backbone docking, 2) conformer selection model (CS) using a novel ensemble docking algorithm, 3) induced fit model (IF) using energy gradient-based backbone minimization, and 4) a combined conformer selection/induced fit model (CS/IF). Backbone flexibility was limited to the smaller partner of the complex, structural ensembles were generated using Rosetta refinement methods, and docking consisted of local perturbations around the complexed conformation using unbound component crystal structures for a set of 21 target complexes. The lowest-energy structure contained more than 30% of the native residue-residue contacts for 9, 13, 13, and 14 targets for KL, CS, IF and CS/IF docking respectively. When applied to 15 targets using NMR ensembles of the smaller protein, the lowest-energy structure recovered at least 30% native residue contacts in 3, 8, 4 and 8 targets for KL, CS, IF and CS/IF docking respectively. CS/IF docking of the NMR ensemble performed equally well or better than KL docking with the unbound crystal structure in 10 of 15 cases. The marked success of CS and CS/IF docking shows that ensemble docking can be a versatile and effective method for accommodating conformational plasticity in docking and serves as a demonstration for the conformer selection theory - that binding-competent conformers exist in the unbound ensemble and can be selected based on their favorable binding energies.

Chaudhury, Sidhartha; Gray, Jeffrey J.

2008-01-01

360

Deuterium Spin Probes of Backbone Order in Proteins: A 2H NMR Relaxation Study of Deuterated Carbon ? Sites  

PubMed Central

2H spin relaxation NMR experiments to study the dynamics of deuterated backbone ?-positions, D?, are developed. To date, solution-state 2H relaxation measurements in proteins have been confined to side-chain deuterons - primarily 13CH2D or 13CHD2 methyl groups. It is shown that quantification of 2H relaxation rates at D? backbone positions and the derivation of associated order parameters of C?-D? bond vector motions in small [U-15N,13C,2H]-labeled proteins is feasible with reasonable accuracy. The utility of the developed methodology is demonstrated on a pair of proteins - ubiquitin (8.5 kDa) at 10°C, 27°C, and 40°C, and a variant of GB1 (6.5 kDa) at 22°C. In both proteins, the D?-derived parameters of the global rotational diffusion tensor are in good agreement with those obtained from 15N relaxation rates. Semi-quantitative solution state NMR measurements yield an average value of the quadrupolar coupling constant, QCC, for D? sites in proteins equal to 174 kHz. Using the uniform value of QCC for all D? sites, we show that C?-D? bond vectors are motionally distinct from the backbone amide N-H bond vectors, with 2H-derived squared order parameters of C?-D? bond vector motions, S2 C?D?, on average slightly higher than their N-H amides counterparts, S2 NH. For ubiquitin, the 2H-derived backbone mobility compares well with that found in a 1-?s molecular dynamics simulation.

Sheppard, Devon; Li, Da-Wei; Bruschweiler, Rafael; Tugarinov, Vitali

2009-01-01

361

Rheological and molecular characterization of linear backbone flexible polymers with the Cole-Cole model relaxation spectrum  

Microsoft Academic Search

The empirical Cole-Cole distribution is an analytical three parameter model of the relaxation spectra that provides accurate\\u000a fits to experimental dynamic viscosity data for many systems of commercial linear backbone flexible polymers. We demonstrate\\u000a that for disparate systems of polyethylenes, the three Cole-Cole model parameters have simple power law relationships to moments\\u000a of the molecular weight distribution enabling direct molecular

Cesar A. Garcia-Franco; David W. Mead

1999-01-01

362

Ramachandran backbone potential energy surfaces of aspartic acid and aspartate residues: implications on allosteric sites in receptor–ligand complexations  

Microsoft Academic Search

Ramachandran backbone potential energy surfaces (PES) were generated for N-acetyl-l-aspartic acid-N?-methylamide and N-acetyl-l-aspartate-N?-methylamide. Relatively few minima were observed from the Ramachandran PES of the aspartate ion while many existed for both endo and exo forms of the aspartic acid residue. By comparing the relative stabilization energies as well as the vertical and adiabetic proton affinities of the two forms the

Joseph C. P Koo; Janice S. W Lam; Gregory A Chass; David H Setiadi; Jacqueline M. S Law; Julius Gy Papp; Botond Penke; Imre G Csizmadia

2003-01-01

363

Backbone and sidechain ¹H, ¹³C and ¹?N chemical shift assignments of the hydrophobin DewA from Aspergillus nidulans.  

