Sample records for mrna secondary structure

  1. mRNA secondary structure optimization using a correlated stem–loop prediction

    PubMed Central

    Gaspar, Paulo; Moura, Gabriela; Santos, Manuel A. S.; Oliveira, José Luís

    2013-01-01

    Secondary structure of messenger RNA plays an important role in the bio-synthesis of proteins. Its negative impact on translation can reduce the yield of protein by slowing or blocking the initiation and movement of ribosomes along the mRNA, becoming a major factor in the regulation of gene expression. Several algorithms can predict the formation of secondary structures by calculating the minimum free energy of RNA sequences, or perform the inverse process of obtaining an RNA sequence for a given structure. However, there is still no approach to redesign an mRNA to achieve minimal secondary structure without affecting the amino acid sequence. Here we present the first strategy to optimize mRNA secondary structures, to increase (or decrease) the minimum free energy of a nucleotide sequence, without changing its resulting polypeptide, in a time-efficient manner, through a simplistic approximation to hairpin formation. Our data show that this approach can efficiently increase the minimum free energy by >40%, strongly reducing the strength of secondary structures. Applications of this technique range from multi-objective optimization of genes by controlling minimum free energy together with CAI and other gene expression variables, to optimization of secondary structures at the genomic level. PMID:23325845

  2. Dynamics of translation by single ribosomes through mRNA secondary structures

    PubMed Central

    Chen, Chunlai; Zhang, Haibo; Broitman, Steven L.; Reiche, Michael; Farrell, Ian; Cooperman, Barry S.; Goldman, Yale E.

    2013-01-01

    During protein synthesis, the ribosome translates nucleotide triplets in single-stranded mRNA into polypeptide sequences. Strong downstream mRNA secondary (2°) structures, which must be unfolded for translation, can slow or even halt protein synthesis. Here we employ single molecule fluorescence resonance energy transfer to determine reaction rates for specific steps within the elongation cycle as the Escherichia coli ribosome encounters stem loop or pseudoknot mRNAstructures. Downstream stem-loops containing 100% G-C base pairs decrease the rates of both tRNA translocation within the ribosome and deacylated tRNA dissociation from the ribosomal exit (E) site. Downstream stem-loops or pseudoknots containing both G-C and A-U pairs also decrease the rate of tRNA dissociation, but they have little effect on tRNA translocation rate. Thus, somewhat surprisingly, unfolding of mRNAstructures is more closely coupled to E-site tRNA dissociation than to tRNA translocation. PMID:23542154

  3. Volatility in mRNA secondary structure as a design principle for antisense

    PubMed Central

    Johnson, Erik; Srivastava, Ranjan

    2013-01-01

    Designing effective antisense sequences is a formidable problem. A method for predicting efficacious antisense holds the potential to provide fundamental insight into this biophysical process. More practically, such an understanding increases the chance of successful antisense design as well as saving considerable time, money and labor. The secondary structure of an mRNA molecule is believed to be in a constant state of flux, sampling several different suboptimal states. We hypothesized that particularly volatile regions might provide better accessibility for antisense targeting. A computational framework, GenAVERT was developed to evaluate this hypothesis. GenAVERT used UNAFold and RNAforester to generate and compare the predicted suboptimal structures of mRNA sequences. Subsequent analysis revealed regions that were particularly volatile in terms of intramolecular hydrogen bonding, and thus potentially superior antisense targets due to their high accessibility. Several mRNA sequences with known natural antisense target sites as well as artificial antisense target sites were evaluated. Upon comparison, antisense sequences predicted based upon the volatility hypothesis closely matched those of the naturally occurring antisense, as well as those artificial target sites that provided efficient down-regulation. These results suggest that this strategy may provide a powerful new approach to antisense design. PMID:23161691

  4. A MYLK variant regulates asthmatic inflammation via alterations in mRNA secondary structure.

    PubMed

    Wang, Ting; Zhou, Tong; Saadat, Laleh; Garcia, Joe Gn

    2015-06-01

    Myosin light-chain kinase (MYLK) is a gene known to be significantly associated with severe asthma in African Americans. Here we further examine the molecular function of a single-nucleotide polymorphism (SNP), located in the non-muscle myosin light-chain kinase isoform (nmMLCK), in asthma susceptibility and pathobiology. We identified nmMLCK variant (reference SNP: rs9840993, NM_053025: 721C>T, c.439C>T) with a distinct mRNA secondary structure from the other variants. The nmMLCK variant (721C) secondary structure exhibits increased stability with an elongated half-life in the human endothelial cell, and greater efficiency in protein translation initiation owing to an increased accessibility to translation start site. Finally, nmMLCK expression of 721C- and 721T-containing MYLK transgenes were compared in nmMLCK(-/-) mice and confirmed deleterious effects of nmMLCK expression on asthmatic indices and implicated the augmented influence of MYLK 721C>T (c.439C>T) SNP on asthma severity. The confirmation of the novel mechanism of the regulation of asthmatic inflammation by a MYLK advances knowledge of the genetic basis for asthma disparities, and further suggests the potential of nmMLCK as a therapeutic target. Our study suggests that in addition to altering protein structure and function, non-synonymous SNPs may also lead to phenotypic disparity by altering protein expression. PMID:25271083

  5. Secondary structure model for the complete simian virus 50 late precursor mRNA.

    PubMed Central

    Nussinov, R; Tinoco, I; Jacobson, A B

    1982-01-01

    Structures for all sequences containing less than 1790 nucleotides in the 2600 nucleotide late region of the SV40 virus have been computed and saved on magnetic tape. Previously the longest sequence whose secondary structure was calculated in a single computer run contained 950 nucleotides. In the past, analysis of long molecules required numerous repeated, partially overlapping computations on much shorter segments. The structure obtained for the late half of the SV40 is Y-shaped with two unequal arms. It has 52 short hairpins. Two long range interactions between nucleotides near 650 and 1350 and between 1450 and 2450 appear to play an important role. The first is within the 16S intron; the second is in the 3' exon. The 5' and 3' ends of the molecule are close to each other and are found in the major elongated stem in the vicinity of the fork. PMID:6278409

  6. Secondary Structure of a Conserved Domain in an Intron of Influenza A M1 mRNA

    PubMed Central

    2014-01-01

    Influenza A virus utilizes RNA throughout infection. Little is known, however, about the roles of RNA structures. A previous bioinformatics survey predicted multiple regions of influenza A virus that are likely to generate evolutionarily conserved and stable RNA structures. One predicted conserved structure is in the pre-mRNA coding for essential proteins, M1 and M2. This structure starts 79 nucleotides downstream of the M2 mRNA 5? splice site. Here, a combination of biochemical structural mapping, mutagenesis, and NMR confirms the predicted three-way multibranch structure of this RNA. Imino proton NMR spectra reveal no change in secondary structure when 80 mM KCl is supplemented with 4 mM MgCl2. Optical melting curves in 1 M NaCl and in 100 mM KCl with 10 mM MgCl2 are very similar, with melting temperatures ?14 °C higher than that for 100 mM KCl alone. These results provide a firm basis for designing experiments and potential therapeutics to test for function in cell culture. PMID:25026548

  7. Signs of Selection in Synonymous Sites of the Mitochondrial Cytochrome b Gene of Baikal Oilfish (Comephoridae) by mRNA Secondary Structure Alterations

    PubMed Central

    Teterina, Veronika I.; Mamontov, Anatoliy M.; Sukhanova, Lyubov V.; Kirilchik, Sergei V.

    2015-01-01

    Studies over the past decade have shown a significant role of synonymous mutations in posttranscriptional regulation of gene expression, which is particularly associated with messenger RNA (mRNA) secondary structure alterations. Most studies focused on prokaryote genomes and the nuclear genomes of eukaryotes while little is known about the regulation of mitochondrial DNA (mtDNA) gene expression. This paper reveals signs of selection in synonymous sites of the mitochondrial cytochrome b gene (Cytb) of Baikal oilfish or golomyankas (Comephoridae) directed towards altering the secondary structure of the mRNA and probably altering the character of mtDNA gene expression. Our findings are based on comparisons of intraspecific genetic variation patterns of small golomyanka (Comephorus dybowski) and two genetic groups of big golomyanka (Comephorus dybowskii). Two approaches were used: (i) analysis of the distribution of synonymous mutations between weak-AT (W) and strong-GC (S) nucleotides within species and groups in accordance with mutation directions from central to peripheral haplotypes and (ii) approaches based on the predicted mRNA secondary structure. PMID:26114105

  8. Recycling Secondary Index Structures

    Microsoft Academic Search

    Paul M. Aoki

    Many database reorganization techniques move tuples in a table from one loca- tion to another in a single pass. For example, distributed database systems move or copy tables between sites to optimize data placement. However, such systems typically drop and then rebuild the secondary indices defined over the table being moved. There are two primary reasons for this. First, moving

  9. 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.

  10. Sequence and structure-specific elements of HERG mRNA determine channel synthesis and trafficking efficiency

    PubMed Central

    Sroubek, Jakub; Krishnan, Yamini; McDonald, Thomas V.

    2013-01-01

    Human ether-á-gogo-related gene (HERG) encodes a potassium channel that is highly susceptible to deleterious mutations resulting in susceptibility to fatal cardiac arrhythmias. Most mutations adversely affect HERG channel assembly and trafficking. Why the channel is so vulnerable to missense mutations is not well understood. Since nothing is known of how mRNA structural elements factor in channel processing, we synthesized a codon-modified HERG cDNA (HERG-CM) where the codons were synonymously changed to reduce GC content, secondary structure, and rare codon usage. HERG-CM produced typical IKr-like currents; however, channel synthesis and processing were markedly different. Translation efficiency was reduced for HERG-CM, as determined by heterologous expression, in vitro translation, and polysomal profiling. Trafficking efficiency to the cell surface was greatly enhanced, as assayed by immunofluorescence, subcellular fractionation, and surface labeling. Chimeras of HERG-NT/CM indicated that trafficking efficiency was largely dependent on 5? sequences, while translation efficiency involved multiple areas. These results suggest that HERG translation and trafficking rates are independently governed by noncoding information in various regions of the mRNA molecule. Noncoding information embedded within the mRNA may play a role in the pathogenesis of hereditary arrhythmia syndromes and could provide an avenue for targeted therapeutics.—Sroubek, J., Krishnan, Y., McDonald, T V. Sequence- and structure-specific elements of HERG mRNA determine channel synthesis and trafficking efficiency. PMID:23608144

  11. 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. PMID:25726462

  12. Data Mining for Protein Secondary Structure Prediction

    Microsoft Academic Search

    Haitao Cheng; Taner Z. Sen; Robert L. Jernigan; Andrzej Kloczkowski

    \\u000a Accurate protein secondary structure prediction from the amino acid sequence is essential for almost all theoretical and experimental\\u000a studies on protein structure and function. After a brief discussion of application of data mining for optimization of crystallization\\u000a conditions for target proteins we show that data mining of structural fragments of proteins from known structures in the protein\\u000a data bank (PDB)

  13. Fatigue of structures and secondary bending in structural elements

    Microsoft Academic Search

    J. Schijve; G. Campoli; A. Monaco

    2009-01-01

    Secondary bending occurs in structural elements with geometric eccentricities when the element is loaded in tension. Eccentricities are present in lap joints, but also in plates with a locally increased thickness. Due to the eccentricities out-of-plane displacements occur with local bending as a result. This secondary bending phenomenon is unfavourable for the fatigue properties of a structure. In the paper

  14. Exact Folding Dynamics of RNA Secondary Structures

    Microsoft Academic Search

    Michael T. Wolfinger; W. Andreas Svrcek-Seiler; Christoph Flamma; Ivo L. Hofacker; Peter F. Stadler

    Barrier trees consisting of local minima and their connecting saddle points imply a natural coarse-graining for the description of the energy landscape of RNA secondary structures. Here we show that, based on this approach, it is possible to predict the folding behavior of RNA molecules by numerical integration. Comparison with stochastic folding simulations shows reasonable agreement of the resulting folding

  15. Conserved RNA Secondary Structures in Flaviviridae Genomes

    Microsoft Academic Search

    Caroline Thurner; Christina Witwer; Ivo L. Hofacker; Peter F. Stadler

    2003-01-01

    We report here on a comprehensive computational survey of evolution- arily conserved secondary structure motifs in the genomic RNAs of the family Flaviviridae. This virus family consists of the three genera Fla- vivirus, Pestivirus, Hepacivirus and the group of Hepatitis G Viruses with a currently uncertain taxonomic classification. Based on the control of replication and translation, two subgroups were considered

  16. Rapid purification of RNA secondary structures

    Microsoft Academic Search

    Stacy L. Gelhaus; William R. LaCourse; Nathan A. Hagan; Gaya K. Amarasinghe; Daniele Fabris

    2003-01-01

    A new method for rapid purification and structural analysis of oligoribonucleotides of 19 and 20 nt is applied to RNA hairpins SL3 and SL2, which are stable secondary structures present on the y recog- nition element of HIV-1. This approach uses ion-pairing reversed-phase liquid chromatography (IP-RPLC) to achieve the separation of the stem- loop from the transcription mix. Evidence is

  17. 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.

  18. 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

  19. RNA secondary structure regulates the translation of sxy and competence development in Haemophilus influenzae.

    PubMed

    Cameron, Andrew D S; Volar, Milica; Bannister, Laura A; Redfield, Rosemary J

    2008-01-01

    The sxy (tfoX) gene product is the central regulator of DNA uptake by naturally competent gamma-proteobacteria such as Haemophilus influenzae, Vibrio cholerae and probably Escherichia coli. However, the mechanisms regulating sxy gene expression are not understood despite being key to understanding the physiological role of DNA uptake. We have isolated mutations in H. influenzae sxy that greatly elevate translation and thus cause competence to develop in otherwise non-inducing conditions (hypercompetence). In vitro nuclease analysis confirmed the existence of an extensive secondary structure at the 5' end of sxy mRNA that sequesters the ribosome-binding site and start codon in a stem-loop. All of the hypercompetence mutations reduced mRNA base pairing, and one was shown to cause a global destabilization that increased translational efficiency. Conversely, mutations engineered to add mRNA base pairs strengthened the secondary structure, resulting in reduced translational efficiency and greatly reduced competence for genetic transformation. Transfer of wild-type cells to starvation medium improved translational efficiency of sxy while independently triggering the sugar starvation regulator (CRP) to stimulate transcription at the sxy promoter. Thus, mRNA secondary structure is responsive to conditions where DNA uptake will be favorable, and transcription of sxy is simultaneously enhanced if CRP activation signals that energy supplies are limited. PMID:17981840

  20. Method for predicting RNA secondary structure.

    PubMed Central

    Pipas, J M; McMahon, J E

    1975-01-01

    We report a method for predicting the most stable secondary structure of RNA from its primary sequence of nucleotides. The technique consists of a series of three computer programs interfaced to take the nucleotide sequence of any RNA and (a) list all possible helical regions, using modified Watson-Crick base-pairing rules; (b) create all possible secondary structures by forming permutations of compatible helical regions; and (c)evaluate each structure for total free energy of formation from a completely extended chain. A free energy distribution and the base-by-base bonding interactions of each possible structure are catalogued by the system and are readily available for examination. The method has been applied to 62 tRNA sequences. The total free-energy of the predicted most stable structures ranged from -19 to -41 kcal/mole (-22 to -49 kJ/mole). The number of structures created was also highly sequence-dependent and ranged from 200 to 13,000. In nearly all cases the cloverleaf is predicted to be the structure with the lowest free energy of formation. PMID:1056009

  1. Cascaded multiple classifiers for secondary structure prediction.

    PubMed Central

    Ouali, M.; King, R. D.

    2000-01-01

    We describe a new classifier for protein secondary structure prediction that is formed by cascading together different types of classifiers using neural networks and linear discrimination. The new classifier achieves an accuracy of 76.7% (assessed by a rigorous full Jack-knife procedure) on a new nonredundant dataset of 496 nonhomologous sequences (obtained from G.J. Barton and J.A. Cuff). This database was especially designed to train and test protein secondary structure prediction methods, and it uses a more stringent definition of homologous sequence than in previous studies. We show that it is possible to design classifiers that can highly discriminate the three classes (H, E, C) with an accuracy of up to 78% for beta-strands, using only a local window and resampling techniques. This indicates that the importance of long-range interactions for the prediction of beta-strands has been probably previously overestimated. PMID:10892809

  2. Energy profile and secondary structure impact shRNA efficacy

    PubMed Central

    Zhou, Hong; Zeng, Xiao

    2009-01-01

    Background RNA interference (RNAi) is a cellular mechanism in which a short/small double stranded RNA induces the degradation of its sequence specific target mRNA, leading to specific gene silencing. Since its discovery, RNAi has become a powerful biological technique for gene function studies and drug discovery. The very first requirement of applying RNAi is to design functional small interfering RNA (siRNA) that can uniquely induce the degradation of the targeted mRNA. It has been shown that many functional synthetic siRNAs share some common characteristics, such as GC content limitation and free energy preferences at both terminals, etc. Results Our three-phase algorithm was developed to design siRNA on a whole-genome scale based on those identified characteristics of functional siRNA. When this algorithm was applied to design short hairpin RNA (shRNA), the validated success rate of shRNAs was over 70%, which was almost double the rate reported for TRC library. This indicates that the designs of siRNA and shRNA may share the same concerns. Further analysis of the shRNA dataset of 444 designs reveals that the high free energy states of the two terminals have the largest positive impact on the shRNA efficacy. Enforcing these energy characteristics of both terminals can further improve the shRNA design success rate to 83.1%. We also found that functional shRNAs have less probability for their 3' terminals to be involved in mRNA secondary structure formation. Conclusion Functional shRNAs prefer high free energy states at both terminals. High free energy states of the two terminals were found to be the largest positive impact factor on shRNA efficacy. In addition, the accessibility of the 3' terminal is another key factor to shRNA efficacy. PMID:19594886

  3. Structure and stability correlation of an mRNA pseudoknot

    E-print Network

    Suram, Saritha

    2002-01-01

    to substantially contribute to the net stability of the molecule. Here, we provide thermodynamic and structural evidence for the contribution of the tertiary loop 2-stem 1 interactions towards the global stability of the pseudoknot. BWYV RNAs containing 2' deoxy...

  4. Parsing nucleic acid pseudoknotted secondary structure: algorithm and applications

    E-print Network

    Condon, Anne

    Parsing nucleic acid pseudoknotted secondary structure: algorithm and applications Baharak of pseudoknotted nucleic acid secondary structure is an impor- tant computational challenge. Prediction algorithms Nucleic acids - that is, DNA and RNA molecules - play fundamental roles in the cell: in translation

  5. HMMs and secondary structure Fold Recognition using Hidden Markov Models and Secondary

    E-print Network

    Karplus, Kevin

    HMMs and secondary structure Fold Recognition using Hidden Markov Models and Secondary Structure affecting the ratio. 7 #12;Standard Null Model ¯ Null model is a zero-order Markov model, that is, each (Bayesian statistical modeling) ¯ SAM-T2K for finding and aligning homologs ¯ Multi-track HMMs and secondary

  6. Analysis of Secondary Structure Elements of Proteins Using Indexing Techniques

    E-print Network

    Lonardi, Stefano

    Analysis of Secondary Structure Elements of Proteins Using Indexing Techniques Concettina Guerra, pattern recogni- tion, secondary-structure elements, globular proteins. 1. Introduction The exponentially. Moreover, the table can be used for a statistical analysis of the arrangement of the secondary structures

  7. Structure and stability correlation of an mRNA pseudoknot 

    E-print Network

    Suram, Saritha

    2002-01-01

    that affect major food crops and result in heavy economic losses (56). The viral genome structure, organization and the mode of gene expression have been extensively studied in a number of plant RNA viruses (57-59). The viral genome is limited in size, yet...S electroeluter. The RNAs recovered, were desalted using a C18-column (Alltech) using 0. 25 M triethylamine (TEA) buffer, pH 6. 0, eluted with 50'lo methanol and evaporated to dryness. The RNAs were then subjected to extensive dialysis in an appropriate buffer...

  8. 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

  9. RNA-SSPT: RNA Secondary Structure Prediction Tools

    PubMed Central

    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

  10. Notch Transmembrane Domain: Secondary Structure and Topology.

    PubMed

    Deatherage, Catherine L; Lu, Zhenwei; Kim, Ji-Hun; Sanders, Charles R

    2015-06-16

    The Notch signaling pathway is critical in development, neuronal maintenance, and hematopoiesis. An obligate step in the activation of this pathway is cleavage of its transmembrane (TM) domain by ?-secretase. While the soluble domains have been extensively studied, little has been done to characterize its TM and flanking juxtamembrane (JM) segments. Here, we present the results of nuclear magnetic resonance (NMR) studies of the human Notch1 TM/JM domain. The TM domain is largely ?-helical. While the flanking JM segments do not adopt regular secondary structure, they interact with the membrane surface, suggesting membrane interactions may play a role in modulating its cleavage by ?-secretase and subsequent NOTCH signaling function. PMID:26023825

  11. Drawing and editing the secondary structure(s) of RNA.

    PubMed

    Ponty, Yann; Leclerc, Fabrice

    2015-01-01

    Secondary structure diagrams are essential, in RNA biology, to communicate functional hypotheses and summarize structural data, and communicate them visually as drafts or finalized publication-ready figures. While many tools are currently available to automate the production of such diagrams, their capacities are usually partial, making it hard for a user to decide which to use in a given context. In this chapter, we guide the reader through the steps involved in the production of expressive publication-quality illustrations featuring the RNA secondary structure. We present major existing representations and layouts, and give precise instructions to produce them using available free software, including jViz.RNA, the PseudoViewer, RILogo, R-chie, RNAplot, R2R, and VARNA. We describe the file formats and structural descriptions accepted by popular RNA visualization tools. We also provide command lines and Python scripts to ease the user's access to advanced features. Finally, we discuss and illustrate alternative approaches to visualize the secondary structure in the presence of probing data, pseudoknots, RNA-RNA interactions, and comparative data. PMID:25577373

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

    SciTech Connect

    Wang, J.T.L.; Chang, Chia-Yo [New Jersey Inst. of Technology, Newark, NJ (United States); Shapiro, B.A. [National Inst. of Health, Frederick, MD (United States)] [and others

    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.

  13. Protein Secondary Structure Prediction Method Based on Neural Networks

    Microsoft Academic Search

    Vasilka Dzikovska; M. Oreskovic; S. Kalajdziski; K. Trivodaliev; D. Davcev

    2008-01-01

    Protein secondary structure prediction remains an open and important problem in life sciences as a first step towards the crucial tertiary structure prediction. In [3], a protein secondary structure prediction algorithm called PSIPRED presents an innovative approach - feeding the neural network (NN) with a position specific scoring matrix as input data. Starting from this idea, in this paper we

  14. 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

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

    SciTech Connect

    Lapedes, A. [Los Alamos National Lab., NM (United States)]|[Santa Fe Inst., NM (United States); Steeg, E. [Toronto Univ., ON (Canada). Dept. of Computer Science; Farber, R. [Los Alamos National Lab., NM (United States)

    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.

  16. A novel approach to represent and compare RNA secondary structures

    PubMed Central

    Mattei, Eugenio; Ausiello, Gabriele; Ferrè, Fabrizio; Helmer-Citterich, Manuela

    2014-01-01

    Structural information is crucial in ribonucleic acid (RNA) analysis and functional annotation; nevertheless, how to include such structural data is still a debated problem. Dot-bracket notation is the most common and simple representation for RNA secondary structures but its simplicity leads also to ambiguity requiring further processing steps to dissolve. Here we present BEAR (Brand nEw Alphabet for RNA), a new context-aware structural encoding represented by a string of characters. Each character in BEAR encodes for a specific secondary structure element (loop, stem, bulge and internal loop) with specific length. Furthermore, exploiting this informative and yet simple encoding in multiple alignments of related RNAs, we captured how much structural variation is tolerated in RNA families and convert it into transition rates among secondary structure elements. This allowed us to compute a substitution matrix for secondary structure elements called MBR (Matrix of BEAR-encoded RNA secondary structures), of which we tested the ability in aligning RNA secondary structures. We propose BEAR and the MBR as powerful resources for the RNA secondary structure analysis, comparison and classification, motif finding and phylogeny. PMID:24753415

  17. Structural analysis by energy dot plot of a large mRNA.

    PubMed

    Jacobson, A B; Zuker, M

    1993-09-20

    We have predicted the secondary structure of the entire 4217 nucleotide sequence of the genomic RNA of coliphage Q beta in one computer run using the computer program MFOLD that computes RNA structures within any prescribed increment of the computed minimum free energy. The results are presented in the form of an "energy dot plot" that shows both an optimal folding as well as the superposition of all base-pairs that can form in slightly suboptimal foldings. The plot reveals five large, well-determined, independent structural domains that cover approximately 50% of the viral genome. The predicted structural domains are consistent with and provide support for five large structural domains identified previously by quantitative electron microscopy in Q beta RNA. The dot plot also contains cluttered regions that indicate large numbers of alternative foldings within or between segments of an RNA molecule. These reflect the impossibility of accurate structure prediction and/or the biological reality of more than one folding. Weaker, long range structures, that are observed by electron microscopy in two alternate competing conformations, are located in the regions of the Q beta sequence that correspond to cluttered regions of the dot plot. The potential biological significance of these secondary structures is discussed. PMID:8377202

  18. Structural model of an mRNA in complex with the bacterial chaperone Hfq.

    PubMed

    Peng, Yi; Curtis, Joseph E; Fang, Xianyang; Woodson, Sarah A

    2014-12-01

    The Sm-like protein Hfq (host factor Q-beta phage) facilitates regulation by bacterial small noncoding RNAs (sRNAs) in response to stress and other environmental signals. Here, we present a low-resolution model of Escherichia coli Hfq bound to the rpoS mRNA, a bacterial stress response gene that is targeted by three different sRNAs. Selective 2'-hydroxyl acylation and primer extension, small-angle X-ray scattering, and Monte Carlo molecular dynamics simulations show that the distal face and lateral rim of Hfq interact with three sites in the rpoS leader, folding the RNA into a compact tertiary structure. These interactions are needed for sRNA regulation of rpoS translation and position the sRNA target adjacent to an sRNA binding region on the proximal face of Hfq. Our results show how Hfq specifically distorts the structure of the rpoS mRNA to enable sRNA base pairing and translational control. PMID:25404287

  19. Protein secondary structure classification revisited: processing DSSP information with PSSC.

    PubMed

    Zacharias, Jan; Knapp, Ernst-Walter

    2014-07-28

    A first step toward three-dimensional protein structure description is the characterization of secondary structure. The most widely used program for secondary structure assignment remains DSSP, introduced in 1983, with currently more than 400 citations per year. DSSP output is in a one-letter representation, where much of the information on DSSP's internal description is lost. Recently it became evident that DSSP overlooks most ?-helical structures, which are more prevalent and important than anticipated before. We introduce an alternative concept, representing the internal structure characterization of DSSP as an eight-character string that is human-interpretable and easy to parse by software. We demonstrate how our protein secondary structure characterization (PSSC) code allows for inspection of complicated structural features. It recognizes ten times more ?-helical residues than does the standard DSSP. The plausibility of introduced changes in interpreting DSSP information is demonstrated by better clustering of secondary structures in (?, ?) dihedral angle space. With a sliding sequence window (SSW), helical assignments with PSSC remain invariant compared with an assignment based on the complete structure. In contrast, assignment with DSSP can be changed by residues in the neighborhood that are in fact not interacting with the residue under consideration. We demonstrate how one can easily define new secondary structure classification schemes with PSSC and perform the classifications. Our approach works without changing the DSSP source code and allows for more detailed protein characterization. PMID:24866861

  20. 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

  1. Symmetry-breaking motility and RNA secondary structures

    E-print Network

    Lee, Allen, S.M. Massachusetts Institute of Technology

    2005-01-01

    This thesis contains work on three separate topics: the spontaneous motility of functionalized particles, the designability of RNA secondary structures, and the statistical mechanics of homopolymer RNAs. For the work on ...

  2. Capped mRNAs with Reduced Secondary Structure Can Function in Extracts from Poliovirus-Infected Cells

    PubMed Central

    Sonenberg, Nahum; Guertin, Denise; Lee, Kevin A. W.

    1982-01-01

    Extracts from poliovirus-infected HeLa cells were used to study ribosome binding of native and denatured reovirus mRNAs and translation of capped mRNAs with different degrees of secondary structure. Here, we demonstrate that ribosomes in extracts from poliovirus-infected cells could form initiation complexes with denatured reovirus mRNA, in contrast to their inability to bind native reovirus mRNA. Furthermore, the capped alfalfa mosaic virus 4 RNA, which is most probably devoid of stable secondary structure at its 5? end, could be translated at much higher efficiency than could other capped mRNAs in extracts from poliovirus-infected cells. Images PMID:14582204

  3. Spectrum of disease-causing mutations in protein secondary structures

    PubMed Central

    Khan, Sofia; Vihinen, Mauno

    2007-01-01

    Background Most genetic disorders are linked to missense mutations as even minor changes in the size or properties of an amino acid can alter or prevent the function of the protein. Further, the effect of a mutation is also dependent on the sequence and structure context of the alteration. Results We investigated the spectrum of disease-causing missense mutations in secondary structure elements in proteins with numerous known mutations and for which an experimentally defined three-dimensional structure is available. We obtained a comprehensive map of the differences in mutation frequencies, location and contact energies, and the changes in residue volume and charge – both in the mutated (original) amino acids and in the mutant amino acids in the different secondary structure types. We collected information for 44 different proteins involved in a large number of diseases. The studied proteins contained a total of 2413 mutations of which 1935 (80%) appeared in secondary structures. Differences in mutation patterns between secondary structures and whole proteins were generally not statistically significant whereas within the secondary structural elements numerous highly significant features were observed. Conclusion Numerous trends in mutated and mutant amino acids are apparent. Among the original residues, arginine clearly has the highest relative mutability. The overall relative mutability among mutant residues is highest for cysteine and tryptophan. The mutability values are higher for mutated residues than for mutant residues. Arginine and glycine are among the most mutated residues in all secondary structures whereas the other amino acids have large variations in mutability between structure types. Statistical analysis was used to reveal trends in different secondary structural elements, residue types as well as for the charge and volume changes. PMID:17727703

  4. Bayesian Model of Protein Primary Sequence for Secondary Structure Prediction

    E-print Network

    Vannucci, Marina

    improving secondary structure reduction given the primary structure, we propose a Bayesian model based made obtaining protein sequences relatively cheap, accurate and fast, in comparison to the costly design of protein structure [4] and enzymatic function [5] as well as in drug development [6]. Depending

  5. PCI-SS: MISO dynamic nonlinear protein secondary structure prediction

    Microsoft Academic Search

    James R. Green; Michael J. Korenberg; Mohammed O. Aboul-magd

    2009-01-01

    BACKGROUND: Since the function of a protein is largely dictated by its three dimensional configuration, determining a protein's structure is of fundamental importance to biology. Here we report on a novel approach to determining the one dimensional secondary structure of proteins (distinguishing ?-helices, ?-strands, and non-regular structures) from primary sequence data which makes use of Parallel Cascade Identification (PCI), a

  6. A new algorithm for RNA secondary structure design.

    PubMed

    Andronescu, Mirela; Fejes, Anthony P; Hutter, Frank; Hoos, Holger H; Condon, Anne

    2004-02-20

    The function of many RNAs depends crucially on their structure. Therefore, the design of RNA molecules with specific structural properties has many potential applications, e.g. in the context of investigating the function of biological RNAs, of creating new ribozymes, or of designing artificial RNA nanostructures. Here, we present a new algorithm for solving the following RNA secondary structure design problem: given a secondary structure, find an RNA sequence (if any) that is predicted to fold to that structure. Unlike the (pseudoknot-free) secondary structure prediction problem, this problem appears to be hard computationally. Our new algorithm, "RNA Secondary Structure Designer (RNA-SSD)", is based on stochastic local search, a prominent general approach for solving hard combinatorial problems. A thorough empirical evaluation on computationally predicted structures of biological sequences and artificially generated RNA structures as well as on empirically modelled structures from the biological literature shows that RNA-SSD substantially out-performs the best known algorithm for this problem, RNAinverse from the Vienna RNA Package. In particular, the new algorithm is able to solve structures, consistently, for which RNAinverse is unable to find solutions. The RNA-SSD software is publically available under the name of RNA Designer at the RNASoft website (www.rnasoft.ca). PMID:15095976

  7. Crystal Structure of the Lysine Riboswitch Regulatory mRNA Element

    SciTech Connect

    Garst, A.; Heroux, A; Rambo, R; Batey, R

    2008-01-01

    Riboswitches are metabolite-sensitive elements found in mRNAs that control gene expression through a regulatory secondary structural switch. Along with regulation of lysine biosynthetic genes, mutations within the lysine-responsive riboswitch (L-box) play a role in the acquisition of resistance to antimicrobial lysine analogs. To understand the structural basis for lysine binding, we have determined the 2.8{angstrom} resolution crystal structure of lysine bound to the Thermotoga maritima asd lysine riboswitch ligand-binding domain. The structure reveals a complex architecture scaffolding a binding pocket completely enveloping lysine. Mutations conferring antimicrobial resistance cluster around this site as well as highly conserved long range interactions, indicating that they disrupt lysine binding or proper folding of the RNA. Comparison of the free and bound forms by x-ray crystallography, small angle x-ray scattering, and chemical probing reveals almost identical structures, indicating that lysine induces only limited and local conformational changes upon binding.

  8. Description of protein secondary structure using dual quaternions

    NASA Astrophysics Data System (ADS)

    Prošková, Jitka

    2014-11-01

    The main aim of this paper is to introduce the application of dual quaternions in one interesting problem in structural biology, i.e., the description of protein structure. The secondary protein structure is a specific geometric shape and the description uses Chasles theorem which states that any rigid body displacement can be described by a screw motion. We will briefly introduce the theory of dual quaternions in connection with the screw motion. Consequently, it is shown that modeling based on dual quaternions is an elegant mathematical method and a compact formula for the description of secondary protein structure is derived using the dual quaternion calculus.

  9. RNAstructure: software for RNA secondary structure prediction and analysis

    PubMed Central

    2010-01-01

    Background To understand an RNA sequence's mechanism of action, the structure must be known. Furthermore, target RNA structure is an important consideration in the design of small interfering RNAs and antisense DNA oligonucleotides. RNA secondary structure prediction, using thermodynamics, can be used to develop hypotheses about the structure of an RNA sequence. Results RNAstructure is a software package for RNA secondary structure prediction and analysis. It uses thermodynamics and utilizes the most recent set of nearest neighbor parameters from the Turner group. It includes methods for secondary structure prediction (using several algorithms), prediction of base pair probabilities, bimolecular structure prediction, and prediction of a structure common to two sequences. This contribution describes new extensions to the package, including a library of C++ classes for incorporation into other programs, a user-friendly graphical user interface written in JAVA, and new Unix-style text interfaces. The original graphical user interface for Microsoft Windows is still maintained. Conclusion The extensions to RNAstructure serve to make RNA secondary structure prediction user-friendly. The package is available for download from the Mathews lab homepage at http://rna.urmc.rochester.edu/RNAstructure.html. PMID:20230624

  10. Secondary Structure Prediction of Proposed RNAi

    E-print Network

    supported by additional information from RNase sensitivity and nucleotide chemical base reactivity assays of multiple sequence alignments. The aim of this exploration is to examine the effectiveness of two web;3 published structures based on multiple methods of structure determination are available. BACKGROUND

  11. Spliced mRNA Encoding the Murine Cytomegalovirus Chemokine Homolog Predicts a ? Chemokine of Novel Structure

    PubMed Central

    MacDonald, Margaret R.; Burney, Mary W.; Resnick, Stuart B.; Virgin, Herbert W.

    1999-01-01

    A viral mRNA of the late kinetic class expressed by murine cytomegalovirus (MCMV) contains an open reading frame (ORF) whose predicted protein, designated MCK-1, has homology to ? chemokines (M. R. MacDonald, X.-Y. Li, and H. W. Virgin IV, J. Virol. 71:1671–1678, 1997). The present study analyzed further the structure of the transcript in infected fibroblast cells. A splicing event removed the MCK-1 stop codon, bringing a downstream ORF into frame with the chemokine homolog and demonstrating that the MCK-1 ORF was an exon of a larger gene. The predicted 31.4-kDa protein, designated MCK-2, contains a putative amino-terminal signal sequence and a ? chemokine domain, followed by a carboxyl-terminal domain without significant homology to known proteins. Quantitative analysis of mRNA forms in MCMV-infected fibroblast cells at late times after infection indicated that the viral chemokine RNA was predominantly spliced. There was no evidence for expression of RNA encoding either MCK-1 or MCK-2 at immediate early or early times after infection with MCMV. Monoclonal antibodies generated against bacterially expressed MCK-2 recognized multiple proteins in the range of ?30 to ?45 kDa in Western blot analysis of MCK-2 expressed in transfected COS cells. The monoclonal antibodies immunoprecipitated a similar group of proteins in transfected COS cells metabolically labeled with radioactive cysteine. Radiolabelled protein of apparent higher molecular mass was immunoprecipitated from culture medium overlying the transfected cells, suggesting that posttranslationally modified MCK-2 can be secreted. Two proteins with apparent molecular mass suggestive of posttranslational modification were detected by Western blot analysis of cells harvested at late times after infection with MCMV. These studies show that MCMV encodes and expresses a ? chemokine homolog with a novel predicted structure. PMID:10196260

  12. Elimination of cap structures generated by mRNA decay involves the new scavenger mRNA decapping enzyme Aph1/FHIT together with DcpS

    PubMed Central

    Taverniti, Valerio; Séraphin, Bertrand

    2015-01-01

    Eukaryotic 5? mRNA cap structures participate to the post-transcriptional control of gene expression before being released by the two main mRNA decay pathways. In the 3?-5? pathway, the exosome generates free cap dinucleotides (m7GpppN) or capped oligoribonucleotides that are hydrolyzed by the Scavenger Decapping Enzyme (DcpS) forming m7GMP. In the 5?-3? pathway, the decapping enzyme Dcp2 generates m7GDP. We investigated the fate of m7GDP and m7GpppN produced by RNA decay in extracts and cells. This defined a pathway involving DcpS, NTPs and the nucleoside diphosphate kinase for m7GDP elimination. Interestingly, we identified and characterized in vitro and in vivo a new scavenger decapping enzyme involved in m7GpppN degradation. We show that activities mediating cap elimination identified in yeast are essentially conserved in human. Their alteration may contribute to pathologies, possibly through the interference of cap (di)nucleotide with cellular function. PMID:25432955

  13. TRACES Centre Secondary structure of proteins and peptides1

    E-print Network

    Wells, Mathew G. - Department of Physical and Environmental Sciences, University of Toronto

    VCD (upper) and absorption (lower) spectra of hemoglobin (left), lysozyme (mid) and concanavalin in comparable amounts. #12;Much more apparent are the differences for the secondary structures in VCD spectra in the VCD spectrum of concanavalin A is very specific for -sheet structures. So it is no surprise

  14. Higher plant Ca(2+)-ATPase: primary structure and regulation of mRNA abundance by salt.

    PubMed Central

    Wimmers, L E; Ewing, N N; Bennett, A B

    1992-01-01

    Calcium-dependent regulatory mechanisms participate in diverse developmentally, hormonally, and environmentally regulated processes, with the precise control of cytosolic Ca2+ concentration being critical to such mechanisms. In plant cells, P-type Ca(2+)-ATPases localized in the plasma membrane and the endoplasmic reticulum are thought to play a central role in regulating cytoplasmic Ca2+ concentrations. Ca(2+)-ATPase activity has been identified in isolated plant cell membranes, but the protein has not been characterized at the molecular level. We have isolated a partial-length cDNA (LCA1) and a complete genomic clone (gLCA13) encoding a putative endoplasmic reticulum-localized Ca(2+)-ATPase in tomato. The deduced amino acid sequence specifies a protein (Lycopersicon Ca(2+)-ATPase) of 1048 amino acids with a molecular mass of 116 kDa, eight probable transmembrane domains, and all of the highly conserved functional domains common to P-type cation-translocating ATPases. In addition, the protein shares approximately 50% amino acid sequence identify with animal sarcoplasmic/endoplasmic reticulum Ca(2+)-ATPases but less than 30% identity with other P-type ATPases. Genomic DNA blot hybridization analysis indicates that the Lycopersicon Ca(2+)-ATPase is encoded by a single gene. RNA blot hybridization analysis indicates the presence of three transcript sizes in root tissue and a single, much less abundant, transcript in leaves. Lycopersicon Ca(2+)-ATPase mRNA levels increase dramatically upon a 1-day exposure to 50 mM NaCl. Thus this report describes the primary structure of a higher-plant Ca(2+)-ATPase and the regulation of its mRNA abundance by salt stress. Images PMID:1384045

  15. Quantifying variances in comparative RNA secondary structure prediction

    PubMed Central

    2013-01-01

    Background With the advancement of next-generation sequencing and transcriptomics technologies, regulatory effects involving RNA, in particular RNA structural changes are being detected. These results often rely on RNA secondary structure predictions. However, current approaches to RNA secondary structure modelling produce predictions with a high variance in predictive accuracy, and we have little quantifiable knowledge about the reasons for these variances. Results In this paper we explore a number of factors which can contribute to poor RNA secondary structure prediction quality. We establish a quantified relationship between alignment quality and loss of accuracy. Furthermore, we define two new measures to quantify uncertainty in alignment-based structure predictions. One of the measures improves on the “reliability score” reported by PPfold, and considers alignment uncertainty as well as base-pair probabilities. The other measure considers the information entropy for SCFGs over a space of input alignments. Conclusions Our predictive accuracy improves on the PPfold reliability score. We can successfully characterize many of the underlying reasons for and variances in poor prediction. However, there is still variability unaccounted for, which we therefore suggest comes from the RNA secondary structure predictive model itself. PMID:23634662

  16. De novo secondary structure motif discovery using RNAProfile.

    PubMed

    Zambelli, Federico; Pavesi, Giulio

    2015-01-01

    RNA secondary structure plays critical roles in several biological processes. For example, many trans-acting noncoding RNA genes and cis-acting RNA regulatory elements present functional motifs, conserved both in structure and sequence, that can be hardly detected by primary sequence analysis alone. We describe here how conserved secondary structure motifs shared by functionally related RNA sequences can be detected through the software tool RNAProfile. RNAProfile takes as input a set of unaligned RNA sequences expected to share a common motif, and outputs the regions that are most conserved throughout the sequences, according to a similarity measure that takes into account both the sequence of the regions and the secondary structure they can form according to base-pairing and thermodynamic rules. The method is split into two parts. First, it identifies candidate regions within the input sequences, and associates with each region a locally optimal secondary structure. Then, it compares candidate regions to one another, both at sequence and structure level, and builds motifs exploring the search space through a greedy heuristic. We provide a detailed guide to the different parameters that can be employed, and usage examples showing the different software capabilities. PMID:25577372

  17. Mechanical tuning of elastomers via peptide secondary structure

    NASA Astrophysics Data System (ADS)

    Wanasekara, Nandula; Johnson, J. Casey; Korley, Lashanda T. J.

    2014-03-01

    Nature utilizes an array of design tools for engineering materials with multiple functions and tunable mechanical properties. The precise control of hierarchical structure, self-assembly, and secondary structure is essential to achieve the desired properties in bio-inspired materials design. We have developed a series of peptidic-poyurea hybrids to determine the effects of peptide secondary structure and hydrogen bonding arrangement on morphology, thermal and mechanical properties. These materials were fabricated by incorporating peptide segments containing either poly(?-benzyl-L-aspartate) or poly(?-carbobenzyloxy-L-lysine) into non-chain extended polyureas to form either ?-sheets or ?-helix conformations based on peptide length. Infrared analysis proved the retention of peptide secondary structure when incorporated into peptidic-polyureas. The polymers containing ?-sheet forming peptide blocks exhibited higher modulus and toughness due to intermolecular H-bonding. Additionally, higher peptide weight fractions lead to higher plateau moduli due to a transition of continuous domain morphology from a soft segment continuous to a fibrous and interconnected stiffer peptide domain. All the polymers exhibited microphase separated morphology with nanofibrous or ribbon-like structures. It is observed that fiber aspect ratio and percolation were influenced by the peptide secondary structure and the weight fraction.

  18. THE KINK-TURN: A NEW RNA SECONDARY STRUCTURE MOTIF

    Microsoft Academic Search

    D. J. Klein; T. M. Schmeing; P. B. Moore; T. A. Steitz

    2001-01-01

    Abstract: IntroductionRNA molecules form complex structures containingA-form helices and non-helical regions that are oftendesignated as loops or bulges in secondary structurediagrams (Shen ## ##., 1995). These regions, however,form denite three-dimensional structures, and severalnon-A-form RNA structural motifs have been identied,including U-turns, S-turns, A-platforms and tetraloops(Hermann and Patel, 1999; Moore, 1999). The prevalenceof these motifs in RNA generally, and their association...

  19. Functional and Structural Analysis of the Internal Ribosome Entry Site Present in the mRNA of Natural Variants of the HIV-1

    PubMed Central

    Vallejos, Maricarmen; Carvajal, Felipe; Pino, Karla; Navarrete, Camilo; Ferres, Marcela; Huidobro-Toro, Juan Pablo; Sargueil, Bruno; López-Lastra, Marcelo

    2012-01-01

    The 5?untranslated regions (UTR) of the full length mRNA of the HIV-1 proviral clones pNL4.3 and pLAI, harbor an internal ribosomal entry site (IRES). In this study we extend this finding by demonstrating that the mRNA 5?UTRs of natural variants of HIV-1 also exhibit IRES-activity. Cap-independent translational activity was demonstrated using bicistronic mRNAs in HeLa cells and in Xenopus laevis oocytes. The possibility that expression of the downstream cistron in these constructs was due to alternative splicing or to cryptic promoter activity was ruled out. The HIV-1 variants exhibited significant 5?UTR nucleotide diversity with respect to the control sequence recovered from pNL4.3. Interestingly, translational activity from the 5?UTR of some of the HIV-1 variants was enhanced relative to that observed for the 5?UTR of pNL4.3. In an attempt to explain these findings we probed the secondary structure of the variant HIV-1 5?UTRs using enzymatic and chemical approaches. Yet subsequent structural analyses did not reveal significant variations when compared to the pNL4.3-5?UTR. Thus, the increased IRES-activity observed for some of the HIV-1 variants cannot be ascribed to a specific structural modification. A model to explain these findings is proposed. PMID:22496887

  20. Structural basis for specific recognition of multiple mRNA targets by a PUF regulatory protein

    SciTech Connect

    Wang, Yeming; Opperman, Laura; Wickens, Marvin; Tanaka Hall, Traci M.; (NIH); (UW)

    2010-08-19

    Caenorhabditis elegans fem-3 binding factor (FBF) is a founding member of the PUMILIO/FBF (PUF) family of mRNA regulatory proteins. It regulates multiple mRNAs critical for stem cell maintenance and germline development. Here, we report crystal structures of FBF in complex with 6 different 9-nt RNA sequences, including elements from 4 natural mRNAs. These structures reveal that FBF binds to conserved bases at positions 1-3 and 7-8. The key specificity determinant of FBF vs. other PUF proteins lies in positions 4-6. In FBF/RNA complexes, these bases stack directly with one another and turn away from the RNA-binding surface. A short region of FBF is sufficient to impart its unique specificity and lies directly opposite the flipped bases. We suggest that this region imposes a flattened curvature on the protein; hence, the requirement for the additional nucleotide. The principles of FBF/RNA recognition suggest a general mechanism by which PUF proteins recognize distinct families of RNAs yet exploit very nearly identical atomic contacts in doing so.

  1. 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 (?-helix, ?-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

  2. Structure formation and transient dynamics of secondary electromagnetic radiation

    E-print Network

    Structure formation and transient dynamics of secondary electromagnetic radiation related to HF and transient dynamics associated with ionospheric modification experiments. The interaction of a high frequency electromagnetic radiation. We study the initial stage of the formation of striations for pump frequen- cies near

  3. Prediction of RNA secondary structure including kissing hairpin motifs

    E-print Network

    Moeller, Ralf

    Prediction of RNA secondary structure including kissing hairpin motifs Corinna Theis, Stefan including kissing hairpin motifs. The new idea is to construct a kissing hairpin motif from an overlay's Principle of Optimality, and the kissing hairpin cannot simply be built from optimal pseudoknots. Our

  4. 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 (?-helix, ?-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

  5. Clustering to identify RNA conformations constrained by secondary structure.

    PubMed

    Sim, Adelene Y L; Levitt, Michael

    2011-03-01

    RNA often folds hierarchically, so that its sequence defines its secondary structure (helical base-paired regions connected by single-stranded junctions), which subsequently defines its tertiary fold. To preserve base-pairing and chain connectivity, the three-dimensional conformations that RNA can explore are strongly confined compared to when secondary structure constraints are not enforced. Using three examples, we studied how secondary structure confines and dictates an RNA's preferred conformations. We made use of Macromolecular Conformations by SYMbolic programming (MC-Sym) fragment assembly to generate RNA conformations constrained by secondary structure. Then, to understand the correlations between different helix placements and orientations, we robustly clustered all RNA conformations by employing unique methods to remove outliers and estimate the best number of conformational clusters. We observed that the preferred conformation (as judged by largest cluster size) for each type of RNA junction molecule tested is consistent with its biological function. Further, the improved quality of models in our pruned datasets facilitates subsequent discrimination using scoring functions based either on statistical analysis (knowledge based) or experimental data. PMID:21317361

  6. Asymptotics of Canonical and Saturated RNA Secondary Structures

    E-print Network

    Clote, Peter

    that no base pairs can be added without violating the definition of secondary structure (i.e. introducing of Biology, Boston College, Chestnut Hill, MA 02467, USA. Research partially supported by National Science is an arbitrary word, or sequence of characters drawn from , then |w| designate

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

    PubMed Central

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

    2007-01-01

    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

  8. Crystal structure of Dcp1p and its functional implications in mRNA decapping

    PubMed Central

    She, Meipei; Decker, Carolyn J; Sundramurthy, Kumar; Liu, Yuying; Chen, Nan; Parker, Roy; Song, Haiwei

    2007-01-01

    A major pathway of eukaryotic mRNA turnover begins with deadenylation, followed by decapping and 5??3? exonucleolytic degradation. A critical step in this pathway is decapping, which is carried out by an enzyme composed of Dcp1p and Dcp2p. The crystal structure of Dcp1p shows that it markedly resembles the EVH1 family of protein domains. Comparison of the proline-rich sequence (PRS)-binding sites in this family of proteins with Dcp1p indicates that it belongs to a novel class of EVH1 domains. Mapping of the sequence conservation on the molecular surface of Dcp1p reveals two prominent sites. One of these is required for the function of the Dcp1p-Dcp2p complex, and the other, corresponding to the PRS-binding site of EVH1 domains, is probably a binding site for decapping regulatory proteins. Moreover, a conserved hydrophobic patch is shown to be critical for decapping. PMID:14758354

  9. Secondary structure assignment that accurately reflects physical and evolutionary characteristics

    E-print Network

    2005-12-01

    development for disseminating the results of biomedical research in our lifetime." Sir Paul Nurse, Cancer Research UK Your research papers will be: available free of charge to the entire biomedical community peer reviewed and published immediately upon... evolutionary diversity: templates, key residues and structure prediction. Proc R Soc Lond B Biol Sci 1990, 241:132-145. 25. Cubellis MV, Caillez F, Blundell TL, Lovell SC: Properties of poly- proline II, a secondary structure element implicated in pro- tein...

  10. Protein structure prediction: assembly of secondary structure elements by basin-hopping.

    PubMed

    Hoffmann, Falk; Vancea, Ioan; Kamat, Sanjay G; Strodel, Birgit

    2014-10-20

    The prediction of protein tertiary structure from primary structure remains a challenging task. One possible approach to this problem is the application of basin-hopping global optimization combined with an all-atom force field. In this work, the efficiency of basin-hopping is improved by introducing an approach that derives tertiary structures from the secondary structure assignments of individual residues. This approach is termed secondary-to-tertiary basin-hopping and benchmarked for three miniproteins: trpzip, trp-cage and ER-10. For each of the three miniproteins, the secondary-to-tertiary basin-hopping approach successfully and reliably predicts their three-dimensional structure. When it is applied to larger proteins, correctly folded structures are obtained. It can be concluded that the assembly of secondary structure elements using basin-hopping is a promising tool for de novo protein structure prediction. PMID:25056272

  11. Molecular structure of the human argininosuccinate synthetase gene: Occurrence of alternative mRNA splicing

    SciTech Connect

    Freytag, S.O.; Beaudet, A.L.; Bock, H.G.O.; O'Brien, W.E.

    1984-10-01

    The human genome contains one expressed argininosuccinate synthetase gene and ca. 14 pseudogenes that are dispersed to at least 11 human chromosomes. Eleven clones isolated from a human genomic DNA library were characterized extensively by restriction mapping, Southern blotting, and nucleotide sequencing. These 11 clones represent the entire expressed argininosuccinate synthetase gene that spans 63 kilobases and contains at least 13 exons. The expressed gene codes for two mRNAs that differ in their 5' untranslated sequences and arise by alternative splicing involving the inclusion or deletion of an entire exon. In normal human liver and cultured fibroblasts, the predominant mature argininosuccinate synthetase mRNA lacks sequences encoded by exon 2 in the expressed gene. In contrast, the predominant argininosuccinate synthetase mRNA in baboon liver contains exon 2 sequences. A transformed canavanine-resistant human cell line in which argininosuccinate synthetase activity is 180-fold higher than that in wild-type cells contains abundant amounts of both forms of the argininosuccinate synthetase mRNA. The mRNA lacking exon 2 sequences is the more abundant mRNA species in the canavanine-resistant cells. These observations show that splicing of the argininosuccinate synthetase mRNA is species specific in primates and varies among different human cell types.

  12. Light can transform the secondary structure of silk protein

    NASA Astrophysics Data System (ADS)

    Tsuboi, Y.; Ikejiri, T.; Shiga, S.; Yamada, K.; Itaya, A.

    Fibroin is the main component of silk and is expected to be used as a novel functional material in medicine and bioelectronics. The main secondary structures of this protein are of the random-coil and the ?-sheet types. In this study, we carried out laser-induced transformation of the secondary structure, from the random-coil type to the ?-sheettype, in solid fibroin films. We prepared two types of fibroin films with the random-coil structure. One is a fibroin film doped with a dye as a photosensitizer with a small amount (1 wt%), and the other is a neat fibroin film. The former was excited at 532 nm and the latter was excited at 266 nm. Irradiations were carried out with fluences much lower than each ablation threshold. The excitation of the dye at 532 nm did not affect the secondary structure of the random-coil type. By contrast, 266-nm laser irradiation, which excites tryptophan (an amino-acid residue) involved in fibroin, created the ?-sheetdomain in the film. The structural transformation was revealed by infrared absorption spectroscopy and atomic force microscopy.

  13. Accelerating calculations of RNA secondary structure partition functions using GPUs

    PubMed Central

    2013-01-01

    Background RNA performs many diverse functions in the cell in addition to its role as a messenger of genetic information. These functions depend on its ability to fold to a unique three-dimensional structure determined by the sequence. The conformation of RNA is in part determined by its secondary structure, or the particular set of contacts between pairs of complementary bases. Prediction of the secondary structure of RNA from its sequence is therefore of great interest, but can be computationally expensive. In this work we accelerate computations of base-pair probababilities using parallel graphics processing units (GPUs). Results Calculation of the probabilities of base pairs in RNA secondary structures using nearest-neighbor standard free energy change parameters has been implemented using CUDA to run on hardware with multiprocessor GPUs. A modified set of recursions was introduced, which reduces memory usage by about 25%. GPUs are fastest in single precision, and for some hardware, restricted to single precision. This may introduce significant roundoff error. However, deviations in base-pair probabilities calculated using single precision were found to be negligible compared to those resulting from shifting the nearest-neighbor parameters by a random amount of magnitude similar to their experimental uncertainties. For large sequences running on our particular hardware, the GPU implementation reduces execution time by a factor of close to 60 compared with an optimized serial implementation, and by a factor of 116 compared with the original code. Conclusions Using GPUs can greatly accelerate computation of RNA secondary structure partition functions, allowing calculation of base-pair probabilities for large sequences in a reasonable amount of time, with a negligible compromise in accuracy due to working in single precision. The source code is integrated into the RNAstructure software package and available for download at http://rna.urmc.rochester.edu. PMID:24180434

  14. Random generation of RNA secondary structures according to native distributions

    PubMed Central

    2011-01-01

    Background Random biological sequences are a topic of great interest in genome analysis since, according to a powerful paradigm, they represent the background noise from which the actual biological information must differentiate. Accordingly, the generation of random sequences has been investigated for a long time. Similarly, random object of a more complicated structure like RNA molecules or proteins are of interest. Results In this article, we present a new general framework for deriving algorithms for the non-uniform random generation of combinatorial objects according to the encoding and probability distribution implied by a stochastic context-free grammar. Briefly, the framework extends on the well-known recursive method for (uniform) random generation and uses the popular framework of admissible specifications of combinatorial classes, introducing weighted combinatorial classes to allow for the non-uniform generation by means of unranking. This framework is used to derive an algorithm for the generation of RNA secondary structures of a given fixed size. We address the random generation of these structures according to a realistic distribution obtained from real-life data by using a very detailed context-free grammar (that models the class of RNA secondary structures by distinguishing between all known motifs in RNA structure). Compared to well-known sampling approaches used in several structure prediction tools (such as SFold) ours has two major advantages: Firstly, after a preprocessing step in time O(n2) for the computation of all weighted class sizes needed, with our approach a set of m random secondary structures of a given structure size n can be computed in worst-case time complexity Om?n? log(n) while other algorithms typically have a runtime in O(m?n2). Secondly, our approach works with integer arithmetic only which is faster and saves us from all the discomforting details of using floating point arithmetic with logarithmized probabilities. Conclusion A number of experimental results shows that our random generation method produces realistic output, at least with respect to the appearance of the different structural motifs. The algorithm is available as a webservice at http://wwwagak.cs.uni-kl.de/NonUniRandGen and can be used for generating random secondary structures of any specified RNA type. A link to download an implementation of our method (in Wolfram Mathematica) can be found there, too. PMID:21992500

  15. 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.

  16. The identification of recurrent tertiary motifs by interactions of protein secondary structure units

    E-print Network

    Hodges, Hamilton Courtney

    2013-02-22

    secondary structure units: alpha helices, beta strands, beta hairpins, and loops. We also identified three physical interactions between the secondary structure units: (1) hydrogen bonds were found by a continuous energy potential; (2) salt bridges were...

  17. RNA Secondary Structure Prediction Using High-throughput SHAPE

    PubMed Central

    Purzycka, Katarzyna J.; Rausch, Jason W.; Le Grice, Stuart F.J.

    2013-01-01

    Understanding the function of RNA involved in biological processes requires a thorough knowledge of RNA structure. Toward this end, the methodology dubbed "high-throughput selective 2' hydroxyl acylation analyzed by primer extension", or SHAPE, allows prediction of RNA secondary structure with single nucleotide resolution. This approach utilizes chemical probing agents that preferentially acylate single stranded or flexible regions of RNA in aqueous solution. Sites of chemical modification are detected by reverse transcription of the modified RNA, and the products of this reaction are fractionated by automated capillary electrophoresis (CE). Since reverse transcriptase pauses at those RNA nucleotides modified by the SHAPE reagents, the resulting cDNA library indirectly maps those ribonucleotides that are single stranded in the context of the folded RNA. Using ShapeFinder software, the electropherograms produced by automated CE are processed and converted into nucleotide reactivity tables that are themselves converted into pseudo-energy constraints used in the RNAStructure (v5.3) prediction algorithm. The two-dimensional RNA structures obtained by combining SHAPE probing with in silico RNA secondary structure prediction have been found to be far more accurate than structures obtained using either method alone. PMID:23748604

  18. HOTAIR forms an intricate and modular secondary structure.

    PubMed

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

    2015-04-16

    Long noncoding 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-nt-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

  19. Study of coal structure using secondary ion mass spectrometry

    SciTech Connect

    Tingey, G.L.; Lytle, J.M.; Baer, D.R.; Thomas, M.T.

    1980-12-01

    Secondary-ion Mass Spectrometry (SIMS) is examined as a tool for studying the chemical structure of coal. SIMS has potential for analysis of coal because of the following characteristics: sensitivity to chemical structure; high sensitivity to all masses; application to solids; excellent depth resolution; and reasonable spatial resolution. SIMS spectra of solid coals show differences with respect to coal rank, the spectra of high rank coal being similar to that of graphite, and the spectra of low rank coal being similar to that of wood. Some functional group analysis is also possible using SIMS. Low rank coals show a larger peak at 15 amu indicating more methyl groups than found in the higher rank coals. Fragments with two and three carbon atoms have also been examined; much larger fragments are undoubtedly present but were not evaluated in this study. Examination of these groups, which are expected to contain valuable information on coal structure, is planned for future work. It has been observed that mineral atoms present in the coal have large secondary ion yields which complicate the interpretation of the spectra. Studies on mineral-free coals and model compounds are therefore recommended to facilitate determination of organic coal structure. In addition, mass spectrometry with much greater mass resolution will aid in distinguishing between various ion species.

