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ngs_backbone: a pipeline for read cleaning, mapping and SNP calling using Next Generation Sequence  

PubMed Central

Background The possibilities offered by next generation sequencing (NGS) platforms are revolutionizing biotechnological laboratories. Moreover, the combination of NGS sequencing and affordable high-throughput genotyping technologies is facilitating the rapid discovery and use of SNPs in non-model species. However, this abundance of sequences and polymorphisms creates new software needs. To fulfill these needs, we have developed a powerful, yet easy-to-use application. Results The ngs_backbone software is a parallel pipeline capable of analyzing Sanger, 454, Illumina and SOLiD (Sequencing by Oligonucleotide Ligation and Detection) sequence reads. Its main supported analyses are: read cleaning, transcriptome assembly and annotation, read mapping and single nucleotide polymorphism (SNP) calling and selection. In order to build a truly useful tool, the software development was paired with a laboratory experiment. All public tomato Sanger EST reads plus 14.2 million Illumina reads were employed to test the tool and predict polymorphism in tomato. The cleaned reads were mapped to the SGN tomato transcriptome obtaining a coverage of 4.2 for Sanger and 8.5 for Illumina. 23,360 single nucleotide variations (SNVs) were predicted. A total of 76 SNVs were experimentally validated, and 85% were found to be real. Conclusions ngs_backbone is a new software package capable of analyzing sequences produced by NGS technologies and predicting SNVs with great accuracy. In our tomato example, we created a highly polymorphic collection of SNVs that will be a useful resource for tomato researchers and breeders. The software developed along with its documentation is freely available under the AGPL license and can be downloaded from or



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

PubMed Central

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

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



Assessment of flexible backbone protein design methods for sequence library prediction in the therapeutic antibody Herceptin-HER2 interface.  


Computational protein design methods can complement experimental screening and selection techniques by predicting libraries of low-energy sequences compatible with a desired structure and function. Incorporating backbone flexibility in computational design allows conformational adjustments that should broaden the range of predicted low-energy sequences. Here, we evaluate computational predictions of sequence libraries from different protocols for modeling backbone flexibility using the complex between the therapeutic antibody Herceptin and its target human epidermal growth factor receptor 2 (HER2) as a model system. Within the program RosettaDesign, three methods are compared: The first two use ensembles of structures generated by Monte Carlo protocols for near-native conformational sampling: kinematic closure (KIC) and backrub, and the third method uses snapshots from molecular dynamics (MD) simulations. KIC or backrub methods were better able to identify the amino acid residues experimentally observed by phage display in the Herceptin-HER2 interface than MD snapshots, which generated much larger conformational and sequence diversity. KIC and backrub, as well as fixed backbone simulations, captured the key mutation Asp98Trp in Herceptin, which leads to a further threefold affinity improvement of the already subnanomolar parental Herceptin-HER2 interface. Modeling subtle backbone conformational changes may assist in the design of sequence libraries for improving the affinity of antibody-antigen interfaces and could be suitable for other protein complexes for which structural information is available. PMID:21465611

Babor, Mariana; Mandell, Daniel J; Kortemme, Tanja



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

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



ngs_backbone: a pipeline for read cleaning, mapping and SNP calling using Next Generation Sequence  

Microsoft Academic Search

Background  The possibilities offered by next generation sequencing (NGS) platforms are revolutionizing biotechnological laboratories.\\u000a Moreover, the combination of NGS sequencing and affordable high-throughput genotyping technologies is facilitating the rapid\\u000a discovery and use of SNPs in non-model species. However, this abundance of sequences and polymorphisms creates new software\\u000a needs. To fulfill these needs, we have developed a powerful, yet easy-to-use application.\\u000a \\u000a \\u000a \\u000a \\u000a Results  The

Jose M Blanca; Laura Pascual; Peio Ziarsolo; Fernando Nuez; Joaquin Cañizares



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


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



Suppression of transfer of non-T-DNA ‘vector backbonesequences by multiple left border repeats in vectors for transformation of higher plants mediated by Agrobacterium tumefaciens  

Microsoft Academic Search

Vectors for transformation of higher plants mediated by Agrobacterium tumefaciens were modified so that one, two or three additional copies of the left border (LB) sequences were inserted close to the original LB of the T-DNA. A gene for ß-glucuronidase (gusA) was placed outside the T-DNA to monitor the transfer to plants of 'vector backbone' sequences. The expression of GUS

Yoshiki Kuraya; Shozo Ohta; Miyuki Fukuda; Yukoh Hiei; Nobuhiko Murai; Kazuyuki Hamada; Jun Ueki; Hidemasa Imaseki; Toshihiko Komari



De novo backbone scaffolds for protein design  

PubMed Central

In recent years, there have been significant advances in the field of computational protein design including the successful computational design of enzymes based on backbone scaffolds from experimentally solved structures. It is likely that large-scale sampling of protein backbone conformations will become necessary as further progress is made on more complicated systems. Removing the constraint of having to use scaffolds based on known protein backbones is a potential method of solving the problem. With this application in mind, we describe a method to systematically construct a large number of de novo backbone structures from idealized topological forms in a top–down hierarchical approach. The structural properties of these novel backbone scaffolds were analyzed and compared with a set of high-resolution experimental structures from the protein data bank (PDB). It was found that the Ramachandran plot distribution and relative ?- and ?-turn frequencies were similar to those found in the PDB. The de novo scaffolds were sequence designed with RosettaDesign, and the energy distributions and amino acid compositions were comparable with the results for redesigned experimentally solved backbones. Proteins 2010. © 2009 Wiley-Liss, Inc.

MacDonald, James T; Maksimiak, Katarzyna; Sadowski, Michael I; Taylor, William R



Compositional complexity of DNA sequence models  

NASA Astrophysics Data System (ADS)

Recently, we proposed a new measure of complexity for symbolic sequences (Sequence Compositional Complexity, SCC) based on the entropic segmentation of a sequence into compositionally homogeneous domains. Such segmentation is carried out by means of a conceptually simple, computationally efficient heuristic algorithm. SCC is now applied to the sequences generated by several stochastic models which describe the statistical properties of DNA, in particular the observed long-range fractal correlations. This approach allows us to test the capability of the different models in describing the complex compositional heterogeneity found in DNA sequences. Moreover, SCC detects clear differences where conventionalstandard methods fail.

Bernaola-Galván, P.; Carpena, P.; Román-Roldán, R.; Oliver, J. L.



Arbitrarily accurate narrowband composite pulse sequences  

SciTech Connect

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

Vitanov, Nikolay V. [Department of Physics, Sofia University, 5 James Bourchier Boulevard, BG-1164 Sofia (Bulgaria)



Composition for nucleic acid sequencing  


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



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 HN, 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.



N-terminal Peptide sequence repetition influences the kinetics of backbone fragmentation: a manifestation of the jahn-teller effect?  


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



N-Terminal Peptide Sequence Repetition Influences the Kinetics of Backbone Fragmentation: A Manifestation of the Jahn-Teller Effect?  

NASA Astrophysics Data System (ADS)

Analysis of large (>10,000 entries) databases consisting of high-resolution tandem mass spectra of peptide dications revealed with high statistical significance ( P < 1?10-3) that peptides with non-identical first two N-terminal amino acids undergo cleavages of the second peptide bond at higher rates than repetitive 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.

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



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



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

Microsoft Academic Search

An ionic polymer-metal composite (IPMC) consisting of a thin perfluorinated ionomer (usually, Nafion or Flemion) strip, platinum, and\\/or gold plated on both faces and neutralized by a certain amount of appropriate cations undergoes large bending motion when, in a hydrated state, a small electric field is applied across its thickness. When the same membrane is suddenly bent, a small voltage

Sia Nemat-Nasser; Yongxian Wu



TALI: Protein Structure Alignment Using Backbone Torsion Angles  

Microsoft Academic Search

This article introduces a novel protein structure alignment method (named TALI) based on protein backbone torsion angle instead of the more traditional distance matrix. Representing protein structure by a serial backbone torsion angles (?, ?), protein structure have a simple mapping relationship to protein sequence. Thus, TALI can naturally incorporate sequence information and sequence analysis method into structure comparison. Here

Xijiang Miao; Michael Bryson; Homayoun Valafar



RNA backbone is rotameric  

PubMed Central

Despite the importance of local structural detail to a mechanistic understanding of RNA catalysis and binding functions, RNA backbone conformation has been quite recalcitrant to analysis. There are too many variable torsion angles per residue, and their raw empirical distributions are poorly clustered. This study applies quality-filtering techniques (using resolution, crystallographic B factor, and all-atom steric clashes) to the backbone torsion angle distributions from an 8,636-residue RNA database. With noise levels greatly reduced, clear signal appears for the underlying angle preferences. Half-residue torsion angle distributions for ?-?-? and for ?-?-? are plotted and contoured in 3D; each shows about a dozen distinct peaks, which can then be combined in pairs to define complete RNA backbone conformers. Traditional nucleic acid residues are defined from phosphate to phosphate, but here we use a base-to-base (or sugar-to-sugar) division into “suites” to parse the RNA backbone repeats, both because most backbone steric clashes are within suites and because the relationship of successive bases is both reliably determined and conformationally important. A suite conformer has seven variables, with sugar pucker specified at both ends. Potential suite conformers were omitted if not represented by at least a small cluster of convincing data points after application of quality filters. The final result is a small library of 42 RNA backbone conformers, which should provide valid conformations for nearly all RNA backbone encountered in experimental structures.

Murray, Laura J. W.; Arendall, W. Bryan; Richardson, David C.; Richardson, Jane S.



Sequence-specific 1HN, 13C and 15N backbone resonance assignments of the 34 kDa Paramecium bursaria Chlorella virus 1 (PBCV1) DNA ligase  

PubMed Central

Chlorella virus DNA ligase (ChVLig) is a minimal (298-amino acid) pluripotent ATP-dependent ligase composed of three structural modules – a nucleotidyltransferase domain, an OB domain, and a ?-hairpin latch – that forms a circumferential clamp around nicked DNA. ChVLig provides an instructive model to understand the chemical and conformational steps of nick repair. Here we report the assignment of backbone 13C, 15N, 1HN resonances of this 34.2 kDa protein, the first for a DNA ligase in full-length form.

Piserchio, Andrea; Nair, Pravin A.; Shuman, Stewart; Ghose, Ranajeet



Nucleotide sequence composition and method for detection of neisseria gonorrhoeae  

SciTech Connect

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

Lo, A.; Yang, H.L.



Dolphin Skeleton - Backbone  

NSDL National Science Digital Library

The dolphin is built to be sleek. Its body is made of almost entirely backbone (a gliding joint) which makes it very flexible under water. The ribs protect the inner organs of the dolphin and the tail beats from side to side, thrusting the animal forward.

Ketan Patel (California State University, Fullerton;Student, Biological Sciences)



Crocodile Skeleton - Backbone  

NSDL National Science Digital Library

The crocodile is a reptile that has a long and narrow skeleton. The backbone (a gliding joint) of this animal extends into a powerful tail, allowing it to swim through water. The ribs of the crocodile are small and serve to protect its inner organs.

Ketan Patel (California State University, Fullerton;Student, Biological Sciences)



The NSFNET backbone network  

Microsoft Academic Search

The NSFNET Backbone Network interconnects six supercomputer sites, several regional networks and ARPANET. It supports the DARPA Internet protocol suite and DCN subnet protocols, which provide delay-based routing and very accurate time-synchronization services. This paper describes the design and implementation of this network, with special emphasis on robustness issues and congestion-control mechanisms.

David L. Mills; Hans-Werner Braun



Two modes of protein sequence evolution and their compositional dependencies.  


Protein sequence evolution has resulted in a vast repertoire of molecular functionality crucial to life. Despite the central importance of sequence evolution to biology, our fundamental understanding of how sequence composition affects evolution is incomplete. This report describes the utilization of lattice model simulations of directed evolution, which indicate that, on average, peptide and protein evolvability is strongly dependent on initial sequence composition. The report also discusses two distinct regimes of sequence evolution by point mutation: (a) the "classical" mode where sequences "crawl" over free energy barriers towards acquiring a target fold, and (b) the "quantum" mode where sequences appear to "tunnel" through large energy barriers generally insurmountable by means of a crawl. Finally, the simulations indicate that oily and charged peptides are the most efficient substrates for evolution at the "classical" and "quantum" regimes, respectively, and that their respective response to temperature is commensurate with analogies made to barrier crossing in classical and quantum systems. On the whole, these results show that sequence composition can tune both the evolvability and the optimal mode of evolution of peptides and proteins. PMID:23848722

Mannige, Ranjan V



Orientation-dependent backbone-only residue pair scoring functions for fixed backbone protein design  

PubMed Central

Background Empirical scoring functions have proven useful in protein structure modeling. Most such scoring functions depend on protein side chain conformations. However, backbone-only scoring functions do not require computationally intensive structure optimization and so are well suited to protein design, which requires fast score evaluation. Furthermore, scoring functions that account for the distinctive relative position and orientation preferences of residue pairs are expected to be more accurate than those that depend only on the separation distance. Results Residue pair scoring functions for fixed backbone protein design were derived using only backbone geometry. Unlike previous studies that used spherical harmonics to fit 2D angular distributions, Gaussian Mixture Models were used to fit the full 3D (position only) and 6D (position and orientation) distributions of residue pairs. The performance of the 1D (residue separation only), 3D, and 6D scoring functions were compared by their ability to identify correct threading solutions for a non-redundant benchmark set of protein backbone structures. The threading accuracy was found to steadily increase with increasing dimension, with the 6D scoring function achieving the highest accuracy. Furthermore, the 3D and 6D scoring functions were shown to outperform side chain-dependent empirical potentials from three other studies. Next, two computational methods that take advantage of the speed and pairwise form of these new backbone-only scoring functions were investigated. The first is a procedure that exploits available sequence data by averaging scores over threading solutions for homologs. This was evaluated by applying it to the challenging problem of identifying interacting transmembrane alpha-helices and found to further improve prediction accuracy. The second is a protein design method for determining the optimal sequence for a backbone structure by applying Belief Propagation optimization using the 6D scoring functions. The sensitivity of this method to backbone structure perturbations was compared with that of fixed-backbone all-atom modeling by determining the similarities between optimal sequences for two different backbone structures within the same protein family. The results showed that the design method using 6D scoring functions was more robust to small variations in backbone structure than the all-atom design method. Conclusions Backbone-only residue pair scoring functions that account for all six relative degrees of freedom are the most accurate and including the scores of homologs further improves the accuracy in threading applications. The 6D scoring function outperformed several side chain-dependent potentials while avoiding time-consuming and error prone side chain structure prediction. These scoring functions are particularly useful as an initial filter in protein design problems before applying all-atom modeling.



Problems with Parsimony in Sequences of Biased Base Composition  

Microsoft Academic Search

.   Parsimony is commonly used to infer the direction of substitution and mutation. However, it is known that parsimony is biased\\u000a when the base composition of the DNA sequence is skewed. Here I quantify this effect for several simple cases. The analysis\\u000a demonstrates that parsimony can be misleading even when levels of sequence divergence are as low as 10%; parsimony

Adam Eyre-Walker



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  

PubMed Central

In genetically transformed plants, transgene silencing 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 five lines, but only one of these displayed silencing. Truncated T-DNA copies, positioned in inverse orientation to an intact T-DNA copy, were discovered in three lines. The whole nptII gene with pnos promoter was present in the truncated copy of one such line in which heavy silencing has been observed. In the two other lines no silencing has been observed over five generations. Thus, vector sequences and short additional T-DNA sequences are not sufficient or necessary to induce transgene silencing. DNA methylation of selected restriction endonuclease sites could not be correlated with silencing. Our collection of T-DNA/plant DNA junctions has also been used to evaluate current models of T-DNA integration. Data for some of our lines are compatible with T-DNA integration in double-strand breaks, while for others initial invasion of plant DNA by the left or by the right T-DNA end seem important.

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



Soil amino acid composition across a boreal forest successional sequence  

Microsoft Academic Search

Soil amino acids are important sources of organic nitrogen for plant nutrition, yet few studies have examined which amino acids are most prevalent in the soil. In this study, we examined the composition, concentration, and seasonal patterns of soil amino acids across a primary successional sequence encompassing a natural gradient of plant productivity and soil physicochemical characteristics. Soil was collected

Nancy R. Werdin-Pfisterer; Knut Kielland; Richard D. Boone



Optimized control of multistate quantum systems by composite pulse sequences  

SciTech Connect

We introduce a technique for derivation of high-fidelity composite pulse sequences for two types of multistate quantum systems: systems with the SU(2) and Morris-Shore dynamic symmetries. For the former type, we use the Majorana decomposition to reduce the dynamics to an effective two-state system, which allows us to find the propagator analytically and use the pool of available composite pulses for two-state systems. For the latter type of multistate systems, we use the Morris-Shore decomposition, which reduces the multistate dynamics to a set of two-state systems. We present examples which demonstrate that the multistate composite sequences open a variety of possibilities for coherent control of quantum systems with multiple states.

Genov, G. T.; Vitanov, N. V. [Department of Physics, Sofia University, James Bourchier 5 Boulevard, BG-1164 Sofia (Bulgaria); Torosov, B. T. [Department of Physics, Sofia University, James Bourchier 5 Boulevard, BG-1164 Sofia (Bulgaria); Institute of Solid State Physics, Bulgarian Academy of Sciences, Tsarigradsko chaussee 72, BG-1784 Sofia (Bulgaria)



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

PubMed Central

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

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



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

Microsoft Academic Search

Conventional Agrobacterium-mediated plant transformation often produces a significant frequency of transgenic events containing vector backbone sequence,\\u000a which is generally undesirable for biotechnology applications. We tested methods to reduce the frequency of transgenic plants\\u000a containing vector backbone by incorporating genes into the backbone that inhibit the development of transgenic plants. Four\\u000a backbone frequency reduction genes, bacterial levansucrase (sacB), maize cytokinin oxidase

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



Adding backbone to protein folding: why proteins are polypeptides.  


It is argued that the chemical nature of the polypeptide backbone is the central determinant of the three-dimensional structures of proteins. The requirement that buried polar groups form intramolecular hydrogen bonds limits the fold of the backbone to the well known units of secondary structure while the amino acid sequence chooses among the set of conformations available to the backbone. 'Sidechain-only' models, based for example on hydrophobicity patterns, fail to account for the properties of the backbone and thus will have difficulty capturing essential features of a folding pathway. This is evident from the incorrect predictions they make for the conformations of the limiting cases of all-hydrophobic or all-polar sequences. PMID:9162145

Honig; Cohen



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


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


Monomer composition and sequence of alginates from Pseudomonas aeruginosa.  


Alginates from four strains of Pseudomonas aeruginosa, one mucoid strain isolated from a technical water system, one strain isolated from a patient with cystic fibrosis and two mutants of this strain with a defect which affects the O-acetylation of the extracellular alginate, have been isolated and analysed for monomer composition and sequence by 13C-nuclear magnetic resonance (NMR) spectroscopy. The detected contributions of different monomer triplets (triads) were compared with values expected from a statistical chain constitution based on the given monomer ratio. While a typical algal alginate presents a nearly statistical distribution of uronic acids in the polymer chain, a strong deviation from the statistical arrangement of mannuronate (M) and guluronate (G) was found in the alginate of the mucoid strains of P. aeruginosa, being most expressed for the triad MMM. This feature is partially lost in the alginate from the mutant strains, indicating that the O-acetylation is linked to a mechanism which takes influence on the chain sequence. The strong preference for MG-pairs in the parent strain of P. aeruginosa may be connected to a stronger binding of cations in the MG-vicinity. PMID:11911901

Schürks, N; Wingender, J; Flemming, H-C; Mayer, C



Predicting membrane protein types by fusing composite protein sequence features into pseudo amino acid composition.  


Membrane proteins are vital type of proteins that serve as channels, receptors, and energy transducers in a cell. Prediction of membrane protein types is an important research area in bioinformatics. Knowledge of membrane protein types provides some valuable information for predicting novel example of the membrane protein types. However, classification of membrane protein types can be both time consuming and susceptible to errors due to the inherent similarity of membrane protein types. In this paper, neural networks based membrane protein type prediction system is proposed. Composite protein sequence representation (CPSR) is used to extract the features of a protein sequence, which includes seven feature sets; amino acid composition, sequence length, 2 gram exchange group frequency, hydrophobic group, electronic group, sum of hydrophobicity, and R-group. Principal component analysis is then employed to reduce the dimensionality of the feature vector. The probabilistic neural network (PNN), generalized regression neural network, and support vector machine (SVM) are used as classifiers. The highest success rate using the jackknife test obtained through SVM is 86.01%. In case of independent dataset test, PNN yields the highest accuracy of 95.73%. These classifiers exhibit improved performance using other performance measures such as sensitivity, specificity, Mathew's correlation coefficient, and F-measure. The experimental results show that the prediction performance of the proposed scheme for classifying membrane protein types is the best reported, so far. This performance improvement may largely be credited to the learning capabilities of neural networks and the composite feature extraction strategy, which exploits seven different properties of protein sequences. The proposed Mem-Predictor can be accessed at PMID:21110985

Hayat, Maqsood; Khan, Asifullah



Protein-like Tertiary Folding Behavior from Heterogeneous Backbones.  


Because proteins play vital roles in life, much effort has been invested in their mimicry by synthetic agents. One approach is to design unnatural backbone oligomers ("foldamers") that fold like natural peptides. Despite success in secondary structure mimicry by such species, protein-like tertiary folds remain elusive. A fundamental challenge underlying this task is the design of a sequence of side chains that will specify a complex tertiary folding pattern on an unnatural backbone. We report here a sequence-based approach to convert a natural protein with a compact tertiary fold to an analogue with a backbone composed of ?20% unnatural building blocks but folding behavior similar to that of the parent protein. PMID:23937097

Reinert, Zachary E; Lengyel, George A; Horne, W Seth



A design backbone for the biomedical engineering curriculum  

Microsoft Academic Search

In this paper, we summarize our experiences as advisors supervising biomedical engineering design projects in the design backbone of our curriculum, the six-semester design course sequence required for all biomedical engineering majors at the University of Wisconsin-Madison.

W. J. Tompkins; D. Beebe; J. A. Gimm; M. Nicosia; N. Ramanujam; P. Thompson; M. E. Tyler; J. G. Webster



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

Microsoft Academic Search

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.

Zhang Zhang; Jun Yu



The Composition of Main-Sequence Stars of Types A-K in the Hyades Cluster.  

National Technical Information Service (NTIS)

The investigation is designed to test the common assumption that all main-sequence stars in a cluster have the same chemical composition. The chemical composition of main-sequence Hyades stars with B-V colors between 0.0 and +0.9 (spectral types A0V and K...

P. S. Conti G. Wallerstein R. F. Wing



Base composition of Coffea AFLP sequences and their conservation within the genus.  


Amplified fragment length polymorphism (AFLP) is often used for genetic mapping and diversity analysis, but very little information is currently available on their sequence characteristics. Species-specific sequences were analyzed from a single Coffea genome (Coffea pseudozanguebariae) associated with clustered or nonclustered AFLP loci of known genetic position. Compared with the expressed sequence tag (EST) sequence composition, their AT content exhibited a bimodal distribution with AT-poor sequences corresponding mainly to putative coding sequences. AT-rich sequences, apart from the EST distribution, were usually clustered on the genetic map and might correspond to noncoding sequences. Conversion of these AFLP markers into sequence-characterized amplified region (SCAR) anchor markers allowed us to assess sequence conservation within Coffea species with respect to species relatedness. PMID:15601908

Poncet, V; Hamon, P; de Saint Marc, M-B Sauvage; Bernard, T; Hamon, S; Noirot, M



The backbone of a city  

NASA Astrophysics Data System (ADS)

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

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



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)



Adding diverse noncanonical backbones to rosetta: enabling peptidomimetic design.  


Peptidomimetics are classes of molecules that mimic structural and functional attributes of polypeptides. Peptidomimetic oligomers can frequently be synthesized using efficient solid phase synthesis procedures similar to peptide synthesis. Conformationally ordered peptidomimetic oligomers are finding broad applications for molecular recognition and for inhibiting protein-protein interactions. One critical limitation is the limited set of design tools for identifying oligomer sequences that can adopt desired conformations. Here, we present expansions to the ROSETTA platform that enable structure prediction and design of five non-peptidic oligomer scaffolds (noncanonical backbones), oligooxopiperazines, oligo-peptoids, [Formula: see text]-peptides, hydrogen bond surrogate helices and oligosaccharides. This work is complementary to prior additions to model noncanonical protein side chains in ROSETTA. The main purpose of our manuscript is to give a detailed description to current and future developers of how each of these noncanonical backbones was implemented. Furthermore, we provide a general outline for implementation of new backbone types not discussed here. To illustrate the utility of this approach, we describe the first tests of the ROSETTA molecular mechanics energy function in the context of oligooxopiperazines, using quantum mechanical calculations as comparison points, scanning through backbone and side chain torsion angles for a model peptidomimetic. Finally, as an example of a novel design application, we describe the automated design of an oligooxopiperazine that inhibits the p53-MDM2 protein-protein interaction. For the general biological and bioengineering community, several noncanonical backbones have been incorporated into web applications that allow users to freely and rapidly test the presented protocols ( This work helps address the peptidomimetic community's need for an automated and expandable modeling tool for noncanonical backbones. PMID:23869206

Drew, Kevin; Renfrew, P Douglas; Craven, Timothy W; Butterfoss, Glenn L; Chou, Fang-Chieh; Lyskov, Sergey; Bullock, Brooke N; Watkins, Andrew; Labonte, Jason W; Pacella, Michael; Kilambi, Krishna Praneeth; Leaver-Fay, Andrew; Kuhlman, Brian; Gray, Jeffrey J; Bradley, Philip; Kirshenbaum, Kent; Arora, Paramjit S; Das, Rhiju; Bonneau, Richard



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.



A two-backbone polymer model for interphase chromosome geometry  

SciTech Connect

A polymer model for the overall geometric structure of a human chromosome during the G0/G1 portion of cell-cycle interphase is constructed, based on fluorescence in situ hybridization data on distances between defined genomic sequences. The model consists of flexible giant loops, averaging about 6 million base pairs, with two random-walk backbones; it involves essentially three parameters. Numerical results based on properly selected values of parameters fit the data well.

Liu, B. [Coll. of St. Scholastica, Duluth, MN (United States). Dept. of Mathematics; Sachs, R.K. [Univ. of California, Berkeley, CA (United States). Dept. of Mathematics



Composition of the Sequence Downstream of the Dengue Virus 5? Cyclization Sequence (dCS) Affects Viral RNA Replication  

PubMed Central

RNA replication of dengue virus (DENV) requires an RNA-RNA mediated circularization of the viral genome, which includes at least three sets of complementary RNA sequences on both ends of the genome. The 5? and the 3? untranslated regions form several additional RNA elements that are involved in regulation of translation and required for RNA replication. Communication between the genomic termini results in a structural reorganization of the RNA elements, forming a functional RNA panhandle structure. Here we report that the sequence composition downstream of the 5? CS element in the capsid gene, designated as downstream CS (dCS) sequence -- but not the capsid protein -- also influences the ability of the viral genome to circularize and hence replicate by modulating the topology of the 5? end. These results provide insights for the design of reporter sub-genomic and genomic mosquito-borne flavivirus constructs and contribute to the understanding of viral RNA replication.

Friebe, Peter; Pena, Jose; Pohl, Marie O. F.; Harris, Eva



Mapping Disulfide Connectivity Using Backbone Ester Hydrolysis †  

Microsoft Academic Search

The site-specific incorporation of R-hydroxy acids into proteins using nonsense suppression can provide a powerful probe of protein structure and function. The resulting backbone ester may be selectively hydrolyzed in the presence of the peptide backbone, providing an \\

Pamela M. England; Henry A. Lester; Dennis A. Dougherty



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 ...



The "universal polymer backbone" concept  

NASA Astrophysics Data System (ADS)

This thesis begins with a brief analysis of the synthetic methodologies utilized in polymer science. A conclusion is drawn inferring that upper limits in molecular design are inevitable, arising as a direct consequence of the predominance of covalent strategies in the field. To address these concerns, the 'universal polymer backbone' (UPB) concept has been hypothesized. A UPB has been defined as any copolymer, side-chain functionalized with multiple recognition elements that are individually capable of forming strong, directional, and reversible non-covalent bonds. Non-covalent functionalization of these scaffolds can lead to the formation of a multitude of new polymer structures, each stemming from a single parent or 'universal polymer backbone'. To prepare such a UPB, isomerically pure exo-norbornene esters containing either a PdII SCS pincer complex or a diaminopyridine residue were synthesized, polymerized, and copolymerized via ROMP. All polymerizations were living under mild reaction conditions. Kinetic studies showed that the kp values are highly dependent upon the isomeric purity but completely independent of the terminal recognition units. Non-covalent functionalization of these copolymers was accomplished via (1) directed self-assembly, (2) multi-step self-assembly , and (3) one-step orthogonal self-assembly. This system shows complete specificity of each recognition motif for its complementary unit with no observable changes in the association constant upon functionalization. To explore potential applications of this UPB concept, random terpolymers possessing high concentrations of pendant alkyl chains and small amounts of recognition units were synthesized. Non-covalent crosslinking using a directed functionalization strategy resulted in dramatic increases in solution viscosities for metal crosslinked polymers with only minor changes in viscosity for hydrogen bonding motifs. The crosslinked materials were further functionalized via self-assembly by employing the second recognition motif, which gave rise to functionalized materials with tailored crosslinks. This non-covalent crosslinking/functionalization strategy could allow for rapid and tunable materials synthesis by overcoming many difficulties inherent to the preparation of covalently crosslinked polymers. Finally, the current status of the UPB concept is reviewed and methodological extensions of the concept are suggested. Evaluation of how UPBs may be used to optimize materials and their potential use in fabricating unique electro-optical materials, sensors, and drug delivery vesicles are explored.

Pollino, Joel Matthew


INDUS - a composition-based approach for rapid and accurate taxonomic classification of metagenomic sequences  

PubMed Central

Background Taxonomic classification of metagenomic sequences is the first step in metagenomic analysis. Existing taxonomic classification approaches are of two types, similarity-based and composition-based. Similarity-based approaches, though accurate and specific, are extremely slow. Since, metagenomic projects generate millions of sequences, adopting similarity-based approaches becomes virtually infeasible for research groups having modest computational resources. In this study, we present INDUS - a composition-based approach that incorporates the following novel features. First, INDUS discards the 'one genome-one composition' model adopted by existing compositional approaches. Second, INDUS uses 'compositional distance' information for identifying appropriate assignment levels. Third, INDUS incorporates steps that attempt to reduce biases due to database representation. Results INDUS is able to rapidly classify sequences in both simulated and real metagenomic sequence data sets with classification efficiency significantly higher than existing composition-based approaches. Although the classification efficiency of INDUS is observed to be comparable to those by similarity-based approaches, the binning time (as compared to alignment based approaches) is 23-33 times lower. Conclusion Given it's rapid execution time, and high levels of classification efficiency, INDUS is expected to be of immense interest to researchers working in metagenomics and microbial ecology. Availability A web-server for the INDUS algorithm is available at



Data Acquisition Backbone Core DABC  

NASA Astrophysics Data System (ADS)

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

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



Analysis of Chromatin Composition of Repetitive Sequences: The ChIP-Chop Assay.  


Chromatin immunoprecipitation (ChIP) is a powerful method that allows to probe specific protein-DNA interactions in vivo and to estimate the occupancy of proteins at specific sites of the genome. However, the traditional ChIP assay is not able to distinguish whether repeats that share identical sequences display a different composition of associated factors and, consequently, different functions. The ChIP-chop method provides a useful application to analyze the interaction of proteins with repetitive sequences based on their CpG methylation content. The detailed ChIP-chop protocol that serves to determine the chromatin composition of active and silent ribosomal RNA (rRNA) genes, repeats that share identical sequences but display distinct functions and chromatin compositions, is reported here. PMID:24162999

Santoro, Raffaella



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.



Compositional segmentation and long-range fractal correlations in DNA sequences  

Microsoft Academic Search

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

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



Cervical Exercise: The Backbone of Spine Treatment  


North American Spine Society Public Education Series Cervical Exercise: The Backbone of Spine Treatment How important is ... physician before starting any exercises. The Importance of Exercise for the Neck Spine experts agree that physical ...


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



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


Efficient Distributed Low-Cost Backbone Formation for Wireless Networks  

Microsoft Academic Search

Backbone has been used extensively in various aspects (e.g., routing, route maintenance, broadcast, scheduling) for wireless ad hoc or sensor networks recently. Previous methods are mostly designed to minimize the size of the backbone. However, in many applications, it is desirable to construct a backbone with small cost when each wireless node has a cost of being in the backbone.

Yu Wang; Weizhao Wang; Xiang-Yang Li



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.



Radio frequency field intensity mapping using a composite spin-echo sequence.  


A novel radio frequency (RF) field intensity mapping or imaging method using a composite NMR spin-echo sequence is proposed. A composite spin-echo RF pulse with 90 degrees y-180 degrees x-90 degrees y sequence makes phase change in the final image depending on the RF field intensity on the object. The resultant phase change or phase map can be used to obtain the actual RF flip-angle map for a given condition which includes the status of tuning and RF inhomogeneity, etc. Bloch equation has been solved numerically to obtain the effects of the RF field intensity as well as the main magnetic field inhomogeneity and the results are used for the mapping (imaging) of the RF field intensity. Phantom studies have been performed using a 1.5 Tesla whole body MRI system and the results are presented. PMID:2325512

Oh, C H; Hilal, S K; Cho, Z H; Mun, I K



An Error-Tolerant Video Retrieval Method Based on the Shot Composition Sequence in a Scene  

Microsoft Academic Search

This paper presents an error-tolerant video retrieval method based on the shot composition sequence in a scene. Conventional video players in the home can not access interesting scenes directly because they offer only play, fast-forward, and rewind. What is needed is an easy-to-use video scene player that can directly access scenes important to the user. This paper presents an error-tolerant

Isao Kondo; Satoshi Shimada; Masashi Morimoto



Bias explorer: measurements of compositional bias in EMBL and GenBank sequence files  

Microsoft Academic Search

A Windows application for compositional analysis of sequenced genomes (EMBL or GenBank flat files) is available as freeware.\\u000a The application allows the user to quantify word bias using Markov chain analysis and it allows the user to generate sliding\\u000a window data for GC-skew, AT-skew, purine excess, keto excess and discrete word counts. The mathematical routines reside in\\u000a a dynamic link

Anders Fuglsang



Effects of material and stacking sequence on behavior of composite plates with holes  

Microsoft Academic Search

Strain distributions to failure, tensile and compressive strain-concentration factors, and strength-reduction factors were determined for glass-, boron-, and graphite-epoxy plates with holes loaded in tension. Strain gages, photoelastic coatings and moiré techniques were used. Ten variations of layup and stacking sequence were studied.The boron-epoxy composite was found to be the stiffest and strongest of the three. The graphite laminate with

I. M. Daniel; R. E. Rowlands; J. B. Whiteside



Composite sequence proteomic analysis of protein biomarkers of Campylobacter coli, C. lari and C. concisus for bacterial identification.  


Protein biomarkers observed in the matrix-assisted laser desorption/ionization time-of-flight mass spectra (MALDI-TOF-MS) of cell lysates of three strains of Campylobacter coli, two strains of C. lari and one strain of C. concisus have been identified by 'bottom-up' proteomic techniques. The significant findings are as follows. First, the protein biomarkers identified were: PhnA-related protein, 4-oxalocrotonate tautomerase (DmpI)-related protein, NifU-like protein, cytochrome c, DNA-binding protein HU, 10 kDa chaperonin, thioredoxin, as well as several conserved hypothetical and ribosomal proteins. Second, variations in the biomarker ion m/z in MALDI-TOF-MS spectra across species and strains are the result of variations in the amino acid sequence of the protein due to non-synonymous mutations of the biomarker gene. Third, the most common post-translational modifications (PTMs) were the removal of the N-terminal methionine and N-terminal signal peptides. However, in the case of the NifU protein (an iron-sulfur cluster transport protein), post-translational cleavage occurred from the C-terminus. Fourth, only the genomes of the C. coli strain RM2228 and C. lari strain RM2100 have been sequenced; thus, proteomic identification of the proteins of the other strains in this study relied upon sequence homology to the genomic sequence of these strains as well as the genomes of sequences of other Campylobacter strains. In some cases, the determination of the full amino acid sequence of a protein biomarker from a genomically non-sequenced strain was accomplished by combining non-overlapping partial sequences from proteomic identifications of genomically-sequenced strains that were of the same species (or of a different species) to that of the non-sequenced strain. The accuracy of this composite sequence was confirmed by both MS and MS/MS. It was necessary, in some cases, to perform de novo sequencing on 'gaps' in the composite sequence that were not homologous to any genomically-sequenced strain. In order to validate the composite sequence approach, composite sequences were further confirmed by subsequent DNA sequencing of the biomarker gene. Thus, using the composite sequence approach, it was possible to determine the full amino acid sequence of an unknown protein from a genomically non-sequenced bacterial strain without the necessity of either sequencing the biomarker gene or performing full de novo MS/MS sequencing. The sequence obtained could then be used as a strain-specific biomarker for analysis by 'top-down' proteomics techniques. PMID:17893805

Fagerquist, Clifton K; Yee, Emma; Miller, William G



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


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

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



Changing protein backbone topology: Structural and dynamic consequences of the backbone cyclization in SH3 domain  

NASA Astrophysics Data System (ADS)

Changing the topology of the normal linear backbone architecture of the polypeptide chain could provide a powerful tool for understanding and manipulating protein structure and function. In particular, backbone circularization (i.e. formation of a peptide bond between the N- and C- termini) is of considerable interest for understanding of the mechanisms underlying protein folding and stability. Here we describe the effect of the backbone circularization on the structure and backbone dynamics of the N-terminal SH3 domain from the murine c-Crk adapter protein. Several circular constructs of various lengths were obtained using intein-based chemical ligation (Camarero et al. J. Mol. Biol. 308, 1045 (2001)). We applied NMR to determine and compare the solution structure and backbone dynamics of the linear and circular forms of the protein. Our data indicate that the circularization does not significantly alter the structure of the protein core. The analysis of the backbone mobility in the sub-nanosecond time range suggests a slight rigidification of the entire backbone upon cyclization. Significant contributions from conformational exchange motions are observed in the region between beta-strands 2 and 3 in the circular constructs, probably caused by the circularization-induced strain in the protein structure.

