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Sample records for mrna secondary structure

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

    PubMed

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

    2015-10-01

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

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

    PubMed Central

    Fedyunin, Ivan; Ignatova, Zoya

    2015-01-01

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

  3. A potential regulatory role for mRNA secondary structures within the prothrombin 3'UTR.

    PubMed

    Liu, Xingge; Jiang, Yong; Russell, J Eric

    2010-08-01

    The distal 3'UTR of prothrombin mRNA exhibits significant sequence heterogeneity reflecting an inexact 3'-cleavage/polyadenylation reaction. This same region encompasses a single-nucleotide polymorphism that enhances the normal post-transcriptional processing of nascent prothrombin transcripts. Both observations indicate the importance of 3'UTR structures to physiologically relevant properties of prothrombin mRNA. Using a HepG2-based model system, we mapped both the primary structures of reporter mRNAs containing the prothrombin 3'UTR, as well as the secondary structures of common, informative 3'UTR processing variants. A chromatographic method was subsequently employed to assess the effects of structural heterogeneities on the binding of candidate trans-acting regulatory factors. We observed that prothrombin 3'UTRs are constitutively polyadenylated at seven or more positions, and can fold into at least two distinct stem-loop conformations. These alternate structures expose/sequester a consensus binding site for hnRNP-I/PTB-1, a trans-acting factor with post-transcriptional regulatory properties. hnRNP-I/PTB-1 exhibits different affinities for the alternate 3'UTR secondary structures in vitro, predicting a corresponding regulatory role in vivo. These analyses demonstrate a critical link between the structure of the prothrombin 3'UTR and its normal function, providing a basis for further investigations into the molecular pathophysiology of naturally occurring polymorphisms within this region. PMID:20553951

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

    PubMed

    Johnson, Erik; Srivastava, Ranjan

    2013-02-01

    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

  5. Trade-offs between tRNA abundance and mRNA secondary structure support smoothing of translation elongation rate

    PubMed Central

    Gorochowski, Thomas E.; Ignatova, Zoya; Bovenberg, Roel A.L.; Roubos, Johannes A.

    2015-01-01

    Translation of protein from mRNA is a complex multi-step process that occurs at a non-uniform rate. Variability in ribosome speed along an mRNA enables refinement of the proteome and plays a critical role in protein biogenesis. Detailed single protein studies have found both tRNA abundance and mRNA secondary structure as key modulators of translation elongation rate, but recent genome-wide ribosome profiling experiments have not observed significant influence of either on translation efficiency. Here we provide evidence that this results from an inherent trade-off between these factors. We find codons pairing to high-abundance tRNAs are preferentially used in regions of high secondary structure content, while codons read by significantly less abundant tRNAs are located in lowly structured regions. By considering long stretches of high and low mRNA secondary structure in Saccharomyces cerevisiae and Escherichia coli and comparing them to randomized-gene models and experimental expression data, we were able to distinguish clear selective pressures and increased protein expression for specific codon choices. The trade-off between secondary structure and tRNA-concentration based codon choice allows for compensation of their independent effects on translation, helping to smooth overall translational speed and reducing the chance of potentially detrimental points of excessively slow or fast ribosome movement. PMID:25765653

  6. hiCLIP reveals the in vivo atlas of mRNA secondary structures recognized by Staufen 1

    PubMed Central

    Sugimoto, Yoichiro; Vigilante, Alessandra; Darbo, Elodie; Zirra, Alexandra; Militti, Cristina; D’Ambrogio, Andrea; Luscombe, Nicholas M; Ule, Jernej

    2015-01-01

    mRNA structure is important for post-transcriptional regulation, largely because it affects binding of trans-acting factors1. However, little is known about the in vivo structure of full-length mRNAs. Here we present hiCLIP, a high-throughput technique to identify RNA secondary structures interacting with RNA-binding proteins (RBPs) in vivo. Using this technique to investigate RNA structures bound by Staufen 1 (STAU1), we uncover a dominance of intra-molecular RNA duplexes, a depletion of duplexes from coding regions of highly translated mRNAs, an unforeseen prevalence of long-range duplexes in 3? untranslated regions (UTRs), and a decreased incidence of SNPs in duplex-forming regions. We also discover a duplex spanning 858nts in the 3? UTR of the X-box binding Protein 1 (XBP1) mRNA that regulates its cytoplasmic splicing and stability. Our study reveals the fundamental role of mRNA secondary structures in gene regulation and introduces hiCLIP as a widely applicable method for discovering novel, especially long-range, RNA duplexes. PMID:25799984

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

    PubMed

    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. 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

  9. A secondary structure in the 5' untranslated region of adhE mRNA required for RNase G-dependent regulation.

    PubMed

    Ito, Kazutaka; Hamasaki, Kohshin; Kayamori, Aya; Nguyen, Phuong Anh Thi; Amagai, Kaoru; Wachi, Masaaki

    2013-01-01

    Escherichia coli RNase G is involved in the degradation of several mRNAs, including adhE and eno, which encode alcohol dehydrogenase and enolase respectively. Previous research indicates that the 5' untranslated region (5'-UTR) of adhE mRNA gives RNase G-dependency to lacZ mRNA when tagged at the 5'-end, but it has not been elucidated yet how RNase G recognizes adhE mRNA. Primer extension analysis revealed that RNase G cleaved a phosphodiester bond between -19A and -18C in the 5'-UTR (the A of the start codon was defined as +1). Site-directed mutagenesis indicated that RNase G did not recognize the nucleotides at -19 and -18. Random deletion analysis indicated that the sequence from -145 to -125 was required for RNase G-dependent degradation. Secondary structure prediction and further site-directed deletion suggested that the stem-loop structure, with a bubble in the stem, is required for RNaseG-dependent degradation of adhE mRNA. PMID:24317071

  10. The requirement for eukaryotic initiation factor 4A (elF4A) in translation is in direct proportion to the degree of mRNA 5' secondary structure.

    PubMed Central

    Svitkin, Y V; Pause, A; Haghighat, A; Pyronnet, S; Witherell, G; Belsham, G J; Sonenberg, N

    2001-01-01

    Eukaryotic initiation factor (elF) 4A functions as a subunit of the initiation factor complex elF4F, which mediates the binding of mRNA to the ribosome. elF4A possesses ATPase and RNA helicase activities and is the prototype for a large family of putative RNA helicases (the DEAD box family). It is thought that the function of elF4A during translation initiation is to unwind the mRNA secondary structure in the 5' UTR to facilitate ribosome binding. However, the evidence to support this hypothesis is rather indirect, and it was reported that elF4A is also required for the translation of mRNAs possessing minimal 5' UTR secondary structure. Were this hypothesis correct, the requirement for elF4A should correlate with the degree of mRNA secondary structure. To test this hypothesis, the effect of a dominant-negative mutant of mammalian elF4A on translation of mRNAs with various degrees of secondary structure was studied in vitro. Here, we show that mRNAs containing stable secondary structure in the 5' untranslated region are more susceptible to inhibition by the elF4A mutant. The mutant protein also strongly inhibits translation from several picornavirus internal ribosome entry sites (IRES), although to different extents. UV crosslinking of elF4F subunits and elF4B to the mRNA cap structure is dramatically reduced by the elF4A mutant and RNA secondary structure. Finally, the elF4A mutant forms a more stable complex with elF4G, as compared to the wild-type elF4A, thus explaining the mechanism by which substoichiometric amounts of mutant elF4A inhibit translation. PMID:11333019

  11. A Conserved Secondary Structural Element in the Coding Region of the Influenza A Virus Nucleoprotein (NP) mRNA Is Important for the Regulation of Viral Proliferation

    PubMed Central

    Soszynska-Jozwiak, Marta; Michalak, Paula; Moss, Walter N.; Kierzek, Ryszard; Kierzek, Elzbieta

    2015-01-01

    Influenza A virus is a threat to humans due to seasonal epidemics and infrequent, but dangerous, pandemics that lead to widespread infection and death. Eight segments of RNA constitute the genome of this virus and they encode greater than eight proteins via alternative splicing of coding (+)RNAs generated from the genomic (-)RNA template strand. RNA is essential in its life cycle. A bioinformatics analysis of segment 5, which encodes nucleoprotein, revealed a conserved structural motif in the (+)RNA. The secondary structure proposed by energy minimization and comparative analysis agrees with structure predicted based on experimental data using a 121 nucleotide in vitro RNA construct comprising an influenza A virus consensus sequence and also an entire segment 5 (+)RNA (strain A/VietNam/1203/2004 (H5N1)). The conserved motif consists of three hairpins with one being especially thermodynamically stable. The biological importance of this conserved secondary structure is supported in experiments using antisense oligonucleotides in cell line, which found that disruption of this motif led to inhibition of viral fitness. These results suggest that this conserved motif in the segment 5 (+)RNA might be a candidate for oligonucleotide-based antiviral therapy. PMID:26488402

  12. A cis-encoded sRNA, Hfq and mRNA secondary structure act independently to suppress IS200 transposition

    PubMed Central

    Ellis, Michael J.; Trussler, Ryan S.; Haniford, David B.

    2015-01-01

    IS200 is found throughout Enterobacteriaceae and transposes at a notoriously low frequency. In addition to the transposase protein (TnpA), IS200 encodes an uncharacterized Hfq-binding sRNA that is encoded opposite to the tnpA 5'UTR. In the current work we asked if this sRNA represses tnpA expression. We show here that the IS200 sRNA (named art200 for antisense regulator of transposase IS200) basepairs with tnpA to inhibit translation initiation. Unexpectedly, art200-tnpA pairing is limited to 40 bp, despite 90 nt of perfect complementarity. Additionally, we show that Hfq and RNA secondary structure in the tnpA 5'UTR each repress tnpA expression in an art200-independent manner. Finally, we show that disrupting translational control of tnpA expression leads to increased IS200 transposition in E.?coli. The current work provides new mechanistic insight into why IS200 transposition is so strongly suppressed. The possibility of art200 acting in trans to regulate a yet-unidentified target is discussed as well as potential applications of the IS200 system for designing novel riboregulators. PMID:26044710

  13. A cis-encoded sRNA, Hfq and mRNA secondary structure act independently to suppress IS200 transposition.

    PubMed

    Ellis, Michael J; Trussler, Ryan S; Haniford, David B

    2015-07-27

    IS200 is found throughout Enterobacteriaceae and transposes at a notoriously low frequency. In addition to the transposase protein (TnpA), IS200 encodes an uncharacterized Hfq-binding sRNA that is encoded opposite to the tnpA 5'UTR. In the current work we asked if this sRNA represses tnpA expression. We show here that the IS200 sRNA (named art200 for antisense regulator of transposase IS200) basepairs with tnpA to inhibit translation initiation. Unexpectedly, art200-tnpA pairing is limited to 40 bp, despite 90 nt of perfect complementarity. Additionally, we show that Hfq and RNA secondary structure in the tnpA 5'UTR each repress tnpA expression in an art200-independent manner. Finally, we show that disrupting translational control of tnpA expression leads to increased IS200 transposition in E.?coli. The current work provides new mechanistic insight into why IS200 transposition is so strongly suppressed. The possibility of art200 acting in trans to regulate a yet-unidentified target is discussed as well as potential applications of the IS200 system for designing novel riboregulators. PMID:26044710

  14. Statistical correlation between protein secondary structure and messenger RNA stem-loop structure.

    PubMed

    Jia, Mengwen; Luo, Liaofu; Liu, Ciquan

    2004-01-01

    A new integrated sequence-structure database, called IADE (Integrated ASTRAL-DSSP-EMBL), incorporating matching mRNA sequence, amino acid sequence, and protein secondary structural data, is constructed. It includes 648 protein domains. Based on the IADE database, we studied the relation between RNA stem-loop frequencies and protein secondary structure. It was found that the alpha-helices and beta-strands on proteins tend to be preferably "coded" by mRNA stem region, while the coils on proteins tend to be preferably "coded" by mRNA loop region. These tendencies are more obvious if we observe the structural words (SWs). An SW is defined by a four-amino-acid-fragment that shows the pronounced secondary structural (alpha-helix or beta-strand) propensity. It is demonstrated that the deduced correlation between protein and mRNA structure can hardly be explained as the stochastic fluctuation effect. PMID:14691936

  15. Secondary Structure Switch

    ERIC Educational Resources Information Center

    King, Angela G.

    2006-01-01

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

  16. On predicting secondary structure transition.

    PubMed

    Loganantharaj, Raja; Philip, Vivek

    2007-01-01

    A function of a protein is dependent on its structure; therefore, predicting a protein structure from an amino acid sequence is an active area of research. To improve the accuracy of validation of structures, we are studying the predictability of secondary structure transitions using the following machine learning algorithms: naive Bayes, C4.5 decision tree, and random forest. The annotated data sets from PDB that have agreement with DSSP and STRIDE are used for training and testing. We have demonstrated that predicting structure transition with high degree of certainty is possible and we were able to get as high as 97.5% of prediction accuracy. PMID:18048311

  17. Genome-wide probing of RNA structure reveals active unfolding of mRNA structures in vivo

    PubMed Central

    Rouskin, Silvi; Zubradt, Meghan; Washietl, Stefan; Kellis, Manolis; Weissman, Jonathan S.

    2014-01-01

    RNA plays a dual role as an informational molecule and a direct effector of biological tasks. The latter function is enabled by RNA’s ability to adopt complex secondary and tertiary folds and thus has motivated extensive computational1–2 and experimental3–8 efforts for determining RNA structures. Existing approaches for evaluating RNA structure have been largely limited to in vitro systems, yet the thermodynamic forces which drive RNA folding in vitro may not be sufficient to predict stable RNA structures in vivo5. Indeed, the presence of RNA binding proteins and ATP-dependent helicases can influence which structures are present inside cells. Here we present an approach for globally monitoring RNA structure in native conditions in vivo with single nucleotide precision. This method is based on in vivo modification with dimethyl sulfate (DMS), which reacts with unpaired adenine and cytosine residues9, followed by deep sequencing to monitor modifications. Our data from yeast and mammalian cells are in excellent agreement with known mRNA structures and with the high-resolution crystal structure of the Saccharomyces cerevisiae ribosome10. Comparison between in vivo and in vitro data reveals that in rapidly dividing cells there are vastly fewer structured mRNA regions in vivo than in vitro. Even thermostable RNA structures are often denatured in cells, highlighting the importance of cellular processes in regulating RNA structure. Indeed, analysis of mRNA structure under ATP-depleted conditions in yeast reveals that energy-dependent processes strongly contribute to the predominantly unfolded state of mRNAs inside cells. Our studies broadly enable the functional analysis of physiological RNA structures and reveal that, in contrast to the Anfinsen view of protein folding, thermodynamics play an incomplete role in determining mRNA structure in vivo. PMID:24336214

  18. Computational Chemistry with RNA Secondary Structures

    E-print Network

    Stadler, Peter F.

    Computational Chemistry with RNA Secondary Structures Christoph Flamm + , Ivo L. Hofacker + , Peter chemistry of RNA secondary structures using a simplified algorithmic approach for explanation. Keywords: Nucleic Acids, RNA Folding, Structure Prediction, RNA Evolution. 1. Introduction Computational Chemistry

  19. Genome-wide Measurement of RNA Secondary Structure in Yeast

    PubMed Central

    Mazor, Elad; Rinn, John L.; Nutter, Robert C.; Chang, Howard Y.; Segal, Eran

    2013-01-01

    The structures of RNA molecules are often important for their function and regulation1-6, yet there are no experimental techniques for genome-scale measurement of RNA structure. Here, we describe a novel strategy termed Parallel Analysis of RNA Structure (PARS), which is based on deep sequencing fragments of RNAs that were treated with structure-specific enzymes, thus providing simultaneous in-vitro profiling of the secondary structure of thousands of RNA species at single nucleotide resolution. We apply PARS to profile the secondary structure of the mRNAs of the budding yeast S. cerevisiae and obtain structural profiles for over 3000 distinct transcripts. Analysis of these profiles reveals several RNA structural properties of yeast transcripts, including the existence of more secondary structure over coding regions compared to untranslated regions, a three-nucleotide periodicity of secondary structure across coding regions, and a relationship between the efficiency with which an mRNA is translated and the lack of structure over its translation start site. PARS is readily applicable to other organisms and to profiling RNA structure in diverse conditions, thus enabling studies of the dynamics of secondary structure at a genomic scale. PMID:20811459

  20. Computational Chemistry with RNA Secondary Structures

    E-print Network

    Stadler, Peter F.

    Computational Chemistry with RNA Secondary Structures Christoph Flamm , Ivo L. Hofacker , Peter F and in the test tube. In this contribution we review the computational chemistry of RNA secondary structures using become 1 #12;Computational Chemistry with RNA Secondary Structures 2 rather complicated due to the many

  1. Coupling of mRNA Structure Rearrangement to Ribosome Movement during Bypassing of Non-coding Regions.

    PubMed

    Chen, Jin; Coakley, Arthur; O'Connor, Michelle; Petrov, Alexey; O'Leary, Seán E; Atkins, John F; Puglisi, Joseph D

    2015-11-19

    Nearly half of the ribosomes translating a particular bacteriophage T4 mRNA bypass a region of 50 nt, resuming translation 3' of this gap. How this large-scale, specific hop occurs and what determines whether a ribosome bypasses remain unclear. We apply single-molecule fluorescence with zero-mode waveguides to track individual Escherichia coli ribosomes during translation of T4's gene 60 mRNA. Ribosomes that bypass are characterized by a 10- to 20-fold longer pause in a non-canonical rotated state at the take-off codon. During the pause, mRNA secondary structure rearrangements are coupled to ribosome forward movement, facilitated by nascent peptide interactions that disengage the ribosome anticodon-codon interactions for slippage. Close to the landing site, the ribosome then scans mRNA in search of optimal base-pairing interactions. Our results provide a mechanistic and conformational framework for bypassing, highlighting a non-canonical ribosomal state to allow for mRNA structure refolding to drive large-scale ribosome movements. PMID:26590426

  2. Amino acid code of protein secondary structure.

    PubMed

    Shestopalov, B V

    2003-01-01

    The calculation of protein three-dimensional structure from the amino acid sequence is a fundamental problem to be solved. This paper presents principles of the code theory of protein secondary structure, and their consequence--the amino acid code of protein secondary structure. The doublet code model of protein secondary structure, developed earlier by the author (Shestopalov, 1990), is part of this theory. The theory basis are: 1) the name secondary structure is assigned to the conformation, stabilized only by the nearest (intraresidual) and middle-range (at a distance no more than that between residues i and i + 5) interactions; 2) the secondary structure consists of regular (alpha-helical and beta-structural) and irregular (coil) segments; 3) the alpha-helices, beta-strands and coil segments are encoded, respectively, by residue pairs (i, i + 4), (i, i + 2), (i, i = 1), according to the numbers of residues per period, 3.6, 2, 1; 4) all such pairs in the amino acid sequence are codons for elementary structural elements, or structurons; 5) the codons are divided into 21 types depending on their strength, i.e. their encoding capability; 6) overlappings of structurons of one and the same structure generate the longer segments of this structure; 7) overlapping of structurons of different structures is forbidden, and therefore selection of codons is required, the codon selection is hierarchic; 8) the code theory of protein secondary structure generates six variants of the amino acid code of protein secondary structure. There are two possible kinds of model construction based on the theory: the physical one using physical properties of amino acid residues, and the statistical one using results of statistical analysis of a great body of structural data. Some evident consequences of the theory are: a) the theory can be used for calculating the secondary structure from the amino acid sequence as a partial solution of the problem of calculation of protein three-dimensional structure from the amino acid sequence, and the calculated secondary structure and codon strength distribution can be used for simulating the next step of protein folding; b) one can propose that the same secondary structures can be folded into different tertiary structures and, vice versa, different secondary structures can be folded into the same tertiary structures, provided codon distributions are considered also; c) codons can be considered as first elements of protein three-dimensional structure language. PMID:14989164