  20. Structure and expression of the human L-myc gene reveal a complex pattern of alternative mRNA processing

    SciTech Connect

    Kaye, F.; Battey, J.; Nau, M.; Brooks, B.; Seifter, E.; De Greve, J.; Birrer, M.; Sausville, E.; Minna, J.

    1988-01-01

    The authors' analyzed in detail the structure of the L-myc gene isolated from human placental DNA and characterized its expression in several small-cell lung cancer cell lines. The gene is composed of three exons and two introns spanning 6.6 kilobases in human DNA. Several distinct mRNA species are produced in all small-cell lung cancer cell lines that express L-myc. These transcripts are generated from a single gene by alternative splicing of introns 1 and 2 and by use of alternative polyadenylation signals. In some mRNAs that is a long open reading frame with a predicted translated protein of 364 residues. Amino acid sequence comparison with c-myc and N-myc demonstrated multiple discrete regions with extensive homology. In contrast, other mRNA transcripts, generated by alternative processing, could encode a truncated protein with a novel carboxy-terminal end.

  1. A semi-supervised learning approach for RNA secondary structure prediction.

    PubMed

    Yonemoto, Haruka; Asai, Kiyoshi; Hamada, Michiaki

    2015-08-01

    RNA secondary structure prediction is a key technology in RNA bioinformatics. Most algorithms for RNA secondary structure prediction use probabilistic models, in which the model parameters are trained with reliable RNA secondary structures. Because of the difficulty of determining RNA secondary structures by experimental procedures, such as NMR or X-ray crystal structural analyses, there are still many RNA sequences that could be useful for training whose secondary structures have not been experimentally determined. In this paper, we introduce a novel semi-supervised learning approach for training parameters in a probabilistic model of RNA secondary structures in which we employ not only RNA sequences with annotated secondary structures but also ones with unknown secondary structures. Our model is based on a hybrid of generative (stochastic context-free grammars) and discriminative models (conditional random fields) that has been successfully applied to natural language processing. Computational experiments indicate that the accuracy of secondary structure prediction is improved by incorporating RNA sequences with unknown secondary structures into training. To our knowledge, this is the first study of a semi-supervised learning approach for RNA secondary structure prediction. This technique will be useful when the number of reliable structures is limited. PMID:25748534

  2. RNA secondary structures of the bacteriophage phi6 packaging regions.

    PubMed Central

    Pirttimaa, M J; Bamford, D H

    2000-01-01

    Bacteriophage phi6 genome consists of three segments of double-stranded RNA. During maturation, single-stranded copies of these segments are packaged into preformed polymerase complex particles. Only phi6 RNA is packaged, and each particle contains only one copy of each segment. An in vitro packaging and replication assay has been developed for phi6, and the packaging signals (pac sites) have been mapped to the 5' ends of the RNA segments. In this study, we propose secondary structure models for the pac sites of phi6 single-stranded RNA segments. Our models accommodate data from structure-specific chemical modifications, free energy minimizations, and phylogenetic comparisons. Previously reported pac site deletion studies are also discussed. Each pac site possesses a unique architecture, that, however, contains common structural elements. PMID:10864045

  3. RNA CoSSMos: Characterization of Secondary Structure Motifs—a searchable database of secondary structure motifs in RNA three-dimensional structures

    PubMed Central

    Vanegas, Pamela L.; Hudson, Graham A.; Davis, Amber R.; Kelly, Shannon C.; Kirkpatrick, Charles C.; Znosko, Brent M.

    2012-01-01

    RNA secondary structure is important for designing therapeutics, understanding protein–RNA binding and predicting tertiary structure of RNA. Several databases and downloadable programs exist that specialize in the three-dimensional (3D) structure of RNA, but none focus specifically on secondary structural motifs such as internal, bulge and hairpin loops. The RNA Characterization of Secondary Structure Motifs (RNA CoSSMos) database is a freely accessible and searchable online database and website of 3D characteristics of secondary structure motifs. To create the RNA CoSSMos database, 2156 Protein Data Bank (PDB) files were searched for internal, bulge and hairpin loops, and each loop's structural information, including sugar pucker, glycosidic linkage, hydrogen bonding patterns and stacking interactions, was included in the database. False positives were defined, identified and reclassified or omitted from the database to ensure the most accurate results possible. Users can search via general PDB information, experimental parameters, sequence and specific motif and by specific structural parameters in the subquery page after the initial search. Returned results for each search can be viewed individually or a complete set can be downloaded into a spreadsheet to allow for easy comparison. The RNA CoSSMos database is automatically updated weekly and is available at http://cossmos.slu.edu. PMID:22127861

  4. RNA CoSSMos: Characterization of Secondary Structure Motifs--a searchable database of secondary structure motifs in RNA three-dimensional structures.

    PubMed

    Vanegas, Pamela L; Hudson, Graham A; Davis, Amber R; Kelly, Shannon C; Kirkpatrick, Charles C; Znosko, Brent M

    2012-01-01

    RNA secondary structure is important for designing therapeutics, understanding protein-RNA binding and predicting tertiary structure of RNA. Several databases and downloadable programs exist that specialize in the three-dimensional (3D) structure of RNA, but none focus specifically on secondary structural motifs such as internal, bulge and hairpin loops. The RNA Characterization of Secondary Structure Motifs (RNA CoSSMos) database is a freely accessible and searchable online database and website of 3D characteristics of secondary structure motifs. To create the RNA CoSSMos database, 2156 Protein Data Bank (PDB) files were searched for internal, bulge and hairpin loops, and each loop's structural information, including sugar pucker, glycosidic linkage, hydrogen bonding patterns and stacking interactions, was included in the database. False positives were defined, identified and reclassified or omitted from the database to ensure the most accurate results possible. Users can search via general PDB information, experimental parameters, sequence and specific motif and by specific structural parameters in the subquery page after the initial search. Returned results for each search can be viewed individually or a complete set can be downloaded into a spreadsheet to allow for easy comparison. The RNA CoSSMos database is automatically updated weekly and is available at http://cossmos.slu.edu. PMID:22127861

  5. DNA secondary structures: stability and function of G-quadruplex structures

    PubMed Central

    Bochman, Matthew L.; Paeschke, Katrin; Zakian, Virginia A.

    2013-01-01

    In addition to the canonical double helix, DNA can fold into various other inter- and intramolecular secondary structures. Although many such structures were long thought to be in vitro artefacts, bioinformatics demonstrates that DNA sequences capable of forming these structures are conserved throughout evolution, suggesting the existence of non-B-form DNA in vivo. In addition, genes whose products promote formation or resolution of these structures are found in diverse organisms, and a growing body of work suggests that the resolution of DNA secondary structures is critical for genome integrity. This Review focuses on emerging evidence relating to the characteristics of G-quadruplex structures and the possible influence of such structures on genomic stability and cellular processes, such as transcription. PMID:23032257

  6. PROTEIN FOLD RECOGNITION USING RESIDUE-BASED ALIGNMENTS OF SEQUENCE AND SECONDARY STRUCTURE

    E-print Network

    Erdogan, Hakan

    PROTEIN FOLD RECOGNITION USING RESIDUE-BASED ALIGNMENTS OF SEQUENCE AND SECONDARY STRUCTURE Zafer)ece.gatech.edu ABSTRACT Protein structure prediction aims to determine the three-dimensional structure of proteins form methods [3,4]. Index Terms- protein fold recognition, secondary structure alignment, amino acid alignment

  7. 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 ?-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 ?-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

  8. Structure of $^{13}$Be probed via secondary beam reactions

    E-print Network

    Randisi, G; Falou, H Al; 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; Brennand, E de Góes; Haigh, P; Hanappe, F; Harlin, C; Laurent, B; Lecouey, J -L; Ninane, A; Patterson, N; Price, D; Stuttgé, L; Thomas, J S

    2013-01-01

    The low-lying level structure of the unbound neutron-rich nucleus $^{13}$Be has been investigated via breakup on a carbon target of secondary beams of $^{14,15}$B at 35 MeV/nucleon. The coincident detection of the beam velocity $^{12}$Be fragments and neutrons permitted the invariant mass of the $^{12}$Be+$n$ and $^{12}$Be+$n$+$n$ systems to be reconstructed. In the case of the breakup of $^{15}$B, a very narrow structure at threshold was observed in the $^{12}$Be+$n$ channel. Contrary to earlier stable beam fragmentation studies which identified this as a strongly interacting $s$-wave virtual state in $^{13}$Be, analysis here of the $^{12}$Be+$n$+$n$ events demonstrated that this was an artifact resulting from the sequential-decay of the $^{14}$Be(2$^+$) state. Single-proton removal from $^{14}$B was found to populate a broad low-lying structure some 0.70 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 ...

  9. DM-pred Method: A New Method to Predict Secondary Structures Based on Data Mining Techniques

    Microsoft Academic Search

    Sondes Fayech; Nadia Essoussi; Mohamed Limam

    2011-01-01

    Protein secondary structure prediction is a key step in prediction of protein tertiary structure. There have emerged many methods based on machine learning techniques, such as neural networks (NN) and support vector machines (SVM), to focus on the prediction of the secondary structures. In this paper a new method, DM-pred, was proposed based on a protein clustering method to detect

  10. Computational analysis of conserved RNA secondary structure in transcriptomes and genomes

    E-print Network

    Eddy, Sean

    Computational analysis of conserved RNA secondary structure in transcriptomes and genomes Sean R RNA secondary structure. An interesting new front is the application of chemical and enzymatic RNA structure probing experiments on a transcriptome-wide scale. I review several proposed approaches

  11. Predicting the secondary structure of globular proteins using neural network models

    Microsoft Academic Search

    Ning Qian; Terrence J. Sejnowski

    1988-01-01

    We present a new method for predicting the secondary structure of globular proteins based on non-linear neural network models. Network models learn from existing protein structures how to predict the secondary structure of local sequences of amino acids. The average success rate of our method on a testing set of proteins non-homologous with the corresponding training set was 643% on

  12. The sequence and secondary structure of the 3'-UTR affect 3'-end maturation, RNA accumulation, and translation in tobacco chloroplasts.

    PubMed

    Monde, R A; Greene, J C; Stern, D B

    2000-11-01

    RNA maturation and modulation of RNA stability play important roles in chloroplast gene expression. In vitro and in vivo studies have shown that both the 5'- and 3'-untranslated regions (UTRs) contain sequence and structural elements that guide these processes, and interact with specific proteins. We have previously characterized the spinach chloroplast petD 3'-UTR in detail by in vitro approaches. This stem-loop forming sequence is a weak terminator but is required for RNA maturation and also exhibits sequence-specific protein binding. To test petD 3'-UTR function in vivo, tobacco chloroplast transformants were generated containing uidA reporter genes flanked by variants of the petD 3'-UTR, including one which does not form an RNA-protein complex in vitro, and one which lacks a stem-loop structure. Analysis of uidA mRNA indicated that a stable secondary structure is required to accumulate a discrete mRNA, and that changes in the 3'-UTR sequence which affect protein binding in vitro can also affect RNA metabolism in vivo. The 3'-UTR also influenced beta-glucuronidase protein accumulation, but not in proportion to RNA levels. These results raise the possibility that in tobacco chloroplasts, the 3'-UTR may influence translational yield. PMID:11197327

  13. Gene structure, chromosomal location, and basis for alternative mRNA splicing of the human VCAM1 gene

    SciTech Connect

    Cybulsky, M.I.; Fries, J.W.U.; Williams, A.J.; Sultan, P.; Gimbrone, M.A. Jr.; Collins, T. (Harvard Medical School, Boston, MA (United States)); Eddy, R.; Byers, M.; Shows, T. (Roswell Park Memorial Inst., Buffalo, NY (United States))

    1991-09-01

    Vascular cell adhesion molecule 1 (VCAM-1) is a cell surface glycoprotein adhesive for certain blood leukocytes and tumor cells, which is expressed by activated endothelium in a variety of pathologic conditions including atherosclerosis. Genomic clones encoding the VCAM1 gene were isolated and the organization of the gene was determined. The gene, which is present in a single copy in the human genome, contains 9 exons spanning {approx}25 kilobases of DNA. Exons 2-8 contain C2 or H-type immunoglobulin domains. At least two different VCAM-1 precursors can be generated from the human gene as a result of alternative mRNA splicing events, which include or exclude exon 5. A consensus TATAA element is located upstream of the transcriptional start site. The VCAM1 promoter contains consensus binding sites for NF-{kappa}B, the GATA family of transcription factors, as well as an AP1 site. The VCAM1 gene was assigned to the 1p31-32 region of chromosome 1 based on the analysis of human-mouse hybrid cell lines and in situ hybridization. Structural analysis of the human VCAM1 gene provides the basis for alternative mRNA splicing and an initial approach to elucidating the regulation of VCAM-1 expression.

  14. Protein 8-class secondary structure prediction using conditional neural fields.

    PubMed

    Wang, Zhiyong; Zhao, Feng; Peng, Jian; Xu, Jinbo

    2011-10-01

    Compared with the protein 3-class secondary structure (SS) prediction, the 8-class prediction gains less attention and is also much more challenging, especially for proteins with few sequence homologs. This paper presents a new probabilistic method for 8-class SS prediction using conditional neural fields (CNFs), a recently invented probabilistic graphical model. This CNF method not only models the complex relationship between sequence features and SS, but also exploits the interdependency among SS types of adjacent residues. In addition to sequence profiles, our method also makes use of non-evolutionary information for SS prediction. Tested on the CB513 and RS126 data sets, our method achieves Q8 accuracy of 64.9 and 64.7%, respectively, which are much better than the SSpro8 web server (51.0 and 48.0%, respectively). Our method can also be used to predict other structure properties (e.g. solvent accessibility) of a protein or the SS of RNA. PMID:21805636

  15. Secretin: structure of the precursor and tissue distribution of the mRNA.

    PubMed Central

    Kopin, A S; Wheeler, M B; Leiter, A B

    1990-01-01

    Secretin is a 27-amino acid gastrointestinal hormone that stimulates the secretion of bicarbonate-rich pancreatic fluid. The unusually high number of serine, leucine, and arginine residues in secretin has precluded the use of oligonucleotides to screen cDNA libraries to isolate a secretin cDNA. In the present study, a short cDNA encoding porcine secretin was amplified from duodenal mucosal first-strand cDNA template by using 16,384- and 4096-fold degenerate primers in the DNA polymerase chain reaction. From the sequence of the amplified cDNA, an unambiguous oligonucleotide probe was designed to screen a cDNA library. Here we report the sequences of cDNAs encoding the porcine and rat secretin precursors. The predicted amino acid sequences reveal that each precursor consists of a signal peptide, an N-terminal peptide, secretin, and a 72-amino acid C-terminal peptide. Secretin has been highly conserved through evolution. Rat secretin differs from its porcine counterpart by a single glutamine-for-arginine substitution at position 14. In contrast, the amino acid sequences of the C-terminal peptides are only 39% conserved between the two species, suggesting that the C-terminal peptide does not have an essential physiologic function. RNA blot hybridizations reveal that the rat secretin gene is expressed throughout the small intestine. Although secretin immunoreactivity has been localized in the central nervous system by some laboratories, we are unable to detect secretin mRNA in tissues of the central nervous system by Northern blot hybridization. Images PMID:2315322

  16. Structurally Coloured Secondary Particles Composed of Black and White Colloidal Particles

    PubMed Central

    Takeoka, Yukikazu; Yoshioka, Shinya; Teshima, Midori; Takano, Atsushi; Harun-Ur-Rashid, Mohammad; Seki, Takahiro

    2013-01-01

    This study investigated the colourful secondary particles formed by controlling the aggregation states of colloidal silica particles and the enhancement of the structural colouration of the secondary particles caused by adding black particles. We obtained glossy, partially structurally coloured secondary particles in the absence of NaCl, but matte, whitish secondary particles were obtained in the presence of NaCl. When a small amount of carbon black was incorporated into both types of secondary particles, the incoherent multiple scattering of light from the amorphous region was considerably reduced. However, the peak intensities in the reflection spectra, caused by Bragg reflection and by coherent single wavelength scattering, were only slightly decreased. Consequently, a brighter structural colour of these secondary particles was observed with the naked eye. Furthermore, when magnetite was added as a black particle, the coloured secondary particles could be moved and collected by applying an external magnetic field. PMID:23917891

  17. Modification of secondary head-forming activity of microinjected ??-catenin mRNA by co-injected spermine and spermidine in Xenopus early embryos

    Microsoft Academic Search

    Takamichi Mishina; Kota Fuchimukai; Kazuei Igarashi; Kosuke Tashiro; Koichiro Shiokawa

    Polyamines are essential for cell growth and differentiation. In Xenopus early embryos, per embryo level of spermine is extremely low as compared with that of spermidine. To disclose the possible\\u000a function of polyamines in Xenopus early embryos, we tested the effect of co-injection of spermine and spermidine on the functioning of exogenously microinjected\\u000a in vitro-synthesized, ??-catenin mRNA which is known

  18. Quantitation of the global secondary structure of globular proteins by FTIR spectroscopy: Comparison with X-ray crystallographic structure

    Microsoft Academic Search

    Thomas F. Kumosinski; Joseph J. Unruh

    1996-01-01

    Fourier transform infrared spectroscopy (FTIR) is potentially a powerful tool for determining the global secondary structure of proteins in solution, providing the spectra are analyzed using a statistically and theoretically justified methodology. We have performed FTIR experiments on 14 globular proteins and two synthetic polypeptides whose X-ray crystal structures are known to exhibit varying types and amounts of secondary structures.

  19. Boundary Layer Dynamical Structure During Secondary Eyewall Formation

    NASA Astrophysics Data System (ADS)

    Abarca, S. F.; Montgomery, M. T.; McWilliams, J. C.

    2014-12-01

    Secondary eyewall formation (SEF) is widely recognized as an important research problem in the dynamics of mature tropical cyclones. It has been shown that the development of the wind maxima in SEF occurs within the boundary layer and that it follows a chain of events initiated by a substantial radial expansion of the tangential wind field. In this context, there is not yet a consensus on the phenomenon's essential physics. It has been proposed that the boundary-layer dynamics of a maturing hurricane vortex is an important controlling element in SEF. However, recent literature also argues that hurricane boundary layers and the related coupling with the interior flow can be described through an Ekman-like balance and that shock-like structures are relevant in the swirling boundary layer of the inner core of mature storms. We analyze the radial and vertical structure of the specific forces and accelerations in in the boundary layer in a mature hurricane that includes a canonical eyewall replacement cycle. The case occurred in a mesoscale, convection-permitting numerical simulation of a tropical cyclone, integrated from an initial weak mesoscale vortex in an idealized quiescent environment. The simulation has been studied extensively in the literature. We find that momentum advection is almost everywhere important (some of it is associated with asymmetric eddies). We discuss the implication of our findings on the proposed importance of Ekman-like balance dynamics during SEF. Finally, our analysis does not support the recently proposed idea that the radial advection of radial momentum, and shock-like structures, are closely related to the supergradient wind phenomena observed during SEF.

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

    PubMed Central

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

    2015-01-01

    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, ?-strand and coil), CSI 3.0 now identifies total of 11 types of secondary and super-secondary structures, including helices, ?-strands, coil regions, five common ?-turns (type I, II, I?, II? and VIII), ? hairpins as well as interior and edge ?-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

  1. 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, ?-strand and coil), CSI 3.0 now identifies total of 11 types of secondary and super-secondary structures, including helices, ?-strands, coil regions, five common ?-turns (type I, II, I', II' and VIII), ? hairpins as well as interior and edge ?-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

  2. The secondary structure of ribosomal ribonucleic acid in solution

    PubMed Central

    Cox, R. A.

    1966-01-01

    1. The u.v.-absorption spectrum of ribosomal RNA from rabbit reticulocytes was studied as a function of temperature at different pH values. The changes in the spectrum over the range 220–320m? were interpreted on the basis of the assumption that the effect of denaturation and ionization are additive. The results suggest that in neutral salt solutions the secondary structure of the ribosomal RNA samples studied is due to two species of helical segments stabilized principally, if not solely, by complementary base pairs but differing in nucleotide composition: each species appears to be heterogeneous in other respects in view of the breadth of the melting ranges. 2. The number of base pairs per helical segment was estimated to be small (between 4 and 17) on the basis of the relation between melting temperature and chain length previously established by Lipsett and others for model compounds. Small fragments (about 2s) obtained by alkaline hydrolysis appeared to form the same helical segments as the intact molecule in accord with the estimated size of these segments. 3. Specific nucleotide sequences appear necessary to account for the hysteresis observed on titrating ribosomal RNA with acid or alkali within the range pH3·0–7·0 since this phenomenon was less pronounced for Escherichia coli transfer RNA and for RNA from turnip yellow-mosaic virus. PMID:5330109

  3. Avocado sunblotch viroid: primary sequence and proposed secondary structure.

    PubMed

    Symons, R H

    1981-12-11

    The sequence of the 247 nucleotide residues of the single strand circular RNA of avocado sunblotch viroid (ASBV) was determined using partial enzymic cleavage methods on overlapping viroid fragments obtained by partial ribonuclease digestion followed by 32p-labelling in vitro at their 5'-ends. ASBV is much smaller than potato spindle tuber viroid (PSTV; 359 residues) and chrysanthemum stunt viroid (CSV; 356 residues). A secondary structure model for ASBV is proposed and contains 67% of its residues base paired. In contrast to the extensive (69%) sequence homology of CSV with PSTV, only 18% of the ASBV sequence is homologous to PSTV and CSV. There are eight potential polypeptide translation products with chain lengths from 4 to 63 amino acid residues coded for by the plus (infectious) strand and four potential translation products (2 to 60 residues) coded for by the minus strand. An improved method is described for the synthesis of gamma-32p-ATP of high specific activity. PMID:7322921

  4. Secondary structure effects on DNA hybridization kinetics: a solution versus surface comparison

    Microsoft Academic Search

    Yang Gao; Lauren K. Wolf; Rosina M. Georgiadis

    2006-01-01

    The hybridization kinetics for a series of designed 25mer probetarget pairs having varying degrees of secondary structure have been measured by UV absorbance and surface plasmon resonance (SPR) spectroscopy in solution and on the surface, res- pectively. Kinetic rate constants derived from the resultant data decrease with increasing probe and target secondary structure similarly in both solution and surface environments.

  5. PROTEIN SECONDARY STRUCTURE PREDICTION BASED ON THE AMINO ACIDS CONFORMATIONAL CLASSIFICATION AND NEURAL NETWORK TECHNIQUE

    E-print Network

    Hefei Institute of Intelligent Machines

    PROTEIN SECONDARY STRUCTURE PREDICTION BASED ON THE AMINO ACIDS CONFORMATIONAL CLASSIFICATION@iim.ac.cn ABSTRACT In this paper, based on the 340 protein sequences and their corresponding secondary structures got from the Protein Data Bank (PDB), we group the 20 different amino acids into f (Former), b (Breaker

  6. HMMs and secondary structure (OSU) Using Hidden Markov Models to Recognize Protein Folds

    E-print Network

    Karplus, Kevin

    HMMs and secondary structure (OSU) Using Hidden Markov Models to Recognize Protein Folds Kevin affecting the ratio. 7 #12;Standard Null Model ¯ Null model is a zero-order Markov model, that is, each statistical modeling) ¯ SAM-T99 and SAM-T2K methods ¯ Multi-track HMMs and secondary structure ¯ Reverse

  7. Secondary RNA structure and nucleotide specificity contribute to internal initiation mediated by the human tau 5? leader

    PubMed Central

    Veo, Bethany L.; Krushel, Leslie A.

    2012-01-01

    Mechanisms by which eukaryotic internal ribosomal entry sites (IRESs) initiate translation have not been well described. Viral IRESs utilize a combination of secondary/tertiary structure concomitant with sequence specific elements to initiate translation. Eukaryotic IRESs are proposed to utilize the same components, although it appears that short sequence specific elements are more common. In this report we perform an extensive analysis of the IRES in the human tau mRNA. We demonstrate that the tau IRES exhibits characteristics similar to viral IRESs. It contains two main structural domains that exhibit secondary interactions, which are essential for internal initiation. Moreover, the tau IRES is extremely sensitive to small nucleotide substitutions. Our data also indicates that the 40S ribosome is recruited to the middle of the IRES, but whether it scans to the initiation codon in a linear fashion is questioned. Overall, these results identify structural and sequence elements critical for tau IRES activity and consequently, provide a novel target to regulate tau protein expression in disease states including Alzheimer disease and other tauopathies. PMID:22995835

  8. Dimeric Structure of a Human Apolipoprotein B mRNA Editing Protein and Cloning and Chromosomal Localization of Its Gene

    Microsoft Academic Search

    Paul P. Lau; Hui-Jia Zhu; Antonio Baldini; Chutaporn Charnsangavej; Lawrence Chan

    1994-01-01

    Apolipoprotein B (apoB) mRNA editing consists of a posttranscriptional C --> U conversion involving the first base of the codon CAA encoding glutamine-2153 to UAA, a stop codon, in apoB mRNA. Using a cloned rat cDNA as a probe, we cloned the cDNA and genomic sequences of the gene for a human apoB mRNA editing protein. Expression of the cDNA

  9. Mechanisms of Lin28-mediated miRNA and mRNA regulation--a structural and functional perspective.

    PubMed

    Mayr, Florian; Heinemann, Udo

    2013-01-01

    Lin28 is an essential RNA-binding protein that is ubiquitously expressed in embryonic stem cells. Its physiological function has been linked to the regulation of differentiation, development, and oncogenesis as well as glucose metabolism. Lin28 mediates these pleiotropic functions by inhibiting let-7 miRNA biogenesis and by modulating the translation of target mRNAs. Both activities strongly depend on Lin28's RNA-binding domains (RBDs), an N-terminal cold-shock domain (CSD) and a C-terminal Zn-knuckle domain (ZKD). Recent biochemical and structural studies revealed the mechanisms of how Lin28 controls let-7 biogenesis. Lin28 binds to the terminal loop of pri- and pre-let-7 miRNA and represses their processing by Drosha and Dicer. Several biochemical and structural studies showed that the specificity of this interaction is mainly mediated by the ZKD with a conserved GGAGA or GGAGA-like motif. Further RNA crosslinking and immunoprecipitation coupled to high-throughput sequencing (CLIP-seq) studies confirmed this binding motif and uncovered a large number of new mRNA binding sites. Here we review exciting recent progress in our understanding of how Lin28 binds structurally diverse RNAs and fulfills its pleiotropic functions. PMID:23939427

  10. Does lack of secondary structure imply intrinsic disorder in proteins? A sequence analysis.

    PubMed

    Rani, Pooja; Baruah, Anupaul; Biswas, Parbati

    2014-10-01

    Intrinsically disordered proteins (IDPs)/protein regions (IDPRs) lack unique three-dimensional structure at the level of secondary and/or tertiary structure and are represented as an ensemble of interchanging conformations. To investigate the role of presence/absence of secondary structures in promoting intrinsic disorder in proteins, a comparative sequence analysis of IDPs, IDPRs and proteins with minimal secondary structures (less than 5%) is required. A sequence analysis reveals proteins with minimal secondary structure content have high mean net positive charge, low mean net hydrophobicity and low sequence complexity. Interestingly, analysis of the relative local electrostatic interactions reveal that an increase in the relative repulsive interactions between amino acids separated by three or four residues lead to either loss of secondary structure or intrinsic disorder. IDPRs show increase in both local negative-negative and positive-positive repulsive interactions. While IDPs show a marked increase in the local negative-negative interactions, proteins with minimal secondary structure depict an increase in the local positive-positive interactions. IDPs and IDPRs are enriched in D, E and Q residues, while proteins with minimal secondary structure are depleted of these residues. Proteins with minimal secondary structures have higher content of G and C, while IDPs and IDPRs are depleted of these residues. These results confirm that proteins with minimal secondary structure have a distinctly different propensity for charge, hydrophobicity, specific amino acids and local electrostatic interactions as compared to IDPs/IDPRs. Thus we conclude that lack of secondary structure may be a necessary but not a sufficient condition for intrinsic disorder in proteins. PMID:25110178

  11. Structure-based energetics of mRNA decoding on the ribosome.

    PubMed

    Satpati, Priyadarshi; Sund, Johan; Aqvist, Johan

    2014-03-18

    The origin of high fidelity in bacterial protein synthesis on the ribosome remains a fundamental unsolved problem despite available three-dimensional structures of different stages of the translation process. However, these structures open up the possibility of directly computing the energetics of tRNA selection that is required for an authentic understanding of fidelity in decoding. Here, we report extensive computer simulations that allow us to quantitatively calculate tRNA discrimination and uncover the energetics underlying accuracy in code translation. We show that the tRNA-mRNA interaction energetics varies drastically along the path from initial selection to peptide bond formation. While the selection process is obviously controlled by kinetics, the underlying thermodynamics explains the origin of the high degree of accuracy. The existence of both low- and high-selectivity states provides an efficient mechanism for initial selection and proofreading that does not require codon-dependent long-range structural signaling within the ribosome. It is instead the distinctly unequal population of the high-selectivity states for cognate and noncognate substrates that is the key discriminatory factor. The simulations reveal the essential roles played both by the 30S subunit conformational switch and by the common tRNA modification at position 37 in amplifying the accuracy. PMID:24564511

  12. Phytoene Desaturase Is Localized Exclusively in the Chloroplast and Up-Regulated at the mRNA Level during Accumulation of Secondary Carotenoids in Haematococcus pluvialis (Volvocales, Chlorophyceae)

    Microsoft Academic Search

    Kay Grunewald; Manfred Eckert; Joseph Hirschberg; Christoph Hagen

    2000-01-01

    The unicellular green alga Haematococcus pluvialis Flotow is known for its massive accumulation of ketocarotenoids under var- ious stress conditions. Therefore, this microalga is one of the fa- vored organisms for biotechnological production of these antioxi- dative compounds. Astaxanthin makes up the main part of the secondary carotenoids and is accumulated mostly in an esterified form in extraplastidic lipid vesicles.

  13. Destabilization of Interleukin-6 mRNA Requires a Putative RNA Stem-Loop Structure, an AU-Rich Element, and the RNA-Binding Protein AUF1?

    PubMed Central

    Paschoud, Serge; Dogar, Afzal M.; Kuntz, Catherine; Grisoni-Neupert, Barbara; Richman, Larry; Kühn, Lukas C.

    2006-01-01

    Interleukin-6 mRNA is unstable and degraded with a half-life of 30 min. Instability determinants can entirely be attributed to the 3? untranslated region. By grafting segments of this region to stable green fluorescent protein mRNA and subsequent scanning mutagenesis, we have identified two conserved elements, which together account for most of the instability. The first corresponds to a short noncanonical AU-rich element. The other, 80 nucleotides further 5?, comprises a sequence predicted to form a stem-loop structure. Neither element alone was sufficient to confer full instability, suggesting that they might cooperate. Overexpression of myc-tagged AUF1 p37 and p42 isoforms as well as suppression of endogenous AUF1 by RNA interference stabilized interleukin-6 mRNA. Both effects required the AU-rich instability element. Similarly, the proteasome inhibitor MG132 stabilized interleukin-6 mRNA probably through an increase of AUF1 levels. The mRNA coimmunoprecipitated specifically with myc-tagged AUF1 p37 and p42 in cell extracts but only when the AU-rich instability element was present. These results indicate that AUF1 binds to the AU-rich element in vivo and promotes IL-6 mRNA degradation. PMID:16954375

  14. Characterization of a Trifunctional Mimivirus mRNA Capping Enzyme and Crystal Structure of the RNA Triphosphatase Domain

    SciTech Connect

    Benarroch,D.; Smith, P.; Shuman, S.

    2008-01-01

    The RNA triphosphatase (RTPase) components of the mRNA capping apparatus are a bellwether of eukaryal taxonomy. Fungal and protozoal RTPases belong to the triphosphate tunnel metalloenzyme (TTM) family, exemplified by yeast Cet1. Several large DNA viruses encode metal-dependent RTPases unrelated to the cysteinyl-phosphatase RTPases of their metazoan host organisms. The origins of DNA virus RTPases are unclear because they are structurally uncharacterized. Mimivirus, a giant virus of amoeba, resembles poxviruses in having a trifunctional capping enzyme composed of a metal-dependent RTPase module fused to guanylyltransferase (GTase) and guanine-N7 methyltransferase domains. The crystal structure of mimivirus RTPase reveals a minimized tunnel fold and an active site strikingly similar to that of Cet1. Unlike homodimeric fungal RTPases, mimivirus RTPase is a monomer. The mimivirus TTM-type RTPase-GTase fusion resembles the capping enzymes of amoebae, providing evidence that the ancestral large DNA virus acquired its capping enzyme from a unicellular host.

  15. A predictive model for secondary RNA structure using graph theory and a neural network

    PubMed Central

    2010-01-01

    Background Determining the secondary structure of RNA from the primary structure is a challenging computational problem. A number of algorithms have been developed to predict the secondary structure from the primary structure. It is agreed that there is still room for improvement in each of these approaches. In this work we build a predictive model for secondary RNA structure using a graph-theoretic tree representation of secondary RNA structure. We model the bonding of two RNA secondary structures to form a larger secondary structure with a graph operation we call merge. We consider all combinatorial possibilities using all possible tree inputs, both those that are RNA-like in structure and those that are not. The resulting data from each tree merge operation is represented by a vector. We use these vectors as input values for a neural network and train the network to recognize a tree as RNA-like or not, based on the merge data vector. The network estimates the probability of a tree being RNA-like. Results The network correctly assigned a high probability of RNA-likeness to trees previously identified as RNA-like and a low probability of RNA-likeness to those classified as not RNA-like. We then used the neural network to predict the RNA-likeness of the unclassified trees. Conclusions There are a number of secondary RNA structure prediction algorithms available online. These programs are based on finding the secondary structure with the lowest total free energy. In this work, we create a predictive tool for secondary RNA structures using graph-theoretic values as input for a neural network. The use of a graph operation to theoretically describe the bonding of secondary RNA is novel and is an entirely different approach to the prediction of secondary RNA structures. Our method correctly predicted trees to be RNA-like or not RNA-like for all known cases. In addition, our results convey a measure of likelihood that a tree is RNA-like or not RNA-like. Given that the majority of secondary RNA folding algorithms return more than one possible outcome, our method provides a means of determining the best or most likely structures among all of the possible outcomes. PMID:20946605

  16. R-chie: a web server and R package for visualizing RNA secondary structures

    PubMed Central

    Lai, Daniel; Proctor, Jeff R.; Zhu, Jing Yun A.; Meyer, Irmtraud M.

    2012-01-01

    Visually examining RNA structures can greatly aid in understanding their potential functional roles and in evaluating the performance of structure prediction algorithms. As many functional roles of RNA structures can already be studied given the secondary structure of the RNA, various methods have been devised for visualizing RNA secondary structures. Most of these methods depict a given RNA secondary structure as a planar graph consisting of base-paired stems interconnected by roundish loops. In this article, we present an alternative method of depicting RNA secondary structure as arc diagrams. This is well suited for structures that are difficult or impossible to represent as planar stem-loop diagrams. Arc diagrams can intuitively display pseudo-knotted structures, as well as transient and alternative structural features. In addition, they facilitate the comparison of known and predicted RNA secondary structures. An added benefit is that structure information can be displayed in conjunction with a corresponding multiple sequence alignments, thereby highlighting structure and primary sequence conservation and variation. We have implemented the visualization algorithm as a web server R-chie as well as a corresponding R package called R4RNA, which allows users to run the software locally and across a range of common operating systems. PMID:22434875

  17. 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…

  18. Testing Mediation Using Multiple Regression and Structural Equation Modeling Analyses in Secondary Data

    ERIC Educational Resources Information Center

    Li, Spencer D.

    2011-01-01

    Mediation analysis in child and adolescent development research is possible using large secondary data sets. This article provides an overview of two statistical methods commonly used to test mediated effects in secondary analysis: multiple regression and structural equation modeling (SEM). Two empirical studies are presented to illustrate the…

  19. Structure-Based Alignment and Consensus Secondary Structures for Three HIV-Related RNA Genomes.

    PubMed

    Lavender, Christopher A; Gorelick, Robert J; Weeks, Kevin M

    2015-05-01

    HIV and related primate lentiviruses possess single-stranded RNA genomes. Multiple regions of these genomes participate in critical steps in the viral replication cycle, and the functions of many RNA elements are dependent on the formation of defined structures. The structures of these elements are still not fully understood, and additional functional elements likely exist that have not been identified. In this work, we compared three full-length HIV-related viral genomes: HIV-1NL4-3, SIVcpz, and SIVmac (the latter two strains are progenitors for all HIV-1 and HIV-2 strains, respectively). Model-free RNA structure comparisons were performed using whole-genome structure information experimentally derived from nucleotide-resolution SHAPE reactivities. Consensus secondary structures were constructed for strongly correlated regions by taking into account both SHAPE probing structural data and nucleotide covariation information from structure-based alignments. In these consensus models, all known functional RNA elements were recapitulated with high accuracy. In addition, we identified multiple previously unannotated structural elements in the HIV-1 genome likely to function in translation, splicing and other replication cycle processes; these are compelling targets for future functional analyses. The structure-informed alignment strategy developed here will be broadly useful for efficient RNA motif discovery. PMID:25992893

  20. Hormones, Sex Accessory Structures, and Secondary Sexual Characteristics

    E-print Network

    Sever, David M.

    gland secretions) and secondary sexual characteristics (e.g., genial glands and skin glands of newts pads of American newts (e.g., Notophthalmus viridescens), whereas oxytocin antagonizes the influence of prolactin. In the Japanese newt (Cynops pyrrhogaster), however, estrogens block the action of prolactin

  1. RNAVLab: A virtual laboratory for studying RNA secondary structures based on grid computing technology

    PubMed Central

    Taufer, Michela; Leung, Ming-Ying; Solorio, Thamar; Licon, Abel; Mireles, David; Araiza, Roberto; Johnson, Kyle L.

    2009-01-01

    As ribonucleic acid (RNA) molecules play important roles in many biological processes including gene expression and regulation, their secondary structures have been the focus of many recent studies. Despite the computing power of supercomputers, computationally predicting secondary structures with thermodynamic methods is still not feasible when the RNA molecules have long nucleotide sequences and include complex motifs such as pseudoknots. This paper presents RNAVLab (RNA Virtual Laboratory), a virtual laboratory for studying RNA secondary structures including pseudoknots that allows scientists to address this challenge. Two important case studies show the versatility and functionalities of RNAVLab. The first study quantifies its capability to rebuild longer secondary structures from motifs found in systematically sampled nucleotide segments. The extensive sampling and predictions are made feasible in a short turnaround time because of the grid technology used. The second study shows how RNAVLab allows scientists to study the viral RNA genome replication mechanisms used by members of the virus family Nodaviridae. PMID:19885376

  2. Strong Eukaryotic IRESs Have Weak Secondary Structure Xuhua Xia1,2

    E-print Network

    Xia, Xuhua

    immediately upstream of the initiation codons was calculated as a proxy of secondary structure stability. MFE bypassing the requirement for m7 G cap and its associated protein factors [1­3]. While IRES

  3. Application of multiple sequence alignment profiles to improve protein secondary structure prediction

    Microsoft Academic Search

    James A. Cuff; Geoffrey J. Barton

    2000-01-01

    ABSTRACT The effect of training a neural net- work secondary structure prediction algorithm with different types of multiple sequence alignment pro- files derived from the same sequences, is shown to provide a range of accuracy from 70.5% to 76.4%. The best accuracy of 76.4% (standard deviation 8.4%), is 3.1% (2000 Wiley-Liss, Inc. Key words: protein; secondary structure predic-

  4. PseudoViewer: web application and web service for visualizing RNA pseudoknots and secondary structures

    Microsoft Academic Search

    Yanga Byun; Kyungsook Han

    2006-01-01

    Visualizing RNA secondary structures and pseudo- knot structures is essential to bioinformatics systems that deal with RNA structures. However, many bioin- formatics systems use heterogeneous data struc- tures and incompatible software components, so integration of software components (including a visu- alization component) into a system can be hindered by incompatibilities between the components of the system. This paper presents an

  5. High-efficiency translational bypassing of non-coding nucleotides specified by mRNA structure and nascent peptide.

    PubMed

    Samatova, Ekaterina; Konevega, Andrey L; Wills, Norma M; Atkins, John F; Rodnina, Marina V

    2014-01-01

    The gene product 60 (gp60) of bacteriophage T4 is synthesized as a single polypeptide chain from a discontinuous reading frame as a result of bypassing of a non-coding mRNA region of 50 nucleotides by the ribosome. To identify the minimum set of signals required for bypassing, we recapitulated efficient translational bypassing in an in vitro reconstituted translation system from Escherichia coli. We find that the signals, which promote efficient and accurate bypassing, are specified by the gene 60 mRNA sequence. Systematic analysis of the mRNA suggests unexpected contributions of sequences upstream and downstream of the non-coding gap region as well as of the nascent peptide. During bypassing, ribosomes glide forward on the mRNA track in a processive way. Gliding may have a role not only for gp60 synthesis, but also during regular mRNA translation for reading frame selection during initiation or tRNA translocation during elongation. PMID:25041899

  6. Including RNA secondary structures improves accuracy and robustness in reconstruction of phylogenetic trees

    PubMed Central

    2010-01-01

    Background In several studies, secondary structures of ribosomal genes have been used to improve the quality of phylogenetic reconstructions. An extensive evaluation of the benefits of secondary structure, however, is lacking. Results This is the first study to counter this deficiency. We inspected the accuracy and robustness of phylogenetics with individual secondary structures by simulation experiments for artificial tree topologies with up to 18 taxa and for divergency levels in the range of typical phylogenetic studies. We chose the internal transcribed spacer 2 of the ribosomal cistron as an exemplary marker region. Simulation integrated the coevolution process of sequences with secondary structures. Additionally, the phylogenetic power of marker size duplication was investigated and compared with sequence and sequence-structure reconstruction methods. The results clearly show that accuracy and robustness of Neighbor Joining trees are largely improved by structural information in contrast to sequence only data, whereas a doubled marker size only accounts for robustness. Conclusions Individual secondary structures of ribosomal RNA sequences provide a valuable gain of information content that is useful for phylogenetics. Thus, the usage of ITS2 sequence together with secondary structure for taxonomic inferences is recommended. Other reconstruction methods as maximum likelihood, bayesian inference or maximum parsimony may equally profit from secondary structure inclusion. Reviewers This article was reviewed by Shamil Sunyaev, Andrea Tanzer (nominated by Frank Eisenhaber) and Eugene V. Koonin. Open peer review Reviewed by Shamil Sunyaev, Andrea Tanzer (nominated by Frank Eisenhaber) and Eugene V. Koonin. For the full reviews, please go to the Reviewers' comments section. PMID:20078867

  7. Structure of a complex between a cap analogue and mRNA guanylyl transferase demonstrates the structural chemistry of RNA capping.

    PubMed

    Hâkansson, K; Wigley, D B

    1998-02-17

    Paramecium bursaria Chlorella virus PBCV-1 mRNA guanylyl transferase (capping enzyme) has been complexed with an mRNA cap analogue G[5']ppp[5']G and crystallized. The crystals belong to space group C2221 with unit cell dimensions a = 78.4 A, b = 164.1 A, c = 103.3 A, and diffraction data to 3.1 A has been collected by using synchrotron radiation. The structure has been solved by molecular replacement by using each of the two domains in the previously determined structure of the enzyme in complex with GTP. The conformation is open with respect to the active site cleft, and all contacts between enzyme and ligand are mediated by domain 1. One of the guanine bases is bound in the same pocket that is utilized by GTP. The conformation of the ligand positions the beta phosphate and the active site lysine on opposite sides of the alpha phosphate. This geometry is optimal for nucleophilic substitution reactions and has previously been found for GTP in the closed conformational form of the capping enzyme, where the lysine can be guanylylated upon treatment with excess manganese(II) ions. The remainder of the cap analogue runs along the conserved active site Lys82 Thr83 Asp84 Gly85 Ile86 Arg87 motif, and the second guanine, corresponding to the 5' RNA base, is stacked against the hydrophobic Ile86. The ligand displays approximate 2-fold symmetry with intramolecular hydrogen bonding between the 2' and 3' hydroxyls of the two ribose rings. PMID:9465045

  8. A method for aligning RNA secondary structures and its application to RNA motif detection

    PubMed Central

    Liu, Jianghui; Wang, Jason TL; Hu, Jun; Tian, Bin

    2005-01-01

    Background Alignment of RNA secondary structures is important in studying functional RNA motifs. In recent years, much progress has been made in RNA motif finding and structure alignment. However, existing tools either require a large number of prealigned structures or suffer from high time complexities. This makes it difficult for the tools to process RNAs whose prealigned structures are unavailable or process very large RNA structure databases. Results We present here an efficient tool called RSmatch for aligning RNA secondary structures and for motif detection. Motivated by widely used algorithms for RNA folding, we decompose an RNA secondary structure into a set of atomic structure components that are further organized by a tree model to capture the structural particularities. RSmatch can find the optimal global or local alignment between two RNA secondary structures using two scoring matrices, one for single-stranded regions and the other for double-stranded regions. The time complexity of RSmatch is O(mn) where m is the size of the query structure and n that of the subject structure. When applied to searching a structure database, RSmatch can find similar RNA substructures, and is capable of conducting multiple structure alignment and iterative database search. Therefore it can be used to identify functional RNA motifs. The accuracy of RSmatch is tested by experiments using a number of known RNA structures, including simple stem-loops and complex structures containing junctions. Conclusion With respect to computing efficiency and accuracy, RSmatch compares favorably with other tools for RNA structure alignment and motif detection. This tool shall be useful to researchers interested in comparing RNA structures obtained from wet lab experiments or RNA folding programs, particularly when the size of the structure dataset is large. PMID:15817128

  9. When secondary comes first – the importance of non-canonical DNA structures

    PubMed Central

    Saini, Natalie; Zhang, Yu; Usdin, Karen; Lobachev, Kirill S.

    2012-01-01

    Secondary structure-forming DNA motifs have achieved infamy because of their association with a variety of human diseases and cancer. The 3rd FASEB summer conference on dynamic DNA structures focused on the mechanisms responsible for the instabilities inherent to repetitive DNA and presented many exciting and novel aspects related to the metabolism of secondary structures. In addition, the meeting encompassed talks and posters on the dynamic structures that are generated during DNA metabolism including nicked DNA, Holliday junctions and RNA:DNA hybrids. New approaches for analysis and sequencing technologies put forth secondary structures and other DNA intermediates as vital regulators of a variety of cellular processes that contribute to evolution, polymorphisms and diseases. PMID:23084930

  10. mRNA Structural Constraints on EBNA1 Synthesis Impact on In Vivo Antigen Presentation and Early Priming of CD8+ T Cells

    PubMed Central

    Lekieffre, Lea; Bhat, Purnima; Martinez, Michelle; Croft, Nathan P.; Kaplan, Warren; Tellam, Ross L.; Khanna, Rajiv

    2014-01-01

    Recent studies have shown that virally encoded mRNA sequences of genome maintenance proteins from herpesviruses contain clusters of unusual structural elements, G-quadruplexes, which modulate viral protein synthesis. Destabilization of these G-quadruplexes can override the inhibitory effect on self-synthesis of these proteins. Here we show that the purine-rich repetitive mRNA sequence of Epstein-Barr virus encoded nuclear antigen 1 (EBNA1) comprising G-quadruplex structures, limits both the presentation of MHC class I-restricted CD8+ T cell epitopes by CD11c+ dendritic cells in draining lymph nodes and early priming of antigen-specific CD8+ T-cells. Destabilization of the G-quadruplex structures through codon-modification significantly enhanced in vivo antigen presentation and activation of virus-specific T cells. Ex vivo imaging of draining lymph nodes by confocal microscopy revealed enhanced antigen-specific T-cell trafficking and APC-CD8+ T-cell interactions in mice primed with viral vectors encoding a codon-modified EBNA1 protein. More importantly, these antigen-specific T cells displayed enhanced expression of the T-box transcription factor and superior polyfunctionality consistent with the qualitative impact of translation efficiency. These results provide an important insight into how viruses exploit mRNA structure to down regulate synthesis of their viral maintenance proteins and delay priming of antigen-specific T cells, thereby establishing a successful latent infection in vivo. Furthermore, targeting EBNA1 mRNA rather than protein by small molecules or antisense oligonucleotides will enhance EBNA1 synthesis and the early priming of effector T cells, to establish a more rapid immune response and prevent persistent infection. PMID:25299404

  11. Structural Characterization of the Chaetomium thermophilum TREX-2 Complex and its Interaction with the mRNA Nuclear Export Factor Mex67:Mtr2.

    PubMed

    Dimitrova, Lyudmila; Valkov, Eugene; Aibara, Shintaro; Flemming, Dirk; McLaughlin, Stephen H; Hurt, Ed; Stewart, Murray

    2015-07-01

    The TREX-2 complex integrates mRNA nuclear export into the gene expression pathway and is based on a Sac3 scaffold to which Thp1, Sem1, Sus1, and Cdc31 bind. TREX-2 also binds the mRNA nuclear export factor, Mex67:Mtr2, through the Sac3 N-terminal region (Sac3N). Here, we characterize Chaetomium thermophilum TREX-2, show that the in vitro reconstituted complex has an annular structure, and define the structural basis for interactions between Sac3, Sus1, Cdc31, and Mex67:Mtr2. Crystal structures show that the binding of C. thermophilum Sac3N to the Mex67 NTF2-like domain (Mex67(NTF2L)) is mediated primarily through phenylalanine residues present in a series of repeating sequence motifs that resemble those seen in many nucleoporins, and Mlp1 also binds Mex67:Mtr2 using a similar motif. Deletion of Sac3N generated growth and mRNA export defects in Saccharomyces cerevisiae, and we propose TREX-2 and Mlp1 function to facilitate export by concentrating mature messenger ribonucleoparticles at the nuclear pore entrance. PMID:26051714

  12. RNA secondary structure formation: a solvable model of heteropolymer folding

    E-print Network

    Bundschuh, Ralf

    : -- Temperature -- Bias for native structure ffl Use long hairpin as native (designed) structure ffl Create for temperature native molten glass denatured #12; Introduction IV 5 ffl Same effects play a role in DNA \\Gamma! remain single­stranded ffl Existence of hybrids detected by enzyme ffl Weak homology: need

  13. Quantitative Dimethyl Sulfate Mapping for Automated RNA Secondary Structure Inference

    E-print Network

    Das, Rhiju

    manual modeling of RNA structure in vitro and in vivo. Here, we incorporate DMS data into automated to be most strongly protected or reactive to DMS can be inferred to be base-paired or unpaired, respectively. This qualitative or "binary" information can be used for RNA structure modeling by manual or automatic methods.10

  14. Analysis of an optimal hidden Markov model for secondary structure prediction

    PubMed Central

    Martin, Juliette; Gibrat, Jean-François; Rodolphe, François

    2006-01-01

    Background Secondary structure prediction is a useful first step toward 3D structure prediction. A number of successful secondary structure prediction methods use neural networks, but unfortunately, neural networks are not intuitively interpretable. On the contrary, hidden Markov models are graphical interpretable models. Moreover, they have been successfully used in many bioinformatic applications. Because they offer a strong statistical background and allow model interpretation, we propose a method based on hidden Markov models. Results Our HMM is designed without prior knowledge. It is chosen within a collection of models of increasing size, using statistical and accuracy criteria. The resulting model has 36 hidden states: 15 that model ?-helices, 12 that model coil and 9 that model ?-strands. Connections between hidden states and state emission probabilities reflect the organization of protein structures into secondary structure segments. We start by analyzing the model features and see how it offers a new vision of local structures. We then use it for secondary structure prediction. Our model appears to be very efficient on single sequences, with a Q3 score of 68.8%, more than one point above PSIPRED prediction on single sequences. A straightforward extension of the method allows the use of multiple sequence alignments, rising the Q3 score to 75.5%. Conclusion The hidden Markov model presented here achieves valuable prediction results using only a limited number of parameters. It provides an interpretable framework for protein secondary structure architecture. Furthermore, it can be used as a tool for generating protein sequences with a given secondary structure content. PMID:17166267

  15. Funnel sculpting for in silico assembly of secondary structure elements of proteins

    PubMed Central

    Fain, Boris; Levitt, Michael

    2003-01-01

    We present a method for designing a funnel-shaped free-energy surface that reproducibly assembles secondary structure elements of proteins into their native conformations from a random extended configuration. Assuming a priori knowledge of secondary structure, our method can design a funnel-shaped surface for folding of ?, ?, and ?? structures individually. We design energy surfaces that fold up to five unrelated sequences with the same energy parameters. We develop a measure of the foldability of an energy landscape in silico and present an alternative way to view energy landscapes. PMID:12925740

  16. Multiple Structurally Distinct ER? mRNA Variants in Zebrafish are Differentially Expressed by Tissue Type, Stage of Development and Estrogen Exposure

    PubMed Central

    Cotter, Kellie A.; Yershov, Anya; Novillo, Apolonia; Callard, Gloria V.

    2013-01-01

    It is well established that estrogen-like environmental chemicals interact with the ligand-binding site of estrogen receptors (ER) to disrupt transcriptional control of estrogen responsive targets. Here we investigate the possibility that estrogens also impact splicing decisions on estrogen responsive genes, such as that encoding ER? itself. Targeted PCR cloning was applied to identify six ER? mRNA variants in zebrafish. Sequencing revealed alternate use of transcription and translation start sites, multiple exon deletions, intron retention and alternate polyadenylation. As determined by quantitative (q)PCR, N-terminal mRNA variants predicting long (ER?L) and short (ER?S) isoforms were differentially expressed by tissue-type, sex, stage of development and estrogen exposure. Whereas ER?L mRNA was diffusely distributed in liver, brain, heart, eye, and gonads, ER?S mRNA was preferentially expressed in liver (female > male) and ovary. Neither ER?L nor ER?S transcripts varied significantly during development, but 17?-estradiol selectively increased accumulation of ER?S mRNA (~170-fold by 120 hpf), an effect mimicked by bisphenol-A and diethylstilbestrol. Significantly, a C-truncated variant (ER?S-Cx) lacking most of the ligand binding and AF-2 domains was transcribed exclusively from the short isoform promoter and was similar to ER?S in its tissue-, stage- and estrogen inducible expression. These results support the idea that promoter choice and alternative splicing of the esr1 gene of zebrafish are part of the autoregulatory mechanism by which estrogen modulates subsequent ER? expression, and further suggest that environmental estrogens could exert some of their toxic effects by altering the relative abundance of structurally and functionally distinct ER? isoforms. PMID:24090614

  17. Nanosecond UV Resonance Raman Examination of Initial Steps in r-Helix Secondary Structure

    E-print Network

    Asher, Sanford A.

    the earliest events in protein structural evolution. We examine the thermal unfolding of the 21 amino acid R find that the unfolding rate constants show Arrhenius-type behavior with an apparent 7 kcal/mol barrier.14-16 These amide Raman bands sensitively depend on secondary structure. We recently determined

  18. b-Peptides with Different Secondary-Structure Preferences: How Different Are Their Conformational Spaces?