PubMed

Hydrophobins are proteins secreted by filamentous fungi that are able to self-assemble into monolayers at hydrophobic:hydrophilic interfaces. The layers are amphipathic and can reverse the wettability of surfaces. Hydrophobins have several roles in fungal development, including the formation of coatings on fungal structures to render them hydrophobic. Here we report the backbone and sidechain assignments for the class I hydrophobin DewA from the fungus Aspergillus nidulans. PMID:21845363

Morris, Vanessa K; Kwan, Ann H; Mackay, Joel P; Sunde, Margaret

2012-04-01

364

Direct Formation of the C5?-Radical in the Sugar-Phosphate Backbone of DNA by High Energy Radiation  

PubMed Central

Neutral sugar radicals formed in DNA sugar-phosphate backbone are well-established as precursors of biologically important damage such as DNA-strand scission and crosslinking. In this work, we present electron spin resonance (ESR) evidence showing that the sugar radical at C5? (C5?•) is one of the most abundant (ca. 30%) sugar radicals formed by ?- and Ar ion-beam irradiated hydrated DNA samples. Taking dimethyl phosphate as a model of sugar-phosphate backbone, ESR and theoretical (DFT) studies of ?-irradiated dimethyl phosphate were carried out. CH3OP(O2?)OCH2• is formed via deprotonation from the methyl group of directly ionized dimethyl phosphate at 77 K. Formation of CH3OP(O2?)OCH2• is independent of dimethyl phosphate concentration (neat or in aqueous solution) or pH. ESR spectra of C5?• found in DNA and of CH3OP(O2?)OCH2• do not show an observable ?-phosphorous hyperfine coupling (HFC). Further, C5?• found in DNA does not show a significant C4?-H ?–proton HFC. Applying the DFT/B3LYP/6-31G(d) method, a study of conformational dependence of the phosphorous HFC in CH3OP(O2?)OCH2• shows that in its minimum energy conformation, CH3OP(O2?)OCH2• has a negligible ?-phosphorous HFC. Based on these results, formation of radiation-induced C5?• is proposed to occur via a very rapid deprotonation from the directly ionized sugar-phosphate backbone and rate of this deprotonation must be faster than that of energetically downhill transfer of the unpaired spin (hole) from ionized sugar-phosphate backbone to the DNA bases. Moreover, C5?• in irradiated DNA is found to be in a conformation that does not exhibit ? proton or ? phosphorous HFCs.

Adhikary, Amitava; Becker, David; Palmer, Brian J.; Heizer, Alicia N.; Sevilla, Michael D.

2012-01-01

365

Direct formation of the C5'-radical in the sugar-phosphate backbone of DNA by high-energy radiation.  

PubMed

Neutral sugar radicals formed in DNA sugar-phosphate backbone are well-established as precursors of biologically important damage such as DNA strand scission and cross-linking. In this work, we present electron spin resonance (ESR) evidence showing that the sugar radical at C5' (C5'(•)) is one of the most abundant (ca. 30%) sugar radicals formed by ?- and Ar ion-beam irradiated hydrated DNA samples. Taking dimethyl phosphate as a model of sugar-phosphate backbone, ESR and theoretical (DFT) studies of ?-irradiated dimethyl phosphate were carried out. CH(3)OP(O(2)(-))OCH(2)(•) is formed via deprotonation from the methyl group of directly ionized dimethyl phosphate at 77 K. The formation of CH(3)OP(O(2)(-))OCH(2)(•) is independent of dimethyl phosphate concentration (neat or in aqueous solution) or pH. ESR spectra of C5'(•) found in DNA and of CH(3)OP(O(2)(-))OCH(2)(•) do not show an observable ?-phosphorus hyperfine coupling (HFC). Furthermore, C5'(•) found in DNA does not show a significant C4'-H ?-proton HFC. Applying the DFT/B3LYP/6-31G(d) method, a study of conformational dependence of the phosphorus HFC in CH(3)OP(O(2)(-))OCH(2)(•) shows that in its minimum energy conformation, CH(3)OP(O(2)(-))OCH(2)(•), has a negligible ?-phosphorus HFC. On the basis of these results, the formation of radiation-induced C5'(•) is proposed to occur via a very rapid deprotonation from the directly ionized sugar-phosphate backbone, and the rate of this deprotonation must be faster than that of energetically downhill transfer of the unpaired spin (hole) from ionized sugar-phosphate backbone to the DNA bases. Moreover, C5'(•) in irradiated DNA is found to be in a conformation that does not exhibit ?-proton or ?-phosphorus HFCs. PMID:22553971

Adhikary, Amitava; Becker, David; Palmer, Brian J; Heizer, Alicia N; Sevilla, Michael D

2012-05-24

366

Catalytic mechanism of RNA backbone cleavage by ribonuclease H from quantum mechanics/molecular mechanics simulations.  