Schumann, Frank; Varadan, Ranjani; Pudiavettil, Praveen; Camarero, Julio; Fushman, David



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



ITS (Intelligent Transportation Systems) Backbone Infrastructure.  

National Technical Information Service (NTIS)

In this brief report, we provide a description of the activities in each of the areas to which the Backbone contributes, and we provide supporting statistics for each of these contributions. The form of these statistics varies by application area: (1) pot...

D. J. Dailey



NASA's Webb Telescope's Last Backbone Component Completed  

NASA Website

Assembly of the backbone of NASA's James Webb Space Telescope, the primary mirror backplane support structure, is a step closer to completion with the recent addition of the backplane support frame, a fixture that will be used to connect all the ...


Correlation between nucleotide composition and folding energy of coding sequences with special attention to wobble bases  

PubMed Central

Background The secondary structure and complexity of mRNA influences its accessibility to regulatory molecules (proteins, micro-RNAs), its stability and its level of expression. The mobile elements of the RNA sequence, the wobble bases, are expected to regulate the formation of structures encompassing coding sequences. Results The sequence/folding energy (FE) relationship was studied by statistical, bioinformatic methods in 90 CDS containing 26,370 codons. I found that the FE (dG) associated with coding sequences is significant and negative (407 kcal/1000 bases, mean ± S.E.M.) indicating that these sequences are able to form structures. However, the FE has only a small free component, less than 10% of the total. The contribution of the 1st and 3rd codon bases to the FE is larger than the contribution of the 2nd (central) bases. It is possible to achieve a ~4-fold change in FE by altering the wobble bases in synonymous codons. The sequence/FE relationship can be described with a simple algorithm, and the total FE can be predicted solely from the sequence composition of the nucleic acid. The contributions of different synonymous codons to the FE are additive and one codon cannot replace another. The accumulated contributions of synonymous codons of an amino acid to the total folding energy of an mRNA is strongly correlated to the relative amount of that amino acid in the translated protein. Conclusion Synonymous codons are not interchangable with regard to their role in determining the mRNA FE and the relative amounts of amino acids in the translated protein, even if they are indistinguishable in respect of amino acid coding.

Biro, Jan C



Sequence Assembly with CAFTOOLS  

Microsoft Academic Search

Large-scale genomic sequencing requires a software infrastructure to support and integrate applications that are not directly compatible. We describe a suite of software tools built around the Common Assembly Format (CAF), a comprehensive representation of a sequence assembly as a text file. These tools form the backbone of sequencing informatics at the Sanger Centre and the Genome Sequencing Center. The

Simon Dear; Richard Durbin; LaDeana Hillier; Gabor Marth; Jean Thierry-Mieg; Richard Mott



Stacking Sequence Effects on Fatigue Intra-laminar Damage Progression in Composite Joints  

NASA Astrophysics Data System (ADS)

In this paper the effects of the stacking sequence on the fatigue intra-laminar damage accumulation in pinned composite joints is investigated. A fatigue damage propagation numerical model based on gradual material degradation rules and Hashin fatigue failure criteria is formulated, implemented in a finite element platform and then used to simulate the intra-laminar fatigue damage evolution in the analysed composite joints. The model has been preliminary validated against literature experimental data in terms of s-n curves providing confirmation of its effectiveness in predicting the joints fatigue life. Different stacking sequences: zero-dominated, quasi-isotropic, cross-ply with different 0 ° and 90 ° plies distributions, have been considered when investigating the influence of the stacking sequence on the fatigue behaviour of the joints. The simulation of the joints' fatigue life provided detailed information on the intra-laminar damage mechanisms on-set and evolution related to fatigue gradual degradation of material stiffness and strength for different values of the applied maximum stresses.

Riccio, A.; Mozzillo, G.; Scaramuzzino, F.



Simple Sequence Repeats in Escherichia coli: Abundance, Distribution, Composition, and Polymorphism  

PubMed Central

Computer-based genome-wide screening of the DNA sequence of Escherichia coli strain K12 revealed tens of thousands of tandem simple sequence repeat (SSR) tracts, with motifs ranging from 1 to 6 nucleotides. SSRs were well distributed throughout the genome. Mononucleotide SSRs were over-represented in noncoding regions and under-represented in open reading frames (ORFs). Nucleotide composition of mono- and dinucleotide SSRs, both in ORFs and in noncoding regions, differed from that of the genomic region in which they occurred, with 93% of all mononucleotide SSRs proving to be of A or T. Computer-based analysis of the fine position of every SSR locus in the noncoding portion of the genome relative to downstream ORFs showed SSRs located in areas that could affect gene regulation. DNA sequences at 14 arbitrarily chosen SSR tracts were compared among E. coli strains. Polymorphisms of SSR copy number were observed at four of seven mononucleotide SSR tracts screened, with all polymorphisms occurring in noncoding regions. SSR polymorphism could prove important as a genome-wide source of variation, both for practical applications (including rapid detection, strain identification, and detection of loci affecting key phenotypes) and for evolutionary adaptation of microbes.[The sequence data described in this paper have been submitted to the GenBank data library under accession numbers AF209020–209030 and AF209508–209518.

Gur-Arie, Riva; Cohen, Cyril J.; Eitan, Yuval; Shelef, Leora; Hallerman, Eric M.; Kashi, Yechezkel



High-fidelity local addressing of trapped ions and atoms by composite sequences of laser pulses.  


A vital requirement for a quantum computer is the ability to locally address, with high fidelity, any of its qubits without affecting their neighbors. We propose an addressing method using composite sequences of laser pulses that dramatically reduces the addressing error in a lattice of closely spaced atoms or ions and at the same time significantly enhances the robustness of qubit manipulations. To this end, we design novel (to our knowledge) high-fidelity composite pulses for the most important single-qubit operations. In principle, this method allows one to beat the diffraction limit, for only atoms situated in a small spatial region around the center of the laser beam are excited, well within the laser beam waist. PMID:21479056

Ivanov, Svetoslav S; Vitanov, Nikolay V



Bias explorer: measurements of compositional bias in EMBL and GenBank sequence files.  


A Windows application for compositional analysis of sequenced genomes (EMBL or GenBank flat files) is available as freeware. The application allows the user to quantify word bias using Markov chain analysis and it allows the user to generate sliding window data for GC-skew, AT-skew, purine excess, keto excess and discrete word counts. The mathematical routines reside in a dynamic link library (DLL), which can be used independently by other applications. The software is available for download at PMID:15702383

Fuglsang, Anders



Effects of stacking sequence and clamping force on the bearing strengths of mechanically fastened joints in composite laminates  

Microsoft Academic Search

The weakest parts of a composite laminate structure are often the joints. Hence the need to design reliable and efficient load-carrying joints has become increasingly important and the effects of stacking sequence and clamping force on joint strengths have to be clarified. In this study, the effects of stacking sequence and clamping force on delamination bearing strength and ultimate bearing

Heung-Joon Park



Backbone resonance assignment of Staphylococcal Enterotoxin H  

Microsoft Academic Search

The staphylococcal enterotoxin H (SEH; 217 aa, 25 kD) belongs to a family of superantigens that cause a massive immune response upon simultaneous\\u000a binding to the T cell receptor (TCR) and the major histocompatibility complex class II. The SEH-TCR interaction is weak and\\u000a amenable to studies using NMR methodology. Essentially, 2 mg of U{2H, 13C,15N}-labeled SEH was used for the complete sequential backbone

Maria Saline; Vladislav Orekhov; Karin Lindkvist-Petersson; B. Göran Karlsson



ANSS Backbone Station Installation and Site Characterization  

NASA Astrophysics Data System (ADS)

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

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



Efficient virtual-backbone routing in mobile ad hoc networks  

Microsoft Academic Search

Since the physical topology of Mobile Ad hoc Networks (MANETs) is generally unstable, an appealing approach is the construction of a stable and robust virtual topology or backbone. A virtual backbone can play important roles related to routing and connectivity management. In this paper, the problem of providing such a virtual backbone with low overhead is investigated. In particular, we

Jamal N. Al-karaki; Ahmed E. Kamal



Quantum chemical studies of peptide nucleic acid monomers and role of cyclohexyl modification on backbone flexibility  

NASA Astrophysics Data System (ADS)

Peptide nucleic acids (PNA) bind sequence specifically to DNA/RNA and are of major interest for all fields of molecular biology and could form the basis for gene-targeted drugs. Modifications are introduced in PNA to overcome problems associated with orientational selectivity in binding, to restrict conformational flexibility of backbone, and to discriminate binding for either DNA or RNA. The addition of geometrical isomers (1R,2S and 1S,2R) of cyclohexyl ring in the backbone of PNA could bring rigidification to PNA backbone and may impart specificity toward RNA. Therefore, quantum chemical studies are aimed to explore the conformational space, to find out preferred stable conformations of PNA and modified (1R,2S and 1S,2R) cyclohexyl PNA monomer. Content:text/plain; charset="UTF-8"

Sharma, Smriti; Sonavane, Uddhavesh B.; Joshi, Rajendra R.


Automated Real-Space Refinement of Protein Structures Using a Realistic Backbone Move Set  

PubMed Central

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

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



Phylogeny of Prokaryotes and Chloroplasts Revealed by a Simple Composition Approach on All Protein Sequences from Complete Genomes Without Sequence Alignment  

Microsoft Academic Search

The complete genomes of living organisms have provided much information on their phylogenetic relationships. Similarly, the complete genomes of chloroplasts have helped to resolve the evolution of this organelle in photosynthetic eukaryotes. In this paper we propose an alternative method of phylogenetic analysis using compositional statistics for all protein sequences from complete genomes. This new method is conceptually simpler than

Z. G. Yu; L. Q. Zhou; V. V. Anh; K. H. Chu; S. C. Long; J. Q. Deng



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


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

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



Sequence composition and environment effects on residue fluctuations in protein structures  

PubMed Central

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.



VITCOMIC: visualization tool for taxonomic compositions of microbial communities based on 16S rRNA gene sequences  

PubMed Central

Background Understanding the community structure of microbes is typically accomplished by sequencing 16S ribosomal RNA (16S rRNA) genes. These community data can be represented by constructing a phylogenetic tree and comparing it with other samples using statistical methods. However, owing to high computational complexity, these methods are insufficient to effectively analyze the millions of sequences produced by new sequencing technologies such as pyrosequencing. Results We introduce a web tool named VITCOMIC (VIsualization tool for Taxonomic COmpositions of MIcrobial Community) that can analyze millions of bacterial 16S rRNA gene sequences and calculate the overall taxonomic composition for a microbial community. The 16S rRNA gene sequences of genome-sequenced strains are used as references to identify the nearest relative of each sample sequence. With this information, VITCOMIC plots all sequences in a single figure and indicates relative evolutionary distances. Conclusions VITCOMIC yields a clear representation of the overall taxonomic composition of each sample and facilitates an intuitive understanding of differences in community structure between samples. VITCOMIC is freely available at




NSDL National Science Digital Library

DESK Standard: Summarize important ideas/events; summarize supporting details in sequence. . DATES: You can begin this activity on January 22. You should complete it by January 26. OBJECTIVE: It is important to remember the events of a story in the order they happen. You wouldn\\'t want to know how a good story ends before reading all of the ...

Hughes, Mr.



Building a backbone for integrated business communications  

SciTech Connect

This article describes how an effective fiberoptic broadband solution can help utilities redesign business environments, add value to existing products and services, and introduce new possibilities. The Scarborough Public Utilities Commission (PUC) manages the electric and water distribution business within the city of Scarborough, Canada. In 1992, the commission made a strategic decision to develop an integrated business communication system that allows corporate business units to exchange information and helps automate the distribution network. The communication system will allow the commission to realize new and improved services that are customer focused and operations focused. Operations focused services are those supporting internal applications for supervisory control, data acquisition, distribution automation, automatic meter reading, and the corporate business information system. Customer focused services are demand-side management and the efficient utilization of energy. Operations and customer focused services are considered a potential source of competitive advantage. A communication system linking a whole enterprise requires an effective infrastructure (backbone) on which other suitable technologies may be integrated. This article reviews the plan and implementation of the Scarborough PUC backbone system.

Sabir, S. [Scarborough Public Utilities Commission, Ontario (Canada); Mahoney, H.



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.



Predicting regional mutability in antibody V genes based solely on di- and trinucleotide sequence composition.  


Somatic mutations are not distributed randomly throughout Ab V region genes. A sequence-specific target bias is revealed by a defined hierarchy of mutability among di- and trinucleotide sequences located within Ig intronic DNA. Here we report that the di- and trinucleotide mutability preference pattern is shared by mouse intronic JH and Jkappa clusters and by human VH genes, suggesting that a common mutation mechanism exists for all Ig V genes of both species. Using di- and trinucleotide target preferences, we performed a comprehensive analysis of human and murine germline V genes to predict regional mutabilities. Heavy chain genes of both species exhibit indistinguishable patterns in which complementarity-determining region 1 (CDR1), CDR2, and framework region 3 (FR3) are predicted to be more mutable than FR1 and FR2. This prediction is borne out by empirical mutation data from nonproductively rearranged human VH genes. Analysis of light chain genes in both species also revealed a common, but unexpected, pattern in which FR2 is predicted to be highly mutable. While our analyses of nonfunctional Ig genes accurately predicts regional mutation preferences in VH genes, observed relative mutability differences between regions are more extreme than expected. This cannot be readily accounted for by nascent mRNA secondary structure or by a supplemental gene conversion mechanism that might favor nucleotide replacements in CDR. Collectively, our data support the concept of a common mutation mechanism for heavy and light chain genes of mice and humans with regional bias that is qualitatively, but not quantitatively, accounted for by short nucleotide sequence composition. PMID:10384124

Shapiro, G S; Aviszus, K; Ikle, D; Wysocki, L J



A backbone-based theory of protein folding.  


Under physiological conditions, a protein undergoes a spontaneous disorder order transition called "folding." The protein polymer is highly flexible when unfolded but adopts its unique native, three-dimensional structure when folded. Current experimental knowledge comes primarily from thermodynamic measurements in solution or the structures of individual molecules, elucidated by either x-ray crystallography or NMR spectroscopy. From the former, we know the enthalpy, entropy, and free energy differences between the folded and unfolded forms of hundreds of proteins under a variety of solvent/cosolvent conditions. From the latter, we know the structures of approximately 35,000 proteins, which are built on scaffolds of hydrogen-bonded structural elements, alpha-helix and beta-sheet. Anfinsen showed that the amino acid sequence alone is sufficient to determine a protein's structure, but the molecular mechanism responsible for self-assembly remains an open question, probably the most fundamental open question in biochemistry. This perspective is a hybrid: partly review, partly proposal. First, we summarize key ideas regarding protein folding developed over the past half-century and culminating in the current mindset. In this view, the energetics of side-chain interactions dominate the folding process, driving the chain to self-organize under folding conditions. Next, having taken stock, we propose an alternative model that inverts the prevailing side-chain/backbone paradigm. Here, the energetics of backbone hydrogen bonds dominate the folding process, with preorganization in the unfolded state. Then, under folding conditions, the resultant fold is selected from a limited repertoire of structural possibilities, each corresponding to a distinct hydrogen-bonded arrangement of alpha-helices and/or strands of beta-sheet. PMID:17075053

Rose, George D; Fleming, Patrick J; Banavar, Jayanth R; Maritan, Amos



Evaluation of impact of backbone outages in IP networks  

NASA Astrophysics Data System (ADS)

Nationwide IP networks typically include nodes in major cities and the following elements: customer equipment, access routers, backbone routers, peering routers, access links connecting customer equipment to access routers, access routers to backbone routers, and backbone links interconnecting backbone routers. The part of this network consisting of backbone routers and related interconnecting links is referred to as the "backbone". We develop a new approach for accurately computing the Availability measure of IP networks by directly simulating each type of backbone outage event and its impact on traffic loss. We use this approach to quantify availability improvement as a result of introducing various technological changes in the network such as IGP tuning, high availability router architecture, MPLS-TE and Fast Reroute. A situation, where operational backbone links do not have enough spare capacity to carry additional traffic during the outage time, is referred to as bandwidth loss. We concentrate on one unidirectional backbone link and derive asymptotic approximations for the expected bandwidth loss in the framework of generalized Erlang and Engset models when the total number of resource units and request arrival rates are proportionally large. Simulation results demonstrate good accuracy of the approximations.

Kogan, Yaakov; Choudhury, Gagan L.; Tarapore, Percy



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


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

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



Computational backbone mutagenesis of A? peptides: Probing the role of backbone hydrogen bonds in aggregation  

PubMed Central

Using REMD and united atom implicit solvent model we examine the role of backbone hydrogen bonds (HBs) in A? aggregation. The importance of HBs appears to depend on the aggregation stage. The backbone HBs have little effect on the stability of A? dimers or on their aggregation interface. The HBs also do not play a critical role in initial binding of A? peptides to the amyloid fibril. Their elimination does not change the continuous character of A? binding nor its temperature. However, cancellation of HBs forming between incoming A? peptides and the fibril disrupts the locked fibril-like states in the bound peptides. Without the support of HBs bound A? peptides form few long ?-strands on the fibril edge. As a result the deletion of peptide-fibril HBs is expected to impede fibril growth. As for the peptides bound to A? fibril the deletion of interpeptide HBs reduces the ? propensity in the dimers making them less competent for amyloid assembly. These simulation findings together with the backbone mutagenesis experiments suggest that a viable strategy for arresting fibril growth is the disruption of interpeptide HBs.

Takeda, Takako; Klimov, Dmitri K.



Agrobacterium T-DNA integration in Arabidopsis is correlated with DNA sequence compositions that occur frequently in gene promoter regions.  


Mobile insertion elements such as transposons and T-DNA generate useful genetic variation and are important tools for functional genomics studies in plants and animals. The spectrum of mutations obtained in different systems can be highly influenced by target site preferences inherent in the mechanism of DNA integration. We investigated the target site preferences of Agrobacterium T-DNA insertions in the chromosomes of the model plant Arabidopsis thaliana. The relative frequencies of insertions in genic and intergenic regions of the genome were calculated and DNA composition features associated with the insertion site flanking sequences were identified. Insertion frequencies across the genome indicate that T-strand integration is suppressed near centromeres and rDNA loci, progressively increases towards telomeres, and is highly correlated with gene density. At the gene level, T-DNA integration events show a statistically significant preference for insertion in the 5' and 3' flanking regions of protein coding sequences as well as the promoter region of RNA polymerase I transcribed rRNA gene repeats. The increased insertion frequencies in 5' upstream regions compared to coding sequences are positively correlated with gene expression activity and DNA sequence composition. Analysis of the relationship between DNA sequence composition and gene activity further demonstrates that DNA sequences with high CG-skew ratios are consistently correlated with T-DNA insertion site preference and high gene expression. The results demonstrate genomic and gene-specific preferences for T-strand integration and suggest that DNA sequences with a pronounced transition in CG- and AT-skew ratios are preferred targets for T-DNA integration. PMID:15744539

Schneeberger, Richard G; Zhang, Ke; Tatarinova, Tatiana; Troukhan, Max; Kwok, Shing F; Drais, Josh; Klinger, Kevin; Orejudos, Francis; Macy, Kimberly; Bhakta, Amit; Burns, James; Subramanian, Gopal; Donson, Jonathan; Flavell, Richard; Feldmann, Kenneth A



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

PubMed Central

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

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



Toward future IP optical backbone networks  

NASA Astrophysics Data System (ADS)

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

Urushidani, Shigeo



The Backbone of the Climate Networks  

NASA Astrophysics Data System (ADS)

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

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



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



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


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



Solution Structure and Backbone Dynamics of Streptopain  

PubMed Central

Streptococcal pyrogenic exotoxin B (SPE B) is a cysteine protease expressed by Streptococcus pyogenes. The D9N, G163S, G163S/A172S, and G239D mutant proteins were expressed to study the effect of the allelic variants on their protease activity. In contrast to other mutants, the G239D mutant was ?12-fold less active. The Gly-239 residue is located within the C-terminal S230-G239 region, which cannot be observed in the x-ray structure. The three-dimensional structure and backbone dynamics of the 28-kDa mature SPE B (mSPE B) were determined. Unlike the x-ray structure of the 40-kDa zymogen SPE B (proSPE B), we observed the interactions between the C-terminal loop and the active site residues in mSPE B. The structural differences between mSPE B and proSPE B were the conformation of the C-terminal loop and the orientation of the catalytic His-195 residue, suggesting that activation and inactivation of SPE B is involved in the His-195 side-chain rotation. Dynamics analysis of mSPE B and the mSPE B/inhibitor complexes showed that the catalytic and C-terminal loops were the most flexible regions with low order parameter values of 0.5 to 0.8 and exhibited the motion on the ps/ns timescale. These findings suggest that the flexible C-terminal loop of SPE B may play an important role in controlling the substrate binding, resulting in its broad substrate specificity.

Wang, Chih-Chieh; Houng, Hsiang-Chee; Chen, Chun-Liang; Wang, Pei-Ju; Kuo, Chih-Feng; Lin, Yee-Shin; Wu, Jiunn-Jong; Lin, Ming T.; Liu, Ching-Chuan; Huang, Wenya; Chuang, Woei-Jer



Monomer composition and sequence of sodium alginate extracted at pilot plant scale from three commercially important seaweeds from Mexico  

Microsoft Academic Search

The marine waters of the Baja California peninsula (Mexico) are a rich source of brown seaweeds with a great potential for\\u000a exploitation. For that reason, Sargassum sinicola, Eisenia arborea, and Macrocystis pyrifera collected from different locations were subjected to extraction of sodium alginate using a pilot-plant scale process developed\\u000a in our facilities. The composition and sequence parameters of the recovered

Jesús Iván Murillo-Álvarez; Gustavo Hernández-Carmona



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

SciTech Connect

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

Fidanza, J.A.



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


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

Aita, Takuyo; Nishigaki, Koichi



A backbone lever-arm effect enhances polymer mechanochemistry  

NASA Astrophysics Data System (ADS)

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

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



RosettaBackrub--a web server for flexible backbone protein structure modeling and design  

PubMed Central

The RosettaBackrub server ( implements the Backrub method, derived from observations of alternative conformations in high-resolution protein crystal structures, for flexible backbone protein modeling. Backrub modeling is applied to three related applications using the Rosetta program for structure prediction and design: (I) modeling of structures of point mutations, (II) generating protein conformational ensembles and designing sequences consistent with these conformations and (III) predicting tolerated sequences at protein–protein interfaces. The three protocols have been validated on experimental data. Starting from a user-provided single input protein structure in PDB format, the server generates near-native conformational ensembles. The predicted conformations and sequences can be used for different applications, such as to guide mutagenesis experiments, for ensemble-docking approaches or to generate sequence libraries for protein design.

Lauck, Florian; Smith, Colin A.; Friedland, Gregory F.; Humphris, Elisabeth L.; Kortemme, Tanja



Simulation of a Campus Backbone Network, a case-study  

Microsoft Academic Search

This paper describes the work performed in the framework of a Master's thesis. The aim of the thesis was to make a simulation model in OPNET Modeler of the backbone at the K.U.Leuven, Belgium. The backbone consists of five Cisco Catalyst 5500 switches in a ring topology interconnected by full-duplex Gigabit Ethernet links. Accurate real-life measurements are used to add

J. Potemans; J. Theunis; B. Rodiers; B. Van den Broeck; P. Leys; E. Van Lil; A. Van de Capelle


Design issues of optical IP routers for Internet backbone applications  

Microsoft Academic Search

The rapid increase of Internet traffic is pushing the deployment of WDM technology in the next-generation high-speed Internet backbone. Routers in the backbone could still be the potential bottleneck. In this article we consider some design issues of high-throughput optical routers which combine the advantages of WDM with the new optical switching technology. We first introduce a proposed Internet architecture

Franco Callegati; A. C. Cankaya; Yijun Xiong; Marc Vandenhoute



Photocleavage of the polypeptide backbone by 2-nitrophenylalanine.  


Photocleavage of the polypeptide backbone is potentially a powerful and general method to activate or deactivate functional peptides and proteins with high spatial and temporal resolution. Here we show that 2-nitrophenylalanine is able to photochemically cleave the polypeptide backbone by an unusual cinnoline-forming reaction. This unnatural amino acid was genetically encoded in E. coli, and protein containing 2-nitrophenylalanine was expressed and site-specifically photocleaved. PMID:19246005

Peters, Francis B; Brock, Ansgar; Wang, Jiangyun; Schultz, Peter G



Polyarylether composition and membrane  

SciTech Connect

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)



HIV-1 Phenotypic Reverse Transcriptase Inhibitor Drug Resistance Test Interpretation Is Not Dependent on the Subtype of the Virus Backbone  

PubMed Central

To date, the majority of HIV-1 phenotypic resistance testing has been performed with subtype B virus backbones (e.g. HXB2). However, the relevance of using this backbone to determine resistance in non-subtype B HIV-1 viruses still needs to be assessed. From 114 HIV-1 subtype C clinical samples (36 ARV-naïve, 78 ARV-exposed), pol amplicons were produced and analyzed for phenotypic resistance using both a subtype B- and C-backbone in which the pol fragment was deleted. Phenotypic resistance was assessed in resulting recombinant virus stocks (RVS) for a series of antiretroviral drugs (ARV's) and expressed as fold change (FC), yielding 1660 FC comparisons. These Antivirogram® derived FC values were categorized as having resistant or sensitive susceptibility based on biological cut-off values (BCOs). The concordance between resistance calls obtained for the same clinical sample but derived from two different backbones (i.e. B and C) accounted for 86.1% (1429/1660) of the FC comparisons. However, when taking the assay variability into account, 95.8% (1590/1660) of the phenotypic data could be considered as being concordant with respect to their resistance call. No difference in the capacity to detect resistance associated with M184V, K103N and V106M mutations was noted between the two backbones. The following was concluded: (i) A high level of concordance was shown between the two backbone phenotypic resistance profiles; (ii) Assay variability is largely responsible for discordant results (i.e. for FC values close to BCO); (iii) Confidence intervals should be given around the BCO's, when assessing resistance in HIV-1 subtype C; (iv) No systematic resistance under- or overcalling of subtype C amplicons in the B-backbone was observed; (v) Virus backbone subtype sequence variability outside the pol region does not contribute to phenotypic FC values. In conclusion the HXB2 virus backbone remains an acceptable vector for phenotyping HIV-1 subtype C pol amplicons.

Bronze, Michelle; Steegen, Kim; Wallis, Carole L.; De Wolf, Hans; Papathanasopoulos, Maria A.; Van Houtte, Margriet; Stevens, Wendy S.; de Wit, Tobias Rinke; Stuyver, Lieven J.



Sequence stratigraphy and composition of late quaternary shelf-margin deltas, Northern Gulf of Mexico  

Microsoft Academic Search

High-resolution seismic profiles and foundation borings from the northwestern Gulf of Mexico record the physical attributes and depositional histories of several late Quaternary sequences that were deposited by wave-modified, river-dominated shelf-margin deltas during successive periods of lowered sea level. Each progressively younger deltaic sequence is thinner and exhibits a systematic decrease in the abundance and concentration of sand, which is

R. A. Morton; J. R. Suter



Peptide Amphiphile Nanofibers with Conjugated Polydiacetylene Backbones in Their Core  

PubMed Central

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 ?-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 ?-sheets, which are normally twisted in helical fashion. Heating and cooling shows simultaneous changes in ?-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.

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



Backbone assignment of the N-terminal polyomavirus large T antigen.  


Polyoma Large T antigen (PyLT) is a viral oncoprotein that targets cell proteins important for growth regulation. PyLT has two functional domains. Here we report (1)H, (15)N, (13)C backbone and (13)C beta assignments of 76% of the residues of the polyomavirus large T antigen N-terminal domain (PyLTNT) that is sufficient to regulate cell phenotype. PyLTNT is substantially unfolded even in regions known to be critical for its biological function. The protein also includes a previously characterised J domain that although conformationally influenced by the residue extension, retains its folded state unlike the majority of the protein sequence. PMID:19636961

Knoblich, Konstantin; Whittaker, Sara; Ludwig, Christian; Michiels, Paul; Jiang, Tao; Schaffhausen, Brian; Günther, Ulrich



The Dicyclopropylmethyl (Dcpm) Peptide Backbone Protectant†  

PubMed Central

The N-dicyclopropylmethyl (Dcpm) residue, introduced into amino acids via reaction of dicyclopropylmethanimine hydrochloride with an amino acid ester followed by sodium cyanoborohydride or triacetoxyborohydride reduction, can be used as an amide bond protectant for peptide synthesis. Examples which demonstrate the amelioration of aggregation effects include syntheses of the alanine decapeptide and the prion peptide (106–126). Avoidance of cyclization to the aminosuccinimide followed substitution of Fmoc-(Dcpm)Gly-OH for Fmoc-Gly-OH in the assembly of sequences containing the sensitive Asp-Gly unit.

Carpino, Louis A.; Nasr, Khaled; Abdel-Maksoud, Adel Ali; El-Faham, Ayman; Ionescu, Dumitru; Henklein, Peter; Wenschuh, Holger; Beyermann, Michael; Krause, Eberhard; Bienert, Michael



Composition-based classification of short metagenomic sequences elucidates the landscapes of taxonomic and functional enrichment of microorganisms  

PubMed Central

Compared with traditional algorithms for long metagenomic sequence classification, characterizing microorganisms’ taxonomic and functional abundance based on tens of millions of very short reads are much more challenging. We describe an efficient composition and phylogeny-based algorithm [Metagenome Composition Vector (MetaCV)] to classify very short metagenomic reads (75–100 bp) into specific taxonomic and functional groups. We applied MetaCV to the Meta-HIT data (371-Gb 75-bp reads of 109 human gut metagenomes), and this single-read-based, instead of assembly-based, classification has a high resolution to characterize the composition and structure of human gut microbiota, especially for low abundance species. Most strikingly, it only took MetaCV 10 days to do all the computation work on a server with five 24-core nodes. To our knowledge, MetaCV, benefited from the strategy of composition comparison, is the first algorithm that can classify millions of very short reads within affordable time.

Liu, Jiemeng; Wang, Haifeng; Yang, Hongxing; Zhang, Yizhe; Wang, Jinfeng; Zhao, Fangqing; Qi, Ji



Modeling the sulfur and oxygen isotopic composition of sulfates through a halite-potash sequence: Implications for the hydrological evolution of the upper eocene Southpyrenean basin  

Microsoft Academic Search

The isotopic composition of sulfates sampled throughout a complete evaporite sequence has contributed to the understanding of the evolution of the Southpyrenean Upper Eocene basin. The ?34S and ?18O values appear to be constant in thick segments of the sequence. This pattern is clearly different from the continuous decrease in ? values predicted by the evaporation processes in a closed

Carlos Ayora; Conxita Taberner; Catherine Pierre; Juan-José Pueyo



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

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



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


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 PMID:23892401

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



Distributed low-cost backbone formation for wireless ad hoc networks  

Microsoft Academic Search

Backbone has been used extensively in various aspects (e.g., routing, route maintenance, broadcast, scheduling) for wireless networks. Previous methods are mostly designed to minimize the backbone size. However, in many applications, it is desirable to construct a backbone with small cost when each wireless node has a cost of being in the backbone. In this paper, we first show that

Yu Wang; Weizhao Wang; Xiang-yang Li




Microsoft Academic Search

In recent years, fibre - reinforced composite laminated plates have been widely used in the aerospace, marine, automobile and other engineering industries. During the operational life, the variation of temperature and moisture reduces the elastic moduli and degrades the strength of the laminated materials (1-2). Also, in previous studies (3-4), the transient hygroscopic stresses induced by the hygrothermal stresses have



Some fractal properties of the percolating backbone in two dimensions  

SciTech Connect

A new algorithm is presented, based on elements of artificial intelligence theory, to determine the fractal properties of the backbone of the incipient infinite cluster. It is found that fractal dimensionality of the backbone is d/sub f//sup BB/ = 1.61 +/- 0.01, the chemical dimensionality is d/sub t/ = 1.40 +/- 0.01, and the fractal dimension of the minimum path d/sub min/ = 1.15 +/- 0.02 for the two-dimensional triangular lattice.

Laidlaw, D.; MacKay, G.; Jan, N.



Backbone 1 H, 15 N, and 13 C resonance assignments and secondary structure of the tollip CUE domain  

Microsoft Academic Search

The Toll-interacting protein (Tollip) is a negative regulator of the Toll-like receptor (TLR)-mediated inflammation response.\\u000a Tollip is a modular protein that contains an Nterminal Tom1-binding domain (TBD), a central conserved domain 2 (C2), and a C-terminal coupling of ubiquitin to endoplasmic reticulum degradation (CUE) domain. Here, we report the sequence-specific backbone 1H, 15N, and 13C assignments of the human Tollip

Hugo F. Azurmendi; Sharmistha Mitra; Iriscilla Ayala; Liwu Li; Carla V. Finkielstein; Daniel G. S. Capelluto



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

PubMed Central

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



Stretches of oligogalacturonan are present in the backbone of rhamnogalacturonan I from cotton suspension culture cell walls  

SciTech Connect

A polysaccharide fraction, solubilized from cotton suspension culture cell walls by sequential treatments by endopolygalacturonase and cellulase and purified by gel filtration chromatography, contained the sugars characteristic of rhamnogalacturonan I (RGI). A known structural feature of the backbone of RGI is the repeating disaccharide galA-rha; however, the ratio of galA to rha residues was found to be 1 {center dot} 9:1. Treatment of the RGI preparation with liquid HF (containing 1% water) at {minus}23{degree} caused cleavage of most of the rhamnosyl linkages without cleavage of galacturonosyl linkages. Neutral sugar linkages of the sidechains were also mostly cleaved. Characterization of the products from the backbone by nmr spectroscopy, compositional analysis, and liquid secondary ion mass spectrometry suggested that the backbone of the RGI is made up of short segments ({approximately} 10 units) of the galA-rha repeat interspersed with short homogalacturonan segments of {approximately} 10 galA residues of which about 40% are methyl esterified. The sequential enzyme treatments only solubilize {approximately} 40% of the RGI. The residual RGI contains a higher proportion of falA-rha repeats in its backbone.

An, Jinhua; Mort, A. (Oklahoma State Univ., Stillwater (United States))



A study of archaeal enzymes involved in polar lipid synthesis linking amino acid sequence information, genomic contexts and lipid composition  

PubMed Central

Cellular membrane lipids, of which phospholipids are the major constituents, form one of the characteristic features that distinguish Archaea from other organisms. In this study, we focused on the steps in archaeal phospholipid synthetic pathways that generate polar lipids such as archaetidylserine, archaetidylglycerol, and archaetidylinositol. Only archaetidylserine synthase (ASS), from Methanothermobacter thermautotrophicus,has been experimentally identified. Other enzymes have not been fully examined. Through database searching, we detected many archaeal hypothetical proteins that show sequence similarity to members of the CDP alcohol phosphatidyltransferase family, such as phosphatidylserine synthase (PSS), phosphatidylglycerol synthase (PGS) and phosphatidylinositol synthase (PIS) derived from Bacteria and Eukarya. The archaeal hypothetical proteins were classified into two groups, based on the sequence similarity. Members of the first group, including ASS from M. thermautotrophicus, were closely related to PSS. The rough agreement between PSS homologue distribution within Archaea and the experimentally identified distribution of archaetidylserine suggested that the hypothetical proteins are ASSs. We found that an open reading frame (ORF) tends to be adjacent to that of ASS in the genome, and that the order of the two ORFs is conserved. The sequence similarity of phosphatidylserine decarboxylase to the product of the ORF next to the ASS gene, together with the genomic context conservation, suggests that the ORF encodes archaetidylserine decarboxylase, which may transform archaetidylserine to archaetidylethanolamine. The second group of archaeal hypothetical proteins was related to PGS and PIS. The members of this group were subjected to molecular phylogenetic analysis, together with PGSs and PISs and it was found that they formed two distinct clusters in the molecular phylogenetic tree. The distribution of members of each cluster within Archaea roughly corresponded to the experimentally identified distribution of archaetidylglycerol or archaetidylinositol. The molecular phylogenetic tree patterns and the correspondence to the membrane compositions suggest that the two clusters in this group correspond to archaetidylglycerol synthases and archaetidylinositol synthases. No archaeal hypothetical protein with sequence similarity to known phosphatidylcholine synthases was detected in this study.

