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Sample records for additional secondary structure

  1. Combinatorics of saturated secondary structures of RNA.

    PubMed

    Clote, P

    2006-11-01

    Following Zuker (1986), a saturated secondary structure for a given RNA sequence is a secondary structure such that no base pair can be added without violating the definition of secondary structure, e.g., without introducing a pseudoknot. In the Nussinov-Jacobson energy model (Nussinov and Jacobson, 1980), where the energy of a secondary structure is -1 times the number of base pairs, saturated secondary structures are local minima in the energy landscape, hence form kinetic traps during the folding process. Here we present recurrence relations and closed form asymptotic limits for combinatorial problems related to the number of saturated secondary structures. In addition, Python source code to compute the number of saturated secondary structures having k base pairs can be found at the web servers link of bioinformatics.bc.edu/clotelab/.

  2. Secondary Structure Switch

    ERIC Educational Resources Information Center

    King, Angela G.

    2006-01-01

    Neurogenerative diseases like Alzheimer's disease and Parkinson's disease involve a transformation between two peptide and protein structures of alpha-helices and beta-sheets, where the peptide backbone can also participate in metal ion binding in addition to histidine residues. However, the complete absence of change in conformation of Coiled…

  3. Conserved Secondary Structures in Aspergillus

    PubMed Central

    McGuire, Abigail Manson; Galagan, James E.

    2008-01-01

    Background Recent evidence suggests that the number and variety of functional RNAs (ncRNAs as well as cis-acting RNA elements within mRNAs ) is much higher than previously thought; thus, the ability to computationally predict and analyze RNAs has taken on new importance. We have computationally studied the secondary structures in an alignment of six Aspergillus genomes. Little is known about the RNAs present in this set of fungi, and this diverse set of genomes has an optimal level of sequence conservation for observing the correlated evolution of base-pairs seen in RNAs. Methodology/Principal Findings We report the results of a whole-genome search for evolutionarily conserved secondary structures, as well as the results of clustering these predicted secondary structures by structural similarity. We find a total of 7450 predicted secondary structures, including a new predicted ∼60 bp long hairpin motif found primarily inside introns. We find no evidence for microRNAs. Different types of genomic regions are over-represented in different classes of predicted secondary structures. Exons contain the longest motifs (primarily long, branched hairpins), 5′ UTRs primarily contain groupings of short hairpins located near the start codon, and 3′ UTRs contain very little secondary structure compared to other regions. There is a large concentration of short hairpins just inside the boundaries of exons. The density of predicted intronic RNAs increases with the length of introns, and the density of predicted secondary structures within mRNA coding regions increases with the number of introns in a gene. Conclusions/Sigificance There are many conserved, high-confidence RNAs of unknown function in these Aspergillus genomes, as well as interesting spatial distributions of predicted secondary structures. This study increases our knowledge of secondary structure in these aspergillus organisms. PMID:18665251

  4. Combinatorics of locally optimal RNA secondary structures.

    PubMed

    Fusy, Eric; Clote, Peter

    2014-01-01

    It is a classical result of Stein and Waterman that the asymptotic number of RNA secondary structures is 1.104366∙n-3/2∙2.618034n. Motivated by the kinetics of RNA secondary structure formation, we are interested in determining the asymptotic number of secondary structures that are locally optimal, with respect to a particular energy model. In the Nussinov energy model, where each base pair contributes -1 towards the energy of the structure, locally optimal structures are exactly the saturated structures, for which we have previously shown that asymptotically, there are 1.07427∙n-3/2∙2.35467n many saturated structures for a sequence of length n. In this paper, we consider the base stacking energy model, a mild variant of the Nussinov model, where each stacked base pair contributes -1 toward the energy of the structure. Locally optimal structures with respect to the base stacking energy model are exactly those secondary structures, whose stems cannot be extended. Such structures were first considered by Evers and Giegerich, who described a dynamic programming algorithm to enumerate all locally optimal structures. In this paper, we apply methods from enumerative combinatorics to compute the asymptotic number of such structures. Additionally, we consider analogous combinatorial problems for secondary structures with annotated single-stranded, stacking nucleotides (dangles).

  5. Combinatorics of locally optimal RNA secondary structures.

    PubMed

    Fusy, Eric; Clote, Peter

    2014-01-01

    It is a classical result of Stein and Waterman that the asymptotic number of RNA secondary structures is 1.104366∙n-3/2∙2.618034n. Motivated by the kinetics of RNA secondary structure formation, we are interested in determining the asymptotic number of secondary structures that are locally optimal, with respect to a particular energy model. In the Nussinov energy model, where each base pair contributes -1 towards the energy of the structure, locally optimal structures are exactly the saturated structures, for which we have previously shown that asymptotically, there are 1.07427∙n-3/2∙2.35467n many saturated structures for a sequence of length n. In this paper, we consider the base stacking energy model, a mild variant of the Nussinov model, where each stacked base pair contributes -1 toward the energy of the structure. Locally optimal structures with respect to the base stacking energy model are exactly those secondary structures, whose stems cannot be extended. Such structures were first considered by Evers and Giegerich, who described a dynamic programming algorithm to enumerate all locally optimal structures. In this paper, we apply methods from enumerative combinatorics to compute the asymptotic number of such structures. Additionally, we consider analogous combinatorial problems for secondary structures with annotated single-stranded, stacking nucleotides (dangles). PMID:23263300

  6. Interaction between Polymeric Additives and Secondary Fluids in Capillary Suspensions.

    PubMed

    Bitsch, Boris; Braunschweig, Björn; Willenbacher, Norbert

    2016-02-16

    Capillary suspensions are ternary systems including a solid and two liquid phases representing a novel formulation platform for pastes with unique processing and end-use properties. Here we have investigated aqueous suspensions of non-Brownian graphite particles including different polymers commonly used as thickening agents or binders in paste formulations. We have studied the interaction between these additives and organic solvents in order to elucidate its effect on the characteristic formation of a particle network structure in corresponding ternary capillary suspension systems. Organic solvents with different polarity have been employed, and in the presence of nonadsorbing poly(ethylene oxide), all of them, whether they preferentially wet the graphite surface or not, induce the formation of a network structure within the suspension as indicated by a strong change in rheological properties. However, when the adsorbing polymers carboxymethylcellulose and poly(vinylpyrrolidone) are included, the drastic change in rheological behavior occurs only when polar organic solvents are used as secondary liquids. Obviously, these solvents can form pendular bridges, finally resulting in a sample-spanning particle network. Vibrational sum frequency spectroscopy provides evidence that these polar liquids remove the adsorbed polymer from the graphite particles. In contrast, nonpolar and nonwetting solvents do not force polymer desorption. In these cases, the formation of a percolating network structure within the suspensions is presumably prevented by the strong steric repulsion among graphite particles, not allowing for the formation of particle clusters encapsulating the secondary liquid. Accordingly, polymeric additives and secondary fluids have to be carefully selected in capillary suspension formulations, then offering a new pathway to customize paste formulations. The polymer may serve to adjust an appropriate viscosity level, and the capillary bridging induces the

  7. Secondary structure formation in peptide amphiphile micelles

    NASA Astrophysics Data System (ADS)

    Tirrell, Matthew

    2012-02-01

    Peptide amphiphiles (PAs) are capable of self-assembly into micelles for use in the targeted delivery of peptide therapeutics and diagnostics. PA micelles exhibit a structural resemblance to proteins by having folded bioactive peptides displayed on the exterior of a hydrophobic core. We have studied two factors that influence PA secondary structure in micellar assemblies: the length of the peptide headgroup and amino acids closest to the micelle core. Peptide length was systematically varied using a heptad repeat PA. For all PAs the addition of a C12 tail induced micellization and secondary structure. PAs with 9 amino acids formed beta-sheet interactions upon aggregation, whereas the 23 and 30 residue peptides were displayed in an apha-helical conformation. The 16 amino acid PA experienced a structural transition from helix to sheet, indicating that kinetics play a role in secondary structure formation. A p53 peptide was conjugated to a C16 tail via various linkers to study the effect of linker chemistry on PA headgroup conformation. With no linker the p53 headgroup was predominantly alpha helix and a four alanine linker drastically changed the structure of the peptide headgroup to beta-sheet, highlighting the importance of hydrogen boding potential near the micelle core.

  8. Prediction of RNA secondary structures with pseudoknots

    NASA Astrophysics Data System (ADS)

    Bon, M.; Orland, H.

    2010-08-01

    We present a new algorithm to predict RNA secondary structures with pseudoknots. The method is based on a classification of RNA structures according to their topological genus. The algorithm utilizes a simplified parametrization of the free energies for pair stacking, loop penalties, etc. and in addition a free energy penalty proportional to the topological genus of the pairing graph. Our method can take into account all pseudoknot topologies and achieves high success rates compared to state-of-the-art methods. This shows that the genus is a promising concept to classify pseudoknots.

  9. Improving RNA secondary structure prediction with structure mapping data.

    PubMed

    Sloma, Michael F; Mathews, David H

    2015-01-01

    Methods to probe RNA secondary structure, such as small molecule modifying agents, secondary structure-specific nucleases, inline probing, and SHAPE chemistry, are widely used to study the structure of functional RNA. Computational secondary structure prediction programs can incorporate probing data to predict structure with high accuracy. In this chapter, an overview of current methods for probing RNA secondary structure is provided, including modern high-throughput methods. Methods for guiding secondary structure prediction algorithms using these data are explained, and best practices for using these data are provided. This chapter concludes by listing a number of open questions about how to best use probing data, and what these data can provide.

  10. Maximum expected accuracy structural neighbors of an RNA secondary structure

    PubMed Central

    2012-01-01

    Background Since RNA molecules regulate genes and control alternative splicing by allostery, it is important to develop algorithms to predict RNA conformational switches. Some tools, such as paRNAss, RNAshapes and RNAbor, can be used to predict potential conformational switches; nevertheless, no existent tool can detect general (i.e., not family specific) entire riboswitches (both aptamer and expression platform) with accuracy. Thus, the development of additional algorithms to detect conformational switches seems important, especially since the difference in free energy between the two metastable secondary structures may be as large as 15-20 kcal/mol. It has recently emerged that RNA secondary structure can be more accurately predicted by computing the maximum expected accuracy (MEA) structure, rather than the minimum free energy (MFE) structure. Results Given an arbitrary RNA secondary structure S0 for an RNA nucleotide sequence a = a1,..., an, we say that another secondary structure S of a is a k-neighbor of S0, if the base pair distance between S0 and S is k. In this paper, we prove that the Boltzmann probability of all k-neighbors of the minimum free energy structure S0 can be approximated with accuracy ε and confidence 1 - p, simultaneously for all 0 ≤ k < K, by a relative frequency count over N sampled structures, provided that N>N(ε,p,K)=Φ-1p2K24ε2, where Φ(z) is the cumulative distribution function (CDF) for the standard normal distribution. We go on to describe the algorithm RNAborMEA, which for an arbitrary initial structure S0 and for all values 0 ≤ k < K, computes the secondary structure MEA(k), having maximum expected accuracy over all k-neighbors of S0. Computation time is O(n3 · K2), and memory requirements are O(n2 · K). We analyze a sample TPP riboswitch, and apply our algorithm to the class of purine riboswitches. Conclusions The approximation of RNAbor by sampling, with rigorous bound on accuracy, together with the computation of

  11. An algebraic representation of RNA secondary structures.

    PubMed

    Magarshak, Y; Benham, C J

    1992-12-01

    This paper develops mathematical methods for describing and analyzing RNA secondary structures. It was motivated by the need to develop rigorous yet efficient methods to treat transitions from one secondary structure to another, which we propose here may occur as motions of loops within RNAs having appropriate sequences. In this approach a molecular sequence is described as a vector of the appropriate length. The concept of symmetries between nucleic acid sequences is developed, and the 48 possible different types of symmetries are described. Each secondary structure possible for a particular nucleotide sequence determines a symmetric, signed permutation matrix. The collection of all possible secondary structures is comprised of all matrices of this type whose left multiplication with the sequence vector leaves that vector unchanged. A transition between two secondary structures is given by the product of the two corresponding structure matrices. This formalism provides an efficient method for describing nucleic acid sequences that allows questions relating to secondary structures and transitions to be addressed using the powerful methods of abstract algebra. In particular, it facilitates the determination of possible secondary structures, including those containing pseudoknots. Although this paper concentrates on RNA structure, this formalism also can be applied to DNA. PMID:1283516

  12. Enumeration of Secondary Structure Element Bundles

    SciTech Connect

    Brown, William Michael; Faulon, Jean-Loup

    2004-10-26

    A deterministic algorithm for enumeration of transmembrane protein folds is implemented. Using a set of sparse pairwise atomic distance constraints (such as those obtained from chemical cross-linking, FRET, or dipolar EPR experiments), the algorithm performs an exhaustive search of secondary structure element packing conformations distributed throughout the entire conformational space. The end result is a set of distinct protein conformations which can be scored and refined as part of a process designed for computational elucidation of transmembrane protein structures. Algorithm Overview: The ESSEB algorithm works by dividing the conforrnational space of each secondary structure element (SSE) into a set of cells. For each cell there is a representative conformation and for each atom in the SSE for which a distance restraint is available, there is an associated internal error, The internal error for a distance restraint is the maximum distance that the atom, when positioned in any conformation within a cell, can be from the atom in the representative conformation. The algorithm works recursively by positioning one representative conformation of an SSE. AdI distance restraints are checked with a tolerance that includes both the experimental and internal error. If all restraints are satisfied, every representative conformation of the next SSE is checked, otherwise, the program moves on to the next representative conformation of the current SSE. In addition to the distance restraints, other constraints on protein conformation can be enforced. These include the distance of closest approach between SSE axes, a restraint which prevents the crossover of loops connecting adjacent SSEs, and a restriction on the minimum and maximum distances between axis end-points. Any protein conformation satisfying all of the restraints is enumerated for later scoring and possible refinement. Additionally, in order to make run-times feasible, a divide-and-conquer approach is used in which

  13. Pairwise amino acid secondary structural propensities

    NASA Astrophysics Data System (ADS)

    Chemmama, Ilan E.; Chapagain, Prem P.; Gerstman, Bernard S.

    2015-04-01

    We investigate the propensities for amino acids to form a specific secondary structure when they are paired with other amino acids. Our investigations use molecular dynamics (MD) computer simulations, and we compare the results to those from the Protein Data Bank (PDB). Proper comparison requires weighting of the MD results in a manner consistent with the relative frequency of appearance in the PDB of each possible pair of amino acids. We find that the propensity for an amino acid to assume a secondary structure varies dramatically depending on the amino acid that is before or after it in the primary sequence. This cooperative effect means that when selecting amino acids to facilitate the formation of a secondary structure in peptide engineering experiments, the adjacent amino acids must be considered. We also examine the preference for a secondary structure in bacterial proteins and compare the results to those of human proteins.

  14. Current perspectives on RNA secondary structure probing.

    PubMed

    Kenyon, Julia; Prestwood, Liam; Lever, Andrew

    2014-08-01

    The range of roles played by structured RNAs in biological systems is vast. At the same time as we are learning more about the importance of RNA structure, recent advances in reagents, methods and technology mean that RNA secondary structural probing has become faster and more accurate. As a result, the capabilities of laboratories that already perform this type of structural analysis have increased greatly, and it has also become more widely accessible. The present review summarizes established and recently developed techniques. The information we can derive from secondary structural analysis is assessed, together with the areas in which we are likely to see exciting developments in the near future. PMID:25110033

  15. Hydrogen bonding in peptide secondary structures

    NASA Astrophysics Data System (ADS)

    Varga, Zoltán; Kovács, Attila

    Hydrogen bonding interactions in various peptide secondary structures (β-sheet, 27-ribbon, 310-helix, α-helix, π-helix, β-turn II, and γ-turn) have been investigated in small oligopeptides by quantum chemical calculations at the B3LYP/6-31G** level. Besides the primary O...HN interactions, the optimized structures revealed the importance of N...HN hydrogen bonding in several structures. The effect of substitution on the energy and structural properties was investigated comparing the properties of glycine, alanine, valine, and serine. The aliphatic substituents generally weaken the hydrogen bonds, the strongest effects being observed in crowded valine conformers. Additional hydrogen bonding interactions introduced by the OH group of serine can both strengthen (by polarizing the amide moiety through N...H interaction) and weaken (constraining the CO oxygen by O...HO interaction) the backbone hydrogen bonds. The effect of water as a polarizable medium on the energy properties was assessed by the COSMO model.

  16. RNA Secondary Structure Determination by NMR.

    PubMed

    Chen, Jonathan L; Bellaousov, Stanislav; Turner, Douglas H

    2016-01-01

    Dynamic programming methods for predicting RNA secondary structure often use thermodynamics and experimental restraints and/or constraints to limit folding space. Chemical mapping results typically restrain certain nucleotides not to be in AU or GC pairs. Two-dimensional nuclear magnetic resonance (NMR) spectra can reveal the order of AU, GC, and GU pairs in double helixes. This chapter describes a program, NMR-assisted prediction of secondary structure and chemical shifts (NAPSS-CS), that constrains possible secondary structures on the basis of the NMR determined order and 5'-3' direction of AU, GC, and GU pairs in helixes. NAPSS-CS minimally requires input of the order of base pairs as determined from nuclear Overhauser effect spectroscopy (NOESY) of imino protons. The program deduces the 5'-3' direction of the base pairs if certain chemical shifts are also input. Secondary structures predicted by the program provide assignments of input chemical shifts to particular nucleotides in the sequence, thus facilitating an important step for determination of the three dimensional structure by NMR. The method is particularly useful for revealing pseudoknots and an example is provided. The method may also allow determination of secondary structures when a sequence folds into two structures that exchange slowly. PMID:27665599

  17. RNA Secondary Structure Analysis Using RNAstructure.

    PubMed

    Mathews, David H

    2014-06-17

    RNAstructure is a user-friendly program for the prediction and analysis of RNA secondary structure. It is available as a Web server, as a program with a graphical user interface, or as a set of command-line tools. The programs are available for Microsoft Windows, Macintosh OS X, or Linux. This unit provides protocols for RNA secondary structure prediction (using the Web server or the graphical user interface) and prediction of high-affinity oligonucleotide biding sites to a structured RNA target (using the graphical user interface).

  18. Enumeration of Secondary Structure Element Bundles

    2004-10-26

    A deterministic algorithm for enumeration of transmembrane protein folds is implemented. Using a set of sparse pairwise atomic distance constraints (such as those obtained from chemical cross-linking, FRET, or dipolar EPR experiments), the algorithm performs an exhaustive search of secondary structure element packing conformations distributed throughout the entire conformational space. The end result is a set of distinct protein conformations which can be scored and refined as part of a process designed for computational elucidationmore » of transmembrane protein structures. Algorithm Overview: The ESSEB algorithm works by dividing the conforrnational space of each secondary structure element (SSE) into a set of cells. For each cell there is a representative conformation and for each atom in the SSE for which a distance restraint is available, there is an associated internal error, The internal error for a distance restraint is the maximum distance that the atom, when positioned in any conformation within a cell, can be from the atom in the representative conformation. The algorithm works recursively by positioning one representative conformation of an SSE. AdI distance restraints are checked with a tolerance that includes both the experimental and internal error. If all restraints are satisfied, every representative conformation of the next SSE is checked, otherwise, the program moves on to the next representative conformation of the current SSE. In addition to the distance restraints, other constraints on protein conformation can be enforced. These include the distance of closest approach between SSE axes, a restraint which prevents the crossover of loops connecting adjacent SSEs, and a restriction on the minimum and maximum distances between axis end-points. Any protein conformation satisfying all of the restraints is enumerated for later scoring and possible refinement. Additionally, in order to make run-times feasible, a divide-and-conquer approach is used

  19. Computing the Partition Function for Kinetically Trapped RNA Secondary Structures

    PubMed Central

    Lorenz, William A.; Clote, Peter

    2011-01-01

    An RNA secondary structure is locally optimal if there is no lower energy structure that can be obtained by the addition or removal of a single base pair, where energy is defined according to the widely accepted Turner nearest neighbor model. Locally optimal structures form kinetic traps, since any evolution away from a locally optimal structure must involve energetically unfavorable folding steps. Here, we present a novel, efficient algorithm to compute the partition function over all locally optimal secondary structures of a given RNA sequence. Our software, RNAlocopt runs in time and space. Additionally, RNAlocopt samples a user-specified number of structures from the Boltzmann subensemble of all locally optimal structures. We apply RNAlocopt to show that (1) the number of locally optimal structures is far fewer than the total number of structures – indeed, the number of locally optimal structures approximately equal to the square root of the number of all structures, (2) the structural diversity of this subensemble may be either similar to or quite different from the structural diversity of the entire Boltzmann ensemble, a situation that depends on the type of input RNA, (3) the (modified) maximum expected accuracy structure, computed by taking into account base pairing frequencies of locally optimal structures, is a more accurate prediction of the native structure than other current thermodynamics-based methods. The software RNAlocopt constitutes a technical breakthrough in our study of the folding landscape for RNA secondary structures. For the first time, locally optimal structures (kinetic traps in the Turner energy model) can be rapidly generated for long RNA sequences, previously impossible with methods that involved exhaustive enumeration. Use of locally optimal structure leads to state-of-the-art secondary structure prediction, as benchmarked against methods involving the computation of minimum free energy and of maximum expected accuracy. Web server

  20. Computing the partition function for kinetically trapped RNA secondary structures.

    PubMed

    Lorenz, William A; Clote, Peter

    2011-01-01

    An RNA secondary structure is locally optimal if there is no lower energy structure that can be obtained by the addition or removal of a single base pair, where energy is defined according to the widely accepted Turner nearest neighbor model. Locally optimal structures form kinetic traps, since any evolution away from a locally optimal structure must involve energetically unfavorable folding steps. Here, we present a novel, efficient algorithm to compute the partition function over all locally optimal secondary structures of a given RNA sequence. Our software, RNAlocopt runs in O(n3) time and O(n2) space. Additionally, RNAlocopt samples a user-specified number of structures from the Boltzmann subensemble of all locally optimal structures. We apply RNAlocopt to show that (1) the number of locally optimal structures is far fewer than the total number of structures--indeed, the number of locally optimal structures approximately equal to the square root of the number of all structures, (2) the structural diversity of this subensemble may be either similar to or quite different from the structural diversity of the entire Boltzmann ensemble, a situation that depends on the type of input RNA, (3) the (modified) maximum expected accuracy structure, computed by taking into account base pairing frequencies of locally optimal structures, is a more accurate prediction of the native structure than other current thermodynamics-based methods. The software RNAlocopt constitutes a technical breakthrough in our study of the folding landscape for RNA secondary structures. For the first time, locally optimal structures (kinetic traps in the Turner energy model) can be rapidly generated for long RNA sequences, previously impossible with methods that involved exhaustive enumeration. Use of locally optimal structure leads to state-of-the-art secondary structure prediction, as benchmarked against methods involving the computation of minimum free energy and of maximum expected accuracy

  1. General combinatorics of RNA secondary structure.

    PubMed

    Liao, Bo; Wang, Tian-ming

    2004-09-01

    The total number of RNA secondary structures of a given length with minimal hairpin loop length m(m>0) and with minimal stack length l(l>0) is computed, under the assumption that all base pairs can occur. Asymptotics are derived from the determination of recurrence relations of decomposition properties.

  2. Folding and Finding RNA Secondary Structure

    PubMed Central

    Mathews, David H.; Moss, Walter N.; Turner, Douglas H.

    2010-01-01

    SUMMARY Optimal exploitation of the expanding database of sequences requires rapid finding and folding of RNAs. Methods are reviewed that automate folding and discovery of RNAs with algorithms that couple thermodynamics with chemical mapping, NMR, and/or sequence comparison. New functional noncoding RNAs in genome sequences can be found by combining sequence comparison with the assumption that functional noncoding RNAs will have more favorable folding free energies than other RNAs. When a new RNA is discovered, experiments and sequence comparison can restrict folding space so that secondary structure can be rapidly determined with the help of predicted free energies. In turn, secondary structure restricts folding in three dimensions, which allows modeling of three-dimensional structure. An example from a domain of a retrotransposon is described. Discovery of new RNAs and their structures will provide insights into evolution, biology, and design of therapeutics. Applications to studies of evolution are also reviewed. PMID:20685845

  3. PSS-SQL: protein secondary structure - structured query language.

    PubMed

    Mrozek, Dariusz; Wieczorek, Dominika; Malysiak-Mrozek, Bozena; Kozielski, Stanislaw

    2010-01-01

    Secondary structure representation of proteins provides important information regarding protein general construction and shape. This representation is often used in protein similarity searching. Since existing commercial database management systems do not offer integrated exploration methods for biological data e.g. at the level of the SQL language, the structural similarity searching is usually performed by external tools. In the paper, we present our newly developed PSS-SQL language, which allows searching a database in order to identify proteins having secondary structure similar to the structure specified by the user in a PSS-SQL query. Therefore, we provide a simple and declarative language for protein structure similarity searching.

  4. Structural perspectives on secondary active transporters

    PubMed Central

    Boudker, Olga; Verdon, Grégory

    2010-01-01

    Secondary active transporters catalyze concentrative transport of substrates across lipid membranes by harnessing the energy of electrochemical ion gradients. These transporters bind their ligands on one side of the membrane, and undergo a global conformational change to release them on the other side of the membrane. Over the last few years, crystal structures have captured several bacterial secondary transporters in different states along their transport cycle, providing insight into possible molecular mechanisms. In this review, we will summarize recent findings focusing on the emerging structural and mechanistic similarities between evolutionary diverse transporters. We will also discuss the structural basis of substrate binding, ion coupling and inhibition viewed from the perspective of these similarities. PMID:20655602

  5. Chemoselective synthesis of ketones and ketimines by addition of organometallic reagents to secondary amides

    NASA Astrophysics Data System (ADS)

    Bechara, William S.; Pelletier, Guillaume; Charette, André B.

    2012-03-01

    The development of efficient and selective transformations is crucial in synthetic chemistry as it opens new possibilities in the total synthesis of complex molecules. Applying such reactions to the synthesis of ketones is of great importance, as this motif serves as a synthetic handle for the elaboration of numerous organic functionalities. In this context, we report a general and chemoselective method based on an activation/addition sequence on secondary amides allowing the controlled isolation of structurally diverse ketones and ketimines. The generation of a highly electrophilic imidoyl triflate intermediate was found to be pivotal in the observed exceptional functional group tolerance, allowing the facile addition of readily available Grignard and diorganozinc reagents to amides, and avoiding commonly observed over-addition or reduction side reactions. The methodology has been applied to the formal synthesis of analogues of the antineoplastic agent Bexarotene and to the rapid and efficient synthesis of unsymmetrical diketones in a one-pot procedure.

  6. RNA secondary structure prediction using soft computing.

    PubMed

    Ray, Shubhra Sankar; Pal, Sankar K

    2013-01-01

    Prediction of RNA structure is invaluable in creating new drugs and understanding genetic diseases. Several deterministic algorithms and soft computing-based techniques have been developed for more than a decade to determine the structure from a known RNA sequence. Soft computing gained importance with the need to get approximate solutions for RNA sequences by considering the issues related with kinetic effects, cotranscriptional folding, and estimation of certain energy parameters. A brief description of some of the soft computing-based techniques, developed for RNA secondary structure prediction, is presented along with their relevance. The basic concepts of RNA and its different structural elements like helix, bulge, hairpin loop, internal loop, and multiloop are described. These are followed by different methodologies, employing genetic algorithms, artificial neural networks, and fuzzy logic. The role of various metaheuristics, like simulated annealing, particle swarm optimization, ant colony optimization, and tabu search is also discussed. A relative comparison among different techniques, in predicting 12 known RNA secondary structures, is presented, as an example. Future challenging issues are then mentioned. PMID:23702539

  7. Automatic display of RNA secondary structures.

    PubMed

    Muller, G; Gaspin, C; Etienne, A; Westhof, E

    1993-10-01

    A set of programs written in C language with the GL library and under UNIX has been developed for generating compact, pleasant and non-overlapping displays of secondary structures of ribonucleic acids. The first program, rnasearch, implements a new search procedure that dynamically rearranges overlapping portions of the two-dimensional drawing while preserving clear and readable displays of the two-dimensional structure. The algorithm is fast (the execution time for the command rnasearch is 38.6 s for the 16S rRNA of Escherichia coli with 1542 bases), accepts outputs from two-dimensional prediction programs and therefore allows for rapid comparison between the various two-dimensional folds generated. A second program, rnadisplay, allows the graphical display of the computed two-dimensional structures on a graphics workstation. Otherwise, it is possible to obtain a paper output of the two-dimensional structure by using the program print2D which builds a Postscript file. Moreover the two-dimensional drawing can be labelled for representing data coming from chemical modifications and/or enzymatic cleavages. Application to a few secondary structures such as RNaseP, 5S rRNA and 16S rRNA are given.

  8. Secondary flow structures in large rivers

    NASA Astrophysics Data System (ADS)

    Chauvet, H.; Devauchelle, O.; Metivier, F.; Limare, A.; Lajeunesse, E.

    2012-04-01

    Measuring the velocity field in large rivers remains a challenge, even with recent measurement techniques such as Acoustic Doppler Current Profiler (ADCP). Indeed, due to the diverging angle between its ultrasonic beams, an ADCP cannot detect small-scale flow structures. However, when the measurements are limited to a single location for a sufficient period of time, averaging can reveal large, stationary flow structures. Here we present velocity measurements in a straight reach of the Seine river in Paris, France, where the cross-section is close to rectangular. The transverse modulation of the streamwise velocity indicates secondary flow cells, which seem to occupy the entire width of the river. This observation is reminiscent of the longitudinal vortices observed in laboratory experiments (e.g. Blanckaert et al., Advances in Water Resources, 2010, 33, 1062-1074). Although the physical origin of these secondary structures remains unclear, their measured velocity is sufficient to significantly impact the distribution of streamwise momentum. We propose a model for the transverse profile of the depth-averaged velocity based on a crude representation of the longitudinal vortices, with a single free parameter. Preliminary results are in good agreement with field measurements. This model also provides an estimate for the bank shear stress, which controls bank erosion.

  9. Prediction of packing of secondary structure.

    PubMed

    Nagano, K; Ponnuswamy, P K

    1984-01-01

    An improved method of picking up candidates for predicting the packing arrangement of beta-strands and alpha-helices of the alpha/beta type domains is described here. The method of judging whether the region of the protein would fold into the alpha/beta type or not is also described. The folding constraints of globular proteins are analysed and presented in this article for application to the prediction of packing of secondary structure. The analysis of the residue-fluctuations is also applicable for the purpose.

  10. JPred4: a protein secondary structure prediction server.

    PubMed

    Drozdetskiy, Alexey; Cole, Christian; Procter, James; Barton, Geoffrey J

    2015-07-01

    JPred4 (http://www.compbio.dundee.ac.uk/jpred4) is the latest version of the popular JPred protein secondary structure prediction server which provides predictions by the JNet algorithm, one of the most accurate methods for secondary structure prediction. In addition to protein secondary structure, JPred also makes predictions of solvent accessibility and coiled-coil regions. The JPred service runs up to 94 000 jobs per month and has carried out over 1.5 million predictions in total for users in 179 countries. The JPred4 web server has been re-implemented in the Bootstrap framework and JavaScript to improve its design, usability and accessibility from mobile devices. JPred4 features higher accuracy, with a blind three-state (α-helix, β-strand and coil) secondary structure prediction accuracy of 82.0% while solvent accessibility prediction accuracy has been raised to 90% for residues <5% accessible. Reporting of results is enhanced both on the website and through the optional email summaries and batch submission results. Predictions are now presented in SVG format with options to view full multiple sequence alignments with and without gaps and insertions. Finally, the help-pages have been updated and tool-tips added as well as step-by-step tutorials. PMID:25883141

  11. JPred4: a protein secondary structure prediction server

    PubMed Central

    Drozdetskiy, Alexey; Cole, Christian; Procter, James; Barton, Geoffrey J.

    2015-01-01

    JPred4 (http://www.compbio.dundee.ac.uk/jpred4) is the latest version of the popular JPred protein secondary structure prediction server which provides predictions by the JNet algorithm, one of the most accurate methods for secondary structure prediction. In addition to protein secondary structure, JPred also makes predictions of solvent accessibility and coiled-coil regions. The JPred service runs up to 94 000 jobs per month and has carried out over 1.5 million predictions in total for users in 179 countries. The JPred4 web server has been re-implemented in the Bootstrap framework and JavaScript to improve its design, usability and accessibility from mobile devices. JPred4 features higher accuracy, with a blind three-state (α-helix, β-strand and coil) secondary structure prediction accuracy of 82.0% while solvent accessibility prediction accuracy has been raised to 90% for residues <5% accessible. Reporting of results is enhanced both on the website and through the optional email summaries and batch submission results. Predictions are now presented in SVG format with options to view full multiple sequence alignments with and without gaps and insertions. Finally, the help-pages have been updated and tool-tips added as well as step-by-step tutorials. PMID:25883141

  12. Experiment-Assisted Secondary Structure Prediction with RNAstructure.

    PubMed

    Xu, Zhenjiang Zech; Mathews, David H

    2016-01-01

    Experimental probing data can be used to improve the accuracy of RNA secondary structure prediction. The software package RNAstructure can take advantage of enzymatic cleavage data, FMN cleavage data, traditional chemical modification reactivity data, and SHAPE reactivity data for secondary structure modeling. This chapter provides protocols for using experimental probing data with RNAstructure to restrain or constrain RNA secondary structure prediction. PMID:27665598

  13. Secondary use of structured patient data: interim results of a systematic review.

    PubMed

    Vuokko, Riikka; Mäkelä-Bengs, Päivi; Hyppönen, Hannele; Doupi, Persephone

    2015-01-01

    In addition to patient care, EHR data are increasingly in demand for secondary purposes, e.g. administration, research and enterprise resource planning. We conducted a systematic literature review and subsequent analysis of 85 articles focusing on the secondary use of structured patient records. We grounded the analysis on how patient records have been structured, how these structures have been evaluated and what are the main results achieved from the secondary use viewpoint. We conclude that secondary use requires complete and interoperable patient records, which in turn depend on better alignment of primary and secondary users' needs and benefits. PMID:25991152

  14. Circular dichroism and DNA secondary structure.

    PubMed

    Baase, W A; Johnson, W C

    1979-02-01

    The change in average rotation of the DNA helix has been determined for the transfer from 0.05 M NaCl to 3.0 M CsCl, 6.2 M LiCl and 5.4 M NH4Cl. This work, combined with data at lower salt from other laboratories, allows us to relate the intensity of the CD of DNA at 275 nm directly to the change in the number of base pairs per turn. The change in secondary structure for the transfer of DNA from 0.05 M NaCl (where it is presumably in the B-form) to high salt (where the characteristic CD has been interpreted as corresponding to C-form geometry) is found to be -0.22 (+/- 0.02) base pairs per turn. In the case of mononucleosomes, where the CD indicates the "C-form", the change in secondary structure (including temperature effects) would add -0.31 (+/- 0.03) turns about the histone core to the -1.25 turns estimated from work on SV40 chromatin. Accurate winding angles and molar extinction coefficients were determined for ethidium.

  15. Using Circular Dichroism Spectra to Estimate Protein Secondary Structure

    SciTech Connect

    Greenfield, N.

    2006-01-01

    Circular dichroism (CD) is an excellent tool for rapid determination of the secondary structure and folding properties of proteins that have been obtained using recombinant techniques or purified from tissues. The most widely used applications of protein CD are to determine whether an expressed, purified protein is folded, or if a mutation affects its conformation or stability. In addition, it can be used to study protein interactions. This protocol details the basic steps of obtaining and interpreting CD data and methods for analyzing spectra to estimate the secondary structural composition of proteins. CD has the advantage that it is that measurements may be made on multiple samples containing 20 {mu}g or less of proteins in physiological buffers in a few hours. However, it does not give the residue-specific information that can be obtained by X-ray crystallography or NMR.

  16. Using circular dichroism spectra to estimate protein secondary structure

    PubMed Central

    Greenfield, Norma J.

    2009-01-01

    Circular dichroism (CD) is an excellent tool for rapid determination of the secondary structure and folding properties of proteins that have been obtained using recombinant techniques or purified from tissues. The most widely used applications of protein CD are to determine whether an expressed, purified protein is folded, or if a mutation affects its conformation or stability. In addition, it can be used to study protein interactions. This protocol details the basic steps of obtaining and interpreting CD data and methods for analyzing spectra to estimate the secondary structural composition of proteins. CD has the advantage that it is that measurements may be made on multiple samples containing 20 µg or less of proteins in physiological buffers in a few hours. However, it does not give the residue-specific information that can be obtained by X-ray crystallography or NMR. PMID:17406547

  17. RNA-SSPT: RNA Secondary Structure Prediction Tools.

    PubMed

    Ahmad, Freed; Mahboob, Shahid; Gulzar, Tahsin; Din, Salah U; Hanif, Tanzeela; Ahmad, Hifza; Afzal, Muhammad

    2013-01-01

    The prediction of RNA structure is useful for understanding evolution for both in silico and in vitro studies. Physical methods like NMR studies to predict RNA secondary structure are expensive and difficult. Computational RNA secondary structure prediction is easier. Comparative sequence analysis provides the best solution. But secondary structure prediction of a single RNA sequence is challenging. RNA-SSPT is a tool that computationally predicts secondary structure of a single RNA sequence. Most of the RNA secondary structure prediction tools do not allow pseudoknots in the structure or are unable to locate them. Nussinov dynamic programming algorithm has been implemented in RNA-SSPT. The current studies shows only energetically most favorable secondary structure is required and the algorithm modification is also available that produces base pairs to lower the total free energy of the secondary structure. For visualization of RNA secondary structure, NAVIEW in C language is used and modified in C# for tool requirement. RNA-SSPT is built in C# using Dot Net 2.0 in Microsoft Visual Studio 2005 Professional edition. The accuracy of RNA-SSPT is tested in terms of Sensitivity and Positive Predicted Value. It is a tool which serves both secondary structure prediction and secondary structure visualization purposes. PMID:24250115

  18. COOLAIR Antisense RNAs Form Evolutionarily Conserved Elaborate Secondary Structures.

    PubMed

    Hawkes, Emily J; Hennelly, Scott P; Novikova, Irina V; Irwin, Judith A; Dean, Caroline; Sanbonmatsu, Karissa Y

    2016-09-20

    There is considerable debate about the functionality of long non-coding RNAs (lncRNAs). Lack of sequence conservation has been used to argue against functional relevance. We investigated antisense lncRNAs, called COOLAIR, at the A. thaliana FLC locus and experimentally determined their secondary structure. The major COOLAIR variants are highly structured, organized by exon. The distally polyadenylated transcript has a complex multi-domain structure, altered by a single non-coding SNP defining a functionally distinct A. thaliana FLC haplotype. The A. thaliana COOLAIR secondary structure was used to predict COOLAIR exons in evolutionarily divergent Brassicaceae species. These predictions were validated through chemical probing and cloning. Despite the relatively low nucleotide sequence identity, the structures, including multi-helix junctions, show remarkable evolutionary conservation. In a number of places, the structure is conserved through covariation of a non-contiguous DNA sequence. This structural conservation supports a functional role for COOLAIR transcripts rather than, or in addition to, antisense transcription. PMID:27653675

  19. Structural changes in gluten protein structure after addition of emulsifier. A Raman spectroscopy study

    NASA Astrophysics Data System (ADS)

    Ferrer, Evelina G.; Gómez, Analía V.; Añón, María C.; Puppo, María C.

    2011-06-01

    Food protein product, gluten protein, was chemically modified by varying levels of sodium stearoyl lactylate (SSL); and the extent of modifications (secondary and tertiary structures) of this protein was analyzed by using Raman spectroscopy. Analysis of the Amide I band showed an increase in its intensity mainly after the addition of the 0.25% of SSL to wheat flour to produced modified gluten protein, pointing the formation of a more ordered structure. Side chain vibrations also confirmed the observed changes.

  20. 77 FR 71695 - Secondary Direct Food Additives Permitted in Food for Human Consumption; Sodium...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-12-04

    ... February 2, 2012 (77 FR 5201), FDA announced that a food additive petition (FAP 2A4785) had been filed by... HUMAN SERVICES Food and Drug Administration 21 CFR Part 173 Secondary Direct Food Additives Permitted in Food for Human Consumption; Sodium Dodecylbenzenesulfonate AGENCY: Food and Drug Administration,...

  1. Distinct circular dichroism spectroscopic signatures of polyproline II and unordered secondary structures: Applications in secondary structure analyses

    PubMed Central

    Lopes, Jose L S; Miles, Andrew J; Whitmore, Lee; Wallace, B A

    2014-01-01

    Circular dichroism (CD) spectroscopy is a valuable method for defining canonical secondary structure contents of proteins based on empirically-defined spectroscopic signatures derived from proteins with known three-dimensional structures. Many proteins identified as being “Intrinsically Disordered Proteins” have a significant amount of their structure that is neither sheet, helix, nor turn; this type of structure is often classified by CD as “other”, “random coil”, “unordered”, or “disordered”. However the “other” category can also include polyproline II (PPII)-type structures, whose spectral properties have not been well-distinguished from those of unordered structures. In this study, synchrotron radiation circular dichroism spectroscopy was used to investigate the spectral properties of collagen and polyproline, which both contain PPII-type structures. Their native spectra were compared as representatives of PPII structures. In addition, their spectra before and after treatment with various conditions to produce unfolded or denatured structures were also compared, with the aim of defining the differences between CD spectra of PPII and disordered structures. We conclude that the spectral features of collagen are more appropriate than those of polyproline for use as the representative spectrum for PPII structures present in typical amino acid-containing proteins, and that the single most characteristic spectroscopic feature distinguishing a PPII structure from a disordered structure is the presence of a positive peak around 220nm in the former but not in the latter. These spectra are now available for inclusion in new reference data sets used for CD analyses of the secondary structures of soluble proteins. PMID:25262612

  2. Automated discovery of active motifs in multiple RNA secondary structures

    SciTech Connect

    Wang, J.T.L.; Chang, Chia-Yo; Shapiro, B.A.

    1996-12-31

    In this paper we present a method for discovering approximately common motifs (also known as active motifs) in multiple RNA secondary structures. The secondary structures can be represented as ordered trees (i.e., the order among siblings matters). Motifs in these trees are connected subgraphs that can differ in both substitutions and deletions/insertions. The proposed method consists of two steps: (1) find candidate motifs in a small sample of the secondary structures; (2) search all of the secondary structures to determine how frequently these motifs occur (within the allowed approximation) in the secondary structures. To reduce the running time, we develop two optimization heuristics based on sampling and pattern matching techniques. Experimental results obtained by running these algorithms on both generated data and RNA secondary structures show the good performance of the algorithms. To demonstrate the utility of our algorithms, we discuss their applications to conducting the phylogenetic study of RNA sequences obtained from GenBank.

  3. Structure Property Studies for Additively Manufactured Parts

    SciTech Connect

    Milenski, Helen M; Schmalzer, Andrew Michael; Kelly, Daniel

    2015-08-17

    Since the invention of modern Additive Manufacturing (AM) processes engineers and designers have worked hard to capitalize on the unique building capabilities that AM allows. By being able to customize the interior fill of parts it is now possible to design components with a controlled density and customized internal structure. The creation of new polymers and polymer composites allow for even greater control over the mechanical properties of AM parts. One of the key reasons to explore AM, is to bring about a new paradigm in part design, where materials can be strategically optimized in a way that conventional subtractive methods cannot achieve. The two processes investigated in my research were the Fused Deposition Modeling (FDM) process and the Direct Ink Write (DIW) process. The objectives of the research were to determine the impact of in-fill density and morphology on the mechanical properties of FDM parts, and to determine if DIW printed samples could be produced where the filament diameter was varied while the overall density remained constant.

  4. Neural network definitions of highly predictable protein secondary structure classes

    SciTech Connect

    Lapedes, A. |; Steeg, E.; Farber, R.

    1994-02-01

    We use two co-evolving neural networks to determine new classes of protein secondary structure which are significantly more predictable from local amino sequence than the conventional secondary structure classification. Accurate prediction of the conventional secondary structure classes: alpha helix, beta strand, and coil, from primary sequence has long been an important problem in computational molecular biology. Neural networks have been a popular method to attempt to predict these conventional secondary structure classes. Accuracy has been disappointingly low. The algorithm presented here uses neural networks to similtaneously examine both sequence and structure data, and to evolve new classes of secondary structure that can be predicted from sequence with significantly higher accuracy than the conventional classes. These new classes have both similarities to, and differences with the conventional alpha helix, beta strand and coil.

  5. ncRNA consensus secondary structure derivation using grammar strings.

    PubMed

    Achawanantakun, Rujira; Sun, Yanni; Takyar, Seyedeh Shohreh

    2011-04-01

    Many noncoding RNAs (ncRNAs) function through both their sequences and secondary structures. Thus, secondary structure derivation is an important issue in today's RNA research. The state-of-the-art structure annotation tools are based on comparative analysis, which derives consensus structure of homologous ncRNAs. Despite promising results from existing ncRNA aligning and consensus structure derivation tools, there is a need for more efficient and accurate ncRNA secondary structure modeling and alignment methods. In this work, we introduce a consensus structure derivation approach based on grammar string, a novel ncRNA secondary structure representation that encodes an ncRNA's sequence and secondary structure in the parameter space of a context-free grammar (CFG) and a full RNA grammar including pseudoknots. Being a string defined on a special alphabet constructed from a grammar, grammar string converts ncRNA alignment into sequence alignment. We derive consensus secondary structures from hundreds of ncRNA families from BraliBase 2.1 and 25 families containing pseudoknots using grammar string alignment. Our experiments have shown that grammar string-based structure derivation competes favorably in consensus structure quality with Murlet and RNASampler. Source code and experimental data are available at http://www.cse.msu.edu/~yannisun/grammar-string. PMID:21523935

  6. ncRNA consensus secondary structure derivation using grammar strings.

    PubMed

    Achawanantakun, Rujira; Sun, Yanni; Takyar, Seyedeh Shohreh

    2011-04-01

    Many noncoding RNAs (ncRNAs) function through both their sequences and secondary structures. Thus, secondary structure derivation is an important issue in today's RNA research. The state-of-the-art structure annotation tools are based on comparative analysis, which derives consensus structure of homologous ncRNAs. Despite promising results from existing ncRNA aligning and consensus structure derivation tools, there is a need for more efficient and accurate ncRNA secondary structure modeling and alignment methods. In this work, we introduce a consensus structure derivation approach based on grammar string, a novel ncRNA secondary structure representation that encodes an ncRNA's sequence and secondary structure in the parameter space of a context-free grammar (CFG) and a full RNA grammar including pseudoknots. Being a string defined on a special alphabet constructed from a grammar, grammar string converts ncRNA alignment into sequence alignment. We derive consensus secondary structures from hundreds of ncRNA families from BraliBase 2.1 and 25 families containing pseudoknots using grammar string alignment. Our experiments have shown that grammar string-based structure derivation competes favorably in consensus structure quality with Murlet and RNASampler. Source code and experimental data are available at http://www.cse.msu.edu/~yannisun/grammar-string.

  7. A dynamic programming algorithm for finding alternative RNA secondary structures.

    PubMed

    Williams, A L; Tinoco, I

    1986-01-10

    Dynamic programming algorithms that predict RNA secondary structure by minimizing the free energy have had one important limitation. They were able to predict only one optimal structure. Given the uncertainties of the thermodynamic data and the effects of proteins and other environmental factors on structure, the optimal structure predicted by these methods may not have biological significance. We present a dynamic programming algorithm that can determine optimal and suboptimal secondary structures for an RNA. The power and utility of the method is demonstrated in the folding of the intervening sequence of the rRNA of Tetrahymena. By first identifying the major secondary structures corresponding to the lowest free energy minima, a secondary structure of possible biological significance is derived.

  8. Non-B DNA Secondary Structures and Their Resolution by RecQ Helicases

    PubMed Central

    Sharma, Sudha

    2011-01-01

    In addition to the canonical B-form structure first described by Watson and Crick, DNA can adopt a number of alternative structures. These non-B-form DNA secondary structures form spontaneously on tracts of repeat sequences that are abundant in genomes. In addition, structured forms of DNA with intrastrand pairing may arise on single-stranded DNA produced transiently during various cellular processes. Such secondary structures have a range of biological functions but also induce genetic instability. Increasing evidence suggests that genomic instabilities induced by non-B DNA secondary structures result in predisposition to diseases. Secondary DNA structures also represent a new class of molecular targets for DNA-interactive compounds that might be useful for targeting telomeres and transcriptional control. The equilibrium between the duplex DNA and formation of multistranded non-B-form structures is partly dependent upon the helicases that unwind (resolve) these alternate DNA structures. With special focus on tetraplex, triplex, and cruciform, this paper summarizes the incidence of non-B DNA structures and their association with genomic instability and emphasizes the roles of RecQ-like DNA helicases in genome maintenance by resolution of DNA secondary structures. In future, RecQ helicases are anticipated to be additional molecular targets for cancer chemotherapeutics. PMID:21977309

  9. Visualizing the global secondary structure of a viral RNA genome with cryo-electron microscopy.

    PubMed

    Garmann, Rees F; Gopal, Ajaykumar; Athavale, Shreyas S; Knobler, Charles M; Gelbart, William M; Harvey, Stephen C

    2015-05-01

    The lifecycle, and therefore the virulence, of single-stranded (ss)-RNA viruses is regulated not only by their particular protein gene products, but also by the secondary and tertiary structure of their genomes. The secondary structure of the entire genomic RNA of satellite tobacco mosaic virus (STMV) was recently determined by selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE). The SHAPE analysis suggested a single highly extended secondary structure with much less branching than occurs in the ensemble of structures predicted by purely thermodynamic algorithms. Here we examine the solution-equilibrated STMV genome by direct visualization with cryo-electron microscopy (cryo-EM), using an RNA of similar length transcribed from the yeast genome as a control. The cryo-EM data reveal an ensemble of branching patterns that are collectively consistent with the SHAPE-derived secondary structure model. Thus, our results both elucidate the statistical nature of the secondary structure of large ss-RNAs and give visual support for modern RNA structure determination methods. Additionally, this work introduces cryo-EM as a means to distinguish between competing secondary structure models if the models differ significantly in terms of the number and/or length of branches. Furthermore, with the latest advances in cryo-EM technology, we suggest the possibility of developing methods that incorporate restraints from cryo-EM into the next generation of algorithms for the determination of RNA secondary and tertiary structures.

  10. Rhodium-catalyzed anti-Markovnikov addition of secondary amines to arylacetylenes at room temperature.

    PubMed

    Sakai, Kazunori; Kochi, Takuya; Kakiuchi, Fumitoshi

    2011-08-01

    An efficient method for synthesis of E-enamines by the anti-Markovnikov addition of secondary amines to terminal alkynes is described. The reaction of a variety of aryl- and heteroarylacetylenes proceeded at room temperature using a combination of a 8-quinolinolato rhodium complex and P(p-MeOC(6)H(4))(3) as a catalyst. The products were obtained as enamines by simple bulb-to-bulb distillation. PMID:21699251

  11. Coding of odor stimulus features among secondary olfactory structures.

    PubMed

    Xia, Christina Z; Adjei, Stacey; Wesson, Daniel W

    2015-07-01

    Sensory systems must represent stimuli in manners dependent upon a wealth of factors, including stimulus intensity and duration. One way the brain might handle these complex functions is to assign the tasks throughout distributed nodes, each contributing to information processing. We sought to explore this important aspect of sensory network function in the mammalian olfactory system, wherein the intensity and duration of odor exposure are critical contributors to odor perception. This is a quintessential model for exploring processing schemes given the distribution of odor information by olfactory bulb mitral and tufted cells into several anatomically distinct secondary processing stages, including the piriform cortex (PCX) and olfactory tubercle (OT), whose unique contributions to odor coding are unresolved. We explored the coding of PCX and OT neuron responses to odor intensity and duration. We found that both structures similarly partake in representing descending intensities of odors by reduced recruitment and modulation of neurons. Additionally, while neurons in the OT adapt to odor exposure, they display reduced capacity to adapt to either repeated presentations of odor or a single prolonged odor presentation compared with neurons in the PCX. These results provide insights into manners whereby secondary olfactory structures may, at least in some cases, uniquely represent stimulus features. PMID:26041832

  12. Coding of odor stimulus features among secondary olfactory structures

    PubMed Central

    Xia, Christina Z.; Adjei, Stacey

    2015-01-01

    Sensory systems must represent stimuli in manners dependent upon a wealth of factors, including stimulus intensity and duration. One way the brain might handle these complex functions is to assign the tasks throughout distributed nodes, each contributing to information processing. We sought to explore this important aspect of sensory network function in the mammalian olfactory system, wherein the intensity and duration of odor exposure are critical contributors to odor perception. This is a quintessential model for exploring processing schemes given the distribution of odor information by olfactory bulb mitral and tufted cells into several anatomically distinct secondary processing stages, including the piriform cortex (PCX) and olfactory tubercle (OT), whose unique contributions to odor coding are unresolved. We explored the coding of PCX and OT neuron responses to odor intensity and duration. We found that both structures similarly partake in representing descending intensities of odors by reduced recruitment and modulation of neurons. Additionally, while neurons in the OT adapt to odor exposure, they display reduced capacity to adapt to either repeated presentations of odor or a single prolonged odor presentation compared with neurons in the PCX. These results provide insights into manners whereby secondary olfactory structures may, at least in some cases, uniquely represent stimulus features. PMID:26041832

  13. Epigenetic Manipulation of a Filamentous Fungus by the Proteasome-Inhibitor Bortezomib Induces the Production of an Additional Secondary Metabolite

    PubMed Central

    VanderMolen, Karen M.; Darveaux, Blaise A.; Chen, Wei-Lun; Swanson, Steven M.; Pearce, Cedric J.; Oberlies, Nicholas H.

    2014-01-01

    The use of epigenetic modifiers, such as histone deacetylase inhibitors and DNA methyltransferase inhibitors, has been explored increasingly as a technique to induce the production of additional microbial secondary metabolites. The application of such molecules to microbial cultures has been shown to upregulate otherwise suppressed genes, and in several cases has led to the production of new molecular structures. In this study, the proteasome inhibitor bortezomib was used to induce the production of an additional metabolite from a filamentous fungus (Pleosporales). The induced metabolite was previously isolated from a plant, but the configuration was not assigned until now; in addition, an analogue was isolated from a degraded sample, yielding a new compound. Proteasome inhibitors have not previously been used in this application and offer an additional tool for microbial genome mining. PMID:24955237

  14. Efficient detection of secondary structure folded nucleic acids related to Alzheimer's disease based on junction probes.

    PubMed

    Li, Juan; Qi, Xiu-Juan; Du, Yan-Yan; Fu, Hua-E; Chen, Guo-Nan; Yang, Huang-Hao

    2012-01-01

    Single stranded DNA often forms stable secondary structures under physiological conditions. These DNA secondary structures play important physiological roles. However, the analysis of such secondary structure folded DNA is often complicated because of its high thermodynamic stability and slow hybridization kinetics. In this article, we demonstrate that Y-shaped junction probes could be used for rapid and highly efficient detection of secondary structure folded DNA. Our approach contained a molecular beacon (MB) probe and an assistant probe. In the absence of target, the MB probe failed to hybridize with the assistant probe. Whereas, the MB probe and the assistant probe could cooperatively unwind the secondary structure folded DNA target to form a ternary Y-shaped junction structure. In this condition, the MB probe was also opened, resulting in separating the fluorophores from the quenching moiety and emitting the fluorescence signal. This approach allowed for the highly sensitive detection of secondary structure folded DNA target, such as a tau specific DNA fragment related to Alzheimer's disease in this case. Additionally, this approach showed strong SNPs identifying capability. Furthermore, it was noteworthy that this newly proposed approach was capable of detecting secondary structure folded DNA target in cell lysate samples.

  15. Unified approach to partition functions of RNA secondary structures.

    PubMed

    Bundschuh, Ralf

    2014-11-01

    RNA secondary structure formation is a field of considerable biological interest as well as a model system for understanding generic properties of heteropolymer folding. This system is particularly attractive because the partition function and thus all thermodynamic properties of RNA secondary structure ensembles can be calculated numerically in polynomial time for arbitrary sequences and homopolymer models admit analytical solutions. Such solutions for many different aspects of the combinatorics of RNA secondary structure formation share the property that the final solution depends on differences of statistical weights rather than on the weights alone. Here, we present a unified approach to a large class of problems in the field of RNA secondary structure formation. We prove a generic theorem for the calculation of RNA folding partition functions. Then, we show that this approach can be applied to the study of the molten-native transition, denaturation of RNA molecules, as well as to studies of the glass phase of random RNA sequences.

  16. Unified approach to partition functions of RNA secondary structures.

    PubMed

    Bundschuh, Ralf

    2014-11-01

    RNA secondary structure formation is a field of considerable biological interest as well as a model system for understanding generic properties of heteropolymer folding. This system is particularly attractive because the partition function and thus all thermodynamic properties of RNA secondary structure ensembles can be calculated numerically in polynomial time for arbitrary sequences and homopolymer models admit analytical solutions. Such solutions for many different aspects of the combinatorics of RNA secondary structure formation share the property that the final solution depends on differences of statistical weights rather than on the weights alone. Here, we present a unified approach to a large class of problems in the field of RNA secondary structure formation. We prove a generic theorem for the calculation of RNA folding partition functions. Then, we show that this approach can be applied to the study of the molten-native transition, denaturation of RNA molecules, as well as to studies of the glass phase of random RNA sequences. PMID:24177391

  17. Dynamics in Sequence Space for RNA Secondary Structure Design.

    PubMed

    Matthies, Marco C; Bienert, Stefan; Torda, Andrew E

    2012-10-01

    We have implemented a method for the design of RNA sequences that should fold to arbitrary secondary structures. A popular energy model allows one to take the derivative with respect to composition, which can then be interpreted as a force and used for Newtonian dynamics in sequence space. Combined with a negative design term, one can rapidly sample sequences which are compatible with a desired secondary structure via simulated annealing. Results for 360 structures were compared with those from another nucleic acid design program using measures such as the probability of the target structure and an ensemble-weighted distance to the target structure.

  18. Combinatorics of RNA Secondary Structures with Base Triples.

    PubMed

    Müller, Robert; Nebel, Markus E

    2015-07-01

    The structure of RNA has been the subject of intense research over the last decades due to its importance for the correct functioning of RNA molecules in biological processes. Hence, a large number of models for RNA folding and corresponding algorithms for structure prediction have been developed. However, previous models often only consider base pairs, although every base is capable of up to three edge-to-edge interactions with other bases. Recently, Höner zu Siederdissen et al. presented an extended model of RNA secondary structure, including base triples together with a folding algorithm-the first thermodynamics-based algorithm that allows the prediction of secondary structures with base triples. In this article, we investigate the search space processed by this new algorithm, that is, the combinatorics of extended RNA secondary structures with base triples. We present generalized definitions for structural motifs like hairpins, stems, bulges, or interior loops occurring in structures with base triples. Furthermore, we prove precise asymptotic results for the number of different structures (size of search space) and expectations for various parameters associated with structural motifs (typical shape of folding). Our analysis shows that the asymptotic number of secondary structures of size n increases exponentially to [Formula: see text] compared to the classic model by Stein and Waterman for which [Formula: see text] structures exist. A comparison with the classic model reveals large deviations in the expected structural appearance, too. The inclusion of base triples constitutes a significant refinement of the combinatorial model of RNA secondary structure, which, by our findings, is quantitatively characterized. Our results are of special theoretical interest, because a closer look at the numbers involved suggests that extended RNA secondary structures constitute a new combinatorial class not bijective with any other combinatorial objects studied so far.

  19. Combinatorics of RNA Secondary Structures with Base Triples.

    PubMed

    Müller, Robert; Nebel, Markus E

    2015-07-01

    The structure of RNA has been the subject of intense research over the last decades due to its importance for the correct functioning of RNA molecules in biological processes. Hence, a large number of models for RNA folding and corresponding algorithms for structure prediction have been developed. However, previous models often only consider base pairs, although every base is capable of up to three edge-to-edge interactions with other bases. Recently, Höner zu Siederdissen et al. presented an extended model of RNA secondary structure, including base triples together with a folding algorithm-the first thermodynamics-based algorithm that allows the prediction of secondary structures with base triples. In this article, we investigate the search space processed by this new algorithm, that is, the combinatorics of extended RNA secondary structures with base triples. We present generalized definitions for structural motifs like hairpins, stems, bulges, or interior loops occurring in structures with base triples. Furthermore, we prove precise asymptotic results for the number of different structures (size of search space) and expectations for various parameters associated with structural motifs (typical shape of folding). Our analysis shows that the asymptotic number of secondary structures of size n increases exponentially to [Formula: see text] compared to the classic model by Stein and Waterman for which [Formula: see text] structures exist. A comparison with the classic model reveals large deviations in the expected structural appearance, too. The inclusion of base triples constitutes a significant refinement of the combinatorial model of RNA secondary structure, which, by our findings, is quantitatively characterized. Our results are of special theoretical interest, because a closer look at the numbers involved suggests that extended RNA secondary structures constitute a new combinatorial class not bijective with any other combinatorial objects studied so far. PMID

  20. Secondary structure models for the internal transcribed spacer (ITS) region 1 from symbiotic dinoflagellates.

    PubMed

    Thornhill, Daniel J; Lord, Jenna B

    2010-07-01

    Ribosomal genes and their spacers have been extensively utilized to examine the biodiversity and phylogenetics of protists. Among these, the internal transcribed spacer regions 1 and 2 (ITS1 and ITS2) are known to form secondary structures that are critically important for proper processing of the pre-rRNA into mature ribosomes. Although the secondary structure of ITS2 has been widely investigated, considerably less is known about ITS1 and its secondary structure. Here, secondary structures of the ITS1 were modeled for 46 ITS "types" from Symbiodinium, a diverse dinoflagellate genus that forms symbioses with many protists and metazoans, using comparative phylogenetic and minimum free energy approaches. The predicted ITS1 secondary structures for each Symbiodinium "type" were highly stable (DeltaG=-46.40 to -85.30 kcal mol(-1) at 37 degrees C) and consisted of an open loop with five helices separated by single-stranded regions. Several structural characteristics were conserved within monophyletic sub-groups, providing additional support for the predicted structures and the relationships within this genus. Finally, the structures were applied to identify potential pseudogenes from five Symbiodinium ITS1 datasets. Consequently, ITS1 secondary structures are useful in understanding the biology and phylogenetics, as well as recognizing and excluding questionable sequences from datasets, of protists such as Symbiodinium.

  1. Secondary Structure Prediction of Single Sequences Using RNAstructure.

    PubMed

    Xu, Zhenjiang Zech; Mathews, David H

    2016-01-01

    RNA secondary structure is often predicted using folding thermodynamics. RNAstructure is a software package that includes structure prediction by free energy minimization, prediction of base pairing probabilities, prediction of structures composed of highly probably base pairs, and prediction of structures with pseudoknots. A user-friendly graphical user interface is provided, and this interface works on Windows, Apple OS X, and Linux. This chapter provides protocols for using RNAstructure for structure prediction. PMID:27665590

  2. Novel and efficient RNA secondary structure prediction using hierarchical folding.

    PubMed

    Jabbari, Hosna; Condon, Anne; Zhao, Shelly

    2008-03-01

    Algorithms for prediction of RNA secondary structure-the set of base pairs that form when an RNA molecule folds-are valuable to biologists who aim to understand RNA structure and function. Improving the accuracy and efficiency of prediction methods is an ongoing challenge, particularly for pseudoknotted secondary structures, in which base pairs overlap. This challenge is biologically important, since pseudoknotted structures play essential roles in functions of many RNA molecules, such as splicing and ribosomal frameshifting. State-of-the-art methods, which are based on free energy minimization, have high run-time complexity (typically Theta(n(5)) or worse), and can handle (minimize over) only limited types of pseudoknotted structures. We propose a new approach for prediction of pseudoknotted structures, motivated by the hypothesis that RNA structures fold hierarchically, with pseudoknot-free (non-overlapping) base pairs forming first, and pseudoknots forming later so as to minimize energy relative to the folded pseudoknot-free structure. Our HFold algorithm uses two-phase energy minimization to predict hierarchically formed secondary structures in O(n(3)) time, matching the complexity of the best algorithms for pseudoknot-free secondary structure prediction via energy minimization. Our algorithm can handle a wide range of biological structures, including kissing hairpins and nested kissing hairpins, which have previously required Theta(n(6)) time.

  3. Predicting RNA secondary structures from sequence and probing data.

    PubMed

    Lorenz, Ronny; Wolfinger, Michael T; Tanzer, Andrea; Hofacker, Ivo L

    2016-07-01

    RNA secondary structures have proven essential for understanding the regulatory functions performed by RNA such as microRNAs, bacterial small RNAs, or riboswitches. This success is in part due to the availability of efficient computational methods for predicting RNA secondary structures. Recent advances focus on dealing with the inherent uncertainty of prediction by considering the ensemble of possible structures rather than the single most stable one. Moreover, the advent of high-throughput structural probing has spurred the development of computational methods that incorporate such experimental data as auxiliary information.

  4. Principles for Predicting RNA Secondary Structure Design Difficulty.

    PubMed

    Anderson-Lee, Jeff; Fisker, Eli; Kosaraju, Vineet; Wu, Michelle; Kong, Justin; Lee, Jeehyung; Lee, Minjae; Zada, Mathew; Treuille, Adrien; Das, Rhiju

    2016-02-27

    Designing RNAs that form specific secondary structures is enabling better understanding and control of living systems through RNA-guided silencing, genome editing and protein organization. Little is known, however, about which RNA secondary structures might be tractable for downstream sequence design, increasing the time and expense of design efforts due to inefficient secondary structure choices. Here, we present insights into specific structural features that increase the difficulty of finding sequences that fold into a target RNA secondary structure, summarizing the design efforts of tens of thousands of human participants and three automated algorithms (RNAInverse, INFO-RNA and RNA-SSD) in the Eterna massive open laboratory. Subsequent tests through three independent RNA design algorithms (NUPACK, DSS-Opt and MODENA) confirmed the hypothesized importance of several features in determining design difficulty, including sequence length, mean stem length, symmetry and specific difficult-to-design motifs such as zigzags. Based on these results, we have compiled an Eterna100 benchmark of 100 secondary structure design challenges that span a large range in design difficulty to help test future efforts. Our in silico results suggest new routes for improving computational RNA design methods and for extending these insights to assess "designability" of single RNA structures, as well as of switches for in vitro and in vivo applications. PMID:26902426

  5. Principles for Predicting RNA Secondary Structure Design Difficulty.

    PubMed

    Anderson-Lee, Jeff; Fisker, Eli; Kosaraju, Vineet; Wu, Michelle; Kong, Justin; Lee, Jeehyung; Lee, Minjae; Zada, Mathew; Treuille, Adrien; Das, Rhiju

    2016-02-27

    Designing RNAs that form specific secondary structures is enabling better understanding and control of living systems through RNA-guided silencing, genome editing and protein organization. Little is known, however, about which RNA secondary structures might be tractable for downstream sequence design, increasing the time and expense of design efforts due to inefficient secondary structure choices. Here, we present insights into specific structural features that increase the difficulty of finding sequences that fold into a target RNA secondary structure, summarizing the design efforts of tens of thousands of human participants and three automated algorithms (RNAInverse, INFO-RNA and RNA-SSD) in the Eterna massive open laboratory. Subsequent tests through three independent RNA design algorithms (NUPACK, DSS-Opt and MODENA) confirmed the hypothesized importance of several features in determining design difficulty, including sequence length, mean stem length, symmetry and specific difficult-to-design motifs such as zigzags. Based on these results, we have compiled an Eterna100 benchmark of 100 secondary structure design challenges that span a large range in design difficulty to help test future efforts. Our in silico results suggest new routes for improving computational RNA design methods and for extending these insights to assess "designability" of single RNA structures, as well as of switches for in vitro and in vivo applications.

  6. DNA Secondary Structure at Chromosomal Fragile Sites in Human Disease

    PubMed Central

    Thys, Ryan G; Lehman, Christine E; Pierce, Levi C. T; Wang, Yuh-Hwa

    2015-01-01

    DNA has the ability to form a variety of secondary structures that can interfere with normal cellular processes, and many of these structures have been associated with neurological diseases and cancer. Secondary structure-forming sequences are often found at chromosomal fragile sites, which are hotspots for sister chromatid exchange, chromosomal translocations, and deletions. Structures formed at fragile sites can lead to instability by disrupting normal cellular processes such as DNA replication and transcription. The instability caused by disruption of replication and transcription can lead to DNA breakage, resulting in gene rearrangements and deletions that cause disease. In this review, we discuss the role of DNA secondary structure at fragile sites in human disease. PMID:25937814

  7. Prediction of Secondary Structures Conserved in Multiple RNA Sequences.

    PubMed

    Xu, Zhenjiang Zech; Mathews, David H

    2016-01-01

    RNA structure is conserved by evolution to a greater extent than sequence. Predicting the conserved structure for multiple homologous sequences can be much more accurate than predicting the structure for a single sequence. RNAstructure is a software package that includes the programs Dynalign, Multilign, TurboFold, and PARTS for predicting conserved RNA secondary structure. This chapter provides protocols for using these programs. PMID:27665591

  8. Secondary structural analyses of ITS1 in Paramecium.

    PubMed

    Hoshina, Ryo

    2010-01-01

    The nuclear ribosomal RNA gene operon is interrupted by internal transcribed spacer (ITS) 1 and ITS2. Although the secondary structure of ITS2 has been widely investigated, less is known about ITS1 and its structure. In this study, the secondary structure of ITS1 sequences for Paramecium and other ciliates was predicted. Each Paramecium ITS1 forms an open loop with three helices, A through C. Helix B was highly conserved among Paramecium, and similar helices were found in other ciliates. A phylogenetic analysis using the ITS1 sequences showed high-resolution, implying that ITS1 is a good tool for species-level analyses.

  9. 1. Building #3, original structure and first addition, north side, ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    1. Building #3, original structure and first addition, north side, looking south. Photo shows (from left) the original 1911 structure, the 1939 infill addition, and the 1934 structure. - S. W. Shattuck Chemical Company, Incorporated, Building No. 3, 1805 South Bannock Street, Denver, Denver County, CO

  10. Conservation of mRNA secondary structures may filter out mutations in Escherichia coli evolution.

    PubMed

    Chursov, Andrey; Frishman, Dmitrij; Shneider, Alexander

    2013-09-01

    Recent reports indicate that mutations in viral genomes tend to preserve RNA secondary structure, and those mutations that disrupt secondary structural elements may reduce gene expression levels, thereby serving as a functional knockout. In this article, we explore the conservation of secondary structures of mRNA coding regions, a previously unknown factor in bacterial evolution, by comparing the structural consequences of mutations in essential and nonessential Escherichia coli genes accumulated over 40 000 generations in the course of the 'long-term evolution experiment'. We monitored the extent to which mutations influence minimum free energy (MFE) values, assuming that a substantial change in MFE is indicative of structural perturbation. Our principal finding is that purifying selection tends to eliminate those mutations in essential genes that lead to greater changes of MFE values and, therefore, may be more disruptive for the corresponding mRNA secondary structures. This effect implies that synonymous mutations disrupting mRNA secondary structures may directly affect the fitness of the organism. These results demonstrate that the need to maintain intact mRNA structures imposes additional evolutionary constraints on bacterial genomes, which go beyond preservation of structure and function of the encoded proteins.