    E-print Network

    Simons, Jack

    b-Peptides with Different Secondary-Structure Preferences: How Different Are Their Conformational-dynamics simulation with an atomistic model of both solute and solvent. The structural properties of these peptides to a model (P)-12/10-helix for one of the peptides and a model hairpin with a ten-membered H- bonded turn

  19. Detection of Secondary and Supersecondary Structures of Proteins from Cryo-Electron Microscopy

    E-print Network

    Texas at Austin, University of

    in proteins. Keywords: protein structures detection, electron microscopy, stable/unstable manifolds, criticalDetection of Secondary and Supersecondary Structures of Proteins from Cryo-Electron Microscopy in three-dimensional electron microscopy (3D EM) have enabled the quantitative visualization

  20. Regulation of splicing enhancer activities by RNA secondary structures.

    PubMed

    Liu, Wei; Zhou, Yu; Hu, Zexi; Sun, Tao; Denise, Alain; Fu, Xiang-Dong; Zhang, Yi

    2010-11-01

    In this report, we studied the effect of RNA structures on the activity of exonic splicing enhancers on the SMN1 minigene model by engineering known ESEs into different positions of stable hairpins. We found that as short as 7-bp stem is sufficient to abolish the enhancer activity. When placing ESEs in the loop region, AG-rich ESEs are fully active, but a UCG-rich ESE is not because of additional structural constraints. ESEs placed adjacent to the 3' end of the hairpin structure display high enhancer activity, regardless of their sequence identities. These rules explain the suppression of multiple ESEs by point mutations that result in a stable RNA structure, and provide an additional mechanism for the C6T mutation in SMN2. PMID:20888818

  1. Asymptotics of Canonical and Saturated RNA Secondary Structures

    E-print Network

    Paris-Sud XI, Université de

    of saturated stem-loop structures is 0.323954·1.69562n , in contrast to the number 2n-2 of (arbitrary) stem Foundation Grants DBI-0543506, DMS-0817971, and the RNA Ontology Consortium. Additional support is gratefully

  2. PSP_MCSVM: brainstorming consensus prediction of protein secondary structures using two-stage multiclass support vector machines

    Microsoft Academic Search

    Piyali Chatterjee; Subhadip Basu; Mahantapas Kundu; Mita Nasipuri; Dariusz Plewczynski

    Secondary structure prediction is a crucial task for understanding the variety of protein structures and performed biological\\u000a functions. Prediction of secondary structures for new proteins using their amino acid sequences is of fundamental importance\\u000a in bioinformatics. We propose a novel technique to predict protein secondary structures based on position-specific scoring\\u000a matrices (PSSMs) and physico-chemical properties of amino acids. It is

  3. Atomic model of a cypovirus built from cryo-EM structure provides insight into the mechanism of mRNA capping

    PubMed Central

    Cheng, Lingpeng; Sun, Jingchen; Zhang, Kai; Mou, Zongjun; Huang, Xiaoxing; Ji, Gang; Sun, Fei; Zhang, Jingqiang; Zhu, Ping

    2011-01-01

    The cytoplasmic polyhedrosis virus (CPV) from the family Reoviridae belongs to a subgroup of “turreted” reoviruses, in which the mRNA capping activity occurs in a pentameric turret. We report a full atomic model of CPV built from a 3D density map obtained using cryoelectron microscopy. The image data for the 3D reconstruction were acquired exclusively from a CCD camera. Our structure shows that the enzymatic domains of the pentameric turret of CPV are topologically conserved and that there are five unique channels connecting the guanylyltransferase and methyltransferase regions. This structural organization reveals how the channels guide nascent mRNA sequentially to guanylyltransferase, 7-N-methyltransferase, and 2?-O-methyltransferase in the turret, undergoing the highly coordinated mRNA capping activity. Furthermore, by fitting the deduced amino acid sequence of the protein VP5 to 120 large protrusion proteins on the CPV capsid shell, we confirmed that this protrusion protein is encoded by CPV RNA segment 7. PMID:21220303

  4. Thermodynamic and phylogenetic prediction of RNA secondary structures in the coding region of hepatitis C virus.

    PubMed Central

    Tuplin, Andrew; Wood, Jonny; Evans, David J; Patel, Arvind H; Simmonds, Peter

    2002-01-01

    The existence and functional importance of RNA secondary structure in the replication of positive-stranded RNA viruses is increasingly recognized. We applied several computational methods to detect RNA secondary structure in the coding region of hepatitis C virus (HCV), including thermodynamic prediction, calculation of free energy on folding, and a newly developed method to scan sequences for covariant sites and associated secondary structures using a parsimony-based algorithm. Each of the prediction methods provided evidence for complex RNA folding in the core- and NS5B-encoding regions of the genome. The positioning of covariant sites and associated predicted stem-loop structures coincided with thermodynamic predictions of RNA base pairing, and localized precisely in parts of the genome with marked suppression of variability at synonymous sites. Combined, there was evidence for a total of six evolutionarily conserved stem-loop structures in the NS5B-encoding region and two in the core gene. The virus most closely related to HCV, GB virus-B (GBV-B) also showed evidence for similar internal base pairing in its coding region, although predictions of secondary structures were limited by the absence of comparative sequence data for this virus. While the role(s) of stem-loops in the coding region of HCV and GBV-B are currently unknown, the structure predictions in this study could provide the starting point for functional investigations using recently developed self-replicating clones of HCV. PMID:12088154

  5. 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

  6. Role of mRNA Stability during Bacterial Adaptation

    PubMed Central

    Dressaire, Clémentine; Picard, Flora; Redon, Emma; Loubière, Pascal; Queinnec, Isabelle; Girbal, Laurence; Cocaign-Bousquet, Muriel

    2013-01-01

    Bacterial adaptation involves extensive cellular reorganization. In particular, growth rate adjustments are associated with substantial modifications of gene expression and mRNA abundance. In this work we aimed to assess the role of mRNA degradation during such variations. A genome-wide transcriptomic-based method was used to determine mRNA half-lives. The model bacterium Lactococcus lactis was used and different growth rates were studied in continuous cultures under isoleucine-limitation and in batch cultures during the adaptation to the isoleucine starvation. During continuous isoleucine-limited growth, the mRNAs of different genes had different half-lives. The stability of most of the transcripts was not constant, and increased as the growth rate decreased. This half-life diversity was analyzed to investigate determinants of mRNA stability. The concentration, length, codon adaptation index and secondary structures of mRNAs were found to contribute to the determination of mRNA stability in these conditions. However, the growth rate was, by far, the most influential determinant. The respective influences of mRNA degradation and transcription on the regulation of intra-cellular transcript concentration were estimated. The role of degradation on mRNA homeostasis was clearly evidenced: for more than 90% of the mRNAs studied during continuous isoleucine-limited growth of L. lactis, degradation was antagonistic to transcription. Although both transcription and degradation had, opposite effects, the mRNA changes in response to growth rate were driven by transcription. Interestingly, degradation control increased during the dynamic adaptation of bacteria as the growth rate reduced due to progressive isoleucine starvation in batch cultures. This work shows that mRNA decay differs between gene transcripts and according to the growth rate. It demonstrates that mRNA degradation is an important regulatory process involved in bacterial adaptation. However, its impact on the regulation of mRNA levels is smaller than that of transcription in the conditions studied. PMID:23516597

  7. ITS2 Secondary Structure Improves Discrimination between Medicinal “Mu Tong” Species when Using DNA Barcoding

    PubMed Central

    Zhang, Wei; Yuan, Yuan; Yang, Shuo; Huang, Jianjun; Huang, Luqi

    2015-01-01

    DNA barcoding is a promising species identification method, but it has proved difficult to find a standardized DNA marker in plant. Although the ITS/ITS2 RNA transcript has been proposed as the core barcode for seed plants, it has been criticized for being too conserved in some species to provide enough information or too variable in some species to align it within the different taxa ranks. We selected 30 individuals, representing 16 species and four families, to explore whether ITS2 can successfully resolve species in terms of secondary structure. Secondary structure was predicted using Mfold software and sequence-structure was aligned by MARNA. RNAstat software transformed the secondary structures into 28 symbol code data for maximum parsimony (MP) analysis. The results showed that the ITS2 structures in our samples had a common four-helix folding type with some shared motifs. This conserved structure facilitated the alignment of ambiguous sequences from divergent families. The structure alignment yielded a MP tree, in which most topological relationships were congruent with the tree constructed using nucleotide sequence data. When the data was combined, we obtained a well-resolved and highly supported phylogeny, in which individuals of a same species were clustered together into a monophyletic group. As a result, the different species that are often referred to as the herb “Mu tong” were successfully identified using short fragments of 250 bp ITS2 sequences, together with their secondary structure. Thus our analysis strengthens the potential of ITS2 as a promising DNA barcode because it incorporates valuable secondary structure information that will help improve discrimination between species. PMID:26132382

  8. Accurate secondary structure prediction and fold recognition for circular dichroism spectroscopy

    PubMed Central

    Micsonai, András; Wien, Frank; Kernya, Linda; Lee, Young-Ho; Goto, Yuji; Réfrégiers, Matthieu; Kardos, József

    2015-01-01

    Circular dichroism (CD) spectroscopy is a widely used technique for the study of protein structure. Numerous algorithms have been developed for the estimation of the secondary structure composition from the CD spectra. These methods often fail to provide acceptable results on ?/?-mixed or ?-structure–rich proteins. The problem arises from the spectral diversity of ?-structures, which has hitherto been considered as an intrinsic limitation of the technique. The predictions are less reliable for proteins of unusual ?-structures such as membrane proteins, protein aggregates, and amyloid fibrils. Here, we show that the parallel/antiparallel orientation and the twisting of the ?-sheets account for the observed spectral diversity. We have developed a method called ?-structure selection (BeStSel) for the secondary structure estimation that takes into account the twist of ?-structures. This method can reliably distinguish parallel and antiparallel ?-sheets and accurately estimates the secondary structure for a broad range of proteins. Moreover, the secondary structure components applied by the method are characteristic to the protein fold, and thus the fold can be predicted to the level of topology in the CATH classification from a single CD spectrum. By constructing a web server, we offer a general tool for a quick and reliable structure analysis using conventional CD or synchrotron radiation CD (SRCD) spectroscopy for the protein science research community. The method is especially useful when X-ray or NMR techniques fail. Using BeStSel on data collected by SRCD spectroscopy, we investigated the structure of amyloid fibrils of various disease-related proteins and peptides. PMID:26038575

  9. Accurate secondary structure prediction and fold recognition for circular dichroism spectroscopy.

    PubMed

    Micsonai, András; Wien, Frank; Kernya, Linda; Lee, Young-Ho; Goto, Yuji; Réfrégiers, Matthieu; Kardos, József

    2015-06-16

    Circular dichroism (CD) spectroscopy is a widely used technique for the study of protein structure. Numerous algorithms have been developed for the estimation of the secondary structure composition from the CD spectra. These methods often fail to provide acceptable results on ?/?-mixed or ?-structure-rich proteins. The problem arises from the spectral diversity of ?-structures, which has hitherto been considered as an intrinsic limitation of the technique. The predictions are less reliable for proteins of unusual ?-structures such as membrane proteins, protein aggregates, and amyloid fibrils. Here, we show that the parallel/antiparallel orientation and the twisting of the ?-sheets account for the observed spectral diversity. We have developed a method called ?-structure selection (BeStSel) for the secondary structure estimation that takes into account the twist of ?-structures. This method can reliably distinguish parallel and antiparallel ?-sheets and accurately estimates the secondary structure for a broad range of proteins. Moreover, the secondary structure components applied by the method are characteristic to the protein fold, and thus the fold can be predicted to the level of topology in the CATH classification from a single CD spectrum. By constructing a web server, we offer a general tool for a quick and reliable structure analysis using conventional CD or synchrotron radiation CD (SRCD) spectroscopy for the protein science research community. The method is especially useful when X-ray or NMR techniques fail. Using BeStSel on data collected by SRCD spectroscopy, we investigated the structure of amyloid fibrils of various disease-related proteins and peptides. PMID:26038575

  10. 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 ?-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 ?-helices, other fragments can be exploited in an analogous way: libraries of helices with modelled side chains, ?-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

  11. High-accuracy prediction of protein structural classes using PseAA structural properties and secondary structural patterns.

    PubMed

    Wang, Junru; Li, Yan; Liu, Xiaoqing; Dai, Qi; Yao, Yuhua; He, Pingan

    2014-06-01

    Since introduction of PseAAs and functional domains, promising results have been achieved in protein structural class predication, but some challenges still exist in the representation of the PseAA structural correlation and structural domains. This paper proposed a high-accuracy prediction method using novel PseAA structural properties and secondary structural patterns, reflecting the long-range and local structural properties of the PseAAs and certain compact structural domains. The proposed prediction method was tested against the competing prediction methods with four experiments. The experiment results indicate that the proposed method achieved the best performance. Its overall accuracies for datasets 25 PDB, D640, FC699 and 1189 are 88.8%, 90.9%, 96.4% and 87.4%, which are 4.5%, 7.6%, 2% and 3.9% higher than the existing best-performing method. This understanding can be used to guide development of more powerful methods for protein structural class prediction. The software and supplement material are freely available at http://bioinfo.zstu.edu.cn/PseAA-SSP. PMID:24412731

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

    PubMed

    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

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

    PubMed

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

    2015-07-01

    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. 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

  15. RNACompress: Grammar-based compression and informational complexity measurement of RNA secondary structure

    PubMed Central

    Liu, Qi; Yang, Yu; Chen, Chun; Bu, Jiajun; Zhang, Yin; Ye, Xiuzi

    2008-01-01

    Background With the rapid emergence of RNA databases and newly identified non-coding RNAs, an efficient compression algorithm for RNA sequence and structural information is needed for the storage and analysis of such data. Although several algorithms for compressing DNA sequences have been proposed, none of them are suitable for the compression of RNA sequences with their secondary structures simultaneously. This kind of compression not only facilitates the maintenance of RNA data, but also supplies a novel way to measure the informational complexity of RNA structural data, raising the possibility of studying the relationship between the functional activities of RNA structures and their complexities, as well as various structural properties of RNA based on compression. Results RNACompress employs an efficient grammar-based model to compress RNA sequences and their secondary structures. The main goals of this algorithm are two fold: (1) present a robust and effective way for RNA structural data compression; (2) design a suitable model to represent RNA secondary structure as well as derive the informational complexity of the structural data based on compression. Our extensive tests have shown that RNACompress achieves a universally better compression ratio compared with other sequence-specific or common text-specific compression algorithms, such as Gencompress, winrar and gzip. Moreover, a test of the activities of distinct GTP-binding RNAs (aptamers) compared with their structural complexity shows that our defined informational complexity can be used to describe how complexity varies with activity. These results lead to an objective means of comparing the functional properties of heteropolymers from the information perspective. Conclusion A universal algorithm for the compression of RNA secondary structure as well as the evaluation of its informational complexity is discussed in this paper. We have developed RNACompress, as a useful tool for academic users. Extensive tests have shown that RNACompress is a universally efficient algorithm for the compression of RNA sequences with their secondary structures. RNACompress also serves as a good measurement of the informational complexity of RNA secondary structure, which can be used to study the functional activities of RNA molecules. PMID:18373878

  16. Mapping in Solution Shows the Peach Latent Mosaic Viroid To Possess a New Pseudoknot in a Complex, Branched Secondary Structure

    Microsoft Academic Search

    F. Bussiere; J. Ouellet; F. Cote; D. Levesque; J. P. Perreault

    2000-01-01

    We have investigated the secondary structure of peach latent mosaic viroid (PLMVd) in solution, and we present here the first description of the structure of a branched viroid in solution. Different PLMVd transcripts of plus polarity were produced by using the circularly permuted RNA method and the exploitation of RNA internal secondary structure to position the 5* and 3* termini

  17. The vitellogenin of the bumblebee, Bombus hypocrita: studies on structural analysis of the cDNA and expression of the mRNA.

    PubMed

    Li, Jilian; Huang, Jiaxing; Cai, Wanzhi; Zhao, Zhangwu; Peng, Wenjun; Wu, Jie

    2010-02-01

    In this present study, the cDNA of Bombus hypocrita vitellogenin (Vg) was cloned and sequenced. It is composed of 5,478 bp and contains an ORF of 1,772 amino acids within a putative signal peptide of 16 residues. The deduced amino acid sequence shows significant similarity with Bombus ignitus (95%) and Apis mellifera (52%) and a high number of conserved motifs. Close to the C terminus there is a GL/ICG motif followed by nine cysteines, and a DGXR motif is located 18 residues upstream from the GL/ICG motif. Moreover, we predicted the 3D structure of B. hypocrita Vg. Furthermore, the Vg mRNA of B. hypocrita was spatio-temporally analyzed in different castes (such as queen, worker and drone) from pupae to adult. The Vg mRNA was found in the white-eyed pupal (Pw) stage in queens, and the expression increased during the entire pupal development and attained its peak in the dark brown pupal stage. It also had a high expression in the adult fat body. In workers, the Vg expression was detected in the Pw stage, and its levels increased with age with the highest in 15 days. Afterward, it decreased progressively. Vg mRNA was also observed in drones, with a higher level of expression shown in only freshly molted adult drones. PMID:20012056

  18. Quantitative Correlation Between the Protein Primary Sequences and Secondary Structures in Spider Dragline Silks

    PubMed Central

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

    2009-01-01

    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 ?-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. DNA secondary structures and epigenetic determinants of cancer genome evolution

    PubMed Central

    De, Subhajyoti; Michor, Franziska

    2014-01-01

    An unstable genome is a hallmark of many cancers. It is unclear, however, whether some mutagenic features driving somatic alterations in cancer are encoded in the genome sequence and whether they can operate in a tissue-specific manner. We performed a genome-wide analysis of 663,446 DNA breakpoints associated with somatic copy-number alterations (SCNAs) from 2,792 cancer samples classified into 26 cancer types. Many SCNA breakpoints are spatially clustered in cancer genomes. We observed a significant enrichment for G-quadruplex sequences (G4s) in the vicinity of SCNA breakpoints and established that SCNAs show a strand bias consistent with G4-mediated structural alterations. Notably, abnormal hypomethylation near G4s-rich regions is a common signature for many SCNA breakpoint hotspots. We propose a mechanistic hypothesis that abnormal hypomethylation in genomic regions enriched for G4s acts as a mutagenic factor driving tissue-specific mutational landscapes in cancer. PMID:21725294

  20. The influence of ignoring secondary structure on divergence time estimates from ribosomal RNA genes.

    PubMed

    Dohrmann, Martin

    2014-02-01

    Genes coding for ribosomal RNA molecules (rDNA) are among the most popular markers in molecular phylogenetics and evolution. However, coevolution of sites that code for pairing regions (stems) in the RNA secondary structure can make it challenging to obtain accurate results from such loci. While the influence of ignoring secondary structure on multiple sequence alignment and tree topology has been investigated in numerous studies, its effect on molecular divergence time estimates is still poorly known. Here, I investigate this issue in Bayesian Markov Chain Monte Carlo (BMCMC) and penalized likelihood (PL) frameworks, using empirical datasets from dragonflies (Odonata: Anisoptera) and glass sponges (Porifera: Hexactinellida). My results indicate that highly biased inferences under substitution models that ignore secondary structure only occur if maximum-likelihood estimates of branch lengths are used as input to PL dating, whereas in a BMCMC framework and in PL dating based on Bayesian consensus branch lengths, the effect is far less severe. I conclude that accounting for coevolution of paired sites in molecular dating studies is not as important as previously suggested, as long as the estimates are based on Bayesian consensus branch lengths instead of ML point estimates. This finding is especially relevant for studies where computational limitations do not allow the use of secondary-structure specific substitution models, or where accurate consensus structures cannot be predicted. I also found that the magnitude and direction (over- vs. underestimating node ages) of bias in age estimates when secondary structure is ignored was not distributed randomly across the nodes of the phylogenies, a phenomenon that requires further investigation. PMID:24361769

  1. Mouse hepatitis virus A59: mRNA structure and genetic localization of the sequence divergence from hepatotropic strain MHV-3.

    PubMed Central

    Lai, M M; Brayton, P R; Armen, R C; Patton, C D; Pugh, C; Stohlman, S A

    1981-01-01

    The composition and structure of the mouse hepatitis virus (MHV)-specific RNA in actinomycin D-treated, infected L-2 cells were studied. SEven virus-specific RNA species with molecular weights of 0.6 X 10(6), 0.9 X 10(6), 1.2 X 10(6), 1.5 X 10(6), 3.0 X 10(6), 4.0 X 10(6), and 5.4 X 10(6) (equivalent to the viral genome) were detected. T1 oligonucleotide fingerprinting studies suggested that the sequences of each RNA species were totally included within the next large RNa species. The oligonucleotides of each RNA species were mapped on the 60S RNA genome of the virus. Each RNA species contained the oligonucleotides starting from the 3' end of the genome and extending continuously for various lengths in the 3' leads to 5' direction. All of the viral RNA species contained a polyadenylate stretch of 100 to 130 nucleotides and probably identical sequences immediately next to the polyadenylate. These data suggested that the virus-specific RNAs are mRNA's and have a stairlike structure similar to that of infectious bronchitis virus, an avian coronavirus. A proposal is presented, based on the mRNA structure, for the designation of the genes on the MHV genome. Using this proposal, the sequence differences between A59, a weakly pathogenic strain, and MHV-3, a strongly hepatotropic strain, were localized primarily in mRNA's 1 and 3, corresponding t genes A and C. Images PMID:6169842

  2. Viral IRES prediction system - a web server for prediction of the IRES secondary structure in silico.

    PubMed

    Hong, Jun-Jie; Wu, Tzong-Yuan; Chang, Tsair-Yuan; Chen, Chung-Yung

    2013-01-01

    The internal ribosomal entry site (IRES) functions as cap-independent translation initiation sites in eukaryotic cells. IRES elements have been applied as useful tools for bi-cistronic expression vectors. Current RNA structure prediction programs are unable to predict precisely the potential IRES element. We have designed a viral IRES prediction system (VIPS) to perform the IRES secondary structure prediction. In order to obtain better results for the IRES prediction, the VIPS can evaluate and predict for all four different groups of IRESs with a higher accuracy. RNA secondary structure prediction, comparison, and pseudoknot prediction programs were implemented to form the three-stage procedure for the VIPS. The backbone of VIPS includes: the RNAL fold program, aimed to predict local RNA secondary structures by minimum free energy method; the RNA Align program, intended to compare predicted structures; and pknotsRG program, used to calculate the pseudoknot structure. VIPS was evaluated by using UTR database, IRES database and Virus database, and the accuracy rate of VIPS was assessed as 98.53%, 90.80%, 82.36% and 80.41% for IRES groups 1, 2, 3, and 4, respectively. This advance useful search approach for IRES structures will facilitate IRES related studies. The VIPS on-line website service is available at http://140.135.61.250/vips/. PMID:24223923

  3. STRUCTURAL CHARACTERIZATION OF SULFONATED AZO DYES USING LIQUID SECONDARY ION MASS SPECTROMETRY/TANDEM MASS SPECTROMETRY

    EPA Science Inventory

    Eight monosulfonated and disulfonated azo dyes were analyzed using liquid secondary ion mass spectrometry/tandem mass spectrometry, in the negative ion mode, under low-energy conditions (110-150 eV). any structurally characteristic fragment ions were obtained, several of which ha...

  4. Sequence-Based Prediction of Protein Folding Rates Using Contacts, Secondary Structures and Support Vector Machines

    E-print Network

    Cheng, Jianlin Jack

    Sequence-Based Prediction of Protein Folding Rates Using Contacts, Secondary Structures and Support, Columbia, Missouri * Corresponding author: chengji@missouri.edu Abstract Predicting protein folding rate is useful for understanding protein folding process and guiding protein design. Here we developed a method

  5. Interplay between Secondary and Tertiary Structure Formation in Protein Folding Cooperativity

    E-print Network

    Bachmann, Michael

    Interplay between Secondary and Tertiary Structure Formation in Protein Folding Cooperativity¨lich, 52425 Ju¨lich, Germany Received June 14, 2010; E-mail: deserno@andrew.cmu.edu Abstract: Protein folding be difficult to measure. Therefore, protein folding cooperativity is often probed using the calorimetric

  6. Protein Secondary Structure Prediction Based on Position-specific Scoring Matrices

    Microsoft Academic Search

    David T. Jones

    1999-01-01

    A two-stage neural network has been used to predict protein secondary structure based on the position specific scoring matrices generated by PSI-BLAST. Despite the simplicity and convenience of the approach used, the results are found to be superior to those produced by other methods, including the popular PHD method according to our own benchmarking results and the results from the

  7. Dynalign II: common secondary structure prediction for RNA homologs with domain insertions

    PubMed Central

    Fu, Yinghan; Sharma, Gaurav; Mathews, David H.

    2014-01-01

    Homologous non-coding RNAs frequently exhibit domain insertions, where a branch of secondary structure is inserted in a sequence with respect to its homologs. Dynamic programming algorithms for common secondary structure prediction of multiple RNA homologs, however, do not account for these domain insertions. This paper introduces a novel dynamic programming algorithm methodology that explicitly accounts for the possibility of inserted domains when predicting common RNA secondary structures. The algorithm is implemented as Dynalign II, an update to the Dynalign software package for predicting the common secondary structure of two RNA homologs. This update is accomplished with negligible increase in computational cost. Benchmarks on ncRNA families with domain insertions validate the method. Over base pairs occurring in inserted domains, Dynalign II improves accuracy over Dynalign, attaining 80.8% sensitivity (compared with 14.4% for Dynalign) and 91.4% positive predictive value (PPV) for tRNA; 66.5% sensitivity (compared with 38.9% for Dynalign) and 57.0% PPV for RNase P RNA; and 50.1% sensitivity (compared with 24.3% for Dynalign) and 58.5% PPV for SRP RNA. Compared with Dynalign, Dynalign II also exhibits statistically significant improvements in overall sensitivity and PPV. Dynalign II is available as a component of RNAstructure, which can be downloaded from http://rna.urmc.rochester.edu/RNAstructure.html. PMID:25416799

  8. Effects and mechanisms of the secondary structure on the antimicrobial activity and specificity of antimicrobial peptides.

    PubMed

    Mai, Xuan-Thanh; Huang, Jinfeng; Tan, Juanjuan; Huang, Yibing; Chen, Yuxin

    2015-07-01

    A 15-mer cationic ?-helical antimicrobial peptide HPRP-A1 was used as the parent peptide to study the effects of peptide secondary structure on the biophysical properties and biological activities. Without changing the amino acid composition of HPRP-A1, we designed two ?-helical peptides with either higher or lower helicity compared with the parent peptide, a ?-sheet peptide and a random coiled peptide using de novo design approach. The secondary structures were confirmed by circular dichroism spectroscopy. The three ?-helical peptides exhibited comparable antibacterial activities, but their hemolytic activity varied from extreme hemolysis to no hemolysis, which is correlated with their helicity. The ?-sheet peptide shows poor antibacterial and strong hemolytic activities. More interestingly, the random coil peptide shows no antibacterial activity against Gram-negative bacteria, weak antibacterial activity against Gram-positive bacteria, and extremely weak hemolytic activity. Bacterial membrane permeabilization was also testified on peptides with different secondary structures. Tryptophan fluorescence experiment revealed that the peptide binding preference to the lipid vesicles for mimicking the prokaryotic or eukaryotic membranes was consistent with their biological activities. With the de novo design approach, we proved that it is important to maintain certain contents of amphipathic secondary structure for a desirable biological activity. We believe that the de novo design approach of relocation of the amino acids within a template sequence could be an effective approach in optimizing the specificity of an antimicrobial peptide. Copyright © 2015 European Peptide Society and John Wiley & Sons, Ltd. PMID:25826179

  9. 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…

  10. Structure and floristics of secondary and old-growth forest stands in lowland Costa Rica

    Microsoft Academic Search

    Manuel R. Guariguata; Robin L. Chazdon; Julie S. Denslow; Juan M. Dupuy; Laura Anderson

    1997-01-01

    We characterized stand structure and floristic composition of woody life forms in three, 16–18 yr old secondary stands that regenerated after pasture abandonment, and three nearby old-growth stands of tropical rain forest in lowland Costa Rica. Basal area and stem density for each of four plant size classes (seedlings, saplings, treelets, trees) were similar among stand types, but density of

  11. Chinese American Post-Secondary Achievement and Attainment: A Cultural and Structural Analysis

    ERIC Educational Resources Information Center

    Pearce, Richard R.; Lin, Zeng

    2007-01-01

    In this article, the authors compare Chinese American post-secondary educational attainment with that of White Americans and, in identifying those factors that most strongly account for success, argue that commonalities exist among social structural factors, while distinct differences are evident among cultural capital factors. The article rejects…

  12. 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…

  13. Graviresponsiveness and columella cell structure in primary and secondary roots of Ricinus communis

    Microsoft Academic Search

    Randy Moore; John Pasieniuk

    1984-01-01

    In order to determine what structural changes are associated with the onset of graviresponsiveness by plant roots, we have monitored the quantitative ultrastructures of columella (i.e., graviperceptive) cells in primary and secondary roots of Ricinus communis. The relative volumes of cellular components in lateral (i.e., minimally graviresponsive) roots were not significantly different from those of primary roots. The relative volumes

  14. 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'…

  15. DETERMINATION OF SECONDARY STRUCTURAL CHANGES IN GLUTEN PROTEINS DURING MIXING USING FT-HATR SPECTROSCOPY

    Technology Transfer Automated Retrieval System (TEKTRAN)

    An infrared spectroscopic method was developed to examine changes in the secondary structure of gluten proteins in a flour-water dough system during mixing. Fourier transform horizontal attenuated total reflectance (FT-HATR) mid-infrared spectra of mixed doughs revealed changes in four bands in the ...

  16. A Qualitative Assessment of Administrative and Organizational Structure of Secondary Vocational Schools in Turkey.

    ERIC Educational Resources Information Center

    Simsek, Hasan; Yildirim, Ali

    A study critically evaluated the administrative practices and organizational structure of the Turkish secondary vocational education system from the perspectives of school administrators, teachers, and industry managers. The study population included 14 vocational high schools and 12 companies that hired graduates of these schools in 4 relatively…

  17. Secondary structure of NADPH: protochlorophyllide oxidoreductase examined by circular dichroism and prediction methods.

    PubMed Central

    Birve, S J; Selstam, E; Johansson, L B

    1996-01-01

    To study the secondary structure of the enzyme NADPH: protochlorophyllide oxidoreductase (PCOR), a novel method of enzyme isolation was developed. The detergent isotridecyl poly-(ethylene glycol) ether (Genapol X-080) selectively solubilizes the enzyme from a prolamellar-body fraction isolated from wheat (Triticum aestivum L.). The solubilized fraction was further purified by ion-exchange chromatography. The isolated enzyme was studied by fluorescence spectroscopy at 77 K, and by CD spectroscopy. The fluorescence-emission spectra revealed that the binding properties of the substrate and co-substrate were preserved and that photo-reduction occurred. The CD spectra of PCOR were analysed for the relative amounts of the secondary structures, alpha-helix, beta-sheet, turn and random coil. The secondary structure composition was estimated to be 33% alpha-helix, 19% beta-sheet, 20% turn and 28% random coil. These values are in agreement with those predicted by the Predict Heidelberg Deutschland and self-optimized prediction method from alignments methods. The enzyme has some amino acid identity with other NADPH-binding enzymes containing the Rossmann fold. The Rossmann-fold fingerprint motif is localized in the N-terminal region and at the expected positions in the predicted secondary structure. It is suggested that PCOR is anchored to the interfacial region of the membrane by either a beta-sheet or an alpha-helical region containing tryptophan residues. A hydrophobic loop-region could also be involved in membrane anchoring. PMID:8713084

  18. Abstract Minute inversions (4 bp in length), associated with probable hairpin secondary structures, were inferred

    E-print Network

    Kelchner, Scot A.

    Abstract Minute inversions (4 bp in length), associated with probable hairpin secondary structures, were inferred from comparative analysis of rpl16 intron sequences from the chloroplast genomes-coding region of the chloroplast genome, suggesting that the inversional process may be a common feature of non

  19. PolyprOnline: polyproline helix II and secondary structure assignment database

    PubMed Central

    Chebrek, Romain; Leonard, Sylvain; de Brevern, Alexandre G.; Gelly, Jean-Christophe

    2014-01-01

    The polyproline helix type II (PPII) is a regular protein secondary structure with remarkable features. Many studies have highlighted different crucial biological roles supported by this local conformation, e.g. in the interactions between biological macromolecules. Although PPII is less frequently present than regular secondary structures such as canonical alpha helices and beta strands, it corresponds to 3–10% of residues. Up to now, PPII is not assigned by most popular assignment tools, and therefore, remains insufficiently studied. PolyprOnline database is, therefore, dedicated to PPII structure assignment and analysis to facilitate the study of PPII structure and functional roles. This database is freely accessible from www.dsimb.inserm.fr/dsimb_tools/polyproline. PMID:25380779

  20. Detection of Secondary and Supersecondary Structures of Proteins from Cryo-Electron Microscopy

    PubMed Central

    Bajaj, Chandrajit; Goswami, Samrat; Zhang, Qin

    2012-01-01

    Recent advances in three-dimensional electron microscopy (3D EM) have enabled the quantitative visualization of the structural building blocks of proteins at improved resolutions. We provide algorithms to detect the secondary structures (?-helices and ?-sheets) from proteins for which the volumetric maps are reconstructed at 6–10Å resolution. Additionally, we show that when the resolution is coarser than 10Å, some of the super-secondary structures can be detected from 3D EM maps. For both these algorithms, we employ tools from computational geometry and differential topology, specifically the computation of stable/unstable manifolds of certain critical points of the distance function induced by the molecular surface. Our results connect mathematically well-defined constructions with bio-chemically induced structures observed in proteins. PMID:22186625

  1. The predicted secondary structures of class I fructose-bisphosphate aldolases.

    PubMed Central

    Sawyer, L; Fothergill-Gilmore, L A; Freemont, P S

    1988-01-01

    The results of several secondary-structure prediction programs were combined to produce an estimate of the regions of alpha-helix, beta-sheet and reverse turns for fructose-bisphosphate aldolases from human and rat muscle and liver, from Trypanosoma brucei and from Drosophila melanogaster. All the aldolase sequences gave essentially the same pattern of secondary-structure predictions despite having sequences up to 50% different. One exception to this pattern was an additional strongly predicted helix in the rat liver and Drosophila enzymes. Regions of relatively high sequence variation generally were predicted as reverse turns, and probably occur as surface loops. Most of the positions corresponding to exon boundaries are located between regions predicted to have secondary-structural elements consistent with a compact structure. The predominantly alternating alpha/beta structure predicted is consistent with the alpha/beta-barrel structure indicated by preliminary high-resolution X-ray diffraction studies on rabbit muscle aldolase [Sygusch, Beaudry & Allaire (1986) Biophys. J. 49, 287a]. Images Fig. 1. (cont.) Fig. 1. PMID:3128269

  2. Targeting Nucleic Acid Secondary Structures by Antisense Oligonucleotides Designed through in vitro Selection

    NASA Astrophysics Data System (ADS)

    Mishra, Rakesh K.; Le Tinevez, Rejane; Toulme, Jean-Jacques

    1996-10-01

    Using an in vitro selection approach, we have isolated oligonucleotides that can bind to a DNA hairpin structure. Complex formation of these oligonucleotides with the target hairpin involves some type of triple-stranded structure with noncanonical interaction, as indicated by band-shift assays and footprinting studies. The selected oligomers can block restriction endonuclease cleavage of the target hairpin in a sequence-specific manner. We demonstrate that in vitro selection can extend the antisense approach to functional targeting of secondary structure motifs. This could provide a basis for interfering with regulatory processes mediated by a variety of nucleic acid structures.

  3. 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…

  4. The role of G-quadruplex/i-motif secondary structures as cis-acting regulatory elements

    PubMed Central

    Kendrick, Samantha; Hurley, Laurence H.

    2011-01-01

    The nature of DNA has captivated scientists for more than fifty years. The discovery of the double-helix model of DNA by Watson and Crick in 1953 not only established the primary structure of DNA, but also provided the mechanism behind DNA function. Since then, researchers have continued to further the understanding of DNA structure and its pivotal role in transcription. The demonstration of DNA secondary structure formation has allowed for the proposal that the dynamics of DNA itself can function to modulate transcription. This review presents evidence that DNA can exist in a dynamic equilibrium between duplex and secondary conformations. In addition, data demonstrating that intracellular proteins as well as small molecules can shift this equilibrium in either direction to alter gene transcription will be discussed, with a focus on the modulation of proto-oncogene expression. PMID:21796223

  5. 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. PMID:25964384

  6. Secondary Structural Preferences of Some Antibacterial Cyclooctapeptides in the Presence of Calcium(II)

    PubMed Central

    Stevens, Tarshona; McNeil, Nykia; Lin, Xiuli; Ngu-Schwemlein, Maria

    2012-01-01

    The purpose of this study is to understand the interactions of some antibacterial cationic amphipathic cyclooctapeptides with calcium(II) and their secondary structural preferences. The thermodynamic parameters associated with calcium(II) interactions, between the antibacterial active cyclooctapeptides (COP 1–6) and those that did not exhibit significant activities (COP 7–9), were studied by isothermal titration calorimetry. Calcium(II) binding in the absence and presence of micellar dodecylphosphocholine (DPC), a membrane mimicking detergent, was conducted by circular dichroism (CD). Both groups of cyclopeptides showed weak binding affinities for calcium(II) (Kb ca. 10?3?M?1). However, CD data showed that the antimicrobial peptides COP 1–6 adopted a twisted beta-sheet structure (positive CD absorption band at ca. 203?nm) in the presence of calcium(II) in micellar DPC. In contrast, COP 7–9, which lacked antibacterial activity, adopted a different conformational structure (negative CD absorption band at ca. 203?nm). These results indicate that these cyclopeptides could adopt secondary structural preferences in the presence of calcium(II) amidst a hydrophobic environment to elicit their antibacterial activity. These findings could be useful in facilitating the design of cyclopeptide derivatives that can adopt this beta-sheet-like secondary structure and, thereby, provide a useful molecular template for crafting antibacterial compounds. PMID:25379288

  7. The Pekin duck programmed death-ligand 1: cDNA cloning, genomic structure, molecular characterization and mRNA expression analysis.

    PubMed

    Yao, Q; Fischer, K P; Tyrrell, D L; Gutfreund, K S

    2015-04-01

    Programmed death ligand-1 (PD-L1) plays an important role in the attenuation of adaptive immune responses in higher vertebrates. Here, we describe the identification of the Pekin duck PD-L1 orthologue (duPD-L1) and its gene structure. The duPD-L1 cDNA encodes a 311-amino acid protein that has an amino acid identity of 78% and 42% with chicken and human PD-L1, respectively. Mapping of the duPD-L1 cDNA with duck genomic sequences revealed an exonic structure of its coding sequence similar to those of other vertebrates but lacked a noncoding exon 1. Homology modelling of the duPD-L1 extracellular domain was compatible with the tandem IgV-like and IgC-like IgSF domain structure of human PD-L1 (PDB ID: 3BIS). Residues known to be important for receptor binding of human PD-L1 were mostly conserved in duPD-L1 within the N-terminus and the G sheet, and partially conserved within the F sheet but not within sheets C and C'. DuPD-L1 mRNA was constitutively expressed in all tissues examined with highest expression levels in lung and spleen and very low levels of expression in muscle, kidney and brain. Mitogen stimulation of duck peripheral blood mononuclear cells transiently increased duPD-L1 mRNA expression. Our observations demonstrate evolutionary conservation of the exonic structure of its coding sequence, the extracellular domain structure and residues implicated in receptor binding, but the role of the longer cytoplasmic tail in avian PD-L1 proteins remains to be determined. PMID:25556810

  8. Altered features in the secondary structure of Vicia faba 5.8s rRNA.

    PubMed

    Nazar, R N; Wildeman, A G

    1981-10-24

    We have re-examined the nucleotide sequence of Vicia faba (broad bean) 5.8S rRNA using partial chemical degradation and a new approach to high temperature (65-80 degrees C) sequencing gels. The results indicate that the secondary structure was not completely disrupted in previous studies (Tanaka, Y., Dyer, T.A. and Brownlee, G.G. (1980) Nucleic Acid Res. 8, 1259-1272) and explain ambiguities between the nucleotide sequence and T1 ribonuclease digests. Despite this revision, estimates in the secondary structure suggest that this 5.8S rRNA differs from previously examined examples in two respects, more open conformations in both the "GC-rich" and "AU-rich" stems. The secondary structure was probed under a variety of ionic conditions using limited pancreatic and T1 ribonuclease digestion and rapid gel sequencing techniques. These studies and theoretical considerations generally supported the "burp gun" model previously proposed for all 5.8S rRNAs and were inconsistent with the recently suggested "cloverleaf" configuration. More importantly, they were also consistent with more open stem structures in this higher plant. PMID:7301589

  9. Prediction of protein secondary structure content for the twilight zone sequences.

    PubMed

    Homaeian, Leila; Kurgan, Lukasz A; Ruan, Jishou; Cios, Krzysztof J; Chen, Ke

    2007-11-15

    Secondary protein structure carries information about local structural arrangements, which include three major conformations: alpha-helices, beta-strands, and coils. Significant majority of successful methods for prediction of the secondary structure is based on multiple sequence alignment. However, multiple alignment fails to provide accurate results when a sequence comes from the twilight zone, that is, it is characterized by low (<30%) homology. To this end, we propose a novel method for prediction of secondary structure content through comprehensive sequence representation, called PSSC-core. The method uses a multiple linear regression model and introduces a comprehensive feature-based sequence representation to predict amount of helices and strands for sequences from the twilight zone. The PSSC-core method was tested and compared with two other state-of-the-art prediction methods on a set of 2187 twilight zone sequences. The results indicate that our method provides better predictions for both helix and strand content. The PSSC-core is shown to provide statistically significantly better results when compared with the competing methods, reducing the prediction error by 5-7% for helix and 7-9% for strand content predictions. The proposed feature-based sequence representation uses a comprehensive set of physicochemical properties that are custom-designed for each of the helix and strand content predictions. It includes composition and composition moment vectors, frequency of tetra-peptides associated with helical and strand conformations, various property-based groups like exchange groups, chemical groups of the side chains and hydrophobic group, auto-correlations based on hydrophobicity, side-chain masses, hydropathy, and conformational patterns for beta-sheets. The PSSC-core method provides an alternative for predicting the secondary structure content that can be used to validate and constrain results of other structure prediction methods. At the same time, it also provides useful insight into design of successful protein sequence representations that can be used in developing new methods related to prediction of different aspects of the secondary protein structure. PMID:17623861

  10. 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.

  11. NMR structure of the apoB mRNA stem–loop and its interaction with the C to U editing APOBEC1 complementary factor

    PubMed Central

    MARIS, CHRISTOPHE; MASSE, JAMES; CHESTER, ANN; NAVARATNAM, NAVEENAN; ALLAIN, FRÉDÉRIC H.-T.

    2005-01-01

    We have solved the NMR structure of the 31-nucleotide (nt) apoB mRNA stem–loop, a substrate of the cytidine deaminase APOBEC1. We found that the edited base located at the 5? end of the octa-loop is stacked between two adenosines in both the unedited (cytidine 6666) and the edited (uridine 6666) forms and that the rest of the loop is unstructured. The 11-nt “mooring” sequence essential for editing is partially flexible although it is mostly in the stem of the RNA. The octa-loop and the internal loop in the middle of the stem confer this flexibility. These findings shed light on why APOBEC1 alone cannot edit efficiently the cytidine 6666 under physiological conditions, the editing base being buried in the loop and not directly accessible. We also show that APOBEC1 does not specifically bind apoB mRNA and requires the auxiliary factor, APOBEC1 complementary factor (ACF), to edit specifically cytidine 6666. The binding of ACF to both the mooring sequence and APOBEC1 explains the specificity of the reaction. Our NMR study lead us to propose a mechanism in which ACF recognizes first the flexible nucleotides of the mooring sequence (the internal loop and the 3? end octa-loop) and subsequently melts the stem–loop, exposing the amino group of the cytidine 6666 to APOBEC1. Thus, the flexibility of the mooring sequence plays a central role in the RNA recognition by ACF. PMID:15659357

  12. A Replica Exchange Monte Carlo Algorithm for the Optimization of Secondary Structure Packing in Proteins

    Microsoft Academic Search

    Leonidas Kapsokalivas; Kathleen Steinhöfel

    2010-01-01

    \\u000a We approach the problem of packing secondary structure fragments into low energy conformations with a local search optimization\\u000a algorithm. Protein conformations are represented in a simplified off-lattice model. In that model we propose a move set that\\u000a transforms a protein conformation into another in order to enable the use of local search algorithms for protein folding simulations\\u000a and conformational search.

  13. Oxidation of goat hepatic galectin-1 induces change in secondary structure.

    PubMed

    Pande, Abhay H; Gupta, Rajesh K; Sumati; Hajela, Krishnan

    2003-06-01

    Galectin-1 requires a reducing environment for its lectin activity and the carbohydrate binding function is destroyed in oxidizing condition. In this report we provide direct evidence that the oxidation of goat hepatic galectin-1 perturbs its carbohydrate recognition domain and this could be due to changes in secondary structure of goat hepatic galectin-1. Conformational changes in goat hepatic galectin-1 due to oxidation were investigated by absorption, fluorescence and circular dichroism measurements. PMID:12871146

  14. DIALIGN-TX and multiple protein alignment using secondary structure information at GOBICS

    PubMed Central

    Subramanian, Amarendran R.; Hiran, Suvrat; Steinkamp, Rasmus; Meinicke, Peter; Corel, Eduardo; Morgenstern, Burkhard

    2010-01-01

    We introduce web interfaces for two recent extensions of the multiple-alignment program DIALIGN. DIALIGN-TX combines the greedy heuristic previously used in DIALIGN with a more traditional ‘progressive’ approach for improved performance on locally and globally related sequence sets. In addition, we offer a version of DIALIGN that uses predicted protein secondary structures together with primary sequence information to construct multiple protein alignments. Both programs are available through ‘Göttingen Bioinformatics Compute Server’ (GOBICS). PMID:20497995

  15. Influence of secondary structure on kinetics and reaction mechanism of DNA hybridization

    Microsoft Academic Search

    Chunlai Chen; Wenjuan Wang; Zhang Wang; Fang Wei; Xin Sheng Zhao

    2007-01-01

    Hybridization of nucleic acids with secondary structure is involved in many biological processes and technological applications. To gain more insight into its mechanism, we have investigated the kinetics of DNA hybridization\\/denaturation via fluorescence resonance energy transfer (FRET) on perfectly matched and single-base-mismatched DNA strands. DNA hybridization shows non- Arrhenius behavior. At high temperature, the appar- ent activation energies of DNA

  16. Molecular Dynamics Simulation of Protein Denaturation: Solvation of the Hydrophobic Cores and Secondary Structure of Barnase

    Microsoft Academic Search

    Amedeo Caflisch; Martin Karplus

    1994-01-01

    The transition in barnase from the native state to a compact globule has been studied with high-temperature molecular dynamics simulations. A partial destruction of the alpha-helices and the outer strands of the beta-sheet is observed with water molecules replacing the hydrogen bonds of the secondary structural elements. Simultaneously, the main alpha-helix moves away from the beta-sheet and exposes the principal

  17. MUC7 20Mer: Investigation of Antimicrobial Activity, Secondary Structure, and Possible Mechanism of Antifungal Action

    Microsoft Academic Search

    Libuse A. Bobek; Hongsa Situ

    2003-01-01

    This study was aimed at examining the spectrum of antimicrobial activity of MUC7 20-mer (N-LAHQKP- FIRKSYKCLHKRCR-C; residues 32 to 51 of MUC7, the low-molecular-weight human salivary mucin, com- prised of 357 residues) and comparing its antifungal properties to those of salivary histatin 5 (Hsn-5). We also examined the secondary structure of the 20-mer and the possible mechanism of its antifungal

  18. RNA secondary structures in the proximal 3?UTR of Indonesian Dengue 1 virus strains

    Microsoft Academic Search

    Penelope Koraka; Marisol M. Williams; Kis Djamiatun; Tatty E. Setiati; F. H. D van Batenburg; Koert J. Stittelaar; Albert D. M. E. Osterhaus; Byron E. E. Martina

    2009-01-01

    The characteristics of DENV-1 viruses, isolated during the 2001–2002 outbreak in Indonesia were studied. The secondary structure of the 3?UTR of different DENV-1 strains derived from Indonesian patients was compared with the 3?UTR of previously described DENV-1 sequences. The complete 3?UTR of DENV-1 was sequenced from 13 patients suffering from the severe form of dengue virus infection (dengue hemorrhagic fever).

  19. A novel representation of RNA secondary structure based on element-contact graphs

    PubMed Central

    Shu, Wenjie; Bo, Xiaochen; Zheng, Zhiqiang; Wang, Shengqi

    2008-01-01

    Background Depending on their specific structures, noncoding RNAs (ncRNAs) play important roles in many biological processes. Interest in developing new topological indices based on RNA graphs has been revived in recent years, as such indices can be used to compare, identify and classify RNAs. Although the topological indices presented before characterize the main topological features of RNA secondary structures, information on RNA structural details is ignored to some degree. Therefore, it is necessity to identify topological features with low degeneracy based on complete and fine-grained RNA graphical representations. Results In this study, we present a complete and fine scheme for RNA graph representation as a new basis for constructing RNA topological indices. We propose a combination of three vertex-weighted element-contact graphs (ECGs) to describe the RNA element details and their adjacent patterns in RNA secondary structure. Both the stem and loop topologies are encoded completely in the ECGs. The relationship among the three typical topological index families defined by their ECGs and RNA secondary structures was investigated from a dataset of 6,305 ncRNAs. The applicability of topological indices is illustrated by three application case studies. Based on the applied small dataset, we find that the topological indices can distinguish true pre-miRNAs from pseudo pre-miRNAs with about 96% accuracy, and can cluster known types of ncRNAs with about 98% accuracy, respectively. Conclusion The results indicate that the topological indices can characterize the details of RNA structures and may have a potential role in identifying and classifying ncRNAs. Moreover, these indices may lead to a new approach for discovering novel ncRNAs. However, further research is needed to fully resolve the challenging problem of predicting and classifying noncoding RNAs. PMID:18402706

  20. Super-secondary structure peptidomimetics: design and synthesis of an ?-? hairpin analogue

    PubMed Central

    Nevola, Laura; Rodriguez, Johanna M.; Thompson, Sam; Hamilton, Andrew D.

    2015-01-01

    The ?-? helix motif presents key recognition domains in protein-protein and protein-oligonucleotide binding, and is one of the most common super-secondary structures. Herein we describe the design, synthesis and structural characterization of an ?-? hairpin analogue based on a tetra-coordinated Pd(II) bis-(iminoisoquinoline) complex as a template for the display of two ?-helix mimics. This approach is exemplified by the attachment of two biphenyl peptidomimetics to reproduce the side-chains of the i and i+4 residues of two helices.

  1. Topology-dependent swichability of peptide secondary structures in bioconjugates with complex architectures.

    PubMed

    Börner, Hans G; Sütterlin, Romina I; Theato, Patrick; Wiss, Kerstin T

    2014-01-01

    Peptide sequences, which exhibit a reversible pH-responsive coil to ?-helix secondary structure transition, are conjugated to polymer precursors to yield linear AB and graft ABA peptide-poly(ethylene oxide) conjugates. While the PEO B-block is comparable, the conjugates differ in topologies of the peptide bearing A-blocks. The influences of topology on the structure transitions in the peptide segments are investigated, comparing linear AB-bioconjugates with graft ABA-bioconjugates having multiple peptide segments combined in star or pom-pom topologies. PMID:24323643

  2. A proton nuclear magnetic resonance assignment and secondary structure determination of recombinant human thioredoxin

    SciTech Connect

    Forman-Kay, J.D.; Clore, G.M.; Driscoll, P.C.; Wingfield, P.; Richards, F.M.; Gronenborn, A.M. (National Institutes of Health, Bethesda, MD (USA))

    1989-08-22

    Two-dimensional {sup 1}H NMR spectroscopy has been applied to a structural analysis of the reduced form of a recombinant human thioredoxin, a ubiquitous dithiol oxidoreductase recently isolated from an immunocompetent lymphoblastoid cell line. The sequential assignment of the spectrum, including all proline residues, has been accomplished by using experiments to demonstrate through-bond and through-space connectivities. The secondary structure has been determined by a qualitative interpretation of nuclear Overhauser effects, NH exchange data, and {sup 3}J{sub HN{alpha}} coupling constants. The secondary structure was found to be similar to that of the X-ray structure of Escherichia coli thioredoxin, consisting of a mixed five-stranded {beta}-sheet surrounded by four {alpha}-helices. The assignment and structural characterization of human thioredoxin was facilitated by the increased resolution and sensitivity afforded by a magnetic field strength of 600 MHz and required the use of two temperatures and two pH conditions to resolve ambiguities caused by a duplication of resonances. This duplication, extending from Phe-41 to Val-59, and including Lys-3-Ile-5, Val-24, Val-25, Asn-39, and Ile-101-Glu-103, appears to be due to heterogeneity arising from the presence or absence of the N-terminal methionine.

  3. Secondary structure of rhBMP-2 in a protective biopolymeric carrier material.

    PubMed

    Gilde, Flora; Maniti, Ofélia; Guillot, Raphael; Mano, Joao F; Logeart-Avramoglou, Delphine; Sailhan, Frédéric; Picart, Catherine

    2012-11-12

    Efficient delivery of growth factors is one of the great challenges of tissue engineering. Polyelectrolyte multilayer films (PEM) made of biopolymers have recently emerged as an interesting carrier for delivering recombinant human bone morphogenetic protein 2 (rhBMP-2 noted here BMP-2) to cells in a matrix-bound manner. We recently showed that PEM made of poly(l-lysine) and hyaluronan (PLL/HA) can retain high and tunable quantities of BMP-2 and can deliver it to cells to induce their differentiation in osteoblasts. Here, we investigate quantitatively by Fourier transform infrared spectroscopy (FTIR) the secondary structure of BMP-2 in solution as well as trapped in a biopolymeric thin film. We reveal that the major structural elements of BMP-2 in solution are intramolecular ?-sheets and unordered structures as well as ?-helices. Furthermore, we studied the secondary structure of rhBMP-2 trapped in hydrated films and in dry films since drying is an important step for future applications of these bioactive films onto orthopedic biomaterials. We demonstrate that the structural elements were preserved when BMP-2 was trapped in the biopolymeric film in hydrated conditions and, to a lesser extent, in dry state. Importantly, its bioactivity was maintained after drying of the film. Our results appear highly promising for future applications of these films as coatings of biomedical materials, to deliver bioactive proteins while preserving their bioactivity upon storage in dry state. PMID:22967015

  4. Fast and accurate clustering of noncoding RNAs using ensembles of sequence alignments and secondary structures

    PubMed Central

    2011-01-01

    Background Clustering of unannotated transcripts is an important task to identify novel families of noncoding RNAs (ncRNAs). Several hierarchical clustering methods have been developed using similarity measures based on the scores of structural alignment. However, the high computational cost of exact structural alignment requires these methods to employ approximate algorithms. Such heuristics degrade the quality of clustering results, especially when the similarity among family members is not detectable at the primary sequence level. Results We describe a new similarity measure for the hierarchical clustering of ncRNAs. The idea is that the reliability of approximate algorithms can be improved by utilizing the information of suboptimal solutions in their dynamic programming frameworks. We approximate structural alignment in a more simplified manner than the existing methods. Instead, our method utilizes all possible sequence alignments and all possible secondary structures, whereas the existing methods only use one optimal sequence alignment and one optimal secondary structure. We demonstrate that this strategy can achieve the best balance between the computational cost and the quality of the clustering. In particular, our method can keep its high performance even when the sequence identity of family members is less than 60%. Conclusions Our method enables fast and accurate clustering of ncRNAs. The software is available for download at http://bpla-kernel.dna.bio.keio.ac.jp/clustering/. PMID:21342580

  5. 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 ?-helix and ?-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. PMID:24985932

  6. Molecular characterization and in situ mRNA localization of the neural recognition molecule J1-160/180: a modular structure similar to tenascin

    PubMed Central

    1993-01-01

    The oligodendrocyte-derived extracellular matrix glycoprotein J1- 160/180 is a recognition molecule expressed exclusively in the central nervous system. J1-160/180 has been shown to be adhesive for astrocytes and repellent towards neurons and growth cones. We report here the complete nucleotide sequence of J1-160/180 in the rat. The predicted amino acid sequence showed a structural architecture very similar to tenascin: a cysteine-rich amino terminal region is followed by 4.5 epidermal growth factor-like repeats, 9 fibronectin type III homologous repeats and a domain homologous to fibrinogen. Sequence comparison analysis revealed highest homology of rat J1-160/180 to mouse tenascin and chicken restrictin with a similarity of 66% and 85%, respectively. The J1-160/180-coding mRNA is derived from a single copy gene. Using the polymerase chain reaction we could show that two J1-160/180 isoforms are generated by alternative splicing of the sixth fibronectin type III homologous repeat. Localization of J1-160/180 mRNA by in situ hybridization in the cerebellum, hippocampus and olfactory bulb confirmed the expression of J1-160/180 by oligodendrocytes with a peak of transcription at 7-14 d after birth, indicating a functional role during myelination. In addition, J1-160/180-specific RNA was found in a small subset of neurons in all three structures of the CNS analyzed. These neurons continue to express J1-160/180 in the adult. PMID:7679676

  7. Combining secondary-structure and protein solvent-accessibility predictions in methionine substitution for anomalous dispersion.

    PubMed

    Wu, Hsin-Yi; Cheng, Yi-Sheng

    2014-03-01

    In X-ray crystallographic analysis, the single-wavelength and multi-wavelength anomalous diffraction (SAD and MAD) methods have been widely used in order to solve the phase problem. Selenium-labelled methionine has been shown to be very effective for anomalous dispersion phasing, and at least one selenomethionine is required for every 100 amino acids. Some proteins, such as the Arabidopsis thaliana thylakoid lumen protein AtTLP18.3, can be overexpressed in an Escherichia coli system and high-quality protein crystals can be obtained. However, AtTLP18.3 contains no methionine residues, and site-directed mutagenesis was required in order to introduce methionine residues into the protein. A criterion for the mutated residues is that they should avoid affecting the structure and function. In this study, several leucine and isoleucine residues were selected for methionine substitution by combining secondary-structure and solvent-accessibility predictions. From the secondary-structure prediction, mutated residues were first determined in the coil or loop regions at the junction of two secondary structures. Since leucine and isoleucine residues are hydrophobic and are normally buried within the protein core, these residues should have a higher solvent-accessibility prediction so that they would be partially buried or exposed in the protein. In addition, five residues (Leu107, Leu202, Ile133, Leu128 and Ile159) of AtTLP18.3 were mutated to methionine residues. After overexpression and purification, only two single-mutant lines, L128M and I159M, could be crystallized. Finally, a double-mutation line of truncated AtTLP18.3 with L128M and I159M mutations was constructed. The structure of the double mutant AtTLP18.3 protein was resolved using the single-wavelength anomalous diffraction method at 2.6?Å resolution. The results indicated that a combination of secondary-structure and solvent-accessibility prediction for methionine substitution is a useful method in SAD and MAD phasing. PMID:24598932

  8. 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

  9. Unit-cell intergrowth of pyrochlore and hexagonal tungsten bronze structures in secondary tungsten minerals

    SciTech Connect

    Grey, Ian E. [CSIRO Minerals, Box 312, Clayton South, Vic. 3169 (Australia)]. E-mail: ian.grey@csiro.au; Birch, William D. [Geosciences Department, Museum Victoria, GPO Box 666, Melbourne, Vic. 3001 (Australia); Bougerol, Catherine [Equipe CEA-CNRS NPSC SP2M/DRFMC/CEA, 17 rue des Martyrs, 38054 Grenoble (France); Mills, Stuart J. [CSIRO Minerals, Box 312, Clayton South, Vic. 3169 (Australia); Geosciences Department, Museum Victoria, GPO Box 666, Melbourne, Vic. 3001 (Australia)

    2006-12-15

    Structural relations between secondary tungsten minerals with general composition A{sub x}[(W,Fe)(O,OH){sub 3}]{sub .y}H{sub 2}O are described. Phyllotungstite (A=predominantly Ca) is hexagonal, a=7.31(3)A, c=19.55(1)A, space group P6{sub 3}/mmc. Pittongite, a new secondary tungsten mineral from a wolframite deposit near Pittong in Victoria, southeastern Australia (A=predominantly Na) is hexagonal, a=7.286(1)A, c=50.49(1)A, space group P-6m2. The structures of both minerals can be described as unit-cell scale intergrowths of (111){sub py} pyrochlore slabs with pairs of hexagonal tungsten bronze (HTB) layers. In phyllotungstite, the (111){sub py} blocks have the same thickness, 6A, whereas pittongite contains pyrochlore blocks of two different thicknesses, 6 and 12A. The structures can alternatively be described in terms of chemical twinning of the pyrochlore structure on (111){sub py} oxygen planes. At the chemical twin planes, pairs of HTB layers are corner connected as in hexagonal WO{sub 3}.

  10. Discrete state model and accurate estimation of loop entropy of RNA secondary structures

    PubMed Central

    Zhang, Jian; Lin, Ming; Chen, Rong; Wang, Wei; Liang, Jie

    2008-01-01

    Conformational entropy makes important contribution to the stability and folding of RNA molecule, but it is challenging to either measure or compute conformational entropy associated with long loops. We develop optimized discrete k-state models of RNA backbone based on known RNA structures for computing entropy of loops, which are modeled as self-avoiding walks. To estimate entropy of hairpin, bulge, internal loop, and multibranch loop of long length (up to 50), we develop an efficient sampling method based on the sequential Monte Carlo principle. Our method considers excluded volume effect. It is general and can be applied to calculating entropy of loops with longer length and arbitrary complexity. For loops of short length, our results are in good agreement with a recent theoretical model and experimental measurement. For long loops, our estimated entropy of hairpin loops is in excellent agreement with the Jacobson–Stockmayer extrapolation model. However, for bulge loops and more complex secondary structures such as internal and multibranch loops, we find that the Jacobson–Stockmayer extrapolation model has large errors. Based on estimated entropy, we have developed empirical formulae for accurate calculation of entropy of long loops in different secondary structures. Our study on the effect of asymmetric size of loops suggest that loop entropy of internal loops is largely determined by the total loop length, and is only marginally affected by the asymmetric size of the two loops. Our finding suggests that the significant asymmetric effects of loop length in internal loops measured by experiments are likely to be partially enthalpic. Our method can be applied to develop improved energy parameters important for studying RNA stability and folding, and for predicting RNA secondary and tertiary structures. The discrete model and the program used to calculate loop entropy can be downloaded at http://gila.bioengr.uic.edu/resources/RNA.html. PMID:18376982

  11. Structures in secondary flow under simple harmonic inflow in a 180 degree curved pipe model of an artery

    NASA Astrophysics Data System (ADS)

    Glenn, Autumn L.; Seagrave, Sarah L.; Bulusu, Kartik V.; Plesniak, Michael W.

    2011-11-01

    Inward centrifuging of fluid in a 180 degree curved pipe leads to development of secondary flow vortical structures. These Dean's vortices have been widely studied in steady flows. Complex secondary flow structures were observed under (unsteady) physiological flow forcing associated with the cardiac cycle, as well as simple harmonic forcing. These structures were investigated under several simple harmonic inflow conditions with phase-locked 2-D PIV measurements to examine the formation of coherent structures in the secondary flow. Experimental velocity field data were acquired at various cross-sectional planes along the bend. Multiple vortex pairs were observed at 90 degrees into the bend for all waveforms investigated. The overarching goal of this study is to understand the effect of driving waveform characteristics, i.e. period, flow acceleration, etc. on secondary flow morphologies and to characterize these morphologies in terms of dimensionless parameters describing the flow. Supported by the National Science Foundation under Grant No. CBET-0828903.

  12. The overall structure of the human lens is one of succes-sive generations of secondary fiber cells stratified chrono-

    E-print Network

    Hammock, Bruce D.