PubMed

We use quantum mechanics/molecular mechanics simulations to study the cleavage of the ribonucleic acid (RNA) backbone catalyzed by ribonuclease H. This protein is a prototypical member of a large family of enzymes that use two-metal catalysis to process nucleic acids. By combining Hamiltonian replica exchange with a finite-temperature string method, we calculate the free energy surface underlying the RNA-cleavage reaction and characterize its mechanism. We find that the reaction proceeds in two steps. In a first step, catalyzed primarily by magnesium ion A and its ligands, a water molecule attacks the scissile phosphate. Consistent with thiol-substitution experiments, a water proton is transferred to the downstream phosphate group. The transient phosphorane formed as a result of this nucleophilic attack decays by breaking the bond between the phosphate and the ribose oxygen. In the resulting intermediate, the dissociated but unprotonated leaving group forms an alkoxide coordinated to magnesium ion B. In a second step, the reaction is completed by protonation of the leaving group, with a neutral Asp132 as a likely proton donor. The overall reaction barrier of ?15 kcal mol(-1), encountered in the first step, together with the cost of protonating Asp132, is consistent with the slow measured rate of ?1-100/min. The two-step mechanism is also consistent with the bell-shaped pH dependence of the reaction rate. The nonmonotonic relative motion of the magnesium ions along the reaction pathway agrees with X-ray crystal structures. Proton-transfer reactions and changes in the metal ion coordination emerge as central factors in the RNA-cleavage reaction. PMID:21539371

Rosta, Edina; Nowotny, Marcin; Yang, Wei; Hummer, Gerhard

2011-06-15

367

The multiscale backbone of the human phenotype network based on biological pathways  

PubMed Central

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.

2014-01-01

368

Catalytic Mechanism of RNA Backbone Cleavage by Ribonuclease H from QM/MM Simulations  

PubMed Central

We use quantum mechanics/molecular mechanics (QM/MM) simulations to study the cleavage of the ribonucleic acid (RNA) backbone catalyzed by ribonuclease H. This protein is a prototypical member of a large family of enzymes that use two-metal catalysis to process nucleic acids. By combining Hamiltonian replica exchange with a finite-temperature string method, we calculate the free energy surface underlying the RNA cleavage reaction and characterize its mechanism. We find that the reaction proceeds in two steps. In a first step, catalyzed primarily by magnesium ion A and its ligands, a water molecule attacks the scissile phosphate. Consistent with thiol-substitution experiments, a water proton is transferred to the downstream phosphate group. The transient phosphorane formed as a result of this nucleophilic attack decays by breaking the bond between the phosphate and the ribose oxygen. In the resulting intermediate, the dissociated but unprotonated leaving group forms an alkoxide coordinated to magnesium ion B. In a second step, the reaction is completed by protonation of the leaving group, with a neutral Asp132 as a likely proton donor. The overall reaction barrier of ~15 kcal mol?1, encountered in the first step, together with the cost of protonating Asp132, is consistent with the slow measured rate of ~1–100/min. The two-step mechanism is also consistent with the bell-shaped pH dependence of the reaction rate. The non-monotonic relative motion of the magnesium ions along the reaction pathway agrees with X-ray crystal structures. Proton transfer reactions and changes in the metal ion coordination emerge as central factors in the RNA cleavage reaction.

Rosta, Edina; Nowotny, Marcin; Yang, Wei; Hummer, Gerhard

2011-01-01

369

Functional implications of large backbone amplitude motions of the glycoprotein 130-binding epitope of interleukin-6.  

PubMed

Human interleukin (IL)-6 plays a pivotal role in the immune response, hematopoiesis, the acute-phase response, and inflammation. IL-6 has three distinct receptor epitopes, termed sites I, II, and III, that facilitate the formation of a signaling complex. IL-6 signals via a homodimer of glycoprotein 130 (gp130) after initially forming a heterodimer with the nonsignaling ?-receptor [IL-6 ?-receptor (IL-6R)] via site I. Here, we present the backbone dynamics of apo-IL-6 as determined by analysis of NMR relaxation data with the extended model-free formalism of Lipari and Szabo. To alleviate significant resonance overlap in the HSQC-type spectra, cell-free protein synthesis was used to selectively (15) N-label residues, thereby ensuring a complete set of residue-specific dynamics. The calculated order parameters [square of the generalized model-free order parameter (S(2) )] showed significant conformational heterogeneity among clusters of residues in IL-6. In particular, the N-terminal region of the long AB-loop, which corresponds spatially to one of the gp130 receptor binding epitopes (i.e. site III), experiences substantial fluctuations along the conformation of the main chain (S(2)  = 0.3-0.8) that are not observed at the other two epitopes or in other cytokines. Thus, we postulate that dynamic properties of the AB-loop are responsible for inhibiting the interaction of IL-6 with gp130 in the absence of the IL-6R, and that binding of IL-6R at site I shifts the dynamic equilibrium to favor interaction with gp130 at site III. In addition, molecular dynamics simulations corroborated the NMR-derived dynamics, and showed that the BC-loop adopts different substates that possibly play a role in facilitating receptor assembly. PMID:24712547

Bobby, Romel; Robustelli, Paul; Kralicek, Andrew V; Mobli, Mehdi; King, Glenn F; Grötzinger, Joachim; Dingley, Andrew J

2014-05-01

370

Backbone-branched DNA building blocks for facile angular control in nanostructures.  