  3. A balanced secondary structure predictor.

    PubMed

    Nasrul Islam, Md; Iqbal, Sumaiya; Katebi, Ataur R; Tamjidul Hoque, Md

    2016-01-21

    Secondary structure (SS) refers to the local spatial organization of a polypeptide backbone atoms of a protein. Accurate prediction of SS can provide crucial features to form the next higher level of 3D structure of a protein accurately. SS has three different major components, helix (H), beta (E) and coil (C). Most of the SS predictors express imbalanced accuracies by claiming higher prediction performances in predicting H and C, and on the contrary having low accuracy in E predictions. E component being in low count, a predictor may show very good overall performance by over-predicting H and C and under predicting E, which can make such predictors biologically inapplicable. In this work we are motivated to develop a balanced SS predictor by incorporating 33 physicochemical properties into 15-tuble peptides via Chou?s general PseAAC, which allowed obtaining higher accuracies in predicting all three SS components. Our approach uses three different support vector machines for binary classification of the major classes and then form optimized multiclass predictor using genetic algorithm (GA). The trained three binary SVMs are E versus non-E (i.e., E/¬E), C/¬C and H/¬H. This GA based optimized and combined three class predictor, called cSVM, is further combined with SPINE X to form the proposed final balanced predictor, called MetaSSPred. This novel paradigm assists us in optimizing the precision and recall. We prepared two independent test datasets (CB471 and N295) to compare the performance of our predictors with SPINE X. MetaSSPred significantly increases beta accuracy (QE) for both the datasets. QE score of MetaSSPred on CB471 and N295 were 71.7% and 74.4% respectively. These scores are 20.9% and 19.0% improvement over the QE scores given by SPINE X alone on CB471 and N295 datasets respectively. Standard deviations of the accuracies across three SS classes of MetaSSPred on CB471 and N295 datasets were 4.2% and 2.3% respectively. On the other hand, for SPINE X, these values are 12.9% and 10.9% respectively. These findings suggest that the proposed MetaSSPred is a well-balanced SS predictor compared to the state-of-the-art SPINE X predictor. PMID:26549467

  4. The peptidyl-prolyl isomerase Pin1 determines parathyroid hormone mRNA levels and stability in rat models of secondary hyperparathyroidism

    PubMed Central

    Nechama, Morris; Uchida, Takafumi; Mor Yosef-Levi, Irit; Silver, Justin; Naveh-Many, Tally

    2009-01-01

    Secondary hyperparathyroidism is a major complication of chronic kidney disease (CKD). In experimental models of secondary hyperparathyroidism induced by hypocalcemia or CKD, parathyroid hormone (PTH) mRNA levels increase due to increased PTH mRNA stability. K-homology splicing regulator protein (KSRP) decreases the stability of PTH mRNA upon binding a cis-acting element in the PTH mRNA 3? UTR region. As the peptidyl-prolyl isomerase (PPIase) Pin1 has recently been shown to regulate the turnover of multiple cytokine mRNAs, we investigated the role of Pin1 in regulating PTH mRNA stability in rat parathyroids and transfected cells. The data generated were consistent with Pin1 being a PTH mRNA destabilizing protein. Initial analysis indicated that Pin1 activity was decreased in parathyroid protein extracts from both hypocalcemic and CKD rats and that pharmacologic inhibition of Pin1 increased PTH mRNA levels posttranscriptionally in rat parathyroid and in transfected cells. Pin1 mediated its effects via interaction with KSRP, which led to KSRP dephosphorylation and activation. In the rat parathyroid, Pin1 inhibition decreased KSRP–PTH mRNA interactions, increasing PTH mRNA levels. Furthermore, Pin1–/– mice displayed increased serum PTH and PTH mRNA levels, suggesting that Pin1 determines basal PTH expression in vivo. These results demonstrate that Pin1 is a key mediator of PTH mRNA stability and indicate a role for Pin1 in the pathogenesis of secondary hyperparathyroidism in individuals with CKD. PMID:19770516

  5. Protein secondary structure prediction with SPARROW.

    PubMed

    Bettella, Francesco; Rasinski, Dawid; Knapp, Ernst Walter

    2012-02-27

    A first step toward predicting the structure of a protein is to determine its secondary structure. The secondary structure information is generally used as starting point to solve protein crystal structures. In the present study, a machine learning approach based on a complete set of two-class scoring functions was used. Such functions discriminate between two specific structural classes or between a single specific class and the rest. The approach uses a hierarchical scheme of scoring functions and a neural network. The parameters are determined by optimizing the recall of learning data. Quality control is performed by predicting separate independent test data. A first set of scoring functions is trained to correlate the secondary structures of residues with profiles of sequence windows of width 15, centered at these residues. The sequence profiles are obtained by multiple sequence alignment with PSI-BLAST. A second set of scoring functions is trained to correlate the secondary structures of the center residues with the secondary structures of all other residues in the sequence windows used in the first step. Finally, a neural network is trained using the results from the second set of scoring functions as input to make a decision on the secondary structure class of the residue in the center of the sequence window. Here, we consider the three-class problem of helix, strand, and other secondary structures. The corresponding prediction scheme "SPARROW" was trained with the ASTRAL40 database, which contains protein domain structures with less than 40% sequence identity. The secondary structures were determined with DSSP. In a loose assignment, the helix class contains all DSSP helix types (?, 3-10, ?), the strand class contains ?-strand and ?-bridge, and the third class contains the other structures. In a tight assignment, the helix and strand classes contain only ?-helix and ?-strand classes, respectively. A 10-fold cross validation showed less than 0.8% deviation in the fraction of correct structure assignments between true prediction and recall of data used for training. Using sequences of 140,000 residues as a test data set, 80.46% ± 0.35% of secondary structures are predicted correctly in the loose assignment, a prediction performance, which is very close to the best results in the field. Most applications are done with the loose assignment. However, the tight assignment yields 2.25% better prediction performance. With each individual prediction, we also provide a confidence measure providing the probability that the prediction is correct. The SPARROW software can be used and downloaded on the Web page http://agknapp.chemie.fu-berlin.de/sparrow/ . PMID:22224407

  6. Secondary structural predictions for the clostridial neurotoxins.

    PubMed

    Lebeda, F J; Olson, M A

    1994-12-01

    The primary structures of a family of ten clostridial neurotoxins have recently been deduced yet little information is presently available concerning their secondary or tertiary structures. Because the overall similarity percentage of multiply aligned sequences is high, the secondary structures of these metalloendopeptidases are also expected to be conserved. The neural net program, PHD (Rost and Sander, Proc. Natl. Acad. Sci. USA 90:7558-7562, 1993), predicted that the secondary structures of the neurotoxins were indeed conserved in both single and multiple sequence modes of analysis. Predictions for the amounts of helical, extended, and loop states from the single sequence analyses were consistent with previously published data from circular dichroism studies on some of these neurotoxins. In the single analysis mode, only the aligned regions were predicted to show conservation of the three-state structure. In contrast, the multiple sequence analysis predicted that a conserved state (variable loops) also exists in non-aligned regions. Alignments with the primary structure of the prototypic metalloendopeptidase thermolysin showed that about 25% of the residues within this enzyme are similar to those in the neurotoxins. A comparison of thermolysin's known secondary structure with the predictions from this study showed that about 80% of thermolysin's residues could be structurally aligned with those in the neurotoxins. These predictions provide the necessary framework to build a homologous low-resolution tertiary structure of the neurotoxin active site that will be essential in the development of synthetic inhibitors. PMID:7731948

  7. Continuum secondary structure captures protein flexibility.

    PubMed

    Andersen, Claus A F; Palmer, Arthur G; Brunak, Sřren; Rost, Burkhard

    2002-02-01

    The DSSP program assigns protein secondary structure to one of eight states. This discrete assignment cannot describe the continuum of thermal fluctuations. Hence, a continuous assignment is proposed. Technically, the continuum results from averaging over ten discrete DSSP assignments with different hydrogen bond thresholds. The final continuous assignment for a single NMR model successfully reflected the structural variations observed between all NMR models in the ensemble. The structural variations between NMR models were verified to correlate with thermal motion; these variations were captured by the continuous assignments. Because the continuous assignment reproduces the structural variation between many NMR models from one single model, functionally important variation can be extracted from a single X-ray structure. Thus, continuous assignments of secondary structure may affect future protein structure analysis, comparison, and prediction. PMID:11839303

  8. A conserved secondary structure for telomerase RNA.

    PubMed

    Romero, D P; Blackburn, E H

    1991-10-18

    The RNA moiety of the ribonucleoprotein enzyme telomerase contains the template for telomeric DNA synthesis. We present a secondary structure model for telomerase RNA, derived by a phylogenetic comparative analysis of telomerase RNAs from seven tetrahymenine ciliates. The telomerase RNA genes from Tetrahymena malaccensis, T. pyriformis, T. hyperangularis, T. pigmentosa, T. hegewishii, and Glaucoma chattoni were cloned, sequenced, and compared with the previously cloned RNA gene from T. thermophila and with each other. To define secondary structures of these RNAs, homologous complementary sequences were identified by the occurrence of covariation among putative base pairs. Although their primary sequences have diverged rapidly overall, a strikingly conserved secondary structure was identified for all these telomerase RNAs. Short regions of nucleotide conservation include a block of 22 totally conserved nucleotides that contains the telomeric templating region. PMID:1840508

  9. The structure of the SOLE element of oskar mRNA

    PubMed Central

    Simon, Bernd; Masiewicz, Pawel; Ephrussi, Anne; Carlomagno, Teresa

    2015-01-01

    mRNA localization by active transport is a regulated process that requires association of mRNPs with protein motors for transport along either the microtubule or the actin cytoskeleton. oskar mRNA localization at the posterior pole of the Drosophila oocyte requires a specific mRNA sequence, termed the SOLE, which comprises nucleotides of both exon 1 and exon 2 and is assembled upon splicing. The SOLE folds into a stem–loop structure. Both SOLE RNA and the exon junction complex (EJC) are required for oskar mRNA transport along the microtubules by kinesin. The SOLE RNA likely constitutes a recognition element for a yet unknown protein, which either belongs to the EJC or functions as a bridge between the EJC and the mRNA. Here, we determine the solution structure of the SOLE RNA by Nuclear Magnetic Resonance spectroscopy. We show that the SOLE forms a continuous helical structure, including a few noncanonical base pairs, capped by a pentanucleotide loop. The helix displays a widened major groove, which could accommodate a protein partner. In addition, the apical helical segment undergoes complex dynamics, with potential functional significance. PMID:26089324

  10. The structure of the SOLE element of oskar mRNA.

    PubMed

    Simon, Bernd; Masiewicz, Pawel; Ephrussi, Anne; Carlomagno, Teresa

    2015-08-01

    mRNA localization by active transport is a regulated process that requires association of mRNPs with protein motors for transport along either the microtubule or the actin cytoskeleton. oskar mRNA localization at the posterior pole of the Drosophila oocyte requires a specific mRNA sequence, termed the SOLE, which comprises nucleotides of both exon 1 and exon 2 and is assembled upon splicing. The SOLE folds into a stem-loop structure. Both SOLE RNA and the exon junction complex (EJC) are required for oskar mRNA transport along the microtubules by kinesin. The SOLE RNA likely constitutes a recognition element for a yet unknown protein, which either belongs to the EJC or functions as a bridge between the EJC and the mRNA. Here, we determine the solution structure of the SOLE RNA by Nuclear Magnetic Resonance spectroscopy. We show that the SOLE forms a continuous helical structure, including a few noncanonical base pairs, capped by a pentanucleotide loop. The helix displays a widened major groove, which could accommodate a protein partner. In addition, the apical helical segment undergoes complex dynamics, with potential functional significance. PMID:26089324

  11. The mRNA of the translationally controlled tumor protein P23/TCTP is a highly structured RNA, which activates the dsRNA-dependent protein kinase PKR.

    PubMed Central

    Bommer, Ulrich-Axel; Borovjagin, Anton V; Greagg, Martin A; Jeffrey, Ian W; Russell, Paul; Laing, Kenneth G; Lee, Melanie; Clemens, Michael J

    2002-01-01

    The dsRNA-activated protein kinase PKR is involved in signal transduction pathways that mediate cellular processes as diverse as cell growth and differentiation, the stress response, and apoptosis. PKR was originally described as an interferon-inducible elF2alpha kinase involved in the antiviral defense mechanism of the cell. The interaction of the kinase with specific viral RNAs has been studied in much detail, but information about cellular mRNAs, which are able to bind and activate PKR, is scarce. In search for such cellular mRNAs, we developed a cloning strategy to identify individual mRNA species from the dsRNA-rich fraction of Daudi cell poly(A)+ RNA. Two out of five cDNA clones we obtained contained sequences derived from the mRNA of the translationally controlled tumor protein P23/TCTP, indicating that this mRNA is present in the dsRNA-rich fraction. Secondary structure predictions and gel electrophoretic mobility investigations on P23/TCTP transcripts confirmed the potential of this mRNA to form extensive secondary structure. A full-length P23 transcript, but not a truncated version thereof, was able to bind to PKR in vitro and in vivo. Transient transfection experiments in human 293 cells showed that coexpression of full-length P23 mRNA leads to partial inhibition of the expression of a beta-galactosidase reporter gene in trans. Additional coexpression of a dominant negative mutant of PKR or of adenovirus VA1 RNA suppressed this inhibition, indicating that it is mediated by PKR. Studies on P23/TCTP expression in cells from PKR-knockout mice suggest that P23/TCTP mRNA translation is regulated by PKR. Hence, our results demonstrate that the mRNA of P23/TCTP may both activate PKR and be subject to translational regulation by this kinase. PMID:11991642

  12. DSSPcont: Continuous secondary structure assignments for proteins.

    PubMed

    Carter, Phil; Andersen, Claus A F; Rost, Burkhard

    2003-07-01

    The DSSP program automatically assigns the secondary structure for each residue from the three-dimensional co-ordinates of a protein structure to one of eight states. However, discrete assignments are incomplete in that they cannot capture the continuum of thermal fluctuations. Therefore, DSSPcont (http://cubic.bioc.columbia.edu/services/DSSPcont) introduces a continuous assignment of secondary structure that replaces 'static' by 'dynamic' states. Technically, the continuum results from calculating weighted averages over 10 discrete DSSP assignments with different hydrogen bond thresholds. A DSSPcont assignment for a particular residue is a percentage likelihood of eight secondary structure states, derived from a weighted average of the ten DSSP assignments. The continuous assignments have two important features: (i) they reflect the structural variations due to thermal fluctuations as detected by NMR spectroscopy; and (ii) they reproduce the structural variation between many NMR models from one single model. Therefore, functionally important variation can be extracted from a single X-ray structure using the continuous assignment procedure. PMID:12824310

  13. Cost Structure of Post-Secondary Education

    E-print Network

    12-2013 Cost Structure of Post- Secondary Education Guide to Making Activity-Based Costing: Executive Summary The higher education industry and its observers have wrung hands over rising costs for years. While there are many reasons for escalating costs, there is at least one that higher education

  14. Recycling Secondary Index Structures Paul M. Aoki

    E-print Network

    Aoki, Paul M.

    Recycling Secondary Index Structures * Paul M. Aoki Department of Electrical Engineering. For example, distributed database systems move or copy tables between sites to optimize data placement, means that data layout optimization has been considered expensive as well. In this paper, we present

  15. 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.

  16. 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

  17. The ribosome structure controls and directs mRNA entry, translocation and exit dynamics

    NASA Astrophysics Data System (ADS)

    Kurkcuoglu, Ozge; Doruker, Pemra; Sen, Taner Z.; Kloczkowski, Andrzej; Jernigan, Robert L.

    2008-12-01

    The protein-synthesizing ribosome undergoes large motions to effect the translocation of tRNAs and mRNA; here, the domain motions of this system are explored with a coarse-grained elastic network model using normal mode analysis. Crystal structures are used to construct various model systems of the 70S complex with/without tRNA, elongation factor Tu and the ribosomal proteins. Computed motions reveal the well-known ratchet-like rotational motion of the large subunits, as well as the head rotation of the small subunit and the high flexibility of the L1 and L7/L12 stalks, even in the absence of ribosomal proteins. This result indicates that these experimentally observed motions during translocation are inherently controlled by the ribosomal shape and only partially dependent upon GTP hydrolysis. Normal mode analysis further reveals the mobility of A- and P-tRNAs to increase in the absence of the E-tRNA. In addition, the dynamics of the E-tRNA is affected by the absence of the ribosomal protein L1. The mRNA in the entrance tunnel interacts directly with helicase proteins S3 and S4, which constrain the mRNA in a clamp-like fashion, as well as with protein S5, which likely orients the mRNA to ensure correct translation. The ribosomal proteins S7, S11 and S18 may also be involved in assuring translation fidelity by constraining the mRNA at the exit site of the channel. The mRNA also interacts with the 16S 3' end forming the Shine-Dalgarno complex at the initiation step; the 3' end may act as a 'hook' to reel in the mRNA to facilitate its exit.

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

    PubMed Central

    Kanehisa, M I; Goad, W B

    1982-01-01

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

  19. Capped mRNAs with reduced secondary structure can function in extracts from poliovirus-infected cells

    SciTech Connect

    Sonenberg, N.; Guertin, D.; Lee, K.A.W.

    1982-12-01

    Extracts form 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, the authors 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 mosiac virus 4 RNA, which is most probable 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.