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

    PubMed Central

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

    2016-01-01

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

  12. NMR Methods for Characterization of RNA Secondary Structure.

    PubMed

    Kennedy, Scott D

    2016-01-01

    Knowledge of RNA secondary structure is often sufficient to identify relationships between the structure of RNA and processing pathways, and the design of therapeutics. Nuclear magnetic resonance (NMR) can identify types of nucleotide base pairs and the sequence, thus limiting possible secondary structures. Because NMR experiments, like chemical mapping, are performed in solution, not in single crystals, experiments can be initiated as soon as the biomolecule is expressed and purified. This chapter summarizes NMR methods that permit rapid identification of RNA secondary structure, information that can be used as supplements to chemical mapping, and/or as preliminary steps required for 3D structure determination. The primary aim is to provide guidelines to enable a researcher with minimal knowledge of NMR to quickly extract secondary structure information from basic datasets. Instrumental and sample considerations that can maximize data quality are discussed along with some details for optimal data acquisition and processing parameters. Approaches for identifying base pair types in both unlabeled and isotopically labeled RNA are covered. Common problems, such as missing signals and overlaps, and approaches to address them are considered. Programs under development for merging NMR data with structure prediction algorithms are briefly discussed. PMID:27665604

  13. Identification of Secondary Structure Elements in Intermediate Resolution Density Maps

    PubMed Central

    Baker, Matthew L.; Ju, Tao; Chiu, Wah

    2007-01-01

    An increasing number of structural studies of large macromolecular complexes, both in X-ray crystallography and electron cryomicroscopy, have resulted in intermediate resolution (5–10 Å) structures. Despite being limited in resolution, significant structural and functional information may be extractable from these maps. To aid in the analysis and annotation of these complexes, we have developed SSEhunter, a tool for the quantitative detection of α-helices and β-sheets. Based on density skeletonization, local geometry calculations and a template-based search, SSEhunter has been tested and validated on a variety of simulated and authentic subnanometer resolution density maps. The result is a robust, user-friendly approach that allows users to quickly visualize, assess and annotate intermediate resolution density maps. Beyond secondary structure element identification, the skeletonization algorithm in SSEhunter provides secondary structure topology, potentially useful in leading to structural models of individual molecular components directly from the density. PMID:17223528

  14. Secondary structure adventures with Carl Woese

    PubMed Central

    Noller, Harry F

    2014-01-01

    Not long after my arrival at UCSC as an assistant professor, I came across Carl Woese's paper “Molecular Mechanics of Translation: A Reciprocating Ratchet Mechanism.”1 In the days before the crystal structure of tRNA was known, Fuller and Hodgson2 had proposed two alternative conformations for its anticodon loop; one was stacked on the 3′ side (as later found in the crystal structure) and the other on the 5′ side. In an ingenious and elegant model, Woese proposed that the conformation of the loop flips between Fuller and Hodgson's 5′- and 3′-stacked forms during protein synthesis, changing the local direction of the mRNA such that the identities of the tRNA binding sites alternated between binding aminoacyl-tRNA and peptidyl-tRNA. The model predicted that there are no A and P sites, only two binding sites whose identities changed following translation of each codon, and that there would be no translocation of tRNAs in the usual sense—only binding and release. I met Carl in person the following year when he presented a seminar on his ratchet model in Santa Cruz. He was chatting in my colleague Ralph Hinegardner's office in what Carl termed a “Little Jack Horner appointment” (the visitor sits and listens to his host describing “What a good boy am I”). He was of compact stature, and bore a striking resemblance to Oskar Werner in Truffaut's film “Jules and Jim.” He projected the impression of a New-Age guru—a shiny black amulet suspended over the front of his black turtleneck sweater and a crown of prematurely white hair. Ralph asked me to explain to Carl what we were doing with ribosomes. I quickly summarized our early experiments that were pointing to a functional role for 16S rRNA. Carl regarded me silently, with a penetrating stare. He then turned to Ralph and said, in an ominous low voice, “I'm going to have some more tanks made as soon as I get back.” Carl's beautiful model was, unfortunately, wrong—it was simpler and more

  15. Enhanced performance of a submerged membrane bioreactor with powdered activated carbon addition for municipal secondary effluent treatment.

    PubMed

    Lin, Hongjun; Wang, Fangyuan; Ding, Linxian; Hong, Huachang; Chen, Jianrong; Lu, Xiaofeng

    2011-09-15

    The aim of this study was to investigate the feasibility of PAC-MBR process treating municipal secondary effluent. Two laboratory-scale submerged MBRs (SMBR) with and without PAC addition were continuously operated in parallel for secondary effluent treatment. Approximately 63%TOC, 95% NH(4)(+)-N and 98% turbidity in secondary effluent were removed by the PAC-MBR process. Most organics in the secondary effluent were found to be low molecular weight (MW) substances, which could be retained in the reactor and then removed to some extent by using PAC-MBR process. Parallel experiments showed that the addition of PAC significantly increased organic removal and responsible for the largest fraction of organic removal. Membrane fouling analysis showed the enhanced membrane performance in terms of sustainable operational time and filtration resistances by PAC addition. Based on these results, the PAC-MBR process was considered as an attractive option for the reduction of pollutants in secondary effluent. PMID:21794980

  16. Structure of 13Be probed via secondary-beam reactions

    NASA Astrophysics Data System (ADS)

    Randisi, G.; Leprince, A.; Al Falou, H.; Orr, N. A.; Marqués, F. M.; Achouri, N. L.; Angélique, J.-C.; Ashwood, N.; Bastin, B.; Bloxham, T.; Brown, B. A.; Catford, W. N.; Curtis, N.; Delaunay, F.; Freer, M.; de Góes Brennand, E.; Haigh, P.; Hanappe, F.; Harlin, C.; Laurent, B.; Lecouey, J.-L.; Ninane, A.; Patterson, N.; Price, D.; Stuttgé, L.; Thomas, J. S.

    2014-03-01

    The low-lying level structure of the unbound neutron-rich nucleus 13Be has been investigated via breakup on a carbon target of secondary beams of 14,15B at 35 MeV/nucleon. The coincident detection of the beam velocity 12Be fragments and neutrons permitted the invariant mass of the 12Be+n and 12Be+n+n systems to be reconstructed. In the case of the breakup of 15B, a very narrow structure at threshold was observed in the 12Be+n channel. Analysis of the 12Be+n+n events demonstrated that this resulted from the sequential decay of the unbound 14Be(2+) state rather than a strongly interacting s-wave virtual state in 13Be, as had been surmised in stable beam fragmentation studies. Single-proton removal from 14B was found to populate a broad low-lying structure some 0.7 MeV above the neutron-decay threshold, in addition to a less prominent feature at around 2.4 MeV. Based on the selectivity of the reaction and a comparison with (0-3)ℏω shell-model calculations, the low-lying structure is concluded to arise from closely spaced Jπ=1/2+ and 5/2+ resonances (Er=0.40±0.03 and 0.85-0.11+0.15 MeV), while the broad higher-lying feature is a second 5/2+ level (Er=2.35±0.14 MeV). Taken in conjunction with earlier studies, the results suggest that the lowest 1/2+ and 1/2- levels lie relatively close together below 1 MeV.

  17. Secondary Structure across the Bacterial Transcriptome Reveals Versatile Roles in mRNA Regulation and Function.

    PubMed

    Del Campo, Cristian; Bartholomäus, Alexander; Fedyunin, Ivan; Ignatova, Zoya

    2015-10-01

    Messenger RNA acts as an informational molecule between DNA and translating ribosomes. Emerging evidence places mRNA in central cellular processes beyond its major function as informational entity. Although individual examples show that specific structural features of mRNA regulate translation and transcript stability, their role and function throughout the bacterial transcriptome remains unknown. Combining three sequencing approaches to provide a high resolution view of global mRNA secondary structure, translation efficiency and mRNA abundance, we unraveled structural features in E. coli mRNA with implications in translation and mRNA degradation. A poorly structured site upstream of the coding sequence serves as an additional unspecific binding site of the ribosomes and the degree of its secondary structure propensity negatively correlates with gene expression. Secondary structures within coding sequences are highly dynamic and influence translation only within a very small subset of positions. A secondary structure upstream of the stop codon is enriched in genes terminated by UAA codon with likely implications in translation termination. The global analysis further substantiates a common recognition signature of RNase E to initiate endonucleolytic cleavage. This work determines for the first time the E. coli RNA structurome, highlighting the contribution of mRNA secondary structure as a direct effector of a variety of processes, including translation and mRNA degradation. PMID:26495981

  18. RNA Movies 2: sequential animation of RNA secondary structures.

    PubMed

    Kaiser, Alexander; Krüger, Jan; Evers, Dirk J

    2007-07-01

    RNA Movies is a simple, yet powerful visualization tool in likeness to a media player application, which enables to browse sequential paths through RNA secondary structure landscapes. It can be used to visualize structural rearrangement processes of RNA, such as folding pathways and conformational switches, or to browse lists of alternative structure candidates. Besides extending the feature set, retaining and improving usability and availability in the web is the main aim of this new version. RNA Movies now supports the DCSE and RNAStructML input formats besides its own RNM format. Pseudoknots and 'entangled helices' can be superimposed on the RNA secondary structure layout. Publication quality output is provided through the Scalable Vector Graphics output format understood by most current drawing programs. The software has been completely re-implemented in Java to enable pure client-side operation as applet and web-start application available at the Bielefeld Bioinformatics Server http://bibiserv.techfak.uni-bielefeld.de/rnamovies. PMID:17567618

  19. Refinement by shifting secondary structure elements improves sequence alignments.

    PubMed

    Tong, Jing; Pei, Jimin; Otwinowski, Zbyszek; Grishin, Nick V

    2015-03-01

    Constructing a model of a query protein based on its alignment to a homolog with experimentally determined spatial structure (the template) is still the most reliable approach to structure prediction. Alignment errors are the main bottleneck for homology modeling when the query is distantly related to the template. Alignment methods often misalign secondary structural elements by a few residues. Therefore, better alignment solutions can be found within a limited set of local shifts of secondary structures. We present a refinement method to improve pairwise sequence alignments by evaluating alignment variants generated by local shifts of template-defined secondary structures. Our method SFESA is based on a novel scoring function that combines the profile-based sequence score and the structure score derived from residue contacts in a template. Such a combined score frequently selects a better alignment variant among a set of candidate alignments generated by local shifts and leads to overall increase in alignment accuracy. Evaluation of several benchmarks shows that our refinement method significantly improves alignments made by automatic methods such as PROMALS, HHpred and CNFpred. The web server is available at http://prodata.swmed.edu/sfesa. PMID:25546158

  20. Refinement by shifting secondary structure elements improves sequence alignments

    PubMed Central

    Tong, Jing; Pei, Jimin; Otwinowski, Zbyszek; Grishin, Nick V.

    2015-01-01

    Constructing a model of a query protein based on its alignment to a homolog with experimentally determined spatial structure (the template) is still the most reliable approach to structure prediction. Alignment errors are the main bottleneck for homology modeling when the query is distantly related to the template. Alignment methods often misalign secondary structural elements by a few residues. Therefore, better alignment solutions can be found within a limited set of local shifts of secondary structures. We present a refinement method to improve pairwise sequence alignments by evaluating alignment variants generated by local shifts of template-defined secondary structures. Our method SFESA is based on a novel scoring function that combines the profile-based sequence score and the structure score derived from residue contacts in a template. Such a combined score frequently selects a better alignment variant among a set of candidate alignments generated by local shifts and leads to overall increase in alignment accuracy. Evaluation of several benchmarks shows that our refinement method significantly improves alignments made by automatic methods such as PROMALS, HHpred and CNFpred. The web server is available at http://prodata.swmed.edu/sfesa. PMID:25546158

  1. Computation of statistical secondary structure of nucleic acids.

    PubMed Central

    Yamamoto, K; Kitamura, Y; Yoshikura, H

    1984-01-01

    This paper presents a computer analysis of statistical secondary structure of nucleic acids. For a given single stranded nucleic acid, we generated "structure map" which included all the annealing structures in the sequence. The map was transformed into "energy map" by rough approximation; here, the energy level of every pairing structure consisting of more than 2 successive nucleic acid pairs was calculated. By using the "energy map", the probability of occurrence of each annealed structure was computed, i.e., the structure was computed statistically. The basis of computation was the 8-queen problem in the chess game. The validity of our computer programme was checked by computing tRNA structure which has been well established. Successful application of this programme to small nuclear RNAs of various origins is demonstrated. PMID:6198622

  2. Interconnection of Salt-induced Hydrophobic Compaction and Secondary Structure Formation Depends on Solution Conditions

    PubMed Central

    Haldar, Shubhasis; Chattopadhyay, Krishnananda

    2012-01-01

    What happens in the early stage of protein folding remains an interesting unsolved problem. Rapid kinetics measurements with cytochrome c using submillisecond continuous flow mixing devices suggest simultaneous formation of a compact collapsed state and secondary structure. These data seem to indicate that collapse formation is guided by specific short and long range interactions (heteropolymer collapse). A contrasting interpretation also has been proposed, which suggests that the collapse formation is rapid, nonspecific, and a trivial solvent related compaction, which could as well be observed by a homopolymer (homopolymer collapse). We address this controversy using fluorescence correlation spectroscopy (FCS), which enables us to monitor the salt-induced compaction accompanying collapse formation and the associated time constant directly at single molecule resolution. In addition, we follow the formation of secondary structure using far UV CD. The data presented here suggest that both these models (homopolymer and heteropolymer) could be applicable depending on the solution conditions. For example, the formation of secondary structure and compact state is not simultaneous in aqueous buffer. In aqueous buffer, formation of the compact state occurs through a two-state co-operative transition following heteropolymer formalism, whereas secondary structure formation takes place gradually. In contrast, in the presence of urea, a compaction of the protein radius occurs gradually over an extended range of salt concentration following homopolymer formalism. The salt-induced compaction and the formation of secondary structure take place simultaneously in the presence of urea. PMID:22303014

  3. Students' understanding of primary and secondary protein structure: drawing secondary protein structure reveals student understanding better than simple recognition of structures.

    PubMed

    Harle, Marissa; Towns, Marcy H

    2013-01-01

    The interdisciplinary nature of biochemistry courses requires students to use both chemistry and biology knowledge to understand biochemical concepts. Research that has focused on external representations in biochemistry has uncovered student difficulties in comprehending and interpreting external representations in addition to a fragmented understanding of fundamental biochemistry concepts. This project focuses on students' understanding of primary and secondary protein structure and drawings (representations) of hydrogen-bonding in alpha helices and beta sheets. Analysis demonstrated that students can recognize and identify primary protein structure concepts when given a polypeptide. However, when asked to draw alpha helices and beta sheets and explain the role of hydrogen bonding their drawings students exhibited a fragmented understanding that lacked coherence. Faculty are encouraged to have students draw molecular level representations to make their mental models more explicit, complete, and coherent. This is in contrast to recognition and identification tasks, which do not adequately probe mental models and molecular level understanding.

  4. Data-directed RNA secondary structure prediction using probabilistic modeling.

    PubMed

    Deng, Fei; Ledda, Mirko; Vaziri, Sana; Aviran, Sharon

    2016-08-01

    Structure dictates the function of many RNAs, but secondary RNA structure analysis is either labor intensive and costly or relies on computational predictions that are often inaccurate. These limitations are alleviated by integration of structure probing data into prediction algorithms. However, existing algorithms are optimized for a specific type of probing data. Recently, new chemistries combined with advances in sequencing have facilitated structure probing at unprecedented scale and sensitivity. These novel technologies and anticipated wealth of data highlight a need for algorithms that readily accommodate more complex and diverse input sources. We implemented and investigated a recently outlined probabilistic framework for RNA secondary structure prediction and extended it to accommodate further refinement of structural information. This framework utilizes direct likelihood-based calculations of pseudo-energy terms per considered structural context and can readily accommodate diverse data types and complex data dependencies. We use real data in conjunction with simulations to evaluate performances of several implementations and to show that proper integration of structural contexts can lead to improvements. Our tests also reveal discrepancies between real data and simulations, which we show can be alleviated by refined modeling. We then propose statistical preprocessing approaches to standardize data interpretation and integration into such a generic framework. We further systematically quantify the information content of data subsets, demonstrating that high reactivities are major drivers of SHAPE-directed predictions and that better understanding of less informative reactivities is key to further improvements. Finally, we provide evidence for the adaptive capability of our framework using mock probe simulations.

  5. Integrating chemical footprinting data into RNA secondary structure prediction.

    PubMed

    Zarringhalam, Kourosh; Meyer, Michelle M; Dotu, Ivan; Chuang, Jeffrey H; Clote, Peter

    2012-01-01

    Chemical and enzymatic footprinting experiments, such as shape (selective 2'-hydroxyl acylation analyzed by primer extension), yield important information about RNA secondary structure. Indeed, since the [Formula: see text]-hydroxyl is reactive at flexible (loop) regions, but unreactive at base-paired regions, shape yields quantitative data about which RNA nucleotides are base-paired. Recently, low error rates in secondary structure prediction have been reported for three RNAs of moderate size, by including base stacking pseudo-energy terms derived from shape data into the computation of minimum free energy secondary structure. Here, we describe a novel method, RNAsc (RNA soft constraints), which includes pseudo-energy terms for each nucleotide position, rather than only for base stacking positions. We prove that RNAsc is self-consistent, in the sense that the nucleotide-specific probabilities of being unpaired in the low energy Boltzmann ensemble always become more closely correlated with the input shape data after application of RNAsc. From this mathematical perspective, the secondary structure predicted by RNAsc should be 'correct', in as much as the shape data is 'correct'. We benchmark RNAsc against the previously mentioned method for eight RNAs, for which both shape data and native structures are known, to find the same accuracy in 7 out of 8 cases, and an improvement of 25% in one case. Furthermore, we present what appears to be the first direct comparison of shape data and in-line probing data, by comparing yeast asp-tRNA shape data from the literature with data from in-line probing experiments we have recently performed. With respect to several criteria, we find that shape data appear to be more robust than in-line probing data, at least in the case of asp-tRNA.

  6. Biobased extreme pressure additives: Structure-property considerations

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Extreme pressure additives are widely used in lubricant formulations for engine oils, hydraulic fluids, gear oils, metalworking fluids, and many others. Extreme pressure additives contain selected elements such as sulfur, phosphorus, and halogens in their structures. These elements, under extreme tr...

  7. Secondary Fast Magnetoacoustic Waves Trapped in Randomly Structured Plasmas

    NASA Astrophysics Data System (ADS)

    Yuan, Ding; Li, Bo; Walsh, Robert W.

    2016-09-01

    Fast magnetoacoustic waves are an important tool for inferring parameters of the solar atmosphere. We numerically simulate the propagation of fast wave pulses in randomly structured plasmas that mimic the highly inhomogeneous solar corona. A network of secondary waves is formed by a series of partial reflections and transmissions. These secondary waves exhibit quasi-periodicities in both time and space. Since the temporal and spatial periods are related simply through the speed of the fast wave, we quantify the properties of secondary waves by examining the dependence of the average temporal period (\\bar{p}) on the initial pulse width (w 0) and studying the density contrast ({δ }ρ ) and correlation length (L c ) that characterize the randomness of the equilibrium density profiles. For small-amplitude pulses, {δ }ρ does not alter \\bar{p} significantly. Large-amplitude pulses, on the other hand, enhance the density contrast when {δ }ρ is small but have a smoothing effect when {δ }ρ is sufficiently large. We found that \\bar{p} scales linearly with L c and that the scaling factor is larger for a narrower pulse. However, in terms of the absolute values of \\bar{p}, broader pulses generate secondary waves with longer periods, and this effect is stronger in random plasmas with shorter correlation lengths. Secondary waves carry the signatures of both the leading wave pulse and the background plasma. Our study may find applications in magnetohydrodynamic seismology by exploiting the secondary waves detected in the dimming regions after coronal mass ejections or extreme ultraviolet waves.

  8. Coating concrete secondary containment structures exposed to agrichemicals

    SciTech Connect

    Broder, M.F.; Nguyen, D.T.

    1995-06-01

    Concrete has traditionally been the material of choice for building secondary containment structures because it is relatively inexpensive and has structural properties which make it ideal for supporting the loads of vehicles and large tanks. However, concrete`s chemical properties make it susceptible to corrosion by some common fertilizers. Though fairly impervious to water movement, concrete is easily penetrated by vapors and solvents. It is also prone to cracking. For these reasons, the Environmental Protection Agency (EPA) believes that concrete alone may not provide an effective barrier to pesticide movement and has proposed that concrete in pesticide secondary containment structures be sealed or coated to reduce its permeability. Some state secondary containment regulations require that concrete exposed to fertilizers and pesticides be sealed or protected with a coating. Lacking guidelines, some retailers have used penetrating sealants to satisfy the law, even though these products provide little protection from chemical attack nor do they prevent pesticide egress. Other retailers who have applied thick film coatings which were properly selected have had disastrous results because the application was poorly done. Consequently, much skepticism exists regarding the performance and benefit of protective coatings.

  9. Secondary structure models of the 3′ untranslated regions of diverse R2 RNAs

    PubMed Central

    RUSCHAK, AMY M.; MATHEWS, DAVID H.; BIBILLO, ARKADIUSZ; SPINELLI, SHERRY L.; CHILDS, JESSICA L.; EICKBUSH, THOMAS H.; TURNER, DOUGLAS H.

    2004-01-01

    The RNA structure of the 3′ untranslated region (UTR) of the R2 retrotransposable element is recognized by the R2-encoded reverse transcriptase in a reaction called target primed reverse transcription (TPRT). To provide insight into structure–function relationships important for TPRT, we have created alignments that reveal the secondary structure for 22 Drosophila and five silkmoth 3′ UTR R2 sequences. In addition, free energy minimization has been used to predict the secondary structure for the 3′ UTR R2 RNA of Forficula auricularia. The predicted structures for Bombyx mori and F. auricularia are consistent with chemical modification data obtained with β-ethoxy-α-ketobutyraldehyde (kethoxal), dimethyl sulfate, and 1-cyclohexyl-3-(2-morpholinoethyl)carbodiimide metho-p-toluene sulfonate. The structures appear to have common helices that are likely important for function. PMID:15146081

  10. Identification of local variations within secondary structures of proteins.

    PubMed

    Kumar, Prasun; Bansal, Manju

    2015-05-01

    Secondary-structure elements (SSEs) play an important role in the folding of proteins. Identification of SSEs in proteins is a common problem in structural biology. A new method, ASSP (Assignment of Secondary Structure in Proteins), using only the path traversed by the C(α) atoms has been developed. The algorithm is based on the premise that the protein structure can be divided into continuous or uniform stretches, which can be defined in terms of helical parameters, and depending on their values the stretches can be classified into different SSEs, namely α-helices, 310-helices, π-helices, extended β-strands and polyproline II (PPII) and other left-handed helices. The methodology was validated using an unbiased clustering of these parameters for a protein data set consisting of 1008 protein chains, which suggested that there are seven well defined clusters associated with different SSEs. Apart from α-helices and extended β-strands, 310-helices and π-helices were also found to occur in substantial numbers. ASSP was able to discriminate non-α-helical segments from flanking α-helices, which were often identified as part of α-helices by other algorithms. ASSP can also lead to the identification of novel SSEs. It is believed that ASSP could provide a better understanding of the finer nuances of protein secondary structure and could make an important contribution to the better understanding of comparatively less frequently occurring structural motifs. At the same time, it can contribute to the identification of novel SSEs. A standalone version of the program for the Linux as well as the Windows operating systems is freely downloadable and a web-server version is also available at http://nucleix.mbu.iisc.ernet.in/assp/index.php.

  11. Identification of local variations within secondary structures of proteins.

    PubMed

    Kumar, Prasun; Bansal, Manju

    2015-05-01

    Secondary-structure elements (SSEs) play an important role in the folding of proteins. Identification of SSEs in proteins is a common problem in structural biology. A new method, ASSP (Assignment of Secondary Structure in Proteins), using only the path traversed by the C(α) atoms has been developed. The algorithm is based on the premise that the protein structure can be divided into continuous or uniform stretches, which can be defined in terms of helical parameters, and depending on their values the stretches can be classified into different SSEs, namely α-helices, 310-helices, π-helices, extended β-strands and polyproline II (PPII) and other left-handed helices. The methodology was validated using an unbiased clustering of these parameters for a protein data set consisting of 1008 protein chains, which suggested that there are seven well defined clusters associated with different SSEs. Apart from α-helices and extended β-strands, 310-helices and π-helices were also found to occur in substantial numbers. ASSP was able to discriminate non-α-helical segments from flanking α-helices, which were often identified as part of α-helices by other algorithms. ASSP can also lead to the identification of novel SSEs. It is believed that ASSP could provide a better understanding of the finer nuances of protein secondary structure and could make an important contribution to the better understanding of comparatively less frequently occurring structural motifs. At the same time, it can contribute to the identification of novel SSEs. A standalone version of the program for the Linux as well as the Windows operating systems is freely downloadable and a web-server version is also available at http://nucleix.mbu.iisc.ernet.in/assp/index.php. PMID:25945573

  12. Secondary Pollutants from Ozone Reaction with Ventilation Filters and Degradation of Filter Media Additives

    SciTech Connect

    Destaillats, Hugo; Chen, Wenhao; Apte, Michael; Li, Nuan; Spears, Michael; Almosni, Jérémie; Brunner, Gregory; Zhang, Jianshun; Fisk, William J.

    2011-05-01

    Prior research suggests that chemical processes taking place on the surface of particle filters employed in buildings may lead to the formation of harmful secondary byproducts. We investigated ozone reactions with fiberglass, polyester, cotton/polyester and polyolefin filter media, as well as hydrolysis of filter media additives. Studies were carried out on unused media, and on filters that were installed for 3 months in buildings at two different locations in the San Francisco Bay Area. Specimens from each filter media were exposed to {approx}150 ppbv ozone in a flow tube under a constant flow of dry or humidified air (50percent RH). Ozone breakthrough was recorded for each sample over periods of {approx}1000 min; the ozone uptake rate was calculated for an initial transient period and for steady-state conditions. While ozone uptake was observed in all cases, we did not observe significant differences in the uptake rate and capacity for the various types of filter media tested. Most experiments were performed at an airflow rate of 1.3 L/min (face velocity = 0.013 m/s), and a few tests were also run at higher rates (8 to 10 L/min). Formaldehyde and acetaldehyde, two oxidation byproducts, were quantified downstream of each sample. Those aldehydes (m/z 31 and 45) and other volatile byproducts (m/z 57, 59, 61 and 101) were also detected in real-time using Proton-Transfer Reaction - Mass Spectrometry (PTR-MS). Low-ppbv byproduct emissions were consistently higher under humidified air than under dry conditions, and were higher when the filters were loaded with particles, as compared with unused filters. No significant differences were observed when ozone reacted over various types of filter media. Fiberglass filters heavily coated with impaction oil (tackifier) showed higher formaldehyde emissions than other samples. Those emissions were particularly high in the case of used filters, and were observed even in the absence of ozone, suggesting that hydrolysis of additives

  13. How well are protein structures annotated in secondary databases?

    PubMed

    Rother, Kristian; Michalsky, Elke; Leser, Ulf

    2005-09-01

    We investigated to what extent Protein Data Bank (PDB) entries are annotated with second-party information based on existing cross-references between PDB and 15 other databases. We report 2 interesting findings. First, there is a clear "annotation gap" for structures less than 7 years old for secondary databases that are manually curated. Second, the examined databases overlap with each other quite well, dividing the PDB into 2 well-annotated thirds and one poorly annotated third. Both observations should be taken into account in any study depending on the selection of protein structures by their annotation.

  14. Pd(Quinox)-Catalyzed Allylic Relay Suzuki Reactions of Secondary Homostyrenyl Tosylates via Alkene-Assisted Oxidative Addition.

    PubMed

    Stokes, Benjamin J; Bischoff, Amanda J; Sigman, Matthew S

    2014-06-01

    Pd-catalyzed allylic relay Suzuki cross-coupling reactions of secondary alkyl tosylates, featuring a sterically-hindered oxidative addition and precise control of β-hydride elimination, are reported. The identification of a linear free energy relationship between the relative rates of substrate consumption and the electronic nature of the substrate alkene suggests that the oxidative addition requires direct alkene involvement. A study of the effect of chain length on the reaction outcome supports a chelation-controlled oxidative addition.

  15. RNA secondary structure prediction based on SHAPE data in helix regions.

    PubMed

    Lotfi, Mohadeseh; Zare-Mirakabad, Fatemeh; Montaseri, Soheila

    2015-09-01

    RNA molecules play important and fundamental roles in biological processes. Frequently, the functional form of single-stranded RNA molecules requires a specific tertiary structure. Classically, RNA structure determination has mostly been accomplished by X-Ray crystallography or Nuclear Magnetic Resonance approaches. These experimental methods are time consuming and expensive. In the past two decades, some computational methods and algorithms have been developed for RNA secondary structure prediction. In these algorithms, minimum free energy is known as the best criterion. However, the results of algorithms show that minimum free energy is not a sufficient criterion to predict RNA secondary structure. These algorithms need some additional knowledge about the structure, which has to be added in the methods. Recently, the information obtained from some experimental data, called SHAPE, can greatly improve the consistency between the native and predicted RNA secondary structure. In this paper, we investigate the influence of SHAPE data on four types of RNA substructures, helices, loops, base pairs from the start and end of helices and two base pairs from the start and end of helices. The results show that SHAPE data in helix regions can improve the prediction. We represent a new method to apply SHAPE data in helix regions for finding RNA secondary structure. Finally, we compare the results of the method on a set of RNAs to predict minimum free energy structure based on considering all SHAPE data and only SHAPE data in helix regions as pseudo free energy and without SHAPE data (without any pseudo free energy). The results show that RNA secondary structure prediction based on considering only SHAPE data in helix regions is more successful than not considering SHAPE data and it provides competitive results in comparison with considering all SHAPE data.

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

    PubMed

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

    2013-09-01

    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.

  17. Secondary Impacts on Structures on the Lunar Surface

    NASA Technical Reports Server (NTRS)

    Christiansen, Eric; Walker, James D.; Grosch, Donald J.

    2010-01-01

    The Altair Lunar Lander is being designed for the planned return to the Moon by 2020. Since it is hoped that lander components will be re-used by later missions, studies are underway to examine the exposure threat to the lander sitting on the Lunar surface for extended periods. These threats involve both direct strikes of meteoroids on the vehicle as well as strikes from Lunar regolith and rock thrown by nearby meteorite strikes. Currently, the lander design is comprised of up to 10 different types of pressure vessels. These vessels included the manned habitation module, fuel, cryogenic fuel and gas storage containers, and instrument bays. These pressure vessels have various wall designs, including various aluminum alloys, honeycomb, and carbon-fiber composite materials. For some of the vessels, shielding is being considered. This program involved the test and analysis of six pressure vessel designs, one of which included a Whipple bumper shield. In addition to the pressure vessel walls, all the pressure vessels are wrapped in multi-layer insulation (MLI). Two variants were tested without the MLI to better understand the role of the MLI in the impact performance. The tests of performed were to examine the secondary impacts on these structures as they rested on the Lunar surface. If a hypervelocity meteor were to strike the surface nearby, it would throw regolith and rock debris into the structure at a much lower velocity. Also, when the manned module departs for the return to Earth, its rocket engines throw up debris that can impact the remaining lander components and cause damage. Glass spheres were used as a stimulant for the regolith material. Impact tests were performed with a gas gun to find the V50 of various sized spheres striking the pressure vessels. The impacts were then modeled and a fast-running approximate model for the V50 data was developed. This model was for performing risk analysis to assist in the vessel design and in the identification of ideal

  18. Additives

    NASA Technical Reports Server (NTRS)

    Smalheer, C. V.

    1973-01-01

    The chemistry of lubricant additives is discussed to show what the additives are chemically and what functions they perform in the lubrication of various kinds of equipment. Current theories regarding the mode of action of lubricant additives are presented. The additive groups discussed include the following: (1) detergents and dispersants, (2) corrosion inhibitors, (3) antioxidants, (4) viscosity index improvers, (5) pour point depressants, and (6) antifouling agents.

  19. HOTAIR forms an intricate and modular secondary structure

    PubMed Central

    Somarowthu, Srinivas; Legiewicz, Michal; Chillón, Isabel; Marcia, Marco; Liu, Fei; Pyle, Anna Marie

    2015-01-01

    SUMMARY Long non-coding RNAs (lncRNAs) have recently emerged as key players in fundamental cellular processes and diseases, but their functions are poorly understood. HOTAIR is a 2,148-nucleotide-long lncRNA molecule involved in physiological epidermal development and in pathogenic cancer progression, where it has been demonstrated to repress tumor and metastasis suppressor genes. To gain insights into the molecular mechanisms of HOTAIR, we purified it in a stable and homogenous form in vitro and we determined its functional secondary structure through chemical probing and phylogenetic analysis. The HOTAIR structure reveals a degree of structural organization comparable to well-folded RNAs, like the group II intron, rRNA or lncRNA steroid receptor activator. It is composed of four independently-folding modules, two of which correspond to predicted protein-binding domains. Secondary structure elements that surround protein-binding motifs are evolutionarily conserved. Our work serves as a guide for “navigating” through the lncRNA HOTAIR and ultimately for understanding its function. PMID:25866246

  20. Structuring Numbers 1 to 20: Developing Facile Addition and Subtraction

    ERIC Educational Resources Information Center

    Ellemor-Collins, David; Wright, Robert

    2009-01-01

    The Numeracy Intervention Research Project (NIRP) aims to develop assessment and instructional tools for use with low-attaining 3rd- and 4th-graders. The NIRP approach to instruction in addition and subtraction in the range 1 to 20 is described. The approach is based on a notion of structuring numbers, which draws on the work of Freudenthal and…

  1. Metallic sulfide additives for positive electrode material within a secondary electrochemical cell

    DOEpatents

    Walsh, William J.; McPheeters, Charles C.; Yao, Neng-ping; Koura, Kobuyuki

    1976-01-01

    An improved active material for use within the positive electrode of a secondary electrochemical cell includes a mixture of iron disulfide and a sulfide of a polyvalent metal. Various metal sulfides, particularly sulfides of cobalt, nickel, copper, cerium and manganese, are added in minor weight proportion in respect to iron disulfide for improving the electrode performance and reducing current collector requirements.

  2. Protein secondary structure prediction using logic-based machine learning.

    PubMed

    Muggleton, S; King, R D; Sternberg, M J

    1992-10-01

    Many attempts have been made to solve the problem of predicting protein secondary structure from the primary sequence but the best performance results are still disappointing. In this paper, the use of a machine learning algorithm which allows relational descriptions is shown to lead to improved performance. The Inductive Logic Programming computer program, Golem, was applied to learning secondary structure prediction rules for alpha/alpha domain type proteins. The input to the program consisted of 12 non-homologous proteins (1612 residues) of known structure, together with a background knowledge describing the chemical and physical properties of the residues. Golem learned a small set of rules that predict which residues are part of the alpha-helices--based on their positional relationships and chemical and physical properties. The rules were tested on four independent non-homologous proteins (416 residues) giving an accuracy of 81% (+/- 2%). This is an improvement, on identical data, over the previously reported result of 73% by King and Sternberg (1990, J. Mol. Biol., 216, 441-457) using the machine learning program PROMIS, and of 72% using the standard Garnier-Osguthorpe-Robson method. The best previously reported result in the literature for the alpha/alpha domain type is 76%, achieved using a neural net approach. Machine learning also has the advantage over neural network and statistical methods in producing more understandable results. PMID:1480619

  3. Secondary Structure of Rat and Human Amylin across Force Fields.

    PubMed

    Hoffmann, Kyle Quynn; McGovern, Michael; Chiu, Chi-Cheng; de Pablo, Juan J

    2015-01-01

    The aggregation of human amylin has been strongly implicated in the progression of Type II diabetes. This 37-residue peptide forms a variety of secondary structures, including random coils, α-helices, and β-hairpins. The balance between these structures depends on the chemical environment, making amylin an ideal candidate to examine inherent biases in force fields. Rat amylin differs from human amylin by only 6 residues; however, it does not form fibrils. Therefore it provides a useful complement to human amylin in studies of the key events along the aggregation pathway. In this work, the free energy of rat and human amylin was determined as a function of α-helix and β-hairpin content for the Gromos96 53a6, OPLS-AA/L, CHARMM22/CMAP, CHARMM22*, Amberff99sb*-ILDN, and Amberff03w force fields using advanced sampling techniques, specifically bias exchange metadynamics. This work represents a first systematic attempt to evaluate the conformations and the corresponding free energy of a large, clinically relevant disordered peptide in solution across force fields. The NMR chemical shifts of rIAPP were calculated for each of the force fields using their respective free energy maps, allowing us to quantitatively assess their predictions. We show that the predicted distribution of secondary structures is sensitive to the choice of force-field: Gromos53a6 is biased towards β-hairpins, while CHARMM22/CMAP predicts structures that are overly α-helical. OPLS-AA/L favors disordered structures. Amberff99sb*-ILDN, AmberFF03w and CHARMM22* provide the balance between secondary structures that is most consistent with available experimental data. In contrast to previous reports, our findings suggest that the equilibrium conformations of human and rat amylin are remarkably similar, but that subtle differences arise in transient alpha-helical and beta-strand containing structures that the human peptide can more readily adopt. We hypothesize that these transient states enable

  4. Secondary Structure of Rat and Human Amylin across Force Fields.

    PubMed

    Hoffmann, Kyle Quynn; McGovern, Michael; Chiu, Chi-Cheng; de Pablo, Juan J

    2015-01-01

    The aggregation of human amylin has been strongly implicated in the progression of Type II diabetes. This 37-residue peptide forms a variety of secondary structures, including random coils, α-helices, and β-hairpins. The balance between these structures depends on the chemical environment, making amylin an ideal candidate to examine inherent biases in force fields. Rat amylin differs from human amylin by only 6 residues; however, it does not form fibrils. Therefore it provides a useful complement to human amylin in studies of the key events along the aggregation pathway. In this work, the free energy of rat and human amylin was determined as a function of α-helix and β-hairpin content for the Gromos96 53a6, OPLS-AA/L, CHARMM22/CMAP, CHARMM22*, Amberff99sb*-ILDN, and Amberff03w force fields using advanced sampling techniques, specifically bias exchange metadynamics. This work represents a first systematic attempt to evaluate the conformations and the corresponding free energy of a large, clinically relevant disordered peptide in solution across force fields. The NMR chemical shifts of rIAPP were calculated for each of the force fields using their respective free energy maps, allowing us to quantitatively assess their predictions. We show that the predicted distribution of secondary structures is sensitive to the choice of force-field: Gromos53a6 is biased towards β-hairpins, while CHARMM22/CMAP predicts structures that are overly α-helical. OPLS-AA/L favors disordered structures. Amberff99sb*-ILDN, AmberFF03w and CHARMM22* provide the balance between secondary structures that is most consistent with available experimental data. In contrast to previous reports, our findings suggest that the equilibrium conformations of human and rat amylin are remarkably similar, but that subtle differences arise in transient alpha-helical and beta-strand containing structures that the human peptide can more readily adopt. We hypothesize that these transient states enable

  5. Secondary Structure of Rat and Human Amylin across Force Fields

    PubMed Central

    Hoffmann, Kyle Quynn; McGovern, Michael; Chiu, Chi-cheng; de Pablo, Juan J.

    2015-01-01

    The aggregation of human amylin has been strongly implicated in the progression of Type II diabetes. This 37-residue peptide forms a variety of secondary structures, including random coils, α-helices, and β-hairpins. The balance between these structures depends on the chemical environment, making amylin an ideal candidate to examine inherent biases in force fields. Rat amylin differs from human amylin by only 6 residues; however, it does not form fibrils. Therefore it provides a useful complement to human amylin in studies of the key events along the aggregation pathway. In this work, the free energy of rat and human amylin was determined as a function of α-helix and β-hairpin content for the Gromos96 53a6, OPLS-AA/L, CHARMM22/CMAP, CHARMM22*, Amberff99sb*-ILDN, and Amberff03w force fields using advanced sampling techniques, specifically bias exchange metadynamics. This work represents a first systematic attempt to evaluate the conformations and the corresponding free energy of a large, clinically relevant disordered peptide in solution across force fields. The NMR chemical shifts of rIAPP were calculated for each of the force fields using their respective free energy maps, allowing us to quantitatively assess their predictions. We show that the predicted distribution of secondary structures is sensitive to the choice of force-field: Gromos53a6 is biased towards β-hairpins, while CHARMM22/CMAP predicts structures that are overly α-helical. OPLS-AA/L favors disordered structures. Amberff99sb*-ILDN, AmberFF03w and CHARMM22* provide the balance between secondary structures that is most consistent with available experimental data. In contrast to previous reports, our findings suggest that the equilibrium conformations of human and rat amylin are remarkably similar, but that subtle differences arise in transient alpha-helical and beta-strand containing structures that the human peptide can more readily adopt. We hypothesize that these transient states enable

  6. Secondary structure of rat and human amylin across force fields

    DOE PAGES

    Hoffmann, Kyle Quynn; McGovern, Michael; Chiu, Chi -cheng; de Pablo, Juan J.; Paci, Emanuele

    2015-07-29

    The aggregation of human amylin has been strongly implicated in the progression of Type II diabetes. This 37-residue peptide forms a variety of secondary structures, including random coils, α-helices, and β-hairpins. The balance between these structures depends on the chemical environment, making amylin an ideal candidate to examine inherent biases in force fields. Rat amylin differs from human amylin by only 6 residues; however, it does not form fibrils. Therefore it provides a useful complement to human amylin in studies of the key events along the aggregation pathway. In this work, the free energy of rat and human amylin wasmore » determined as a function of α-helix and β-hairpin content for the Gromos96 53a6, OPLS-AA/L, CHARMM22/CMAP, CHARMM22*, Amberff99sb*-ILDN, and Amberff03w force fields using advanced sampling techniques, specifically bias exchange metadynamics. This work represents a first systematic attempt to evaluate the conformations and the corresponding free energy of a large, clinically relevant disordered peptide in solution across force fields. The NMR chemical shifts of rIAPP were calculated for each of the force fields using their respective free energy maps, allowing us to quantitatively assess their predictions. We show that the predicted distribution of secondary structures is sensitive to the choice of force-field: Gromos53a6 is biased towards β-hairpins, while CHARMM22/CMAP predicts structures that are overly α-helical. OPLS-AA/L favors disordered structures. Amberff99sb*-ILDN, AmberFF03w and CHARMM22* provide the balance between secondary structures that is most consistent with available experimental data. In contrast to previous reports, our findings suggest that the equilibrium conformations of human and rat amylin are remarkably similar, but that subtle differences arise in transient alpha-helical and beta-strand containing structures that the human peptide can more readily adopt. We hypothesize that these transient states

  7. Secondary structure of rat and human amylin across force fields

    SciTech Connect

    Hoffmann, Kyle Quynn; McGovern, Michael; Chiu, Chi -cheng; de Pablo, Juan J.; Paci, Emanuele

    2015-07-29

    The aggregation of human amylin has been strongly implicated in the progression of Type II diabetes. This 37-residue peptide forms a variety of secondary structures, including random coils, α-helices, and β-hairpins. The balance between these structures depends on the chemical environment, making amylin an ideal candidate to examine inherent biases in force fields. Rat amylin differs from human amylin by only 6 residues; however, it does not form fibrils. Therefore it provides a useful complement to human amylin in studies of the key events along the aggregation pathway. In this work, the free energy of rat and human amylin was determined as a function of α-helix and β-hairpin content for the Gromos96 53a6, OPLS-AA/L, CHARMM22/CMAP, CHARMM22*, Amberff99sb*-ILDN, and Amberff03w force fields using advanced sampling techniques, specifically bias exchange metadynamics. This work represents a first systematic attempt to evaluate the conformations and the corresponding free energy of a large, clinically relevant disordered peptide in solution across force fields. The NMR chemical shifts of rIAPP were calculated for each of the force fields using their respective free energy maps, allowing us to quantitatively assess their predictions. We show that the predicted distribution of secondary structures is sensitive to the choice of force-field: Gromos53a6 is biased towards β-hairpins, while CHARMM22/CMAP predicts structures that are overly α-helical. OPLS-AA/L favors disordered structures. Amberff99sb*-ILDN, AmberFF03w and CHARMM22* provide the balance between secondary structures that is most consistent with available experimental data. In contrast to previous reports, our findings suggest that the equilibrium conformations of human and rat amylin are remarkably similar, but that subtle differences arise in transient alpha-helical and beta-strand containing structures that the human peptide can more readily adopt. We hypothesize that these transient states enable

  8. [Conserved motifs in the primary and secondary ITS1 structures in bryophytes].

    PubMed

    Milyutina, I A; Ignatov, M S

    2015-01-01

    A study of the ITS1 nucleotide sequences of 1000 moss species of 62 families, 11 liverwort species from five orders, and one hornwort Anthoceros agrestis identified five highly conserved motifs (CM1-CM5), which are presumably involved in pre-rRNA processing. Although the ITS1 sequences substantially differ in length and the extent of divergence, the conserved motifs are found in all of them. ITS1 secondary structures were constructed for 76 mosses, and main regularities at conserved motif positioning were observed. The positions of processing sites in the ITS1 secondary structure of the yeast Saccharomyces cerevisiae were found to be similar to the positions of the conserved motifs in the ITS1 secondary structures of mosses and liverworts. In addition, a potential hairpin formation in the putative secondary structure of a pre-rRNA fragment was considered for the region between ITS1 CM4-CM5 and a highly conserved region between hairpins 49 and 50 (H49 and H50) of the 18S rRNA.

  9. [Conserved motifs in the primary and secondary ITS1 structures in bryophytes].

    PubMed

    Milyutina, I A; Ignatov, M S

    2015-01-01

    A study of the ITS1 nucleotide sequences of 1000 moss species of 62 families, 11 liverwort species from five orders, and one hornwort Anthoceros agrestis identified five highly conserved motifs (CM1-CM5), which are presumably involved in pre-rRNA processing. Although the ITS1 sequences substantially differ in length and the extent of divergence, the conserved motifs are found in all of them. ITS1 secondary structures were constructed for 76 mosses, and main regularities at conserved motif positioning were observed. The positions of processing sites in the ITS1 secondary structure of the yeast Saccharomyces cerevisiae were found to be similar to the positions of the conserved motifs in the ITS1 secondary structures of mosses and liverworts. In addition, a potential hairpin formation in the putative secondary structure of a pre-rRNA fragment was considered for the region between ITS1 CM4-CM5 and a highly conserved region between hairpins 49 and 50 (H49 and H50) of the 18S rRNA. PMID:26107892

  10. RNA Secondary Structure Prediction by Using Discrete Mathematics: An Interdisciplinary Research Experience for Undergraduate Students

    ERIC Educational Resources Information Center

    Ellington, Roni; Wachira, James; Nkwanta, Asamoah

    2010-01-01

    The focus of this Research Experience for Undergraduates (REU) project was on RNA secondary structure prediction by using a lattice walk approach. The lattice walk approach is a combinatorial and computational biology method used to enumerate possible secondary structures and predict RNA secondary structure from RNA sequences. The method uses…

  11. Intron positions in actin genes seem unrelated to the secondary structure of the protein.

    PubMed Central

    Weber, K; Kabsch, W

    1994-01-01

    A catalogue of intron positions along the coding sequence was assembled from the large number of actin genes known for different eukaryotes. 36 positions in the amino acid sequence were compared with the known three-dimensional structure of actin. At least 20 but not more than 23 intron positions are at the start or end of a secondary structural element (beta-strand, alpha-helix or 3/10 helix) while eight positions interrupt such an element. Statistical analysis shows that due to the large number of end positions the boundaries of secondary structural elements are not correlated with the intron positions. In addition, the observed intron pattern seems compatible with the null hypothesis, i.e. intron positions are randomly distributed along the actin sequence. Images PMID:8137812

  12. A phase transition in energy-filtered RNA secondary structures.

    PubMed

    Han, Hillary S W; Reidys, Christian M

    2012-10-01

    In this article we study the effect of energy parameters on minimum free energy (mfe) RNA secondary structures. Employing a simplified combinatorial energy model that is only dependent on the diagram representation and is not sequence-specific, we prove the following dichotomy result. Mfe structures derived via the Turner energy parameters contain only finitely many complex irreducible substructures, and just minor parameter changes produce a class of mfe structures that contain a large number of small irreducibles. We localize the exact point at which the distribution of irreducibles experiences this phase transition from a discrete limit to a central limit distribution and, subsequently, put our result into the context of quantifying the effect of sparsification of the folding of these respective mfe structures. We show that the sparsification of realistic mfe structures leads to a constant time and space reduction, and that the sparsification of the folding of structures with modified parameters leads to a linear time and space reduction. We, furthermore, identify the limit distribution at the phase transition as a Rayleigh distribution.

  13. The design of impact absorbing structures for additive manufacture

    NASA Astrophysics Data System (ADS)

    Brennan-Craddock, J.; Brackett, D.; Wildman, R.; Hague, R.

    2012-08-01

    Additive manufacturing (AM) is increasingly becoming a viable manufacturing process due to dramatic advantages that it facilitates in the area of design complexity. This paper investigates the potential of additively manufactured lattice structures for the application of tailored impact absorption specifically for conformal body protection. It explores lattice cell types based on foam microstructures and assesses their suitability for impact absorption. The effect of varying the cell strut edge design is also investigated. The implications of scaling these cells up for AM are discussed as well as the design issues regarding the handling of geometric complexity and the requirement for body conformity. The suitability of AM materials for this application is also discussed.

  14. RNApdbee—a webserver to derive secondary structures from pdb files of knotted and unknotted RNAs

    PubMed Central

    Antczak, Maciej; Zok, Tomasz; Popenda, Mariusz; Lukasiak, Piotr; Adamiak, Ryszard W.; Blazewicz, Jacek; Szachniuk, Marta

    2014-01-01

    In RNA structural biology and bioinformatics an access to correct RNA secondary structure and its proper representation is of crucial importance. This is true especially in the field of secondary and 3D RNA structure prediction. Here, we introduce RNApdbee—a new tool that allows to extract RNA secondary structure from the pdb file, and presents it in both textual and graphical form. RNApdbee supports processing of knotted and unknotted structures of large RNAs, also within protein complexes. The method works not only for first but also for high order pseudoknots, and gives an information about canonical and non-canonical base pairs. A combination of these features is unique among existing applications for RNA structure analysis. Additionally, a function of converting between the text notations, i.e. BPSEQ, CT and extended dot-bracket, is provided. In order to facilitate a more comprehensive study, the webserver integrates the functionality of RNAView, MC-Annotate and 3DNA/DSSR, being the most common tools used for automated identification and classification of RNA base pairs. RNApdbee is implemented as a publicly available webserver with an intuitive interface and can be freely accessed at http://rnapdbee.cs.put.poznan.pl/. PMID:24771339

  15. 113. Stage level floor structure. In addition to the movable ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    113. Stage level floor structure. In addition to the movable sections, there were hinged slots that could be opened in the stage floor (see sheet 4 of 9, note 4; sheet 5 of 9, note 2; and sheet 7 of 9, note 1). A remaining cast iron bracket is visible in the left foreground of the photograph. The actual structure for a hinged section is visible in the background, to the right of center. The hydraulic ram (type D) visible below the floor level is the south ram in the middle row; the view is facing north. - Auditorium Building, 430 South Michigan Avenue, Chicago, Cook County, IL

  16. Peptoid nanosheets exhibit a new secondary-structure motif

    NASA Astrophysics Data System (ADS)

    Mannige, Ranjan V.; Haxton, Thomas K.; Proulx, Caroline; Robertson, Ellen J.; Battigelli, Alessia; Butterfoss, Glenn L.; Zuckermann, Ronald N.; Whitelam, Stephen

    2015-10-01

    A promising route to the synthesis of protein-mimetic materials that are capable of complex functions, such as molecular recognition and catalysis, is provided by sequence-defined peptoid polymers--structural relatives of biologically occurring polypeptides. Peptoids, which are relatively non-toxic and resistant to degradation, can fold into defined structures through a combination of sequence-dependent interactions. However, the range of possible structures that are accessible to peptoids and other biological mimetics is unknown, and our ability to design protein-like architectures from these polymer classes is limited. Here we use molecular-dynamics simulations, together with scattering and microscopy data, to determine the atomic-resolution structure of the recently discovered peptoid nanosheet, an ordered supramolecular assembly that extends macroscopically in only two dimensions. Our simulations show that nanosheets are structurally and dynamically heterogeneous, can be formed only from peptoids of certain lengths, and are potentially porous to water and ions. Moreover, their formation is enabled by the peptoids' adoption of a secondary structure that is not seen in the natural world. This structure, a zigzag pattern that we call a Σ(`sigma')-strand, results from the ability of adjacent backbone monomers to adopt opposed rotational states, thereby allowing the backbone to remain linear and untwisted. Linear backbones tiled in a brick-like way form an extended two-dimensional nanostructure, the Σ-sheet. The binary rotational-state motif of the Σ-strand is not seen in regular protein structures, which are usually built from one type of rotational state. We also show that the concept of building regular structures from multiple rotational states can be generalized beyond the peptoid nanosheet system.

  17. RNAex: an RNA secondary structure prediction server enhanced by high-throughput structure-probing data.

    PubMed

    Wu, Yang; Qu, Rihao; Huang, Yiming; Shi, Binbin; Liu, Mengrong; Li, Yang; Lu, Zhi John

    2016-07-01

    Several high-throughput technologies have been developed to probe RNA base pairs and loops at the transcriptome level in multiple species. However, to obtain the final RNA secondary structure, extensive effort and considerable expertise is required to statistically process the probing data and combine them with free energy models. Therefore, we developed an RNA secondary structure prediction server that is enhanced by experimental data (RNAex). RNAex is a web interface that enables non-specialists to easily access cutting-edge structure-probing data and predict RNA secondary structures enhanced by in vivo and in vitro data. RNAex annotates the RNA editing, RNA modification and SNP sites on the predicted structures. It provides four structure-folding methods, restrained MaxExpect, SeqFold, RNAstructure (Fold) and RNAfold that can be selected by the user. The performance of these four folding methods has been verified by previous publications on known structures. We re-mapped the raw sequencing data of the probing experiments to the whole genome for each species. RNAex thus enables users to predict secondary structures for both known and novel RNA transcripts in human, mouse, yeast and Arabidopsis The RNAex web server is available at http://RNAex.ncrnalab.org/.

  18. RNAex: an RNA secondary structure prediction server enhanced by high-throughput structure-probing data

    PubMed Central

    Wu, Yang; Qu, Rihao; Huang, Yiming; Shi, Binbin; Liu, Mengrong; Li, Yang; Lu, Zhi John

    2016-01-01

    Several high-throughput technologies have been developed to probe RNA base pairs and loops at the transcriptome level in multiple species. However, to obtain the final RNA secondary structure, extensive effort and considerable expertise is required to statistically process the probing data and combine them with free energy models. Therefore, we developed an RNA secondary structure prediction server that is enhanced by experimental data (RNAex). RNAex is a web interface that enables non-specialists to easily access cutting-edge structure-probing data and predict RNA secondary structures enhanced by in vivo and in vitro data. RNAex annotates the RNA editing, RNA modification and SNP sites on the predicted structures. It provides four structure-folding methods, restrained MaxExpect, SeqFold, RNAstructure (Fold) and RNAfold that can be selected by the user. The performance of these four folding methods has been verified by previous publications on known structures. We re-mapped the raw sequencing data of the probing experiments to the whole genome for each species. RNAex thus enables users to predict secondary structures for both known and novel RNA transcripts in human, mouse, yeast and Arabidopsis. The RNAex web server is available at http://RNAex.ncrnalab.org/. PMID:27137891

  19. Computer-aided prediction of RNA secondary structures.

    PubMed Central

    Auron, P E; Rindone, W P; Vary, C P; Celentano, J J; Vournakis, J N

    1982-01-01

    A brief survey of computer algorithms that have been developed to generate predictions of the secondary structures of RNA molecules is presented. Two particular methods are described in some detail. The first utilizes a thermodynamic energy minimization algorithm that takes into account the likelihood that short-range folding tends to be favored over long-range interactions. The second utilizes an interactive computer graphic modelling algorithm that enables the user to consider thermodynamic criteria as well as structural data obtained by nuclease susceptibility, chemical reactivity and phylogenetic studies. Examples of structures for prokaryotic 16S and 23S ribosomal RNAs, several eukaryotic 5S ribosomal RNAs and rabbit beta-globin messenger RNA are presented as case studies in order to describe the two techniques. Anm argument is made for integrating the two approaches presented in this paper, enabling the user to generate proposed structures using thermodynamic criteria, allowing interactive refinement of these structures through the application of experimentally derived data. PMID:6174937

  20. Oxygen additions in serial femtosecond crystallographic protein structures.

    PubMed

    Wang, Jimin

    2016-10-01

    In principle, serial femtosecond crystallography (SFX) could yield data sets that are completely free of the effects caused by slow, radiation-induced chemical reactions, for example, oxygen additions, responsible for radiation damage. However, experimental evidence is presented here that SFX data sets obtained by techniques that expose different parts of the same specimen to single pulses of radiation do not have this property, even if the specimen in question is frozen. The diffraction image of each such crystal obtained with the first pulse of radiation is certain to represent the structure of a protein that has not been modified chemically, but all of the images obtained subsequently from the same crystal will represent structures that have been modified to a lesser or greater extent by oxygen additions because of the rapid diffusion of oxygenic free radicals through the specimen. The higher the level of oxygen additions a crystal suffers during data collection, the poorer the statistical quality of data set obtained from it will, and the higher the free R-factors of the resulting structural model. PMID:27438534

  1. 1H and 13C NMR characterization and secondary structure of the K2 polysaccharide of Klebsiella pneumoniae strain 52145.

    PubMed

    Corsaro, Maria Michela; De Castro, Cristina; Naldi, Teresa; Parrilli, Michelangelo; Tomás, Juan M; Regué, Miguel

    2005-09-26

    The complete (1)H and (13)C NMR characterization of the tetrasaccharide repeating unit from the K2 polysaccharide of Klebsiella pneumoniae strain 52145 is reported. [chemical structure] In addition a model for its secondary structure was suggested on the basis of dynamic and molecular calculations.

  2. Nucleotide sequence of a crustacean 18S ribosomal RNA gene and secondary structure of eukaryotic small subunit ribosomal RNAs.

    PubMed

    Nelles, L; Fang, B L; Volckaert, G; Vandenberghe, A; De Wachter, R

    1984-12-11

    The primary structure of the gene for 18 S rRNA of the crustacean Artemia salina was determined. The sequence has been aligned with 13 other small ribosomal subunit RNA sequences of eukaryotic, archaebacterial, eubacterial, chloroplastic and plant mitochondrial origin. Secondary structure models for these RNAs were derived on the basis of previously proposed models and additional comparative evidence found in the alignment. Although there is a general similarity in the secondary structure models for eukaryotes and prokaryotes, the evidence seems to indicate a different topology in a central area of the structures.

  3. Secondary structure of the HIV-2 leader RNA comprising the tRNA-primer binding site.

    PubMed Central

    Berkhout, B; Schoneveld, I

    1993-01-01

    The initiation of reverse transcription of a retroviral RNA genome occurs by a tRNA primer bound near the 5' end of the genomic RNA at a position called the primer-binding site (PBS). To understand the molecular basis for this RNA-RNA interaction, the secondary structure of the leader RNA of the human immunodeficiency virus type 2 (HIV-2) RNA was analyzed. In vitro synthesized HIV-2 RNA was probed with various structure-specific enzymes and chemicals. A computer program was then used to predict the secondary structure consistent with these data. In addition, the nucleotide sequences of different HIV-2 isolates were used to screen for the occurrence of covariation among putative base pairs. The primary sequences have diverged rapidly in some HIV-2 isolates, however, some strikingly conserved secondary structure elements were identified. Most nucleotides in the leader region are involved in base pairing. An exception is the PBS sequence, of which 15 out of 18 nucleotides are exposed in an internal loop. These findings suggest that the overall structure of the HIV-2 genome has evolved to facilitate an optimal interaction with its tRNA primer. Images PMID:8464701

  4. Protein Secondary Structure Prediction Using Deep Convolutional Neural Fields.

    PubMed

    Wang, Sheng; Peng, Jian; Ma, Jianzhu; Xu, Jinbo

    2016-01-01

    Protein secondary structure (SS) prediction is important for studying protein structure and function. When only the sequence (profile) information is used as input feature, currently the best predictors can obtain ~80% Q3 accuracy, which has not been improved in the past decade. Here we present DeepCNF (Deep Convolutional Neural Fields) for protein SS prediction. DeepCNF is a Deep Learning extension of Conditional Neural Fields (CNF), which is an integration of Conditional Random Fields (CRF) and shallow neural networks. DeepCNF can model not only complex sequence-structure relationship by a deep hierarchical architecture, but also interdependency between adjacent SS labels, so it is much more powerful than CNF. Experimental results show that DeepCNF can obtain ~84% Q3 accuracy, ~85% SOV score, and ~72% Q8 accuracy, respectively, on the CASP and CAMEO test proteins, greatly outperforming currently popular predictors. As a general framework, DeepCNF can be used to predict other protein structure properties such as contact number, disorder regions, and solvent accessibility. PMID:26752681

  5. Protein Secondary Structure Prediction Using Deep Convolutional Neural Fields

    NASA Astrophysics Data System (ADS)

    Wang, Sheng; Peng, Jian; Ma, Jianzhu; Xu, Jinbo

    2016-01-01

    Protein secondary structure (SS) prediction is important for studying protein structure and function. When only the sequence (profile) information is used as input feature, currently the best predictors can obtain ~80% Q3 accuracy, which has not been improved in the past decade. Here we present DeepCNF (Deep Convolutional Neural Fields) for protein SS prediction. DeepCNF is a Deep Learning extension of Conditional Neural Fields (CNF), which is an integration of Conditional Random Fields (CRF) and shallow neural networks. DeepCNF can model not only complex sequence-structure relationship by a deep hierarchical architecture, but also interdependency between adjacent SS labels, so it is much more powerful than CNF. Experimental results show that DeepCNF can obtain ~84% Q3 accuracy, ~85% SOV score, and ~72% Q8 accuracy, respectively, on the CASP and CAMEO test proteins, greatly outperforming currently popular predictors. As a general framework, DeepCNF can be used to predict other protein structure properties such as contact number, disorder regions, and solvent accessibility.

  6. Secondary structure encodes a cooperative tertiary folding funnel in the Azoarcus ribozyme

    PubMed Central

    Mustoe, Anthony M.; Al-Hashimi, Hashim M.; Brooks, Charles L.

    2016-01-01

    A requirement for specific RNA folding is that the free-energy landscape discriminate against non-native folds. While tertiary interactions are critical for stabilizing the native fold, they are relatively non-specific, suggesting additional mechanisms contribute to tertiary folding specificity. In this study, we use coarse-grained molecular dynamics simulations to explore how secondary structure shapes the tertiary free-energy landscape of the Azoarcus ribozyme. We show that steric and connectivity constraints posed by secondary structure strongly limit the accessible conformational space of the ribozyme, and that these so-called topological constraints in turn pose strong free-energy penalties on forming different tertiary contacts. Notably, native A-minor and base-triple interactions form with low conformational free energy, while non-native tetraloop/tetraloop–receptor interactions are penalized by high conformational free energies. Topological constraints also give rise to strong cooperativity between distal tertiary interactions, quantitatively matching prior experimental measurements. The specificity of the folding landscape is further enhanced as tertiary contacts place additional constraints on the conformational space, progressively funneling the molecule to the native state. These results indicate that secondary structure assists the ribozyme in navigating the otherwise rugged tertiary folding landscape, and further emphasize topological constraints as a key force in RNA folding. PMID:26481360

  7. An RNA secondary structure prediction method based on minimum and suboptimal free energy structures.

    PubMed

    Fu, Haoyue; Yang, Lianping; Zhang, Xiangde

    2015-09-01

    The function of an RNA-molecule is mainly determined by its tertiary structures. And its secondary structure is an important determinant of its tertiary structure. The comparative methods usually give better results than the single-sequence methods. Based on minimum and suboptimal free energy structures, the paper presents a novel method for predicting conserved secondary structure of a group of related RNAs. In the method, the information from the known RNA structures is used as training data in a SVM (Support Vector Machine) classifier. Our method has been tested on the benchmark dataset given by Puton et al. The results show that the average sensitivity of our method is higher than that of other comparative methods such as CentroidAlifold, MXScrana, RNAalifold, and TurboFold. PMID:26100179

  8. Bioinspired Cellular Structures: Additive Manufacturing and Mechanical Properties

    NASA Astrophysics Data System (ADS)

    Stampfl, J.; Pettermann, H. E.; Liska, R.

    Biological materials (e.g., wood, trabecular bone, marine skeletons) rely heavily on the use of cellular architecture, which provides several advantages. (1) The resulting structures can bear the variety of "real life" load spectra using a minimum of a given bulk material, featuring engineering lightweight design principles. (2) The inside of the structures is accessible to body fluids which deliver the required nutrients. (3) Furthermore, cellular architectures can grow organically by adding or removing individual struts or by changing the shape of the constituting elements. All these facts make the use of cellular architectures a reasonable choice for nature. Using additive manufacturing technologies (AMT), it is now possible to fabricate such structures for applications in engineering and biomedicine. In this chapter, we present methods that allow the 3D computational analysis of the mechanical properties of cellular structures with open porosity. Various different cellular architectures including disorder are studied. In order to quantify the influence of architecture, the apparent density is always kept constant. Furthermore, it is shown that how new advanced photopolymers can be used to tailor the mechanical and functional properties of the fabricated structures.

  9. Fretting Wear Properties of TiCN-Ni Cermets: Influence of Load and Secondary Carbide Addition

    NASA Astrophysics Data System (ADS)

    Manoj Kumar, B. V.; Basu, Bikramjit

    2008-03-01

    The increasing demand for TiCN-based cermets in tribological applications necessitates a thorough understanding of the influence of experimental as well as material parameters on the friction and wear properties. In optimizing microstructure and properties, secondary carbides are added to baseline TiCN-Ni cermet. The present work aims at evaluating the fretting wear behavior of Ti(CN)-Ni cermets containing various secondary carbides, such as WC, NbC, TaC, and HfC, against steel at different loading (2, 6, and 10 N) conditions. The evolution of tangential frictional force for the investigated cermets was analyzed in terms of fretting logs and fretting loops. The topographical characterization of worn surfaces was performed, using laser surface profilometry and a scanning electron microscope (SEM) equipped with energy-dispersive spectroscopy (EDS) capability. The steady-state coefficient of friction (COF) was minimum (0.33) for a TiCN-20Ni cermet/steel tribocouple, while a maximum COF (0.47) was recorded for TiCN-20Ni-10HfC cermet/steel at a 2-N load. The wear rate of the cermets varied in the range of 1.7 × 10-6 to 3.5 × 10-6 mm3/Nm. The TiCN-20Ni-10HfC cermet exhibited poor wear resistance among investigated cermets. The dominant wear mechanisms were found as abrasion and tribolayer formation. The dominance of abrasion is explained in terms of cumulative energy dissipation.

  10. "Well-determined" regions in RNA secondary structure prediction: analysis of small subunit ribosomal RNA.

    PubMed Central

    Zuker, M; Jacobson, A B

    1995-01-01

    Recent structural analyses of genomic RNAs from RNA coliphages suggest that both well-determined base paired helices and well-determined structural domains that are identified by "energy dot plot" analysis using the RNA folding package mfold, are likely to be predicted correctly. To test these observations with another group of large RNAs, we have analyzed 15 ribosomal RNAs. Published secondary structure models that were derived by comparative sequence analysis were used to evaluate the predicted structures. Both the optimal predicted fold and the predicted "energy dot plot" of each sequence were examined. Each prediction was obtained from a single computer run on an entire ribosomal RNA sequence. All predicted base pairs in optimal foldings were examined for agreement with proven base pairs in the comparative models. Our analyses show that the overall correspondence between the predicted and comparative models varied for different RNAs and ranges from a low of 27% to high of 70%, with a mean value of 49%. The correspondence improves to a mean value of 81% when the analysis is limited to well-determined helices. In addition to well-determined helices, large well-determined structural domains can be observed in "energy dot plots" of some 16S ribosomal RNAs. The predicted domains correspond closely with structural domains that are found by the comparative method in the same RNAs. Our analyses also show that measuring the agreement between predicted and comparative secondary structure models underestimates the reliability of structural prediction by mfold. PMID:7544463

  11. Structure of ternary additive hard-sphere fluid mixtures

    NASA Astrophysics Data System (ADS)

    Malijevský, Alexander; Malijevský, Anatol; Yuste, Santos B.; Santos, Andrés; López de Haro, Mariano

    2002-12-01

    Monte Carlo simulations on the structural properties of ternary fluid mixtures of additive hard spheres are reported. The results are compared with those obtained from a recent analytical approximation [S. B. Yuste, A. Santos, and M. López de Haro, J. Chem. Phys. 108, 3683 (1998)] to the radial distribution functions of hard-sphere mixtures and with the results derived from the solution of the Ornstein-Zernike integral equation with both the Martynov-Sarkisov and the Percus-Yevick closures. Very good agreement between the results of the first two approaches and simulation is observed, with a noticeable improvement over the Percus-Yevick predictions especially near contact.

  12. Protein secondary structural types are differentially coded on messenger RNA.

    PubMed Central

    Thanaraj, T. A.; Argos, P.

    1996-01-01

    Tricodon regions on messenger RNAs corresponding to a set of proteins from Escherichia coli were scrutinized for their translation speed. The fractional frequency values of the individual codons as they occur in mRNAs of highly expressed genes from Escherichia coli were taken as an indicative measure of the translation speed. The tricodons were classified by the sum of the frequency values of the constituent codons. Examination of the conformation of the encoded amino acid residues in the corresponding protein tertiary structures revealed a correlation between codon usage in mRNA and topological features of the encoded proteins. Alpha helices on proteins tend to be preferentially coded by translationally fast mRNA regions while the slow segments often code for beta strands and coil regions. Fast regions correspondingly avoid coding for beta strands and coil regions while the slow regions similarly move away from encoding alpha helices. Structural and mechanistic aspects of the ribosome peptide channel support the relevance of sequence fragment translation and subsequent conformation. A discussion is presented relating the observation to the reported kinetic data on the formation and stabilization of protein secondary structural types during protein folding. The observed absence of such strong positive selection for codons in non-highly expressed genes is compatible with existing theories that mutation pressure may well dominate codon selection in non-highly expressed genes. PMID:8897597

  13. Consequential secondary structure alterations and aggregation during prolonged casein glycation.

    PubMed

    Jindal, Supriya; Naeem, Aabgeena

    2013-05-01

    Non-enzymatic glycosylation (glycation) of casein is a process used not just to ameliorate the quality of dairy products but also to increase the shelf life of canned foods, including baby milk supplements. Incubation of κ-casein with reducing sugars for 15 days at physiological temperature showed the formation of a molten globule state at day 9 and 12 during fructation and glucation respectively. This state exhibits substantial secondary structure and maximum ANS binding. Later on, glycation resulted in the formation of aggregates at day 12 in presence of fructose and day 15 in presence of glucose. Aggregates possess extensive β-sheet structure as revealed by far-UV CD and FTIR. These aggregates showed altered tryptophan environment, decrease ANS binding relative to molten globule state and increase in Thioflavin T fluorescence. Aggregates were also accompanied by the accumulation of AGEs, indicative of structural damage to the protein and formation of potentially harmful species at the physiological level. Fructose was more reactive than glucose and thus caused early and significant changes in the protein. From our studies, we conclude that controlling the extent of the Maillard reaction in the food industry is essential to counter its negative effects and expand its safety spectrum. PMID:23408088

  14. Visualizing the formation of an RNA folding intermediate through a fast highly modular secondary structure switch

    PubMed Central

    Xue, Yi; Gracia, Brant; Herschlag, Daniel; Russell, Rick; Al-Hashimi, Hashim M.