PubMed

Nanotechnology based on the highly specific pairing of nucleobases in DNA has been used to generate a wide variety of well-defined two- and three-dimensional assemblies, both static and dynamic. However, control over the junction angles to achieve them has been limited. To achieve higher order assemblies, the strands of the DNA duplex are typically made to deviate at junctions with configurations based on crossovers or non-DNA moieties. Such strand crossovers tend to be intrinsically unstructured with the overall structural rigidity determined by the architecture of the nanoassembly, rather than the junction itself. Specific approaches to define nanoassembly junction angles are based either on the cooperative twist- and strain-promoted tuning of DNA persistence length leading to bent DNA rods for fairly large nano-objects, or de novo synthesis of individual junction inserts that are typically non-DNA and based on small organic molecules or metal-coordinating ligand moieties. Here, we describe a general strategy for direct control of junction angles in DNA nanostructures that are completely tunable about the DNA helix. This approach is used to define angular vertices through readily accessible backbone-branched DNAs (bbDNAs). We demonstrate how such bbDNAs can be used as a new building block in DNA nanoconstruction to obtain well-defined nanostructures. Angular control through readily accessible bbDNA building block provides a general and versatile approach for incorporating well-defined junctions in nanoconstructs and expands the toolkit toward achieving strain free, highly size- and shape-tunable DNA based architectures. PMID:23600590

Paredes, Eduardo; Zhang, Xiaojuan; Ghodke, Harshad; Yadavalli, Vamsi K; Das, Subha R

2013-05-28

371

Languaging: A Composition Curriculum.  

ERIC Educational Resources Information Center

This curriculum guide reviews current theories on the teaching of writing, focuses on the nature of composition, and enumerates sequences of writing exercises for seventh and eighth grade teachers to consider for assigning to their students. Contents include "Rhetoric in the 1960's," which defines composition and explains what languaging is about;…

Mount Diablo Unified School District, Concord, CA.

372

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

NASA Technical Reports Server (NTRS)

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.

Huo, Winifred M.; Dateo, Christopher E.

2005-01-01

373

Backbone Dynamics of Alamethicin Bound to Lipid Membranes: Spin-Echo Electron Paramagnetic Resonance of TOAC-Spin Labels  

PubMed Central

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, 2?. 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.

Bartucci, Rosa; Guzzi, Rita; De Zotti, Marta; Toniolo, Claudio; Sportelli, Luigi; Marsh, Derek

2008-01-01

374

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

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

Balzano, Sergio; Marie, Dominique; Gourvil, Priscillia; Vaulot, Daniel

2012-08-01

375

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

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.

Balzano, Sergio; Marie, Dominique; Gourvil, Priscillia; Vaulot, Daniel

2012-01-01

376

MSLICE Sequencing  

NASA Technical Reports Server (NTRS)

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.

Crockett, Thomas M.; Joswig, Joseph C.; Shams, Khawaja S.; Norris, Jeffrey S.; Morris, John R.

2011-01-01

377

Segmentation algorithm for DNA sequences  

NASA Astrophysics Data System (ADS)

A new measure, to quantify the difference between two probability distributions, called the quadratic divergence, has been proposed. Based on the quadratic divergence, a new segmentation algorithm to partition a given genome or DNA sequence into compositionally distinct domains is put forward. The new algorithm has been applied to segment the 24 human chromosome sequences, and the boundaries of isochores for each chromosome were obtained. Compared with the results obtained by using the entropic segmentation algorithm based on the Jensen-Shannon divergence, both algorithms resulted in all identical coordinates of segmentation points. An explanation of the equivalence of the two segmentation algorithms is presented. The new algorithm has a number of advantages. Particularly, it is much simpler and faster than the entropy-based method. Therefore, the new algorithm is more suitable for analyzing long genome sequences, such as human and other newly sequenced eukaryotic genome sequences.

Zhang, Chun-Ting; Gao, Feng; Zhang, Ren

2005-10-01

378

Antimicrobial Treatment and Containment Measures for an Extremely Drug-Resistant Klebsiella pneumoniae ST101 Isolate Carrying pKPN101-IT, a Novel Fully Sequenced blaKPC-2 Plasmid  

PubMed Central

An extremely drug-resistant Klebsiella pneumoniae isolate, sequence type ST101, was isolated from a patient in Italy. We describe antibiotic treatment, measures to clear and contain the infection, and a complete sequence analysis of a novel large plasmid, pKPN101-IT, harboring the blaKPC-2 gene and arising from the threatening recombination of different worldwide-distributed backbones.

Frasson, Ilaria; Lavezzo, Enrico; Franchin, Elisa; Toppo, Stefano; Barzon, Luisa; Cavallaro, Antonietta; Palu, Giorgio

2012-01-01

379

Tenofovir disoproxil fumarate-emtricitabine coformulation for once-daily dual NRTI backbone.  