  20. Protein secondary structure: category assignment and predictability.

    PubMed

    Andersen, C A; Bohr, H; Brunak, S

    2001-10-19

    In the last decade, the prediction of protein secondary structure has been optimized using essentially one and the same assignment scheme known as DSSP. We present here a different scheme, which is more predictable. This scheme predicts directly the hydrogen bonds, which stabilize the secondary structures. Single sequence prediction of the new three category assignment gives an overall prediction improvement of 3.1% and 5.1% compared to the DSSP assignment and schemes where the helix category consists of alpha-helix and 3(10)-helix, respectively. These results were achieved using a standard feed-forward neural network with one hidden layer on a data set identical to the one used in earlier work. PMID:11682049

  1. 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

  2. Secondary flow structures in large rivers

    NASA Astrophysics Data System (ADS)

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

    2012-04-01

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

  3. An intronic RNA structure modulates expression of the mRNA biogenesis factor Sus1

    PubMed Central

    AbuQattam, Ali; Gallego, José; Rodríguez-Navarro, Susana

    2016-01-01

    Sus1 is a conserved protein involved in chromatin remodeling and mRNA biogenesis. Unlike most yeast genes, the SUS1 pre-mRNA of Saccharomyces cerevisiae contains two introns and is alternatively spliced, retaining one or both introns in response to changes in environmental conditions. SUS1 splicing may allow the cell to control Sus1 expression, but the mechanisms that regulate this process remain unknown. Using in silico analyses together with NMR spectroscopy, gel electrophoresis, and UV thermal denaturation experiments, we show that the downstream intron (I2) of SUS1 forms a weakly stable, 37-nucleotide stem–loop structure containing the branch site near its apical loop and the 3? splice site after the stem terminus. A cellular assay revealed that two of four mutants containing altered I2 structures had significantly impaired SUS1 expression. Semiquantitative RT-PCR experiments indicated that all mutants accumulated unspliced SUS1 pre-mRNA and/or induced distorted levels of fully spliced mRNA relative to wild type. Concomitantly, Sus1 cellular functions in histone H2B deubiquitination and mRNA export were affected in I2 hairpin mutants that inhibited splicing. This work demonstrates that I2 structure is relevant for SUS1 expression, and that this effect is likely exerted through modulation of splicing. PMID:26546116

  4. An intronic RNA structure modulates expression of the mRNA biogenesis factor Sus1.

    PubMed

    AbuQattam, Ali; Gallego, José; Rodríguez-Navarro, Susana

    2016-01-01

    Sus1 is a conserved protein involved in chromatin remodeling and mRNA biogenesis. Unlike most yeast genes, the SUS1 pre-mRNA of Saccharomyces cerevisiae contains two introns and is alternatively spliced, retaining one or both introns in response to changes in environmental conditions. SUS1 splicing may allow the cell to control Sus1 expression, but the mechanisms that regulate this process remain unknown. Using in silico analyses together with NMR spectroscopy, gel electrophoresis, and UV thermal denaturation experiments, we show that the downstream intron (I2) of SUS1 forms a weakly stable, 37-nucleotide stem-loop structure containing the branch site near its apical loop and the 3' splice site after the stem terminus. A cellular assay revealed that two of four mutants containing altered I2 structures had significantly impaired SUS1 expression. Semiquantitative RT-PCR experiments indicated that all mutants accumulated unspliced SUS1 pre-mRNA and/or induced distorted levels of fully spliced mRNA relative to wild type. Concomitantly, Sus1 cellular functions in histone H2B deubiquitination and mRNA export were affected in I2 hairpin mutants that inhibited splicing. This work demonstrates that I2 structure is relevant for SUS1 expression, and that this effect is likely exerted through modulation of splicing. PMID:26546116

  5. Translation with secondary structure: Dynamic blockages in totally asymmetric simple exclusion process

    NASA Astrophysics Data System (ADS)

    Shaw, Leah

    2011-03-01

    The totally asymmetric simple exclusion process (TASEP) is often used as a model for protein synthesis, with the lattice and particles representing the mRNA and ribosomes, respectively. Here we model the effect of secondary structure (folding) of the mRNA by introducing a dynamic blockage region in the lattice. If the region is unoccupied by particles, the blockage can close and prevent upstream particles from moving into it, representing the folding of that section of mRNA. Reopening of the blockage, allowing particles to pass, represents unfolding. We study the effects of the blockage size, closing/opening probabilities, and TASEP parameters on the particle current and blockage switching rates.

  6. Co-evolution of Bacterial Ribosomal Protein S15 with Diverse mRNA Regulatory Structures

    PubMed Central

    Slinger, Betty L.; Newman, Hunter; Lee, Younghan; Pei, Shermin; Meyer, Michelle M.

    2015-01-01

    RNA-protein interactions are critical in many biological processes, yet how such interactions affect the evolution of both partners is still unknown. RNA and protein structures are impacted very differently by mechanisms of genomic change. While most protein families are identifiable at the nucleotide level across large phylogenetic distances, RNA families display far less nucleotide similarity and are often only shared by closely related bacterial species. Ribosomal protein S15 has two RNA binding functions. First, it is a ribosomal protein responsible for organizing the rRNA during ribosome assembly. Second, in many bacterial species S15 also interacts with a structured portion of its own transcript to negatively regulate gene expression. While the first interaction is conserved in most bacteria, the second is not. Four distinct mRNA structures interact with S15 to enable regulation, each of which appears to be independently derived in different groups of bacteria. With the goal of understanding how protein-binding specificity may influence the evolution of such RNA regulatory structures, we examine whether examples of these mRNA structures are able to interact with, and regulate in response to, S15 homologs from organisms containing distinct mRNA structures. We find that despite their shared RNA binding function in the rRNA, S15 homologs have distinct RNA recognition profiles. We present a model to explain the specificity patterns observed, and support this model by with further mutagenesis. After analyzing the patterns of conservation for the S15 protein coding sequences, we also identified amino acid changes that alter the binding specificity of an S15 homolog. In this work we demonstrate that homologous RNA-binding proteins have different specificity profiles, and minor changes to amino acid sequences, or to RNA structural motifs, can have large impacts on RNA-protein recognition. PMID:26675164

  7. 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

  8. Polymorphisms within the COL5A1 3'-UTR that alters mRNA structure and the MIR608 gene are associated with Achilles tendinopathy.

    PubMed

    Abrahams, Yoonus; Laguette, Mary-Jessica; Prince, Sharon; Collins, Malcolm

    2013-05-01

    COL5A1 encodes for the ?1 chain of type V collagen, an important regulator of fibril assembly in tendons, ligaments and other connective tissues. A polymorphism (rs12722) within the functional COL5A1 3'-untranslated region (UTR) has been shown to associate with chronic Achilles tendinopathy and other exercise-related phenotypes. The COL5A1 3'-UTR contains several putative cis-acting elements including a functional Hsa-miR-608 binding site. The aim of this study was to determine whether previously uncharacterized polymorphisms within a functional region of the COL5A1 3'-UTR or the MIR608 gene are associated with chronic Achilles tendinopathy. The effect of these COL5A1 3'-UTR polymorphisms on the 3'-UTR predicted mRNA secondary structure was also investigated. One hundred and sixty Caucasian chronic Achilles tendinopathic and 342 control participants were genotyped for the COL5A1 3'-UTR markers rs71746744, rs16399 and rs1134170, as well as marker rs4919510 within MIR608. All four genetic markers were independently associated with chronic Achilles tendinopathy. The COL5A1 polymorphisms appear to alter the predicted secondary structure of the 3'-UTR. We propose that the secondary structure plays a role in the regulation of the COL5A1 mRNA stability and by implication type V collagen production. PMID:23347277

  9. Regulation of cytochrome P450 mRNA expression in primary porcine hepatocytes by selected secondary plant metabolites from chicory (Cichorium intybus L.).

    PubMed

    Rasmussen, Martin Krřyer; Klausen, Christina Lindgaard; Ekstrand, Bo

    2014-03-01

    Chicory (Cichorium intybus) has been shown to induce enzymes of pharmacokinetic relevance (cytochrome P450; CYP). The aim of this study was to investigate the effects of selected secondary plant metabolites with a global extract of chicory root, on the expression of hepatic CYP mRNA (1A2, 2A19, 2C33, 2D25, 2E1 and 3A29), using primary porcine hepatocytes. Of the tested secondary plant metabolites, artemisinin, scoparone, lactucin and esculetin all induced increased expression of specific CYPs, while esculin showed no effect. In contrast, a global extract of chicory root decreased the expression of CYP1A2, 2C33, 2D25 and 3A29 at high concentrations. The results suggest that purified secondary metabolites from chicory affect CYP expression and thereby might affect detoxification in general, and that global extracts of plants can have effects different from individual components. PMID:24176340

  10. Enumeration of Secondary Structure Element Bundles

    SciTech Connect

    2004-10-26

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

  11. 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).

    PubMed

    Grünewald, K; Eckert, M; Hirschberg, J; Hagen, C

    2000-04-01

    The unicellular green alga Haematococcus pluvialis Flotow is known for its massive accumulation of ketocarotenoids under various stress conditions. Therefore, this microalga is one of the favored organisms for biotechnological production of these antioxidative compounds. Astaxanthin makes up the main part of the secondary carotenoids and is accumulated mostly in an esterified form in extraplastidic lipid vesicles. We have studied phytoene desaturase, an early enzyme of the carotenoid biosynthetic pathway. The increase in the phytoene desaturase protein levels that occurs following induction is accompanied by a corresponding increase of its mRNA during the accumulation period, indicating that phytoene desaturase is regulated at the mRNA level. We also investigated the localization of the enzyme by western-blot analysis of cell fractions and by immunogold labeling of ultrathin sections for electron microscopy. In spite of the fact that secondary carotenoids accumulate outside the chloroplast, no extra pathway specific for secondary carotenoid biosynthesis in H. pluvialis was found, at least at this early stage in the biosynthesis. A transport process of carotenoids from the site of biosynthesis (chloroplast) to the site of accumulation (cytoplasmatic located lipid vesicles) is implicated. PMID:10759523

  12. A Bayesian Model for Protein Secondary Structure Prediction

    E-print Network

    Dahl, David B.

    Structure (DSSP) for protein secondary structure with single letter codes. We consider the following 4 block types (in italics) from the original 8 structures defined in DSSP (in parentheses): 1. Helix "H": 310

  13. 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

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

    PubMed

    Ellington, Roni; Wachira, James; Nkwanta, Asamoah

    2010-01-01

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

  15. RNAstructure: Web servers for RNA secondary structure prediction and analysis.

    PubMed

    Bellaousov, Stanislav; Reuter, Jessica S; Seetin, Matthew G; Mathews, David H

    2013-07-01

    RNAstructure is a software package for RNA secondary structure prediction and analysis. This contribution describes a new set of web servers to provide its functionality. The web server offers RNA secondary structure prediction, including free energy minimization, maximum expected accuracy structure prediction and pseudoknot prediction. Bimolecular secondary structure prediction is also provided. Additionally, the server can predict secondary structures conserved in either two homologs or more than two homologs. Folding free energy changes can be predicted for a given RNA structure using nearest neighbor rules. Secondary structures can be compared using circular plots or the scoring methods, sensitivity and positive predictive value. Additionally, structure drawings can be rendered as SVG, postscript, jpeg or pdf. The web server is freely available for public use at: http://rna.urmc.rochester.edu/RNAstructureWeb. PMID:23620284

  16. Enumeration of Secondary Structure Element Bundles

    Energy Science and Technology Software Center (ESTSC)

    2004-10-26

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

  17. Widespread signatures of local mRNA folding structure selection in four Dengue virus serotypes

    PubMed Central

    2015-01-01

    Background It is known that mRNA folding can affect and regulate various gene expression steps both in living organisms and in viruses. Previous studies have recognized functional RNA structures in the genome of the Dengue virus. However, these studies usually focused either on the viral untranslated regions or on very specific and limited regions at the beginning of the coding sequences, in a limited number of strains, and without considering evolutionary selection. Results Here we performed the first large scale comprehensive genomics analysis of selection for local mRNA folding strength in the Dengue virus coding sequences, based on a total of 1,670 genomes and 4 serotypes. Our analysis identified clusters of positions along the coding regions that may undergo a conserved evolutionary selection for strong or weak local folding maintained across different viral variants. Specifically, 53-66 clusters for strong folding and 49-73 clusters for weak folding (depending on serotype) aggregated of positions with a significant conservation of folding energy signals (related to partially overlapping local genomic regions) were recognized. In addition, up to 7% of these positions were found to be conserved in more than 90% of the viral genomes. Although some of the identified positions undergo frequent synonymous / non-synonymous substitutions, the selection for folding strength therein is preserved, and thus cannot be trivially explained based on sequence conservation alone. Conclusions The fact that many of the positions with significant folding related signals are conserved among different Dengue variants suggests that a better understanding of the mRNA structures in the corresponding regions may promote the development of prospective anti- Dengue vaccination strategies. The comparative genomics approach described here can be employed in the future for detecting functional regions in other pathogens with very high mutations rates. PMID:26449467

  18. SCFGs in RNA secondary structure prediction RNA secondary structure prediction: a hands-on approach.

    PubMed

    Sükösd, Zsuzsanna; Andersen, Ebbe S; Lyngsř, Rune

    2014-01-01

    Stochastic context-free grammars (SCFGs) were first established in the context of natural language modelling, and only later found their applications in RNA secondary structure prediction. In this chapter, we discuss the basic SCFG algorithms (CYK and inside-outside algorithms) in an application-centered manner and use the pfold grammar as a case study to show how the algorithms can be adapted to a grammar in a nonstandard form. We extend our discussion to the use of grammars with additional information (such as evolutionary information) to improve the quality of predictions. Finally, we provide a brief survey of programs that use stochastic context-free grammars for RNA secondary structure prediction and modelling. PMID:24639159

  19. Peptide-chain secondary structure of bacteriorhodopsin.

    PubMed Central

    Jap, B K; Maestre, M F; Hayward, S B; Glaeser, R M

    1983-01-01

    Ultraviolet circular dichroism spectroscopy in the interval from 190 to 240 nm and infrared spectroscopy in the region of the amide I band (1,600 cm-1 to 1,700 cm-1) has been used to estimate the alpha-helix content and the beta-sheet content of bacteriorhodopsin. Circular dichroism spectroscopy strongly suggests that the alpha-helix content is sufficient for only five helices, if each helix is composed of 20 or more residues. It also suggests that there is substantial beta-sheet conformation in bacteriorhodopsin. The presence of beta-sheet secondary structure is further suggested by the presence of a 1,639 cm-1 shoulder on the amide I band in the infrared spectrum. Although a structural model consisting of seven alpha-helical rods has been generally accepted up to this point, the spectroscopic data are more consistent with a model consisting of five alpha-helices and four strands of beta-sheet. We note that the primary amino acid sequence can be assigned to segments of alpha-helix and beta-sheet in a way that does not require burying more than two charged groups in the hydrophobic membrane interior, contrary to the situation for any seven-helix model. Images FIGURE 6 PMID:6882864

  20. Secondary structure adventures with Carl Woese

    PubMed Central

    Noller, Harry F

    2014-01-01

    Not long after my arrival at UCSC as an assistant professor, I came across Carl Woese's paper “Molecular Mechanics of Translation: A Reciprocating Ratchet Mechanism.”1 In the days before the crystal structure of tRNA was known, Fuller and Hodgson2 had proposed two alternative conformations for its anticodon loop; one was stacked on the 3? side (as later found in the crystal structure) and the other on the 5? side. In an ingenious and elegant model, Woese proposed that the conformation of the loop flips between Fuller and Hodgson's 5?- and 3?-stacked forms during protein synthesis, changing the local direction of the mRNA such that the identities of the tRNA binding sites alternated between binding aminoacyl-tRNA and peptidyl-tRNA. The model predicted that there are no A and P sites, only two binding sites whose identities changed following translation of each codon, and that there would be no translocation of tRNAs in the usual sense—only binding and release. I met Carl in person the following year when he presented a seminar on his ratchet model in Santa Cruz. He was chatting in my colleague Ralph Hinegardner's office in what Carl termed a “Little Jack Horner appointment” (the visitor sits and listens to his host describing “What a good boy am I”). He was of compact stature, and bore a striking resemblance to Oskar Werner in Truffaut's film “Jules and Jim.” He projected the impression of a New-Age guru—a shiny black amulet suspended over the front of his black turtleneck sweater and a crown of prematurely white hair. Ralph asked me to explain to Carl what we were doing with ribosomes. I quickly summarized our early experiments that were pointing to a functional role for 16S rRNA. Carl regarded me silently, with a penetrating stare. He then turned to Ralph and said, in an ominous low voice, “I'm going to have some more tanks made as soon as I get back.” Carl's beautiful model was, unfortunately, wrong—it was simpler and more elegant than the complex mechanism that Nature actually uses. Unyielding, Carl railed against the A-site-P-site model at every opportunity,3,4 and although we ended up enjoying a long, intense, and fruitful collaboration, and became close, life-long friends, I finally gave up trying to describe to him our biochemical and crystallographic results on the A, P, and E sites. PMID:24637459

  1. Secondary structure adventures with Carl Woese.

    PubMed

    Noller, Harry F

    2014-01-01

    Not long after my arrival at UCSC as an assistant professor, I came across Carl Woese's paper "Molecular Mechanics of Translation: A Reciprocating Ratchet Mechanism." (1) In the days before the crystal structure of tRNA was known, Fuller and Hodgson (2) had proposed two alternative conformations for its anticodon loop; one was stacked on the 3' side (as later found in the crystal structure) and the other on the 5' side. In an ingenious and elegant model, Woese proposed that the conformation of the loop flips between Fuller and Hodgson's 5'- and 3'-stacked forms during protein synthesis, changing the local direction of the mRNA such that the identities of the tRNA binding sites alternated between binding aminoacyl-tRNA and peptidyl-tRNA. The model predicted that there are no A and P sites, only two binding sites whose identities changed following translation of each codon, and that there would be no translocation of tRNAs in the usual sense--only binding and release. I met Carl in person the following year when he presented a seminar on his ratchet model in Santa Cruz. He was chatting in my colleague Ralph Hinegardner's office in what Carl termed a "Little Jack Horner appointment" (the visitor sits and listens to his host describing "What a good boy am I"). He was of compact stature, and bore a striking resemblance to Oskar Werner in Truffaut's film "Jules and Jim." He projected the impression of a New-Age guru--a shiny black amulet suspended over the front of his black turtleneck sweater and a crown of prematurely white hair. Ralph asked me to explain to Carl what we were doing with ribosomes. I quickly summarized our early experiments that were pointing to a functional role for 16S rRNA. Carl regarded me silently, with a penetrating stare. He then turned to Ralph and said, in an ominous low voice, "I'm going to have some more tanks made as soon as I get back." Carl's beautiful model was, unfortunately, wrong--it was simpler and more elegant than the complex mechanism that Nature actually uses. Unyielding, Carl railed against the A-site-P-site model at every opportunity, and although we ended up enjoying a long, intense, and fruitful collaboration, and became close, life-long friends, I finally gave up trying to describe to him our biochemical and crystallographic results on the A, P, and E sites. PMID:24637459

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

    SciTech Connect

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

    1994-02-01

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

  3. Statistical model of amino acid code of protein secondary structure.

    PubMed

    Shestopalov, B V

    2003-01-01

    In the previous paper (Shestopalov, 2003) we presented the amino acid code of protein secondary structure as a partial solution of the fundamental problem of the protein three-dimensional structure calculation from the amino acid sequence. Here a statistical model of the code is described. The model is based on the structural data from 2258 protein chains (417,112 amino acid residues used). 60 and 61% of the secondary structure, calculated using the model, coincide, respectively, with the observed secondary structure in the training subset and test subset (104 protein chains and 21,166 residues used). This is equal to the threshold value for all the secondary structure calculations, based on the models, where, similarly as here, only the nearest and middle-range interactions are considered. Therefore the constructed model can be applied for the protein structure prediction from the amino acid sequence, especially when additional information is used along with expert analysis, as in the most successful prediction methods. The model can be used for analysis of the secondary structure changes during protein folding by comparison of the calculated and observed secondary structures. The information about the conformationally invariant segments can serve for the simulation of the supersecondary structure formation. One can try to obtain and examine the protein subset, in which the calculated and observed secondary structures are very similar. PMID:14989165

  4. Thickness-dependent secondary structure formation of tubelike polymers

    E-print Network

    Janke, Wolfhard

    OFFPRINT Thickness-dependent secondary structure formation of tubelike polymers T. Vogel, T.epljournal.org doi: 10.1209/0295-5075/85/10003 Thickness-dependent secondary structure formation of tubelike polymers the conformational phase diagram of a simple model for flexible polymers with explicit thickness. The thickness

  5. Characterising RNA secondary structure space using information entropy.

    PubMed

    Sükösd, Zsuzsanna; Knudsen, Bjarne; Anderson, James W J; Novák, Adám; Kjems, Jřrgen; Pedersen, Christian N S

    2013-01-01

    Comparative methods for RNA secondary structure prediction use evolutionary information from RNA alignments to increase prediction accuracy. The model is often described in terms of stochastic context-free grammars (SCFGs), which generate a probability distribution over secondary structures. It is, however, unclear how this probability distribution changes as a function of the input alignment. As prediction programs typically only return a single secondary structure, better characterisation of the underlying probability space of RNA secondary structures is of great interest. In this work, we show how to efficiently compute the information entropy of the probability distribution over RNA secondary structures produced for RNA alignments by a phylo-SCFG, and implement it for the PPfold model. We also discuss interpretations and applications of this quantity, including how it can clarify reasons for low prediction reliability scores. PPfold and its source code are available from http://birc.au.dk/software/ppfold/. PMID:23368905

  6. Metabolism of DNA secondary structures at the eukaryotic replication fork.

    PubMed

    León-Ortiz, Ana María; Svendsen, Jennifer; Boulton, Simon J

    2014-07-01

    DNA secondary structures are largely advantageous for numerous cellular processes but can pose specific threats to the progression of the replication machinery and therefore genome duplication and cell division. A number of specialized enzymes dismantle these structures to allow replication fork progression to proceed faithfully. In this review, we discuss the in vitro and in vivo data that has lead to the identification of these enzymes in eukaryotes, and the evidence that suggests that they act specifically at replication forks to resolve secondary structures. We focus on the role of helicases, which catalyze the dissociation of nucleotide complexes, and on the role of nucleases, which cleave secondary structures to allow replication fork progression at the expense of local rearrangements. Finally, we discuss outstanding questions in terms of dismantling DNA secondary structures, as well as the interplay between diverse enzymes that act upon specific types of structures. PMID:24815912

  7. Pre-mRNA Secondary Structures Influence Exon Recognition

    E-print Network

    Will, Sebastian

    determined splicing enhancer and silencer motifs in their natural pre-mRNA context. We found that affect splicing and indicate that the structural context of splicing motifs is part of the mRNA splicing can adopt various conformations in solution by base pairings and hydrophobic interactions. For example

  8. A Partition Function Algorithm for Nucleic Acid Secondary Structure Including Pseudoknots

    E-print Network

    Pierce, Niles A.