Daiyasu, Hiromi; Kuma, Kei-Ichi; Yokoi, Toshiro; Morii, Hiroyuki; Koga, Yosuke; Toh, Hiroyuki



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



Traffic Characteristics of the T1 NSFNET Backbone  

Microsoft Academic Search

This paper presents the results of a measurementstudy of the T1 NSFNET backbone. We first discussthe measurement environment and approach to datacollection. We then present measurements results for:long-term growth in traffic volume, including attributionto domains and protocols; trend in average packetsize on the network, both over long and medium termintervals; most popular sources, destinations, and sitepairs; traffic locality; international distribution

Kimberly C. Claffy; George C. Polyzos; Hans-werner Braun



Radiation damage to DNA: Electron scattering from the backbone subunits  

Microsoft Academic Search

In the context of damage to DNA by low energy electrons, we carry out calculations of electron scattering from tetrahydrofuran and phosphoric acid, models of the subunits in the DNA backbone, as a first step in simulating the electron capture process that occurs in the cell. In the case of tetrahydrofuran, we also compare with previous theoretical and experimental data.

Stefano Tonzani; Chris H. Greene



Evaluating the competitive effects of mergers of internet backbone providers  

Microsoft Academic Search

This article analyzes the usefulness of the traffic measurement methodologies used by the European Commission (EC) and the United States Department of Justice (DOJ) in assessing the competitive effects of mergers of Internet backbone providers. The analysis concludes that the traffic ratios used by the EC to estimate market shares when it reviewed the merger application of MCI and WorldCom,

Stanley M. Besen; Jeffrey S. Spigel; Padmanabhan Srinagesh



Diffusive process on a backbone structure with drift terms.  


The effects of an external force on a diffusive process subjected to a backbone structure are investigated by considering the system governed by a Fokker-Planck equation with drift terms. Our results show an anomalous spreading which may present different diffusive regimes connected to anomalous diffusion and stationary states. PMID:23410297

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



Determination of protein backbone structures from residual dipolar couplings.  


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

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



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



Cell cycle-dependent changes in conformation and composition of nucleosomes containing human histone gene sequences.  

PubMed Central

Unfolding of the nucleosomes in transcriptionally active chromatin uncovers the sulfhydryl groups of histone H3 and permits the selective recovery of the unfolded nucleosomes by mercury-affinity chromatography. This new technique has been used to compare the nucleosomal proteins and their postsynthetic modifications in the unfolded and the compactly beaded nucleosomes of HeLa cells in logarithmic growth, and at different stages of the growth cycle. The Hg-bound nucleosomes are shown to be deficient in replicating DNA sequences, but to remain associated with fragments of nascent RNA chains (or RNP particles) during gradient centrifugations. Both nucleosome fractions contain a full complement of "core" histones but differ with respect to postsynthetic modifications. The Hg-bound nucleosomes contain high levels of the tri- and tetra-acetylated forms of histones H3 and H4. The unbound nucleosomes are deficient in acetylated histones but enriched in phosphorylated H2A. In synchronized HeLa cells, histone H2A and H4 gene sequences occur in the Hg-bound nucleosomes during the S-phase when their transcription takes place, but not in the G2-phase when the genes are repressed. Images

Sterner, R; Boffa, L C; Chen, T A; Allfrey, V G



Triazole linkages and backbone branches in nucleic acids for biological and extra-biological applications  

NASA Astrophysics Data System (ADS)

The recently increasing evidence of nucleic acids' alternative roles in biology and potential as useful nanomaterials and therapeutic agents has enabled the development of useful probes, elaborate nanostructures and therapeutic effectors based on nucleic acids. The study of alternative nucleic acid structure and function, particularly RNA, hinges on the ability to introduce site-specific modifications that either provide clues to the nucleic acid structure function relationship or alter the nucleic acid's function. Although the available chemistries allow for the conjugation of useful labels and molecules, their limitations lie in their tedious conjugation conditions or the lability of the installed probes. The development and optimization of click chemistry with RNA now provides the access to a robust and orthogonal conjugation methodology while providing stable conjugates. Our ability to introduce click reactive groups enzymatically, rather than only in the solid-phase, allows for the modification of larger, more cell relevant RNAs. Additionally, ligation of modified RNAs with larger RNA constructs through click chemistry represents an improvement over traditional ligation techniques. We determined that the triazole linkage generated through click chemistry is compatible in diverse nucleic acid based biological systems. Click chemistry has also been developed for extra-biological applications, particularly with DNA. We have expanded its use to generate useful polymer-DNA conjugates which can form controllable soft nanoparticles which take advantage of DNA's properties, i.e. DNA hybridization and computing. Additionally, we have generated protein-DNA conjugates and assembled protein-polymer hybrids mediated by DNA hybridization. The use of click chemistry in these reactions allows for the facile synthesis of these unnatural conjugates. We have also developed backbone branched DNA through click chemistry and showed that these branched DNAs are useful in generating well-defined architectures based solely on DNA. While backbone branched DNAs are useful for nanotechnological applications, backbone branches in RNA occur in nature and are involved in the distinct but related processes of splicing, debranching and RNAi. Therefore we have developed protocols for the synthesis of backbone branched nucleic acids in the solid-phase using photoprotecting groups. Using the synthesized backbone branched RNAs we have uncovered a specific substrate requirement of debranching enzyme which distinguishes it from other homologous proteins with alternative functions. Finally, through the marriage of click chemistry and backbone branches, we have produced useful progeny in the synthesis of lariat RNAs. We investigated the potential of these lariats as therapeutic agents by synthesizing siRNA sequences as lariats. We showed that these lariats are efficiently debranched by debranching enzyme and are able to induce an RNAi response in vivo. Altogether, the development of click chemistry and backbone branched nucleic acids represents a significant advantage in the ability to modify nucleic acid structure and affect its function. I envision that these methods can become generally useful to probe nucleic acid systems, useful nanomaterials and functional effectors in nucleic acid based therapies.

Paredes, Eduardo


First Survey of the Wheat Chromosome 5A Composition through a Next Generation Sequencing Approach  

PubMed Central

Wheat is one of the world's most important crops and is characterized by a large polyploid genome. One way to reduce genome complexity is to isolate single chromosomes using flow cytometry. Low coverage DNA sequencing can provide a snapshot of individual chromosomes, allowing a fast characterization of their main features and comparison with other genomes. We used massively parallel 454 pyrosequencing to obtain a 2x coverage of wheat chromosome 5A. The resulting sequence assembly was used to identify TEs, genes and miRNAs, as well as to infer a virtual gene order based on the synteny with other grass genomes. Repetitive elements account for more than 75% of the genome. Gene content was estimated considering non-redundant reads showing at least one match to ESTs or proteins. The results indicate that the coding fraction represents 1.08% and 1.3% of the short and long arm respectively, projecting the number of genes of the whole chromosome to approximately 5,000. 195 candidate miRNA precursors belonging to 16 miRNA families were identified. The 5A genes were used to search for syntenic relationships between grass genomes. The short arm is closely related to Brachypodium chromosome 4, sorghum chromosome 8 and rice chromosome 12; the long arm to regions of Brachypodium chromosomes 4 and 1, sorghum chromosomes 1 and 2 and rice chromosomes 9 and 3. From these similarities it was possible to infer the virtual gene order of 392 (5AS) and 1,480 (5AL) genes of chromosome 5A, which was compared to, and found to be largely congruent with the available physical map of this chromosome.

Vitulo, Nicola; Albiero, Alessandro; Forcato, Claudio; Campagna, Davide; Dal Pero, Francesca; Bagnaresi, Paolo; Colaiacovo, Moreno; Faccioli, Primetta; Lamontanara, Antonella; Simkova, Hana; Kubalakova, Marie; Perrotta, Gaetano; Facella, Paolo; Lopez, Loredana; Pietrella, Marco; Gianese, Giulio; Dolezel, Jaroslav; Giuliano, Giovanni; Cattivelli, Luigi; Valle, Giorgio; Stanca, A. Michele



Comparative genomics of pAKD4, the prototype IncP-1delta plasmid with a complete backbone.  


Plasmids of the incompatibility group IncP-1 are important agents of horizontal gene transfer and contribute to the spread of antibiotic resistance and xenobiotic degradation within bacterial communities. Even though some prototype plasmids have been studied in much detail, the diversity of this plasmid group was still greatly underestimated until recently, as only two of the five currently known divergent sub-groups had been described. To further improve our insight into the diversity and evolutionary history of this family of broad-host-range plasmids, we compared the complete nucleotide sequence of a new IncP-1delta plasmid pAKD4 to the genomes of other IncP-1 plasmids. Plasmid pAKD4 was previously isolated by exogenous plasmid isolation from an agricultural soil in Norway. Its 56,803bp nucleotide sequence shows high similarity in gene sequence and gene order to both plasmids pEST4011 and pIJB1, the only other IncP-1delta plasmids sequenced so far. While all three plasmids have a typical IncP-1 backbone comprising replication, transfer, and stable inheritance/control genes, the low sequence similarity in some regions and presence/absence of some backbone genes compared to other IncP-1 plasmids cluster them in a divergent sub-group. Therefore this study validates the presence of a real IncP-1delta clade with multiple plasmids. Moreover, since both pEST4011 and pIJB1 are missing a portion of their transfer genes, pAKD4 represents the first completely sequenced self-transferable plasmid with a complete IncP-1delta backbone. We therefore propose it to be the prototype IncP-1delta plasmid. PMID:20018208

Sen, Diya; Yano, Hirokazu; Suzuki, Haruo; Król, Jaroslaw E; Rogers, Linda; Brown, Celeste J; Top, Eva M



Comparative genomics of pAKD4, the prototype IncP-1?plasmid with a complete backbone  

PubMed Central

Plasmids of the incompatibility group IncP-1 are important agents of horizontal gene transfer and contribute to the spread of antibiotic resistance and xenobiotic degradation within bacterial communities. Even though some prototype plasmids have been studied in much detail, the diversity of this plasmid group was still greatly underestimated until recently, as only two of the five currently known divergent sub-groups had been described. To further improve our insight into the diversity and evolutionary history of this family of broad-host-range plasmids, we compared the complete nucleotide sequence of a new IncP-1? plasmid pAKD4 to the genomes of other IncP-1 plasmids. Plasmid pAKD4 was previously isolated by exogenous plasmid isolation from an agricultural soil in Norway. Its 56,803 bp nucleotide sequence shows high similarity in gene sequence and gene order to both plasmids pEST4011 and pIJB1, the only other IncP-1? plasmids sequenced so far. While all three plasmids have a typical IncP-1 backbone comprising replication, transfer and stable inheritance/control genes, the low sequence similarity in some regions and presence/absence of some backbone genes compared to other IncP-1 plasmids cluster them in a divergent sub-group. Therefore this study validates the presence of a real IncP-1? clade with multiple plasmids. Moreover, since both pEST4011 and pIJB1 are missing a portion of their transfer genes, pAKD4 represents the first completely sequenced self-transferable plasmid with a complete IncP-1? backbone. We therefore propose it to be the prototype IncP-1? plasmid.

Sen, Diya; Yano, Hirokazu; Suzuki, Haruo; Krol, Jaroslaw E.; Rogers, Linda; Brown, Celeste J.; Top, Eva M.



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.



UV resonance Raman monitors polyglutamine backbone and side chain hydrogen bonding and fibrillization1  

PubMed Central

We utilize 198 and 204 nm excited UV resonance Raman spectroscopy (UVRR) and circular dichroism spectroscopy (CD) to monitor the backbone conformation and the GLN side chain hydrogen bonding (HB) of a short, mainly polyGLN peptide of sequence D2Q10K2 (Q10). We measured the UVRR spectra of valeramide to determine the dependence of the primary amide vibrations on amide HB. We observe that non-disaggregated Q10 (NDQ10) solution (prepared by directly dissolving the original synthesized peptide in pure water) occurs in a ?-sheet conformation, where the GLN side chains form HB to either the backbone or other GLN side chains. At 60 °C, these solutions readily form amyloid fibrils. We used the polyGLN disaggregation protocol of Wetzel et al (Methods Enzymol, 2006, 413, 34–74) to dissolve the Q10 ?-sheet aggregates. We observe that the disaggregated Q10 (DQ10) solutions adopt PPII-like and 2.51-helix conformations where the GLN side chains form HB to water. In contrast, these samples do not form fibrils. The NDQ10 ?-sheet solution structure is essentially identical to that found in the NDQ10 solid formed upon solution evaporation. The DQ10 PPII and 2.51-helix solution structure is essentially identical to that in the DQ10 solid. Although the NDQ10 solution readily forms fibrils when heated, the DQ10 solution does not form fibrils unless seeded by NDQ10 solution. This result demonstrates very high activation barriers between these solution conformations. The NDQ10 fibril secondary structure is essentially identical to that of the NDQ10 solution, except that the NDQ10 fibril backbone conformational distribution is narrower than in the dissolved species. The NDQ10 fibril GLN side chain geometry is more constrained than when NDQ10 is in solution. The NDQ10 fibril structure is identical to that of the DQ10 fibril seeded by the NDQ10 solution.

Xiong, Kan; Punihaole, David



Role of Backbone Hydration and Salt-Bridge Formation in Stability of ?-Helix in Solution  

PubMed Central

We test molecular level hypotheses for the high thermal stability of ?-helical conformations of alanine-based peptides by performing detailed atomistic simulations of a 20-amino-acid peptide with explicit treatment of water. To assess the contribution of large side chains to ?-helix stability through backbone desolvation and salt-bridge formation, we simulate the alanine-rich peptide, Ac-YAEAAKAAEAAKAAEAAKAF-Nme, referred to as the EK peptide, that has three pairs of “i, i + 3” glutamic acid(?) and lysine(+) substitutions. Efficient configurational sampling of the EK peptide over a wide temperature range enabled by the replica exchange molecular dynamics technique allows characterization of the stability of ?-helix with respect to heat-induced unfolding. We find that near ambient temperatures, the EK peptide predominately samples ?-helical configurations with 80% fractional helicity at 300 K. The helix melts over a broad range of temperatures with melting temperature, Tm, equal to 350 K, that is significantly higher than the Tm of a 21-residue polyalanine peptide, A21. Salt-bridges between oppositely charged Glu? and Lys+ side chains can, in principle, provide thermal stability to ?-helical conformers. For the specific EK peptide sequence, we observe infrequent formation of Glu-Lys salt-bridges (with ?10–20% probability) and therefore we conclude that salt-bridge formation does not contribute significantly to the EK peptide's helical stability. However, lysine side chains are found to shield specific “i, i + 4” backbone hydrogen bonds from water, indicating that large side-chain substituents can play an important role in stabilizing ?-helical configurations of short peptides in aqueous solution through mediation of water access to backbone hydrogen bonds. These observations have implications on molecular engineering of peptides and biomolecules in the design of their thermostable variants where the shielding mechanism can act in concert with other factors such as salt-bridge formation, thereby increasing thermal stability considerably.

Ghosh, Tuhin; Garde, Shekhar; Garcia, Angel E.



Silkmoth chorion proteins. Their diversity, amino acid composition, and the NH-terminal sequence of one component.  


Silkmoth eggshell (chorion) proteins have been characterized by electrophoresis on sodium dodecyl sulfate and isoelectric focusing polyacrylamide gels; up to 33 and 41 components, respectively, were detected from a single chorion. Some of these components are polymorphic, being absent from chorions of certain animals. A system of nomenclature for all chorion proteins is presented, based on their separation on sodium dodecyl sulfate and isoelectric focusing gels. The chorion is enriched in glycine, alanine, cysteine, and tyrosine and poor in methionine and histidine. The proteins were fractionated into four partially overlapping groups; all four are enriched in the above amino acids, although significant differences exist. Further fractionation by isoelectric focusing of one of the above groups, s/s, yielded seven components, two of which are homogeneous both on sodium dodecyl sulfate and isoelectric focusing gels. The amino acid compositions, molecular weights, and solubility properties of the components share certain features which distinguish s/s as a group from the other three groups. The sequence of the first 67 NH2-terminal residues of a homogeneous protein purified from s/s has been determined. The protein contains a cysteine-rich tail (3 cysteines in the first 18 residues) followed by a 49-residue segment which contains only a single cysteine residue. This latter segment also contains two different tetrapeptide sequences which are each repeated, one twice and the other four times. PMID:624733

Regier, J C; Kafatos, F C; Kramer, K J; Heinrikson, R L; Keim, P S



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



Backbone structure of the infectious epsilon15 virus capsid revealed by electron cryomicroscopy.  


A half-century after the determination of the first three-dimensional crystal structure of a protein, more than 40,000 structures ranging from single polypeptides to large assemblies have been reported. The challenge for crystallographers, however, remains the growing of a diffracting crystal. Here we report the 4.5-A resolution structure of a 22-MDa macromolecular assembly, the capsid of the infectious epsilon15 (epsilon15) particle, by single-particle electron cryomicroscopy. From this density map we constructed a complete backbone trace of its major capsid protein, gene product 7 (gp7). The structure reveals a similar protein architecture to that of other tailed double-stranded DNA viruses, even in the absence of detectable sequence similarity. However, the connectivity of the secondary structure elements (topology) in gp7 is unique. Protruding densities are observed around the two-fold axes that cannot be accounted for by gp7. A subsequent proteomic analysis of the whole virus identifies these densities as gp10, a 12-kDa protein. Its structure, location and high binding affinity to the capsid indicate that the gp10 dimer functions as a molecular staple between neighbouring capsomeres to ensure the particle's stability. Beyond epsilon15, this method potentially offers a new approach for modelling the backbone conformations of the protein subunits in other macromolecular assemblies at near-native solution states. PMID:18305544

Jiang, Wen; Baker, Matthew L; Jakana, Joanita; Weigele, Peter R; King, Jonathan; Chiu, Wah



Backbone modification of nucleic acids: synthesis, structure and therapeutic applications.  


Nucleic acids have been extensively modified by replacing the phosphodiester group or the whole sugar phosphodiester with alternative anionic, neutral and cationic structures. Several of these modified oligonucleotides exhibit improved properties including enhanced recognition and binding to RNA, duplex DNA and proteins. This has resulted in the development of new and more potent antisense and antigene agents, as well as aptamers. Furthermore, backbone modified oligonucleotides have also been used in the development of several alternative strategies, which rely on altogether different mechanisms of action and show significant promise for therapeutic intervention. In this review the latest advances in the synthesis and evaluation of the most promising backbone modified oligos will be discussed, with a view to their future as novel pharmaceuticals. PMID:11472234

Micklefield, J



Economic and policy analysis of mergers among Internet backbone providers  

Microsoft Academic Search

The increasing record of mergers and acquisitions in the Internet backbone provider marketraises concern among the Internet community regarding market concentration and potentialmonopoly power abuse. The question addressed in this thesis is whether mergers among Internetbackbone providers should be regulated.To tackle this question, two methodologies are used:- An economic cost\\/benefit analysis mainly based on the MCI WorldCom Sprint proposedmerger using

Beatrice Cossa



Energy-Efficient Virtual Backbones for Reception-Aware MANET  

Microsoft Academic Search

A simple, yet popular way to design energy-efficient routing for Mobile Ad Hoc Networks (MANET) is to use a virtual backbone that forms a minimum sized Connected Dominating Set (CDS) of the network topology. By minimising the number of forwarding nodes, it looks at extending the (battery-dependent) life-span of the network by minimising the number (and energy cost) of transmitting

Joanne Lee; Bernard Mans



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



Minimum interference algorithm for integrated topology control and routing in wireless optical backbone networks  

Microsoft Academic Search

We consider a wireless backbone network with free space optical point-to-point links. Each backbone node has a limited number of transceivers with which to establish links to neighbors. Requests for aggregate bandwidth between pairs of backbone nodes arrive one-by-one and future demands are unknown. When a demand arrives, a bandwidth guaranteed path is established between the source and destination backbone

Fangting Sun; Mark Shayman



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 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



Predicting secretory proteins of malaria parasite by incorporating sequence evolution information into pseudo amino acid composition via grey system model.  


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 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. PMID:23189138

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



Evolution of the structure and composition of house mouse satellite DNA sequences in the subgenus Mus (Rodentia: Muridea): a cytogenomic approach.  


The composition and orientation of the house mouse satellite DNA sequences (minor, major, TLC) were investigated by a FISH and CO-FISH approach in 11 taxa belonging to three clades of the subgenus Mus. Using a phylogenetic framework, our results highlighted two distribution patterns. The TLC satellite, the most recently discovered satellite, was present in all clades but varied quantitatively among species. This distribution supported its appearance in the ancestor of the subgenus followed by independent evolution in species of each clade. In contrast, the minor and major satellites occurred in only two clades of the subgenus indicating the simultaneous and recent amplification of these sequences. In addition, although qualitative differences in the composition and orientation of the satellite sequences were observed among the taxa, none of the features studied were unique to the house mouse and could account for the extensive chromosomal plasticity evidenced in Mus musculus domesticus. PMID:23515652

Cazaux, B; Catalan, J; Justy, F; Escudé, C; Desmarais, E; Britton-Davidian, J



Malate dehydrogenase from the thermophilic green bacterium Chloroflexus aurantiacus: purification, molecular weight, amino acid composition, and partial amino acid sequence.  

PubMed Central

Malate dehydrogenase (MDH; EC from the thermophilic green nonsulfur bacterium Chloroflexus aurantiacus was purified by a two-step procedure involving affinity chromatography and gel filtration. The enzyme consists of identical subunits which had molecular weights of approximately 35,000. In its active form at 55 degrees C, it formed tetramers. At lower temperatures, inactive dimers and trimers existed. Antibodies against the purified enzyme were produced, and immunotitration and enzyme-linked immunosorbent assays showed that there was an immunochemical homology between the MDH from C. aurantiacus and MDHs from several other bacteria. The amino acid composition of C. aurantiacus MDH was similar to those of other MDHs. The N-terminal amino acid sequence was enriched with hydrophobic amino acids, which showed a high degree of functional similarity to amino acids at the N-terminal ends of both Escherichia coli and Thermus flavus MDHs. The activity of the native enzyme was inhibited by high concentrations of substrate and had temperature and pH optima consistent with the optimal growth conditions for the organism. Images

Rolstad, A K; Howland, E; Sirevag, R



Native protein sequences are close to optimal for their structures  

Microsoft Academic Search

How large is the volume of sequence space that is compatible with a given protein structure? Starting from random sequences, low free energy sequences were generated for 108 protein backbone structures by using a Monte Carlo optimization procedure and a free energy function based primarily on Lennard-Jones packing interactions and the Lazaridis-Karplus implicit solvation model. Remarkably, in the designed sequences

Brian Kuhlman; David Baker



Assigning Backbone NMR Resonances for Full Length Tau Isoforms: Efficient Compromise between Manual Assignments and Reduced Dimensionality  

PubMed Central

Tau protein is the longest disordered protein for which nearly complete backbone NMR resonance assignments have been reported. Full-length tau protein was initially assigned using a laborious combination of bootstrapping assignments from shorter tau fragments and conventional triple resonance NMR experiments. Subsequently it was reported that assignments of comparable quality could be obtained in a fully automated fashion from data obtained using reduced dimensionality NMR (RDNMR) experiments employing a large number of indirect dimensions. Although the latter strategy offers many advantages, it presents some difficulties if manual intervention, confirmation, or correction of the assignments is desirable, as may often be the case for long disordered and degenerate polypeptide sequences. Here we demonstrate that nearly complete backbone resonance assignments for full-length tau isoforms can be obtained without resorting either to bootstrapping from smaller fragments or to very high dimensionality experiments and automation. Instead, a set of RDNMR triple resonance experiments of modest dimensionality lend themselves readily to efficient and unambiguous manual assignments. An analysis of the backbone chemical shifts obtained in this fashion indicates several regions in full length tau with a notable propensity for helical or strand-like structure that are in good agreement with previous observations.

Harbison, Nicholas W.; Bhattacharya, Shibani; Eliezer, David



A unique signal distorts the perception of species richness and composition in high-throughput sequencing surveys of microbial communities: a case study of fungi in indoor dust.  


Sequence-based surveys of microorganisms in varied environments have found extremely diverse assemblages. A standard practice in current high-throughput sequence (HTS) approaches in microbial ecology is to sequence the composition of many environmental samples at once by pooling amplicon libraries at a common concentration before processing on one run of a sequencing platform. Biomass of the target taxa, however, is not typically determined prior to HTS, and here, we show that when abundances of the samples differ to a large degree, this standard practice can lead to a perceived bias in community richness and composition. Fungal signal in settled dust of five university teaching laboratory classrooms, one of which was used for a mycology course, was surveyed. The fungal richness and composition in the dust of the nonmycology classrooms were remarkably similar to each other, while the mycology classroom was dominated by abundantly sporulating specimen fungi, particularly puffballs, and appeared to have a lower overall richness based on rarefaction curves and richness estimators. The fungal biomass was three to five times higher in the mycology classroom than the other classrooms, indicating that fungi added to the mycology classroom swamped the background fungi present in indoor air. Thus, the high abundance of a few taxa can skew the perception of richness and composition when samples are sequenced to an even depth. Next, we used in silico manipulations of the observed data to confirm that a unique signature can be identified with HTS approaches when the source is abundant, whether or not the taxon identity is distinct. Lastly, aerobiology of indoor fungi is discussed. PMID:23880792

Adams, Rachel I; Amend, Anthony S; Taylor, John W; Bruns, Thomas D



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



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.



Long-term forecasting of internet backbone traffic.  


We introduce a methodology to predict when and where link additions/upgrades have to take place in an Internet protocol (IP) backbone network. Using simple network management protocol (SNMP) statistics, collected continuously since 1999, we compute aggregate demand between any two adjacent points of presence (PoPs) and look at its evolution at time scales larger than 1 h. We show that IP backbone traffic exhibits visible long term trends, strong periodicities, and variability at multiple time scales. Our methodology relies on the wavelet multiresolution analysis (MRA) and linear time series models. Using wavelet MRA, we smooth the collected measurements until we identify the overall long-term trend. The fluctuations around the obtained trend are further analyzed at multiple time scales. We show that the largest amount of variability in the original signal is due to its fluctuations at the 12-h time scale. We model inter-PoP aggregate demand as a multiple linear regression model, consisting of the two identified components. We show that this model accounts for 98% of the total energy in the original signal, while explaining 90% of its variance. Weekly approximations of those components can be accurately modeled with low-order autoregressive integrated moving average (ARIMA) models. We show that forecasting the long term trend and the fluctuations of the traffic at the 12-h time scale yields accurate estimates for at least 6 months in the future. PMID:16252820

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



Origin of the neighboring residue effect on peptide backbone conformation.  


Unfolded peptides in water have some residual structure that may be important in the folding process, and the nature of the residual structure is currently of much interest. There is a neighboring residue effect on backbone conformation, discovered in 1997 from measurements of (3)J(HN alpha) coupling constants. The neighboring residue effect appears also in the "coil library" of Protein Data Bank structures of residues not in alpha-helix and not in beta-structure. When a neighboring residue (i - 1 or i + 1) belongs to class L (aromatic and beta-branched amino acids, FHITVWY) rather than class S (all others, G and P excluded), then the backbone angle of residue i is more negative for essentially all amino acids. Calculated values of peptide solvation (electrostatic solvation free energy, ESF) predict basic properties of the neighboring residue effect. We show that L amino acids reduce the solvation of neighboring peptide groups more than S amino acids. When tripeptides from the coil library are excised to allow solvation, the central residues have more negative values of but less negative values of with L than with S neighbors. The coil library values of <(3)J(HN alpha)>, which vary strikingly among the amino acids, are correlated with the neighboring residue effect seen by ESF. Moreover, values for the "blocking effect" of side chains on the hydrogen exchange rates of peptide NH protons are correlated with ESF values. PMID:15254296

Avbelj, Franc; Baldwin, Robert L



Strong liquid-crystalline polymeric compositions  


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)



Strong liquid-crystalline polymeric compositions  


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.



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


In this contribution, we present an algorithm for protein backbone reconstruction that comprises very high computational efficiency with high accuracy. Reconstruction of the main chain atomic coordinates from the alpha carbon trace is a common task in protein modeling, including de novo structure prediction, comparative modeling, and processing experimental data. The method employed in this work follows the main idea of some earlier approaches to the problem. The details and careful design of the present approach are new and lead to the algorithm that outperforms all commonly used earlier applications. BBQ (Backbone Building from Quadrilaterals) program has been extensively tested both on native structures as well as on near-native decoy models and compared with the different available existing methods. Obtained results provide a comprehensive benchmark of existing tools and evaluate their applicability to a large scale modeling using a reduced representation of protein conformational space. The BBQ package is available for downloading from our website at This webpage also provides a user manual that describes BBQ functions in detail. PMID:17342707

Gront, Dominik; Kmiecik, Sebastian; Kolinski, Andrzej



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


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

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



Maximizing open capacity in mobile optical backbone networks using controllable mobile agents  

Microsoft Academic Search

We consider a mobile backbone network with free space optical point-to-point links. 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; otherwise, the request is rejected. In addition to the ordinary backbone nodes, there are a limited number of controllable mobile agents; these are nodes

Fangting Sun; Abhishek Kashyap; Mark Shayman



Probing backbone dynamics with hydrogen/deuterium exchange mass spectrometry.  


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



Probing backbone hydrogen bonds in the hydrophobic core of GCN4.  


Backbone amide hydrogen bonds play a central role in protein secondary and tertiary structure. Previous studies have shown that substitution of a backbone ester (-COO-) in place of a backbone amide (-CONH-) can selectively destabilize backbone hydrogen bonds in a protein while maintaining a similar conformation to the native backbone structure. The majority of these studies have focused on backbone substitutions that were accessible to solvent. The GCN4 coiled coil domain is an example of a stable alpha-helical dimer that possesses a well-packed hydrophobic core. Amino acids in the a and d positions of the GCN4 helix, which pack the hydrophobic core, were replaced with the corresponding alpha-hydroxy acids in the context of a chemoselectively ligated heterodimer. While the overall structure and oligomerization state of the heterodimer were maintained, the overall destabilization of the ester analogues was greater (average DeltaDeltaG of 3+ kcal mol(-1)) and more variable than previous studies. Since burial of the more hydrophobic ester should stabilize the backbone and reduce the DeltaDeltaG, the increased destabilization must come from another source. However, the observed destabilization is correlated with the protection factors for individual amide hydrogens from previous hydrogen exchange experiments. Therefore, our results suggest that backbone engineering through ester substitution is a useful approach for probing the relative strength of backbone hydrogen bonds. PMID:12501196

Blankenship, John W; Balambika, Rema; Dawson, Philip E



Complex of B-DNA with polyamides freezes DNA backbone flexibility.  


The development of sequence-specific minor groove binding ligands is a modern and rapidly growing field of research because of their extraordinary importance as transcription-controlling drugs. We performed three molecular dynamics simulations in order to clarify the influence of minor groove binding of two ImHpPyPy-beta-Dp polyamides to the d(CCAGTACTGG)(2) decamer in the B-form. This decamer contains the recognition sequence for the trp repressor (5'-GTACT-3'), and it was investigated recently by X-ray crystallography. On one hand we are able to reproduce X-ray-determined DNA--drug contacts, and on the other hand we provide new contact information which is important for the development of potential ligands. The new insights show how the beta-tail of the polyamide ligands contributes to binding. Our simulations also indicate that complexation freezes the DNA backbone in a specific B(I) or B(II) substate conformation and thus optimizes nonbonded contacts. The existence of this distinct B(I)/B(II) substate pattern also allows the formation of water-mediated contacts. Thus, we suggest the B(I) <==> B(II) substate behavior to be an important part of the indirect readout of DNA. PMID:11457333

Wellenzohn, B; Flader, W; Winger, R H; Hallbrucker, A; Mayer, E; Liedl, K R



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


Protein backbone 15N NMR spin relaxation rates are useful in characterizing the protein dynamics and structures. To observe the protein nuclear-spin resonances a pulse sequence has to include a water suppression scheme. There are two commonly employed methods, saturating or dephasing the water spins with pulse field gradients and keeping them unperturbed with flip-back pulses. Here different water suppression methods were incorporated into pulse sequences to measure 15N longitudinal T1 and transversal rotating-frame T1? spin relaxation. Unexpectedly the 15N T1 relaxation time constants varied significantly with the choice of water suppression method. For a 25-kDa Escherichiacoli. glutamine binding protein (GlnBP) the T1 values acquired with the pulse sequence containing a water dephasing gradient are on average 20% longer than the ones obtained using a pulse sequence containing the water flip-back pulse. In contrast the two T1? data sets are correlated without an apparent offset. The average T1 difference was reduced to 12% when the experimental recycle delay was doubled, while the average T1 values from the flip-back measurements were nearly unchanged. Analysis of spectral signal to noise ratios (s/n) showed the apparent slower 15N relaxation obtained with the water dephasing experiment originated from the differences in 1HN recovery for each relaxation time point. This in turn offset signal reduction from 15N relaxation decay. The artifact becomes noticeable when the measured 15N relaxation time constant is comparable to recycle delay, e.g., the 15N T1 of medium to large proteins. The 15N relaxation rates measured with either water suppression schemes yield reasonable fits to the structure. However, data from the saturated scheme results in significantly lower Model-Free order parameters (=0.81) than the non-saturated ones (=0.88), indicating such order parameters may be previously underestimated. PMID:22015249

Chen, Kang; Tjandra, Nico



Synthesis, biophysical properties, and nuclease resistance properties of mixed backbone oligodeoxynucleotides containing cationic internucleoside guanidinium linkages: Deoxynucleic guanidine/DNA chimeras  

PubMed Central

The synthesis of mixed backbone oligodeoxynucleotides (18-mers) consisting of positively charged guanidinium linkages along with negatively charged phosphodiester linkages is carried out. The use of a base labile-protecting group for guanidinium linkage offers a synthetic strategy similar to standard oligonucleotide synthesis. The nuclease resistance of the oligodeoxyribonucleotides capped with guanidinium linkages at 5? and 3? ends are reported. The hybridization properties and sequence specificity of binding of these deoxynucleic guanidine/DNA chimeras with complementary DNA or RNA are described.

Barawkar, Dinesh A.; Bruice, Thomas C.



Mixed backbone antisense oligonucleotides: design, biochemical and biological properties of oligonucleotides containing 24-54-ribo- and 34-54-deoxyribonucleotide segments  

Microsoft Academic Search

We have designed and synthesized mixed backbone oligonucleotides (MBOs) containing 24-54-ribo- and 34-54-deoxyribonucleotide segments. Thermal melting studies of the phosphodiester MBOs (three 24-54 linkages at each end) with the complementary 34-54-DNA and -RNA target strands suggest that 24-54-ri- bonucleoside incorporation into 34-54-oligodeoxyri- bonucleotides reduces binding to the target strands compared with an all 34-54-oligodeoxyribonucleotide of the same sequence and length.

Ekambar R. Kandimalla; Adrienne Manning; Qiuyan Zhao; Denise R. Shaw; Randal A. Byrn; V. Sasisekharan; Sudhir Agrawal


Synthesis of rapid responsive gels comprising hydrophilic backbone and poly( N-isopropylacrylamide) graft chains by RAFT polymerization and end-linking processes  

Microsoft Academic Search

A thermosensitive poly(N-isopropylacrylamide) (PNIPAM) grafted gel, which comprises hydrophilic backbone and freely mobile PNIPAM graft chains, was synthesized by reversible addition fragmentation chain transfer (RAFT) polymerization and end-linking processes. Functional PNIPAM bearing dithiobenzoate end group (–C(S)S–R) was prepared first, and then it was reacted with divinyl compounds to obtain gel. In order to adjust the composition of the gels, two

Qunfeng Liu; Ping Zhang; Aixiang Qing; Yanxun Lan; Jianbo Shi; Mangeng Lu



5D 13C-detected experiments for backbone assignment of unstructured proteins with a very low signal dispersion.  