PubMed

Truvada is the coformulation of tenofovir disoproxil fumarate (TDF; 300 mg) and emtricitabine (FTC; 200 mg) in a single tablet, providing the nucleotide backbone for once-daily dosing, as a component of highly active antiretroviral therapy (HAART). TDF (the bioavailable prodrug of tenofovir) is hydrolyzed to tenofovir intracellularly and phosphorylated to the active metabolite, tenofovir diphosphate. Tenofovir is a nucleotide analog of deoxyadenosine monophosphate, with activity against HIV-1, -2 and hepatitis B virus. FTC, the fluorinated derivative of lamivudine, is an analog of deoxycitidine, active against HIV-1, -2 and hepatitis B virus. Their long half-lives in plasma and in peripheral blood mononuclear cells allow once-daily dosing. Both are eliminated renally. Resistance mutation K65R is selected for by tenofovir and confers a two- to fourfold reduced susceptibility to this drug. The incidence of K65R is low (3%) and has not been observed in clinical trials with the concomitant use of tenofovir and FTC. FTC selects for M184V mutation less frequently than lamivudine. Tenofovir drug interactions include increased exposure to didanosine and inferior immune recovery that preclude their concomitant use. Boosted protease inhibitors increase exposure to tenofovir without dose adjustment required. FTC has no significant drug interactions. They are not metabolized by cytochrome P450, which confers little potential for interactions with drugs metabolized by these enzymes. As tenofovir and FTC are renally eliminated, drugs eliminated by tubular secretion must be avoided. Both antiretrovirals, as individual agents and in coadministration have evidenced antiviral potency in clinical trials. Pivotal study 934 evidenced superior efficacy of the combination TDF/FTC/efavirenz (EFV) versus zidovudine/FTC/EFV. The toxicity profile of tenofovir and FTC has been extensively studied. Lipid profile is more favorable with tenofovir than thymidine analog. Tenofovir requires surveillance of glomerular filtration rate and dosing interval adjustment when creatinine clearance is less than 50 ml/min and avoidance less than 30 ml/min. Fat loss is less likely with tenofovir than with thymidine analog. Clinical trials have assessed the performance of the coformulation of TDF and FTC. PMID:17009933

Muñoz de Benito, Rosa María; Arribas López, Jose Ramón

2006-08-01

380

Enhanced production of single copy backbone-free transgenic plants in multiple crop species using binary vectors with a pRi replication origin in Agrobacterium tumefaciens  

Microsoft Academic Search

Single transgene copy, vector backbone-free transgenic crop plants are highly desired for functional genomics and many biotechnological\\u000a 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

Xudong Ye; Edward J. Williams; Junjiang Shen; Susan Johnson; Brenda Lowe; Sharon Radke; Steve Strickland; James A. Esser; Michael W. Petersen; Larry A. Gilbertson

381

Effect of distortions in the deoxyribose phosphate backbone conformation of duplex oligodeoxyribonucleotide dodecamers containing GT, GG, GA, AC, and GU base-pair mismatches on sup 31 P NMR spectra  

SciTech Connect

The authors have previously suggested that variations in the {sup 31}P chemical shifts of individual phosphates in duplex oligonucleotides are attributable to torsional angle changes in the deoxyribose phosphate backbone. This hypothesis is now directly supported by analysis of the {sup 1}H/{sup 31}P two-dimensional J-resolved spectra of a number of mismatch dodecamer oligonucleotide duplexes including the following sequences: d(CGTGAATTCGCG), d(CGUGAATTCGCG), d(CGGGAATTCGCG), d(CGAGAATTCGCG), and d(CGCGAATTCACG). The {sup 31}P NMR signals of the dodecamer mismatch duplexes were assigned by 2D {sup 1}H/{sup 31}P pure absorption phase constant time (PAC) heteronuclear correlation spectra. From the assigned H3{prime} and H4{prime} signals, the {sup 31}P signals of the base-pair mismatch dodecamers were identified. J{sub H3{prime}-P} coupling constants for each of the phosphates of the dodecamers were obtained from {sup 1}H/{sup 31}P J-resolved selective proton flip 2D spectra. By use of a modified Karplus relationship, the C4{prime}-C3{prime}-O3{prime}-P torsional angles ({epsilon}) were obtained. J{sub H3{prime}-P} coupling constants were measured for many of the oligonucleotides as a function of temperature. The {sup 31}P chemical shifts follows the general observation that the more internally the phosphate is located within the oligonucleotide sequence, the more upfield the {sup 31}P resonance occurs. Analysis of the backbone torsional angle variations from the coupling constant analysis has provided additional information regarding the origin of these variations in {sup 31}P chemical shifts.