    A Partition Function Algorithm for Nucleic Acid Secondary Structure Including Pseudoknots ROBERT M 2003 Abstract: Nucleic acid secondary structure models usually exclude pseudoknots due implemented to predict the secondary structure or structures that a given nucleic acid sequence will adopt

  9. 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.

    2011-11-02

    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.

  10. Structure-function Studies of Nucleocytoplasmic Transport of Retroviral Genomic RNA by mRNA Export Factor TAP

    SciTech Connect

    M Teplova; L Wohlbold; N Khin; E Izaurralde; D Patel

    2011-12-31

    mRNA export is mediated by the TAP-p15 heterodimer, which belongs to the family of NTF2-like export receptors. TAP-p15 heterodimers also bind to the constitutive transport element (CTE) present in simian type D retroviral RNAs, and they mediate the export of viral unspliced RNAs to the host cytoplasm. We have solved the crystal structure of the RNA recognition and leucine-rich repeat motifs of TAP bound to one symmetrical half of the CTE RNA. L-shaped conformations of protein and RNA are involved in a mutual molecular embrace on complex formation. We have monitored the impact of structure-guided mutations on binding affinities in vitro and transport assays in vivo. Our studies define the principles by which CTE RNA subverts the mRNA export receptor TAP, thereby facilitating the nuclear export of viral genomic RNAs, and, more generally, provide insights on cargo RNA recognition by mRNA export receptors.

  11. 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

  12. 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 ...

  13. Combinatorics of RNA Secondary Structures with Base Triples.

    PubMed

    Müller, Robert; Nebel, Markus E

    2015-07-01

    The structure of RNA has been the subject of intense research over the last decades due to its importance for the correct functioning of RNA molecules in biological processes. Hence, a large number of models for RNA folding and corresponding algorithms for structure prediction have been developed. However, previous models often only consider base pairs, although every base is capable of up to three edge-to-edge interactions with other bases. Recently, Höner zu Siederdissen et al. presented an extended model of RNA secondary structure, including base triples together with a folding algorithm-the first thermodynamics-based algorithm that allows the prediction of secondary structures with base triples. In this article, we investigate the search space processed by this new algorithm, that is, the combinatorics of extended RNA secondary structures with base triples. We present generalized definitions for structural motifs like hairpins, stems, bulges, or interior loops occurring in structures with base triples. Furthermore, we prove precise asymptotic results for the number of different structures (size of search space) and expectations for various parameters associated with structural motifs (typical shape of folding). Our analysis shows that the asymptotic number of secondary structures of size n increases exponentially to [Formula: see text] compared to the classic model by Stein and Waterman for which [Formula: see text] structures exist. A comparison with the classic model reveals large deviations in the expected structural appearance, too. The inclusion of base triples constitutes a significant refinement of the combinatorial model of RNA secondary structure, which, by our findings, is quantitatively characterized. Our results are of special theoretical interest, because a closer look at the numbers involved suggests that extended RNA secondary structures constitute a new combinatorial class not bijective with any other combinatorial objects studied so far. PMID:26098199

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

    E-print Network

    2005-12-01

    are the most widely used are Stride and especially DSSP based both on the calculation of hydrogen bonds. DSSP [14] calculates energies of hydrogen bonds using a classical electrostatic function. The residues are assigned in a secondary structure category... , although no restriction is be considered as an improvement on DSSP, it can also produce incorrect assignments in some cases. The obligation to be involved in two hydrogen bonds for a residue in the middle of a secondary structure is very restrictive...

  15. 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

  16. A stem–loop structure directs oskar mRNA to microtubule minus ends

    PubMed Central

    Jambor, Helena; Mueller, Sandra; Bullock, Simon L.; Ephrussi, Anne

    2014-01-01

    mRNA transport coupled with translational control underlies the intracellular localization of many proteins in eukaryotic cells. This is exemplified in Drosophila, where oskar mRNA transport and translation at the posterior pole of the oocyte direct posterior patterning of the embryo. oskar localization is a multistep process. Within the oocyte, a spliced oskar localization element (SOLE) targets oskar mRNA for plus end-directed transport by kinesin-1 to the posterior pole. However, the signals mediating the initial minus end-directed, dynein-dependent transport of the mRNA from nurse cells into the oocyte have remained unknown. Here, we show that a 67-nt stem–loop in the oskar 3? UTR promotes oskar mRNA delivery to the developing oocyte and that it shares functional features with the fs(1)K10 oocyte localization signal. Thus, two independent cis-acting signals, the oocyte entry signal (OES) and the SOLE, mediate sequential dynein- and kinesin-dependent phases of oskar mRNA transport during oogenesis. The OES also promotes apical localization of injected RNAs in blastoderm stage embryos, another dynein-mediated process. Similarly, when ectopically expressed in polarized cells of the follicular epithelium or salivary glands, reporter RNAs bearing the oskar OES are apically enriched, demonstrating that this element promotes mRNA localization independently of cell type. Our work sheds new light on how oskar mRNA is trafficked during oogenesis and the RNA features that mediate minus end-directed transport. PMID:24572808

  17. Hierarchical Protein Structure Superposition using both Secondary Structure and Atomic Representations

    E-print Network

    Brutlag, Doug

    Hierarchical Protein Structure Superposition using both Secondary Structure and Atomic the secondary structure level to the atomic level. Our technique represents -helices and -strands as vectors of vectors. The second step in our algorithm is based on the atomic coordinates of the protein structures

  18. Elucidating protein secondary structures using alpha-carbon recurrence quantifications.

    PubMed

    Webber, C L; Giuliani, A; Zbilut, J P; Colosimo, A

    2001-08-15

    Secondary structures of proteins were studied by recurrence quantification analysis (RQA). High-resolution, 3-dimensional coordinates of alpha-carbon atoms comprising a set of 68 proteins were downloaded from the Protein Data Bank. By fine-tuning four recurrence parameters (radius, line, residue, separation), it was possible to establish excellent agreement between percent contribution of alpha-helix and beta-sheet structures determined independently by RQA and that of the DSSP algorithm (Define Secondary Structure of Proteins). These results indicate that there is an equivalency between these two techniques, which are based upon totally different pattern recognition strategies. RQA enhances qualitative contact maps by quantifying the arrangements of recurrent points of alpha carbons close in 3-dimensional space. For example, the radius was systematically increased, moving the analysis beyond local alpha-carbon neighborhoods in order to capture super-secondary and tertiary structures. However, differences between proteins could only be detected within distances up to about 6-11 A, but not higher. This result underscores the complexity of alpha-carbon spacing when super-secondary structures appear at larger distances. Finally, RQA-defined secondary structures were found to be robust against random displacement of alpha carbons upwards of 1 A. This finding has potential import for the dynamic functions of proteins in motion. PMID:11455602

  19. Secondary Structure Determination of Peptides and Proteins After Immobilization.

    PubMed

    North, Stella H; Taitt, Chris R

    2016-01-01

    The presentation of immobilized peptides and other small biomolecules attached to surfaces can be greatly affected by the attachment chemistry and linking moieties, resulting in altered activity and specificity. For this reason, it is critical to understand how the various aspects of surface immobilization-underlying substrate properties, tether structure, and site of linkage-affect the secondary and quaternary structures of the immobilized species. Here, we present methods for attaching cysteine-containing peptides to quartz surfaces and determining the secondary structure of surface-immobilized peptides. We specifically show that, even when covalently immobilized, changes in peptide conformation can still occur, with measurement occurring in real time. PMID:26490466

  20. PROCEEDINGS Open Access Characterising RNA secondary structure space

    E-print Network

    Schierup, Mikkel Heide

    PROCEEDINGS Open Access Characterising RNA secondary structure space using information entropy, we show how to efficiently compute the information entropy of the probability distribution over RNA structures, however, it is difficult to report useful quantities to describe this. Information entropy is one

  1. Bayesian Network Multi-classifiers for Protein Secondary Structure Prediction

    E-print Network

    Grosu, Radu

    and evolutionary in- formation from the divergence of proteins in the same structural family. At the alignmentBayesian Network Multi-classifiers for Protein Secondary Structure Prediction V´ictor Robles a , Pedro Larra~naga b , Jos´e M. Pe~na a , Ernestina Menasalvas a , Mar´ia S. P´erez a , Vanessa Herves

  2. From RNA Secondary Structure to Coding Theory: A Combinatorial Approach

    E-print Network

    Hoos, Holger H.

    analysis to transform a special case of the computational problem of designing RNA base sequences pairings of the secondary structure. Hence, this is crucial initial work in the design of RNA molecules with desired three-dimensional structures and specific functional properties. The biological importance of RNA

  3. Communication Secondary structure of dengue virus type 4

    E-print Network

    Hanley, Kathryn A.

    Short Communication Secondary structure of dengue virus type 4 39 untranslated region: impact of the 39 untranslated region (UTR) of Dengue virus (DEN); however, experimental verification structure, yet viruses carrying these mutations were viable. The four serotypes of mosquito-borne Dengue

  4. Evidence for an alternative genomic structure, mRNA and protein sequence of human ABCA13.

    PubMed

    Maeß, Marten B; Stolle, Katrin; Cullen, Paul; Lorkowski, Stefan

    2013-02-25

    ABC transporters form one of the major families of transport proteins. In humans, the ABC family comprises seven subfamilies named A to G, of which the A subfamily contains twelve members. Among these are several well-characterized transporters, including ABCA1, which is involved in cellular cholesterol transport and HDL formation, and ABCA4, which is a transporter for vitamin A derivatives in photoreceptor cells. The function of another subfamily member termed ABCA13 is unknown. The human ABCA13 gene has been reported to span 450kb of genomic DNA at chromosomal locus 7p12.3 and to encode a 5058 amino acid protein that includes two unusually large exons close to the N-terminus. We now show that the gene as well as the corresponding mRNA and protein may be considerably shorter than previously thought. We used PCR and RACE to identify a genomic sequence spanning about 350kb and encoding a protein of 2323 amino acids. This corresponds to the C-terminal half of the previously reported ABCA13 protein but lacks the residues reportedly encoded by the two very big N-terminal exons. Using immunoprecipitation and Western blot analyses we identified a protein of about 260kDa in size likely representing the shorter protein proposed here. Computer analyses showed that our proposed sequence contains all the structural elements of an ABCA protein and agrees well with the mouse ABCA13 protein sequence. Additionally, we identified a putative promoter region containing well-conserved TATA and CAAT boxes just upstream of our transcription start site. Overall, our data provide good evidence for an alternative human ABCA13 transcript and protein. PMID:23266639

  5. Predicting RNA secondary structures with pseudoknots by MCMC sampling.

    PubMed

    Metzler, Dirk; Nebel, Markus E

    2008-01-01

    The most probable secondary structure of an RNA molecule, given the nucleotide sequence, can be computed efficiently if a stochastic context-free grammar (SCFG) is used as the prior distribution of the secondary structure. The structures of some RNA molecules contain so-called pseudoknots. Allowing all possible configurations of pseudoknots is not compatible with context-free grammar models and makes the search for an optimal secondary structure NP-complete. We suggest a probabilistic model for RNA secondary structures with pseudoknots and present a Markov-chain Monte-Carlo Method for sampling RNA structures according to their posterior distribution for a given sequence. We favor Bayesian sampling over optimization methods in this context, because it makes the uncertainty of RNA structure predictions assessable. We demonstrate the benefit of our method in examples with tmRNA and also with simulated data. McQFold, an implementation of our method, is freely available from http://www.cs.uni-frankfurt.de/~metzler/McQFold. PMID:17589847

  6. An AU-rich stem–loop structure is a critical feature of the perinuclear localization signal of c-myc mRNA

    PubMed Central

    Chabanon, Hervé; Mickleburgh, Ian; Burtle, Brian; Pedder, Christopher; Hesketh, John

    2005-01-01

    In eukaryotic cells, several mRNAs including those of c-myc and c-fos are localized to the perinuclear cytoplasm and associated with the cytoskeleton. The localization element of c-myc mRNA is present within its 3?UTR (3?-untranslated region) but the precise nature of this signal has remained unidentified. Chemical/enzymatic cleavage with RNases (ribonucleases) and lead have identified single-stranded and double-stranded regions in RNA transcripts of nucleotides 194–280 of the c-myc 3?UTR. Combined with computer predicted structure these results indicate that this region folds so that part of it forms a stem-loop structure. A mutation, that has been previously shown to prevent localization, leads to a different secondary RNA structure in this region as indicated by altered cleavage patterns. Competitive gel-retardation assays, using labelled transcripts corresponding to nucleotides 205–280 of c-myc 3?UTR, and fibroblast extracts revealed that the stem-loop region was sufficient for RNA–protein complex formation. In situ hybridization studies in cells transfected with reporter constructs, in which all or parts of the region corresponding to this stem-loop were linked to ?-globin, indicated that this region was sufficient for localization and that deletion of the nucleotides corresponding to the proposed upper-stem or terminal loop prevented localization. Our hypothesis is that an AU-rich stem-loop structure within nt 222–267 in the c-myc 3?UTR forms the perinuclear localization signal. Bioinformatic analysis suggests that this signal shares features with 3?UTRs of other localized mRNAs and that these features may represent a conserved form of signal in mRNA localization mechanisms. PMID:16042622

  7. Asymptotic number of hairpins of saturated RNA secondary structures.

    PubMed

    Clote, Peter; Kranakis, Evangelos; Krizanc, Danny

    2013-12-01

    In the absence of chaperone molecules, RNA folding is believed to depend on the distribution of kinetic traps in the energy landscape of all secondary structures. Kinetic traps in the Nussinov energy model are precisely those secondary structures that are saturated, meaning that no base pair can be added without introducing either a pseudoknot or base triple. In this paper, we compute the asymptotic expected number of hairpins in saturated structures. For instance, if every hairpin is required to contain at least ?=3 unpaired bases and the probability that any two positions can base-pair is p=3/8, then the asymptotic number of saturated structures is 1.34685[Symbol: see text]n (-3/2)[Symbol: see text]1.62178 (n) , and the asymptotic expected number of hairpins follows a normal distribution with mean [Formula: see text]. Similar results are given for values ?=1,3, and p=1,1/2,3/8; for instance, when ?=1 and p=1, the asymptotic expected number of hairpins in saturated secondary structures is 0.123194[Symbol: see text]n, a value greater than the asymptotic expected number 0.105573[Symbol: see text]n of hairpins over all secondary structures. Since RNA binding targets are often found in hairpin regions, it follows that saturated structures present potentially more binding targets than nonsaturated structures, on average. Next, we describe a novel algorithm to compute the hairpin profile of a given RNA sequence: given RNA sequence a 1,…,a n , for each integer k, we compute that secondary structure S k having minimum energy in the Nussinov energy model, taken over all secondary structures having k hairpins. We expect that an extension of our algorithm to the Turner energy model may provide more accurate structure prediction for particular RNAs, such as tRNAs and purine riboswitches, known to have a particular number of hairpins. Mathematica(™) computations, C and Python source code, and additional supplementary information are available at the website http://bioinformatics.bc.edu/clotelab/RNAhairpinProfile/ . PMID:24142625

  8. RNALOSS: a web server for RNA locally optimal secondary structures

    E-print Network

    Clote, Peter

    , function and regulation of all RNA in a living organism. Given recently discovered roles played by micro, riboswitches, micro RNA, small interfering RNA (4), tRNA, rRNA, etc. Riboswitches have recently been discoveredRNALOSS: a web server for RNA locally optimal secondary structures P. Clote* Department of Biology

  9. Problems on RNA Secondary Structure Prediction and Design

    E-print Network

    Condon, Anne

    Problems on RNA Secondary Structure Prediction and Design Anne Condon The Department of Computer world - the Chemistry Department. This short walk was the start of a rewarding ongoing journey. Along their home in the heads of us theoreticians, there to remain indefinitely. In this article, I will describe

  10. 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

  11. 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

  12. Small Molecule Ligands for Bulged RNA Secondary Structures

    E-print Network

    Hergenrother, Paul J.