Two novel 5D NMR experiments (CACONCACO, NCOCANCO) for backbone assignment of disordered proteins are presented. The pulse sequences exploit relaxation properties of the unstructured proteins and combine the advantages of (13)C-direct detection, non-uniform sampling, and longitudinal relaxation optimization to maximize the achievable resolution and minimize the experimental time. The pulse sequences were successfully tested on the sample of partially disordered delta subunit from RNA polymerase from Bacillus subtilis. The unstructured part of this 20 kDa protein consists of 81 amino acids with frequent sequential repeats. A collection of 0.0003% of the data needed for a conventional experiment with linear sampling was sufficient to perform an unambiguous assignment of the disordered part of the protein from a single 5D spectrum. PMID:21424579

Nová?ek, Ji?í; Zawadzka-Kazimierczuk, Anna; Papoušková, Veronika; Zídek, Lukáš; Sanderová, Hana; Krásný, Libor; Ko?mi?ski, Wiktor; Sklená?, Vladimír



Performance evaluation by petri nets of a full duplex wireless link for an industrial backbone  

Microsoft Academic Search

This paper addresses the performance evaluation of a full duplex wireless protocol for an industrial backbone making a comparison with the traditional IEEE802.11 half duplex protocol. A Petri net model is used as the basis for the evaluation. The paper first examines the features of a wireless backbone and some issues they impose. Then, the paper describes the limits of

O. Mirabella; M. Brischetto; A. Raucea



Implementation and Experiments of Path Computation Element Based Backbone Network Architecture  

NASA Astrophysics Data System (ADS)

This paper proposes the Path Computation Element (PCE)-based backbone network architecture and verifies its feasibility through implementation and experiments. PCE communication Protocol (PCEP) is implemented for communication between the PCE and the management system to control and manage Generalized Multi-Protocol Label Switching (GMPLS)-based backbone networks.

Takeda, Tomonori; Oki, Eiji; Inoue, Ichiro; Shiomoto, Kohei; Fujihara, Kazuhiro; Kato, Shin-Ichi


Controlling the secondary-structure-forming tendencies of proteins by a backbone torsion-energy term  

Microsoft Academic Search

We examined a new backbone torsion-energy term proposed by us in the force field for protein systems. This torsion-energy term is represented by a double Fourier series in two variables, namely the backbone dihedral angles ? and ?. It gives a natural representation of the torsion energy in the Ramachandran space in the sense that any two-dimensional energy surface periodic

Yoshitake Sakae; Yuko Okamoto



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



DNA Sequence Analysis of Regions Surrounding blaCMY-2 from Multiple Salmonella Plasmid Backbones  

Microsoft Academic Search

The emergence in the United States of resistance to expanded-spectrum cephalosporin (e.g., ceftriaxone) within the salmonellae has been associated primarily with three large (>100-kb) plasmids (designated types A, B, and C) and one 10.1-kb plasmid (type D) that carry the blaCMY-2 gene. In the present study, the distri- bution of these four known blaCMY-2-carrying plasmids among 35 ceftriaxone-resistant Salmonella isolates

W. P. Giles; A. K. Benson; M. E. Olson; R. W. Hutkins; J. M. Whichard; P. L. Winokur; P. D. Fey



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

SciTech Connect

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

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



RDC derived protein backbone resonance assignment using fragment assembly.  


Experimental residual dipolar couplings (RDCs) in combination with structural models have the potential for accelerating the protein backbone resonance assignment process because RDCs can be measured accurately and interpreted quantitatively. However, this application has been limited due to the need for very high-resolution structural templates. Here, we introduce a new approach to resonance assignment based on optimal agreement between the experimental and calculated RDCs from a structural template that contains all assignable residues. To overcome the inherent computational complexity of such a global search, we have adopted an efficient two-stage search algorithm and included connectivity data from conventional assignment experiments. In the first stage, a list of strings of resonances (CA-links) is generated via exhaustive searches for short segments of sequentially connected residues in a protein (local templates), and then ranked by the agreement of the experimental (13)C(?) chemical shifts and (15)N-(1)H RDCs to the predicted values for each local template. In the second stage, the top CA-links for different local templates in stage I are combinatorially connected to produce CA-links for all assignable residues. The resulting CA-links are ranked for resonance assignment according to their measured RDCs and predicted values from a tertiary structure. Since the final RDC ranking of CA-links includes all assignable residues and the assignment is derived from a "global minimum", our approach is far less reliant on the quality of experimental data and structural templates. The present approach is validated with the assignments of several proteins, including a 42 kDa maltose binding protein (MBP) using RDCs and structural templates of varying quality. Since backbone resonance assignment is an essential first step for most of biomolecular NMR applications and is often a bottleneck for large systems, we expect that this new approach will improve the efficiency of the assignment process for small and medium size proteins and will extend the size limits assignable by current methods for proteins with structural models. PMID:21191805

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



The Contributions of Replication Orientation, Gene Direction, and Signal Sequences to Base-Composition Asymmetries in Bacterial Genomes  

Microsoft Academic Search

.   Asymmetries in base composition between the leading and the lagging strands have been observed previously in many prokaryotic\\u000a genomes. Since a majority of genes is encoded on the leading strand in these genomes, previous analyses have not been able\\u000a to determine the relative contribution to the base composition skews of replication processes and transcriptional and\\/or translational\\u000a forces. Using qualitative

Elisabeth R. M. Tillier; Richard A. Collins



Syntheses and structural diversity of salicylideneaniline derivatives with cobaltadithiolene backbone  

NASA Astrophysics Data System (ADS)

Salicylideneaniline (SA) or benzylideneaniline (BA) derivatives with [CpCo(dithiolene)] backbone, which are formulated as [CpCo(S2C2(H)(R))] (R = 5-chlorosalicylideneaniline (2a), salicylideneaniline (2b), benzylideneaniline (2c) and 3,5-di-t-butylsalicylideneaniline (2d)), were prepared from the aniline precursor [CpCo(S2C2(H)(C6H4-NH2))] (1) and the corresponding aldehydes. 1 and 2a-2d were identified with spectral data and electrochemical redox potentials. 1 and 2a-2c were structurally determined by X-ray diffraction studies. 1 and 2a showed dithiolene-H\\ctdot X hydrogen bondings (X = N (1), O (2a)), because the dithiolene proton is usually acidic (ca. 9 ppm by 1H NMR). In 2a-2c, the dihedral angles between two benzene rings (?1) in the SA (or BA) moieties were depending on the substituents on these benzene rings. 2a has small ?1 angle (7.321°) and the result indicates a short intramolecular OH···N hydrogen bonding distance (1.743 Å). In the crystal of 2b (or 2c), there are two (or four) crystallographically independent molecules, and their ?1 angles are different by the flexible SA (or BA) unit. The crystal 2b contains a non-planar molecule (?1 = 37.043°) and a relatively planar molecule (?1 = 22.822°) as well.

Nomura, Mitsushiro; Nakamura, Tomoko; Kashimura, Yohei; Sugiyama, Toru; Kajitani, Masatsugu



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

SciTech Connect

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

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



Coordination polymers containing ferrocene backbone. Synthesis, structure and electrochemistry.  


The reaction of 1,1'-ferrocenedicarboxylic acid (LH(2)) with bis(triphenyltin) oxide afforded a molecular heterobimetallic compound [(Ph(3)Sn)(2)L]. In the latter the two carboxylate units of [L](2-) are involved in an anisobidentate chelating coordination mode to two triphenyl tin units. The reaction of LH(2) with trimethyltin hydroxide or bis(tri-n-butyltin) oxide afforded 2D-coordination polymers [(Me(3)Sn)(2)L](n) and [(n-Bu(3)Sn)(2)L](n) which are formed as a result of anisobidentate bridging coordination action of the two carboxylate units of [L](2-). Interestingly the 2D-coordination polymers contain 24-membered macrocycles each of which is comprised of four trialkyl tin units. The coordination unsaturation of [(Ph(3)Sn)(2)L] can be utilized to form coordination polymers. Accordingly the reaction of LH(2) with bis(triphenyltin) oxide in the presence of ditopic nitrogen ligands such as 4,4'-bipyridine, 4,4'-trimethylenebipyridine or 4,4'-vinylenebipyridine afforded one-dimensional coordination polymers which contain in their backbone three distinct structural components viz., two triorganotin units, a ferrocenyl unit and a bridging nitrogen ligand unit. The coordination polymers, however, do not retain their structural integrity in solution and fall apart to their monomeric units. Electrochemical studies on these hybrid orgaonotin/ferrocene systems reveal that most of them exhibit a single quasi-reversible oxidation peak. PMID:20179864

Chandrasekhar, Vadapalli; Thirumoorthi, Ramalingam



Compositional variations across a dunite - harzburgite - lherzolite - plagioclase lherzolite sequence at the Trinity ophiolite: Evidence for multiple episodes of melt flow and melt-rock reaction in the mantle  

Microsoft Academic Search

In the preceding report we showed experimentally that the dunite-harzburgite-lherzolite (DHL) sequence found in the mantle sections of ophiolite could be formed by reactive dissolution of lherzolite in a basaltic liquid. The most striking results of our lherzolite dissolution experiments are the sharp mineralogical boundaries between adjacent lithologies and simple monotonic composition variations in minerals across the DHL sequence. Here

Z. T. Morgan; Y. Liang; P. Kelemen



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



4D experiments measured with APSY for automated backbone resonance assignments of large proteins.  


Detailed structural and functional characterization of proteins by solution NMR requires sequence-specific resonance assignment. We present a set of transverse relaxation optimization (TROSY) based four-dimensional automated projection spectroscopy (APSY) experiments which are designed for resonance assignments of proteins with a size up to 40 kDa, namely HNCACO, HNCOCA, HNCACB and HN(CO)CACB. These higher-dimensional experiments include several sensitivity-optimizing features such as multiple quantum parallel evolution in a 'just-in-time' manner, aliased off-resonance evolution, evolution-time optimized APSY acquisition, selective water-handling and TROSY. The experiments were acquired within the concept of APSY, but they can also be used within the framework of sparsely sampled experiments. The multidimensional peak lists derived with APSY provided chemical shifts with an approximately 20 times higher precision than conventional methods usually do, and allowed the assignment of 90 % of the backbone resonances of the perdeuterated primase-polymerase ORF904, which contains 331 amino acid residues and has a molecular weight of 38.4 kDa. PMID:23625454

Krähenbühl, Barbara; Boudet, Julien; Wider, Gerhard



Temperature dependence of protein backbone motion from carbonyl 13C and amide 15N NMR relaxation  

NASA Astrophysics Data System (ADS)

The NMR spin lattice relaxation rate (R1) and the rotating-frame spin lattice relaxation rate (R1?) of amide 15N and carbonyl 13C (13C?) of the uniformly 13C- and 15N-labeled ubiquitin were measured at different temperatures and field strengths to investigate the temperature dependence of overall rotational diffusion and local backbone motion. Correlation between the order parameter of the N H vector, SNH2, and that of the carbonyl carbon, SC2, was investigated. The effective SC2 was estimated from the direct fit of the experimental relaxation rates and from the slope of 2R2 - R1 vs. B2 using Lipari Szabo formalism. The average SNH2 decreased by 5.9%, while the average SC2 decreased by 4.6% from 15 to 47 °C. At the extreme low and high temperatures the difference in the temperature dependence of the order parameters vanishes. At the intermediate temperatures they do not change by the same amount but they follow the same trend. On the same peptide plane along the protein sequence, SC2 and SNH2 are highly correlated. The results suggest that fast local motion experienced at the site of the N H vector and carbonyl nucleus is more complicated than previously thought and it cannot be easily described by one single type of motion in a broad range of temperature.

Chang, Shou-Lin; Tjandra, Nico



Evaluation of diverse ?/?-backbone patterns for functional ?-helix mimicry: analogues of the Bim BH3 domain.  


Peptidic oligomers that contain both ?- and ?-amino acid residues, in regular patterns throughout the backbone, are emerging as structural mimics of ?-helix-forming conventional peptides (composed exclusively of ?-amino acid residues). Here we describe a comprehensive evaluation of diverse ?/?-peptide homologues of the Bim BH3 domain in terms of their ability to bind to the BH3-recognition sites on two partner proteins, Bcl-x(L) and Mcl-1. These proteins are members of the anti-apoptotic Bcl-2 family, and both bind tightly to the Bim BH3 domain itself. All ?/?-peptide homologues retain the side-chain sequence of the Bim BH3 domain, but each homologue contains periodic ?-residue ? ?(3)-residue substitutions. Previous work has shown that the ??????? pattern, which aligns the ?(3)-residues in a 'stripe' along one side of the helix, can support functional ?-helix mimicry, and the results reported here strengthen this conclusion. The present study provides the first evaluation of functional mimicry by ??? and ???? patterns, which cause the ?(3)-residues to spiral around the helix periphery. We find that the ???? pattern can support effective mimicry of the Bim BH3 domain, as manifested by the crystal structure of an ?/?-peptide bound to Bcl-x(L), affinity for a variety of Bcl-2 family proteins, and induction of apoptotic signaling in mouse embryonic fibroblast extracts. The best ???? homologue shows substantial protection from proteolytic degradation relative to the Bim BH3 ?-peptide. PMID:22040025

Boersma, Melissa D; Haase, Holly S; Peterson-Kaufman, Kimberly J; Lee, Erinna F; Clarke, Oliver B; Colman, Peter M; Smith, Brian J; Horne, W Seth; Fairlie, W Douglas; Gellman, Samuel H



Effect of a neutralized phosphate backbone on the minor groove of B-DNA: molecular dynamics simulation studies  

PubMed Central

Alternative models have been presented to provide explanations for the sequence-dependent variation of the DNA minor groove width. In a structural model groove narrowing in A-tracts results from direct, short-range interactions among DNA bases. In an electrostatic model, the narrow minor groove of A-tracts is proposed to respond to sequence-dependent localization of water and cations. Molecular dynamics simulations on partially methylphosphonate substituted helical chains of d(TATAGGCCTATA) and d(CGCGAATTCGCG) duplexes have been carried out to help evaluate the effects of neutralizing DNA phosphate groups on the minor groove width. The results show that the time-average minor groove width of the GGCC duplex becomes significantly more narrow on neutralizing the phosphate backbone with methylphosphonates. The minor groove of the AATT sequence is normally narrow and the methylphosphonate substitutions have a smaller but measurable affect on this sequence. These results and models provide a system that can be tested by experiment and they support the hypothesis that the electrostatic environment around the minor groove affects the groove width in a sequence-dependent dynamic and time-average manner.

Hamelberg, Donald; Williams, Loren Dean; Wilson, W. David



Chlorobenzoate Catabolic Transposon Tn5271 is a Composite Class I Element with Flanking Class II Insertion Sequences  

Microsoft Academic Search

The structure of a transposon specifying the biodegradation of chlorobenzoate contaminants is described. Tn5271 is a 17-kilobase (kb) transposon that resides in the plasmid or chromosome of Alcaligenes sp. strain BR60 and allows this organism to grow on 3- and 4-chlorobenzoate. The transposon is flanked by a directly repeated sequence of 3201 base pairs (bp), which in turn is flanked

Cindy Nakatsu; James Ng; Rama Singh; Neil Straus; Campbell Wyndham



Trophozoite and nuclear size, DNA base composition, and nucleotide sequence homology of several Entamoeba strains in axenic culture  

Microsoft Academic Search

We carried out a comparative study of nuclear and trophozoite diameters and of DNA thermal denaturation in eight Entamoeba strains cultured axenically (four of them E. histolytica, two initially designated as E. invadens, one E. moshkovskii, and one E. histolytica-like), as well as an analysis of the overall DNA sequence homology of the non-E. histolytica strains. The average nuclear (N)

R. López-Revilla; R. Gómez-Domínguez



Backbone cyclic peptide antagonists, derived from the insect pheromone biosynthesis activating neuropeptide, inhibit sex pheromone biosynthesis in moths.  


We describe an application of the backbone cyclization and cycloscan concept for the design and synthesis of pheromone biosynthesis activating neuropeptide (PBAN) antagonists capable of inhibiting sex pheromone biosynthesis in Heliothis peltigera female moths. Two backbone cyclic (BBC) sub-libraries were designed and synthesized. The structure of the first sub-library ([Arg27]PBAN27-33NH2, termed the Ser sub-library) was based on the active C-terminal hexapeptide sequence (Tyr-Phe-Ser-Pro-Arg-Leu-NH2) of PBAN1-33NH2, which was found to comprise its active core. The second sub-library ([Arg27, D-Phe30]PBAN27-33NH2, termed the D-Phe sub-library) was based on the sequence of the lead antagonist Arg-Tyr-Phe-(D)Phe-Pro-Arg-Leu-NH2. In both sub-libraries the Pro residue was replaced by an Nalpha(omega-amino-alkyl)Gly building unit having various lengths of the alkyl chain. All the cyclic peptides in each sub-library had the same primary sequence and the same location of the ring. The members of each library differed from each other by the bridge size and bridge chemistry. Screening of the two libraries for pheromonotropic antagonists resulted in the disclosure of four compounds that fully inhibited sex pheromone biosynthesis at 1 nmol and were devoid of agonistic activity. All antagonistic peptides originated from the D-Phe sub-library. Substitution of the D-Phe30 amino acid with a Ser resulted in a loss of antagonistic activity. Agonistic activities were exhibited by peptides from both sub-libraries. PMID:10364192

Altstein, M; Ben-Aziz, O; Daniel, S; Schefler, I; Zeltser, I; Gilon, C



Ruthenium-catalyzed olefin metathesis accelerated by the steric effect of the backbone substituent in cyclic (alkyl)(amino) carbenes.  


Three ruthenium complexes bearing backbone-monosubstituted CAACs were prepared and displayed dramatic improvement in catalytic efficiency not only in RCM reaction but also in the ethenolysis of methyl oleate, compared to those bearing backbone-disubstituted CAACs. PMID:24013192

Zhang, Jun; Song, Shangfei; Wang, Xiao; Jiao, Jiajun; Shi, Min



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



A precise reconstruction of the emergence and constrained radiations of Escherichia coli O157 portrayed by backbone concatenomic analysis  

PubMed Central

Single nucleotide polymorphisms (SNPs) in stable genome regions provide durable measurements of species evolution. We systematically identified each SNP in concatenations of all backbone ORFs in 7 newly or previously sequenced evolutionarily instructive pathogenic Escherichia coli O157:H7, O157:H?, and O55:H7. The 1,113 synonymous SNPs demonstrate emergence of the largest cluster of this pathogen only in the last millennium. Unexpectedly, shared SNPs within circumscribed clusters of organisms suggest severely restricted survival and limited effective population sizes of pathogenic O157:H7, tenuous survival of these organisms in nature, source-sink evolutionary dynamics, or, possibly, a limited number of mutations that confer selective advantage. A single large segment spanning the rfb-gnd gene cluster is the only backbone region convincingly acquired by recombination as O157 emerged from O55. This concatenomic analysis also supports using SNPs to differentiate closely related pathogens for infection control and forensic purposes. However, constrained radiations raise the possibility of making false associations between isolates.

Leopold, Shana R.; Magrini, Vincent; Holt, Nicholas J.; Shaikh, Nurmohammad; Mardis, Elaine R.; Cagno, Joseph; Ogura, Yoshitoshi; Iguchi, Atsushi; Hayashi, Tetsuya; Mellmann, Alexander; Karch, Helge; Besser, Thomas E.; Sawyer, Stanley A.; Whittam, Thomas S.; Tarr, Phillip I.



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.



MCBT: Multi-Hop Cluster Based Stable Backbone Trees for Data Collection and Dissemination in WSNs.  


We propose a stable backbone tree construction algorithm using multi-hop clusters for wireless sensor networks (WSNs). The hierarchical cluster structure has advantages in data fusion and aggregation. Energy consumption can be decreased by managing nodes with cluster heads. Backbone nodes, which are responsible for performing and managing multi-hop communication, can reduce the communication overhead such as control traffic and minimize the number of active nodes. Previous backbone construction algorithms, such as Hierarchical Cluster-based Data Dissemination (HCDD) and Multicluster, Mobile, Multimedia radio network (MMM), consume energy quickly. They are designed without regard to appropriate factors such as residual energy and degree (the number of connections or edges to other nodes) of a node for WSNs. Thus, the network is quickly disconnected or has to reconstruct a backbone. We propose a distributed algorithm to create a stable backbone by selecting the nodes with higher energy or degree as the cluster heads. This increases the overall network lifetime. Moreover, the proposed method balances energy consumption by distributing the traffic load among nodes around the cluster head. In the simulation, the proposed scheme outperforms previous clustering schemes in terms of the average and the standard deviation of residual energy or degree of backbone nodes, the average residual energy of backbone nodes after disseminating the sensed data, and the network lifetime. PMID:22454570

Shin, Inyoung; Kim, Moonseong; Mutka, Matt W; Choo, Hyunseung; Lee, Tae-Jin



Compositional analysis of re-refined and non-conventional lubricant base oils. Correlations to sequence VE and IIIE gasoline engine tests  

SciTech Connect

In 1993, a Presidential Executive Order was issued requiring that federal agencies purchase lubricants containing at least 25% re-refined base oil. In light of this initiative, we have undertaken a program to characterize the chemical composition of re-refined base stocks, provided by a number of manufacturers, using column chromatography coupled with mass spectrometry techniques. The hydrocarbon-type distribution observed for the re-refined oils provides an index of their relative quality when benchmarked against conventionally processed `virgin` and certain non-conventional, high viscosity index (VI) base oils. Using statistical models which can predict lubricant performance in the ASTM Sequence VE and IIIE Gasoline Engine Tests from base oil compositional features and VI, it was determined that highly paraffinic synthetic and non-conventional base oils provide enhanced performance while re-refined oils generally exhibit predicted behavior comparable to an `average` `virgin` base oil, for most commercially available products. Sequence VE and IIIE test parameter predictions were found to be especially sensitive to the thioaromatic and multiring aromatic content of the base oil under evaluation. 11 refs., 5 figs., 6 tabs.

Stipanovic, A.J.; Smith, M.P.; Firmstone, G.P.; Patel, J.A.



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

SciTech Connect

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

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



Stretching single polypeptides: The effect of rotational constraints in the backbone  

NASA Astrophysics Data System (ADS)

Polypeptides consist of three types of backbone bonds that are distinguished by the degree to which their dihedral rotation is hindered. We discuss the effect of this inhomogeneous rotational restriction on the stretching response as measurable by single-molecule force spectroscopic experiments. The ab initio-derived molecular backbone structure yields geometric input parameters. For the cases where one or two out of three bonds are rotationally frozen, which are two extreme cases of the actual peptidic backbone statistics, we derive analytic and numerical results and show that the Kuhn and persistence lengths are substantially increased. A simple explicit formula is derived that accurately describes the extension over the entire force range.

Hanke, F.; Serr, A.; Kreuzer, H. J.; Netz, R. R.



Compositional sequence distribution and second-order Markov statistics in vinyl chloride-vinylidene chloride copolymers by Carbon13 NMR  

Microsoft Academic Search

Summary 90 MHz-1H-NMR and 22.635 MHz-13C-NMR spectroscopy were used in a study of vinyl chloride-vinylidene chloride co-polymers. Triad sequence distribution of CCl2 and CHCl carbon was generated for these copolymers and compared to calculated distributions based on Bernoullian, first-order Markov and second-order Markov statistics. It was observed that for samples different in the conditions of preparation including commercial materials in

K. Schlothauer; F. Keller; H. Schneider; B. Wandelt



Enhanced immunogenicity of a sequence derived from hepatitis B virus surface antigen in a composite peptide that includes the immunostimulatory region from human interleukin 1.  

PubMed Central

The effect on immunogenicity of coupling the immunostimulatory nonapeptide sequence (residues 163-171) from human interleukin 1 beta (IL-1 beta) to a small immunogen was examined. A 21-amino acid sequence spanning positions 12-32 on the large protein of hepatitis B surface antigen was chosen as a model. Three peptides were synthesized corresponding to the IL-1 beta-derived sequence [peptide IL-(163-171)], the hepatitis B surface antigen-derived sequence [peptide S1-(12-32)] and a composite peptide that included both these sequences separated by a spacer of two glycine residues [peptide S1-(12-32)-IL-(163-171)]. In an in vitro thymocyte proliferation assay, both peptides S1-(12-32)-IL-(163-171) and IL-(163-171) showed comparable activity, whereas peptide S1-(12-32) was inactive. Groups of five to seven mice each from C3H/CH, BALB/c, SJL/J, and C57BL/6 strains were immunized with equimolar amounts of either peptide S1-(12-32), peptide S1-(12-32)-IL-(163-171), or a mixture of peptides S1-(12-32) and IL-(163-171), and sera were screened for anti-S1-(12-32) antibodies. In all strains, peptide S1-(12-32)-IL-(163-171) elicited an increased primary and secondary anti-S1-(12-32) antibody response compared to the other two groups. Further, peptide S1-(12-32)-IL-(163-171) also induced an increased number of responders to primary immunization, though the number of responders was quantitative in all groups following secondary immunization. At least part of the enhanced immunogenicity of the S1-(12-32) sequence in peptide S1-(12-32)-IL-(163-171) appears to be due to augmented T-helper cell activity. These results suggest that coupling of the immunostimulatory IL-1 beta-derived sequence in tandem with an immunogen may confer inbuilt adjuvanticity.

Rao, K V; Nayak, A R



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

PubMed Central

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

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



A comprehensive library of blocked dipeptides reveals intrinsic backbone conformational propensities of unfolded proteins.  


Despite prolonged scientific efforts to elucidate the intrinsic peptide backbone preferences of amino-acids based on understanding of intermolecular forces, many open questions remain, particularly concerning neighboring peptide interaction effects on the backbone conformational distribution of short peptides and unfolded proteins. Here, we show that spectroscopic studies of a complete library of 400 dipeptides reveal that, irrespective of side-chain properties, the backbone conformation distribution is narrow and they adopt polyproline II and ?-strand, indicating the importance of backbone peptide solvation and electronic effects. By directly comparing the dipeptide circular dichroism and NMR results with those of unfolded proteins, the comprehensive dipeptides form a complete set of structural motifs of unfolded proteins. We thus anticipate that the present dipeptide library with spectroscopic data can serve as a useful database for understanding the nature of unfolded protein structures and for further refinements of molecular mechanical parameters. PMID:22223291

Oh, Kwang-Im; Lee, Kyung-Koo; Park, Eun-Kyung; Jung, Youngae; Hwang, Geum-Sook; Cho, Minhaeng



Backbone structure of the Edwards-Anderson spin-glass model  

NASA Astrophysics Data System (ADS)

We study the ground-state spatial heterogeneities of the Edwards-Anderson spin-glass model with both bimodal and Gaussian bond distributions. We characterize these heterogeneities by using a general definition of bond rigidity, which allows us to classify the bonds of the system into two sets, the backbone and its complement, with very different properties. This generalizes to continuous distributions of bonds the well-known definition of a backbone for discrete bond distributions. By extensive numerical simulations we find that the topological structure of the backbone for a given lattice dimensionality is very similar for both discrete and continuous bond distributions. We then analyze how these heterogeneities influence the equilibrium properties at finite temperature and we discuss the possibility that a suitable backbone picture can be relevant to describe spin-glass phenomena.

Romá, F.; Risau-Gusman, S.



Packet optical networks for high-speed TCP-IP backbones  

Microsoft Academic Search

This article presents a new proposal for TCP-IP backbone implementation based on optical packet switching technology. The proposed network architecture merges the flexibility in resource management of packet switching with the high capacity offered by full optical technology

F. Callegati; M. Casoni; C. Raffaelli



STAB-WIN: Self Organized, Topology Control Ability Backbone Node in Wireless Networks  

Microsoft Academic Search

The objective of the paper is to construct a backbone node with self organization, topology control and reconfiguration capabilities.\\u000a The key issues in wireless networks are maintain a topology with minimum degree, self organization during link or node failure\\u000a and reconstruction ability when the backbone changes the position. Existing research works concentrate on any one of the issues\\u000a by a

S. Smys; G. Josemin Bala


On the Geometry and Electronic Structure of the As-DNA Backbone  

SciTech Connect

High-level quantum chemical calculations have been applied to investigate the geometry and electronic properties of the arsenate analogue of the DNA backbone. The optimized geometries as well as hyperconjugation effects along the C30 O30 X O50 C50 linkage (X = P,As) exhibit a remarkable similarity for both arsenates and phosphates. This suggests that arsenates, if present, might serve as a potential substitute for phosphates in the DNA backbone.

Fuentes-Cabrera, Miguel A [ORNL; Sponer, Jiri [Academy of Sciences of the Czech Republic; Sponer, Judit [Academy of Sciences of the Czech Republic; Sumpter, Bobby G [ORNL; Mladek, Arnost [Academy of Sciences of the Czech Republic



Purifying Selection, Sequence Composition, and Context-Specific Indel Mutations Shape Intraspecific Variation in a Bacterial Endosymbiont  

PubMed Central

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

Williams, Laura E.; Wernegreen, Jennifer J.



Implementing knot-theoretical characterization methods to analyze the backbone structure of proteins: application to CTF L7/L12 and carboxypeptidase A inhibitor proteins.  


In this work we apply a recently developed method for characterizing the shape of the tertiary structure of proteins. The approach is based on a combination of graph- and knot-theoretical characterizations of Cartesian projections of the space curve describing the protein backbone. The proposed technique reduces the essential shape features to a topologically based code formed by a sequence of knot symbols and polynomials. These polynomials are topological invariants that describe the overcrossing and knotting patterns of curves derived from the molecular space curve. These descriptors are algorithmically computed. The procedure is applied to describe the structure of the carboxy terminal fragment of the L7/L12 chloroplast ribosomal protein (CTF L7/L12) and the potato carboxypeptidase A inhibitor protein (PCI), which has a set of three disulfide bridges. In the former case, we describe the protein's shape features in terms of its alpha-helices, and a backbone simplified by considering helices without internal structure. An extension of the methodology to describe disulfide bridges is discussed and applied to PCI. Changes in the knot-theoretical characterization due to possible uncertainties in the resolution of the X-ray structure, as well as the inclusion of low-frequency motions of the backbone, are also discussed. PMID:1772837

Arteca, G A; Tapia, O; Mezey, P G



Capturing protein sequence-structure specificity using computational sequence design.  


It is well known that protein fold recognition can be greatly improved if models for the underlying evolution history of the folds are taken into account. The improvement, however, exists only if such evolutionary information is available. To circumvent this limitation for protein families that only have a small number of representatives in current sequence databases, we follow an alternate approach in which the benefits of including evolutionary information can be recreated by using sequences generated by computational protein design algorithms. We explore this strategy on a large database of protein templates with 1747 members from different protein families. An automated method is used to design sequences for these templates. We use the backbones from the experimental structures as fixed templates, thread sequences on these backbones using a self-consistent mean field approach, and score the fitness of the corresponding models using a semi-empirical physical potential. Sequences designed for one template are translated into a hidden Markov model-based profile. We describe the implementation of this method, the optimization of its parameters, and its performance. When the native sequences of the protein templates were tested against the library of these profiles, the class, fold, and family memberships of a large majority (>90%) of these sequences were correctly recognized for an E-value threshold of 1. In contrast, when homologous sequences were tested against the same library, a much smaller fraction (35%) of sequences were recognized; The structural classification of protein families corresponding to these sequences, however, are correctly recognized (with an accuracy of >88%). Proteins 2013; © 2013 Wiley Periodicals, Inc. PMID:23609941

Mach, Paul; Koehl, Patrice



Diversity and composition of the bacterial community of Poyang Lake (China) as determined by 16S rRNA gene sequence analysis.  


Poyang Lake is the largest fresh water lake in China. In this study, the objective was to examine the diversity of bacterial community in this environment. The phylogenetic composition of bacterioplankton communities from two sites and two dates (northern and southern sub-basins in October 2006 and in May 2007, respectively) in the water column of Poyang Lake were investigated by partially sequencing cloned 16SrRNA genes. Moreover, restriction fragment length polymorphism (RFLP) was applied in the 16SrRNA gene clones. In total, four clone libraries were constructed and 347 clones were screened by RFLP, yielding 153 operational taxonomic units, which mainly belonged to the proteobacteria, Actinobacteria, Bacteroidetes, Cyanobacteria, Verrucomicrobia and Planctomycetes. Our results showed that Beta-proteobacteria was the most significant lineage, with dominant numbers of operational taxonomic units in the northern October 2006, southern October 2006 and May 2007 libraries. The highest bacterial diversity occurred in the library from the southern sub-basin in May 2007 and the lowest in the library from the northern sub-basin in May 2007. Horizontal and temporal differences associated with the concentration of total phosphorus, water temperature and pH suggested that the trophic state and the physicochemical properties of lake play key roles in sustaining bacterial community composition structure. PMID:22806799

Wu, Lan; Ge, Gang; Zhu, Guofeng; Gong, Shijie; Li, Siguang; Wan, Jinbao



Genotyping by RAD sequencing enables mapping of fatty acid composition traits in perennial ryegrass (Lolium perenne (L.)).  


Perennial ryegrass (Lolium perenne L.) is the most important forage crop in temperate livestock agriculture. Its nutritional quality has significant impact on the quality of meat and milk for human consumption. Evidence suggests that higher energy content in forage can assist in reducing greenhouse gas emissions from ruminants. Increasing the fatty acid content (especially ?-linolenic acid, an omega-3 fatty acid) may thus contribute to better forage, but little is known about the genetic basis of variation for this trait. To this end, quantitative trait loci (QTLs) were identified associated with major fatty acid content in perennial ryegrass using a population derived from a cross between the heterozygous and outbreeding high-sugar grass variety AberMagic and an older variety, Aurora. A genetic map with 434 restriction-associated DNA (RAD) and SSR markers was generated. Significant QTLs for the content of palmitic (C16:0) on linkage groups (LGs) 2 and 7; stearic (C18:0) on LGs 3, 4 and 7; linoleic (C18:2n-6) on LGs 2 and 5; and ?-linolenic acids (C18:3n-3) on LG 1 were identified. Two candidate genes (a lipase and a beta-ketoacyl CoA synthase), both associated with C16:0, and separately with C18:2n-6 and C18:0 contents, were identified. The physical positions of these genes in rice and their genetic positions in perennial ryegrass were consistent with established syntenic relationships between these two species. Validation of these associations is required, but the utility of RAD markers for rapid generation of genetic maps and QTL analysis has been demonstrated for fatty acid composition in a global forage crop. PMID:23331642

Hegarty, Matthew; Yadav, Rattan; Lee, Michael; Armstead, Ian; Sanderson, Ruth; Scollan, Nigel; Powell, Wayne; Skøt, Leif



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



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

PubMed Central

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

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



Understanding GFP posttranslational chemistry: structures of designed variants that achieve backbone fragmentation, hydrolysis, and decarboxylation.  


The green fluorescent protein (GFP) creates a fluorophore out of three sequential amino acids by promoting spontaneous posttranslational modifications. Here, we use high-resolution crystallography to characterize GFP variants that not only undergo peptide backbone cyclization but additional denaturation-induced peptide backbone fragmentation, native peptide hydrolysis, and decarboxylation reactions. Our analyses indicate that architectural features that favor GFP peptide cyclization also drive peptide hydrolysis. These results are relevant for the maturation pathways of GFP homologues, such as the kindling fluorescent protein and the Kaede protein, which use backbone cleavage to red-shift the spectral properties of their chromophores. We further propose a photochemical mechanism for the decarboxylation reaction, supporting a role for the GFP protein environment in facilitating radical formation and one-electron chemistry, which may be important in activating oxygen for the oxidation step of chromophore biosynthesis. Together, our results characterize GFP posttranslational modification chemistry with implications for the energetic landscape of backbone cyclization and subsequent reactions, and for the rational design of predetermined spontaneous backbone cyclization and cleavage reactions. PMID:16594705

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



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



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



Diffraction in resonant electron scattering from helical macromolecules: Effects of the DNA backbone  

NASA Astrophysics Data System (ADS)

We recently developed a theoretical framework to treat low-energy electron scattering from helical macromolecules. In this article, we use this framework to extend our previous model of simple base-pair scatterers, organized into the DNA structure, to include the backbone. The internal diffraction pattern due to base pairs is still present, but addition of the backbone screens the base pairs by a factor of 2. More interestingly, the effect of constructive interference on the phosphate groups within the backbone itself is seen to be strong at lower energies. We perform a calculation for electrons incident perpendicular and parallel to the axis of a fragment and find comparable electron patterns on the phosphate groups at the surface of films consisting of vertically or horizontally arranged segments relative to the substrate.

Caron, Laurent; Sanche, Léon



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

PubMed Central

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

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



Characterization of the binding properties of SIRT2 inhibitors with a N-(3-phenylpropenoyl)-glycine tryptamide backbone  

Microsoft Academic Search

SIRT2 inhibitors with a N-(3-phenylpropenoyl)-glycine tryptamide backbone were studied. This backbone has been developed in our group, and it is derived from a compound originally found by virtual screening. In addition, compounds with a smaller 3-phenylpropenoic acid tryptamide backbone were also included in the study. Binding modes for the new compounds and the previously reported compounds were analyzed with molecular

Päivi H. Kiviranta; Heikki S. Salo; Jukka Leppänen; Valtteri M. Rinne; Sergiy Kyrylenko; Erkki Kuusisto; Tiina Suuronen; Antero Salminen; Antti Poso; Maija Lahtela-Kakkonen; Erik A. A. Wallén



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



Structural mimicry of the ?-helix in aqueous solution with an isoatomic ?/?/?-peptide backbone.  