Roongta, V.A.; Jones, C.R.; Gorenstein, D.G. (Purdue Univ., West Lafayette, IN (USA))

1990-06-05

382

Hidden Markov models that use predicted local structure for fold recognition: Alphabets of backbone geometry  

Microsoft Academic Search

An important problem in computa- tional biology is predicting the structure of the large number of putative proteins discovered by genome sequencing projects. Fold-recognition meth- ods 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 simi- larity are often not detectable

Rachel Karchin; Melissa Cline; Yael Mandel-Gutfreund; Kevin Karplus

2003-01-01

383

Molecular basis for nanoscopic membrane curvature generation from quantum mechanical models and synthetic transporter sequences  

PubMed Central

We investigate the physical origin of peptide-induced membrane curvature by contrasting differences between H-bonding interactions of prototypical cationic amino acids, arginine (Arg) and lysine (Lys), with phosphate groups of phospholipid heads using quantum mechanical (QM) calculations of a minimum model, and test the results via synthetic oxaorbornene-based transporter sequences without the geometric constraints of polypeptide backbones. QM calculations suggest that although individual Lys can in principle coordinate two phosphates, they are not able to do so at small inter-Lys distances without drastic energetic penalties. In contrast, Arg can coordinate two phosphates down to less than 5 Å, where guanidinium groups can stack ‘face to face’. In agreement with these observations, poly-Lys cannot generate the nanoscale positive curvature necessary for inducing negative Gaussian membrane curvature, in contrast to poly-Arg. Also consistent with QM calculations, polyguanidine-oxanorbornene homopolymers (PGONs) showed that curvature generation is exquisitely sensitive to the guanidinium group spacing when the phosphate groups are near close packing. Addition of phenyl or butyl hydrophobic groups into guanidine-oxanorbornene polymers increased the amount of induced saddle-splay membrane curvature, and broadened the range of lipid compositions where saddle-splay curvature was induced. The enhancement of saddle-splay curvature generation and relaxation of lipid composition requirements via addition of hydrophobicity is consistent with activity profiles. While PGON polymers displayed selective antimicrobial activity against prototypical (Gram positive and negative) bacteria, polymers with phenyl and butyl groups were also active against red blood cells. Our results suggest that it is possible to achieve deterministic molecular design of pore forming peptides.

Schmidt, Nathan W.; Lis, Michael; Zhao, Kun; Lai, Ghee Hwee; Alexandrova, Anastassia; Tew, Gregory N.; Wong, Gerard C. L.

2013-01-01

384

Protein Side-Chain Resonance Assignment and NOE Assignment Using RDC-Defined Backbones without TOCSY Data3  

PubMed Central

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.

Zeng, Jianyang; Zhou, Pei; Donald, Bruce Randall

2011-01-01

385

Effects of backbone and side chain on the molecular environments of chiral cavities in polysaccharide-based biopolymers.  

PubMed

The effects of the backbone and side chain on the molecular environments in the chiral cavities of three commercially important polysaccharide-based chiral sorbents--cellulose tris(3,5-dimethylphenylcarbamate) (CDMPC), amylose tris(3,5-dimethylphenylcarbamate) (ADMPC), and amylose tris[(S)-alpha-methylbenzylcarbamate] (ASMBC)--are studied by attenuated total reflection infrared spectroscopy (ATR-IR), X-ray diffraction (XRD), 13C cross-polarization/magic-angle spinning (CP/MAS) and MAS solid-state NMR, and density functional theory (DFT) modeling. These sorbents are used widely in preparative-scale chiral separations. ATR-IR is used to determine how the H-bonding states of the C=O and NH groups of the polymer depend on the backbone and side chain. The changes in the polymer crystallinity are characterized with XRD. The changes in the polymer helicity and molecular mobility for polymer-coated silica beads (commercially called Chiralcel OD, Chirapak AD, and Chiralpak AS) are probed with 13C CP/MAS and MAS solid-state NMR. The IR wavenumbers and the NMR chemical shifts for the polymer backbone monomers and dimers and the side chains are predicted at the DFT/B3LYP/6-311+g(d,p) level of theory. It is concluded that the molecular environments of the C=O, NH, and phenyl groups show significant differences in intramolecular and intermolecular interactions and in the nanostructures of the chiral cavities of these biopolymers. These results have implications for understanding how the molecular environments of chiral cavities of these polymers affect their molecular recognition mechanisms. PMID:17439279

Kasat, Rahul B; Wang, Nien-Hwa Linda; Franses, Elias I

2007-05-01

386

Regression fronts in random sphere packs: Application to composite solid propellant burning rate  

Microsoft Academic Search

The burning rate of a composite solid propellant may be estimated by global modeling, such as the widely used BDP model. The backbone of such models is the “mixture law” that links the propellant burning rate rp with the burning rate of its own components, i.e., oxidizer rox and binder rb. However, different laws are available in literature which all

Stany Gallier; Jean-François Guery

2009-01-01

387

Incorporation of heterocycles into the backbone of peptoids to generate diverse peptoid-inspired one bead one compound libraries.  