    2016-01-01

    Intermediates play important roles in RNA folding but can be difficult to characterize when short-lived or not significantly populated. By combining 15N relaxation dispersion NMR with chemical probing, we visualized a fast (kex=k1+k−1≈423 s−1) secondary structural switch directed towards a low-populated (∼3%) partially folded intermediate in tertiary folding of the P5abc subdomain of the ‘Tetrahymena' group I intron ribozyme. The secondary structure switch changes the base-pairing register across the P5c hairpin, creating a native-like structure, and occurs at rates of more than two orders of magnitude faster than tertiary folding. The switch occurs robustly in the absence of tertiary interactions, Mg2+ or even when the hairpin is excised from the three-way junction. Fast, highly modular secondary structural switches may be quite common during RNA tertiary folding where they may help smoothen the folding landscape by allowing folding to proceed efficiently via additional pathways. PMID:27292179

  15. Additive manufacturing of ceramic structures by laser engineered net shaping

    NASA Astrophysics Data System (ADS)

    Niu, Fangyong; Wu, Dongjiang; Ma, Guangyi; Zhang, Bi

    2015-11-01

    Ceramic is an important material with outstanding physical properties whereas impurities and porosities generated by traditional manufacturing methods limits its further industrial applications. In order to solve this problem, direct fabrication of Al2O3 ceramic structures is conducted by laser engineered net shaping system and pure ceramic powders. Grain refinement strengthening method by doping ZrO2 and dispersion strengthening method by doping SiC are proposed to suppress cracks in fabricating Al2O3 structure. Phase compositions, microstructures as well as mechanical properties of fabricated specimens are then analyzed. The results show that the proposed two methods are effective in suppressing cracks and structures of single-bead wall, arc and cylinder ring are successfully deposited. Stable phase of α-Al2O3 and t-ZrO2 are obtained in the fabricated specimens. Micro-hardness higher than 1700 HV are also achieved for both Al2O3 and Al2O3/ZrO2, which are resulted from fine directional crystals generated by the melting-solidification process. Results presented indicate that additive manufacturing is a very attractive technique for the production of high-performance ceramic structures in a single step.

  16. Toward a better understanding of structural divergences in proteins using different secondary structure assignment methods

    NASA Astrophysics Data System (ADS)

    Rocha, L. F. O.

    2014-04-01

    Structural disagreements on the location and quantity of secondary structure segments comprise a current challenging problem leading to several limitations for theoretical and applied research. This paper presents 116 structural evaluations by steric and hydrophobic interactions in secondary structures within a specific template group; determines simple prediction rules that calculate 88 occurrence frequencies of large and hydrophobic residues into target intra- and inter-subgroups with structure disagreements; and utilizes 42 comparisons between the methods PROMOTIF, DSSP and STRIDE. In the stereochemical predictions inside the subgroups there are predominantly excellent and/or good success amounts with their expected values, and the disclosure of a triple molecular mechanism by residue volumetric and hydrophobic ingredients. The method comparisons show high compatibility scores between them, therefore validating their seemingly incompatible assignments. Thus, the nonconsensual ascriptions are better understood and appreciated. Furthermore, such results suggest a broad utility of our assignment method for other benchmark datasets and known methods.

  17. Identify five kinds of simple super-secondary structures with quadratic discriminant algorithm based on the chemical shifts.

    PubMed

    Kou, Gaoshan; Feng, Yonge

    2015-09-01

    The biological function of protein is largely determined by its spatial structure. The research on the relationship between structure and function is the basis of protein structure prediction. However, the prediction of super secondary structure is an important step in the prediction of protein spatial structure. Many algorithms have been proposed for the prediction of protein super secondary structure. However, the parameters used by these methods were primarily based on amino acid sequences. In this paper, we proposed a novel model for predicting five kinds of protein super secondary structures based on the chemical shifts (CSs). Firstly, we analyzed the statistical distribution of chemical shifts of six nuclei in five kinds of protein super secondary structures by using the analysis of variance (ANOVA). Secondly, we used chemical shifts of six nuclei as features, and combined with quadratic discriminant analysis (QDA) to predict five kinds of protein super secondary structures. Finally, we achieved the averaged sensitivity, specificity and the overall accuracy of 81.8%, 95.19%, 82.91%, respectively in seven-fold cross-validation. Moreover, we have performed the prediction by combining the five different chemical shifts as features, the maximum overall accuracy up to 89.87% by using the C,Cα,Cβ,N,Hα of Hα chemical shifts, which are clearly superior to that of the quadratic discriminant analysis (QDA) algorithm by using 20 amino acid compositions (AAC) as feature in the seven-fold cross-validation. These results demonstrated that chemical shifts (CSs) are indeed an outstanding parameter for the prediction of five kinds of super secondary structures. In addition, we compared the prediction of the quadratic discriminant analysis (QDA) with that of support vector machine (SVM) by using the same six CSs as features. The result suggested that the quadratic discriminant analysis method by using chemical shifts as features is a good predictor for protein super

  18. PSRna: Prediction of small RNA secondary structures based on reverse complementary folding method.

    PubMed

    Li, Jin; Xu, Chengzhen; Wang, Lei; Liang, Hong; Feng, Weixing; Cai, Zhongxi; Wang, Ying; Cong, Wang; Liu, Yunlong

    2016-08-01

    Prediction of RNA secondary structures is an important problem in computational biology and bioinformatics, since RNA secondary structures are fundamental for functional analysis of RNA molecules. However, small RNA secondary structures are scarce and few algorithms have been specifically designed for predicting the secondary structures of small RNAs. Here we propose an algorithm named "PSRna" for predicting small-RNA secondary structures using reverse complementary folding and characteristic hairpin loops of small RNAs. Unlike traditional algorithms that usually generate multi-branch loops and 5[Formula: see text] end self-folding, PSRna first estimated the maximum number of base pairs of RNA secondary structures based on the dynamic programming algorithm and a path matrix is constructed at the same time. Second, the backtracking paths are extracted from the path matrix based on backtracking algorithm, and each backtracking path represents a secondary structure. To improve accuracy, the predicted RNA secondary structures are filtered based on their free energy, where only the secondary structure with the minimum free energy was identified as the candidate secondary structure. Our experiments on real data show that the proposed algorithm is superior to two popular methods, RNAfold and RNAstructure, in terms of sensitivity, specificity and Matthews correlation coefficient (MCC). PMID:27045556

  19. PSRna: Prediction of small RNA secondary structures based on reverse complementary folding method.

    PubMed

    Li, Jin; Xu, Chengzhen; Wang, Lei; Liang, Hong; Feng, Weixing; Cai, Zhongxi; Wang, Ying; Cong, Wang; Liu, Yunlong

    2016-08-01

    Prediction of RNA secondary structures is an important problem in computational biology and bioinformatics, since RNA secondary structures are fundamental for functional analysis of RNA molecules. However, small RNA secondary structures are scarce and few algorithms have been specifically designed for predicting the secondary structures of small RNAs. Here we propose an algorithm named "PSRna" for predicting small-RNA secondary structures using reverse complementary folding and characteristic hairpin loops of small RNAs. Unlike traditional algorithms that usually generate multi-branch loops and 5[Formula: see text] end self-folding, PSRna first estimated the maximum number of base pairs of RNA secondary structures based on the dynamic programming algorithm and a path matrix is constructed at the same time. Second, the backtracking paths are extracted from the path matrix based on backtracking algorithm, and each backtracking path represents a secondary structure. To improve accuracy, the predicted RNA secondary structures are filtered based on their free energy, where only the secondary structure with the minimum free energy was identified as the candidate secondary structure. Our experiments on real data show that the proposed algorithm is superior to two popular methods, RNAfold and RNAstructure, in terms of sensitivity, specificity and Matthews correlation coefficient (MCC).

  20. Expected distance between terminal nucleotides of RNA secondary structures.

    PubMed

    Clote, Peter; Ponty, Yann; Steyaert, Jean-Marc

    2012-09-01

    In "The ends of a large RNA molecule are necessarily close", Yoffe et al. (Nucleic Acids Res 39(1):292-299, 2011) used the programs RNAfold [resp. RNAsubopt] from Vienna RNA Package to calculate the distance between 5' and 3' ends of the minimum free energy secondary structure [resp. thermal equilibrium structures] of viral and random RNA sequences. Here, the 5'-3' distance is defined to be the length of the shortest path from 5' node to 3' node in the undirected graph, whose edge set consists of edges {i, i + 1} corresponding to covalent backbone bonds and of edges {i, j} corresponding to canonical base pairs. From repeated simulations and using a heuristic theoretical argument, Yoffe et al. conclude that the 5'-3' distance is less than a fixed constant, independent of RNA sequence length. In this paper, we provide a rigorous, mathematical framework to study the expected distance from 5' to 3' ends of an RNA sequence. We present recurrence relations that precisely define the expected distance from 5' to 3' ends of an RNA sequence, both for the Turner nearest neighbor energy model, as well as for a simple homopolymer model first defined by Stein and Waterman. We implement dynamic programming algorithms to compute (rather than approximate by repeated application of Vienna RNA Package) the expected distance between 5' and 3' ends of a given RNA sequence, with respect to the Turner energy model. Using methods of analytical combinatorics, that depend on complex analysis, we prove that the asymptotic expected 5'-3' distance of length n homopolymers is approximately equal to the constant 5.47211, while the asymptotic distance is 6.771096 if hairpins have a minimum of 3 unpaired bases and the probability that any two positions can form a base pair is 1/4. Finally, we analyze the 5'-3' distance for secondary structures from the STRAND database, and conclude that the 5'-3' distance is correlated with RNA sequence length.

  1. Expected distance between terminal nucleotides of RNA secondary structures.

    PubMed

    Clote, Peter; Ponty, Yann; Steyaert, Jean-Marc

    2012-09-01

    In "The ends of a large RNA molecule are necessarily close", Yoffe et al. (Nucleic Acids Res 39(1):292-299, 2011) used the programs RNAfold [resp. RNAsubopt] from Vienna RNA Package to calculate the distance between 5' and 3' ends of the minimum free energy secondary structure [resp. thermal equilibrium structures] of viral and random RNA sequences. Here, the 5'-3' distance is defined to be the length of the shortest path from 5' node to 3' node in the undirected graph, whose edge set consists of edges {i, i + 1} corresponding to covalent backbone bonds and of edges {i, j} corresponding to canonical base pairs. From repeated simulations and using a heuristic theoretical argument, Yoffe et al. conclude that the 5'-3' distance is less than a fixed constant, independent of RNA sequence length. In this paper, we provide a rigorous, mathematical framework to study the expected distance from 5' to 3' ends of an RNA sequence. We present recurrence relations that precisely define the expected distance from 5' to 3' ends of an RNA sequence, both for the Turner nearest neighbor energy model, as well as for a simple homopolymer model first defined by Stein and Waterman. We implement dynamic programming algorithms to compute (rather than approximate by repeated application of Vienna RNA Package) the expected distance between 5' and 3' ends of a given RNA sequence, with respect to the Turner energy model. Using methods of analytical combinatorics, that depend on complex analysis, we prove that the asymptotic expected 5'-3' distance of length n homopolymers is approximately equal to the constant 5.47211, while the asymptotic distance is 6.771096 if hairpins have a minimum of 3 unpaired bases and the probability that any two positions can form a base pair is 1/4. Finally, we analyze the 5'-3' distance for secondary structures from the STRAND database, and conclude that the 5'-3' distance is correlated with RNA sequence length. PMID:21984358

  2. Mechanistic study of secondary organic aerosol components formed from nucleophilic addition reactions of methacrylic acid epoxide

    NASA Astrophysics Data System (ADS)

    Birdsall, A. W.; Miner, C. R.; Mael, L. E.; Elrod, M. J.

    2014-08-01

    Recently, methacrylic acid epoxide (MAE) has been proposed as a precursor to an important class of isoprene-derived compounds found in secondary organic aerosol (SOA): 2-methylglyceric acid (2-MG) and a set of oligomers, nitric acid esters and sulfuric acid esters related to 2-MG. However, the specific chemical mechanisms by which MAE could form these compounds have not been previously studied. In order to determine the relevance of these processes to atmospheric aerosol, MAE and 2-MG have been synthesized and a series of bulk solution-phase experiments aimed at studying the reactivity of MAE using nuclear magnetic resonance (NMR) spectroscopy have been performed. The present results indicate that the acid-catalyzed MAE reaction is more than 600 times slower than a similar reaction of an important isoprene-derived epoxide, but is still expected to be kinetically feasible in the atmosphere on more acidic SOA. The specific mechanism by which MAE leads to oligomers was identified, and the reactions of MAE with a number of atmospherically relevant nucleophiles were also investigated. Because the nucleophilic strengths of water, sulfate, alcohols (including 2-MG), and acids (including MAE and 2-MG) in their reactions with MAE were found to be of a similar magnitude, it is expected that a diverse variety of MAE + nucleophile product species may be formed on ambient SOA. Thus, the results indicate that epoxide chain reaction oligomerization will be limited by the presence of high concentrations of non-epoxide nucleophiles (such as water); this finding is consistent with previous environmental chamber investigations of the relative humidity-dependence of 2-MG-derived oligomerization processes and suggests that extensive oligomerization may not be likely on ambient SOA because of other competitive MAE reaction mechanisms.

  3. Mechanistic study of secondary organic aerosol components formed from nucleophilic addition reactions of methacrylic acid epoxide

    NASA Astrophysics Data System (ADS)

    Birdsall, A. W.; Miner, C. R.; Mael, L. E.; Elrod, M. J.

    2014-12-01

    Recently, methacrylic acid epoxide (MAE) has been proposed as a precursor to an important class of isoprene-derived compounds found in secondary organic aerosol (SOA): 2-methylglyceric acid (2-MG) and a set of oligomers, nitric acid esters, and sulfuric acid esters related to 2-MG. However, the specific chemical mechanisms by which MAE could form these compounds have not been previously studied with experimental methods. In order to determine the relevance of these processes to atmospheric aerosol, MAE and 2-MG have been synthesized and a series of bulk solution-phase experiments aimed at studying the reactivity of MAE using nuclear magnetic resonance (NMR) spectroscopy have been performed. The present results indicate that the acid-catalyzed MAE reaction is more than 600 times slower than a similar reaction of an important isoprene-derived epoxide, but is still expected to be kinetically feasible in the atmosphere on more acidic SOA. The specific mechanism by which MAE leads to oligomers was identified, and the reactions of MAE with a number of atmospherically relevant nucleophiles were also investigated. Because the nucleophilic strengths of water, sulfate, alcohols (including 2-MG), and acids (including MAE and 2-MG) in their reactions with MAE were found to be of similar magnitudes, it is expected that a diverse variety of MAE + nucleophile product species may be formed on ambient SOA. Thus, the results indicate that epoxide chain reaction oligomerization will be limited by the presence of high concentrations of non-epoxide nucleophiles (such as water); this finding is consistent with previous environmental chamber investigations of the relative humidity dependence of 2-MG-derived oligomerization processes and suggests that extensive oligomerization may not be likely on ambient SOA because of other competitive MAE reaction mechanisms.

  4. Electrical inhibition of lens epithelial cell proliferation: an additional factor in secondary cataract?

    PubMed Central

    Wang, Entong; Reid, Brian; Lois, Noemi; Forrester, John V.; McCaig, Colin D.; Zhao, Min

    2005-01-01

    Cataract is the most common cause of blindness but is at least curable by surgery. Unfortunately, many patients gradually develop the complication of posterior capsule opacification (PCO) or secondary cataract. This arises from stimulated cell growth within the lens capsule and can greatly impair vision. It is not fully understood why residual lens epithelial cell growth occurs after surgery. We propose and show that cataract surgery might remove an important inhibitory factor for lens cell growth, namely electric fields. The lens generates a unique pattern of electric currents constantly flowing out from the equator and entering the anterior and posterior poles. We show here that cutting and removing part of the anterior capsule as in cataract surgery significantly decreases the equatorial outward electric currents. Application of electric fields in culture inhibits proliferation of human lens epithelial cells. This inhibitory effect is likely to be mediated through a cell cycle control mechanism that decreases entry of cells into S phase from G1 phase by decreasing the G1-specific cell cycle protein cyclin E and increasing the cyclin-Cdk complex inhibitor p27kip1. Capsulorrhexis in vivo, which reduced endogenous lens electric fields, significantly increased LEC growth. This, together with our previous findings that electric fields have significant effects on the direction of lens cell migration, points to a controlling mechanism for the aberrant cell growth in posterior capsule opacification. A novel approach to control growth of lens epithelial cells using electric fields combined with other controlling mechanisms may be more effective in the prevention and treatment of this common complication of cataract surgery. PMID:15764648

  5. Tuning structure and mobility of solvation shells surrounding tracer additives

    SciTech Connect

    Carmer, James; Jain, Avni; Bollinger, Jonathan A.; Truskett, Thomas M.; Swol, Frank van

    2015-03-28

    Molecular dynamics simulations and a stochastic Fokker-Planck equation based approach are used to illuminate how position-dependent solvent mobility near one or more tracer particle(s) is affected when tracer-solvent interactions are rationally modified to affect corresponding solvation structure. For tracers in a dense hard-sphere fluid, we compare two types of tracer-solvent interactions: (1) a hard-sphere-like interaction, and (2) a soft repulsion extending beyond the hard core designed via statistical mechanical theory to enhance tracer mobility at infinite dilution by suppressing coordination-shell structure [Carmer et al., Soft Matter 8, 4083–4089 (2012)]. For the latter case, we show that the mobility of surrounding solvent particles is also increased by addition of the soft repulsive interaction, which helps to rationalize the mechanism underlying the tracer’s enhanced diffusivity. However, if multiple tracer surfaces are in closer proximity (as at higher tracer concentrations), similar interactions that disrupt local solvation structure instead suppress the position-dependent solvent dynamics.

  6. Tuning structure and mobility of solvation shells surrounding tracer additives

    NASA Astrophysics Data System (ADS)

    Carmer, James; Jain, Avni; Bollinger, Jonathan A.; van Swol, Frank; Truskett, Thomas M.

    2015-03-01

    Molecular dynamics simulations and a stochastic Fokker-Planck equation based approach are used to illuminate how position-dependent solvent mobility near one or more tracer particle(s) is affected when tracer-solvent interactions are rationally modified to affect corresponding solvation structure. For tracers in a dense hard-sphere fluid, we compare two types of tracer-solvent interactions: (1) a hard-sphere-like interaction, and (2) a soft repulsion extending beyond the hard core designed via statistical mechanical theory to enhance tracer mobility at infinite dilution by suppressing coordination-shell structure [Carmer et al., Soft Matter 8, 4083-4089 (2012)]. For the latter case, we show that the mobility of surrounding solvent particles is also increased by addition of the soft repulsive interaction, which helps to rationalize the mechanism underlying the tracer's enhanced diffusivity. However, if multiple tracer surfaces are in closer proximity (as at higher tracer concentrations), similar interactions that disrupt local solvation structure instead suppress the position-dependent solvent dynamics.

  7. Control of cerium oxidation state through metal complex secondary structures

    DOE PAGES

    Levin, Jessica R.; Dorfner, Walter L.; Carroll, Patrick J.; Schelter, Eric J.

    2015-08-11

    A series of alkali metal cerium diphenylhydrazido complexes, Mx(py)y[Ce(PhNNPh)4], M = Li, Na, and K, x = 4 (Li and Na) or 5 (K), and y = 4 (Li), 8 (Na), or 7 (K), were synthesized to probe how a secondary coordination sphere would modulate electronic structures at a cerium cation. The resulting electronic structures of the heterobimetallic cerium diphenylhydrazido complexes were found to be strongly dependent on the identity of the alkali metal cations. When M = Li+ or Na+, the cerium(III) starting material was oxidized with concomitant reduction of 1,2-diphenylhydrazine to aniline. Reduction of 1,2-diphenylhydrazine was not observedmore » when M = K+, and the complex remained in the cerium(III) oxidation state. Oxidation of the cerium(III) diphenylhydrazido complex to the Ce(IV) diphenylhydrazido one was achieved through a simple cation exchange reaction of the alkali metals. As a result, UV-Vis spectroscopy, FTIR spectroscopy, electrochemistry, magnetic susceptibility, and DFT studies were used to probe the oxidation state and the electronic changes that occurred at the metal centre.« less

  8. Changes in secondary structure of gluten proteins due to emulsifiers

    NASA Astrophysics Data System (ADS)

    Gómez, Analía V.; Ferrer, Evelina G.; Añón, María C.; Puppo, María C.

    2013-02-01

    Changes in the secondary structure of gluten proteins due to emulsifiers were analyzed by Raman Spectroscopy. The protein folding induced by 0.25% SSL (Sodium Stearoyl Lactylate) (GS0.25, Gluten + 0.25% SSL) included an increase in α-helix conformation and a decrease in β-sheet, turns and random coil. The same behavior, although in a less degree, was observed for 0.5% gluten-DATEM (Diacetyl Tartaric Acid Esters of Monoglycerides) system. The low burial of Tryptophan residues to a more hydrophobic environment and the low percentage area of the C-H stretching band for GS0.25 (Gluten + 0.25% SSL), could be related to the increased in α-helix conformation. This behavior was also confirmed by changes in stretching vibrational modes of disulfide bridges (S-S) and the low exposure of Tyrosine residues. High levels of SSL (0.5% and 1.0%) and DATEM (1.0%) led to more disordered protein structures, with different gluten networks. SSL (1.0%) formed a more disordered and opened gluten matrix than DATEM, the last one being laminar and homogeneous.

  9. Control of cerium oxidation state through metal complex secondary structures

    SciTech Connect

    Levin, Jessica R.; Dorfner, Walter L.; Carroll, Patrick J.; Schelter, Eric J.

    2015-08-11

    A series of alkali metal cerium diphenylhydrazido complexes, Mx(py)y[Ce(PhNNPh)4], M = Li, Na, and K, x = 4 (Li and Na) or 5 (K), and y = 4 (Li), 8 (Na), or 7 (K), were synthesized to probe how a secondary coordination sphere would modulate electronic structures at a cerium cation. The resulting electronic structures of the heterobimetallic cerium diphenylhydrazido complexes were found to be strongly dependent on the identity of the alkali metal cations. When M = Li+ or Na+, the cerium(III) starting material was oxidized with concomitant reduction of 1,2-diphenylhydrazine to aniline. Reduction of 1,2-diphenylhydrazine was not observed when M = K+, and the complex remained in the cerium(III) oxidation state. Oxidation of the cerium(III) diphenylhydrazido complex to the Ce(IV) diphenylhydrazido one was achieved through a simple cation exchange reaction of the alkali metals. As a result, UV-Vis spectroscopy, FTIR spectroscopy, electrochemistry, magnetic susceptibility, and DFT studies were used to probe the oxidation state and the electronic changes that occurred at the metal centre.

  10. Sheath structure in plasma with two species of positive ions and secondary electrons

    NASA Astrophysics Data System (ADS)

    Xiao-Yun, Zhao; Nong, Xiang; Jing, Ou; De-Hui, Li; Bin-Bin, Lin

    2016-02-01

    The properties of a collisionless plasma sheath are investigated by using a fluid model in which two species of positive ions and secondary electrons are taken into account. It is shown that the positive ion speeds at the sheath edge increase with secondary electron emission (SEE) coefficient, and the sheath structure is affected by the interplay between the two species of positive ions and secondary electrons. The critical SEE coefficients and the sheath widths depend strongly on the positive ion charge number, mass and concentration in the cases with and without SEE. In addition, ion kinetic energy flux to the wall and the impact of positive ion species on secondary electron density at the sheath edge are also discussed. Project supported by the National Natural Science Foundation of China (Grant Nos. 11475220 and 11405208), the Program of Fusion Reactor Physics and Digital Tokamak with the CAS “One-Three-Five” Strategic Planning, the National ITER Program of China (Grant No. 2015GB101003), and the Higher Education Natural Science Research Project of Anhui Province, China (Grant No. 2015KJ009).

  11. Faxing Structures to the Moon: Freeform Additive Construction System (FACS)

    NASA Technical Reports Server (NTRS)

    Howe, A. Scott; Wilcox, Brian; McQuin, Christopher; Townsend, Julie; Rieber, Richard; Barmatz, Martin; Leichty, John

    2013-01-01

    Using the highly articulated All-Terrain Hex-Limbed Extra-Terrestrial Explorer (ATHLETE) robotic mobility system as a precision positioning tool, a variety of print head technologies can be used to 3D print large-scale in-situ structures on planetary surfaces such as the moon or Mars. In effect, in the same way CAD models can be printed in a 3D printer, large-scale structures such as walls, vaults, domes, berms, paving, trench walls, and other insitu derived elements can be FAXed to the planetary surface and built in advance of the arrival of crews, supplementing equipment and materials brought from earth. This paper discusses the ATHLETE system as a mobility / positioning platform, and presents several options for large-scale additive print head technologies, including tunable microwave "sinterator" approaches and in-situ concrete deposition. The paper also discusses potential applications, such as sintered-in-place habitat shells, radiation shielding, road paving, modular bricks, and prefabricated construction components.

  12. Energy-based RNA consensus secondary structure prediction in multiple sequence alignments.

    PubMed

    Washietl, Stefan; Bernhart, Stephan H; Kellis, Manolis

    2014-01-01

    Many biologically important RNA structures are conserved in evolution leading to characteristic mutational patterns. RNAalifold is a widely used program to predict consensus secondary structures in multiple alignments by combining evolutionary information with traditional energy-based RNA folding algorithms. Here we describe the theory and applications of the RNAalifold algorithm. Consensus secondary structure prediction not only leads to significantly more accurate structure models, but it also allows to study structural conservation of functional RNAs. PMID:24639158

  13. Energy-based RNA consensus secondary structure prediction in multiple sequence alignments.

    PubMed

    Washietl, Stefan; Bernhart, Stephan H; Kellis, Manolis

    2014-01-01

    Many biologically important RNA structures are conserved in evolution leading to characteristic mutational patterns. RNAalifold is a widely used program to predict consensus secondary structures in multiple alignments by combining evolutionary information with traditional energy-based RNA folding algorithms. Here we describe the theory and applications of the RNAalifold algorithm. Consensus secondary structure prediction not only leads to significantly more accurate structure models, but it also allows to study structural conservation of functional RNAs.

  14. Rtools: a web server for various secondary structural analyses on single RNA sequences.

    PubMed

    Hamada, Michiaki; Ono, Yukiteru; Kiryu, Hisanori; Sato, Kengo; Kato, Yuki; Fukunaga, Tsukasa; Mori, Ryota; Asai, Kiyoshi

    2016-07-01

    The secondary structures, as well as the nucleotide sequences, are the important features of RNA molecules to characterize their functions. According to the thermodynamic model, however, the probability of any secondary structure is very small. As a consequence, any tool to predict the secondary structures of RNAs has limited accuracy. On the other hand, there are a few tools to compensate the imperfect predictions by calculating and visualizing the secondary structural information from RNA sequences. It is desirable to obtain the rich information from those tools through a friendly interface. We implemented a web server of the tools to predict secondary structures and to calculate various structural features based on the energy models of secondary structures. By just giving an RNA sequence to the web server, the user can get the different types of solutions of the secondary structures, the marginal probabilities such as base-paring probabilities, loop probabilities and accessibilities of the local bases, the energy changes by arbitrary base mutations as well as the measures for validations of the predicted secondary structures. The web server is available at http://rtools.cbrc.jp, which integrates software tools, CentroidFold, CentroidHomfold, IPKnot, CapR, Raccess, Rchange and RintD. PMID:27131356

  15. Rtools: a web server for various secondary structural analyses on single RNA sequences

    PubMed Central

    Hamada, Michiaki; Ono, Yukiteru; Kiryu, Hisanori; Sato, Kengo; Kato, Yuki; Fukunaga, Tsukasa; Mori, Ryota; Asai, Kiyoshi

    2016-01-01

    The secondary structures, as well as the nucleotide sequences, are the important features of RNA molecules to characterize their functions. According to the thermodynamic model, however, the probability of any secondary structure is very small. As a consequence, any tool to predict the secondary structures of RNAs has limited accuracy. On the other hand, there are a few tools to compensate the imperfect predictions by calculating and visualizing the secondary structural information from RNA sequences. It is desirable to obtain the rich information from those tools through a friendly interface. We implemented a web server of the tools to predict secondary structures and to calculate various structural features based on the energy models of secondary structures. By just giving an RNA sequence to the web server, the user can get the different types of solutions of the secondary structures, the marginal probabilities such as base-paring probabilities, loop probabilities and accessibilities of the local bases, the energy changes by arbitrary base mutations as well as the measures for validations of the predicted secondary structures. The web server is available at http://rtools.cbrc.jp, which integrates software tools, CentroidFold, CentroidHomfold, IPKnot, CapR, Raccess, Rchange and RintD. PMID:27131356

  16. Comparative analysis of secondary structure of insect mitochondrial small subunit ribosomal RNA using maximum weighted matching.

    PubMed

    Page, R D

    2000-10-15

    Comparative analysis is the preferred method of inferring RNA secondary structure, but its use requires considerable expertise and manual effort. As the importance of secondary structure for accurate sequence alignment and phylogenetic analysis becomes increasingly realised, the need for secondary structure models for diverse taxonomic groups becomes more pressing. The number of available structures bears little relation to the relative diversity or importance of the different taxonomic groups. Insects, for example, comprise the largest group of animals and yet are very poorly represented in secondary structure databases. This paper explores the utility of maximum weighted matching (MWM) to help automate the process of comparative analysis by inferring secondary structure for insect mitochondrial small subunit (12S) rRNA sequences. By combining information on correlated changes in substitutions and helix dot plots, MWM can rapidly generate plausible models of secondary structure. These models can be further refined using standard comparative techniques. This paper presents a secondary structure model for insect 12S rRNA based on an alignment of 225 insect sequences and an alignment for 16 exemplar insect sequences. This alignment is used as a template for a web server that automatically generates secondary structures for insect sequences.

  17. Sucrose prevents protein fibrillation through compaction of the tertiary structure but hardly affects the secondary structure.

    PubMed

    Estrela, Nídia; Franquelim, Henri G; Lopes, Carlos; Tavares, Evandro; Macedo, Joana A; Christiansen, Gunna; Otzen, Daniel E; Melo, Eduardo P

    2015-11-01

    Amyloid fibers, implicated in a wide range of diseases, are formed when proteins misfold and stick together in long rope-like structures. As a natural mechanism, osmolytes can be used to modulate protein aggregation pathways with no interference with other cellular functions. The osmolyte sucrose delays fibrillation of the ribosomal protein S6 leading to softer and less shaped-defined fibrils. The molecular mechanism used by sucrose to delay S6 fibrillation was studied based on the two-state unfolding kinetics of the secondary and tertiary structures. It was concluded that the delay in S6 fibrillation results from stabilization and compaction of the slightly expanded tertiary native structure formed under fibrillation conditions. Interestingly, this compaction extends to almost all S6 tertiary structure but hardly affects its secondary structure. The part of the S6 tertiary structure that suffered more compaction by sucrose is known to be the first part to unfold, indicating that the native S6 has entered the unfolding pathway under fibrillation conditions.

  18. Self-Renewing Secondary Schools: The Relationship between Structural and Cultural Change.

    ERIC Educational Resources Information Center

    Hannay, Lynne M.; Ross, John A.

    This paper explores the deep-reform efforts of 9 secondary schools over a 3-year period. The reforms occurred in an Ontario, Canada, school district that empowered their secondary schools to develop site-specific organizational structures that deviated from the traditional subject, departmental structure. The sample for the study included all…

  19. CSI 3.0: a web server for identifying secondary and super-secondary structure in proteins using NMR chemical shifts.

    PubMed

    Hafsa, Noor E; Arndt, David; Wishart, David S

    2015-07-01

    The Chemical Shift Index or CSI 3.0 (http://csi3.wishartlab.com) is a web server designed to accurately identify the location of secondary and super-secondary structures in protein chains using only nuclear magnetic resonance (NMR) backbone chemical shifts and their corresponding protein sequence data. Unlike earlier versions of CSI, which only identified three types of secondary structure (helix, β-strand and coil), CSI 3.0 now identifies total of 11 types of secondary and super-secondary structures, including helices, β-strands, coil regions, five common β-turns (type I, II, I', II' and VIII), β hairpins as well as interior and edge β-strands. CSI 3.0 accepts experimental NMR chemical shift data in multiple formats (NMR Star 2.1, NMR Star 3.1 and SHIFTY) and generates colorful CSI plots (bar graphs) and secondary/super-secondary structure assignments. The output can be readily used as constraints for structure determination and refinement or the images may be used for presentations and publications. CSI 3.0 uses a pipeline of several well-tested, previously published programs to identify the secondary and super-secondary structures in protein chains. Comparisons with secondary and super-secondary structure assignments made via standard coordinate analysis programs such as DSSP, STRIDE and VADAR on high-resolution protein structures solved by X-ray and NMR show >90% agreement between those made with CSI 3.0. PMID:25979265

  20. CSI 3.0: a web server for identifying secondary and super-secondary structure in proteins using NMR chemical shifts.

    PubMed

    Hafsa, Noor E; Arndt, David; Wishart, David S

    2015-07-01

    The Chemical Shift Index or CSI 3.0 (http://csi3.wishartlab.com) is a web server designed to accurately identify the location of secondary and super-secondary structures in protein chains using only nuclear magnetic resonance (NMR) backbone chemical shifts and their corresponding protein sequence data. Unlike earlier versions of CSI, which only identified three types of secondary structure (helix, β-strand and coil), CSI 3.0 now identifies total of 11 types of secondary and super-secondary structures, including helices, β-strands, coil regions, five common β-turns (type I, II, I', II' and VIII), β hairpins as well as interior and edge β-strands. CSI 3.0 accepts experimental NMR chemical shift data in multiple formats (NMR Star 2.1, NMR Star 3.1 and SHIFTY) and generates colorful CSI plots (bar graphs) and secondary/super-secondary structure assignments. The output can be readily used as constraints for structure determination and refinement or the images may be used for presentations and publications. CSI 3.0 uses a pipeline of several well-tested, previously published programs to identify the secondary and super-secondary structures in protein chains. Comparisons with secondary and super-secondary structure assignments made via standard coordinate analysis programs such as DSSP, STRIDE and VADAR on high-resolution protein structures solved by X-ray and NMR show >90% agreement between those made with CSI 3.0.

  1. Transcriptome-wide interrogation of RNA secondary structure in living cells with icSHAPE

    PubMed Central

    Flynn, Ryan A; Zhang, Qiangfeng Cliff; Spitale, Robert C; Lee, Byron; Mumbach, Maxwell R; Chang, Howard Y

    2016-01-01

    icSHAPE (in vivo click selective 2-hydroxyl acylation and profiling experiment) captures RNA secondary structure at a transcriptome-wide level by measuring nucleotide flexibility at base resolution. Living cells are treated with the icSHAPE chemical NAI-N3 followed by selective chemical enrichment of NAI-N3–modified RNA, which provides an improved signal-to-noise ratio compared with similar methods leveraging deep sequencing. Purified RNA is then reverse-transcribed to produce cDNA, with SHAPE-modified bases leading to truncated cDNA. After deep sequencing of cDNA, computational analysis yields flexibility scores for every base across the starting RNA population. The entire experimental procedure can be completed in ~5 d, and the sequencing and bioinformatics data analysis take an additional 4–5 d with no extensive computational skills required. Comparing in vivo and in vitro icSHAPE measurements can reveal in vivo RNA-binding protein imprints or facilitate the dissection of RNA post-transcriptional modifications. icSHAPE reactivities can additionally be used to constrain and improve RNA secondary structure prediction models. PMID:26766114

  2. Transcriptome-wide interrogation of RNA secondary structure in living cells with icSHAPE.

    PubMed

    Flynn, Ryan A; Zhang, Qiangfeng Cliff; Spitale, Robert C; Lee, Byron; Mumbach, Maxwell R; Chang, Howard Y

    2016-02-01

    icSHAPE (in vivo click selective 2-hydroxyl acylation and profiling experiment) captures RNA secondary structure at a transcriptome-wide level by measuring nucleotide flexibility at base resolution. Living cells are treated with the icSHAPE chemical NAI-N3 followed by selective chemical enrichment of NAI-N3-modified RNA, which provides an improved signal-to-noise ratio compared with similar methods leveraging deep sequencing. Purified RNA is then reverse-transcribed to produce cDNA, with SHAPE-modified bases leading to truncated cDNA. After deep sequencing of cDNA, computational analysis yields flexibility scores for every base across the starting RNA population. The entire experimental procedure can be completed in ∼5 d, and the sequencing and bioinformatics data analysis take an additional 4-5 d with no extensive computational skills required. Comparing in vivo and in vitro icSHAPE measurements can reveal in vivo RNA-binding protein imprints or facilitate the dissection of RNA post-transcriptional modifications. icSHAPE reactivities can additionally be used to constrain and improve RNA secondary structure prediction models.

  3. Effective stiffness and formation of secondary structures in a protein-like model

    NASA Astrophysics Data System (ADS)

    Škrbić, Tatjana; Hoang, Trinh X.; Giacometti, Achille

    2016-08-01

    We use Wang-Landau and replica exchange techniques to study the effect of an increasing stiffness on the formation of secondary structures in protein-like systems. Two possible models are considered. In both models, a polymer chain is formed by tethered beads where non-consecutive backbone beads attract each other via a square-well potential representing the tendency of the chain to fold. In addition, smaller hard spheres are attached to each non-terminal backbone bead along the direction normal to the chain to mimic the steric hindrance of side chains in real proteins. The two models, however, differ in the way bending rigidity is enforced. In the first model, partial overlap between consecutive beads is allowed. This reduces the possible bending angle between consecutive bonds thus producing an effective entropic stiffness that competes with a short-range attraction, and leads to the formation of secondary structures characteristic of proteins. We discuss the low-temperature phase diagram as a function of increasing interpenetration and find a transition from a planar, beta-like structure, to helical shape. In the second model, an energetic stiffness is explicitly introduced by imposing an infinitely large energy penalty for bending above a critical angle between consecutive bonds, and no penalty below it. The low-temperature phase of this model does not show any sign of protein-like secondary structures. At intermediate temperatures, however, where the chain is still in the coil conformation but stiffness is significant, we find the two models to predict a quite similar dependence of the persistence length as a function of the stiffness. This behaviour is rationalized in terms of a simple geometrical mapping between the two models. Finally, we discuss the effect of shrinking side chains to zero and find the above mapping to still hold true.

  4. Effective stiffness and formation of secondary structures in a protein-like model.

    PubMed

    Škrbić, Tatjana; Hoang, Trinh X; Giacometti, Achille

    2016-08-28

    We use Wang-Landau and replica exchange techniques to study the effect of an increasing stiffness on the formation of secondary structures in protein-like systems. Two possible models are considered. In both models, a polymer chain is formed by tethered beads where non-consecutive backbone beads attract each other via a square-well potential representing the tendency of the chain to fold. In addition, smaller hard spheres are attached to each non-terminal backbone bead along the direction normal to the chain to mimic the steric hindrance of side chains in real proteins. The two models, however, differ in the way bending rigidity is enforced. In the first model, partial overlap between consecutive beads is allowed. This reduces the possible bending angle between consecutive bonds thus producing an effective entropic stiffness that competes with a short-range attraction, and leads to the formation of secondary structures characteristic of proteins. We discuss the low-temperature phase diagram as a function of increasing interpenetration and find a transition from a planar, beta-like structure, to helical shape. In the second model, an energetic stiffness is explicitly introduced by imposing an infinitely large energy penalty for bending above a critical angle between consecutive bonds, and no penalty below it. The low-temperature phase of this model does not show any sign of protein-like secondary structures. At intermediate temperatures, however, where the chain is still in the coil conformation but stiffness is significant, we find the two models to predict a quite similar dependence of the persistence length as a function of the stiffness. This behaviour is rationalized in terms of a simple geometrical mapping between the two models. Finally, we discuss the effect of shrinking side chains to zero and find the above mapping to still hold true. PMID:27586943

  5. ExSer: A standalone tool to mine protein data bank (PDB) for secondary structural elements

    PubMed Central

    Vignesh, Dhandapani; Daniel, Paul; Raja, Natarajan; Balasubramanian, Ponnusamy; Arul, Loganathan

    2010-01-01

    Detailed structural analysis of protein necessitates investigation at primary, secondary and tertiary levels, respectively. Insight into protein secondary structures pave way for understanding the type of secondary structural elements involved (α-helices, β-strands etc.), the amino acid sequence that encode the secondary structural elements, number of residues, length and, percentage composition of the respective elements in the protein. Here we present a standalone tool entitled “ExSer” which facilitate an automated extraction of the amino acid sequence that encode for the secondary structural regions of a protein from the protein data bank (PDB) file. Availability ExSer is freely downloadable from http://code.google.com/p/tool-exser/ PMID:20975886

  6. Evaluation of the information content of RNA structure mapping data for secondary structure prediction.

    PubMed

    Quarrier, Scott; Martin, Joshua S; Davis-Neulander, Lauren; Beauregard, Arthur; Laederach, Alain

    2010-06-01

    Structure mapping experiments (using probes such as dimethyl sulfate [DMS], kethoxal, and T1 and V1 RNases) are used to determine the secondary structures of RNA molecules. The process is iterative, combining the results of several probes with constrained minimum free-energy calculations to produce a model of the structure. We aim to evaluate whether particular probes provide more structural information, and specifically, how noise in the data affects the predictions. Our approach involves generating "decoy" RNA structures (using the sFold Boltzmann sampling procedure) and evaluating whether we are able to identify the correct structure from this ensemble of structures. We show that with perfect information, we are always able to identify the optimal structure for five RNAs of known structure. We then collected orthogonal structure mapping data (DMS and RNase T1 digest) under several solution conditions using our high-throughput capillary automated footprinting analysis (CAFA) technique on two group I introns of known structure. Analysis of these data reveals the error rates in the data under optimal (low salt) and suboptimal solution conditions (high MgCl(2)). We show that despite these errors, our computational approach is less sensitive to experimental noise than traditional constraint-based structure prediction algorithms. Finally, we propose a novel approach for visualizing the interaction of chemical and enzymatic mapping data with RNA structure. We project the data onto the first two dimensions of a multidimensional scaling of the sFold-generated decoy structures. We are able to directly visualize the structural information content of structure mapping data and reconcile multiple data sets.

  7. Evaluation of the information content of RNA structure mapping data for secondary structure prediction.

    PubMed

    Quarrier, Scott; Martin, Joshua S; Davis-Neulander, Lauren; Beauregard, Arthur; Laederach, Alain

    2010-06-01

    Structure mapping experiments (using probes such as dimethyl sulfate [DMS], kethoxal, and T1 and V1 RNases) are used to determine the secondary structures of RNA molecules. The process is iterative, combining the results of several probes with constrained minimum free-energy calculations to produce a model of the structure. We aim to evaluate whether particular probes provide more structural information, and specifically, how noise in the data affects the predictions. Our approach involves generating "decoy" RNA structures (using the sFold Boltzmann sampling procedure) and evaluating whether we are able to identify the correct structure from this ensemble of structures. We show that with perfect information, we are always able to identify the optimal structure for five RNAs of known structure. We then collected orthogonal structure mapping data (DMS and RNase T1 digest) under several solution conditions using our high-throughput capillary automated footprinting analysis (CAFA) technique on two group I introns of known structure. Analysis of these data reveals the error rates in the data under optimal (low salt) and suboptimal solution conditions (high MgCl(2)). We show that despite these errors, our computational approach is less sensitive to experimental noise than traditional constraint-based structure prediction algorithms. Finally, we propose a novel approach for visualizing the interaction of chemical and enzymatic mapping data with RNA structure. We project the data onto the first two dimensions of a multidimensional scaling of the sFold-generated decoy structures. We are able to directly visualize the structural information content of structure mapping data and reconcile multiple data sets. PMID:20413617

  8. Pfold: RNA secondary structure prediction using stochastic context-free grammars.

    PubMed

    Knudsen, Bjarne; Hein, Jotun

    2003-07-01

    RNA secondary structures are important in many biological processes and efficient structure prediction can give vital directions for experimental investigations. Many available programs for RNA secondary structure prediction only use a single sequence at a time. This may be sufficient in some applications, but often it is possible to obtain related RNA sequences with conserved secondary structure. These should be included in structural analyses to give improved results. This work presents a practical way of predicting RNA secondary structure that is especially useful when related sequences can be obtained. The method improves a previous algorithm based on an explicit evolutionary model and a probabilistic model of structures. Predictions can be done on a web server at http://www.daimi.au.dk/~compbio/pfold.

  9. Deciphering the shape and deformation of secondary structures through local conformation analysis

    PubMed Central

    2011-01-01

    Background Protein deformation has been extensively analysed through global methods based on RMSD, torsion angles and Principal Components Analysis calculations. Here we use a local approach, able to distinguish among the different backbone conformations within loops, α-helices and β-strands, to address the question of secondary structures' shape variation within proteins and deformation at interface upon complexation. Results Using a structural alphabet, we translated the 3 D structures of large sets of protein-protein complexes into sequences of structural letters. The shape of the secondary structures can be assessed by the structural letters that modeled them in the structural sequences. The distribution analysis of the structural letters in the three protein compartments (surface, core and interface) reveals that secondary structures tend to adopt preferential conformations that differ among the compartments. The local description of secondary structures highlights that curved conformations are preferred on the surface while straight ones are preferred in the core. Interfaces display a mixture of local conformations either preferred in core or surface. The analysis of the structural letters transition occurring between protein-bound and unbound conformations shows that the deformation of secondary structure is tightly linked to the compartment preference of the local conformations. Conclusion The conformation of secondary structures can be further analysed and detailed thanks to a structural alphabet which allows a better description of protein surface, core and interface in terms of secondary structures' shape and deformation. Induced-fit modification tendencies described here should be valuable information to identify and characterize regions under strong structural constraints for functional reasons. PMID:21284872

  10. Ambient modal identification of a primary-secondary structure by Fast Bayesian FFT method

    NASA Astrophysics Data System (ADS)

    Au, Siu-Kui; Zhang, Feng-Liang

    2012-04-01

    The Mong Man Wai Building is a seven-storied reinforced concrete structure situated on the campus of the City University of Hong Kong. On its roof a two-storied steel frame has been recently constructed to host a new wind tunnel laboratory. The roof frame and the main building form a primary-secondary structure. The dynamic characteristics of the resulting system are of interest from a structural dynamics point of view. This paper presents work on modal identification of the structure using ambient vibration measurement. An array of tri-axial acceleration data has been obtained using a number of setups to cover all locations of interest with a limited number of sensors. Modal identification is performed using a recently developed Fast Bayesian FFT method. In addition to the most probable modal properties, their posterior uncertainties can also be assessed using the method. The posterior uncertainty of mode shape is assessed by the expected value of the Modal Assurance Criteria (MAC) of the most probable mode shape with a random mode shape consistent with the posterior distribution. The mode shapes of the overall structural system are obtained by assembling those from individual setups using a recently developed least-square method. The identification results reveal a number of interesting features about the structural system and provide important information defining the baseline modal properties of the building. Practical interpretation of the statistics of modal parameters calculated from frequentist and Bayesian context is also discussed.

  11. Quantifying the energetic interplay of RNA tertiary and secondary structure interactions.

    PubMed Central

    Silverman, S K; Zheng, M; Wu, M; Tinoco, I; Cech, T R

    1999-01-01

    To understand the RNA-folding problem, we must know the extent to which RNA structure formation is hierarchical (tertiary folding of preformed secondary structure). Recently, nuclear magnetic resonance (NMR) spectroscopy was used to show that Mg2+-dependent tertiary interactions force secondary structure rearrangement in the 56-nt tP5abc RNA, a truncated subdomain of the Tetrahymena group I intron. Here we combine mutagenesis with folding computations, nondenaturing gel electrophoresis, high-resolution NMR spectroscopy, and chemical-modification experiments to probe further the energetic interplay of tertiary and secondary interactions in tP5abc. Point mutations predicted to destabilize the secondary structure of folded tP5abc greatly disrupt its Mg2+-dependent folding, as monitored by nondenaturing gels. Imino proton assignments and sequential NOE walks of the two-dimensional NMR spectrum of one of the tP5abc mutants confirm the predicted secondary structure, which does not change in the presence of Mg2+. In contrast to these data on tP5abc, the same point mutations in the context of the P4-P6 domain (of which P5abc is a subdomain) shift the Mg2+ dependence of P4-P6 folding only moderately, and dimethyl sulfate (DMS) modification experiments demonstrate that Mg2+ does cause secondary structure rearrangement of the P4-P6 mutants' P5abc subdomains. Our data provide experimental support for two simple conclusions: (1) Even single point mutations at bases involved only in secondary structure can be enough to tip the balance between RNA tertiary and secondary interactions. (2) Domain context must be considered in evaluating the relative importance of tertiary and secondary contributions. This tertiary/secondary interplay is likely relevant to the folding of many large RNA and to bimolecular snRNA-snRNA and snRNA-intron RNA interactions. PMID:10606276

  12. Addition of in-vitro generated endothelial microparticles to von-Willebrand plasma improves primary and secondary hemostasis.

    PubMed

    Trummer, Arne; Werwitzke, Sonja; Wermes, Cornelia; Ganser, Arnold; Birschmann, Ingvild; Budde, Ulrich; Tiede, Andreas

    2014-03-01

    Increased endothelial microparticles (EMP) as markers for endothelial activation have been associated with worse outcomes in clinical prothrombotic situations. The procoagulant properties of EMP can be attributed to the expression of phospholipids, tissue factor and von-Willebrand factor on their surface. We therefore investigated whether addition of in-vitro generated EMP modifies hemostasis in plasma from patients with severe von-Willebrand disease (VWD). A large EMP pool was obtained from stimulated endothelial cell lines and EMP concentration was quantified by flow cytometry. The influence of EMP on primary and secondary hemostasis in VWD plasma was assessed using ristocetin-induced platelet aggregation (RIPA) and thrombin generation in a calibrated automated thrombogram (CAT), respectively. After addition of EMP, there was a significant increase in the maximal aggregation level in RIPA as well as a significant shortening of lag time and time-to-peak in CAT in comparison to control buffer. In summary, in vitro-generated EMP have the potential to improve hemostasis in severe VWD plasma and these results warrant further clinical reseach regarding their contribution to the clinical bleeding phenotype as well as their potential to improve replacement therapy.

  13. Prediction of RNA secondary structures: from theory to models and real molecules

    NASA Astrophysics Data System (ADS)

    Schuster, Peter

    2006-05-01

    empirical parameters can be determined and by principal deficiencies, for example by the lack of energy contributions resulting from tertiary interactions. In addition, native structures may be determined by folding kinetics rather than by thermodynamics. We address the first problem by considering base pair probabilities or base pairing entropies, which are derived from the partition function of conformations. A high base pair probability corresponding to a low pairing entropy is taken as an indicator of a high reliability of prediction. Pseudoknots are discussed as an example of a tertiary interaction that is highly important for RNA function. Moreover, pseudoknot formation is readily incorporated into structure prediction algorithms. Some examples of experimental data on RNA secondary structures that are readily explained using the landscape concept are presented. They deal with (i) properties of RNA molecules with random sequences, (ii) RNA molecules from restricted alphabets, (iii) existence of neutral networks, (iv) shape space covering, (v) riboswitches and (vi) evolution of non-coding RNAs as an example of evolution restricted to neutral networks.

  14. Improving the prediction of secondary structure of 'TIM-barrel' enzymes.

    PubMed

    Niermann, T; Kirschner, K

    1991-02-01

    The information contained in aligned sets of homologous protein sequences should improve the score of secondary structure prediction. Seven different enzymes having the (beta/alpha)8 or TIM-barrel fold were used to optimize the prediction with regard to this class of enzymes. The alpha-helix, beta-strand and loop propensities of the Garnier-Osguthorpe-Robson method were averaged at aligned residue positions, leading to a significant improvement over the average score obtained from single sequences. The increased accuracy correlates with the average sequence variability of the aligned set. Further improvements were obtained by using the following averaged properties as weights for the averaged state propensities: amphipathic moment and alpha-helix; hydropathy and beta-strand; chain flexibility and loop. The clustering of conserved residues at the C-terminal ends of the beta-strands was used as an additional positive weight for beta-strand propensity and increased the prediction of otherwise unpredicted beta-strands decisively. The automatic weighted prediction method identifies greater than 95% of the secondary structure elements of the set of seven TIM-barrel enzymes.

  15. A Tool Preference Choice Method for RNA Secondary Structure Prediction by SVM with Statistical Tests

    PubMed Central

    Hor, Chiou-Yi; Yang, Chang-Biau; Chang, Chia-Hung; Tseng, Chiou-Ting; Chen, Hung-Hsin

    2013-01-01

    The Prediction of RNA secondary structures has drawn much attention from both biologists and computer scientists. Many useful tools have been developed for this purpose. These tools have their individual strengths and weaknesses. As a result, based on support vector machines (SVM), we propose a tool choice method which integrates three prediction tools: pknotsRG, RNAStructure, and NUPACK. Our method first extracts features from the target RNA sequence, and adopts two information-theoretic feature selection methods for feature ranking. We propose a method to combine feature selection and classifier fusion in an incremental manner. Our test data set contains 720 RNA sequences, where 225 pseudoknotted RNA sequences are obtained from PseudoBase, and 495 nested RNA sequences are obtained from RNA SSTRAND. The method serves as a preprocessing way in analyzing RNA sequences before the RNA secondary structure prediction tools are employed. In addition, the performance of various configurations is subject to statistical tests to examine their significance. The best base-pair accuracy achieved is 75.5%, which is obtained by the proposed incremental method, and is significantly higher than 68.8%, which is associated with the best predictor, pknotsRG. PMID:23641141

  16. RNA-protein interactions and secondary structures of cowpea chlorotic mottle virus for in vitro assembly.

    PubMed

    Verduin, B J; Prescott, B; Thomas, G J

    1984-09-11

    Laser Raman spectroscopy of the cowpea chlorotic mottle virus (CCMV) in native (pH 5.0) and partially swollen (pH 7.5) states reveals the presence of small percentages of protonated adenine (less than 15%) and cytosine (less than 7%) bases in the encapsidated RNA molecule of the native virion. The protonated bases are titrated with pH-induced swelling of the virus. Titration of putative COOH groups of aspartic and glutamic side chains of the virion subunit cannot be detected over the same pH range, which suggests that carboxyl anions (CO-2) and protonated bases are both available at pH 5 to stabilize the ribonucleoprotein particles by electrostatic interactions. The highly (95%) ordered secondary structure of encapsidated RNA may undergo a small additional increase (less than 3%) in ordered structure with release from the virion, suggesting at most a marginal structure-distorting influence from protein contacts in the native particle. The Raman spectra of the virion are also compared by difference spectroscopy with spectra of capsids (empty shells devoid of RNA), subunit dimers, and protein-free RNA. The results indicate that the subunit structure is altered by the release of RNA from the virion, as well as by the swelling of the virion. Amino acid residues and protein secondary structures that are affected in these in vitro assembly and disassembly processes are identified from their characteristic Raman lines. Two classes of cysteinyl SH groups, solvent exposed and solvent protected, are revealed for the capsid and virion subunit.(ABSTRACT TRUNCATED AT 250 WORDS)

  17. Mechanical properties of amyloid-like fibrils defined by secondary structures

    NASA Astrophysics Data System (ADS)

    Bortolini, C.; Jones, N. C.; Hoffmann, S. V.; Wang, C.; Besenbacher, F.; Dong, M.

    2015-04-01

    are extensively studied - among these parameters, the secondary structures and the pH have been revealed to be crucial, since a variation in pH changes the fibril morphology and net chirality during protein aggregation. It is important to quantify the mechanical properties of these fibrils in order to help the design of effective strategies for treating diseases related to the presence of amyloid fibrils. In this work, we show that by changing pH the mechanical properties of amyloid-like fibrils vary as well. In particular, we reveal that these mechanical properties are strongly related to the content of secondary structures. We analysed and estimated the Young's modulus (E) by comparing the persistence length (Lp) - measured from the observation of TEM images by using statistical mechanics arguments - with the mechanical information provided by peak force quantitative nanomechanical property mapping (PF-QNM). The secondary structure content and the chirality are investigated by means of synchrotron radiation circular dichroism (SR-CD). Results arising from this study could be fruitfully used as a protocol to investigate other medical or engineering relevant peptide fibrils. Electronic supplementary information (ESI) available: A molecular model for the peptide studied and the charge chart associated to it. In addition, an AFM image of pH 4 fibrils is presented. See DOI: 10.1039/c4nr05109b

  18. Teachers' Personal Agency: Making Sense of Slope through Additive Structures

    ERIC Educational Resources Information Center

    Walter, Janet G.; Gerson, Hope

    2007-01-01

    In the context of a three-year professional development program in mathematics, practicing elementary teachers persistently engaged in collaborative inquiry and reflection to build connected meanings for slope. One teacher invented a compelling representation for slope as a process of repeated addition, using Cuisenaire rods, based on teachers'…

  19. Determination of Secondary School Students' Cognitive Structure, and Misconception in Ecological Concepts through Word Association Test

    ERIC Educational Resources Information Center

    Yücel, Elif Özata; Özkan, Mulis

    2015-01-01

    In this study, we determined cognitive structures and misconceptions about basic ecological concepts by using "word association" tests on secondary school students, age between 12-14 years. Eighty-nine students participated in this study. Before WAT was generated, basic ecological concepts that take place in the secondary science…

  20. R2R - software to speed the depiction of aesthetic consensus RNA secondary structures

    PubMed Central

    2011-01-01

    Background With continuing identification of novel structured noncoding RNAs, there is an increasing need to create schematic diagrams showing the consensus features of these molecules. RNA structural diagrams are typically made either with general-purpose drawing programs like Adobe Illustrator, or with automated or interactive programs specific to RNA. Unfortunately, the use of applications like Illustrator is extremely time consuming, while existing RNA-specific programs produce figures that are useful, but usually not of the same aesthetic quality as those produced at great cost in Illustrator. Additionally, most existing RNA-specific applications are designed for drawing single RNA molecules, not consensus diagrams. Results We created R2R, a computer program that facilitates the generation of aesthetic and readable drawings of RNA consensus diagrams in a fraction of the time required with general-purpose drawing programs. Since the inference of a consensus RNA structure typically requires a multiple-sequence alignment, the R2R user annotates the alignment with commands directing the layout and annotation of the RNA. R2R creates SVG or PDF output that can be imported into Adobe Illustrator, Inkscape or CorelDRAW. R2R can be used to create consensus sequence and secondary structure models for novel RNA structures or to revise models when new representatives for known RNA classes become available. Although R2R does not currently have a graphical user interface, it has proven useful in our efforts to create 100 schematic models of distinct noncoding RNA classes. Conclusions R2R makes it possible to obtain high-quality drawings of the consensus sequence and structural models of many diverse RNA structures with a more practical amount of effort. R2R software is available at http://breaker.research.yale.edu/R2R and as an Additional file. PMID:21205310

  1. Putative secondary structures of unusually long strepsipteran SSU rRNAs and its phylogenetic implications.

    PubMed

    Choe, C P; Hwang, U W; Kim, W

    1999-04-30

    We constructed the putative secondary structures of the small subunit rRNAs (SSU rRNA) from three strepsipteran insects. The primary sequences of the strepsipteran SSU rRNAs are unusually long due to unique and long insertions. In spite of these insertions, the basic shapes of their secondary structures are well maintained as shown in those of other eukaryotes, because these insertions appear mainly in the variable regions. The secondary structures for the V1, V3, V5, V8, and V9 regions are well conserved, even though the primary structures of V1, V5, and V8 regions are quite variable. However, the predicted secondary structures for the V2, V4, and V7 regions are quite different from those of other insects. In the V4 and V7 regions, helices specific to the Strepsiptera exist. These helices have not been reported in other organisms so far. Similarly, four eukaryotic specific helices (E8-1, E10-2, E23-4 and E45-1) not reported in insects exist in the V2, V4, and V8 regions. These helices are formed by the inserted sequences. The secondary structures of the expanded segments of the strepsipteran SSU rRNA were applied to infer the phylogenetic position of Strepsiptera, one of the most enigmatic problems in insect phylogeny. Only the secondary structure of the V7 region showed the weak Strepsiptera/Diptera sister-group relationship. PMID:10340475

  2. Nuclear rRNA transcript processing versus internal transcribed spacer secondary structure.

    PubMed

    Coleman, Annette W

    2015-03-01

    rRNA is one of the few universal features of life, making it uniquely suited to assess phylogenetic relationships. The processing of the initial polycistronic rRNA transcript is also a conserved process, involving numerous cleavage events and the generation of secondary structures. The secondary structure of the internal transcribed spacer (ITS) regions of nuclear rRNA transcripts are well known for a wide variety of eukaryotes and have been used to aid in the alignment of these sequences for phylogenetic comparisons. By contrast, study of the processing of the initial rRNA transcripts has been largely limited to yeast, mice, rats, and humans. Here I examine the known cleavage sites in the two ITS regions and their positions relative to the secondary structure. A better understanding of the conservation of secondary structures and cleavage sites within the ITS regions will improve evolutionary inferences based on these sequences.

  3. Conductivity and structure of bilinear organic addition compounds

    PubMed Central

    Phillips, J. C.

    1976-01-01

    The relationship between crystal structures and metallic conductivities of linear organic materials such as tetrathiafulvalene-tetracyanoquinodimethane is explained in terms of strong lateral elastic interactions between chains. A microdomain model is presented in which at high temperatures there are, in general, two coexisting phases on each stacked molecular chain. The ordering of (in general, four) phases on two interacting chains leads to a variety of phase transitions at low temperatures. By examining temperature-dependent electrical conductivities and magnetic susceptibilities one can establish the character of each such transition. PMID:16592359

  4. Characterization and comparative study of coal combustion residues from a primary and additional flue gas secondary desulfurization process

    SciTech Connect

    Gomes, S.; Francois, M.; Evrard, O.; Pellissier, C.

    1998-11-01

    An extensive characterization and comparative study was done on two flue gas desulfurization (FGD) residues derived from the same coal. LR residues (originated from Loire/Rhone in the south of Lyon, France) are obtained after a primary desulfurization process (SO{sub 2} is trapped by reaction with CaO at a temperature of about 1100 C), and LM residues (originating from La Maxe, near Metz in the east of France) are obtained after an additional secondary desulfurization process (SO{sub 2} is removed further by reaction with Ca(OH){sub 2} at a temperature of about 120 C). Various and complementary investigation methods were used to determine their chemical, physical, and mineralogical properties: x-ray fluorescence and diffraction, scanning electron microscopy, differential scanning calorimetry, thermogravimetry analysis, granulometric distribution, pycnometric density, BET specific surface area and pH, conductivity measurements, and chemical analysis of their insoluble fraction. The FGD residues contain basically two main components: a silico-aluminous fly ash part and calcic FGD phases. In the LR residues the two components can be considered as independent, whereas they are linked in the LM residues because chemical reactions have occurred, leading to the formation of silico-calcic gel CSH, hydrated aluminate AFm, and AFt phases.

  5. Sheath structure transition controlled by secondary electron emission

    NASA Astrophysics Data System (ADS)

    Schweigert, I. V.; Langendorf, S. J.; Walker, M. L. R.; Keidar, M.

    2015-04-01

    In particle-in-cell Monte Carlo collision (PIC MCC) simulations and in an experiment we study sheath formation over an emissive floating Al2O3 plate in a direct current discharge plasma at argon gas pressure 10-4 Torr. The discharge glow is maintained by the beam electrons emitted from a negatively biased hot cathode. We observe three types of sheaths near the floating emissive plate and the transition between them is driven by changing the negative bias. The Debye sheath appears at lower voltages, when secondary electron emission is negligible. With increasing applied voltage, secondary electron emission switches on and a first transition to a new sheath type, beam electron emission (BEE), takes place. For the first time we find this specific regime of sheath operation near the floating emissive surface. In this regime, the potential drop over the plate sheath is about four times larger than the temperature of plasma electrons. The virtual cathode appears near the emissive plate and its modification helps to maintain the BEE regime within some voltage range. Further increase of the applied voltage U initiates the second smooth transition to the plasma electron emission sheath regime and the ratio Δφs/Te tends to unity with increasing U. The oscillatory behavior of the emissive sheath is analyzed in PIC MCC simulations. A plasmoid of slow electrons is formed near the plate and transported to the bulk plasma periodically with a frequency of about 25 kHz.

  6. Peptide secondary structure modulates single-walled carbon nanotube fluorescence as a chaperone sensor for nitroaromatics

    PubMed Central

    Heller, Daniel A.; Pratt, George W.; Zhang, Jingqing; Nair, Nitish; Hansborough, Adam J.; Boghossian, Ardemis A.; Reuel, Nigel F.; Barone, Paul W.; Strano, Michael S.

    2011-01-01

    A class of peptides from the bombolitin family, not previously identified for nitroaromatic recognition, allows near-infrared fluorescent single-walled carbon nanotubes to transduce specific changes in their conformation. In response to the binding of specific nitroaromatic species, such peptide–nanotube complexes form a virtual “chaperone sensor,” which reports modulation of the peptide secondary structure via changes in single-walled carbon nanotubes, near-infrared photoluminescence. A split-channel microscope constructed to image quantized spectral wavelength shifts in real time, in response to nitroaromatic adsorption, results in the first single-nanotube imaging of solvatochromic events. The described indirect detection mechanism, as well as an additional exciton quenching-based optical nitroaromatic detection method, illustrate that functionalization of the carbon nanotube surface can result in completely unique sites for recognition, resolvable at the single-molecule level. PMID:21555544

  7. Internal transcribed spacer 1 secondary structure analysis reveals a common core throughout the anaerobic fungi (Neocallimastigomycota).

    PubMed

    Koetschan, Christian; Kittelmann, Sandra; Lu, Jingli; Al-Halbouni, Djamila; Jarvis, Graeme N; Müller, Tobias; Wolf, Matthias; Janssen, Peter H

    2014-01-01

    The internal transcribed spacer (ITS) is a popular barcode marker for fungi and in particular the ITS1 has been widely used for the anaerobic fungi (phylum Neocallimastigomycota). A good number of validated reference sequences of isolates as well as a large number of environmental sequences are available in public databases. Its highly variable nature predisposes the ITS1 for low level phylogenetics; however, it complicates the establishment of reproducible alignments and the reconstruction of stable phylogenetic trees at higher taxonomic levels (genus and above). Here, we overcame these problems by proposing a common core secondary structure of the ITS1 of the anaerobic fungi employing a Hidden Markov Model-based ITS1 sequence annotation and a helix-wise folding approach. We integrated the additional structural information into phylogenetic analyses and present for the first time an automated sequence-structure-based taxonomy of the ITS1 of the anaerobic fungi. The methodology developed is transferable to the ITS1 of other fungal groups, and the robust taxonomy will facilitate and improve high-throughput anaerobic fungal community structure analysis of samples from various environments.

  8. Function of RNA secondary structures in transcriptional attenuation of the Bacillus subtilis pyr operon.

    PubMed

    Lu, Y; Turner, R J; Switzer, R L

    1996-12-10

    The Bacillus subtilis pyr operon is regulated by exogenous pyrimidines by a transcriptional attenuation mechanism. Transcription in vitro from pyr DNA templates specifying attenuation regions yielded terminated and read-through transcripts of the expected lengths. Addition of the PyrR regulatory protein plus UMP led to greatly increased termination. Synthetic antisense deoxyoligonucleotides were used to probe possible secondary structures in the pyr mRNA that were proposed to play roles in controlling attenuation. Oligonucleotides predicted to disrupt terminator structures suppressed termination, whereas oligonucleotides predicted to disrupt the stem of antiterminator stem-loops strongly promoted termination at the usual termination site. Oligonucleotides that disrupt a previously unrecognized stem-loop structure, called the anti-antiterminator, the formation of which interferes with formation of the downstream antiterminator, suppressed termination. We propose that transcriptional attenuation of the pyr operon is governed by switching between alternative antiterminator versus anti-antiterminator plus terminator structures, and that PyrR acts by UMP-dependent binding to and stabilization of the anti-antiterminator.

  9. Knowledge base and neural network approach for protein secondary structure prediction.

    PubMed

    Patel, Maulika S; Mazumdar, Himanshu S

    2014-11-21

    Protein structure prediction is of great relevance given the abundant genomic and proteomic data generated by the genome sequencing projects. Protein secondary structure prediction is addressed as a sub task in determining the protein tertiary structure and function. In this paper, a novel algorithm, KB-PROSSP-NN, which is a combination of knowledge base and modeling of the exceptions in the knowledge base using neural networks for protein secondary structure prediction (PSSP), is proposed. The knowledge base is derived from a proteomic sequence-structure database and consists of the statistics of association between the 5-residue words and corresponding secondary structure. The predicted results obtained using knowledge base are refined with a Backpropogation neural network algorithm. Neural net models the exceptions of the knowledge base. The Q3 accuracy of 90% and 82% is achieved on the RS126 and CB396 test sets respectively which suggest improvement over existing state of art methods.

  10. Pattern recognition in nucleic acid sequences. II. An efficient method for finding locally stable secondary structures.

    PubMed Central

    Kanehisa, M I; Goad, W B

    1982-01-01

    We present a method for calculating all possible single hairpin loop secondary structures in a nucleic acid sequence by the order of N2 operations where N is the total number of bases. Each structure may contain any number of bulges and internal loops. Most natural sequences are found to be indistinguishable from random sequences in the potential of forming secondary structures, which is defined by the frequency of possible secondary structures calculated by the method. There is a strong correlation between the higher G+C content and the higher structure forming potential. Interestingly, the removal of intervening sequences in mRNAs is almost always accompanied by an increase in the G+C content, which may suggest an involvement of structural stabilization in the mRNA maturation. PMID:6174936

  11. Crystal structure of advanced lithium titanate with lithium oxide additives

    NASA Astrophysics Data System (ADS)

    Hoshino, Tsuyoshi; Sasaki, Kazuya; Tsuchiya, Kunihiko; Hayashi, Kimio; Suzuki, Akihiro; Hashimoto, Takuya; Terai, Takayuki

    2009-04-01

    Li 2TiO 3 is one of the most promising candidates among solid breeder materials proposed for fusion reactors. However, the mass of Li 2TiO 3 was found to decrease with time in the sweep gas mixed with hydrogen. This mass change indicates that the oxygen content of the sample decreased, suggesting the change from Ti 4+ to Ti 3+. In the present paper, the crystal structure and the non-stoichiometry of Li 2TiO 3 added with Li 2O have been extensively investigated by means of X-ray diffraction (XRD) and thermogravimetry. In the case of the Li 2TiO 3 samples used in the present study, LiO-C 2H 5 or LiO-i-C 3H 7 and Ti(O-i-C 3H 7) 4 were mixed in the proportion corresponding to the molar ratio Li 2O/TiO 2 of either 2.00 or 1.00. In thermogravimetry, the mass of this sample decreased with time due to lithium deficiency, where no presence of oxygen deficiency was indicated.