    The overall structure of the human lens is one of succes- sive generations of secondary fiber cells specialized fiber cells located at the core (nucleus) of the lens undergo pseudo-apoptosis to become devoid

  13. 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

  14. Solution and crystal structures of mRNA exporter Dbp5p and its interaction with nucleotides.

    PubMed

    Fan, Jing-Song; Cheng, Zhihong; Zhang, Jingfeng; Noble, Christian; Zhou, Zhihong; Song, Haiwei; Yang, Daiwen

    2009-04-24

    DEAD-box protein 5 (Dbp5p) plays very important roles in RNA metabolism from transcription, to translation, to RNA decay. It is an RNA helicase and functions as an essential RNA export factor from nucleus. Here, we report the solution NMR structures of the N- and C-terminal domains (NTD and CTD, respectively) of Dbp5p from Saccharomyces cerevisiae (ScDbp5p) and X-ray crystal structure of Dbp5p from Schizosaccharomyces pombe (SpDbp5p) in the absence of nucleotides and RNA. The crystal structure clearly shows that SpDbp5p comprises two RecA-like domains that do not interact with each other. NMR results show that the N-terminal flanking region of ScDpbp5 (M1-E70) is intrinsically unstructured and the region Y71-R121 including the Q motif is highly dynamic on millisecond-microsecond timescales in solution. The C-terminal flanking region of ScDbp5p forms a short beta-strand and a long helix. This helix is unique for ScDbp5p and has not been observed in other DEAD-box proteins. Compared with other DEAD-box proteins, Dbp5p has an extra insert with six residues in the CTD. NMR structure reveals that the insert is located in a solvent-exposed loop capable of interacting with other proteins. ATP and ADP titration experiments show that both ADP and ATP bind to the consensus binding site in the NTD of ScDbp5p but do not interact with the CTD at all. Binding of ATP or ADP to NTD induces significant conformational rearrangement too. PMID:19281819

  15. Differential protein occupancy profiling of the mRNA transcriptome

    PubMed Central

    2014-01-01

    Background RNA-binding proteins (RBPs) mediate mRNA biogenesis, translation and decay. We recently developed an approach to profile transcriptome-wide RBP contacts on polyadenylated transcripts by next-generation sequencing. A comparison of such profiles from different biological conditions has the power to unravel dynamic changes in protein-contacted cis-regulatory mRNA regions without a priori knowledge of the regulatory protein component. Results We compared protein occupancy profiles of polyadenylated transcripts in MCF7 and HEK293 cells. Briefly, we developed a bioinformatics workflow to identify differential crosslinking sites in cDNA reads of 4-thiouridine crosslinked polyadenylated RNA samples. We identified 30,000 differential crosslinking sites between MCF7 and HEK293 cells at an estimated false discovery rate of 10%. 73% of all reported differential protein-RNA contact sites cannot be explained by local changes in exon usage as indicated by complementary RNA-seq data. The majority of differentially crosslinked positions are located in 3? UTRs, show distinct secondary-structure characteristics and overlap with binding sites of known RBPs, such as ELAVL1. Importantly, mRNA transcripts with the most significant occupancy changes show elongated mRNA half-lives in MCF7 cells. Conclusions We present a global comparison of protein occupancy profiles from different cell types, and provide evidence for altered mRNA metabolism as a result of differential protein-RNA contacts. Additionally, we introduce POPPI, a bioinformatics workflow for the analysis of protein occupancy profiling experiments. Our work demonstrates the value of protein occupancy profiling for assessing cis-regulatory RNA sequence space and its dynamics in growth, development and disease. PMID:24417896

  16. Enzymatic synthesis of DNA complementary to mitochondrial mRNA via reverse transcription.

    PubMed Central

    Frolova, L; Arsenyan, S; Avdonina, T; Gaitskhoki, V; Kisselev, O; Neifach, S; Kisselev, L

    1978-01-01

    The poly(A)-containing mitochondrial mRNAs of rat liver were tested for their ability to serve as templates for the DNA synthesis by means of reverse transcription in the presence of the oligo(dT) primer and the RNA-directed DNA-polymerase from avian myeloblastosis virus. The mT-mRNA does not support the DNA synthesis in the standard conditions sufficient for effective reverse transcription of rabbit globin mRNA and of poly(A) in the presence of oligo(dT) primers. After a mild alkaline treatment of the mRNA and subsequent polyadenylation of the 3'-termini of the generated fragments with ATP:RNA adenyltransferase from E.coli the poly(A) (+) polyribonucleotides are able to serve as templates for reverse transcription in the presence of oligo(dT) and the reverse transcriptase. A conclusion is made that a "structural stop" exists in mitochondrial mRNA non-translable regions adjacent to the poly(A) terminal sequence. The "structural stop" is suggested to be caused by post-transcriptional modification of mRNA (methylation, etc.) or by a particularly stable secondary structure in this region of the mRNA molecules. PMID:77007

  17. Investigation of secondary structures and macromolecular interactions in bacteriophage P22 by laser Raman spectroscopy

    SciTech Connect

    Fish, S.R. (Univ. of Rhode Island, Kingston); Fuller, M.T.; King, J.; Thomas, G.J. Jr

    1980-10-01

    Laser Raman spectra of the DNA bacteriophage P22 and of its precursor particles and related structures have been obtained using 514.5-nm excitation. The spectra show that P22 DNA exists in the B form both inside of the phage head and after extraction from the phage. The major coat protein (gp5) contains a secondary structure composed of 18% ..cap alpha..-helix, 20% BETA-sheet and 62% irregular conformations. The scaffolding protein (gp8) in the phage prohead is substantially richer than gp5 in ..cap alpha..-helical content. Among the amino acid residues which give prominent Raman lines, the spectra show that tryptophans are exposed to solvent and most tyrosines are hydrogen bonded to positive donor groups. The above features of phage DNA and protein structures are nearly invariant to changes in temperature up to 80/sup 0/C, indicating a remarkable thermal stability of the phage head and its encapsulated DNA.

  18. 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 ?-helical proteins; which are softer than ?-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

  19. Rigidity, secondary structure, and the universality of the boson peak in proteins.

    PubMed

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

    2014-06-17

    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 ?-helical proteins; which are softer than ?-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

  20. Use of techniques derived from graph theory to compare secondary structure motifs in proteins.

    PubMed

    Mitchell, E M; Artymiuk, P J; Rice, D W; Willett, P

    1990-03-01

    A substructure matching algorithm is described that can be used for the automatic identification of secondary structural motifs in three-dimensional protein structures from the Protein Data Bank. The proteins and motifs are stored for searching as labelled graphs, with the nodes of a graph corresponding to linear representations of helices and strands and the edges to the inter-line angles and distances. A modification of Ullman's subgraph isomorphism algorithm is described that can be used to search these graph representations. Tests with patterns from the protein structure literature demonstrate both the efficiency and the effectiveness of the search procedure, which has been implemented in FORTRAN 77 on a MicroVAX-II system, coupled to the molecular fitting program FRODO on an Evans and Sutherland PS300 graphics system. PMID:2319595

  1. Protein secondary structure prediction using different encoding schemes and neural network architectures

    NASA Astrophysics Data System (ADS)

    Zhong, Wei; Pan, Yi; Harrison, Robert; Tai, Phang C.

    2004-04-01

    Protein secondary structure prediction is very important for drug design, protein engineering and immunological studies. This research uses fully connected multilayer perceptron (MLP) neural network with one, two and three hidden layers to predict protein secondary structure. Orthogonal matrix, BLOSUM62 matrix and hydrophobicity matrix are used for input profiles. To increase the input information for neural networks, the combined matrix from BLOSUM62 and orthogonal matrix and the combined matrix from BLOSUM62 and hydrophobicity matrix are also experimented. Binary classifiers indicate test accuracy of one hidden layer is better than that of two and three hidden layers. This may indicate that increasing complexity of architecture may not help neural network to recognize structural pattern of protein sequence more accurately. The results also show that the combined input profile of BLOSUM62 matrix and orthogonal matrix is the best one among five encoding schemes. While accuracy of the tertiary classifier reaches 63.20%, binary classifier for H/~H is 78.70%, which is comparable to other researchers" results.

  2. 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

  3. Secondary Structure Preferences of Mn2+ Binding Sites in Bacterial Proteins

    PubMed Central

    Khrustaleva, Tatyana Aleksandrovna

    2014-01-01

    3D structures of proteins with coordinated Mn2+ ions from bacteria with low, average, and high genomic GC-content have been analyzed (149 PDB files were used). Major Mn2+ binders are aspartic acid (6.82% of Asp residues), histidine (14.76% of His residues), and glutamic acid (3.51% of Glu residues). We found out that the motif of secondary structure “beta strand-major binder-random coil” is overrepresented around all the three major Mn2+ binders. That motif may be followed by either alpha helix or beta strand. Beta strands near Mn2+ binding residues should be stable because they are enriched by such beta formers as valine and isoleucine, as well as by specific combinations of hydrophobic and hydrophilic amino acid residues characteristic to beta sheet. In the group of proteins from GC-rich bacteria glutamic acid residues situated in alpha helices frequently coordinate Mn2+ ions, probably, because of the decrease of Lys usage under the influence of mutational GC-pressure. On the other hand, the percentage of Mn2+ sites with at least one amino acid in the “beta strand-major binder-random coil” motif of secondary structure (77.88%) does not depend on genomic GC-content. PMID:24778647

  4. RNA secondary structure critical exponents of random sequences near the glass transition

    NASA Astrophysics Data System (ADS)

    Baez, William; Bundschuh, Ralf

    2014-03-01

    RNA forms elaborate secondary structures through intramolecular base pairing. These structures are important for the RNA's biological function but, due to the availability of a polynomial algorithm to calculate the partition function, they are also a model system for the study of statistical physics of disordered systems. In this context, it is known that below the denaturation temperature random RNA secondary structures can exist in one of two phases: a strongly disordered, low-temperature glass phase and a weakly disordered, high-temperature molten phase. The probability of two bases pairing in these phases have been shown to scale with the distance between the two bases as -3/2 and -1.33 in the molten and glass phases, respectively. In this study, we attempt to answer the question as to the value and behavior of this scaling exponent at and around the transition temperature. We present a precise determination of the location of the critical point and then use several methods to measure the exponent at this critical point including a comparison of different analytical models to describe finite-size effects developed within both phases. This material is based upon work supported by the National Science Foundation under Grant No. 1105458.

  5. The secondary structure and sequence optimization of an RNA ligase ribozyme.

    PubMed Central

    Ekland, E H; Bartel, D P

    1995-01-01

    In vitro selection can generate functional sequence variants of an RNA structural motif that are useful for comparative analysis. The technique is particularly valuable in cases where natural variation is unavailable or non-existent. We report the extension of this approach to a new extreme--the identification of a 112 nt ribozyme secondary structure imbedded within a 186 nt RNA. A pool of 10(14) variants of an RNA ligase ribozyme was generated using combinatorial chemical synthesis coupled with combinatorial enzymatic ligation such that 172 of the 186 relevant positions were partially mutagenized. Active variants of this pool were enriched using an in vitro selection scheme that retains the sequence variability at positions very close to the ligation junction. Ligases isolated after four rounds of selection catalyzed self-ligation up to 700 times faster than the starting sequence. Comparative analysis of the isolates indicated that when complexed with substrate RNAs the ligase forms a nested, double pseudo-knot secondary structure with seven stems and several important joining segments. Comparative analysis also suggested the identity of mutations that account for the increased activity of the selected ligase variants; designed constructs incorporating combinations of these changes were more active than any of the individual ligase isolates. Images PMID:7667099

  6. Structure of the Yeast SR protein Npl3 and Interaction with mRNA 3?-End Processing Signals

    PubMed Central

    Deka, Pritilekha; Bucheli, Miriam E.; Moore, Claire; Buratowski, Stephen; Varani, Gabriele

    2007-01-01

    Yeast Npl3 is homologous to SR proteins in higher eukaryotes, a family of RNA-binding proteins that play multiple essential roles in RNA metabolism. This protein competes with 3?-end processing factors for binding to the nascent RNA, protecting the transcript from premature termination and coordinating transcription termination and the packaging of the fully processed transcript for export. The NMR structure of its RNA-binding domain shows two unusually compact RNA Recognition Motifs, identifies the RNA recognition surface in Npl3. Biochemical and NMR studies identify a class of G/U-rich RNA sequences with high specificity for this protein. The protein binds to RNA by forming a single globular structure, but the two RRMs of Npl3 are not equivalent, with the second domain forming much stronger interactions with G/U-rich RNA sequences that occur independently of the interaction of the first RRM. The specific binding to G/U-rich RNAs observed for the two RRMs of Npl3 is masked in the full-length protein by a much stronger but non-sequence-specific RNA-binding activity residing outside of its RRMs. The preference of Npl3 for G/U-rich sequences supports the model for its function in regulating recognition of 3?-end processing sites through competition with the Rna15 (yeast analog of human CstF-64 protein) subunit of the processing complex. PMID:18022637

  7. Evaluation and improvement of multiple sequence methods for protein secondary structure prediction

    Microsoft Academic Search

    James A. Cuff; Geoffrey J. Barton

    1999-01-01

    ABSTRACT A new,dataset,of 396 protein,do- mains,is developed,and,used to evaluate,the perfor- mance,of the,protein,secondary,structure,predic- tion algorithms DSC, PHD, NNSSP, and PREDATOR. The maximum,theoretical Q3 accuracy,for combina- tion of these methods,is shown,to be 78%. A simple consensus prediction on the 396 domains, with auto- matically,generated,multiple,sequence,alignments gives an,average,Q3 prediction,accuracy,of 72.9%. This is a 1% improvement over PHD, which was the best single method,evaluated. Segment,Overlap

  8. Accurate ab Initio Study on the Hydrogen-Bond Pairs in Protein Secondary Structures

    PubMed Central

    Wang, Zhi-Xiang; Wu, Chun; Lei, Hongxing; Duan, Yong

    2014-01-01

    Ab initio calculations up to the MP2/aug-cc-pVQZ//MP2/6-311+G** level have been carried out to characterize the four patterns of hydrogen-bond (H-bond) pairs in protein secondary structures. The unblocked and methyl-blocked glycine dipeptide dimers were arranged to model the H-bond pairs in ?-helix (?HH) and antiparallel (A??-C5 and A??-C7) and parallel ?-sheet (P??) secondary structures. The study uncovers that, in addition to the primary CO?NH H-bonds and the crossing secondary interactions, the CH?OC H-bonds and the tertiary effect (as we call it) also contribute substantially. The tertiary effect is due to the interpolarization between the donor and acceptor of a H-bond. This effect, which enhances the dipole–dipole interactions between two nearby H-bonds, stabilizes the ?-sheet-like but destabilizes the helix-like H-bond pairs. The MP2 binding energies of the complexes were further refined by extrapolating to the complete basis set limit (CBS) according to Truhlar and co-workers and by a three-basis-set-based method. The best extrapolated CBS(aD-aT-aQ) binding energies of the unblocked dimers are ?13.1 (?HH), ?11.3 (A??-C5), ?19.2 (A??-C7), and ?14.8 kcal/mol (P??). For the methyl-blocked counterparts, the best extrapolated CBS(D-T-Q) binding energies are ?14.8, ?13.4, ?20.8, and ?16.7 kcal/mol, respectively. The interactions in the parallel ? conformations are very close to the averages of the C5 and C7 antiparallel ? conformations, and both are stronger than the helical dimers. Because the additive force fields are unable to account for the tertiary effect owing to the lack of polarization, all examined additive force fields significantly overestimate the interaction energies of the helix conformations relative to the ?-sheet conformations. Notably, the agreement between molecular mechanical and quantum mechanical binding energies is improved after turning on the polarization. The study provides reference ab initio structures and binding energies for characterizing the backbone H-bonds of the protein secondary structures, which can be used for the parametrization of empirical molecular mechanics force fields.

  9. Evaluation of a Cyclopentane-Based ?-Amino Acid for the Ability to Promote ?/?-Peptide Secondary Structure

    PubMed Central

    Giuliano, Michael W.; Maynard, Stacy J.; Almeida, Aaron M.; Reidenbach, Andrew G.; Guo, Li; Ulrich, Emily C.; Guzei, Ilia A.; Gellman, Samuel H.

    2014-01-01

    We report the asymmetric synthesis of the y-amino acid (1R,2R)-2-aminomethyl-1-cyclopentane carboxylic acid (AMCP) and an evaluation of this residue's potential to promote secondary structure in ?/?-peptides. Simulated annealing calculations using NMR-derived distance restraints obtained for ?/?-peptides in chloroform reveal that AMCP-containing oligomers are conformationally flexible. However, additional evidence that suggests an internally hydrogen-bonded helical conformation is partially populated in solution. From these data, we propose characteristic NOE patterns for formation of the ?/?-peptide 12/10-helix and present discussion of the apparent conformational frustration of AMCP-containing oligomers. PMID:24303945

  10. RNAMotifScan: automatic identification of RNA structural motifs using secondary structural alignment.

    PubMed

    Zhong, Cuncong; Tang, Haixu; Zhang, Shaojie

    2010-10-01

    Recent studies have shown that RNA structural motifs play essential roles in RNA folding and interaction with other molecules. Computational identification and analysis of RNA structural motifs remains a challenging task. Existing motif identification methods based on 3D structure may not properly compare motifs with high structural variations. Other structural motif identification methods consider only nested canonical base-pairing structures and cannot be used to identify complex RNA structural motifs that often consist of various non-canonical base pairs due to uncommon hydrogen bond interactions. In this article, we present a novel RNA structural alignment method for RNA structural motif identification, RNAMotifScan, which takes into consideration the isosteric (both canonical and non-canonical) base pairs and multi-pairings in RNA structural motifs. The utility and accuracy of RNAMotifScan is demonstrated by searching for kink-turn, C-loop, sarcin-ricin, reverse kink-turn and E-loop motifs against a 23S rRNA (PDBid: 1S72), which is well characterized for the occurrences of these motifs. Finally, we search these motifs against the RNA structures in the entire Protein Data Bank and the abundances of them are estimated. RNAMotifScan is freely available at our supplementary website (http://genome.ucf.edu/RNAMotifScan). PMID:20696653

  11. Formation of C-terminally truncated version of the Taz1 protein employs cleavage-box structure in mRNA

    SciTech Connect

    Gunisova, Stanislava; Bartosova, Zdenka [Department of Genetics, Comenius University, Faculty of Natural Sciences, 842 15 Bratislava (Slovakia)] [Department of Genetics, Comenius University, Faculty of Natural Sciences, 842 15 Bratislava (Slovakia); Kramara, Juraj; Nosek, Jozef [Department of Biochemistry, Comenius University, Faculty of Natural Sciences, 842 15 Bratislava (Slovakia)] [Department of Biochemistry, Comenius University, Faculty of Natural Sciences, 842 15 Bratislava (Slovakia); Tomaska, Lubomir, E-mail: tomaska@fns.uniba.sk [Department of Genetics, Comenius University, Faculty of Natural Sciences, 842 15 Bratislava (Slovakia)] [Department of Genetics, Comenius University, Faculty of Natural Sciences, 842 15 Bratislava (Slovakia)

    2010-02-12

    When expressed in various hosts the taz1{sup +} gene encoding the fission yeast telomere-binding protein produces two forms of polypeptides: full-length (Taz1p) and truncated (Taz1p{Delta}C) version lacking almost entire Myb-domain. Whereas Taz1p binds telomeric DNA in vitro, Taz1p{Delta}C forms long filaments unable of DNA binding. The formation of Taz1p{Delta}C is a result of neither site-specific proteolysis, nor premature termination of transcription. In silico analysis of the taz1{sup +} RNA transcript revealed a stem-loop structure at the site of cleavage (cleavage box; CB). In order to explore whether it possesses inherent destabilizing effects, we cloned CB sequence into the open reading frame (ORF) of glutathione-S-transferase (GST) and observed that when expressed in Escherichia coli the engineered gene produced two forms of the reporter protein. The formation of the truncated version of GST was abolished, when CB was replaced with recoded sequence containing synonymous codons thus indicating that the truncation is based on structural properties of taz1{sup +} mRNA.

  12. 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.

  13. STITCHER: Dynamic assembly of likely amyloid and prion beta-structures from secondary structure predictions

    E-print Network

    Bryan, Allen W.

    The supersecondary structure of amyloids and prions, proteins of intense clinical and biological interest, are difficult to determine by standard experimental or computational means. In addition, significant conformational ...

  14. Protein-coding structured RNAs: A computational survey of conserved RNA secondary structures overlapping coding regions in drosophilids.

    PubMed

    Findeiss, Sven; Engelhardt, Jan; Prohaska, Sonja J; Stadler, Peter F

    2011-11-01

    Functional RNA elements can be embedded also within exonic sequences coding for functional proteins. While not uncommon in viruses, only a few examples of this type have been described in some detail for eukaryotic genomes. Here we use RNAz and RNAcode, two comparative genomics methods that measure signatures of stabilizing selection acting on RNA secondary structure and peptide sequence, resp., to survey the fruit fly genomes. We estimate that there might be on the order of 1000 loci that are subject to dual selection pressure. The used genome-wide screens also expose the limitations of the currently available methods. PMID:21835221

  15. Compensatory mutations cause excess of antagonistic epistasis in RNA secondary structure folding

    E-print Network

    Claus O Wilke; Richard E Lenski; Christoph Adami

    2003-02-18

    Background: The rate at which fitness declines as an organism's genome accumulates random mutations is an important variable in several evolutionary theories. At an intuitive level, it might seem natural that random mutations should tend to interact synergistically, such that the rate of mean fitness decline accelerates as the number of random mutations is increased. However, in a number of recent studies, a prevalence of antagonistic epistasis (the tendency of multiple mutations to have a mitigating rather than reinforcing effect) has been observed. Results: We studied in silico the net amount and form of epistatic interactions in RNA secondary structure folding by measuring the fraction of neutral mutants as a function of mutational distance d. We found a clear prevalence of antagonistic epistasis in RNA secondary structure folding. By relating the fraction of neutral mutants at distance d to the average neutrality at distance d, we showed that this prevalence derives from the existence of many compensatory mutations at larger mutational distances. Conclusions: Our findings imply that the average direction of epistasis in simple fitness landscapes is directly related to the density with which fitness peaks are distributed in these landscapes.

  16. 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.

  17. Ultraviolet Raman examination of the environmental dependence of bombolitin I and bombolitin III secondary structure.

    PubMed Central

    Holtz, J S; Holtz, J H; Chi, Z; Asher, S A

    1999-01-01

    Bombolitin I and III (BI and BIII) are small amphiphilic peptides isolated from bumblebee venom. Although they exist in predominately nonhelical conformations in dilute aqueous solutions, we demonstrate, using UV Raman spectroscopy, that they become predominately alpha-helical in solution at pH > 10, in high ionic strength solutions, and in the presence of trifluoroethanol (TFE) and dodecylphosphocholine (DPC) micelles. In this paper, we examine the effects of electrostatic and hydrophobic interactions that control folding of BI and BIII by systematically monitoring their secondary structures as a function of solution conditions. We determine the BI and BIII secondary structure contents by using the quantitative UV Raman methodology of Chi et al. (1998. Biochemistry. 37:2854-2864). Our findings suggest that the alpha-helix turn in BIII at neutral pH is stabilized by a salt bridge between residues Asp2 and Lys5. This initial alpha-helical turn results in different BI and BIII alpha-helical folding mechanisms observed in high pH and high salt concentrations: BIII folds from its single alpha-helix turn close to its N-terminal, whereas the BI alpha-helix probably nucleates within the C-terminal half. We also used quasielastic light scattering to demonstrate that the BI and BIII alpha-helix formation in 0.2 M Ca(ClO4)2 is accompanied by formation of trimers and hexamers, respectively. PMID:10354447

  18. The influence of residual water on the secondary structure and crystallinity of freeze-dried fibrinogen.

    PubMed

    Wahl, Verena; Scheibelhofer, Otto; Roessl, Ulrich; Leitgeb, Stefan; De Beer, Thomas; Khinast, Johannes

    2015-04-30

    The purpose of this work was to investigate the influence of water content on the secondary structure of a freeze-dried protein (fibrinogen) after a storage period of two weeks. To that end, attenuated reflectance Fourier transformed infrared (ATR-FTIR) and Raman spectra were generated and evaluated and the crystalline state of the fibrinogen bulks was determined via X-ray diffraction. First, a PCA (principal component analysis) of the spectral data was performed. While the ?-helix and ?-turn contents were increasing with the increasing water content, the ?-sheet content was decreasing. A partial least squares (PLS) model was developed to correlate the mid-infrared and Raman spectral changes with the degree of crystallinity. The obtained R(2) value of 0.953 confirmed a correlation between changes in the secondary structure and crystallinity of the samples. The results demonstrated that the combined ATR-FTIR and Raman approach could be used to predict the crystalline state in freeze-dried fibrinogen products. PMID:25701629

  19. Quaternion-based definition of protein secondary structure straightness and its relationship to Ramachandran angles.

    PubMed

    Hanson, Robert M; Kohler, Daniel; Braun, Steven G

    2011-07-01

    We describe here definitions of "local helical axis" and "straightness" that are developed using a simple quaternion-based analysis of protein structure without resort to least-squares fitting. As part of this analysis, it is shown how quaternion differences can be visualized to depict accurately the local helical axis relating any two adjacent amino acid residues in standard, nonidealized proteins. Three different options for the definition of amino acid residue orientation in terms of quaternion frames are described. Two of these, the "C(?) frame" and the "P frame," are shown to be correlated strongly with a simple approximate measure derived solely from Ramachandran angles. The relationship between quaternion-based straightness and recognized DSSP-derived secondary structure motifs is discussed. PMID:21557319

  20. Structural Basis for Inhibition of the MDM2:p53 Interaction by an Optimized MDM2-Binding Peptide Selected with mRNA Display

    PubMed Central

    Kobayashi, Naohiro; Shiheido, Hirokazu; Tabata, Noriko; Sakuma-Yonemura, Yuko; Horisawa, Kenichi; Katahira, Masato; Doi, Nobuhide; Yanagawa, Hiroshi

    2014-01-01

    The oncoprotein MDM2 binds to tumor suppressor protein p53 and inhibits its anticancer activity, which leads to promotion of tumor cell growth and tumor survival. Abrogation of the p53:MDM2 interaction reportedly results in reactivation of the p53 pathway and inhibition of tumor cell proliferation. We recently performed rigorous selection of MDM2-binding peptides by means of mRNA display and identified an optimal 12-mer peptide (PRFWEYWLRLME), named MDM2 Inhibitory Peptide (MIP), which shows higher affinity for MDM2 (and also its homolog, MDMX) and higher tumor cell proliferation suppression activity than known peptides. Here we determined the NMR solution structure of a MIP-MDM2 fusion protein to elucidate the structural basis of the tight binding of MIP to MDM2. A region spanning from Phe3 to Met11 of MIP forms a single ?-helix, which is longer than those of the other MDM2-binding peptides. MIP shares a conserved Phe3-Trp7-Leu10 triad, whose side chains are oriented towards and fit into the hydrophobic pockets of MDM2. Additionally, hydrophobic surface patches that surround the hydrophobic pockets of MDM2 are covered by solvent-exposed MIP residues, Trp4, Tyr6, and Met11. Their hydrophobic interactions extend the interface of the two molecules and contribute to the strong binding. The potential MDM2 inhibition activity observed for MIP turned out to originate from its enlarged binding interface. The structural information obtained in the present study provides a road map for the rational design of strong inhibitors of MDM2:p53 binding. PMID:25275651

  1. Short oligonucleotides aligned in stretched humid matrix: secondary DNA structure in poly(vinyl alcohol) environment.

    PubMed

    Hanczyc, Piotr; Akerman, Björn; Nordén, Bengt

    2012-04-24

    We report that short, synthetic, double- as well as single-stranded DNA can be aligned in stretched humid poly(vinyl alcohol) (PVA) matrix, and the secondary structure (nucleobase orientation) can be characterized with linear dichroism (LD) spectroscopy. Oligonucleotides of lengths varying between 10 (3.4 nm) and 60 bases (20.4 nm) were investigated with respect to structural properties in the gel-like polymer environment. The DNA conformation as a function of relative humidity reveals a strong dependence of helical structure of DNA on PVA hydration level, results of relevance for nanotechnical studies of DNA-based supramolecular systems. Also, the PVA gel could provide possibilities to test models for nucleic acid interactions and distribution in cell contexts, including structural stability of genetic material in the cell and PVA-packaging for gene delivery. A method by which duplex oligonucleotides, with sequences designed to provide specific binding sites, become amenable to polarized-light spectroscopy opens up new possibilities for studying structure in DNA complexes with small adduct molecules as well as proteins. PMID:22452613

  2. Clustering RNA structural motifs in ribosomal RNAs using secondary structural alignment.

    PubMed

    Zhong, Cuncong; Zhang, Shaojie

    2012-02-01

    RNA structural motifs are the building blocks of the complex RNA architecture. Identification of non-coding RNA structural motifs is a critical step towards understanding of their structures and functionalities. In this article, we present a clustering approach for de novo RNA structural motif identification. We applied our approach on a data set containing 5S, 16S and 23S rRNAs and rediscovered many known motifs including GNRA tetraloop, kink-turn, C-loop, sarcin-ricin, reverse kink-turn, hook-turn, E-loop and tandem-sheared motifs, with higher accuracy than the state-of-the-art clustering method. We also identified a number of potential novel instances of GNRA tetraloop, kink-turn, sarcin-ricin and tandem-sheared motifs. More importantly, several novel structural motif families have been revealed by our clustering analysis. We identified a highly asymmetric bulge loop motif that resembles the rope sling. We also found an internal loop motif that can significantly increase the twist of the helix. Finally, we discovered a subfamily of hexaloop motif, which has significantly different geometry comparing to the currently known hexaloop motif. Our discoveries presented in this article have largely increased current knowledge of RNA structural motifs. PMID:21976732

  3. 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

  4. A new protein folding algorithm based on hydrophobic compactness: Rigid Unconnected Secondary Structure Iterative Assembly (RUSSIA). I: Methodology

    Microsoft Academic Search

    Denis Znamenskiy; Jacques Chomilier; Khan Le Tuan; Jean-Paul Mornon

    2003-01-01

    We present an algorithm that is able to propose compact models of protein 3D structures, only starting from the prediction of the nature and length of regular secondary structures. Helices are modeled by cylinders and sheets by helicoid surfaces, all strands of a sheet being considered as a single block. It means that relative topology of the strands inside one

  5. Secondary Structure ofHistones and DNA in Chromatin Abstract. Laser Raman spectroscopy indicates that the inner histones which are

    E-print Network

    Olins, Ada L.

    Secondary Structure ofHistones and DNA in Chromatin Abstract. Laser Raman spectroscopy indicates, and characterized by various physical methods (2). Here we report the laser Raman spectra of these v, preparations and of chromatin, and identify the conformational structures of the constituent DNA and histone mole- cules. Laser

  6. Secondary structure of proteins analyzed ex vivo in vascular wall in diabetic animals using FT-IR spectroscopy.

    PubMed

    Majzner, Katarzyna; Wrobel, Tomasz P; Fedorowicz, Andrzej; Chlopicki, Stefan; Baranska, Malgorzata

    2013-11-12

    In recent years many methods for ex vivo tissue analysis or diagnosis of diseases have been applied, including infrared absorption spectroscopy. Fourier-transform infrared (FT-IR) absorption microspectroscopy allows the simultaneous monitoring of the content of various chemical compounds in tissues with both high selectivity and resolution. Imaging of tissue samples in very short time can be performed using a spectrometer equipped with a Focal Plane Array (FPA) detector. Additionally, a detection of minor components or subtle changes associated with the functional status of a tissue sample is possible when advanced methods of data analysis, such as chemometric techniques, are applied. Monitoring of secondary structures of proteins has already proved to be useful in the analysis of animal tissues in disease states. The aim of this work was to build a mathematical model based on FT-IR measurements for the prediction of alterations in the content of secondary structures of proteins analyzed by FT-IR in the vascular wall of diabetic animals. For that purpose a spectral database of proteins of known crystallography and secondary structures was assembled. Thirty-seven proteins were measured by means of two FT-IR techniques: transflection and Attenuated Total Reflectance (ATR). The obtained model was tested on cross-sections of rat tail, for which the content of proteins and their secondary structures was well characterized. Then, the model was applied for the detection of possible alterations in the secondary structures of proteins in the vascular wall of diabetic rats and mice. The obtained results suggest a prominent increase in E- and S-structures and a decrease in the content of H-structures in the vascular wall from diabetic mice and rats. FT-IR-based studies of secondary structures of proteins may be a novel approach to study complex processes ongoing in the vascular wall. The obtained results are satisfactory; however, the existing limitations of the method are also discussed. PMID:24179990

  7. mRNA

    PubMed Central

    Van Lint, Sandra; Heirman, Carlo; Thielemans, Kris; Breckpot, Karine

    2013-01-01

    Two decades ago, mRNA became the focus of research in molecular medicine and was proposed as an active pharmaceutical ingredient for the therapy of cancer. In this regard, mRNA has been mainly used for ex vivo modification of antigen-presenting cells (APCs), such as dendritic cells (DCs). This vaccination strategy has proven to be safe, well tolerated and capable of inducing tumor antigen-specific immune responses. Recently, the direct application of mRNA for in situ modification of APCs, hence immunization was shown to be feasible and at least as effective as DC-based immunization in pre-clinical models. It is believed that application of mRNA as an off-the-shelf vaccine represents an important step in the development of future cancer immunotherapeutic strategies. Here, we will discuss the use of ex vivo mRNA-modified DCs and “naked mRNA” for cancer immunotherapy focusing on parameters such as the employed DC subtype, DC activation stimulus and route of immunization. In addition, we will provide an overview on the clinical trials published so far, trying to link their outcome to the aforementioned parameters. PMID:23291946

  8. Internal Transcribed Spacer 1 Secondary Structure Analysis Reveals a Common Core throughout the Anaerobic Fungi (Neocallimastigomycota)

    PubMed Central

    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. PMID:24663345

  9. Suppression of secondary electron yield by micro-porous array structure

    SciTech Connect

    Ye, M.; He, Y. N.; Hu, S. G. [School of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an 710049 (China); Wang, R.; Hu, T. C.; Yang, J.; Cui, W. Z. [Science and Technology on Space Microwave Laboratory, China Academy of Space Technology, Xi'an 710100 (China)

    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.

  10. Artificial Neural Networks and Hidden Markov Models for Predicting the Protein Structures: The Secondary Structure

    E-print Network

    1 Artificial Neural Networks and Hidden Markov Models for Predicting the Protein Structures advice on the development of this project #12;2 Artificial Neural Networks and Hidden Markov Models learning methods: artificial neural networks (ANN) and hidden Markov models (HMM) (Rost 2002; Karplus et al

  11. Conformational changes and catalytic competency of hydrolases adsorbing on fumed silica nanoparticles: II. Secondary structure.

    PubMed

    Cruz, Juan C; Pfromm, Peter H; Tomich, John M; Rezac, Mary E

    2010-11-01

    Secondary conformational analysis via Circular Dichroism (CD) and Amide-I FTIR was applied to preparations of Candida antarctica Lipase B (CALB), subtilisin Carlsberg, and the Lipase from Thermomyces lanuginosus (TLL) on fumed silica to confirm that the "hardness" and packing density of the enzymes on the solid fumed silica nanoparticle surface can be used to rationalize the variable enzyme-dependent changes of catalytic competency with surface coverage. "Soft" enzymes should be immobilized at a surface coverage where enzyme-enzyme interactions predominate thereby preventing detrimental structural changes caused by enzyme-support interactions, while "hard" enzymes can be immobilized at low to intermediate surface coverage with good catalytic performance. Multi-layered coverage reduces the superficial average catalytic performance in all cases due to mass transfer limitations. PMID:20638251

  12. Nucleotide sequence determination and secondary structure of Xenopus U3 snRNA.

    PubMed Central

    Jeppesen, C; Stebbins-Boaz, B; Gerbi, S A

    1988-01-01

    Using a combination of RNA sequencing and construction of cDNA clones followed by DNA sequencing, we have determined the primary nucleotide sequence of U3 snRNA in Xenopus laevis and Xenopus borealis. This molecule has a length of 219 nucleotides. Alignment of the Xenopus sequences with U3 snRNA sequences from other organisms reveals three evolutionarily conserved blocks. We have probed the secondary structure of U3 snRNA in intact Xenopus laevis nuclei using single-strand specific chemical reagents; primer extension was used to map the positions of chemical modification. The three blocks of conserved sequences fall within single-stranded regions, and are therefore accessible for interaction with other molecules. Models of U3 snRNA function are discussed in light of these data. Images PMID:3357768

  13. Structural evidences for a secondary gold binding site in the hydrophobic box of lysozyme.

    PubMed

    Ferraro, Giarita; Massai, Lara; Messori, Luigi; Cinellu, Maria Agostina; Merlino, Antonello

    2015-08-01

    A new crystal structure is reported here for the adduct formed in the reaction between NH4 [Au(Sac)2], AuSac2, a cytotoxic homoleptic gold(I) complex with the saccharinate ligand, and the model protein hen egg white lysozyme. To produce this adduct, AuSac2 breaks down and releases both saccharinate ligands. The resulting Au(I) ions bind the protein to ND1 and NE2 atoms of His15 but also to SD atom of the zero-solvent accessible Met105 side chain, which is located in the protein hydrophobic box. The unexpected existence of this secondary gold(I) binding site is confirmed by spectroscopic and spectrometric measurements in solution. PMID:26054833

  14. 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.

  15. Polysaccharide hydrogels with tunable stiffness and provasculogenic properties via ?-helix to ?-sheet switch in secondary structure.

    PubMed

    Forget, Aurelien; Christensen, Jon; Lüdeke, Steffen; Kohler, Esther; Tobias, Simon; Matloubi, Maziar; Thomann, Ralf; Shastri, V Prasad

    2013-08-01

    Mechanical aspects of the cellular environment can influence cell function, and in this context hydrogels can serve as an instructive matrix. Here we report that physicochemical properties of hydrogels derived from polysaccharides (agarose, ?-carrageenan) having an ?-helical backbone can be tailored by inducing a switch in the secondary structure from ?-helix to ?-sheet through carboxylation. This enables the gel modulus to be tuned over four orders of magnitude (G' 6 Pa-3.6 × 10(4) Pa) independently of polymer concentration and molecular weight. Using carboxylated agarose gels as a screening platform, we demonstrate that soft-carboxylated agarose provides a unique environment for the polarization of endothelial cells in the presence of soluble and bound signals, which notably does not occur in fibrin and collagen gels. Furthermore, endothelial cells organize into freestanding lumens over 100 ?m in length. The finding that a biomaterial can modulate soluble and bound signals provides impetus for exploring mechanobiology paradigms in regenerative therapies. PMID:23886665

  16. Effect of secondary structure on the self-assembly of amphiphilic molecules: A multiscale simulation study

    NASA Astrophysics Data System (ADS)

    Mondal, Jagannath; Yethiraj, Arun

    2012-02-01

    The self-assembly of amphiphilic molecules is of interest from a fundamental and practical standpoint. There has been recent interest in a class of molecules made from ?-amino acids (which contain an additional backbone carbon atom when compared with natural amino acids). Block copolymers of ?-peptides, where one block is hydrophobic and the other is hydrophilic, self-assemble into micelles. In this work, we use computer simulations to provide insight into the effect of secondary structure on the self-assembly of these molecules. Atomistic simulations for the free energy of association of a pair of molecules show that a homochiral hydrophobic block promotes self assembly compared to a heterochiral hydrophobic block, consistent with experiment. Simulations of a coarse-grained model show that these molecules spontaneously form spherical micelles.

  17. 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 ?-structure in the phosphorylated samples, concomitant to a decrease in ?-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

  18. Regulation of mRNA transport, localization and translation in the nervous system of mammals (Review)

    PubMed Central

    DI LIEGRO, CARLO MARIA; SCHIERA, GABRIELLA; DI LIEGRO, ITALIA

    2014-01-01

    Post-transcriptional control of mRNA trafficking and metabolism plays a critical role in the actualization and fine tuning of the genetic program of cells, both in development and in differentiated tissues. Cis-acting signals, responsible for post-transcriptional regulation, reside in the RNA message itself, usually in untranslated regions, 5? or 3? to the coding sequence, and are recognized by trans-acting factors: RNA-binding proteins (RBPs) and/or non-coding RNAs (ncRNAs). ncRNAs bind short mRNA sequences usually present in the 3?-untranslated (3?-UTR) region of their target messages. RBPs recognize specific nucleotide sequences and/or secondary/tertiary structures. Most RBPs assemble on mRNA at the moment of transcription and shepherd it to its destination, somehow determining its final fate. Regulation of mRNA localization and metabolism has a particularly important role in the nervous system where local translation of pre-localized mRNAs has been implicated in developing axon and dendrite pathfinding, and in synapse formation. Moreover, activity-dependent mRNA trafficking and local translation may underlie long-lasting changes in synaptic efficacy, responsible for learning and memory. This review focuses on the role of RBPs in neuronal development and plasticity, as well as possible connections between ncRNAs and RBPs. PMID:24452120

  19. Identification of a cis-acting element that localizes mRNA to synapses

    PubMed Central

    Meer, Elliott J.; Wang, Dan Ohtan; Kim, Sangmok; Barr, Ian; Guo, Feng; Martin, Kelsey C.

    2012-01-01

    Messenger RNA (mRNA) localization and regulated translation can spatially restrict gene expression to each of the thousands of synaptic compartments formed by a single neuron. Although cis-acting RNA elements have been shown to direct localization of mRNAs from the soma into neuronal processes, less is known about signals that target transcripts specifically to synapses. In Aplysia sensory-motor neuronal cultures, synapse formation rapidly redistributes the mRNA encoding the peptide neurotransmitter sensorin from neuritic shafts into synapses. We find that the export of sensorin mRNA from soma to neurite and the localization to synapse are controlled by distinct signals. The 3? UTR is sufficient for export into distal neurites, whereas the 5? UTR is required for concentration of reporter mRNA at synapses. We have identified a 66-nt element in the 5? UTR of sensorin that is necessary and sufficient for synaptic mRNA localization. Mutational and chemical probing analyses are consistent with a role for secondary structure in this process. PMID:22383561

  20. 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 C? 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 ? and ? angles, respectively, and 8° and 32° for mean absolute errors of C?-based ? and ? angles, respectively, for an independent test dataset of 1199 proteins. The accuracy of the method is slightly lower for 72 CASP 11 targets but much higher than those of model structures from current state-of-the-art techniques. This suggests the potentially beneficial use of these predicted properties for model assessment and ranking. PMID:26098304

  1. 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 C? 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 ? and ? angles, respectively, and 8° and 32° for mean absolute errors of C?-based ? and ? 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

  2. Protein secondary structure prediction from circular dichroism spectra using a self-organizing map with concentration correction.

    PubMed

    Hall, Vincent; Sklepari, Meropi; Rodger, Alison

    2014-09-01

    Collecting circular dichroism (CD) spectra for protein solutions is a simple experiment, yet reliable extraction of secondary structure content is dependent on knowledge of the concentration of the protein--which is not always available with accuracy. We previously developed a self-organizing map (SOM), called Secondary Structure Neural Network (SSNN), to cluster a database of CD spectra and use that map to assign the secondary structure content of new proteins from CD spectra. The performance of SSNN is at least as good as other available protein CD structure-fitting algorithms. In this work we apply SSNN to a collection of spectra of experimental samples where there was suspicion that the nominal protein concentration was incorrect. We show that by plotting the normalized root mean square deviation of the SSNN predicted spectrum from the experimental one versus a concentration scaling-factor it is possible to improve the estimate of the protein concentration while providing an estimate of the secondary structure. For our implementation (51 data points 240-190?nm in nm increments) good fits and structure estimates were obtained if the NRMSD (normalized root mean square displacement, RMSE/data range) is <0.03; reasonable for NRMSD <0.05; and variable above this. We also augmented the reference database with 100% helical spectra and truly random coil spectra. PMID:24890763

  3. How a Spatial Arrangement of Secondary Structure Elements Is Dispersed in the Universe of Protein Folds

    PubMed Central

    Minami, Shintaro; Sawada, Kengo; Chikenji, George

    2014-01-01

    It has been known that topologically different proteins of the same class sometimes share the same spatial arrangement of secondary structure elements (SSEs). However, the frequency by which topologically different structures share the same spatial arrangement of SSEs is unclear. It is important to estimate this frequency because it provides both a deeper understanding of the geometry of protein folds and a valuable suggestion for predicting protein structures with novel folds. Here we clarified the frequency with which protein folds share the same SSE packing arrangement with other folds, the types of spatial arrangement of SSEs that are frequently observed across different folds, and the diversity of protein folds that share the same spatial arrangement of SSEs with a given fold, using a protein structure alignment program MICAN, which we have been developing. By performing comprehensive structural comparison of SCOP fold representatives, we found that approximately 80% of protein folds share the same spatial arrangement of SSEs with other folds. We also observed that many protein pairs that share the same spatial arrangement of SSEs belong to the different classes, often with an opposing N- to C-terminal direction of the polypeptide chain. The most frequently observed spatial arrangement of SSEs was the 2-layer ?/? packing arrangement and it was dispersed among as many as 27% of SCOP fold representatives. These results suggest that the same spatial arrangements of SSEs are adopted by a wide variety of different folds and that the spatial arrangement of SSEs is highly robust against the N- to C-terminal direction of the polypeptide chain. PMID:25243952

  4. ITS2, 18S, 16S or any other RNA - simply aligning sequences and their individual secondary structures simultaneously by an automatic approach.

    PubMed

    Wolf, Matthias; Koetschan, Christian; Müller, Tobias

    2014-08-10

    Secondary structures of RNA sequences are increasingly being used as additional information in reconstructing phylogenies and/or in distinguishing species by compensatory base change (CBC) analyses. However, in most cases just one secondary structure is used in manually correcting an automatically generated multiple sequence alignment and/or just one secondary structure is used in guiding a sequence alignment still completely generated by hand. With the advent of databases and tools offering individual RNA secondary structures, here we re-introduce a twelve letter code already implemented in 4SALE - a tool for synchronous sequence and secondary structure alignment and editing - that enables one to align RNA sequences and their individual secondary structures synchronously and fully automatic, while dramatically increasing the phylogenetic information content. We further introduce a scaled down non-GUI version of 4SALE particularly designed for big data analysis, and available at: http://4sale.bioapps.biozentrum.uni-wuerzburg.de. PMID:24881812

  5. Phylogenetic hypotheses of gorgoniid octocorals according to ITS2 and their predicted RNA secondary structures.

    PubMed

    Aguilar, Catalina; Sánchez, Juan Armando

    2007-06-01

    Gorgoniid octocorals taxonomy (Cnidaria; Octocorallia; Gorgoniidae) includes diagnostic characters not well defined at the generic level, and based on the family diagnosis some species could be classified in either Gorgoniidae or Plexauridae. In this study, we used sequences from the Internal Transcribed Spacer 2 (ITS2) and their predicted RNA secondary structure to both correct the alignment and reconstruct phylogenies using molecular morphometrics for 24 octocorals mostly from the Atlantic. ITS2 exhibited the six-helicoidal ring-model structure found in eukaryotes, and provided 38 parsimony-informative characters. The proposed phylogenies, though differing between sequence- and structure-base results, provided consistent support for several clades. Genera considered part of the polyphyletic genus Leptogorgia, such as Filigorgia, were distantly related to the former in all phylogenetic hypotheses. Main differences among the hypotheses consisted in the placement of Muriceopsis (previously considered from the Plexauridae family) and Filigorgia. Excluding Muriceopsis and an undescribed octocoral from Tobago, Plexaurella and Pterogorgia grouped together as a sister branch of Pinnigorgia spp. but long-branch attraction was evident for the grouping of Plexaurella nutans (another plexaurid) and Pterogorgia citrina. Unexpected results were the divergence between Caribbean genera, Gorgonia and Pseudopterogorgia, which were placed basal respect to Pacifigorgia and Leptogorgia (=Lophogorgia). ITS2 provided support to corroborate observations based on sclerite morphology: species with "capstan sclerites" (e.g., Pacifigorgia and Leptogorgia) were characterized by a long helix IV with one internal loop and a helix V with four internal loops; "scaphoid sclerites" had a predominantly long helix V if compared to helix IV; "asymmetric spiny sclerites" (Muriceopsis, Pinnigorgia and the undescribed octocoral) exhibited one or two lateral bulges in the V helix. Remarkably, Muriceopsis and Pinnigorgia were supported by a complete Compensatory Base Change (CBC) (A-U to G-C) in helix V. Filigorgia with simple "spindles" had a short helix IV and a large central ring. DNA sequences from the nuclear ITS2 region, including information from predicted RNA secondary structure, despite their reduced length, provided numerous characters and phylogenetic information among Gorgoniidae genera and species. PMID:17254805

  6. 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.

  7. An investigation into the influence of secondary structures for DNA hybridization using surface plasmon resonance and surface-enhanced Raman scattering

    Microsoft Academic Search

    J.-N. Yih; K.-C. Chiu; F.-C. Chien; W.-Y. Chen; S.-J. Chen

    2006-01-01

    This study utilizes a surface plasmon resonance (SPR) biosensing to investigate the influence of secondary structures on the DNA hybridization and a surface-enhanced Raman scattering (SERS) spectrum to yield analytical data regarding the structure of the oligonucleotides. It is found that the SPR angular shifts associated with the three pairs of 60mer oligonucleotides with prominent secondary structures are lower than

  8. Structural features of helical secondary structures and leucine-rich repeat superhelix in proteins as revealed by HELFIT analyses

    NASA Astrophysics Data System (ADS)

    Matsushima, Norio; Enkhbayar, Purevjav

    2012-09-01

    The HELFIT program determines the helical parameters - pitch, residues per turn (n), radius, and handedness - and p = rmsd / (N - 1)1/2 estimating helical regularity, where "rmsd" is the root mean square deviation from the best fit helix or superhelix and "N" is helix/superhelix length. Helical secondary structures - ?-helix and 310-helix - and solenoid structures of leucine rich repeats (LRRs) in The Protein Data Bank (PDB) were analyzed by the HELFIT program. The results indicate that the definition of 310-helices in terms of average, uniform dihedral angles is not appropriate and that it is inherently unstable for a polypeptide to form an extended, regular 310-helix. The 310-helices observed in proteins are better referred to parahelices. A modification of the ?-helix, termed the ?-helix, that has four residues in one turn of a helix, has been identified only in synthetic polypeptides. The results also demonstrate that the right-handed ?-helix occur really in proteins. The solenoid structures of LRR domains in brasinosteroid insensitive 1 (BRI1), internalin J (InlJ), and internalin A (InlA) are well represented by a superhelix rather than by a circular arc.

  9. 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 absorption band. Current breeding lines show a substantial variance in this feature and its determination allows the prediction of relative quality for breadmaking to be taken into consideration for subsequent steps in the wheat breeding process. Data treatments include deconvolution, modeling of the individual resulting bands that contribute to the amide I band to enable measurement of the relative amounts of both forms. Results with specimens representing multiple crop years of hard winter wheat breeding are reported. It is evident that a range is available for the breeder to choose from, that allows including this protein molecular structural attribute in the selection process.

  10. 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 breeding lines show a substantial variance in this feature and its determination allows the prediction of relative quality for breadmaking to be taken into consideration for subsequent steps in the wheat breeding process. Data treatments include deconvolution, modeling of the individual resulting bands that contribute to the amide I band to enable measurement of the relative amounts of both forms. Results with specimens representing multiple crop years of hard winter wheat breeding are reported. It is evident that a range is available for the breeder to choose from, that allows including this protein molecular structural attribute in the selection process.

  11. Acute Endoplasmic Reticulum Stress-Independent Unconventional Splicing of XBP1 mRNA in the Nucleus of Mammalian Cells

    PubMed Central

    Wang, Yuanyuan; Xing, Pan; Cui, Wenjing; Wang, Wenwen; Cui, Yanfen; Ying, Guoguang; Wang, Xin; Li, Binghui

    2015-01-01

    The regulation of expression of X-box-binding protein-1 (XBP1), a transcriptional factor, involves an unconventional mRNA splicing that removes the 26 nucleotides intron. In contrast to the conventional splicing that exclusively takes place in the nucleus, determining the location of unconventional splicing still remains controversial. This study was designed to examine whether the unconventional spicing of XBP1 mRNA could occur in the nucleus and its possible biological relevance. We use RT-PCR reverse transcription system and the expand high fidelity PCR system to detect spliced XBP1 mRNA, and fraction cells to determine the location of the unconventional splicing of XBP1 mRNA. We employ reporter constructs to show the presence of unconventional splicing machinery in mammal cells independently of acute endoplasmic reticulum (ER) stress. Our results reveal the presence of basal unconventional splicing of XBP1 mRNA in the nucleus that also requires inositol-requiring transmembrane kinase and endonuclease 1? (IRE1?) and can occur independently of acute ER stress. Furthermore, we confirm that acute ER stress induces the splicing of XBP1 mRNA predominantly occurring in the cytoplasm, but it also promotes the splicing in the nucleus. The deletion of 5?-nucleotides in XBP1 mRNA significantly increases its basal unconventional splicing, suggesting that the secondary structure of XBP1 mRNA may determine the location of unconventional splicing. These results suggest that the unconventional splicing of XBP1 mRNA can take place in the nucleus and/or cytoplasm, which possibly depends on the elaborate regulation. The acute ER stress-independent unconventional splicing in the nucleus is most likely required for the maintaining of day-to-day folding protein homeostasis. PMID:26068456

  12. Interplay between Secondary and Tertiary Structure Formation in Protein Folding Cooperativity

    E-print Network

    Tristan Bereau; Michael Bachmann; Markus Deserno

    2011-07-01

    Protein folding cooperativity is defined by the nature of the finite-size thermodynamic transition exhibited upon folding: two-state transitions show a free energy barrier between the folded and unfolded ensembles, while downhill folding is barrierless. A microcanonical analysis, where the energy is the natural variable, has shown better suited to unambiguously characterize the nature of the transition compared to its canonical counterpart. Replica exchange molecular dynamics simulations of a high resolution coarse-grained model allow for the accurate evaluation of the density of states, in order to extract precise thermodynamic information, and measure its impact on structural features. The method is applied to three helical peptides: a short helix shows sharp features of a two-state folder, while a longer helix and a three-helix bundle exhibit downhill and two-state transitions, respectively. Extending the results of lattice simulations and theoretical models, we find that it is the interplay between secondary structure and the loss of non-native tertiary contacts which determines the nature of the transition.

  13. Micelle density regulated by a reversible switch of protein secondary structure.

    PubMed

    Sallach, Rory E; Wei, Min; Biswas, Nilanjana; Conticello, Vincent P; Lecommandoux, Sébastien; Dluhy, Richard A; Chaikof, Elliot L

    2006-09-13

    Protein secondary structures may exhibit reversible transitions that occur in an abrupt and controllable manner. In this report, we demonstrate that such transitions may be utilized in the design of a "smart" protein micellar system, in which a stimulus-induced change in protein structure triggers a rapid change in micelle compacticity and size. Specifically, recombinant DNA methods were used to prepare a protein triblock copolymer containing a central hydrophilic block and two hydrophobic end blocks derived from elastin-mimetic peptide sequences. Below the copolymer inverse transition temperature (T(t)), dilute solutions of this amphiphilic protein formed monodispersed micelles in a narrow range of R(H) of approximately 100 nm. When the the temperature was raised above T(t), an abrupt increase in micelle internal density was observed with a concomitant reduction in micelle size. This reversible change in micelle compacticity was triggered by helix-to-sheet protein folding transition. Significantly, these protein polymer-based micelles, which are rapidly responsive to environmental stimuli, establish a new mechanism for the design of controlled drug delivery vehicles. PMID:16953644

  14. Fine-grained parallel RNAalifold algorithm for RNA secondary structure prediction on FPGA

    PubMed Central

    Xia, Fei; Dou, Yong; Zhou, Xingming; Yang, Xuejun; Xu, Jiaqing; Zhang, Yang

    2009-01-01

    Background In the field of RNA secondary structure prediction, the RNAalifold algorithm is one of the most popular methods using free energy minimization. However, general-purpose computers including parallel computers or multi-core computers exhibit parallel efficiency of no more than 50%. Field Programmable Gate-Array (FPGA) chips provide a new approach to accelerate RNAalifold by exploiting fine-grained custom design. Results RNAalifold shows complicated data dependences, in which the dependence distance is variable, and the dependence direction is also across two dimensions. We propose a systolic array structure including one master Processing Element (PE) and multiple slave PEs for fine grain hardware implementation on FPGA. We exploit data reuse schemes to reduce the need to load energy matrices from external memory. We also propose several methods to reduce energy table parameter size by 80%. Conclusion To our knowledge, our implementation with 16 PEs is the only FPGA accelerator implementing the complete RNAalifold algorithm. The experimental results show a factor of 12.2 speedup over the RNAalifold (ViennaPackage – 1.6.5) software for a group of aligned RNA sequences with 2981-residue running on a Personal Computer (PC) platform with Pentium 4 2.6 GHz CPU. PMID:19208138

  15. Features of the secondary structure of a protein molecule from powder diffraction data.

    PubMed

    Basso, Sebastian; Besnard, Céline; Wright, Jonathan P; Margiolaki, Irene; Fitch, Andrew; Pattison, Philip; Schiltz, Marc

    2010-07-01

    Protein powder diffraction is shown to be suitable for obtaining de novo solutions to the phase problem at low resolution via phasing methods such as the isomorphous replacement method. Two heavy-atom derivatives (a gadolinium derivative and a holmium derivative) of the tetragonal form of hen egg-white lysozyme were crystallized at room temperature. Using synchrotron radiation, high-quality powder patterns were collected in which pH-induced anisotropic lattice-parameter changes were exploited in order to reduce the challenging and powder-specific problem of overlapping reflections. The phasing power of two heavy-atom derivatives in a multiple isomorphous replacement analysis enabled molecular structural information to be obtained up to approximately 5.3 A resolution. At such a resolution, features of the secondary structure of the lysozyme molecule can be accurately located using programs dedicated to that effect. In addition, the quoted resolution is sufficient to determine the correct hand of the heavy-atom substructure which leads to an electron-density map representing the protein molecule of proper chirality. PMID:20606255

  16. FTIR Study On The Secondary Structure Of Mucin From Mucinous Cystadenoma Of The Ovary

    NASA Astrophysics Data System (ADS)

    Shen, Keng; Wu, Paochen; Zhou, Weij in; Liu, Fuan; Guo, Hai; Wu, Jinguang

    1989-12-01

    The mucinous cystadenoma, a common benign neoplasm of the ovary, may sometime bring about a fatal outcome known as pseudomyxoma peritonei which is characterized by massive accumulation of mucinous substance in the peritoneal cavity, resulting in extensive adhesions, chronic progressive intestinal obstruction and finally death of the patient. Surgical approach to this condition proves to be a palliative procedure. Repeated operation can only remove part of the geletinous material and reaccumulation of mucus within 1-2 years after the initial surgery is almost a rule. In view of the benign histologic nature of the disease, chemotherapy, either systemic or intraperitoneal, and radiotherapy are generally ineffective in arresting the progression of the pathologic process and preventing the reaccumulation of mucus. Therefore, the only hope lies on the introduction into the peritoneal cavity some agents which may dissolve the accumulated mucin, relieve the intestinal obstruction, and consequently, prolong and even save the life f the patient. Based on this conception, sporadic articles by a few authors(1,2)ap-peared in the literature reporting their clinical experience with different mucolytic agents. However, some blindness would inevitably be involved in such investigations due to the lack of a comprehensive understanding of the chemical structures of the substance. The purpose of the present paper is to report our preliminary results of study of the secondary structures of mucin secreted by this special type of tumor.

  17. Changes in the community structure of ammonia-oxidizing bacteria during secondary succession of calcareous grasslands.

    PubMed

    Kowalchuk, G A; Stienstra, A W; Heilig, G H; Stephen, J R; Woldendorp, J W

    2000-02-01

    The community structure of beta-subclass Proteobacteria ammonia-oxidizing bacteria was determined in semi-natural chalk grassland soils at different stages of secondary succession. Both culture-mediated (most probable number; MPN) and direct nucleic acid-based approaches targeting genes encoding 16S rRNA and the AmoA subunit of ammonia monooxygenase were used. Similar shifts were detected in the composition of the ammonia oxidizer communities by both culture-dependent and independent approaches. A predominance of Nitrosospira sequence cluster 3 in early successional fields was replaced by Nitrosospira sequence cluster 4 in late successional fields. The rate of this shift differed between the two areas examined. This shift occurred in a background of relative stability in the dominant bacterial populations in the soil, as determined by domain-level polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE). Molecular analysis of enrichment cultures obtained using different ammonia concentrations revealed biases towards Nitrosospira sequence cluster 3 or Nitrosospira sequence cluster 4 under high- or low-ammonia conditions respectively. High-ammonia MPNs suggested a decease in ammonia oxidizer numbers with succession, but low-ammonia MPNs and competitive PCR targeting amoA failed to support such a trend. Ammonia turnover rate, not specific changes in plant diversity and species composition, is implicated as the major determinant of ammonia oxidizer community structure in successional chalk grassland soils. PMID:11243267

  18. Mapping in Solution Shows the Peach Latent Mosaic Viroid To Possess a New Pseudoknot in a Complex, Branched Secondary Structure

    PubMed Central

    Bussière, F.; Ouellet, J.; Côté, F.; Lévesque, D.; Perreault, J. P.