PubMed

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. 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

Aditya, Animesh; Kodadek, Thomas

2012-03-12

388

Incorporation of Heterocycles into the Backbone of Peptoids to Generate Diverse Peptoid-Inspired One Bead One Compound Libraries  

PubMed Central

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.

Aditya, Animesh; Kodadek, Thomas

2012-01-01

389

Characteristics of novel di-?-fluoroacrylate derivatives with polyfluoroalkyl aromatic backbone as a binder resin of direct filling materials.  

PubMed

To realize good mechanical properties and water resistance of a dental resin, novel di-?-fluoroacrylates with polyfluoroalkyl aromatic backbone were studied. The monomers were 2,2-bis(4-?-fluoroacryloxy phenyl)propane, 2,2-bis(4-?-fluoroacryloxy phenyl) hexafluoropropane, and 1,3-bis(2-?-fluoroacryloxy-2-hexafluoropropyl)benzene. The copolymers of the monomers and methyl methacrylate (MMA) were excellent in hardness, Izod impact strength, abrasion resistance, and water resistance, and showed similar values of compressive, diametral tensile, tensile, and bending strength compared with copolymers prepared from the corresponding dimethacrylate derivatives and MMA. PMID:21597214

Kurata, Shigeaki; Yamazaki, Noboru

2011-01-01

390

Depurination of N7-methylguanine by DNA glycosylase AlkD is dependent on the DNA backbone.  

PubMed

DNA glycosylase AlkD excises N7-methylguanine (7mG) by a unique but unknown mechanism, in which the damaged nucleotide is positioned away from the protein and the phosphate backbone is distorted. Here, we show by methylphosphonate substitution that a phosphate proximal to the lesion has a significant effect on the rate enhancement of 7mG depurination by the enzyme. Thus, instead of a conventional mechanism whereby protein side chains participate in N-glycosidic bond cleavage, AlkD remodels the DNA into an active site composed exclusively of DNA functional groups that provide the necessary chemistry to catalyze depurination. PMID:24090276

Rubinson, Emily H; Christov, Plamen P; Eichman, Brandt F

2013-10-22

391

Sequencing of Oligourea Foldamers by Tandem Mass Spectrometry  

NASA Astrophysics Data System (ADS)

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.

Bathany, Katell; Owens, Neil W.; Guichard, Gilles; Schmitter, Jean-Marie

2013-03-01

392

Sequencing of oligourea foldamers by tandem mass spectrometry.  

PubMed

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. PMID:23400773

Bathany, Katell; Owens, Neil W; Guichard, Gilles; Schmitter, Jean-Marie

2013-03-01

393

Mixed backbone antisense oligonucleotides: design, biochemical and biological properties of oligonucleotides containing 2'-5'-ribo- and 3'-5'-deoxyribonucleotide segments.  

PubMed Central

We have designed and synthesized mixed backbone oligonucleotides (MBOs) containing 2'-5'-ribo- and 3'-5'-deoxyribonucleotide segments. Thermal melting studies of the phosphodiester MBOs (three 2'-5'linkages at each end) with the complementary 3'-5'-DNA and -RNA target strands suggest that 2'-5'-ribonucleoside incorporation into 3'-5'-oligodeoxyribonucleotides reduces binding to the target strands compared with an all 3'-5'-oligodeoxyribonucleotide of the same sequence and length. Increasing the number of 2'-5'linkages (from six to nine) further reduces binding to the DNA target strand more than the RNA target strand [Kandimalla,E.R. and Agrawal,S. (1996)Nucleic Acids Symp. Ser., 35, 125-126]. Phosphorothioate (PS) analogs of MBOs destabilize the duplex with the DNA target strand more than the duplex with the RNA target strand. Circular dichroism studies indicate that the duplexes of MBOs with the DNA and RNA target strands have spectral characteristics of both A- and B-type conformations. Compared with the control oligonucleotide, MBOs exhibit moderately higher stability against snake venom phosphodiesterase, S1 nuclease and in fetal calf serum. Although 2'-5'modification does not evoke RNase H activity, this modification does not effect the RNase H activation property of the 3'-5'-deoxyribonucleotide segment adjacent to the modification. In vitro studies with MBOs suggest that they have lesser effects on cell proliferation, clotting prolongation and hemolytic complement lysis than do control PS oligodeoxyribonucleotides. PS analogs of MBOs show HIV-1 inhibition comparable with that of a control PS oligodeoxyribonucleotide with all 3'-5'linkages. The current results suggest that a limited number of 2'-5'linkages could be used in conjunction with PS oligonucleotides to further modulate the properties of antisense oligonucleotides as therapeutic agents.