  12. RNACluster: An integrated tool for RNA secondary structure comparison and clustering.

    PubMed

    Liu, Qi; Olman, V; Liu, Huiqing; Ye, Xiuzi; Qiu, Shilun; Xu, Ying

    2008-07-15

    RNA structure comparison is a fundamental problem in structural biology, structural chemistry, and bioinformatics. It can be used for analysis of RNA energy landscapes, conformational switches, and facilitating RNA structure prediction. The purpose of our integrated tool RNACluster is twofold: to provide a platform for computing and comparison of different distances between RNA secondary structures, and to perform cluster identification to derive useful information of RNA structure ensembles, using a minimum spanning tree (MST) based clustering algorithm. RNACluster employs a cluster identification approach based on a MST representation of the RNA ensemble data and currently supports six distance measures between RNA secondary structures. RNACluster provides a user-friendly graphical interface to allow a user to compare different structural distances, analyze the structure ensembles, and visualize predicted structural clusters. PMID:18271070

  13. RNACluster: An integrated tool for RNA secondary structure comparison and clustering.

    PubMed

    Liu, Qi; Olman, V; Liu, Huiqing; Ye, Xiuzi; Qiu, Shilun; Xu, Ying

    2008-07-15

    RNA structure comparison is a fundamental problem in structural biology, structural chemistry, and bioinformatics. It can be used for analysis of RNA energy landscapes, conformational switches, and facilitating RNA structure prediction. The purpose of our integrated tool RNACluster is twofold: to provide a platform for computing and comparison of different distances between RNA secondary structures, and to perform cluster identification to derive useful information of RNA structure ensembles, using a minimum spanning tree (MST) based clustering algorithm. RNACluster employs a cluster identification approach based on a MST representation of the RNA ensemble data and currently supports six distance measures between RNA secondary structures. RNACluster provides a user-friendly graphical interface to allow a user to compare different structural distances, analyze the structure ensembles, and visualize predicted structural clusters.

  14. Raman spectroscopic evaluation of meat batter structural changes induced by thermal treatment and salt addition.

    PubMed

    Herrero, A M; Carmona, P; López-López, I; Jiménez-Colmenero, F

    2008-08-27

    Raman spectroscopy, texture, proximate composition, and water binding analysis were carried out to evaluate the effect of thermal treatment and/or salt addition to meat batter. For this purpose, different meat batters were elaborated: control meat batter (no salt) and meat batters with low (1.0%) and high (2.5%) NaCl content with and without thermal treatment (70 degrees C/30 min). Increase (P < 0.05) in penetration force and hardness upon heating was observed. Results also showed hardness increasing (P < 0.05) as a function of salt addition in heated meat batter. Raman spectroscopy analysis revealed a significant (P < 0.05) decrease in alpha-helix content accompanied by an increase (P < 0.05) in beta-sheets resulting from heating. Significant (P < 0.05) correlations were found between these secondary structural changes in meat proteins and water binding and textural properties of meat batter. In this way, a significant correlation was found between beta-sheets, salt content, hardness, and chewiness in heated samples.

  15. A cell-compatible PEO-PPO-PEO (Pluronic®)-based hydrogel stabilized through secondary structures.

    PubMed

    Peng, Sydney; Lin, Ji-Yu; Cheng, Ming-Huei; Wu, Chih-Wei; Chu, I-Ming

    2016-12-01

    Pluronic F-127 (PF127) is a thermosensitive polymer that has been widely recognized as a potential candidate for various bio-applications. However, in hydrogel form, its rapid disintegration and inhospitality toward cells have significantly limited its usage. As a means to increase the integrity and cell compatibility of a PF127 hydrogel, we propose the introduction of stabilizing secondary structures to the gel network by the addition of secondary structure-forming oligo-alanine and oligo-phenylalanine. Results indicate that increasing the oligo(peptides) attached to PF127 led to a significant decrease in the gelation concentration and temperature. A selected oligo(peptide)-modified PF127 was capable of forming a stable hydrogel network at 5% and suffered only 20% weight loss after 7days of incubation in media. Scanning electron microscopy (SEM) revealed comparably more interconnected morphology in modified hydrogels which may be attributed to the presence of secondary structures, as verified by circular dichroism (CD) and Fourier-transformed infrared (FT-IR) spectroscopy. Nuclear magnetic resonance (NMR) provided insights into the extensive interactions at the micelle core, which is the key to altered gelation behavior. Furthermore, modified hydrogels maintained structural integrity within culturing media and supported the proliferation of encapsulated chondrocytes. In addition, in vivo residence time was extended to well beyond 2weeks after oligo(peptide) modification, thereby broadening the application scope of the PF127 hydrogel to encompass long-term drug delivery and cell culturing. PMID:27612731

  16. The role of a metastable RNA secondary structure in hepatitis delta virus genotype III RNA editing

    PubMed Central

    Linnstaedt, Sarah D.; Kasprzak, Wojciech K.; Shapiro, Bruce A.; Casey, John L.

    2006-01-01

    RNA editing plays a critical role in the life cycle of hepatitis delta virus (HDV). The host editing enzyme ADAR1 recognizes specific RNA secondary structure features around the amber/W site in the HDV antigenome and deaminates the amber/W adenosine. A previous report suggested that a branched secondary structure is necessary for editing in HDV genotype III. This branched structure, which is distinct from the characteristic unbranched rod structure required for HDV replication, was only partially characterized, and knowledge concerning its formation and stability was limited. Here, we examine the secondary structures, conformational dynamics, and amber/W site editing of HDV genotype III RNA using a miniaturized HDV genotype III RNA in vitro. Computational analysis of this RNA using the MPGAfold algorithm indicated that the RNA has a tendency to form both metastable and stable unbranched secondary structures. Moreover, native polyacrylamide gel electrophoresis demonstrated that this RNA forms both branched and unbranched rod structures when transcribed in vitro. As predicted, the branched structure is a metastable structure that converts readily to the unbranched rod structure. Only branched RNA was edited at the amber/W site by ADAR1 in vitro. The structural heterogeneity of HDV genotype III RNA is significant because not only are both conformations of the RNA functionally important for viral replication, but the ratio of the two forms could modulate editing by determining the amount of substrate RNA available for modification. PMID:16790843

  17. Mature MiRNAs Form Secondary Structure, which Suggests Their Function beyond RISC

    PubMed Central

    Belter, Agnieszka; Gudanis, Dorota; Rolle, Katarzyna; Piwecka, Monika; Gdaniec, Zofia; Naskręt-Barciszewska, Mirosława Z.; Barciszewski, Jan

    2014-01-01

    The generally accepted model of the miRNA-guided RNA down-regulation suggests that mature miRNA targets mRNA in a nucleotide sequence-specific manner. However, we have shown that the nucleotide sequence of miRNA is not the only determinant of miRNA specificity. Using specific nucleases, T1, V1 and S1 as well as NMR, UV/Vis and CD spectroscopies, we found that miR-21, miR-93 and miR-296 can adopt hairpin and/or homoduplex structures. The secondary structure of those miRNAs in solution is a function of RNA concentration and ionic conditions. Additionally, we have shown that a formation of miRNA hairpin is facilitated by cellular environment.Looking for functional consequences of this observation, we have perceived that structure of these miRNAs resemble RNA aptamers, short oligonucleotides forming a stable 3D structures with a high affinity and specificity for their targets. We compared structures of anti-tenascin C (anti-Tn-C) aptamers, which inhibit brain tumor glioblastoma multiforme (GBM, WHO IV) and selected miRNA. A strong overexpression of miR-21, miR-93 as well Tn-C in GBM may imply some connections between them. The structural similarity of these miRNA hairpins and anti-Tn-C aptamers indicates that miRNAs may function also beyond RISC and are even more sophisticated regulators, that it was previously expected. We think that the knowledge of the miRNA structure may give a new insight into miRNA-dependent gene regulation mechanism and be a step forward in the understanding their function and involvement in cancerogenesis. This may improve design process of anti-miRNA therapeutics. PMID:25423301

  18. Secondary structures of proteins from the 30S subunit of the Escherichia coli ribosome.

    PubMed

    Dzionara, M; Robinson, S M; Wittmann-Liebold, B

    1977-08-01

    The secondary structures of the proteins S4, S6, S8, S9, S12, S13, S15, S16, S18, S20 and S21 from the subunit of the E. coli ribosome were predicted according to four different methods. From the resultant diagrams indicating regions of helix, turn, extended structure and random coil, average values for the respective secondary structures could be calculated for each protein. Using the known relative distances for residues in the helical, turn and sheet or allowed random conformations, estimates are made of the maximum possible lengths of the proteins in order to correlate these with results obtained from antibody binding studies to the 30S subunit as determined by electron microscopy. The influence of amino acid changes on the predicted secondary structures of proteins from a few selected mutants was studied. The altered residues tend to be structurally conservative or to induce only minimal local changes.

  19. Structural evolution of gold nanorods during controlled secondary growth.

    PubMed

    Keul, Heidrun A; Möller, Martin; Bockstaller, Michael R

    2007-09-25

    Single-crystalline gold nanorods synthesized by the Ag(I)-mediated seeded-growth method (see: El-Sayed, M. A.; Nikoobakht, B. Chem. Mater. 2003, 15, 1957) were used as seeds for the preferential overgrowth of gold on particular crystallographic facets by systematic variation of the conditions during overgrowth. The results support previous reports about the relevance of the cationic surfactant cetyltrimethylammonium bromide (CTAB) and Ag(I) in stabilizing anisotropic particle shapes and demonstrate that the regulation of the amount of ascorbic acid facilitates the preferential overgrowth of {111} crystal facets to form Xi-type particle shapes. Interestingly, secondary overgrowth is found to inevitably result in a loss of particle shape anisotropy. A mechanism based on surface reconstruction is proposed to rationalize the "shape-reversal" that is generally observed in the nanorod growth process, that is, the initial increase and subsequent decrease of particle anisotropy with increasing reaction time. High-resolution electron microscopy analysis of gold nanorods reveals clear evidence for (1 x 2) missing row surface reconstruction of high energetic {110} facets that form during the initial phase during particle growth. PMID:17713936

  20. The RNAsnp web server: predicting SNP effects on local RNA secondary structure.

    PubMed

    Sabarinathan, Radhakrishnan; Tafer, Hakim; Seemann, Stefan E; Hofacker, Ivo L; Stadler, Peter F; Gorodkin, Jan

    2013-07-01

    The function of many non-coding RNA genes and cis-regulatory elements of messenger RNA largely depends on the structure, which is in turn determined by their sequence. Single nucleotide polymorphisms (SNPs) and other mutations may disrupt the RNA structure, interfere with the molecular function and hence cause a phenotypic effect. RNAsnp is an efficient method to predict the effect of SNPs on local RNA secondary structure based on the RNA folding algorithms implemented in the Vienna RNA package. The SNP effects are quantified in terms of empirical P-values, which, for computational efficiency, are derived from extensive pre-computed tables of distributions of substitution effects as a function of gene length and GC content. Here, we present a web service that not only provides an interface for RNAsnp but also features a graphical output representation. In addition, the web server is connected to a local mirror of the UCSC genome browser database that enables the users to select the genomic sequences for analysis and visualize the results directly in the UCSC genome browser. The RNAsnp web server is freely available at: http://rth.dk/resources/rnasnp/.

  1. Probing the glycosidic linkage: secondary structures in the gas phase

    NASA Astrophysics Data System (ADS)

    Simons, John P.; Cristina Stanca-Kaposta, E.; Cocinero, Emilio J.; Liu, B.; Davis, Benjamin G.; Gamblin, David P.; Kroemer, Romano T.

    2008-10-01

    The functional importance of carbohydrates in biological processes, particularly those involving specific molecular recognition, is immense. Characterizing the three-dimensional (3D) structures of carbohydrates and glycoproteins, and their interactions with other molecules, not least the ubiquitous solvent, water, is a key starting point for understanding these processes. The combination of laser-based electronic and vibrational spectroscopy of mass-selected carbohydrate molecules and their hydrated complexes, conducted under molecular beam conditions, with ab initio computation is providing a uniquely powerful means of characterizing 3D carbohydrate conformations; the structures of their hydrated complexes, the hydrogen-bonded networks they support (or which support them); and the factors that determine their conformational and structural preferences.

  2. Porous carbonaceous electrode structure and method for secondary electrochemical cell

    DOEpatents

    Kaun, Thomas D.

    1977-03-08

    Positive and negative electrodes are provided as rigid, porous carbonaceous matrices with particulate active material fixedly embedded. Active material such as metal chalcogenides, solid alloys of alkali metal or alkaline earth metals along with other metals and their oxides in particulate form are blended with a thermosetting resin and a solid volatile to form a paste mixture. Various electrically conductive powders or current collector structures can be blended or embedded into the paste mixture which can be molded to the desired electrode shape. The molded paste is heated to a temperature at which the volatile transforms into vapor to impart porosity as the resin begins to cure into a rigid solid structure.

  3. Identification of novel DNA repair proteins via primary sequence, secondary structure, and homology

    PubMed Central

    Brown, JB; Akutsu, Tatsuya

    2009-01-01

    Background DNA repair is the general term for the collection of critical mechanisms which repair many forms of DNA damage such as methylation or ionizing radiation. DNA repair has mainly been studied in experimental and clinical situations, and relatively few information-based approaches to new extracting DNA repair knowledge exist. As a first step, automatic detection of DNA repair proteins in genomes via informatics techniques is desirable; however, there are many forms of DNA repair and it is not a straightforward process to identify and classify repair proteins with a single optimal method. We perform a study of the ability of homology and machine learning-based methods to identify and classify DNA repair proteins, as well as scan vertebrate genomes for the presence of novel repair proteins. Combinations of primary sequence polypeptide frequency, secondary structure, and homology information are used as feature information for input to a Support Vector Machine (SVM). Results We identify that SVM techniques are capable of identifying portions of DNA repair protein datasets without admitting false positives; at low levels of false positive tolerance, homology can also identify and classify proteins with good performance. Secondary structure information provides improved performance compared to using primary structure alone. Furthermore, we observe that machine learning methods incorporating homology information perform best when data is filtered by some clustering technique. Analysis by applying these methodologies to the scanning of multiple vertebrate genomes confirms a positive correlation between the size of a genome and the number of DNA repair protein transcripts it is likely to contain, and simultaneously suggests that all organisms have a non-zero minimum number of repair genes. In addition, the scan result clusters several organisms' repair abilities in an evolutionarily consistent fashion. Analysis also identifies several functionally unconfirmed

  4. Free energy minimization to predict RNA secondary structures and computational RNA design.

    PubMed

    Churkin, Alexander; Weinbrand, Lina; Barash, Danny

    2015-01-01

    Determining the RNA secondary structure from sequence data by computational predictions is a long-standing problem. Its solution has been approached in two distinctive ways. If a multiple sequence alignment of a collection of homologous sequences is available, the comparative method uses phylogeny to determine conserved base pairs that are more likely to form as a result of billions of years of evolution than by chance. In the case of single sequences, recursive algorithms that compute free energy structures by using empirically derived energy parameters have been developed. This latter approach of RNA folding prediction by energy minimization is widely used to predict RNA secondary structure from sequence. For a significant number of RNA molecules, the secondary structure of the RNA molecule is indicative of its function and its computational prediction by minimizing its free energy is important for its functional analysis. A general method for free energy minimization to predict RNA secondary structures is dynamic programming, although other optimization methods have been developed as well along with empirically derived energy parameters. In this chapter, we introduce and illustrate by examples the approach of free energy minimization to predict RNA secondary structures.

  5. GTfold: Enabling parallel RNA secondary structure prediction on multi-core desktops

    PubMed Central

    2012-01-01

    Background Accurate and efficient RNA secondary structure prediction remains an important open problem in computational molecular biology. Historically, advances in computing technology have enabled faster and more accurate RNA secondary structure predictions. Previous parallelized prediction programs achieved significant improvements in runtime, but their implementations were not portable from niche high-performance computers or easily accessible to most RNA researchers. With the increasing prevalence of multi-core desktop machines, a new parallel prediction program is needed to take full advantage of today’s computing technology. Findings We present here the first implementation of RNA secondary structure prediction by thermodynamic optimization for modern multi-core computers. We show that GTfold predicts secondary structure in less time than UNAfold and RNAfold, without sacrificing accuracy, on machines with four or more cores. Conclusions GTfold supports advances in RNA structural biology by reducing the timescales for secondary structure prediction. The difference will be particularly valuable to researchers working with lengthy RNA sequences, such as RNA viral genomes. PMID:22747589

  6. Evaluation of the Information Content in Infrared Spectra for Protein Secondary Structure Determination

    PubMed Central

    Goormaghtigh, Erik; Ruysschaert, Jean-Marie; Raussens, Vincent

    2006-01-01

    Fourier-transform infrared spectroscopy is a method of choice for the experimental determination of protein secondary structure. Numerous approaches have been developed during the past 15 years. A critical parameter that has not been taken into account systematically is the selection of the wavenumbers used for building the mathematical models used for structure prediction. The high quality of the current Fourier-transform infrared spectrometers makes the absorbance at every single wavenumber a valid and almost noiseless type of information. We address here the question of the amount of independent information present in the infrared spectra of proteins for the prediction of the different secondary structure contents. It appears that, at most, the absorbance at three distinct frequencies of the spectra contain all the nonredundant information that can be related to one secondary structure content. The ascending stepwise method proposed here identifies the relevance of each wavenumber of the infrared spectrum for the prediction of a given secondary structure and yields a particularly simple method for computing the secondary structure content. Using the 50-protein database built beforehand to contain as little fold redundancy as possible, the standard error of prediction in cross-validation is 5.5% for the α-helix, 6.6% for the β-sheet, and 3.4% for the β-turn. PMID:16428280

  7. Argumentation in Secondary School Students' Structured and Unstructured Chat Discussions

    ERIC Educational Resources Information Center

    Salminen, Timo; Marttunen, Miika; Laurinen, Leena

    2012-01-01

    Joint construction of new knowledge demands that persons can express their statements in a convincing way and explore other people's arguments constructively. For this reason, more knowledge on different means to support collaborative argumentation is needed. This study clarifies whether structured interaction supports students' critical and…

  8. Parameter-Free Hydrogen-Bond Definition to Classify Protein Secondary Structure.

    PubMed

    Haghighi, Hasti; Higham, Jonathan; Henchman, Richard H

    2016-08-25

    DSSP is the most commonly used method to assign protein secondary structure. It is based on a hydrogen-bond definition with an energy cutoff. To assess whether hydrogen bonds defined in a parameter-free way may give more generality while preserving accuracy, we examine a series of hydrogen-bond definitions to assign secondary structure for a series of proteins. Assignment by the strongest-acceptor bifurcated definition with provision for unassigned donor hydrogens, termed the SABLE method, is found to match DSSP with 95% agreement. The small disagreement mainly occurs for helices, turns, and bends. While there is no absolute way to assign protein secondary structure, avoiding molecule-specific cutoff parameters should be advantageous in generalizing structure-assignment methods to any hydrogen-bonded system. PMID:27067825

  9. Charge‐Induced Unzipping of Isolated Proteins to a Defined Secondary Structure

    PubMed Central

    González Flórez, Ana Isabel; Mucha, Eike; Ahn, Doo‐Sik; Gewinner, Sandy; Schöllkopf, Wieland; Pagel, Kevin

    2016-01-01

    Abstract Here we present a combined experimental and theoretical study on the secondary structure of isolated proteins as a function of charge state. In infrared spectra of the proteins ubiquitin and cytochrome c, amide I (C=O stretch) and amide II (N–H bend) bands can be found at positions that are typical for condensed‐phase proteins. For high charge states a new band appears, substantially red‐shifted from the amide II band observed at lower charge states. The observations are interpreted in terms of Coulomb‐driven transitions in secondary structures from mostly helical to extended C5‐type hydrogen‐bonded structures. Support for this interpretation comes from simple energy considerations as well as from quantum chemical calculations on model peptides. This transition in secondary structure is most likely universal for isolated proteins that occur in mass spectrometric experiments. PMID:26847383

  10. Residue-residue contacts: application to analysis of secondary structure interactions.

    PubMed

    Potapov, Vladimir; Edelman, Marvin; Sobolev, Vladimir

    2013-01-01

    Protein structures and their complexes are formed and stabilized by interactions, both inside and outside of the protein. Analysis of such interactions helps in understanding different levels of structures (secondary, super-secondary, and oligomeric states). It can also assist molecular biologists in understanding structural consequences of modifying proteins and/or ligands. In this chapter, our definition of atom-atom and residue-residue contacts is described and applied to analysis of protein-protein interactions in dimeric β-sandwich proteins.

  11. Use of secondary structural information and C alpha-C alpha distance restraints to model protein structures with MODELLER.

    PubMed

    Reddy, Boojala V B; Kaznessis, Yiannis N

    2007-08-01

    Protein secondary structure predictions and amino acid long range contact map predictions from primary sequence of proteins have been explored to aid in modelling protein tertiary structures. In order to evaluate the usefulness of secondary structure and 3D-residue contact prediction methods to model protein structures we have used the known Q3 (alpha-helix,beta-strands and irregular turns/loops) secondary structure information, along with residue-residue contact information as restraints for MODELLER. We present here results of our modelling studies on 30 best resolved single domain protein structures of varied lengths. The results shows that it is very difficult to obtain useful models even with 100% accurate secondary structure predictions and accurate residue contact predictions for up to 30% of residues in a sequence. The best models that we obtained for proteins of lengths 37, 70, 118, 136 and 193 amino acid residues are of RMSDs 4.17, 5.27, 9.12, 7.89 and 9.69,respectively. The results show that one can obtain better models for the proteins which have high percent of alpha-helix content. This analysis further shows that MODELLER restrain optimization program can be useful only if we have truly homologous structure(s) as a template where it derives numerous restraints, almost identical to the templates used. This analysis also clearly indicates that even if we satisfy several true residue-residue contact distances, up to 30%of their sequence length with fully known secondary structural information, we end up predicting model structures much distant from their corresponding native structures.

  12. Macromolecular ab initio phasing enforcing secondary and tertiary structure

    PubMed Central

    Millán, Claudia; Sammito, Massimo; Usón, Isabel

    2015-01-01

    Ab initio phasing of macromolecular structures, from the native intensities alone with no experimental phase information or previous particular structural knowledge, has been the object of a long quest, limited by two main barriers: structure size and resolution of the data. Current approaches to extend the scope of ab initio phasing include use of the Patterson function, density modification and data extrapolation. The authors’ approach relies on the combination of locating model fragments such as polyalanine α-helices with the program PHASER and density modification with the program SHELXE. Given the difficulties in discriminating correct small substructures, many putative groups of fragments have to be tested in parallel; thus calculations are performed in a grid or supercomputer. The method has been named after the Italian painter Arcimboldo, who used to compose portraits out of fruit and vegetables. With ARCIMBOLDO, most collections of fragments remain a ‘still-life’, but some are correct enough for density modification and main-chain tracing to reveal the protein’s true portrait. Beyond α-helices, other fragments can be exploited in an analogous way: libraries of helices with modelled side chains, β-strands, predictable fragments such as DNA-binding folds or fragments selected from distant homologues up to libraries of small local folds that are used to enforce nonspecific tertiary structure; thus restoring the ab initio nature of the method. Using these methods, a number of unknown macromolecules with a few thousand atoms and resolutions around 2 Å have been solved. In the 2014 release, use of the program has been simplified. The software mediates the use of massive computing to automate the grid access required in difficult cases but may also run on a single multicore workstation (http://chango.ibmb.csic.es/ARCIMBOLDO_LITE) to solve straightforward cases. PMID:25610631

  13. Macromolecular ab initio phasing enforcing secondary and tertiary structure.

    PubMed

    Millán, Claudia; Sammito, Massimo; Usón, Isabel

    2015-01-01

    Ab initio phasing of macromolecular structures, from the native intensities alone with no experimental phase information or previous particular structural knowledge, has been the object of a long quest, limited by two main barriers: structure size and resolution of the data. Current approaches to extend the scope of ab initio phasing include use of the Patterson function, density modification and data extrapolation. The authors' approach relies on the combination of locating model fragments such as polyalanine α-helices with the program PHASER and density modification with the program SHELXE. Given the difficulties in discriminating correct small substructures, many putative groups of fragments have to be tested in parallel; thus calculations are performed in a grid or supercomputer. The method has been named after the Italian painter Arcimboldo, who used to compose portraits out of fruit and vegetables. With ARCIMBOLDO, most collections of fragments remain a 'still-life', but some are correct enough for density modification and main-chain tracing to reveal the protein's true portrait. Beyond α-helices, other fragments can be exploited in an analogous way: libraries of helices with modelled side chains, β-strands, predictable fragments such as DNA-binding folds or fragments selected from distant homologues up to libraries of small local folds that are used to enforce nonspecific tertiary structure; thus restoring the ab initio nature of the method. Using these methods, a number of unknown macromolecules with a few thousand atoms and resolutions around 2 Å have been solved. In the 2014 release, use of the program has been simplified. The software mediates the use of massive computing to automate the grid access required in difficult cases but may also run on a single multicore workstation (http://chango.ibmb.csic.es/ARCIMBOLDO_LITE) to solve straightforward cases.

  14. Macromolecular ab initio phasing enforcing secondary and tertiary structure.

    PubMed

    Millán, Claudia; Sammito, Massimo; Usón, Isabel

    2015-01-01

    Ab initio phasing of macromolecular structures, from the native intensities alone with no experimental phase information or previous particular structural knowledge, has been the object of a long quest, limited by two main barriers: structure size and resolution of the data. Current approaches to extend the scope of ab initio phasing include use of the Patterson function, density modification and data extrapolation. The authors' approach relies on the combination of locating model fragments such as polyalanine α-helices with the program PHASER and density modification with the program SHELXE. Given the difficulties in discriminating correct small substructures, many putative groups of fragments have to be tested in parallel; thus calculations are performed in a grid or supercomputer. The method has been named after the Italian painter Arcimboldo, who used to compose portraits out of fruit and vegetables. With ARCIMBOLDO, most collections of fragments remain a 'still-life', but some are correct enough for density modification and main-chain tracing to reveal the protein's true portrait. Beyond α-helices, other fragments can be exploited in an analogous way: libraries of helices with modelled side chains, β-strands, predictable fragments such as DNA-binding folds or fragments selected from distant homologues up to libraries of small local folds that are used to enforce nonspecific tertiary structure; thus restoring the ab initio nature of the method. Using these methods, a number of unknown macromolecules with a few thousand atoms and resolutions around 2 Å have been solved. In the 2014 release, use of the program has been simplified. The software mediates the use of massive computing to automate the grid access required in difficult cases but may also run on a single multicore workstation (http://chango.ibmb.csic.es/ARCIMBOLDO_LITE) to solve straightforward cases. PMID:25610631

  15. RNA Secondary Structure Prediction by Using Discrete Mathematics: An Interdisciplinary Research Experience for Undergraduate Students

    PubMed Central

    Ellington, Roni; Wachira, James

    2010-01-01

    The focus of this Research Experience for Undergraduates (REU) project was on RNA secondary structure prediction by using a lattice walk approach. The lattice walk approach is a combinatorial and computational biology method used to enumerate possible secondary structures and predict RNA secondary structure from RNA sequences. The method uses discrete mathematical techniques and identifies specified base pairs as parameters. The goal of the REU was to introduce upper-level undergraduate students to the principles and challenges of interdisciplinary research in molecular biology and discrete mathematics. At the beginning of the project, students from the biology and mathematics departments of a mid-sized university received instruction on the role of secondary structure in the function of eukaryotic RNAs and RNA viruses, RNA related to combinatorics, and the National Center for Biotechnology Information resources. The student research projects focused on RNA secondary structure prediction on a regulatory region of the yellow fever virus RNA genome and on an untranslated region of an mRNA of a gene associated with the neurological disorder epilepsy. At the end of the project, the REU students gave poster and oral presentations, and they submitted written final project reports to the program director. The outcome of the REU was that the students gained transferable knowledge and skills in bioinformatics and an awareness of the applications of discrete mathematics to biological research problems. PMID:20810968

  16. RNA secondary structure prediction by using discrete mathematics: an interdisciplinary research experience for undergraduate students.

    PubMed

    Ellington, Roni; Wachira, James; Nkwanta, Asamoah

    2010-01-01

    The focus of this Research Experience for Undergraduates (REU) project was on RNA secondary structure prediction by using a lattice walk approach. The lattice walk approach is a combinatorial and computational biology method used to enumerate possible secondary structures and predict RNA secondary structure from RNA sequences. The method uses discrete mathematical techniques and identifies specified base pairs as parameters. The goal of the REU was to introduce upper-level undergraduate students to the principles and challenges of interdisciplinary research in molecular biology and discrete mathematics. At the beginning of the project, students from the biology and mathematics departments of a mid-sized university received instruction on the role of secondary structure in the function of eukaryotic RNAs and RNA viruses, RNA related to combinatorics, and the National Center for Biotechnology Information resources. The student research projects focused on RNA secondary structure prediction on a regulatory region of the yellow fever virus RNA genome and on an untranslated region of an mRNA of a gene associated with the neurological disorder epilepsy. At the end of the project, the REU students gave poster and oral presentations, and they submitted written final project reports to the program director. The outcome of the REU was that the students gained transferable knowledge and skills in bioinformatics and an awareness of the applications of discrete mathematics to biological research problems.

  17. Structuring Free-text Microbiology Culture Reports For Secondary Use

    PubMed Central

    Yim, Wen-wai; Evans, Heather L.; Yetisgen, Meliha

    2015-01-01

    Microbiology lab culture reports are a frequently used diagnostic tool for clinical providers. However, their incorporation into clinical surveillance applications and evidence-based medicine can be severely hindered by the free-text nature of these reports. In this work, we (1) created a microbiology culture template to structure free-text microbiology reports, (2) generated an annotated microbiology report corpus, and (3) built a microbiology information extraction system. Specifically, we combined rule-based, hybrid, and statistical techniques to extract microbiology entities and fill templates for structuring data. System performances were favorable, with entity f1-score 0.889 and relation f1-score 0.795. We plan to incorporate these extractions as features for our ongoing ventilator-associated pneumonia surveillance project, though this tool can be used as an upstream process in other applications. Our newly created corpus includes 1442 unique gram stain and culture microbiology reports generated from a cohort of 715 patients at the University of Washington Medical Facilities. PMID:26306288

  18. Parity-Violation Energy of Biomolecules - IV: Protein Secondary Structure

    NASA Astrophysics Data System (ADS)

    Faglioni, Francesco; Cuesta, Inmaculada García

    2011-06-01

    The parity-violation energy difference between enantiomeric forms of the same amino acid sequence, from the amyloid β-peptide involved in Alzheimer's desease, in both α-helix and β-sheet configurations, is investigated with ab-initio techniques. To this end, we develop an extension of the N2 computational scheme that selectively includes neighboring amino acids to preserve the relevant H-bonds. In agreement with previous speculations, it is found that the helical α structure is associated with larger parity-violation energy differences than the corresponding β form. Implications for the evolution of biological homochirality are discussed as well as the relative importance of various effects in determining the parity-violation energy.

  19. Including secondary structure, fossils and molecular dating in the centipede tree of life.

    PubMed

    Murienne, Jerome; Edgecombe, Gregory D; Giribet, Gonzalo

    2010-10-01

    A well-corroborated morphological scheme of interrelationships for centipedes, once broadly accepted, has been in conflict with molecular data with respect to deep branching events. Expanded taxonomic coverage compared to previous analyses adds longer fragments for 28S rRNA and a structural alignment as part of a sample of four genes (two nuclear ribosomal and two mitochondrial) for 111 extant species; these sequence data are combined with morphology under parsimony and maximum likelihood, exploring both traditional multiple sequence alignment and direct optimization approaches. Novel automated procedures to incorporate secondary structure information are also explored. The molecular data in combination yield trees that are highly congruent with morphology as regards the monophyly of all centipede orders as well as the major groups within each of the large orders. Regardless of the optimality criterion or alignment strategy, the Tasmanian/New Zealand Craterostigmomorpha is resolved in a different position by the molecular data than by morphology. Addition of morphology overturns the placement of Craterostigmomorpha in favour of the traditional morphological resolution and eliminates the need to posit major character reversals with respect to developmental mode and maternal care. Calibration of the tree with Palaeozoic and Mesozoic fossils for a relaxed clock analysis corroborates the palaeontological signal that divergences between centipede orders date to the Silurian and earliest Devonian, and familial divergences are likewise almost wholly Palaeozoic.

  20. Regulation of tyrosine hydroxylase transcription by hnRNP K and DNA secondary structure

    PubMed Central

    Banerjee, Kasturi; Wang, Meng; Cai, Elizabeth; Fujiwara, Nana; Baker, Harriet; Cave, John W.

    2014-01-01

    Regulation of tyrosine hydroxylase gene (Th) transcription is critical for specifying and maintaining the dopaminergic neuronal phenotype. Here we define a molecular regulatory mechanism for Th transcription conserved in tetrapod vertebrates. We show that heterogeneous nuclear ribonucleoprotein (hnRNP) K is a transactivator of Th transcription. It binds to previously unreported and evolutionarily conserved G:C-rich regions in the Th proximal promoter. hnRNP K directly binds C-rich single DNA strands within these conserved regions and also associates with double-stranded sequences when proteins, such as CREB, are bound to an adjacent cis-regulatory element. The single DNA strands within the conserved G:C-rich regions adopt either G-quadruplex or i-motif secondary structures. We also show that small molecule-mediated stabilization of these secondary structures represses Th promoter activity. These data suggest that these secondary structures are targets for pharmacological modulation of the dopaminergic phenotype. PMID:25493445

  1. The FT-IR spectrometric analysis of the changes of polyphenol oxidase II secondary structure

    NASA Astrophysics Data System (ADS)

    Shi, Chunhua; Dai, Ya; Liu, Qingliang; Xie, Yongshu; Xu, Xiaolong

    2003-01-01

    Polyphenol oxidase II is a novel protein purified from tobacco, which acts as a key role in plant defense system. From the analysis of FT-IR spectrums, Fourier self-deconvolution (FSD) spectrums and second-derivative spectrums of PPO II at different pH and peroxide PPO II adduct, the secondary structure fractions are analyzed. PPO II at low pH (pH=3.0) and peroxide PPO II adduct almost keep the same secondary structure of native PPO II. The percentages of β-turn and random coil increase rapidly and the percentages of α-helix and anti-parallel β-sheet decrease rapidly at high pH (pH=10.0) comparing with that of native PPO II. All these conclusions are proved by the secondary structure calculations of circular dichroism spectrums in different states.

  2. Relationship between chain collapse and secondary structure formation in a partially folded protein.

    PubMed

    Nakagawa, Kanako; Yamada, Yoshiteru; Matsumura, Yoshitaka; Tsukamoto, Seiichi; Yamamoto-Ohtomo, Mio; Ohtomo, Hideaki; Okabe, Takahiro; Fujiwara, Kazuo; Ikeguchi, Masamichi

    2014-06-01

    Chain collapse and secondary structure formation are frequently observed during the early stages of protein folding. Is the chain collapse brought about by interactions between secondary structure units or is it due to polymer behavior in a poor solvent (coil-globule transition)? To answer this question, we measured small-angle X-ray scattering for a series of β-lactoglobulin mutants under conditions in which they assume a partially folded state analogous to the folding intermediates. Mutants that were designed to disrupt the secondary structure units showed the gyration radii similar to that of the wild type protein, indicating that chain collapse is due to coil-globule transitions. PMID:25100622

  3. Tracing specific synonymous codon-secondary structure correlations through evolution.

    PubMed

    Oresic, Matej; Dehn, Michael; Korenblum, Daniel; Shalloway, David

    2003-04-01

    We previously showed that GAU codons are preferred (relative to synonymous GAC codons) for encoding aspartates specifically at the N-termini of alpha-helices in human, but not in E. coli, proteins. To test if this difference reflected a general difference between eucaryotes and procaryotes, we now extended the analysis to include the proteins and coding sequences of mammals, vertebrates, S. cerevisiae, and plants. We found that the GAU-alpha-helix correlation is also strong in non-human mammalian and vertebrate proteins but is much weaker or insignificant in S. cerevisiae and plants. The vertebrate correlations are of sufficient strength to enhance alpha-helix N-terminus prediction. Additional results, including the observation that the correlation is significantly enhanced when proteins that are known to be correctly expressed in recombinant procaryotic systems are excluded, suggest that the correlation is induced at the level of protein translation and folding and not at the nucleic acid level. To the best of our knowledge, it is not explicable by the canonical picture of protein expression and folding, suggesting the existence of a novel evolutionary selection mechanism. One possible explanation is that some alpha-helix N-terminal GAU codons may facilitate correct co-translational folding in vertebrates.

  4. Dynamics of beta and proliferating cell nuclear antigen sliding clamps in traversing DNA secondary structure.

    PubMed

    Yao, N; Hurwitz, J; O'Donnell, M

    2000-01-14

    Chromosomal replicases of cellular organisms utilize a ring shaped protein that encircles DNA as a mobile tether for high processivity in DNA synthesis. These "sliding clamps" have sufficiently large linear diameters to encircle duplex DNA and are perhaps even large enough to slide over certain DNA secondary structural elements. This report examines the Escherichia coli beta and human proliferating cell nuclear antigen clamps for their ability to slide over various DNA secondary structures. The results show that these clamps are capable of traversing a 13-nucleotide ssDNA loop, a 4-base pair stem-loop, a 4-nucleotide 5' tail, and a 15-mer bubble within the duplex. However, upon increasing the size of these structures (20-nucleotide loop, 12-base pair stem-loop, 28-nucleotide 5' tail, and 20-nucleotide bubble) the sliding motion of the beta and proliferating cell nuclear antigen over these elements is halted. Studies of the E. coli replicase, DNA polymerase III holoenzyme, in chain elongation with the beta clamp demonstrate that upon encounter with an oligonucleotide annealed in its path, it traverses the duplex and resumes synthesis on the 3' terminus of the oligonucleotide. This sliding and resumption of synthesis occurs even when the oligonucleotide contains a secondary structure element, provided the beta clamp can traverse the structure. However, upon encounter with a downstream oligonucleotide containing a large internal secondary structure, the holoenzyme clears the obstacle by strand displacing the oligonucleotide from the template. Implications of these protein dynamics to DNA transactions are discussed. PMID:10625694

  5. A set of nearest neighbor parameters for predicting the enthalpy change of RNA secondary structure formation

    PubMed Central

    Lu, Zhi John; Turner, Douglas H.; Mathews, David H.

    2006-01-01

    A complete set of nearest neighbor parameters to predict the enthalpy change of RNA secondary structure formation was derived. These parameters can be used with available free energy nearest neighbor parameters to extend the secondary structure prediction of RNA sequences to temperatures other than 37°C. The parameters were tested by predicting the secondary structures of sequences with known secondary structure that are from organisms with known optimal growth temperatures. Compared with the previous set of enthalpy nearest neighbor parameters, the sensitivity of base pair prediction improved from 65.2 to 68.9% at optimal growth temperatures ranging from 10 to 60°C. Base pair probabilities were predicted with a partition function and the positive predictive value of structure prediction is 90.4% when considering the base pairs in the lowest free energy structure with pairing probability of 0.99 or above. Moreover, a strong correlation is found between the predicted melting temperatures of RNA sequences and the optimal growth temperatures of the host organism. This indicates that organisms that live at higher temperatures have evolved RNA sequences with higher melting temperatures. PMID:16982646

  6. RNAmutants: a web server to explore the mutational landscape of RNA secondary structures.

    PubMed

    Waldispühl, Jerome; Devadas, Srinivas; Berger, Bonnie; Clote, Peter

    2009-07-01

    The history and mechanism of molecular evolution in DNA have been greatly elucidated by contributions from genetics, probability theory and bioinformatics--indeed, mathematical developments such as Kimura's neutral theory, Kingman's coalescent theory and efficient software such as BLAST, ClustalW, Phylip, etc., provide the foundation for modern population genetics. In contrast to DNA, the function of most noncoding RNA depends on tertiary structure, experimentally known to be largely determined by secondary structure, for which dynamic programming can efficiently compute the minimum free energy secondary structure. For this reason, understanding the effect of pointwise mutations in RNA secondary structure could reveal fundamental properties of structural RNA molecules and improve our understanding of molecular evolution of RNA. The web server RNAmutants provides several efficient tools to compute the ensemble of low-energy secondary structures for all k-mutants of a given RNA sequence, where k is bounded by a user-specified upper bound. As we have previously shown, these tools can be used to predict putative deleterious mutations and to analyze regulatory sequences from the hepatitis C and human immunodeficiency genomes. Web server is available at http://bioinformatics.bc.edu/clotelab/RNAmutants/, and downloadable binaries at http://rnamutants.csail.mit.edu/.

  7. RNAmutants: a web server to explore the mutational landscape of RNA secondary structures.

    PubMed

    Waldispühl, Jerome; Devadas, Srinivas; Berger, Bonnie; Clote, Peter

    2009-07-01

    The history and mechanism of molecular evolution in DNA have been greatly elucidated by contributions from genetics, probability theory and bioinformatics--indeed, mathematical developments such as Kimura's neutral theory, Kingman's coalescent theory and efficient software such as BLAST, ClustalW, Phylip, etc., provide the foundation for modern population genetics. In contrast to DNA, the function of most noncoding RNA depends on tertiary structure, experimentally known to be largely determined by secondary structure, for which dynamic programming can efficiently compute the minimum free energy secondary structure. For this reason, understanding the effect of pointwise mutations in RNA secondary structure could reveal fundamental properties of structural RNA molecules and improve our understanding of molecular evolution of RNA. The web server RNAmutants provides several efficient tools to compute the ensemble of low-energy secondary structures for all k-mutants of a given RNA sequence, where k is bounded by a user-specified upper bound. As we have previously shown, these tools can be used to predict putative deleterious mutations and to analyze regulatory sequences from the hepatitis C and human immunodeficiency genomes. Web server is available at http://bioinformatics.bc.edu/clotelab/RNAmutants/, and downloadable binaries at http://rnamutants.csail.mit.edu/. PMID:19531740

  8. Fabrication of experimental three-meter space telescope primary and secondary mirror support structure

    NASA Technical Reports Server (NTRS)

    Mishler, H. W.

    1974-01-01

    The fabrication of prototype titanium alloy primary and secondary mirror support structures for a proposed experimental three-meter space telescope is discussed. The structure was fabricated entirely of Ti-6Al-4V tubing and plate. Fabrication included the development of procedures including welding, forming, and machining. Most of the structures was fabricated by gas-shielding tungsten-arc (GTA) welding with several major components fabricated by high frequency resistance (HFR) welding.

  9. New charge-bearing amino acid residues that promote β-sheet secondary structure.

    PubMed

    Maynard, Stacy J; Almeida, Aaron M; Yoshimi, Yasuharu; Gellman, Samuel H

    2014-11-26

    Proteinogenic amino acid residues that promote β-sheet secondary structure are hydrophobic (e.g., Ile or Val) or only moderately polar (e.g., Thr). The design of peptides intended to display β-sheet secondary structure in water typically requires one set of residues to ensure conformational stability and an orthogonal set, with charged side chains, to ensure aqueous solubility and discourage self-association. Here we describe new amino acids that manifest substantial β-sheet propensity, by virtue of β-branching, and also bear an ionizable group in the side chain. PMID:25393077

  10. Artificial Intelligence in Prediction of Secondary Protein Structure Using CB513 Database

    PubMed Central

    Avdagic, Zikrija; Purisevic, Elvir; Omanovic, Samir; Coralic, Zlatan

    2009-01-01

    In this paper we describe CB513 a non-redundant dataset, suitable for development of algorithms for prediction of secondary protein structure. A program was made in Borland Delphi for transforming data from our dataset to make it suitable for learning of neural network for prediction of secondary protein structure implemented in MATLAB Neural-Network Toolbox. Learning (training and testing) of neural network is researched with different sizes of windows, different number of neurons in the hidden layer and different number of training epochs, while using dataset CB513. PMID:21347158

  11. FASTR: A novel data format for concomitant representation of RNA sequence and secondary structure information.

    PubMed

    Bose, Tungadri; Dutta, Anirban; Mh, Mohammed; Gandhi, Hemang; Mande, Sharmila S

    2015-09-01

    Given the importance of RNA secondary structures in defining their biological role, it would be convenient for researchers seeking RNA data if both sequence and structural information pertaining to RNA molecules are made available together. Current nucleotide data repositories archive only RNA sequence data. Furthermore, storage formats which can frugally represent RNA sequence as well as structure data in a single file, are currently unavailable. This article proposes a novel storage format, 'FASTR', for concomitant representation of RNA sequence and structure. The storage efficiency of the proposed FASTR format has been evaluated using RNA data from various microorganisms. Results indicate that the size of FASTR formatted files (containing both RNA sequence as well as structure information) are equivalent to that of FASTA-format files, which contain only RNA sequence information. RNA secondary structure is typically represented using a combination of a string of nucleotide characters along with the corresponding dot-bracket notation indicating structural attributes. 'FASTR' - the novel storage format proposed in the present study enables a frugal representation of both RNA sequence and structural information in the form of a single string. In spite of having a relatively smaller storage footprint, the resultant 'fastr' string(s) retain all sequence as well as secondary structural information that could be stored using a dot-bracket notation. An implementation of the 'FASTR' methodology is available for download at http://metagenomics.atc.tcs.com/compression/fastr.

  12. Secondary Structural Change Can Occur Diffusely and Not Modularly during Protein Folding and Unfolding Reactions.

    PubMed

    Malhotra, Pooja; Udgaonkar, Jayant B

    2016-05-11

    A major goal of protein folding studies is to understand the structural basis of the coupling between stabilizing interactions, which leads to cooperative conformational change. The goal is challenging because of the difficulty in simultaneously measuring global cooperativity by determining population distributions of the conformations present, and the structures of these conformations. Here, hydrogen exchange (HX) into the small protein monellin was carried out under conditions where structure-opening is rate limiting for most backbone amide sites. Detection by mass spectrometry allowed characterization of not only segment-specific structure-opening rates but also the cooperativity of unfolding of the different secondary structural segments of the protein. The segment-specific pattern of HX reveals that the backbone hydrogen-bonding network disassembles in a structurally diffuse, asynchronous manner. A comparison of the site-specific transient opening rates of secondary and tertiary structure in the protein provides a structural rationale for the observation that unfolding is hierarchical and describable by exponential kinetics, despite being diffuse. Since unfolding was studied in native conditions, the sequence of events during folding in the same conditions will be the reverse of the sequence of events observed during unfolding. Hence, the formation of secondary structural units during folding would also occur in a non-cooperative, diffuse, and asynchronous manner. PMID:27093885

  13. Web-Beagle: a web server for the alignment of RNA secondary structures

    PubMed Central

    Mattei, Eugenio; Pietrosanto, Marco; Ferrè, Fabrizio; Helmer-Citterich, Manuela

    2015-01-01

    Web-Beagle (http://beagle.bio.uniroma2.it) is a web server for the pairwise global or local alignment of RNA secondary structures. The server exploits a new encoding for RNA secondary structure and a substitution matrix of RNA structural elements to perform RNA structural alignments. The web server allows the user to compute up to 10 000 alignments in a single run, taking as input sets of RNA sequences and structures or primary sequences alone. In the latter case, the server computes the secondary structure prediction for the RNAs on-the-fly using RNAfold (free energy minimization). The user can also compare a set of input RNAs to one of five pre-compiled RNA datasets including lncRNAs and 3′ UTRs. All types of comparison produce in output the pairwise alignments along with structural similarity and statistical significance measures for each resulting alignment. A graphical color-coded representation of the alignments allows the user to easily identify structural similarities between RNAs. Web-Beagle can be used for finding structurally related regions in two or more RNAs, for the identification of homologous regions or for functional annotation. Benchmark tests show that Web-Beagle has lower computational complexity, running time and better performances than other available methods. PMID:25977293

  14. Implementation of an FTIR calibration curve for fast and objective determination of changes in protein secondary structure during formulation development.

    PubMed

    Vonhoff, Sebastian; Condliffe, Jamie; Schiffter, Heiko

    2010-01-01

    The aim of this study was to develop a quick and objective method for the determination of changes in protein secondary structure by Fourier transform infrared spectroscopy (FTIR). Structural shifts from native regions (alpha-helix, intramolecular beta-sheet) to aggregated strands (intermolecular beta-sheet) were used to evaluate protein damage. FTIR spectra of 16 different proteins were recorded and quantified by peak fitting of the non-deconvolved and baseline corrected amide I bands. The resulting percentile secondary structures were correlated with the shape and intensity of the area normalized amide I bands using an interval partial least squares algorithm (iPLS). Structural elements were focused on the following regions: alpha-helix 1660-1650 cm(-1), intramolecular beta-sheet 1695-1683 cm(-1) and 1644-1620 cm(-1), intermolecular beta-sheet 1620-1595 cm(-1). Three calibration curves were created from the data sets. Calculated alpha-helix content ranged from 0% to 79.59%, intramolecular beta-sheet from 10.64% to 63.89% and intermolecular beta-sheet from 0.23% to 9.70%. The linear relationship between actual values (as determined by peak fitting) and calculated values was evaluated by correlation coefficient and root mean square error of calibration while cross-validation was performed to detect possible outliers. Results were verified by including two proteins as validation standards and comparing the calculated values to peak fitting and X-ray data. Structural changes of human serum albumin (HSA) due to elevated temperatures and the fibrillation of glucagon were quantified by calibration curve analysis. Performance and reliability of the iPLS algorithm were evaluated by comparing calculated secondary structure elements with results from peak fitting and circular dichroism. Different methods for the determination of secondary structure gave slightly different results but overall tendencies concurred. Additionally, formation of HSA aggregates could be linked to

  15. Computer-aided nucleic acid secondary structure modeling incorporating enzymatic digestion data.

    PubMed Central

    Quigley, G J; Gehrke, L; Roth, D A; Auron, P E

    1984-01-01

    We present a computer-aided method for determining nucleic acid secondary structure. The method utilizes a program which has the capability to filter matrix diagonal data on the basis of diagonal length, stabilization energy, and chemical and enzymatic data. The program also allows the user to assign selected regions of the structure as uniquely single-stranded or paired, and to filter out "trade-off" structures on the basis of such pairing. In order to demonstrate the utility of the program we present a preliminary secondary structure for the 3' end of alfalfa mosaic virus RNA 4 (AMV-4 RNA). This structure is based on an analysis which includes the use of in vitro partial enzymatic digestion of the RNA. Images PMID:6320093

  16. New insights from cluster analysis methods for RNA secondary structure prediction.

    PubMed

    Rogers, Emily; Heitsch, Christine

    2016-05-01

    A widening gap exists between the best practices for RNA secondary structure prediction developed by computational researchers and the methods used in practice by experimentalists. Minimum free energy predictions, although broadly used, are outperformed by methods which sample from the Boltzmann distribution and data mine the results. In particular, moving beyond the single structure prediction paradigm yields substantial gains in accuracy. Furthermore, the largest improvements in accuracy and precision come from viewing secondary structures not at the base pair level but at lower granularity/higher abstraction. This suggests that random errors affecting precision and systematic ones affecting accuracy are both reduced by this 'fuzzier' view of secondary structures. Thus experimentalists who are willing to adopt a more rigorous, multilayered approach to secondary structure prediction by iterating through these levels of granularity will be much better able to capture fundamental aspects of RNA base pairing. WIREs RNA 2016, 7:278-294. doi: 10.1002/wrna.1334 For further resources related to this article, please visit the WIREs website.

  17. The four ingredients of single-sequence RNA secondary structure prediction. A unifying perspective

    PubMed Central

    Rivas, Elena

    2013-01-01

    Any method for RNA secondary structure prediction is determined by four ingredients. The architecture is the choice of features implemented by the model (such as stacked basepairs, loop length distributions, etc.). The architecture determines the number of parameters in the model. The scoring scheme is the nature of those parameters (whether thermodynamic, probabilistic, or weights). The parameterization stands for the specific values assigned to the parameters. These three ingredients are referred to as “the model.” The fourth ingredient is the folding algorithms used to predict plausible secondary structures given the model and the sequence of a structural RNA. Here, I make several unifying observations drawn from looking at more than 40 years of methods for RNA secondary structure prediction in the light of this classification. As a final observation, there seems to be a performance ceiling that affects all methods with complex architectures, a ceiling that impacts all scoring schemes with remarkable similarity. This suggests that modeling RNA secondary structure by using intrinsic sequence-based plausible “foldability” will require the incorporation of other forms of information in order to constrain the folding space and to improve prediction accuracy. This could give an advantage to probabilistic scoring systems since a probabilistic framework is a natural platform to incorporate different sources of information into one single inference problem. PMID:23695796

  18. Quantitative Correlation between the protein primary sequences and secondary structures in spider dragline silks.

    PubMed

    Jenkins, Janelle E; Creager, Melinda S; Lewis, Randolph V; Holland, Gregory P; Yarger, Jeffery L

    2010-01-11

    Synthetic spider silk holds great potential for use in various applications spanning medical uses to ultra lightweight armor; however, producing synthetic fibers with mechanical properties comparable to natural spider silk has eluded the scientific community. Natural dragline spider silks are commonly made from proteins that contain highly repetitive amino acid motifs, adopting an array of secondary structures. Before further advances can be made in the production of synthetic fibers based on spider silk proteins, it is imperative to know the percentage of each amino acid in the protein that forms a specific secondary structure. Linking these percentages to the primary amino acid sequence of the protein will establish a structural foundation for synthetic silk. In this study, nuclear magnetic resonance (NMR) techniques are used to quantify the percentage of Ala, Gly, and Ser that form both beta-sheet and helical secondary structures. The fraction of these three amino acids and their secondary structure are quantitatively correlated to the primary amino acid sequence for the proteins that comprise major and minor ampullate silk from the Nephila clavipes spider providing a blueprint for synthetic spider silks. PMID:20000730

  19. The four ingredients of single-sequence RNA secondary structure prediction. A unifying perspective.

    PubMed

    Rivas, Elena

    2013-07-01

    Any method for RNA secondary structure prediction is determined by four ingredients. The architecture is the choice of features implemented by the model (such as stacked basepairs, loop length distributions, etc.). The architecture determines the number of parameters in the model. The scoring scheme is the nature of those parameters (whether thermodynamic, probabilistic, or weights). The parameterization stands for the specific values assigned to the parameters. These three ingredients are referred to as "the model." The fourth ingredient is the folding algorithms used to predict plausible secondary structures given the model and the sequence of a structural RNA. Here, I make several unifying observations drawn from looking at more than 40 years of methods for RNA secondary structure prediction in the light of this classification. As a final observation, there seems to be a performance ceiling that affects all methods with complex architectures, a ceiling that impacts all scoring schemes with remarkable similarity. This suggests that modeling RNA secondary structure by using intrinsic sequence-based plausible "foldability" will require the incorporation of other forms of information in order to constrain the folding space and to improve prediction accuracy. This could give an advantage to probabilistic scoring systems since a probabilistic framework is a natural platform to incorporate different sources of information into one single inference problem.

  20. Orientation Determination of Protein Helical Secondary Structure Using Linear and Nonlinear Vibrational Spectroscopy

    PubMed Central

    Nguyen, Khoi Tan; Le Clair, Stéphanie V.; Ye, Shuji; Chen, Zhan

    2009-01-01

    In this paper, we systematically presented the orientation determination of protein helical secondary structures using vibrational spectroscopic methods, particularly the nonlinear Sum Frequency Generation (SFG) vibrational spectroscopy, along with linear vibrational spectroscopic techniques such as infrared spectroscopy and Raman scattering. SFG amide I signals can be collected using different polarization combinations of the input laser beams and output signal beam to measure the second order nonlinear optical susceptibility components of the helical amide I modes, which are related to their molecular hyperpolarizability elements through the orientation distribution of these helices. The molecular hyperpolarizability elements of amide I modes of a helix can be calculated based on the infrared transition dipole moment and Raman polarizability tensor of the helix; these quantities are determined by using the bond additivity model to sum over the individual infrared dipole transition moments and Raman polarizability tensors, respectively, of the peptide units (or the amino acid residues). The computed overall infrared transition dipole moment and Raman polarizability tensor of a helix can be validated by experimental data using polarized infrared and polarized Raman spectroscopy on samples with well-aligned helical structures. From the deduced SFG hyperpolarizability elements and measured SFG second order nonlinear susceptibility components, orientation information regarding helical structures can be determined. Even though such orientation information can also be measured using polarized infrared or polarized Raman amide I signals, SFG has a much lower detection limit, which can be used to study the orientation of a helix when its surface coverage is much lower than a monolayer. In addition, the combination of different vibrational spectroscopic techniques, e.g., SFG and Attenuated Total Reflectance – Fourier Transform Infrared spectroscopy, provides more

  1. Synthesis and characterization of nitroaromatic peptoids: fine tuning peptoid secondary structure through monomer position and functionality.

    PubMed

    Fowler, Sarah A; Luechapanichkul, Rinrada; Blackwell, Helen E

    2009-02-20

    N-substituted glycine oligomers, or peptoids, have emerged as an important class of foldamers for the study of biomolecular interactions and for potential use as therapeutic agents. However, the design of peptoids with well-defined conformations a priori remains a formidable challenge. New approaches are required to address this problem, and the systematic study of the role of individual monomer units in the global peptoid folding process represents one strategy. Here, we report our efforts toward this approach through the design, synthesis, and characterization of peptoids containing nitroaromatic monomer units. This work required the synthesis of a new chiral amine building block, (S)-1-(2-nitrophenyl)ethanamine (s2ne), which could be readily installed into peptoids using standard solid-phase peptoid synthesis techniques. We designed a series of peptoid nonamers that allowed us to probe the effects of this relatively electron-deficient and sterically encumbered alpha-chiral side chain on peptoid structure, namely, the peptoid threaded loop and helix. Circular dichroism spectroscopy of the peptoids revealed that the nitroaromatic monomer has a significant effect on peptoid secondary structure. Specifically, the threaded loop structure was disrupted in a nonamer containing alternating N-(S)-1-phenylethylglycine (Nspe) and Ns2ne monomers, and the major conformation was helical instead. Indeed, placement of a single Ns2ne at the N-terminal position of (Nspe)(9) resulted in a destabilized form of the threaded loop structure relative to the homononamer (Nspe)(9). Conversely, we observed that incorporation of N-(S)-1-(4-nitrophenyl)ethylglycine (Nsnp, a p-nitro monomer) at the N-terminal position stabilized the threaded loop structure relative to (Nspe)(9). Additional experiments revealed that nitroaromatic side chains can influence peptoid nonamer folding by modulating the strength of key intramolecular hydrogen bonds in the peptoid threaded loop structure. Steric

  2. Flow structure in submarine meandering channels, a continuous discussion on secondary flow

    NASA Astrophysics Data System (ADS)

    Abad, J. D.; Parker, G.; Sequeiros, O.; Spinewine, B.; Garcia, M. H.; Pirmez, C.

    2011-12-01

    The understanding of the flow structure in deep-sea turbidity currents is important for the formation of submarine meandering channels. Similarly to the case of subaerial channels, several types of secondary flows include turbulence-, curvature- and bed morphodynamic-driven flow structures that modulate sediment transport and channel bed morphodynamics. This study focuses on [1] a review of long-time research effort (Abad et al., 2011) that tackles the description of the secondary flow associated with a subaqueous bottom current (saline) in a high-curvature meandering channel and [2] ongoing numerical simulations of similar settings as the experiments to describe the entire flow structure. In the case of subaerial channels, the classical Rozovskiian paradigm is often invoked which indicates that the near-bottom secondary flow in a bend is directed inward. It has recently been suggested based on experimental and theoretical considerations, however, that this pattern is reversed (near-bottom secondary flow is directed outward) in the case of submarine meandering channels. Experimental results presented here, on the other hand, indicate near-bottom secondary flows that have the same direction as observed in a river (normal secondary flow). The implication is an apparent contradiction between experimental results. This study combines theory, experiments, reconstructions of field flows and ongoing simulations to resolve this apparent contradiction based on the flow densimetric Froude number. Three ranges of densimetric Froude number are found, such that a) in an upper regime, secondary flow is reversed, b) in a middle regime, it is normal and c) in a lower regime, it is reversed. These results are applied to field scale channel-forming turbidity currents in the Amazon submarine canyon-fan system (Amazon Channel) and the Monterey canyon and a saline underflow in the Black Sea flowing from the Bosphorus. Our analysis indicates that secondary flow should be normal

  3. Reactivity of molybdovanadophosphoric acids: Influence of the presence of vanadium in the primary and secondary structure

    SciTech Connect

    Casarini, D.; Centi, G.; Lena, V.; Tvaruzkova, Z. ); Jiru, P. )

    1993-10-01

    The catalytic behavior in butadiene and n-butane oxidation of molybdovanadophosphoric acids with vanadium localized inside the primary (oxoanion) and/or the secondary structure is reported. The samples are characterized by infrared, [sup 31]P-NMR, [sup 51]V-NMR, and UV-visible diffuse reflectance spectroscopies in order to obtain information on the nature and localization of vanadium in the samples before reaction and the possible changes occurring during the course of the catalytic reaction. In particular, it is shown that vanadium localized initially in the secondary structure can exchange with the molybdenum atoms of the oxoanion during the catalytic reaction. Introduction of vanadium in the molybdophosphoric acid structure enhances the selective formation of maleic anhydride from the butadiene when vanadium is present both inside the oxoanion or localized in the secondary structure (before the catalytic tests), but the maximum in catalytic performance is found for different amounts of vanadium, depending on where the vanadium is localized initially. However, when present in the secondary structure, vanadium also has a negative influence on the activity of the heteropoly acid. On the contrary, in n-butane oxidation, the presence of vanadium enhances the rate of alkane activation due to the different rate-determining step. The presence of V ions also affects the maximum selectivity and yield to maleic anhydride from butane. V ions in the secondary structure are more selective at low conversion, while V ions inside the oxoanion are more selective at higher conversions and thus allow better maximum yields to maleic anhydride. 40 refs., 11 figs., 2 tabs.

  4. Bioinformatics approaches for structural and functional analysis of proteins in secondary metabolism in Withania somnifera.

    PubMed

    Sanchita; Singh, Swati; Sharma, Ashok

    2014-11-01

    Withania somnifera (Ashwagandha) is an affluent storehouse of large number of pharmacologically active secondary metabolites known as withanolides. These secondary metabolites are produced by withanolide biosynthetic pathway. Very less information is available on structural and functional aspects of enzymes involved in withanolides biosynthetic pathways of Withiana somnifera. We therefore performed a bioinformatics analysis to look at functional and structural properties of these important enzymes. The pathway enzymes taken for this study were 3-Hydroxy-3-methylglutaryl coenzyme A reductase, 1-Deoxy-D-xylulose-5-phosphate synthase, 1-Deoxy-D-xylulose-5-phosphate reductase, farnesyl pyrophosphate synthase, squalene synthase, squalene epoxidase, and cycloartenol synthase. The prediction of secondary structure was performed for basic structural information. Three-dimensional structures for these enzymes were predicted. The physico-chemical properties such as pI, AI, GRAVY and instability index were also studied. The current information will provide a platform to know the structural attributes responsible for the function of these protein until experimental structures become available.

  5. RNA secondary structure modeling at consistent high accuracy using differential SHAPE.

    PubMed

    Rice, Greggory M; Leonard, Christopher W; Weeks, Kevin M

    2014-06-01

    RNA secondary structure modeling is a challenging problem, and recent successes have raised the standards for accuracy, consistency, and tractability. Large increases in accuracy have been achieved by including data on reactivity toward chemical probes: Incorporation of 1M7 SHAPE reactivity data into an mfold-class algorithm results in median accuracies for base pair prediction that exceed 90%. However, a few RNA structures are modeled with significantly lower accuracy. Here, we show that incorporating differential reactivities from the NMIA and 1M6 reagents--which detect noncanonical and tertiary interactions--into prediction algorithms results in highly accurate secondary structure models for RNAs that were previously shown to be difficult to model. For these RNAs, 93% of accepted canonical base pairs were recovered in SHAPE-directed models. Discrepancies between accepted and modeled structures were small and appear to reflect genuine structural differences. Three-reagent SHAPE-directed modeling scales concisely to structurally complex RNAs to resolve the in-solution secondary structure analysis problem for many classes of RNA.

  6. Protein-associated water and secondary structure effect removal of blood proteins from metallic substrates.

    PubMed

    Anand, Gaurav; Zhang, Fuming; Linhardt, Robert J; Belfort, Georges

    2011-03-01

    behaved similarly on addition of the alkaline-surfactant cleaning solution, in that platinum and gold exhibited an increase, while tungsten, titanium, and stainless steel showed a decrease in weight. According to dissipation measurements with the QCM-D, the adsorbed layer for platinum and gold was rigid, while that for the tungsten, titanium, and stainless steel was much more flexible. The removal efficiency of adsorbed-protein by alkaline solution of SDS depended on the water content of the adsorbed layers for W, Ti, and SS, while for Pt and Au, it depended on secondary structural content. When protein adsorption was high (Pt, Au), protein-protein interactions and protein-surface interactions were dominant and the removal of protein layers was limited. Water content of the adsorbed protein layer was the determining factor for how efficiently the layer was removed by alkaline SDS when protein adsorption was low. Hence, protein-protein and protein-surface interactions were minimal and protein structure was less perturbed in comparison with those for high protein adsorption. Secondary structural content determined the efficient removal of adsorbed protein for high adsorbed amount. PMID:21182242

  7. Protein-associated water and secondary structure effect removal of blood proteins from metallic substrates.

    PubMed

    Anand, Gaurav; Zhang, Fuming; Linhardt, Robert J; Belfort, Georges

    2011-03-01

    behaved similarly on addition of the alkaline-surfactant cleaning solution, in that platinum and gold exhibited an increase, while tungsten, titanium, and stainless steel showed a decrease in weight. According to dissipation measurements with the QCM-D, the adsorbed layer for platinum and gold was rigid, while that for the tungsten, titanium, and stainless steel was much more flexible. The removal efficiency of adsorbed-protein by alkaline solution of SDS depended on the water content of the adsorbed layers for W, Ti, and SS, while for Pt and Au, it depended on secondary structural content. When protein adsorption was high (Pt, Au), protein-protein interactions and protein-surface interactions were dominant and the removal of protein layers was limited. Water content of the adsorbed protein layer was the determining factor for how efficiently the layer was removed by alkaline SDS when protein adsorption was low. Hence, protein-protein and protein-surface interactions were minimal and protein structure was less perturbed in comparison with those for high protein adsorption. Secondary structural content determined the efficient removal of adsorbed protein for high adsorbed amount.

  8. Classroom Structure and Teacher Efficacy in Serving Students with Disabilities: Differences in Elementary and Secondary Teachers

    ERIC Educational Resources Information Center

    Shippen, Margaret E.; Flores, Margaret M.; Crites, Steven A.; Patterson, DaShaunda; Ramsey, Michelle L.; Houchins, David E.; Jolivette, Kristine

    2011-01-01

    The purpose of this study was to investigate the differential classroom structure and efficacy reported by general and special educators at the elementary and secondary level. General and special educators (n = 774, return rate of 37%) from a large school district in the southeast US participated in the study. The participants completed a modified…

  9. Understanding of Relation Structures of Graphical Models by Lower Secondary Students

    ERIC Educational Resources Information Center

    van Buuren, Onne; Heck, André; Ellermeijer, Ton

    2016-01-01

    A learning path has been developed on system dynamical graphical modelling, integrated into the Dutch lower secondary physics curriculum. As part of the developmental research for this learning path, students' understanding of the relation structures shown in the diagrams of graphical system dynamics based models has been investigated. One of our…

  10. Teachers Working in Collaborative Structures: A Case Study of a Secondary School in the USA

    ERIC Educational Resources Information Center

    Cameron, David Hagen

    2005-01-01

    This article reports on a study that explores collaborative structures of shared decision-making in an urban secondary school in the USA. The data in the study came from unstructured interviews with 20 teachers, the principal, the assistant principal, a counsellor and 10 students. The interviews took place over a three-week period in June of 2001…

  11. The Turn of the Screw: An Exercise in Protein Secondary Structure

    ERIC Educational Resources Information Center

    Pikaart, Michael

    2011-01-01

    An exercise using simple paper strips to illustrate protein helical and sheet secondary structures is presented. Drawing on the rich historical context of the use of physical models in protein biochemistry by early practitioners, in particular Linus Pauling, the purpose of this activity is to cultivate in students a hands-on, intuitive sense of…

  12. Secondary School Students' Understanding of Mathematical Induction: Structural Characteristics and the Process of Proof Construction

    ERIC Educational Resources Information Center

    Palla, Marina; Potari, Despina; Spyrou, Panagiotis

    2012-01-01

    In this study, we investigate the meaning students attribute to the structure of mathematical induction (MI) and the process of proof construction using mathematical induction in the context of a geometric recursion problem. Two hundred and thirteen 17-year-old students of an upper secondary school in Greece participated in the study. Students'…

  13. Assessing the impact of secondary structure and solvent accessibility on protein evolution.

    PubMed Central

    Goldman, N; Thorne, J L; Jones, D T

    1998-01-01

    Empirically derived models of amino acid replacement are employed to study the association between various physical features of proteins and evolution. The strengths of these associations are statistically evaluated by applying the models of protein evolution to 11 diverse sets of protein sequences. Parametric bootstrap tests indicate that the solvent accessibility status of a site has a particularly strong association with the process of amino acid replacement that it experiences. Significant association between secondary structure environment and the amino acid replacement process is also observed. Careful description of the length distribution of secondary structure elements and of the organization of secondary structure and solvent accessibility along a protein did not always significantly improve the fit of the evolutionary models to the data sets that were analyzed. As indicated by the strength of the association of both solvent accessibility and secondary structure with amino acid replacement, the process of protein evolution-both above and below the species level-will not be well understood until the physical constraints that affect protein evolution are identified and characterized. PMID:9584116

  14. Topology and Secondary Structure of the N-terminal Domain of Diacylglycerol Kinase

    SciTech Connect

    Oxenoid, Kirill; Soennichsen, Frank D.; Sanders, Charles R.

    2002-09-28

    Prokaryotic diacylglycerol kinase (DAGK) functions as a homotrimer of 13 kDa subunits, each of which has three transmembrane segments. This enzyme is conditionally essential to some bacteria and serves as a model system for studies of membrane protein biocatalysis, stability, folding, and misfolding. In this work, the detailed topology and secondary structure of DAGKs N-terminus up through the loop

  15. Amide I'-II' 2D IR spectroscopy provides enhanced protein secondary structural sensitivity.

    PubMed

    Deflores, Lauren P; Ganim, Ziad; Nicodemus, Rebecca A; Tokmakoff, Andrei

    2009-03-11

    We demonstrate how multimode 2D IR spectroscopy of the protein amide I' and II' vibrations can be used to distinguish protein secondary structure. Polarization-dependent amide I'-II' 2D IR experiments on poly-l-lysine in the beta-sheet, alpha-helix, and random coil conformations show that a combination of amide I' and II' diagonal and cross peaks can effectively distinguish between secondary structural content, where amide I' infrared spectroscopy alone cannot. The enhanced sensitivity arises from frequency and amplitude correlations between amide II' and amide I' spectra that reflect the symmetry of secondary structures. 2D IR surfaces are used to parametrize an excitonic model for the amide I'-II' manifold suitable to predict protein amide I'-II' spectra. This model reveals that the dominant vibrational interaction contributing to this sensitivity is a combination of negative amide II'-II' through-bond coupling and amide I'-II' coupling within the peptide unit. The empirically determined amide II'-II' couplings do not significantly vary with secondary structure: -8.5 cm(-1) for the beta sheet, -8.7 cm(-1) for the alpha helix, and -5 cm(-1) for the coil.

  16. Secondary flow structure in a model curved artery: 3D morphology and circulation budget analysis

    NASA Astrophysics Data System (ADS)

    Bulusu, Kartik V.; Plesniak, Michael W.