Artificial mimicry of ?-helices offers a basis for development of protein-protein interaction antagonists. Here we report a new type of unnatural peptidic backbone, containing ?-, ?-, and ?-amino acid residues in an ?????? repeat pattern, for this purpose. This unnatural hexad has the same number of backbone atoms as a heptad of ? residues. Two-dimensional NMR data clearly establish the formation of an ?-helix-like conformation in aqueous solution. The helix formed by our 12-mer ?/?/?-peptide is considerably more stable than the ?-helix formed by an analogous 14-mer ?-peptide, presumably because of the preorganized ? and ? residues employed. PMID:21520956

Sawada, Tomohisa; Gellman, Samuel H



A backbone based protein model with explicit solvent  

NASA Astrophysics Data System (ADS)

The computational expense of folding atomistically detailed protein models is prohibitive. Hence minimalist models of proteins are a popular choice. The minimalist models developed so far have excluded water, and treated the hydrophobic effect as an effective attraction between hydrophobic monomers. This simplified treatment does not capture the temperature-dependent variations in entropy and enthalpy of water molecules. Proteins have a predominantly water-screened hydrophobic core and water-exposed polar groups. This structural feature should alter the dynamics of proteins and surrounding water from that of a hydrophobic homopolymer in water. To include these features in a minimalist model, we designed heteropolymers of polar and hydrophobic monomers in explicit water-like medium. The polar monomers and water molecules were modeled with the Jagla potential, which has been shown to reproduce many water-like thermodynamic properties, and the hydrophobic monomers as hard spheres. We discuss a methodology for optimizing the sequence of these heteropolymers and how the hydrophobic collapse of these heteropolymers differs from that of a random heteropolymer.

Sharma, Sumit; Buldyrev, Sergey; Rossky, Peter J.; Stanley, H. Eugene; Debenedetti, Pablo G.; Angell, C. Austen; Kumar, Sanat K.



Complete Nucleotide Sequence of CTX-M-15-Plasmids from Clinical Escherichia coli Isolates: Insertional Events of Transposons and Insertion Sequences  

PubMed Central

Background CTX-M-producing Escherichia coli strains are regarded as major global pathogens. Methodology/Principal Findings The nucleotide sequence of three plasmids (pEC_B24: 73801-bp; pEC_L8: 118525-bp and pEC_L46: 144871-bp) from Escherichia coli isolates obtained from patients with urinary tract infections and one plasmid (pEC_Bactec: 92970-bp) from an Escherichia coli strain isolated from the joint of a horse with arthritis were determined. Plasmid pEC_Bactec belongs to the IncI1 group and carries two resistance genes: blaTEM-1 and blaCTX-M-15. It shares more than 90% homology with a previously published blaCTX-M-plasmid from E. coli of human origin. Plasmid pEC_B24 belongs to the IncFII group whereas plasmids pEC_L8 and pEC_L46 represent a fusion of two replicons of type FII and FIA. On the pEC_B24 backbone, two resistance genes, blaTEM-1 and blaCTX-M-15, were found. Six resistance genes, blaTEM-1, blaCTX-M-15, blaOXA-1, aac6'-lb-cr, tetA and catB4, were detected on the pEC_L8 backbone. The same antimicrobial drug resistance genes, with the exception of tetA, were also identified on the pEC_L46 backbone. Genome analysis of all 4 plasmids studied provides evidence of a seemingly frequent transposition event of the blaCTX-M-15-ISEcp1 element. This element seems to have a preferred insertion site at the tnpA gene of a blaTEM-carrying Tn3-like transposon, the latter itself being inserted by a transposition event. The IS26-composite transposon, which contains the blaOXA-1, aac6'-lb-cr and catB4 genes, was inserted into plasmids pEC_L8 and pEC_L46 by homologous recombination rather than a transposition event. Results obtained for pEC_L46 indicated that IS26 also plays an important role in structural rearrangements of the plasmid backbone and seems to facilitate the mobilisation of fragments from other plasmids. Conclusions Collectively, these data suggests that IS26 together with ISEcp1 could play a critical role in the evolution of diverse multiresistant plasmids found in clinical Enterobacteriaceae.

Smet, Annemieke; Martel, An; Deforce, Dieter; Butaye, Patrick; Haesebrouck, Freddy



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


Collective Modes Of Ordered Water As A Synchronization Backbone For Quantum Neuromolecular Computation And Consciousness  

Microsoft Academic Search

Theoretical modeling suggests spin-glass resonance properties of ordered water play a key role in the phase regulation of neuromolecular computation in processes related to consciousness in complex self-organized living systems. Water provides the central tier in the synchronization backbone required for quantum data processing and information transduction in the domain of Quantum Brain Dynamics (QBD). For over forty years it




Phase Transitions and Backbones of 3SAT and Maximum 3SAT  

Microsoft Academic Search

Many real-world problems involve constraints that cannot be all satisfied. Solving an overconstrained problem then means to find solutions minimizing the number of constraints violated, which is an optimization problem. In this research, we study the behavior of the phase transitions and backbones of constraint optimization problems. We rst investigate the relationship between the phase transitions of Boolean satisfiability, or

Weixiong Zhang



Side chain and backbone structure-dependent subcellular localization and toxicity of conjugated polymer nanoparticles.  


The subcellular localization and toxicity of conjugated polymer nanoparticles (CPNs) are dependent on the chemical structure of the side chains and backbone. Primary amine-containing CPNs exhibit high Golgi localization with no toxicity. Incorporation of short ethylene oxide and tertiary amine side chains contributes to decreased Golgi localization and increased toxicity, respectively. PMID:23722239

Mendez, Eladio; Moon, Joong Ho



Solid-state NMR triple-resonance backbone assignments in a protein  

Microsoft Academic Search

Triple-resonance solid-state NMR spectroscopy is demonstrated to sequentially assign the 13C' and 15N amide backbone resonances of adjacent residues in an oriented protein sample. The observed 13C' chemical shift frequency provides an orientational constraint complementary to those measured from the 1H and 15N amide resonances in double-resonance experiments.

Wee Meng Tan; Zhengtian Gu; Ana Carolina Zeri



Estimating market power in the Internet backbone. Using the IP transit Band-X database  

Microsoft Academic Search

Recent studies have found the Internet backbone to be more competitive than was thought before. This paper explores a novel route to monitor market power using prices and quality data from the online trading site Band-X. First the hypothesis that Europe is a connectivity market on its own, is tested and then, by using a Panel data regression, the paper

Emanuele Giovannetti; Cristiano Andrea Ristuccia



Sparsely sampled high-resolution 4-D experiments for efficient backbone resonance assignment of disordered proteins.  


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. PMID:21277815

Wen, Jie; Wu, Jihui; Zhou, Pei



Experimental investigation of hull girder vibrations of a flexible backbone model in bending and torsion  

Microsoft Academic Search

Although the coupled horizontal–torsional vibrations of open ships have been investigated numerically for decades, the available experimental data in oblique seas seem rare. Model tests, considering natural frequencies of bending and torsional modes, have been conducted by the Centre for Ships and Ocean Structures (CeSOS) in the towing tank and ocean basin. A flexible backbone model was designed with five

Suji Zhu; MingKang Wu; Torgeir Moan



Backbone-directed perylene dye self-assembly into oligomer stacks.  


Arm wrestling: Backbone-directed "arm-to-arm" aggregation of a newly designed perylene bisimide (PBI) dyad with a defined intramolecular space leads to the growth of kinetically stable extended PBI ?-stacks. This PBI dyad was shown to assemble into oligomers up to 21 units in length. PMID:23943193

Shao, Changzhun; Stolte, Matthias; Würthner, Frank



Topological performance of mobile backbone based wireless ad hoc network with unmanned vehicles  

Microsoft Academic Search

We have recently introduced a hierarchical structure for ad hoc wireless networks that classifies nodes into two categories: backbone capable nodes (BCNs) and regular nodes (RNs). BNCs are better equipped, have higher capacities, and have the ability to operate at multiple power levels and employ multiple radio modules. Under our protocol, identified as TBONE, when a BCN is elected to

Izhak Rubin; Runhe Zhang; Huei-jiun Ju



Switched optical backbone for cost-effective scalable core IP networks  

Microsoft Academic Search

With the advent of WDM technology, IP backbone carriers are now connecting core routers directly over point-to-point WDM links (IP over WDM). The advances and standardization in optical control plane technologies like GMPLS have substantially increased the intelligence of the optical layer and shown promise toward making dynamic provisioning and restoration of optical layer circuits a basic capability to be

Sudipta Sengupta; Vijay Kumar; Debanjan Saha



Inferring the evolutionary history of IncP-1 plasmids despite incongruence among backbone gene trees.  


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

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



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


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

Mant, Colin T; Hodges, Robert S



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

PubMed Central

The backbone dynamics of the four-helical bundle cytokine leukemia inhibitory factor (LIF) have been investigated using 15N NMR relaxation and amide proton exchange measurements on a murine-human chimera, MH35-LIF. For rapid backbone motions (on a time scale of 10 ps to 100 ns), as probed by 15N relaxation measurements, the dynamics parameters were calculated using the model-free formalism incorporating the model selection approach. The principal components of the inertia tensor of MH35-LIF, as calculated from its NMR structure, were 1:0.98:0.38. The global rotational motion of the molecule was, therefore, assumed to be axially symmetric in the analysis of its relaxation data. This yielded a diffusion anisotropy D(parallel)/D(perpendicular) of 1.31 and an effective correlation time (4D(perpendicular) + 2D(parallel))(-1) of 8.9 ns. The average values of the order parameters (S2) for the four helices, the long interhelical loops, and the N-terminus were 0.91, 0.84, and 0.65, respectively, indicating that LIF is fairly rigid in solution, except at the N-terminus. The S2 values for the long interhelical loops of MH35-LIF were higher than those of their counterparts in short-chain members of the four-helical bundle cytokine family. Residues involved in LIF receptor binding showed no consistent pattern of backbone mobilities, with S2 values ranging from 0.71 to 0.95, but residues contributing to receptor binding site III had relatively lower S2 values, implying higher amplitude motions than for the backbone of sites I and II. In the relatively slow motion regime, backbone amide exchange measurements showed that a number of amides from the helical bundle exchanged extremely slowly, persisting for several months in 2H2O at 37 degrees C. Evidence for local unfolding was considered, and correlations among various structure-related parameters and the backbone amide exchange rates were examined. Both sets of data concur in showing that LIF is one of the most rigid four-helical bundle cytokines.

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



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)



Solution structure and backbone dynamics of Calsensin, an invertebrate neuronal calcium-binding protein.  


Calsensin is an EF-hand calcium-binding protein expressed by a subset of peripheral sensory neurons that fasciculate into a single tract in the leech central nervous system. Calsensin is a 9-kD protein with two EF-hand calcium-binding motifs. Using multidimensional NMR spectroscopy we have determined the solution structure and backbone dynamics of calcium-bound Calsensin. Calsensin consists of four helices forming a unicornate-type four-helix bundle. The residues in the third helix undergo slow conformational exchange indicating that the motion of this helix is associated with calciumbinding. The backbone dynamics of the protein as measured by (15)N relaxation rates and heteronuclear NOEs correlate well with the three-dimensional structure. Furthermore, comparison of the structure of Calsensin with other members of the EF-hand calcium-binding protein family provides insight into plausible mechanisms of calcium and target protein binding. PMID:15937283

Venkitaramani, Deepa V; Fulton, D Bruce; Andreotti, Amy H; Johansen, Kristen M; Johansen, Jørgen



Molecular bottlebrushes with polypeptide backbone prepared via ring-opening polymerization of NCA and ATRP.  


A new type of molecular bottlebrush with poly-L-lysine (PLL) as backbone was synthesized via ROP followed by ATRP. A N?-bromoisobutyryl functionalized N?-CBZ-L-lysine was firstly synthesized and converted in polymerizable ?-amino acid N-carboxyanhydride (NCA), which was then polymerized using Ni(0) transition metal complex to give well-defined bromo-functionalized homopolypeptide (PBrLL), from which we prepared two types of polypeptide bottlebrushes with polystyrene and poly(oligoethylene glycol methacrylate) as side-chains. PBrLL macroinitiator was demonstrated to have high initiation efficiency for ATRP, which allowed good control over side-chain length. CD and FTIR characterization revealed that both PBrLL macroinitiator and PLL backbone of bottlebrushes adopted ?-helical conformation in appropriate solvents. PMID:22139826

Liu, Yu; Chen, Ping; Li, Zhibo



The molecular structure of spider dragline silk: Folding and orientation of the protein backbone  

PubMed Central

The design principles of spider dragline silk, nature's high-performance fiber, are still largely unknown, in particular for the noncrystalline glycine-rich domains, which form the bulk of the material. Here we apply two-dimensional solid-state NMR to determine the distribution of the backbone torsion angles (?,?) as well as the orientation of the polypeptide backbone toward the fiber at both the glycine and alanine residues. Instead of an “amorphous matrix,” suggested earlier for the glycine-rich domains, these new data indicate that all domains in dragline silk have a preferred secondary structure and are strongly oriented, with the chains predominantly parallel to the fiber. As proposed previously, the alanine residues are predominantly found in a ? sheet conformation. The glycine residues are partly incorporated into the ? sheets and otherwise form helical structures with an approximate 3-fold symmetry.

van Beek, J. D.; Hess, S.; Vollrath, F.; Meier, B. H.



Protein backbone torsion angle-based structure comparison and secondary structure database web server.  


Structural information has been a major concern for biological and pharmaceutical studies for its intimate relationship to the function of a protein. Three-dimensional representation of the positions of protein atoms is utilized among many structural information repositories that have been published. The reliability of the torsional system, which represents the native processes of structural change in the structural analysis, was partially proven with previous structural alignment studies. Here, a web server providing structural information and analysis based on the backbone torsional representation of a protein structure is newly introduced. The web server offers functions of secondary structure database search, secondary structure calculation, and pair-wise protein structure comparison, based on a backbone torsion angle representation system. Application of the implementation in pair-wise structural alignment showed highly accurate results. The information derived from this web server might be further utilized in the field of ab initio protein structure modeling or protein homology-related analyses. PMID:24124412

Jung, Sunghoon; Bae, Se-Eun; Ahn, Insung; Son, Hyeon S



Protein Backbone Torsion Angle-Based Structure Comparison and Secondary Structure Database Web Server  

PubMed Central

Structural information has been a major concern for biological and pharmaceutical studies for its intimate relationship to the function of a protein. Three-dimensional representation of the positions of protein atoms is utilized among many structural information repositories that have been published. The reliability of the torsional system, which represents the native processes of structural change in the structural analysis, was partially proven with previous structural alignment studies. Here, a web server providing structural information and analysis based on the backbone torsional representation of a protein structure is newly introduced. The web server offers functions of secondary structure database search, secondary structure calculation, and pair-wise protein structure comparison, based on a backbone torsion angle representation system. Application of the implementation in pair-wise structural alignment showed highly accurate results. The information derived from this web server might be further utilized in the field of ab initio protein structure modeling or protein homology-related analyses.

Jung, Sunghoon; Bae, Se-Eun; Ahn, Insung



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

NASA Astrophysics Data System (ADS)

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

Hernández, Belén; Pflüger, Fernando; Kruglik, Sergei G.; Ghomi, Mahmoud



Inherent stretching elasticity of a single polymer chain with a carbon-carbon backbone.  


We study the single-chain elasticities of three kinds of neutral polymers with a carbon-carbon (C-C) backbone by atomic force microscopy-based single-molecule force spectroscopy in a nonpolar solvent (octane), aiming at measuring the inherent chain elasticity of this very important class of polymers. The finding that the single-chain elasticities of all three polymers in octane are virtually identical in the entire force region implies that the side chains of the polymers have no detectable effects on the single-chain elasticity. By utilizing the single-chain elasticity from quantum mechanics calculations, the freely rotating chain model can provide the best fitting curve when each C-C bond is set to be the rotating unit. Although there are some exceptions when the side chain is very huge, our work provides a general result for the inherent elasticity of single neutral flexible polymer chains with C-C backbones. PMID:23477592

Wang, Kefeng; Pang, Xiangchao; Cui, Shuxun



Synthesis and anti-tumor-promoting activity of glycoglycerolipid analogues lacking the glycerol backbone  

Microsoft Academic Search

Glycoglycerolipid analogues lacking the glycerol backbone were prepared through a lipase catalyzed transesterification of ?-d-galactosylethylene glycol. The inhibitory effect of the resultant isomeric hexanoates at the primary alcoholic positions, ?-d-galactosylethylene glycol itself and nonyl ?-d-galactopyranoside, was tested on Epstein–Barr virus early antigen (EBV-EA) activation in Raji cells promoted by the tumor promoter 12-O-tetradecanoylphorbol-13-acetate (TPA), as a primary screening test for

Diego Colombo; Fiamma Ronchetti; Antonio Scala; Lucio Toma; Harukuni Tokuda; Hoyoku Nishino



An overlay approach for enabling access to dynamically shared backbone GMPLS networks  

Microsoft Academic Search

In this paper, we address the question of how to introduce new Quality-of-Service enhancements into the existing Internet. Specifically, dynamically shared circuit- switched\\/virtual-circuit (VC) networks are being deployed in some of the backbone research and education networks. We describe an overlay solution for enabling access of end hosts that are not physically connected to these networks to nev- ertheless benefit

Xiuduan Fang; Malathi Veeraraghavan; Mark E. Mcginley; Robert W. Gisiger



Role of Backbone Hydration and Salt-Bridge Formation in Stability of ?-Helix in Solution  

Microsoft Academic Search

We test molecular level hypotheses for the high thermal stability of ?-helical conformations of alanine-based peptides by performing detailed atomistic simulations of a 20-amino-acid peptide with explicit treatment of water. To assess the contribution of large side chains to ?-helix stability through backbone desolvation and salt-bridge formation, we simulate the alanine-rich peptide, Ac-YAEAAKAAEAAKAAEAAKAF-Nme, referred to as the EK peptide, that

Tuhin Ghosh; Shekhar Garde; Angel E. García



A framework for real-time worm attack detection and backbone monitoring  

Microsoft Academic Search

We developed an open source Internet backbone monitoring and traffic analysis framework named UPFrame. It captures UDP NetFlow packets, buffers it in shared memory and feeds it to customised plug-ins. UPFrame is highly tolerant to misbehaving plug-ins and provides a watchdog mechanism for restarting crashed plug-ins. This makes UP-Frame an ideal platform for experiments. It also features a traffic shaper

Thomas Dubendorfer; Arno Wagner; Bernhard Plattner



Protein backbone motions viewed by intraresidue and sequential H N –H ? residual dipolar couplings  

Microsoft Academic Search

Triple resonance E.COSY-based techniques were used to measure intra-residue and sequential HN–H? residual dipolar couplings (RDCs) for the third IgG-binding domain of protein G (GB3), aligned in Pf1 medium. Measurements closely correlate with values predicted on the basis of an NMR structure, previously determined on the\\u000a basis of a large number of one-bond backbone RDCs measured in five alignment media.

Beat Vögeli; Lishan Yao; Ad Bax



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



Tritium containing polymers having a polymer backbone substantially void of tritium  


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.



The backbone N-(4-azidobutyl) linker for the preparation of Peptide chimera.  


A robust synthetic strategy for the introduction of the N-(4-azidobutyl) linker into peptides using standard SPPS techniques is described. Based on the example of Cilengitide it is shown that the N-(4-azidobutyl) group exerts similar conformational restraints as a backbone N-Me group and allows conjugation of a desired molecule either via click chemistry or-after azide reduction-via acylation or reductive alkylation. PMID:24006938

Fernández-Llamazares, Ana I; García, Jesús; Adan, Jaume; Meunier, David; Mitjans, Francesc; Spengler, Jan; Albericio, Fernando



Synthesis of a backbone hexasaccharide fragment of the pectic polysaccharide rhamnogalacturonan I.  


Synthesis of the fully unprotected hexasaccharide backbone of the pectic polysaccharide rhamnogalacturonan I is described. The strategy relies on iterative coupling of a common pentenyl disaccharide glycosyl donor followed by a late-stage oxidation of the C-6 positions of the galactose residues. The disaccharide donor is prepared by an efficient chemoselective armed-disarmed coupling of a thiophenyl rhamnoside donor with a pentenyl galactoside acceptor bearing the strongly electron-withdrawing pentafluorobenzoyl ester (PFBz) protective group. PMID:23544444

Zakharova, Alexandra N; Madsen, Robert; Clausen, Mads H



Mechanical compressibility of the glycosylphosphatidylinositol (GPI) anchor backbone governed by independent glycosidic linkages.  


About 1% of the human proteome is anchored to the outer leaflet of cell membranes via a class of glycolipids called GPI anchors. In spite of their ubiquity, experimental information about the conformational dynamics of these glycolipids is rather limited. Here, we use a variety of computer simulation techniques to elucidate the conformational flexibility of the Man-?(1?2)-Man-?(1?6)-Man-?(1?4)-GlcNAc-?-OMe tetrasaccharide backbone 2 that is an essential and invariant part of all GPI-anchors. In addition to the complete tetrasaccharide structure, all disaccharide and trisaccharide subunits of the GPI backbone have been studied as independent moieties. The extended free energy landscape as a function of the corresponding dihedral angles has been determined for each glycosidic linkage relevant for the conformational preferences of the tetrasaccharide backbone (Man-?(1?2)-Man, Man-?(1?6)Man and Man-?(1?4)-GlcNAc). We compared the free energy landscapes obtained for the same glycosidic linkage within different oligosaccharides. This comparison reveals that the conformational properties of a linkage are primarily determined by its two connecting carbohydrate moieties, just as in the corresponding disaccharide. Furthermore, we can show that the torsions of the different glycosidic linkages within the GPI tetrasaccharide can be considered as statistically independent degrees of freedom. Using this insight, we are able to map the atomistic description to an effective, reduced model and study the response of the tetrasaccharide 2 to external forces. Even though the backbone assumes essentially a single, extended conformation in the absence of mechanical stress, it can be easily bent by forces of physiological magnitude. PMID:23061547

Wehle, Marko; Vilotijevic, Ivan; Lipowsky, Reinhard; Seeberger, Peter H; Silva, Daniel Varon; Santer, Mark



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



Oxo-biodegradable carbon backbone polymers – Oxidative degradation of polyethylene under accelerated test conditions  

Microsoft Academic Search

Oxo-biodegradation of carbon-only backbone polymers is receiving ever increasing attention for the practical implications that some re-engineered thermoplastic polymer formulations based on conventional biostable polymeric materials may satisfy in terms of environmental friendliness and acceptance by commodity plastic manufacturers.In this respect, as part of our continuing activity in the area of bioactive polymeric materials for biomedical and environmental applications, we

E. Chiellini; A. Corti; S. D'Antone; R. Baciu



Effect of Steric Constraint at the ?-Backbone Position on the Conformations and Hybridization Properties of PNAs  

PubMed Central

Conformationally preorganized peptide nucleic acids (PNAs) have been synthesized through backbone modifications at the ?-position, where R = alanine, valine, isoleucine, and phenylalanine side chains. The effects of these side-chains on the conformations and hybridization properties of PNAs were determined using a combination of CD and UV-Vis spectroscopic techniques. Our results show that the ?-position can accommodate varying degrees of sterically hindered side-chains, reaffirming the bimodal function of PNAs as the true hybrids of “peptides” and “nucleic acids.”

Crawford, Matthew J.; Rapireddy, Srinivas; Bahal, Raman; Sacui, Iulia; Ly, Danith H.



High-Resolution Conformation and Backbone Dynamics of a Soluble Aggregate of Apomyoglobin119  

PubMed Central

The structure and dynamics of soluble misfolded aggregates are poorly understood, despite their importance in protein science and disease. Water-soluble self-associated species that do not become insoluble over time are invaluable tools for high-resolution conformational studies aimed at dissecting the determinants of self-association. Here, we characterize the soluble model aggregate apomyoglobin119 (apoMb119), generated upon truncating the residues corresponding to the C-terminal helix of sperm whale apomyoglobin. The secondary structure and backbone dynamics of apoMb119, determined by multidimensional NMR at pH 6.0, reveal the presence of an N-terminal slow-tumbling core and a highly disordered flexible C-terminus displaying residual helicity and large-amplitude backbone motions on the picosecond-to-nanosecond timescale. The backbone of the apoMb119 aggregate assumes progressively increased mobility as residues get further removed from the nonpolar core and closer to the more hydrophilic C-terminal end. This structural motif establishes a useful paradigm for the topology of soluble misfolded protein aggregates in aqueous solution in the absence of stabilizing additives. The partially helical and flexible C-terminus of apoMb119's aggregate is in interesting contrast with the amyloid-related globulomers, which display dangling ends rich in ?-strand. Finally, we investigate how a molecular chaperone, the substrate-binding domain of DnaK, interferes with apoMb119's aggregation.

Rajagopalan, Senapathy; Kurt, Nese; Cavagnero, Silvia



A practical implementation of cross-spectrum in protein backbone resonance assignment  

NASA Astrophysics Data System (ADS)

The concept of cross-spectrum is applied in protein NMR spectroscopy to assist in the backbone sequential resonance assignment. Cross-spectrum analysis is used routinely to reveal correlations in frequency domains as a means to reveal common features contained in multiple time series. Here the cross-spectrum between related NMR spectra, for example HNCO and HN(CA)CO, can be calculated with point-by-point multiplications along their common C? carbon axis. In the resulting higher order cross-spectrum, an enhanced correlation signal occurs at every common i-1 carbon frequency allowing the amide proton HN (and nitrogen N) resonances from residues i and i-1 to be identified. The cross-spectrum approach is demonstrated using 2D spectra H(N)CO, H(NCA)CO, H(NCO)CACB, and H(N)CACB measured on a 15N/13C double-labeled Ubiquitin sample. These 2D spectra are used to calculate two pseudo-3D cross-spectra, Hi-Hi-1-C?i-1 and Hi-Hi-1-CAi-1CBi-1. We show using this approach, backbone resonances of H, C?, CA, and CB can be fully assigned without ambiguity. The cross-spectrum principle is expected to offer an easy, practical, and more quantitative approach for heteronuclear backbone resonance assignment.

Chen, Kang; Delaglio, Frank; Tjandra, Nico



Quantitative analysis of protein backbone dynamics in microcrystalline ubiquitin by solid-state NMR spectroscopy.  


Characterization of protein dynamics by solid-state NMR spectroscopy requires robust and accurate measurement protocols, which are not yet fully developed. In this study, we investigate the backbone dynamics of microcrystalline ubiquitin using different approaches. A rotational-echo double-resonance type (REDOR-type) methodology allows one to accurately measure (1)H-(15)N order parameters in highly deuterated samples. We show that the systematic errors in the REDOR experiment are as low as 1% or even less, giving access to accurate data for the amplitudes of backbone mobility. Combining such dipolar-coupling-derived order parameters with autocorrelated and cross-correlated (15)N relaxation rates, we are able to quantitate amplitudes and correlation times of backbone dynamics on picosecond and nanosecond time scales in a residue-resolved manner. While the mobility on picosecond time scales appears to have rather uniform amplitude throughout the protein, we unambiguously identify and quantitate nanosecond mobility with order parameters S(2) as low as 0.8 in some regions of the protein, where nanosecond dynamics has also been revealed in solution state. The methodology used here, a combination of accurate dipolar-coupling measurements and different relaxation parameters, yields details about dynamics on different time scales and can be applied to solid protein samples such as amyloid fibrils or membrane proteins. PMID:20977205

Schanda, Paul; Meier, Beat H; Ernst, Matthias



Biocleavable comb-shaped gene carriers from dextran backbones with bioreducible ATRP initiation sites.  


It is of crucial importance to design reduction-sensitive polysaccharide-based copolymers for intracellular triggered gene and drug delivery. In this work, a simple two-step method involving the reaction of hydroxyl groups of dextran with cystamine was first developed to introduce reduction-sensitive disulfide linked initiation sites of atom transfer radical polymerization (ATRP) onto dextran. Well-defined biocleavable comb-shaped vectors consisting of nonionic dextran backbones and disulfide-linked cationic P(DMAEMA) side chains were subsequently prepared via ATRP for highly efficient gene delivery. The P(DMAEMA) side chains can be readily cleavable from the dextran backbones under reducible conditions. Moreover, the bioreducible P(DMAEMA) side chains can be functionalized by poly(poly(ethylene glycol)ethyl ether methacrylate) (P(PEGEEMA)) end blocks to reduce the cytotoxicity and further enhance the gene transfection efficiency. This present study demonstrated that properly grafting short bioreducible polycation side chains from a nonionic polysaccharide backbone with biocleavable ATRP initiation sites is an effective means to produce a class of polysaccharide-based gene delivery vectors. PMID:22136712

Wang, Zeng-Hui; Zhu, Yun; Chai, Ming-Ying; Yang, Wan-Tai; Xu, Fu-Jian



Relationships between 31P chemical shift tensors and conformation of nucleic acid backbone: a DFT study.  


Density functional theory (DFT) has been applied to study the conformational dependence of 31P chemical shift tensors in B-DNA. The gg and gt conformations of backbone phosphate groups representing BI- and BII-DNA have been examined. Calculations have been carried out on static models of dimethyl phosphate (dmp) and dinucleoside-3',5'-monophosphate with bases replaced by hydrogen atoms in vacuo as well as in an explicit solvent. Trends in 31P chemical shift anisotropy (CSA) tensors with respect to the backbone torsion angles alpha, zeta, beta, and epsilon are presented. Although these trends do not change qualitatively upon solvation, quantitative changes result in the reduction of the chemical shift anisotropy. For alpha and zeta in the range from 270 degrees to 330 degrees and from 240 degrees to 300 degrees , respectively, the delta22 and delta33 principal components vary within as much as 30 ppm, showing a marked dependence on backbone conformation. The calculated 31P chemical shift tensor principal axes deviate from the axes of O-P-O bond angles by at most 5 degrees . For solvent models, our results are in a good agreement with experimental estimates of relative gg and gt isotropic chemical shifts. Solvation also brings the theoretical deltaiso of the gg conformation closer to the experimental gg data of barium diethyl phosphate. PMID:17315915

Precechtelová, Jana; Munzarová, Markéta L; Novák, Petr; Sklenár, Vladimír



Development of an optimized backbone of FRET biosensors for kinases and GTPases  

PubMed Central

Biosensors based on the principle of Förster (or fluorescence) resonance energy transfer (FRET) have shed new light on the spatiotemporal dynamics of signaling molecules. Among them, intramolecular FRET biosensors have been increasingly used due to their high sensitivity and user-friendliness. Time-consuming optimizations by trial and error, however, obstructed the development of intramolecular FRET biosensors. Here we report an optimized backbone for rapid development of highly sensitive intramolecular FRET biosensors. The key concept is to exclude the “orientation-dependent” FRET and to render the biosensors completely “distance-dependent” with a long, flexible linker. We optimized a pair of fluorescent proteins for distance-dependent biosensors, and then developed a long, flexible linker ranging from 116 to 244 amino acids in length, which reduced the basal FRET signal and thereby increased the gain of the FRET biosensors. Computational simulations provided insight into the mechanisms by which this optimized system was the rational strategy for intramolecular FRET biosensors. With this backbone system, we improved previously reported FRET biosensors of PKA, ERK, JNK, EGFR/Abl, Ras, and Rac1. Furthermore, this backbone enabled us to develop novel FRET biosensors for several kinases of RSK, S6K, Akt, and PKC and to perform quantitative evaluation of kinase inhibitors in living cells.

Komatsu, Naoki; Aoki, Kazuhiro; Yamada, Masashi; Yukinaga, Hiroko; Fujita, Yoshihisa; Kamioka, Yuji; Matsuda, Michiyuki



DNA conformations and their sequence preferences  

PubMed Central

The geometry of the phosphodiester backbone was analyzed for 7739 dinucleotides from 447 selected crystal structures of naked and complexed DNA. Ten torsion angles of a near-dinucleotide unit have been studied by combining Fourier averaging and clustering. Besides the known variants of the A-, B- and Z-DNA forms, we have also identified combined A + B backbone-deformed conformers, e.g. with ?/? switches, and a few conformers with a syn orientation of bases occurring e.g. in G-quadruplex structures. A plethora of A- and B-like conformers show a close relationship between the A- and B-form double helices. A comparison of the populations of the conformers occurring in naked and complexed DNA has revealed a significant broadening of the DNA conformational space in the complexes, but the conformers still remain within the limits defined by the A- and B- forms. Possible sequence preferences, important for sequence-dependent recognition, have been assessed for the main A and B conformers by means of statistical goodness-of-fit tests. The structural properties of the backbone in quadruplexes, junctions and histone-core particles are discussed in further detail.

Svozil, Daniel; Kalina, Jan; Omelka, Marek; Schneider, Bohdan



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



Profiles of Backbone Distribution of Different Side-Chain Liquid-Crystal Polymers in the Smectic Phase  

Microsoft Academic Search

The measurements of the smectic reflection intensities of side-chain liquid-crystal polymers give access, after inverse Fourier transform, to the profile of coherent scattering length density along the normal to the layers. We give here three backbone density profiles associated to three liquid-crystal polymers: two polymethacrylates and one polyacrylate differing only by the nature of the backbone or by the mesogen

Laurence Noirez



"Splicing up" drug discovery. Cell-Based Expression and Screening of Genetically-Encoded Libraries of Backbone Cyclized Polypeptides  

PubMed Central

The present paper reviews the use of protein splicing for the biosynthesis of backbone cyclic polypeptides. This general method allows the in vivo and in vitro biosynthesis of cyclic polypeptides using recombinant DNA expression techniques. Biosynthetic access to backbone cyclic peptides opens the possibility to generate cell-based combinatorial libraries that can be screened inside living cells for their ability to attenuate or inhibit cellular processes thus providing a new way for finding therapeutic agents.

Sancheti, Harshkumar; Camarero, Julio A.



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



Cryptic Open Reading Frames in Plasmid Vector Backbone Sequences Can Provide Highly Immunogenic Cytotoxic T-Lymphocyte Epitopes1  

Microsoft Academic Search

Murine tumor cells obtained through transfection of expression plas- mids carrying activated cellular and\\/or viral oncogenes constitute formi dable tools for immunological tumor research. As reported previously, mouse embryo cells of C57BL\\/6 origin, transformed by mutated p53 or human papilloma virus type 16 (HPV16), present, at their surface, MHC- bound peptides that are derived from the p53 and the HPV16

Nastasja E. van de Rhee; Stephen P. Schoenberger; Michel P. M. Vierboom; Frank A. W. Verreck; Cornelis J. M. Melief; Rienk Offringa



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.



Compositional variations across a dunite - harzburgite - lherzolite - plagioclase lherzolite sequence at the Trinity ophiolite: Evidence for multiple episodes of melt flow and melt-rock reaction in the mantle.  

NASA Astrophysics Data System (ADS)

In the preceding report we showed experimentally that the dunite-harzburgite-lherzolite (DHL) sequence found in the mantle sections of ophiolite could be formed by reactive dissolution of lherzolite in a basaltic liquid. The most striking results of our lherzolite dissolution experiments are the sharp mineralogical boundaries between adjacent lithologies and simple monotonic composition variations in minerals across the DHL sequence. Here we present a detailed compositional traverse across a dunite (3.64 m wide) - harzburgite-lherzolite (5.64 m) - plagioclase lherzolite (> 10 m) sequence (referred to as DHL-PL) at the Trinity ophiolite that shows complicated composition trends and melt flow history. With the exception of a small (1 m wide) anomalous region within the dunite, less than 1 m away from the dunite-harzburgite contact, the Mg#s of olivine (90), cpx (92.8), opx (90.4 in harzburgite) and spinel (40), as well as Al2O3 and TiO2 abundance in cpx, opx and spinel are essentially constant from dunite to lherzolite. The CaO content in olivine (0.02%), opx (1%) and cpx (23.5%) are also uniform throughout the harzburgite-plagioclase lherzolite sequence. However, the Mg# of olivine and opx, Al2O3, TiO2 and Cr2O3 in cpx and opx, as well as Na2O in cpx increase 2 meters into the plagioclase lherzolite. In addition, asymmetric concentration gradients are observed for CaO in olivine and Cr2O3, Al2O3, MgO, and FeO in spinel. These asymmetric concentration gradients are mostly in the dunite-side of the dunite-harzburgite contact. And finally, the 1 m wide anomalous region within the dunite is characterized by elevated Mg# and NiO in olivine, Al2O3, TiO2, Cr2O3, and REE in cpx, and very distinct elemental abundance in spinel. The composition variations reported here are substantially different from those of Quick (1981) who measured a smaller (1 m) DHL-PL sequence at the Trinity ophiolite. Together these two Trinity data sets show a large variation in DHL-PL chemistry within the same ophiolite. Concentration gradients across DHL-PL sequences have been observed in the mantle sections of ophiolites around the world. Based on our lherzolite dissolution experiments, preliminary numerical calculations, and previous studies we suggest that the DHL-PL sequence at Trinity was formed by pervasive melt flow and reactive dissolution of a plagioclase lherzolite in basaltic liquids. Although the details are still unknown, the complicated concentration profiles reported in this study can be explained by a model that involves multiple episodes of melt flow and melt-rock reaction in an evolving dunite channel system. Multiple episodes of melt flow in the mantle, each with distinct elemental and isotopic characteristics, have already been documented in olivine-hosted melt inclusions. The spatial distributions of the compositional variations reported here can be used to further constrain the time interval between different episodes of melt flow in the dunite channel. For example, the two (or more) episodes of melt flow that created the anomalous region in the dunite and the DHL-PL sequence could at most be separated by less than a few hundred years.