Kandimalla, E R; Manning, A; Zhao, Q; Shaw, D R; Byrn, R A; Sasisekharan, V; Agrawal, S

1997-01-01

394

alpha Helical stabilization by side chain shielding of backbone hydrogen bonds  

Microsoft Academic Search

We study atomic models of the thermodynamics of the structural transition of peptides that form -helices. The effect of sequence variation on -helix formation for alanine-rich peptides, Ac-Ala21- methyl amide (A21) and Ac-A5 (AAARA)3A-methyl amide (Fs peptide), is investigated by atomic simulation studies of the ther- modynamics of the helix-coil transition in explicit water. The simulations show that the guanidinium

Angel E. Garcia; Kevin Y. Sanbonmatsu

2002-01-01

395

Complete Genome Sequence and Comparative Genomics of Shigella flexneri Serotype 2a Strain 2457T  

Microsoft Academic Search

We determined the complete genome sequence of Shigella flexneri serotype 2a strain 2457T (4,599,354 bp). Shigella species cause >1 million deaths per year from dysentery and diarrhea and have a lifestyle that is markedly different from those of closely related bacteria, including Escherichia coli. The genome exhibits the backbone and island mosaic structure of E. coli pathogens, albeit with much

J. Wei; M. B. Goldberg; V. Burland; M. M. Venkatesan; W. Deng; G. Fournier; G. F. Mayhew; G. Plunkett; D. J. Rose; A. Darling; B. Mau; N. T. Perna; S. M. Payne; L. J. Runyen-Janecky; S. Zhou; D. C. Schwartz; F. R. Blattner

2003-01-01

396

Formatt: Correcting protein multiple structural alignments by incorporating sequence alignment  

PubMed Central

Background The quality of multiple protein structure alignments are usually computed and assessed based on geometric functions of the coordinates of the backbone atoms from the protein chains. These purely geometric methods do not utilize directly protein sequence similarity, and in fact, determining the proper way to incorporate sequence similarity measures into the construction and assessment of protein multiple structure alignments has proved surprisingly difficult. Results We present Formatt, a multiple structure alignment based on the Matt purely geometric multiple structure alignment program, that also takes into account sequence similarity when constructing alignments. We show that Formatt outperforms Matt and other popular structure alignment programs on the popular HOMSTRAD benchmark. For the SABMark twilight zone benchmark set that captures more remote homology, Formatt and Matt outperform other programs; depending on choice of embedded sequence aligner, Formatt produces either better sequence and structural alignments with a smaller core size than Matt, or similarly sized alignments with better sequence similarity, for a small cost in average RMSD. Conclusions Considering sequence information as well as purely geometric information seems to improve quality of multiple structure alignments, though defining what constitutes the best alignment when sequence and structural measures would suggest different alignments remains a difficult open question.

2012-01-01

397

Complete nucleotide sequences of two blaKPC-2-bearing IncN Plasmids isolated from sequence type 442 Klebsiella pneumoniae clinical strains four years apart.  

PubMed

We sequenced the oldest blaKPC-2-bearing plasmid isolated in Brazil and another plasmid also carried by a Klebsiella pneumoniae strain of sequence type 442 (ST442), isolated 52 months later. Both plasmids present an IncN backbone and few acquired regions. Because the 2005 plasmid presented deletions and a truncated gene within Tn4401b compared to the 2009 plasmid, we can thus infer that IncN blaKPC-2-bearing plasmids pFCF1305 and pFCF3SP had a common ancestor circulating in Brazil prior to May 2005. PMID:24566176

Pérez-Chaparro, Paula Juliana; Cerdeira, Louise Teixeira; Queiroz, Maíse Gomes; de Lima, Clayton Pereira Silva; Levy, Carlos Emílio; Pavez, Mónica; Lincopan, Nilton; Gonçalves, Evonnildo Costa; Mamizuka, Elsa Masae; Sampaio, Jorge Luiz Mello; Nunes, Marcio Roberto Teixeira; McCulloch, John Anthony

2014-05-01

398

Novel Recombinant Poxvirus Composition and Uses Thereof.  

National Technical Information Service (NTIS)

The present invention provides a recombinant pox virus composition comprising a nucleic acid sequence encoding chemokines as costimulatory molecules. The present invention further provides a host cell, a host animal, and a pharmaceutical composition compr...

H. Kaufman K. Flanagan

2004-01-01

399

Vanishing amplitude of backbone dynamics causes a true protein dynamical transition: H2 NMR studies on perdeuterated C-phycocyanin.  

PubMed

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. PMID:24730877

Kämpf, Kerstin; Kremmling, Beke; Vogel, Michael

2014-03-01

400

Localization of electrons in the sugar/phosphate backbone in DNA investigated via resonant Auger decay spectra  

SciTech Connect

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.

Baba, Yuji; Sekiguchi, Tetsuhiro; Shimoyama, Iwao; Hirao, Norie [Japan Atomic Energy Agency, Tokai-mura, Naka-gun, Ibaraki-ken, 319-1195 (Japan); Nath, Krishna G. [INRS-EMT, University of Quebec, 1650 Boul. Lionel Boulet, Varennes, QC, J3X 1S2 (Canada)

2006-11-15