    2000-01-01

    We have investigated the secondary structure of peach latent mosaic viroid (PLMVd) in solution, and we present here the first description of the structure of a branched viroid in solution. Different PLMVd transcripts of plus polarity were produced by using the circularly permuted RNA method and the exploitation of RNA internal secondary structure to position the 5? and 3? termini and studied by nuclease mapping and binding shift assays using DNA and RNA oligonucleotides. We show that PLMVd folds into a complex, branched secondary structure. In general, this structure is similar to that reported previously, which was based on sequence comparison and computer modelling. The structural microheterogeneity is apparently limited to only some small domains. More importantly, this structure includes a novel pseudoknot that is conserved in all PLMVd isolates and seems to allow folding into a very compact form. This pseudoknot is also found in chrysanthemum chlorotic mottle viroid, suggesting that it is a unique feature of the viroid members of the PLMVd subgroup. PMID:10684279

  19. Protein energetic conformational analysis from NMR chemical shifts (PECAN) and its use in determining secondary structural elements

    Microsoft Academic Search

    Hamid R. Eghbalnia; Liya Wang; Arash Bahrami; Amir Assadi; John L. Markley

    2005-01-01

    We present an energy model that combines information from the amino acid sequence of a protein and available NMR chemical shifts for the purposes of identifying low energy conformations and determining elements of secondary structure. The model (“PECAN”, Protein Energetic Conformational Analysis from NMR chemical shifts) optimizes a combination of sequence information and residue-specific statistical energy function to yield energetic

  20. Summary Archaeal and bacterial RNase P RNAs are similar in sequence and secondary structure, but in the absence of pro-

    E-print Network

    Brown, James W.

    of Bacteria and Archaea are globally optimized and the basis for the large bio- chemical differences betweenSummary Archaeal and bacterial RNase P RNAs are similar in sequence and secondary structure these two types of RNaseP RNA is distributed in the molecule. Keywords: Archaea, archaebacteria

  1. Secondary structure model of the RNA recognized by the reverse transcriptase from the R2 retrotransposable element.

    PubMed Central

    Mathews, D H; Banerjee, A R; Luan, D D; Eickbush, T H; Turner, D H

    1997-01-01

    RNA transcripts corresponding to the 250-nt 3' untranslated region of the R2 non-LTR retrotransposable element are recognized by the R2 reverse transcriptase and are sufficient to serve as templates in the target DNA-primed reverse transcription (TPRT) reaction. The R2 protein encoded by the Bombyx mori R2 can recognize this region from both the B. mori and Drosophila melanogaster R2 elements even though these regions show little nucleotide sequence identity. A model for the RNA secondary structure of the 3' untranslated region of the D. melanogaster R2 retrotransposon was developed by sequence comparison of 10 species aided by free energy minimization. Chemical modification experiments are consistent with this prediction. A secondary structure model for the 3' untranslated region of R2 RNA from the R2 element from B. mori was obtained by a combination of chemical modification data and free energy minimization. These two secondary structure models, found independently, share several common sites. This study shows the utility of combining free energy minimization, sequence comparison, and chemical modification to model an RNA secondary structure. PMID:8990394

  2. 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…

  3. Changes of trypsin in activity and secondary structure induced by complex with trypsin inhibitors and tea polyphenol

    Microsoft Academic Search

    Huihua Huang; Mouming Zhao

    2008-01-01

    To reveal the relationships between the activity of trypsin and its structural change, changes of trypsin in biological activity\\u000a induced by complex with Bowman-Birk trypsin inhibitor (BBTI), Kunitz soybean trypsin inhibitor (KSTI, type I-S) and tea polyphenol\\u000a (TP) were detected and their relationship with the secondary structure changes were studied by far-UV circular dichroism (CD)\\u000a spectra measurement. BBTI and KSTI

  4. Structure of the gene encoding VGF, a nervous system-specific mRNA that is rapidly and selectively induced by nerve growth factor in PC12 cells.

    PubMed Central

    Salton, S R; Fischberg, D J; Dong, K W

    1991-01-01

    Nerve growth factor (NGF) plays a critical role in the development and survival of neurons in the peripheral nervous system. Following treatment with NGF but not epidermal growth factor, rat pheochromocytoma (PC12) cells undergo neural differentiation. We have cloned a nervous system-specific mRNA, NGF33.1, that is rapidly and relatively selectively induced by treatment of PC12 cells with NGF and basic fibroblast growth factor in comparison with epidermal growth factor. Analysis of the nucleic acid and predicted amino acid sequences of the NGF33.1 cDNA clone suggested that this clone corresponded to the NGF-inducible mRNA called VGF (A. Levi, J. D. Eldridge, and B. M. Paterson, Science 229:393-395, 1985; R. Possenti, J. D. Eldridge, B. M. Paterson, A. Grasso, and A. Levi, EMBO J. 8:2217-2223, 1989). We have used the NGF33.1 cDNA clone to isolate and characterize the VGF gene, and in this paper we report the complete sequence of the VGF gene, including 853 bases of 5' flank revealed TATAA and CCAAT elements, several GC boxes, and a consensus cyclic AMP response element-binding protein binding site. The VGF promoter contains sequences homologous to other NGF-inducible, neuronal promoters. We further show that VGF mRNA is induced in PC12 cells to a greater extent by depolarization and by phorbol-12-myristate-13-acetate treatment than by 8-bromo-cyclic AMP treatment. By Northern (RNA) and RNase protection analysis, VGF mRNA is detectable in embryonic and postnatal central and peripheral nervous tissues but not in a number of nonneural tissues. In the cascade of events which ultimately leads to the neural differentiation of NGF-treated PC12 cells, the VGF gene encodes the most rapidly and selectively regulated, nervous-system specific mRNA yet identified. Images PMID:2017159

  5. Global analysis of the RNA-protein interaction and RNA secondary structure landscapes of the Arabidopsis nucleus.

    PubMed

    Gosai, Sager J; Foley, Shawn W; Wang, Dongxue; Silverman, Ian M; Selamoglu, Nur; Nelson, Andrew D L; Beilstein, Mark A; Daldal, Fevzi; Deal, Roger B; Gregory, Brian D

    2015-01-22

    Posttranscriptional regulation in eukaryotes requires cis- and trans-acting features and factors including RNA secondary structure and RNA-binding proteins (RBPs). However, a comprehensive view of the structural and RBP interaction landscape of nuclear RNAs has yet to be compiled for any organism. Here, we use our ribonuclease-mediated structure and RBP-binding site mapping approaches to globally profile these features in Arabidopsis seedling nuclei in vivo. We reveal anticorrelated patterns of secondary structure and RBP binding throughout nuclear mRNAs that demarcate sites of alternative splicing and polyadenylation. We also uncover a collection of protein-bound sequence motifs, and identify their structural contexts, co-occurrences in transcripts encoding functionally related proteins, and interactions with putative RBPs. Finally, using these motifs, we find that the chloroplast RBP CP29A also interacts with nuclear mRNAs. In total, we provide a simultaneous view of the RNA secondary structure and RBP interaction landscapes in a eukaryotic nucleus. PMID:25557549

  6. 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

  7. A New Criterion to Evaluate Water Vapor Interference in Protein Secondary Structural Analysis by FTIR Spectroscopy

    PubMed Central

    Zou, Ye; Ma, Gang

    2014-01-01

    Second derivative and Fourier self-deconvolution (FSD) are two commonly used techniques to resolve the overlapped component peaks from the often featureless amide I band in Fourier transform infrared (FTIR) curve-fitting approach for protein secondary structural analysis. Yet, the reliability of these two techniques is greatly affected by the omnipresent water vapor in the atmosphere. Several criteria are currently in use as quality controls to ensure the protein absorption spectrum is negligibly affected by water vapor interference. In this study, through a second derivative study of liquid water, we first argue that the previously established criteria cannot guarantee a reliable evaluation of water vapor interference due to a phenomenon that we refer to as sample’s absorbance-dependent water vapor interference. Then, through a comparative study of protein and liquid water, we show that a protein absorption spectrum can still be significantly affected by water vapor interference even though it satisfies the established criteria. At last, we propose to use the comparison between the second derivative spectra of protein and liquid water as a new criterion to better evaluate water vapor interference for more reliable second derivative and FSD treatments on the protein amide I band. PMID:24901531

  8. Spontaneous deposition of polylysine on surfaces: role of the secondary structure to optimize noncovalent coating strategies.

    PubMed

    Di Mauro, Alessandro; Mirabella, Francesca; D'Urso, Alessandro; Randazzo, Rosalba; Purrello, Roberto; Fragalà, Maria Elena

    2015-01-01

    Understanding the factors that governs spontaneous molecular transfer from solution to solid surface is fundamental to control noncovalent surface functionalization strategies, both in term of robustness and reproducibility. The comprehension of the nature of interaction involved in the mechanism of spontaneous adsorption will allow for a fine modulation of the deposition process. Herein, we provide experimental evidences to demonstrate that poly-lysine secondary structure represents a crucial factor profoundly influencing the outcome of its spontaneous deposition on quartz surfaces. In particular, random coil to ?-helix transition is required to drive an effective transfer of the poly-l-lysine at the liquid-solid interface. ?-sheet deposition requires longer times to be accomplished, while random-coil deposition is highly unfavored. Accordingly, polylysine deposition on quartz and silicon is effective when ?-helix is formed in solution (pH>10). This surface noncovalent functionalization represents a simple strategy to fabricate hybrid organic-inorganic or biocompatible materials. In fact, the proposed methodology is proven robust and repeatable and compatible for combination with solution or vapor phases (i.e. MOCVD) nanomaterial deposition approaches. PMID:25441360

  9. Patterns of brain infiltration and secondary structure formation in supratentorial ependymal tumors.

    PubMed

    Lehman, Norman L

    2008-09-01

    Ependymomas are generally considered to be noninfiltrative tumors that have discrete borders with adjacent brain tissue. Most occur in the posterior fossa or spinal cord. Supratentorial ependymal tumors arise near the ventricular system or, more rarely, within the cerebral white matter or cortex. Presented here are 6 supratentorial ependymal tumors, 3 that primarily involve the cerebral cortex and 3 that extend into the cortex from the underlying white matter. By microscopy, all of these tumors locally infiltrate the cortex and/or white matter along small blood vessels and axonal fiber tracts. They also form other glioma secondary structures including perineuronal tumor cell satellitosis and subpial tumor cell mounds. The 3 cortical ependymal tumors show a spectrum of features ranging from conventional and clear-cell ependymoma-like patterns to more angiocentric glioma-like histology. Because ependymal tumors generally have a significantly better prognosis than other infiltrating gliomas, recognition of their capacity to infiltrate adjacent cortex and white matter is important to prevent the misdiagnosis of oligodendroglioma, astrocytoma, or infiltrating glioma, not otherwise specified. Cortical ependymomas and angiocentric gliomas may comprise a group of locally infiltrative ependymal tumors that are associated with an excellent prognosis after gross total surgical resection. PMID:18716554

  10. 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. PMID:24969746

  11. Ebola Virus RNA Editing Depends on the Primary Editing Site Sequence and an Upstream Secondary Structure

    PubMed Central

    Mehedi, Masfique; Hoenen, Thomas; Robertson, Shelly; Ricklefs, Stacy; Dolan, Michael A.; Taylor, Travis; Falzarano, Darryl; Ebihara, Hideki; Porcella, Stephen F.; Feldmann, Heinz

    2013-01-01

    Ebolavirus (EBOV), the causative agent of a severe hemorrhagic fever and a biosafety level 4 pathogen, increases its genome coding capacity by producing multiple transcripts encoding for structural and nonstructural glycoproteins from a single gene. This is achieved through RNA editing, during which non-template adenosine residues are incorporated into the EBOV mRNAs at an editing site encoding for 7 adenosine residues. However, the mechanism of EBOV RNA editing is currently not understood. In this study, we report for the first time that minigenomes containing the glycoprotein gene editing site can undergo RNA editing, thereby eliminating the requirement for a biosafety level 4 laboratory to study EBOV RNA editing. Using a newly developed dual-reporter minigenome, we have characterized the mechanism of EBOV RNA editing, and have identified cis-acting sequences that are required for editing, located between 9 nt upstream and 9 nt downstream of the editing site. Moreover, we show that a secondary structure in the upstream cis-acting sequence plays an important role in RNA editing. EBOV RNA editing is glycoprotein gene-specific, as a stretch encoding for 7 adenosine residues located in the viral polymerase gene did not serve as an editing site, most likely due to an absence of the necessary cis-acting sequences. Finally, the EBOV protein VP30 was identified as a trans-acting factor for RNA editing, constituting a novel function for this protein. Overall, our results provide novel insights into the RNA editing mechanism of EBOV, further understanding of which might result in novel intervention strategies against this viral pathogen. PMID:24146620

  12. Changes in secondary structure of ?-synuclein during oligomerization induced by reactive aldehydes.

    PubMed

    Cai, Yixiao; Lendel, Christofer; Österlund, Lars; Kasrayan, Alex; Lannfelt, Lars; Ingelsson, Martin; Nikolajeff, Fredrik; Karlsson, Mikael; Bergström, Joakim

    2015-08-14

    The oxidative stress-related reactive aldehydes 4-hydroxy-2-nonenal (HNE) and 4-oxo-2-nonenal (ONE) have been shown to promote formation of ?-synuclein oligomers in vitro. However, the changes in secondary structure of ?-synuclein and the kinetics of the oligomerization process are not known and were the focus of this study. Size exclusion chromatography showed that after 1 h of incubation, HNE induced the formation of an oligomeric ?-synuclein peak with a molecular weight of about ?2000 kDa, which coincided with a decreasing ?50 kDa monomeric peak. With prolonged incubation (up to 24 h) the oligomeric peak became the dominating molecular species. In contrast, in the presence of ONE, a ?2000 oligomeric peak was exclusively observed after 15 min of incubation and this peak remained constant with prolonged incubation. Western blot analysis of HNE-induced ?-synuclein oligomers showed the presence of monomers (15 kDa), SDS-resistant low molecular (30-160 kDa) and high molecular weight oligomers (?260 kDa), indicating that the oligomers consisted of both covalent and non-covalent protein. In contrast, ONE-induced ?-synuclein oligomers only migrated as covalent cross-linked high molecular-weight material (?300 kDa). Both circular dichroism (CD) and Attenuated total reflectance Fourier transform infrared (ATR-FTIR) spectroscopy showed that the formation of HNE- and ONE-induced oligomers coincided with a spectral change from random coil to ?-sheet. However, ONE-induced ?-synuclein oligomers exhibited a slightly higher degree of ?-sheet. Taken together, our results indicate that both HNE and ONE induce a change from random coil to ?-sheet structure that coincides with the formation of ?-synuclein oligomers; albeit through different kinetic pathways depending on the degree of cross-linking. PMID:26129771

  13. 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 (NWU); (SKI)

    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.

  14. Two-dimensional sup 1 H NMR studies on HPr protein from Staphylococcus aureus: Complete sequential assignments and secondary structure

    SciTech Connect

    Kalbitzer, H.R.; Neidig, K.P. (Max-Planck-Inst. for Medical Research, Heidelberg (West Germany)); Hengstenberg, W. (Univ. of Bochum (West Germany))

    1991-11-19

    Complete sequence-specific assignments of the {sup 1}H NMR spectrum of HPr protein from Staphylococcus aureus were obtained by two-dimensional NMR methods. Important secondary structure elements that can be derived from the observed nuclear Overhauser effects are a large antiparallel {beta}-pleated sheet consisting of four strands, A, B, C, D, a segment S{sub AB} consisting of an extended region around the active-center histidine (His-15) and an {alpha}-helix, a half-turn between strands B and C, a segment S{sub CD} which shows no typical secondary structure, and the {alpha}-helical, C-terminal segment S{sub term}. These general structural features are similar to those found earlier in HPr proteins from different microorganisms such as Escherichia coli, Bacillus subtilis, and Streptococcus faecalis.

  15. Targeting of antisense DNA: comparison of activity of anti-rabbit beta-globin oligodeoxyribonucleoside phosphorothioates with computer predictions of mRNA folding.

    PubMed

    Jaroszewski, J W; Syi, J L; Ghosh, M; Ghosh, K; Cohen, J S

    1993-01-01

    To assess the usefulness of computer-assisted modeling of mRNA as an aid in design of antisense DNA, the efficiency of inhibition of translation of rabbit beta-globin mRNA by various antisense sequences was compared with calculated structures of the mRNA. The model obtained by consideration of 30 lowest-energy computer-simulated structures is consistent with the high accessibility of the AUG initiation codon region known from digestion with nucleases and with previous antisense inhibition studies reported in the literature. Additional antisense inhibition data were obtained with 20-mer phosphorothioate oligonucleotides, targeted to regions of beta-globin mRNA differing moderately in their degree of participation in intramolecular folding. The efficiency of translation arrest by the oligonucleotides in cell-free expression systems (wheat germ extract and rabbit reticulocyte lysate) was obtained by measuring incorporation of [35S]methionine into total protein, and corrected for sequence-nonspecific inhibition using brome mosaic virus mRNA. In the presence of RNase H (wheat germ system), the inhibitory activity of the oligonucleotides showed correlation with the calculated secondary structure of mRNA, in particular at low oligonucleotide-to-mRNA ratios (correlation coefficient, 0.95). No correlation was observed in the reticulocyte lysate system, in which the inhibition is mediated by translational arrest. PMID:8155975

  16. Fabrication of sub-20 nm nano-gap structures through the elastomeric nano-stamp assisted secondary sputtering phenomenon.

    PubMed

    Jeon, Hwan-Jin; Lee, Eun Hyung; Yoo, Hae-Wook; Kim, Kyoung Hwan; Jung, Hee-Tae

    2014-06-01

    We describe a highly efficient method for fabricating controllable and reliable sub-20 nm scale nano-gap structures through an elastomeric nano-stamp with an embedded ultra-thin pattern. The stamp consists of ultrahigh resolution (approximately 10 nm) and high aspect ratio (ca. 15) metal nano-structures, which are obtained by secondary sputtering lithography (SSL). The nano-gap structures fabricated in this fashion achieve a high resolution and meet the requirements of minimal cost, high reliability, controllability, reproducibility, and applicability to different materials. Further, we demonstrate that this method enables the fabrication of SERS substrates for detection at the single-molecule level. PMID:24770563

  17. Graph-distance distribution of the Boltzmann ensemble of RNA secondary structures

    PubMed Central

    2014-01-01

    Background Large RNA molecules are often composed of multiple functional domains whose spatial arrangement strongly influences their function. Pre-mRNA splicing, for instance, relies on the spatial proximity of the splice junctions that can be separated by very long introns. Similar effects appear in the processing of RNA virus genomes. Albeit a crude measure, the distribution of spatial distances in thermodynamic equilibrium harbors useful information on the shape of the molecule that in turn can give insights into the interplay of its functional domains. Result Spatial distance can be approximated by the graph-distance in RNA secondary structure. We show here that the equilibrium distribution of graph-distances between a fixed pair of nucleotides can be computed in polynomial time by means of dynamic programming. While a naïve implementation would yield recursions with a very high time complexity of O(n6D5) for sequence length n and D distinct distance values, it is possible to reduce this to O(n4) for practical applications in which predominantly small distances are of of interest. Further reductions, however, seem to be difficult. Therefore, we introduced sampling approaches that are much easier to implement. They are also theoretically favorable for several real-life applications, in particular since these primarily concern long-range interactions in very large RNA molecules. Conclusions The graph-distance distribution can be computed using a dynamic programming approach. Although a crude approximation of reality, our initial results indicate that the graph-distance can be related to the smFRET data. The additional file and the software of our paper are available from http://www.rna.uni-jena.de/RNAgraphdist.html. PMID:25285153

  18. Secondary amenorrhea

    MedlinePLUS

    Amenorrhea - secondary; No periods - secondary; Absent periods - secondary; Absent menses - secondary; Absence of periods - secondary ... In addition to having no menstrual periods, other symptoms can ... Weight gain or weight loss Discharge from the breast or change ...

  19. Effect of Wake Disturbance Frequency on the Secondary Flow Vortex Structure in a Turbine Blade Cascade

    Microsoft Academic Search

    Christopher G. Murawski; Kambiz Vafai

    2000-01-01

    An experimental study of the effect of wake disturbance frequency on the secondary flow vortices in a two-dimensional linear cascade is presented. The flow Reynolds numbers, based on exit velocity and suction side surface length were 25,000, 50,000 and 85,000. Secondary flow was visualized by injecting smoke into the boundary layer and illuminat- ing it with a laser light sheet

  20. Pulsed laser deposition of silk protein: Effect of photosensitized-ablation on the secondary structure in thin deposited films

    NASA Astrophysics Data System (ADS)

    Tsuboi, Yasuyuki; Goto, Masaharu; Itaya, Akira

    2001-06-01

    Silk fibroin is a simple protein expected to have functional applications in medicine and bioelectronics. The primary structure of this protein is quite simple, and the main secondary structures are ?-sheet crystals and amorphous random coils. In the present study, we investigated pulsed laser deposition (PLD) of fibroin with the ?-sheet structures as targets. The primary and secondary structures in films deposited were analyzed using infrared spectroscopy. Normal laser deposition at 351 nm using neat fibroin targets produced thin films of fibroin with a random coiled structure. Ablation was triggered by two-photonic excitation of the peptide chains, which resulted in the destruction of ?-sheet structure in PLD. In order to avoid the two-photonic excitation, we adopted a PLD method utilizing anthracene (5-0.1 wt %) in a photosensitized reaction involving doped fibroin targets. Laser light (351 or 355 nm) was absorbed only by anthracene, which plays an important role converting photon energy to thermal energy with great ablation efficiency. Thin fibroin films deposited by this method had both random coil and ?-sheet structures. As the dopant concentration and laser fluence decreased, the ratio of ?-sheet domain to random coil increased in thin deposited films.

  1. Pulsed laser deposition of silk protein: Effect of photosensitized-ablation on the secondary structure in thin deposited films

    SciTech Connect

    Tsuboi, Yasuyuki; Goto, Masaharu; Itaya, Akira

    2001-06-15

    Silk fibroin is a simple protein expected to have functional applications in medicine and bioelectronics. The primary structure of this protein is quite simple, and the main secondary structures are {beta}-sheet crystals and amorphous random coils. In the present study, we investigated pulsed laser deposition (PLD) of fibroin with the {beta}-sheet structures as targets. The primary and secondary structures in films deposited were analyzed using infrared spectroscopy. Normal laser deposition at 351 nm using neat fibroin targets produced thin films of fibroin with a random coiled structure. Ablation was triggered by two-photonic excitation of the peptide chains, which resulted in the destruction of {beta}-sheet structure in PLD. In order to avoid the two-photonic excitation, we adopted a PLD method utilizing anthracene (5{endash}0.1 wt%) in a photosensitized reaction involving doped fibroin targets. Laser light (351 or 355 nm) was absorbed only by anthracene, which plays an important role converting photon energy to thermal energy with great ablation efficiency. Thin fibroin films deposited by this method had both random coil and {beta}-sheet structures. As the dopant concentration and laser fluence decreased, the ratio of {beta}-sheet domain to random coil increased in thin deposited films. {copyright} 2001 American Institute of Physics.

  2. Plasmodesmata during development: re-examination of the importance of primary, secondary, and branched plasmodesmata structure versus function

    PubMed Central

    Burch-Smith, Tessa M.; Stonebloom, Solomon; Xu, Min

    2010-01-01

    Plasmodesmata (PD) structure and function vary temporally and spatially during all stages of plant development. PD that originate during, or post, cell division are designated as primary or secondary according to classical terminology. PD structure may be simple, twinned, or branched. Studies of PD during leaf, root, and embryo development have lead to the generalization that cells in less mature tissues contain predominantly simple PD. New quantitative analyses reveal that twinned and branched PD also occur in immature tissues. New data also highlight the versatility of viral movement proteins as tags for labeling PD in immature tissues as well as PD in mature tissues. A summary of the formation and function of primary, secondary, and branched PD during leaf, trichome, embryo, apical meristem, vascular cambium, and root development underscores the remarkable and indispensible plant-specific intercellular communication system that is mediated by PD. PMID:21174132

  3. The response of greek key proteins to changes in connectivity depends on the nature of their secondary structure.

    PubMed

    Kemplen, Katherine R; De Sancho, David; Clarke, Jane

    2015-06-19

    What governs the balance between connectivity and topology in regulating the mechanism of protein folding? We use circular permutation to vary the order of the helices in the all-? Greek key protein FADD (Fas-associated death domain) to investigate this question. Unlike all-? Greek key proteins, where changes in the order of secondary structure cause a shift in the folding nucleus, the position of the nucleus in FADD is unchanged, even when permutation reduces the complexity significantly. We suggest that this is because local helical contacts are so dominant that permutation has little effect on the entropic cost of forming the folding nucleus whereas, in all-? Greek key proteins, all interactions in the nucleus are long range. Thus, the type of secondary structure modulates the sensitivity of proteins to changes in connectivity. PMID:25861761

  4. The Response of Greek Key Proteins to Changes in Connectivity Depends on the Nature of Their Secondary Structure

    PubMed Central

    Kemplen, Katherine R.; De Sancho, David; Clarke, Jane

    2015-01-01

    What governs the balance between connectivity and topology in regulating the mechanism of protein folding? We use circular permutation to vary the order of the helices in the all-? Greek key protein FADD (Fas-associated death domain) to investigate this question. Unlike all-? Greek key proteins, where changes in the order of secondary structure cause a shift in the folding nucleus, the position of the nucleus in FADD is unchanged, even when permutation reduces the complexity significantly. We suggest that this is because local helical contacts are so dominant that permutation has little effect on the entropic cost of forming the folding nucleus whereas, in all-? Greek key proteins, all interactions in the nucleus are long range. Thus, the type of secondary structure modulates the sensitivity of proteins to changes in connectivity. PMID:25861761

  5. Structural integrity of the PCI domain of eIF3a/TIF32 is required for mRNA recruitment to the 43S pre-initiation complexes

    PubMed Central

    Khoshnevis, Sohail; Gunišová, Stanislava; Vl?ková, Vladislava; Kouba, Tomáš; Neumann, Piotr; Beznosková, Petra; Ficner, Ralf; Valášek, Leoš Shivaya

    2014-01-01

    Transfer of genetic information from genes into proteins is mediated by messenger RNA (mRNA) that must be first recruited to ribosomal pre-initiation complexes (PICs) by a mechanism that is still poorly understood. Recent studies showed that besides eIF4F and poly(A)-binding protein, eIF3 also plays a critical role in this process, yet the molecular mechanism of its action is unknown. We showed previously that the PCI domain of the eIF3c/NIP1 subunit of yeast eIF3 is involved in RNA binding. To assess the role of the second PCI domain of eIF3 present in eIF3a/TIF32, we performed its mutational analysis and identified a 10-Ala-substitution (Box37) that severely reduces amounts of model mRNA in the 43–48S PICs in vivo as the major, if not the only, detectable defect. Crystal structure analysis of the a/TIF32-PCI domain at 2.65-Å resolution showed that it is required for integrity of the eIF3 core and, similarly to the c/NIP1-PCI, is capable of RNA binding. The putative RNA-binding surface defined by positively charged areas contains two Box37 residues, R363 and K364. Their substitutions with alanines severely impair the mRNA recruitment step in vivo suggesting that a/TIF32-PCI represents one of the key domains ensuring stable and efficient mRNA delivery to the PICs. PMID:24423867

  6. Genomic HIV RNA Induces Innate Immune Responses through RIG-I-Dependent Sensing of Secondary-Structured RNA

    PubMed Central

    Berg, Randi K.; Melchjorsen, Jesper; Rintahaka, Johanna; Diget, Elisabeth; Søby, Stine; Horan, Kristy A.; Gorelick, Robert J.; Matikainen, Sampsa; Larsen, Carsten S.; Ostergaard, Lars; Paludan, Søren R.; Mogensen, Trine H.

    2012-01-01

    Background Innate immune responses have recently been appreciated to play an important role in the pathogenesis of HIV infection. Whereas inadequate innate immune sensing of HIV during acute infection may contribute to failure to control and eradicate infection, persistent inflammatory responses later during infection contribute in driving chronic immune activation and development of immunodeficiency. However, knowledge on specific HIV PAMPs and cellular PRRs responsible for inducing innate immune responses remains sparse. Methods/Principal Findings Here we demonstrate a major role for RIG-I and the adaptor protein MAVS in induction of innate immune responses to HIV genomic RNA. We found that secondary structured HIV-derived RNAs induced a response similar to genomic RNA. In primary human peripheral blood mononuclear cells and primary human macrophages, HIV RNA induced expression of IFN-stimulated genes, whereas only low levels of type I IFN and tumor necrosis factor ? were produced. Furthermore, secondary structured HIV-derived RNA activated pathways to NF-?B, MAP kinases, and IRF3 and co-localized with peroxisomes, suggesting a role for this organelle in RIG-I-mediated innate immune sensing of HIV RNA. Conclusions/Significance These results establish RIG-I as an innate immune sensor of cytosolic HIV genomic RNA with secondary structure, thereby expanding current knowledge on HIV molecules capable of stimulating the innate immune system. PMID:22235281

  7. Secondary structure analysis of ITS2 in the rDNA of three Indian paramphistomid species found in local livestock.

    PubMed

    Shylla, Jollin A; Ghatani, Sudeep; Chatterjee, Anupam; Tandon, Veena

    2011-04-01

    Of paramphistomid trematodes, three species viz., Homalogaster paloniae, Calicophoron calicophorum and Orthocoelium streptocoelium are commonly prevalent in bovine hosts in Northeast India. The aim of the present study was to genetically characterise these species using rDNA second internal transcribed spacer (ITS2) so as to supplement the morphological criteria substantiated by molecular findings. The annotated ITS2 region from H. paloniae, C. calicophorum and O. streptocoelium were found to be 289 bp, 288 bp and 288 bp long, respectively. On comparison, the Indian isolates of the three species were observed to have a maximum identity of 99% with each of their respective counterparts from Japan. The secondary structure models were inferred using minimum free energy modelling algorithms. The paramphistomes displayed the typical four helix ITS2 secondary structure and differed from each other due to minor nucleotide differences. The consensus ITS2 secondary structure model revealed the presence of conservative motifs GACGAGGGUG and GCGGUAGAGUC in helix III. Monophyly is well supported for a clade consisting of the Japanese and Indian paramphistomes with significant bootstrap values. PMID:21069539

  8. High-resolution NMR reveals secondary structure and folding of amino acid transporter from outer chloroplast membrane.

    PubMed

    Zook, James D; Molugu, Trivikram R; Jacobsen, Neil E; Lin, Guangxin; Soll, Jürgen; Cherry, Brian R; Brown, Michael F; Fromme, Petra

    2013-01-01

    Solving high-resolution structures for membrane proteins continues to be a daunting challenge in the structural biology community. In this study we report our high-resolution NMR results for a transmembrane protein, outer envelope protein of molar mass 16 kDa (OEP16), an amino acid transporter from the outer membrane of chloroplasts. Three-dimensional, high-resolution NMR experiments on the (13)C, (15)N, (2)H-triply-labeled protein were used to assign protein backbone resonances and to obtain secondary structure information. The results yield over 95% assignment of N, HN, CO, C?, and C? chemical shifts, which is essential for obtaining a high resolution structure from NMR data. Chemical shift analysis from the assignment data reveals experimental evidence for the first time on the location of the secondary structure elements on a per residue basis. In addition T 1Z and T2 relaxation experiments were performed in order to better understand the protein dynamics. Arginine titration experiments yield an insight into the amino acid residues responsible for protein transporter function. The results provide the necessary basis for high-resolution structural determination of this important plant membrane protein. PMID:24205117

  9. Single-Molecule Measurements of the CCR5 mRNA Unfolding Pathways

    PubMed Central

    de Messieres, Michel; Chang, Jen-Chien; Belew, Ashton Trey; Meskauskas, Arturas; Dinman, Jonathan D.; La Porta, Arthur

    2014-01-01

    Secondary or tertiary structure in an mRNA, such as a pseudoknot, can create a physical barrier that requires the ribosome to generate additional force to translocate. The presence of such a barrier can dramatically increase the probability that the ribosome will shift into an alternate reading frame, in which a different set of codons is recognized. The detailed biophysical mechanism by which frameshifting is induced remains unknown. Here we employ optical trapping techniques to investigate the structure of a ?1 programmed ribosomal frameshift (?1 PRF) sequence element located in the CCR5 mRNA, which encodes a coreceptor for HIV-1 and is, to our knowledge, the first known human ?1 PRF signal of nonviral origin. We begin by presenting a set of computationally predicted structures that include pseudoknots. We then employ what we believe to be new analytical techniques for measuring the effective free energy landscapes of biomolecules. We find that the ?1 PRF element manifests several distinct unfolding pathways when subject to end-to-end force, one of which is consistent with a proposed pseudoknot conformation, and another of which we have identified as a folding intermediate. The dynamic ensemble of conformations that CCR5 mRNA exhibits in the single-molecule experiments may be a significant feature of the frameshifting mechanism. PMID:24411256

  10. Sequences of three molluscan 5 S ribosomal RNAs confirm the validity of a dynamic secondary structure model.

    PubMed

    Fang, B L; De Baere, R; Vandenberghe, A; De Wachter, R

    1982-08-11

    The collection of known 5 S rRNA primary structures is enriched with the sequences from three mollusca, the snails Helix pomatia and Arion rufus, and the mussel Mytilus edulis. The three sequences can be fitted in a five-helix secondary structure model previously shown (De Wachter et al. (1982) Biochimie 64, 311-329) to apply to all 5 S RNAs regardless of their origin. One of the helices in this model can undergo a bulge-internal loop transition. Within the metazoan kingdom, the dimensions of each helix and loop are rigidly conserved, except for one helix which can comprise either 6 or 7 base pairs. PMID:7133995

  11. Sequences of three molluscan 5 S ribosomal RNAs confirm the validity of a dynamic secondary structure model.

    PubMed Central

    Fang, B L; De Baere, R; Vandenberghe, A; De Wachter, R

    1982-01-01

    The collection of known 5 S rRNA primary structures is enriched with the sequences from three mollusca, the snails Helix pomatia and Arion rufus, and the mussel Mytilus edulis. The three sequences can be fitted in a five-helix secondary structure model previously shown (De Wachter et al. (1982) Biochimie 64, 311-329) to apply to all 5 S RNAs regardless of their origin. One of the helices in this model can undergo a bulge-internal loop transition. Within the metazoan kingdom, the dimensions of each helix and loop are rigidly conserved, except for one helix which can comprise either 6 or 7 base pairs. PMID:7133995

  12. STRUCTURAL CHARACTERIZATION OF REACTIVE DYES USING SECONDARY ION MASS SPECTROMETRY/TANDEM MASS SPECTROMETRY

    EPA Science Inventory

    Reactive Blue 19 (RB 19), its reactive form (RB 19-VS) and its hydrolyzed form, (RB 19-OH) were examined using liquid secondary ion mass spectrometry/tandem mass spectrometry (LSIMS/MS/MS) in the negative-ion mode under low-energy collision conditions (240-300 eV). tructurally ch...

  13. Combining evolutionary information and neural networks to predict protein secondary structure

    Microsoft Academic Search

    Burkhard Rost; Chris Sander

    1994-01-01

    Using evolutionary informa- tion contained in multiple sequence alignments as input to neural networks, secondary struc- ture can be predicted at significantly increased accuracy. Here, we extend our previous three- level system of neural networks by using addi- tional input information derived from multiple alignments. Using a position-specific conserva- tion weight as part of the input increases per- formance. Using

  14. Secondary structure formation of homopolymeric single-stranded nucleic acids including force and loop entropy: implications for DNA hybridization

    E-print Network

    Einert, Thomas R; Netz, Roland R

    2011-01-01

    Loops are essential secondary structure elements in folded DNA and RNA molecules and proliferate close to the melting transition. Using a theory for nucleic acid secondary structures that accounts for the logarithmic entropy c ln m for a loop of length m, we study homopolymeric single-stranded nucleic acid chains under external force and varying temperature. In the thermodynamic limit of a long strand, the chain displays a phase transition between a low temperature / low force compact (folded) structure and a high temperature / high force molten (unfolded) structure. The influence of c on phase diagrams, critical exponents, melting, and force extension curves is derived analytically. For vanishing pulling force, only for the limited range of loop exponents 2 < c < 2.479 a melting transition is possible; for c <= 2 the chain is always in the folded phase and for 2.479 < c always in the unfolded phase. A force induced melting transition with singular behavior is possible for all loop exponents c <...

  15. Structure and reactivity of boron-ate complexes derived from primary and secondary boronic esters.

    PubMed

    Feeney, Kathryn; Berionni, Guillaume; Mayr, Herbert; Aggarwal, Varinder K

    2015-06-01

    Boron-ate complexes derived from primary and secondary boronic esters and aryllithiums have been isolated, and the kinetics of their reactions with carbenium ions studied. The second-order rate constants have been used to derive nucleophilicity parameters for the boron-ate complexes, revealing that nucleophilicity increased with (i) electron-donating aromatics on boron, (ii) neopentyl glycol over pinacol boronic esters, and (iii) 12-crown-4 ether. PMID:25973673

  16. Position-specific residue preference features around the ends of helices and strands and a novel strategy for the prediction of secondary structures.

    PubMed

    Duan, Mojie; Huang, Min; Ma, Chuang; Li, Lun; Zhou, Yanhong

    2008-09-01

    It has been many years since position-specific residue preference around the ends of a helix was revealed. However, all the existing secondary structure prediction methods did not exploit this preference feature, resulting in low accuracy in predicting the ends of secondary structures. In this study, we collected a relatively large data set consisting of 1860 high-resolution, non-homology proteins from the PDB, and further analyzed the residue distributions around the ends of regular secondary structures. It was found that there exist position-specific residue preferences (PSRP) around the ends of not only helices but also strands. Based on the unique features, we proposed a novel strategy and developed a tool named E-SSpred that treats the secondary structure as a whole and builds models to predict entire secondary structure segments directly by integrating relevant features. In E-SSpred, the support vector machine (SVM) method is adopted to model and predict the ends of helices and strands according to the unique residue distributions around them. A simple linear discriminate analysis method is applied to model and predict entire secondary structure segments by integrating end-prediction results, tri-peptide composition, and length distribution features of secondary structures, as well as the prediction results of the most famous program PSIPRED. The results of fivefold cross-validation on a widely used data set demonstrate that the accuracy of E-SSpred in predicting ends of secondary structures is about 10% higher than PSIPRED, and the overall prediction accuracy (Q(3) value) of E-SSpred (82.2%) is also better than PSIPRED (80.3%). The E-SSpred web server is available at http://bioinfo.hust.edu.cn/bio/tools/E-SSpred/index.html. PMID:18519808

  17. The identification of recurrent tertiary motifs by interactions of protein secondary structure units 

    E-print Network

    Hodges, Hamilton Courtney

    2013-02-22

    of amino acids that fold into unique three-dimensional structures. One of the goals of structural biology is to predict a protein's three-dimensional structure from its amino acid sequence. One important aspect of protein structure is the manner by which...

  18. Primary and secondary structure of 5.8S rRNA from the silkgland of Bombyx mori.

    PubMed

    Fujiwara, H; Kawata, Y; Ishikawa, H

    1982-04-10

    Nucleotide sequence of 5.8S rRNA of the silkworm, Bombyx mori has been determined by gel sequencing methods. The 5.8S rRNA was the longest so far reported, with the 5'-terminal sequence several nucleotides longer than those of the other organisms. Upon constructing the secondary structure in accordance with the "burp gun" model (12), the Bombyx 5.8S rRNA formed a wide-open "muzzle" due to several unpaired bases at the ends. The overall structure also appeared less stable with less G . C pairs and more unpaired bases than that of the HeLa 5.8S rRNA. These structural features may be essential for those 5.8S rRNAs which interact with 28S rRNAs containing the hidden break to form a stable complex. PMID:7088713

  19. Effect of surface produced secondary electrons on the sheath structure induced by high-power microwave window breakdown

    SciTech Connect

    Cheng Guoxin; Liu Lie [College of Opto-Electronic Science and Engineering, National University of Defense Technology, Changsha, Hunan 410073 (China)

    2011-03-15

    Dielectric window breakdown, whose mechanism is not thoroughly understood, is a major factor of limiting the transmission and radiation of high-power microwave on the order of 1 GW. In this paper, a one-dimensional fluid-like sheath model is developed to investigate the sheath structures formed at different gas pressures. The dominant processes during the surface flashover are isolated by this model. In vacuum, electron multipactor is self-sustained by secondary electron emission, a positive space-charge potential is formed on the dielectric surface. With increasing gas pressure, electron-neutral ionization prevails against secondary electron emission. The multipactor effect is suppressed by the shielding of plasma electrons. This leads to the sheath potential changing gradually from a positive space-charge potential to a negative space-charge potential. For argon gas pressure lower than 14 Torr, the sheath is space charge limited. A potential minimum could be formed in front of the dielectric which traps secondary electrons emitted from the wall. With the higher argon gas pressure, the number density of ions becomes comparable to that of electrons, all surface produced electrons are accelerated toward the presheath region. Therefore, the normal sheath is formed and the resulting surface flashover on the dielectric surface becomes rf-driven volumetric breakdown.

  20. Protein folding simulations of 2D HP model by the genetic algorithm based on optimal secondary structures.

    PubMed

    Huang, Chenhua; Yang, Xiangbo; He, Zhihong

    2010-06-01

    In this paper, based on the evolutionary Monte Carlo (EMC) algorithm, we have made four points of ameliorations and propose a so-called genetic algorithm based on optimal secondary structure (GAOSS) method to predict efficiently the protein folding conformations in the two-dimensional hydrophobic-hydrophilic (2D HP) model. Nine benchmarks are tested to verify the effectiveness of the proposed approach and the results show that for the listed benchmarks GAOSS can find the best solutions so far. It means that reasonable, effective and compact secondary structures (SSs) can avoid blind searches and can reduce time consuming significantly. On the other hand, as examples, we discuss the diversity of protein GSC for the 24-mer and 85-mer sequences. Several GSCs have been found by GAOSS and some of the conformations are quite different from each other. It would be useful for the designing of protein molecules. GAOSS would be an efficient tool for the protein structure predictions (PSP). PMID:20627698

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

    PubMed Central

    Nickrent, D L; Sargent, M L

    1991-01-01

    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. PMID:2014163

  2. Effect of centrifugal forces on formation of secondary flow structures in a 180-degree curved artery model under pulsatile inflow conditions

    NASA Astrophysics Data System (ADS)

    Callahan, Shannon; Sajjad, Roshan; Bulusu, Kartik V.; Plesniak, Michael W.

    2013-11-01

    An experimental investigation of secondary flow structures within a 180-degree bent tube model of a curved artery was performed using phase-averaged, two-component, two-dimensional, particle image velocimetry (2C-2D PIV) under pulsatile inflow conditions. Pulsatile waveforms ranging from simple sinusoidal to physiological inflows were supplied. We developed a novel continuous wavelet transform algorithm (PIVlet 1.2) and applied it to vorticity fields for coherent secondary flow structure detection. Regime maps of secondary flow structures revealed new, deceleration-phase-dependent flow morphologies. The temporal instances where streamwise centrifugal forces dominated were associated with large-scale coherent structures, such as deformed Dean-, Lyne- and Wall-type (D-L-W) vortical structures. Magnitudes of streamwise and cross-stream centrifugal forces tend to balance during deceleration phases. Deceleration events were also associated with spatial reorganization and asymmetry in large-scale D-L-W secondary flow structures. Hence, the interaction between streamwise and cross-stream centrifugal forces that affects secondary flow morphologies is explained using a ``residual force'' parameter i.e., the difference in magnitudes of these forces. An experimental investigation of secondary flow structures within a 180-degree bent tube model of a curved artery was performed using phase-averaged, two-component, two-dimensional, particle image velocimetry (2C-2D PIV) under pulsatile inflow conditions. Pulsatile waveforms ranging from simple sinusoidal to physiological inflows were supplied. We developed a novel continuous wavelet transform algorithm (PIVlet 1.2) and applied it to vorticity fields for coherent secondary flow structure detection. Regime maps of secondary flow structures revealed new, deceleration-phase-dependent flow morphologies. The temporal instances where streamwise centrifugal forces dominated were associated with large-scale coherent structures, such as deformed Dean-, Lyne- and Wall-type (D-L-W) vortical structures. Magnitudes of streamwise and cross-stream centrifugal forces tend to balance during deceleration phases. Deceleration events were also associated with spatial reorganization and asymmetry in large-scale D-L-W secondary flow structures. Hence, the interaction between streamwise and cross-stream centrifugal forces that affects secondary flow morphologies is explained using a ``residual force'' parameter i.e., the difference in magnitudes of these forces. Supported by the NSF Grant No. CBET- 0828903 and GW Center for Biomimetics and Bioinspired Engineering.

  3. Resonant production of secondary electrons generating a discrete energy structure in a magnetized electron beam system.

    PubMed

    Ito, A; Yoshida, Z

    2001-02-01

    In a system of magnetized electron beams, multiplication of electrons can occur if the incident and return beams (the latter one is produced by secondary electrons emitted at the end of the incident beam) satisfy a resonance condition on the gyration phase. The beams propagate between two boundaries; one is an electron gun and the other is a Faraday cup detector. The resonance condition demands discrete energies (eigenvalues) of the Hamiltonian that generates a propagator of the beam. This model has been compared with Varma's formulation of discrete energies [R. K. Varma and A. M. Punithavelu, Mod. Phys. Lett. A 8, 167 (1993)]. PMID:11308593

  4. Prediction and Fourier-transform infrared-spectroscopy estimation of the secondary structure of a recombinant beta-glucosidase from Streptomyces sp. (ATCC 11238).

    PubMed Central

    Perez-Pons, J A; Padros, E; Querol, E

    1995-01-01

    The secondary structure of a recombinant beta-glucosidase (EC 3.2.1.21) from Streptomyces sp. (ATCC 11238) has been predicted by computer algorithms and also estimated by Fourier-transform IR spectroscopy. From curve fitting of the deconvoluted IR spectra, the most probable distribution of the secondary-structural classes appears to be about 34% alpha-helix, 30% beta-sheet, 25% reverse turns and 11% non-ordered structures. These data showed a good agreement with data from computer prediction (35% alpha-helix, 23% beta-sheet, 31% reverse turns and 11% non-ordered structures). PMID:8948434

  5. Protein Structure Analysis Iosif Vaisman

    E-print Network

    Vaisman, Iosif

    Protein Structure Analysis Iosif Vaisman 2012 BINF 731 http://binf.gmu.edu/vaisman/binf731/ Secondary Structure: Computational Problems Secondary structure characterization Secondary structure assignment Secondary structure prediction Protein structure classification Secondary Structure Conformations

  6. Protein Structure Analysis Iosif Vaisman

    E-print Network

    Vaisman, Iosif

    Protein Structure Analysis Iosif Vaisman 2013 BINF 731 http://binf.gmu.edu/vaisman/binf731/ Secondary Structure: Computational Problems Secondary structure characterization Secondary structure assignment Secondary structure prediction Protein structure classification Secondary Structure Conformations

  7. Cyclization of the intrinsically disordered ?1S dihydropyridine receptor II-III loop enhances secondary structure and in vitro function.

    PubMed

    Tae, Han-Shen; Cui, Yanfang; Karunasekara, Yamuna; Board, Philip G; Dulhunty, Angela F; Casarotto, Marco G

    2011-06-24

    A key component of excitation contraction (EC) coupling in skeletal muscle is the cytoplasmic linker (II-III loop) between the second and third transmembrane repeats of the ?(1S) subunit of the dihydropyridine receptor (DHPR). The II-III loop has been previously examined in vitro using a linear II-III loop with unrestrained N- and C-terminal ends. To better reproduce the loop structure in its native environment (tethered to the DHPR transmembrane domains), we have joined the N and C termini using intein-mediated technology. Circular dichroism and NMR spectroscopy revealed a structural shift in the cyclized loop toward a protein with increased ?-helical and ?-strand structure in a region of the loop implicated in its in vitro function and also in a critical region for EC coupling. The affinity of binding of the II-III loop binding to the SPRY2 domain of the skeletal ryanodine receptor (RyR1) increased 4-fold, and its ability to activate RyR1 channels in lipid bilayers was enhanced 3-fold by cyclization. These functional changes were predicted consequences of the structural enhancement. We suggest that tethering the N and C termini stabilized secondary structural elements in the DHPR II-III loop and may reflect structural and dynamic characteristics of the loop that are inherent in EC coupling. PMID:21525002

  8. New Comparative Analysis Based on the Secondary Structure of SSU-rRNA Gene Reveals the Evolutionary Trend and the Family-Genus Characters of Mobilida (Ciliophora, Peritrichia).

    PubMed

    Zhang, Yong; Zhao, Yuan-Jun; Wang, Qin; Tang, Fa-Hui

    2015-08-01

    In order to reveal the structural evolutionary trend of Mobilida ciliates, twenty-six SSU-rRNA sequences of mobilid species, including seven ones newly sequenced in the present work, were used for comparative phylogenic analysis based on the RNA secondary structure. The research results indicate that all the secondary structures except domains Helix 10, Helix 12, and Helix 37 could be regarded as the criterions in classification between the family Trichodinidae and Urceolariida, and four regions including Helix E10-1, Helix 29, Helix 43, and Helix 45-Helix 46 could be as criterions in classification between the genus Trichodinella and Trichodina in family Trichodinidae. After the analysis of common structural feature within the Mobilida, it was found that the secondary structure of V6 could prove the family Urceolariidae primitive status. This research has further suggested that the genus Trichodina could be divergent earlier than Trichodinella in the family Trichodinidae. In addition, the relationship between the secondary structure and topology of phylogenic tree that the branching order of most clades corresponds with the secondary structure of species within each clade of phylogenetic tree was first uncovered and discussed in the present study. PMID:26037381

  9. Elastic properties and secondary structure formation of single-stranded DNA at monovalent and divalent salt conditions.

    PubMed

    Bosco, Alessandro; Camunas-Soler, Joan; Ritort, Felix

    2014-02-01

    Single-stranded DNA (ssDNA) plays a major role in several biological processes. It is therefore of fundamental interest to understand how the elastic response and the formation of secondary structures are modulated by the interplay between base pairing and electrostatic interactions. Here we measure force-extension curves (FECs) of ssDNA molecules in optical tweezers set up over two orders of magnitude of monovalent and divalent salt conditions, and obtain its elastic parameters by fitting the FECs to semiflexible models of polymers. For both monovalent and divalent salts, we find that the electrostatic contribution to the persistence length is proportional to the Debye screening length, varying as the inverse of the square root of cation concentration. The intrinsic persistence length is equal to 0.7 nm for both types of salts, and the effectivity of divalent cations in screening electrostatic interactions appears to be 100-fold as compared with monovalent salt, in line with what has been recently reported for single-stranded RNA. Finally, we propose an analysis of the FECs using a model that accounts for the effective thickness of the filament at low salt condition and a simple phenomenological description that quantifies the formation of non-specific secondary structure at low forces. PMID:24225314

  10. Studies on the secondary structure of 5.8 S rRNA from a thermophile, Thermomyces lanuginosus.

    PubMed

    Wildeman, A G; Nazar, R N

    1981-06-10

    The nucleotide sequence of ribosomal 5.8 S RNA from a thermophilic fungus, Thermomyces lanuginosus, was determined to be (formula: see text). The secondary structure was probed under a variety of ionic conditions using limited pancreatic and T1 ribonuclease digestion and rapid gel sequencing techniques. The results generally supported the "burp gun" model previously proposed for all 5.8 S rRNAs (Nazar, R. N., Sitz, T. O., and Busch, H. (1975) J. Biol. Chem. 250, 8591-8597) and were inconsistent with a recently suggested "cloverleaf" configuration (Luoma, G. A., and Marshall, A. G. (1978) Proc. Natl. Acad. Sci. U.S.A. 75, 4901-4905). Theoretical considerations of the overall stability also appear to favor the former estimate. As previously observed with other 5.8 S RNAs the sequence of T. lanuginosus RNA is strikingly homologous with other species; it differs in only 13 positions from that of yeast. When compared to yeast, the differences appear not to contribute to the stability of the secondary structure but probably lead to a more stable 5.8 S-25 S rRNA interaction in the large ribosomal subunit. A general comparison of T. lanuginosus 5.8 S RNA with all known 5.8 S RNA sequences indicates that, although modified nucleotides differ significantly between species, they are always located in four highly conserved regions of the 5.8 S molecule, probably contributing to the unique character of these very essential sequences. PMID:7195399

  11. Elastic properties and secondary structure formation of single-stranded DNA at monovalent and divalent salt conditions

    PubMed Central

    Bosco, Alessandro; Camunas-Soler, Joan; Ritort, Felix

    2014-01-01

    Single-stranded DNA (ssDNA) plays a major role in several biological processes. It is therefore of fundamental interest to understand how the elastic response and the formation of secondary structures are modulated by the interplay between base pairing and electrostatic interactions. Here we measure force-extension curves (FECs) of ssDNA molecules in optical tweezers set up over two orders of magnitude of monovalent and divalent salt conditions, and obtain its elastic parameters by fitting the FECs to semiflexible models of polymers. For both monovalent and divalent salts, we find that the electrostatic contribution to the persistence length is proportional to the Debye screening length, varying as the inverse of the square root of cation concentration. The intrinsic persistence length is equal to 0.7 nm for both types of salts, and the effectivity of divalent cations in screening electrostatic interactions appears to be 100-fold as compared with monovalent salt, in line with what has been recently reported for single-stranded RNA. Finally, we propose an analysis of the FECs using a model that accounts for the effective thickness of the filament at low salt condition and a simple phenomenological description that quantifies the formation of non-specific secondary structure at low forces. PMID:24225314

  12. [FTIR analysis of cosrelation between emulsifying properties and the secondary structure of the proteins in modified egg yolk powder ].

    PubMed

    Ge, Shao-Yang; Liu, Mei-Yu; Zhu, Jun; Wang, Fang; Ren, Fa-Zheng; Zhang, Lu-Da; Guo, Hui-Yuan

    2011-08-01

    Spray drying is an important processing of producing modificatied yolk powder (MEYP). To investigate the correlation between the secondary structure and emulsifying property of MEYP made at different spray-drying-temperatures, Fourier transform infrared spectroscopy (FTIR) was applied in the present study. The result indicated that emulsifiability and the percentage of alpha-helix were both significantly increased firstly and then remarkably decreased with rising of spray-drying-temperature, and the emulsifying property of MEYP was relative to the percentage of alpha-helix. After heat-treating, the percentage of alpha-helix was significantly decreased and the percentage of p-sheet was remarkably increased, however, the total percentage of the two structures was maintained. The stable total percentage of alpha-helix and beta-sheet would be a good explanation for the great heat stability of emulsion presented in the MEYP made at different spray-drying temperature. PMID:22007391

  13. G-SIMS-FPM: Molecular structure at surfaces—a combined positive and negative secondary ion study

    NASA Astrophysics Data System (ADS)

    Gilmore, I. S.; Green, F. M.; Seah, M. P.

    2006-07-01

    G-SIMS is an easy to use method that considerably simplifies complex static SIMS spectra. The G-SIMS peaks relate directly to the parent molecular structure and so provide a library independent method for direct interpretation and identification. For larger molecules (>100 u) the mass alone may be insufficient to identify the molecule unambiguously. A development of G-SIMS, G-SIMS-fragmentation pathway mapping (FPM), solves this problem. G-SIMS-FPM allows the molecular structure to be re-assembled by following fragmentation pathways as the G-SIMS surface plasma temperature is varied. In this study, we develop the inclusion of negative secondary ion fragmentation data to provide a more complete analysis. This approach is exampled with data for complex molecules of Irganox 1010 and folic acid.

  14. Model-Free RNA Sequence and Structure Alignment Informed by SHAPE Probing Reveals a Conserved Alternate Secondary Structure for 16S rRNA.

    PubMed

    Lavender, Christopher A; Lorenz, Ronny; Zhang, Ge; Tamayo, Rita; Hofacker, Ivo L; Weeks, Kevin M

    2015-05-01

    Discovery and characterization of functional RNA structures remains challenging due to deficiencies in de novo secondary structure modeling. Here we describe a dynamic programming approach for model-free sequence comparison that incorporates high-throughput chemical probing data. Based on SHAPE probing data alone, ribosomal RNAs (rRNAs) from three diverse organisms - the eubacteria E. coli and C. difficile and the archeon H. volcanii - could be aligned with accuracies comparable to alignments based on actual sequence identity. When both base sequence identity and chemical probing reactivities were considered together, accuracies improved further. Derived sequence alignments and chemical probing data from protein-free RNAs were then used as pseudo-free energy constraints to model consensus secondary structures for the 16S and 23S rRNAs. There are critical differences between these experimentally-informed models and currently accepted models, including in the functionally important neck and decoding regions of the 16S rRNA. We infer that the 16S rRNA has evolved to undergo large-scale changes in base pairing as part of ribosome function. As high-quality RNA probing data become widely available, structurally-informed sequence alignment will become broadly useful for de novo motif and function discovery. PMID:25992778

  15. Carbon Policy and Technical Change: Market Structure, Increasing Returns, and Secondary Benefits. Final Report

    SciTech Connect

    Peretto, P.; Smith, V. K.

    2001-11-19

    An economic evaluation of the impact of policies intended to control emissions of CO{sub 2} and other ''greenhouse gases'' (GHGS) depends on the net costs of these controls and their distribution throughout the production sectors of developed and developing economics. The answers derived from appraisals of these net costs, in turn, stem from what is assumed about the timing of the controls, the pace of technological change, and any short-term secondary benefits from their control. There have only been a few serious attempts to estimate the economic benefits from the policies associated with such long run outcomes. All of the approaches to date have made fairly strong assumptions or relied on contingent valuation estimates of hypothetical situations.

  16. Secondary structure and domain architecture of the 23S and 5S rRNAs

    E-print Network

    Williams, Loren

    -resolution 3D structures (10­18) from all three primary domains of the tree of life; Bacteria, Archaea similarity with the 16S rRNA. The revised 2 structure also reveals a clear relation- ship with the 3D

  17. Design of 11-residue peptides with unusual biophysical properties: induced secondary structure in the absence of water.

    PubMed

    Mo, Xiaoqun; Hiromasa, Yasuaki; Warner, Matt; Al-Rawi, Ahlam N; Iwamoto, Takeo; Rahman, Talat S; Sun, Xiuzhi; Tomich, John M

    2008-03-01

    A series of oligopeptides with beta-forming and adhesive properties, were synthesized and analyzed for adhesion shear strength, secondary structure, and association properties. The sequences contained related hydrophobic core segments varying in length from 5 to 12 residues and flanked by di- or tri-lysine segments. Three remarkable peptides consisting of just 11 residues with hydrophobic core sequences of FLIVI, IGSII, and IVIGS flanked by three lysine residues gave the highest dry adhesion shear strength and displayed unusual biophysical properties in the presence and absence of water. KKKFLIVIKKK had its highest adhesion strength at 2% (w/v) at pH 12.0 and showed the highest adhesion strength after exposure to water (water resistance). Both KKKIGSIIKKK and KKKIVIGSKKK, at 4% (w/v) at pH 12.0, displayed nearly identical dry shear strength values to that with the FLIVI core sequence. The peptide with IGSII core, however, displayed a lower water resistance and the latter, IVIGS, showed no water resistance, completely delaminating upon soaking in water. These are the smallest peptides with adhesive properties reported to date and show remarkable adhesion strength even at lower concentrations of 0.2% (w/v), which corresponds to 1.6 mM. The FLIVI containing peptide adopted a beta-sheet secondary structure in water while the IGSII- and IVIGS-containing sequences folded similarly only in the absence of water. Analytical ultracentrifugation studies showed that when the FLIVI sequence adopts beta-structure in aqueous solution, it associates into a large molecular weight assembly. The random coils of IGSII and IVIGS showed no tendency to associate at any pH. PMID:18024497

  18. Design of 11-Residue Peptides with Unusual Biophysical Properties: Induced Secondary Structure in the Absence of Water?

    PubMed Central

    Mo, Xiaoqun; Hiromasa, Yasuaki; Warner, Matt; Al-Rawi, Ahlam N.; Iwamoto, Takeo; Rahman, Talat S.; Sun, Xiuzhi; Tomich, John M.