Morgan, Z. T.; Liang, Y.; Kelemen, P.



Effect of temperature and solvent composition on acid dissociation equilibria, I: Sequenced (s)(s)pKa determination of compounds commonly used as buffers in high performance liquid chromatography coupled to mass spectroscopy detection.  


A new automated and rapid potentiometric method for determining the effect of organic-solvent composition on pK(a) has been developed. It is based on the measurements of pH values of buffer solutions of variable solvent compositions using a combined glass electrode. Additions of small volumes of one precisely thermostated solution into another, both containing exactly the same analytical concentrations of the buffer components, can produce continuous changes in the solvent composition. Two sequences of potential measurements, one of increasing and the other of decreasing solvent content, are sufficient to obtain the pK(a) values of the acidic compound within the complete solvent-composition range in about 2h. The experimental design, procedures, and calculations needed to convert the measured pH into the thermodynamic pK(a) values are thoroughly discussed. This rapid and automated method allows the systematic study of the effect of solvent compositions and temperatures on the pK(a). It has been applied to study the dissociation constants of two monoprotic acids: formic acid and triethylamine:HCl in acetonitrile/water mixtures within the range from 0 to 90% (v/v) at temperatures between 20°C and 60°C. These volatile compounds are frequently used to control the pH of the mobile phase in HPLC, especially in methods coupled to mass-spectrometry detection. The obtained pK(a) values are in excellent agreement with those previously reported. The results were fitted to empirical functions between pK(a) and temperature and composition. These equations, which can be used to estimate the pK(a) of these substances at any composition and temperature, would be highly useful in practical work during chromatographic method development. PMID:22502616

Padró, Juan M; Acquaviva, Agustín; Tascon, Marcos; Gagliardi, Leonardo G; Castells, Cecilia B



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

PubMed Central

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

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



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


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



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

Microsoft Academic Search

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

Derek Marsh; Micha Jost; Cristina Peggion; Claudio Tonioloy



Backbone-base inclination as a fundamental determinant of nucleic acid self- and cross-pairing  

Microsoft Academic Search

The crystal structure of the duplex formed by oligo(2',3'-dideoxy-b-D-glucopyranosyl)nucleotides (homo-DNA) revealed strongly inclined backbone and base-pair axes (Egli,M., Pallan,P.S., Pattanayek,R., Wilds,C.J., Lubini,P., Minasov,G., Dobler,M., Leumann,C.J. and Eschenmoser,A. (2006) Crystal structure of homo-DNA and nature's choice of pentose over hexose in the genetic system. J. Am. Chem. Soc., 128, 10847-10856). This inclination is easily perceived because homo- DNA exhibits only a

Pradeep S. Pallan; Paolo Lubini; Martin Bolli; Martin Egli



Backbone resonance assignments of the ? sub-domain of Brevibacillus thermoruber Lon protease.  


Lon is an ATPases associated with diverse cellular activities protease and belongs to a unique group that binds DNA. The ? sub-domain of Lon protease is responsible for DNA-binding, but the structural information for its DNA-recognition mode is still limited. Here, we report (1)H, (15)N and (13)C backbone assignment for the ? sub-domain from Brevibacillus thermoruber Lon protease as the basis for the elucidation of its structure and interactions with DNA, necessary for understanding the allosteric regulatory mechanism of the enzymatic function. PMID:23771856

Chen, Yu-Da; Wu, Shih-Hsiung; Hsu, Chun-Hua



A triangular macrocycle altering planar and bulky sections in its molecular backbone.  


A triangular macrocyclic molecule has been synthesized which consists of substituted phenanthrene vertices interconnected by 1,3-diethynylbicyclo[1.1.1]pentane sides. The molecule is the very first example of exploiting the bicyclopentane motif in the construction of a shape persistent macrocycle's backbone. It carries new features such as bulkiness, nonconjugated ?-bonding, and a certain conformational flexibility due to its easy longitudinal rotation. We have used some of the features in order to rationalize the observed tendency of the compound to form films on various surfaces. PMID:21338056

Kaleta, Ji?í; Mazal, Ctibor



Backbone 1H, 15N, and 13C resonance assignments for the NOXO1? PX domain  

PubMed Central

NOXO1 (Nox Organizer 1) is a homolog of the NAPDH oxidase protein p47phox. NADPH oxidases transfer electrons from NADPH to molecular oxygen, generating the superoxide anion. NOXO1 contains an N-terminal PX (phox homology) domain and is one of several PX domain-containing proteins found in the cytosolic subunits of the NADPH oxidase complex. These PX domains bind to membrane lipids and target the protein to membranes, recruiting other cytosolic components to the membrane bound components and aiding formation of a active enzyme complex. This recruitment represents a level of regulation of these oxidases. Here we report the backbone assignments of NOXO1? PX.

Davis, Nicole Y.; McPhail, Linda C.



Backbone 1H, 15N, and 13C resonance assignments for the NOXO1? PX domain.  


NOXO1 (Nox Organizer 1) is a homolog of the NAPDH oxidase protein p47(phox). NADPH oxidases transfer electrons from NADPH to molecular oxygen, generating the superoxide anion. NOXO1 contains an N-terminal PX (phox homology) domain and is one of several PX domain-containing proteins found in the cytosolic subunits of the NADPH oxidase complex. These PX domains bind to membrane lipids and target the protein to membranes, recruiting other cytosolic components to the membrane bound components and aiding formation of a active enzyme complex. This recruitment represents a level of regulation of these oxidases. Here we report the backbone assignments of NOXO1? PX. PMID:21188560

Davis, Nicole Y; McPhail, Linda C; Horita, David A



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.



Synthesis and properties of carbohydrate-phosphate backbone-modified oligonucleotide analogues and nucleic acid mimetics  

NASA Astrophysics Data System (ADS)

Advances in the synthesis of oligo(deoxy)ribonucleotide analogues and nucleic acid mimetics made in the last decade are summarized. Attention is focused on new methods for the synthesis of derivatives with a modified ribose-phosphate backbone (phosphorothioate, boranophosphate, and nucleoside phosphonate derivatives) and derivatives devoid of the phosphate group. Among nucleic acid mimetics, conformationally restricted modified peptide nucleic acids, including those bearing a negative or positive charge, and morpholino oligomers are considered. Advantages and drawbacks of the main types of analogues as regards the complexity of the synthesis and the possibility of their application as antisense agents or reagents for hybridization analysis are compared.

Abramova, Tatyana V.; Silnikov, Vladimir N.



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.



Lipovitellin constitutes the protein backbone of glycoproteins involved in sperm-egg interaction in the amphibian Discoglossus pictus.  


Our knowledge of the molecules that interact with sperm at the egg membrane is restricted to a short list. In the eggs of Discoglossus pictus, fusion with sperm is limited to a differentiated structure, the dimple, offering several advantages for detecting molecules involved in fertilization. Previous studies have identified fucosylated glycoproteins of 200, 260, and 270?kDa located at the surface of the dimple that are able to bind sperm in vitro. Here, we show that dimple glycoproteins and a protein represented by a 120-kDa band released following gel-into-gel SDS-PAGE of both glycoproteins share the same N-terminal amino acid sequence, which itself is similar to the N-termini of Xenopus liver-synthesized vitellogenin (VTG) and the lipovitellin 1. MALDI/MS mass spectrometry indicated that the 120-kDa band is part of both gps 200 and 270/260. A 117-kDa major protein of the egg lysate exhibits the same MALDI/MS spectrum, and LC-MSMS indicates that this is a lipovitellin 1 (DpLIV) that coincides with the 120-kDa band and is responsible for the formation of the 200-270-kDa dimers. Therefore, lipovitellin 1 constitutes the protein backbone of the dimple glycoconjugates. In vitro assays using polystyrene beads coated with DpLIV or with its dimers indicate that significant sperm binding occurs only with DpLIV dimers. In amphibians, VTG is taken up by the oocyte, where it releases lipovitellins destined to form yolk. In Discoglossus, our data suggest that yolk proteins are also synthesized by the oocyte. The dimple forms in the ovulated oocyte following the exocytosis of vesicles that likely expose DpLIVs at their membrane. Indeed, in whole mounts of immunostained eggs, anti-vitellogenin antibodies label only the surface of the dimple. PMID:21308852

Campanella, C; Caputo, M; Vaccaro, M C; De Marco, N; Tretola, L; Romano, M; Prisco, M; Camardella, L; Flagiello, A; Carotenuto, R; Limatola, E; Polzonetti-Magni, A; Infante, V



C?-C bond cleavage of the peptide backbone in MALDI in-source decay using salicylic acid derivative matrices.  


The use of 5-formylsalicylic acid (5-FSA) and 5-nitrosalicylic acid (5-NSA) as novel matrices for in-source decay (ISD) of peptides in matrix-assisted laser desorption/ionization (MALDI) is described. The use of 5-FSA and 5-NSA generated a- and x-series ions accompanied by oxidized peptides [M - 2 H + H](+). The preferential formation of a- and x-series ions was found to be dependent on the hydrogen-accepting ability of matrix. The hydrogen-accepting ability estimated from the ratio of signal intensity of oxidized product [M - 2 H + H](+) to that of non-oxidized protonated molecule [M + H](+) of peptide was of the order 5-NSA > 5-FSA > 5-aminosalicylic acid (5-ASA) ? 2,5-dihydroxyl benzoic acid (2,5-DHB) ? 0. The results suggest that the hydrogen transfer reaction from peptide to 5-FSA and 5-NSA occurs during the MALDI-ISD processes. The hydrogen abstraction from peptides results in the formation of oxidized peptides containing a radical site on the amide nitrogen with subsequent radical-induced cleavage at the C?-C bond, leading to the formation of a- and x-series ions. The most significant feature of MALDI-ISD with 5-FSA and 5-NSA is the specific cleavage of the C?-C bond of the peptide backbone without degradation of side-chain and post-translational modifications (PTM). The matrix provides a useful complementary method to conventional MALDI-ISD for amino acid sequencing and site localization of PTMs in peptides. PMID:21953105

Asakawa, Daiki; Takayama, Mitsuo



The Composition of Coding Joints Formed in V(D)J Recombination Is Strongly Affected by the Nucleotide Sequence of the Coding Ends and Their Relationship to the Recombination Signal Sequences  

Microsoft Academic Search

V(D)J recombination proceeds in two stages. Precise cleavage at the border of the conserved recombination signal sequences (RSSs) and the coding ends results in flush double-stranded signal ends and coding ends terminating in hairpins. In the second stage, the signal and coding ends are processed into signal and coding joints. Coding ends containing certain nucleotide homopolymers affect the efficiency of




The mouse DNA binding protein Rc for the kappa B motif of transcription and for the V(D)J recombination signal sequences contains composite DNA-protein interaction domains and belongs to a new family of large transcriptional proteins  

SciTech Connect

Rc is a DNA binding protein with dual specificities for the V(D)J recombination signal sequences and for the B motif of the immunoglobulin kappa chain gene enhancer. The largest Rc transcript present in lymphoid cells/tissues is {approximately} 9 kb. Molecular cloning and sequence determination for 8822 bp of mouse Rc cDNA revealed an open reading frame of 2282 amino acids and long 5{prime}- and 3{prime}- untranslated regions. The derived amino acid sequence contains multiple DNA and protein interaction domains. Composite ZAS structures with tandem zinc fingers, and acidic motif, and a Ser/Thr-rich segment are located near the N-terminal and the C-terminal regions. The middle region of Rc contains a lone zinc finger, an acidic motif, a Ser-rich region, a nucleus localization signal, and GTPase motifs. Cloning and characterization of a mouse Rc gene show that the Rc cDNA corresponds to seven exons located in a genomic region spanning 70 kb. Exon 2 is exceptionally large, with 5487 bp. cDNA cloning and Northern blot analyses revealed multiple Rc transcripts, probably generated by alternative splicings. Sequence comparisons show that Rc belongs to a ZAS protein family that is involved in gene transcription and/or DNA recombination. The major histocompatibility complex class I gene enhancer binding proteins MBP1 and MBP2 are other representatives of this ZAS protein family. 43 refs., 6 figs., 2 tabs.

Wu, Lai-Chu; Liu, Yiling; Li, Zhiling [Ohio State Univ., Columbus, OH (United States)] [and others



Polypeptide helices in hybrid peptide sequences.  


A new class of polypeptide helices in hybrid sequences containing alpha-, beta-, and gamma-residues is described. The molecular conformations in crystals determined for the synthetic peptides Boc-Leu-Phe-Val-Aib-betaPhe-Leu-Phe-Val-OMe 1 (betaPhe: (S)-beta3-homophenylalanine) and Boc-Aib-Gpn-Aib-Gpn-OMe 2(Gpn: 1-(aminomethyl)cyclohexaneacetic acid) reveal expanded helical turns in the hybrid sequences (alpha alphabeta)n and (alphagamma)n. In 1, a repetitive helical structure composed of C14 hydrogen-bonded units is observed, whereas 2 provides an example of a repetitive C12 hydrogen-bonded structure. Using experimentally determined backbone torsion angles for the hydrogen-bonded units formed by hybrid sequences, we have generated energetically favorable hybrid helices. Conformational parameters are provided for C11, C12, C13, C14, and C15 helices in hybrid sequences. PMID:16305256

Ananda, Kuppanna; Vasudev, Prema G; Sengupta, Anindita; Raja, K Muruga Poopathi; Shamala, Narayanaswamy; Balaram, Padmanabhan



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

SciTech Connect

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

Radhakrishnan, R.; Bhaduri, S.B. [Idaho Univ., Moscow, ID (United States). Dept. of Mining and Metallurgy; Henager, C.H. Jr. [Pacific Northwest Lab., Richland, WA (United States)



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


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



Fair Sequences  

Microsoft Academic Search

This chapter studies fair sequences and their applications in manu- facturing, hard real-time systems, computer and operating systems, the Internet and network services. One builds a fair sequence with n letters, where letter i = 1,...,n is to occur given number di of times in the sequence. The fair sequences will be those that allocate a fair share of positions

Wieslaw Kubiak


Genetic characterization by composite sequence analysis of a new pathogenic field strain of equine infectious anemia virus from the 2006 outbreak in Ireland.  


Equine infectious anemia virus (EIAV), the causative agent of equine infectious anaemia (EIA), possesses the least-complex genomic organization of any known extant lentivirus. Despite this relative genetic simplicity, all of the complete genomic sequences published to date are derived from just two viruses, namely the North American EIAV(WYOMING) (EIAV(WY)) and Chinese EIAV(LIAONING) (EIAV(LIA)) strains. In 2006, an outbreak of EIA occurred in Ireland, apparently as a result of the importation of contaminated horse plasma from Italy and subsequent iatrogenic transmission to foals. This EIA outbreak was characterized by cases of severe, sometimes fatal, disease. To begin to understand the molecular mechanisms underlying this pathogenic phenotype, complete proviral genomic sequences in the form of 12 overlapping PCR-generated fragments were obtained from four of the EIAV-infected animals, including two of the index cases. Sequence analysis of multiple molecular clones produced from each fragment demonstrated the extent of diversity within individual viral genes and permitted construction of consensus whole-genome sequences for each of the four viral isolates. In addition, complete env gene sequences were obtained from 11 animals with differing clinical profiles, despite exposure to a common EIAV source. Although the overall genomic organization of the Irish EIAV isolates was typical of that seen in all other strains, the European viruses possessed ?80?% nucleotide sequence identity with either EIAV(WY) or EIAV(LIA). Furthermore, phylogenetic analysis suggested that the Irish EIAV isolates developed independently of the North American and Chinese viruses and that they constitute a separate monophyletic group. PMID:23175240

Quinlivan, Michelle; Cook, Frank; Kenna, Rachel; Callinan, John J; Cullinane, Ann



Digital Sequences  

NASA Astrophysics Data System (ADS)

This section discusses the applications of digital sequences in acoustical system identification and characterization and describes Golay codes and binary maximum-length sequences (MLSs) in some detail. Legendre sequences and other coded signals are briefly described. Golay codes and MLS have been used for acoustic applications for years. Applications of Legendre sequences have also been reported. Digital sequences of other classes such as, e.g., binary Gold sequences and Kasami sequences have only recently found applications in acoustical system identification and characterization.

Xiang, Ning


Protein backbone motions viewed by intraresidue and sequential HN-H? residual dipolar couplings  

PubMed Central

Summary Triple resonance E.COSY-based techniques were used to measure intra-residue and sequential HN-H? residual dipolar couplings (RDCs) for the third IgG-binding domain of protein G (GB3), aligned in Pf1 medium. Measurements closely correlate with values predicted on the basis of an NMR structure, previously determined on the basis of a large number of one-bond backbone RDCs measured in five alignment media. However, in particular the sequential HN-H? RDCs are smaller than predicted for a static structure, suggesting a degree of motion for these internuclear vectors that exceeds that of the backbone amide N-H vectors. Of all experimentally determined GB3 structures available, the best correlation between experimental 1H-1H couplings is observed for a GB3 ensemble, previously derived to generate a realistic picture of the conformational space sampled by GB3. However, for both NMR and X-ray-derived structures the 1H-1H couplings are found to be systematically smaller by ca 10% than expected on the basis of alignment tensors derived from 15N-1H amide RDCs, assuming librationally corrected N-H bond lengths of 1.041 ?.

Vogeli, Beat; Yao, Lishan; Bax, Ad



Antibacterial studies of cationic polymers with alternating, random, and uniform backbones.  


Antibacterial polymers have potential as pharmaceuticals and as coatings for implantation devices. The design of these materials will be optimized when we have a complete understanding of the structural features that impart activity toward target organisms and those that are benign with respect to the mammalian host. In this work, four series of polymers in which cationic and hydrophobic groups were distributed along the backbone were tested against six different bacterial species (both Gram-positive and Gram-negative) and for host cytotoxicities (red blood cell lysis). The most effective of the polymers studied are regularly spaced, featuring a 6-8 carbon stretch along the backbone between side chains that present positively charged groups. They cause potassium efflux, disorder the bacterial cytoplasmic membrane, and disrupt the membrane potential. These polymers, available from alternating ring-opening metathesis polymerization (AROMP), offer proof of principle for the importance of regular spacing in antibacterial polymers and for the synthesis of additional functional materials based on regularly spaced scaffolds. PMID:21370918

Song, Airong; Walker, Stephen G; Parker, Kathlyn A; Sampson, Nicole S



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 (HN, 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 (HN, 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.



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


HNN has proven to be an extremely valuable experiment for rapid and unambiguous backbone (H(N), (15)N) assignment in ((13)C, (15)N) labeled proteins. However, low sensitivity of the experiment is often a limiting factor, especially when the transverse relaxation times (T(2)) 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 8-10h. 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), (15)N) 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. PMID:20236846

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



Electrical properties of metal-molecule-silicon structures with varying molecular backbones, dipoles, and atomic tethers  

NASA Astrophysics Data System (ADS)

We present the results of an extensive experimental investigation of metal-monolayer-silicon junctions. By varying the molecular dipole, the molecular backbone, the Si-molecule linkage, and the Si-doping, we indentified critical features that determine the electrical transport and injection properties of the junctions. Two basic structures were used. One is an enclosed planar structure in which an organic monolayer is directly assembled on silicon and contacted with evaporated silver. The other was made via Flip Chip Lamination, a novel approach that relies on the formation of monolayers on a gold surface first, which enables the study of a wider range of molecular layers on silicon of very high-quality. Two charge transport regimes dominate: (1) a Schottky barrier limited regime where the molecular dipole results in silicon band bending at the junction interface, and (2) a tunneling regime where the molecular dipole creates a small local electric field that screens the electrical transport. Transition Voltage spectroscopy was used to identify electrical differences between ?-conjugated and alkyl backbones attributed to the extended ?-delocalization and variations due to the chemical nature of Si-atom linkage.

Richter, Curt A.; Gergel-Hackett, Nadine; Coll, Mariona; Hacker, Christina A.



Supramolecular organization of the repetitive backbone unit of the Streptococcus pneumoniae pilus.  


Streptococcus pneumoniae, like many other Gram-positive bacteria, assembles long filamentous pili on their surface through which they adhere to host cells. Pneumococcal pili are formed by a backbone, consisting of the repetition of the major component RrgB, and two accessory proteins (RrgA and RrgC). Here we reconstruct by transmission electron microscopy and single particle image reconstruction method the three dimensional arrangement of two neighbouring RrgB molecules, which represent the minimal repetitive structural domain of the native pilus. The crystal structure of the D2-D4 domains of RrgB was solved at 1.6 A resolution. Rigid-body fitting of the X-ray coordinates into the electron density map enabled us to define the arrangement of the backbone subunits into the S. pneumoniae native pilus. The quantitative fitting provide evidence that the pneumococcal pilus consists uniquely of RrgB monomers assembled in a head-to-tail organization. The presence of short intra-subunit linker regions connecting neighbouring domains provides the molecular basis for the intrinsic pilus flexibility. PMID:20559564

Spraggon, Glen; Koesema, Eric; Scarselli, Maria; Malito, Enrico; Biagini, Massimiliano; Norais, Nathalie; Emolo, Carla; Barocchi, Michèle Anne; Giusti, Fabiola; Hilleringmann, Markus; Rappuoli, Rino; Lesley, Scott; Covacci, Antonello; Masignani, Vega; Ferlenghi, Ilaria



Automatic assignment of protein backbone resonances by direct spectrum inspection in targeted acquisition of NMR data.  


The necessity to acquire large multidimensional datasets, a basis for assignment of NMR resonances, results in long data acquisition times during which substantial degradation of a protein sample might occur. Here we propose a method applicable for such a protein for automatic assignment of backbone resonances by direct inspection of multidimensional NMR spectra. In order to establish an optimal balance between completeness of resonance assignment and losses of cross-peaks due to dynamic processes/degradation of protein, assignment of backbone resonances is set as a stirring criterion for dynamically controlled targeted nonlinear NMR data acquisition. The result is demonstrated with the 12 kDa (13)C,(15) N-labeled apo-form of heme chaperone protein CcmE, where hydrolytic cleavage of 29 C-terminal amino acids is detected. For this protein, 90 and 98% of manually assignable resonances are automatically assigned within 10 and 40 h of nonlinear sampling of five 3D NMR spectra, respectively, instead of 600 h needed to complete the full time domain grid. In addition, resonances stemming from degradation products are identified. This study indicates that automatic resonance assignment might serve as a guiding criterion for optimal run-time allocation of NMR resources in applications to proteins prone to degradation. PMID:18784977

Wong, Leo E; Masse, James E; Jaravine, Victor; Orekhov, Vladislav; Pervushin, Konstantin



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


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

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



High-quality protein backbone reconstruction from alpha carbons using Gaussian mixture models.  


Coarse-grained protein structure models offer increased efficiency in structural modeling, but these must be coupled with fast and accurate methods to revert to a full-atom structure. Here, we present a novel algorithm to reconstruct mainchain models from C traces. This has been parameterized by fitting Gaussian mixture models (GMMs) to short backbone fragments centered on idealized peptide bonds. The method we have developed is statistically significantly more accurate than several competing methods, both in terms of RMSD values and dihedral angle differences. The method produced Ramachandran dihedral angle distributions that are closer to that observed in real proteins and better Phaser molecular replacement log-likelihood gains. Amino acid residue sidechain reconstruction accuracy using SCWRL4 was found to be statistically significantly correlated to backbone reconstruction accuracy. Finally, the PD2 method was found to produce significantly lower energy full-atom models using Rosetta which has implications for multiscale protein modeling using coarse-grained models. A webserver and C++ source code is freely available for noncommercial use from: PMID:23703289

Moore, Benjamin L; Kelley, Lawrence A; Barber, James; Murray, James W; MacDonald, James T



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.



The chemical and hydrological evolution of an ancient potash-forming evaporite basin as constrained by mineral sequence, fluid inclusion composition, and numerical simulation  

Microsoft Academic Search

The chemical evolution of the brine in a potash evaporite basin has been investigated by X-ray microanalysis of frozen primary inclusions trapped in halite. A Computer program based on thermodynamic equilibrium and mass balance principles has been used to simulate evaporation paths. The comparison between the results of calculations, the observed mineralogy and mineral sequence, and the solute content in

Carlos Ayora; Javier Garcia-Veigas; Juan-Jose Pueyo



Effect of feeding regime and the sludge age on the fate of acetate and the microbial composition in sequencing batch reactor  

Microsoft Academic Search

The study investigated the effects of the feeding regime on the substrate metabolism under aerobic conditions. Throughout the study, two parallel sequencing batch reactors were operated using either short-term (pulse) or long-term (almost continuous) feeding of acetate at two different sludge ages of two days and eight days. The microbial characterization studies showed that the feeding regime did not change

Asli S. Ciggin; Simona Rossetti; Mauro Majone; Derin Orhon



Application of chitosan/Fe?O? microsphere-graphene composite modified carbon ionic liquid electrode for the electrochemical detection of the PCR product of soybean Lectin gene sequence.  


In this paper a Fe(3)O(4) microsphere, graphene (GR) and chitosan (CTS) nanocomposite material modified carbon ionic liquid electrode (CILE) was used as the platform for the construction of a new electrochemical DNA biosensor. The single-stranded DNA (ssDNA) probe was immobilized directly on the surface of the CTS/Fe(3)O(4)-GR/CILE, which could hybridize with the target ssDNA sequence at the selected conditions. By using methylene blue (MB) as the electrochemical indicator the hybridization reaction was investigated with the reduction peak current measured. By combining the specific properties such as the biocompatibility and big surface area of Fe(3)O(4) microspheres, the excellent electron transfer ability of GR, the good film-forming ability of CTS and the high conductivity of CILE, the synergistic effects of nanocomposite increased the amounts of ssDNA adsorbed on the electrode surface and then resulted in the greatly increase of the electrochemical responses. Under the optimal conditions differential pulse voltammetric responses of MB were proportional to the specific ssDNA sequences concentration in the range from 1.0×10(-12) to 1.0×10(-6)mol/L with the detection limit as 3.59×10(-13)mol/L (3?). This DNA biosensor showed good stability and discrimination ability to one-base and three-base mismatched ssDNA sequences. The polymerase chain reaction (PCR) product of soybean Lectin gene sequence was detected by the proposed method with satisfactory result, suggesting that the CTS/Fe(3)O(4)-GR/CILE was a suitable sensing platform for the sensitive detection of specific gene sequence. PMID:22099656

Sun, Wei; Qi, Xiaowei; Chen, Ying; Liu, Shengyun; Gao, Hongwei



Polarizable Simulations with Second order Interaction Model (POSSIM) force field: Developing parameters for alanine peptides and protein backbone  

PubMed Central

A previously introduced POSSIM (POlarizable Simulations with Second order Interaction Model) force field has been extended to include parameters for alanine peptides and protein backbones. New features were introduced into the fitting protocol, as compared to the previous generation of the polarizable force field for proteins. A reduced amount of quantum mechanical data was employed in fitting the electrostatic parameters. Transferability of the electrostatics between our recently developed NMA model and the protein backbone was confirmed. Binding energy and geometry for complexes of alanine dipeptide with a water molecule were estimated and found in a good agreement with high-level quantum mechanical results (for example, the intermolecular distances agreeing within ca. 0.06Å). Following the previously devised procedure, we calculated average errors in alanine di- and tetra-peptide conformational energies and backbone angles and found the agreement to be adequate (for example, the alanine tetrapeptide extended-globular conformational energy gap was calculated to be 3.09 kcal/mol quantim mechanically and 3.14 kcal/mol with the POSSIM force field). However, we have now also included simulation of a simple alpha-helix in both gas-phase and water as the ultimate test of the backbone conformational behavior. The resulting alanine and protein backbone force field is currently being employed in further development of the POSSIM fast polarizable force field for proteins.

Ponomarev, Sergei Y.; Kaminski, George A.



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



Diversity and composition of the bacterial community of Poyang Lake (China) as determined by 16S rRNA gene sequence analysis  

Microsoft Academic Search

Poyang Lake is the largest fresh water lake in China. In this study, the objective was to examine the diversity of bacterial\\u000a community in this environment. The phylogenetic composition of bacterioplankton communities from two sites and two dates (northern\\u000a and southern sub-basins in October 2006 and in May 2007, respectively) in the water column of Poyang Lake were investigated\\u000a by

Lan WuGang; Gang Ge; Guofeng Zhu; Shijie Gong; Siguang Li; Jinbao Wan


Effect of laminate stacking sequence on the high frequency fatigue behavior of SCS6 fiber-reinforced Si 3 N 4 matrix composites  

Microsoft Academic Search

In many potential applications, continuous fiber-reinforced ceramic matrix composites (CFCMCs) will encounter cyclic fatigue\\u000a loadings at high frequencies (25 Hz or higher). While most of the work in the area of fatigue of CFCMCs has concentrated on\\u000a low frequency behavior, high frequency behavior is equally important. In CFCMCs, stress-strain hysteresis occurs during fatigue\\u000a and is associated with energy dissipation in

Nikhilesh Chawla



Solution structure and backbone dynamics of human epidermal-type fatty acid-binding protein (E-FABP).  

PubMed Central

Human epidermal-type fatty acid-binding protein (E-FABP) belongs to a family of intracellular 14-15 kDa lipid-binding proteins, whose functions have been associated with fatty acid signalling, cell growth, regulation and differentiation. As a contribution to understanding the structure-function relationship, we report in the present study features of its solution structure and backbone dynamics determined by NMR spectroscopy. Applying multi-dimensional high-resolution NMR techniques on unlabelled and 15N-enriched recombinant human E-FABP, the 1H and 15N resonance assignments were completed. On the basis of 2008 distance restraints, the three-dimensional solution structure of human E-FABP was subsequently obtained (backbone atom root-mean-square deviation of 0.92+/-0.11 A; where 1 A=0.1 nm), consisting mainly of 10 anti-parallel beta-strands that form a beta-barrel structure. 15N relaxation experiments (T1, T2 and heteronuclear nuclear Overhauser effects) at 500, 600 and 800 MHz provided information on the internal dynamics of the protein backbone. Nearly all non-terminal backbone amide groups showed order parameters S(2)>0.8, with an average value of 0.88+/-0.04, suggesting a uniformly low backbone mobility in the nanosecond-to-picosecond time range. Moreover, hydrogen/deuterium exchange experiments indicated a direct correlation between the stability of the hydrogen-bonding network in the beta-sheet structure and the conformational exchange in the millisecond-to-microsecond time range. The features of E-FABP backbone dynamics elaborated in the present study differ markedly from those of the phylogenetically closely related heart-type FABP and the more distantly related ileal lipid-binding protein, implying a strong interdependence with the overall protein stability and possibly also with the ligand-binding affinity for members of the lipid-binding protein family.

Gutierrez-Gonzalez, Luis H; Ludwig, Christian; Hohoff, Carsten; Rademacher, Martin; Hanhoff, Thorsten; Ruterjans, Heinz; Spener, Friedrich; Lucke, Christian



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."



Repetitive Sequences  

Technology Transfer Automated Retrieval System (TEKTRAN)

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


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.


Protein Backbone Dynamics through 13C?-13C? Cross-Relaxation in NMR Spectroscopy  

PubMed Central

Internal dynamics of proteins are usually characterized by the analysis of 15N relaxation rates that reflect the motions of NHN vectors. It was suggested a decade ago that additional information on backbone motions can be obtained by measuring cross-relaxation rates associated with intra-residue C?C? vectors. Here we propose a new approach to such measurements, based on the observation of the transfer between two-spin orders 2NzCz? and 2NzCz?. This amounts to “anchoring” the Cz? and Cz? operators to the Nz term from the amide of the next residue. In combination with symmetrical reconversion, this method greatly reduces various artifacts. The experiment is carried out on human ubiquitin at 284.1 K, where the correlation time is 7.1 ns. The motions of the C?C? vector appear more restricted than those of the NHN vector.

Ferrage, Fabien; Pelupessy, Philippe; Cowburn, David; Bodenhausen, Geoffrey



Facile backbone structure determination of human membrane proteins by NMR spectroscopy  

PubMed Central

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

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



Protection against Staphylococcus aureus by antibody to the polyglycerolphosphate backbone of heterologous lipoteichoic acid.  


Type 1 lipoteichoic acid (LTA) is present in many clinically important gram-positive bacteria, including enterococci, streptococci, and staphylococci, and antibodies against LTA have been shown to opsonize nonencapsulated Enterococcus faecalis strains. In the present study, we show that antibodies against E. faecalis LTA also bind to type 1 LTA from other gram-positive species and opsonized Staphylocccus epidermidis and Staphylcoccus aureus strains as well as group B streptococci. Inhibition studies using teichoic acid oligomers indicated that cross-reactive opsonic antibodies bind to the teichoic acid backbone. Passive immunization with rabbit antibodies against E. faecalis LTA promoted the clearance of bacteremia by E. faecalis and S. epidermidis in mice. Furthermore, passive protection also reduced mortality in a murine S. aureus peritonitis model. The effectiveness of rabbit antibody against LTA suggests that this conserved bacterial structure could function as a single vaccine antigen that targets multiple gram-positive pathogens. PMID:22362863

Theilacker, Christian; Kropec, Andrea; Hammer, Felix; Sava, Irina; Wobser, Dominique; Sakinc, Tuerkan; Codée, Jeroen D C; Hogendorf, Wouter F J; van der Marel, Gijsbert A; Huebner, Johannes



YcaO domains utilize ATP to activate amide backbones during peptide cyclodehydrations  

PubMed Central

Thiazole/oxazole-modified microcins (TOMMs) encompass a recently defined class of ribosomally synthesized natural products with a diverse set of biological activities. Although TOMM biosynthesis has been investigated for over a decade, the mechanism of heterocycle formation by the synthetase enzymes remains poorly understood. Using substrate analogs and isotopic labeling, we demonstrate that adenosine 5?-triphosphate (ATP) is utilized to directly phosphorylate the peptide amide backbone during TOMM heterocycle formation. Moreover, we present the first experimental evidence that the D-protein component of the heterocycle-forming synthetase (YcaO/DUF181 family member), formerly annotated as a docking/scaffolding protein involved in complex formation and regulation, is able to perform the ATP-dependent cyclodehydration reaction in the absence of the other TOMM biosynthetic proteins. Together, these data provide a greater level of detail into the biosynthesis of azol(in)e heterocycles in ribosomal natural products and prompt a reclassification of the enzymes involved in their installation.

Dunbar, Kyle L; Melby, Joel O; Mitchell, Douglas A



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)



Modeling the Backbone Dynamics of Reduced and Oxidized Solvated Rat Microsomal Cytochrome b5  

PubMed Central

In this article, a description of the statistics and dynamics of cytochrome b5 in both reduced and oxidized forms is given. Results of molecular dynamics computer simulations in the explicit solvent have been combined with mode-coupling diffusion models including and neglecting the molecule-solvent correlations. R1 and R1? nuclear magnetic relaxation parameters of 15N in the protein backbone have been calculated and compared with experiments. Slight changes in charge density in the heme upon oxidation produces a cascade of changes in charge distributions from heme propionates up to charged residues ?1.5 nm from Fe. These changes in charge distributions modify the molecular surface and the water shell surrounding the protein. The statistical changes upon oxidation can be included in diffusive models that physically explain the upper and lower limits of R1? relaxation parameters at high off-resonance fields.

Giachetti, Andrea; Penna, Giovanni La; Perico, Angelo; Banci, Lucia



RNABC: forward kinematics to reduce all-atom steric clashes in RNA backbone.  