    2015-11-01

    In this study, we examined the rate of change of circulation within control regions encompassing the large-scale vortical structures associated with secondary flows, i.e. deformed Dean-, Lyne- and Wall-type (D-L-W) vortices at planar cross-sections in a 180° curved artery model (curvature ratio, 1/7). Magnetic resonance velocimetry (MRV) and particle image velocimetry (PIV) experiments were performed independently, under the same physiological inflow conditions (Womersley number, 4.2) and using Newtonian blood-analog fluids. The MRV-technique performed at Stanford University produced phase-averaged, three-dimensional velocity fields. Secondary flow field comparisons of MRV-data to PIV-data at various cross-sectional planes and inflow phases were made. A wavelet-decomposition-based approach was implemented to characterize various secondary flow morphologies. We hypothesize that the persistence and decay of arterial secondary flow vortices is intrinsically related to the influence of the out-of-plane flow, tilting, in-plane convection and diffusion-related factors within the control regions. Evaluation of these factors will elucidate secondary flow structures in arterial hemodynamics. Supported by the National Science Foundation under Grant Number CBET-0828903, and GW Center for Biomimetics and Bioinspired Engineering (COBRE). The MRV data were acquired at Stanford University in collaboration with Christopher Elkins and John Eaton.

  17. Secondary structure of the 3' untranslated region of flaviviruses: similarities and differences.

    PubMed

    Proutski, V; Gould, E A; Holmes, E C

    1997-03-15

    Genetic algorithm-based RNA secondary structure prediction was used in combination with comparative sequence analysis to construct models of folding for the distal part of the 3'-untranslated region of flaviviruses belonging to four serological groups. Elements of RNA secondary structure that are preserved among all the flaviviruses studied were revealed, despite the high degree of sequence divergence between them. At the same time, structural elements were observed that distinguish members of different serological groups and, in particular, a region of remarkable structural divergence between the tick-borne and mosquito-borne flaviviruses was found. Application of the genetic algorithm also revealed that the 3'-terminus of flaviviral genomic RNA may take on alternative conformations, which are not observed in the 3'-terminus of complementary minus strand RNA. These alternative folding patterns may have roles in the regulation of transcription and translation initiation and in the switch between them.

  18. Comparative Genome Structure, Secondary Metabolite, and Effector Coding Capacity across Cochliobolus Pathogens

    SciTech Connect

    Condon, Bradford J.; Leng, Yueqiang; Wu, Dongliang; Bushley, Kathryn E.; Ohm, Robin A.; Otillar, Robert; Martin, Joel; Schackwitz, Wendy; Grimwood, Jane; MohdZainudin, NurAinlzzati; Xue, Chunsheng; Wang, Rui; Manning, Viola A.; Dhillon, Braham; Tu, Zheng Jin; Steffenson, Brian J.; Salamov, Asaf; Sun, Hui; Lowry, Steve; LaButti, Kurt; Han, James; Copeland, Alex; Lindquist, Erika; Barry, Kerrie; Schmutz, Jeremy; Baker, Scott E.; Ciuffetti, Lynda M.; Grigoriev, Igor V.; Zhong, Shaobin; Turgeon, B. Gillian

    2013-01-24

    The genomes of five Cochliobolus heterostrophus strains, two Cochliobolus sativus strains, three additional Cochliobolus species (Cochliobolus victoriae, Cochliobolus carbonum, Cochliobolus miyabeanus), and closely related Setosphaeria turcica were sequenced at the Joint Genome Institute (JGI). The datasets were used to identify SNPs between strains and species, unique genomic regions, core secondary metabolism genes, and small secreted protein (SSP) candidate effector encoding genes with a view towards pinpointing structural elements and gene content associated with specificity of these closely related fungi to different cereal hosts. Whole-genome alignment shows that three to five of each genome differs between strains of the same species, while a quarter of each genome differs between species. On average, SNP counts among field isolates of the same C. heterostrophus species are more than 25 higher than those between inbred lines and 50 lower than SNPs between Cochliobolus species. The suites of nonribosomal peptide synthetase (NRPS), polyketide synthase (PKS), and SSP encoding genes are astoundingly diverse among species but remarkably conserved among isolates of the same species, whether inbred or field strains, except for defining examples that map to unique genomic regions. Functional analysis of several strain-unique PKSs and NRPSs reveal a strong correlation with a role in virulence.

  19. Comparative Genome Structure, Secondary Metabolite, and Effector Coding Capacity across Cochliobolus Pathogens

    PubMed Central

    Bushley, Kathryn E.; Ohm, Robin A.; Otillar, Robert; Martin, Joel; Schackwitz, Wendy; Grimwood, Jane; MohdZainudin, NurAinIzzati; Xue, Chunsheng; Wang, Rui; Manning, Viola A.; Dhillon, Braham; Tu, Zheng Jin; Steffenson, Brian J.; Salamov, Asaf; Sun, Hui; Lowry, Steve; LaButti, Kurt; Han, James; Copeland, Alex; Lindquist, Erika; Barry, Kerrie; Schmutz, Jeremy; Baker, Scott E.; Ciuffetti, Lynda M.; Grigoriev, Igor V.; Zhong, Shaobin; Turgeon, B. Gillian

    2013-01-01

    The genomes of five Cochliobolus heterostrophus strains, two Cochliobolus sativus strains, three additional Cochliobolus species (Cochliobolus victoriae, Cochliobolus carbonum, Cochliobolus miyabeanus), and closely related Setosphaeria turcica were sequenced at the Joint Genome Institute (JGI). The datasets were used to identify SNPs between strains and species, unique genomic regions, core secondary metabolism genes, and small secreted protein (SSP) candidate effector encoding genes with a view towards pinpointing structural elements and gene content associated with specificity of these closely related fungi to different cereal hosts. Whole-genome alignment shows that three to five percent of each genome differs between strains of the same species, while a quarter of each genome differs between species. On average, SNP counts among field isolates of the same C. heterostrophus species are more than 25× higher than those between inbred lines and 50× lower than SNPs between Cochliobolus species. The suites of nonribosomal peptide synthetase (NRPS), polyketide synthase (PKS), and SSP–encoding genes are astoundingly diverse among species but remarkably conserved among isolates of the same species, whether inbred or field strains, except for defining examples that map to unique genomic regions. Functional analysis of several strain-unique PKSs and NRPSs reveal a strong correlation with a role in virulence. PMID:23357949

  20. Shape and secondary structure prediction for ncRNAs including pseudoknots based on linear SVM

    PubMed Central

    2013-01-01

    Background Accurate secondary structure prediction provides important information to undefirstafinding the tertiary structures and thus the functions of ncRNAs. However, the accuracy of the native structure derivation of ncRNAs is still not satisfactory, especially on sequences containing pseudoknots. It is recently shown that using the abstract shapes, which retain adjacency and nesting of structural features but disregard the length details of helix and loop regions, can improve the performance of structure prediction. In this work, we use SVM-based feature selection to derive the consensus abstract shape of homologous ncRNAs and apply the predicted shape to structure prediction including pseudoknots. Results Our approach was applied to predict shapes and secondary structures on hundreds of ncRNA data sets with and without psuedoknots. The experimental results show that we can achieve 18% higher accuracy in shape prediction than the state-of-the-art consensus shape prediction tools. Using predicted shapes in structure prediction allows us to achieve approximate 29% higher sensitivity and 10% higher positive predictive value than other pseudoknot prediction tools. Conclusions Extensive analysis of RNA properties based on SVM allows us to identify important properties of sequences and structures related to their shapes. The combination of mass data analysis and SVM-based feature selection makes our approach a promising method for shape and structure prediction. The implemented tools, Knot Shape and Knot Structure are open source software and can be downloaded at: http://www.cse.msu.edu/~achawana/KnotShape. PMID:23369147

  1. Secondary deuterium kinetic isotope effects in irreversible additions of hydride and carbon nucleophiles to aldehydes: A spectrum of transition states from complete bond formation to single electron transfer

    SciTech Connect

    Gajewski, J.J.; Bocian, W.; Harris, N.J.; Olson, L.P.; Gajewski, J.P.

    1999-01-20

    The competitive kinetics of hydride and organometallic additions to benzaldehyde-H and -D were determined at {minus}78 C using LiAlH{sub 4}, LiBEt{sub 3}H, NaBH{sub 4}, LiBH{sub 4}, LiAl(O-tert-butoxy){sub 3}H, NaB(OMe){sub 3}H, NaB-(Ac){sub 3}H (at 20 C) methyl, phenyl, and allyl Grignard, and methyl-, phenyl-, n-butyl-, tert-butyl-, and allyllithium. The additions of hydride were found to have an inverse secondary deuterium kinetic isotope effects in all cases, but the magnitude of the effect varied inversely with the apparent reactivity of the hydride. In the additions of methyl Grignard reagent and of methyllithium and phenyllithium, inverse secondary deuterium isotope effects were observed; little if any isotope effect was observed with phenyl Grignard or n-butyl- and tert-butyllithium. With allyl Grignard and allyllithium, a normal secondary deuterium kinetic isotope effect was observed. The results indicate that rate-determining single-electron transfer occurs with allyl reagents, but direct nucleophilic reaction occurs with all of the other reagents, with the extent of bond formation dependent on the reactivity of the reagent. In the addition of methyllithium to cyclohexanecarboxyaldehyde, a less inverse secondary deuterium kinetic isotope effect was observed than that observed in the addition of methyllithium to benzaldehyde, and allyllithium addition to cyclohexanecarboxaldehyde had a kinetic isotope effect near unity. The data with organometallic additions, which are not incompatible with observations of carbonyl carbon isotope effects, suggest that electrochemically determined redox potentials which indicate endoergonic electron transfer with energies less than ca. 13 kcal/mol allow electron-transfer mechanisms to compete well with direct polar additions to aldehydes, provided that the reagent is highly stabilized, like allyl species. Methyllithium and phenyllithium and methyl and phenyl Grignard reagents are estimated to undergo electron transfer with

  2. Single-molecule reconstruction of oligonucleotide secondary structure by atomic force microscopy.

    PubMed

    Pyne, Alice; Thompson, Ruth; Leung, Carl; Roy, Debdulal; Hoogenboom, Bart W

    2014-08-27

    Based on soft-touch atomic force microscopy, a method is described to reconstruct the secondary structure of single extended biomolecules, without the need for crystallization. The method is tested by accurately reproducing the dimensions of the B-DNA crystal structure. Importantly, intramolecular variations in groove depth of the DNA double helix are resolved, which would be inaccessible for methods that rely on ensemble-averaging.

  3. A permutation based simulated annealing algorithm to predict pseudoknotted RNA secondary structures.

    PubMed

    Tsang, Herbert H; Wiese, Kay C

    2015-01-01

    Pseudoknots are RNA tertiary structures which perform essential biological functions. This paper discusses SARNA-Predict-pk, a RNA pseudoknotted secondary structure prediction algorithm based on Simulated Annealing (SA). The research presented here extends previous work of SARNA-Predict and further examines the effect of the new algorithm to include prediction of RNA secondary structure with pseudoknots. An evaluation of the performance of SARNA-Predict-pk in terms of prediction accuracy is made via comparison with several state-of-the-art prediction algorithms using 20 individual known structures from seven RNA classes. We measured the sensitivity and specificity of nine prediction algorithms. Three of these are dynamic programming algorithms: Pseudoknot (pknotsRE), NUPACK, and pknotsRG-mfe. One is using the statistical clustering approach: Sfold and the other five are heuristic algorithms: SARNA-Predict-pk, ILM, STAR, IPknot and HotKnots algorithms. The results presented in this paper demonstrate that SARNA-Predict-pk can out-perform other state-of-the-art algorithms in terms of prediction accuracy. This supports the use of the proposed method on pseudoknotted RNA secondary structure prediction of other known structures. PMID:26558299

  4. Protein secondary-structure description with a coarse-grained model.

    PubMed

    Kneller, Gerald R; Hinsen, Konrad

    2015-07-01

    A coarse-grained geometrical model for protein secondary-structure description and analysis is presented which uses only the positions of the C(α) atoms. A space curve connecting these positions by piecewise polynomial interpolation is constructed and the folding of the protein backbone is described by a succession of screw motions linking the Frenet frames at consecutive C(α) positions. Using the ASTRAL subset of the SCOPe database of protein structures, thresholds are derived for the screw parameters of secondary-structure elements and demonstrate that the latter can be reliably assigned on the basis of a C(α) model. For this purpose, a comparative study with the widely used DSSP (Define Secondary Structure of Proteins) algorithm was performed and it was shown that the parameter distribution corresponding to the ensemble of all pure C(α) structures in the RCSB Protein Data Bank matches that of the ASTRAL database. It is expected that this approach will be useful in the development of structure-refinement techniques for low-resolution data. PMID:26143913

  5. Nitrogen and phosphorus addition impact soil N2O emission in a secondary tropical forest of South China

    PubMed Central

    Wang, Faming; Li, Jian; Wang, Xiaoli; Zhang, Wei; Zou, Bi; Neher, Deborah A.; Li, Zhian

    2014-01-01

    Nutrient availability greatly regulates ecosystem processes and functions of tropical forests. However, few studies have explored impacts of N addition (aN), P addition (aP) and N×P interaction on tropical forests N2O fluxes. We established an N and P addition experiment in a tropical forest to test whether: (1) N addition would increase N2O emission and nitrification, and (2) P addition would increase N2O emission and N transformations. Nitrogen and P addition had no effect on N mineralization and nitrification. Soil microbial biomass was increased following P addition in wet seasons. aN increased 39% N2O emission as compared to control (43.3 μgN2O-N m−2h−1). aP did not increase N2O emission. Overall, N2O emission was 60% greater for aNP relative to the control, but significant difference was observed only in wet seasons, when N2O emission was 78% greater for aNP relative to the control. Our results suggested that increasing N deposition will enhance soil N2O emission, and there would be N×P interaction on N2O emission in wet seasons. Given elevated N deposition in future, P addition in this tropical soil will stimulate soil microbial activities in wet seasons, which will further enhance soil N2O emission. PMID:25001013

  6. An Adaptive Defect Weighted Sampling Algorithm to Design Pseudoknotted RNA Secondary Structures

    PubMed Central

    Zandi, Kasra; Butler, Gregory; Kharma, Nawwaf

    2016-01-01

    Computational design of RNA sequences that fold into targeted secondary structures has many applications in biomedicine, nanotechnology and synthetic biology. An RNA molecule is made of different types of secondary structure elements and an important RNA element named pseudoknot plays a key role in stabilizing the functional form of the molecule. However, due to the computational complexities associated with characterizing pseudoknotted RNA structures, most of the existing RNA sequence designer algorithms generally ignore this important structural element and therefore limit their applications. In this paper we present a new algorithm to design RNA sequences for pseudoknotted secondary structures. We use NUPACK as the folding algorithm to compute the equilibrium characteristics of the pseudoknotted RNAs, and describe a new adaptive defect weighted sampling algorithm named Enzymer to design low ensemble defect RNA sequences for targeted secondary structures including pseudoknots. We used a biological data set of 201 pseudoknotted structures from the Pseudobase library to benchmark the performance of our algorithm. We compared the quality characteristics of the RNA sequences we designed by Enzymer with the results obtained from the state of the art MODENA and antaRNA. Our results show our method succeeds more frequently than MODENA and antaRNA do, and generates sequences that have lower ensemble defect, lower probability defect and higher thermostability. Finally by using Enzymer and by constraining the design to a naturally occurring and highly conserved Hammerhead motif, we designed 8 sequences for a pseudoknotted cis-acting Hammerhead ribozyme. Enzymer is available for download at https://bitbucket.org/casraz/enzymer. PMID:27499762

  7. An Adaptive Defect Weighted Sampling Algorithm to Design Pseudoknotted RNA Secondary Structures.

    PubMed

    Zandi, Kasra; Butler, Gregory; Kharma, Nawwaf

    2016-01-01

    Computational design of RNA sequences that fold into targeted secondary structures has many applications in biomedicine, nanotechnology and synthetic biology. An RNA molecule is made of different types of secondary structure elements and an important RNA element named pseudoknot plays a key role in stabilizing the functional form of the molecule. However, due to the computational complexities associated with characterizing pseudoknotted RNA structures, most of the existing RNA sequence designer algorithms generally ignore this important structural element and therefore limit their applications. In this paper we present a new algorithm to design RNA sequences for pseudoknotted secondary structures. We use NUPACK as the folding algorithm to compute the equilibrium characteristics of the pseudoknotted RNAs, and describe a new adaptive defect weighted sampling algorithm named Enzymer to design low ensemble defect RNA sequences for targeted secondary structures including pseudoknots. We used a biological data set of 201 pseudoknotted structures from the Pseudobase library to benchmark the performance of our algorithm. We compared the quality characteristics of the RNA sequences we designed by Enzymer with the results obtained from the state of the art MODENA and antaRNA. Our results show our method succeeds more frequently than MODENA and antaRNA do, and generates sequences that have lower ensemble defect, lower probability defect and higher thermostability. Finally by using Enzymer and by constraining the design to a naturally occurring and highly conserved Hammerhead motif, we designed 8 sequences for a pseudoknotted cis-acting Hammerhead ribozyme. Enzymer is available for download at https://bitbucket.org/casraz/enzymer. PMID:27499762

  8. An Adaptive Defect Weighted Sampling Algorithm to Design Pseudoknotted RNA Secondary Structures.

    PubMed

    Zandi, Kasra; Butler, Gregory; Kharma, Nawwaf

    2016-01-01

    Computational design of RNA sequences that fold into targeted secondary structures has many applications in biomedicine, nanotechnology and synthetic biology. An RNA molecule is made of different types of secondary structure elements and an important RNA element named pseudoknot plays a key role in stabilizing the functional form of the molecule. However, due to the computational complexities associated with characterizing pseudoknotted RNA structures, most of the existing RNA sequence designer algorithms generally ignore this important structural element and therefore limit their applications. In this paper we present a new algorithm to design RNA sequences for pseudoknotted secondary structures. We use NUPACK as the folding algorithm to compute the equilibrium characteristics of the pseudoknotted RNAs, and describe a new adaptive defect weighted sampling algorithm named Enzymer to design low ensemble defect RNA sequences for targeted secondary structures including pseudoknots. We used a biological data set of 201 pseudoknotted structures from the Pseudobase library to benchmark the performance of our algorithm. We compared the quality characteristics of the RNA sequences we designed by Enzymer with the results obtained from the state of the art MODENA and antaRNA. Our results show our method succeeds more frequently than MODENA and antaRNA do, and generates sequences that have lower ensemble defect, lower probability defect and higher thermostability. Finally by using Enzymer and by constraining the design to a naturally occurring and highly conserved Hammerhead motif, we designed 8 sequences for a pseudoknotted cis-acting Hammerhead ribozyme. Enzymer is available for download at https://bitbucket.org/casraz/enzymer.

  9. Evidence of Pervasive Biologically Functional Secondary Structures within the Genomes of Eukaryotic Single-Stranded DNA Viruses

    PubMed Central

    Muhire, Brejnev Muhizi; Golden, Michael; Murrell, Ben; Lefeuvre, Pierre; Lett, Jean-Michel; Gray, Alistair; Poon, Art Y. F.; Ngandu, Nobubelo Kwanele; Semegni, Yves; Tanov, Emil Pavlov; Monjane, Adérito Luis; Harkins, Gordon William; Varsani, Arvind; Shepherd, Dionne Natalie

    2014-01-01

    Single-stranded DNA (ssDNA) viruses have genomes that are potentially capable of forming complex secondary structures through Watson-Crick base pairing between their constituent nucleotides. A few of the structural elements formed by such base pairings are, in fact, known to have important functions during the replication of many ssDNA viruses. Unknown, however, are (i) whether numerous additional ssDNA virus genomic structural elements predicted to exist by computational DNA folding methods actually exist and (ii) whether those structures that do exist have any biological relevance. We therefore computationally inferred lists of the most evolutionarily conserved structures within a diverse selection of animal- and plant-infecting ssDNA viruses drawn from the families Circoviridae, Anelloviridae, Parvoviridae, Nanoviridae, and Geminiviridae and analyzed these for evidence of natural selection favoring the maintenance of these structures. While we find evidence that is consistent with purifying selection being stronger at nucleotide sites that are predicted to be base paired than at sites predicted to be unpaired, we also find strong associations between sites that are predicted to pair with one another and site pairs that are apparently coevolving in a complementary fashion. Collectively, these results indicate that natural selection actively preserves much of the pervasive secondary structure that is evident within eukaryote-infecting ssDNA virus genomes and, therefore, that much of this structure is biologically functional. Lastly, we provide examples of various highly conserved but completely uncharacterized structural elements that likely have important functions within some of the ssDNA virus genomes analyzed here. PMID:24284329

  10. Male secondary sexual structures and the systematics of the Thereus oppia species group (Lepidoptera, Lycaenidae, Eumaeini).

    PubMed

    Robbins, Robert K; Heredia, María Dolores; Busby, Robert C

    2015-01-01

    The Thereus oppia species group includes species with and without a scent pad, which is a histologically and morphologically characterized male secondary sexual structure on the dorsal surface of the forewing. To assess the hypothesis that these structures are lost evolutionarily, but not regained (Dollo's Law), the taxonomy of this species group is revised. Thereus lomalarga sp. n., and Thereus brocki sp. n., are described. Diagnostic traits, especially male secondary structures, within the Thereus oppia species group are illustrated. Distributional and biological information is summarized for each species. Three species have been reared, and the caterpillars eat Loranthaceae. An inferred phylogeny is consistent with the hypothesis that scent pads in the Thereus oppia species group have been lost evolutionarily twice (in allopatry), and not re-gained. PMID:26448715

  11. Male secondary sexual structures and the systematics of the Thereus oppia species group (Lepidoptera, Lycaenidae, Eumaeini)

    PubMed Central

    Robbins, Robert K.; Heredia, María Dolores; Busby, Robert C.

    2015-01-01

    Abstract The Thereus oppia species group includes species with and without a scent pad, which is a histologically and morphologically characterized male secondary sexual structure on the dorsal surface of the forewing. To assess the hypothesis that these structures are lost evolutionarily, but not regained (Dollo’s Law), the taxonomy of this species group is revised. Thereus lomalarga sp. n., and Thereus brocki sp. n., are described. Diagnostic traits, especially male secondary structures, within the Thereus oppia species group are illustrated. Distributional and biological information is summarized for each species. Three species have been reared, and the caterpillars eat Loranthaceae. An inferred phylogeny is consistent with the hypothesis that scent pads in the Thereus oppia species group have been lost evolutionarily twice (in allopatry), and not re-gained. PMID:26448715

  12. Influence of MLS laser radiation on erythrocyte membrane fluidity and secondary structure of human serum albumin.

    PubMed

    Pasternak, Kamila; Nowacka, Olga; Wróbel, Dominika; Pieszyński, Ireneusz; Bryszewska, Maria; Kujawa, Jolanta

    2014-03-01

    The biostimulating activity of low level laser radiation of various wavelengths and energy doses is widely documented in the literature, but the mechanisms of the intracellular reactions involved are not precisely known. The aim of this paper is to evaluate the influence of low level laser radiation from an multiwave locked system (MLS) of two wavelengths (wavelength = 808 nm in continuous emission and 905 nm in pulsed emission) on the human erythrocyte membrane and on the secondary structure of human serum albumin (HSA). Human erythrocytes membranes and HSA were irradiated with laser light of low intensity with surface energy density ranging from 0.46 to 4.9 J cm(-2) and surface energy power density 195 mW cm(-2) (1,000 Hz) and 230 mW cm(-2) (2,000 Hz). Structural and functional changes in the erythrocyte membrane were characterized by its fluidity, while changes in the protein were monitored by its secondary structure. Dose-dependent changes in erythrocyte membrane fluidity were induced by near-infrared laser radiation. Slight changes in the secondary structure of HSA were also noted. MLS laser radiation influences the structure and function of the human erythrocyte membrane resulting in a change in fluidity.

  13. Conserved RNA secondary structures and long-range interactions in hepatitis C viruses.

    PubMed

    Fricke, Markus; Dünnes, Nadia; Zayas, Margarita; Bartenschlager, Ralf; Niepmann, Michael; Marz, Manja

    2015-07-01

    Hepatitis C virus (HCV) is a hepatotropic virus with a plus-strand RNA genome of ∼9.600 nt. Due to error-prone replication by its RNA-dependent RNA polymerase (RdRp) residing in nonstructural protein 5B (NS5B), HCV isolates are grouped into seven genotypes with several subtypes. By using whole-genome sequences of 106 HCV isolates and secondary structure alignments of the plus-strand genome and its minus-strand replication intermediate, we established refined secondary structures of the 5' untranslated region (UTR), the cis-acting replication element (CRE) in NS5B, and the 3' UTR. We propose an alternative structure in the 5' UTR, conserved secondary structures of 5B stem-loop (SL)1 and 5BSL2, and four possible structures of the X-tail at the very 3' end of the HCV genome. We predict several previously unknown long-range interactions, most importantly a possible circularization interaction between distinct elements in the 5' and 3' UTR, reminiscent of the cyclization elements of the related flaviviruses. Based on analogy to these viruses, we propose that the 5'-3' UTR base-pairing in the HCV genome might play an important role in viral RNA replication. These results may have important implications for our understanding of the nature of the cis-acting RNA elements in the HCV genome and their possible role in regulating the mutually exclusive processes of viral RNA translation and replication.

  14. A Dynamic Programming Algorithm for Finding the Optimal Placement of a Secondary Structure Topology in Cryo-EM Data.

    PubMed

    Biswas, Abhishek; Ranjan, Desh; Zubair, Mohammad; He, Jing

    2015-09-01

    The determination of secondary structure topology is a critical step in deriving the atomic structures from the protein density maps obtained from electron cryomicroscopy technique. This step often relies on matching the secondary structure traces detected from the protein density map to the secondary structure sequence segments predicted from the amino acid sequence. Due to inaccuracies in both sources of information, a pool of possible secondary structure positions needs to be sampled. One way to approach the problem is to first derive a small number of possible topologies using existing matching algorithms, and then find the optimal placement for each possible topology. We present a dynamic programming method of Θ(Nq(2)h) to find the optimal placement for a secondary structure topology. We show that our algorithm requires significantly less computational time than the brute force method that is in the order of Θ(q(N) h).

  15. Interconnection of salt-induced hydrophobic compaction and secondary structure formation depends on solution conditions: revisiting early events of protein folding at single molecule resolution.

    PubMed

    Haldar, Shubhasis; Chattopadhyay, Krishnananda

    2012-03-30

    What happens in the early stage of protein folding remains an interesting unsolved problem. Rapid kinetics measurements with cytochrome c using submillisecond continuous flow mixing devices suggest simultaneous formation of a compact collapsed state and secondary structure. These data seem to indicate that collapse formation is guided by specific short and long range interactions (heteropolymer collapse). A contrasting interpretation also has been proposed, which suggests that the collapse formation is rapid, nonspecific, and a trivial solvent related compaction, which could as well be observed by a homopolymer (homopolymer collapse). We address this controversy using fluorescence correlation spectroscopy (FCS), which enables us to monitor the salt-induced compaction accompanying collapse formation and the associated time constant directly at single molecule resolution. In addition, we follow the formation of secondary structure using far UV CD. The data presented here suggest that both these models (homopolymer and heteropolymer) could be applicable depending on the solution conditions. For example, the formation of secondary structure and compact state is not simultaneous in aqueous buffer. In aqueous buffer, formation of the compact state occurs through a two-state co-operative transition following heteropolymer formalism, whereas secondary structure formation takes place gradually. In contrast, in the presence of urea, a compaction of the protein radius occurs gradually over an extended range of salt concentration following homopolymer formalism. The salt-induced compaction and the formation of secondary structure take place simultaneously in the presence of urea.

  16. Three new crystal structures in the Na-Pb system: solving structures without additional experimental input.

    PubMed

    Ward, Logan; Michel, Kyle; Wolverton, Chris

    2015-09-01

    The structures of three Na-Pb compounds, γ, δ and δ', have remained incompletely solved for nearly 60 years. The space group, lattice parameters and positions of the Pb atoms of these three structures have been determined, but the positions of the Na atoms are still unknown. In this work, the First-Principles Assisted Structure Solution (FPASS) method [Meredig & Wolverton (2013). Nat. Mater. 12, 123-127] has been used to complete the description of these three structures using only experimental information available from the literature as input. The paper also discusses the relative advantages of constrained crystal structure prediction tools, like FPASS, in comparison to conventional crystal structure prediction methods in reference to their abilities to complete the solution of other unsolved structures. PMID:26317197

  17. Self-Efficacy, School Resources, Job Stressors and Burnout among Spanish Primary and Secondary School Teachers: A Structural Equation Approach

    ERIC Educational Resources Information Center

    Betoret, Fernando Domenech

    2009-01-01

    This study examines the relationship between school resources, teacher self-efficacy, potential multi-level stressors and teacher burnout using structural equation modelling. The causal structure for primary and secondary school teachers was also examined. The sample was composed of 724 primary and secondary Spanish school teachers. The changes…

  18. Minimum-free-energy distribution of RNA secondary structures: Entropic and thermodynamic properties of rare events

    NASA Astrophysics Data System (ADS)

    Wolfsheimer, S.; Hartmann, A. K.

    2010-08-01

    We study the distribution of the minimum free energy (MFE) for the Turner model of pseudoknot free RNA secondary structures over ensembles of random RNA sequences. In particular, we are interested in those rare and intermediate events of unexpected low MFEs. Generalized ensemble Markov-chain Monte Carlo methods allow us to explore the rare-event tail of the MFE distribution down to probabilities such as 10-70 and to study the relationship between the sequence entropy and structural properties for sequence ensembles with fixed MFEs. Entropic and structural properties of those ensembles are compared with natural RNA of the same reduced MFE ( z score).

  19. An atomic view of additive mutational effects in a protein structure

    SciTech Connect

    Skinner, M.M.; Terwilliger, T.C.

    1996-04-01

    Substitution of a single amino acid in a protein will often lead to substantial changes in properties. If these properties could be altered in a rational way then proteins could be readily generated with functions tailored to specific uses. When amino acid substitutions are made at well-separated locations in a single protein, their effects are generally additive. Additivity of effects of amino acid substitutions is very useful because the properties of proteins with any combination of substitutions can be inferred directly from those of the proteins with single changes. It would therefore be of considerable interest to have a means of knowing whether substitutions at a particular pair of sites in a protein are likely to lead to additive effects. The structural basis for additivity of effects of mutations on protein function was examined by determining crystal structures of single and double mutants in the hydrophobic core of gene V protein. Structural effects of mutations were found to be cumulative when two mutations were made in a single protein. Additivity occurs in this case because the regions structurally affected by mutations at the two sites do not overlap even though the sites are separated by only 9 {angstrom}. Structural distortions induced by mutations in gene V protein decrease rapidly, but not isotropically, with distance from the site of mutation. It is anticipated that cases where structural and functional effects of mutations will be additive could be identified simply by examining whether the regions structurally affected by each component mutation overlap.

  20. Determination of Protein Secondary Structure from Infrared Spectra Using Partial Least-Squares Regression.

    PubMed

    Wilcox, Kieaibi E; Blanch, Ewan W; Doig, Andrew J

    2016-07-12

    Infrared (IR) spectra contain substantial information about protein structure. This has previously most often been exploited by using known band assignments. Here, we convert spectral intensities in bins within Amide I and II regions to vectors and apply machine learning methods to determine protein secondary structure. Partial least squares was performed on spectra of 90 proteins in H2O. After preprocessing and removal of outliers, 84 proteins were used for this work. Standard normal variate and second-derivative preprocessing methods on the combined Amide I and II data generally gave the best performance, with root-mean-square values for prediction of ∼12% for α-helix, ∼7% for β-sheet, 7% for antiparallel β-sheet, and ∼8% for other conformations. Analysis of Fourier transform infrared (FTIR) spectra of 16 proteins in D2O showed that secondary structure determination was slightly poorer than in H2O. Interval partial least squares was used to identify the critical regions within spectra for secondary structure prediction and showed that the sides of bands were most valuable, rather than their peak maxima. In conclusion, we have shown that multivariate analysis of protein FTIR spectra can give α-helix, β-sheet, other, and antiparallel β-sheet contents with good accuracy, comparable to that of circular dichroism, which is widely used for this purpose. PMID:27322779

  1. Synthesis of Heterocycles Through Classical Ugi and Passerini Reactions Followed by Secondary Transformations Involving One or Two Additional Functional Groups

    NASA Astrophysics Data System (ADS)

    Banfi, Luca; Basso, Andrea; Riva, Renata

    The combination of classical isocyanide-based multicomponent reactions (Ugi and Passerini) with a variety of post-condensation transformations, which take advantage of suitably positioned additional functional groups, allows the straightforward synthesis, often in 1-2 synthetic steps, of many diverse nitrogen-containing heterocycles. This review will cover all the applications of this strategy reported to date (September 2009).

  2. Leader length and secondary structure modulate mRNA function under conditions of stress

    SciTech Connect

    Kozak, M.

    1988-07-01

    Simina virus 40-based plasmids that direct the synthesis of preproinsulin in cultured monkey cells were used to study the effects of mRNA structure on translational efficiency. Lengthening the leader sequence enhanced translation in this system. The enhancement was most obvious when an unstructured sequence (two, four, or eight copies of the oligonculeotide AGCTAAGTAAGTAAGTA) was inserted upstream from a region of deliberate secondary structure; the degree of enhancement was proportional to the number of copies of the inserted oligonucleotide. Lengthening the leader sequence on the 3' side of a stem-and-loop structure, in contrast, did not offset the potentially inhibitory effect of the hairpin structure. Both the facilitating effect of length and the inhibitory effect of secondary structure were demonstrated most easily under conditions of mRNA competition, which was brought about by an abrupt shift in the tonicity of the culture medium. These experiments suggest a simple structural basis for the long-recognized differential response of viral and cellular mRNAs to hypertonic stress. The fact that the translatability of structure-prone mRNAs varies with changes in the environment may also have general implications for gene expression in eucaryotic cells.

  3. Circumstances and mechanisms of inhibition of translation by secondary structure in eucaryotic mRNAs.

    PubMed Central

    Kozak, M

    1989-01-01

    This paper describes in vitro experiments with two types of intramolecular duplex structures that inhibit translation in cis by preventing the formation of an initiation complex or by causing the complex to be abortive. One stem-loop structure (delta G = -30 kcal/mol) prevented mRNA from engaging 40S subunits when the hairpin occurred 12 nucleotides (nt) from the cap but had no deleterious effect when it was repositioned 52 nt from the cap. This result confirms prior in vivo evidence that the 40S subunit-factor complex, once bound to mRNA, has considerable ability to penetrate secondary structure. Consequently, translation is most sensitive to secondary structure at the entry site for ribosomes, i.e., the 5' end of the mRNA. The second stem-loop structure (hp7; delta G = -61 kcal/mol, located 72 nt from the cap) was too stable to be unwound by 40S ribosomes, hp7 did not prevent a 40S ribosomal subunit from binding but caused the 40S subunit to stall on the 5' side of the hairpin, exactly as the scanning model predicts. Control experiments revealed that 80S elongating ribosomes could disrupt duplex structures, such as hp7, that were too stable to be penetrated by the scanning 40S ribosome-factor complex. A third type of base-paired structure shown to inhibit translation in vivo involves a long-range interaction between the 5' and 3' noncoding sequences. Images PMID:2601712

  4. Small-angle X-ray scattering: a bridge between RNA secondary structures and three-dimensional topological structures

    SciTech Connect

    Fang, Xianyang; Stagno, Jason R.; Bhandari, Yuba R.; Zuo, Xiaobing; Wang, Yun-Xing

    2015-02-01

    Whereas the structures of small to medium-sized well folded RNA molecules often can be determined by either X-ray crystallography or NMR spectroscopy, obtaining structural information for large RNAs using experimental, computational, or combined approaches remains a major interest and challenge. RNA is very sensitive to small-angle X-ray scattering (SAXS) due to high electron density along phosphate-sugar backbones, whose scattering contribution dominates SAXS intensity. For this reason, SAXS is particularly useful in obtaining global RNA structural information that outlines backbone topologies and, therefore, molecular envelopes. Such information is extremely valuable in bridging the gap between the secondary structures and three-dimensional topological structures of RNAmolecules, particularly those that have proven difficult to study using other structuredetermination methods. Here we review published results of RNA topological structures derived from SAXS data or in combination with other experimental data, as well as details on RNA sample preparation for SAXS experiments.

  5. Determination of the Secondary Structure of the king Cobra Neurotoxin CM-11.

    PubMed

    Pang, Yu-Xi; Liu, Wei-Dong; Liu, Ai-Zhuo; Pei, Feng-Kui

    1997-01-01

    The king cobra neurotoxin CM-11 is a small protein with 72 amino acid residues. After its complete assignments of (1)H-NMR resonance's were obtained using various 2D-NMR technologies, including DQF-COSY, clean-TOCSY and NOESY, the secondary structure was analysed by studying the various NOEs extracted from the NOESY spectra and the distribution of chemical shifts. The secondary structure was finally determined by MCD as follows: a triple-strand antiparallel beta sheet with I20-W26, R37-A43 and V53-S59 as its beta strands, a short alpha helix formed by W30-G35 and four turns formed by P7-K1O, C14-G17, K50-V53 and D61-N64.

  6. Analysis of the secondary structure of a protein's N-terminal

    NASA Astrophysics Data System (ADS)

    Floare, C. G.; Bogdan, M.; Horovitz, O.; Mocanu, A.; Tomoaia-Cotisel, M.

    2009-08-01

    The major protein component from aleurone cells of barley (Hordeum vulgare L.), PACB, is related to 7S globulins present in other cereals and to the vicilin-type 7S globulins of legumes and cotton seed. It contains 4 subunits of about 20, 25, 40 and 50 kDa molecular weights. The N-terminal sequence of 16 amino acids (over 260 atoms) in the protein was previously determined, and our aim is the prediction of its secondary structure. The empirical Chou-Fasman method was applied in an improved version as well as the empirical DSC method (discrimination of protein secondary structure class) with quite similar results. A molecular dynamics simulation was also performed, using the FF99SB forcefield within AMBER version 9.0. Solvation effects were incorporated using the Born model. The results are compared and a 3D model is proposed.

  7. Sequence and secondary structure of the mitochondrial 16S ribosomal RNA gene of Ixodes scapularis.

    PubMed

    Krakowetz, Chantel N; Chilton, Neil B

    2015-02-01

    The complete DNA sequences and secondary structure of the mitochondrial (mt) 16S ribosomal (r) RNA gene were determined for six Ixodes scapularis adults. There were 44 variable nucleotide positions in the 1252 bp sequence alignment. Most (95%) nucleotide alterations did not affect the integrity of the secondary structure of the gene because they either occurred at unpaired positions or represented compensatory changes that maintained the base pairing in helices. A large proportion (75%) of the intraspecific variation in DNA sequence occurred within Domains I, II and VI of the 16S gene. Therefore, several regions within this gene may be highly informative for studies of the population genetics and phylogeography of I. scapularis, a major vector of pathogens of humans and domestic animals in North America.

  8. An overview of the secondary structure of the V4 region of eukaryotic small-subunit ribosomal RNA.

    PubMed

    Nickrent, D L; Sargent, M L

    1991-01-25

    The V4 region of the small subunit (18S) ribosomal RNA was examined in 72 different sequences representing a broad sample eukaryotic diversity. This domain is the most variable region of the 18S rRNA molecule and ranges in length from ca. 230 to over 500 bases. Based upon comparative analysis, secondary structural models were constructed for all sequences and the resulting generalized model shows that most organisms possess seven helices for this region. The protists and two insects show from one to as many as four helices in addition to the above seven. In this report, we summarize secondary structure information presented elsewhere for the V4 region, describe the general features for helical and apical regions, and identify signature sequences useful in helix identification. Our model generally agrees with other current concepts; however, we propose modifications or alternative structures for the start of the V4 region, the large protist inserts, and the sector that may possibly contain a pseudoknot.

  9. NMR assignments, secondary structure, and global fold of calerythrin, an EF-hand calcium-binding protein from Saccharopolyspora erythraea.

    PubMed Central

    Aitio, H.; Annila, A.; Heikkinen, S.; Thulin, E.; Drakenberg, T.; Kilpeläinen, I.

    1999-01-01

    Calerythrin is a 20 kDa calcium-binding protein isolated from gram-positive bacterium Saccharopolyspora erythraea. Based on amino acid sequence homology, it has been suggested that calerythrin belongs to the family of invertebrate sarcoplasmic EF-hand calcium-binding proteins (SCPs), and therefore it is expected to function as a calcium buffer. NMR spectroscopy was used to obtain structural information on the protein in solution. Backbone and side chain 1H, 13C, and 15N assignments were obtained from triple resonance experiments HNCACB, HN(CO)CACB, HNCO, CC(CO)NH, and [15N]-edited TOCSY, and HCCH-TOCSY. Secondary structure was determined by using secondary chemical shifts and characteristic NOEs. In addition, backbone N-H residual dipolar couplings were measured from a spin-state selective [1H, 15N] correlation spectrum acquired from a sample dissolved in a dilute liquid crystal. Four EF-hand motifs with characteristic helix-loop-helix patterns were observed. Three of these are typical calcium-binding EF-hands, whereas site 2 is an atypical nonbinding site. The global fold of calerythrin was assessed by dipolar couplings. Measured dipolar couplings were compared with values calculated from four crystal structures of proteins with sequence homology to calerythrin. These data allowed us to recognize an overall similarity between the folds of calerythrin and sarcoplasmic calcium-binding proteins from the sandworm Nereis diversicolor and the amphioxus Branchiostoma lanceolatum. PMID:10631973

  10. Extremely Slow Dynamics of an Abiotic Helical Assembly: Unusual Relevance to the Secondary Structure of Proteins.

    PubMed

    Avinash, M B; Govindaraju, T

    2013-02-21

    Serendipitously, we found that isoleucine methylester functionalized perylenediimide 1 undergoes an extremely slow supramolecular helical assembly over a day's time. Surprisingly, heating led to irreversible chiral denaturation. However, reversible helical assembly could be achieved only in the presence of nondenatured aggregates of 1, which act as seeds. The intriguing functional relevance deduced from 1 was employed to draw parallels with the secondary structure of proteins, envisaging its plausible implications.

  11. A generalized threading model using integer programming that allows for secondary structure element deletion.

    PubMed

    Ellrott, Kyle; Guo, Jun-tao; Olman, Victor; Xu, Ying

    2006-01-01

    Integer programming is a combinatorial optimization method that has been successfully applied to the protein threading problem. We seek to expand the model optimized by this technique to allow for a more accurate description of protein threading. We have developed and implemented an expanded model of integer programming that has the capability to model secondary structure element deletion, which was not possible in previous version of integer programming based optimization. PMID:17503397

  12. TMPyP4, a Stabilizer of Nucleic Acid Secondary Structure, Is a Novel Acetylcholinesterase Inhibitor

    PubMed Central

    Fujiwara, Nana; Mazzola, Michael; Cai, Elizabeth; Wang, Meng; Cave, John W.

    2015-01-01

    The porphyrin compound, TMPyP4 (5,10,15,20-Tetrakis-(N-methyl-4-pyridyl)porphine), is widely used as a photosensitizer and a modulator of nucleic acid secondary structure stability. Our group recently showed in cultured cells and forebrain slice cultures that this compound can also down regulate expression of Tyrosine hydroxylase (Th), which encodes the rate-limiting enzyme in catecholamine biosynthesis, by stabilizing DNA secondary structures in the Th proximal promoter. The current study sought to establish whether treatment with TMPyP4 could modify mouse Th expression levels in vivo. Intraperitoneal administration of low TMPyP4 doses (10mg/kg), similar to those used for photosensitization, did not significantly reduce Th transcript levels in several catecholaminergic regions. Administration of a high dose (40 mg/kg), similar to those used for tumor xenograph reduction, unexpectedly induced flaccid paralysis in an age and sex-dependent manner. In vitro analyses revealed that TMPyP4, but not putative metabolites, inhibited Acetylcholinesterase activity and pre-treatment of TMPyP4 with Hemeoxygenase-2 (HO-2) rescued Acetylcholinesterase function. Age-dependent differences in HO-2 expression levels may account for some of the variable in vivo effects of high TMPyP4 doses. Together, these studies indicate that only low doses of TMPyP4, such as those typically used for photosensitization, are well tolerated in vivo. Thus, despite its widespread use in vitro, TMPyP4 is not ideal for modifying neuronal gene expression in vivo by manipulating nucleic acid secondary structure stability, which highlights the need to identify more clinically suitable compounds that can modulate nucleic acid secondary structure and gene expression. PMID:26402367

  13. TMPyP4, a Stabilizer of Nucleic Acid Secondary Structure, Is a Novel Acetylcholinesterase Inhibitor.

    PubMed

    Fujiwara, Nana; Mazzola, Michael; Cai, Elizabeth; Wang, Meng; Cave, John W

    2015-01-01

    The porphyrin compound, TMPyP4 (5,10,15,20-Tetrakis-(N-methyl-4-pyridyl)porphine), is widely used as a photosensitizer and a modulator of nucleic acid secondary structure stability. Our group recently showed in cultured cells and forebrain slice cultures that this compound can also down regulate expression of Tyrosine hydroxylase (Th), which encodes the rate-limiting enzyme in catecholamine biosynthesis, by stabilizing DNA secondary structures in the Th proximal promoter. The current study sought to establish whether treatment with TMPyP4 could modify mouse Th expression levels in vivo. Intraperitoneal administration of low TMPyP4 doses (10mg/kg), similar to those used for photosensitization, did not significantly reduce Th transcript levels in several catecholaminergic regions. Administration of a high dose (40 mg/kg), similar to those used for tumor xenograph reduction, unexpectedly induced flaccid paralysis in an age and sex-dependent manner. In vitro analyses revealed that TMPyP4, but not putative metabolites, inhibited Acetylcholinesterase activity and pre-treatment of TMPyP4 with Hemeoxygenase-2 (HO-2) rescued Acetylcholinesterase function. Age-dependent differences in HO-2 expression levels may account for some of the variable in vivo effects of high TMPyP4 doses. Together, these studies indicate that only low doses of TMPyP4, such as those typically used for photosensitization, are well tolerated in vivo. Thus, despite its widespread use in vitro, TMPyP4 is not ideal for modifying neuronal gene expression in vivo by manipulating nucleic acid secondary structure stability, which highlights the need to identify more clinically suitable compounds that can modulate nucleic acid secondary structure and gene expression. PMID:26402367

  14. Secondary relaxation dynamics in rigid glass-forming molecular liquids with related structures

    NASA Astrophysics Data System (ADS)

    Li, Xiangqian; Wang, Meng; Liu, Riping; Ngai, Kia L.; Tian, Yongjun; Wang, Li-Min; Capaccioli, Simone

    2015-09-01

    The dielectric relaxation in three glass-forming molecular liquids, 1-methylindole (1MID), 5H-5-Methyl-6,7-dihydrocyclopentapyrazine (MDCP), and Quinaldine (QN) is studied focusing on the secondary relaxation and its relation to the structural α-relaxation. All three glass-formers are rigid and more or less planar molecules with related chemical structures but have dipoles of different strengths at different locations. A strong and fast secondary relaxation is detected in the dielectric spectra of 1MID, while no resolved β-relaxation is observed in MDCP and QN. If the observed secondary relaxation in 1MID is identified with the Johari-Goldstein (JG) β-relaxation, then apparently the relation between the α- and β-relaxation frequencies of 1MID is not in accord with the Coupling Model (CM). The possibility of the violation of the prediction in 1MID as due to either the formation of hydrogen-bond induced clusters or the involvement of intramolecular degree of freedom is ruled out. The violation is explained by the secondary relaxation originating from the in-plane rotation of the dipole located on the plane of the rigid molecule, contributing to dielectric loss at higher frequencies and more intense than the JG β-relaxation generated by the out-of-plane rotation. MDCP has smaller dipole moment located in the plane of the molecule; however, presence of the change of curvature of dielectric loss, ɛ″(f), at some frequency on the high-frequency flank of the α-relaxation reveals the JG β-relaxation in MDCP and which is in accord with the CM prediction. QN has as large an in-plane dipole moment as 1MID, and the absence of the resolved secondary relaxation is explained by the smaller coupling parameter than the latter in the framework of the CM.

  15. The constant region affects antigen binding of antibodies to DNA by altering secondary structure.

    PubMed

    Xia, Yumin; Janda, Alena; Eryilmaz, Ertan; Casadevall, Arturo; Putterman, Chaim

    2013-11-01

    We previously demonstrated an important role of the constant region in the pathogenicity of anti-DNA antibodies. To determine the mechanisms by which the constant region affects autoantibody binding, a panel of isotype-switch variants (IgG1, IgG2a, IgG2b) was generated from the murine PL9-11 IgG3 autoantibody. The affinity of the PL9-11 antibody panel for histone was measured by surface plasmon resonance (SPR). Tryptophan fluorescence was used to determine wavelength shifts of the antibody panel upon binding to DNA and histone. Finally, circular dichroism spectroscopy was used to measure changes in secondary structure. SPR analysis revealed significant differences in histone binding affinity between members of the PL9-11 panel. The wavelength shifts of tryptophan fluorescence emission were found to be dependent on the antibody isotype, while circular dichroism analysis determined that changes in antibody secondary structure content differed between isotypes upon antigen binding. Thus, the antigen binding affinity is dependent on the particular constant region expressed. Moreover, the effects of antibody binding to antigen were also constant region dependent. Alteration of secondary structures influenced by constant regions may explain differences in fine specificity of anti-DNA antibodies between antibodies with similar variable regions, as well as cross-reactivity of anti-DNA antibodies with non-DNA antigens.

  16. CPU-GPU hybrid accelerating the Zuker algorithm for RNA secondary structure prediction applications

    PubMed Central

    2012-01-01

    Background Prediction of ribonucleic acid (RNA) secondary structure remains one of the most important research areas in bioinformatics. The Zuker algorithm is one of the most popular methods of free energy minimization for RNA secondary structure prediction. Thus far, few studies have been reported on the acceleration of the Zuker algorithm on general-purpose processors or on extra accelerators such as Field Programmable Gate-Array (FPGA) and Graphics Processing Units (GPU). To the best of our knowledge, no implementation combines both CPU and extra accelerators, such as GPUs, to accelerate the Zuker algorithm applications. Results In this paper, a CPU-GPU hybrid computing system that accelerates Zuker algorithm applications for RNA secondary structure prediction is proposed. The computing tasks are allocated between CPU and GPU for parallel cooperate execution. Performance differences between the CPU and the GPU in the task-allocation scheme are considered to obtain workload balance. To improve the hybrid system performance, the Zuker algorithm is optimally implemented with special methods for CPU and GPU architecture. Conclusions Speedup of 15.93× over optimized multi-core SIMD CPU implementation and performance advantage of 16% over optimized GPU implementation are shown in the experimental results. More than 14% of the sequences are executed on CPU in the hybrid system. The system combining CPU and GPU to accelerate the Zuker algorithm is proven to be promising and can be applied to other bioinformatics applications. PMID:22369626

  17. Mechanical properties of amyloid-like fibrils defined by secondary structures.

    PubMed

    Bortolini, C; Jones, N C; Hoffmann, S V; Wang, C; Besenbacher, F; Dong, M

    2015-05-01

    Amyloid and amyloid-like fibrils represent a generic class of highly ordered nanostructures that are implicated in some of the most fatal neurodegenerative diseases. On the other hand, amyloids, by possessing outstanding mechanical robustness, have also been successfully employed as functional biomaterials. For these reasons, physical and chemical factors driving fibril self-assembly and morphology are extensively studied - among these parameters, the secondary structures and the pH have been revealed to be crucial, since a variation in pH changes the fibril morphology and net chirality during protein aggregation. It is important to quantify the mechanical properties of these fibrils in order to help the design of effective strategies for treating diseases related to the presence of amyloid fibrils. In this work, we show that by changing pH the mechanical properties of amyloid-like fibrils vary as well. In particular, we reveal that these mechanical properties are strongly related to the content of secondary structures. We analysed and estimated the Young's modulus (E) by comparing the persistence length (Lp) - measured from the observation of TEM images by using statistical mechanics arguments - with the mechanical information provided by peak force quantitative nanomechanical property mapping (PF-QNM). The secondary structure content and the chirality are investigated by means of synchrotron radiation circular dichroism (SR-CD). Results arising from this study could be fruitfully used as a protocol to investigate other medical or engineering relevant peptide fibrils. PMID:25839069

  18. Compensatory evolution of a precursor messenger RNA secondary structure in the Drosophila melanogaster Adh gene

    PubMed Central

    Chen, Ying; Stephan, Wolfgang

    2003-01-01

    Evidence for the evolutionary maintenance of a hairpin structure possibly involved in intron processing had been found in intron 1 of the alcohol dehydrogenase gene (Adh) in diverse Drosophila species. In this study, the putative hairpin structure was evaluated systematically in Drosophila melanogaster by elimination of either side of the stem using site-directed mutagenesis. The effects of these mutations and the compensatory double mutant on intron splicing efficiency and ADH protein production were assayed in Drosophila melanogaster Schneider L2 cells and germ-line transformed adult flies. Mutations that disrupt the putative hairpin structure right upstream of the intron branch point were found to cause a significant reduction in both splicing efficiency and ADH protein production. In contrast, the compensatory double mutant that restores the putative hairpin structure was indistinguishable from the WT in both splicing efficiency and ADH level. It was also observed by mutational analysis that a more stable secondary structure (with a longer stem) in this intron decreases both splicing efficiency and ADH protein production. Implications for RNA secondary structure and intron evolution are discussed. PMID:12972637

  19. Secondary structure of protamine in sperm nuclei: an infrared spectroscopy study

    PubMed Central

    2011-01-01

    Background Protamines are small basic proteins that condense the DNA in mature spermatozoa. Typical protamines are of simple composition and very arginine-rich, usually in the range of 60-80%. Arginine residues are distributed in a number of stretches separated by neutral amino acids. We have used Fourier transform infrared spectroscopy (FTIR) to gain access for the first time to the secondary structure of protamines in sperm nuclei. This technique is particularly well suited to the study of DNA-bound protamine in whole nuclei since it is not affected by turbidity. Results We show that DNA -bound salmon (salmine) and squid protamines contain α-helix, β-turns and a proportion of other structures not stabilized by intramolecular hydrogen bonding. No β-sheet was observed. In salmine, the α-helix amounted to ~20%, while in squid protamine it reached ~40%. In contrast, the structure not stabilized by intermolecular hydrogen bonding was more abundant in salmine (~40%) than in squid protamine (~20%). Both protamines contained ~40% β-turns. The different helical potential of salmine and squid protamine was confirmed by structure predictions and CD in the presence of trifluoroethanol. Conclusion DNA-bound protamine in sperm nuclei contains large amounts of defined secondary structure stabilized by intramolecular hydrogen bonding. Both salmine and squid protamine contain similar amounts of β-turns, but differ in the proportions of α-helix and non-hydrogen bonded conformations. In spite of the large differences in the proportions of secondary structure motifs between salmon and squid protamines, they appear to be equally efficient in promoting tight hexagonal packing of the DNA molecules in sperm nuclei. PMID:21435240

  20. Using probe secondary structure information to enhance Affymetrix GeneChip background estimates

    PubMed Central

    Gharaibeh, Raad Z.; Fodor, Anthony A.; Gibas, Cynthia J.

    2007-01-01

    High-density short oligonucleotide microarrays are a primary research tool for assessing global gene expression. Background noise on microarrays comprises a significant portion of the measured raw data. A number of statistical techniques have been developed to correct for this background noise. Here, we demonstrate that probe minimum folding energy and structure can be used to enhance a previously existing model for background noise correction. We estimate that probe secondary structure accounts for up to 3% of all variation on Affymetrix microarrays. PMID:17387043

  1. The Use of Additive Manufacturing for Fabrication of Multi-Function Small Satellite Structures

    SciTech Connect

    Horais, Brian J; Love, Lonnie J; Dehoff, Ryan R

    2013-01-01

    The use of small satellites in constellations is limited only by the growing functionality of smallsats themselves. Additive manufacturing provides exciting new design opportunities for development of multifunction CubeSat structures that integrate such functions as propulsion and thermal control into the satellite structures themselves. Manufacturing of these complex multifunction structures is now possible in lightweight, high strength, materials such as titanium by using existing electron beam melting additive manufacturing processes. However, the use of today's additive manufacturing capabilities is often cost-prohibitive for small companies due to the large capital investments required. To alleviate this impediment the U.S. Department of Energy has established a Manufacturing Demonstration Facility (MDF) at their Oak Ridge National Laboratory (ORNL) in Tennessee that provides industry access to a broad range of energy-efficient additive manufacturing equipment for collaborative use by both small and large organizations. This paper presents a notional CubeSat multifunction design that integrates the propulsion system into a three-unit (3U) CubeSat structure. The full-scale structure has been designed and fabricated at the ORNL MDF. The use of additive manufacturing for spacecraft fabrication is opening up many new possibilities in design and fabrication capabilities for what had previously been impossible structures to fabricate.

  2. VMD-SS: A graphical user interface plug-in to calculate the protein secondary structure in VMD program

    PubMed Central

    Yahyavi, Masoumeh; Falsafi-Zadeh, Sajad; Karimi, Zahra; Kalatarian, Giti; Galehdari, Hamid

    2014-01-01

    The investigation on the types of secondary structure (SS) of a protein is important. The evolution of secondary structures during molecular dynamics simulations is a useful parameter to analyze protein structures. Therefore, it is of interest to describe VMD-SS (a software program) for the identification of secondary structure elements and its trajectories during simulation for known structures available at the Protein Data Bank (PDB). The program helps to calculate (1) percentage SS, (2) SS occurrence in each residue, (3) percentage SS during simulation, and (4) percentage residues in all SS types during simulation. The VMD-SS plug-in was designed using TCL script and stride to calculate secondary structure features. Availability The database is available for free at http://science.scu.ac.ir/HomePage.aspx?TabID=13755 PMID:25258493

  3. Dissolved organic matter removal during coal slag additive soil aquifer treatment for secondary effluent recharging: Contribution of aerobic biodegradation.

    PubMed

    Wei, Liangliang; Li, Siliang; Noguera, Daniel R; Qin, Kena; Jiang, Junqiu; Zhao, Qingliang; Kong, Xiangjuan; Cui, Fuyi

    2015-06-01

    Recycling wastewater treatment plant (WWTP) effluent at low cost via the soil aquifer treatment (SAT), which has been considered as a renewable approach in regenerating potable and non-potable water, is welcome in arid and semi-arid regions throughout the world. In this study, the effect of a coal slag additive on the bulk removal of the dissolved organic matter (DOM) in WWTP effluent during SAT operation was explored via the matrix configurations of both coal slag layer and natural soil layer. Azide inhibition and XAD-resins fractionation experiments indicated that the appropriate configuration designing of an upper soil layer (25 cm) and a mixture of soil/coal slag underneath would enhance the removal efficiency of adsorption and anaerobic biodegradation to the same level as that of aerobic biodegradation (31.7% vs 32.2%), while it was only 29.4% compared with the aerobic biodegradation during traditional 50 cm soil column operation. The added coal slag would preferentially adsorb the hydrophobic DOM, and those adsorbed organics could be partially biodegraded by the biomass within the SAT systems. Compared with the relatively lower dissolved organic carbon (DOC), ultraviolet light adsorption at 254 nm (UV-254) and trihalomethane formation potential (THMFP) removal rate of the original soil column (42.0%, 32.9%, and 28.0%, respectively), SSL2 and SSL4 columns would enhance the bulk removal efficiency to more than 60%. Moreover, a coal slag additive in the SAT columns could decline the aromatic components (fulvic-like organics and tryptophan-like proteins) significantly. PMID:25845997

  4. Dissolved organic matter removal during coal slag additive soil aquifer treatment for secondary effluent recharging: Contribution of aerobic biodegradation.

    PubMed

    Wei, Liangliang; Li, Siliang; Noguera, Daniel R; Qin, Kena; Jiang, Junqiu; Zhao, Qingliang; Kong, Xiangjuan; Cui, Fuyi

    2015-06-01

    Recycling wastewater treatment plant (WWTP) effluent at low cost via the soil aquifer treatment (SAT), which has been considered as a renewable approach in regenerating potable and non-potable water, is welcome in arid and semi-arid regions throughout the world. In this study, the effect of a coal slag additive on the bulk removal of the dissolved organic matter (DOM) in WWTP effluent during SAT operation was explored via the matrix configurations of both coal slag layer and natural soil layer. Azide inhibition and XAD-resins fractionation experiments indicated that the appropriate configuration designing of an upper soil layer (25 cm) and a mixture of soil/coal slag underneath would enhance the removal efficiency of adsorption and anaerobic biodegradation to the same level as that of aerobic biodegradation (31.7% vs 32.2%), while it was only 29.4% compared with the aerobic biodegradation during traditional 50 cm soil column operation. The added coal slag would preferentially adsorb the hydrophobic DOM, and those adsorbed organics could be partially biodegraded by the biomass within the SAT systems. Compared with the relatively lower dissolved organic carbon (DOC), ultraviolet light adsorption at 254 nm (UV-254) and trihalomethane formation potential (THMFP) removal rate of the original soil column (42.0%, 32.9%, and 28.0%, respectively), SSL2 and SSL4 columns would enhance the bulk removal efficiency to more than 60%. Moreover, a coal slag additive in the SAT columns could decline the aromatic components (fulvic-like organics and tryptophan-like proteins) significantly.

  5. RNA folding with soft constraints: reconciliation of probing data and thermodynamic secondary structure prediction

    PubMed Central

    Washietl, Stefan; Hofacker, Ivo L.; Stadler, Peter F.; Kellis, Manolis

    2012-01-01

    Thermodynamic folding algorithms and structure probing experiments are commonly used to determine the secondary structure of RNAs. Here we propose a formal framework to reconcile information from both prediction algorithms and probing experiments. The thermodynamic energy parameters are adjusted using ‘pseudo-energies’ to minimize the discrepancy between prediction and experiment. Our framework differs from related approaches that used pseudo-energies in several key aspects. (i) The energy model is only changed when necessary and no adjustments are made if prediction and experiment are consistent. (ii) Pseudo-energies remain biophysically interpretable and hold positional information where experiment and model disagree. (iii) The whole thermodynamic ensemble of structures is considered thus allowing to reconstruct mixtures of suboptimal structures from seemingly contradicting data. (iv) The noise of the energy model and the experimental data is explicitly modeled leading to an intuitive weighting factor through which the problem can be seen as folding with ‘soft’ constraints of different strength. We present an efficient algorithm to iteratively calculate pseudo-energies within this framework and demonstrate how this approach can be used in combination with SHAPE chemical probing data to improve secondary structure prediction. We further demonstrate that the pseudo-energies correlate with biophysical effects that are known to affect RNA folding such as chemical nucleotide modifications and protein binding. PMID:22287623

  6. A novel secondary structure based on fused five-membered rings motif

    PubMed Central

    Dhar, Jesmita; Kishore, Raghuvansh; Chakrabarti, Pinak

    2016-01-01

    An analysis of protein structures indicates the existence of a novel, fused five-membered rings motif, comprising of two residues (i and i + 1), stabilized by interresidue Ni+1–H∙∙∙Ni and intraresidue Ni+1–H∙∙∙O=Ci+1 hydrogen bonds. Fused-rings geometry is the common thread running through many commonly occurring motifs, such as β-turn, β-bulge, Asx-turn, Ser/Thr-turn, Schellman motif, and points to its structural robustness. A location close to the beginning of a β-strand is rather common for the motif. Devoid of side chain, Gly seems to be a key player in this motif, occurring at i, for which the backbone torsion angles cluster at ~(−90°, −10°) and (70°, 20°). The fused-rings structures, distant from each other in sequence, can hydrogen bond with each other, and the two segments aligned to each other in a parallel fashion, give rise to a novel secondary structure, topi, which is quite common in proteins, distinct from two major secondary structures, α-helix and β-sheet. Majority of the peptide segments making topi are identified as aggregation-prone and the residues tend to be conserved among homologous proteins. PMID:27511362

  7. Prediction of Spontaneous Protein Deamidation from Sequence-Derived Secondary Structure and Intrinsic Disorder

    PubMed Central

    Lorenzo, J. Ramiro; Alonso, Leonardo G.; Sánchez, Ignacio E.

    2015-01-01

    Asparagine residues in proteins undergo spontaneous deamidation, a post-translational modification that may act as a molecular clock for the regulation of protein function and turnover. Asparagine deamidation is modulated by protein local sequence, secondary structure and hydrogen bonding. We present NGOME, an algorithm able to predict non-enzymatic deamidation of internal asparagine residues in proteins in the absence of structural data, using sequence-based predictions of secondary structure and intrinsic disorder. Compared to previous algorithms, NGOME does not require three-dimensional structures yet yields better predictions than available sequence-only methods. Four case studies of specific proteins show how NGOME may help the user identify deamidation-prone asparagine residues, often related to protein gain of function, protein degradation or protein misfolding in pathological processes. A fifth case study applies NGOME at a proteomic scale and unveils a correlation between asparagine deamidation and protein degradation in yeast. NGOME is freely available as a webserver at the National EMBnet node Argentina, URL: http://www.embnet.qb.fcen.uba.ar/ in the subpage “Protein and nucleic acid structure and sequence analysis”. PMID:26674530

  8. Prediction of Spontaneous Protein Deamidation from Sequence-Derived Secondary Structure and Intrinsic Disorder.

    PubMed

    Lorenzo, J Ramiro; Alonso, Leonardo G; Sánchez, Ignacio E

    2015-01-01

    Asparagine residues in proteins undergo spontaneous deamidation, a post-translational modification that may act as a molecular clock for the regulation of protein function and turnover. Asparagine deamidation is modulated by protein local sequence, secondary structure and hydrogen bonding. We present NGOME, an algorithm able to predict non-enzymatic deamidation of internal asparagine residues in proteins in the absence of structural data, using sequence-based predictions of secondary structure and intrinsic disorder. Compared to previous algorithms, NGOME does not require three-dimensional structures yet yields better predictions than available sequence-only methods. Four case studies of specific proteins show how NGOME may help the user identify deamidation-prone asparagine residues, often related to protein gain of function, protein degradation or protein misfolding in pathological processes. A fifth case study applies NGOME at a proteomic scale and unveils a correlation between asparagine deamidation and protein degradation in yeast. NGOME is freely available as a webserver at the National EMBnet node Argentina, URL: http://www.embnet.qb.fcen.uba.ar/ in the subpage "Protein and nucleic acid structure and sequence analysis".

  9. Mitochondrial RNase P RNAs in ascomycete fungi: lineage-specific variations in RNA secondary structure.

    PubMed

    Seif, Elias R; Forget, Lise; Martin, Nancy C; Lang, B Franz

    2003-09-01

    The RNA subunit of mitochondrial RNase P (mtP-RNA) is encoded by a mitochondrial gene (rnpB) in several ascomycete fungi and in the protists Reclinomonas americana and Nephroselmis olivacea. By searching for universally conserved structural elements, we have identified previously unknown rnpB genes in the mitochondrial DNAs (mtDNAs) of two fission yeasts, Schizosaccharomyces pombe and Schizosaccharomyces octosporus; in the budding yeast Pichia canadensis; and in the archiascomycete Taphrina deformans. The expression of mtP-RNAs of the predicted size was experimentally confirmed in the two fission yeasts, and their precise 5' and 3' ends were determined by sequencing of cDNAs generated from circularized mtP-RNAs. Comparative RNA secondary structure modeling shows that in contrast to mtP-RNAs of the two protists R. americana and N. olivacea, those of ascomycete fungi all have highly reduced secondary structures. In certain budding yeasts, such as Saccharomycopsis fibuligera, we find only the two most conserved pairings, P1 and P4. A P18 pairing is conserved in Saccharomyces cerevisiae and its close relatives, whereas nearly half of the minimum bacterial consensus structure is retained in the RNAs of fission yeasts, Aspergillus nidulans and Taphrina deformans. The evolutionary implications of the reduction of mtP-RNA structures in ascomycetes will be discussed.

  10. RNA secondary structure prediction by centroids in a Boltzmann weighted ensemble.

    PubMed

    Ding, Ye; Chan, Chi Yu; Lawrence, Charles E

    2005-08-01

    Prediction of RNA secondary structure by free energy minimization has been the standard for over two decades. Here we describe a novel method that forsakes this paradigm for predictions based on Boltzmann-weighted structure ensemble. We introduce the notion of a centroid structure as a representative for a set of structures and describe a procedure for its identification. In comparison with the minimum free energy (MFE) structure using diverse types of structural RNAs, the centroid of the ensemble makes 30.0% fewer prediction errors as measured by the positive predictive value (PPV) with marginally improved sensitivity. The Boltzmann ensemble can be separated into a small number (3.2 on average) of clusters. Among the centroids of these clusters, the "best cluster centroid" as determined by comparison to the known structure simultaneously improves PPV by 46.5% and sensitivity by 21.7%. For 58% of the studied sequences for which the MFE structure is outside the cluster containing the best centroid, the improvements by the best centroid are 62.5% for PPV and 31.4% for sensitivity. These results suggest that the energy well containing the MFE structure under the current incomplete energy model is often different from the one for the unavailable complete model that presumably contains the unique native structure. Centroids are available on the Sfold server at http://sfold.wadsworth.org.

  11. Perturbation-induced secondary flow structures due to fractured stents in arterial curvatures

    NASA Astrophysics Data System (ADS)

    Bulusu, Kartik V.; Popma, Christopher; Penna, Leanne; Plesniak, Michael W.

    2012-11-01

    An in vitro experimental investigation of secondary flow structures was performed downstream of a model stent that embodied a ``Type-IV'' stent fracture, i.e. complete transverse fracture of elements and element displacement (of 3 diameters). One part of the fractured stent was located in the curved region of a test section comprised of a 180-degree bent tube, and the velocity field measured with PIV. Secondary flow morphologies downstream of the stent were identified with a continuous wavelet transform (CWT) algorithm (PIVlet 1.2) using a 2D Ricker wavelet. A comparison of wavelet transformed vorticity fields of fractured and unfractured model stents is presented under physiological inflow conditions. During systolic deceleration, a breakdown in symmetry of vortical structures occurred with the unfractured stent, but not with the fractured model stent. Potential mechanisms to explain the differences in secondary flow morphologies include redirection of vorticity from the meridional plane of the bend to the normal plane and diffusion of vorticity. Supported by the National Science Foundation, Grant No. CBET-0828903 and GW Center for Biomimetics and Bioinspired Engineering (COBRE).

  12. Responses of secondary chemicals in sugar maple (Acer saccharum) seedlings to UV-B, springtime warming and nitrogen additions.

    PubMed

    Sager, E P S; Hutchinson, T C

    2006-10-01

    Anticipated effects of climate change involve complex interactions in the field. To assess the effects of springtime warming, ambient ultraviolet-B radiation (UV-B) and nitrogen fertilization on the foliar chemistry and herbivore activity of native sugar maple (Acer saccharum Marsh.) seedlings, we carried out a field experiment for 2 years at two sugar maple forests growing on soils of contrasting acidity. At the Oliver site, soils are derived from a strongly calcareous till, whereas the naturally acidic soils and base-poor soils of the Haliburton site are derived from the largely granitic Precambrian Shield. At both sites, removal of ambient UV-B led to increases in chlorogenic acid and some flavonoids and reduced herbivore activity. At Haliburton, ammonium nitrate fertilization led to further increases in foliar manganese (Mn), whereas at Oliver there were no such changes. Nitrogen additions led to decreases in the concentrations of some flavonoids at both sites, but seedlings at Oliver had significantly higher concentrations of flavonoids and chlorogenic acid than seedlings at Haliburton. We suggest that this could be associated with increased mobilization of Mn due to increased soil acidity, which interferes with the role of calcium (Ca) in the phenolic biosynthetic pathway. It appears that the composition of the forest soil governs the response of seedlings when they are exposed to abiotic stressors.