    2008-01-01

    A series of oligopeptides with ?-forming and adhesive properties, were synthesized and analyzed for adhesion shear strength, secondary structure, and association properties. The sequences contained related hydrophobic core segments varying in length from 5 to 12 residues and flanked by di- or tri-lysine segments. Three remarkable peptides consisting of just 11 residues with hydrophobic core sequences of FLIVI, IGSII, and IVIGS flanked by three lysine residues gave the highest dry adhesion shear strength and displayed unusual biophysical properties in the presence and absence of water. KKKFLIVIKKK had its highest adhesion strength at 2% (w/v) at pH 12.0 and showed the highest adhesion strength after exposure to water (water resistance). Both KKKIGSIIKKK and KKKIVIGSKKK, at 4% (w/v) at pH 12.0, displayed nearly identical dry shear strength values to that with the FLIVI core sequence. The peptide with IGSII core, however, displayed a lower water resistance and the latter, IVIGS, showed no water resistance, completely delaminating upon soaking in water. These are the smallest peptides with adhesive properties reported to date and show remarkable adhesion strength even at lower concentrations of 0.2% (w/v), which corresponds to 1.6 mM. The FLIVI containing peptide adopted a ?-sheet secondary structure in water while the IGSII- and IVIGS-containing sequences folded similarly only in the absence of water. Analytical ultracentrifugation studies showed that when the FLIVI sequence adopts ?-structure in aqueous solution, it associates into a large molecular weight assembly. The random coils of IGSII and IVIGS showed no tendency to associate at any pH. PMID:18024497

  19. Iterative sequence\\/secondary structure search for protein homologs: comparison with amino acid sequence alignments and application to fold recognition in genome databases

    Microsoft Academic Search

    Anders Wallqvist; Yoshifumi Fukunishi; Lynne Reed Murphy; Addi Fadel; Ronald M. Levy

    2000-01-01

    Motivation: Sequence alignment techniques have been developed into extremely powerful tools for identifying the folding families and function of proteins in newly sequenced genomes. For a sufficiently low sequence iden- tity it is necessary to incorporate additional structural information to positively detect homologous proteins. We have carried out an extensive analysis of the effectiveness of incorporating secondary structure information directly

  20. Ultraviolet Raman Examination of the Environmental Dependence of Bombolitin I and Bombolitin III Secondary Structure

    E-print Network

    Asher, Sanford A.

    of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260 USA ABSTRACT Bombolitin I and III (BI of electrostatic and hydrophobic interactions on pep- tide/protein structure can be studied by examining the de

  1. A domain-level DNA strand displacement reaction enumerator allowing arbitrary non-pseudoknotted secondary structures

    E-print Network

    Winfree, Erik

    network (equivalently a Petri net), connecting these initial complexes to some set of intermediate activation. To avoid polymerization that is inherent when considering general structures, we employ a time

  2. Evolutionary Relationships among Chlamydophila abortus Variant Strains Inferred by rRNA Secondary Structure-Based Phylogeny

    PubMed Central

    Siarkou, Victoria I.; Hadweh, Paul; Laroucau, Karine

    2011-01-01

    The evolutionary relationships among known Chlamydophila abortus variant strains including the LLG and POS, previously identified as being highly distinct, were investigated based on rRNA secondary structure information. PCR-amplified overlapping fragments of the 16S, 16S-23S intergenic spacer (IS), and 23S domain I rRNAs were subjected to cloning and sequencing. Secondary structure analysis revealed the presence of transitional single nucleotide variations (SNVs), two of which occurred in loops, while seven in stem regions that did not result in compensatory substitutions. Notably, only two SNVs, in 16S and 23S, occurred within evolutionary variable regions. Maximum likelihood and Bayesian phylogeny reconstructions revealed that C. abortus strains could be regarded as representing two distinct lineages, one including the “classical” C. abortus strains and the other the “LLG/POS variant”, with the type strain B577T possibly representing an intermediate of the two lineages. The two C. abortus lineages shared three unique (apomorphic) characters in the 23S domain I and 16S-23S IS, but interestingly lacked synapomorphies in the 16S rRNA. The two lineages could be distinguished on the basis of eight positions; four of these comprised residues that appeared to be signature or unique for the “classical” lineage, while three were unique for the “LLG/POS variant”. The U277 (E. coli numbering) signature character, corresponding to a highly conserved residue of the 16S molecule, and the unique G681 residue, conserved in a functionally strategic region also of 16S, are the most pronounced attributes (autapomorphies) of the “classical” and the “LLG/POS variant” lineages, respectively. Both lineages were found to be descendants of a common ancestor with the Prk/Daruma C. psittaci variant. Compared with the “classical”, the “LLG/POS variant” lineage has retained more ancestral features. The current rRNA secondary structure-based analysis and phylogenetic inference reveal new insights into how these two C. abortus lineages have differentiated during their evolution. PMID:21629695

  3. Molecular characterization of Bemisia tabaci populations in Tunisia: genetic structure and evidence for multiple acquisition of secondary symbionts.

    PubMed

    Gorsane, F; Ben Halima, A; Ben Khalifa, M; Bel-Kadhi, M S; Fakhfakh, H

    2011-08-01

    A survey was conducted during 2009-2010 seasons to identify the distribution of Bemisia tabaci (Gennadius) biotypes in Tunisia. The genetic affiliation of collected populations was determined by polymerase chain reaction (PCR)-restriction fragment-length polymorphism (TaqI) of the mitochondrial cytochrom oxidase I (mtCOI) gene. Results, validated by sequencing and phylogenetic analysis, allowed the clustering of sampled sweetpotato whiteflies into B and Q biotypes. As B. tabaci harbors the obligatory bacterium Portiera aleyrodidarum, and a diverse array of secondary symbionts including Rickettsia, Hamiltonella, Wolbachia, Cardinium, Arsenophonus, and Fritschea, we report here the infectious status of Tunisian populations by secondary symbionts to find out a correlation between bacterial composition to biotype. The genetic variability and structure of B. tabaci populations in Tunisia was driven by analysis of molecular variance (AMOVA) and the hypothesis of isolation by distance was explored. Selective neutrality and genetic haplotype network tests suggested that Tunisian sweetpotato whiteflies have been undergoing a potential expansion followed by gene flow restriction. PMID:22251681

  4. Structural and functional characterization of BaiA, an enzyme involved in secondary bile acid synthesis in human gut microbe.

    PubMed

    Bhowmik, Shiva; Jones, David H; Chiu, Hsien-Po; Park, In-Hee; Chiu, Hsiu-Ju; Axelrod, Herbert L; Farr, Carol L; Tien, Henry J; Agarwalla, Sanjay; Lesley, Scott A

    2014-02-01

    Despite significant influence of secondary bile acids on human health and disease, limited structural and biochemical information is available for the key gut microbial enzymes catalyzing its synthesis. Herein, we report apo- and cofactor bound crystal structures of BaiA2, a short chain dehydrogenase/reductase from Clostridium scindens VPI 12708 that represent the first protein structure of this pathway. The structures elucidated the basis of cofactor specificity and mechanism of proton relay. A conformational restriction involving Glu42 located in the cofactor binding site seems crucial in determining cofactor specificity. Limited flexibility of Glu42 results in imminent steric and electrostatic hindrance with 2'-phosphate group of NADP(H). Consistent with crystal structures, steady state kinetic characterization performed with both BaiA2 and BaiA1, a close homolog with 92% sequence identity, revealed specificity constant (kcat /KM ) of NADP(+) at least an order of magnitude lower than NAD(+) . Substitution of Glu42 with Ala improved specificity toward NADP(+) by 10-fold compared to wild type. The cofactor bound structure uncovered a novel nicotinamide-hydroxyl ion (NAD(+) -OH(-) ) adduct contraposing previously reported adducts. The OH(-) of the adduct in BaiA2 is distal to C4 atom of nicotinamide and proximal to 2'-hydroxyl group of the ribose moiety. Moreover, it is located at intermediary distances between terminal functional groups of active site residues Tyr157 (2.7 Å) and Lys161 (4.5 Å). Based on these observations, we propose an involvement of NAD(+) -OH(-) adduct in proton relay instead of hydride transfer as noted for previous adducts. PMID:23836456

  5. FTIR observation of compression recovery of the secondary structure of heat denaturated ribonuclease A in sucrose solution

    NASA Astrophysics Data System (ADS)

    Yamamoto, T.; Chatani, E.; Kato, M.

    2010-03-01

    We have investigated the effect of pressure on the secondary structure of ribonuclease A using FTIR spectroscopy. In the presence of 47 %w/w sucrose, the intensity of an amide I' peak assigned to ?-sheets of ribonuclease A was slightly recovered by applying pressure up to 200 MPa, while the peak was monotonically decreased with increasing pressure in the absence of sucrose. The present study is the first observation of the compression recovery of ?-sheets in a protein by pressure in high concentration of sucrose. This result is consistent with a pressure perturbation calorimetric study (Ravindra et al. 2004 Phys. Chem. Chem. Phys. 6 1952) reported that the sign of volume change of the protein thermal denaturation changed from negative to positive by adding sugars.

  6. Effect of glass structure on the dynamics of the secondary relaxation in diisobutyl and diisoctyl phthalates

    NASA Astrophysics Data System (ADS)

    Paluch, M.; Pawlus, S.; Hensel-Bielowka, S.; Kaminski, K.; Psurek, T.; Rzoska, S. J.; Ziolo, J.; Roland, C. M.

    2005-12-01

    The ? relaxation is a principal source of information about the dynamics in the glassy state; however, the nature of this process remains a controversial issue. In this paper, we show that properties of the ? relaxation measured below Tg are sensitive to the structure of the glass; that is, the thermodynamic path from the equilibrium liquid strongly affects the ? relaxation times, their distribution, and the activation energy quantifying their temperature dependence. These results support the idea that the Johari-Goldstein ? process is the precursor to the structural relaxation transpiring at longer times. We discuss the experimental findings in light of the heterogeneous and homogeneous scenarios for the ? process.

  7. 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. PMID:25043709

  8. Embedded Learning Strategy Instruction: Story-Structure Pedagogy in Heterogeneous Secondary Literature Classes

    ERIC Educational Resources Information Center

    Faggella-Luby, Michael; Schumaker, Jean S.; Deshler, Donald D.

    2007-01-01

    The effects of using the Embedded Story-Structure (ESS) Routine in a literature course were investigated. A heterogeneous group of 79 ninth graders, including 14 students with LD, were randomly assigned to one of two conditions, with instruction occurring in groups of 12 to 14 students in general education literature classes over a nine-day…

  9. 7088 Biochemistry 1989, 28, 7088-7097 A Proton Nuclear Magnetic Resonance Assignment and Secondary Structure

    E-print Network

    Clore, G. Marius

    has been determined by a qualitative interpretation of nuclear Overhauser effects, NH exchange data-ray structure of Escherichia coli thioredoxin, consisting of a mixed five-stranded @-sheetsurrounded by four a pH conditions to resolve ambiguities caused by a duplication of resonances. This duplication

  10. The Development of a Proposed Model for Secondary School Level Physical Science Content Structure.

    ERIC Educational Resources Information Center

    Day, Gary Dean

    Developed was a diagrammatic model of basic physical science content structure which included substantive components common to physics and chemistry selected from the Physical Science Study Committee (PSSC) physics and the Chemical Education Materials Study (CHEMS) chemistry texts. A descriptive rationale for the model was written which gave a…

  11. Staufen-mediated mRNA decay

    PubMed Central

    Park, Eonyoung; Maquat, Lynne E.

    2013-01-01

    Staufen1 (STAU1)-mediated mRNA decay (SMD) is an mRNA degradation process in mammalian cells that is mediated by the binding of STAU1 to a STAU1-binding site (SBS) within the 3'-untranslated region (3'UTR) of target mRNAs. During SMD, STAU1, a double-stranded (ds) RNA-binding protein, recognizes dsRNA structures formed either by intramolecular base-pairing of 3'UTR sequences or by intermolecular base-pairing of 3'UTR sequences with a long noncoding RNA (lncRNA) via partially complementary Alu elements. Recently, STAU2, a paralog of STAU1, has also been reported to mediate SMD. Both STAU1 and STAU2 interact directly with the ATP-dependent RNA helicase UPF1, a key SMD factor, enhancing its helicase activity to promote effective SMD. Moreover, STAU1 and STAU2 form homodimeric and heterodimeric interactions via domain-swapping. Since both SMD and the mechanistically related nonsense-mediated mRNA decay (NMD) employ UPF1, SMD and NMD are competitive pathways. Competition contributes to cellular differentiation processes, such as myogenesis and adipogenesis, placing SMD at the heart of various physiologically important mechanisms. PMID:23681777

  12. Selective mRNA translation in erythropoiesis.

    PubMed

    Thiadens, Klaske A M H; von Lindern, Marieke

    2015-06-01

    The daily production of up to 1011 erythrocytes is tightly controlled to maintain the number of erythrocytes in peripheral blood between narrow boundaries. Availability of growth factors and nutrients, particularly iron, control the proliferation and survival of precursor cells partly through control of mRNA translation. General translation initiation mechanisms can selectively control translation of transcripts that carry specific structures in the UTRs. This selective mRNA translation is an important layer of gene expression regulation in erythropoiesis. Ribosome profiling is a recently developed high throughput sequencing technique for global mapping of translation initiation sites across the transcriptome. Here we describe what is known about control of mRNA translation in erythropoiesis and how ribosome profiling will help to further our knowledge. Ribosome footprinting will give insight in transcript-specific translation at codon resolution, which is of great value to understand many cellular processes during erythropoiesis. It will be of particular interest to understand responses to iron availability and reactive oxygen species (ROS), which affects translation initiation of transcripts harbouring upstream ORFs (uORF) and potential alternative downstream ORFs (aORF). PMID:26009174

  13. Gene regulation by mRNA editing

    SciTech Connect

    Ashkenas, J. [Univ. of Washington, Seattle, WA (United States)

    1997-02-01

    The commonly cited figure of 10{sup 5} genes in the human genome represents a tremendous underestimate of our capacity to generate distinct gene products with unique functions. Our cells possess an impressive collection of tools for altering the products of a single gene to create a variety of proteins. The different gene products may have related but distinct functions, allowing cells of different types or at different developmental stages to fine-tune their patterns of gene expression. These tools may act in the cytoplasm, as when proteins undergo post-translational modifications, or in the nucleus, in the processing of pre-mRNA. Two forms of intranuclear fine-tuning are well established and widely studied: alternative splicing of pre-mRNAs and alternative polyadenylation site selection. In recent years it has become clear that cells possess yet another tool to create RNA sequence diversity, mRNA editing. The term {open_quotes}editing{close_quotes} is applied to posttranscriptional modifications of a purine or pyrimidine, which alter an mRNA sequence as it is read, for example, by ribosomes. Covalent changes to the structure of nucleotide bases are well known to occur on tRNA and rRNA molecules, but such changes in mRNA sequence are novel in that they have the capacity to change specific protein sequences. 43 refs., 1 fig.

  14. Small Amphipathic Molecules Modulate Secondary Structure and Amyloid Fibril-forming Kinetics of Alzheimer Disease Peptide A?1–42

    PubMed Central

    Ryan, Timothy M.; Friedhuber, Anna; Lind, Monica; Howlett, Geoffrey J.; Masters, Colin; Roberts, Blaine R.

    2012-01-01

    Amyloid fibril formation is associated with a number of debilitating systemic and neurodegenerative diseases. One of the most prominent is Alzheimer disease in which aggregation and deposition of the A? peptide occur. A? is widely considered to mediate the extensive neuronal loss observed in this disease through the formation of soluble oligomeric species, with the final fibrillar end product of the aggregation process being relatively inert. Factors that influence the aggregation of these amyloid-forming proteins are therefore very important. We have screened a library of 96 amphipathic molecules for effects on A?1–42 aggregation and self-association. We find, using thioflavin T fluorescence and electron microscopy assays, that 30 of the molecules inhibit the aggregation process, whereas 36 activate fibril formation. Several activators and inhibitors were subjected to further analysis using analytical ultracentrifugation and circular dichroism. Activators typically display a 1:10 peptide:detergent stoichiometry for maximal activation, whereas the inhibitors are effective at a 1:1 stoichiometry. Analytical ultracentrifugation and circular dichroism experiments show that activators promote a mixture of unfolded and ?-sheet structures and rapidly form large aggregates, whereas inhibitors induce ?-helical structures that form stable dimeric/trimeric oligomers. The results suggest that A?1–42 contains at least one small molecule binding site, which modulates the secondary structure and aggregation processes. Further studies of the binding of these compounds to A? may provide insight for developing therapeutic strategies aimed at stabilizing A? in a favorable conformation. PMID:22461629

  15. Loss of activities for mRNA synthesis accompanies loss of lambda2 spikes from reovirus cores: an effect of lambda2 on lambda1 shell structure.

    PubMed

    Luongo, Cindy L; Zhang, Xing; Walker, Stephen B; Chen, Ya; Broering, Teresa J; Farsetta, Diane L; Bowman, Valorie D; Baker, Timothy S; Nibert, Max L

    2002-04-25

    The 144-kDa lambda2 protein, a component of the transcriptionally active reovirus core particle, catalyzes the last three enzymatic activities for formation of the 5' cap 1 structure on the viral plus-strand transcripts. Limited evidence suggests it may also play a role in transcription per se. Particle-associated lambda2 forms pentameric turrets ("spikes") around the fivefold axes of the icosahedral core. To address the requirements for lambda2 in core functions other than the known functions in RNA capping, particles depleted of lambda2 were generated from cores in vitro by a series of treatments involving heat, protease, and ionic detergent. The resulting particles contained less than 5% of pretreatment levels of lambda2 but showed negligible loss of the other four core proteins or the 10 double-stranded RNA genome segments. Transmission cryo-electron microscopy (cryo-TEM) and scanning cryo-electron microscopy demonstrated loss of the lambda2 spikes from these otherwise intact particles. In functional analyses, the "spikeless cores" showed greatly reduced activities not only for RNA capping but also for transcription and nucleoside triphosphate hydrolysis, suggesting enzymatic or structural roles for lambda2 in all these activities. Comparison of the core and spikeless core structures obtained by cryo-TEM and three-dimensional image reconstruction revealed changes in the lambda1 core shell that accompany lambda2 loss, most notably the elimination of small pores that span the shell near the icosahedral fivefold axes. Changes in the shell may explain the reductions in transcriptase-related activities by spikeless cores. PMID:12036315

  16. 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 proteoglycan shows a broad unfolding transition between 1-6 M urea, probably indicating the presence of stable unfolding intermediates.

  17. Discovery of Novel ncRNA Sequences in Multiple Genome Alignments on the Basis of Conserved and Stable Secondary Structures

    PubMed Central

    Fu, Yinghan; Xu, Zhenjiang Zech; Lu, Zhi J.; Zhao, Shan; Mathews, David H.

    2015-01-01

    Recently, non-coding RNAs (ncRNAs) have been discovered with novel functions, and it has been appreciated that there is pervasive transcription of genomes. Moreover, many novel ncRNAs are not conserved on the primary sequence level. Therefore, de novo computational ncRNA detection that is accurate and efficient is desirable. The purpose of this study is to develop a ncRNA detection method based on conservation of structure in more than two genomes. A new method called Multifind, using Multilign, was developed. Multilign predicts the common secondary structure for multiple input sequences. Multifind then uses measures of structure conservation to estimate the probability that the input sequences are a conserved ncRNA using a classification support vector machine. Multilign is based on Dynalign, which folds and aligns two sequences simultaneously using a scoring scheme that does not include sequence identity; its structure prediction quality is therefore not affected by input sequence diversity. Additionally, ensemble defect was introduced to Multifind as an additional discriminating feature that quantifies the compactness of the folding space for a sequence. Benchmarks showed Multifind performs better than RNAz and LocARNATE+RNAz, a method that uses RNAz on structure alignments generated by LocARNATE, on testing sequences extracted from the Rfam database. For de novo ncRNA discovery in three genomes, Multifind and LocARNATE+RNAz had an advantage over RNAz in low similarity regions of genome alignments. Additionally, Multifind and LocARNATE+RNAz found different subsets of known ncRNA sequences, suggesting the two approaches are complementary. PMID:26075601

  18. 3D CAFE modeling of grain structures: application to primary dendritic and secondary eutectic solidification

    NASA Astrophysics Data System (ADS)

    Carozzani, T.; Digonnet, H.; Gandin, Ch-A.

    2012-01-01

    A three-dimensional model is presented for the prediction of grain structures formed in casting. It is based on direct tracking of grain boundaries using a cellular automaton (CA) method. The model is fully coupled with a solution of the heat flow computed with a finite element (FE) method. Several unique capabilities are implemented including (i) the possibility to track the development of several types of grain structures, e.g. dendritic and eutectic grains, (ii) a coupling scheme that permits iterations between the FE method and the CA method, and (iii) tabulated enthalpy curves for the solid and liquid phases that offer the possibility to work with multicomponent alloys. The present CAFE model is also fully parallelized and runs on a cluster of computers. Demonstration is provided by direct comparison between simulated and recorded cooling curves for a directionally solidified aluminum-7 wt% silicon alloy.

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

    Microsoft Academic Search

    Zsuzsanna Sukosd; Bjarne Knudsen; Morten Vaerum; Jorgen Kjems; Ebbe Sloth Andersen

    2011-01-01

    Background  The prediction of the structure of large RNAs remains a particular challenge in bioinformatics, due to the computational complexity\\u000a 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\\u000a complexity of the algorithm and underflow errors have prevented its use for long

  20. Protein Secondary Structure Determination by Constrained Single-Particle Cryo-Electron Tomography

    PubMed Central

    Bartesaghi, Alberto; Lecumberry, Federico; Sapiro, Guillermo; Subramaniam, Sriram

    2012-01-01

    SUMMARY Cryo-electron microscopy (cryo-EM) is a powerful technique for 3D structure determination of protein complexes by averaging information from individual molecular images. The resolutions that can be achieved with single-particle cryo-EM are frequently limited by inaccuracies in assigning molecular orientations based solely on 2D projection images. Tomographic data collection schemes, however, provide powerful constraints that can be used to more accurately determine molecular orientations necessary for 3D reconstruction. Here, we propose “constrained single-particle tomography” as a general strategy for 3D structure determination in cryo-EM. A key component of our approach is the effective use of images recorded in tilt series to extract high-resolution information and correct for the contrast transfer function. By incorporating geometric constraints into the refinement to improve orientational accuracy of images, we reduce model bias and overrefinement artifacts and demonstrate that protein structures can be determined at resolutions of ~8 Å starting from low-dose tomographic tilt series. PMID:23217682

  1. Conformations and vibrational spectra of a model tripeptide: change of secondary structure upon micro-solvation.

    PubMed

    Zhu, Hui; Blom, Martine; Compagnon, Isabel; Rijs, Anouk M; Roy, Santanu; von Helden, Gert; Schmidt, Burkhard

    2010-04-14

    Mid-infrared (IR) hole burning spectra of the model tripeptide Z-Aib-Pro-NHMe (Z = benzyloxycarbonyl) in gas phase and its micro-clusters with one and two methanol molecules are presented. To establish a relation between experimental spectra and the underlying conformations, calculations at the DFT [B3LYP/6-311++G(d,p)] level of theory are performed. In particular, the intra-peptide and the peptide-methanol hydrogen bonds can be identified from spectral shifts in the amide I, II, and III regions. While the unsolvated tripeptide as well as its one-methanol cluster prefer a gamma-turn structure, a beta-turn structure is found for the two-methanol cluster, in agreement with previous condensed phase studies. Comparison of measured and simulated spectra reveals that the favorable methanol binding sites are at the head and tail parts of the tripeptide. The interconversions between gamma-turn and beta-turn structures are governed by potential barriers below 10 kJ mol(-1) inside one of the low energy basins of the potential energy surface. PMID:20352678

  2. Crystal structure of vaccinia virus mRNA capping enzyme provides insights into the mechanism and evolution of the capping apparatus

    PubMed Central

    Kyrieleis, Otto J.P.; Chang, Jonathan; de la Peña, Marcos; Shuman, Stewart; Cusack, Stephen

    2014-01-01

    Summary Vaccinia virus capping enzyme is a heterodimer of D1 (844-aa) and D12 (287-aa) polypeptides that executes all three steps in m7GpppRNA synthesis. The D1 subunit comprises an N-terminal RNA triphosphatase (TPase)–guanylyltransferase (GTase) module and a C-terminal guanine-N7-methyltransferase (MTase) module. The D12 subunit binds and allosterically stimulates the MTase module. Crystal structures of the complete D1•D12 heterodimer disclose the TPase and GTase as members of the triphosphate tunnel metalloenzyme and covalent nucleotidyltransferase superfamilies, respectively, albeit with distinctive active site features. An extensive TPase-GTase interface clamps the GTase nucleotidyltransferase and OB domains in a closed conformation around GTP. Mutagenesis confirms the importance of the TPase-GTase interface for GTase activity. The D1•D12 structure complements and rationalizes four decades of biochemical studies of this enzyme (the first capping enzyme to be purified and characterized) and provides new insights to the origins of the capping systems of other large DNA viruses. PMID:24607143

  3. Human promyelocytic leukemia HL-60 cell proliferation and c-myc protein expression are inhibited by an antisense pentadecadeoxynucleotide targeted against c-myc mRNA

    SciTech Connect

    Wickstrom, E.L.; Bacon, T.A.; Gonzalez, A.; Freeman, D.L.; Lyman, G.H.; Wickstrom, E.

    1988-02-01

    The human promyelocytic leukemia cell line HL-60 overexpresses the c-myc protooncogene. A calculated secondary structure for c-myc mRNA placed the initiation codon in a bulge of a weakly based-paired region. Treatment of HL-60 cells with 5' d(AACGTTGAGGGGCAT) 3', complementary to the initiation codon and the next four codons of c-myc mRNA, inhibited c-myc protein expression in a dose-dependent manner. However, treatment of HL-60 cells with 5' d(TTGGGATAACACTTA) 3', complementary to nucleotides 17-31 of vesicular stomatits virus matrix protein mRNA, displayed no such effects. These results agree with analogous studies of normal human T lymphocytes, except that only one-third as much oligomer was needed for a comparable effect. Proliferation of HL-60 cells in culture was inhibited in a sequence-specific, dose-dependent manner by the c-myc-complementary oligomer, but neither the oligomer complementary to vesicular stomatitis virus matrix protein mRNA nor 5' d(CATTTCTTGCTCTCC) 3', complementary to nucleotides 5399-5413 of human immunodeficiency virus tat gene mRNA, inhibited proliferation. It thus appears that antisense oligodeoxynucleotides added to myc-transformed cells via culture medium are capable of eliciting sequence-specific, dose-dependent inhibition of c-myc protein expression and cell proliferation.

  4. Secondary and tertiary structure of the A-state of cytochrome c from resonance Raman spectroscopy.

    PubMed Central

    Jordan, T.; Eads, J. C.; Spiro, T. G.

    1995-01-01

    Ferricytochrome c can be converted to the partially folded A-state at pH 2.2 in the presence of 1.5 M NaCl. The structure of the A-state has been studied in comparison with the native and unfolded states, using resonance Raman spectroscopy with visible and ultraviolet excitation wavelengths. Spectra obtained with 200 nm excitation show a decrease in amide II intensity consistent with loss of structure for the 50s and 70s helices. The 230-nm spectra contain information on vibrational modes of the single Trp 59 side chain and the four tyrosine side chains (Tyr 48, 67, 74, and 97). The Trp 59 modes indicate that the side chain remains in a hydrophobic environment but loses its tertiary hydrogen bond and is rotationally disordered. The tyrosine modes Y8b and Y9a show disruption of tertiary hydrogen bonding for the Tyr 48, 67, and 74 side chains. The high-wavenumber region of the 406.7-nm resonance Raman spectrum reveals a mixed spin heme iron atom, which arises from axial coordination to His 18 and a water molecule. The low-frequency spectral region reports on heme distortions and indicates a reduced degree of interaction between the heme and the polypeptide chain. A structural model for the A-state is proposed in which a folded protein subdomain, consisting of the heme and the N-terminal, C-terminal, and 60s helices, is stabilized through nonbonding interactions between helices and with the heme. PMID:7613469

  5. Secondary Structure Specificity of the Nuclease Activity of the 1,10-phenanthroline--Copper Complex

    Microsoft Academic Search

    Laura E. Pope; David S. Sigman

    1984-01-01

    The artificial DNase activity of the 1,10-phenanthroline-cuprous ion complex [(OP)2Cu+] and H2O2 cleaves the A, B, and Z forms of DNA at different rates. The B structure, formed by most DNAs including poly(dA-dT) and poly(dA)\\\\cdot poly(dT), is the most susceptible to cleavage. It is completely degraded within 1 min by 40 mu M 1,10-phenanthroline\\/4 mu M Cu2+\\/7 mM H2O2\\/7 mM

  6. Protein Structure Analysis Iosif Vaisman

    E-print Network

    Vaisman, Iosif

    Protein Structure Analysis Iosif Vaisman 2013 BINF 731 Secondary Structure: Computational Problems Secondary structure characterization Secondary structure assignment Secondary structure prediction Protein structure classification Structural classes of proteins all all Protein Structure Classification SCOP

  7. Protein Structure Analysis Iosif Vaisman

    E-print Network

    Vaisman, Iosif

    Protein Structure Analysis Iosif Vaisman 2012 BINF 731 Secondary Structure: Computational Problems Secondary structure characterization Secondary structure assignment Secondary structure prediction Protein structure classification Structural classes of proteins all all Protein Structure Classification SCOP

  8. Protein Structure Analysis Iosif Vaisman

    E-print Network

    Vaisman, Iosif

    Protein Structure Analysis Iosif Vaisman 2009 BINF 731 Secondary Structure: Computational Problems Secondary structure characterization Secondary structure assignment Secondary structure prediction Protein structure classification Structural classes of proteins all all / Protein Structure Classification SCOP

  9. Template secondary structure can increase the error frequency of the DNA polymerase from Thermus aquaticus.

    PubMed

    Loewen, P C; Switala, J

    1995-10-16

    Amplification of portions of the intergenic spacer between the katE gene and cryptic cel operon of Escherichia coli was accomplished by the polymerase chain reaction using the DNA polymerase from Thermus aquaticus. Nine different segments were amplified and cloned without error, but one 83-bp fragment was amplified with a high error rate such that 32 of 34 selected clones had three or more nucleotide changes from the expected sequence. The changes were all located in two 9-bp segments immediately adjacent to the 3'-ends of the two primers. Moving the end points of the primers to increase the spacing between them resulted in the isolation of significantly fewer error-containing products. It is proposed that stem-loop structures in the template immediately downstream from the primers interfere with an early stage of elongation and cause misincorporation. This is supported by the observation that destabilisation of one of the stem-loop structures reduced the frequency of errors. PMID:7590322

  10. The effect of Berberine on the secondary structure of human serum albumin

    NASA Astrophysics Data System (ADS)

    Li, Ying; He, WenYing; Tian, Jianniao; Tang, Jianghong; Hu, Zhide; Chen, Xingguo

    2005-05-01

    The presence of several high affinity binding sites on human serum albumin (HSA) makes it a possible target for many drugs. This study is designed to examine the effect of Berberine (an ancient Chinese drug used for antimicrobial, antiplasmodial, antidiarrheal and cardiovascular) on the solution structure of HSA using fluorescence, Fourier transform infrared (FT-IR), circular dichroism (CD) spectroscopic methods. The fluorescence spectroscopic results show that the fluorescence intensity of HSA was significantly decreased in the presence of Berberine. The Scatchard's plots indicated that the binding of Berberine to HSA at 296, 303, 318 K is characterized by one binding site with the binding constant is 4.071(±0.128)×10 4, 3.741(±0.089)×10 4, 3.454(±0.110)×10 4 M -1, respectively. The protein conformation is altered (FT-IR and CD data) with reductions of ?-helices from 54 to 47% for free HSA to 45-32% and with increases of turn structure5% for free HSA to 18% in the presence of Berberine. The binding process was exothermic, enthalpy driven and spontaneous, as indicated by the thermodynamic analyses, Berberine bound to HSA was mainly based on hydrophobic interaction and electrostatic interaction cannot be excluded from the binding. Furthermore, the displace experiments indicate that Berberine can bind to the subdomain IIA, that is, high affinity site (site II).

  11. X-ray evidence for a "super"-secondary structure in silk fibers.

    PubMed

    Valluzzi, Regina; Jin, Hyoung-Joon

    2004-01-01

    X-ray studies on degummed B. mori silk fibers and on hydrogels prepared under a variety of conditions reveal moderately small angle reflections. These reflections are often highly oriented and are correlated to silk II lattice reflections. A superstructure can explain these features. Silk fibroin hydrogels were monitored as they dried to form the silk II structure. The silk II wide angle and moderately small angle patterns obtained from dried hydrogels and silk fibers are identical. The "superstructure" reflections at moderately small angle (3-7 nm) were first to appear, followed by the "intersheet" spacing, and then the remainder of the silk II wide angle scattering pattern. Thus, any superstructure hypothesized for the hydrogels (and for Silk II in fibers) must be both stable in a highly hydrated environment and must convert to silk II with little large scale diffusion. A folded structure, similar to amyloids and cross-beta-sheets but with much longer beta-strand stems, is proposed for silk II in fibers. PMID:15132649

  12. Principal component analysis of Fourier transform infrared and/or circular dichroism spectra of proteins applied in a calibration of protein secondary structure.

    PubMed

    Pribi?, R

    1994-11-15

    Gaining information on the secondary structure of a protein from its spectra is presented as a calibration problem. The secondary structures known from X-ray studies and the spectra of 21 proteins are represented by a linear model. Fourier transform infrared (FTIR) spectra from 1700 to 1600 cm-1, circular dichroism (CD) spectra from 178 to 260 nm, and combined spectra are used; the secondary structure classes of interest are alpha-helices, antiparallel beta-sheets, parallel beta-sheets, beta-turns, and "other." The calibration is solved in two steps: (i) the dependencies between the structures and the spectra of reference proteins are found using the least-squares estimator, and (ii) the secondary structure of a protein is predicted from its spectra using the information gained in the first step and principal component analysis. The problem of information content of the reference spectra is analyzed using the linearly independent pieces of information, the so-called principal components, provided by singular value decomposition. Attention is paid to a number of the principal components sufficient for the prediction, which may be less than the total number. A relative estimable parameter is used to determine unambiguously the number of the components corresponding to the minimum mean square error of the predictor. The analysis gives the solutions to this linear calibration relevant to the underlying protein problem, thus reducing subjective assessments as well as computations. PMID:7695098

  13. Toward non-Newtonian effects on secondary flow structures in a 180 degree bent tube model for curved arteries

    NASA Astrophysics Data System (ADS)

    van Wyk, Stevin; Prahl Wittberg, Lisa; Fuchs, Laszlo; Bulusu, Kartik V.; Plesniak, Michael W.

    2013-11-01

    The purpose of this study is to investigate the development of vortical flow structures of blood like fluids in a 180 degree tube bend, analogous to the aortic arch. Cardiovascular diseases are localized to regions of curvature in the arterial tree. The pathology of atherogenesis is widely considered an inflammatory response, hypothesized to be modulated by the interplay between Wall Shear Stress (WSS) variations and particulate transport mechanisms from the bulk fluid core to the near wall. The WSS is determined by the local flow characteristics as well as the rheological properties of the blood, which in turn are dependent on the bulk secondary flows. In this work, the time dependent fluid flow under various physiological flow conditions are investigated both experimentally and numerically. A Newtonian blood analog fluid model is considered in both studies to validate both methods and thereby study flow structure development during steady as well as pulsatile conditions. Particle image velocimetry (2C - 2D PIV) is used to acquire velocity field data from an acrylic tube bend. The numerical study is extended to consider the non-Newtonian properties of blood according to an empirical model to identify the relative importance of the non-Newtonian behavior. The studies show complex Dean and Lyne vortex interaction that are enhanced with increasing peak Reynolds numbers.

  14. Microsatellite diversity and genetic structure among common bean (Phaseolus vulgaris L.) landraces in Brazil, a secondary center of diversity

    PubMed Central

    Burle, Marília Lobo; Fonseca, Jaime Roberto; Kami, James A.

    2010-01-01

    Brazil is the largest producer and consumer of common bean (Phaseolus vulgaris L.), which is the most important source of human dietary protein in that country. This study assessed the genetic diversity and the structure of a sample of 279 geo-referenced common bean landraces from Brazil, using molecular markers. Sixty-seven microsatellite markers spread over the 11 linkage groups of the common bean genome, as well as Phaseolin, PvTFL1y, APA and four SCAR markers were used. As expected, the sample showed lower genetic diversity compared to the diversity in the primary center of diversification. Andean and Mesoamerican gene pools were both present but the latter gene pool was four times more frequent than the former. The two gene pools could be clearly distinguished; limited admixture was observed between these groups. The Mesoamerican group consisted of two sub-populations, with a high level of admixture between them leading to a large proportion of stabilized hybrids not observed in the centers of domestication. Thus, Brazil can be considered a secondary center of diversification of common bean. A high degree of genome-wide multilocus associations even among unlinked loci was observed, confirming the high level of structure in the sample and suggesting that association mapping should be conducted in separate Andean and Mesoamerican Brazilian samples. Electronic supplementary material The online version of this article (doi:10.1007/s00122-010-1350-5) contains supplementary material, which is available to authorized users. PMID:20502861

  15. Structural, optical and magnetic properties of Co-doped ZnO nanorods with hidden secondary phases.

    PubMed

    Wang, Xuefeng; Zheng, Rongkun; Liu, Zongwen; Ho, Ho-Pui; Xu, Jianbin; Ringer, Simon P

    2008-11-12

    Co-doped ZnO nanorods (composition: Zn(0.955)Co(0.045)O) were grown by a simple surfactant-assisted hydrothermal technique. The morphological, structural, optical and magnetic properties of the as-prepared nanorods were investigated by means of scanning electron microscopy, high-resolution transmission electron microscopy, x-ray diffraction, x-ray photoelectron spectroscopy, micro-Raman spectroscopy, micro-cathodoluminescence, and vibrating sample magnetometry (VSM). The results showed that the sample had rod-like morphology and that the preferential growth direction was along the c axis. While Co was successfully doped into the ZnO wurtzite lattice structure as revealed by several characterization techniques, hidden secondary phases of Zn(y)Co(3-y)O(4) (0?y?1) were also clearly detected by the micro-Raman spectroscopic technique. We propose that the predominant diffusion-limited Ostwald ripening crystal growth mechanism under the hydrothermal coarsening yielded such phase segregation. VSM results showed that the nanorods displayed relatively weak room-temperature ferromagnetism. We suggest that the origin of the ferromagnetism is probably due to the presence of the mixed cation valence of Co via a d-d double-exchange mechanism rather than the real doping effect. It is essential to control the crystal growth mechanism and defect states associated with the ferromagnetism in order to realize the intrinsic diluted magnetic semiconductors. PMID:21832791

  16. Imposing function down a (cupin)-barrel: secondary structure and metal stereochemistry in the ?KG-dependent oxygenases.

    PubMed

    Hangasky, John A; Taabazuing, Cornelius Y; Valliere, Meaghan A; Knapp, Michael J

    2013-04-01

    The Fe(ii)/?ketoglutarate (?KG) dependent oxygenases catalyze a diverse range of reactions significant in biological processes such as antibiotic biosynthesis, lipid metabolism, oxygen sensing, and DNA and RNA repair. Although functionally diverse, the eight-stranded ?-barrel (cupin) and HX(D/E)XnH facial triad motifs are conserved in this super-family of enzymes. Crystal structure analysis of 25 ?KG oxygenases reveals two stereoisomers of the Fe cofactor, Anti and Clock, which differ in the relative position of the exchangeable ligand position and the primary substrate. Herein, we discuss the relationship between the chemical mechanism and the secondary coordination sphere of the ?KG oxygenases, within the constraints of the stereochemistry of the Fe cofactor. Sequence analysis of the cupin barrel indicates that a small subset of positions constitute the second coordination sphere, which has significant ramifications for the structure of the ferryl intermediate. The competence of both Anti and Clock stereoisomers of Fe points to a ferryl intermediate that is 5 coordinate. The small number of conserved close contacts within the active sites of ?KG oxygenases can be extended to chemically related enzymes, such as the ?KG-dependent halogenases SyrB2 and CytC3, and the non-?KG dependent dioxygenases isopenicillin N synthase (IPNS) and cysteine dioxygenase (CDO). PMID:23446356

  17. Design of a secondary debris containment shield for large space structures

    NASA Technical Reports Server (NTRS)

    Schonberg, William P.; Taylor, Roy A.

    1989-01-01

    All long-duration spacecraft are susceptible to impacts by meteoroids and pieces of orbiting space debris. Such impacts are expected to occur at extremely high speeds and can damage internal and external flight-critical systems of spacecraft. An effective mechanism is developed to protect external spacecraft subsystems against damage by ricochet particles formed during such impacts. Equations and design procedures for protective shield panels are developed based on observed ricochet phenomena and calculated ricochet particle sizes and speeds. Panel dimensions are shown to be strongly dependent on their inclination and on their distribution around a spacecraft module. It is concluded that obliquity effects of high-speed impacts must be considered in the design of any structure exposed to the meteoroid and space debris environment.

  18. Evidence for evolutionarily conserved secondary structure in the H19 tumor suppressor RNA.

    PubMed

    Juan, V; Crain, C; Wilson, C

    2000-03-01

    The molecular basis for function of the mammalian H19 as a tumor suppressor is poorly understood. Large, conserved open reading frames (ORFs) are absent from both the human and mouse cDNAs, suggesting that it may act as an RNA. Contradicting earlier reports, however, recent studies have shown that the H19 transcript exists in polysomal form and is likely translated. To distinguish between possible functional roles for the gene product, we have characterized the sequence requirements for H19-mediated in vitro suppression of tumor cell clonogenicity and analyzed the sequence of the gene cloned from a range of mammals. A cDNA version of the human gene, lacking the unusually short introns characteristic of imprinted genes, is as effective as a genomic copy in blocking anchorage-independent growth by G401 cells. The first 710 nucleotides of the gene can be deleted with no effect on in vitro activity. Further truncations from either the 5'- or 3'-end, however, cause a loss of suppression of clonogenicity. Using conserved sequences within the H19 gene as PCR primers, genomic DNA fragments were amplified from a range of mammalian species that span the functional domain defined by deletion analysis. Sequences from cat, lynx, elephant, gopher and orangutan complement the previous database of sequences from human, mouse, rat and rabbit. Hypothetical translation of the resulting sequences shows an absence of conserved ORFs of any size. Free energy and covariational analysis of the RNA sequences was used to identify potential helical pairings within the H19 transcript. A set of 16 helices are supported by covariation (i.e. conservation of base pairing potential in the absence of primary sequence conservation). The predicted RNA pairings consist largely of local hairpins but also include several long range interactions that bridge the 5'- and 3'-ends of the functional domain. Given the evolutionary conservation of structure at the RNA level and the absence of conservation at the protein level, we presume that the functional product of the H19 gene is a structured RNA. PMID:10666466

  19. Fate and effects of the insecticide Dursban 4E in indoor Elodea-dominated and macrophyte-free freshwater model ecosystems: II. Secondary effects on community structure.

    PubMed

    Brock, T C; van den Bogaert, M; Bos, A R; van Breukelen, S W; Reiche, R; Terwoert, J; Suykerbuyk, R E; Roijackers, R M

    1992-11-01

    Secondary effects of a single dose of the insecticide Dursban 4E (active ingredient chlorpyrifos) were studied in indoor experimental freshwater ecosystems intended to mimic drainage ditches. Two experiments were performed, one in which all model ecosystems were dominated by the macrophyte Elodea muttallii, and one using systems devoid of macrophytes. In the Elodea-dominated and macrophyte-free model ecosystems, populations of primary producers, herbivores, carnivores and detritivores were indirectly affected via the loss of populations of Arthropoda as a direct result of insecticide application. However, the taxa in which secondary effects were observed differed considerably between these two types of model ecosystem. In macrophyte-dominated systems secondary effects were observed on populations of periphytic algae, the macrophyte Elodea nuttallii, the gastropod Bithynia tentaculata, Turbellaria, and sediment dwelling Oligochaeta. In open water systems it were populations of phytoplankton, the rotators Polyarthra and Asplanchna, bivalves (Sphaeriidae), Hirudinea, sediment dwelling Oligochaeta, and that of the isopod Proasellus coxalis in which secondary effects were observed. In aquatic ecosystems the presence or absence of a well-developed macrophyte vegetation may be a very important characteristic that determines the nature and route of secondary effects induced by pesticides. The differences in secondary effects observed between Elodea-dominated and macrophyte-free model ecosystems indicate that the system's structure and trophic dynamics should be taken into account when predicting ecological effects. PMID:1280070

  20. Preparation, Purification, and Secondary Structure Determination of Bacillus Circulans Xylanase. A Molecular Laboratory Incorporating Aspects of Molecular Biology, Biochemistry, and Biophysical Chemistry

    ERIC Educational Resources Information Center

    Russo, Sal; Gentile, Lisa

    2006-01-01

    A project module designed for biochemistry or cellular and molecular biology student which involves determining the secondary structure of Bacillus circulans xylanase (BCX) by circular dichroism (CD) spectroscopy under conditions that compromise its stabilizing intramolecular forces is described. The lab model enhanced students knowledge of the…

  1. Insight into the secondary structure of non-native proteins bound to a molecular chaperone alpha-crystallin. An isotope-edited infrared spectroscopic study.

    PubMed

    Das, K P; Choo-Smith, L P; Petrash, J M; Surewicz, W K

    1999-11-19

    alpha-Crystallin, the major lens protein, acts as a molecular chaperone by preventing the aggregation of proteins damaged by heat and other stress conditions. To characterize the backbone conformation of protein folding intermediates that are recognized by the chaperone, we prepared the uniformly (13)C-labeled alphaA-crystallin. The labeling greatly reduced the overlapping between the conformation-sensitive amide I bands of alpha-crystallin and unlabeled substrate proteins. This procedure has allowed us to gain insight into the secondary structure of alpha-crystallin-bound species, an understanding which has previously been unattainable. Analysis of the infrared spectra of two substrate proteins (gamma- and beta(L)-crystallins) indicates that heat-destabilized conformers captured by alpha-crystallin are characterized by a high proportion of native-like secondary structure. In contrast to the chaperone-bound species, the same proteins subjected to heat treatment in the absence of alpha-crystallin preserve very little native secondary structure. These data show that alpha-crystallin specifically recognizes very early intermediates on the denaturation pathway of proteins. These aggregation-prone species are characterized by native-like secondary structure but compromised tertiary interactions. The experimental approach described in this study can be further applied to probe the backbone conformation of proteins bound to chaperones other than alpha-crystallin. PMID:10559193

  2. The Structure of Primary and Secondary Teachers' Attributions for Pupils' Misbehaviour: A Preliminary Cross-Phase and Cross-Cultural Investigation

    ERIC Educational Resources Information Center

    Gibbs, Simon; Gardiner, Marianne

    2008-01-01

    The purpose of this study was to see if systematic contrasts in educational culture and curricular emphases might affect the underlying structure of teachers' attributions for children's behaviour. Thus, responses to a questionnaire developed from earlier work by Miller and colleagues (2000, 2002) were gathered from primary and secondary school…

  3. Secondary successional trajectories of structural and catabolic bacterial communities in oil-polluted soil planted with hybrid poplar.

    PubMed

    Mukherjee, Shinjini; Sipilä, Timo; Pulkkinen, Pertti; Yrjälä, Kim

    2015-02-01

    Poplars have widely been used for rhizoremediation of a broad range of organic contaminants for the past two decades. Still, there is a knowledge gap regarding the rhizosphere-associated bacterial communities of poplars and their dynamics during the remediation process. It is envisaged that a detailed understanding of rhizosphere-associated microbial populations will greatly contribute to a better design and implementation of rhizoremediation. To investigate the long-term succession of structural and catabolic bacterial communities in oil-polluted soil planted with hybrid poplar, we carried out a 2-year field study. Hybrid aspen (Populus tremula × Populus tremuloides) seedlings were planted in polluted soil excavated from an accidental oil-spill site. Vegetated and un-vegetated soil samples were collected for microbial community analyses at seven different time points during the course of 2 years and sampling time points were chosen to cover the seasonal variation in the boreal climate zone. Bacterial community structure was accessed by means of 16S rRNA gene amplicon pyrosequencing, whereas catabolic diversity was monitored by pyrosequencing of alkane hydroxylase and extradiol dioxygenase genes. We observed a clear succession of bacterial communities on both structural and functional levels from early to late-phase communities. Sphingomonas type extradiol dioxygenases and alkane hydroxylase homologs of Rhodococcus clearly dominated the early-phase communities. The high-dominance/low-diversity functional gene communities underwent a transition to low-dominance/high-diversity communities in the late phase. These results pointed towards increased catabolic capacities and a change from specialist to generalist strategy of bacterial communities during the course of secondary succession. PMID:25545194

  4. The Influence of Primary and Secondary DNA Structure in Deletion and Duplication between Direct Repeats in Escherichia Coli

    PubMed Central

    Trinh, T. Q.; Sinden, R. R.

    1993-01-01

    We describe a system to measure the frequency of both deletions and duplications between direct repeats. Short 17- and 18-bp palindromic and nonpalindromic DNA sequences were cloned into the EcoRI site within the chloramphenicol acetyltransferase gene of plasmids pBR325 and pJT7. This creates an insert between direct repeated EcoRI sites and results in a chloramphenicol-sensitive phenotype. Selection for chloramphenicol resistance was utilized to select chloramphenicol resistant revertants that included those with precise deletion of the insert from plasmid pBR325 and duplication of the insert in plasmid pJT7. The frequency of deletion or duplication varied more than 500-fold depending on the sequence of the short sequence inserted into the EcoRI site. For the nonpalindromic inserts, multiple internal direct repeats and the length of the direct repeats appear to influence the frequency of deletion. Certain palindromic DNA sequences with the potential to form DNA hairpin structures that might stabilize the misalignment of direct repeats had a high frequency of deletion. Other DNA sequences with the potential to form structures that might destabilize misalignment of direct repeats had a very low frequency of deletion. Duplication mutations occurred at the highest frequency when the DNA between the direct repeats contained no direct or inverted repeats. The presence of inverted repeats dramatically reduced the frequency of duplications. The results support the slippage-misalignment model, suggesting that misalignment occurring during DNA replication leads to deletion and duplication mutations. The results also support the idea that the formation of DNA secondary structures during DNA replication can facilitate and direct specific mutagenic events. PMID:8325478

  5. Secondary Structures in Phe-Containing Isolated Dipeptide Chains: Laser Spectroscopy vs Quantum Chemistry.

    PubMed

    Loquais, Yohan; Gloaguen, Eric; Habka, Sana; Vaquero-Vara, Vanesa; Brenner, Valérie; Tardivel, Benjamin; Mons, Michel

    2015-06-11

    The intrinsic conformational landscape of two phenylalanine-containing protein chain models (-Gly-Phe- and -Ala-Phe- sequences) has been investigated theoretically and experimentally in the gas phase. The near UV spectroscopy (first ??* transition of the Phe ring) is obtained experimentally under jet conditions where the conformational features can be resolved. Single-conformation IR spectroscopy in the NH stretch region is then obtained by IR/UV double resonance in the ground state, leading to resolved vibrational spectra that are assigned in terms of conformation and H-bonding content from comparison with quantum chemistry calculations. For the main conformer, whose UV spectrum exhibits a significant Franck-Condon activity in low frequency modes involving peptide backbone motions relative to the Phe chromophore, excited state IR spectroscopy has also been recorded in a UV/IR/UV experiment. The NH stretch spectral changes observed in such a ??* labeling experiment enable us to determine those NH bonds that are coupled to the phenyl ring; they are compared to CC2 excited state calculations to quantify the geometry change upon ??* excitation. The complete and consistent series of data obtained enable us to propose an unambiguous assignment for the gallery of conformers observed and to demonstrate that, in these two sequences, three conceptually important local structural motifs of proteins (?-strands, 27 ribbons, and ?-turns) are represented. The satisfactory agreement between the experimental conformational distribution and the predicted landscape anticipated from the DFT-D approach demonstrates the capabilities of a theoretical method that accounts for dispersive interactions. It also shows that the flaws, inherent to a resonant two-photon ionization detection scheme, often evoked for aromatic chromophores, do not seem to be significant in the case of Phe. PMID:25336282

  6. The influence of secondary processing on the structural relaxation dynamics of fluticasone propionate.

    PubMed

    Depasquale, Roberto; Lee, Sau L; Saluja, Bhawana; Shur, Jagdeep; Price, Robert

    2015-06-01

    This study investigated the structural relaxation of micronized fluticasone propionate (FP) under different lagering conditions and its influence on aerodynamic particle size distribution (APSD) of binary and tertiary carrier-based dry powder inhaler (DPI) formulations. Micronized FP was lagered under low humidity (LH 25 C, 33% RH [relative humidity]), high humidity (HH 25°C, 75% RH) for 30, 60, and 90 days, respectively, and high temperature (HT 60°C, 44% RH) for 14 days. Physicochemical, surface interfacial properties via cohesive-adhesive balance (CAB) measurements and amorphous disorder levels of the FP samples were characterized. Particle size, surface area, and rugosity suggested minimal morphological changes of the lagered FP samples, with the exception of the 90-day HH (HH90) sample. HH90 FP samples appeared to undergo surface reconstruction with a reduction in surface rugosity. LH and HH lagering reduced the levels of amorphous content over 90-day exposure, which influenced the CAB measurements with lactose monohydrate and salmeterol xinafoate (SX). CAB analysis suggested that LH and HH lagering led to different interfacial interactions with lactose monohydrate but an increasing adhesive affinity with SX. HT lagering led to no detectable levels of the amorphous disorder, resulting in an increase in the adhesive interaction with lactose monohydrate. APSD analysis suggested that the fine particle mass of FP and SX was affected by the lagering of the FP. In conclusion, environmental conditions during the lagering of FP may have a profound effect on physicochemical and interfacial properties as well as product performance of binary and tertiary carrier-based DPI formulations. PMID:25398478

  7. The poly(A)-dependent degradation pathway of rpsO mRNA is primarily mediated by RNase R

    PubMed Central

    Andrade, José M.; Hajnsdorf, Eliane; Régnier, Philippe; Arraiano, Cecília M.

    2009-01-01

    Polyadenylation is an important factor controlling RNA degradation and RNA quality control mechanisms. In this report we demonstrate for the first time that RNase R has in vivo affinity for polyadenylated RNA and can be a key enzyme involved in poly(A) metabolism. RNase II and PNPase, two major RNA exonucleases present in Escherichia coli, could not account for all the poly(A)-dependent degradation of the rpsO mRNA. RNase II can remove the poly(A) tails but fails to degrade the mRNA as it cannot overcome the RNA termination hairpin, while PNPase plays only a modest role in this degradation. We now demonstrate that in the absence of RNase E, RNase R is the relevant factor in the poly(A)-dependent degradation of the rpsO mRNA. Moreover, we have found that the RNase R inactivation counteracts the extended degradation of this transcript observed in RNase II-deficient cells. Elongated rpsO transcripts harboring increasing poly(A) tails are specifically recognized by RNase R and strongly accumulate in the absence of this exonuclease. The 3? oligo(A) extension may stimulate the binding of RNase R, allowing the complete degradation of the mRNA, as RNase R is not susceptible to RNA secondary structures. Moreover, this regulation is shown to occur despite the presence of PNPase. Similar results were observed with the rpsT mRNA. This report shows that polyadenylation favors in vivo the RNase R-mediated pathways of RNA degradation. PMID:19103951

  8. 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. (Univ. of Nijmegen, Toernooiveld (Netherlands))

    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.

  9. Structural and functional dissection of a conserved destabilizing element of cyclo-oxygenase-2 mRNA: evidence against the involvement of AUF-1 [AU-rich element/poly(U)-binding/degradation factor-1], AUF-2, tristetraprolin, HuR (Hu antigen R) or FBP1 (far-upstream-sequence-element-binding protein 1).

    PubMed Central

    Sully, Gareth; Dean, Jonathan L E; Wait, Robin; Rawlinson, Lesley; Santalucia, Tomas; Saklatvala, Jeremy; Clark, Andrew R

    2004-01-01

    COX-2 (cyclo-oxygenase-2) mRNA is degraded rapidly in resting cells, but is stabilized by the mitogen-activated protein kinase p38 signalling pathway in response to pro-inflammatory stimuli. A conserved ARE (AU-rich element) of the COX-2 3' untranslated region, CR1 (conserved region 1), acts as a potent instability determinant, and mediates stabilization in response to p38 activation. A detailed structural and functional analysis of this element was performed in an attempt to identify RNA-binding proteins involved in the regulation of COX-2 mRNA stability. Destabilization of a beta-globin reporter mRNA was dependent upon two distinct AREs within CR1, each containing three copies of the sequence AUUUA. CR1 was shown to bind AUF-1 [ARE/poly(U)-binding/degradation factor-1] and/or AUF-2, HuR (Hu antigen R), TTP (tristetraprolin) and FBP1 (far-upstream-sequence-element-binding protein 1), yet these factors did not appear to account for the effects of CR1 upon mRNA stability. Mutant sequences were identified that were incapable of destabilizing a reporter mRNA, yet showed unimpaired binding of FBP1 and AUF-1 and/or -2. TTP was absent from the HeLa cell line used in this analysis. Finally, RNA interference experiments argued against a prominent role for HuR in the CR1-mediated regulation of mRNA stability. We conclude that at least one critical regulator of COX-2 mRNA stability is likely to remain unidentified at present. PMID:14594446

  10. Counteracting effects of thiocyanate and sucrose on chymotrypsinogen secondary structure and aggregation during freezing, drying, and rehydration.

    PubMed Central

    Allison, S D; Dong, A; Carpenter, J F

    1996-01-01

    Studies of numerous proteins with infrared spectroscopy have documented that unfolding is a general response of unprotected proteins to freeze-drying. Some proteins that are unfolded in the dried solid aggregate during rehydration, whereas others refold. It has been proposed for the latter case that aggregation is avoided because refolding kinetically outcompetes intermolecular interactions. In contrast, with proteins that normally aggregate after rehydration, minimizing unfolding during freeze-drying with stabilizer has been shown to be needed to favor the recovery of native protein molecules after rehydration. The purpose of the current study was to examine first the opposite situation, in which a denaturant is used to foster additional unfolding in the protein population during freeze-drying. If the protein is not intrinsically resistant to aggregation under the study conditions (e.g., because of intermolecular charge repulsion) and the denaturant does not disrupt intermolecular interactions during rehydration, this treatment should favor aggregation upon rehydration. With infrared spectroscopy we found that at concentrations of the denaturant Na thiocyanate (NaSCN) that only slightly perturbed chymotrypsinogen secondary structure in solution before freeze-drying, there was a large increase in protein unfolding in the dried solid and in protein aggregation measured after rehydration. Bands assigned to intermolecular beta sheet were present in the spectra of samples dried with NaSCN, indicating that aggregation could also arise in the dried solid. By examining the protein structure in the frozen state, we determined that in the absence of NaSCN the protein remains native. NaSCN caused structural perturbations during freezing, without the formation of intermolecular beta sheet, that were intermediate to structural changes noted after freeze-drying. In contrast, samples treated in the presence of NaSCN and sucrose had native-like spectra in the frozen and dried states, and much reduced aggregation after rehydration. These results indicate that during freezing and drying the sugar can counteract and mostly reverse the structural perturbations induced by NaSCN before and during these treatments. PMID:8889176

  11. A simple system for the identification of fluorescent dyes capable of reporting differences in secondary structure and hydrophobicity among amyloidogenic protein oligomers

    NASA Astrophysics Data System (ADS)

    Yates, Emma

    2012-02-01

    Thioflavin T and Congo Red are fluorescent dyes that are commonly used to identify the presence of amyloid structures, ordered protein aggregates. Despite the ubiquity of their use, little is known about their mechanism of interaction with amyloid fibrils, or whether other dyes, whose photophysics indicate that they may be more responsive to differences in macromolecular secondary structure and hydrophobicity, would be better suited to the identification of pathologically relevant oligomeric species in amyloid diseases. In order to systematically address this question, we have designed a strategy that discretely introduces differences in secondary structure and hydrophobicity amidst otherwise identical polyamino acids. This strategy will enable us to quantify and compare the affinities of Thioflavin T, Congo Red, and other, incompletely explored, fluorescent dyes for different secondary structural elements and hydrophobic motifs. With this information, we will identify dyes that give the most robust and quantitative information about structural differences among the complex population of oligomeric species present along an aggregation pathway between soluble monomers and amyloid fibrils, and correlate the resulting structural information with differential oligomeric toxicity.

  12. Structural Complexity, Differential Response to Infection, and Tissue Specificity of Indolic and Phenylpropanoid Secondary Metabolism in Arabidopsis Roots1[w

    PubMed Central

    Bednarek, Pawe?; Schneider, Bernd; Svatoš, Aleš; Oldham, Neil J.; Hahlbrock, Klaus

    2005-01-01

    Levels of indolic and phenylpropanoid secondary metabolites in Arabidopsis (Arabidopsis thaliana) leaves undergo rapid and drastic changes during pathogen defense, yet little is known about this process in roots. Using Arabidopsis wild-type and mutant root cultures as an experimental system, and the root-pathogenic oomycete, Pythium sylvaticum, for infections, we analyzed the aromatic metabolite profiles in soluble extracts from uninfected and infected roots, as well as from the surrounding medium. A total of 16 indolic, one heterocyclic, and three phenylpropanoid compounds were structurally identified by mass spectrometry and nuclear magnetic resonance analyses. Most of the indolics increased strongly upon infection, whereas the three phenylpropanoids decreased. Concomitant increases in both indolic and phenylpropanoid biosynthetic mRNAs suggested that phenylpropanoids other than those examined here in “soluble extracts” were coinduced with the indolics. These and previous results indicate that roots differ greatly from leaves with regard to the nature and relative abundance of all major soluble phenylpropanoid constituents. For indolics, by contrast, our data reveal far-reaching similarities between roots and leaves and, beyond this comparative aspect, provide an insight into this highly diversified yet under-explored metabolic realm. The data point to metabolic interconnections among the compounds identified and suggest a partial revision of the previously proposed camalexin pathway. PMID:15923335

  13. Dihydrofolate reductase: Sequential resonance assignments using 2D and 3D NMR and secondary structure determination in solution

    SciTech Connect

    Carr, M.D.; Birdsall, B.; Jimenez-Barbero, J.; Polshakov, V.I.; McCormick, J.E.; Feeney, J.; Frenkiel, T.A.; Bauer, C.J. (National Inst. for Medical Research, London (England)); Roberts, G.C.K. (Univ. of Leicester (England))

    1991-06-25

    Three-dimensional (3D) heteronuclear NMR techniques have been used to make sequential {sup 1}H and {sup 15}H resonance assignments for most of the residues of Lactobacillus casei dihydrofolate reductase (DHFR), a monomeric protein of molecular mass 18,300 Da. A uniformly {sup 15}N-labeled sample of the protein was prepared and its complex with methotrexate (MTX) studied by 3D {sup 15}N/{sup 1}H nuclear Overhauserheteronuclear multiple quantum coherence (NOESY-HMQC), Harmann-Hahn-heteronuclear multiple quantum coherence (HOHAHA-HMQC), and HMQC-NOESY-HMQC experiments. These experiments overcame most of the spectral overlap problems caused by chemical shift degeneracies in 2D spectra and allowed the {sup 1}H-{sup 1}H through-space and through-bond connectivities to be identified unambiguously, leading to the resonance assignments. The novel HMQC-NOESY-HMQC experiment allows NOE cross peaks to be detected between NH protons even when their {sup 1}H chemical shifts are degenerate as long as the amide {sup 15}N chemical shifts are nondegenerate. The 3D experiments, in combination with conventional 2D NOESY, COSY, and HOHAHA experiments on unlabelled and selectively deuterated DHFR, provide backbone assignments for 146 of the 162 residues and side-chain assignments for 104 residues of the protein. Data from the NOE-based experiments and identification of the slowly exchanging amide protons provide detailed information about the secondary structure of the binary complex of the protein with methotrexate.