    .; Harris, J. L.; Pennington, W. T.; Fouad, F. S.; Qabaja, G.; Wright, J. M.; Jones, G. B. Chem. Biol. 2002Small Molecule Ligands for Bulged RNA Secondary Structures S. Todd Meyer and Paul J. Hergenrother) For reviews of small molecule-RNA binding, see: (a) Thomas, J. R.; Hergenrother, P. J. Chem. ReV. 2008, 108

  13. Structural basis for Pan3 binding to Pan2 and its function in mRNA recruitment and deadenylation.

    PubMed

    Wolf, Jana; Valkov, Eugene; Allen, Mark D; Meineke, Birthe; Gordiyenko, Yuliya; McLaughlin, Stephen H; Olsen, Tayla M; Robinson, Carol V; Bycroft, Mark; Stewart, Murray; Passmore, Lori A

    2014-07-17

    The conserved eukaryotic Pan2-Pan3 deadenylation complex shortens cytoplasmic mRNA 3' polyA tails to regulate mRNA stability. Although the exonuclease activity resides in Pan2, efficient deadenylation requires Pan3. The mechanistic role of Pan3 is unclear. Here, we show that Pan3 binds RNA directly both through its pseudokinase/C-terminal domain and via an N-terminal zinc finger that binds polyA RNA specifically. In contrast, isolated Pan2 is unable to bind RNA. Pan3 binds to the region of Pan2 that links its N-terminal WD40 domain to the C-terminal part that contains the exonuclease, with a 2:1 stoichiometry. The crystal structure of the Pan2 linker region bound to a Pan3 homodimer shows how the unusual structural asymmetry of the Pan3 dimer is used to form an extensive high-affinity interaction. This binding allows Pan3 to supply Pan2 with substrate polyA RNA, facilitating efficient mRNA deadenylation by the intact Pan2-Pan3 complex. PMID:24872509

  14. Role of the highly structured 5'-end region of MDR1 mRNA in P-glycoprotein expression.

    PubMed

    Randle, Rebecca A; Raguz, Selina; Higgins, Christopher F; Yagüe, Ernesto

    2007-09-15

    Overexpression of P-glycoprotein, encoded by the MDR1 (multidrug resistance 1) gene, is often responsible for multidrug resistance in acute myeloid leukaemia. We have shown previously that MDR1 (P-glycoprotein) mRNA levels in K562 leukaemic cells exposed to cytotoxic drugs are up-regulated but P-glycoprotein expression is translationally blocked. In the present study we show that cytotoxic drugs down-regulate the Akt signalling pathway, leading to hypophosphorylation of the translational repressor 4E-BP [eIF (eukaryotic initiation factor) 4E-binding protein] and decreased eIF4E availability. The 5'-end of MDR1 mRNA adopts a highly-structured fold. Fusion of this structured 5'-region upstream of a reporter gene impeded its efficient translation, specifically under cytotoxic stress, by reducing its competitive ability for the translational machinery. The effect of cytotoxic stress could be mimicked in vivo by blocking the phosphorylation of 4E-BP by mTOR (mammalian target of rapamycin) using rapamycin or eIF4E siRNA (small interfering RNA), and relieved by overexpression of either eIF4E or constitutively-active Akt. Upon drug exposure MDR1 mRNA was up-regulated, apparently stochastically, in a small proportion of cells. Only in these cells could MDR1 mRNA compete successfully for the reduced amounts of eIF4E and translate P-glycoprotein. Consequent drug efflux and restoration of eIF4E availability results in a feed-forward relief from stress-induced translational repression and to the acquisition of drug resistance. PMID:17573715

  15. Effect of acute resistance exercise and sex on human patellar tendon structural and regulatory mRNA expression

    PubMed Central

    Sullivan, Bridget E.; Carroll, Chad C.; Jemiolo, Bozena; Trappe, Scott W.; Magnusson, S. Peter; Dřssing, Simon; Kjaer, Michael; Trappe, Todd A.

    2009-01-01

    Tendon is mainly composed of collagen and an aqueous matrix of proteoglycans that are regulated by enzymes called matrix metalloproteinases (MMPs) and tissue inhibitors of metalloproteinases (TIMPs). Although it is known that resistance exercise (RE) and sex influence tendon metabolism and mechanical properties, it is uncertain what structural and regulatory components contribute to these responses. We measured the mRNA expression of tendon's main fibrillar collagens (type I and type III) and the main proteoglycans (decorin, biglycan, fibromodulin, and versican) and the regulatory enzymes MMP-2, MMP-9, MMP-3, and TIMP-1 at rest and after RE. Patellar tendon biopsy samples were taken from six individuals (3 men and 3 women) before and 4 h after a bout of RE and from a another six individuals (3 men and 3 women) before and 24 h after RE. Resting mRNA expression was used for sex comparisons (6 men and 6 women). Collagen type I, collagen type III, and MMP-2 were downregulated (P < 0.05) 4 h after RE but were unchanged (P > 0.05) 24 h after RE. All other genes remained unchanged (P > 0.05) after RE. Women had higher resting mRNA expression (P < 0.05) of collagen type III and a trend (P = 0.08) toward lower resting expression of MMP-3 than men. All other genes were not influenced (P > 0.05) by sex. Acute RE appears to stimulate a change in collagen type I, collagen type III, and MMP-2 gene regulation in the human patellar tendon. Sex influences the structural and regulatory mRNA expression of tendon. PMID:19023016

  16. The structural basis of secondary active transport mechanisms.

    PubMed

    Forrest, Lucy R; Krämer, Reinhard; Ziegler, Christine

    2011-02-01

    Secondary active transporters couple the free energy of the electrochemical potential of one solute to the transmembrane movement of another. As a basic mechanistic explanation for their transport function the model of alternating access was put forward more than 40 years ago, and has been supported by numerous kinetic, biochemical and biophysical studies. According to this model, the transporter exposes its substrate binding site(s) to one side of the membrane or the other during transport catalysis, requiring a substantial conformational change of the carrier protein. In the light of recent structural data for a number of secondary transport proteins, we analyze the model of alternating access in more detail, and correlate it with specific structural and chemical properties of the transporters, such as their assignment to different functional states in the catalytic cycle of the respective transporter, the definition of substrate binding sites, the type of movement of the central part of the carrier harboring the substrate binding site, as well as the impact of symmetry on fold-specific conformational changes. Besides mediating the transmembrane movement of solutes, the mechanism of secondary carriers inherently involves a mechanistic coupling of substrate flux to the electrochemical potential of co-substrate ions or solutes. Mainly because of limitations in resolution of available transporter structures, this important aspect of secondary transport cannot yet be substantiated by structural data to the same extent as the conformational change aspect. We summarize the concepts of coupling in secondary transport and discuss them in the context of the available evidence for ion binding to specific sites and the impact of the ions on the conformational state of the carrier protein, which together lead to mechanistic models for coupling. PMID:21029721

  17. Improved Chou-Fasman method for protein secondary structure prediction

    PubMed Central

    Chen, Hang; Gu, Fei; Huang, Zhengge

    2006-01-01

    Background Protein secondary structure prediction is a fundamental and important component in the analytical study of protein structure and functions. The prediction technique has been developed for several decades. The Chou-Fasman algorithm, one of the earliest methods, has been successfully applied to the prediction. However, this method has its limitations due to low accuracy, unreliable parameters, and over prediction. Thanks to the recent development in protein folding type-specific structure propensities and wavelet transformation, the shortcomings in Chou-Fasman method are able to be overcome. Results We improved Chou-Fasman method in three aspects. (a) Replace the nucleation regions with extreme values of coefficients calculated by the continuous wavelet transform. (b) Substitute the original secondary structure conformational parameters with folding type-specific secondary structure propensities. (c) Modify Chou-Fasman rules. The CB396 data set was tested by using improved Chou-Fasman method and three indices: Q3, Qpre, SOV were used to measure this method. We compared the indices with those obtained from the original Chou-Fasman method and other four popular methods. The results showed that our improved Chou-Fasman method performs better than the original one in all indices, about 10–18% improvement. It is also comparable to other currently popular methods considering all the indices. Conclusion Our method has greatly improved Chou-Fasman method. It is able to predict protein secondary structure as good as current popular methods. By locating nucleation regions with refined wavelet transform technology and by calculating propensity factors with larger size data set, it is likely to get a better result. PMID:17217506

  18. Complete nucleotide sequence of mRNA for caerulein precursor from Xenopus skin: the mRNA contains an unusual repetitive structure.

    PubMed Central

    Wakabayashi, T; Kato, H; Tachibana, S

    1985-01-01

    The complete nucleotide sequence of mRNA for caerulein precursor in the skin of Xenopus laevis was determined. The sequence was composed of 705 bp of coding region, accounting for 234 amino acids, 58 bp of 5'-untranslated region and 158 bp of 3'-untranslated region containing two putative poly(A) signals. It coded for four caerulein peptides interspersed with three 147 bp segments (intercaerulein segment; ICS). Analyses of several caerulein encoding cDNAs revealed some interesting features of caerulein mRNA species, which were highly heterogeneous and consisted of a repetition of two fundamental RNA sequences, a 45-nucleotide caerulein fragment and a 147-nucleotide ICS. The result of Northern blotting indicated that caerulein mRNA was only present in frog skin, not in stomach, upper intestine or liver. It appears that caerulein has different physiological function(s) from mammalian gastrin and cholecystokinin-pancreozymin (CCK). The relationship of caerulein to mammalian gastrointestinal hormones is discussed. Images PMID:4000945

  19. Assessing secondary structure assignment of protein structures by using pairwise sequence-alignment benchmarks.

    PubMed

    Zhang, Wei; Dunker, A Keith; Zhou, Yaoqi

    2008-04-01

    How to make an objective assignment of secondary structures based on a protein structure is an unsolved problem. Defining the boundaries between helix, sheet, and coil structures is arbitrary, and commonly accepted standard assignments do not exist. Here, we propose a criterion that assesses secondary structure assignment based on the similarity of the secondary structures assigned to pairwise sequence-alignment benchmarks, where these benchmarks are determined by prior structural alignments of the protein pairs. This criterion is used to rank six secondary structure assignment methods: STRIDE, DSSP, SECSTR, KAKSI, P-SEA, and SEGNO with three established sequence-alignment benchmarks (PREFAB, SABmark, and SALIGN). STRIDE and KAKSI achieve comparable success rates in assigning the same secondary structure elements to structurally aligned residues in the three benchmarks. Their success rates are between 1-4% higher than those of the other four methods. The consensus of STRIDE, KAKSI, SECSTR, and P-SEA, called SKSP, improves assignments over the best single method in each benchmark by an additional 1%. These results support the usefulness of the sequence-alignment benchmarks as a means to evaluate secondary structure assignment. The SKSP server and the benchmarks can be accessed at http://sparks.informatics.iupui.edu PMID:17932927

  20. Automatic RNA secondary structure determination stochastic context-free grammars

    SciTech Connect

    Grate, L.

    1995-12-31

    We have developed a method for predicting the common secondary structure of large RNA multiple alignments using only the information in the alignment. It uses a series of progressively more sensitive searches of the data in an iterative manner to discover regions of base pairing; the first pass examines the entire multiple alignment. The searching uses two methods to find base pairings. Mutual information is used to measure covariation between pairs of columns in the multiple alignment and a minimum length encoding method is used to detect column pairs with high potential to base pair. Dynamic programming is used to recover the optimal tree made up of the best potential base pairs and to create a stochastic context-free grammar. The information in the tree guides the next iteration of searching. The method is similar to the traditional comparative sequence analysis technique. The method correctly identifies most of the common secondary structure in 16S and 23S rRNA.

  1. Approximation algorithms for predicting RNA secondary structures with arbitrary pseudoknots.

    PubMed

    Jiang, Minghui

    2010-01-01

    We study three closely related problems motivated by the prediction of RNA secondary structures with arbitrary pseudoknots: the problem 2-Interval Pattern proposed by Vialette, the problem Maximum Base Pair Stackings proposed by Leong et al., and the problem Maximum Stacking Base Pairs proposed by Lyngsř. For the 2-Interval Pattern, we present polynomialtime approximation algorithms for the problem over the preceding-and-crossing model and on input with the unitary restriction. For Maximum Base Pair Stackings and Maximum Stacking Base Pairs, we present polynomial-time approximation algorithms for the two problems on explicit input of candidate base pairs. We also propose a new problem called Length-Weighted Balanced 2-Interval Pattern, which is natural in the context of RNA secondary structure prediction. PMID:20431151

  2. Extracting physicochemical features to predict protein secondary structure.

    PubMed

    Huang, Yin-Fu; Chen, Shu-Ying

    2013-01-01

    We propose a protein secondary structure prediction method based on position-specific scoring matrix (PSSM) profiles and four physicochemical features including conformation parameters, net charges, hydrophobic, and side chain mass. First, the SVM with the optimal window size and the optimal parameters of the kernel function is found. Then, we train the SVM using the PSSM profiles generated from PSI-BLAST and the physicochemical features extracted from the CB513 data set. Finally, we use the filter to refine the predicted results from the trained SVM. For all the performance measures of our method, Q 3 reaches 79.52, SOV94 reaches 86.10, and SOV99 reaches 74.60; all the measures are higher than those of the SVMpsi method and the SVMfreq method. This validates that considering these physicochemical features in predicting protein secondary structure would exhibit better performances. PMID:23766688

  3. Improving the accuracy of protein secondary structure prediction using structural alignment

    PubMed Central

    Montgomerie, Scott; Sundararaj, Shan; Gallin, Warren J; Wishart, David S

    2006-01-01

    Background The accuracy of protein secondary structure prediction has steadily improved over the past 30 years. Now many secondary structure prediction methods routinely achieve an accuracy (Q3) of about 75%. We believe this accuracy could be further improved by including structure (as opposed to sequence) database comparisons as part of the prediction process. Indeed, given the large size of the Protein Data Bank (>35,000 sequences), the probability of a newly identified sequence having a structural homologue is actually quite high. Results We have developed a method that performs structure-based sequence alignments as part of the secondary structure prediction process. By mapping the structure of a known homologue (sequence ID >25%) onto the query protein's sequence, it is possible to predict at least a portion of that query protein's secondary structure. By integrating this structural alignment approach with conventional (sequence-based) secondary structure methods and then combining it with a "jury-of-experts" system to generate a consensus result, it is possible to attain very high prediction accuracy. Using a sequence-unique test set of 1644 proteins from EVA, this new method achieves an average Q3 score of 81.3%. Extensive testing indicates this is approximately 4–5% better than any other method currently available. Assessments using non sequence-unique test sets (typical of those used in proteome annotation or structural genomics) indicate that this new method can achieve a Q3 score approaching 88%. Conclusion By using both sequence and structure databases and by exploiting the latest techniques in machine learning it is possible to routinely predict protein secondary structure with an accuracy well above 80%. A program and web server, called PROTEUS, that performs these secondary structure predictions is accessible at . For high throughput or batch sequence analyses, the PROTEUS programs, databases (and server) can be downloaded and run locally. PMID:16774686

  4. 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.

  5. A graphic approach to evaluate algorithms of secondary structure prediction.

    PubMed

    Zhang, C T; Zhang, R

    2000-04-01

    Algorithms of secondary structure prediction have undergone the developments of nearly 30 years. However, the problem of how to appropriately evaluate and compare algorithms has not yet completely solved. A graphic method to evaluate algorithms of secondary structure prediction has been proposed here. Traditionally, the performance of an algorithm is evaluated by a number, i.e., accuracy of various definitions. Instead of a number, we use a graph to completely evaluate an algorithm, in which the mapping points are distributed in a three-dimensional space. Each point represents the predictive result of the secondary structure of a protein. Because the distribution of mapping points in the 3D space generally contains more information than a number or a set of numbers, it is expected that algorithms may be evaluated and compared by the proposed graphic method more objectively. Based on the point distribution, six evaluation parameters are proposed, which describe the overall performance of the algorithm evaluated. Furthermore, the graphic method is simple and intuitive. As an example of application, two advanced algorithms, i.e., the PHD and NNpredict methods, are evaluated and compared. It is shown that there is still much room for further improvement for both algorithms. It is pointed out that the accuracy for predicting either the alpha-helix or beta-strand in proteins with higher alpha-helix or beta-strand content, respectively, should be greatly improved for both algorithms. PMID:10798528

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

    PubMed

    Kumar, Prasun; Bansal, Manju

    2015-05-01

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

  7. Secondary electron emission from surfaces with small structure

    NASA Astrophysics Data System (ADS)

    Dzhanoev, A. R.; Spahn, F.; Yaroshenko, V.; Lühr, H.; Schmidt, J.

    2015-09-01

    It is found that for objects possessing small surface structures with differing radii of curvature the secondary electron emission (SEE) yield may be significantly higher than for objects with smooth surfaces of the same material. The effect is highly pronounced for surface structures of nanometer scale, often providing a more than 100 % increase of the SEE yield. The results also show that the SEE yield from surfaces with structure does not show a universal dependence on the energy of the primary, incident electrons as it is found for flat surfaces in experiments. We derive conditions for the applicability of the conventional formulation of SEE using the simplifying assumption of universal dependence. Our analysis provides a basis for studying low-energy electron emission from nanometer structured surfaces under a penetrating electron beam important in many technological applications.

  8. Machine learning approach for the prediction of protein secondary structure.

    PubMed

    King, R D; Sternberg, M J

    1990-11-20

    PROMIS (protein machine induction system), a program for machine learning, was used to generalize rules that characterize the relationship between primary and secondary structure in globular proteins. These rules can be used to predict an unknown secondary structure from a known primary structure. The symbolic induction method used by PROMIS was specifically designed to produce rules that are meaningful in terms of chemical properties of the residues. The rules found were compared with existing knowledge of protein structure: some features of the rules were already recognized (e.g. amphipathic nature of alpha-helices). Other features are not understood, and are under investigation. The rules produced a prediction accuracy for three states (alpha-helix, beta-strand and coil) of 60% for all proteins, 73% for proteins of known alpha domain type, 62% for proteins of known beta domain type and 59% for proteins of known alpha/beta domain type. We conclude that machine learning is a useful tool in the examination of the large databases generated in molecular biology. PMID:2254939

  9. Formation and stability of secondary structures in globular proteins

    NASA Astrophysics Data System (ADS)

    Bascle, J.; Garel, T.; Orland, H.

    1993-02-01

    We study two models for the formation and packing of helices and sheets in globular (compact) proteins. These models, based on weighted Hamiltonian paths on a regular lattice both exhibit a first order transition between a compact high temperature phase, with no extended secondary structures, and a quasi-frozen compact phase, with secondary structures invading the whole lattice. The quasi-frozen phase with very weak temperature dependence, is identified as the native phase of proteins, whereas the high-temperature phase may be relevant to the so-called molten globule state of proteins. Nous étudions deux modčles pour la formation et l'empilement d'hélices ou de feuillets dans la phase globulaire (compacte) des protéines. ces modčles, fondés sur des chemins hamiltoniens pondérés sur réseau, possčdent une transition de phase du premier ordre, entre (i) une phase haute température compacte, avec structures secondaires non étendues, et (ii) une phase compacte quasi-gelée, oů les structures secondaires envahissent tout le réseau. La phase quasi-gelée, qui a une dépendance en température trčs faible, est identifiée ŕ la phase native des protéines; la phase haute température est peut-ętre reliée ŕ la phase native “globule fondu” (molten globule) des protéines.