  13. TT2NE: a novel algorithm to predict RNA secondary structures with pseudoknots

    PubMed Central

    Bon, Michaël; Orland, Henri

    2011-01-01

    We present TT2NE, a new algorithm to predict RNA secondary structures with pseudoknots. The method is based on a classification of RNA structures according to their topological genus. TT2NE is guaranteed to find the minimum free energy structure regardless of pseudoknot topology. This unique proficiency is obtained at the expense of the maximum length of sequences that can be treated, but comparison with state-of-the-art algorithms shows that TT2NE significantly improves the quality of predictions. Analysis of TT2NE's incorrect predictions sheds light on the need to study how sterical constraints limit the range of pseudoknotted structures that can be formed from a given sequence. An implementation of TT2NE on a public server can be found at http://ipht.cea.fr/rna/tt2ne.php. PMID:21593129

  14. The effect of structural disorder on the secondary electron emission of graphite

    NASA Astrophysics Data System (ADS)

    Gonzalez, L. A.; Larciprete, R.; Cimino, R.

    2016-09-01

    The dependance of the secondary electron yield (SEY) on the degree of crystallinity of graphite has been investigated during the amorphization of a highly oriented pyrolytic graphite (HOPG) samples by means of Ar+ bombardment. Photoemission and Raman spectroscopies were used to follow the structural damage while the SEY curves were measured from very low energies up to 1000 eV. We found that the increase of lattice defects lowers the contribution of the π electrons in the valence band and loss spectra and smears out the intense modulations in the low energy secondary electron yield (LE-SEY) curve. Raman spectroscopy results showed that ion induced lattice amorphization is confined in a near-surface layer. The evolution of SEY curves was observed with the progressive Ar+ dosage after crystal damage as due to the modification of the electronic transport properties within the damaged near surface layer.

  15. Effect of stabilizing additives on the structure and hydration of proteins: a study involving monoclinic lysozyme.

    PubMed

    Saraswathi, N T; Sankaranarayanan, R; Vijayan, M

    2002-07-01

    In pursuance of a long-range programme on the hydration, mobility and action of proteins, the structural basis of the stabilizing effect of sugars and polyols is being investigated. With two crystallographically independent molecules with slightly different packing environments in the crystal, monoclinic lysozyme constitutes an ideal system for exploring the problem. The differences in the structure and hydration of the two molecules provide a framework for examining the changes caused by stabilizing additives. Monoclinic crystals were grown under native conditions and also in the presence of 10% sucrose, 15% trehalose, 10% trehalose, 10% sorbitol and 5% glycerol. The crystal structures were refined at resolutions ranging from 1.8 to 2.1 A. The average B values, and hence the mobility of the structure, are lower in the presence of additives than in the native crystals. However, a comparison of the structures indicates that the effect of the additives on the structure and the hydration shell around the protein molecule is considerably less than that caused by differences in packing. It is also less than that caused by the replacement of NaNO(3) by NaCl as the precipitant in the crystallization experiments. This result is not in conformity with the commonly held belief that additives exert their stabilizing effect through the reorganization of the hydration shell, at least as far as the ordered water molecules are concerned.

  16. Assignment of the sup 1 H NMR spectrum and secondary structure elucidation of the single-stranded DNA binding protein encoded by the filamentous bacteriophage IKe

    SciTech Connect

    van Duynhoven, J.P.M.; Folkers, P.J.M.; Prinse, C.W.J.M.; Harmsen, B.J.M.; Konings, R.N.H.; Hilbers, C.W. )

    1992-02-04

    By means of 2D NMR techniques, all backbone resonances in the {sup 1}H NMR spectrum of the single-stranded DNA binding protein encoded by gene V of the filamentous phage IKe have been assigned sequence specifically. In addition, a major part of the side chain resonances could be assigned as well. Analysis of NOESY data permitted the elucidation of the secondary structure of IKe gene V protein. The major part of the secondary structure is present as an antiparallel {beta}-sheet, i.e., as two {beta}-loops which partly combine into a triple-stranded {beta}-sheet structure, one {beta}-loop and one triple-stranded {beta}-sheet structure. It is shown that a high degree of homology exists with the single-stranded DNA binding protein encoded by gene V of the distantly related filamentous phase M13.

  17. Structural effects of liana presence in secondary tropical dry forests using ground LiDAR

    NASA Astrophysics Data System (ADS)

    Sánchez-Azofeifa, A.; Portillo-Quintero, C.; Durán, S. M.

    2015-10-01

    Lianas, woody vines, are a key component of tropical forest because they may reduce carbon storage potential. Lianas are increasing in density and biomass in tropical forests, but it is unknown what the potential consequences of these increases are for forest dynamics. Lianas may proliferate in disturbed areas, such as regenerating forests, but little is known about the role of lianas in secondary succession. In this study, we evaluated the potential of the ground LiDAR to detect differences in the vertical structure of stands of different ages with and without lianas in tropical dry forests. Specifically, we used a terrestrial laser scanner called VEGNET to assess whether liana presence influences the vertical signature of stands of different ages, and whether successional trajectories as detected by the VEGNET could be altered by liana presence. We deployed the VEGNET ground LiDAR system in 15 secondary forests of different ages early (21 years old since land abandonment), intermediate (32-35 years old) and late stages (> 80 years old) with and without lianas. We compared laser-derived vegetation components such as Plant Area Index (PAI), plant area volume density (PAVD), and the radius of gyration (RG) across forest stands between liana and no-liana treatments. In general forest stands without lianas show a clearer distinction of vertical strata and the vertical height of accumulated PAVD. A significant increase of PAI was found from intermediate to late stages in stands without lianas, but in stands where lianas were present there was not a significant trend. This suggests that lianas may be influencing successional trajectories in secondary forests, and these effects can be captured by terrestrial laser scanners such as the VEGNET. This research contributes to estimate the potential effects of lianas in secondary dry forests and highlight the role of ground LiDAR to monitor structural changes in tropical forests due to liana presence.

  18. In situ protein secondary structure determination in ice: Raman spectroscopy-based process analytical tool for frozen storage of biopharmaceuticals.

    PubMed

    Roessl, Ulrich; Leitgeb, Stefan; Pieters, Sigrid; De Beer, Thomas; Nidetzky, Bernd

    2014-08-01

    A Raman spectroscopy-based method for in situ monitoring of secondary structural composition of proteins during frozen and thawed storage was developed. A set of reference proteins with different α-helix and β-sheet compositions was used for calibration and validation in a chemometric approach. Reference secondary structures were quantified with circular dichroism spectroscopy in the liquid state. Partial least squares regression models were established that enable estimation of secondary structure content from Raman spectra. Quantitative secondary structure determination in ice was accomplished for the first time and correlation with existing (qualitative) protein structural data from the frozen state was achieved. The method can be used in the presence of common stabilizing agents and is applicable in an industrial freezer setup. Raman spectroscopy represents a powerful, noninvasive, and flexibly applicable tool for protein stability monitoring during frozen storage.

  19. Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure

    PubMed Central

    Mathews, David H.; Disney, Matthew D.; Childs, Jessica L.; Schroeder, Susan J.; Zuker, Michael; Turner, Douglas H.

    2004-01-01

    A dynamic programming algorithm for prediction of RNA secondary structure has been revised to accommodate folding constraints determined by chemical modification and to include free energy increments for coaxial stacking of helices when they are either adjacent or separated by a single mismatch. Furthermore, free energy parameters are revised to account for recent experimental results for terminal mismatches and hairpin, bulge, internal, and multibranch loops. To demonstrate the applicability of this method, in vivo modification was performed on 5S rRNA in both Escherichia coli and Candida albicans with 1-cyclohexyl-3-(2-morpholinoethyl) carbodiimide metho-p-toluene sulfonate, dimethyl sulfate, and kethoxal. The percentage of known base pairs in the predicted structure increased from 26.3% to 86.8% for the E. coli sequence by using modification constraints. For C. albicans, the accuracy remained 87.5% both with and without modification data. On average, for these sequences and a set of 14 sequences with known secondary structure and chemical modification data taken from the literature, accuracy improves from 67% to 76%. This enhancement primarily reflects improvement for three sequences that are predicted with <40% accuracy on the basis of energetics alone. For these sequences, inclusion of chemical modification constraints improves the average accuracy from 28% to 78%. For the 11 sequences with <6% pseudoknotted base pairs, structures predicted with constraints from chemical modification contain on average 84% of known canonical base pairs. PMID:15123812

  20. Importance of the RNA secondary structure for the relative accumulation of clustered viral microRNAs

    PubMed Central

    Contrant, Maud; Fender, Aurélie; Chane-Woon-Ming, Béatrice; Randrianjafy, Ramy; Vivet-Boudou, Valérie; Richer, Delphine; Pfeffer, Sébastien

    2014-01-01

    Micro (mi)RNAs are small non-coding RNAs with key regulatory functions. Recent advances in the field allowed researchers to identify their targets. However, much less is known regarding the regulation of miRNAs themselves. The accumulation of these tiny regulators can be modulated at various levels during their biogenesis from the transcription of the primary transcript (pri-miRNA) to the stability of the mature miRNA. Here, we studied the importance of the pri-miRNA secondary structure for the regulation of mature miRNA accumulation. To this end, we used the Kaposi's sarcoma herpesvirus, which encodes a cluster of 12 pre-miRNAs. Using small RNA profiling and quantitative northern blot analysis, we measured the absolute amount of each mature miRNAs in different cellular context. We found that the difference in expression between the least and most expressed viral miRNAs could be as high as 60-fold. Using high-throughput selective 2′-hydroxyl acylation analyzed by primer extension, we then determined the secondary structure of the long primary transcript. We found that highly expressed miRNAs derived from optimally structured regions within the pri-miRNA. Finally, we confirmed the importance of the local structure by swapping stem-loops or by targeted mutagenesis of selected miRNAs, which resulted in a perturbed accumulation of the mature miRNA. PMID:24831544

  1. Sequence-specific polypeptoids: A diverse family of heteropolymers with stable secondary structure

    PubMed Central

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

    1998-01-01

    We have synthesized and characterized a family of structured oligo-N-substituted-glycines (peptoids) up to 36 residues in length by using an efficient solid-phase protocol to incorporate chemically diverse side chains in a sequence-specific fashion. We investigated polypeptoids containing side chains with a chiral center adjacent to the main chain nitrogen. Some of these sequences have stable secondary structure, despite the achirality of the polymer backbone and its lack of hydrogen bond donors. In both aqueous and organic solvents, peptoid oligomers as short as five residues give rise to CD spectra that strongly resemble those of peptide α-helices. Differential scanning calorimetry and CD measurements show that polypeptoid secondary structure is highly stable and that unfolding is reversible and cooperative. Thermodynamic parameters obtained for unfolding are similar to those obtained for the α-helix to coil transitions of peptides. This class of biomimetic polymers may enable the design of self-assembling macromolecules with novel structures and functions. PMID:9539732

  2. The RNAmute web server for the mutational analysis of RNA secondary structures.

    PubMed

    Churkin, Alexander; Gabdank, Idan; Barash, Danny

    2011-07-01

    RNA mutational analysis at the secondary-structure level can be useful to a wide-range of biological applications. It can be used to predict an optimal site for performing a nucleotide mutation at the single molecular level, as well as to analyze basic phenomena at the systems level. For the former, as more sequence modification experiments are performed that include site-directed mutagenesis to find and explore functional motifs in RNAs, a pre-processing step that helps guide in planning the experiment becomes vital. For the latter, mutations are generally accepted as a central mechanism by which evolution occurs, and mutational analysis relating to structure should gain a better understanding of system functionality and evolution. In the past several years, the program RNAmute that is structure based and relies on RNA secondary-structure prediction has been developed for assisting in RNA mutational analysis. It has been extended from single-point mutations to treat multiple-point mutations efficiently by initially calculating all suboptimal solutions, after which only the mutations that stabilize the suboptimal solutions and destabilize the optimal one are considered as candidates for being deleterious. The RNAmute web server for mutational analysis is available at http://www.cs.bgu.ac.il/~xrnamute/XRNAmute.

  3. The Interplay between Adolescent Needs and Secondary School Structures: Fostering Developmentally Responsive Middle and High School Environments across the Transition

    ERIC Educational Resources Information Center

    Ellerbrock, Cheryl R.; Kiefer, Sarah M.

    2013-01-01

    Understanding the developmental responsiveness of secondary school environments may be an important factor in supporting students as they make the transition from one school to the next. Students' needs may or may not be met depending on the nature of the fit between their basic and developmental needs and secondary school structures at the…

  4. Terrestrial exposure of oilfield flowline additives diminish soil structural stability and remediative microbial function.

    PubMed

    George, S J; Sherbone, J; Hinz, C; Tibbett, M

    2011-10-01

    Onshore oil production pipelines are major installations in the petroleum industry, stretching many thousands of kilometres worldwide which also contain flowline additives. The current study focuses on the effect of the flowline additives on soil physico-chemical and biological properties and quantified the impact using resilience and resistance indices. Our findings are the first to highlight deleterious effect of flowline additives by altering some fundamental soil properties, including a complete loss of structural integrity of the impacted soil and a reduced capacity to degrade hydrocarbons mainly due to: (i) phosphonate salts (in scale inhibitor) prevented accumulation of scale in pipelines but also disrupted soil physical structure; (ii) glutaraldehyde (in biocides) which repressed microbial activity in the pipeline and reduced hydrocarbon degradation in soil upon environmental exposure; (iii) the combinatory effects of these two chemicals synergistically caused severe soil structural collapse and disruption of microbial degradation of petroleum hydrocarbons.

  5. Multithreaded comparative RNA secondary structure prediction using stochastic context-free grammars

    PubMed Central

    2011-01-01

    Background The prediction of the structure of large RNAs remains a particular challenge in bioinformatics, due to the computational complexity and low levels of accuracy of state-of-the-art algorithms. The pfold model couples a stochastic context-free grammar to phylogenetic analysis for a high accuracy in predictions, but the time complexity of the algorithm and underflow errors have prevented its use for long alignments. Here we present PPfold, a multithreaded version of pfold, which is capable of predicting the structure of large RNA alignments accurately on practical timescales. Results We have distributed both the phylogenetic calculations and the inside-outside algorithm in PPfold, resulting in a significant reduction of runtime on multicore machines. We have addressed the floating-point underflow problems of pfold by implementing an extended-exponent datatype, enabling PPfold to be used for large-scale RNA structure predictions. We have also improved the user interface and portability: alongside standalone executable and Java source code of the program, PPfold is also available as a free plugin to the CLC Workbenches. We have evaluated the accuracy of PPfold using BRaliBase I tests, and demonstrated its practical use by predicting the secondary structure of an alignment of 24 complete HIV-1 genomes in 65 minutes on an 8-core machine and identifying several known structural elements in the prediction. Conclusions PPfold is the first parallelized comparative RNA structure prediction algorithm to date. Based on the pfold model, PPfold is capable of fast, high-quality predictions of large RNA secondary structures, such as the genomes of RNA viruses or long genomic transcripts. The techniques used in the parallelization of this algorithm may be of general applicability to other bioinformatics algorithms. PMID:21501497

  6. Landscape and variation of RNA secondary structure across the human transcriptome.

    PubMed

    Wan, Yue; Qu, Kun; Zhang, Qiangfeng Cliff; Flynn, Ryan A; Manor, Ohad; Ouyang, Zhengqing; Zhang, Jiajing; Spitale, Robert C; Snyder, Michael P; Segal, Eran; Chang, Howard Y

    2014-01-30

    In parallel to the genetic code for protein synthesis, a second layer of information is embedded in all RNA transcripts in the form of RNA structure. RNA structure influences practically every step in the gene expression program. However, the nature of most RNA structures or effects of sequence variation on structure are not known. Here we report the initial landscape and variation of RNA secondary structures (RSSs) in a human family trio (mother, father and their child). This provides a comprehensive RSS map of human coding and non-coding RNAs. We identify unique RSS signatures that demarcate open reading frames and splicing junctions, and define authentic microRNA-binding sites. Comparison of native deproteinized RNA isolated from cells versus refolded purified RNA suggests that the majority of the RSS information is encoded within RNA sequence. Over 1,900 transcribed single nucleotide variants (approximately 15% of all transcribed single nucleotide variants) alter local RNA structure. We discover simple sequence and spacing rules that determine the ability of point mutations to impact RSSs. Selective depletion of 'riboSNitches' versus structurally synonymous variants at precise locations suggests selection for specific RNA shapes at thousands of sites, including 3' untranslated regions, binding sites of microRNAs and RNA-binding proteins genome-wide. These results highlight the potentially broad contribution of RNA structure and its variation to gene regulation.

  7. Understanding of Relation Structures of Graphical Models by Lower Secondary Students

    NASA Astrophysics Data System (ADS)

    van Buuren, Onne; Heck, André; Ellermeijer, Ton

    2016-10-01

    A learning path has been developed on system dynamical graphical modelling, integrated into the Dutch lower secondary physics curriculum. As part of the developmental research for this learning path, students' understanding of the relation structures shown in the diagrams of graphical system dynamics based models has been investigated. One of our main findings is that only some students understand these structures correctly. Reality-based interpretation of the diagrams can conceal an incorrect understanding of diagram structures. As a result, students seemingly have no problems interpreting the diagrams until they are asked to construct a graphical model. Misconceptions have been identified that are the consequence of the fact that the equations are not clearly communicated by the diagrams or because the icons used in the diagrams mislead novice modellers. Suggestions are made for improvements.

  8. [The effect of crystallization of calcium carbonate on the secondary structure of pepsin].

    PubMed

    Zhu, Shu-fa; Tang, Jun-ming; Ma, Xiao-ming; Guo, Yu-ming; Zhang, Xiu-ying; Yang, Lin

    2003-06-01

    The effect of crystallization of calcium carbonate on the secondary structure of pepsin was studied by Fourier transform infrared spectroscopy, derivative, deconvolution and curve-fitting techniques in this paper. The result shows that the pure protein is composed of 24.38% alpha-helices, 29.91% beta-sheets, 39.22% beta-turns and 6.49% random structures, and the pepsin in the CaCO3/pepsin solution is composed of 2.09% alpha-helices, 93.304% beta-sheets, 4.60% beta-turns and 0.006% random structures. From these data we can see that the alpha-helices decrease and the beta-turns increase with the formation of the crystal of calcium carbonate. The essence of these changes is discussed in the paper.

  9. Rigidity, Secondary Structure, and the Universality of the Boson Peak in Proteins

    PubMed Central

    Perticaroli, Stefania; Nickels, Jonathan D.; Ehlers, Georg; Sokolov, Alexei P.

    2014-01-01

    Complementary neutron- and light-scattering results on nine proteins and amino acids reveal the role of rigidity and secondary structure in determining the time- and lengthscales of low-frequency collective vibrational dynamics in proteins. These dynamics manifest in a spectral feature, known as the boson peak (BP), which is common to all disordered materials. We demonstrate that BP position scales systematically with structural motifs, reflecting local rigidity: disordered proteins appear softer than α-helical proteins; which are softer than β-sheet proteins. Our analysis also reveals a universal spectral shape of the BP in proteins and amino acid mixtures; superimposable on the shape observed in typical glasses. Uniformity in the underlying physical mechanism, independent of the specific chemical composition, connects the BP vibrations to nanometer-scale heterogeneities, providing an experimental benchmark for coarse-grained simulations, structure/rigidity relationships, and engineering of proteins for novel applications. PMID:24940784

  10. Neural-network design applied to protein-secondary-structure predictions

    SciTech Connect

    Yu, R.C.; Head-Gordon, T.

    1995-04-01

    The success of neural networks is often limited by a sparse database of training examples, deficient neural-network architectures, and nonglobal optimization of the network variables. The convolution of these three problems has curtailed the application of network models to protein-structure predictions, where homology modeling or information theory approaches are considered better controlled alternatives. This paper introduces our broad objective of disentangling the three degrading features of neural networks cited above, beginning with improved designs of network architectures used in the prediction of protein secondary structure. This work demonstrates that network architecture design considerations greatly improve generalization and more efficiently extract complex sequence-structure relationships from the existing database, as compared to arbitrary architectures with the same size input window.

  11. Sequence-specific sup 1 H NMR assignments and secondary structure of eglin c

    SciTech Connect

    Hyberts, S.G.; Wagner, G. )

    1990-02-13

    Sequence-specific nuclear magnetic resonance assignments were obtained for eglin c, a polypeptide inhibitor of the granulocytic proteinases elastase and cathepsin G and some other proteinases. The protein consists of a single polypeptide chain of 70 residues. All proton resonances were assigned except for some labile protons of arginine side chains. The patterns of nuclear Overhauser enhancements and coupling constants and the observation of slow hydrogen exchange were used to characterize the secondary structure of the protein. The results indicate that the solution structure of the free inhibitor is very similar to the crystal structure reported for the same protein in the complex with subtilisin Carlsberg. However, a part of the binding loop seems to have a significantly different conformation in the free protein.

  12. Proton NMR assignment and secondary structural elements of human transforming growth factor. alpha

    SciTech Connect

    Brown, S.C.; Mueller, L.; Jeffs, P.W. )

    1989-01-24

    The {sup 1}H NMR spectrum of human transforming growth factor {alpha} (hTGF-{alpha}) has been completely assigned, and secondary structural elements have been identified as a preliminary step in determining the structure of this protein by distance geometry methods. Many of these structural elements closely correspond to those previously found in a truncated human EGF and murine EGF. These include the presence of an antiparallel {beta}-sheet between residues G19 and C34 with a type I {beta}-turn at V25-D28, a type II {beta}-turn at H35-Y38, and another short {beta}-sheet between residues Y38-V39 and H45-A46.

  13. The recognition of multi-class protein folds by adding average chemical shifts of secondary structure elements

    PubMed Central

    Feng, Zhenxing; Hu, Xiuzhen; Jiang, Zhuo; Song, Hangyu; Ashraf, Muhammad Aqeel

    2015-01-01

    The recognition of protein folds is an important step in the prediction of protein structure and function. Recently, an increasing number of researchers have sought to improve the methods for protein fold recognition. Following the construction of a dataset consisting of 27 protein fold classes by Ding and Dubchak in 2001, prediction algorithms, parameters and the construction of new datasets have improved for the prediction of protein folds. In this study, we reorganized a dataset consisting of 76-fold classes constructed by Liu et al. and used the values of the increment of diversity, average chemical shifts of secondary structure elements and secondary structure motifs as feature parameters in the recognition of multi-class protein folds. With the combined feature vector as the input parameter for the Random Forests algorithm and ensemble classification strategy, we propose a novel method to identify the 76 protein fold classes. The overall accuracy of the test dataset using an independent test was 66.69%; when the training and test sets were combined, with 5-fold cross-validation, the overall accuracy was 73.43%. This method was further used to predict the test dataset and the corresponding structural classification of the first 27-protein fold class dataset, resulting in overall accuracies of 79.66% and 93.40%, respectively. Moreover, when the training set and test sets were combined, the accuracy using 5-fold cross-validation was 81.21%. Additionally, this approach resulted in improved prediction results using the 27-protein fold class dataset constructed by Ding and Dubchak. PMID:26980999

  14. Computer analysis of phytochrome sequences and reevaluation of the phytochrome secondary structure by Fourier transform infrared spectroscopy.

    PubMed

    Sühnel, J; Hermann, G; Dornberger, U; Fritzsche, H

    1997-07-18

    A repertoire of various methods of computer sequence analysis was applied to phytochromes in order to gain new insights into their structure and function. A statistical analysis of 23 complete phytochrome sequences revealed regions of non-random amino acid composition, which are supposed to be of particular structural or functional importance. All phytochromes other than phyD and phyE from Arabidopsis have at least one such region at the N-terminus between residues 2 and 35. A sequence similarity search of current databases indicated striking homologies between all phytochromes and a hypothetical 84.2-kDa protein from the cyanobacterium Synechocystis. Furthermore, scanning the phytochrome sequences for the occurrence of patterns defined in the PROSITE database detected the signature of the WD repeats of the beta-transducin family within the functionally important 623-779 region (sequence numbering of phyA from Avena) in a number of phytochromes. A multiple sequence alignment performed with 23 complete phytochrome sequences is made available via the IMB Jena World-Wide Web server (http://www.imb-jena.de/PHYTO.html). It can be used as a working tool for future theoretical and experimental studies. Based on the multiple alignment striking sequence differences between phytochromes A and B were detected directly at the N-terminal end, where all phytochromes B have an additional stretch of 15-42 amino acids. There is also a variety of positions with totally conserved but different amino acids in phytochromes A and B. Most of these changes are found in the sequence segment 150-200. It is, therefore, suggested that this region might be of importance in determining the photosensory specificity of the two phytochromes. The secondary structure prediction based on the multiple alignment resulted in a small but significant beta-sheet content. This finding is confirmed by a reevaluation of the secondary structure using FTIR spectroscopy.

  15. Pitch accent alignment in romance: primary and secondary associations with metrical structure.

    PubMed

    Prieto, Pilar; D'Imperio, Mariapaola; Fivela, Barbara Gili

    2005-01-01

    The article describes the contrastive possibilities of alignment of high accents in three Romance varieties, namely, Central Catalan, Neapolitan Italian, and Pisa Italian. The Romance languages analyzed in this article provide crucial evidence that small differences in alignment in rising accents should be encoded phonologically. To account for such facts within the AM model, the article develops the notion of "phonological anchoring" as an extension of the concept of secondary association originally proposed by Pierrehumbert and Beckman (1988), and later adopted by Grice (1995), Grice, Ladd, and Arvaniti (2000), and others to explain the behavior of edge tones. The Romance data represent evidence that not only peripheral edge tones seek secondary associations. We claim that the phonological representation of pitch accents should include two independent mechanisms to encode alignment properties with metrical structure: (1) encoding of the primary phonological association (or affiliation) between the tone and its tone-bearing unit; and (2), for some specific cases, encoding of the secondary phonological anchoring of tones to prosodic edges (moras, syllables, and prosodic words). The Romance data described in the article provide crucial evidence of mora-edge, syllable-edge, and word-edge H tonal associations.

  16. Interplay between desolvation and secondary structure in mediating cosolvent and temperature induced alpha-synuclein aggregation

    NASA Astrophysics Data System (ADS)

    Anderson, V. L.; Webb, W. W.; Eliezer, D.

    2012-10-01

    Both increased temperature and moderate concentrations of fluorinated alcohols enhance aggregation of the Parkinson's disease-associated protein α-synuclein (αS). Here, we investigate the secondary structural rearrangements induced by heating and trifluoroethanol [TFE]. At low TFE concentrations, CD spectra feature a negative peak characteristic of disordered polypeptides near 200 nm and a slight shoulder around 220 nm suggesting some polyproline-II content. Upon heating, these peaks weaken, while a weak negative signal develops at 222 nm. At high TFE concentrations, the spectra show distinct minima at 208 and 222 nm, indicative of considerable α-helical structure, which diminish upon heating. We observe a crossover between the low-TFE and high-TFE behavior near 15% TFE, where we previously showed that a partially helical intermediate is populated. We postulate that the protein is well solvated by water at low TFE concentrations and by TFE at high TFE concentrations, but may become desolvated at the crossover point. We discuss the potential roles and interplay of desolvation and helical secondary structure in driving αS aggregation.

  17. Protein Secondary Structure Prediction Using Local Adaptive Techniques in Training Neural Networks

    NASA Astrophysics Data System (ADS)

    Aik, Lim Eng; Zainuddin, Zarita; Joseph, Annie

    2008-01-01

    One of the most significant problems in computer molecular biology today is how to predict a protein's three-dimensional structure from its one-dimensional amino acid sequence or generally call the protein folding problem and difficult to determine the corresponding protein functions. Thus, this paper involves protein secondary structure prediction using neural network in order to solve the protein folding problem. The neural network used for protein secondary structure prediction is multilayer perceptron (MLP) of the feed-forward variety. The training set are taken from the protein data bank which are 120 proteins while 60 testing set is the proteins which were chosen randomly from the protein data bank. Multiple sequence alignment (MSA) is used to get the protein similar sequence and Position Specific Scoring matrix (PSSM) is used for network input. The training process of the neural network involves local adaptive techniques. Local adaptive techniques used in this paper comprises Learning rate by sign changes, SuperSAB, Quickprop and RPROP. From the simulation, the performance for learning rate by Rprop and Quickprop are superior to all other algorithms with respect to the convergence time. However, the best result was obtained using Rprop algorithm.

  18. Prediction algorithm for amino acid types with their secondary structure in proteins (PLATON) using chemical shifts.

    PubMed

    Labudde, D; Leitner, D; Krüger, M; Oschkinat, H

    2003-01-01

    The algorithm PLATON is able to assign sets of chemical shifts derived from a single residue to amino acid types with its secondary structure (amino acid species). A subsequent ranking procedure using optionally two different penalty functions yields predictions for possible amino acid species for the given set of chemical shifts. This was demonstrated in the case of the alpha-spectrin SH3 domain and applied to 9 further protein data sets taken from the BioMagRes database. A database consisting of reference chemical shift patterns (reference CSPs) was generated from assigned chemical shifts of proteins with known 3D-structure. This reference CSP database is used in our approach for extracting distributions of amino acid types with their most likely secondary structure elements (namely alpha-helix, beta-sheet, and coil) for single amino acids by comparison with query CSPs. Results obtained for the 10 investigated proteins indicates that the percentage of correct amino acid species in the first three positions in the ranking list, ranges from 71.4% to 93.2% for the more favorable penalty function. Where only the top result of the ranking list for these 10 proteins is considered, 36.5% to 83.1% of the amino acid species are correctly predicted. The main advantage of our approach, over other methods that rely on average chemical shift values is the ability to increase database content by incorporating newly derived CSPs, and therefore to improve PLATON's performance over time.

  19. Pan-eukaryote ITS2 homologies revealed by RNA secondary structure

    PubMed Central

    Coleman, Annette W.

    2007-01-01

    For evolutionary comparisons, phylogenetics and evaluation of potential interbreeding taxa of a species, various loci have served for animals and plants and protistans. One [second internal transcribed spacer (ITS2) of the nuclear ribosomal DNA] is highly suitable for all. Its sequence is species specific. It has already been used extensively and very successfully for plants and some protistans, and a few animals (where historically, the mitochondrial genes have dominated species studies). Despite initial impressions that ITS2 is too variable, it has proven to provide useful biological information at higher taxonomic levels, even across all eukaryotes, thanks to the conserved aspects of its transcript secondary structure. The review of all eukaryote groups reveals that ITS2 is expandable, but always retains in its RNA transcript a common core structure of two helices with hallmark characteristics important for ribosomal RNA processing. This aspect of its RNA transcript secondary structure can rescue difficult alignment problems, making the ITS2 a more powerful tool for phylogenetics. Equally important, the recognition of eukaryote-wide homology regions provides extensive and detailed information to test experimental studies of ribosomal rRNA processing. PMID:17459886

  20. A global sampling approach to designing and reengineering RNA secondary structures.

    PubMed

    Levin, Alex; Lis, Mieszko; Ponty, Yann; O'Donnell, Charles W; Devadas, Srinivas; Berger, Bonnie; Waldispühl, Jérôme

    2012-11-01

    The development of algorithms for designing artificial RNA sequences that fold into specific secondary structures has many potential biomedical and synthetic biology applications. To date, this problem remains computationally difficult, and current strategies to address it resort to heuristics and stochastic search techniques. The most popular methods consist of two steps: First a random seed sequence is generated; next, this seed is progressively modified (i.e. mutated) to adopt the desired folding properties. Although computationally inexpensive, this approach raises several questions such as (i) the influence of the seed; and (ii) the efficiency of single-path directed searches that may be affected by energy barriers in the mutational landscape. In this article, we present RNA-ensign, a novel paradigm for RNA design. Instead of taking a progressive adaptive walk driven by local search criteria, we use an efficient global sampling algorithm to examine large regions of the mutational landscape under structural and thermodynamical constraints until a solution is found. When considering the influence of the seeds and the target secondary structures, our results show that, compared to single-path directed searches, our approach is more robust, succeeds more often and generates more thermodynamically stable sequences. An ensemble approach to RNA design is thus well worth pursuing as a complement to existing approaches. RNA-ensign is available at http://csb.cs.mcgill.ca/RNAensign. PMID:22941632

  1. Effects of high hydrostatic pressure on secondary structure and emulsifying behavior of sweet potato protein

    NASA Astrophysics Data System (ADS)

    Mehmood Khan, Nasir; Mu, Tai-Hua; Sun, Hong-Nan; Zhang, Miao; Chen, Jing-Wang

    2015-04-01

    In this study, secondary structures of sweet potato protein (SPP) after high hydrostatic pressure (HHP) treatment (200-600 MPa) were evaluated and emulsifying properties of emulsions with HHP-treated SPP solutions in different pH values (3, 6, and 9) were investigated. Circular dichroism analysis confirmed the modification of the SPP secondary structure. Surface hydrophobicity increased at pH 3 and decreased at 6 and 9. Emulsifying activity index at pH 6 increased with an increase in pressure, whereas emulsifying stability index increased at pH 6 and 9. Oil droplet sizes decreased, while volume frequency distribution of the smaller droplets increased at pH 3 and 6 with the HHP treatment. Emulsion viscosity increased at pH 6 and 9 and pseudo-plastic flow behaviors were not altered for all emulsions produced with HHP-treated SPP. These results suggested that HHP could modify the SPP structure for better emulsifying properties, which could increase the use of SPP emulsion in the food industry.

  2. Molecular topography and secondary structure comparisons of botulinum neurotoxin types A, B and E.

    PubMed

    Singh, B R; DasGupta, B R

    1989-03-16

    Botulinum neurotoxin (NT) serotypes A, B and E differ in microstructure and biological activities. The three NTs were examined for secondary structure parameters (alpha-helix, beta-sheet, beta-turn and random coil content) on the basis of circular dichroism; degree of exposed Tyr residues (second derivative spectroscopy) and state of the Trp residues (fluorescence and fluorescence quantum yield). The proteins are high in beta-pleated sheet content (41-44%) and low in alpha-helical content (21-28%). About 30-36% of the amino acids are in random coils. The beta-sheet contents in the NTs are similar irrespective of their structural forms (i.e. single or dichain forms) or level of toxicity. About 84%, 58% and 61% of Tyr residues of types A, B, and E NT, respectively, were exposed to the solvent (pH 7.2 phosphate buffer). Although the fluorescence emission maximum of Trp residues of type B NT was most blue shifted (331 nm compared to 334 for types A and E NT, and 346 nm for free tryptophan) the fluorescence quantum yields of types A and B were similar and higher than type E. In general the NTs have similar secondary (low alpha-helix and high beta-sheets) and tertiary (exposed tyrosine residues and tryptophan fluorescence quantum yield) structures. Within this generalized picture there are significant differences which might be related to the differences in their biological activities.

  3. Secondary Structure of Corona Proteins Determines the Cell Surface Receptors Used by Nanoparticles

    PubMed Central

    2015-01-01

    Nanoparticles used for biological and biomedical applications encounter a host of extracellular proteins. These proteins rapidly adsorb onto the nanoparticle surface, creating a protein corona. Poly(ethylene glycol) can reduce, but not eliminate, the nonspecific adsorption of proteins. As a result, the adsorbed proteins, rather than the nanoparticle itself, determine the cellular receptors used for binding, the internalization mechanism, the intracellular transport pathway, and the subsequent immune response. Using fluorescence microscopy and flow cytometry, we first characterize a set of polystyrene nanoparticles in which the same adsorbed protein, bovine serum albumin, leads to binding to two different cell surface receptors: native albumin receptors and scavenger receptors. Using a combination of circular dichroism spectroscopy, isothermal titration calorimetry, and fluorescence spectroscopy, we demonstrate that the secondary structure of the adsorbed bovine serum albumin protein controls the cellular receptors used by the protein–nanoparticle complexes. These results show that protein secondary structure is a key parameter in determining the cell surface receptor used by a protein–nanoparticle complex. We expect this link between protein structure and cellular outcomes will provide a molecular basis for the design of nanoparticles for use in biological and biomedical applications. PMID:24779411

  4. Comparative structure and biomechanics of plant primary and secondary cell walls.

    PubMed

    Cosgrove, Daniel J; Jarvis, Michael C

    2012-01-01

    Recent insights into the physical biology of plant cell walls are reviewed, summarizing the essential differences between primary and secondary cell walls and identifying crucial gaps in our knowledge of their structure and biomechanics. Unexpected parallels are identified between the mechanism of expansion of primary cell walls during growth and the mechanisms by which hydrated wood deforms under external tension. There is a particular need to revise current "cartoons" of plant cell walls to be more consistent with data from diverse approaches and to go beyond summarizing limited aspects of cell walls, serving instead as guides for future experiments and for the application of new techniques.

  5. Monte Carlo simulation of secondary electron images for real sample structures in scanning electron microscopy.

    PubMed

    Zhang, P; Wang, H Y; Li, Y G; Mao, S F; Ding, Z J

    2012-01-01

    Monte Carlo simulation methods for the study of electron beam interaction with solids have been mostly concerned with specimens of simple geometry. In this article, we propose a simulation algorithm for treating arbitrary complex structures in a real sample. The method is based on a finite element triangular mesh modeling of sample geometry and a space subdivision for accelerating simulation. Simulation of secondary electron image in scanning electron microscopy has been performed for gold particles on a carbon substrate. Comparison of the simulation result with an experiment image confirms that this method is effective to model complex morphology of a real sample.

  6. Comparative structure and biomechanics of plant primary and secondary cell walls

    PubMed Central

    Cosgrove, Daniel J.; Jarvis, Michael C.

    2012-01-01

    Recent insights into the physical biology of plant cell walls are reviewed, summarizing the essential differences between primary and secondary cell walls and identifying crucial gaps in our knowledge of their structure and biomechanics. Unexpected parallels are identified between the mechanism of expansion of primary cell walls during growth and the mechanisms by which hydrated wood deforms under external tension. There is a particular need to revise current “cartoons” of plant cell walls to be more consistent with data from diverse approaches and to go beyond summarizing limited aspects of cell walls, serving instead as guides for future experiments and for the application of new techniques. PMID:22936943

  7. GraphClust: alignment-free structural clustering of local RNA secondary structures

    PubMed Central

    Rose, Dominic; Backofen, Rolf

    2012-01-01

    Motivation: Clustering according to sequence–structure similarity has now become a generally accepted scheme for ncRNA annotation. Its application to complete genomic sequences as well as whole transcriptomes is therefore desirable but hindered by extremely high computational costs. Results: We present a novel linear-time, alignment-free method for comparing and clustering RNAs according to sequence and structure. The approach scales to datasets of hundreds of thousands of sequences. The quality of the retrieved clusters has been benchmarked against known ncRNA datasets and is comparable to state-of-the-art sequence–structure methods although achieving speedups of several orders of magnitude. A selection of applications aiming at the detection of novel structural ncRNAs are presented. Exemplarily, we predicted local structural elements specific to lincRNAs likely functionally associating involved transcripts to vital processes of the human nervous system. In total, we predicted 349 local structural RNA elements. Availability: The GraphClust pipeline is available on request. Contact: backofen@informatik.uni-freiburg.de Supplementary information: Supplementary data are available at Bioinformatics online. PMID:22689765

  8. Structural evaluation of mixer pump installed in Tank 241-AN-107 for caustic addition project

    SciTech Connect

    Leshikar, G.A.

    1995-06-16

    This report documents the structural analysis and evaluation of a mixer pump and caustic addition system to be used in Tank 107-AN. This pump will be installed in the central pump pit of this double- shell tank for the purpose of bringing the hydroxide ion concentration into compliance with Tank Farm operating specifications.

  9. Secondary structures of short peptide chains in the gas phase: Double resonance spectroscopy of protected dipeptides

    NASA Astrophysics Data System (ADS)

    Chin, Wutharath; Dognon, Jean-Pierre; Canuel, Clélia; Piuzzi, François; Dimicoli, Iliana; Mons, Michel; Compagnon, Isabelle; von Helden, Gert; Meijer, Gerard

    2005-02-01

    The conformational structure of short peptide chains in the gas phase is studied by laser spectroscopy of a series of protected dipeptides, Ac-Xxx-Phe-NH2, Xxx=Gly, Ala, and Val. The combination of laser desorption with supersonic expansion enables us to vaporize the peptide molecules and cool them internally; IR/UV double resonance spectroscopy in comparison to density functional theory calculations on Ac-Gly-Phe-NH2 permits us to identify and characterize the conformers populated in the supersonic expansion. Two main conformations, corresponding to secondary structures of proteins, are found to compete in the present experiments. One is composed of a doubly γ-fold corresponding to the 27 ribbon structure. Topologically, this motif is very close to a β-strand backbone conformation. The second conformation observed is the β-turn, responsible for the chain reversal in proteins. It is characterized by a relatively weak hydrogen bond linking remote NH and CO groups of the molecule and leading to a ten-membered ring. The present gas phase experiment illustrates the intrinsic folding properties of the peptide chain and the robustness of the β-turn structure, even in the absence of a solvent. The β-turn population is found to vary significantly with the residues within the sequence; the Ac-Val-Phe-NH2 peptide, with its two bulky side chains, exhibits the largest β-turn population. This suggests that the intrinsic stabilities of the 27 ribbon and the β-turn are very similar and that weakly polar interactions occurring between side chains can be a decisive factor capable of controlling the secondary structure.

  10. Secondary functionalization of allyl-terminated GaP(111)A surfaces via heck cross-coupling metathesis, hydrosilylation, and electrophilic addition of bromine.

    PubMed

    Peczonczyk, Sabrina L; Brown, Elizabeth S; Maldonado, Stephen

    2014-01-14

    The functionalization of single crystalline gallium phosphide (GaP) (111)A surfaces with allyl groups has been performed using a sequential chlorine-activation/Grignard reaction process. Increased hydrophobicity following reaction of a GaP(111)A surface with C3H5MgCl was observed through water contact angle measurements. Infrared spectra of GaP(111)A samples after reaction with C3H5MgCl showed the asymmetric C═C and C═C-H modes diagnostic of surface-attached allyl groups. The stability of allyl-terminated GaP(111)A surfaces under ambient and aqueous conditions was investigated. XP spectra of allyl-terminated GaP(111)A highlighted a significant resistance against interfacial oxidation both in air and in water relative to the native interface. Electrochemical impedance spectroscopy indicated a change in the flat-band potential of allyl-terminated GaP(111)A electrodes immersed in water relative to native GaP(111)A surfaces. Further, the flat-band potentials for allyl-terminated electrodes were insensitive to changes in solution pH. The utility of surface-bound allyl groups for covalent secondary functionalization of GaP(111)A interfaces was assessed through three separate reactions: Heck cross-coupling metathesis, hydrosilylation, and electrophilic addition of bromine reactions. Addition of aryl groups across the olefins on allyl-terminated GaP(111)A via Heck cross coupling was performed and confirmed through high-resolution F 1s and C 1s XP spectra and IR spectra. Control experiments with GaP(111)A surfaces functionalized with short alkanes indicated no evidence for metathesis. Hydrosilylation reactions were separately performed. Si 2s XP spectra, in conjunction with infrared spectra, similarly showed secondary evidence of surface functionalization for allyl-terminated GaP(111)A but not for CH3-terminated GaP(111)A surfaces. Similar analyses showed electrophilic addition of Br2 across the terminal olefin on an allyl-terminated GaP(111)A surface after exposure to

  11. Students' Understanding of Primary and Secondary Protein Structure: Drawing Secondary Protein Structure Reveals Student Understanding Better than Simple Recognition of Structures

    ERIC Educational Resources Information Center

    Harle, Marissa; Towns, Marcy H.

    2013-01-01

    The interdisciplinary nature of biochemistry courses requires students to use both chemistry and biology knowledge to understand biochemical concepts. Research that has focused on external representations in biochemistry has uncovered student difficulties in comprehending and interpreting external representations in addition to a fragmented…

  12. Secondary contact and changes in coastal habitat availability influence the nonequilibrium population structure of a salmonid (Oncorhynchus keta)

    PubMed Central

    Petrou, E L; Hauser, L; Waples, R S; Seeb, J E; Templin, W D; Gomez-Uchida, D; Seeb, L W

    2013-01-01

    Numerous empirical studies have reported lack of migration–drift equilibrium in wild populations. Determining the causes of nonequilibrium population structure is challenging because different evolutionary processes acting at a variety of spatiotemporal scales can produce similar patterns. Studies of contemporary populations in northern latitudes suggest that nonequilibrium population structure is probably caused by recent colonization of the region after the last Pleistocene ice age ended ∼13 000 years ago. The chum salmon's (Oncorhynchus keta) range was fragmented by dramatic environmental changes during the Pleistocene. We investigated the population structure of chum salmon on the North Alaska Peninsula (NAP) and, using both empirical data and simulations, evaluated the effects of colonization timing and founder population heterogeneity on patterns of genetic differentiation. We screened 161 single nucleotide polymorphisms and found evidence of nonequilibrium population structure when the slope of the isolation-by-distance relationship was examined at incremental spatial scales. In addition, simulations suggested that this pattern closely matched models of recent colonization of the NAP by secondary contact. Our results agree with geological and archaeological data indicating that the NAP was a dynamic landscape that may have been more recently colonized than during the last deglaciation because of dramatic changes in coastal hydrology over the last several thousand years. PMID:24118255

  13. Secondary Airflow Structure around Clustered Shrubs and Its Significance for Vegetated Dune Evolution

    NASA Astrophysics Data System (ADS)

    Luo, Wanyin; Dong, Zhibao; Qian, Guangqiang; Lu, Junfeng

    2016-04-01

    Shrubs have an important significance in aeolian processes due to their disturbance of the local airflow. In the formation of vegetated dunes, there is an iterative interaction between shrub geometry, the structure of the secondary airflow, and the interaction between neighboring shrubs. Understanding the dynamics of vegetated dunes thus requires an insight into the airflow fields around shrubs. Based on aerodynamic and aeolian sand physics theory, this project measured the complex secondary flow field and aeolian sand deposition pattern around single and cluster shrubs with varied densities (i.e., 0.05, 0.08, 0.15, 0.20) and gap ratios (the ratio of the gap spacing between the shrub models to the center-to-center distance for the shrub models, ranged from 1.1 to 1.8 with side-by-side arrangement and 1.2 to 4.3 with tandem arrangement) using the particle image velocimetry system through wind tunnle simulation. The relationship between the secondary airflow structure and the shrub's porosity and arrangement was analyzed quantitatively. Research results revealed that porosity (density) is the key parameter to affect the flow patterns around single shrub. Compared to solid obstacles, bleed flow through the shrubs has great influence on the secondary airflow patterns around itself. Under cluster modes, the distance between two adjacent shrubs has great influence on flow field structures around them. The flow patterns around two side-by-side arranged shrubs can be classified into three kinds of modes, that is: single-bluff-body, biased flow pattern and parallel vortex streets. The flow patterns around two tandem arranged shrubs can be classified into three regimes, that is: the extended body regime, reattachment regime and co-shedding regime. The "shadow zone" with low velocity in the lee of shrubs is the optimal position for sand deposition, but its form, size and orientation would varied with the shrub porosity and gap ratio between them. With the increase of the gap

  14. Sequence-specific 1H assignment and secondary structure of the bacteriocin AS-48 cyclic peptide.

    PubMed

    Langdon, G M; Bruix, M; Gálvez, A; Valdivia, E; Maqueda, M; Rico, M

    1998-07-01

    The bacteriocin AS-48 is a cationic peptide (7149 Da) having a broad antimicrobial spectrum, encoded by the 68 kb conjugative plasmid pMB2 from Enterococcus faecalis S-48. It is a unique peptide since it has a cyclic structure, which is achieved by the formation of a tail-head peptide bond after ribosomal synthesis (Gálvez et al., 1989; Martínez-Bueno et al., 1994; Samyn et al., 1994). Preliminary CD and calorimetric studies (data not shown) pointed towards a highly helical and very stable three dimensional structure. All the information gathered until now indicates that the target of AS-48 is the cytoplasmic membrane in which it opens channels or pores, leading to dissipation of the proton motive force and cell death, which in some cases is also followed by bacterial lysis (Gálvez et al., 1991). This peptide is a suitable tool for studying protein-membrane interactions, and it also offers promising perspectives for biotechnological applications. Knowledge of the 3D structure of AS-48 is a first step in the conduct of further structure-function studies. Here we report the complete 1H NMR assignment of its proton resonances together with the resulting secondary structure pattern as prerequisites for the determination of a high-resolution 3D solution structure.

  15. Accounting for solvent accessibility and secondary structure in protein phylogenetics is clearly beneficial.

    PubMed

    Le, Si Quang; Gascuel, Olivier

    2010-05-01

    Amino acid substitution models are essential to most methods to infer phylogenies from protein data. These models represent the ways in which proteins evolve and substitutions accumulate along the course of time. It is widely accepted that the substitution processes vary depending on the structural configuration of the protein residues. However, this information is very rarely used in phylogenetic studies, though the 3-dimensional structure of dozens of thousands of proteins has been elucidated. Here, we reinvestigate the question in order to fill this gap. We use an improved estimation methodology and a very large database comprising 1471 nonredundant globular protein alignments with structural annotations to estimate new amino acid substitution models accounting for the secondary structure and solvent accessibility of the residues. These models incorporate a confidence coefficient that is estimated from the data and reflects the reliability and usefulness of structural annotations in the analyzed sequences. Our results with 300 independent test alignments show an impressive likelihood gain compared with standard models such as JTT or WAG. Moreover, the use of these models induces significant topological changes in the inferred trees, which should be of primary interest to phylogeneticists. Our data, models, and software are available for download from http://atgc.lirmm.fr/phyml-structure/.

  16. Experiences and Reflections about Teaching Atomic Structure in a Jigsaw Classroom in Lower Secondary School Chemistry Lessons

    NASA Astrophysics Data System (ADS)

    Eilks, Ingo

    2005-02-01

    This article describes and discusses an example of how atomic structure can be taught in lower secondary chemistry using a modified jigsaw-classroom method. The lesson was taught in grades 9 and 10 (age range 15 17 years) chemistry in 13 learning groups with a total of 313 students in various grammar, middle, and comprehensive schools in Germany. The written evaluation of the lesson focused on determining the students’ opinions on the teaching methods that were used. Emphasis was on gathering information from the students’ viewpoint. Did the students think that these methods could make science lessons more attractive? Could these methods help to promote more active student learning, cooperative learning, or communicative and social abilities? Additional data that were derived from a cognitive test and teacher feedback are also presented. The results of the study show that teaching methods like the jigsaw classroom have potential to improve students’ attitude towards science. The results may also indicate that it is appropriate to demand that student-oriented and cooperative-learning methods be used more often in secondary level science education.

  17. Ten-Structure as Strategy of Addition 1-20 by Involving Spatial Structuring Ability for First Grade Students

    ERIC Educational Resources Information Center

    Salmah, Ummy; Putri, Ratu Ilma Indra; Somakim

    2015-01-01

    The aim of this study is to design learning activities that can support students to develop strategies for the addition of number 1 to 20 in the first grade by involving students' spatial structuring ability. This study was conducted in Indonesia by involving 27 students. In this paper, one of three activities is discussed namely ten-box activity.…

  18. Membrane Association and Destabilization by Aggregatibacter actinomycetemcomitans Leukotoxin Requires Changes in Secondary Structures

    PubMed Central

    Walters, Michael J.; Brown, Angela C.; Edrington, Thomas C.; Baranwal, Somesh; Du, Yurong; Lally, Edward T.; Boesze-Battaglia, Kathleen

    2013-01-01

    SUMMARY Aggregatibacter actinomycetemcomitans is a common inhabitant of the upper aerodigestive tract of humans and non-human primates and is associated with disseminated infections, including lung and brain abscesses, pediatric infective endocarditis in children, and localized aggressive periodontitis. A. actinomycetemcomitans secretes a repeats-in-toxin protein, leukotoxin, which exclusively kills lymphocyte function-associated antigen-1-bearing cells. The toxin's pathological mechanism is not fully understood; however, experimental evidence indicates that it involves the association with and subsequent destabilization of the target cell's plasma membrane. We have long hypothesized that leukotoxin secondary structure is strongly correlated with membrane association and/or destabilization. In this study, we tested this hypothesis by analyzing lipid-induced changes in leukotoxin conformation. Upon incubation of leukotoxin with lipids that favor leukotoxin-membrane association, we observed an increase in leukotoxin α-helical content that was not observed with lipids that favor membrane destabilization. The change in leukotoxin conformation after incubation with these lipids suggests that membrane binding and membrane destabilization have distinct secondary structural requirements, suggesting that they are independent events. These studies thus provide insight into the mechanism of cell damage that leads to disease progression by A. actinomycetemcomitans. PMID:23678967

  19. Secondary flow structures under simple harmonic inflow in a bent pipe model for curved arteries

    NASA Astrophysics Data System (ADS)

    Glenn, Autumn; Seagrave, Penelope; Shu, Fangjun; Bulusu, Kartik; Plesniak, Michael W.

    2010-11-01

    Inward centrifuging of fluid in the inviscid core of a 180 degree curved pipe leads to Lyne-type vortices under zero-mean harmonic oscillations, along with the formation of vortices in the Stokes' layer, that rotate in the same directional sense as their steady flow counterpart (Dean vortices). Under physiological conditions, the development of the Lyne-type vortices is believed to be influenced by the systolic pulse, and its associated rapid acceleration and deceleration. Experimental data acquired using Particle Image Velocimetry (PIV) for three harmonic waveforms of different frequencies clarify the conditions under which Lyne vortices form. Multiple vortex pairs were observed for all waveforms and frequencies investigated, including Dean and Lyne-type vortex structures at a Womersley number of 4.22, much lower than previously reported. Hence, frequency alone is not an adequate governing parameter to characterize secondary flow structures in pulsatile flows. A regime map of the secondary flow was sought by using an acceleration-based parameter and the Dean number.

  20. 18S rRNA secondary structure and phylogenetic position of Peloridiidae (Insecta, hemiptera).

    PubMed

    Ouvrard, D; Campbell, B C; Bourgoin, T; Chan, K L

    2000-09-01

    A secondary structure model for 18S rRNA of peloridiids, relict insects with a present-day circumantarctic distribution, is constructed using comparative sequence analysis, thermodynamic folding, a consensus method using 18S rRNA models of other taxa, and support of helices based on compensatory substitutions. Results show that probable in vivo configuration of 18S rRNA is not predictable using current free-energy models to fold the entire molecule concurrently. This suggests that refinements in free-energy minimization algorithms are needed. Molecular phylogenetic datasets were created using 18S rRNA nucleotide alignments produced by CLUSTAL and rigorous interpretation of homologous position based on certain secondary substructures. Phylogenetic analysis of a hemipteran data matrix of 18S rDNA sequences placed peloridiids sister to Heteroptera. Resolution of affiliations between the three main euhemipteran lineages was unresolved. The peloridiid 18S RNA model presented here provides the most accurate template to date for aligning homologous nucleotides of hemipteran taxa. Using folded 18S rRNA to infer homology of character as morpho-molecular structures or nucleotides and scoring particular sites or substructures is discussed. PMID:10991793

  1. Evolutionary conservation of sequence and secondary structures inCRISPR repeats

    SciTech Connect

    Kunin, Victor; Sorek, Rotem; Hugenholtz, Philip

    2006-09-01

    Clustered Regularly Interspaced Palindromic Repeats (CRISPRs) are a novel class of direct repeats, separated by unique spacer sequences of similar length, that are present in {approx}40% of bacterial and all archaeal genomes analyzed to date. More than 40 gene families, called CRISPR-associated sequences (CAS), appear in conjunction with these repeats and are thought to be involved in the propagation and functioning of CRISPRs. It has been proposed that the CRISPR/CAS system samples, maintains a record of, and inactivates invasive DNA that the cell has encountered, and therefore constitutes a prokaryotic analog of an immune system. Here we analyze CRISPR repeats identified in 195 microbial genomes and show that they can be organized into multiple clusters based on sequence similarity. All individual repeats in any given cluster were inferred to form characteristic RNA secondary structure, ranging from non-existent to pronounced. Stable secondary structures included G:U base pairs and exhibited multiple compensatory base changes in the stem region, indicating evolutionary conservation and functional importance. We also show that the repeat-based classification corresponds to, and expands upon, a previously reported CAS gene-based classification including specific relationships between CRISPR and CAS subtypes.

  2. Proton NMR assignments and secondary structure of the snake venom protein echistatin

    SciTech Connect

    Yuan Chen; Baum, J. ); Pitzenberger, S.M.; Garsky, V.M.; Lumma, P.K.; Sanyal, G. )

    1991-12-17

    The snake venom protein echistatin is a potent inhibitor of platelet aggregation. The inhibitory properties of echistatin have been attributed to the Arg-Gly-Asp sequence at residues 24-26. In this paper, sequence-specific nuclear magnetic resonance assignments are presented for the proton resonances of echistatin in water. The single-chain protein contains 49 amino acids and 4 cystine bridges. All of the backbone amide, C{sub alpha}H, and side-chain resonances, except for the {eta}-NH of the arginines, have been assigned. The secondary structure of the protein was characterized from the pattern of nuclear Overhauser enhancements, from the identification of slowly exchanging amide protons, from {sup 3}J{sub c{alpha}H-NH} coupling constants, and from circular dichroism studies. The data suggest that the secondary structure consists of a type I {beta}-turn, a short {beta}-hairpin, and a short-, irregular, antiparallel {beta}-sheet and that the Arg-Gly-Asp sequence is in a flexible loop connecting two strands of the distorted antiparallel {beta}-sheet.

  3. Direct RNA motif definition and identification from multiple sequence alignments using secondary structure profiles.

    PubMed

    Gautheret, D; Lambert, A

    2001-11-01

    We present here a new approach to the problem of defining RNA signatures and finding their occurrences in sequence databases. The proposed method is based on "secondary structure profiles". An RNA sequence alignment with secondary structure information is used as an input. Two types of weight matrices/profiles are constructed from this alignment: single strands are represented by a classical lod-scores profile while helical regions are represented by an extended "helical profile" comprising 16 lod-scores per position, one for each of the 16 possible base-pairs. Database searches are then conducted using a simultaneous search for helical profiles and dynamic programming alignment of single strand profiles. The algorithm has been implemented into a new software, ERPIN, that performs both profile construction and database search. Applications are presented for several RNA motifs. The automated use of sequence information in both single-stranded and helical regions yields better sensitivity/specificity ratios than descriptor-based programs. Furthermore, since the translation of alignments into profiles is straightforward with ERPIN, iterative searches can easily be conducted to enrich collections of homologous RNAs.

  4. Cygnus Pressured Cargo Module: Validation of Mathematical Model and Dynamic Qualification of Secondary Structures

    NASA Astrophysics Data System (ADS)

    Bellini, Marina; Luison, Dario; Tizzani, Luca

    2012-07-01

    Thales Alenia Space Italy is in charge to develop build- up, integrate and verify Cygnus Pressurized Cargo Module (PCM). This cargo is characterized by the large amount of payload, wrapped in foam, transferred in soft stowage bags, connected to the structure of support by belts. The paper summarizes the several tests performed to acquire the dynamic properties of bags. On the basis of the empirical results a reliable linear model was generated and used for a successful campaign of qualification of secondary structure. It is also demonstrated that the empirical-linear model of the soft-stowage bag was also the reason of a significant reduction of loads, which allowed achieving more easily the goal of carried mass, for PCM. The validation of PCM by Modal Survey Test is presented as well, emphasizing that the more realistic modeling of the soft bags has made easier the definition of a very simple test configuration.

  5. In solution cation-induced secondary and tertiary structure alterations of human calprotectin.

    PubMed

    Imani, Mehdi; Bahrami, Yaser; Jaliani, Hossein Zarei; Ardestani, Sussan Kaboudanian

    2014-10-01

    Calprotectin (CP) is widely considered to have diverse roles including growth inhibitory and apoptosis induction in a number of tumor cell lines and antimicrobial activities. As CP has been proposed to bind metal ions with high affinity, we have studied its functional and primarily its structural behavior upon Zn(2+) and Mn(2+) chelation solely and along with Ca(2+). We employed fluorescence spectroscopy and circular dichroism to determine the resulting modifications. Based upon our findings it is clear that treating CP with ions effectively weakened its natural growth inhibitory activity. Moreover, structural analysis of Zn(2+) and Mn(2+)-treated CPs indicated remarkable alterations in the regular secondary structures in favor of irregular structures while Zn(2+) and Mn(2+) treatment of CP after incubation with Ca(2+) displayed no remarkable shifts. Tertiary structure investigation using fluorescence spectroscopy showed that CP undergoes conformational changes upon Zn(2+) and Mn(2+) treatment whereby Trp residues of protein is slightly exposed to the hydrophilic environment, compactness of CP is compromised, whereas in Ca(2+)-treated CP, the tertiary structure integrity is intact upon Zn(2+) and Mn(2+) chelation. Interestingly, CP structural modifications upon Zn(2+) and Mn(2+) treatment was significantly comparable, probably due to similar radii and charges of ions. Taken all together, we have concluded that CP maintains its normal nature in Ca(2+)-loaded state when treated with Zn(2+) and Mn(2+) ions. It can be suggested that Ca(2+) not only stabilize CP structure but also helps CP to keep its structure upon metal ions chelation which is involved in host organism defense system.

  6. Probing secondary structures of peptide chains using gas phase laser spectroscopy

    NASA Astrophysics Data System (ADS)

    Mons, Michel

    2006-03-01

    A bottom-up approach involving conformer-specific IR studies of short peptide sequences enables us to map the intramolecular interactions that shape the peptide backbone, in particular those H-bonds that are responsible for stability and formation of secondary structures in proteins, like turns or helices. The combination of laser-desorption of solid samples coupled to the efficient cooling in a supersonic expansion makes it possible to isolate in the gas phase the lowest conformations of the energy landscape of small flexible biomolecules. The low temperature achieved enables spectroscopists to record UV spectra in which the contribution of each conformer populated can be distinguished and the corresponding conformation identified using IR/UV double resonance spectroscopy. Data collected are directly comparable to the best quantum chemistry calculations on these species and therefore constitute a severe test for the theoretical methods used. It will be shown how investigation of sequences with an increasing number of building blocks permits to deduce the robust structural trends of a peptide backbone: i) local conformational preference of the backbone in one-residue chains, ii) in capped dipeptides, the competition between a succession of local conformational preferences and overall folded structures, in which a different type of H-bonding scheme, involving distant H-bonding sites along the backbone, takes place: in particular beta-turns, the secondary structure responsible for chain reversals, and finally iii) evidence for the spontaneous helical folding (short 3-10 helix) of three-residue chains will be presented, illustrating the relative weakness of the H-bonding in these molecular assemblies.

  7. Characterization of Effect of Support Structures in Laser Additive Manufacturing of Stainless Steel

    NASA Astrophysics Data System (ADS)

    Järvinen, Jukka-Pekka; Matilainen, Ville; Li, Xiaoyun; Piili, Heidi; Salminen, Antti; Mäkelä, Ismo; Nyrhilä, Olli

    Laser additive manufacturing (LAM) of stainless steel is a layer wisetechnology for fabricating 3D parts from metal powder via selectively melting powder with laser beam. Support structures play a significant role in LAM process as they help to remove heat away from the process and on the other hand hold the work piece in its place. A successful design of support structures can help to achievea building process fast and inexpensive with high quality. Aimof this study was to characterize the usability of two types of support structures: web and tube supports. Purpose of this studywas also to analyze how suitable they are in two industrial application cases: case for dental application and case for jewelry application. It was concluded that the removability of web supports was much better than tube supports. It was noticed that support structures are an important part of LAM process and they strongly affect the manufacturability and the end quality of the part.

  8. Secondary Structure Prediction of Protein Constructs Using Random Incremental Truncation and Vacuum-Ultraviolet CD Spectroscopy.

    PubMed

    Pukáncsik, Mária; Orbán, Ágnes; Nagy, Kinga; Matsuo, Koichi; Gekko, Kunihiko; Maurin, Damien; Hart, Darren; Kézsmárki, István; Vertessy, Beata G

    2016-01-01

    A novel uracil-DNA degrading protein factor (termed UDE) was identified in Drosophila melanogaster with no significant structural and functional homology to other uracil-DNA binding or processing factors. Determination of the 3D structure of UDE is excepted to provide key information on the description of the molecular mechanism of action of UDE catalysis, as well as in general uracil-recognition and nuclease action. Towards this long-term aim, the random library ESPRIT technology was applied to the novel protein UDE to overcome problems in identifying soluble expressing constructs given the absence of precise information on domain content and arrangement. Nine constructs of UDE were chosen to decipher structural and functional relationships. Vacuum ultraviolet circular dichroism (VUVCD) spectroscopy was performed to define the secondary structure content and location within UDE and its truncated variants. The quantitative analysis demonstrated exclusive α-helical content for the full-length protein, which is preserved in the truncated constructs. Arrangement of α-helical bundles within the truncated protein segments suggested new domain boundaries which differ from the conserved motifs determined by sequence-based alignment of UDE homologues. Here we demonstrate that the combination of ESPRIT and VUVCD spectroscopy provides a new structural description of UDE and confirms that the truncated constructs are useful for further detailed functional studies. PMID:27273007

  9. Secondary Structure Prediction of Protein Constructs Using Random Incremental Truncation and Vacuum-Ultraviolet CD Spectroscopy

    PubMed Central

    Pukáncsik, Mária; Orbán, Ágnes; Nagy, Kinga; Matsuo, Koichi; Gekko, Kunihiko; Maurin, Damien; Hart, Darren; Kézsmárki, István; Vertessy, Beata G.

    2016-01-01

    A novel uracil-DNA degrading protein factor (termed UDE) was identified in Drosophila melanogaster with no significant structural and functional homology to other uracil-DNA binding or processing factors. Determination of the 3D structure of UDE is excepted to provide key information on the description of the molecular mechanism of action of UDE catalysis, as well as in general uracil-recognition and nuclease action. Towards this long-term aim, the random library ESPRIT technology was applied to the novel protein UDE to overcome problems in identifying soluble expressing constructs given the absence of precise information on domain content and arrangement. Nine constructs of UDE were chosen to decipher structural and functional relationships. Vacuum ultraviolet circular dichroism (VUVCD) spectroscopy was performed to define the secondary structure content and location within UDE and its truncated variants. The quantitative analysis demonstrated exclusive α-helical content for the full-length protein, which is preserved in the truncated constructs. Arrangement of α-helical bundles within the truncated protein segments suggested new domain boundaries which differ from the conserved motifs determined by sequence-based alignment of UDE homologues. Here we demonstrate that the combination of ESPRIT and VUVCD spectroscopy provides a new structural description of UDE and confirms that the truncated constructs are useful for further detailed functional studies. PMID:27273007

  10. Addition of three-dimensional isoparametric elements to NASA structural analysis program (NASTRAN)

    NASA Technical Reports Server (NTRS)

    Field, E. I.; Johnson, S. E.

    1973-01-01

    Implementation is made of the three-dimensional family of linear, quadratic and cubic isoparametric solid elements into the NASA Structural Analysis program, NASTRAN. This work included program development, installation, testing, and documentation. The addition of these elements to NASTRAN provides a significant increase in modeling capability particularly for structures requiring specification of temperatures, material properties, displacements, and stresses which vary throughout each individual element. Complete program documentation is presented in the form of new sections and updates for direct insertion to the three NASTRAN manuals. The results of demonstration test problems are summarized. Excellent results are obtained with the isoparametric elements for static, normal mode, and buckling analyses.

  11. SeqFold: genome-scale reconstruction of RNA secondary structure integrating high-throughput sequencing data.

    PubMed

    Ouyang, Zhengqing; Snyder, Michael P; Chang, Howard Y

    2013-02-01

    We present an integrative approach, SeqFold, that combines high-throughput RNA structure profiling data with computational prediction for genome-scale reconstruction of RNA secondary structures. SeqFold transforms experimental RNA structure information into a structure preference profile (SPP) and uses it to select stable RNA structure candidates representing the structure ensemble. Under a high-dimensional classification framework, SeqFold efficiently matches a given SPP to the most likely cluster of structures sampled from the Boltzmann-weighted ensemble. SeqFold is able to incorporate diverse types of RNA structure profiling data, including parallel analysis of RNA structure (PARS), selective 2'-hydroxyl acylation analyzed by primer extension sequencing (SHAPE-Seq), fragmentation sequencing (FragSeq) data generated by deep sequencing, and conventional SHAPE data. Using the known structures of a wide range of mRNAs and noncoding RNAs as benchmarks, we demonstrate that SeqFold outperforms or matches existing approaches in accuracy and is more robust to noise in experimental data. Application of SeqFold to reconstruct the secondary structures of the yeast transcriptome reveals the diverse impact of RNA secondary structure on gene regulation, including translation efficiency, transcription initiation, and protein-RNA interactions. SeqFold can be easily adapted to incorporate any new types of high-throughput RNA structure profiling data and is widely applicable to analyze RNA structures in any transcriptome.

  12. Periodicity in DNA primary structure is defined by secondary structure of the coded protein.

    PubMed Central

    Zhurkin, V B

    1981-01-01

    A 10.5-base periodicity found earlier is inherent in both eu- and prokaryotic coding nucleotide sequences. In the case of noncoding eukaryotic sequences no periodicity is found, so the 10.5-base oscillation seemingly does not correlate with the nucleosomal organization of DNA. It is shown that the DNA fragments, coding the alpha-helical protein segments, manifest the pronounced 10.5-base periodicity, while those regions of DNA which code the beta-structure have a 6-base oscillation. The repeating pattern of nucleotide sequences can be used for comparison of the DNA segments with low degree of homology. PMID:7243595

  13. Structure of the velocity distribution of sheath-accelerated secondary electrons in an asymmetric RF-dc discharge

    NASA Astrophysics Data System (ADS)

    Khrabrov, Alexander V.; Kaganovich, Igor D.; Ventzek, Peter L. G.; Ranjan, Alok; Chen, Lee

    2015-10-01

    Low-pressure capacitively-coupled discharges with additional dc bias applied to a separate electrode are utilized in plasma-assisted etching for semiconductor device manufacturing. Measurements of the electron velocity distribution function (EVDF) of the flux impinging on the wafer, as well as in the plasma bulk, show a thermal population and additional peaks within a broad range of energies. That range extends from the thermal level up to the value for the ‘ballistic’ peak, corresponding to the bias potential. The non-thermal electron flux has been correlated to alleviating the electron shading effect and providing etch-resistance properties to masking photoresist layers. ‘Middle-energy peak electrons’ at energies of several hundred eV may provide an additional sustaining mechanism for the discharge. These features in the electron velocity (or energy) distribution functions are possibly caused by secondary electrons emitted from the electrodes and interacting with two high-voltage sheaths: a stationary sheath at the dc electrode and an oscillating self-biased sheath at the powered electrode. Since at those energies the mean free path for large-angle scattering (momentum relaxation length) is comparable to, or exceeds the size of the discharge gap, these ‘ballistic’ electrons will not be fully scattered by the background gas as they traverse the inter-electrode space. We have performed test-particle simulations in which the features in the EVDF of electrons impacting the RF electrode are fully resolved at all energies. An analytical model has been developed to predict existence of peaked and step-like structures in the EVDF. Those features can be explained by analyzing the kinematics of electron trajectories in the discharge gap. Step-like structures in the EVDF near the powered electrode appear due to accumulation of electrons emitted from the dc electrode within a portion of the RF cycle, and their subsequent release. Trapping occurs when the RF

  14. An updated 18S rRNA phylogeny of tunicates based on mixture and secondary structure models

    PubMed Central

    Tsagkogeorga, Georgia; Turon, Xavier; Hopcroft, Russell R; Tilak, Marie-Ka; Feldstein, Tamar; Shenkar, Noa; Loya, Yossi; Huchon, Dorothée; Douzery, Emmanuel JP; Delsuc, Frédéric

    2009-01-01

    Background Tunicates have been recently revealed to be the closest living relatives of vertebrates. Yet, with more than 2500 described species, details of their evolutionary history are still obscure. From a molecular point of view, tunicate phylogenetic relationships have been mostly studied based on analyses of 18S rRNA sequences, which indicate several major clades at odds with the traditional class-level arrangements. Nonetheless, substantial uncertainty remains about the phylogenetic relationships and taxonomic status of key groups such as the Aplousobranchia, Appendicularia, and Thaliacea. Results Thirty new complete 18S rRNA sequences were acquired from previously unsampled tunicate species, with special focus on groups presenting high evolutionary rate. The updated 18S rRNA dataset has been aligned with respect to the constraint on homology imposed by the rRNA secondary structure. A probabilistic framework of phylogenetic reconstruction was adopted to accommodate the particular evolutionary dynamics of this ribosomal marker. Detailed Bayesian analyses were conducted under the non-parametric CAT mixture model accounting for site-specific heterogeneity of the evolutionary process, and under RNA-specific doublet models accommodating the occurrence of compensatory substitutions in stem regions. Our results support the division of tunicates into three major clades: 1) Phlebobranchia + Thaliacea + Aplousobranchia, 2) Appendicularia, and 3) Stolidobranchia, but the position of Appendicularia could not be firmly resolved. Our study additionally reveals that most Aplousobranchia evolve at extremely high rates involving changes in secondary structure of their 18S rRNA, with the exception of the family Clavelinidae, which appears to be slowly evolving. This extreme rate heterogeneity precluded resolving with certainty the exact phylogenetic placement of Aplousobranchia. Finally, the best fitting secondary-structure and CAT-mixture models suggest a sister

  15. Impact of Microscale and Pilot-Scale Freeze-Drying on Protein Secondary Structures: Sucrose Formulations of Lysozyme and Catalase.