  14. iFC²: an integrated web-server for improved prediction of protein structural class, fold type, and secondary structure content.

    PubMed

    Chen, Ke; Stach, Wojciech; Homaeian, Leila; Kurgan, Lukasz

    2011-03-01

    Several descriptors of protein structure at the sequence and residue levels have been recently proposed. They are widely adopted in the analysis and prediction of structural and functional characteristics of proteins. Numerous in silico methods have been developed for sequence-based prediction of these descriptors. However, many of them do not have a public web-server and only a few integrate multiple descriptors to improve the predictions. We introduce iFC² (integrated prediction of fold, class, and content) server that is the first to integrate three modern predictors of sequence-level descriptors. They concern fold type (PFRES), structural class (SCEC), and secondary structure content (PSSC-core). The server exploits relations between the three descriptors to implement a cross-evaluation procedure that improves over the predictions of the individual methods. The iFC² annotates fold and class predictions as potentially correct/incorrect. When tested on datasets with low-similarity chains, for the fold prediction iFC² labels 82% of the PFRES predictions as correct and the accuracy of these predictions equals 72%. The accuracy of the remaining 28% of the PFRES predictions equals 38%. Similarly, our server assigns correct labels for over 79% of SCEC predictions, which are shown to be 98% accurate, while the remaining SCEC predictions are only 15% accurate. These results are shown to be competitive when contrasted against recent relevant web-servers. Predictions on CASP8 targets show that the content predicted by iFC² is competitive when compared with the content computed from the tertiary structures predicted by three best-performing methods in CASP8. The iFC² server is available at http://biomine.ece.ualberta.ca/1D/1D.html . PMID:20730460

  15. Differential expression of BDNF mRNA splice variants in mouse brain and immune cells

    Microsoft Academic Search

    Niels Kruse; Seray Cetin; Andrew Chan; Ralf Gold; Fred Lühder

    2007-01-01

    For the neurotrophin BDNF several splice variants were recently described. We analyzed the expression of mBDNF mRNA splice variants in cells of the immune system in comparison to the central nervous system (CNS). Whereas all splice variants are expressed in the CNS, only mBDNF 3 mRNA could be detected in primary and secondary lymphoid organs as well as in purified

  16. Importance of secondary structural specificity determinants in protein folding: insertion of a native beta-sheet sequence into an alpha-helical coiled-coil.

    PubMed

    Kwok, Stanley C; Mant, Colin T; Hodges, Robert S

    2002-06-01

    To examine how a short secondary structural element derived from a native protein folds when in a different protein environment, we inserted an 11-residue beta-sheet segment (cassette) from human immunoglobulin fold, Fab new, into an alpha-helical coiled-coil host protein (cassette holder). This de novo design protein model, the structural cassette mutagenesis (SCM) model, allows us to study protein folding principles involving both short- and long-range interactions that affect secondary structure stability and conformation. In this study, we address whether the insertion of this beta-sheet cassette into the alpha-helical coiled-coil protein would result in conformational change nucleated by the long-range tertiary stabilization of the coiled-coil, therefore overriding the local propensity of the cassette to form beta-sheet, observed in its native immunoglobulin fold. The results showed that not only did the nucleating helices of the coiled-coil on either end of the cassette fail to nucleate the beta-sheet cassette to fold with an alpha-helical conformation, but also the entire chimeric protein became a random coil. We identified two determinants in this cassette that prevented coiled-coil formation: (1) a tandem dipeptide NN motif at the N-terminal of the beta-sheet cassette, and (2) the hydrophilic Ser residue, which would be buried in the hydrophobic core if the coiled-coil structure were to fold. By amino acid substitution of these helix disruptive residues, that is, either the replacement of the NN motif with high helical propensity Ala residues or the substitution of Ser with Leu to enhance hydrophobicity, we were able to convert the random coil chimeric protein into a fully folded alpha-helical coiled-coil. We hypothesized that this NN motif is a "secondary structural specificity determinant" which is very selective for one type of secondary structure and may prevent neighboring residues from adopting an alternate protein fold. These sequences with secondary structural specificity determinants have very strong local propensity to fold into a specific secondary structure and may affect overall protein folding by acting as a folding initiation site. PMID:12021450

  17. Sequence-specific 1H-NMR assignment and secondary structure of black mamba dendrotoxin I, a highly selective blocker of voltage-gated potassium channels.

    PubMed

    Foray, M F; Lancelin, J M; Hollecker, M; Marion, D

    1993-02-01

    The secondary structure of dendrotoxin I, an important constituent of the venom of the African black mamba snake Dendroaspis polylepis polylepis, was determined in aqueous solution by two-dimensional methods. Complete sequence-specific 1H-NMR assignment was obtained with the exception of the backbone amide proton of Gly39 and Cys40. Dendrotoxin I is based on a central antiparallel beta-sheet and two small helices located at the N- and the C-terminal extremities. These secondary-structural units occur at exactly the same places in the amino acid sequence as those of bovine pancreatic trypsin inhibitor (BPTI), with which dendrotoxin I shares 33% sequence similarity. According to the disulfide-bridge positions and the long-range NOE observed these secondary-structural elements fold in a similar manner to BPTI. This similarity allows an hypothesis according to which dendrotoxin I could derive from an ancestral Künitz-type proteinase inhibitor. This ancestor would have been heavily mutated at amino acid positions not critical for gross structure. The spatial locations of the solvent-exposed amino acids concerned could therefore serve as a guideline for interpretation of the structure/activity relationship of dendrotoxin I for the blockage of voltage-sensitive potassium channels of which dendrotoxin I is a strong inhibitor. The possible connections with other polypeptide toxins that block related ion currents is discussed. PMID:7679640

  18. 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 (?-helix, ?-sheet and ?-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.

  19. Effect of the N-terminal glycine on the secondary structure, orientation, and interaction of the influenza hemagglutinin fusion peptide with lipid bilayers.

    PubMed Central

    Gray, C; Tatulian, S A; Wharton, S A; Tamm, L K

    1996-01-01

    The amino-terminal segment of the membrane-anchored subunit of influenza hemagglutinin (HA) plays a crucial role in membrane fusion and, hence, has been termed the fusion peptide. We have studied the secondary structure, orientation, and effects on the bilayer structure of synthetic peptides corresponding to the wild-type and several fusogenic and nonfusogenic mutants with altered N-termini of the influenza HA fusion peptide by fluorescence, circular dichroism, and Fourier transform infrared spectroscopy. All peptides contained segments of alpha-helical and beta-strand conformation. In the wild-type fusion peptide, 40% of all residues were in alpha-secondary and 30% in beta-secondary structures. By comparison, the nonfusogenic peptides exhibited larger beta/alpha secondary structure ratios. The order parameters of the helices and the amide carbonyl groups of the beta-strands of the wild-type fusion peptide were measured separately, based on the infrared dichroism of the respective absorption bands. Order parameters in the range 0.1-0.7 were found for both segments of the wild-type peptide, which indicates that they are most likely aligned at oblique angles to the membrane normal. The nonfusogenic but not the fusogenic peptides induced splitting of the infrared absorption band at 1735 cm(-1), which is assigned to stretching vibrations of the lipid ester carbonyl bond. This splitting, which reports on an alteration of the hydrogen bonds formed between the lipid ester carbonyls and water and/or hydrogen-donating groups of the fusion peptides, correlated with the beta/alpha ratio of the peptides, suggesting that unpaired beta-strands may replace water molecules and hydrogen-bond to the lipid ester carbonyl groups. The profound structural changes induced by single amino acid replacements at the extreme N-terminus of the fusion peptide further suggest that tertiary or quaternary structural interactions may be important when fusion peptides bind to lipid bilayers. PMID:9172751

  20. Phylogenetic reconstruction using secondary structures and sequence motifs of ITS2 rDNA of Paragonimus westermani (Kerbert, 1878) Braun, 1899 (Digenea: Paragonimidae) and related species

    PubMed Central

    2009-01-01

    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 that give "morphological" information, not found in the primary sequence. In several mountainous regions of Northeastern India, foci of Paragonimus (lung fluke) infection reportedly involve species that are known to prevail in neighbouring countries. The present study was undertaken to demonstrate the sequence analysis of the ribosomal DNA (ITS2) of the infective (metacercarial) stage of the lung fluke collected from the edible crab hosts that are abundant in a mountain stream of the area (Miao, Changlang District in Arunachal Pradesh) and to construct its phylogeny. Using the approach of molecular morphometrics that is based on ITS2 secondary structure homologies, phylogenetic relationships of the various isolates of Paragonimus species that are prevalent in the neighbouring Near-eastern countries have been discussed. Results Initially, ten predicted RNA secondary structures were reconstructed and the topology based only on the predicted RNA secondary structure of the ITS2 region resolved most relationships among the species studied. We obtained three similar topologies for seven species of the genus Paragonimus on the basis of traditional primary sequence analysis using MEGA 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. Paragonimus westermani was found to group with P. siamensis of Thailand; this was best supported by both the molecular morphometrics and combined analyses. P. heterotremus, P. proliferus, P. skrjabini, P. bangkokensis and P. harinasutai formed a separate clade in the molecular phylogenies, and were reciprocally monophyletic with respect to other species. ITS2 sequence motifs allowed an accurate in-silico distinction of lung flukes. Conclusion Data indicate that ITS2 motifs (? 50 bp in size) can be considered a promising tool for trematode species identification. RNA secondary structure analysis could be a valuable tool for distinguishing new species and completing Paragonimus systematics, more so because ITS2 secondary structure contains more information than the usual primary sequence alignment. PMID:19958489

  1. Probing of structural relaxation times in the glassy state of sucrose and trehalose based on dynamical properties of two secondary relaxation processes

    SciTech Connect

    Kaminski, K.; Adrjanowicz, K.; Paluch, M. [Institute of Physics, Silesian University, Uniwersytecka 4, PL-40-007 Katowice (Poland); Kaminska, E. [Department of Pharmacognosy and Phytochemistry, Medical University of Silesia, Jagiellonska 4, PL-41-200 Sosnowiec (Poland)

    2011-06-15

    Time-dependent isothermal dielectric measurements were carried out deeply in the glassy state on two very important saccharides: sucrose and trehalose. In both compounds two prominent secondary relaxation processes were identified. The faster one is an inherent feature of the whole family of carbohydrates. The slower one can also be detected in oligo- and polysaccharides. It was shown earlier that the {beta} process is the Johari-Goldstein (JG) relaxation coupled to motions of the glycosidic linkage, while the {gamma} relaxation originates from motions of the exocyclic hydroxymethyl unit. Recently, it was shown that the JG relaxation process can be used to determine structural relaxation times in the glassy state [R. Casalini and C. M. Roland, Phys. Rev. Lett. 102, 035701 (2009)]. In this paper we present the results of an analysis of the data obtained during aging using two independent approaches. The first was proposed by Casalini and Roland, and the second one is based on the variation of the dielectric strength of the secondary relaxation process during aging [J. K. Vij and G. Power, J. Non-Cryst. Solids 357, 783 (2011)]. Surprisingly, we found that the estimated structural relaxation times in the glassy state of both saccharides are almost the same, independent of the type of secondary mode. This finding calls into question the common view that secondary modes of intramolecular origin do not provide information about the dynamics of the glassy state.

  2. 3512 IEEE TRANSACTIONS ON SIGNAL PROCESSING, VOL. 55, NO. 7, JULY 2007 Bayesian Protein Secondary Structure Prediction

    E-print Network

    Erdogan, Hakan

    3512 IEEE TRANSACTIONS ON SIGNAL PROCESSING, VOL. 55, NO. 7, JULY 2007 Bayesian Protein Secondary was supported by the National Science Foundation­Signal Processing Systems (NSF­SPS) under Grant CCR-0105654

  3. Molecular authentication of three Italian melon accessions by ARMS-PCR and ITS1 (internal transcribed spacer 1) secondary structure prediction

    PubMed Central

    Fantaccione, Stefania; Woodrow, Pasqualina; Pontecorvo, Giovanni

    2008-01-01

    Genetic assessment was carried out on three Italian melon accessions by sequence and structural analysis of the internal transcribed spacer 1 (ITS1) from three populations belonging to two Cucumis melo L. varieties (madras and tendral). Alignment of the 18S-5.8S-26S sequences from three melon accessions showed that there were three single-nucleotide polymorphisms (SNPs) and one short insertion-deletion (indel) at the 5'end ITS1. An amplification refractory mutation system (ARMS)-PCR-based analysis was successfully applied to the SNP markers of the ITS1 sequences for the fingerprinting analysis of three melon populations. Secondary structure models for each ITS1 were derived. The prediction of ITS1 RNA secondary structure from each accession was improved by detecting key functional elements shared by all sequences in the alignments. Our results demonstrated that the ITS1secondary structure models can be used to improve the preliminary genetic assessment of the three melon accessions, suggesting a new tool in plant fingerprinting analysis. PMID:18478086

  4. Complete 1H, 13C, and 15N NMR resonance assignments and secondary structure of human glutaredoxin in the fully reduced form.

    PubMed Central

    Sun, C.; Holmgren, A.; Bushweller, J. H.

    1997-01-01

    Human glutaredoxin is a member of the glutaredoxin family, which is characterized by a glutathione binding site and a redox-active dithiol/disulfide in the active site. Unlike Escherichia coli glutaredoxin-1, this protein has additional cysteine residues that have been suggested to play a regulatory role in its activity. Human glutaredoxin (106 amino acid residues, M(r) = 12,000) has been purified from a pET expression vector with both uniform 15N labeling and 13C/15N double labeling. The combination of three-dimensional 15N-edited TOCSY, 15N-edited NOESY, HNCA, HN(CO)CA, and gradient sensitivity-enhanced HNCACB and HNCO spectra were used to obtain sequential assignments for residues 2-106 of the protein. The gradient-enhanced version of the HCCH-TOCSY pulse sequence and HCCH-COSY were used to obtain side chain 1H and 13C assignments. The secondary structural elements in the reduced protein were identified based on NOE information, amide proton exchange data, and chemical shift index data. Human glutaredoxin contains five helices extending approximately from residues 4-10, 24-36, 53-64, 83-92, and 94-104. The secondary structure also shows four beta-strands comprised of residues 15-19, 43-48, 71-75, 78-80, which form a beta-sheet almost identical to that found in E. coli glutaredoxin-1. Complete 1H, 13C, and 15N assignments and the secondary structure of fully reduced human glutaredoxin are presented. Comparison to the structures of other glutaredoxins is presented and differences in the secondary structure elements are discussed. PMID:9041640

  5. Circular dichroism and electron microscopy studies in vitro of 33-mer gliadin peptide revealed secondary structure transition and supramolecular organization.

    PubMed

    Herrera, María G; Zamarreño, Fernando; Costabel, Marcelo; Ritacco, Hernan; Hütten, Andreas; Sewald, Norbert; Dodero, Verónica I

    2014-01-01

    Gliadin, a protein present in wheat, rye, and barley, undergoes incomplete enzymatic degradation during digestion, producing an immunogenic 33-mer peptide, LQLQPF(PQPQLPY)3 PQPQPF. The special features of 33-mer that provoke a break in its tolerance leading to gliadin sensitivity and celiac disease remains elusive. Herein, it is reported that 33-mer gliadin peptide was not only able to fold into polyproline II secondary structure but also depending on concentration resulted in conformational transition and self-assembly under aqueous condition, pH 7.0. A 33-mer dimer is presented as one initial possible step in the self-assembling process obtained by partial electrostatics charge distribution calculation and molecular dynamics. In addition, electron microscopy experiments revealed supramolecular organization of 33-mer into colloidal nanospheres. In the presence of 1 mM sodium citrate, 1 mM sodium borate, 1 mM sodium phosphate buffer, 15 mM NaCl, the nanospheres were stabilized, whereas in water, a linear organization and formation of fibrils were observed. It is hypothesized that the self-assembling process could be the result of the combination of hydrophobic effect, intramolecular hydrogen bonding, and electrostatic complementarity due to 33-mer's high content of proline and glutamine amino acids and its calculated nonionic amphiphilic character. Although, performed in vitro, these experiments have revealed new features of the 33-mer gliadin peptide that could represent an important and unprecedented event in the early stage of 33-mer interaction with the gut mucosa prior to onset of inflammation. Moreover, these findings may open new perspectives for the understanding and treatment of gliadin intolerance disorders. © 2013 Wiley Periodicals, Inc. Biopolymers 101: 96-106, 2014. PMID:23703327

  6. Structure and floristics of an old secondary rain forest in Central Kalimantan, Indonesia, and a comparison with adjacent primary forest

    Microsoft Academic Search

    Francis Q Brearley; Sukaesih Prajadinata; Petra S Kidd; John Proctor; Suriantata

    2004-01-01

    The study of tropical secondary forests, and of the time taken for them to revert to ‘primary’ forest, is of increasing importance given the current global destruction of tropical rain forests. We describe a 55-year-old secondary rain forest at Barito Ulu, Central Kalimantan, Indonesia, and compare it with the adjacent, undisturbed, primary forest. Three 0.25ha plots were set up in

  7. mRNA stability in mammalian cells.

    PubMed Central

    Ross, J

    1995-01-01

    This review concerns how cytoplasmic mRNA half-lives are regulated and how mRNA decay rates influence gene expression. mRNA stability influences gene expression in virtually all organisms, from bacteria to mammals, and the abundance of a particular mRNA can fluctuate manyfold following a change in the mRNA half-life, without any change in transcription. The processes that regulate mRNA half-lives can, in turn, affect how cells grow, differentiate, and respond to their environment. Three major questions are addressed. Which sequences in mRNAs determine their half-lives? Which enzymes degrade mRNAs? Which (trans-acting) factors regulate mRNA stability, and how do they function? The following specific topics are discussed: techniques for measuring eukaryotic mRNA stability and for calculating decay constants, mRNA decay pathways, mRNases, proteins that bind to sequences shared among many mRNAs [like poly(A)- and AU-rich-binding proteins] and proteins that bind to specific mRNAs (like the c-myc coding-region determinant-binding protein), how environmental factors like hormones and growth factors affect mRNA stability, and how translation and mRNA stability are linked. Some perspectives and predictions for future research directions are summarized at the end. PMID:7565413

  8. High-Resolution Aeromagnetic Survey over the Yucatan Peninsula - Implications for Chicxulub Impact, Secondary Craters and Regional Crustal Structures

    NASA Astrophysics Data System (ADS)

    Fucugauchi, J. U.; Lopez-Loera, H.; Rebolledo-Vieyra, M.

    2011-12-01

    We present the initial results of a low-altitude high-resolution aeromagnetic study over the Yucatan peninsula. Area surveyed extends from 86W to 91W and 18N to 21N, covering the peninsula and adjacent continental margin of Gulf of Mexico and Caribbean Sea. Aeromagnetic surveys are integrated into a regional map, and regional and residual anomalies are separated using spectral and least-squares methods. For the study, aeromagnetic field was reduced to the pole and several data filtering techniques were used, including first and second vertical derivatives, analytical signal, and upward and downward analytical continuations. The region is characterized by large amplitude broad elongated magnetic anomalies oriented north-south in the northern sector of the continental shelf, and northwest-southeast and northeast-southwest over the western and eastern sides of the peninsula, respectively. Major regional anomalies extend from the continental shelf into the peninsula, whereas other anomaly trends in the central northern sector, at northeast limit of Chicxulub crater, are restricted to the shelf. Largest anomaly on the east extends over the Holbox fracture zone. At its southern end, south of Chetumal a parallel trend extends over the Rio Hondo fault zone between Quintana Roo and Belize. On the western peninsula the anomaly is characterized by two parallel trends offset between Yucatan and Campeche. The central zone of Chicxulub is characterized by a semi-circular anomaly pattern, surrounded by long wavelength small amplitude anomalies extending to the east on the peninsula and shelf, isolated from the regional broad anomalies. To the south of Chicxulub anomaly, there is an elongated low with a central high extending southward from the terrace zone inside the crater rim. The elongated magnetic anomaly correlates with a broad gravity low, which is apparent south of the concentric zone of anomalies. To the north of Chicxulub anomaly, a magnetic high inside the crater is followed by a low outside, which extend to the north and northwest. The regional broad anomalies crossing the peninsula and shelf are interpreted as crustal structures on the Yucatan block related to pre- and rifting deformation, which include basement uplift. The southward elongated magnetic anomaly and gravity low may correspond to a pre-impact structure. From analysis of residual anomalies, we found no clear indication of secondary craters or multiple impacts.

  9. All things must pass: contrasts and commonalities in eukaryotic and bacterial mRNA decay

    Microsoft Academic Search

    Joel G. Belasco

    2010-01-01

    Despite its universal importance for controlling gene expression, mRNA degradation was initially thought to occur by disparate mechanisms in eukaryotes and bacteria. This conclusion was based on differences in the structures used by these organisms to protect mRNA termini and in the RNases and modifying enzymes originally implicated in mRNA decay. Subsequent discoveries have identified several striking parallels between the

  10. Secondary smoke

    NASA Astrophysics Data System (ADS)

    Kessel, P. A.

    1993-06-01

    The open literature on secondary smoke formation, prediction, and classification is briefly reviewed. This review was limited to the open literature in order to promote the widest possible discussion within the AGARD engineering community. The recently completed PEP WG 21 proposal for smoke classification is presented. Secondary smoke is defined and the physics of condensation of vapor onto droplets is reviewed. The basis for the existing droplet condensation models is discussed and the existing methodology for predicting secondary smoke light attenuation and scattering is presented. Test data taken to establish the initial conditions for heterogeneous nucleation in rocket plumes is presented. Comparisons between secondary smoke predictions and flight data are presented. The state of the art of secondary smoke modeling is discussed and suggestions are made for improvements.

  11. Improved Secondary Structure Predictions for a Nicotinic Receptor Subunit: Incorporation of Solvent Accessibility and Experimental Data into a Two-Dimensional Representation

    Microsoft Academic Search

    Nicolas Le Novère; Pierre-Jean Corringer; Jean-Pierre Changeux

    1999-01-01

    Abstract A refined prediction of the nicotinic acetylcholine receptor (nAChR) subunits’ secondary structure was computed with third-generation algorithms. The four selected programs, PHD, Predator, DSC, and NNSSP, based on different prediction approaches, were applied to each sequence of an alignment of nAChR and 5-HT3 receptor subunits, as well as a larger alignment with related subunit sequences from glycine and GABA

  12. Structural studies of secondary crystallization products of the Fe23B6-type in a nanocrystalline FeCoB-based alloy

    E-print Network

    Laughlin, David E.

    Structural studies of secondary crystallization products of the Fe23B6-type in a nanocrystalline FeCo and 740 °C, respectively. After annealing the sample at 820 °C for 1 h, a Fe23B6-type phase FeCoNb 23B6 consist of nanometer size -FeSi DO3 FineMet ,1 -Fe bcc NANOPERM ,2 and -FeCo B2 HITPERM Ref. 3 grains

  13. Organophosphorus acid anhydrolase: Secondary structure analysis in solution and Langmuir-Blodgett film and the direct CDS quantum dots conjugation for detection of diisopropylfluorophosphate

    Microsoft Academic Search

    Liang Zhao

    2006-01-01

    Organophosphorus acid anhydrolase (OPAA) can catalyze the hydrolysis of P-F or PCN bonds of organophosphorus (OP) compounds. My main objective is to develop the OPAA-based biosensor to detect and detoxify OP compounds by the conjugation of CdS quantum dots (QDs) and OPAA.First, the surface chemistry and secondary structure of enzyme OPAA was studied. The pH (from 4.6 to 10.5) and

  14. Characterization of rock bream (Oplegnathus fasciatus) cytosolic Cu/Zn superoxide dismutase in terms of molecular structure, genomic arrangement, stress-induced mRNA expression and antioxidant function.

    PubMed

    Umasuthan, Navaneethaiyer; Bathige, S D N K; Thulasitha, William Shanthakumar; Qiang, Wan; Lim, Bong-Soo; Lee, Jehee

    2014-10-01

    Superoxide dismutases (SODs) are dedicated to scavenge and dismutate the superoxide anions in order to protect the cells from oxidative stress by establishing the redox homeostasis. In this study, we describe a cytosolic Cu/ZnSOD, the second SOD member from rock bream Oplegnathus fasciatus (Of-cCu/ZnSOD) at molecular, genomic structural-, transcriptional- and functional-levels. The determination of genomic arrangement of Of-cCu/ZnSOD by means of a BAC library revealed that its primary transcript is represented by five exons and encoded a peptide of 154 amino acids. In silico investigation of Of-cCu/ZnSOD indicated the presence of several family characteristics including two Cu/ZnSOD signatures, seven metal liganding residues and eight ?-sheets forming a ?-barrel topology. Alignment and modeling studies confirmed the conservation of Cu/ZnSOD at primary and tertiary levels. While invertebrate Cu/ZnSOD members mainly demonstrate a tetraexonic structure, the vertebrate members have acquired an additional intron in the third exon resulting in a quinquepartite arrangement with class-specific exon lengths. Although, teleost Cu/ZnSOD members resembled the mammalian orthologs in their genomic organization, they shared a proximal position with molluscan members in the phylogeny. The antioxidant (AO) activity of Of-cCu/ZnSOD was affirmed by a recombinant protein which was also used to examine the biophysical and biochemical properties. The pronounced activity was detected when the rOf-cCu/ZnSOD was expressed with the Cu(2+) and Zn(2+) supplementation. The optimum activities were observed at pH10 and 25°C, and KCN strongly inhibited the activity of the rOf-cCu/ZnSOD. Furthermore, a constitutive mRNA expression of Of-cCu/ZnSOD with higher levels in blood>liver>heart and brain was observed, which was consistent with the transcriptional profile of Of-mMnSOD, suggesting important physiological role(s). This idea was further strengthened by the temporal assessment of Of-cCu/ZnSOD transcripts in animals under pathological (bacteria- or viral-induced) and physiological (H2O2-induced oxidative) stress conditions using qPCR, in which it exhibited significantly up-regulated levels. Screening of Of-cCu/ZnSOD 5'-flanking region revealed the presence of several important transcription factor binding sites that potentially govern the Cu/ZnSOD expression. These findings conjointly contribute to expand our understanding regarding the piscine Cu/ZnSODs and; in particular, the AO enzyme network of rock bream. PMID:25088251

  15. Endoribonucleases--enzymes gaining spotlight in mRNA metabolism.

    PubMed

    Li, Wai Ming; Barnes, Tavish; Lee, Chow H

    2010-02-01

    The efficient turnover of messenger RNA represents an important mechanism that allows the cell to control gene expression. Until recently, the mechanism of mRNA decay was mainly attributed to exonucleases, comprising enzymes that degrade RNAs from the ends of the molecules. This article summarizes the endoribonucleases, comprising enzymes that cleave RNA molecules internally, which were identified in more recent years in eukaryotic mRNA metabolism. Endoribonucleases have received little attention in the past, based on the difficulty in their identification and a lack of understanding of their physiological significance. This review aims to compare the similarities and differences among this group of enzymes, as well as their known cellular functions. Despite the many differences in protein structure, and thus difficulties in identifying them based on amino acid sequence, most endoribonucleases possess essential cellular functions and have been shown to play an important role in mRNA turnover. PMID:19968858

  16. Emerging features of mRNA decay in bacteria.

    PubMed Central

    Steege, D A

    2000-01-01

    The problem of mRNA decay in E. coli has recently seen exciting progress, with the discoveries that key degradation enzymes are associated together in a high molecular weight degradosome and that polyadenylation promotes decay. Recent advances make it clear that mRNA decay in bacteria is far more interesting enzymatically than might have been predicted. In-depth study of specific mRNAs has revealed multiple pathways for degradation. Which pathway a given mRNA follows appears to depend in large part on the location of the initiating endonucleolytic cleavage within the mRNA. During the steps of mRNA decay, stable RNA structures pose formidable barriers to the 3' --> 5' exonucleases. However, polyadenylation is now emerging as a process that plays an important role in maintaining the momentum of exonucleolytic degradation by adding single-stranded extensions to the 3' ends of mRNAs and their decay intermediates, thereby facilitating further exonuclease digestion. PMID:10943888

  17. [Secondary rhinoplasty].

    PubMed

    Duron, J-B; Nguyen, P S; Bardot, J; Aiach, G

    2014-12-01

    Secondary rhinoplasty is very usual. Some patients are not satisfied by the previous surgery because the result is poor with obvious defaults but, sometimes, the result is good but the patient expects perfection. These two different situations will not lead to the same answer from the surgeon. Techniques of secondary rhinoplasty are the same than primary, but are often more difficult to perform because of scar tissue, retraction and loss of lining. The authors analyse the more frequent deformities in secondary rhinoplasty and the way they fix them. PMID:25213488

  18. TOPICAL REVIEW: Mechanisms governing the control of mRNA translation

    NASA Astrophysics Data System (ADS)

    Livingstone, Mark; Atas, Evrim; Meller, Amit; Sonenberg, Nahum

    2010-06-01

    The translation of cellular mRNA to protein is a tightly controlled process often deregulated in diseases such as cancer. Furthering our understanding of mRNA structural elements and the intracellular proteins and signaling pathways that affect protein expression is crucial in the development of new therapies. In this review, we discuss the current state-of-the-art of detecting and determining the role of mRNA sequence elements in regulating the initiation of mRNA translation and the therapeutic strategies that exploit this knowledge to treat disease.

  19. Secondary Headaches

    MedlinePLUS

    ... Migraine and Other Headaches Headache Journal - Public Site Art Gallery Art Gallery Support the AMF American Migraine Foundation The ... but there are usually clues in the medical history or examination to suggest secondary headache. Headache can ...

  20. 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 (?-helix, ?-sheet and ?-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. PMID:25203214

  1. Secondary atomization

    Microsoft Academic Search

    D. R. Guildenbecher; C. López-Rivera; P. E. Sojka

    2009-01-01

    When a drop is subjected to a surrounding dispersed phase that is moving at an initial relative velocity, aerodynamic forces\\u000a will cause it to deform and fragment. This is referred to as secondary atomization. In this paper, the abundant literature\\u000a on secondary atomization experimental methods, breakup morphology, breakup times, fragment size and velocity distributions,\\u000a and modeling efforts is reviewed and

  2. Brazil: Secondary Education Profile. A Summary of "Secondary Education: Time to Move Forward." Secondary Education Series.

    ERIC Educational Resources Information Center

    Larach, Linda

    This paper provides a brief profile of the state of secondary education in Brazil. An overview of the organizational structure, objectives, curricular offerings, system size, and governance structure of secondary education is provided. Issues relating to the quality, equity, management, and financing of the system are discussed, and promising…

  3. The Weight of History: Structures, Patterns and Legacies of Secondary Education in the British Isles, c.1200-c.1980

    ERIC Educational Resources Information Center

    Richardson, William

    2011-01-01

    This article serves as context for the other papers in this special issue, all of which deal with developments in UK secondary education since c.1980. The paper comprises a review of selected impulses and imperatives that saw the substantial legacy of medieval and humanist schooling in Britain re-shaped, during the period c.1830-c.1980, into the…

  4. Effect of temperature and pH on the secondary structure and processes of oligomerization of 19 kDa alpha-zein.

    PubMed

    Cabra, Vanessa; Arreguin, Roberto; Vazquez-Duhalt, Rafael; Farres, Amelia

    2006-06-01

    Highly hydrophobic protein Z19 zein shows a tendency towards oligomerization. The role of temperature and pH on the oligomerization process was studied monitoring the secondary structure content and the appearance of aggregates by Circular Dichroism Spectroscopy (CD) and Dinamic Light Scattering (DLS). Z19 zein suffers irreversible thermal denaturalization, as demonstrated by far-UV CD measurements. DLS data indicate that this denaturalization is accompanied by oligomerization processes which are strongly dependent on temperature. The aggregates that appear when the sample is heated maintain a certain amount of their native structure. Oligomers, showing high stability to temperature changes and other denaturing conditions with molecular weights of 45, 66 kDa and higher, were detected by SDS-PAGE. The secondary structure strongly depends on pH. Thus, at pH above pI (6.8), all the protein structure is in alpha helix. The formation of disulfide bonds plays an important role in the aggregation process, since most of the sulfhydryls in the protein (97.52%) form disulfide bonds and only 2.47% of them are free and superficially exposed. The sensitivity towards thermal denaturalization is also affected by pH rises. PMID:16765112

  5. HISTOLOGIC STRUCTURE AND MINERAL COMPONENTS OF SECONDARY DENTIN FORMED BY ENDOCHONDRAL BONE MATRIX GELATIN IMPLANTATION IN RABBIT PULP CAVITY

    Microsoft Academic Search

    A. G. Sobhani; A. Shoa-Kazemi; B. Niknafs; A. Hedaiatpour

    Many investigators use bone matrix gelatin for bone induction but it is used rarely for repair of teeth defects. This study was designed to evaluate secondary dentin formation by endochondral bone matrix gelatin (E-BMG) in rabbit. E-BMG was prepared from tibia and femur of 4 Deutsche-Poland rabbits with average ages of 4-6 months. The prepared E-BMG was implanted in right

  6. [Secondary achalasia].

    PubMed

    Arnon, R; Fich, A; Bar-Ziv, J

    1993-08-01

    Achalasia is usually a primary disorder of esophageal motility, but has been described in association with other pathological processes, such as malignancy. A 79-year-old man with achalasia secondary to gastric adenocarcinoma is presented. The differential diagnosis of secondary achalasia includes infectious and infiltrative disease and neuropathy, but mainly malignant diseases. The clinical criteria found for achalasia secondary to malignancy included older age at diagnosis, brief duration of symptoms, and weight loss. While upper gastrointestinal x-rays and computerized tomographic scanning may be helpful, the most reliable diagnostic tool is esophago-gastro-duodenoscopy. This is a terminal disease with short life expectancy. Yet making the correct diagnosis can save the patient from futile treatment with muscle relaxants and endoscopic balloon dilatation, the accepted therapeutic measures in primary achalasia. PMID:8225085

  7. A universal model for the secondary structure of 5.8S ribosomal RNA molecules, their contact sites with 28S ribosomal RNAs, and their prokaryotic equivalent.

    PubMed Central

    Vaughn, J C; Sperbeck, S J; Ramsey, W J; Lawrence, C B

    1984-01-01

    The phylogenetic approach (ref. 1) has been utilized in construction of a universal 5.8S rRNA secondary structure model, in which about 65% of the residues exist in paired structures. Conserved nucleotides primarily occupy unpaired regions. Multiple compensating base changes are demonstrated to be present in each of the five postulated helices, thereby forming a major basis for their proof. The results of chemical and enzymatic probing of 5.8S rRNAs (ref. 13, 32) are fully consistent with, and support, our model. This model differs in several ways from recently proposed 5.8S rRNA models (ref. 3, 4), which are discussed. Each of the helices in our model has been extended to the corresponding bacterial, chloroplast and mitochondrial sequences, which are demonstrated to be positionally conserved by alignment with their eukaryotic counterparts. This extension is also made for the base paired 5.8S/28S contact points, and their prokaryotic and organelle counterparts. The demonstrated identity of secondary structure in these diverse molecules strongly suggests that they perform equivalent functions in prokaryotic and eukaryotic ribosomes. PMID:6208532

  8. Label-free determination of lipid composition and secondary protein structure of human salivary noncancerous and cancerous tissues by Raman microspectroscopy.

    PubMed

    Brozek-Pluska, Beata; Kopec, Monika; Niedzwiecka, Izabela; Morawiec-Sztandera, Alina

    2015-04-01

    The applications of optical spectroscopic methods in cancer detection open new possibilities in oncological diagnostics. Raman spectroscopy and Raman imaging represent noninvasive, label-free, and rapidly developing tools in cancer diagnosis. In the study described in this paper Raman microspectroscopy has been employed to examine noncancerous and cancerous human salivary gland tissues of the same patient. The most significant differences between noncancerous and cancerous tissues were found in regions typical for the vibrations of lipids and proteins. The detailed analysis of secondary structures of proteins contained in the cancerous and the noncancerous tissues is also presented. PMID:25478605

  9. Chemical and structural characterisation of DGEBA-based epoxies by time of flight secondary ion mass spectrometry (ToF-SIMS) as a preliminary to polymer interphase characterisation

    Microsoft Academic Search

    Sven Passlack; Alexander Brodyanski; Wolfgang Bock; Michael Kopnarski; Melanie Presser; Paul Ludwig Geiß; Gunnar Possart; Paul Steinmann

    2009-01-01

    Time-of-flight secondary ion mass spectrometry (ToF-SIMS) has become a powerful tool in the field of surface analysis since\\u000a it provides information about the top few monolayers of a sample, i.e. on the chemical composition of the sample surface.\\u000a Thus, the general question arises whether a surface-sensitive technique like ToF-SIMS would be appropriate to detect systematic\\u000a chemical and\\/or structural changes in

  10. Science: Secondary.

    ERIC Educational Resources Information Center

    Curriculum Review, 1980

    1980-01-01

    This article reviews and compares five recent secondary science texts: Addison-Wesley Life Science (Gr. 7-9); Prentice-Hall Life Science (Gr. 7-9); Scott Foresman Biology (Gr. 9-12); Biology: Living Systems (Gr. 10-12); and Biology: The Science of Life (Gr. 10-12). (SJL)

  11. Secondary Products

    Technology Transfer Automated Retrieval System (TEKTRAN)

    In spite of their name, "secondary" products are essential for plant survival. They are required for basic cell functions as well as communicating the plant's presence to the surrounding environment and defense against pests as defined in the broad sense (i.e., diseases, nematodes, insects and plan...

  12. Analysis of mRNA recognition by human thymidylate synthase.

    PubMed

    Brunn, Nicholas D; Dibrov, Sergey M; Kao, Melody B; Ghassemian, Majid; Hermann, Thomas

    2014-01-01

    Expression of hTS (human thymidylate synthase), a key enzyme in thymidine biosynthesis, is regulated on the translational level through a feedback mechanism that is rarely found in eukaryotes. At low substrate concentrations, the ligand-free enzyme binds to its own mRNA and stabilizes a hairpin structure that sequesters the start codon. When in complex with dUMP (2'-deoxyuridine-5'-monophosphate) and a THF (tetrahydrofolate) cofactor, the enzyme adopts a conformation that is unable to bind and repress expression of mRNA. Here, we have used a combination of X-ray crystallography, RNA mutagenesis and site-specific cross-linking studies to investigate the molecular recognition of TS mRNA by the hTS enzyme. The interacting mRNA region was narrowed to the start codon and immediately flanking sequences. In the hTS enzyme, a helix-loop-helix domain on the protein surface was identified as the putative RNA-binding site. PMID:25423174

  13. Molecular dynamics as a tool to detect protein foldability. A mutant of domain B1 of protein G with non-native secondary structure propensities.

    PubMed Central

    Cregut, D.; Serrano, L.

    1999-01-01

    The usefulness of molecular dynamics to assess the structural integrity of mutants containing several mutations has been investigated. Our goal was to determine whether molecular dynamics would be able to discriminate mutants of a protein having a close-to-wild-type fold, from those that are not folded under the same conditions. We used as a model the B1 domain of protein G in which we replaced the unique central alpha-helix by the sequence of the second beta-hairpin, which has a strong intrinsic propensity to form this secondary structure in solution. In the resulting protein, one-third of the secondary structure has been replaced by a non-native one. Models of the mutants were built based on the three-dimensional structure of the wild-type GB1 domain. During 2 ns of molecular dynamics simulations on these models, mutants containing up to 10 mutations in the helix retained the native fold, while another mutant with an additional mutation unfolded. This result is in agreement with our circular dichroism and NMR experiments, which indicated that the former mutants fold into a structure similar to the wild-type, as opposed to the latter mutant which is partly unfolded. Additionally, a mutant containing six mutations scattered through the surface of the domain, and which is unfolded, was also detected by the simulation. This study suggests that molecular dynamics calculations could be performed on molecular models of mutants of a protein to evaluate their foldability, prior to a mutagenesis experiment. PMID:10048320

  14. In situ hybridization of albumin mRNA in normal liver and liver tumors: Identification of hepatocellular origin

    Microsoft Academic Search

    Koji Yamaguchi; Michael A. Nalesnik; Brian I. Carr

    1993-01-01

    Summary  In situ hybridization was performed to detect albumin mRNA in normal liver, liver cirrhosis, primary liver tumors and secondary\\u000a liver neoplasms. In areas of normal liver, and liver cirrhosis, signals for albumin mRNA were present in hepatocytes, whereas\\u000a no signals were seen in other cells such as endothelial and Küpffer cells, bile duct epithelium and smooth muscle cells. In\\u000a 53

  15. How Secondary Level Teachers and Students Impose Personal Structure on Fractional Expressions and Equations--An Expert-Novice Study

    ERIC Educational Resources Information Center

    Ruede, Christian

    2013-01-01

    While an algebraic expression is typically assigned a regular structure, this article introduces the concept of personal structure ("Strukturierung"); here, the structuring of an algebraic expression is understood as the act of forming relationships between its parts. This concept is used for the analysis of interviews in which experts and novices…

  16. Characterization of visna virus mRNA.

    PubMed Central

    Filippi, P; Brahic, M; Vigne, R; Tamalet, J

    1979-01-01

    Visna virus is a retrovirus responsible for a classical slow infection of the central nervous system of sheep. In the present work we focused our attention on the viral mRNA's. We found that, during the acute infection in vitro, (i) viral mRNA's amount to only 0.1% of the total cytoplasmic RNA, (ii) 20% of the total cytoplasmic viral RNA is found in polyribosomes, and (iii) three viral mRNA's can be identified by sucrose gradient sedimentation or polyacrylamide gel electrophoresis. Their sedimentation coefficients are 36S, 27S, and 21S. PMID:228056

  17. Secondary Flow Structure Induced by a Multiple-Harmonic Pulsatile Waveform at Low Womersley Number in a Curved Tube

    NASA Astrophysics Data System (ADS)

    Prince, Chekema; Plesniak, Michael; Peterson, Sean

    2008-11-01

    Under forced harmonic oscillation at sufficiently high Womersley number, the secondary flow pattern in a tube can exhibit Lyne-type vortices, where an inviscid core in the center of the tube experiences inward centrifuging. The present study investigates the evolution of secondary flow development in a curved tube subjected to a physiologically-inspired pulsatile waveform constructed using 10 harmonics. Specifically, the study seeks to address whether a Lyne-type effect is possible at a nominally low Womersley number. Experimental data were acquired using Laser Doppler Velocimetry (LDV) and numerical simulations were conducted using Fluent. Experimental and numerical results show fully developed flow after approximately 150 degrees for all phases of the driving waveform. This is in agreement with previous studies of harmonic forcing. For the lower Reynolds number portions of the waveform, flow development can occur as early as 135 degrees according to experimental data. Lyne-type vortices were observed at portions of the waveform dominated by higher harmonics, such as the peak associated with systole.

  18. Exploring the relationship between protein secondary structures, temperature-dependent viscosities, and technological treatments in egg yolk and LDL by FTIR and rheology.

    PubMed

    Blume, K; Dietrich, K; Lilienthal, S; Ternes, W; Drotleff, A M

    2015-04-15

    Egg yolk and its main component, low-density lipoproteins (LDL), were consecutively pasteurised, optimally freeze-dried, and dispersed in various NaCl solutions (0-10%). Heat-induced changes in the protein secondary structures which accompanied viscosity-increasing aggregation processes were monitored using Fourier transform infrared spectroscopy (FTIR) to determine the intensities of intermolecular ?-sheets (1622 cm(-1)) and results were compared with the temperature-dependent viscosities. Considerable changes in secondary structures observed after reconstitution of freeze-dried LDL had no detectable effect on the characteristic heat-induced viscosity curves but suggest that LDL plays a particular role in the unwanted gel formation of egg yolk after conventional freezing. For all egg yolk samples and all NaCl-containing LDL samples, the sigmoidal changes in the absorbance units vs. temperature curves corresponded with the first increase in heat-induced viscosity. Both analytical methods showed that the presence of ionic strength caused a shift in curve progressions towards higher temperatures, indicating increased thermal stability. PMID:25466063

  19. Studies on the secondary structure of wheat 5.8 S rRNA. Conformational changes in the A + U-rich stem during ribosome assembly.

    PubMed

    Wildeman, A G; Nazar, R N

    1982-01-01

    The nucleotide sequence of wheat (Triticum aestivum) 5.8-S ribosomal RNA has been re-examined using partial chemical degradation with high-temperature sequencing gels and oligonucleotide analysis. The results clarify previously ambiguous residues and add two additional nucleotides, G127 and G135, to the sequence. Estimates of the secondary structure suggest that 5.8-S rRNAs of higher plants differ from previous examples in having more open G + C-rich and A + U-rich stems. S1 ribonuclease digestion was used to probe this secondary structure; the data generally support the 'burp gun' model proposed for all 5.8-S rRNAs but are also consistent with a more open A + U-rich stem. Diethyl pyrocarbonate reactivity was used to probe the topography of this RNA in wheat ribosomes. The results indicate that the G + C-rich and A + U-rich stems are accessible to chemical modification in the wheat ribosome and suggest that the A + U-rich stem undergoes a significant conformational change when the molecule associates into ribosomes. PMID:7060553

  20. Internal and external relationships of the Cnidaria: implications of primary and predicted secondary structure of the 5'-end of the 23S-like rDNA.

    PubMed Central

    Odorico, D M; Miller, D J

    1997-01-01

    Since both internal (class-level) and external relationships of the Cnidaria remain unclear on the basis of analyses of 18S and (partial) 16S rDNA sequence data, we examined the informativeness of the 5'-end of the 23S-like rDNA. Here we describe analyses of both primary and predicted secondary structure data for this region from the ctenophore Bolinopsis sp., the placozoan Trichoplax adhaerens, the sponge Hymeniacidon heliophila, and representatives of all four cnidarian classes. Primary sequence analyses clearly resolved the Cnidaria from other lower Metazoa, supported sister group relationships between the Scyphozoa and Cubozoa and between the Ctenophora and the Placozoa, and confirmed the basal status of the Anthozoa within the Cnidaria. Additionally, in the ctenophore, placozoan and sponge, non-canonical base pairing is required to maintain the secondary structure of the B12 region, whereas amongst the Cnidaria this is not the case. Although the phylogenetic significance of this molecular character is unclear, our analyses do not support the close relationship between Cnidaria and Placozoa suggested by previous studies. PMID:9061962

  1. Secondary hypoadrenalism

    Microsoft Academic Search

    Giuseppe Reimondo; Silvia Bovio; Barbara Allasino; Massimo Terzolo; Alberto Angeli

    2008-01-01

    Secondary adrenal insufficiency (SAI) is a clinical disorder that results from hypothalamic or hypophyseal damage or from\\u000a prolonged administration of supraphysiological doses of glucocorticoids. Since glucocorticoids are widely used for a variety\\u000a of diseases, the prevalence of SAI is by far exceeding that of primary adrenal insufficiency. Although the presentation of\\u000a adrenal insufficiency may be insidious and difficult to recognize,

  2. Two-dimensional NMR studies of squash family inhibitors. Sequence-specific proton assignments and secondary structure of reactive-site hydrolyzed Cucurbita maxima trypsin inhibitor III.

    PubMed

    Krishnamoorthi, R; Gong, Y X; Lin, C L; VanderVelde, D

    1992-01-28

    The solution structure of reactive-site hydrolyzed Cucurbita maxima trypsin inhibitor III (CMTI-III*) was investigated by two-dimensional proton nuclear magnetic resonance (2D NMR) spectroscopy. CMTI-III*, prepared by reacting CMTI-III with trypsin which cleaved the Arg5-Ile6 peptide bond, had the two fragments held together by a disulfide linkage. Sequence-specific 1H NMR resonance assignments were made for all the 29 amino acid residues of the protein. The secondary structure of CMTI-III*, as deduced from NOESY cross peaks and identification of slowly exchanging hydrogens, contains two turns (residues 8-12 and 24-27), a 3(10)-helix (residues 13-16), and a triple-stranded beta-sheet (residues 8-10, 29-27, and 21-25). This secondary structure is similar to that of CMTI-I [Holak, T. A., Gondol, D., Otlewski, J., & Wilusz, T. (1989) J. Mol. Biol. 210, 635-648], which has a Glu instead of a Lys at position 9. Sequential proton assignments were also made for the virgin inhibitor, CMTI-III, at pH 4.71, 30 degrees C. Comparison of backbone hydrogen chemical shifts of CMTI-III and CMTI-III* revealed significant changes for residues located far away from the reactive-site region as well as for those located near it, indicating tertiary structural changes that are transmitted through most of the 29 residues of the inhibitor protein. Many of these residues are functionally important in that they make contact with atoms of the enzyme in the trypsin-inhibitor complex, as revealed by X-ray crystallography [Bode, W., Greyling, H. J., Huber, R., Otlewski, J., & Wilusz, T. (1989) FEBS Lett. 242, 285-292].(ABSTRACT TRUNCATED AT 250 WORDS) PMID:1731946

  3. In the right place at the right time: visualizing and understanding mRNA localization

    PubMed Central

    Buxbaum, Adina R.; Haimovich, Gal

    2015-01-01

    The spatial regulation of protein translation is an efficient way to create functional and structural asymmetries in cells. Recent research has furthered our understanding of how individual cells spatially organize protein synthesis, by applying innovative technology to characterize the relationship between mRNAs and their regulatory proteins, single-mRNA trafficking dynamics, physiological effects of abrogating mRNA localization in vivo and for endogenous mRNA labelling. The implementation of new imaging technologies has yielded valuable information on mRNA localization, for example, by observing single molecules in tissues. The emerging movements and localization patterns of mRNAs in morphologically distinct unicellular organisms and in neurons have illuminated shared and specialized mechanisms of mRNA localization, and this information is complemented by transgenic and biochemical techniques that reveal the biological consequences of mRNA mislocalization. PMID:25549890

  4. 14 CFR 23.405 - Secondary control system.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... 2012-01-01 false Secondary control system. 23.405 Section 23.405 Aeronautics...COMMUTER CATEGORY AIRPLANES Structure Control Surface and System Loads § 23.405 Secondary control system. Secondary controls, such as...

  5. 14 CFR 25.405 - Secondary control system.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... 2014-01-01 false Secondary control system. 25.405 Section 25.405 Aeronautics...TRANSPORT CATEGORY AIRPLANES Structure Control Surface and System Loads § 25.405 Secondary control system. Secondary controls, such as...

  6. 14 CFR 25.405 - Secondary control system.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 2010-01-01 false Secondary control system. 25.405 Section 25.405 Aeronautics...TRANSPORT CATEGORY AIRPLANES Structure Control Surface and System Loads § 25.405 Secondary control system. Secondary controls, such as...

  7. 14 CFR 23.405 - Secondary control system.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 2010-01-01 false Secondary control system. 23.405 Section 23.405 Aeronautics...COMMUTER CATEGORY AIRPLANES Structure Control Surface and System Loads § 23.405 Secondary control system. Secondary controls, such as...

  8. 14 CFR 23.405 - Secondary control system.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... 2013-01-01 false Secondary control system. 23.405 Section 23.405 Aeronautics...COMMUTER CATEGORY AIRPLANES Structure Control Surface and System Loads § 23.405 Secondary control system. Secondary controls, such as...

  9. 14 CFR 25.405 - Secondary control system.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 2011-01-01 false Secondary control system. 25.405 Section 25.405 Aeronautics...TRANSPORT CATEGORY AIRPLANES Structure Control Surface and System Loads § 25.405 Secondary control system. Secondary controls, such as...

  10. 14 CFR 23.405 - Secondary control system.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... 2014-01-01 false Secondary control system. 23.405 Section 23.405 Aeronautics...COMMUTER CATEGORY AIRPLANES Structure Control Surface and System Loads § 23.405 Secondary control system. Secondary controls, such as...

  11. 14 CFR 23.405 - Secondary control system.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 2011-01-01 false Secondary control system. 23.405 Section 23.405 Aeronautics...COMMUTER CATEGORY AIRPLANES Structure Control Surface and System Loads § 23.405 Secondary control system. Secondary controls, such as...

  12. 14 CFR 25.405 - Secondary control system.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... 2013-01-01 false Secondary control system. 25.405 Section 25.405 Aeronautics...TRANSPORT CATEGORY AIRPLANES Structure Control Surface and System Loads § 25.405 Secondary control system. Secondary controls, such as...

  13. 14 CFR 25.405 - Secondary control system.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... 2012-01-01 false Secondary control system. 25.405 Section 25.405 Aeronautics...TRANSPORT CATEGORY AIRPLANES Structure Control Surface and System Loads § 25.405 Secondary control system. Secondary controls, such as...

  14. Ferredoxin-1 mRNA is destabilized by changes in photosynthetic electron transport

    PubMed Central

    Petracek, Marie E.; Dickey, Lynn F.; Nguyen, Tuyen T.; Gatz, Christiane; Sowinski, Dolores A.; Allen, George C.; Thompson, William F.

    1998-01-01

    In transgenic tobacco, pea Ferredoxin-1 (Fed-1) mRNA accumulates rapidly in response to photosynthesis even when the transgene is driven by a constitutive promoter. To investigate the role of photosynthesis on Fed-1 mRNA stability, we used the tetracycline repressible Top10 promoter system to specifically shut off transcription of the Fed-1 transgene. The Fed-1 mRNA has a half-life of approximately 2.4 hr in the light and a half-life of only 1.2 hr in the dark or in the presence of the photosynthetic electron transport inhibitor 3-(3,4-dichlorophenyl)-1,1-dimethylurea (DCMU). These data indicate that cessation of photosynthesis, either by darkness or DCMU results in a destabilization of the Fed-1 mRNA. Furthermore, the Fed-1 mRNA half-life is reduced immediately upon transfer to darkness, suggesting that Fed-1 mRNA destabilization is a primary response to photosynthesis rather than a secondary response to long-term dark adaptation. Finally, the two different methods for efficient tetracycline delivery reported here generally should be useful for half-life measurements of other mRNAs in whole plants. PMID:9671795

  15. A Nascent Peptide Signal Responsive to Endogenous Levels of Polyamines Acts to Stimulate Regulatory Frameshifting on Antizyme mRNA.

    PubMed

    Yordanova, Martina M; Wu, Cheng; Andreev, Dmitry E; Sachs, Matthew S; Atkins, John F

    2015-07-17

    The protein antizyme is a negative regulator of cellular polyamine concentrations from yeast to mammals. Synthesis of functional antizyme requires programmed +1 ribosomal frameshifting at the 3' end of the first of two partially overlapping ORFs. The frameshift is the sensor and effector in an autoregulatory circuit. Except for Saccharomyces cerevisiae antizyme mRNA, the frameshift site alone only supports low levels of frameshifting. The high levels usually observed depend on the presence of cis-acting stimulatory elements located 5' and 3' of the frameshift site. Antizyme genes from different evolutionary branches have evolved different stimulatory elements. Prior and new multiple alignments of fungal antizyme mRNA sequences from the Agaricomycetes class of Basidiomycota show a distinct pattern of conservation 5' of the frameshift site consistent with a function at the amino acid level. As shown here when tested in Schizosaccharomyces pombe and mammalian HEK293T cells, the 5' part of this conserved sequence acts at the nascent peptide level to stimulate the frameshifting, without involving stalling detectable by toe-printing. However, the peptide is only part of the signal. The 3' part of the stimulator functions largely independently and acts at least mostly at the nucleotide level. When polyamine levels were varied, the stimulatory effect was seen to be especially responsive in the endogenous polyamine concentration range, and this effect may be more general. A conserved RNA secondary structure 3' of the frameshift site has weaker stimulatory and polyamine sensitizing effects on frameshifting. PMID:25998126

  16. Bioinformatic and functional analysis of RNA secondary structure elements among different genera of human and animal caliciviruses

    Microsoft Academic Search

    Peter Simmonds; Ioannis Karakasiliotis; Dalan Bailey; Yasmin Chaudhry; David J. Evans; Ian G. Goodfellow

    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 second- ary structures within the Norovirus, Sapovirus, Vesivirus and Lagovirus genera. All showed pro- found suppression of synonymous site variability (SSSV) at genomic 5' ends and the start of the sub-genomic (sg) transcript, consistent

  17. The epidermal cell structure of the secondary pollen presenter in Vangueria infausta (Rubiaceae: Vanguerieae) suggests a functional association with protruding onci in pollen grains.

    PubMed

    Tilney, Patricia M; van Wyk, Abraham E; van der Merwe, Chris F

    2014-01-01

    Secondary pollen presentation is a well-known phenomenon in the Rubiaceae with particularly conspicuous pollen presenters occurring in the tribe Vanguerieae. These knob-like structures are formed by a modification of the upper portion of the style and stigma, together known as the stylar head complex. In the flower bud and shortly before anthesis, the anthers surrounding the stylar head complex dehisce and release pollen grains which adhere to the pollen presenter. The epidermal cells of the pollen presenter facing the anthers are radially elongated with a characteristic wall thickening encircling the anticlinal walls of each cell towards the distal end. These cells were studied in the pollen presenter of Vangueria infausta using electron and light microscopy in conjunction with histochemical tests and immunohistochemical methods. Other prominent thickenings of the cell wall were also observed on the distal and proximal walls. All these thickenings were found to be rich in pectin and possibly xyloglucan. The terms "thickenings of Igersheim" and "bands of Igersheim" are proposed to refer, respectively, to these wall structures in general and those encircling the anticlinal walls of each cell near the distal end. The epidermal cells have an intricate ultrastructure with an abundance of organelles, including smooth and rough endoplasmic reticulum, Golgi apparatus, mitochondria and secretory vesicles. This indicates that these cells are likely to have an active physiological role. The pollen grains possess prominent protruding onci and observations were made on their structure and development. Walls of the protruding onci are also rich in pectin. Pectins are hydrophilic and known to be involved in the dehydration and rehydration of pollen grains. We hypothesise that the thickenings of Igersheim, as well as the protruding onci of the pollen grains, are functionally associated and part of the adaptive syndrome of secondary pollen presentation, at least in the Vanguerieae. PMID:24804803

  18. The Epidermal Cell Structure of the Secondary Pollen Presenter in Vangueria infausta (Rubiaceae: Vanguerieae) Suggests a Functional Association with Protruding Onci in Pollen Grains

    PubMed Central

    Tilney, Patricia M.; van Wyk, Abraham E.; van der Merwe, Chris F.