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

    ERIC Educational Resources Information Center

    Ellington, Roni; Wachira, James; Nkwanta, Asamoah

    2010-01-01

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

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

    PubMed

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

    1992-10-01

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

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

    PubMed Central

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

    2015-01-01

    The aggregation of human amylin has been strongly implicated in the progression of Type II diabetes. This 37-residue peptide forms a variety of secondary structures, including random coils, ?-helices, and ?-hairpins. The balance between these structures depends on the chemical environment, making amylin an ideal candidate to examine inherent biases in force fields. Rat amylin differs from human amylin by only 6 residues; however, it does not form fibrils. Therefore it provides a useful complement to human amylin in studies of the key events along the aggregation pathway. In this work, the free energy of rat and human amylin was determined as a function of ?-helix and ?-hairpin content for the Gromos96 53a6, OPLS-AA/L, CHARMM22/CMAP, CHARMM22*, Amberff99sb*-ILDN, and Amberff03w force fields using advanced sampling techniques, specifically bias exchange metadynamics. This work represents a first systematic attempt to evaluate the conformations and the corresponding free energy of a large, clinically relevant disordered peptide in solution across force fields. The NMR chemical shifts of rIAPP were calculated for each of the force fields using their respective free energy maps, allowing us to quantitatively assess their predictions. We show that the predicted distribution of secondary structures is sensitive to the choice of force-field: Gromos53a6 is biased towards ?-hairpins, while CHARMM22/CMAP predicts structures that are overly ?-helical. OPLS-AA/L favors disordered structures. Amberff99sb*-ILDN, AmberFF03w and CHARMM22* provide the balance between secondary structures that is most consistent with available experimental data. In contrast to previous reports, our findings suggest that the equilibrium conformations of human and rat amylin are remarkably similar, but that subtle differences arise in transient alpha-helical and beta-strand containing structures that the human peptide can more readily adopt. We hypothesize that these transient states enable dynamic pathways that facilitate the formation of aggregates and, eventually, amyloid fibrils. PMID:26221949

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

    DOE PAGESBeta

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

    2015-07-29

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

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

    SciTech Connect

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

    2015-07-29

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

  15. Lack of secondary structure characterizes the 5' ends of mammalian mitochondrial mRNAs.

    PubMed

    Jones, Christie N; Wilkinson, Kevin A; Hung, Kimberly T; Weeks, Kevin M; Spremulli, Linda L

    2008-05-01

    The mammalian mitochondrial genome encodes 13 proteins, which are synthesized at the direction of nine monocistronic and two dicistronic mRNAs. These mRNAs lack both 5' and 3' untranslated regions. The mechanism by which the specialized mitochondrial translational apparatus locates start codons and initiates translation of these leaderless mRNAs is currently unknown. To better understand this mechanism, the secondary structures near the start codons of all 13 open reading frames have been analyzed using RNA SHAPE chemistry. The extent of structure in these mRNAs as assessed experimentally is distinctly lower than would be predicted by current algorithms based on free energy minimization alone. We find that the 5' ends of all mitochondrial mRNAs are highly unstructured. The first 35 nucleotides for all mitochondrial mRNAs form structures with free energies less favorable than -3 kcal/mol, equal to or less than a single typical base pair. The start codons, which lie at the very 5' ends of these mRNAs, are accessible within single stranded motifs in all cases, making them potentially poised for ribosome binding. These data are consistent with a model in which the specialized mitochondrial ribosome preferentially allows passage of unstructured 5' sequences into the mRNA entrance site to participate in translation initiation. PMID:18367717

  16. 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)12

    PubMed Central

    Grünewald, Kay; Eckert, Manfred; Hirschberg, Joseph; Hagen, Christoph

    2000-01-01

    The unicellular green alga Haematococcus pluvialis Flotow is known for its massive accumulation of ketocarotenoids under various stress conditions. Therefore, this microalga is one of the favored organisms for biotechnological production of these antioxidative compounds. Astaxanthin makes up the main part of the secondary carotenoids and is accumulated mostly in an esterified form in extraplastidic lipid vesicles. We have studied phytoene desaturase, an early enzyme of the carotenoid biosynthetic pathway. The increase in the phytoene desaturase protein levels that occurs following induction is accompanied by a corresponding increase of its mRNA during the accumulation period, indicating that phytoene desaturase is regulated at the mRNA level. We also investigated the localization of the enzyme by western-blot analysis of cell fractions and by immunogold labeling of ultrathin sections for electron microscopy. In spite of the fact that secondary carotenoids accumulate outside the chloroplast, no extra pathway specific for secondary carotenoid biosynthesis in H. pluvialis was found, at least at this early stage in the biosynthesis. A transport process of carotenoids from the site of biosynthesis (chloroplast) to the site of accumulation (cytoplasmatic located lipid vesicles) is implicated. PMID:10759523

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

    PubMed Central

    Belter, Agnieszka; Gudanis, Dorota; Rolle, Katarzyna; Piwecka, Monika; Gdaniec, Zofia; Naskr?t-Barciszewska, Miros?awa Z.; Barciszewski, Jan

    2014-01-01

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

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

    PubMed

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

    2015-07-01

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

  19. A new distance for high level RNA secondary structure comparison.

    PubMed

    Allali, Julien; Sagot, Marie-France

    2005-01-01

    We describe an algorithm for comparing two RNA secondary structures coded in the form of trees that introduces two new operations, called node fusion and edge fusion, besides the tree edit operations of deletion, insertion, and relabeling classically used in the literature. This allows us to address some serious limitations of the more traditional tree edit operations when the trees represent RNAs and what is searched for is a common structural core of two RNAs. Although the algorithm complexity has an exponential term, this term depends only on the number of successive fusions that may be applied to a same node, not on the total number of fusions. The algorithm remains therefore efficient in practice and is used for illustrative purposes on ribosomal as well as on other types of RNAs. PMID:17044160

  20. Peptoid nanosheets exhibit a new secondary-structure motif

    NASA Astrophysics Data System (ADS)

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

    2015-10-01

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

  1. Peptoid nanosheets exhibit a new secondary-structure motif.

    PubMed

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

    2015-10-15

    A promising route to the synthesis of protein-mimetic materials that are capable of complex functions, such as molecular recognition and catalysis, is provided by sequence-defined peptoid polymers--structural relatives of biologically occurring polypeptides. Peptoids, which are relatively non-toxic and resistant to degradation, can fold into defined structures through a combination of sequence-dependent interactions. However, the range of possible structures that are accessible to peptoids and other biological mimetics is unknown, and our ability to design protein-like architectures from these polymer classes is limited. Here we use molecular-dynamics simulations, together with scattering and microscopy data, to determine the atomic-resolution structure of the recently discovered peptoid nanosheet, an ordered supramolecular assembly that extends macroscopically in only two dimensions. Our simulations show that nanosheets are structurally and dynamically heterogeneous, can be formed only from peptoids of certain lengths, and are potentially porous to water and ions. Moreover, their formation is enabled by the peptoids' adoption of a secondary structure that is not seen in the natural world. This structure, a zigzag pattern that we call a ?('sigma')-strand, results from the ability of adjacent backbone monomers to adopt opposed rotational states, thereby allowing the backbone to remain linear and untwisted. Linear backbones tiled in a brick-like way form an extended two-dimensional nanostructure, the ?-sheet. The binary rotational-state motif of the ?-strand is not seen in regular protein structures, which are usually built from one type of rotational state. We also show that the concept of building regular structures from multiple rotational states can be generalized beyond the peptoid nanosheet system. PMID:26444241

  2. Template-directed synthesis of a small molecule-antisense conjugate targeting an mRNA structure

    PubMed Central

    Liu, Yang; Rodriguez, Lilia; Wolfe, Michael S.

    2014-01-01

    The targeting of structural features in mRNA with specificity remains a great chemical challenge. A hairpin structure near exon 10 in the pre-mRNA encoding the tau protein controls its splicing, and dementia-causing mutations that disrupt this structure increase exon 10 splicing. We previously reported the discovery of small molecules, mitoxantrone (MTX) and analogs, which bind to the tau RNA hairpin structure and the design of bipartite antisense oligonucleotides (ASOs) that simultaneously bind to the discontinuous sequences that flank this hairpin. Herein we report the synthesis of a bipartite ASO conjugated to MTX using the tau RNA hairpin and flanking sequences as a template. A set of six MTX analogs, each containing a linker-azide, and a set of ten bipartite ASOs, each containing a branched linker-alkyne, were synthesized and tested in combinatorial fashion for their ability to conjugate in the presence or absence of template RNA. A single template-dependent MTX–ASO conjugate was identified from among the 60 reaction mixtures, demonstrating that the MTX and ASO precursors could simultaneously bind the RNA template and allow proper positioning of azide and alkyne for 1,3-cycloaddition. While the MTX–ASO conjugate proved too cytotoxic for cell-based assays, the conjugate inhibited tau exon 10 splicing under cell-free conditions more effectively than MTX or bipartite ASO alone. PMID:24691171

  3. Hot spot of structural ambivalence in prion protein revealed by secondary structure principal component analysis.

    PubMed

    Yamamoto, Norifumi

    2014-08-21

    The conformational conversion of proteins into an aggregation-prone form is a common feature of various neurodegenerative disorders including Alzheimer's, Huntington's, Parkinson's, and prion diseases. In the early stage of prion diseases, secondary structure conversion in prion protein (PrP) causing ?-sheet expansion facilitates the formation of a pathogenic isoform with a high content of ?-sheets and strong aggregation tendency to form amyloid fibrils. Herein, we propose a straightforward method to extract essential information regarding the secondary structure conversion of proteins from molecular simulations, named secondary structure principal component analysis (SSPCA). The definite existence of a PrP isoform with an increased ?-sheet structure was confirmed in a free-energy landscape constructed by mapping protein structural data into a reduced space according to the principal components determined by the SSPCA. We suggest a "spot" of structural ambivalence in PrP-the C-terminal part of helix 2-that lacks a strong intrinsic secondary structure, thus promoting a partial ?-helix-to-?-sheet conversion. This result is important to understand how the pathogenic conformational conversion of PrP is initiated in prion diseases. The SSPCA has great potential to solve various challenges in studying highly flexible molecular systems, such as intrinsically disordered proteins, structurally ambivalent peptides, and chameleon sequences. PMID:25101991

  4. SABA (secondary structure assignment program based on only alpha carbons): a novel pseudo center geometrical criterion for accurate assignment of protein secondary structures.

    PubMed

    Park, Sang Youn; Yoo, Min-Jae; Shin, Jaemin; Cho, Kwang-Hwi

    2011-02-01

    Most widely used secondary structure assignment methods such as DSSP identify structural elements based on N-H and C=O hydrogen bonding patterns from X-ray or NMR-determined coordinates. Secondary structure assignment algorithms using limited C? information have been under development as well, but their accuracy is only ~80% compared to DSSP. We have hereby developed SABA (Secondary Structure Assignment Program Based on only Alpha Carbons) with~90% accuracy. SABA defines a novel geometrical parameter, termed a pseudo center, which is the midpoint of two continuous C?s. SABA is capable of identifying ?-helices, 3(10)-helices, and ?-strands with high accuracy by using cut-off criteria on distances and dihedral angles between two or more pseudo centers. In addition to assigning secondary structures to C?-only structures, algorithms using limited C? information with high accuracy have the potential to enhance the speed of calculations for high capacity structure comparison. PMID:21345311

  5. Secondary structure in the 3' UTR of EGF and the choice of reverse transcriptases affect the detection of message diversity by RT-PCR.

    PubMed

    Brooks, E M; Sheflin, L G; Spaulding, S W

    1995-11-01

    The secondary structure in mRNA is essential for many processes, but it can present a technical problem in making full-length cDNA with reverse transcriptases. Furthermore, different reverse transcriptases have differing abilities to transcribe through regions with secondary structure, which can alter the products obtained by reverse-transcribing RNA and then PCR-amplifying the product (RT-PCR). We have been interested in studying the posttranscriptional regulation of epidermal growth factor by RT-PCR and have tested the ability of several reverse transcriptases to reverse transcribe the 3'-untranslated region (3'UTR), a region that contains substantial secondary structure. When low levels of either total RNA or poly(A)+ mRNA were used, we found avian myeloblastosis virus reverse transcriptase (AMV-RT) to be the most robust of all the enzymes tested. Furthermore, contrary to reports that AMV-RT is inhibited by tRNA--which should make it less effective than Moloney murine leukemia virus reverse transcriptase (MMLV-RT) at reverse-transcribing total RNA--adding tRNA to poly(A)+ RNA actually increased the amount of specific RT-PCR product obtained with AMV-RT while it decreased the amount of product and enhanced mispriming with MMLV-RT. We found that pre-incubation of the oligo(dT) primer with total RNA at elevated temperature prior to reverse transcription improved the efficiency of both native and modified MMLV-RTs. These findings support the concept that secondary structures in RNA differentially affect the abilities of different reverse transcriptases to detect transcript diversity and raise the possibility that such structures could affect quantitation using RT-PCR with internal mRNA standards. PMID:8588921

  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. Secondary Structure of Huntingtin Amino-Terminal Region

    SciTech Connect

    Kim, Mee Whi; Chelliah, Yogarany; Kim, Sang Woo; Otwinowski, Zbyszek; Bezprozvanny, Ilya

    2010-09-21

    Huntington's disease is a genetic neurodegenerative disorder resulting from polyglutamine (polyQ) expansion (>36Q) within the first exon of Huntingtin (Htt) protein. We applied X-ray crystallography to determine the secondary structure of the first exon (EX1) of Htt17Q. The structure of Htt17Q-EX1 consists of an amino-terminal {alpha} helix, poly17Q region, and polyproline helix formed by the proline-rich region. The poly17Q region adopts multiple conformations in the structure, including {alpha} helix, random coil, and extended loop. The conformation of the poly17Q region is influenced by the conformation of neighboring protein regions, demonstrating the importance of the native protein context. We propose that the conformational flexibility of the polyQ region observed in our structure is a common characteristic of many amyloidogenic proteins. We further propose that the pathogenic polyQ expansion in the Htt protein increases the length of the random coil, which promotes aggregation and facilitates abnormal interactions with other proteins in cells.

  8. Structure of the Saccharomyces cerevisiae Cet1-Ceg1 mRNA Capping Apparatus

    SciTech Connect

    Gu, Meigang; Rajashankar, Kanagalaghatta R.; Lima, Christopher D.

    2010-05-04

    The 5{prime} guanine-N7 cap is the first cotranscriptional modification of messenger RNA. In Saccharomyces cerevisiae, the first two steps in capping are catalyzed by the RNA triphosphatase Cet1 and RNA guanylyltransferase Ceg1, which form a complex that is directly recruited to phosphorylated RNA polymerase II (RNAP IIo), primarily via contacts between RNAP IIo and Ceg1. A 3.0 {angstrom} crystal structure of Cet1-Ceg1 revealed a 176 kDa heterotetrameric complex composed of one Cet1 homodimer that associates with two Ceg1 molecules via interactions between the Ceg1 oligonucleotide binding domain and an extended Cet1 WAQKW amino acid motif. The WAQKW motif is followed by a flexible linker that would allow Ceg1 to achieve conformational changes required for capping while maintaining interactions with both Cet1 and RNAP IIo. The impact of mutations as assessed through genetic analysis in S. cerevisiae is consonant with contacts observed in the Cet1-Ceg1 structure.

  9. Causal signals between codon bias, mRNA structure, and the efficiency of translation and elongation

    PubMed Central

    Pop, Cristina; Rouskin, Silvi; Ingolia, Nicholas T; Han, Lu; Phizicky, Eric M; Weissman, Jonathan S; Koller, Daphne

    2014-01-01

    Ribosome profiling data report on the distribution of translating ribosomes, at steady-state, with codon-level resolution. We present a robust method to extract codon translation rates and protein synthesis rates from these data, and identify causal features associated with elongation and translation efficiency in physiological conditions in yeast. We show that neither elongation rate nor translational efficiency is improved by experimental manipulation of the abundance or body sequence of the rare AGG tRNA. Deletion of three of the four copies of the heavily used ACA tRNA shows a modest efficiency decrease that could be explained by other rate-reducing signals at gene start. This suggests that correlation between codon bias and efficiency arises as selection for codons to utilize translation machinery efficiently in highly translated genes. We also show a correlation between efficiency and RNA structure calculated both computationally and from recent structure probing data, as well as the Kozak initiation motif, which may comprise a mechanism to regulate initiation. PMID:25538139

  10. Conformational Features of Topologically Classified RNA Secondary Structures

    PubMed Central

    Chiu, Jimmy Ka Ho; Chen, Yi-Ping Phoebe

    2012-01-01

    Background Current RNA secondary structure prediction approaches predict prevalent pseudoknots such as the H-pseudoknot and kissing hairpin. The number of possible structures increases drastically when more complex pseudoknots are considered, thus leading to computational limitations. On the other hand, the enormous population of possible structures means not all of them appear in real RNA molecules. Therefore, it is of interest to understand how many of them really exist and the reasons for their preferred existence over the others, as any new findings revealed by this study might enhance the capability of future structure prediction algorithms for more accurate prediction of complex pseudoknots. Methodology/Principal Findings A novel algorithm was devised to estimate the exact number of structural possibilities for a pseudoknot constructed with a specified number of base pair stems. Then, topological classification was applied to classify RNA pseudoknotted structures from data in the RNA STRAND database. By showing the vast possibilities and the real population, it is clear that most of these plausible complex pseudoknots are not observed. Moreover, from these classified motifs that exist in nature, some features were identified for further investigation. It was found that some features are related to helical stacking. Other features are still left open to discover underlying tertiary interactions. Conclusions Results from topological classification suggest that complex pseudoknots are usually some well-known motifs that are themselves complex or the interaction results of some special motifs. Heuristics can be proposed to predict the essential parts of these complex motifs, even if the required thermodynamic parameters are currently unknown. PMID:22792195

  11. Template secondary structure promotes polymerase jumping during PCR amplification.

    PubMed

    Viswanathan, V K; Krcmarik, K; Cianciotto, N P

    1999-09-01

    Pairs of primers flanking known miniTn10 transposon insertion sites were used to confirm the presence of the transposon in DNA isolated from Legionella pneumophila mutants. It was expected that the polymerase chain reaction products derived from the mutant template would be larger than those from the wild-type (WT) template due to the presence of the 1.8-kb transposon. Instead, it was observed that the mutant template yielded a product of almost the same size as that yielded by WT template. We present evidence to indicate that the aberrant product from the mutant template is a direct result of secondary structure of the template resulting from an inverted repeat sequence present in the miniTn10 transposon. PMID:10489610

  12. Rapid NMR screening of RNA secondary structure and binding.

    PubMed

    Helmling, Christina; Keyhani, Sara; Sochor, Florian; Fürtig, Boris; Hengesbach, Martin; Schwalbe, Harald

    2015-09-01

    Determination of RNA secondary structures by NMR spectroscopy is a useful tool e.g. to elucidate RNA folding space or functional aspects of regulatory RNA elements. However, current approaches of RNA synthesis and preparation are usually time-consuming and do not provide analysis with single nucleotide precision when applied for a large number of different RNA sequences. Here, we significantly improve the yield and 3' end homogeneity of RNA preparation by in vitro transcription. Further, by establishing a native purification procedure with increased throughput, we provide a shortcut to study several RNA constructs simultaneously. We show that this approach yields ?mol quantities of RNA with purities comparable to PAGE purification, while avoiding denaturation of the RNA. PMID:26188386

  13. Frame disruptions in human mRNA transcripts, and their relationship with splicing and protein structures

    PubMed Central

    Harrison, Paul; Yu, Zhan

    2007-01-01

    Background Efforts to gather genomic evidence for the processes of gene evolution are ongoing, and are closely coupled to improved gene annotation methods. Such annotation is complicated by the occurrence of disrupted mRNAs (dmRNAs), harbouring frameshifts and premature stop codons, which can be considered indicators of decay into pseudogenes. Results We have derived a procedure to annotate dmRNAs, and have applied it to human data. Subsequences are generated from parsing at key frame-disruption positions and are required to align significantly within any original protein homology. We find 419 high-quality human dmRNAs (3% of total). Significant dmRNA subpopulations include: zinc-finger-containing transcription factors with long disrupted exons, and antisense homologies to distal genes. We analysed the distribution of initial frame disruptions in dmRNAs with respect to positions of: (i) protein domains, (ii) alternatively-spliced exons, and (iii) regions susceptible to nonsense-mediated decay (NMD). We find significant avoidance of protein-domain disruption (indicating a selection pressure for this), and highly significant overrepresentation of disruptions in alternatively-spliced exons, and 'non-NMD' regions. We do not find any evidence for evolution of novelty in protein structures through frameshifting. Conclusion Our results indicate largely negative selection pressures related to frame disruption during gene evolution. PMID:17937804

  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. Secondary structure and NMR assignments of Bacillus circulans xylanase.