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 (>or= 0.4 A 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 . PMID:17401565

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



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


A statistical mechanical model of allosteric transition of proteins is developed by extending the structure-based model of protein folding to cases that a protein has two different native conformations. Partition function is calculated exactly within the model and free-energy surfaces associated with allostery are derived. In this paper, the model of allosteric transition proposed in a previous paper [Proc. Natl. Acad. Sci. U.S.A 134, 7775 (2010)] is reformulated to describe both fluctuation in side-chain configurations and that in backbone structures in a balanced way. The model is applied to example proteins, Ras, calmodulin, and CheY: Ras undergoes the allosteric transition between guanosine diphosphate (GDP)-bound and guanosine triphosphate (GTP)-bound forms, and the model results show that the GDP-bound form is stabilized enough to prevent unnecessary signal transmission, but the conformation in the GTP-bound state bears large fluctuation in side-chain configurations, which may help to bind multiple target proteins for multiple pathways of signaling. The calculated results of calmodulin show the scenario of sequential ordering in Ca(2+) binding and the associated allosteric conformational change, which are realized though the sequential appearing of pre-existing structural fluctuations, i.e., fluctuations to show structures suitable to bind Ca(2+) before its binding. Here, the pre-existing fluctuations to accept the second and third Ca(2+) ions are dominated by the side-chain fluctuation. In CheY, the calculated side-chain fluctuation of Tyr106 is coordinated with the backbone structural change in the ?4-?4 loop, which explains the pre-existing Y-T coupling process in this protein. Ability of the model to explain allosteric transitions of example proteins supports the view that the large entropic effects lower the free-energy barrier of allosteric transition. PMID:21456702

Itoh, Kazuhito; Sasai, Masaki



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

PubMed Central

The backbone dynamics of the tetrameric p53 oligomerization domain (residues 319-360) have been investigated by two-dimensional inverse detected heteronuclear 1H-15N NMR spectroscopy at 500 and 600 MHz. 15N T1, T2, 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 T1/T2 ratios, was found to be 14.8 ns at 35 degrees C. The correlation times and amplitudes of the internal motions were extracted from the relaxation data using the model-free formalism (Lipari G, Szabo A, 1982, J Am Chem Soc 104:4546-4559). The internal dynamics of the structural core of the p53 oligomerization domain are uniform and fairly rigid, with residues 327-354 exhibiting an average generalized order parameter (S2) of 0.88 +/- 0.08. The N- and C-termini exhibit substantial mobility and are unstructured in the solution structure of p53. Residues located at the N- and C-termini, in the beta-sheet, in the turn between the alpha-helix and beta-sheet, and at the C-terminal end of the alpha-helix display two distinct internal motions that are faster than the overall correlation time. Fast internal motions (< or = 20 ps) are within the extreme narrowing limit and are of uniform amplitude. The slower motions (0.6-2.2 ns) are outside the extreme narrowing limit and vary in amplitude.(ABSTRACT TRUNCATED AT 250 WORDS)

Clubb, R. T.; Omichinski, J. G.; Sakaguchi, K.; Appella, E.; Gronenborn, A. M.; Clore, G. M.



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

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



Comparison of 13C?H and 15NH backbone dynamics in protein GB1  

PubMed Central

This study presents a site-resolved experimental view of backbone C?H and NH internal motions in the 56-residue immunoglobulin-binding domain of streptococcal protein G, GB1. Using 13C?H and 15NH NMR relaxation data [T1, T2, and NOE] acquired at three resonance frequencies (1H frequencies of 500, 600, and 800 MHz), spectral density functions were calculated as F(?) = 2?J(?) to provide a model-independent way to visualize and analyze internal motional correlation time distributions for backbone groups in GB1. Line broadening in F(?) curves indicates the presence of nanosecond time scale internal motions (0.8 to 5 nsec) for all C?H and NH groups. Deconvolution of F(?) curves effectively separates overall tumbling and internal motional correlation time distributions to yield more accurate order parameters than determined by using standard model free approaches. Compared to NH groups, C?H internal motions are more broadly distributed on the nanosecond time scale, and larger C?H order parameters are related to correlated bond rotations for C?H fluctuations. Motional parameters for NH groups are more structurally correlated, with NH order parameters, for example, being larger for residues in more structured regions of ?-sheet and helix and generally smaller for residues in the loop and turns. This is most likely related to the observation that NH order parameters are correlated to hydrogen bonding. This study contributes to the general understanding of protein dynamics and exemplifies an alternative and easier way to analyze NMR relaxation data.

Idiyatullin, Djaudat; Nesmelova, Irina; Daragan, Vladimir A.; Mayo, Kevin H.



Comparison of (13)C(alpha)H and (15)NH backbone dynamics in protein GB1.  


This study presents a site-resolved experimental view of backbone C(alpha)H and NH internal motions in the 56-residue immunoglobulin-binding domain of streptococcal protein G, GB1. Using (13)C(alpha)H and (15)NH NMR relaxation data [T(1), T(2), and NOE] acquired at three resonance frequencies ((1)H frequencies of 500, 600, and 800 MHz), spectral density functions were calculated as F(omega) = 2omegaJ(omega) to provide a model-independent way to visualize and analyze internal motional correlation time distributions for backbone groups in GB1. Line broadening in F(omega) curves indicates the presence of nanosecond time scale internal motions (0.8 to 5 nsec) for all C(alpha)H and NH groups. Deconvolution of F(omega) curves effectively separates overall tumbling and internal motional correlation time distributions to yield more accurate order parameters than determined by using standard model free approaches. Compared to NH groups, C(alpha)H internal motions are more broadly distributed on the nanosecond time scale, and larger C(alpha)H order parameters are related to correlated bond rotations for C(alpha)H fluctuations. Motional parameters for NH groups are more structurally correlated, with NH order parameters, for example, being larger for residues in more structured regions of beta-sheet and helix and generally smaller for residues in the loop and turns. This is most likely related to the observation that NH order parameters are correlated to hydrogen bonding. This study contributes to the general understanding of protein dynamics and exemplifies an alternative and easier way to analyze NMR relaxation data. PMID:12717014

Idiyatullin, Djaudat; Nesmelova, Irina; Daragan, Vladimir A; Mayo, Kevin H



Biosensors for DNA sequence detection.  


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. PMID:12470736

Vercoutere, Wenonah; Akeson, Mark



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))



Sequence-controlled polymerization using dendritic macromonomers: precise chain-positioning of bulky functional clusters.  


A simple strategy to insert functional dendrons at precise positions along a linear polymer backbone is reported. Sequence controlled copolymerization of styrene and polyester dendrons containing a maleimide unit at their focal points was utilized to yield such polymers. PMID:23775396

Baradel, Nathalie; Gok, Ozgul; Zamfir, Mirela; Sanyal, Amitav; Lutz, Jean-François



Effect of nanotube waviness on the electrical conductivity of carbon nanotube-based composites  

Microsoft Academic Search

This paper reports the effect of nanotube waviness on the electrical conductivity of carbon nanotube-based composites using a percolation model. Wavy nanotubes are approximated by elongated polygons, and the current-carrying backbones of percolation clusters in the composite are identified by the direct electrifying algorithm. The tunneling resistance due to an insulating film of matrix material between crossing nanotubes is considered.

Chunyu Li; Erik T. Thostenson; Tsu-Wei Chou



solution structure, backbone dynamics, and interaction with Cdc42 of Salmonella guanine nucleotide exchange factor SopE2.  


SopE and SopE2 are delivered by the Salmonella type III secretion system into eukaryotic cells to promote cell invasion. SopE and SopE2 are potent guanine nucleotide exchange factors (GEFs) for Rho GTPases Cdc42 and Rac1 and constitute a novel class of Rho GEFs. Although the sequence of SopE-like GEFs is not at all homologous to those of the Dbl homology domain-containing eukaryotic GEFs, the mechanism of nucleotide release seems to have significant similarities. We have determined the solution structure of the catalytic domain (residues 69-240) of SopE2, showing that SopE2(69-240) comprises two three-helix bundles (alpha1alpha4alpha5 and alpha2alpha3alpha6) arranged in a Lambda shape. Compared to the crystal structure of SopE(78-240) in complex with Cdc42, SopE2(69-240) exhibits a less open Lambda shape due to movement of SopE(78-240) helices alpha2 and alpha5 to accommodate binding to the Cdc42 switch regions. In an NMR titration to investigate the SopE2(69-240)-Cdc42 interaction, the SopE2(69-240) residues affected by binding Cdc42 were very similar to the SopE(78-240) residues that contact Cdc42 in the SopE(78-240)-Cdc42 complex. Analysis of the backbone (15)N dynamics of SopE2(69-240) revealed flexibility in residues that link the two three-helix bundles, including the alpha3-alpha4 linker that incorporates a beta-hairpin and the catalytic loop, and the alpha5-alpha6 loop, and flexibility in residues involved in interaction with Cdc42. Together, these observations provide experimental evidence of a previously proposed mechanism of GEF-mediated nucleotide exchange based on the Rac1-Tiam1 complex structure, with SopE/E2 flexibility, particularly in the interbundle loops, enabling conformational rearrangements of the nucleotide binding region of Cdc42 through an induced fit type of binding. Such flexibility in SopE/E2 may also facilitate interaction through adaptive binding with alternative target proteins such as Rab5, allograft inflammatory factor 1, and apolipoprotein A-1. PMID:15379540

Williams, Christopher; Galyov, Edouard E; Bagby, Stefan



End-to-End QoS Architecture for VPNs: MPLS VPN Deployment in a Backbone Network  

Microsoft Academic Search

Virtual private networks (VPNs) enable companies to connect geographically dispersed offices and remote workers via secure links to the private company network, using the public Internet as a backbone. Specially, VPN service in the broadband data communication network is very important and necessary to take in users who want to specify group communication. VPN mechanisms are needed which work over

Haeryong Lee; Jeongyeon Hwang; Byungryong Kang; Kyoungpyo Jun



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

PubMed Central

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

Arges, Christopher G.; Ramani, Vijay



The extension of a DNA double helix by an additional Watson-Crick base pair on the same backbone.  


Additional base pair: The DNA duplex can be extended with an additional Watson-Crick base pair on the same backbone by the use of double-headed nucleotides. These also work as compressed dinucleotides and form two base pairs with cognate nucleobases on the opposite strand. PMID:23712945

Kumar, Pawan; Sharma, Pawan K; Madsen, Charlotte S; Petersen, Michael; Nielsen, Poul



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



Phase behaviors, molecular and supramolecular structures in polymers containing rigid-rod backbones with cyanobiphenyl side chains  

Microsoft Academic Search

One of the most important and challenging topics in materials chemistry involves designing nano-structures in synthetic materials via self-assembly for various highly technical applications. A specially designed combined liquid crystalline polymer containing a polyester backbone with cyanobiphenyl side chains has been studied in aspects of phase behaviors and crystal structures. The triclinic crystal phases identified in this series of polymer

Jrjeng Ruan



(1)H, (13)C, (15)N backbone and side chain NMR resonance assignments of BPSL1050 from Burkholderia pseudomallei.  


BPSL1050 is a 13.9 kDa protein produced by the Gram-negative bacterium Burkholderia pseudomallei, the etiological agent of melioidosis. Immunodetection assays against sera patients using protein microarray suggest BPSL1050 involvement in melioidosis. Herein we report its backbone and side chains NMR assignment. PMID:23616103

Gaudesi, Davide; Quilici, Giacomo; Musco, Giovanna



Sequence landscapes.  

PubMed Central

We describe a method for representing the structure of repeating sequences in nucleic-acids, proteins and other texts. A portion of the sequence is presented at the bottom of a CRT screen. Above the sequence is its landscape, which looks like a mountain range. Each mountain corresponds to a subsequence of the sequence. At the peak of every mountain is written the number of times that the subsequence appears. A data structure called a DAWG, which can be built in time proportional to the length of the sequence, is used to construct the landscape. For the 40 thousand bases of bacteriophage T7, the DAWG can be built in 30 seconds. The time to display any portion of the landscape is less than a second. Using sequence landscapes, one can quickly locate significant repeats.

Clift, B; Haussler, D; McConnell, R; Schneider, T D; Stormo, G D



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.  


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



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



Backbone dynamics of the 269-residue protease Savinase determined from 15N-NMR relaxation measurements.  


Backbone dynamics of Savinase, a subtilisin of 269 residues secreted by Bacillus lentus, have been studied using 15N relaxation measurements derived from proton-detected dimensional 1H-15N-NMR spectroscopy. 15N spin-lattice rate constants (R1), spin-spin relaxation-rate constants(R2), and 1H-15N nuclear Overhauser effects (NOE) were determined for 84% of the backbone amide 15N nuclei. The model-free formalism [Lipari, G. & Szabo, A. (1982) J. Am. Chem. Soc. 104, 4546-4559] was used to derive values for a generalized order parameter, S2, interpretable as a measure of the amplitude of motion on the picosecond-nanosecond timescale, for each N-H bond vector. Additional terms used to fit the data include an effective correlation time for internal motions (taue) and an exchange term (Rex) to account for exchange contributions to R2. The overall rotational correlation time (taum) is 9.59 +/- 0.02 ns; the average order parameter (S2) is 0.90 +/- 0.07, indicative of a rigid structure consistent with Savinase's high degree of secondary structure and compact tertiary fold. Residues S125-S128, located in the substrate-binding region, represent the longest stretch of protein which exhibits disorder on the picosecond-nanosecond timescale. These residues also exhibit significant exchange terms, possibly indicative of motion on the microsecond-millisecond timescale, which could also be influenced by the proximity of the phenyl ring of the substituted aryl boronic acid inhibitor used in this study. S103 and G219 in the substrate-binding region, represent the longest stretch of protein which exhibits disorder on the picosecond-nanosecond timescale. These residues also exhibit significant exchange terms, possibly indicative of motion on the microsecond-millisecond timescale, which could also be influenced by the proximity of the phenyl ring of the substituted aryl boronic acid inhibitor used in this study. S103 and G219 in the substrate-binding region also show flexibility on the picosecond-nanosecond timescale. There is also significant motion in the turn, G258-T260, of a small solvent-exposed loop region which may make the protein vulnerable autolysis at that point. Some residues in both calcium-binding sites and nearby also show mobility. PMID:8654411

Remerowski, M L; Pepermans, H A; Hilbers, C W; Van De Ven, F J



A natural fiber composite in a pelagic limestone-chert sequence. The importance of mechanical stratigraphy for fracture type development in carbonate anticlines.  

NASA Astrophysics Data System (ADS)

Thrust fault-related folds in carbonate rocks are characterized by deformation accommodated by different kinds of structures, such as joints, faults, pressure solution seams (PSSs), and deformation bands, which may form at various stages during the folding process. Defining the distribution, orientation, and the type of fold-related structures and understanding the relationships between folding and fracturing is significant both for theoretical and practical purposes. Furthermore, as the deformation related to the folding process influences fluid flow through rocks, identifying the types of structures formed during folding is as important as predicting their geometries. To unravel the relationship between mechanical stratigraphy and folding process, the well-exposed Cingoli anticline (Northern Apennines), has been studied in detail. The Upper Cretaceous-Middle Eocene stratigraphy of the Cingoli anticline is characterized by a pelagic multilayer made up of fine-grained pelagic limestones and, marly limestones, in places alternated with thin continuous chert layers. The presence of several outcrops located in different structural positions of the anticline makes the Cingoli anticline an excellent natural laboratory to investigate relationships between folding, fracturing, and mechanical stratigraphy relative to the structural setting of the fold. The field data collected show that high angle to bedding PSSs, which formed before tilting and during the first stage of folding, are not homogeneously distributed in the pelagic limestones. Generally, high angle to bedding PSSs form in the marly pelagic limestones and they have been observed in several outcrops and in different structural positions except where the marly limestones are inter-bedded with stiffer chert layers. In order to analyse theoretically what observed in the field, we compared the deformation of limestones and chert layers with the deformation acting on fiber composites. In the mechanics of materials, composites refer to a matrix reinforced with particles, fibers, or laminae. During the early stage of folding, when the compressive stress is almost bedding parallel, chert layers act as a stiff lamina embedded in a weak limestone matrix. As a result, the stress is partitioned and the chert layers bear the greatest stress. Considering the mechanical properties (Poisson and Young's modulus) of the two materials (chert and limestone), and the estimated tectonic stress acting at the onset of the folding process, the stress magnitude in the limestone beds does not reach the expected value for the onset of pressure solution. For this reason, pelagic limestones containing chert layers are mainly characterized by joints whereas PSSs form in pelagic limestones without the stiffer phase (chert). This study suggests that within the same fold, and even within the same formation, different mechanical units can be characterized by different fractures types and fluid flow behaviour as a result of mechanical stratigraphy distribution.

Petracchini, Lorenzo; Antonellini, Marco; Scrocca, Davide; Billi, Andrea



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



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



Polypeptoids: A Diverse Family of Sequence-Specific Heteropolymers with Stable Secondary Structure  

Microsoft Academic Search

We report the synthesis and characterization of a family of structured oligo-N-substituted glycines (peptoids) up to 36 residues in length, produced by an efficient solid-phase protocol that allows the facile incorporation of chemically diverse sidechains in a sequence-specific fashion. Certain polypeptoid sequences demonstrate stable, chiral secondary structure in the polymer backbone, despite its lack of mainchain chiral centers and hydrogen

Annelise E. Barron; Kent Kirshenbaum; Philippe Armand; Fred E. Cohen; Ken A. Dill; Richard E. Goldsmith; Kiet T. V. Truong; Erin K. Bradley; Ronald N. Zuckermann



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


Potter's Sequence  

PubMed Central

Potter's sequence is a rare fatal disorder that occurs in sporadic and autosomal recessive forms with an incidence of 1 in 4000 births. Babies born with this condition are either still born or die very early within the neonatal period. We report a case of Potter's sequence with the typical physical findings and histological findings.

Shastry, Srikanth M.; Kolte, Sachin S.; Sanagapati, Panduranga R.



Sequence biostratigraphy  

SciTech Connect

Sequence biostratigraphy is a relatively new discipline that has rapidly expanded in parallel with the development of sequence stratigraphy. Sequence biostratigraphic concepts result in significant improvements in the authors ability to determine ages, correlate stratigraphic units, and to estimate environments of deposition. Sequence stratigraphy provides a physical framework consisting of a predictable hierarchy of correlation surfaces, ranging from sequence boundaries to parasequence boundaries, within which biostratigraphic observations may be placed. These physical correlation surfaces define true chronostratigraphic units that can be used to assess, using time-distance grids, the relative position of biozone 'tops' or 'bases.' These surfaces also provide a physical link between sedimentary basins and the open-ocean planktonic microfossil chronozones established by the Deep Sea Drilling and Ocean Drilling Programs. Another important role for sequence biostratigraphy is the calibration of nonmarine biozones with open ocean microfossil zones via physical correlation surfaces. Sequence stratigraphic concepts have also played an important role in the estimation of depositional environments, particularly water depths and distance from shoreline. The recognition of large, apparently sudden (but actually gradual), water depth changes within condensed sections results in more accurate and precise paleobathymetric estimation in exploration wells. Sequence biostratigraphers now utilize a wider range of tools to accomplish the traditional tasks of age determination and paleoenvironmental analysis and produce results more efficiently and effectively.

Loutit, T.S.; Hardenbol, J.; Wright, R.C. (Exxon Production Research Co., Houston, TX (United States))



Short sequence motifs, overrepresented in mammalian conservednon-coding sequences  

SciTech Connect

Background: A substantial fraction of non-coding DNAsequences of multicellular eukaryotes is under selective constraint. Inparticular, ~;5 percent of the human genome consists of conservednon-coding sequences (CNSs). CNSs differ from other genomic sequences intheir nucleotide composition and must play important functional roles,which mostly remain obscure.Results: We investigated relative abundancesof short sequence motifs in all human CNSs present in the human/mousewhole-genome alignments vs. three background sets of sequences: (i)weakly conserved or unconserved non-coding sequences (non-CNSs); (ii)near-promoter sequences (located between nucleotides -500 and -1500,relative to a start of transcription); and (iii) random sequences withthe same nucleotide composition as that of CNSs. When compared tonon-CNSs and near-promoter sequences, CNSs possess an excess of AT-richmotifs, often containing runs of identical nucleotides. In contrast, whencompared to random sequences, CNSs contain an excess of GC-rich motifswhich, however, lack CpG dinucleotides. Thus, abundance of short sequencemotifs in human CNSs, taken as a whole, is mostly determined by theiroverall compositional properties and not by overrepresentation of anyspecific short motifs. These properties are: (i) high AT-content of CNSs,(ii) a tendency, probably due to context-dependent mutation, of A's andT's to clump, (iii) presence of short GC-rich regions, and (iv) avoidanceof CpG contexts, due to their hypermutability. Only a small number ofshort motifs, overrepresented in all human CNSs are similar to bindingsites of transcription factors from the FOX family.Conclusion: Human CNSsas a whole appear to be too broad a class of sequences to possess strongfootprints of any short sequence-specific functions. Such footprintsshould be studied at the level of functional subclasses of CNSs, such asthose which flank genes with a particular pattern of expression. Overallproperties of CNSs are affected by patterns in mutation, suggesting thatselection which causes their conservation is not always verystrong.

Minovitsky, Simon; Stegmaier, Philip; Kel, Alexander; Kondrashov,Alexey S.; Dubchak, Inna



Sequence nets.  


We study a class of networks generated by sequences of letters taken from a finite alphabet consisting of m letters (corresponding to m types of nodes) and a fixed set of connectivity rules. Recently, it was shown how a binary alphabet might generate threshold nets in a similar fashion [A. Hagberg, Phys. Rev. E 74, 056116 (2006)]. Just like threshold nets, sequence nets in general possess a modular structure reminiscent of everyday-life nets and are easy to handle analytically (i.e., calculate degree distribution, shortest paths, betweenness centrality, etc.). Exploiting symmetry, we make a full classification of two- and three-letter sequence nets, discovering two classes of two-letter sequence nets. These sequence nets retain many of the desirable analytical properties of threshold nets while yielding richer possibilities for the modeling of everyday-life complex networks more faithfully. PMID:18850894

Sun, Jie; Nishikawa, Takashi; Ben-Avraham, Daniel



Prediction of Xaa-Pro peptide bond conformation from sequence and chemical shifts  

PubMed Central

We present a program, named Promega, to predict the Xaa-Pro peptide bond conformation on the basis of backbone chemical shifts and the amino acid sequence. Using a chemical shift database of proteins of known structure together with the PDB-extracted amino acid preference of cis Xaa-Pro peptide bonds, a cis/trans probability score is calculated from the backbone and 13C? chemical shifts of the proline and its neighboring residues. For an arbitrary number of input chemical shifts, which may include Pro-13C?, Promega calculates the statistical probability that a Xaa-Pro peptide bond is cis. Besides its potential as a validation tool, Promega is particularly useful for studies of larger proteins where Pro-13C? assignments can be challenging, and for on-going efforts to determine protein structures exclusively on the basis of backbone and 13C? chemical shifts.

Shen, Yang; Bax, Ad



Glyoxylate as a Backbone Linkage for a Prebiotic Ancestor of RNA  

NASA Astrophysics Data System (ADS)

The origin of the first RNA polymers is central to most current theories for the origin of life. Difficulties associated with the prebiotic formation of RNA have lead to the general consensus that a simpler polymer preceded RNA. However, polymers proposed as possible ancestors to RNA are not much easier to synthesize than RNA itself. One particular problem with the prebiotic synthesis of RNA is the formation of phosphoester bonds in the absence of chemical activation. Here we demonstrate that glyoxylate (the ionized form of glyoxylic acid), a plausible prebiotic molecule, represents a possible ancestor of the phosphate group in modern RNA. Although in low yields (˜ 1%), acetals are formed from glyoxylate and nucleosides under neutral conditions, provided that metal ions are present (e.g., Mg2+), and provided that water is removed by evaporation at moderate temperatures (e.g., 65 ?C), i.e. under “drying conditions”. Such acetals are termed ga-dinucleotides and possess a linkage that is analogous to the backbone in RNA in both structure and electrostatic charge. Additionally, an energy-minimized model of a gaRNA duplex predicts a helical structure similar to that of A-form RNA. We propose that glyoxylate-acetal linkages would have had certain advantages over phosphate linkages for early self-replicating polymers, but that the distinct functional properties of phosphoester and phosphodiester bonds would have eventually lead to the replacement of glyoxylate by phosphate.

Bean, Heather D.; Anet, Frank A. L.; Gould, Ian R.; Hud, Nicholas V.



Using halogen bonds to address the protein backbone: a systematic evaluation.  


Halogen bonds are specific embodiments of the sigma hole bonding paradigm. They represent directional interactions between the halogens chlorine, bromine, or iodine and an electron donor as binding partner. Using quantum chemical calculations at the MP2 level, we systematically explore how they can be used in molecular design to address the omnipresent carbonyls of the protein backbone. We characterize energetics and directionality and elucidate their spatial variability in sub-optimal geometries that are expected to occur in protein-ligand complexes featuring a multitude of concomitant interactions. By deriving simple rules, we aid medicinal chemists and chemical biologists in easily exploiting them for scaffold decoration and design. Our work shows that carbonyl-halogen bonds may be used to expand the patentable medicinal chemistry space, redefining halogens as key features. Furthermore, this data will be useful for implementing halogen bonds into pharmacophore models or scoring functions making the QM information available for automatic molecular recognition in virtual high throughput screening. PMID:22865255

Wilcken, Rainer; Zimmermann, Markus O; Lange, Andreas; Zahn, Stefan; Boeckler, Frank M



Side-chain to backbone interactions dictate the conformational preferences of a cyclopentane arginine analogue  

PubMed Central

The intrinsic conformational preferences of the non-proteinogenic amino acids constructed by incorporating the arginine side chain in the ? position of 1-aminocyclopentane-1-carboxylic acid (either in a cis or a trans orientation relative to the amino group) have been investigated using computational methods. These compounds may be considered as constrained analogues of arginine (denoted as c5Arg) in which the orientation of the side chain is fixed by the cyclopentane moiety. Specifically, the N-acetyl-N?-methylamide derivatives of cis and trans-c5Arg have been examined in the gas phase and in solution using B3LYP/6-311+G(d,p) calculations and Molecular Dynamics simulations. Results indicate that the conformational space available to these compounds is highly restricted, their conformational preferences being dictated by the ability of the guanidinium group in the side chain to establish hydrogen-bond interactions with the backbone. A comparison with the behavior previously described for the analogous phenylalanine derivatives is presented.

Revilla-Lopez, Guillem; Torras, Juan; Jimenez, Ana I.; Cativiela, Carlos; Nussinov, Ruth; Aleman, Carlos




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



Is there a Climate Network - A Backbone of the Climate System? (Invited)  

NASA Astrophysics Data System (ADS)

We consider an inverse problem: Is there a backbone-like structure underlying the climate system? For this we propose a method to reconstruct and analyze a complex network from data generated by a spatio-temporal dynamical system. This technique is then applied to reanalysis and model surface air temperature data. Parameters of this network, as betweenness centrality, uncover relations to global circulation patterns in oceans and atmosphere. We especially study the role of hubs and of long range connections, called teleconnections, in the flows of energy and matter in the climate system. The global scale view on climate networks offers promising new perspectives for detecting dynamical structures based on nonlinear physical processes in the climate system. References Arenas, A., A. Diaz-Guilera, J. Kurths, Y. Moreno, and C. Zhou, Phys. Reports 2008, 469, 93. Donges, J., Y. Zou, N. Marwan, and J. Kurths, Europ. Phys. J. ST 2009, 174, 157-179. Donges, J., Y. Zou, N. Marwan, and J. Kurths, Europhys. Lett. 2009, 87, 48007. Nawrath, J. et al., Phys. Rev. Lett. 2010, 104, 038701. Donner, R., Y. Zou, J. Donges, N. Marwan, and J. Kurths, Phys. Rev. E 2010, 81, 015101(R ).

Kurths, J.



Hydrogen bond formation between the naturally modified nucleobase and phosphate backbone  

PubMed Central

Natural RNAs, especially tRNAs, are extensively modified to tailor structure and function diversities. Uracil is the most modified nucleobase among all natural nucleobases. Interestingly, >76% of uracil modifications are located on its 5-position. We have investigated the natural 5-methoxy (5-O-CH3) modification of uracil in the context of A-form oligonucleotide duplex. Our X-ray crystal structure indicates first a H-bond formation between the uracil 5-O-CH3 and its 5?-phosphate. This novel H-bond is not observed when the oxygen of 5-O-CH3 is replaced with a larger atom (selenium or sulfur). The 5-O-CH3 modification does not cause significant structure and stability alterations. Moreover, our computational study is consistent with the experimental observation. The investigation on the uracil 5-position demonstrates the importance of this RNA modification at the atomic level. Our finding suggests a general interaction between the nucleobase and backbone and reveals a plausible function of the tRNA 5-O-CH3 modification, which might potentially rigidify the local conformation and facilitates translation.

Sheng, Jia; Zhang, Wen; Hassan, Abdalla E. A.; Gan, Jianhua; Soares, Alexei S.; Geng, Song; Ren, Yi; Huang, Zhen



Rapid chain tracing of polypeptide backbones in electron-density maps  

PubMed Central

A method for the rapid tracing of polypeptide backbones has been developed. The method creates an approximate chain tracing that is useful for visual evaluation of whether a structure has been solved and for use in scoring the quality of electron-density maps. The essence of the method is to (i) sample candidate C? positions at spacings of approximately 0.6?Å along ridgelines of high electron density, (ii) list all possible nonapeptides that satisfy simple geometric and density criteria using these candidate C? positions, (iii) score the nonapeptides and choose the highest scoring ones, and (iv) find the longest chains that can be made by connecting nonamers. An indexing and storage scheme that allows a single calculation of most distances and density values is used to speed up the process. The method was applied to 42 density-modified electron-density maps at resolutions from 1.5 to 3.8?Å. A total of 21?428 residues in these maps were traced in 24 CPU min with an overall r.m.s.d. of 1.61?Å for C? atoms compared with the known refined structures. The method appears to be suitable for rapid evaluation of electron-density map quality.

Terwilliger, Thomas C.



Backbone dynamics of the olfactory marker protein as studied by 15N NMR relaxation measurements.  


Nuclear magnetic resonance (NMR) (15)N relaxation measurements of the olfactory marker protein (OMP) including longitudinal relaxation (T(1)), transverse relaxation (T(2)), and (15)N-{(1)H} NOE data were collected at low protein concentrations (backbone amide groups. Rotational diffusion of the OMP was found to be axially symmetric with D( parallel)/D( perpendicular) = 1.20 +/- 0.02 with an overall global correlation time of 8.93 +/- 0.03 ns. Model-free internal dynamic analyses of these data provided a description of the protein's dynamics on multiple time scales. The results of these studies indicate that there is a large degree of conformational flexibility for alpha-helix 1 (alpha1), loop 1, and the conserved Omega-loop (loop 3). The functional significance that these dynamic regions of OMP have in modulating olfactory signal transduction is discussed. PMID:16008352

Gitti, Rossitza K; Wright, Nathan T; Margolis, Joyce W; Varney, Kristen M; Weber, David J; Margolis, Frank L



An enhanced backbone-assisted reliable framework for wireless sensor networks.  


An extremely reliable source to sink communication is required for most of the contemporary WSN applications especially pertaining to military, healthcare and disaster-recovery. However, due to their intrinsic energy, bandwidth and computational constraints, Wireless Sensor Networks (WSNs) encounter several challenges in reliable source to sink communication. In this paper, we present a novel reliable topology that uses reliable hotlines between sensor gateways to boost the reliability of end-to-end transmissions. This reliable and efficient routing alternative reduces the number of average hops from source to the sink. We prove, with the help of analytical evaluation, that communication using hotlines is considerably more reliable than traditional WSN routing. We use reliability theory to analyze the cost and benefit of adding gateway nodes to a backbone-assisted WSN. However, in hotline assisted routing some scenarios where source and the sink are just a couple of hops away might bring more latency, therefore, we present a Signature Based Routing (SBR) scheme. SBR enables the gateways to make intelligent routing decisions, based upon the derived signature, hence providing lesser end-to-end delay between source to the sink communication. Finally, we evaluate our proposed hotline based topology with the help of a simulation tool and show that the proposed topology provides manifold increase in end-to-end reliability. PMID:22294890

Tufail, Ali; Khayam, Syed Ali; Raza, Muhammad Taqi; Ali, Amna; Kim, Ki-Hyung



An Enhanced Backbone-Assisted Reliable Framework for Wireless Sensor Networks  

PubMed Central

An extremely reliable source to sink communication is required for most of the contemporary WSN applications especially pertaining to military, healthcare and disaster-recovery. However, due to their intrinsic energy, bandwidth and computational constraints, Wireless Sensor Networks (WSNs) encounter several challenges in reliable source to sink communication. In this paper, we present a novel reliable topology that uses reliable hotlines between sensor gateways to boost the reliability of end-to-end transmissions. This reliable and efficient routing alternative reduces the number of average hops from source to the sink. We prove, with the help of analytical evaluation, that communication using hotlines is considerably more reliable than traditional WSN routing. We use reliability theory to analyze the cost and benefit of adding gateway nodes to a backbone-assisted WSN. However, in hotline assisted routing some scenarios where source and the sink are just a couple of hops away might bring more latency, therefore, we present a Signature Based Routing (SBR) scheme. SBR enables the gateways to make intelligent routing decisions, based upon the derived signature, hence providing lesser end-to-end delay between source to the sink communication. Finally, we evaluate our proposed hotline based topology with the help of a simulation tool and show that the proposed topology provides manifold increase in end-to-end reliability.

Tufail, Ali; Khayam, Syed Ali; Raza, Muhammad Taqi; Ali, Amna; Kim, Ki-Hyung



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



An Intelligent System for Searching Genomic Sequences  

Microsoft Academic Search

In this paper, we have developed an intelligent system for searching comparative genomic sequences which departs from the traditional sequence alignment methods of nucleic residues or alphabets. Instead, we use the composition vector method that exploits pattern structures in sequences and indexing techniques for building a genomic database of prokaryotic organisms and their phylogenetic relationships. For the structural analysis of

Vandana Gummuluru; Su-shing Chen



Recurrence Sequences  

NSDL National Science Digital Library

A book on recurrence sequences, an advanced topic in number theory, can be downloaded from this site. It deals mainly with linear recurrence sequences, and provides extensive theory, methods, and equations. While the material is quite complex, it has applications for various disciplines. The authors state, "these sequences appear almost everywhere in mathematics and computer science." The book is in draft form, and will be featured in the Surveys and Monographs series of the American Mathematical Society sometime in 2003. Until then, however, the book can be accessed here for the purpose of correcting any errors.

Ward, Thomas.; Van Der Poorten, A. J.; Shparlinski, Igor E.; Everest, Graham.



Solid state and solution conformations of a hybrid alphagammaalphaalphagammaalpha hexapeptide. Characterization of a backbone expanded analog of the alpha-polypeptide 3(10)-helix.  


The stereochemically constrained gamma amino acid residue gabapentin (1-(aminomethyl)cyclohexaneacetic acid, Gpn) has been incorporated into a host alpha-peptide sequence. The structure of a hybrid alphagammaalphaalphagammaalpha peptide, Boc-Leu-Gpn-Aib-Leu-Gpn-Aib-OMe in crystals reveals a continuous helical conformation stabilized by three intramolecular 4 --> 1 C(12) hydrogen bonds across the alphagamma/alphagamma segments and one C(10) hydrogen bond across the central alphaalpha segment. This conformation corresponds to an expanded analog of the canonical all-alpha polypeptide 3(10)-helix, with insertion of two additional backbone atoms at each gamma residue. Solvent dependence of NH chemical shifts in CDCl(3) solution are consistent with conformation in which the NH groups of Aib (3), Leu (4), Gpn (5), and Aib (6) are hydrogen bonded, a feature observed in the solid state. The nonsequential NOEs between Gpn (2) NH <--> Leu (4) NH and Gpn (2) NH <--> Gpn (5) NH support the presence of additional conformations in solution. Temperature-dependent line broadening of NH resonances confirms the occurrence of rapid exchange between multiple conformations at room temperature. Two conformational models which rationalize the observed nonsequential NOEs are presented, both of which contain three hydrogen bonds and are consistent with the known stereochemical preferences of the Gpn residue. PMID:18767124

Chatterjee, Sunanda; Vasudev, Prema G; Raghothama, Srinivasarao; Shamala, Narayanaswamy; Balaram, Padmanabhan



Antitumor activity and pharmacokinetics of a mixed-backbone antisense oligonucleotide targeted to the RI? subunit of protein kinase A after oral administration  

PubMed Central

Overexpression of the RI? subunit of cAMP-dependent protein kinase (PKA) has been demonstrated in various human cancers. PKA has been suggested as a potential target for cancer therapy. The goal of the present study was to evaluate an anti-PKA antisense oligonucleotide (mixed-backbone oligonucleotide) as a therapeutic approach to human cancer treatment. The identified oligonucleotide inhibited the growth of cell lines of human colon cancer (LS174T, DLD-1), leukemia (HL-60), breast cancer (MCF-7, MDA-MB-468), and lung cancer (A549) in a time-, concentration-, and sequence-dependent manner. In a dose-dependent manner, the oligonucleotide displayed in vivo antitumor activity in severe combined immunodeficient and nude mice bearing xenografts of human cancers of the colon (LS174T), breast (MDA-MB-468), and lung (A549). The routes of drug administration were intraperitoneal and oral. Synergistic effects were found when the antisense oligonucleotide was used in combination with the cancer chemotherapeutic agent cisplatin. The pharmacokinetics of the oligonucleotide after oral administration of 35S-labeled oligonucleotide into tumor-bearing mice indicated an accumulation and retention of the oligonucleotide in tumor tissue. This study further provides a basis for clinical studies of the antisense oligonucleotide targeted to the RI? subunit of PKA (GEM 231) as a cancer therapeutic agent used alone or in combination with conventional chemotherapy.