    2014-01-01

    Secondary pollen presentation is a well-known phenomenon in the Rubiaceae with particularly conspicuous pollen presenters occurring in the tribe Vanguerieae. These knob-like structures are formed by a modification of the upper portion of the style and stigma, together known as the stylar head complex. In the flower bud and shortly before anthesis, the anthers surrounding the stylar head complex dehisce and release pollen grains which adhere to the pollen presenter. The epidermal cells of the pollen presenter facing the anthers are radially elongated with a characteristic wall thickening encircling the anticlinal walls of each cell towards the distal end. These cells were studied in the pollen presenter of Vangueria infausta using electron and light microscopy in conjunction with histochemical tests and immunohistochemical methods. Other prominent thickenings of the cell wall were also observed on the distal and proximal walls. All these thickenings were found to be rich in pectin and possibly xyloglucan. The terms “thickenings of Igersheim” and “bands of Igersheim” are proposed to refer, respectively, to these wall structures in general and those encircling the anticlinal walls of each cell near the distal end. The epidermal cells have an intricate ultrastructure with an abundance of organelles, including smooth and rough endoplasmic reticulum, Golgi apparatus, mitochondria and secretory vesicles. This indicates that these cells are likely to have an active physiological role. The pollen grains possess prominent protruding onci and observations were made on their structure and development. Walls of the protruding onci are also rich in pectin. Pectins are hydrophilic and known to be involved in the dehydration and rehydration of pollen grains. We hypothesise that the thickenings of Igersheim, as well as the protruding onci of the pollen grains, are functionally associated and part of the adaptive syndrome of secondary pollen presentation, at least in the Vanguerieae. PMID:24804803

  19. Phenotypic variation and spatial structure of secondary chemistry in a natural population of a tropical tree species

    E-print Network

    Bermingham, Eldredge

    (Berenbaum and Zangerl 1992), developmental (Bowers and Stamp 1993) and environmental (Agrell et al. 2000) sources of variation. Thus, the age structure, environ- mental heterogeneity and limits in gene flow

  20. Analysis of an Activator:Coactivator Complex Reveals an Essential Role for Secondary Structure in Transcriptional Activation

    Microsoft Academic Search

    David Parker; Ulupi S Jhala; Ishwar Radhakrishnan; Michael B Yaffe; Christine Reyes; Andrew I Shulman; Lewis C Cantley; Peter E Wright; Marc Montminy

    1998-01-01

    Ser-133 phosphorylation of CREB within the kinase-inducible domain (KID) promotes target gene activation via complex formation with the KIX domain of the coactivator CBP. Concurrent phosphorylation of CREB at Ser-142 inhibits transcriptional induction via an unknown mechanism. Unstructured in the free state, KID folds into a helical structure upon binding to KIX. Using site-directed mutagenesis based on the NMR structure

  1. Helical secondary structure of polyalanine peptides in vacuo: Ac-Alan-LysH^+ (n=5,10,15), experiment and theory

    NASA Astrophysics Data System (ADS)

    Rossi, Mariana; Blum, Volker; Kupser, Peter; von Helden, Gert; Bierau, Frauke; Meijer, Gerard; Scheffler, Matthias

    2009-03-01

    The presence of a solvent is often viewed as indispensable to explain the structure of peptides and proteins. However, well defined secondary structure motifs (helices, sheets, ...) also exist in vacuo, offering a unique ``clean room'' condition to quantify the stabilizing interactions. We here unravel the structure of LysineH^+ capped polyalanine peptides Ac-Alan-LysH^+ (n-5,10,15), by combining experimental multi-photon IR spectra obtained using the FELIX free-electron laser at room-temperature with van der Waals-corrected all-electron density-functional theory (DFT) in the generalized gradient approximation in the FHI-aims code [1]. Earlier ion mobility studies of these molecules indicate helical structure [2], which we here demonstrate quantitatively. For n=5, we find a close energetic competition of different helix motifs (?, 310), with similar and good agreement between measured and calculated vibrational spectra. We show how the LysH^+ termination acts to induce helices also for longer peptides, and how vibrational modes develop with helix length (n=10,15), yielding, e.g., a softening of collective modes towards the infinite helix limit. [1] V. Blum et al, Comp. Phys. Comm. (2008), accepted. [2] M. Kohtani et al., JACS 120, 12975 (1998).

  2. The Arctic: Glacial Refugium or Area of Secondary Contact? Inference from the Population Genetic Structure of the Thick-Billed Murre (Uria lomvia), with Implications for Management.

    PubMed

    Tigano, Anna; Damus, Martin; Birt, Tim P; Morris-Pocock, Jamie A; Artukhin, Yuri B; Friesen, Vicki L

    2015-01-01

    Quaternary glaciations affected the distribution of many species. Here, we investigate whether the Arctic represented a glacial refugium during the Last Glacial Maximum or an area of secondary contact following the ice retreat, by analyzing the genetic population structure of the thick-billed murre (Uria lomvia), a seabird that breeds throughout the North Atlantic, North Pacific and Arctic Oceans. The thick-billed murre is a species of socio-economic importance and faces numerous threats including hunting, oil pollution, gill netting, and climate change. We compared variation in the mitochondrial DNA (mtDNA) control region (n = 424), supplemented by 4 microsatellite loci (n = 445), among thick-billed murres sampled throughout their range. MtDNA data indicated that colonies comprise 4 genetically differentiated groups (?st = 0.11-0.81): 1) Atlantic Ocean plus New Siberian Islands region, 2) Cape Parry, 3) Chukchi Sea, and 4) Pacific Ocean. Microsatellite variation differed between Atlantic and Pacific populations. Otherwise, little substructure was found within either ocean. Atlantic and Pacific populations appear to have been genetically isolated since the last interglacial period and should be considered separate evolutionary significant units for management. The Chukchi Sea and Cape Parry appear to represent areas of secondary contact, rather than arctic refugial populations. PMID:25825313

  3. Definition of global and transcript-specific mRNA export pathways in metazoans

    PubMed Central

    Farny, Natalie G.; Hurt, Jessica A.; Silver, Pamela A.

    2008-01-01

    Eukaryotic gene expression requires export of messenger RNAs (mRNAs) from their site of transcription in the nucleus to the cytoplasm where they are translated. While mRNA export has been studied in yeast, the complexity of gene structure and cellular function in metazoan cells has likely led to increased diversification of these organisms’ export pathways. Here we report the results of a genome-wide RNAi screen in which we identify 72 factors required for polyadenylated [poly-(A+)] mRNA export from the nucleus in Drosophila cells. Using structural and functional conservation analysis of yeast and Drosophila mRNA export factors, we expose the evolutionary divergence of eukaryotic mRNA export pathways. Additionally, we demonstrate the differential export requirements of two endogenous heat-inducible transcripts—intronless heat-shock protein 70 (HSP70) and intron-containing HSP83—and identify novel export factors that participate in HSP83 mRNA splicing. We characterize several novel factors and demonstrate their participation in interactions with known components of the Drosophila export machinery. One of these factors, Drosophila melanogaster PCI domain-containing protein 2 (dmPCID2), associates with polysomes and may bridge the transition between exported messenger ribonucleoprotein particles (mRNPs) and polysomes. Our results define the global network of factors involved in Drosophila mRNA export, reveal specificity in the export requirements of different transcripts, and expose new avenues for future work in mRNA export. PMID:18086857

  4. Primary and secondary structures of Tetrahymena and aphid 5.8S rRNAs: structural features of 5.8S rRNA which interacts with the 28S rRNA containing the hidden break.

    PubMed

    Fujiwara, H; Ishikawa, H

    1982-09-11

    The Tetrahymena 5.8S rRNA is 154 nucleotides long, the shortest so far reported except for the split 5.8S rRNAs of Diptera (m5.8S plus 2S rRNA). In this molecule several nucleotides are deleted in the helix e (GC-rich stem) region. Upon constructing the secondary structure in accordance with "burp-gun" model, the Tetrahymena 5.8S rRNA forms a wide-open "muzzle" of the terminal regions due to both extra nucleotides and several unpaired bases. The aphid 5.8S rRNA consists of 161 nucleotides and can form stable helices in both terminal and helix e regions. As a whole, the secondary structure of Tetrahymena 5.8S rRNA resembles that of Bombyx 5.8S molecule while the aphid 5.8S rRNA shares several structural features with the HeLa 5.8S molecule. Likely, the 5.8S rRNA attached to the 28S rRNA with the hidden break differs in structure from those interacting with the 28S partners without the break. Nucleotide sequences of 5.8S rRNA in insects as well as in protozoans are not so conservative evolutionarily as in vertebrates. PMID:6815618

  5. Four butyrolactones and diverse bioactive secondary metabolites from terrestrial Aspergillus flavipes MM2: isolation and structure determination

    PubMed Central

    2012-01-01

    The chemical constituents and biological activities of the terrestrial Aspergillus flavipes MM2 isolated from Egyptian rice hulls are reported. Seven bioactive compounds were obtained, of which one sterol: ergosterol (1), four butyrolactones: butyrolactone I (2), aspulvinone H (3), butyrolactone-V (6) and 4,4'-diydroxypulvinone (7), along with 6-methylsalicylic acid (4) and the cyclopentenone analogue; terrien (5). Structures of the isolated compounds were deduced by intensive studies of their 1D & 2D NMR, MS data and comparison with related structures. The strain extract and the isolated compounds (1-7) were biologically studied against number of microbial strains, and brine shrimp for cytotoxicity. In this article, the taxonomical characterization of A. flavipes MM2 along with its upscale fermentation, isolation and structural assignment of the obtained bioactive metabolites, and evaluate their antimicrobial and cytotoxic activities were described. PMID:22380482

  6. Circular dichroism and infrared spectroscopic characterization of secondary structure components of protein Z during mashing and boiling processes.

    PubMed

    Han, Yupeng; Wang, Jinjing; Li, Yongxian; Hang, Yu; Yin, Xiangsheng; Li, Qi

    2015-12-01

    In beer brewing, protein Z is hypothesized to stabilize beer foam. However, few investigations have revealed the relationship between conformational alterations to protein Z during the brewing process and beer foam. In this report, protein Z from sweet wort was isolated during mashing and boiling processes. Circular dichroism (CD) and Fourier transform infrared spectroscopy (FTIR) were used to monitor the structural characteristics of protein Z. The results showed that the ?-helix and ?-sheet content decreased, whereas the content of ?-turn and random coil increased. The complex environment rich in polysaccharides may facilitate conformational alterations and modifications to protein Z. Additionally, the formation of extended structural features to protein Z provides access to reactive amino acid side chains that can undergo modifications and the exposure of hydrophobic core regions of the protein. Analyzing structural transformations should provide a deeper understanding of the mechanism of protein Z on maintaining beer foam. PMID:26041183

  7. Coupling mRNA Synthesis and Decay

    PubMed Central

    Braun, Katherine A.

    2014-01-01

    What has been will be again, what has been done will be done again; there is nothing new under the sun.—Ecclesiastes 1:9 (New International Version) Posttranscriptional regulation of gene expression has an important role in defining the phenotypic characteristics of an organism. Well-defined steps in mRNA metabolism that occur in the nucleus—capping, splicing, and polyadenylation—are mechanistically linked to the process of transcription. Recent evidence suggests another link between RNA polymerase II (Pol II) and a posttranscriptional process that occurs in the cytoplasm—mRNA decay. This conclusion appears to represent a conundrum. How could mRNA synthesis in the nucleus and mRNA decay in the cytoplasm be mechanistically linked? After a brief overview of mRNA processing, we will review the recent evidence for transcription-coupled mRNA decay and the possible involvement of Snf1, the Saccharomyces cerevisiae ortholog of AMP-activated protein kinase, in this process. PMID:25154419

  8. Secondary Periodicity in the Structural and Vibrational Characteristics of 3,3-DIMETHYLCYCLOPROPENES - and Monosubstituted by -X{(CH_3)}_3 (x = C, Si, Ge, Sn, Pb)

    NASA Astrophysics Data System (ADS)

    Panchenko, Yu. N.; Abramenkov, A. V.; de Maré, G. R.

    2009-06-01

    The regularities of changes in the structural parameters and vibrational wavenumbers have been traced for certain moieties of the title compounds. The optimized geometrical parameters and the force fields of disubstituted 3,3-dimethylcyclopropenes and monosubstituted 3,3-dimethylcyclopropenes were determined at the HF/3-21G* and DDAll levels, respectively. The choice of these theoretical levels was brought about by peculiarities of GAUSSIAN 03 suite of programs for Sn and Pb atoms. The theoretical vibrational wavenumbers were calculated from the corresponding scaled force fields. The regularities obtained in the form of the zigzag lines are analogous to regularities that are characteristic to the atoms of the 14 (IVA) group of the Mendeleyev Periodic Table. This is known as the secondary periodicity phenomenon. Yu. N. Panchenko, G. R. De Maré, A. V. Abramenkov, and A. de Meijere, Spectrochim. Acta 65A, 575 (2006). G. R. De Maré, Yu. N. Panchenko, and A. V. Abramenkov, Spectrochim. Acta 67A, 1094 (2007).

  9. Effect of transcription inhibitors on the iron-dependent degradation of transferrin receptor mRNA.

    PubMed

    Seiser, C; Posch, M; Thompson, N; Kühn, L C

    1995-12-01

    Transferrin receptor (TfR) mRNA expression is tightly linked to intracellular iron levels. Upon iron deprivation, the iron regulatory protein (IRP) stabilizes TfR mRNA by binding to stem-loop structures in its 3'-untranslated region, whereas increased iron levels result in inactivation of the mRNA-binding protein and rapid degradation of TfR mRNA. Although IRP and the regulation of its RNA binding activity have been studied intensively, little is known about the mechanism of TfR mRNA degradation. In order to get more information about factors involved in this process we investigated the in vivo IRP-RNA interaction and the effect of transcription inhibitors on the iron-dependent decay of TfR mRNA. Here we demonstrate that part of the active IRP co-localizes with TfR mRNA to the rough endoplasmic reticulum. High intracellular iron levels led to a drastic reduction of this active RNA-bound IRP in vivo, indicating that IRP dissociates prior to TfR mRNA decay. Furthermore, the transcription inhibitor actinomycin D and translation inhibitor cycloheximide suppressed TfR mRNA degradation but did not interfere with the IRP dissociation step. Other inhibitors of RNA polymerase II had no effect on iron-dependent degradation of TfR mRNA. However, high concentrations of alpha-amanitin known to block transcription by RNA polymerase III interfered with mRNA decay suggesting the involvement of polymerase III transcripts in the degradation pathway. PMID:7493976

  10. Chemical composition, molecular weight distribution, secondary structure and effect of NaCl on functional properties of walnut (Juglans regia L) protein isolates and concentrates.

    PubMed

    Mao, Xiao-Ying; Hua, Yu-Fei

    2014-08-01

    Chemical composition, molecular weight distribution, secondary structure and effect of sodium chloride concentration on functional properties of walnut protein isolates, concentrates and defatted walnut flour were study. Compared with walnut protein concentrates (75.6%) and defatted walnut flour (52.5%), walnut protein isolates contain a relatively high amount of protein (90.5%). The yield of walnut protein isolates and concentrates was 43.2% and 76.6%, respectively. In molecular weight distribution study, Walnut protein isolates showed one peak with molecular weight of 106.33 KDa (100%) and walnut protein concentrates showed four peaks with molecular weight of 16,725 KDa (0.8%),104.943 KDa(63.9%), 7.3 KDa (11.4%), 2.6 KDa (23.9%). The secondary structure of walnut protein isolates was similar to that of walnut protein concentrates, but was differ from that of defatted walnut flour. The addition of sodium chloride (0?~?1 M) could improve the functionality of walnut protein concentrates, isolates and defatted walnut flour. The maximum solubility, water absorption capacity, emulsifying properties and foaming properties of walnut protein isolates, concentrates and defatted walnut flour were at sodium chloride solutions of 1.0 M, 0.6 M, 0.4 M, 0.6 M, respectively. The solubility of walnut protein concentrates (32.5%) in distilled water with 0 M sodium chloride was lower than that of walnut protein isolates (35.2%). The maximum solubility of walnut protein isolates, concentrates and defatted walnut flour in solution were 36.8%, 33.7% and 9.6% at 1.0 M sodium chloride solutions, respectively. As compared with other vegetable proteins, walnut protein isolates and concentrates exhibited better emulsifying properties and foam stability. PMID:25114337

  11. Spectroscopic vibrations of austinite (CaZnAsO4?OH) and its mineral structure: implications for identification of secondary arsenic-containing mineral.

    PubMed

    Liu, Jing; Ming, Dengshi; Cheng, Hongfei; Xu, Zhiqiang; Frost, Ray L

    2015-01-25

    Austinite (CaZnAsO4?OH) is a unique secondary mineral in arsenic-contaminated mine wastes. The infrared and Raman spectroscopies were used to characterize the austenite vibrations. The IR bands at 369, 790 and 416 cm(-1) are assigned to the ?2, ?3 and ?4 vibrations of AsO4(3-) unit, respectively. The Raman bands at 814, 779 and 403 cm(-1) correspond to the ?1, ?3 and ?4 vibrations of AsO4(3(-) unit respectively. The sharp bands at 3265 cm(-1) for IR and 3270 cm(-(1) both reveals that the structural hydroxyl units exist in the austenite structure. The IR and Raman spectra both show that some SO4 units isomorphically replace AsO4 in austinite. X-ray single crystal diffraction provides the arrangement of each atom in the mineral structure, and also confirms that the conclusions made from the vibrational spectra. Micro-powder diffraction was used to confirm our mineral identification due to the small quantity of the austenite crystals. PMID:25087167

  12. SDO/AIA OBSERVATIONS OF SECONDARY WAVES GENERATED BY INTERACTION OF THE 2011 JUNE 7 GLOBAL EUV WAVE WITH SOLAR CORONAL STRUCTURES

    SciTech Connect

    Li Ting; Zhang Jun; Yang Shuhong [Key Laboratory of Solar Activity, National Astronomical Observatories, Chinese Academy of Sciences, Beijing 100012 (China); Liu Wei, E-mail: liting@nao.cas.cn, E-mail: zjun@nao.cas.cn, E-mail: shuhongyang@nao.cas.cn [Lockheed Martin Solar and Astrophysics Laboratory, Department ADBS, Building 252, 3251 Hanover Street, Palo Alto, CA 94304 (United States)

    2012-02-10

    We present Solar Dynamics Observatory/Atmospheric Imaging Assembly observations of the interaction of a global EUV wave on 2011 June 7 with active regions (ARs), coronal holes (CHs), and coronal bright structures. The primary global wave has a three-dimensional dome shape, with propagation speeds ranging from 430 to 780 km s{sup -1} in different directions. The primary coronal wave runs in front of the expanding loops involved in the coronal mass ejection (CME) and its propagation speeds are approximately constant within 10-20 minutes. Upon arrival at an AR on its path, the primary EUV wave apparently disappears and a secondary wave rapidly reemerges within 75 Mm of the AR boundary at a similar speed. When the EUV wave encounters a coronal bright structure, an additional wave front appears there and propagates in front of it at a velocity nearly a factor of two faster. Reflected waves from a polar CH and a coronal bright structure are observed and propagate fractionally slower than the primary waves. Some of these phenomena can be equally explained by either a wave or a non-wave model alone. However, taken together, these observations provide new evidence for the multitudes of global EUV waves, in which a true MHD fast-mode wave or shock propagates in front of an expanding CME bubble.

  13. SDO/AIA Observations of Secondary Waves Generated by Interaction of the 2011 June 7 Global EUV Wave With Solar Coronal Structures

    E-print Network

    Li, Ting; Yang, Shuhong; Liu, Wei

    2011-01-01

    We present SDO/AIA observations of the interaction of a global EUV wave on 2011 June 7 with active regions (ARs), coronal holes (CHs) and coronal bright structures. The primary global wave has a three-dimensional dome shape, with propagation speeds ranging from 430-780 km/s in different directions. The primary coronal wave runs in front of the expanding loops involved in the CME and its propagation speeds are approximately constant within 10-20 minutes. Upon arrival at an AR on its path, the primary EUV wave apparently disappears and a secondary wave rapidly reemerges 75 Mm within the AR boundary at a similar speed. When the EUV wave encounters a coronal bright structure, an additional wave front appears there and propagates in front of it at a velocity nearly a factor of 2 faster. Reflected waves from a polar CH and a coronal bright structure are observed and propagate fractionally slower than the primary waves. Some of these phenomena can be equally explained by either a wave or non-wave model alone. Howeve...

  14. Self-amplifying mRNA vaccines.

    PubMed

    Brito, Luis A; Kommareddy, Sushma; Maione, Domenico; Uematsu, Yasushi; Giovani, Cinzia; Berlanda Scorza, Francesco; Otten, Gillis R; Yu, Dong; Mandl, Christian W; Mason, Peter W; Dormitzer, Philip R; Ulmer, Jeffrey B; Geall, Andrew J

    2015-01-01

    This chapter provides a brief introduction to nucleic acid-based vaccines and recent research in developing self-amplifying mRNA vaccines. These vaccines promise the flexibility of plasmid DNA vaccines with enhanced immunogenicity and safety. The key to realizing the full potential of these vaccines is efficient delivery of nucleic acid to the cytoplasm of a cell, where it can amplify and express the encoded antigenic protein. The hydrophilicity and strong net negative charge of RNA impedes cellular uptake. To overcome this limitation, electrostatic complexation with cationic lipids or polymers and physical delivery using electroporation or ballistic particles to improve cellular uptake has been evaluated. This chapter highlights the rapid progress made in using nonviral delivery systems for RNA-based vaccines. Initial preclinical testing of self-amplifying mRNA vaccines has shown nonviral delivery to be capable of producing potent and robust innate and adaptive immune responses in small animals and nonhuman primates. Historically, the prospect of developing mRNA vaccines was uncertain due to concerns of mRNA instability and the feasibility of large-scale manufacturing. Today, these issues are no longer perceived as barriers in the widespread implementation of the technology. Currently, nonamplifying mRNA vaccines are under investigation in human clinical trials and can be produced at a sufficient quantity and quality to meet regulatory requirements. If the encouraging preclinical data with self-amplifying mRNA vaccines are matched by equivalently positive immunogenicity, potency, and tolerability in human trials, this platform could establish nucleic acid vaccines as a versatile new tool for human immunization. PMID:25620012

  15. Sequence and expression of ferredoxin mRNA in barley

    SciTech Connect

    Zielinski, R.; Funder, P.M.; Ling, V. (Univ. of Illinois, Urbana (USA))

    1990-05-01

    We have isolated and structurally characterized a full-length cDNA clone encoding ferredoxin from a {lambda}gt10 cDNA library prepared from barley leaf mRNA. The ferredoxin clone (pBFD-1) was fused head-to-head with a partial-length cDNA clone encoding calmodulin, and was fortuitously isolated by screening the library with a calmodulin-specific oligonucleotide probe. The mRNA sequence from which pBFD-1 was derived is expressed exclusively in the leaf tissues of 7-d old barley seedlings. Barley pre-ferredoxin has a predicted size of 15.3 kDal, of which 4.6 kDal are accounted for by the transit peptide. The polypeptide encoded by pBFD-1 is identical to wheat ferredoxin, and shares slightly more amino acid sequence similarity with spinach ferredoxin I than with ferredoxin II. Ferredoxin mRNA levels are rapidly increased 10-fold by white light in etiolated barley leaves.

  16. Acylation of myelin basic protein peptide 1-21 with alkyl carboxylates 2-10 carbons long affects secondary structure and posttranslational modification.

    PubMed

    Costentino, M; Pritzker, L; Boulias, C; Moscarello, M A

    1994-04-12

    A peptide consisting of the first 21 residues of human myelin basic protein (MBP) was synthesized. The N-terminal alanine of portions was blocked in separate experiments with alkyl carboxylates varying in size from 2 to 10 carbon atoms. The effects of these different alkyl carboxylates at the N-terminus on the secondary structure was studied by circular dichroism (250-190 nm). In water, the spectra of the unblocked peptide suggested unordered structure with large negative ellipticities at 198 nm. Addition of an acetyl group altered the magnitude of [theta]198 from -21856 +/- 2319 to -11095 +/- 1000 deg cm2 dmol-1, suggesting a significant increase in ordered structure. When peptides with longer alkyl carboxylates, acylated at the N-termini, were studied, the magnitude of theta 198 approached that of the unblocked peptide but greater negative ellipticities were observed for the C8 and C10 alkyl carboxylates. The theta 222 values were generally low (-1803 +/- 463) but increased with increasing length of the alkyl carboxylate to about -3200 deg cm2 dmol-1, suggesting that little alpha-helical structure was present. The spectra were also taken in lipid-mimetic solvents, including 2-propanol, methanol, and lysophosphatidylglycerol (lysoPG). In general the theta 198 and theta 222 values were suggestive of increased structure in these environments compared to water. In 90% 2-propanol the theta 198 of the unblocked peptide did not change when an acetyl group was added to the N-terminus (9088 compared to 8477 deg cm2 dmol-1). Addition of longer alkyl carboxylates correlated with larger, negative ellipticities.(ABSTRACT TRUNCATED AT 250 WORDS) PMID:7512380

  17. Design, Analysis and Fabrication of Secondary Structural Components for the Habitat Demonstration Unit-Deep Space Habitat

    NASA Technical Reports Server (NTRS)

    Smith, Russell W.; Langford, William M.

    2012-01-01

    In support of NASA s Habitat Demonstration Unit - Deep Space Habitat Prototype, a number of evolved structural sections were designed, fabricated, analyzed and installed in the 5 meter diameter prototype. The hardware consisted of three principal structural sections, and included the development of novel fastener insert concepts. The articles developed consisted of: 1) 1/8th of the primary flooring section, 2) an inner radius floor beam support which interfaced with, and supported (1), 3) two upper hatch section prototypes, and 4) novel insert designs for mechanical fastener attachments. Advanced manufacturing approaches were utilized in the fabrication of the components. The structural components were developed using current commercial aircraft constructions as a baseline (for both the flooring components and their associated mechanical fastener inserts). The structural sections utilized honeycomb sandwich panels. The core section consisted of 1/8th inch cell size Nomex, at 9 lbs/cu ft, and which was 0.66 inches thick. The facesheets had 3 plys each, with a thickness of 0.010 inches per ply, made from woven E-glass with epoxy reinforcement. Analysis activities consisted of both analytical models, as well as initial closed form calculations. Testing was conducted to help verify analysis model inputs, as well as to facilitate correlation between testing and analysis. Test activities consisted of both 4 point bending tests as well as compressive core crush sequences. This paper presents an overview of this activity, and discusses issues encountered during the various phases of the applied research effort, and its relevance to future space based habitats.

  18. Functional similarities of human and chicken apolipoprotein AI: dependence on secondary and tertiary rather than primary structure

    Microsoft Academic Search

    Robert S. Kiss; Robert O. Ryan; Gordon A. Francis

    2001-01-01

    To investigate the sequence requirements for apolipoprotein (apo) AI functions, comparisons of human and chicken apoAI were performed. In lipid binding assays, chicken apoAI was capable of transforming phospholipid vesicles into discoidal bilayer structures, similar in both size and apolipoprotein content to those produced with human apoAI under the same conditions. Human and chicken apoAI were indistinguishable in their relative

  19. The complete mitochondrial genome and its remarkable secondary structure for a stonefly Acroneuria hainana Wu (Insecta: Plecoptera, Perlidae).

    PubMed

    Huang, Mingchao; Wang, Yuyu; Liu, Xingyue; Li, Weihai; Kang, Zehui; Wang, Kai; Li, Xuankun; Yang, Ding

    2015-02-15

    The Plecoptera (stoneflies) is a hemimetabolous order of insects, whose larvae are usually used as indicators for fresh water biomonitoring. Herein, we describe the complete mitochondrial (mt) genome of a stonefly species, namely Acroneuria hainana Wu belonging to the family Perlidae. This mt genome contains 13 PCGs, 22 tRNA-coding genes and 2 rRNA-coding genes that are conserved in most insect mt genomes, and it also has the identical gene order with the insect ancestral gene order. However, there are three special initiation codons of ND1, ND5 and COI in PCGs: TTG, GTG and CGA, coding for L, V and R, respectively. Additionally, the 899-bp control region, with 73.30% A+T content, has two long repeated sequences which are found at the 3'-end closing to the tRNA(Ile) gene. Both of them can be folded into a stem-loop structure, whose adjacent upstream and downstream sequences can be also folded into stem-loop structures. It is presumed that the four special structures in series could be associated with the D-loop replication. It might be able to adjust the replication speed of two replicate directions. PMID:25499698

  20. Using protein abundance to indicate underlying mRNA expression levels in E. coli: an SEM modelling approach

    PubMed Central

    Harris, Jacqueline J.; Duarte, Christine W.; Mossing, Michael C.

    2012-01-01

    Do steady-state protein levels accurately predict mRNA levels? Based on the central dogma (DNA ? RNA ? protein) current protein levels are representative of mRNA present at an earlier time. However, most cellular mRNA – protein comparative studies try to relate steady-state protein levels to current mRNA levels in cells. Protein steady-states are more correctly related to protein production, protein degradation and other complex cellular conditions. Using Structural Equation Modelling (SEM) we relate linear protein measurements to latent mRNA in E. coli. This method can be used to find the optimal protein measurements that explain underlying mRNA expression, and better understand the proteomic and transcriptomic relationship in E. coli gene expression. PMID:22199038

  1. Single-molecule modeling of mRNA degradation by miRNA: Lessons from data

    PubMed Central

    2015-01-01

    Recent experimental results on the effect of miRNA on the decay of its target mRNA have been analyzed against a previously hypothesized single molecule degradation pathway. According to that hypothesis, the silencing complex (miRISC) first interacts with its target mRNA and then recruits the protein complexes associated with NOT1 and PAN3 to trigger deadenylation (and subsequent degradation) of the target mRNA. Our analysis of the experimental decay patterns allowed us to refine the structure of the degradation pathways at the single molecule level. Surprisingly, we found that if the previously hypothesized network was correct, only about 7% of the target mRNA would be regulated by the miRNA mechanism, which is inconsistent with the available knowledge. Based on systematic data analysis, we propose the alternative hypothesis that NOT1 interacts with miRISC before binding to the target mRNA. Moreover, we show that when miRISC binds alone to the target mRNA, the mRNA is degraded more slowly, probably through a deadenylation-independent pathway. The new biochemical pathway proposed here both fits the data and paves the way for new experimental work to identify new interactions. PMID:26050661

  2. Single-molecule modeling of mRNA degradation by miRNA: Lessons from data

    E-print Network

    Celine Sin; Davide Chiarugi; Angelo Valleriani

    2014-10-20

    Recent experimental results on the effect of miRNA on the decay of its target mRNA have been analyzed against a previously hypothesized single molecule degradation pathway. According to that hypothesis, the silencing complex (miRISC) first interacts with its target mRNA and then recruits the protein complexes associated with NOT1 and PAN3 to trigger deadenylation (and subsequent degradation) of the target mRNA. Our analysis of the experimental decay patterns allowed us to refine the structure of the degradation pathways at the single molecule level. Surprisingly, we found that if the previously hypothesized network was correct, only about 7% of the target mRNA would be regulated by the miRNA mechanism, which is inconsistent with the available knowledge. Based on systematic data analysis, we propose the alternative hypothesis that NOT1 interacts with miRISC before binding to the target mRNA. Moreover, we show that when miRISC binds alone to the target mRNA, the mRNA is degraded more slowly, probably through a deadenylation-independent pathway. The new biochemical pathway we propose both fits the data and paves the way for new experimental work to identify new interactions.

  3. Structural, optical and magnetic properties of Co-doped ZnO nanorods with hidden secondary phases

    Microsoft Academic Search

    Xuefeng Wang; Rongkun Zheng; Zongwen Liu; Ho-pui Ho; Jianbin Xu; Simon P. Ringer

    2008-01-01

    Co-doped ZnO nanorods (composition: Zn0.955Co0.045O) were grown by a simple surfactant-assisted hydrothermal technique. The morphological, structural, optical and magnetic properties of the as-prepared nanorods were investigated by means of scanning electron microscopy, high-resolution transmission electron microscopy, x-ray diffraction, x-ray photoelectron spectroscopy, micro-Raman spectroscopy, micro-cathodoluminescence, and vibrating sample magnetometry (VSM). The results showed that the sample had rod-like morphology and that

  4. The Response of Greek Key Proteins to Changes in Connectivity Depends on the Nature of Their Secondary Structure

    E-print Network

    Kemplen, Katherine R.; De Sancho, David; Clarke, Jane

    2015-04-07

    reductase from Escherichia coli. J Mol Biol 2003;328:273–88. [13] Bulaj G, Koehn RE, Goldenberg DP. Alteration of the disulfide-coupled folding pathway of BPTI by circular permutation. Protein Sci 2004;13:1182–96. [14] Cellitti J, Llinas M, Echols N, Shank... - tivity on the stability and structure of dihydrofolate reductase from E. coli: fragment complementation and circular permu- tation reveal stable, alternatively folded forms. Protein Sci 2000;10:116–28. [16] Mart? ?n-Sierra FM, Candel AM, Casares S...

  5. Fourier Transform Infrared Microspectroscopy Detects Changes in Protein Secondary Structure Associated with Desiccation Tolerance in Developing Maize Embryos1

    PubMed Central

    Wolkers, Willem F.; Bochicchio, Adriana; Selvaggi, Giuseppe; Hoekstra, Folkert A.

    1998-01-01

    Isolated immature maize (Zea mays L.) embryos have been shown to acquire tolerance to rapid drying between 22 and 25 d after pollination (DAP) and to slow drying from 18 DAP onward. To investigate adaptations in protein profile in association with the acquisition of desiccation tolerance in isolated, immature maize embryos, we applied in situ Fourier transform infrared microspectroscopy. In fresh, viable, 20- and 25-DAP embryo axes, the shapes of the different amide-I bands were identical, and this was maintained after flash drying. On rapid drying, the 20-DAP axes had a reduced relative proportion of ?-helical protein structure and lost viability. Rapidly dried 25-DAP embryos germinated (74%) and had a protein profile similar to the fresh control axes. On slow drying, the ?-helical contribution in both the 20- and 25-DAP embryo axes increased compared with that in the fresh control axes, and survival of desiccation was high. The protein profile in dry, mature axes resembled that after slow drying of the immature axes. Rapid drying resulted in an almost complete loss of membrane integrity in the 20-DAP embryo axes and much less so in the 25-DAP axes. After slow drying, low plasma membrane permeability ensued in both the 20- and 25-DAP axes. We conclude that slow drying of excised, immature embryos leads to an increased proportion of ?-helical protein structures in their axes, which coincides with additional tolerance of desiccation stress. PMID:9501150

  6. De novo sequencing and assembly of Centella asiatica leaf transcriptome for mapping of structural, functional and regulatory genes with special reference to secondary metabolism.

    PubMed

    Sangwan, Rajender S; Tripathi, Sandhya; Singh, Jyoti; Narnoliya, Lokesh K; Sangwan, Neelam S

    2013-08-01

    Centella asiatica (L.) Urban is an important medicinal plant and has been used since ancient times in traditional systems of medicine. C. asiatica mainly contains ursane skeleton based triterpenoid sapogenins and saponins predominantly in its leaves. This investigation employed Illumina next generation sequencing (NGS) strategy on a pool of three cDNAs from expanding leaf of C. asiatica and developed an assembled transcriptome sequence resource of the plant. The short transcript reads (STRs) generated and assembled into contigs and singletons, representing majority of the genes expressed in C. asiatica, were termed as 'tentative unique transcripts' (TUTs). The TUT dataset was analyzed with the objectives of (i) development of a transcriptome assembly of C. asiatica, and (ii) classification/characterization of the genes into categories like structural, functional, regulatory etc. based on their function. Overall, 68.49% of the 46,171,131 reads generated in the NGS process could be assembled into a total of 79,041 contigs. Gene ontology and functional annotation of sequences resulted into the identification of genes related to different sets of cellular functions including identification of genes related to primary and secondary metabolism. The wet lab validation of seventeen assembled gene sequences identified to be involved in secondary metabolic pathways and control of reactive oxygen species (ROS) was established by semi-quantitative and real time PCR (qRT-PCR). The validation also included sequencing/size matching of a set of semi-quantitative PCR amplicons with their in silico assembled contig/gene. This confirmed the appropriateness of assembling the reads and contigs. Thus, the present study constitutes the largest report to date on C. asiatica transcriptome based gene resource that may contribute substantially to the understanding of the basal biological functions and biochemical pathways of secondary metabolites as well as the transcriptional regulatory elements and genetic markers. This work sets the stage for multi-faceted future improvement of the plant, through discovery of new genes, marker-assisted breeding or genetic engineering, on this species as well as for other species of Apiaceae and triterpene producing medicinal plants. PMID:23644021

  7. Neuroimaging in Secondary Headache Disorders.

    PubMed

    Chaudhry, Priyanka; Friedman, Deborah I

    2015-07-01

    A secondary headache may develop de novo or in patients with a history of primary headaches, and a thorough history and neurological exam often helps to suspect a secondary etiology. The causes of secondary headaches include tumors, vascular etiologies, structural brain disorders, infection, inflammation, and alterations of cerebrospinal fluid pressure dynamics. Computed tomography (CT) is very sensitive for detecting acute hemorrhage but magnetic resonance imaging (MRI) is preferred over a head CT in subacute and non-emergent cases. Obtaining the correct diagnosis may include incorporation of intravenous contrast agents, special imaging sequences, and functional imaging techniques. PMID:26049776

  8. Implant-supported overdenture manufactured using CAD/CAM techniques to achieve horizontal path insertion between the primary and secondary structure: A clinical case report

    PubMed Central

    Agustín-Panadero, Rubén; Peñarrocha-Oltra, David; Gomar-Vercher, Sonia; Ferreiroa, Alberto

    2015-01-01

    This report describes the case of an edentulous patient with an atrophic maxilla and severe class III malocclusion. Prosthetic rehabilitation was performed using CAD/CAM techniques for manufacturing an implant-supported overdenture with horizontal insertion. A vestibulo-lingual insertion overdenture is a precision prosthesis with a fixation system affording a good fit between the primary and secondary structure. Both structures exhibit passive horizontal adjustment. This treatment option requires the same number of implants as implant-supported fixed dentures. The horizontal assembly system prevents the prosthesis from loosening or moving in response to axial and non-axial forces. The technique was used to rehabilitate a patient presenting an atrophic upper maxilla, with the insertion of 8 implants. No complications were reported at follow-up 3, 6 and 12 months after fitting of the prosthesis. This system offers solutions to the clinical and laboratory complications associated with hybrid prostheses, concealing emergence of the chimneys and improving implant-prosthesis hygiene.

  9. Implant-supported overdenture manufactured using CAD/CAM techniques to achieve horizontal path insertion between the primary and secondary structure: A clinical case report.

    PubMed

    Agustín-Panadero, Rubén; Peñarrocha-Oltra, David; Gomar-Vercher, Sonia; Ferreiroa, Alberto; Peñarrocha-Diago, Miguel

    2015-06-01

    This report describes the case of an edentulous patient with an atrophic maxilla and severe class III malocclusion. Prosthetic rehabilitation was performed using CAD/CAM techniques for manufacturing an implant-supported overdenture with horizontal insertion. A vestibulo-lingual insertion overdenture is a precision prosthesis with a fixation system affording a good fit between the primary and secondary structure. Both structures exhibit passive horizontal adjustment. This treatment option requires the same number of implants as implant-supported fixed dentures. The horizontal assembly system prevents the prosthesis from loosening or moving in response to axial and non-axial forces. The technique was used to rehabilitate a patient presenting an atrophic upper maxilla, with the insertion of 8 implants. No complications were reported at follow-up 3, 6 and 12 months after fitting of the prosthesis. This system offers solutions to the clinical and laboratory complications associated with hybrid prostheses, concealing emergence of the chimneys and improving implant-prosthesis hygiene. PMID:26140179

  10. Role of pH controlled DNA secondary structures in the reversible dispersion/precipitation and separation of metallic and semiconducting single-walled carbon nanotubes

    NASA Astrophysics Data System (ADS)

    Maji, Basudeb; Samanta, Suman K.; Bhattacharya, Santanu

    2014-03-01

    Single-stranded DNA (ss-DNA) oligomers (dA20, d[(C3TA2)3C3] or dT20) are able to disperse single-walled carbon nanotubes (SWNTs) in water at pH 7 through non-covalent wrapping on the nanotube surface. At lower pH, an alteration of the DNA secondary structure leads to precipitation of the SWNTs from the dispersion. The structural change of dA20 takes place from the single-stranded to the A-motif form at pH 3.5 while in case of d[(C3TA2)3C3] the change occurs from the single-stranded to the i-motif form at pH 5. Due to this structural change, the DNA is no longer able to bind the nanotube and hence the SWNT precipitates from its well-dispersed state. However, this could be reversed on restoring the pH to 7, where the DNA again relaxes in the single-stranded form. In this way the dispersion and precipitation process could be repeated over and over again. Variable temperature UV-Vis-NIR and CD spectroscopy studies showed that the DNA-SWNT complexes were thermally stable even at ~90 °C at pH 7. Broadband NIR laser (1064 nm) irradiation also demonstrated the stability of the DNA-SWNT complex against local heating introduced through excitation of the carbon nanotubes. Electrophoretic mobility shift assay confirmed the formation of a stable DNA-SWNT complex at pH 7 and also the generation of DNA secondary structures (A/i-motif) upon acidification. The interactions of ss-DNA with SWNTs cause debundling of the nanotubes from its assembly. Selective affinity of the semiconducting SWNTs towards DNA than the metallic ones enables separation of the two as evident from spectroscopic as well as electrical conductivity studies.Single-stranded DNA (ss-DNA) oligomers (dA20, d[(C3TA2)3C3] or dT20) are able to disperse single-walled carbon nanotubes (SWNTs) in water at pH 7 through non-covalent wrapping on the nanotube surface. At lower pH, an alteration of the DNA secondary structure leads to precipitation of the SWNTs from the dispersion. The structural change of dA20 takes place from the single-stranded to the A-motif form at pH 3.5 while in case of d[(C3TA2)3C3] the change occurs from the single-stranded to the i-motif form at pH 5. Due to this structural change, the DNA is no longer able to bind the nanotube and hence the SWNT precipitates from its well-dispersed state. However, this could be reversed on restoring the pH to 7, where the DNA again relaxes in the single-stranded form. In this way the dispersion and precipitation process could be repeated over and over again. Variable temperature UV-Vis-NIR and CD spectroscopy studies showed that the DNA-SWNT complexes were thermally stable even at ~90 °C at pH 7. Broadband NIR laser (1064 nm) irradiation also demonstrated the stability of the DNA-SWNT complex against local heating introduced through excitation of the carbon nanotubes. Electrophoretic mobility shift assay confirmed the formation of a stable DNA-SWNT complex at pH 7 and also the generation of DNA secondary structures (A/i-motif) upon acidification. The interactions of ss-DNA with SWNTs cause debundling of the nanotubes from its assembly. Selective affinity of the semiconducting SWNTs towards DNA than the metallic ones enables separation of the two as evident from spectroscopic as well as electrical conductivity studies. Electronic supplementary information (ESI) available: Additional UV-Vis-NIR absorption, CD and Raman spectra, zeta potential, AFM, laser irradiation and electrical conductivity data (S1-S15). See DOI: 10.1039/c3nr05045a

  11. Differential regulation of plastid mRNA stability. Progress report

    SciTech Connect

    Stern, D.B.

    1993-09-01

    Our goal is to identify cis-acting sequences and transacting factors that function in plastid mRNA maturation, stabilization, and/or decay through an in vitro and in vivo analysis of mRNA:protein interactions. Our previous results emphasized the study of 3{prime}end inverted repeat sequences (IRs) that serve both as mRNA processing elements and stability determinants, and associate with plastid proteins that potentially play enzymatic, structural and/or regulatory roles. We seek to define, by single base and internal deletion mutagenesis, the sequence and structural requirements for protein binding to the 3{prime} IRs of petD and psbA mRNAs; to purify RNA-binding proteins that demonstrate gene- or sequence-specific binding, or that are implicated in RNA stabilization or decay; and to investigate the native form of mRNA in the plastid, by attempting to purify ribonucleoprotein (RNP) particles from organelles. Our view of mRNA decay is that it is regulated by three interactive components: RNA structure, ribonucleases and RNA-binding proteins. We have used mutagenesis to study the role of RNA structure in regulating RNA decay rates, and to identify protein binding and endonuclease recognition sites. We have identified at least three endonuclease activities; one that cleaves psbA RNA; and two whose cleavage patterns with petD 3{prime} IR-RNA has been studied (endoC1 and endoC2). Additionally, we have continued to analyze the properties of the major RNA processing exoribonuclease. We have concentrated our efforts on three RNA-binding proteins. A 100 kd protein with properties suggestive of a mammalian RNP component has been purified. A protein of 55 kd that may also be an endonuclease has been partially purified. We have studied the interaction of a 29 kd protein with the petD stem/loop, and its role in RNA processing. Recently, we have used a novel gel shift/SDS-PAGE technique to identify new RNA-binding proteins.

  12. Quaternary and secondary structural imaging of a human hair by a VSFG-detected IR super-resolution microscope

    NASA Astrophysics Data System (ADS)

    Sakai, Makoto; Kikuchi, Katsuya; Fujii, Masaaki

    2013-06-01

    IR super-resolution images of cross sections of a human black hair were measured by using a home-made vibrational sum-frequency generation (VSFG) detected IR microscope in the 6-9 ?m region with a sub-micrometer spatial resolution. For the amide III band, the sample gave clear strong signals at the cortex area. This enabled us to measure the distribution of intermediate filaments, which have an ?-helix based quaternary structure of keratin proteins in the hair. On the other hand, the VSFG signal disappeared completely when the amide I band was monitored by the same polarization of incident light. From the polarization dependence of VSFG, it is concluded that the ?-helix of keratin proteins are well aligned along the axial direction in human hair.

  13. Antimicrobial peptides against Pseudomonas syringae pv. actinidiae and Erwinia amylovora: Chemical synthesis, secondary structure, efficacy, and mechanistic investigations.

    PubMed

    Cameron, Alan; Zoysa, Gayan Heruka De; Sarojini, Vijayalekshmi

    2014-01-01

    We report on structurally modified dodecapeptide amides (KYKLFKKILKFL-NH2 ) and two analogs of a hexapeptide amide (WRWYCR-NH2 ) with antibacterial activity against the Gram negative pathogens Pseudomonas syringae pv. actinidiae (Psa) and Erwinia amylovora (Ea). Dodecapeptide minimal inhibitory concentrations (MICs) ranged from 3.2 to 15.4 µM, with the unmodified peptide being the most potent against both pathogens. The unmodified dodecapeptide also had 32-58% ?-helicity in membrane mimetic environments (50% v/v trifluoroethanol and 30 mM SDS micelles). Structural modifications which included branching, acylation, and conjugation with 5-nitro-2-furaldehyde (NFA) proved detrimental to both antimicrobial activity and ?-helicity. Scanning electron microscopy (SEM) revealed distinct morphological changes to bacterial cells treated with the different peptides, leading to blistering of the membrane and cell lysis. MICs of the hexapeptide amide were 3.9-7.7 µM against both pathogens. The hexapeptide acid did not show anti-bacterial activity against either pathogen. However, the NFA conjugated hexapeptide acid was more active than the parent peptide or NFA alone with MICs of 1.6-3.2 µM against the pathogens. SEM analysis revealed shriveling and collapse of bacterial cells treated with the hexapeptide, whereas shortening and compactness on exposure to streptomycin. A colorimetric assay demonstrated that the dodecapeptides were likely to act by targeting the bacterial membrane, whereas the hexapeptides, streptomycin, and NFA were not, thereby supporting the morphological changes observed during SEM. To the best of our knowledge, this appears to be the first report of antimicrobial peptide activity against Psa, a pathogen that is currently devastating the kiwifruit industry internationally. © 2013 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 102: 88-96, 2014. PMID:24122768

  14. Targeting mRNA for Alzheimer's and Related Dementias

    PubMed Central

    2014-01-01

    Brain deposition of the amyloid beta-protein (A?) and tau are characteristic features in Alzheimer's disease (AD). Mutations in the A? precursor protein (APP) and a protease involved in A? production from APP strongly argue for a pathogenic role of A? in AD, while mutations in tau are associated with related disorders collectively called frontotemporal lobar degeneration (FTLD). Despite intense effort, therapeutic strategies that target A? or tau have not yet yielded medications, suggesting that alternative approaches should be pursued. In recent years, our laboratory has studied the role of mRNA in AD and FTLD, specifically those encoding tau and the A?-producing protease BACE1. As many FTLD-causing tau mutations destabilize a hairpin structure that regulates RNA splicing, we have targeted this structure with small molecules, antisense oligonucleotides, and small molecule-antisense conjugates. We have also discovered that microRNA interaction with the 3?-untranslated region of tau regulates tau expression. Regarding BACE1, we found that alternative splicing leads to inactive splice isoforms and antisense oligonucleotides shift splicing toward these inactive isoforms to decrease A? production. In addition, a G-quadruplex structure in the BACE1 mRNA plays a role in splice regulation. The prospects for targeting tau and BACE1 mRNAs as therapeutic strategies will be discussed. PMID:24876993

  15. Effect of multilayer structure on cyclic performance of Si/Fe anode electrode in lithium-ion secondary batteries.

    PubMed

    Kang, Hee-Kook; Lee, Seong-Rae; Cho, Won Il; Won Cho, Byung

    2013-02-01

    A buffer-strengthened Si/Fe multilayer film, consisting of amorphous silicon layers and polycrystalline Fe layers, is investigated as the anode for Li-ion batteries. This film can achieve a stable cycle-life performance with a high capacity. Decreasing the thickness of the Fe layer can lead to a higher capacity, which is related to the fast transport of the Li ion, but the cyclic performance deteriorates with repeated cycling. In contrast, increasing the thickness of the Fe buffer layers and the number of deposit stacks improves the cycle life with high reversibility. Because of the strain in the Si layers suppressed by the primary multilayer structure, the long-term strength is preserved and the substantial fracture toughness is enhanced by the increasing numbers of effective grain boundaries and interfacial layers. In addition, we demonstrate that the Ti underlayer promotes the electrochemical properties in the Si/Fe multilayer for various Fe layer thicknesses because of the enhanced adhesion of the interfacial electrode and current collector. The mechanically optimized Si/Fe multilayer films can have superior cycle-life performances and higher capacities. Notably, the 16-bilayer deposited electrode exhibits an excellent capacity retention of ~95% with ~204 mAh g(-1) over 300 cycles at a 1 C rate. PMID:23235690

  16. A 3?UTR polymorphism modulates mRNA stability of the oncogene and drug target Polo-like Kinase 1

    PubMed Central

    2014-01-01

    Background The Polo-like Kinase 1 (PLK1) protein regulates cell cycle progression and is overexpressed in many malignant tissues. Overexpression is associated with poor prognosis in several cancer entities, whereby expression of PLK1 shows high inter-individual variability. Although PLK1 is extensively studied, not much is known about the genetic variability of the PLK1 gene. The function of PLK1 and the expression of the corresponding gene could be influenced by genomic variations. Hence, we investigated the gene for functional polymorphisms. Such polymorphisms could be useful to investigate whether PLK1 alters the risk for and the course of cancer and they could have an impact on the response to PLK1 inhibitors. Methods The coding region, the 5? and 3?UTRs and the regulatory regions of PLK1 were systematically sequenced. We determined the allele frequencies and genotype distributions of putatively functional SNPs in 120 Caucasians and analyzed the linkage and haplotype structure using Haploview. The functional analysis included electrophoretic mobility shift assay (EMSA) for detected variants of the silencer and promoter regions and reporter assays for a 3?UTR polymorphism. Results Four putatively functional polymorphisms were detected and further analyzed, one in the silencer region (rs57973275), one in the core promoter region (rs16972787), one in intron 3 (rs40076) and one polymorphism in the 3?untranslated region (3?UTR) of PLK1 (rs27770). Alleles of rs27770 display different secondary mRNA structures and showed a distinct allele-dependent difference in mRNA stability with a significantly higher reporter activity of the A allele (p?

  17. A stable RNA G-quadruplex within the 5'-UTR of Arabidopsis thaliana ATR mRNA inhibits translation.

    PubMed

    Kwok, Chun Kit; Ding, Yiliang; Shahid, Saima; Assmann, Sarah M; Bevilacqua, Philip C

    2015-04-01

    Guanine quadruplex structures (GQSs) play important roles in the regulation of gene expression and cellular processes. Recent studies provide strong evidence for the formation and function of DNA and RNA GQSs in human cells. However, whether GQSs form and are functional in plants remains essentially unexplored. On the basis of circular dichroism (CD)-detected titration, UV-detected melting, in-line probing (ILP) and reporter gene assay studies, we report the first example of a plant RNA GQS that inhibits translation. This GQS is located within the 5'-UTR of the ATAXIA TELANGIECTASIA-MUTATED AND RAD3-RELATED (ATR) mRNA of Arabidopsis thaliana (mouse-ear cress). We show that this GQS is highly stable and is thermodynamically favoured over a competing hairpin structure in the 5'-UTR at physiological K? and Mg²? concentrations. Results from ILP reveal the secondary structure of the RNA and support formation of the GQS in vitro in the context of the complete 5'-UTR. Transient reporter gene assays performed in living plants reveal that the GQS inhibits translation but not transcription, implicating this GQS as a translational repressor in vivo. Our results provide the first complete demonstration of the formation and function of a regulatory RNA GQS in plants and open new avenues to explore potential functional roles of GQS in the plant kingdom. PMID:25793418

  18. Structural, computational, and (59)Co NMR studies of primary and secondary amine complexes of Co(III) porphyrins.

    PubMed

    Munro, O Q; Shabalala, S C; Brown, N J

    2001-07-01

    Four novel low-spin bis(amine) Co(III) porphyrins [Co(TPP)(BzNH(2))(2)](SbF(6)), 1, [Co(TPP)(1-BuNH(2))(2)](SbF(6)), 2, [Co(TPP)(PhCH(2)CH(2)NH(2))(2)](SbF(6)), 3, and [Co(TPP)(1-MePipz)(2)](SbF(6)), 4, have been synthesized and characterized by low-temperature X-ray crystallography, IR, electronic, and NMR ((1)H, (13)C, and (59)Co) spectroscopy. The mean Co-N(p) distance for the four structures is 1.986(1) A. The Co-N(ax) distances for the 1 degrees amine derivatives average to 1.980(5) A; the axial bonds of the 2 degrees amine derivative are significantly longer, averaging 2.040(1) A. The porphyrin core conformation of 4 is significantly nonplanar (mixture of S(4)-ruf and D(2d)-sad distortions) due to a staggered arrangement of the axial ligands over the porphyrin core and meso-phenyl group orientations < 90 degrees. The X-ray structures have been used with the coordinates for [Co(TPP)(Pip)(2)](NO(3)) (Scheidt et al. J. Am. Chem. Soc. 1973, 95, 8289-8294.) to parametrize a molecular mechanics (MM) force field for bis(amine) complexes of Co(III) porphyrins. The calculations show that two types of crystal packing interactions (van der Waals and hydrogen bonding) largely control the crystallographically observed conformations. Gas phase conformational energy surfaces have been computed for these complexes by dihedral angle driving methods and augmented with population distributions calculated by MD simulations at 298 K; the calculations demonstrate that the bis(1 degrees amine) complexes are significantly more flexible than the bis(2 degrees amine) analogues. (59)Co NMR spectra have been acquired for a range of [Co(TPP)(amine)(2)]Cl derivatives as a function of temperature. The (59)Co chemical shifts increase linearly with increasing temperature due to population of thermally excited vibrational levels of the (1)A(1) ground state. Activation energies for molecular reorientation (tumbling) have been determined from an analysis of the (59)Co NMR line widths as a function of 1/T; lower barriers exist for the conformationally rigid 2 degrees amine derivatives (2.6-3.8 kJ mol(-1)). The (59)Co chemical shifts vary linearly with the DFT-calculated radial expectation values (3d) for the Co(III) ion. The correlation leads to the following order for the sigma-donor strengths of the axial ligands: BzNH(2) > or = Cl(-) > 1-BuNH(2) > PhCH(2)CH(2)NH(2) > 1-Bu(2)NH > Et(2)NH. The (59)Co NMR line widths are proportional to the square of the DFT-calculated valence electric field gradient at the Co nucleus. Importantly, this is the first computational rationalization of the (59)Co NMR spectra of Co(III) porphyrins. PMID:11421673

  19. Mobile genetic element proliferation and gene inactivation impact over the genome structure and metabolic capabilities of Sodalis glossinidius, the secondary endosymbiont of tsetse flies

    PubMed Central

    2010-01-01

    Background Genome reduction is a common evolutionary process in symbiotic and pathogenic bacteria. This process has been extensively characterized in bacterial endosymbionts of insects, where primary mutualistic bacteria represent the most extreme cases of genome reduction consequence of a massive process of gene inactivation and loss during their evolution from free-living ancestors. Sodalis glossinidius, the secondary endosymbiont of tsetse flies, contains one of the few complete genomes of bacteria at the very beginning of the symbiotic association, allowing to evaluate the relative impact of mobile genetic element proliferation and gene inactivation over the structure and functional capabilities of this bacterial endosymbiont during the transition to a host dependent lifestyle. Results A detailed characterization of mobile genetic elements and pseudogenes reveals a massive presence of different types of prophage elements together with five different families of IS elements that have proliferated across the genome of Sodalis glossinidius at different levels. In addition, a detailed survey of intergenic regions allowed the characterization of 1501 pseudogenes, a much higher number than the 972 pseudogenes described in the original annotation. Pseudogene structure reveals a minor impact of mobile genetic element proliferation in the process of gene inactivation, with most of pseudogenes originated by multiple frameshift mutations and premature stop codons. The comparison of metabolic profiles of Sodalis glossinidius and tsetse fly primary endosymbiont Wiglesworthia glossinidia based on their whole gene and pseudogene repertoires revealed a novel case of pathway inactivation, the arginine biosynthesis, in Sodalis glossinidius together with a possible case of metabolic complementation with Wigglesworthia glossinidia for thiamine biosynthesis. Conclusions The complete re-analysis of the genome sequence of Sodalis glossinidius reveals novel insights in the evolutionary transition from a free-living ancestor to a host-dependent lifestyle, with a massive proliferation of mobile genetic elements mainly of phage origin although with minor impact in the process of gene inactivation that is taking place in this bacterial genome. The metabolic analysis of the whole endosymbiotic consortia of tsetse flies have revealed a possible phenomenon of metabolic complementation between primary and secondary endosymbionts that can contribute to explain the co-existence of both bacterial endosymbionts in the context of the tsetse host. PMID:20649993

  20. New porphyrins bearing pyridyl peripheral groups linked by secondary or tertiary sulfonamide groups: synthesis and structural characterization.

    PubMed

    Manono, Janet; Marzilli, Patricia A; Fronczek, Frank R; Marzilli, Luigi G

    2009-07-01

    New pyridyl meso-tetraarylporphyrins (TArP, Ar = -C(6)H(4)-) of the general formula, T(R(1)R(2)NSO(2)Ar)P (R(1) = N-py-n-CH(2) (n = 2 or 4) and R(2) = CH(3)), have been synthesized by the versatile approach of utilizing meso-tetra(4-chlorosulfonylphenyl)porphyrin. After characterization by mass spectrometry and by visible absorption and (1)H NMR spectroscopy, the porphyrins were converted to various metalloderivatives, including Cu(II) and Zn(II). Treatment of T(N-py-4-CH(2)(CH(3))NSO(2)Ar)P (5) or TpyP(4) (meso-tetra(4-pyridyl)porphyrin) with CH(3)Co(DH)(2)H(2)O (DH = monoanion of dimethylglyoxime) afforded [CH(3)Co(DH)(2)](4)T(N-py-4-CH(2)(CH(3))NSO(2)Ar)P (6) and [CH(3)Co(DH)(2)](4)TpyP(4) (7). Typically, basic pyridines shift the axial methyl (1)H NMR signal of CH(3)Co(DH)(2)L upfield but leave the equatorial methyl signal unshifted. However, both signals for [CH(3)Co(DH)(2)](4)TpyP(4) are approximately 0.2 ppm more downfield than normal, suggesting perhaps an extremely non-basic pyridyl group. However, TpyP(4) forms CH(3)Co(DH)(2)py adducts with binding ability comparable to that of other pyridine ligands with normal basicity and to that of T(N-py-4-CH(2)(CH(3))NSO(2)Ar)P. Consequently, in 7 the deshielding of the methyl signals, even the axial Co-CH(3) signal, is attributed to anisotropy of the porphyrin core. The methyl signals for [CH(3)Co(DH)(2)](4)T(N-py-4-CH(2)(CH(3))NSO(2)Ar)P (6) have normal shifts. The absence of an anisotropic effect is attributable to the large distance of the CH(3)Co(DH)(2) moieties from the porphyrin core caused by the intervening linker in 6. Indeed, the separation led to only a slightly reduced (25%) fluorescence emission of 6 compared to 5, whereas that of 7 is considerably reduced (90%) compared to TpyP(4). The X-ray structures of 5, its Cu(II) complex, and [CH(3)Co(DH)(2)](4)TpyP(4) (7) (all of which have C(i) symmetry) support the spectroscopy. For example, the Co-N(ax) bond lengths of [CH(3)Co(DH)(2)](4)TpyP(4) (2.055(4) and 2.079(4) A) are comparable to that of CH(3)Co(DH)(2)py (2.068(3) A), consistent with the normal coordinating ability of TpyP(4). In an accompanying study, the new pyridylporphyrins have been converted to DNA-binding, water-soluble cationic porphyrins. PMID:19518078