    PubMed

    Peters, Björn-Hendrik; Leskinen, Jari T T; Molnár, Ferdinand; Ketolainen, Jarkko

    2015-11-01

    Microscale (MS) freeze-drying offers rapid process cycles for early-stage formulation development. The effects of the MS approach on the secondary structures of two model proteins, lysozyme and catalase, were compared with pilot-scale (PS) vial freeze-drying. The secondary structures were assessed by attenuated total reflection Fourier transformed infrared spectroscopy. Formulations were made with increasing sucrose-protein ratios. Freeze-drying protocols involved regular cooling without thermal treatment and annealing with MS and PS equipment, and cooling rate variations with the MS. Principal component analysis of smoothed second-derivative amide I spectra revealed sucrose-protein ratio-dependent shifts toward α-helical structures. Transferability of sucrose-protein formulations from MS to PS vial freeze-drying was evidenced at regular cooling rates. Local differences in protein secondary structures between the bottom and top of sucrose-catalase samples could be detected at the sucrose-catalase ratios of 1 and 2, this being related to the initial filling height and ice crystal morphology. Annealing revealed temperature, protein, formulation, and sample location-dependent effects influencing surface morphology at the top, or causing protein secondary structure perturbation at the bottom. With the MS approach, protein secondary structure differences at different cooling rates could be detected for sucrose-lysozyme samples at the sucrose-lysozyme ratio of 1.

  16. Addition of lipid to the photosynthetic membrane: effects on membrane structure and energy transfer

    PubMed Central

    1981-01-01

    We have carried out a series of experiments in which the lipid composition of the photosynthetic membrane has been altered by the addition of lipid from a defined source under experimental conditions. Liposomes prepared by sonication are mixed with purified photosynthetic membranes obtained from spinach chloroplasts and are taken through cycles of freezing and thawing. Several lines of evidence, including gel electrophoresis and freeze-fracture electron microscopy, indicate that an actual addition of lipid has taken place. Structural analysis by freeze-fracture shows that intramembrane particles are widely separated after the addition of large amounts of lipid, with one exception: large hexagonal lattices of particles appear in some regions of the membrane. These lattices are identical in appearance with lattices formed from a single purified component of the membrane known as chlorophyll-protein complex II. The suggestion that the presence of such lattices in lipid-enriched membranes reflects a profound rearrangement of photosynthetic structures has been confirmed by analysis of the fluorescence emission spectra of natural and lipid- enriched membranes. Specifically, lipid addition in each of the cases we have studied results in the apparent detachment of chlorophyll- protein complex II from photosynthetic reaction centers. It is concluded that specific arrangements of components in the photosynthetic membrane, necessary for the normal functioning of the membrane in the light reaction of photosynthesis, can be regulated to a large extent by the lipid content of the membrane. PMID:7298712

  17. Impact ignition of aluminum-teflon based energetic materials impregnated with nano-structured carbon additives

    NASA Astrophysics Data System (ADS)

    Kappagantula, Keerti; Pantoya, Michelle L.; Hunt, Emily M.

    2012-07-01

    The inclusion of graphene into composite energetic materials to enhance their performance is a new area of interest. Studies have shown that the addition of graphene significantly enhances the thermal transport properties of an energetic composite, but how graphene influences the composite's ignition sensitivity has not been studied. The objective of this study is to examine the influence of carbon additives in composite energetic material composed of aluminum and polytetrafluoroethylene (Teflon™) on ignition sensitivity due to low velocity, drop weight impact. Specifically, three forms of carbon additives were investigated and selected based on different physical and structural properties: spherically shaped amorphous nano particles of carbon, cylindrically shaped multi walled carbon nanotubes, and sheet like graphene flakes. Results show an interesting trend: composites consisting of carbon nanotubes are significantly more sensitive to impact ignition and require the lowest ignition energy. In contrast, graphene is least sensitive to ignition exhibiting negligible reduction in ignition energy with low concentrations of graphene additive. While graphene does not significantly sensitize the energetic composite to ignition, graphene does, however, result in greater overall reactivity as observed through images of the reaction. The enhanced thermal transport properties of graphene containing composites may promote greater energy transport once ignited, but those properties do not also increase ignition sensitivity. These results and the understanding of the structural arrangement of particles within a composite as a key parameter affecting impact ignition sensitivity will have an impact on the safe handling and use of composite energetic materials.

  18. Conformational analysis and clustering of short and medium size loops connecting regular secondary structures: a database for modeling and prediction.

    PubMed Central

    Donate, L. E.; Rufino, S. D.; Canard, L. H.; Blundell, T. L.

    1996-01-01

    Loops are regions of nonrepetitive conformation connecting regular secondary structures. We identified 2,024 loops of one to eight residues in length, with acceptable main-chain bond lengths and peptide bond angles, from a database of 223 protein and protein-domain structures. Each loop is characterized by its sequence, main-chain conformation, and relative disposition of its bounding secondary structures as described by the separation between the tips of their axes and the angle between them. Loops, grouped according to their length and type of their bounding secondary structures, were superposed and clustered into 161 conformational classes, corresponding to 63% of all loops. Of these, 109 (51% of the loops) were populated by at least four nonhomologous loops or four loops sharing a low sequence identity. Another 52 classes, including 12% of the loops, were populated by at least three loops of low sequence similarity from three or fewer nonhomologous groups. Loop class suprafamilies resulting from variations in the termini of secondary structures are discussed in this article. Most previously described loop conformations were found among the classes. New classes included a 2:4 type IV hairpin, a helix-capping loop, and a loop that mediates dinucleotide-binding. The relative disposition of bounding secondary structures varies among loop classes, with some classes such as beta-hairpins being very restrictive. For each class, sequence preferences as key residues were identified; those most frequently at these conserved positions than in proteins were Gly, Asp, Pro, Phe, and Cys. Most of these residues are involved in stabilizing loop conformation, often through a positive phi conformation or secondary structure capping. Identification of helix-capping residues and beta-breakers among the highly conserved positions supported our decision to group loops according to their bounding secondary structures. Several of the identified loop classes were associated with

  19. Suppression of secondary electron yield by micro-porous array structure

    NASA Astrophysics Data System (ADS)

    Ye, M.; He, Y. N.; Hu, S. G.; Wang, R.; Hu, T. C.; Yang, J.; Cui, W. Z.

    2013-02-01

    We study secondary electron yield (SEY) suppression for metal materials using a roughened surface with a micro-porous array. First, we perform a Monte Carlo simulation of the electron trajectory in a single cylindrical well using a phenomenological model of secondary electron emission and the SEY suppression efficiency of a micro-porous array. The simulation results show that the SEY of a roughened surface is affected significantly by the aspect ratio of the micro-pores and the surface porosity of the metal plate. Then, to verify the simulation results, we produce a micro-porous array on metal plates using photolithography and measure their SEYs. We show that the micro-porous array structure can efficiently suppress the SEY of metal materials, and the measurements agree quantitatively with the corresponding simulation results. Finally, we derive an analytical formula to evaluate easily the SEY suppression efficiency of the Ag micro-porous array. In total, the micro-porous array proposed in this paper offers an alternative to SEY suppression in related areas such as multipactor effects in satellite payloads or electron cloud effects in accelerators.

  20. Suppression of secondary electron yield by micro-porous array structure

    SciTech Connect

    Ye, M.; He, Y. N.; Hu, S. G.; Wang, R.; Hu, T. C.; Yang, J.; Cui, W. Z.

    2013-02-21

    We study secondary electron yield (SEY) suppression for metal materials using a roughened surface with a micro-porous array. First, we perform a Monte Carlo simulation of the electron trajectory in a single cylindrical well using a phenomenological model of secondary electron emission and the SEY suppression efficiency of a micro-porous array. The simulation results show that the SEY of a roughened surface is affected significantly by the aspect ratio of the micro-pores and the surface porosity of the metal plate. Then, to verify the simulation results, we produce a micro-porous array on metal plates using photolithography and measure their SEYs. We show that the micro-porous array structure can efficiently suppress the SEY of metal materials, and the measurements agree quantitatively with the corresponding simulation results. Finally, we derive an analytical formula to evaluate easily the SEY suppression efficiency of the Ag micro-porous array. In total, the micro-porous array proposed in this paper offers an alternative to SEY suppression in related areas such as multipactor effects in satellite payloads or electron cloud effects in accelerators.

  1. [Isolation and structural elucidation of secondary metabolites from marine Streptomyces sp. SCSIO 1934].

    PubMed

    Niu, Siwen; Li, Sumei; Tian, Xinpeng; Hu, Tao; Ju, Jianhua; Ynag, Xiaohong; Zhang, Si; Zhang, Changsheng

    2011-07-01

    Marine Actinobacteria are emerging as new resources for bioactive natural products with promise in novel drug discovery. In recent years, the richness and diversity of marine Actinobacteria from the South China Sea and their ability in producing bioactive products have been investigated. The objective of this work is to isolate and identify bioactive secondary metabolites from a marine actinobacterium SCSIO 1934 derived from sediments of South China Sea. The strain was identified as a Streptomyces spieces by analyzing its 16S rDNA sequence. Streptomyces sp. SCSIO 1934 was fermented under optimized conditions and seven bioactive secondary metabolites were isolated and purified by chromatographic methods including colum chromatography over silica gel and Sephadex LH-20. Their structures were elucidated as 17-O-demethylgeldanamycin (1), lebstatin (2), 17-O-demethyllebstatin (3), nigericin (4), nigericin sodium salt (5), abierixin (6), respectively, by detailed NMR spectroscopic data (1H, 13C, COSY, HSQC and HMBC). This work provided a new marine actinobacterium Streptomyces sp. SCSIO 1934, capable of producing diverse bioactive natural products.

  2. Variability in secondary structure of 18S ribosomal RNA as topological marker for identification of Paramecium species.

    PubMed

    Shakoori, Farah R; Tasneem, Fareeda; Al-Ghanim, K; Mahboob, S; Al-Misned, F; Jahan, Nusrat; Shakoori, Abdul Rauf

    2014-12-01

    Besides cytological and molecular applications, Paramecium is being used in water quality assessment and for determination of saprobic levels. An unambiguous identification of these unicellular eukaryotes is not only essential, but its ecological diversity must also be explored in the local environment. 18SrRNA genes of all the strains of Paramecium species isolated from waste water were amplified, cloned and sequenced. Phylogenetic comparison of the nucleotide sequences of these strains with 23 closely related Paramecium species from GenBank Database enabled identification of Paramecium multimicronucleatum and Paramecium jenningsi. Some isolates did not show significant close association with other Paramecium species, and because of their unique position in the phylogenetic tree, they were considered new to the field. In the present report, these isolates are being designated as Paramecium caudatum pakistanicus. In this article, secondary structure of 18SrRNA has also been analyzed as an additional and perhaps more reliable topological marker for species discrimination and for determining possible phylogenetic relationship between the ciliate species. On the basis of comparison of secondary structure of 18SrRNA of various isolated Paramacium strains, and among Paramecium caudatum pakistanicus, Tetrahymena thermophila, Drosophila melanogaster, and Homo sapiens, it can be deduced that variable regions are more helpful in differentiating the species at interspecific level rather than at intraspecific level. It was concluded that V3 was the least variable region in all the organisms, V2 and V7 were the longest expansion segments of D. melanogaster and there was continuous mutational bias towards G.C base pairing in H. sapiens.

  3. Ammonium addition (and aerosol pH) has a dramatic impact on the volatility and yield of glyoxal secondary organic aerosol.

    PubMed

    Ortiz-Montalvo, Diana L; Häkkinen, Silja A K; Schwier, Allison N; Lim, Yong B; McNeill, V Faye; Turpin, Barbara J

    2014-01-01

    Glyoxal is an important precursor to secondary organic aerosol (SOA) formed through aqueous chemistry in clouds, fogs, and wet aerosols, yet the gas-particle partitioning of the resulting mixture is not well understood. This work characterizes the volatility behavior of the glyoxal precursor/product mix formed after aqueous hydroxyl radical oxidation and droplet evaporation under cloud-relevant conditions for 10 min, thus aiding the prediction of SOA via this pathway (SOACld). This work uses kinetic modeling for droplet composition, droplet evaporation experiments and temperature-programmed desorption aerosol-chemical ionization mass spectrometer analysis of gas-particle partitioning. An effective vapor pressure (p'L,eff) of ∼10(-7) atm and an enthalpy of vaporization (ΔHvap,eff) of ∼70 kJ/mol were estimated for this mixture. These estimates are similar to those of oxalic acid, which is a major product. Addition of ammonium until the pH reached 7 (with ammonium hydroxide) reduced the p'L,eff to <10(-9) atm and increased the ΔHvap,eff to >80 kJ/mol, at least in part via the formation of ammonium oxalate. pH 7 samples behaved like ammonium oxalate, which has a vapor pressure of ∼10(-11) atm. We conclude that ammonium addition has a large effect on the gas-particle partitioning of the mixture, substantially enhancing the yield of SOACld from glyoxal. PMID:24328102

  4. Ammonium addition (and aerosol pH) has a dramatic impact on the volatility and yield of glyoxal secondary organic aerosol.

    PubMed

    Ortiz-Montalvo, Diana L; Häkkinen, Silja A K; Schwier, Allison N; Lim, Yong B; McNeill, V Faye; Turpin, Barbara J

    2014-01-01

    Glyoxal is an important precursor to secondary organic aerosol (SOA) formed through aqueous chemistry in clouds, fogs, and wet aerosols, yet the gas-particle partitioning of the resulting mixture is not well understood. This work characterizes the volatility behavior of the glyoxal precursor/product mix formed after aqueous hydroxyl radical oxidation and droplet evaporation under cloud-relevant conditions for 10 min, thus aiding the prediction of SOA via this pathway (SOACld). This work uses kinetic modeling for droplet composition, droplet evaporation experiments and temperature-programmed desorption aerosol-chemical ionization mass spectrometer analysis of gas-particle partitioning. An effective vapor pressure (p'L,eff) of ∼10(-7) atm and an enthalpy of vaporization (ΔHvap,eff) of ∼70 kJ/mol were estimated for this mixture. These estimates are similar to those of oxalic acid, which is a major product. Addition of ammonium until the pH reached 7 (with ammonium hydroxide) reduced the p'L,eff to <10(-9) atm and increased the ΔHvap,eff to >80 kJ/mol, at least in part via the formation of ammonium oxalate. pH 7 samples behaved like ammonium oxalate, which has a vapor pressure of ∼10(-11) atm. We conclude that ammonium addition has a large effect on the gas-particle partitioning of the mixture, substantially enhancing the yield of SOACld from glyoxal.

  5. Phosphate addition and plant species alters microbial community structure in acidic upland grassland soil.

    PubMed

    Rooney, Deirdre C; Clipson, Nicholas J W

    2009-01-01

    Agricultural improvement (addition of fertilizers, liming) of seminatural acidic grasslands across Ireland and the UK has resulted in significant shifts in floristic composition, soil chemistry, and microbial community structure. Although several factors have been proposed as responsible for driving shifts in microbial communities, the exact causes of such changes are not well defined. Phosphate was added to grassland microcosms to investigate the effect on fungal and bacterial communities. Plant species typical of unimproved grasslands (Agrostis capillaris, Festuca ovina) and agriculturally improved grasslands (Lolium perenne) were grown, and phosphate was added 25 days after seed germination, with harvesting after a further 50 days. Phosphate addition significantly increased root biomass (p < 0.001) and shoot biomass (p < 0.05), soil pH (by 0.1 U), and microbial activity (by 5.33 mg triphenylformazan [TPF] g(-1) soil; p < 0.001). A slight decrease (by 0.257 mg biomass-C g(-1) soil; p < 0.05) in microbial biomass after phosphate addition was found. The presence of plant species significantly decreased soil pH (p < 0.05; by up to 0.2 U) and increased microbial activity (by up to 6.02 mg TPF g(-1) soil) but had no significant effect on microbial biomass. Microbial communities were profiled using automated ribosomal intergenic spacer analysis. Multidimensional scaling plots and canonical correspondence analysis revealed that phosphate addition and its interactions with upland grassland plant species resulted in considerable changes in the fungal and bacterial communities of upland soil. The fungal community structure was significantly affected by both phosphate (R = 0.948) and plant species (R = 0.857), and the bacterial community structure was also significantly affected by phosphate (R = 0.758) and plant species (R = 0.753). Differences in microbial community structure following P addition were also revealed by similarity percentage analysis. These data suggest

  6. [Study on the effect of high hydrostatic pressure treatment on the secondary structure of mushroom polyphenoloxidase by SRCD and FTIR].

    PubMed

    Yi, Jian-yong; Dong, Peng; Wang, Yong-tao; Jiang, Bin; Liao, Xiao-jun; Hu, Xiao-song; Zhang, Yan

    2012-02-01

    The secondary structure of the mushroom polyphenoloxidase treated by the high hydrostatic pressure (HHP) was analyzed by the synchrotron radiation circular dichroism (SRCD) and Fourier transform infrared spectroscopy (FTIR). The alpha-helix content of mushroom PPO was decreased after HHP treatment, which indicated that the secondary structure of PPO was changed. There was a discrepancy of the result of the secondary structure content between untreated or HHP-treated mushroom PPO analyzed by SRCD and FTIR spectra, and this discrepancy may be due to the different determination temperature, the concentration of the PPO solution and the spectra analysis method etc. The fluorescence spectra showed that the fluorescence intensity of the mushroom PPO was decreased after HHP treatment, and a red shift was observed after HHP treatment, which indicated that the tertiary structure of the enzyme molecule has been modified.

  7. Poly(L-lysine) and Clay Nanocomposite with Desired Matrix Secondary Structure: Effects of Polypeptide Molecular Weight

    SciTech Connect

    Hule,R.; Pochan, D.

    2007-01-01

    Nanocomposites (NC) were formed using cationic poly(L-lysine) (PLL), a semicrystalline polypeptide, that was reinforced by sodium montmorillonite (MMT) clay via solution intercalation technique. By varying solution conditions such as pH, temperature, and polypeptide concentration in the presence of clay platelets, the secondary structure of PLL was controllably altered into {alpha}-helical, {beta}-sheet, and random coil. The high molecular weight polypeptide shows a strong propensity to fold into the {beta}-sheet structure when cast as films, irrespective of the initial secondary structure in solution. Nanocomposite local morphology confirms intercalated MMT platelets with PLL over a wide range of compositions.

  8. Secondary structure and 3D homology modeling of swine leukocyte antigen class 2 (SLA-2) molecules.

    PubMed

    Gao, Feng-Shan; Xu, Chong-bo; Long, Yi-hou; Xia, Chun

    2009-01-01

    No information to date is available to elucidate the structure of swine leukocyte antigen class I (SLA-I) molecule which is comprised by a heavy chain of SLA-I non-covalently associated with a light chain, beta(2)-microglobulin (beta(2)m) proteins. Presently, one of SLA-I gene SLA-2 and beta(2)m gene were expressed as soluble maltose binding proteins (MBP-proteins) in a pMAL-p2X/Escherichia coli TB1 system and identified by western blotting with anti-MBP polyclonal antibodies. The expressed proteins MBP-SLA-2 and MBP-beta(2)m were purified on amylose affinity columns followed by DEAE-Sepharose. The purified products were cleaved by Factor Xa, respectively, and the interest of proteins SLA-2 and beta(2)m were purified on amylose affinity columns followed by separation from MBP on DEAE-Sepharose. The secondary structures of SLA-2 and beta(2)m were analyzed by circular dichroism (CD) spectrophotometry. The three-dimensional (3D) structure of their peptide-binding domain (PBD) was modeled-based sequence homology. The content of the alpha-helix, beta-sheet, turn, and random coil in the SLA-2 protein were 76, 95, 36, and 67aa, respectively. In the 98aa of beta(2)m, the contents of the alpha-helix, beta-sheet, turn, and random coil were 0, 45, 8, and 45aa, respectively. The SLA-2 protein displayed a typical alpha-helix structure while beta(2)m protein displayed a typical beta-sheet structure. Homology modeling of the SLA-2 and beta(2)m proteins demonstrated similarities with the structure of human and mouse MHC (major histocompatibility complex) class I proteins.

  9. Design and analysis of supporting structure between the primary mirror and the secondary mirror on a space telescope

    NASA Astrophysics Data System (ADS)

    Wang, Chenjie; Chai, Wenyi; Feng, Liangjie; Yang, Wengang; Wang, Wei; Fan, Xuewu

    2015-10-01

    Mechanical stability is a significant segment for an on-axis space telescope to assure its assembly accuracy as well as the image quality in the rigorous space environment, supporting structure between the primary mirror and the secondary mirror as a main structure of the on-axis space telescope must be designed reasonably to meet the mission requirements of the space telescope. Meanwhile, in view of the limitation of the satellite launching cost, it is necessary to reduce the weight and power compensation during the supporting structure design based on the satisfaction of telescope performance. Two types of supporting structure for a space telescope are designed, one is three-tripod structure which has three tripods located on the optical bench to support the secondary mirror assemblies and keep the distance between the primary mirror and the secondary mirror, the other is barrel supporting structure which includes a tube and a secondary mirror support with four spider struts. To compare the mechanical performance and launching cost of the two kinds of supporting structure, both structural and thermal analysis model are established. The analysis results indicates that the three-tripod support is lighter, has better mechanical performance and needs less power compensation than the barrel support.

  10. Translation with secondary structure: Dynamic blockages in totally asymmetric simple exclusion process

    NASA Astrophysics Data System (ADS)

    Shaw, Leah

    2011-03-01

    The totally asymmetric simple exclusion process (TASEP) is often used as a model for protein synthesis, with the lattice and particles representing the mRNA and ribosomes, respectively. Here we model the effect of secondary structure (folding) of the mRNA by introducing a dynamic blockage region in the lattice. If the region is unoccupied by particles, the blockage can close and prevent upstream particles from moving into it, representing the folding of that section of mRNA. Reopening of the blockage, allowing particles to pass, represents unfolding. We study the effects of the blockage size, closing/opening probabilities, and TASEP parameters on the particle current and blockage switching rates.

  11. Innovative FT-IR Imaging of Protein Film Secondary Structure Before and After Heat Treatment

    SciTech Connect

    Bonwell, E.; Wetzel, D

    2009-01-01

    Changes in the secondary structure of globular protein occur during thermal processing. An infrared reflecting mirrored optical substrate that is unaffected by heat allows recording infrared spectra of protein films in a reflection absorption mode on the stage of an FT-IR microspectrometer. Hydrated films of myoglobin protein cast from solution on the mirrored substrate are interrogated before and after thermal denaturation to allow a direct comparison. Focal plane array imaging of 280 protein films allowed selection of the same area in the image from which to extract spectra. After treatment, 110 of 140 spectra from multiple films showed a dramatic shift from the {alpha}-helix form (1650 {+-} 5 cm{sup -1}) to aggregated forms on either side of the original band. Seventy maxima were near 1625 cm{sup -1}, and 40 shifted in the direction of 1670 cm{sup -1}. The method developed was applied to films cast from two other commercial animal and plant protein sources.

  12. Prot-2S: a new python web tool for protein secondary structure studies.

    PubMed

    Munteanu, Cristian R; Magalhães, Alexandre L

    2009-01-01

    Prot-2S is a bioinformatics web application devised to analyse the protein chain secondary structures (2S) (http:/ /www.requimte.pt:8080/Prot-2S/). The tool is built on the RCSB Protein Data Bank PDB and DSSP application/files and includes calculation/graphical display of amino acid propensities in 2S motifs based on any user amino acid classification/code (for any particular protein chain list). The interface can calculate the 2S composition, display the 2S subsequences and search for DSSP non-standard residues and for pairs/triplets/quadruplets (amino acid patterns in 2S motifs). This work presents some Prot-2S applications showing its usefulness in protein research and as an e-learning tool as well. PMID:19640828

  13. Class Anxiety in Secondary Education: Exploring Structural Relations with Perceived Control, Engagement, Disaffection, and Performance.

    PubMed

    González, Antonio; Faílde Garrido, José María; Rodríguez Castro, Yolanda; Carrera Rodríguez, María Victoria

    2015-09-14

    The aim of this study was to assess the relationships between class-related anxiety with perceived control, teacher-reported behavioral engagement, behavioral disaffection, and academic performance. Participants were 355 compulsory secondary students (9th and 10th grades; Mean age = 15.2 years; SD = 1.8 years). Structural equation models revealed performance was predicted by perceived control, anxiety, disaffection, and engagement. Perceived control predicted anxiety, disaffection, and engagement. Anxiety predicted disaffection and engagement, and partially mediated the effects from control on disaffection (β = -.277, p < .005; CI = -.378, -.197) and engagement (β = .170, p < .002; CI = .103 .258). The negative association between anxiety and performance was mediated by engagement and disaffection (β = -.295, p < .002; CI = -.439, -.182). Anxiety, engagement, and disaffection mediated the effects of control on performance (β = .352, p < .003; CI = .279, .440). The implications of these results are discussed in the light of current theory and educational interventions.

  14. Secondary-structure characterization by far-UV CD of highly purified uncoupling protein 1 expressed in yeast.

    PubMed Central

    Douette, Pierre; Navet, Rachel; Bouillenne, Fabrice; Brans, Alain; Sluse-Goffart, Claudine; Matagne, André; Sluse, Francis E

    2004-01-01

    The rat UCP1 (uncoupling protein 1) is a mitochondrial inner-membrane carrier involved in energy dissipation and heat production. We expressed UCP1 carrying a His6 epitope at its C-terminus in Saccharomyces cerevisiae mitochondria. The recombinant-tagged UCP1 was purified by immobilized metal-ion affinity chromatography to homogeneity (>95%). This made it suitable for subsequent biophysical characterization. Fluorescence resonance energy transfer experiments showed that n-dodecyl-beta-D-maltoside-solubilized UCP1-His6 retained its PN (purine nucleotide)-binding capacity. The far-UV CD spectrum of the functional protein clearly indicated the predominance of alpha-helices in the UCP1 secondary structure. The UCP1 secondary structure exhibited an alpha-helical degree of approx. 68%, which is at least 25% higher than the previously reported estimations based on computational predictions. Moreover, the helical content remained unchanged in free and PN-loaded UCP1. A homology model of the first repeat of UCP1, built on the basis of X-ray-solved close parent, the ADP/ATP carrier, strengthened the CD experimental results. Our experimental and computational results indicate that (i) alpha-helices are the major component of UCP1 secondary structure; (ii) PN-binding mechanism does not involve significant secondary-structure rearrangement; and (iii) UCP1 shares similar secondary-structure characteristics with the ADP/ATP carrier, at least for the first repeat. PMID:14766012

  15. Effect of Secondary Cooling Conditions on Solidification Structure and Central Macrosegregation in Continuously Cast High-Carbon Rectangular Billet

    NASA Astrophysics Data System (ADS)

    Zeng, Jie; Chen, Weiqing

    2015-10-01

    Solidification structures of high carbon rectangular billet with a size of 180 mm × 240 mm in different secondary cooling conditions were simulated using cellular automaton-finite element (CAFE) coupling model. The adequacy of the model was compared with the simulated and the actual macrostructures of 82B steel. Effects of the secondary cooling water intensity on solidification structures including the equiaxed grain ratio and the equiaxed grain compactness were discussed. It was shown that the equiaxed grain ratio and the equiaxed grain compactness changed in the opposite direction at different secondary cooling water intensities. Increasing the secondary cooling water intensity from 0.9 or 1.1 to 1.3 L/kg could improve the equiaxed grain compactness and decrease the equiaxed grain ratio. Besides, the industrial test was conducted to investigate the effect of different secondary cooling water intensities on the center carbon macrosegregation of 82B steel. The optimum secondary cooling water intensity was 0.9 L/kg, while the center carbon segregation degree was 1.10. The relationship between solidification structure and center carbon segregation was discussed based on the simulation results and the industrial test.

  16. Secondary correction of unsatisfactory blepharoplasty: removing multilaminated septal structures and grafting of preaponeurotic fat.

    PubMed

    Kim, Y W; Park, H J; Kim, S

    2000-11-01

    Oriental blepharoplasty, commonly known as a "double eyelid operation," is the most frequently practiced cosmetic procedure in Orientals, who have probably become more fold conscious because of social westernization and an influx of Caucasians into their society. Anatomically, the upper eyelids of an Oriental are considerably different from those of a white person, and nearly half of Orientals have single eyelids. When performing blepharoplasty, an appropriate design and operative technique must be carefully selected, taking into consideration the anatomical characteristics of Koreans to obtain an aesthetically pleasing result. However, the incidence of complications is high. Patients who are faced with unsatisfactory results are often perplexed by the fact that such a commonly performed procedure could have a very high rate of dissatisfaction and that an improvement is not easy. An unfavorable result need not imply a postoperative complication, but only that the result is not acceptable to the patient, whose goal may not be based on good aesthetic principles. The most common sources of dissatisfaction are postoperative asymmetry and high placement of the lid fold. From 1991 to 1998, secondary blepharoplasty was performed on 72 patients by slitting transversely, removing the multilaminated septal structures exposed to the previous operative scar, spreading the preaponeurotic fat that extruded, and removing the septal structures into a space where the scar was eliminated to prevent secondary adhesion. The average age of the patients was 26.5 years, and the average follow-up period was 2 years. No remarkable complication was encountered after operation with this method, and the desired aesthetic improvements were achieved in the majority of the patients.

  17. Distinct Secondary Structures of the Leucine-Rich Repeat Proteoglycans Decorin and Biglycan: Glycosylation-Dependent Conformational Stability

    NASA Technical Reports Server (NTRS)

    Krishnan, Priya; Hocking, Anne M.; Scholtz, J. Martin; Pace, C. Nick; Holik, Kimberly K.; McQuillan, David J.

    1998-01-01

    Biglycan and decorin, closely related small leucine-rich repeat proteoglycans, have been overexpressed in eukaryotic cers and two major glycoforms isolated under native conditions: a proteoglycan substituted with glycosaminoglycan chains; and a core protein form secreted devoid of glycosaminoglycans. A comparative biophysical study of these glycoforms has revealed that the overall secondary structures of biglycan and decorin are different. Far-UV Circular Dichroism (CD) spectroscopy of decorin and biglycan proteoglycans indicates that, although they are predominantly Beta-sheet, biglycan has a significantly higher content of alpha-helical structure. Decorin proteoglycan and core protein are very similar, whereas the biglycan core protein exhibits closer similarity to the decorin glycoforms than to. the biglycan proteoglycan form. However, enzymatic removal of the chondroitin sulfate chains from biglycan proteoglycan does not induce a shift to the core protein structure, suggesting that the fmal form is influenced by polysaccharide addition only during biosynthesis. Fluorescence emission spectroscopy demonstrated that the single tryptophan residue, which is at a conserved position at the C-terminal domain of both biglycan and decorin, is found in similar microenvironments. This indicates that at least in this specific domain, the different glycoforms do exhibit apparent conservation of structure. Exposure of decorin and biglycan to 10 M urea resulted in an increase in fluorescent intensity, which indicates that the emission from tryptophan in the native state is quenched. Comparison of urea-induced protein unfolding curves provided further evidence that decorin and biglycan assume different structures in solution. Decorin proteoglycan and core protein unfold in a manner similar to a classic two-state model, in which there is a steep transition to an unfolded state between 1-2 M urea. The biglycan core protein also shows a similar steep transition. However, biglycan

  18. Detection and alignment of 3D domain swapping proteins using angle-distance image-based secondary structural matching techniques.

    PubMed

    Chu, Chia-Han; Lo, Wei-Cheng; Wang, Hsin-Wei; Hsu, Yen-Chu; Hwang, Jenn-Kang; Lyu, Ping-Chiang; Pai, Tun-Wen; Tang, Chuan Yi

    2010-10-14

    This work presents a novel detection method for three-dimensional domain swapping (DS), a mechanism for forming protein quaternary structures that can be visualized as if monomers had "opened" their "closed" structures and exchanged the opened portion to form intertwined oligomers. Since the first report of DS in the mid 1990s, an increasing number of identified cases has led to the postulation that DS might occur in a protein with an unconstrained terminus under appropriate conditions. DS may play important roles in the molecular evolution and functional regulation of proteins and the formation of depositions in Alzheimer's and prion diseases. Moreover, it is promising for designing auto-assembling biomaterials. Despite the increasing interest in DS, related bioinformatics methods are rarely available. Owing to a dramatic conformational difference between the monomeric/closed and oligomeric/open forms, conventional structural comparison methods are inadequate for detecting DS. Hence, there is also a lack of comprehensive datasets for studying DS. Based on angle-distance (A-D) image transformations of secondary structural elements (SSEs), specific patterns within A-D images can be recognized and classified for structural similarities. In this work, a matching algorithm to extract corresponding SSE pairs from A-D images and a novel DS score have been designed and demonstrated to be applicable to the detection of DS relationships. The Matthews correlation coefficient (MCC) and sensitivity of the proposed DS-detecting method were higher than 0.81 even when the sequence identities of the proteins examined were lower than 10%. On average, the alignment percentage and root-mean-square distance (RMSD) computed by the proposed method were 90% and 1.8Å for a set of 1,211 DS-related pairs of proteins. The performances of structural alignments remain high and stable for DS-related homologs with less than 10% sequence identities. In addition, the quality of its hinge loop

  19. Is the structural diversity of tripeptides sufficient for developing functional food additives with satisfactory multiple bioactivities?

    NASA Astrophysics Data System (ADS)

    Wang, Jian-Hui; Liu, Yong-Le; Ning, Jing-Heng; Yu, Jian; Li, Xiang-Hong; Wang, Fa-Xiang

    2013-05-01

    Multifunctional peptides have attracted increasing attention in the food science community because of their therapeutic potential, low toxicity and rapid intestinal absorption. However, previous study demonstrated that the limited structural variations make it difficult to optimize dipeptide molecules in a good balance between desirable and undesirable properties (F. Tian, P. Zhou, F. Lv, R. Song, Z. Li, J. Pept. Sci. 13 (2007) 549-566). In the present work, we attempt to answer whether the structural diversity is sufficient for a tripeptide to have satisfactory multiple bioactivities. Statistical test, structural examination and energetic analysis confirm that peptides of three amino acids long can bind tightly to human angiotensin converting enzyme (ACE) and thus exert significant antihypertensive efficacy. Further quantitative structure-activity relationship (QSAR) modeling and prediction of all 8000 possible tripeptides reveal that their ACE-inhibitory potency exhibits a good (positive) relationship to antioxidative activity, but has only a quite modest correlation with bitterness. This means that it is possible to find certain tripeptide entities possessing the optimal combination of strong ACE-inhibitory potency, high antioxidative activity and weak bitter taste, which are the promising candidates for developing multifunctional food additives with satisfactory multiple bioactivities. The marked difference between dipeptide and tripeptide can be attributed to the fact that the structural diversity of peptides increases dramatically with a slight change in sequence length.

  20. Linker histone partial phosphorylation: effects on secondary structure and chromatin condensation

    PubMed Central

    Lopez, Rita; Sarg, Bettina; Lindner, Herbert; Bartolomé, Salvador; Ponte, Inma; Suau, Pedro; Roque, Alicia

    2015-01-01

    Linker histones are involved in chromatin higher-order structure and gene regulation. We have successfully achieved partial phosphorylation of linker histones in chicken erythrocyte soluble chromatin with CDK2, as indicated by HPCE, MALDI-TOF and Tandem MS. We have studied the effects of linker histone partial phosphorylation on secondary structure and chromatin condensation. Infrared spectroscopy analysis showed a gradual increase of β-structure in the phosphorylated samples, concomitant to a decrease in α-helix/turns, with increasing linker histone phosphorylation. This conformational change could act as the first step in the phosphorylation-induced effects on chromatin condensation. A decrease of the sedimentation rate through sucrose gradients of the phosphorylated samples was observed, indicating a global relaxation of the 30-nm fiber following linker histone phosphorylation. Analysis of specific genes, combining nuclease digestion and qPCR, showed that phosphorylated samples were more accessible than unphosphorylated samples, suggesting local chromatin relaxation. Chromatin aggregation was induced by MgCl2 and analyzed by dynamic light scattering (DLS). Phosphorylated chromatin had lower percentages in volume of aggregated molecules and the aggregates had smaller hydrodynamic diameter than unphosphorylated chromatin, indicating that linker histone phosphorylation impaired chromatin aggregation. These findings provide new insights into the effects of linker histone phosphorylation in chromatin condensation. PMID:25870416

  1. Linker histone partial phosphorylation: effects on secondary structure and chromatin condensation.

    PubMed

    Lopez, Rita; Sarg, Bettina; Lindner, Herbert; Bartolomé, Salvador; Ponte, Inma; Suau, Pedro; Roque, Alicia

    2015-05-19

    Linker histones are involved in chromatin higher-order structure and gene regulation. We have successfully achieved partial phosphorylation of linker histones in chicken erythrocyte soluble chromatin with CDK2, as indicated by HPCE, MALDI-TOF and Tandem MS. We have studied the effects of linker histone partial phosphorylation on secondary structure and chromatin condensation. Infrared spectroscopy analysis showed a gradual increase of β-structure in the phosphorylated samples, concomitant to a decrease in α-helix/turns, with increasing linker histone phosphorylation. This conformational change could act as the first step in the phosphorylation-induced effects on chromatin condensation. A decrease of the sedimentation rate through sucrose gradients of the phosphorylated samples was observed, indicating a global relaxation of the 30-nm fiber following linker histone phosphorylation. Analysis of specific genes, combining nuclease digestion and qPCR, showed that phosphorylated samples were more accessible than unphosphorylated samples, suggesting local chromatin relaxation. Chromatin aggregation was induced by MgCl2 and analyzed by dynamic light scattering (DLS). Phosphorylated chromatin had lower percentages in volume of aggregated molecules and the aggregates had smaller hydrodynamic diameter than unphosphorylated chromatin, indicating that linker histone phosphorylation impaired chromatin aggregation. These findings provide new insights into the effects of linker histone phosphorylation in chromatin condensation.

  2. Linker histone partial phosphorylation: effects on secondary structure and chromatin condensation.

    PubMed

    Lopez, Rita; Sarg, Bettina; Lindner, Herbert; Bartolomé, Salvador; Ponte, Inma; Suau, Pedro; Roque, Alicia

    2015-05-19

    Linker histones are involved in chromatin higher-order structure and gene regulation. We have successfully achieved partial phosphorylation of linker histones in chicken erythrocyte soluble chromatin with CDK2, as indicated by HPCE, MALDI-TOF and Tandem MS. We have studied the effects of linker histone partial phosphorylation on secondary structure and chromatin condensation. Infrared spectroscopy analysis showed a gradual increase of β-structure in the phosphorylated samples, concomitant to a decrease in α-helix/turns, with increasing linker histone phosphorylation. This conformational change could act as the first step in the phosphorylation-induced effects on chromatin condensation. A decrease of the sedimentation rate through sucrose gradients of the phosphorylated samples was observed, indicating a global relaxation of the 30-nm fiber following linker histone phosphorylation. Analysis of specific genes, combining nuclease digestion and qPCR, showed that phosphorylated samples were more accessible than unphosphorylated samples, suggesting local chromatin relaxation. Chromatin aggregation was induced by MgCl2 and analyzed by dynamic light scattering (DLS). Phosphorylated chromatin had lower percentages in volume of aggregated molecules and the aggregates had smaller hydrodynamic diameter than unphosphorylated chromatin, indicating that linker histone phosphorylation impaired chromatin aggregation. These findings provide new insights into the effects of linker histone phosphorylation in chromatin condensation. PMID:25870416

  3. Content-Related Knowledge of Biology Teachers from Secondary Schools: Structure and learning opportunities

    NASA Astrophysics Data System (ADS)

    Großschedl, Jörg; Mahler, Daniela; Kleickmann, Thilo; Harms, Ute

    2014-09-01

    Teachers' content-related knowledge is a key factor influencing the learning progress of students. Different models of content-related knowledge have been proposed by educational researchers; most of them take into account three categories: content knowledge, pedagogical content knowledge, and curricular knowledge. As there is no consensus about the empirical separability (i.e. empirical structure) of content-related knowledge yet, a total of 134 biology teachers from secondary schools completed three tests which were to capture each of the three categories of content-related knowledge. The empirical structure of content-related knowledge was analyzed by Rasch analysis, which suggests content-related knowledge to be composed of (1) content knowledge, (2) pedagogical content knowledge, and (3) curricular knowledge. Pedagogical content knowledge and curricular knowledge are highly related (rlatent = .70). The latent correlations between content knowledge and pedagogical content knowledge (rlatent = .48)-and curricular knowledge, respectively (rlatent = .35)-are moderate to low (all ps < .001). Beyond the empirical structure of content-related knowledge, different learning opportunities for teachers were investigated with regard to their relationship to content knowledge, pedagogical content knowledge, and curricular knowledge acquisition. Our results show that an in-depth training in teacher education, professional development, and teacher self-study are positively related to particular categories of content-related knowledge. Furthermore, our results indicate that teaching experience is negatively related to curricular knowledge, compared to no significant relationship with content knowledge and pedagogical content knowledge.

  4. Mod-seq: A High-Throughput Method for Probing RNA Secondary Structure.

    PubMed

    Lin, Yizhu; May, Gemma E; Joel McManus, C

    2015-01-01

    It has become increasingly clear that large RNA molecules, especially long noncoding RNAs, function in almost all gene regulatory processes (Cech & Steitz, 2014). Many large RNAs appear to be structural scaffolds for assembly of important RNA/protein complexes. However, the structures of most large cellular RNA molecules are currently unknown (Hennelly & Sanbonmatsu, 2012). While chemical probing can reveal single-stranded regions of RNA, traditional approaches to identify sites of chemical modification are time consuming. Mod-seq is a high-throughput method used to map chemical modification sites on RNAs of any size, including complex mixtures of RNA. In this protocol, we describe preparation of Mod-seq high-throughput sequencing libraries from chemically modified RNA. We also describe a software package "Mod-seeker," which is a compilation of scripts written in Python, for the analysis of Mod-seq data. Mod-seeker returns statistically significant modification sites, which can then be used to aid in secondary structure prediction. PMID:26068740

  5. Role of loops connecting secondary structure elements in the stabilization of proteins isolated from thermophilic organisms

    PubMed Central

    Balasco, Nicole; Esposito, Luciana; Simone, Alfonso De; Vitagliano, Luigi

    2013-01-01

    It has been recently discovered that the connection of secondary structure elements (ββ-unit, βα- and αβ-units) in proteins follows quite stringent principles regarding the chirality and the orientation of the structural units (Koga et al., Nature 2012;491:222–227). By exploiting these rules, a number of protein scaffolds endowed with a remarkable thermal stability have been designed (Koga et al., Nature 2012;491:222–227). By using structural databases of proteins isolated from either mesophilic or thermophilic organisms, we here investigate the influence of supersecondary associations on the thermal stability of natural proteins. Our results suggest that β-hairpins of proteins from thermophilic organisms are very frequently characterized by shortenings of the loops. Interestingly, this shortening leads to states that display a very strong preference for the most common connectivity of the strands observed in native protein hairpins. The abundance of selective states in these proteins suggests that they may achieve a high stability by adopting a strategy aimed to reduce the possible conformations of the unfolded ensemble. In this scenario, our data indicate that the shortening is effective if it increases the adherence to these rules. We also show that this mechanism may operate in the stabilization of well-known protein folds (thioredoxin and RNase A). These findings suggest that future investigations aimed at defining mechanism of protein stabilization should also consider these effects. PMID:23661276

  6. A role of BNLT compound addition on structure and properties of PZT ceramics

    NASA Astrophysics Data System (ADS)

    Jaita, P.; Watcharapasorn, A.; Jiansirisomboon, S.

    2010-09-01

    In this research, effects of lead-free bismuth sodium lanthanum titanate (BNLT) addition on structure and properties of lead zirconate titanate (PZT) ceramics were investigated. PZT ceramics with addition of 0.1-3.0 wt%BNLT were fabricated by a solid-state mixed oxide method and sintering at 1050-1200 °C for 2 h to obtain dense ceramics with at least 96% of theoretical density. X-ray diffraction indicated that complete solid solution occurred for all compositions. Phase identification showed both tetragonal and rhombohedral perovskite structure of PZT with no BNLT phase detected. Scanning electron micrographs of fractured PZT/BNLT ceramics showed equiaxed grain shape with both transgranular and intergranular fracture modes. Addition of BNLT was also found to reduce densification and effectively limited grain growth of PZT ceramic. Optimum Hv and KIC values were found to be 4.85 GPa and 1.56 MPa.m 1/2 for PZT/0.5 wt%BNLT sample. Among PZT/BNLT samples, room temperature dielectric constant seemed to be improved with increasing BNLT content. The maximum piezoelectric coefficient values were observed in pure PZT ceramic and were slightly decreased in BNLT-added samples. Small reduction of remanent polarization and coercive field in hysteresis loops was observed in BNLT-added samples, indicating a slightly suppressed ferroelectric interaction in this material system.

  7. An identification method for enclosed voids restriction in manufacturability design for additive manufacturing structures

    NASA Astrophysics Data System (ADS)

    Liu, Shutian; Li, Quhao; Chen, Wenjiong; Tong, Liyong; Cheng, Gengdong

    2015-06-01

    Additive manufacturing (AM) technologies, such as selective laser sintering (SLS) and fused deposition modeling (FDM), have become the powerful tools for direct manufacturing of complex parts. This breakthrough in manufacturing technology makes the fabrication of new geometrical features and multiple materials possible. Past researches on designs and design methods often focused on how to obtain desired functional performance of the structures or parts, specific manufacturing capabilities as well as manufacturing constraints of AM were neglected. However, the inherent constraints in AM processes should be taken into account in design process. In this paper, the enclosed voids, one type of manufacturing constraints of AM, are investigated. In mathematics, enclosed voids restriction expressed as the solid structure is simplyconnected. We propose an equivalent description of simply-connected constraint for avoiding enclosed voids in structures, named as virtual temperature method (VTM). In this method, suppose that the voids in structure are filled with a virtual heating material with high heat conductivity and solid areas are filled with another virtual material with low heat conductivity. Once the enclosed voids exist in structure, the maximum temperature value of structure will be very high. Based upon this method, the simplyconnected constraint is equivalent to maximum temperature constraint. And this method can be easily used to formulate the simply-connected constraint in topology optimization. The effectiveness of this description method is illustrated by several examples. Based upon topology optimization, an example of 3D cantilever beam is used to illustrate the trade-off between manufacturability and functionality. Moreover, the three optimized structures are fabricated by FDM technology to indicate further the necessity of considering the simply-connected constraint in design phase for AM.

  8. Interactive effects between N addition and disturbance on boreal forest ecosystem structure and function

    NASA Astrophysics Data System (ADS)

    Nordin, Annika; Strengbom, Joachim; From, Fredrik

    2014-05-01

    In management of boreal forests, nitrogen (N) enrichment from atmospheric deposition or from forest fertilization can appear in combination with land-use related disturbances, i.e. tree harvesting by clear-felling. Long-term interactive effects between N enrichment and disturbance on boreal forest ecosystem structure and function are, however, poorly known. We investigated effects of N enrichment by forest fertilization done > 25 years ago on forest understory species composition in old-growth (undisturbed) forests, and in forests clear-felled 10 years ago (disturbed). In clear-felled forests we also investigated effects of the previous N addition on growth of tree saplings. The results show that the N enrichment effect on the understory species composition was strongly dependent on the disturbance caused by clear-felling. In undisturbed forests, there were small or no effects on understory species composition from N addition. In contrast, effects were large in forests first exposed to N addition and subsequently disturbed by clear-felling. Effects of N addition differed among functional groups of plants. Abundance of graminoids increased (+232%) and abundance of dwarf shrubs decreased (-44%) following disturbance in N fertilized forests. For vascular plants, the two perturbations had contrasting effects on α-(within forests) and β-diversity (among forests): in disturbed forests, N addition reduced, or had no effect on α-diversity, while β-diversity increased. For bryophytes, negative effects of disturbance on α-diversity were smaller in N fertilized forests than in forests not fertilized, while neither N addition nor disturbance had any effects on β-diversity. Moreover, sapling growth in forests clear-felled 10 years ago was significantly higher in previously N fertilized forests than in forests not fertilized. Our study show that effects of N addition on plant communities may appear small, short-lived, or even absent until exposed to a disturbance. This

  9. Effect of boron addition on the structure and magnetic properties of CoPt nanoparticles

    SciTech Connect

    Khemjeen, Yutthaya; Pinitsoontorn, Supree Chompoosor, Apiwat

    2015-05-07

    The effect of B addition on CoPt nanoparticles was investigated. The CoPt-B nanoparticles were synthesized by means of the polyol process. Transmission electron microscopy has shown that the as-synthesized particles have a spherical morphology with average size about 2–3 nm. The X-ray absorption spectroscopy and the X-ray diffraction technique showed the effect of B concentration on phase transformation. The addition of B at up to 60% promoted the formation of the L1{sub 0} phase when the nanoparticles were subjected to annealing at 600 °C. If the B content is higher than 60%, the phase transition is suppressed. The evidence of B addition on the structure of CoPt nanoparticles was further supported by the magnetic measurements. The results show that the coercivity of the annealed CoPt-B nanoparticles was enhanced by the B additions from 20% to 60%, with the maximum coercivity of 12 000 Oe for the CoPt-40%B sample.

  10. Response of bacterial community structure and function to experimental rainwater additions in a coastal eutrophic embayment

    NASA Astrophysics Data System (ADS)

    Teira, Eva; Hernando-Morales, Víctor; Martínez-García, Sandra; Figueiras, Francisco G.; Arbones, Belén; Álvarez-Salgado, Xosé Antón

    2013-03-01

    Although recognized as a potentially important source of both inorganic and organic nutrients, the impact of rainwater on microbial populations from marine planktonic systems has been poorly assessed. The effect of rainwater additions on bacterioplankton metabolism and community composition was evaluated in microcosm experiments enclosing natural marine plankton populations from the Ría de Vigo (NW Spain). The experiments were conducted during three different seasons (spring, autumn and winter) using rainwater collected at three different locations: marine, urban and rural sites. Bacterial abundance and production significantly increased up to 1.3 and 1.8-fold, respectively, after urban rainwater additions in spring, when ambient nutrient concentration was very low. Overall, the increments in bacterial production were higher than those in bacterial respiration, which implies that a higher proportion of carbon consumed by bacteria would be available to higher trophic levels. The response of the different bacterial groups to distinct rainwater types differed between seasons. The most responsive bacterial groups were Betaproteobacteria which significantly increased their abundance after urban (in spring and winter) and marine (in spring) rainwater additions, and Bacteroidetes which positively responded to all rainwater treatments in spring and to urban rainwater in autumn. Gammaproteobacteria and Roseobacter responded only to urban (in spring) and marine (in winter) rainwater treatment, respectively. The responses to rainwater additions were moderate and transient, and the resulting bacterial community structure was not importantly altered.

  11. Hybrid Residual Flexibility/Mass-Additive Method for Structural Dynamic Testing

    NASA Technical Reports Server (NTRS)

    Tinker, M. L.

    2003-01-01

    A large fixture was designed and constructed for modal vibration testing of International Space Station elements. This fixed-base test fixture, which weighs thousands of pounds and is anchored to a massive concrete floor, initially utilized spherical bearings and pendulum mechanisms to simulate Shuttle orbiter boundary constraints for launch of the hardware. Many difficulties were encountered during a checkout test of the common module prototype structure, mainly due to undesirable friction and excessive clearances in the test-article-to-fixture interface bearings. Measured mode shapes and frequencies were not representative of orbiter-constrained modes due to the friction and clearance effects in the bearings. As a result, a major redesign effort for the interface mechanisms was undertaken. The total cost of the fixture design, construction and checkout, and redesign was over $2 million. Because of the problems experienced with fixed-base testing, alternative free-suspension methods were studied, including the residual flexibility and mass-additive approaches. Free-suspension structural dynamics test methods utilize soft elastic bungee cords and overhead frame suspension systems that are less complex and much less expensive than fixed-base systems. The cost of free-suspension fixturing is on the order of tens of thousands of dollars as opposed to millions, for large fixed-base fixturing. In addition, free-suspension test configurations are portable, allowing modal tests to be done at sites without modal test facilities. For example, a mass-additive modal test of the ASTRO-1 Shuttle payload was done at the Kennedy Space Center launch site. In this Technical Memorandum, the mass-additive and residual flexibility test methods are described in detail. A discussion of a hybrid approach that combines the best characteristics of each method follows and is the focus of the study.

  12. Improved prediction of RNA secondary structure by integrating the free energy model with restraints derived from experimental probing data

    PubMed Central

    Wu, Yang; Shi, Binbin; Ding, Xinqiang; Liu, Tong; Hu, Xihao; Yip, Kevin Y.; Yang, Zheng Rong; Mathews, David H.; Lu, Zhi John

    2015-01-01

    Recently, several experimental techniques have emerged for probing RNA structures based on high-throughput sequencing. However, most secondary structure prediction tools that incorporate probing data are designed and optimized for particular types of experiments. For example, RNAstructure-Fold is optimized for SHAPE data, while SeqFold is optimized for PARS data. Here, we report a new RNA secondary structure prediction method, restrained MaxExpect (RME), which can incorporate multiple types of experimental probing data and is based on a free energy model and an MEA (maximizing expected accuracy) algorithm. We first demonstrated that RME substantially improved secondary structure prediction with perfect restraints (base pair information of known structures). Next, we collected structure-probing data from diverse experiments (e.g. SHAPE, PARS and DMS-seq) and transformed them into a unified set of pairing probabilities with a posterior probabilistic model. By using the probability scores as restraints in RME, we compared its secondary structure prediction performance with two other well-known tools, RNAstructure-Fold (based on a free energy minimization algorithm) and SeqFold (based on a sampling algorithm). For SHAPE data, RME and RNAstructure-Fold performed better than SeqFold, because they markedly altered the energy model with the experimental restraints. For high-throughput data (e.g. PARS and DMS-seq) with lower probing efficiency, the secondary structure prediction performances of the tested tools were comparable, with performance improvements for only a portion of the tested RNAs. However, when the effects of tertiary structure and protein interactions were removed, RME showed the highest prediction accuracy in the DMS-accessible regions by incorporating in vivo DMS-seq data. PMID:26170232

  13. Improved prediction of RNA secondary structure by integrating the free energy model with restraints derived from experimental probing data.

    PubMed

    Wu, Yang; Shi, Binbin; Ding, Xinqiang; Liu, Tong; Hu, Xihao; Yip, Kevin Y; Yang, Zheng Rong; Mathews, David H; Lu, Zhi John

    2015-09-01

    Recently, several experimental techniques have emerged for probing RNA structures based on high-throughput sequencing. However, most secondary structure prediction tools that incorporate probing data are designed and optimized for particular types of experiments. For example, RNAstructure-Fold is optimized for SHAPE data, while SeqFold is optimized for PARS data. Here, we report a new RNA secondary structure prediction method, restrained MaxExpect (RME), which can incorporate multiple types of experimental probing data and is based on a free energy model and an MEA (maximizing expected accuracy) algorithm. We first demonstrated that RME substantially improved secondary structure prediction with perfect restraints (base pair information of known structures). Next, we collected structure-probing data from diverse experiments (e.g. SHAPE, PARS and DMS-seq) and transformed them into a unified set of pairing probabilities with a posterior probabilistic model. By using the probability scores as restraints in RME, we compared its secondary structure prediction performance with two other well-known tools, RNAstructure-Fold (based on a free energy minimization algorithm) and SeqFold (based on a sampling algorithm). For SHAPE data, RME and RNAstructure-Fold performed better than SeqFold, because they markedly altered the energy model with the experimental restraints. For high-throughput data (e.g. PARS and DMS-seq) with lower probing efficiency, the secondary structure prediction performances of the tested tools were comparable, with performance improvements for only a portion of the tested RNAs. However, when the effects of tertiary structure and protein interactions were removed, RME showed the highest prediction accuracy in the DMS-accessible regions by incorporating in vivo DMS-seq data.

  14. Investigations of primary and secondary impact structures on the moon and laboratory experiments to study the ejecta of secondary particles. Ph.D. Thesis - Ruprecht Karl Univ.

    NASA Technical Reports Server (NTRS)

    Koenig, B.

    1977-01-01

    Young lunar impact structures were investigated by using lunar orbiter, Apollo Metric and panorama photographs. Measurements on particularly homogeneous areas low in secondary craters made possible an expansion of primary crater distribution to small diameters. This is now sure for a range between 20m or = D or = 20km and this indicates that the size and velocity distribution of the impacting bodies in the last 3 billion years has been constant. A numerical approximation in the form of a 7th degree polynomial was obtained for the distribution.

  15. Investigating the secondary structures of long oligonucleotides using attenuated-total-reflection surface-enhanced Raman spectroscopy

    NASA Astrophysics Data System (ADS)

    Chiu, K.-C.; Yih, J.-N.; Yu, L.-Y.; Chen, S.-J.

    2006-08-01

    This study utilizes a surface-enhanced Raman spectroscopy (SERS) based on the attenuated-total-reflection method to investigate the secondary structures of long oligonucleotides and their influence on the DNA hybridization. It is found that the ring-breathing modes of adenine, thymine, guanine, and cytosine in Raman fingerprint associated with three 60mer oligonucleotides with prominent secondary structures are lower than those observed for the two oligonucleotides with no obvious secondary structures. It is also determined that increasing the DNA hybridization temperature from 35°C to 45°C reduces secondary structure effects. The kinetics of biomolecular interaction analysis can be performed by using surface plasmons resonance biosensor, but the structural information of the oligonucleotides can not observed directly. The SERS spectrum provides the structural information of the oligonucleotides with the help of a silver colloidal nanoparticle monolayer by control of the size and distribution of the nanoparticles adapted as a Raman active substrate. Also, the detection limit of the DNA Raman signal has been successfully improved to reach sub-micro molarity of DNA concentration.

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

    PubMed

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

    2015-01-01

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

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

    PubMed Central

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

    2015-01-01

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

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

    PubMed

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

    2015-01-01

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

  19. Determination of Endosperm Protein Secondary Structure in Hard Wheat Breeding Lines using Synchrotron Infrared Microspectroscopy

    SciTech Connect

    Wetzel, D.; Bonwell, E; Fritz, T; Fritz, A

    2008-01-01

    One molecular aspect of mature hard wheat protein quality for breadmaking is the relative amount of endosperm protein in the {alpha}-helix form compared with that in other secondary structure forms including {beta}-sheet. Modeling of {alpha}-helix and {beta}-sheet absorption bands that contribute to the amide I band at 1650 cm{sup -1} was applied to more than 1500 spectra in this study. The microscopic view of wheat endosperm is dominated by many large starch granules with protein in between. The spectrum produced from in situ microspectroscopy of this mixture is dominated by carbohydrate bands from the large starch granules that fill up the field. The high spatial resolution achievable with synchrotron infrared microspectroscopy enables revealing good in situ spectra of the protein located interstitially. Synchrotron infrared microspectroscopic mapping of 4 {mu}m thick frozen sections of endosperm in the subaleurone region provides spectra from a large number of pixels. Pixels with protein-dominated spectra are sorted out from among adjacent pixels to minimize the starch absorption and scattering contributions. Subsequent data treatment to extract information from the amide I band requires a high signal to noise ratio. Although spectral interference of the carbohydrate band on the amide band is not a problem, the scattering produced by the large starch granules diminishes the signal to noise ratio throughout the spectrum. High density mapping was done on beamlines U2B and U10B at the National Synchrotron Light Source at Brookhaven National Laboratory, Upton, NY. Mapping with a single masked spot size of 5.5 {mu}m diameter or confocal 5 {mu}mX5{mu}m spot size, respectively, on the two beamlines used produced spectra for new breeding lines under current consideration. Appropriate data treatment allows calculation of a numerical estimate of the {alpha}-helix population relative to other secondary protein structures from the position and shape of the amide I

  20. Determination of Endosperm Protein Secondary Structure in Hard Wheat Breeding Lines using Synchrotron Infrared Microspectroscopy

    SciTech Connect

    Bonwell,E.; Fisher, T.; Fritz, A.; Wetzel, D.

    2008-01-01

    One molecular aspect of mature hard wheat protein quality for breadmaking is the relative amount of endosperm protein in the a-helix form compared with that in other secondary structure forms including {beta}-sheet. Modeling of a-helix and {beta}-sheet absorption bands that contribute to the amide I band at 1650 cm-1 was applied to more than 1500 spectra in this study. The microscopic view of wheat endosperm is dominated by many large starch granules with protein in between. The spectrum produced from in situ microspectroscopy of this mixture is dominated by carbohydrate bands from the large starch granules that fill up the field. The high spatial resolution achievable with synchrotron infrared microspectroscopy enables revealing good in situ spectra of the protein located interstitially. Synchrotron infrared microspectroscopic mapping of 4 {mu}m thick frozen sections of endosperm in the subaleurone region provides spectra from a large number of pixels. Pixels with protein-dominated spectra are sorted out from among adjacent pixels to minimize the starch absorption and scattering contributions. Subsequent data treatment to extract information from the amide I band requires a high signal to noise ratio. Although spectral interference of the carbohydrate band on the amide band is not a problem, the scattering produced by the large starch granules diminishes the signal to noise ratio throughout the spectrum. High density mapping was done on beamlines U2B and U10B at the National Synchrotron Light Source at Brookhaven National Laboratory, Upton, NY. Mapping with a single masked spot size of 5.5 {mu}m diameter or confocal 5 {mu}m x 5 {mu}m spot size, respectively, on the two beamlines used produced spectra for new breeding lines under current consideration. Appropriate data treatment allows calculation of a numerical estimate of the a-helix population relative to other secondary protein structures from the position and shape of the amide I absorption band. Current

  1. Fine Structure in the Secondary Electron Emission Peak for Diamond Crystal with (100) Negative Electron Affinity Surface

    NASA Technical Reports Server (NTRS)

    Asnin, V. M.; Krainsky, I. L.

    1998-01-01

    A fine structure was discovered in the low-energy peak of the secondary electron emission spectra of the diamond surface with negative electron affinity. We studied this structure for the (100) surface of the natural type-IIb diamond crystal. We have found that the low-energy peak consists of a total of four maxima. The relative energy positions of three of them could be related to the electron energy minima near the bottom of the conduction band. The fourth peak, having the lowest energy, was attributed to the breakup of the bulk exciton at the surface during the process of secondary electron emission.

  2. Prediction of protein secondary structure based on residue pair types and conformational states using dynamic programming algorithm.

    PubMed

    Sadeghi, Mehdi; Parto, Sahar; Arab, Shahriar; Ranjbar, Bijan

    2005-06-20

    We have used a statistical approach for protein secondary structure prediction based on information theory and simultaneously taking into consideration pairwise residue types and conformational states. Since the prediction of residue secondary structure by one residue window sliding make ambiguity in state prediction, we used a dynamic programming algorithm to find the path with maximum score. A score system for residue pairs in particular conformations is derived for adjacent neighbors up to ten residue apart in sequence. The three state overall per-residue accuracy, Q3, of this method in a jackknife test with dataset created from PDBSELECT is more than 70%.

  3. Determination of the secondary structure of group II bulge loops using the fluorescent probe 2-aminopurine

    PubMed Central

    Dishler, Abigael L.; McMichael, Elizabeth L.; Serra, Martin J.

    2015-01-01

    Eleven RNA hairpins containing 2-aminopurine (2-AP) in either base-paired or single nucleotide bulge loop positions were optically melted in 1 M NaCl; and, the thermodynamic parameters ΔH°, ΔS°, ΔG°37, and TM for each hairpin were determined. Substitution of 2-AP for an A (adenosine) at a bulge position (where either the 2-AP or A is the bulge) in the stem of a hairpin, does not affect the stability of the hairpin. For group II bulge loops such as AA/U, where there is ambiguity as to which of the A residues is paired with the U, hairpins with 2-AP substituted for either the 5′ or 3′ position in the hairpin stem have similar stability. Fluorescent melts were performed to monitor the environment of the 2-AP. When the 2-AP was located distal to the hairpin loop on either the 5′ or 3′ side of the hairpin stem, the change in fluorescent intensity upon heating was indicative of an unpaired nucleotide. A database of phylogenetically determined RNA secondary structures was examined to explore the presence of naturally occurring bulge loops embedded within a hairpin stem. The distribution of bulge loops is discussed and related to the stability of hairpin structures. PMID:25805856

  4. Enzyme stability, thermodynamics and secondary structures of α-amylase as probed by the CD spectroscopy.

    PubMed

    Kikani, B A; Singh, S P

    2015-11-01

    An amylase of a thermophilic bacterium, Bacillus sp. TSSC-3 (GenBank Number, EU710557) isolated from the Tulsi Shyam hot spring reservoir (Gujarat, India) was purified to the homogeneity in a single step on phenyl sepharose 6FF. The molecular weight of the enzyme was 25kD, while the temperature and pH optima for the enzyme catalysis were 80°C and 7, respectively. The purified enzyme was highly thermostable with broad pH stability and displayed remarkable resistance against surfactants, chelators, urea, guanidine HCl and various solvents as well. The stability and changes in the secondary structure of the enzyme under various extreme conditions were determined by the circular dichroism (CD) spectroscopy. The stability trends and the changes in the α-helices and β-sheets were analyzed by Mean Residual Ellipticity (MRE) and K2D3. The CD data confirmed the structural stability of the enzyme under various harsh conditions, yet it indicated reduced α-helix content and increased β-sheets upon denaturation. The thermodynamic parameters; deactivation rate constant, half-life, changes in entropy, enthalpy, activation energy and Gibb's free energy indicated that the enzyme-substrate reactions were highly stable. The overall profile of the enzyme: high thermostability, alkalitolerance, calcium independent nature, dextrose equivalent values and resistance against chemical denaturants, solvents and surfactants suggest its commercial applications.

  5. Secondary structure and conformational change of mushroom polyphenol oxidase during thermosonication treatment by using FTIR spectroscopy.

    PubMed

    Baltacıoğlu, Hande; Bayındırlı, Alev; Severcan, Feride

    2017-01-01

    To understand the conformational changes of mushroom PPO, the secondary structural change of the enzyme during thermosonication treatment at different power (60, 80 and 100%), temperature (20-60°C) and time (0-30min) combinations was investigated by using FTIR spectroscopy and compared with the change in enzyme activity. The enzyme inactivation higher than 99% was obtained at 100% amplitude at 60°C for 10min. FTIR studies showed that marked spectral changes were noted after ultrasound treatment at 20°C. The α-helix and β-sheet contents decreased, while aggregated β-sheet, turns and random coil contents increased as temperature increased up to 60°C during thermosonication treatment for 10min indicating protein denaturation. Aggregated bands located at 1683 and 1616cm(-1) became evident after ultrasound treatment at 40°C. When temperature was lowered back to 25°C, from ultrasound treatment at 60°C, these bands were still observed, indicating the irreversible change in the structure. PMID:27507504

  6. Bimane Fluorescence Scanning Suggests Secondary Structure near the S3-S4 Linker of BK Channels*

    PubMed Central

    Semenova, Nina P.; Abarca-Heidemann, Karin; Loranc, Eva; Rothberg, Brad S.

    2009-01-01

    Gating of large conductance Ca2+-activated K+ channels (BK or maxi-K channels) is controlled by a Ca2+-sensor, formed by the channel cytoplasmic C-terminal domain, and a voltage sensor, formed by its S0-S4 transmembrane helices. Here we analyze structural properties of a portion of the BK channel voltage sensing domain, the S3-S4 linker, using fluorescence lifetime spectroscopy. Single residues in the S3-S4 linker region were substituted with cysteine, and the cysteine-substituted mutants were expressed in CHO cells and covalently labeled with the sulfhydryl-reactive fluorophore monobromo-trimethylammonio-bimane (qBBr). qBBr fluorescence is quenched by tryptophan and, to a lesser extent, tyrosine side chains. We found that qBBr fluorescence in several of the labeled cysteine-substituted channels shows position-specific quenching, as indicated by increase of the brief lifetime component of the qBBr fluorescence decay. Quenching was reduced with the mutation W203F (in the S4 segment), suggesting that Trp-203 acts as a quenching group. Our results suggest a working hypothesis for the secondary structure of the BK channel S3-S4 region, and places residues Leu-204, Gly-205, and Leu-206 within the extracellular end of the S4 helix. PMID:19244238

  7. A Deep Learning Network Approach to ab initio Protein Secondary Structure Prediction

    PubMed Central

    Spencer, Matt; Eickholt, Jesse; Cheng, Jianlin

    2014-01-01

    Ab initio protein secondary structure (SS) predictions are utilized to generate tertiary structure predictions, which are increasingly demanded due to the rapid discovery of proteins. Although recent developments have slightly exceeded previous methods of SS prediction, accuracy has stagnated around 80% and many wonder if prediction cannot be advanced beyond this ceiling. Disciplines that have traditionally employed neural networks are experimenting with novel deep learning techniques in attempts to stimulate progress. Since neural networks have historically played an important role in SS prediction, we wanted to determine whether deep learning could contribute to the advancement of this field as well. We developed an SS predictor that makes use of the position-specific scoring matrix generated by PSI-BLAST and deep learning network architectures, which we call DNSS. Graphical processing units and CUDA software optimize the deep network architecture and efficiently train the deep networks. Optimal parameters for the training process were determined, and a workflow comprising three separately trained deep networks was constructed in order to make refined predictions. This deep learning network approach was used to predict SS for a fully independent test data set of 198 proteins, achieving a Q3 accuracy of 80.7% and a Sov accuracy of 74.2%. PMID:25750595

  8. Assessing secondary structure of a dyed wool fibre by means of FTIR and FTR spectroscopies

    NASA Astrophysics Data System (ADS)

    Pielesz, A.; Freeman, H. S.; Wesełucha-Birczyńska, A.; Wysocki, M.; Włochowicz, A.