Wang, Hui; Cai, Qiuyin; Zeng, Xiaofei; Yu, Dong; Agrawal, Sudhir; Zhang, Ruiwen



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


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



Antitumor activity and pharmacokinetics of a mixed-backbone antisense oligonucleotide targeted to the RIalpha subunit of protein kinase A after oral administration.  


Overexpression of the RIalpha subunit of cAMP-dependent protein kinase (PKA) has been demonstrated in various human cancers. PKA has been suggested as a potential target for cancer therapy. The goal of the present study was to evaluate an anti-PKA antisense oligonucleotide (mixed-backbone oligonucleotide) as a therapeutic approach to human cancer treatment. The identified oligonucleotide inhibited the growth of cell lines of human colon cancer (LS174T, DLD-1), leukemia (HL-60), breast cancer (MCF-7, MDA-MB-468), and lung cancer (A549) in a time-, concentration-, and sequence-dependent manner. In a dose-dependent manner, the oligonucleotide displayed in vivo antitumor activity in severe combined immunodeficient and nude mice bearing xenografts of human cancers of the colon (LS174T), breast (MDA-MB-468), and lung (A549). The routes of drug administration were intraperitoneal and oral. Synergistic effects were found when the antisense oligonucleotide was used in combination with the cancer chemotherapeutic agent cisplatin. The pharmacokinetics of the oligonucleotide after oral administration of (35)S-labeled oligonucleotide into tumor-bearing mice indicated an accumulation and retention of the oligonucleotide in tumor tissue. This study further provides a basis for clinical studies of the antisense oligonucleotide targeted to the RIalpha subunit of PKA (GEM 231) as a cancer therapeutic agent used alone or in combination with conventional chemotherapy. PMID:10570186

Wang, H; Cai, Q; Zeng, X; Yu, D; Agrawal, S; Zhang, R



Proteoglycan sequence.  


Proteoglycans (PGs) are among the most structurally complex biomacromolecules in nature. They are present in all animal cells and frequently exert their critical biological functions through interactions with protein ligands and receptors. PGs are comprised of a core protein to which one or multiple, heterogeneous, and polydisperse glycosaminoglycan (GAG) chains are attached. Proteins, including the protein core of PGs, are now routinely sequenced either directly using proteomics or indirectly using molecular biology through their encoding DNA. The sequencing of the GAG component of PGs poses a considerably more difficult challenge because of the relatively underdeveloped state of glycomics and because the control of their biosynthesis in the endoplasmic reticulum and the Golgi is poorly understood and not believed to be template driven. Recently, the GAG chain of the simplest PG has been suggested to have a defined sequence based on its top-down Fourier transform mass spectral sequencing. This review examines the advances made over the past decade in the sequencing of GAG chains and the challenges the field face in sequencing complex PGs having critical biological functions in developmental biology and pathogenesis. PMID:22513887

Li, Lingyun; Ly, Mellisa; Linhardt, Robert J



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))



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.



Backbone and side-chain assignments of an effector membrane localization domain from Vibrio vulnificus MARTX toxin.  


(1)H, (13)C, and (15)N chemical shift assignments are presented for the isolated four-helical bundle membrane localization domain from the domain of unknown function 5 (DUF5) effector (MLDVvDUF5) of the MARTX toxin from Vibrio vulnificus in its solution state. We have assigned 97 % of all backbone and side-chain carbon atoms, including 96 % of all backbone residues. Secondary chemical shift analysis using TALOS+ demonstrates four helices that align with those predicted by structure homology modeling using the MLDs of Pasteurella multocida toxin (PMT) and the clostridial TcdB and TcsL toxins as templates. Future studies will be towards solving the structure and determining the dynamics in the solution state. PMID:23765285

Brothers, Michael C; Geissler, Brett; Hisao, Grant S; Wilson, Brenda A; Satchell, Karla J F; Rienstra, Chad M



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


Double sugar and phosphate backbone-constrained nucleotides: synthesis, structure, stability, and their incorporation into oligodeoxynucleotides.  


Two diastereomerically pure carba-LNA dioxaphosphorinane nucleotides [(S(p))- or (R(p))-D(2)-CNA], simultaneously conformationally locked at the sugar and the phosphate backbone, have been designed and synthesized. Structural studies by NMR as well as by ab initio calculations showed that in (S(p))- and (R(p))-D(2)-CNA the following occur: (i) the sugar is locked in extreme North-type conformation with P = 11 degrees and Phi(m) = 54 degrees ; (ii) the six-membered 1,3,2-dioxaphosphorinane ring adopts a half-chair conformation; (iii) the fixed phosphate backbone delta, epsilon, and zeta torsions were found to be delta [gauch(+)], epsilon (cis), zeta [anticlinal(+)] for (S(p))-D(2)-CNA, and delta [gauche(+)], epsilon (cis), zeta [anticlinal(-)] for (R(p))-D(2)-CNA. It has been found that F(-) ion can catalyze the isomerization of pure (S(p))-D(2)-CNA or (R(p))-D(2)-CNA to give an equilibrium mixture (K = 1.94). It turned out that at equilibrium concentration the (S(p))-D(2)-CNA isomer is preferred over the (R(p))-D(2)-CNA isomer by 0.39 kcal/mol. The chemical reactivity of the six-membered dioxaphosphorinane ring in D(2)-CNA was found to be dependent on the internucleotidic phosphate stereochemistry. Thus, both (S(p))- and (R(p))-D(2)-CNA dimers (17a and 17b) were very labile toward nucleophile attack in concentrated aqueous ammonia [t(1/2) = 12 and 6 min, respectively] to give carba-LNA-6',5'-phosphodiester (21) approximately 70-90%, carba-LNA-3',5'-phosphodiester (22) approximately 10%, and carba-LNA-6',3'-phosphodiester (23) <10%. In contrast, the (S(p))-D(2)-CNA was about 2 times more stable than (R(p))-D(2)-CNA under hydrazine hydrate/pyridine/AcOH (pH = 5.6) [t(1/2) = 178 and 99 h, respectively], which was exploited in the deprotection of pure (S(p))-D(2)-CNA-incorporated antisense oligodeoxynucleotides (AON). Thus, after removal of the solid supports from the (S(p))-D(2)-CNA-modified AONs by BDU/MeCN, they were treated with hydrazine hydrate in pyridine/AcOH to give pure AONs in 35-40% yield, which was unequivocally characterized by MALDI-TOF to show that they have an intact six-membered dioxaphosphorinane ring. The effect of pure (S(p))-D(2)-CNA modification in the AONs was estimated by complexing to the complementary RNA and DNA strands by the thermal denaturation studies. This showed that this cyclic phosphotriester modification destabilizes the AON/DNA and AON/RNA duplex by about -6 to -9 degrees C/modification. Treatment of (S(p))-D(2)-CNA-modified AON with concentrated aqueous ammonia gave carba-LNA-6',5'-phosphodiester modified AON ( approximately 80%) plus a small amount of carba-LNA-3',5'-phosphodiester-modified AON ( approximately 20%). It is noteworthy that Carba-LNA-3',5'-phosphodiester modification stabilized the AON/RNA duplex by +4 degrees C/modification (J. Org. Chem. 2009, 74, 118), whereas carba-LNA-6', 5'-phosphodiester modification destabilizes both AON/RNA and AON/DNA significantly (by -10 to -19 degrees C/modification), which, as shown in our comparative CD studies, that the cyclic phosphotriester modified AONs as well as carba-LNA-6',5'-phosphodiester modified AONs are much more weakly stacked than carba-LNA-3',5'-phosphodiester-modified AONs. PMID:19348480

Zhou, Chuanzheng; Plashkevych, Oleksandr; Chattopadhyaya, Jyoti



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


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



Phosphorus chemical shifts in a nucleic acid backbone from combined molecular dynamics and density functional calculations.  


A comprehensive quantum chemical analysis of the influence of backbone torsion angles on (31)P chemical shifts in DNAs has been carried out. An extensive DFT study employed snapshots obtained from the molecular dynamics simulation of [d(CGCGAATTCGCG)]2 to construct geometries of a hydrated dimethyl phosphate, which was used as a model for the phosphodiester linkage. Our calculations provided differences of 2.1 ± 0.3 and 1.6 ± 0.3 ppm between the B(I) and B(II) chemical shifts in two B-DNA residues of interest, which is in a very good agreement with the difference of 1.6 ppm inferred from experimental data. A more negative (31)P chemical shift for a residue in pure BI conformation compared to residues in mixed B(I)/B(II) conformation states is provided by DFT, in agreement with the NMR experiment. Statistical analysis of the MD/DFT data revealed a large dispersion of chemical shifts in both B(I) and B(II) regions of DNA structures. ?P ranges within 3.5 ± 0.8 ppm in the B(I) region and within 4.5 ± 1.5 ppm in the B(II) region. While the (31)P chemical shift becomes more negative with increasing ? in B(I)-DNA, it has the opposite trend in B(II)-DNA when both ? and ? increase simultaneously. The (31)P chemical shift is dominated by the torsion angles ? and ?, while an implicit treatment of ? and ? is sufficient. The presence of an explicit solvent leads to a damping and a 2-3 ppm upfield shift of the torsion angle dependences. PMID:21073198

P?ececht?lová, Jana; Novák, Petr; Munzarová, Markéta L; Kaupp, Martin; Sklená?, Vladimír



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.



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



Probing the role of backbone hydrogen bonds in protein-peptide interactions by amide-to-ester mutations.  


One of the most frequent protein-protein interaction modules in mammalian cells is the postsynaptic density 95/discs large/zonula occludens 1 (PDZ) domain, involved in scaffolding and signaling and emerging as an important drug target for several diseases. Like many other protein-protein interactions, those of the PDZ domain family involve formation of intermolecular hydrogen bonds: C-termini or internal linear motifs of proteins bind as ?-strands to form an extended antiparallel ?-sheet with the PDZ domain. Whereas extensive work has focused on the importance of the amino acid side chains of the protein ligand, the role of the backbone hydrogen bonds in the binding reaction is not known. Using amide-to-ester substitutions to perturb the backbone hydrogen-bonding pattern, we have systematically probed putative backbone hydrogen bonds between four different PDZ domains and peptides corresponding to natural protein ligands. Amide-to-ester mutations of the three C-terminal amides of the peptide ligand severely affected the affinity with the PDZ domain, demonstrating that hydrogen bonds contribute significantly to ligand binding (apparent changes in binding energy, ??G = 1.3 to >3.8 kcal mol(-1)). This decrease in affinity was mainly due to an increase in the dissociation rate constant, but a significant decrease in the association rate constant was found for some amide-to-ester mutations suggesting that native hydrogen bonds have begun to form in the transition state of the binding reaction. This study provides a general framework for studying the role of backbone hydrogen bonds in protein-peptide interactions and for the first time specifically addresses these for PDZ domain-peptide interactions. PMID:23705582

Eildal, Jonas N N; Hultqvist, Greta; Balle, Thomas; Stuhr-Hansen, Nicolai; Padrah, Shahrokh; Gianni, Stefano; Strømgaard, Kristian; Jemth, Per



Conceptualizing digital and physical connectivity: The position of European cities in Internet backbone and air traffic flows  

Microsoft Academic Search

‘Digital’ telecommunication flows and ‘physical’ corporeal flows provide researchers with comprehensive indicators of the economic interactions between cities. However, previous research drawing on telecommunication-based measures of inter-urban connectivity has been hampered by inadequate conceptualizations and data. This paper draws on this observation to devise a new approach for measuring inter-urban connectivity based on a city’s insertion in Internet backbone networks.

Lomme Devriendt; Ben Derudder; Frank Witlox



Synthesis and characterization of new polyimides and polyamide-imides containing azomethine group in the polymer backbone  

Microsoft Academic Search

New aromatic polyimides and polyamide-imides containing azomethine linkages in the polymer backbone have been synthesized by reacting 4,4'-bis(isocyanato) benzylidene aniline (AZMI) with pyromellitic dianhydride (PMDA), 3,3', 4,4'-benzophenone tetracarboxylic dianhydride (BTDA) and trimellitic anhydride (TMA) by one-step method. The AZMI was synthesized from 4,4'-bis(carboxy) benzylidene aniline (AZMA) by a Weinstock modified curtius rearrangement. All the polycondensation reactions were carried out in

Susheela B. Idage; Bhaskar B. Idage; Subhash P. Vernekar



Interaction of sphingomyelinase with sphingomyelin analogs modified at the C-1 and C-3 positions of the sphingosine backbone  

Microsoft Academic Search

In this study, analogs differing at the C-1 or C-3 position of the sphingosine backbone of sphingomyelin were examined in neutral pH-optimum sphingomyelinase assays. Two analogs modified at the C-1 position, ceramide-1-phosphate and ceramide-1-phosphoethanol-N,N-dimethylamine, could act as modest substrates but showed no ability to inhibit the reaction when egg sphingomyelin was used as the substrate. Four analogs of sphingomyelin differing

Mark D. Lister; Zhong-shi Ruan; Robert Bittman



Inherent flame retardation of bio-based poly(lactic acid) by incorporating phosphorus linked pendent group into the backbone  

Microsoft Academic Search

The molecular design for inherently flame-retardant poly(lactic acid) (IFR-PLA) was outlined and achieved by chemically incorporating an effective organophophorus-type flame retardant (FR) into the PLA backbone via the chain extension of the dihydroxyl-terminated prepolymer with 1, 6-hexamethylene diisocyanate (HDI). The structure of IFR-PLA was characterized by 1H- and 31P-nuclear magnetic resonance (NMR) and Fourier transform infrared (FTIR) spectroscopy. IFR-PLA was

Xiao-Ya Yuan; De-Yi Wang; Li Chen; Xiu-Li Wang; Yu-Zhong Wang



Solution structure of the ActD-5?-CCGTT3GTGG-3? complex: drug interaction with tandem G?T mismatches and hairpin loop backbone  

PubMed Central

Binding of actinomycin D (ActD) to the seemingly single-stranded DNA (ssDNA) oligomer 5?-CCGTT3 GTGG-3? has been studied in solution using high-resolution nuclear magnetic resonance (NMR) techniques. A strong binding constant (8 × 106 M–1) and high quality NMR spectra have allowed us to determine the initial DNA structure using distance geometry as well as the final ActD–5?-CCGTT3 GTGG-3? complex structure using constrained molecular dynamics calculations. The DNA oligomer 5?-CCGTT3GTGG-3? in the complex forms a hairpin structure with tandem G·T mismatches at the stem region next to a loop of three stacked thymine bases pointing toward the major groove. Bipartite T2O–GH1 and T2O–G2NH2 hydrogen bonds were detected for the G·T mismatches that further stabilize this unusual DNA hairpin. The phenoxazone chromophore of ActD intercalates nicely between the tandem G·T mismatches in essentially one major orientation. Additional hydrophobic interactions between the ActD quinoid amino acid residues with the loop T5–T6–T7 backbone protons were also observed. The hydrophobic G–phenoxazone–G interaction in the ActD–5?-CCGTT3GTGG-3? complex is more robust than that of the classical ActD– 5?-CCGCT3GCGG-3? complex, consistent with the roughly 2-fold stronger binding of ActD to the 5?-CCGTT3GTGG-3? sequence than to its 5?-CCG CT3GCGG-3? counterpart. Stabilization by ActD of a hairpin containing non-canonical stem base pairs further strengthens the notion that ActD or other related compounds may serve as a sequence- specific ssDNA-binding agent that inhibits human immunodeficiency virus (HIV) and other retroviruses replicating through ssDNA intermediates.

Chin, Ko-Hsin; Chen, Fu-Ming; Chou, Shan-Ho



Extensive backbone dynamics in the GCAA RNA tetraloop analyzed using 13C NMR spin relaxation and specific isotope labeling.  


Conformational dynamics play a key role in the properties and functions of proteins and nucleic acids. Heteronuclear NMR spin relaxation is a uniquely powerful site-specific probe of dynamics in proteins and has found increasing applications to nucleotide base side chains and anomeric sites in RNA. Applications to the nucleic acid ribose backbone, however, have been hampered by strong magnetic coupling among ring carbons in uniformly 13C-labeled samples. In this work, we apply a recently developed, metabolically directed isotope labeling scheme that places 13C with high efficiency and specificity at the nucleotide ribose C2' and C4' sites. We take advantage of this scheme to explore backbone dynamics in the well-studied GCAA RNA tetraloop. Using a combination of CPMG (Carr-Purcell-Meiboom-Gill) and R(1rho) relaxation dispersion spectroscopy to explore exchange processes on the microsecond to millisecond time scale, we find an extensive pattern of dynamic transitions connecting a set of relatively well-defined conformations. In many cases, the observed transitions appear to be linked to C3'-endo/C2'-endo sugar pucker transitions of the corresponding nucleotides, and may also be correlated across multiple nucleotides within the tetraloop. These results demonstrate the power of NMR spin relaxation based on alternate-site isotope labeling to open a new window into the dynamic properties of ribose backbone groups in RNA. PMID:19049467

Johnson, James E; Hoogstraten, Charles G



Altered backbone and side-chain interactions result in route heterogeneity during the folding of interleukin-1? (IL-1?).  


Deletion of the ?-bulge trigger-loop results in both a switch in the preferred folding route, from the functional loop packing folding route to barrel closure, as well as conversion of the agonist activity of IL-1? into antagonist activity. Conversely, circular permutations of IL-1? conserve the functional folding route as well as the agonist activity. These two extremes in the folding-functional interplay beg the question of whether mutations in IL-1? would result in changes in the populations of heterogeneous folding routes and the signaling activity. A series of topologically equivalent water-mediated ?-strand bridging interactions within the pseudosymmetric ?-trefoil fold of IL-1? highlight the backbone water interactions that stabilize the secondary and tertiary structure of the protein. Additionally, conserved aromatic residues lining the central cavity appear to be essential for both stability and folding. Here, we probe these protein backbone-water molecule and side chain-side chain interactions and the role they play in the folding mechanism of this geometrically stressed molecule. We used folding simulations with structure-based models, as well as a series of folding kinetic experiments to examine the effects of the F42W core mutation on the folding landscape of IL-1?. This mutation alters water-mediated backbone interactions essential for maintaining the trefoil fold. Our results clearly indicate that this perturbation in the primary structure alters a structural water interaction and consequently modulates the population of folding routes accessed during folding and signaling activity. PMID:23972849

Capraro, Dominique T; Lammert, Heiko; Heidary, David K; Roy, Melinda; Gross, Larry A; Onuchic, José N; Jennings, Patricia A



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



A generalized approach to sampling backbone conformations with RosettaDock for CAPRI rounds 13-19  

PubMed Central

In CAPRI rounds 13–19, the most native-like structure predicted by RosettaDock resulted in two high, one medium and one acceptable accuracy model out of 13 targets. The current rounds of CAPRI were especially challenging with many unbound and homology modeled starting structures. Novel docking methods, including EnsembleDock and SnugDock, allowed backbone conformational sampling during docking and enabled the creation of more accurate models. For Target 32, ?-amylase/subtilisin inhibitor-subtilisin savinase, we sampled different backbone conformations at an interfacial loop to produce five high-quality models including the most accurate structure submitted in the challenge (2.1 Å ligand rmsd, 0.52 Å interface rmsd). For Target 41, colicin-immunity protein, we used EnsembleDock to sample the ensemble of nuclear magnetic resonance (NMR) models of the immunity protein to generate a medium accuracy structure. Experimental data identifying the catalytic residues at the binding interface for Target 40 (trypsin-inhibitor) were used to filter RosettaDock global rigid body docking decoys to determine high accuracy predictions for the two distinct binding sites in which the inhibitor interacts with trypsin. We discuss our generalized approach to selecting appropriate methods for different types of docking problems. The current toolset provides some robustness to errors in homology models, but significant challenges remain in accommodating larger backbone uncertainties and in sampling adequately for global searches.

Sircar, Aroop; Chaudhury, Sidhartha; Kilambi, Krishna Praneeth; Berrondo, Monica; Gray, Jeffrey J.



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



DNA Sequence Context Conceals ?-Anomeric Lesions  

PubMed Central

DNA sequence context has long been known to modulate detection and repair of DNA damage. Recent studies using experimental and computational approaches have sought to provide a basis for this observation. We have previously shown that an ?-anomeric adenosine (?A) flanked by cytosines (5?C?AC-3?) resulted in a kinked DNA duplex with an enlarged minor groove. Comparison of different flanking sequences revealed that a DNA duplex containing a 5?C?AG-3? motif exhibits unique substrate properties. However, this substrate was not distinguished by unusual thermodynamic properties. To understand the structural basis of the altered recognition, we have determined the solution structure of a DNA duplex with a 5?C?AG-3? core, using an extensive set of restraints including dipolar couplings and backbone torsion angles. The NMR structure exhibits an excellent agreement with the data (total RX <5.3%). The ?A base is intrahelical, in a reverse Watson–Crick orientation, and forms a weak base pair with a thymine of the opposite strand. In comparison to the DNA duplex with a 5?C?AC-3? core, we observe a significant reduction of the local perturbation (backbone, stacking, tilt, roll, and twist), resulting in a straighter DNA with narrower minor groove. Overall, these features result in a less perturbed DNA helix and obscure the presence of the lesion compared to the 5?C?AC-3? sequence. The improved stacking of the 5?C?AG-3? core also affects the energetics of the DNA deformation that is required to form a catalytically competent complex. These traits provide a rationale for the modulation of the recognition by endonuclease IV.

Johnson, Christopher N.; Spring, Alexander M.; Desai, Sunil; Cunningham, Richard P.; Germann, Markus W.



Occultation observations of atmosphere and climate change from space: a backbone for the GCOS  

NASA Astrophysics Data System (ADS)

Since the early use of the occultation measurement principle for sounding planetary atmospheres, its exploitation has seen tremendous advances. A particular boost was felt since the late eighties when a variety of intriguing opportunities for application to the atmosphere of our home planet Earth were increasingly recognized, such as utilizing new signal sources like Global Navigation Satellite System (GNSS) signals. Today we use and plan occultation sensors on Low Earth Orbit (LEO) satellites, which exploit solar, lunar, stellar, GNSS, and LEO-crosslink signals. The sensors, together, smartly utilize the whole electromagnetic spectrum from EUV/UV via VIS/IR and MW to Radio and exploit all kinds of atmosphere-radiation interaction such as absorption and scattering, both by molecules and aerosols, as well as refraction. The parameters obtained, from the Earth's surface up through the entire atmosphere, extend from the fundamental mass field variables temperature, pressure, and geopotential height via the fundamental variable trace gases water vapor and ozone (and many further important trace species) to key particulate species such as aerosols and cloud liquid water. All these measurements rest on one and the same occultation principle with its unique properties of providing self-calibration, high accuracy and vertical resolution, global coverage, and (if using radio signals) all-weather capability. Occultation data thus bear enormous utility for applications in climate monitoring and research but also in other fields such as numerical weather prediction and atmospheric physics and chemistry. The self-calibration property is particularly crucial for climate change monitoring, as it enables unique long-term stability in climate datasets. The latter can be built from occultation data of different satellites and times without inter-calibration efforts. In fact, a controversy such as the recent one on the tropospheric temperature record over the last two decades, involving the heavily calibration-dependent Microwave Sounding Unit (MSU) data, could have been presumably saved had suitable occultation data been available. This talk will highlight, along the lines outlined above, the general principles, properties, capabilities, and exploitation possibilities of occultation methods with a focus on how they provide key contributions to a better understanding of the Earth's climate system and to better prediction of its future evolution. A properly designed occultation observing system has the capacity to become the leading backbone of the Global Climate Observing System (GCOS) for monitoring climate change and variability in fundamental atmospheric variables such as temperature, humidity, ozone, and geopotential height from global scales to meso-scales (order 100 km) and from the planetary boundary layer to the mesopause.

Kirchengast, G.



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.



DNA sequencing  

Microsoft Academic Search

This patent describes a method for sequencing a portion of a nucleotide chain from a primary nucleotide to an nth nucleotide, where n is an integer not greater than about 500. The method comprising: preparing a first mixture of labeled nucleotide chain fragments, each labeled chain extending from a common end adjacent to the primary nucleotide and extending to a

L. E. Orgel; J. W. Patrick



New Helical Foldamers: Heterogeneous Backbones with 1:2 and 2:1 [alpha]:[superscript beta]-Amino Acid Residue Patterns  

SciTech Connect

Foldamers, oligomers with strong folding propensities, are subjects of growing interest because such compounds offer unique scaffolds for the development of molecular function. We report two new foldamer classes, oligopeptides with regular 1:2 or 2:1 patterns of {alpha}- and {beta}-amino acid residues. Two distinct helical conformations are detected via 2D NMR in methanol for each backbone. One of the helices for each backbone is characterized via X-ray crystallography.

Schmitt, Margaret A.; Choi, SooHyuk; Guzei, Ilia A.; Gellman, Samuel H. (UW)



Folding behavior of a backbone-reversed protein: Reversible polyproline type II to ?-sheet thermal transitions in retro-GroES multimers with GroES-like features  

Microsoft Academic Search

The structural consequences of the reversal of polypeptide backbone direction (retro modification) remain insufficiently explored. Here, we describe the behavior of an engineered, backbone-reversed form of the 97 residues-long GroES co-chaperonin of Escherichia coli. FTIR and far-UV CD spectroscopy suggest that retro-GroES adopts a mixed polyproline type II (PPII)-beta-strand structure with a ?II type CD spectrum similar to that of

Shubbir Ahmed; Anshuman Shukla; Purnananda Guptasarma



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


Single transgene copy, vector backbone-free transgenic crop plants are highly desired for functional genomics and many biotechnological applications. We demonstrate that binary vectors that use a replication origin derived from the Ri plasmid of Agrobacterium rhizogenes (oriRi) increase the frequency of single copy, backbone-free transgenic plants in Agrobacterium tumefaciens mediated transformation of soybean, canola, and corn, compared to RK2-derived binary vectors (RK2 oriV). In large scale soybean transformation experiments, the frequency of single copy, backbone-free transgenic plants was nearly doubled in two versions of the oriRi vectors compared to the RK2 oriV control vector. In canola transformation experiments, the oriRi vector produced more single copy, backbone-free transgenic plants than did the RK2 oriV vector. In corn transformation experiments, the frequency of single copy backbone-free transgenic plants was also significantly increased when using the oriRi vector, although the transformation frequency dropped. These results, derived from transformation experiments using three crops, indicate the advantage of oriRi vectors over RK2 oriV binary vectors for the production of single copy, backbone-free transgenic plants using Agrobacterium-mediated transformation. PMID:21042934

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



Decision sequences  

Microsoft Academic Search

Chapter 5 introduced a generally applicable heuristic decision-making procedure suitable for solving complex decision problems.\\u000a Complex problems, as we have seen, typically have multiple causes and in such cases, problem analysis tends to distinguish\\u000a a number of different problems. As a result, these sub-problems will be tackled either in sequence or in parallel. An example\\u000a of this might be a

Rudolf Grünig; Richard Kühn


Protein side-chain resonance assignment and NOE assignment using RDC-defined backbones without TOCSY data.  


One bottleneck in NMR structure determination lies in the laborious and time-consuming process of side-chain resonance and NOE assignments. Compared to the well-studied backbone resonance assignment problem, automated side-chain resonance and NOE assignments are relatively less explored. Most NOE assignment algorithms require nearly complete side-chain resonance assignments from a series of through-bond experiments such as HCCH-TOCSY or HCCCONH. Unfortunately, these TOCSY experiments perform poorly on large proteins. To overcome this deficiency, we present a novel algorithm, called NASCA: (NOE Assignment and Side-Chain Assignment), to automate both side-chain resonance and NOE assignments and to perform high-resolution protein structure determination in the absence of any explicit through-bond experiment to facilitate side-chain resonance assignment, such as HCCH-TOCSY. After casting the assignment problem into a Markov Random Field (MRF), NASCA: extends and applies combinatorial protein design algorithms to compute optimal assignments that best interpret the NMR data. The MRF captures the contact map information of the protein derived from NOESY spectra, exploits the backbone structural information determined by RDCs, and considers all possible side-chain rotamers. The complexity of the combinatorial search is reduced by using a dead-end elimination (DEE) algorithm, which prunes side-chain resonance assignments that are provably not part of the optimal solution. Then an A* search algorithm is employed to find a set of optimal side-chain resonance assignments that best fit the NMR data. These side-chain resonance assignments are then used to resolve the NOE assignment ambiguity and compute high-resolution protein structures. Tests on five proteins show that NASCA: assigns resonances for more than 90% of side-chain protons, and achieves about 80% correct assignments. The final structures computed using the NOE distance restraints assigned by NASCA: have backbone RMSD 0.8-1.5 Å from the reference structures determined by traditional NMR approaches. PMID:21706248

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



Increased hydrophobicity and decreased backbone flexibility explain the lower solubility of a cataract-linked mutant of ?D-crystallin.  


A number of point mutations in ?D-crystallin are associated with human cataract. The Pro23-to-Thr (P23T) mutation is perhaps the most common, is geographically widespread, and presents itself in a variety of phenotypes. It is therefore important to understand the molecular basis of lens opacity due to this mutation. In our earlier studies, we noted that P23T shows retrograde and sharply lowered solubility, most likely due to the emergence of hydrophobic patches involved in protein aggregation. Binding of 4,4'-dianilino-1,1'-binaphthyl-5,5'-disulfonate (Bis-ANS) dye (a probe commonly used for detecting surface hydrophobicity) competed with aggregation, suggesting that the residues involved in Bis-ANS binding are also involved in protein aggregation. Here, using NMR spectroscopy in conjunction with Bis-ANS binding, we identify three residues (Y16, D21, and Y50) in P23T that are involved in binding the dye. Furthermore, using (15)N NMR relaxation experiments, we show that, in the mutant protein, backbone fluctuations are restricted to the picosecond-to-nanosecond and microsecond timescales relative to the wild type. Our present studies specify the residues involved in these two pivotal characteristics of the mutant protein, namely increased surface hydrophobicity and restricted mobility of the protein backbone, which can explain the nucleation and further propagation of protein aggregates. Thus, we have now identified the residues in the P23T mutant that give rise to novel hydrophobic surfaces, as well as those regions of the protein backbone where fluctuations in different timescales are restricted, providing a comprehensive understanding of how lens opacity could result from this mutation. PMID:21827768

Banerjee, Priya R; Puttamadappa, Shadakshara S; Pande, Ajay; Shekhtman, Alexander; Pande, Jayanti



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



Effect of solvents on the chemical and physical properties of ionic polymer-metal composites  

Microsoft Academic Search

Ionic polymer-metal composites (IPMCs) consist of a perfluorinated ionomer membrane (usually Nafion® or Flemion®) plated on both faces with a noble metal such as gold or platinum and neutralized with a certain amount of counterions that balance the electrical charge of anions covalently fixed to the backbone ionomer. IPMCs are electroactive materials with potential applications as actuators and sensors. Their

Sia Nemat-Nasser; Shahram Zamani; Yitzhak Tor



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



Backbone dynamics of free barnase and its complex with barstar determined by 15N NMR relaxation study  

Microsoft Academic Search

Backbone dynamics of uniformly 15N-labeled free barnase and its complex with unlabelled barstar have been studied at 40?°C, pH 6.6, using 15N relaxation data obtained from proton-detected 2D {1H}-15N NMR spectroscopy. 15N spin-lattice relaxation rate constants (R1), spin-spin relaxation rate constants (R2), and steady-state heteronuclear {1H}-15N NOEs have been measured at a magnetic field strength of 14.1 Tesla for 91 residues

Sarata C. Sahua; Abani K. Bhuyan; Jayant B. Udgaonkar; R. V. Hosur



Backbone and side-chain resonance assignments (¹H, ¹?N and ¹³C) of the ubiquitin homology domain of mouse BAG-1.  


BAG-1, an important regulatory protein associates with several signaling molecules and is capable of suppressing apoptosis. A 97-amino acid segment that includes the ubiquitin homology domain of mouse BAG-1 interacts with the cytoplasmic tail domain of proHB-EGF, and this interaction is likely to have functional significance. Here we report the backbone and side-chain resonance assignments for this 97-amino acid segment of mouse BAG-1. The assignment data has been deposited in the BMRB database under the accession number 18416. PMID:22903788

Huang, Hsiao-Wen; Yu, Chin



BON-BONs: cyclic molecules with a boron-oxygen-nitrogen backbone. Computational studies of their thermodynamic properties.  


Although they were first reported in 1963, molecules with a boron-oxygen-nitrogen dimeric backbone do not seem to have been investigated seriously in terms of thermodynamic properties. Here we report on the calculated structures and properties, including thermodynamics, of several so-called "BON-BON" molecules. With the popularity of nitrogen-containing substituents on new high-energy materials, nitro-substituted BON-BONs were a focus of our investigation. A total of 42 BON-BON molecules were evaluated, and thermochemical analysis shows a decrease in the specific enthalpy of combustion or decomposition with increasing NO(2) content, consistent with other systems. PMID:21811776

Lawong, Aloysus K; Ball, David W



Determination of base and backbone contributions to the thermodynamics of premelting and melting transitions in B DNA  

Microsoft Academic Search

In previous papers of this series the temperature- dependent Raman spectra of poly(dA)·poly(dT) and poly(dA-dT)·poly(dA-dT) were used to characterize structurally the melting and premelting transitions in DNAs containing consecutive A·T and alternating A·T\\/T·A base pairs. Here, we describe procedures for obtaining thermodynamic parameters from the Raman data. The method exploits base-specific and backbone-specific Raman markers to determine separate thermodynamic contributions

Liviu Movileanu; James M. Benevides; George J. Thomas Jr



RNA-Binding Affinities and Crystal Structure of Oligonucleotides Containing Five-Atom Amide-Based Backbone Structures  

Microsoft Academic Search

Among the hundreds of nucleic acid analogues that have been studied over the last two decades only very few exhibit backbones with linkers between residues that are either shorter or longer than the four-atom linker O3â²-P-O5â²-C5â² connecting sugar ring moieties in DNA and RNA. 2â²-Deoxyribonucleoside dimers connected by a five-atom linker O3â²-CH*(CHâ)-CO-NH-CHâ (* designates a chiral center) were reported to

Pradeep S. Pallan; Peter von Matt; Christopher J. Wilds; Karl-Heinz Altmann; Martin Egli



Genome Sequence of Yersinia pestis KIM†  

PubMed Central

We present the complete genome sequence of Yersinia pestis KIM, the etiologic agent of bubonic and pneumonic plague. The strain KIM, biovar Mediaevalis, is associated with the second pandemic, including the Black Death. The 4.6-Mb genome encodes 4,198 open reading frames (ORFs). The origin, terminus, and most genes encoding DNA replication proteins are similar to those of Escherichia coli K-12. The KIM genome sequence was compared with that of Y. pestis CO92, biovar Orientalis, revealing homologous sequences but a remarkable amount of genome rearrangement for strains so closely related. The differences appear to result from multiple inversions of genome segments at insertion sequences, in a manner consistent with present knowledge of replication and recombination. There are few differences attributable to horizontal transfer. The KIM and E. coli K-12 genome proteins were also compared, exposing surprising amounts of locally colinear “backbone,” or synteny, that is not discernible at the nucleotide level. Nearly 54% of KIM ORFs are significantly similar to K-12 proteins, with conserved housekeeping functions. However, a number of E. coli pathways and transport systems and at least one global regulator were not found, reflecting differences in lifestyle between them. In KIM-specific islands, new genes encode candidate pathogenicity proteins, including iron transport systems, putative adhesins, toxins, and fimbriae.

Deng, Wen; Burland, Valerie; Plunkett III, Guy; Boutin, Adam; Mayhew, George F.; Liss, Paul; Perna, Nicole T.; Rose, Debra J.; Mau, Bob; Zhou, Shiguo; Schwartz, David C.; Fetherston, Jaqueline D.; Lindler, Luther E.; Brubaker, Robert R.; Plano, Gregory V.; Straley, Susan C.; McDonough, Kathleen A.; Nilles, Matthew L.; Matson, Jyl S.; Blattner, Frederick R.; Perry, Robert D.



{{text{C}}_{? }} - {text{C}} Bond Cleavage of the Peptide Backbone in MALDI In-Source Decay Using Salicylic Acid Derivative Matrices  

NASA Astrophysics Data System (ADS)

The use of 5-formylsalicylic acid (5-FSA) and 5-nitrosalicylic acid (5-NSA) as novel matrices for in-source decay (ISD) of peptides in matrix-assisted laser desorption/ionization (MALDI) is described. The use of 5-FSA and 5-NSA generated a- and x-series ions accompanied by oxidized peptides [M - 2 H + H]+. The preferential formation of a- and x-series ions was found to be dependent on the hydrogen-accepting ability of matrix. The hydrogen-accepting ability estimated from the ratio of signal intensity of oxidized product [M - 2 H + H]+ to that of