    PubMed Central

    Plesniak, L. A.; Wakarchuk, W. W.; McIntosh, L. P.

    1996-01-01

    Bacillus circulans xylanase (BCX) is a member of the family of low molecular weight endo-beta-(1,4)-xylanases. The main-chain 1H, 13C, and 15N resonances of this 20.4-kDa enzyme were assigned using heteronuclear NMR experiments recorded on a combination of selectively and uniformly labeled protein samples. Using chemical shift, NOE, J coupling, and amide hydrogen exchange information, 14 beta-strands, arranged in a network of three beta-sheets, and a single alpha-helix were identified in BCX. The NMR-derived secondary structure and beta-sheet topology agree closely with that observed in the crystal structure of this protein. The HN of Ile 118 has a strongly upfield-shifted resonance at 4.03 ppm, indicative of a potential amide-aromatic hydrogen bond to the indole ring of Trp 71. This interaction, which is conserved in all low molecular weight xylanases of known structure, may play an important role in establishing the active site conformation of these enzymes. Following hen egg white and bacteriophage T4 lysozymes, B. circulans xylanase represents the third family of beta-glycanases for which extensive NMR assignments have been reported. These assignments provide the background for detailed studies of the mechanism of carbohydrate recognition and hydrolysis by this bacterial xylanase. PMID:8762143

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

    NASA Astrophysics Data System (ADS)

    Rocha, L. F. O.

    2014-04-01

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

  17. IFNL3 mRNA structure is remodeled by a functional non-coding polymorphism associated with hepatitis C virus clearance

    PubMed Central

    Lu, Yi-Fan; Mauger, David M.; Goldstein, David B.; Urban, Thomas J.; Weeks, Kevin M.; Bradrick, Shelton S.

    2015-01-01

    Polymorphisms near the interferon lambda 3 (IFNL3) gene strongly predict clearance of hepatitis C virus (HCV) infection. We analyzed a variant (rs4803217 G/T) located within the IFNL3 mRNA 3? untranslated region (UTR); the G allele (protective allele) is associated with elevated therapeutic HCV clearance. We show that the IFNL3 3? UTR represses mRNA translation and the rs4803217 allele modulates the extent of translational regulation. We analyzed the structures of IFNL3 variant mRNAs at nucleotide resolution by SHAPE-MaP. The rs4803217?G allele mRNA forms well-defined 3? UTR structure while the T allele mRNA is more dynamic. The observed differences between alleles are among the largest possible RNA structural alterations that can be induced by a single nucleotide change and transform the UTR from a single well-defined conformation to one with multiple dynamic interconverting structures. These data illustrate that non-coding genetic variants can have significant functional effects by impacting RNA structure. PMID:26531896

  18. Formation of circular polyribosomes on eukaryotic mRNA without cap-structure and poly(A)-tail: a cryo electron tomography study

    PubMed Central

    Afonina, Zhanna A.; Myasnikov, Alexander G.; Shirokov, Vladimir A.; Klaholz, Bruno P.; Spirin, Alexander S.

    2014-01-01

    The polyribosomes newly formed on recombinant GFP-encoding mRNAs in a wheat germ cell-free translation system were analyzed using cryo-electron tomography, with sub-tomogram averaging of polysomal ribosomes and reconstruction of 3D structures of individual polyribosomes. The achieved level of resolution in the reconstructed polyribosomes allowed deducing the mRNA path by connecting adjacent exit and entry sites at the ribosomes inside each polyribosome. In this way, the circularity of a significant fraction (about 50%) of translating polyribosomes was proved in the case of the capped poly(A)-tailed mRNA, in agreement with the existing paradigm of the circularization via interaction of cap-bound initiation factor eIF4F with poly(A)-binding protein. However, translation of the capped mRNA construct without poly(A) tail, but with unspecific 3?-UTR derived from non-coding plasmid sequence, also led to the formation of circular polyribosomes in similar proportion (40%). Moreover, the polyribosomes formed on the uncapped non-polyadenylated mRNA with non-synergistic 5?- and 3?-UTRs proved to be circular as well, and appeared in the same proportion as in the previous cases. Thus, the formation of circular polyribosomes was found to be virtually independent of the presence of cap structure and poly(A) tail in mRNA, in contrast to the longstanding paradigm in the field. PMID:25016525

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

    DOE PAGESBeta

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

    2015-08-11

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

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

    SciTech Connect

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

    2015-08-11

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

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

    NASA Astrophysics Data System (ADS)

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

    2013-02-01

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

  2. Ire1-mediated decay in mammalian cells relies on mRNA sequence, structure, and translational status.

    PubMed

    Moore, Kristin; Hollien, Julie

    2015-08-15

    Endoplasmic reticulum (ER) stress occurs when misfolded proteins overwhelm the capacity of the ER, resulting in activation of the unfolded protein response (UPR). Ire1, an ER transmembrane nuclease and conserved transducer of the UPR, cleaves the mRNA encoding the transcription factor Xbp1 at a dual stem-loop (SL) structure, leading to Xbp1 splicing and activation. Ire1 also cleaves other mRNAs localized to the ER membrane through regulated Ire1-dependent decay (RIDD). We find that during acute ER stress in mammalian cells, Xbp1-like SLs within the target mRNAs are necessary for RIDD. Furthermore, depletion of Perk, a UPR transducer that attenuates translation during ER stress, inhibits RIDD in a substrate-specific manner. Artificially blocking translation of the SL region of target mRNAs fully restores RIDD in cells depleted of Perk, suggesting that ribosomes disrupt SL formation and/or Ire1 binding. This coordination between Perk and Ire1 may serve to spatially and temporally regulate RIDD. PMID:26108623

  3. 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

  4. Single-Molecule Measurements of the CCR5 mRNA Unfolding Pathways Michel de Messieres,

    E-print Network

    La Porta, Arthur

    and Molecular Genetics, University of Maryland, College Park, Maryland ABSTRACT Secondary or tertiary structure trapping techniques to investigate the structure of a Ŕ1 programmed ribosomal frameshift (Ŕ1 PRF) sequence element located in the CCR5 mRNA, which en- codes a coreceptor for HIV-1 and is, to our knowledge

  5. Structural Basis of mRNA Recognition and Cleavage by Toxin MazF and Its Regulation by Antitoxin MazE in Bacillus subtilis

    PubMed Central

    Simanshu, Dhirendra K.; Yamaguchi, Yoshihiro; Park, Jung-Ho; Inouye, Masayori

    2015-01-01

    SUMMARY MazF is an mRNA interferase, which, upon activation during stress conditions, cleaves mRNAs in a sequence-specific manner, resulting in cellular growth arrest. During normal growth conditions, the MazF toxin is inactivated through binding to its cognate antitoxin, MazE. How MazF specifically recognizes its mRNA target and carries out cleavage and how the formation of the MazE-MazF complex inactivates MazF remain unclear. We present crystal structures of MazF in complex with mRNA substrate and antitoxin MazE in Bacillus subtilis. The structure of MazF in complex with uncleavable UUdUACAUAA RNA substrate defines the molecular basis underlying the sequence-specific recognition of UACAU and the role of residues involved in the cleavage through site-specific mutational studies. The structure of the heterohexameric (MazF)2-(MazE)2-(MazF)2 complex in Bacillus subtilis, supplemented by mutational data, demonstrates that the positioning of the C-terminal helical segment of MazE within the RNA-binding channel of the MazF dimer prevents mRNA binding and cleavage by MazF. PMID:24120662

  6. Can computationally designed protein sequences improve secondary structure prediction?

    PubMed

    Bondugula, Rajkumar; Wallqvist, Anders; Lee, Michael S

    2011-05-01

    Computational sequence design methods are used to engineer proteins with desired properties such as increased thermal stability and novel function. In addition, these algorithms can be used to identify an envelope of sequences that may be compatible with a particular protein fold topology. In this regard, we hypothesized that sequence-property prediction, specifically secondary structure, could be significantly enhanced by using a large database of computationally designed sequences. We performed a large-scale test of this hypothesis with 6511 diverse protein domains and 50 designed sequences per domain. After analysis of the inherent accuracy of the designed sequences database, we realized that it was necessary to put constraints on what fraction of the native sequence should be allowed to change. With mutational constraints, accuracy was improved vs. no constraints, but the diversity of designed sequences, and hence effective size of the database, was moderately reduced. Overall, the best three-state prediction accuracy (Q(3)) that we achieved was nearly a percentage point improved over using a natural sequence database alone, well below the theoretical possibility for improvement of 8-10 percentage points. Furthermore, our nascent method was used to augment the state-of-the-art PSIPRED program by a percentage point. PMID:21282334

  7. 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

  8. 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

  9. Structural analysis of human 2'-O-ribose methyltransferases involved in mRNA cap structure formation

    NASA Astrophysics Data System (ADS)

    Smietanski, Miroslaw; Werner, Maria; Purta, Elzbieta; Kaminska, Katarzyna H.; Stepinski, Janusz; Darzynkiewicz, Edward; Nowotny, Marcin; Bujnicki, Janusz M.

    2014-01-01

    The 5' cap of human messenger RNA contains 2'-O-methylation of the first and often second transcribed nucleotide that is important for its processing, translation and stability. Human enzymes that methylate these nucleotides, termed CMTr1 and CMTr2, respectively, have recently been identified. However, the structures of these enzymes and their mechanisms of action remain unknown. In the present study, we solve the crystal structures of the active CMTr1 catalytic domain in complex with a methyl group donor and a capped oligoribonucleotide, thereby revealing the mechanism of specific recognition of capped RNA. This mechanism differs significantly from viral enzymes, thus providing a framework for their specific targeting. Based on the crystal structure of CMTr1, a comparative model of the CMTr2 catalytic domain is generated. This model, together with mutational analysis, leads to the identification of residues involved in RNA and methyl group donor binding.

  10. Algorithms for predicting the secondary structure of pairs and combinatorial sets of nucleic acid strands

    E-print Network

    Hutter, Frank

    Algorithms for predicting the secondary structure of pairs and combinatorial sets of nucleic acid;Abstract Secondary structure prediction of nucleic acid molecules is a very important prob- lem prediction of pairs of nucleic acid molecules (PairFold), and (2) finding which sequences, formed from

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

    E-print Network

    Hein, Jotun

    Pfold: RNA secondary structure prediction using stochastic context-free grammars Bjarne Knudsen Building for Pathogen Research, South Parks Road, Oxford OX1 3SY, UK Received February 15, 2003; Revised and Accepted April 5, 2003 ABSTRACT RNA secondary structures are important in many biological processes

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

    E-print Network

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

  13. RNA Folding with Soft Constraints: Reconciliation of Probing Data and Thermodynamic Secondary Structure Prediction

    E-print Network

    Mag Washietl, Stefan

    Thermodynamic folding algorithms and structure probing experiments are commonly used to determine the secondary structure of RNAs. Here we propose a formal framework to reconcile information from both prediction algorithms ...

  14. PCASSO: a fast and efficient C?-based method for accurately assigning protein secondary structure elements.

    PubMed

    Law, Sean M; Frank, Aaron T; Brooks, Charles L

    2014-09-15

    Proteins are often characterized in terms of their primary, secondary, tertiary, and quaternary structure. Algorithms such as define secondary structure of proteins (DSSP) can automatically assign protein secondary structure based on the backbone hydrogen-bonding pattern. However, the assignment of secondary structure elements (SSEs) becomes a challenge when only the C? coordinates are available. In this work, we present protein C-alpha secondary structure output (PCASSO), a fast and accurate program for assigning protein SSEs using only the C? positions. PCASSO achieves ?95% accuracy with respect to DSSP and takes ?0.1 s using a single processor to analyze a 1000 residue system with multiple chains. Our approach was compared with current state-of-the-art C?-based methods and was found to outperform all of them in both speed and accuracy. A practical application is also presented and discussed. PMID:24995959

  15. PCASSO: A Fast and Efficient C?-based Method for Accurately Assigning Protein Secondary Structure Elements

    PubMed Central

    Law, Sean M.; Frank, Aaron T.; Brooks, Charles L.

    2014-01-01

    Proteins are often characterized in terms of their primary, secondary, tertiary, and quaternary structure. Algorithms such as DSSP can automatically assign protein secondary structure based on the backbone hydrogen-bonding pattern. However, the assignment of secondary structure elements becomes a challenge when only the C? coordinates are available. In the current work, we present PCASSO (Protein C-Alpha Secondary Structure Output), a fast and accurate program for assigning protein secondary structure elements using only the C? positions. PCASSO achieves ~95% accuracy with respect to DSSP and takes ~0.1 s using a single processor to analyze a 1,000 residue system with multiple chains. Our approach was compared with current state-of-the-art C?-based methods and was found to outperform all of them in both speed and accuracy. A practical application is also presented and discussed. PMID:24995959

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

    PubMed

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

    2015-05-01

    The lifecycle, and therefore the virulence, of single-stranded (ss)-RNA viruses is regulated not only by their particular protein gene products, but also by the secondary and tertiary structure of their genomes. The secondary structure of the entire genomic RNA of satellite tobacco mosaic virus (STMV) was recently determined by selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE). The SHAPE analysis suggested a single highly extended secondary structure with much less branching than occurs in the ensemble of structures predicted by purely thermodynamic algorithms. Here we examine the solution-equilibrated STMV genome by direct visualization with cryo-electron microscopy (cryo-EM), using an RNA of similar length transcribed from the yeast genome as a control. The cryo-EM data reveal an ensemble of branching patterns that are collectively consistent with the SHAPE-derived secondary structure model. Thus, our results both elucidate the statistical nature of the secondary structure of large ss-RNAs and give visual support for modern RNA structure determination methods. Additionally, this work introduces cryo-EM as a means to distinguish between competing secondary structure models if the models differ significantly in terms of the number and/or length of branches. Furthermore, with the latest advances in cryo-EM technology, we suggest the possibility of developing methods that incorporate restraints from cryo-EM into the next generation of algorithms for the determination of RNA secondary and tertiary structures. PMID:25752599

  17. Measures for the assessment of fuzzy predictions of protein secondary structure.

    PubMed

    Lee, Julian

    2006-11-01

    Many of the recent secondary structure prediction methods incorporate the idea of fuzzy set theory, where instead of assigning a definite secondary structure to a query residue, probability for the residue being in each of the conformational states is estimated. Moreover, continuous assignment of conformational states to the experimentally observed protein structures can be performed in order to reflect inherent flexibility. Although various measures have been developed for evaluating performances of secondary structure prediction methods, they depend only on the most probable secondary structures. They do not assess the accuracy of the probabilities produced by fuzzy prediction methods, and they cannot incorporate information contained in continuous assignments of conformational states to observed structures. Three important measures for evaluating performance of a secondary structure prediction algorithm, Q score, Segment OVerlap (SOV) measure, and the k-state correlation coefficient (Corr), are deformed into fuzzy measures F score, Fuzzy OVerlap (FOV) measure, and the fuzzy correlation coefficient (Forr), so that the new measures not only assess probabilistic outputs of fuzzy prediction methods, but also incorporate information from continuous assignments of secondary structure. As an example of application, prediction results of four fuzzy secondary structure prediction methods, PSIPRED, PROFking, SABLE, and PREDICT, are assessed using the new fuzzy measures. PMID:16948155

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

    PubMed

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

    2015-11-01

    Amyloid fibers, implicated in a wide range of diseases, are formed when proteins misfold and stick together in long rope-like structures. As a natural mechanism, osmolytes can be used to modulate protein aggregation pathways with no interference with other cellular functions. The osmolyte sucrose delays fibrillation of the ribosomal protein S6 leading to softer and less shaped-defined fibrils. The molecular mechanism used by sucrose to delay S6 fibrillation was studied based on the two-state unfolding kinetics of the secondary and tertiary structures. It was concluded that the delay in S6 fibrillation results from stabilization and compaction of the slightly expanded tertiary native structure formed under fibrillation conditions. Interestingly, this compaction extends to almost all S6 tertiary structure but hardly affects its secondary structure. The part of the S6 tertiary structure that suffered more compaction by sucrose is known to be the first part to unfold, indicating that the native S6 has entered the unfolding pathway under fibrillation conditions. Proteins 2015; 83:2039-2051. © 2015 Wiley Periodicals, Inc. PMID:26344410

  19. The Globular State of the Single-Stranded RNA: Effect of the Secondary Structure Rearrangements

    PubMed Central

    Grigoryan, Zareh A.; Karapetian, Armen T.

    2015-01-01

    The mutual influence of the slow rearrangements of secondary structure and fast collapse of the long single-stranded RNA (ssRNA) in approximation of coarse-grained model is studied with analytic calculations. It is assumed that the characteristic time of the secondary structure rearrangement is much longer than that for the formation of the tertiary structure. A nonequilibrium phase transition of the 2nd order has been observed. PMID:26345143

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

    PubMed Central

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

    2015-01-01

    Summary 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 (Mex67NTF2L) 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

  1. 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

  2. Fragile X Mental Retardation Protein Interactions with a G quadruplex structure in the 3?-Untranslated Region of NR2B mRNA

    PubMed Central

    Stefanovic, Snezana; DeMarco, Brett A.; Underwood, Ayana; Williams, Kathryn R.; Bassell, Gary J.; Mihailescu, Mihaela Rita

    2015-01-01

    Fragile X syndrome, the most common cause of inherited intellectual disability, is caused by a trinucleotide CGG expansion in the 5?-untranslated region of the FMR1 gene, which leads to the loss of expression of the fragile X mental retardation protein (FMRP). FMRP, an RNA-binding protein that regulates the translation of specific mRNAs, has been shown to bind a subset of its mRNA targets by recognizing G quadruplex structures. It has been suggested that FMRP controls the local protein synthesis of several protein components of the Post Synaptic Density (PSD) in response to specific cellular needs. We have previously shown that the interactions between FMRP and mRNAs of the PSD scaffold proteins PSD-95 and Shank1 are mediated via stable G-quadruplex structures formed within the 3?-untranslated regions of these mRNAs. In this study we used biophysical methods to show that a comparable G quadruplex structure forms in the 3?-untranslated region of the glutamate receptor subunit NR2B mRNA encoding for a subunit of N-methyl-D-aspartate (NMDA) receptors that is recognized specifically by FMRP, suggesting a common theme for FMRP recognition of its dendritic mRNA targets. PMID:26412477

  3. Fragile X mental retardation protein interactions with a G quadruplex structure in the 3'-untranslated region of NR2B mRNA.