    2003-06-01

    The paper describes changes in the structure of a wool fibre dyed with model azo dyes. These were direct dyes, non-genotoxic derivatives of carcinogenic benzidine, synthesized specially for the purpose of the experiment. The non-mutagenic benzidine derivatives were: 2,2'-dimethyl-5,5'-dipropoxybenzidine and 5,5'-dipropoxybenzidine. Using FTIR, changes in secondary structure of fibres were assessed in three measuring ranges: 3600-3000, 1700-1400 and 1000-1300 cm -1. The dyes were found to distinctively affect wave-number shifts of amide A, amide I bands and in the fingerprint area around 1050 cm -1. It seems that these three areas are related to the sites in which dyes bind with wool fibre keratin. In FTR spectra, the focus was on assessing the changes of peptide bond configuration in the area of amide I, disulfide area of cystine and the area of the interaction between dyes and wool fibre keratin, i.e. 1250-1600 cm -1. For analysis, three kinds of materials were selected: (1) raw wool fibres, (2) fibres subjected to deuteration and treated with formic acid, (3) wool fabric. Each of them was dyed with the model azo dyes. The results obtained by both spectroscopies allow for identifying the functional groups responsible for the binding of dyes with keratin fibre.

  9. A Deep Learning Network Approach to ab initio Protein Secondary Structure Prediction.

    PubMed

    Spencer, Matt; Eickholt, Jesse; Jianlin Cheng

    2015-01-01

    Ab initio protein secondary structure (SS) predictions are utilized to generate tertiary structure predictions, which are increasingly demanded due to the rapid discovery of proteins. Although recent developments have slightly exceeded previous methods of SS prediction, accuracy has stagnated around 80 percent and many wonder if prediction cannot be advanced beyond this ceiling. Disciplines that have traditionally employed neural networks are experimenting with novel deep learning techniques in attempts to stimulate progress. Since neural networks have historically played an important role in SS prediction, we wanted to determine whether deep learning could contribute to the advancement of this field as well. We developed an SS predictor that makes use of the position-specific scoring matrix generated by PSI-BLAST and deep learning network architectures, which we call DNSS. Graphical processing units and CUDA software optimize the deep network architecture and efficiently train the deep networks. Optimal parameters for the training process were determined, and a workflow comprising three separately trained deep networks was constructed in order to make refined predictions. This deep learning network approach was used to predict SS for a fully independent test dataset of 198 proteins, achieving a Q3 accuracy of 80.7 percent and a Sov accuracy of 74.2 percent.

  10. Strategies for Selection from Protein Libraries Composed of de Novo Designed Secondary Structure Modules

    NASA Astrophysics Data System (ADS)

    Matsuura, Tomoaki; Plückthun, Andreas

    2004-02-01

    As more and more protein structures are determined, it has become clear that there is only a limited number of protein folds in nature. To explore whether the protein folds found in nature are the only solutions to the protein folding problem, or that a lack of evolutionary pressure causes the paucity of different protein folds found, we set out to construct protein libraries without any restriction on topology. We generated different libraries (all α-helix, all β-strand and α-helix plus β-strand) with an average length of 100 amino acid residues, composed of designed secondary structure modules (α-helix, β-strand and β-turn) in various proportions, based primarily on the patterning of polar and non-polar residues. From the analysis of proteins chosen randomly from the libraries, we found that a substantial portion of pure α-helical proteins show properties similar to native proteins. Using these libraries as a starting point, we aim to establish a selection system which allows us to enrich proteins with favorable folding properties (non-aggregating, compactly folded) from the libraries. We have developed such a method based on ribosome display. This selection is based on two concepts: (1) misfolded proteins are more sensitive to proteolysis, (2) misfolded and/or aggregated proteins are more hydrophobic. We show that by applying each of these selection criteria proteins that are compactly folded and soluble can be enriched over insoluble and random coil proteins.

  11. Bimane fluorescence scanning suggests secondary structure near the S3-S4 linker of BK channels.

    PubMed

    Semenova, Nina P; Abarca-Heidemann, Karin; Loranc, Eva; Rothberg, Brad S

    2009-04-17

    Gating of large conductance Ca(2+)-activated K(+) channels (BK or maxi-K channels) is controlled by a Ca(2+)-sensor, formed by the channel cytoplasmic C-terminal domain, and a voltage sensor, formed by its S0-S4 transmembrane helices. Here we analyze structural properties of a portion of the BK channel voltage sensing domain, the S3-S4 linker, using fluorescence lifetime spectroscopy. Single residues in the S3-S4 linker region were substituted with cysteine, and the cysteine-substituted mutants were expressed in CHO cells and covalently labeled with the sulfhydryl-reactive fluorophore monobromo-trimethylammonio-bimane (qBBr). qBBr fluorescence is quenched by tryptophan and, to a lesser extent, tyrosine side chains. We found that qBBr fluorescence in several of the labeled cysteine-substituted channels shows position-specific quenching, as indicated by increase of the brief lifetime component of the qBBr fluorescence decay. Quenching was reduced with the mutation W203F (in the S4 segment), suggesting that Trp-203 acts as a quenching group. Our results suggest a working hypothesis for the secondary structure of the BK channel S3-S4 region, and places residues Leu-204, Gly-205, and Leu-206 within the extracellular end of the S4 helix.

  12. EBSD analysis of magnesium addition on inclusion formation in SS400 structural steel

    SciTech Connect

    Luo, Sin-Jie; Su, Yen-Hao Frank; Lu, Muh-Jung; Kuo, Jui-Chao

    2013-08-15

    In this study, the effect of magnesium addition on the inclusion formation in SS400 steel was investigated. The experimental specimens with and without Mg addition treatment were compared. The microstructure was observed using optical microscopy after etching with 3% nital. The morphology and chemical composition of the inclusions were analyzed via scanning electron microscopy and energy dispersive spectrometry. The lattice structure and orientation of the inclusions were identified by electron backscattering diffraction. The average size of inclusions in SS400 was between 0.67 and 0.75 μm, and between 0.65 and 0.68 μm in SS400 + Mg. The 2 ppm Mg addition resulted in the oxide formation change from Al{sub 2}O{sub 3} to MgO·Al{sub 2}O{sub 3} and in the inclusion formation change from Al{sub 2}O{sub 3}–MnS to MgO·Al{sub 2}O{sub 3}–MnS. Moreover, a simple-phase MnS with an average grain size of 1 μm to 2 μm was observed in rod-like, globular, and polyhedron forms. - Highlights: • The effect of magnesium addition was investigated for SS400 steel. • 2 ppm Mg addition changes the inclusion formation from Al2O3-MnS to MgO·Al2O3-MnS. • MnS observed in inclusions exhibits rod-like, globular, and polyhedron forms.

  13. Investigation of an investment casting method combined with additive manufacturing methods for manufacturing lattice structures

    NASA Astrophysics Data System (ADS)

    Kodira, Ganapathy D.

    Cellular metals exhibit combinations of mechanical, thermal and acoustic properties that provide opportunities for various implementations and applications; light weight aerospace and automobile structures, impact and noise absorption, heat dissipation, and heat exchange. Engineered cell topologies enable one to control mechanical, thermal, and acoustic properties of the gross cell structures. A possible way to manufacture complex 3D metallic cellular solids for mass production with a relatively low cost, the investment casting (IC) method may be used by combining the rapid prototyping (RP) of wax or injection molding. In spite of its potential to produce mass products of various 3D cellular metals, the method is known to have significant casting porosity as a consequence of the complex cellular topology which makes continuous fluid's access to the solidification interface difficult. The effects of temperature on the viscosity of the fluids were studied. A comparative cost analysis between AM-IC and additive manufacturing methods is carried out. In order to manufacture 3D cellular metals with various topologies for multi-functional applications, the casting porosity should be resolved. In this study, the relations between casting porosity and processing conditions of molten metals while interconnecting with complex cellular geometries are investigated. Temperature and pressure conditions on the rapid prototyping -- investment casting (RP-IC) method are reported, thermal stresses induced are also studied. The manufactured samples are compared with those made by additive manufacturing methods.

  14. Reversible intermolecular E-H oxidative addition to a geometrically deformed and structurally dynamic phosphorous triamide.

    PubMed

    Zhao, Wei; McCarthy, Sean M; Lai, Ting Yi; Yennawar, Hemant P; Radosevich, Alexander T

    2014-12-17

    The synthesis and reactivity of geometrically constrained tricoordinate phosphorus (σ(3)-P) compounds supported by tridentate triamide chelates (N[o-NR-C6H4]2(3-); R = Me or (i)Pr) are reported. Studies indicate that 2 (P{N[o-NMe-C6H4]2}) adopts a Cs-symmetric structure in the solid state. Variable-temperature NMR studies demonstrate a low-energy inversion at phosphorus in solution (ΔG(‡)(exptl)(298) = 10.7(5) kcal/mol), for which DFT calculations implicate an edge-inversion mechanism via a metastable C2-symmetric intermediate. In terms of reactivity, compound 2 exhibits poor nucleophilicity, but undergoes oxidative addition at ambient temperature of diverse O-H- and N-H-containing compounds (including alcohols, phenols, carboxylic acids, amines, and anilines). The resulting pentacoordinate adducts 2·[H][OR] and 2·[H][NHR] are characterized by multinuclear NMR spectroscopy and X-ray crystallography, and their structures (which span the pseudorotation coordinate between trigonal bipyramidal and square planar) are evaluated in terms of negative hyperconjugation. At elevated temperatures, the oxidative addition is shown to be reversible for volatile alcohols and amines.

  15. Soil microbial community structure and nitrogen cycling responses to agroecosystem management and carbon substrate addition

    NASA Astrophysics Data System (ADS)

    Berthrong, S. T.; Buckley, D. H.; Drinkwater, L. E.

    2011-12-01

    Fertilizer application in conventional agriculture leads to N saturation and decoupled soil C and N cycling, whereas organic practices, e.g. complex rotations and legume incorporation, often results in increased SOM and tightly coupled cycles of C and N. These legacy effects of management on soils likely affect microbial community composition and microbial process rates. This project tested if agricultural management practices led to distinct microbial communities and if those communities differed in ability to utilize labile plant carbon substrates and to produce more plant available N. We addressed several specific questions in this project. 1) Do organic and conventional management legacies on similar soils produce distinct soil bacterial and fungal community structures and abundances? 2) How do these microbial community structures change in response to carbon substrate addition? 3) How do the responses of the microbial communities influence N cycling? To address these questions we conducted a laboratory incubation of organically and conventionally managed soils. We added C-13 labelled glucose either in one large dose or several smaller pulses. We extracted genomic DNA from soils before and after incubation for TRFLP community fingerprinting. We measured C in soil pools and respiration and N in soil extracts and leachates. Management led to different compositions of bacteria and fungi driven by distinct components in organic soils. Biomass did not differ across treatments indicating that differences in cycling were due to composition rather than abundance. C substrate addition led to convergence in bacterial communities; however management still strongly influenced the difference in communities. Fungal communities were very distinct between managements and plots with substrate addition not altering this pattern. Organic soils respired 3 times more of the glucose in the first week than conventional soils (1.1% vs 0.4%). Organic soils produced twice as much

  16. Effects of essential oil treatments on the secondary protein structure of Vicia faba: a mid-infrared spectroscopic study supported by two-dimensional correlation analysis.

    PubMed

    Mecozzi, Mauro; Sturchio, Elena

    2015-02-25

    In this study we investigated the effects of essential oil treatments on the secondary protein structure of the Vicia faba roots, a bioindicator plant, in order to obtain information for the potential allelopathic uses of these oils as alternative to the use of pesticides in agriculture. We tested two mixtures of essential oils consisting of Tween 20-emulsions of tea tree oil (TTO) and Tween 20-emulsion of Clove and Rosemary (GARROM) essential oils respectively at three different oil concentrations each. The molecular modifications caused in Vicia faba by exposure to oil emulsions were investigated by FTIR spectroscopy in diffuse reflectance (DRIFT) mode. We considered the specific Amide I, Amide II and Amide VI bands by ordinary and second derivative spectroscopy and the results showed that both Tween 20-emulsion of GARROM and Tween 20-emulsion of TTO oils cause transitions among the secondary (α-helix, β-sheet and β-turn) structures with in addition the appearance of random coil structures in exposed samples. The Amide VI bands, placed between 500 and 600 cm(-1), confirmed the structural transitions observed for the Amide I bands. In addition we observed the presence of a protein oxidation effect for TTO treated samples, oxidation which resulted negligible instead for the GARROM oil samples. At last, FTIR spectra were also submitted to two-dimensional correlation analysis (2DCORR) and double two-dimensional correlation analysis (D2DCORR); the results confirmed the different effects caused by the two typologies of essential oils on the secondary protein structures of Vicia faba roots.

  17. Effects of essential oil treatments on the secondary protein structure of Vicia faba: A mid-infrared spectroscopic study supported by two-dimensional correlation analysis

    NASA Astrophysics Data System (ADS)

    Mecozzi, Mauro; Sturchio, Elena

    2015-02-01

    In this study we investigated the effects of essential oil treatments on the secondary protein structure of the Vicia faba roots, a bioindicator plant, in order to obtain information for the potential allelopathic uses of these oils as alternative to the use of pesticides in agriculture. We tested two mixtures of essential oils consisting of Tween 20-emulsions of tea tree oil (TTO) and Tween 20-emulsion of Clove and Rosemary (GARROM) essential oils respectively at three different oil concentrations each. The molecular modifications caused in Vicia faba by exposure to oil emulsions were investigated by FTIR spectroscopy in diffuse reflectance (DRIFT) mode. We considered the specific Amide I, Amide II and Amide VI bands by ordinary and second derivative spectroscopy and the results showed that both Tween 20-emulsion of GARROM and Tween 20-emulsion of TTO oils cause transitions among the secondary (α-helix, β-sheet and β-turn) structures with in addition the appearance of random coil structures in exposed samples. The Amide VI bands, placed between 500 and 600 cm-1, confirmed the structural transitions observed for the Amide I bands. In addition we observed the presence of a protein oxidation effect for TTO treated samples, oxidation which resulted negligible instead for the GARROM oil samples. At last, FTIR spectra were also submitted to two-dimensional correlation analysis (2DCORR) and double two-dimensional correlation analysis (D2DCORR); the results confirmed the different effects caused by the two typologies of essential oils on the secondary protein structures of Vicia faba roots.

  18. Structural and ferromagnetic properties of an orthorhombic phase of MnBi stabilized with Rh additions

    DOE PAGES

    Taufour, Valentin; Thimmaiah, Srinivasa; March, Stephen; Saunders, Scott; Sun, Kewei; Lamichhane, Tej Nath; Kramer, Matthew J.; Bud’ko, Sergey L.; Canfield, Paul C.

    2015-07-28

    The article addresses the possibility of alloy elements in MnBi which may modify the thermodynamic stability of the NiAs-type structure without significantly degrading the magnetic properties. The addition of small amounts of Rh and Mn provides an improvement in the thermal stability with some degradation of the magnetic properties. The small amounts of Rh and Mn additions in MnBi stabilize an orthorhombic phase whose structural and magnetic properties are closely related to the ones of the previously reported high-temperature phase of MnBi (HT MnBi). The properties of the HT MnBi, which is stable between 613 and 719 K, have notmore » been studied in detail because of its transformation to the stable low-temperature MnBi (LT MnBi), making measurements near and below its Curie temperature difficult. The Rh-stabilized MnBi with chemical formula Mn1.0625–xRhxBi [x=0.02(1)] adopts a new superstructure of the NiAs/Ni2In structure family. It is ferromagnetic below a Curie temperature of 416 K. The critical exponents of the ferromagnetic transition are not of the mean-field type but are closer to those associated with the Ising model in three dimensions. The magnetic anisotropy is uniaxial; the anisotropy energy is rather large, and it does not increase when raising the temperature, contrary to what happens in LT MnBi. The saturation magnetization is approximately 3μB/f.u. at low temperatures. Thus, while this exact composition may not be application ready, it does show that alloying is a viable route to modifying the stability of this class of rare-earth-free magnet alloys.« less

  19. Structural and ferromagnetic properties of an orthorhombic phase of MnBi stabilized with Rh additions

    SciTech Connect

    Taufour, Valentin; Thimmaiah, Srinivasa; March, Stephen; Saunders, Scott; Sun, Kewei; Lamichhane, Tej Nath; Kramer, Matthew J.; Bud’ko, Sergey L.; Canfield, Paul C.

    2015-07-28

    The article addresses the possibility of alloy elements in MnBi which may modify the thermodynamic stability of the NiAs-type structure without significantly degrading the magnetic properties. The addition of small amounts of Rh and Mn provides an improvement in the thermal stability with some degradation of the magnetic properties. The small amounts of Rh and Mn additions in MnBi stabilize an orthorhombic phase whose structural and magnetic properties are closely related to the ones of the previously reported high-temperature phase of MnBi (HT MnBi). The properties of the HT MnBi, which is stable between 613 and 719 K, have not been studied in detail because of its transformation to the stable low-temperature MnBi (LT MnBi), making measurements near and below its Curie temperature difficult. The Rh-stabilized MnBi with chemical formula Mn1.0625–xRhxBi [x=0.02(1)] adopts a new superstructure of the NiAs/Ni2In structure family. It is ferromagnetic below a Curie temperature of 416 K. The critical exponents of the ferromagnetic transition are not of the mean-field type but are closer to those associated with the Ising model in three dimensions. The magnetic anisotropy is uniaxial; the anisotropy energy is rather large, and it does not increase when raising the temperature, contrary to what happens in LT MnBi. The saturation magnetization is approximately 3μB/f.u. at low temperatures. Thus, while this exact composition may not be application ready, it does show that alloying is a viable route to modifying the stability of this class of rare-earth-free magnet alloys.

  20. Residual Structure of Streptococcus mutans Biofilm following Complete Disinfection Favors Secondary Bacterial Adhesion and Biofilm Re-Development

    PubMed Central

    Ohsumi, Tatsuya; Takenaka, Shoji; Wakamatsu, Rika; Sakaue, Yuuki; Narisawa, Naoki; Senpuku, Hidenobu; Ohshima, Hayato; Terao, Yutaka; Okiji, Takashi

    2015-01-01

    Chemical disinfection of oral biofilms often leaves biofilm structures intact. This study aimed to examine whether the residual structure promotes secondary bacterial adhesion. Streptococcus mutans biofilms generated on resin-composite disks in a rotating disc reactor were disinfected completely with 70% isopropyl alcohol, and were again cultured in the same reactor after resupplying with the same bacterial solution. Specimens were subjected to fluorescence confocal laser scanning microscopy, viable cell counts and PCR-Invader assay in order to observe and quantify secondarily adhered cells. Fluorescence microscopic analysis, particularly after longitudinal cryosectioning, demonstrated stratified patterns of viable cells on the disinfected biofilm structure. Viable cell counts of test specimens were significantly higher than those of controls, and increased according to the amount of residual structure and culture period. Linear regression analysis exhibited a high correlation between viable and total cell counts. It was concluded that disinfected biofilm structures favored secondary bacterial adhesion. PMID:25635770

  1. Imaging the 3D structure of secondary osteons in human cortical bone using phase-retrieval tomography

    NASA Astrophysics Data System (ADS)

    Arhatari, B. D.; Cooper, D. M. L.; Thomas, C. D. L.; Clement, J. G.; Peele, A. G.

    2011-08-01

    By applying a phase-retrieval step before carrying out standard filtered back-projection reconstructions in tomographic imaging, we were able to resolve structures with small differences in density within a densely absorbing sample. This phase-retrieval tomography is particularly suited for the three-dimensional segmentation of secondary osteons (roughly cylindrical structures) which are superimposed upon an existing cortical bone structure through the process of turnover known as remodelling. The resulting images make possible the analysis of the secondary osteon structure and the relationship between an osteon and the surrounding tissue. Our observations have revealed many different and complex 3D structures of osteons that could not be studied using previous methods. This work was carried out using a laboratory-based x-ray source, which makes obtaining these sorts of images readily accessible.

  2. Lost in folding space? Comparing four variants of the thermodynamic model for RNA secondary structure prediction

    PubMed Central

    2011-01-01

    Background Many bioinformatics tools for RNA secondary structure analysis are based on a thermodynamic model of RNA folding. They predict a single, "optimal" structure by free energy minimization, they enumerate near-optimal structures, they compute base pair probabilities and dot plots, representative structures of different abstract shapes, or Boltzmann probabilities of structures and shapes. Although all programs refer to the same physical model, they implement it with considerable variation for different tasks, and little is known about the effects of heuristic assumptions and model simplifications used by the programs on the outcome of the analysis. Results We extract four different models of the thermodynamic folding space which underlie the programs RNAFOLD, RNASHAPES, and RNASUBOPT. Their differences lie within the details of the energy model and the granularity of the folding space. We implement probabilistic shape analysis for all models, and introduce the shape probability shift as a robust measure of model similarity. Using four data sets derived from experimentally solved structures, we provide a quantitative evaluation of the model differences. Conclusions We find that search space granularity affects the computed shape probabilities less than the over- or underapproximation of free energy by a simplified energy model. Still, the approximations perform similar enough to implementations of the full model to justify their continued use in settings where computational constraints call for simpler algorithms. On the side, we observe that the rarely used level 2 shapes, which predict the complete arrangement of helices, multiloops, internal loops and bulges, include the "true" shape in a rather small number of predicted high probability shapes. This calls for an investigation of new strategies to extract high probability members from the (very large) level 2 shape space of an RNA sequence. We provide implementations of all four models, written in a

  3. Biomechanical investigation into the structural design of porous additive manufactured cages using numerical and experimental approaches.

    PubMed

    Tsai, Pei-I; Hsu, Ching-Chi; Chen, San-Yuan; Wu, Tsung-Han; Huang, Chih-Chieh

    2016-09-01

    Traditional solid cages have been widely used in posterior lumbar interbody fusion (PLIF) surgery. However, solid cages significantly affect the loading mechanism of the human spine due to their extremely high structural stiffness. Previous studies proposed and investigated porous additive manufactured (AM) cages; however, their biomechanical performances were analyzed using oversimplified bone-implant numerical models. Thus, the aim of this study was to investigate the outer shape and inner porous structure of the AM cages. The outer shape of the AM cages was discovered using a simulation-based genetic algorithm; their inner porous structure was subsequently analyzed parametrically using T10-S1 multilevel spine models. Finally, six types of the AM cages, which were manufactured using selective laser melting, were tested to validate the numerical outcomes. The subsidence resistance of the optimum design was superior to the conventional cage designs. A porous AM cage with a pillar diameter of 0.4mm, a pillar angle of 40°, and a porosity of between 69% and 80% revealed better biomechanical performances. Both the numerical and experimental outcomes can help surgeons to understand the biomechanics of PLIF surgery combined with the use of AM cages. PMID:27392226

  4. Understanding the effect of secondary structure on molecular interactions of poly-L-lysine with different substrates by SFA.

    PubMed

    Binazadeh, Mojtaba; Faghihnejad, Ali; Unsworth, Larry D; Zeng, Hongbo

    2013-10-14

    Nonspecific adsorption of proteins on biomaterial surfaces challenges the widespread application of engineered materials, and understanding the impact of secondary structure of proteins and peptides on their adsorption process is of both fundamental and practical importance in bioengineering. In this work, poly-L-lysine (PLL)-based α-helices and β-sheets were chosen as a model system to investigate the effect of secondary structure on peptide interactions with substrates of various surface chemistries. Circular dichroism (CD) was used to confirm the presence of both α-helix and β-sheet structured PLL in aqueous solutions and upon adsorption to quartz, where these secondary structures seemed to be preserved. Atomic force microscopy (AFM) imaging showed different surface patterns for adsorbed α-helix and β-sheet PLL. Interactions between PLL of different secondary structures and various substrates (i.e., PLL, Au, mica, and poly(ethylene glycol) (PEG)) were directly measured using a surface forces apparatus (SFA). It was found that β-sheet PLL films showed higher adsorbed layer thicknesses in general. Adhesion energies of β-sheet versus Au and β-sheet versus β-sheet were considerably higher than that of α-helix versus Au and α-helix versus α-helix systems, respectively. Au and β-sheet PLL interactions seemed to be more dependent on the salt concentration than that of α-helix, while the presence of a grafted PEG layer greatly diminished any attraction with either PLL structure. The molecular interaction mechanism of peptide in different secondary structures is discussed in terms of Derjaguin-Landau-Verwey-Overbeek (DLVO) theory, Alexander-de Gennes (AdG) steric model and hydrogen bonding, which provides important insight into the fundamental understanding of the interaction mechanism between proteins and biomaterials. PMID:24032485

  5. Peptoid oligomers with alpha-chiral, aromatic side chains: effects of chain length on secondary structure.

    PubMed

    Wu, C W; Sanborn, T J; Zuckermann, R N; Barron, A E

    2001-04-01

    Oligomeric N-substituted glycines or "peptoids" with alpha-chiral, aromatic side chains can adopt stable helices in organic or aqueous solution, despite their lack of backbone chirality and their inability to form intrachain hydrogen bonds. Helical ordering appears to be stabilized by avoidance of steric clash as well as by electrostatic repulsion between backbone carbonyls and pi clouds of aromatic rings in the side chains. Interestingly, these peptoid helices exhibit intense circular dichroism (CD) spectra that closely resemble those of peptide alpha-helices. Here, we have utilized CD to systematically study the effects of oligomer length, concentration, and temperature on the chiral secondary structure of organosoluble peptoid homooligomers ranging from 3 to 20 (R)-N-(1-phenylethyl)glycine (Nrpe) monomers in length. We find that a striking evolution in CD spectral features occurs for Nrpe oligomers between 4 and 12 residues in length, which we attribute to a chain length-dependent population of alternate structured conformers having cis versus trans amide bonds. No significant changes are observed in CD spectra of oligomers between 13 and 20 monomers in length, suggesting a minimal chain length of about 13 residues for the formation of stable poly(Nrpe) helices. Moreover, no dependence of circular dichroism on concentration is observed for an Nrpe hexamer, providing evidence that these helices remain monomeric in solution. In light of these new data, we discuss chain length-related factors that stabilize organosoluble peptoid helices of this class, which are important for the design of helical, biomimetic peptoids sharing this structural motif.

  6. Relating the variation of secondary structure of gelatin at fish oil-water interface to adsorption kinetics, dynamic interfacial tension and emulsion stability.

    PubMed

    Liu, Huihua; Wang, Bo; Barrow, Colin J; Adhikari, Benu

    2014-01-15

    The objectives of this study were to quantify the relationship between secondary structure of gelatin and its adsorption at the fish-oil/water interface and to quantify the implication of the adsorption on the dynamic interfacial tension (DST) and emulsion stability. The surface hydrophobicity of the gelatin solutions decreased when the pH increased from 4.0 to 6.0, while opposite tend was observed in the viscosity of the solution. The DST values decreased as the pH increased from 4.0 to 6.0, indicating that higher positive charges (measured trough zeta potential) in the gelatin solution tended to result in higher DST values. The adsorption kinetics of the gelatin solution was examined through the calculated diffusion coefficients (Deff). The addition of acid promoted the random coil and β-turn structures at the expense of α-helical structure. The addition of NaOH decreased the β-turn and increased the α-helix and random coil. The decrease in the random coil and triple helix structures in the gelatin solution resulted into increased Deff values. The highest diffusion coefficients, the highest emulsion stability and the lowest amount of random coil and triple helix structures were observed at pH=4.8. The lowest amount of random coil and triple helix structures in the interfacial protein layer correlated with the highest stability of the emulsion (highest ESI value). The lower amount of random coil and triple helix structures allowed higher coverage of the oil-water interface by relatively highly ordered secondary structure of gelatin.

  7. Genomic-scale comparison of sequence- and structure-based methods of function prediction: Does structure provide additional insight?

    PubMed Central

    Fetrow, Jacquelyn S.; Siew, Naomi; Di Gennaro, Jeannine A.; Martinez-Yamout, Maria; Dyson, H. Jane; Skolnick, Jeffrey

    2001-01-01

    A function annotation method using the sequence-to-structure-to-function paradigm is applied to the identification of all disulfide oxidoreductases in the Saccharomyces cerevisiae genome. The method identifies 27 sequences as potential disulfide oxidoreductases. All previously known thioredoxins, glutaredoxins, and disulfide isomerases are correctly identified. Three of the 27 predictions are probable false-positives. Three novel predictions, which subsequently have been experimentally validated, are presented. Two additional novel predictions suggest a disulfide oxidoreductase regulatory mechanism for two subunits (OST3 and OST6) of the yeast oligosaccharyltransferase complex. Based on homology, this prediction can be extended to a potential tumor suppressor gene, N33, in humans, whose biochemical function was not previously known. Attempts to obtain a folded, active N33 construct to test the prediction were unsuccessful. The results show that structure prediction coupled with biochemically relevant structural motifs is a powerful method for the function annotation of genome sequences and can provide more detailed, robust predictions than function prediction methods that rely on sequence comparison alone. PMID:11316881

  8. The role of additional computed tomography in the decision-making process on the secondary prevention in patients after systemic cerebral thrombolysis

    PubMed Central

    Sobolewski, Piotr; Kozera, Grzegorz; Szczuchniak, Wiktor; Nyka, Walenty M

    2016-01-01

    Introduction Patients with ischemic stroke undergoing intravenous (iv)-thrombolysis are routinely controlled with computed tomography on the second day to assess stroke evolution and hemorrhagic transformation (HT). However, the benefits of an additional computed tomography (aCT) performed over the next days after iv-thrombolysis have not been determined. Methods We retrospectively screened 287 Caucasian patients with ischemic stroke who were consecutively treated with iv-thrombolysis from 2008 to 2012. The results of computed tomography performed on the second (control computed tomography) and seventh (aCT) day after iv-thrombolysis were compared in 274 patients (95.5%); 13 subjects (4.5%), who died before the seventh day from admission were excluded from the analysis. Results aCTs revealed a higher incidence of HT than control computed tomographies (14.2% vs 6.6%; P=0.003). Patients with HT in aCT showed higher median of National Institutes of Health Stroke Scale score on admission than those without HT (13.0 vs 10.0; P=0.01) and higher presence of ischemic changes >1/3 middle cerebral artery territory (66.7% vs 35.2%; P<0.01). Correlations between presence of HT in aCT and National Institutes of Health Stroke Scale score on admission (rpbi 0.15; P<0.01), and the ischemic changes >1/3 middle cerebral artery (phi=0.03) existed, and the presence of HT in aCT was associated with 3-month mortality (phi=0.03). Conclusion aCT after iv-thrombolysis enables higher detection of HT, which is related to higher 3-month mortality. Thus, patients with severe middle cerebral artery infarction may benefit from aCT in the decision-making process on the secondary prophylaxis. PMID:26730196

  9. Computational and molecular analysis of conserved influenza A virus RNA secondary structures involved in infectious virion production.

    PubMed

    Kobayashi, Yuki; Dadonaite, Bernadeta; van Doremalen, Neeltje; Suzuki, Yoshiyuki; Barclay, Wendy S; Pybus, Oliver G

    2016-09-01

    As well as encoding viral proteins, genomes of RNA viruses harbor secondary and tertiary RNA structures that have been associated with functions essential for successful replication and propagation. Here, we identified stem-loop structures that are extremely conserved among 1,884 M segment sequences of influenza A virus (IAV) strains from various subtypes and host species using computational and evolutionary methods. These structures were predicted within the 3' and 5' ends of the coding regions of M1 and M2, respectively, where packaging signals have been previously proposed to exist. These signals are thought to be required for the incorporation of a single copy of 8 different negative-strand RNA segments (vRNAs) into an IAV particle. To directly test the functionality of conserved stem-loop structures, we undertook reverse genetic experiments to introduce synonymous mutations designed to disrupt secondary structures predicted at 3 locations and found them to attenuate infectivity of recombinant virus. In one mutant, predicted to disrupt stem loop structure at nucleotide positions 219-240, attenuation was more evident at increased temperature and was accompanied by an increase in the production of defective virus particles. Our results suggest that the conserved secondary structures predicted in the M segment are involved in the production of infectious viral particles during IAV replication.

  10. Properties of Inconel 625 Mesh Structures Grown by Electron Beam Additive Manufacturing

    SciTech Connect

    List III, Frederick Alyious; Dehoff, Ryan R; Lowe, Larry E; Sames, William J

    2014-01-01

    Relationships between electron beam parameters (beam current, beam speed, and beam focus) and physical properties (mass, diameter, elastic modulus, and yield strength) have been investigated for Inconel 625 mesh cubes fabricated using an additive manufacturing technology based on electron beam melting. The elastic modulus and yield strength of the mesh cubes have been systematically varied by approximately a factor of ten by changing the electron beam parameters. Simple models have been used to understand better these relationships. Structural anisotropies of the mesh associated with the layered build architecture have been observed and may contribute, along with microstructural anisotropies, to the anisotropic mechanical properties of the mesh. Knowledge of this kind is likely applicable to other metal and alloy systems and is essential to rapidly realize the full potential of this burgeoning technology.

  11. Application and testing of additive manufacturing for mirrors and precision structures

    NASA Astrophysics Data System (ADS)

    Sweeney, Michael; Acreman, Martyn; Vettese, Tom; Myatt, Ray; Thompson, Mike

    2015-09-01

    Additive Manufacturing (aka AM, and 3-D printing) is widely touted in the media as the foundation for the next industrial revolution. Beneath the hype, AM does indeed offer profound advantages in lead-time, dramatically reduced consumption of expensive raw materials, while enabling new and innovative design forms that cannot be produced by other means. General Dynamics and their industry partners have begun to embrace this technology for mirrors and precision structures used in the aerospace, defense, and precision optical instrumentation industries. Aggressively lightweighted, open and closed back test mirror designs, 75-150 mm in size, were first produced by AM from several different materials. Subsequent optical finishing and test experiments have exceeded expectations for density, surface finish, dimensional stability and isotropy of thermal expansion on the optical scale of measurement. Materials currently under examination include aluminum, titanium, beryllium, aluminum beryllium, Inconel 625, stainless steel/bronze, and PEKK polymer.

  12. Structural and biocompatibility properties of dextran from Weissella cibaria JAG8 as food additive.

    PubMed

    Tingirikari, Jagan Mohan Rao; Kothari, Damini; Shukla, Rishikesh; Goyal, Arun

    2014-09-01

    Dextran produced from Weissella cibaria JAG8 was purified and characterized. The molecular mass of dextran as determined by the gel filtration and copper bicinchoninate method was approximately, 800 kDa. Monosaccharide analysis revealed that the polysaccharide comprised only glucose units. Dynamic light scattering study confirmed the mono-disperse nature of dextran with hydrodynamic radius of 900 nm. Surface morphology study of dextran by scanning electron microscopy showed the porous web like structure. Cytotoxicity studies on human cervical cancer (HeLa) cell line showed non-toxic and biocompatible nature of dextran. The relative browning for dextran from W. cibaria JAG8 was similar to commercial prebiotic Nutraflora P-95 and 3-fold lower than Raftilose P-95. Synthesis of dextran by dextransucrase treated, sucrose-supplemented skimmed milk revealed the promising potential of dextran as a food additive.

  13. Structure-property relationships in ABA copolymer gels with A homopolymer additions

    NASA Astrophysics Data System (ADS)

    Seitz, Michelle; Rottsolk, Rebecca; Page, Kirt; Shull, Kenneth

    2009-03-01

    ABA acrylic triblock copolymers with poly(methyl methacrylate) endblocks and poly(butyl acrylate) midblocks transition from free flowing liquids to elastic solids with decreasing temperature in alcohol solvents. Homopolymer PMMA chains can be solubilized in the micelle cores if they are shorter than the endblocks. Indentation and compression tests were used to determine gel's modulus and large strain behavior. Gels with volume fractions of PMMA less than ˜0.2 are highly elastic and have moduli dictated by stretching of bridging midblocks. At higher PMMA contents, gels exhibit greater permanent deformation and moduli over an order of magnitude larger than would be expected from rubber elasticity alone. Small angle X-ray and neutron scattering and mean field simulations were used to correlate changes in gel structure and micelle morphology with the addition of homopolymer.

  14. Tailoring of Boehmite-Derived Aluminosilicate Aerogel Structure and Properties: Influence of Ti Addition

    NASA Technical Reports Server (NTRS)

    Hurwitz, Frances I.; Guo, Haiquan; Sheets, Erik J.; Miller, Derek R.; Newlin, Katy N.

    2010-01-01

    Aluminosilicate aerogels offer potential for extremely low thermal conductivities at temperatures greater than 900 C, beyond where silica aerogels reach their upper temperature limits. Aerogels have been synthesized at various Al:Si ratios, including mullite compositions, using Boehmite (AlOOH) as the Al source, and tetraethoxy orthosilicate as the Si precursor. The Boehmite-derived aerogels are found to form by a self-assembly process of AlOOH crystallites, with Si-O groups on the surface of an alumina skeleton. Morphology, surface area and pore size varies with the crystallite size of the starting Boehmite powder, as well as with synthesis parameters. Ternary systems, including Al-Si-Ti aerogels incorporating a soluble Ti precursor, are possible with careful control of pH. The addition of Ti influences sol viscosity, gelation time pore structure and pore size distribution, as well as phase formation on heat treatment.

  15. Observed Lesson Structure during the First Year of Secondary Education: Exploration of Change and Link with Academic Engagement

    ERIC Educational Resources Information Center

    Maulana, Ridwan; Opdenakker, Marie-Christine; Stroet, Kim; Bosker, Roel

    2012-01-01

    This study investigates whether lesson structure (LS) matters and which components are important for academic engagement during the first grade of secondary education. Data from videoed lessons of 10 Dutch and 12 Indonesian teachers analyzed using an observation protocol show that six LS components are found, that between class and over…

  16. DNA secondary structure of the released strand stimulates WRN helicase action on forked duplexes without coordinate action of WRN exonuclease

    SciTech Connect

    Ahn, Byungchan; Bohr, Vilhelm A.

    2011-08-12

    Highlights: {yields} In this study, we investigated the effect of a DNA secondary structure on the two WRN activities. {yields} We found that a DNA secondary structure of the displaced strand during unwinding stimulates WRN helicase without coordinate action of WRN exonuclease. {yields} These results imply that WRN helicase and exonuclease activities can act independently. -- Abstract: Werner syndrome (WS) is an autosomal recessive premature aging disorder characterized by aging-related phenotypes and genomic instability. WS is caused by mutations in a gene encoding a nuclear protein, Werner syndrome protein (WRN), a member of the RecQ helicase family, that interestingly possesses both helicase and exonuclease activities. Previous studies have shown that the two activities act in concert on a single substrate. We investigated the effect of a DNA secondary structure on the two WRN activities and found that a DNA secondary structure of the displaced strand during unwinding stimulates WRN helicase without coordinate action of WRN exonuclease. These results imply that WRN helicase and exonuclease activities can act independently, and we propose that the uncoordinated action may be relevant to the in vivo activity of WRN.

  17. Effect of Programmed Instruction on Students' Attitude towards Structure of the Atom and the Periodic Table among Kenyan Secondary Schools

    ERIC Educational Resources Information Center

    Wangila, M. J.; Martin, W.; Ronald, M.

    2015-01-01

    This study examined the effect of Programmed Instruction on students' attitude towards Structure of the Atom and the Periodic Table (SAPT) among mixed (co-educational) secondary schools of Butere district, Kakamega county, Kenya. The quasi-experimental research design was adopted, using the nonrandomized Solomon four-group as a model. The sample…

  18. Compilation of mRNA Polyadenylation Signals in Arabidopsis Revealed a New Signal Element and Potential Secondary Structures1[w

    PubMed Central

    Loke, Johnny C.; Stahlberg, Eric A.; Strenski, David G.; Haas, Brian J.; Wood, Paul Chris; Li, Qingshun Quinn

    2005-01-01

    Using a novel program, SignalSleuth, and a database containing authenticated polyadenylation [poly(A)] sites, we analyzed the composition of mRNA poly(A) signals in Arabidopsis (Arabidopsis thaliana), and reevaluated previously described cis-elements within the 3′-untranslated (UTR) regions, including near upstream elements and far upstream elements. As predicted, there are absences of high-consensus signal patterns. The AAUAAA signal topped the near upstream elements patterns and was found within the predicted location to only approximately 10% of 3′-UTRs. More importantly, we identified a new set, named cleavage elements, of poly(A) signals flanking both sides of the cleavage site. These cis-elements were not previously revealed by conventional mutagenesis and are contemplated as a cluster of signals for cleavage site recognition. Moreover, a single-nucleotide profile scan on the 3′-UTR regions unveiled a distinct arrangement of alternate stretches of U and A nucleotides, which led to a prediction of the formation of secondary structures. Using an RNA secondary structure prediction program, mFold, we identified three main types of secondary structures on the sequences analyzed. Surprisingly, these observed secondary structures were all interrupted in previously constructed mutations in these regions. These results will enable us to revise the current model of plant poly(A) signals and to develop tools to predict 3′-ends for gene annotation. PMID:15965016

  19. Decentralization and Structural Change in Secondary Education in Argentina: The Case of the Province of Buenos Aires

    ERIC Educational Resources Information Center

    Acedo, Clementina; Gorostiaga, Jorge M.; Senen-Gonzalez, Silvia

    2007-01-01

    Over the past decade, Argentina created and implemented a compulsory lower-secondary education level, within an ambitious educational reform programme. This article addresses the reform at the national level, diverse provincial responses, and the particular way that the powerful province of Buenos Aires appropriated the structural change. The…

  20. Inclusion of persistence length-based secondary structure in replica field theoretic models of heteropolymer freezing

    NASA Astrophysics Data System (ADS)

    Weber, Jeffrey K.; Pande, Vijay S.

    2013-09-01

    The protein folding problem has long represented a "holy grail" in statistical physics due to its physical complexity and its relevance to many human diseases. While past theoretical work has yielded apt descriptions of protein folding landscapes, recent large-scale simulations have provided insights into protein folding that were impractical to obtain from early theories. In particular, the role that non-native contacts play in protein folding, and their relation to the existence of misfolded, β-sheet rich trap states on folding landscapes, has emerged as a topic of interest in the field. In this paper, we present a modified model of heteropolymer freezing that includes explicit secondary structural characteristics which allow observations of "intramolecular amyloid" states to be probed from a theoretical perspective. We introduce a variable persistence length-based energy penalty to a model Hamiltonian, and we illustrate how this modification alters the phase transitions present in the theory. We find, in particular, that inclusion of this variable persistence length increases both generic freezing and folding temperatures in the model, allowing both folding and glass transitions to occur in a more highly optimized fashion. We go on to discuss how these changes might relate to protein evolution, misfolding, and the emergence of intramolecular amyloid states.

  1. Line-Based Object Recognition using Hausdorff Distance: From Range Images to Molecular Secondary Structure

    SciTech Connect

    Guerra, C; Pascucci, V

    2004-12-13

    Object recognition algorithms are fundamental tools in automatic matching of geometric shapes within a background scene. Many approaches have been proposed in the past to solve the object recognition problem. Two of the key aspects that distinguish them in terms of their practical usability are: (i) the type of input model description and (ii) the comparison criteria used. In this paper we introduce a novel scheme for 3D object recognition based on line segment representation of the input shapes and comparison using the Hausdor distance. This choice of model representation provides the flexibility to apply the scheme in different application areas. We define several variants of the Hausdor distance to compare the models within the framework of well defined metric spaces. We present a matching algorithm that efficiently finds a pattern in a 3D scene. The algorithm approximates a minimization procedure of the Hausdor distance. The output error due to the approximation is guaranteed to be within a known constant bound. Practical results are presented for two classes of objects: (i) polyhedral shapes extracted from segmented range images and (ii) secondary structures of large molecules. In both cases the use of our approximate algorithm allows to match correctly the pattern in the background while achieving the efficiency necessary for practical use of the scheme. In particular the performance is improved substantially with minor degradation of the quality of the matching.

  2. Fine-grained parallelism accelerating for RNA secondary structure prediction with pseudoknots based on FPGA.

    PubMed

    Xia, Fei; Jin, Guoqing

    2014-06-01

    PKNOTS is a most famous benchmark program and has been widely used to predict RNA secondary structure including pseudoknots. It adopts the standard four-dimensional (4D) dynamic programming (DP) method and is the basis of many variants and improved algorithms. Unfortunately, the O(N(6)) computing requirements and complicated data dependency greatly limits the usefulness of PKNOTS package with the explosion in gene database size. In this paper, we present a fine-grained parallel PKNOTS package and prototype system for accelerating RNA folding application based on FPGA chip. We adopted a series of storage optimization strategies to resolve the "Memory Wall" problem. We aggressively exploit parallel computing strategies to improve computational efficiency. We also propose several methods that collectively reduce the storage requirements for FPGA on-chip memory. To the best of our knowledge, our design is the first FPGA implementation for accelerating 4D DP problem for RNA folding application including pseudoknots. The experimental results show a factor of more than 50x average speedup over the PKNOTS-1.08 software running on a PC platform with Intel Core2 Q9400 Quad CPU for input RNA sequences. However, the power consumption of our FPGA accelerator is only about 50% of the general-purpose micro-processors.

  3. Essential nucleotide sequences and secondary structure elements of the hairpin ribozyme.

    PubMed Central

    Berzal-Herranz, A; Joseph, S; Chowrira, B M; Butcher, S E; Burke, J M

    1993-01-01

    In vitro selection experiments have been used to isolate active variants of the 50 nt hairpin catalytic RNA motif following randomization of individual ribozyme domains and intensive mutagenesis of the ribozyme-substrate complex. Active and inactive variants were characterized by sequencing, analysis of RNA cleavage activity in cis and in trans, and by substrate binding studies. Results precisely define base-pairing requirements for ribozyme helices 3 and 4, and identify eight essential nucleotides (G8, A9, A10, G21, A22, A23, A24 and C25) within the catalytic core of the ribozyme. Activity and substrate binding assays show that point mutations at these eight sites eliminate cleavage activity but do not significantly decrease substrate binding, demonstrating that these bases contribute to catalytic function. The mutation U39C has been isolated from different selection experiments as a second-site suppressor of the down mutants G21U and A43G. Assays of the U39C mutation in the wild-type ribozyme and in a variety of mutant backgrounds show that this variant is a general up mutation. Results from selection experiments involving populations totaling more than 10(10) variants are summarized, and consensus sequences including 16 essential nucleotides and a secondary structure model of four short helices, encompassing 18 bp for the ribozyme-substrate complex are derived. Images PMID:8508779

  4. An essential secondary structure in the 3' untranslated region of the mouse hepatitis virus genome.

    PubMed

    Hsue, B; Masters, P S

    1998-01-01

    The 3' untranslated regions (3' UTRs) of coronaviruses contain the signals necessary for negative strand RNA synthesis and may also harbor elements essential for positive strand replication and subgenomic RNA transcription. The 3' UTRs of mouse hepatitis virus (MHV) and bovine coronavirus (BCV) are more than 30% divergent. In an effort to learn what parts of these regions might be functionally interchangeable, we attempted to replace the 3' UTR of MHV with its BCV counterpart by targeted RNA recombination. Initially, we tried to substitute the 3' 267 nucleotides (nt) of the 301 nt MHV 3' UTR with the corresponding region of the BCV 3' UTR. This exchange did not yield viable recombinant viruses, and the donor DI RNA was shown to be unable to replicate with MHV as a helper virus. Subsequent analysis revealed that the entire BCV 3' UTR could be inserted into the MHV genome in place of the entire MHV 3' UTR. It resulted that the failure of the initial attempted substitution was due to the inadvertent disruption of an essential conserved bulged stem-loop secondary structure in the MHV and BCV 3' URTs immediately downstream of the N gene stop codon.

  5. Identification of WD40 repeats by secondary structure-aided profile-profile alignment.

    PubMed

    Wang, Chuan; Dong, Xiaobao; Han, Lei; Su, Xiao-Dong; Zhang, Ziding; Li, Jinyan; Song, Jiangning

    2016-06-01

    A WD40 protein typically contains four or more repeats of ~40 residues ended with the Trp-Asp dipeptide, which folds into β-propellers with four β strands in each repeat. They often function as scaffolds for protein-protein interactions and are involved in numerous fundamental biological processes. Despite their important functional role, the "velcro" closure of WD40 propellers and the diversity of WD40 repeats make their identification a difficult task. Here we develop a new WD40 Repeat Recognition method (WDRR), which uses predicted secondary structure information to generate candidate repeat segments, and further employs a profile-profile alignment to identify the correct WD40 repeats from candidate segments. In particular, we design a novel alignment scoring function that combines dot product and BLOSUM62, thereby achieving a great balance of sensitivity and accuracy. Taking advantage of these strategies, WDRR could effectively reduce the false positive rate and accurately identify more remote homologous WD40 repeats with precise repeat boundaries. We further use WDRR to re-annotate the Pfam families in the β-propeller clan (CL0186) and identify a number of WD40 repeat proteins with high confidence across nine model organisms. The WDRR web server and the datasets are available at http://protein.cau.edu.cn/wdrr/.

  6. GADIS: Algorithm for designing sequences to achieve target secondary structure profiles of intrinsically disordered proteins.

    PubMed

    Harmon, Tyler S; Crabtree, Michael D; Shammas, Sarah L; Posey, Ammon E; Clarke, Jane; Pappu, Rohit V

    2016-09-01

    Many intrinsically disordered proteins (IDPs) participate in coupled folding and binding reactions and form alpha helical structures in their bound complexes. Alanine, glycine, or proline scanning mutagenesis approaches are often used to dissect the contributions of intrinsic helicities to coupled folding and binding. These experiments can yield confounding results because the mutagenesis strategy changes the amino acid compositions of IDPs. Therefore, an important next step in mutagenesis-based approaches to mechanistic studies of coupled folding and binding is the design of sequences that satisfy three major constraints. These are (i) achieving a target intrinsic alpha helicity profile; (ii) fixing the positions of residues corresponding to the binding interface; and (iii) maintaining the native amino acid composition. Here, we report the development of a G: enetic A: lgorithm for D: esign of I: ntrinsic secondary S: tructure (GADIS) for designing sequences that satisfy the specified constraints. We describe the algorithm and present results to demonstrate the applicability of GADIS by designing sequence variants of the intrinsically disordered PUMA system that undergoes coupled folding and binding to Mcl-1. Our sequence designs span a range of intrinsic helicity profiles. The predicted variations in sequence-encoded mean helicities are tested against experimental measurements. PMID:27503953

  7. [Study on the effect of electric field on the secondary structure of lipase by circular dichroism].

    PubMed

    Yao, Zhan-quan; Ao, Dun-ge-ri-le; Xu, Qiang; Yang, Ti-qiang

    2006-12-01

    After the lipase was treated with electric field for five minutes, the effect of electric field on the secondary structure of lipase was studied by circular dichroism (CD). The results showed that different electric field strength in the range from 0. 5 to 6. 0 kV x cm(-1) has a different effect on the relative contents of alpha-helix, beta-sheet, beta-turn and random coil of the lipase, and whose changes were non-monotonous with the raising of electric field. In general, the electric treatment tends to transform the alpha-helix and beta-sheet into beta-turn and random coil. The decrease in alpha-helix and beta-sheet ranged respectively from 4. 6% to 48. 0% and from 13. 2% to 35. 1%, and the increase in beta-turn and random coil ranged respectively from 2. 8% to 33. 3% and from 0. 9% to 48. 1%. The result of this study has important meaning to explain the biological effect of electric treatment seeds.

  8. A novel method for protein secondary structure prediction using dual-layer SVM and profiles.

    PubMed

    Guo, Jian; Chen, Hu; Sun, Zhirong; Lin, Yuanlie

    2004-03-01

    A high-performance method was developed for protein secondary structure prediction based on the dual-layer support vector machine (SVM) and position-specific scoring matrices (PSSMs). SVM is a new machine learning technology that has been successfully applied in solving problems in the field of bioinformatics. The SVM's performance is usually better than that of traditional machine learning approaches. The performance was further improved by combining PSSM profiles with the SVM analysis. The PSSMs were generated from PSI-BLAST profiles, which contain important evolution information. The final prediction results were generated from the second SVM layer output. On the CB513 data set, the three-state overall per-residue accuracy, Q3, reached 75.2%, while segment overlap (SOV) accuracy increased to 80.0%. On the CB396 data set, the Q3 of our method reached 74.0% and the SOV reached 78.1%. A web server utilizing the method has been constructed and is available at http://www.bioinfo.tsinghua.edu.cn/pmsvm.

  9. Scoping the Duals: Structural Challenges of Combining Further and Higher Education in Post-Secondary Institutions

    ERIC Educational Resources Information Center

    Garrod, Neil; Macfarlane, Bruce

    2007-01-01

    Dual sector universities (or duals) are a growing international phenomenon that cut across the divide that typically exists in post-secondary education. Duals combine "further" and "higher" education within a single institution providing enhanced opportunities for student transition between post-secondary sectors. This paper reports the results of…

  10. Essential Structural Requirements and Additive Effects for Flavonoids to Scavenge Methylglyoxal.

    PubMed

    Shao, Xi; Chen, Huadong; Zhu, Yingdong; Sedighi, Rashin; Ho, Chi-Tang; Sang, Shengmin

    2014-04-01

    Reactive dicarbonyl species, such as methylglyoxal (MGO), are considered as the major precursors of advanced glycation end products (AGEs), which are believed to be one of the physiological causes of diabetes and its complications. Scavenging of reactive dicarbonyl species using naturally occurring flavonoids has been proposed as an effective way to prevent diabetic complications. To elucidate the structural requirements of flavonoids in scavenging MGO, seven flavonoids (quercetin, luteolin, epicatechin, genistein, daidzein, apigenin, and phloretin) and five sub-components of the flavonoids (gallic acid, phloroglucinol, pyrogallol, pyrocatechol, and resorcinol) were examined in this study. Our results showed the following: (1) 1,2,3-trihydroxybenzene (pyrogallol) has higher MGO scavenging activity than 1,3,5-trihydroxybenzene and 1,2- and 1,3-dihydroxybenzene, and substitution at position 5 of pyrogallol diminished the scavenging activity, indicating that position 5 is the active site of pyrogallol; (2) the A ring is the active site of flavonoids in contributing the MGO-trapping efficacy, and the hydroxyl group at C-5 on the A ring enhances the trapping efficacy; (3) the double bond between C-2 and C-3 on the C ring could facilitate the trapping efficacy; and (4) the number of hydroxyl groups on the B ring does not significantly influence the trapping efficacy. In addition, we found there is an additive effect in MGO trapping by two common flavonoids, quercetin and phloretin, indicating that flavonoid-enriched foods and beverages hold great promise to prevent the development of diabetic complications.

  11. Characterization of the secondary structure of calmodulin in complex with a calmodulin-binding domain peptide

    SciTech Connect

    Roth, S.M.; Schneider, D.M.; Strobel, L.A.; Wand, A.J. Univ. of Illinois, Urbana ); Van Berkum, M.F.A.; Means, A.R. )

    1992-02-11

    The interaction between calcium-saturated chicken calmodulin and a peptide corresponding to the calmodulin-binding domain of the chicken smooth muscle myosin light chain kinase has been studied by multinuclear and multidimensional nuclear magnetic resonance methods. Extensive {sup 1}H and {sup 15}N resonance assignments of calmodulin in the complex have been obtained from the analysis of two- and three-dimensional nuclear magnetic resonance spectra. The assignment of calmodulin in the complex was facilitated by the use of selective labeling of the protein with {alpha}-{sup 15}N-labeled valine, alanine, lysine, leucine, and glycine. These provided reference points during the main-chain-directed analysis of three-dimensional spectra of complexes prepared with uniformly {sup 15}N-labeled calmodulin. The pattern of nuclear Overhauser effects (NOE) seen among main-chain amide NH, C{sub {alpha}}H, and C{sub {beta}}H hydrogens indicates that the secondary structure of the globular domains of calmodulin in the complex closely corresponds to that observed in the calcium-saturated state of the protein in the absence of bound peptide. However, the backbone conformation of residues 76-84 adopts an extended chain conformation upon binding of the peptide in contrast to its helical conformation in the absence of peptide. A sufficient number of NOEs between the globular domains of calmodulin and the bound peptide have been found to indicate that the N- and C-terminal regions of the peptide interact with the C- and N-terminal domains of calmodulin, respectively. The significance of these results are discussed in terms of recently proposed models for the structure of calmodulin-peptide complexes.

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

    PubMed

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

    2013-10-01

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

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

    PubMed

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

    2013-10-01

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

  14. Children's Understanding of the Additive Composition of Number and of the Decimal Structure: What Is the Relationship?

    ERIC Educational Resources Information Center

    Krebs, Georgina; Squire, Sarah; Bryant, Peter

    2003-01-01

    Nunes and Bryant (Children doing mathematics, Blackwell, Oxford, 1996) proposed that an understanding of the additive composition of number could be a precursor to an understanding of the decimal structure. If this is so, children should achieve an understanding of additive composition before they can handle the decimal structure. The aim of our…

  15. effect of hydrogen addition and burner diameter on the stability and structure of lean, premixed flames

    NASA Astrophysics Data System (ADS)

    Kaufman, Kelsey Leigh

    Low swirl burners (LSBs) have gained popularity in heating and gas power generation industries, in part due to their proven capacity for reducing the production of NOx, which in addition to reacting to form smog and acid rain, plays a central role in the formation of the tropospheric ozone layer. With lean operating conditions, LSBs are susceptible to combustion instability, which can result in flame extinction or equipment failure. Extensive work has been performed to understand the nature of LSB combustion, but scaling trends between laboratory- and industrial-sized burners have not been established. Using hydrogen addition as the primary method of flame stabilization, the current work presents results for a 2.54 cm LSB to investigate potential effects of burner outlet diameter on the nature of flame stability, with focus on flashback and lean blowout conditions. In the lean regime, the onset of instability and flame extinction have been shown to occur at similar equivalence ratios for both the 2.54 cm and a 3.81 cm LSB and depend on the resolution of equivalence ratios incremented. Investigations into flame structures are also performed. Discussion begins with a derivation for properties in a multicomponent gas mixture used to determine the Reynolds number (Re) to develop a condition for turbulent intensity similarity in differently-sized LSBs. Based on this requirement, operating conditions are chosen such that the global Reynolds number for the 2.54 cm LSB is within 2% of the Re for the 3.81 cm burner. With similarity obtained, flame structure investigations focus on flame front curvature and flame surface density (FSD). As flame structure results of the current 2.54 cm LSB work are compared to results for the 3.81 cm LSB, no apparent relationship is shown to exist between burner diameter and the distribution of flame surface density. However, burner diameter is shown to have a definite effect on the flame front curvature. In corresponding flow conditions, a

  16. Bioinformatic and functional analysis of RNA secondary structure elements among different genera of human and animal caliciviruses

    PubMed Central

    Simmonds, Peter; Karakasiliotis, Ioannis; Bailey, Dalan; Chaudhry, Yasmin; Evans, David J.; Goodfellow, Ian G.

    2008-01-01

    The mechanism and role of RNA structure elements in the replication and translation of Caliciviridae remains poorly understood. Several algorithmically independent methods were used to predict secondary structures within the Norovirus, Sapovirus, Vesivirus and Lagovirus genera. All showed profound suppression of synonymous site variability (SSSV) at genomic 5′ ends and the start of the sub-genomic (sg) transcript, consistent with evolutionary constraints from underlying RNA structure. A newly developed thermodynamic scanning method predicted RNA folding mapping precisely to regions of SSSV and at the genomic 3′ end. These regions contained several evolutionarily conserved RNA secondary structures, of variable size and positions. However, all caliciviruses contained 3′ terminal hairpins, and stem–loops in the anti-genomic strand invariably six bases upstream of the sg transcript, indicating putative roles as sg promoters. Using the murine norovirus (MNV) reverse-genetics system, disruption of 5′ end stem–loops produced ∼15- to 20-fold infectivity reductions, while disruption of the RNA structure in the sg promoter region and at the 3′ end entirely destroyed replication ability. Restoration of infectivity by repair mutations in the sg promoter region confirmed a functional role for the RNA secondary structure, not the sequence. This study provides comprehensive bioinformatic resources for future functional studies of MNV and other caliciviruses. PMID:18319285

  17. A range of complex probabilistic models for RNA secondary structure prediction that includes the nearest-neighbor model and more.

    PubMed

    Rivas, Elena; Lang, Raymond; Eddy, Sean R

    2012-02-01

    The standard approach for single-sequence RNA secondary structure prediction uses a nearest-neighbor thermodynamic model with several thousand experimentally determined energy parameters. An attractive alternative is to use statistical approaches with parameters estimated from growing databases of structural RNAs. Good results have been reported for discriminative statistical methods using complex nearest-neighbor models, including CONTRAfold, Simfold, and ContextFold. Little work has been reported on generative probabilistic models (stochastic context-free grammars [SCFGs]) of comparable complexity, although probabilistic models are generally easier to train and to use. To explore a range of probabilistic models of increasing complexity, and to directly compare probabilistic, thermodynamic, and discriminative approaches, we created TORNADO, a computational tool that can parse a wide spectrum of RNA grammar architectures (including the standard nearest-neighbor model and more) using a generalized super-grammar that can be parameterized with probabilities, energies, or arbitrary scores. By using TORNADO, we find that probabilistic nearest-neighbor models perform comparably to (but not significantly better than) discriminative methods. We find that complex statistical models are prone to overfitting RNA structure and that evaluations should use structurally nonhomologous training and test data sets. Overfitting has affected at least one published method (ContextFold). The most important barrier to improving statistical approaches for RNA secondary structure prediction is the lack of diversity of well-curated single-sequence RNA secondary structures in current RNA databases. PMID:22194308

  18. A range of complex probabilistic models for RNA secondary structure prediction that includes the nearest-neighbor model and more.

    PubMed

    Rivas, Elena; Lang, Raymond; Eddy, Sean R

    2012-02-01

    The standard approach for single-sequence RNA secondary structure prediction uses a nearest-neighbor thermodynamic model with several thousand experimentally determined energy parameters. An attractive alternative is to use statistical approaches with parameters estimated from growing databases of structural RNAs. Good results have been reported for discriminative statistical methods using complex nearest-neighbor models, including CONTRAfold, Simfold, and ContextFold. Little work has been reported on generative probabilistic models (stochastic context-free grammars [SCFGs]) of comparable complexity, although probabilistic models are generally easier to train and to use. To explore a range of probabilistic models of increasing complexity, and to directly compare probabilistic, thermodynamic, and discriminative approaches, we created TORNADO, a computational tool that can parse a wide spectrum of RNA grammar architectures (including the standard nearest-neighbor model and more) using a generalized super-grammar that can be parameterized with probabilities, energies, or arbitrary scores. By using TORNADO, we find that probabilistic nearest-neighbor models perform comparably to (but not significantly better than) discriminative methods. We find that complex statistical models are prone to overfitting RNA structure and that evaluations should use structurally nonhomologous training and test data sets. Overfitting has affected at least one published method (ContextFold). The most important barrier to improving statistical approaches for RNA secondary structure prediction is the lack of diversity of well-curated single-sequence RNA secondary structures in current RNA databases.

  19. Secondary Structure and Pd(II) Coordination in S-Layer Proteins from Bacillus sphaericus Studied by Infrared and X-Ray Absorption Spectroscopy

    PubMed Central

    Fahmy, Karim; Merroun, Mohamed; Pollmann, Katrin; Raff, Johannes; Savchuk, Olesya; Hennig, Christoph; Selenska-Pobell, Sonja

    2006-01-01

    The S-layer of Bacillus sphaericus strain JG-A12, isolated from a uranium-mining site, exhibits a high metal-binding capacity, indicating that it may provide a protective function by preventing the cellular uptake of heavy metals and radionuclides. This property has allowed the use of this and other S-layers as self-assembling organic templates for the synthesis of nanosized heavy metal cluster arrays. However, little is known about the molecular basis of the metal-protein interactions and their impact on secondary structure. We have studied the secondary structure, protein stability, and Pd(II) coordination in S-layers from the B. sphaericus strains JG-A12 and NCTC 9602 to elucidate the molecular basis of their biological function and of the metal nanocluster growth. Fourier transform infrared spectroscopy reveals similar secondary structures, containing ∼35% β-sheets and little helical structure. pH-induced infrared absorption changes of the side-chain carboxylates evidence a remarkably low pK < 3 in both strains and a structural stabilization when Pd(II) is bound. The COO−-stretching absorptions reveal a predominant Pd(II) coordination by chelation/bridging by Asp and Glu residues. This agrees with XANES and EXAFS data revealing oxygens as coordinating atoms to Pd(II). The additional participation of nitrogen is assigned to side chains rather than to the peptide backbone. The topology of nitrogen- and carboxyl-bearing side chains appears to mediate heavy metal binding to the large number of Asp and Glu in both S-layers at particularly low pH as an adaptation to the environment from which the strain JG-A12 has been isolated. These side chains are thus prime targets for the design of engineered S-layer-based nanoclusters. PMID:16698775

  20. Crystal Structure of a Bacterial Topoisomerase IB in Complex with DNA Reveals a Secondary DNA Binding Site

    SciTech Connect

    Patel, Asmita; Yakovleva, Lyudmila; Shuman, Stewart; Mondragón, Alfonso

    2010-10-22

    Type IB DNA topoisomerases (TopIB) are monomeric enzymes that relax supercoils by cleaving and resealing one strand of duplex DNA within a protein clamp that embraces a {approx}21 DNA segment. A longstanding conundrum concerns the capacity of TopIB enzymes to stabilize intramolecular duplex DNA crossovers and form protein-DNA synaptic filaments. Here we report a structure of Deinococcus radiodurans TopIB in complex with a 12 bp duplex DNA that demonstrates a secondary DNA binding site located on the surface of the C-terminal domain. It comprises a distinctive interface with one strand of the DNA duplex and is conserved in all TopIB enzymes. Modeling of a TopIB with both DNA sites suggests that the secondary site could account for DNA crossover binding, nucleation of DNA synapsis, and generation of a filamentous plectoneme. Mutations of the secondary site eliminate synaptic plectoneme formation without affecting DNA cleavage or supercoil relaxation.

  1. Phylogenetic reconstruction using secondary structures of Internal Transcribed Spacer 2 (ITS2, rDNA): finding the molecular and morphological gap in Caribbean gorgonian corals

    PubMed Central

    Grajales, Alejandro; Aguilar, Catalina; Sánchez, Juan A

    2007-01-01

    Background Most phylogenetic studies using current methods have focused on primary DNA sequence information. However, RNA secondary structures are particularly useful in systematics because they include characteristics, not found in the primary sequence, that give "morphological" information. Despite the number of recent molecular studies on octocorals, there is no consensus opinion about a region that carries enough phylogenetic resolution to solve intrageneric or close species relationships. Moreover, intrageneric morphological information by itself does not always produce accurate phylogenies; intra-species comparisons can reveal greater differences than intra-generic ones. The search for new phylogenetic approaches, such as by RNA secondary structure analysis, is therefore a priority in octocoral research. Results Initially, twelve predicted RNA secondary structures were reconstructed to provide the basic information for phylogenetic analyses; they accorded with the 6 helicoidal ring model, also present in other groups of corals and eukaryotes. We obtained three similar topologies for nine species of the Caribbean gorgonian genus Eunicea (candelabrum corals) with two sister taxa as outgroups (genera Plexaura and Pseudoplexaura) on the basis of molecular morphometrics of ITS2 RNA secondary structures only, traditional primary sequence analyses and maximum likelihood, and a Bayesian analysis of the combined data. The latter approach allowed us to include both primary sequence and RNA molecular morphometrics; each data partition was allowed to have a different evolution rate. In addition, each helix was partitioned as if it had evolved at a distinct rate. Plexaura flexuosa was found to group within Eunicea; this was best supported by both the molecular morphometrics and combined analyses. We suggest Eunicea flexuosa (Lamouroux, 1821) comb. nov., and we present a new species description including Scanning Electron Microscopy (SEM) images of morphological

  2. Changes in bacterial diversity and community structure following pesticides addition to soil estimated by cultivation technique.

    PubMed

    Cycoń, Mariusz; Piotrowska-Seget, Zofia

    2009-07-01

    An experiment was conducted under laboratory conditions to investigate the effect of increasing concentrations of fenitrothion (2, 10 and 200 mg a.i./kg soil), diuron (1.5, 7.5 and 150 mg a.i./kg soil) and thiram (3.5, 17.5 and 350 mg a.i./kg soil) on soil respiration, bacterial counts and changes in culturable fraction of soil bacteria. To ascertain these changes, the community structure, bacterial biodiversity and process of colony formation, based on the r/K strategy concept, EP- and CD-indices and the FOR model, respectively, were determined. The results showed that the measured parameters were generally unaffected by the lowest dosages of pesticides, corresponding to the recommended field rates. The highest dosages of fenitrothion and thiram suppressed the peak SIR by 15-70% and 20-80%, respectively, while diuron increased respiration rate by 17-25% during the 28-day experiment. Also, the total numbers of bacteria increased in pesticide-treated soils. However, the reverse effect on day 1 and, in addition, in case of the highest dosages of insecticide on days 14 and 28, was observed. Analysis of the community structure revealed that in all soil treatments bacterial communities were generally dominated by K-strategists. Moreover, differences in the distribution of individual bacteria classes and the gradual domination of bacteria populations belonging to r-strategists during the experiment, as compared to control, was observed. However, on day 1, at the highest pesticide dosages, fast growing bacteria constituted only 1-10% of the total colonies number during 48 h of plate incubation, whereas in remaining samples they reached from 20 to 40% of total cfu. This effect, in case of fenitrothion, lasted till the end of the experiment. At the highest dosages of fenitrothion, diuron and at all dosages of thiram the decrease of biodiversity, as indicated by EP- and CD-indices on day 1, was found. At the next sampling time, no significant retarding or stimulating effect

  3. Critical review of the safety assessment of nano-structured silica additives in food.

    PubMed

    Winkler, Hans Christian; Suter, Mark; Naegeli, Hanspeter

    2016-01-01

    The development of nano-materials is viewed as one of the most important technological advances of the 21st century and new applications of nano-sized particles in the production, processing, packaging or storage of food are expected to emerge soon. This trend of growing commercialization of engineered nano-particles as part of modern diet will substantially increase oral exposure. Contrary to the proven benefits of nano-materials, however, possible adverse health effects have generally received less attention. This problem is very well illustrated by nano-structured synthetic amorphous silica (SAS), which is a common food additive since several decades although the relevant risk assessment has never been satisfactorily completed. A no observed adverse effect level of 2500 mg SAS particles/kg body weight per day was derived from the only available long-term administration study in rodents. However, extrapolation to a safe daily intake for humans is problematic due to limitations of this chronic animal study and knowledge gaps as to possible local intestinal effects of SAS particles, primarily on the gut-associated lymphoid system. This uncertainty is aggravated by digestion experiments indicating that dietary SAS particles preserve their nano-sized structure when reaching the intestinal lumen. An important aspect is whether food-borne particles like SAS alter the function of dendritic cells that, embedded in the intestinal mucosa, act as first-line sentinels of foreign materials. We conclude that nano-particles do not represent a completely new threat and that most potential risks can be assessed following procedures established for conventional chemical hazards. However, specific properties of food-borne nano-particles should be further examined and, for that purpose, in vitro tests with decision-making cells of the immune system are needed to complement existing in vivo studies. PMID:27287345

  4. Critical review of the safety assessment of nano-structured silica additives in food.

    PubMed

    Winkler, Hans Christian; Suter, Mark; Naegeli, Hanspeter

    2016-06-10

    The development of nano-materials is viewed as one of the most important technological advances of the 21st century and new applications of nano-sized particles in the production, processing, packaging or storage of food are expected to emerge soon. This trend of growing commercialization of engineered nano-particles as part of modern diet will substantially increase oral exposure. Contrary to the proven benefits of nano-materials, however, possible adverse health effects have generally received