    PubMed

    Stefanovic, Snezana; DeMarco, Brett A; Underwood, Ayana; Williams, Kathryn R; Bassell, Gary J; Mihailescu, Mihaela Rita

    2015-11-10

    Fragile X syndrome, the most common cause of inherited intellectual disability, is caused by a trinucleotide CGG expansion in the 5'-untranslated region of the FMR1 gene, which leads to the loss of expression of the fragile X mental retardation protein (FMRP). FMRP, an RNA-binding protein that regulates the translation of specific mRNAs, has been shown to bind a subset of its mRNA targets by recognizing G quadruplex structures. It has been suggested that FMRP controls the local protein synthesis of several protein components of the post synaptic density (PSD) in response to specific cellular needs. We have previously shown that the interactions between FMRP and mRNAs of the PSD scaffold proteins PSD-95 and Shank1 are mediated via stable G-quadruplex structures formed within the 3'-untranslated regions of these mRNAs. In this study we used biophysical methods to show that a comparable G quadruplex structure forms in the 3'-untranslated region of the glutamate receptor subunit NR2B mRNA encoding for a subunit of N-methyl-d-aspartate (NMDA) receptors that is recognized specifically by FMRP, suggesting a common theme for FMRP recognition of its dendritic mRNA targets. PMID:26412477

  4. 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

  5. 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

  6. 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…

  7. 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…

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

    PubMed

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

    2011-01-25

    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

  9. The Role of Structural Elements of the 5'-Terminal Region of p53 mRNA in Translation under Stress Conditions Assayed by the Antisense Oligonucleotide Approach

    PubMed Central

    Swiatkowska, Agata; Zydowicz, Paulina; Gorska, Agnieszka; Suchacka, Julia; Dutkiewicz, Mariola; Ciesio?ka, Jerzy

    2015-01-01

    The p53 protein is one of the major factors responsible for cell cycle regulation and stress response. In the 5’-terminal region of p53 mRNA, an IRES element has been found which takes part in the translational regulation of p53 expression. Two characteristic hairpin motifs are present in this mRNA region: G56-C169, with the first AUG codon, and U180-A218, which interacts with the Hdm2 protein (human homolog of mouse double minute 2 protein). 2?-OMe modified antisense oligomers hybridizing to the 5'-terminal region of p53 mRNA were applied to assess the role of these structural elements in translation initiation under conditions of cellular stress. Structural changes in the RNA target occurring upon oligomers’ binding were monitored by the Pb2+-induced cleavage method. The impact of antisense oligomers on the synthesis of two proteins, the full-length p53 and its isoform ?40p53, was analysed in HT-29, MCF-7 and HepG2 cells, under normal conditions and under stress, as well as in vitro conditions. The results revealed that the hairpin U180-A218 and adjacent single-stranded region A219-A228 were predominantly responsible for high efficacy of IRES-mediated translation in the presence of stress factors. These motifs play a role of cis-acting elements which are able to modulate IRES activity, likely via interactions with protein factors. PMID:26513723

  10. Effect of the peptide secondary structure on the peptide amphiphile supramolecular structure and interactions.

    PubMed

    Missirlis, Dimitris; Chworos, Arkadiusz; Fu, Caroline J; Khant, Htet A; Krogstad, Daniel V; Tirrell, Matthew

    2011-05-17

    Bottom-up fabrication of self-assembled nanomaterials requires control over forces and interactions between building blocks. We report here on the formation and architecture of supramolecular structures constructed from two different peptide amphiphiles. Inclusion of four alanines between a 16-mer peptide and a 16 carbon long aliphatic tail resulted in a secondary structure shift of the peptide headgroups from ? helices to ? sheets. A concomitant shift in self-assembled morphology from nanoribbons to core-shell worm-like micelles was observed by cryogenic transmission electron microscopy (cryo-TEM) and atomic force microscopy (AFM). In the presence of divalent magnesium ions, these a priori formed supramolecular structures interacted in distinct manners, highlighting the importance of peptide amphiphile design in self-assembly. PMID:21488620

  11. Minimum message length inference of secondary structure from protein coordinate data

    PubMed Central

    Konagurthu, Arun S.; Lesk, Arthur M.; Allison, Lloyd

    2012-01-01

    Motivation: Secondary structure underpins the folding pattern and architecture of most proteins. Accurate assignment of the secondary structure elements is therefore an important problem. Although many approximate solutions of the secondary structure assignment problem exist, the statement of the problem has resisted a consistent and mathematically rigorous definition. A variety of comparative studies have highlighted major disagreements in the way the available methods define and assign secondary structure to coordinate data. Results: We report a new method to infer secondary structure based on the Bayesian method of minimum message length inference. It treats assignments of secondary structure as hypotheses that explain the given coordinate data. The method seeks to maximize the joint probability of a hypothesis and the data. There is a natural null hypothesis and any assignment that cannot better it is unacceptable. We developed a program SST based on this approach and compared it with popular programs, such as DSSP and STRIDE among others. Our evaluation suggests that SST gives reliable assignments even on low-resolution structures. Availability: http://www.csse.monash.edu.au/~karun/sst Contact: arun.konagurthu@monash.edu (or lloyd.allison@monash.edu) PMID:22689785

  12. Coherent two-dimensional infrared spectroscopy: Quantitative analysis of protein secondary structure in solution

    E-print Network

    Baiz, Carlos R.

    We present a method to quantitatively determine the secondary structure composition of globular proteins using coherent two-dimensional infrared (2DIR) spectroscopy of backbone amide I vibrations (1550–1720 cm?1). Sixteen ...

  13. 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

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

    PubMed

    Patel, Maulika S; Mazumdar, Himanshu S

    2014-11-21

    Protein structure prediction is of great relevance given the abundant genomic and proteomic data generated by the genome sequencing projects. Protein secondary structure prediction is addressed as a sub task in determining the protein tertiary structure and function. In this paper, a novel algorithm, KB-PROSSP-NN, which is a combination of knowledge base and modeling of the exceptions in the knowledge base using neural networks for protein secondary structure prediction (PSSP), is proposed. The knowledge base is derived from a proteomic sequence-structure database and consists of the statistics of association between the 5-residue words and corresponding secondary structure. The predicted results obtained using knowledge base are refined with a Backpropogation neural network algorithm. Neural net models the exceptions of the knowledge base. The Q3 accuracy of 90% and 82% is achieved on the RS126 and CB396 test sets respectively which suggest improvement over existing state of art methods. PMID:25128736

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

    PubMed

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

    2008-07-15

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

  16. Secondary structure assignment for conformationally irregular peptides: comparison between DSSP, STRIDE and KAKSI.

    PubMed

    Zhang, Yuan; Sagui, Celeste

    2015-02-01

    Secondary structure assignment codes were built to explore the regularities associated with the periodic motifs of proteins, such as those in backbone dihedral angles or in hydrogen bonds between backbone atoms. Precise structure assignment is challenging because real-life secondary structures are susceptible to bending, twist, fraying and other deformations that can distance them from their geometrical prototypes. Although results from codes such as DSSP and STRIDE converge in well-ordered structures, the agreement between the secondary structure assignments is known to deteriorate as the conformations become more distorted. Conformationally irregular peptides therefore offer a great opportunity to explore the differences between these codes. This is especially important for unfolded proteins and intrinsically disordered proteins, which are known to exhibit residual and/or transient secondary structure whose characterization is challenging. In this work, we have carried out Molecular Dynamics simulations of (relatively) disordered peptides, specifically gp41659-671 (ELLELDKWASLWN), the homopeptide polyasparagine (N18), and polyasparagine dimers. We have analyzed the resulting conformations with DSSP and STRIDE, based on hydrogen-bond patterns (and dihedral angles for STRIDE), and KAKSI, based on ?-Carbon distances; and carefully characterized the differences in structural assignments. The full-sequence Segment Overlap (SOV) scores, that quantify the agreement between two secondary structure assignments, vary from 70% for gp41659-671 (STRIDE as reference) to 49% for N18 (DSSP as reference). Major differences are observed in turns, in the distinction between ? and 310 helices, and in short parallel-sheet segments. PMID:25424660

  17. Improving protein secondary structure prediction based on short subsequences with local structure similarity

    PubMed Central

    2010-01-01

    Background When characterizing the structural topology of proteins, protein secondary structure (PSS) plays an important role in analyzing and modeling protein structures because it represents the local conformation of amino acids into regular structures. Although PSS prediction has been studied for decades, the prediction accuracy reaches a bottleneck at around 80%, and further improvement is very difficult. Results In this paper, we present an improved dictionary-based PSS prediction method called SymPred, and a meta-predictor called SymPsiPred. We adopt the concept behind natural language processing techniques and propose synonymous words to capture local sequence similarities in a group of similar proteins. A synonymous word is an n-gram pattern of amino acids that reflects the sequence variation in a protein’s evolution. We generate a protein-dependent synonymous dictionary from a set of protein sequences for PSS prediction. On a large non-redundant dataset of 8,297 protein chains (DsspNr-25), the average Q3 of SymPred and SymPsiPred are 81.0% and 83.9% respectively. On the two latest independent test sets (EVA Set_1 and EVA_Set2), the average Q3 of SymPred is 78.8% and 79.2% respectively. SymPred outperforms other existing methods by 1.4% to 5.4%. We study two factors that may affect the performance of SymPred and find that it is very sensitive to the number of proteins of both known and unknown structures. This finding implies that SymPred and SymPsiPred have the potential to achieve higher accuracy as the number of protein sequences in the NCBInr and PDB databases increases. Conclusions Our experiment results show that local similarities in protein sequences typically exhibit conserved structures, which can be used to improve the accuracy of secondary structure prediction. For the application of synonymous words, we demonstrate an example of a sequence alignment which is generated by the distribution of shared synonymous words of a pair of protein sequences. We can align the two sequences nearly perfectly which are very dissimilar at the sequence level but very similar at the structural level. The SymPred and SymPsiPred prediction servers are available at http://bio-cluster.iis.sinica.edu.tw/SymPred/. PMID:21143813

  18. Structure of the coding region and mRNA variants of the apyrase gene from pea (Pisum sativum)

    NASA Technical Reports Server (NTRS)

    Shibata, K.; Abe, S.; Davies, E.

    2001-01-01

    Partial amino acid sequences of a 49 kDa apyrase (ATP diphosphohydrolase, EC 3.6.1.5) from the cytoskeletal fraction of etiolated pea stems were used to derive oligonucleotide DNA primers to generate a cDNA fragment of pea apyrase mRNA by RT-PCR and these primers were used to screen a pea stem cDNA library. Two almost identical cDNAs differing in just 6 nucleotides within the coding regions were found, and these cDNA sequences were used to clone genomic fragments by PCR. Two nearly identical gene fragments containing 8 exons and 7 introns were obtained. One of them (H-type) encoded the mRNA sequence described by Hsieh et al. (1996) (DDBJ/EMBL/GenBank Z32743), while the other (S-type) differed by the same 6 nucleotides as the mRNAs, suggesting that these genes may be alleles. The six nucleotide differences between these two alleles were found solely in the first exon, and these mutation sites had two types of consensus sequences. These mRNAs were found with varying lengths of 3' untranslated regions (3'-UTR). There are some similarities between the 3'-UTR of these mRNAs and those of actin and actin binding proteins in plants. The putative roles of the 3'-UTR and alternative polyadenylation sites are discussed in relation to their possible role in targeting the mRNAs to different subcellular compartments.

  19. Sheath structure transition controlled by secondary electron emission

    NASA Astrophysics Data System (ADS)

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

    2015-04-01

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

  20. X-ray structure and activity of the yeast Pop2 protein: a nuclease subunit of the mRNA deadenylase complex

    PubMed Central

    Thore, Stéphane; Mauxion, Fabienne; Séraphin, Bertrand; Suck, Dietrich

    2003-01-01

    In Saccharomyces cerevisiae, a large complex, known as the Ccr4–Not complex, containing two nucleases, is responsible for mRNA deadenylation. One of these nucleases is called Pop2 and has been identified by similarity with PARN, a human poly(A) nuclease. Here, we present the crystal structure of the nuclease domain of Pop2 at 2.3 Ĺ resolution. The domain has the fold of the DnaQ family and represents the first structure of an RNase from the DEDD superfamily. Despite the presence of two non-canonical residues in the active site, the domain displays RNase activity on a broad range of RNA substrates. Site-directed mutagenesis of active-site residues demonstrates the intrinsic ability of the Pop2 RNase D domain to digest RNA. This first structure of a nuclease involved in the 3?–5? deadenylation of mRNA in yeast provides information for the understanding of the mechanism by which the Ccr4–Not complex achieves its functions. PMID:14618157

  1. A secondary-structure model for the self-cleaving region of Neurospora VS RNA.

    PubMed Central

    Beattie, T L; Olive, J E; Collins, R A

    1995-01-01

    Neurospora VS RNA performs an RNA-mediated self-cleavage reaction whose products contain 2',3'-cyclic phosphate and 5'-hydroxyl termini. This reaction is similar to those of hammerhead, hairpin, and hepatitis delta virus ribozymes; however, VS RNA is not similar in sequence to these other self-cleaving motifs. Here we propose a model for the secondary structure of the self-cleaving region of VS RNA, supported by site-directed mutagenesis and chemical modification structure probing data. The secondary structure of VS RNA is distinct from those of the other naturally occurring RNA self-cleaving domains. In addition to a unique secondary structure, several Mg-dependent interactions occur during the folding of VS RNA into its active tertiary conformation. Images Fig. 2 PMID:7753865

  2. ScrewFit: combining localization and description of protein secondary structure.

    PubMed

    Calligari, Paolo A; Kneller, Gerald R

    2012-12-01

    A new application of the ScrewFit algorithm [Kneller & Calligari (2006), Acta Cryst. D62, 302-311] is presented which adds the detection of protein secondary-structure elements to their detailed geometrical description in terms of a curve with intrinsic torsion. The extension is based on confidence and persistence criteria for the ScrewFit parameters which are established by analyzing the structural fluctuations of standard motifs in the SCOP fold classes. The agreement with the widely used DSSP method is comparable with the general consensus among other methods in the literature. This combination of secondary-structure detection and analysis is illustrated for the enzyme adenylate kinase. PMID:23151634

  3. Improving protein secondary structure prediction using a multi-modal BP method.

    PubMed

    Qu, Wu; Sui, Haifeng; Yang, Bingru; Qian, Wenbin

    2011-10-01

    Methods for predicting protein secondary structures provide information that is useful both in ab initio structure prediction and as additional restraints for fold recognition algorithms. Secondary structure predictions may also be used to guide the design of site directed mutagenesis studies, and to locate potential functionally important residues. In this article, we propose a multi-modal back propagation neural network (MMBP) method for predicting protein secondary structures. Using a Knowledge Discovery Theory based on Inner Cognitive Mechanism (KDTICM) method, we have constructed a compound pyramid model (CPM), which is composed of three layers of intelligent interface that integrate multi-modal back propagation neural network (MMBP), mixed-modal SVM (MMS), modified Knowledge Discovery in Databases (KDD(?)) process and so on. The CPM method is both an integrated web server and a standalone application that exploits recent advancements in knowledge discovery and machine learning to perform very accurate protein secondary structure predictions. Using a non-redundant test dataset of 256 proteins from RCASP256, the CPM method achieves an average Q(3) score of 86.13% (SOV99=84.66%). Extensive testing indicates that this is significantly better than any other method currently available. Assessments using RS126 and CB513 datasets indicate that the CPM method can achieve average Q(3) score approaching 83.99% (SOV99=80.25%) and 85.58% (SOV99=81.15%). By using both sequence and structure databases and by exploiting the latest techniques in machine learning it is possible to routinely predict protein secondary structure with an accuracy well above 80%. A program and web server, called CPM, which performs these secondary structure predictions, is accessible at http://kdd.ustb.edu.cn/protein_Web/. PMID:21880310

  4. Using neural network predicted secondary structure information in automatic protein NMR assignment.

    PubMed

    Choy, W Y; Sanctuary, B C; Zhu, G

    1997-01-01

    In CAPRI, an automated NMR assignment software package that was developed in our laboratory, both chemical shift values and coupling topologies of spin patterns are used in a procedure for amino acids recognition. By using a knowledge base of chemical shift distributions of the 20 amino acid types, fuzzy mathematics, and pattern recognition theory, the spin coupling topological graphs are mapped onto specific amino acid residues. In this work, we investigated the feasibility of using secondary structure information of proteins as predicted by neural networks in the automated NMR assignment. As the 1H and 13C chemical shifts of proteins are known to correlate to their secondary structures, secondary structure information is useful in improving the amino acid recognition. In this study, the secondary structures of proteins predicted by the PHD protein server and our own trained neural networks are used in the amino acid type recognition. The results show that the predicted secondary structure information can help to improve the accuracy of the amino acid recognition. PMID:9392858

  5. PreSSAPro: a software for the prediction of secondary structure by amino acid properties.

    PubMed

    Costantini, Susan; Colonna, Giovanni; Facchiano, Angelo M

    2007-10-01

    PreSSAPro is a software, available to the scientific community as a free web service designed to provide predictions of secondary structures starting from the amino acid sequence of a given protein. Predictions are based on our recently published work on the amino acid propensities for secondary structures in either large but not homogeneous protein data sets, as well as in smaller but homogeneous data sets corresponding to protein structural classes, i.e. all-alpha, all-beta, or alpha-beta proteins. Predictions result improved by the use of propensities evaluated for the right protein class. PreSSAPro predicts the secondary structure according to the right protein class, if known, or gives a multiple prediction with reference to the different structural classes. The comparison of these predictions represents a novel tool to evaluate what sequence regions can assume different secondary structures depending on the structural class assignment, in the perspective of identifying proteins able to fold in different conformations. The service is available at the URL http://bioinformatica.isa.cnr.it/PRESSAPRO/. PMID:17888742

  6. Protein Secondary Structure Prediction Using Sigmoid Belief Networks to Parameterize

    E-print Network

    Edinburgh, University of

    dependency in residue sequences. The results of numerical experiments indicate the usefulness of a protein from its amino acid sequence. Beginning with the seminal work of Qian and Sejnowski [4], many-side publi., ISBN 2-930307-04-8, pp. 81-86 #12;sequence-structure probability distribution based

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

    E-print Network

    Vannucci, Marina

    but distant in sequence. By performing an assessment of our method on 2 test sets we show how incorporation of the predictions. Software implementing the methods is provided as a web application and a stand. All structural files are available from the Protein Data Bank at http://www.rcsb.org. Funding

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

    ERIC Educational Resources Information Center

    Salminen, Timo; Marttunen, Miika; Laurinen, Leena

    2012-01-01

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

  9. 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

  10. Characterization of primary structure and tissue expression profile of the chicken apical sodium-dependent bile acid transporter mRNA.

    PubMed

    Nakao, N; Kaneda, H; Tsushima, N; Ohta, Y; Tanaka, M

    2015-04-01

    The ileal apical sodium-dependent bile acid cotransporter (ASBT) plays an essential role in the absorption of bile acids from intestinal lumina. ASBT cDNA has been cloned from mammalian and fish species, and the primary structure of the protein and expression properties of the mRNA have been characterized. In this study, we identified chicken ASBT mRNA by cDNA cloning. Chicken ASBT cDNA consisted of 91?bp of the 5'-untranslated region, 1,083?bp of the coding region, and 1,896?bp of the 3'-untranslated region. The cDNA encoded a protein of 360 amino acids showing significant sequence identity with mammalian and fish ASBT. The amino acid residues known to participate in the functions of mammalian ASBT were conserved in chicken ASBT. Real-time polymerase chain reaction analysis revealed that chicken ASBT mRNA was expressed at markedly higher levels in the ileum and proximal colon/rectum, relatively lower levels in the kidney, and very low levels in the jejunum and cecum. Expression levels in the ileum markedly increased after hatching, reached the highest levels on day 7 posthatching, and then decreased to adult levels. A similar expression pattern was observed in the proximal colon/rectum except for the significant decrease from day 7 posthatching to day 21 posthatching. These results suggest that chicken ASBT functions as a bile acid transporter in the ileum and proximal colon/rectum, particularly during the early posthatching period. PMID:25681609

  11. 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

  12. Secondary structure models of the 3' untranslated regions of diverse R2 RNAs.

    PubMed

    Ruschak, Amy M; Mathews, David H; Bibillo, Arkadiusz; Spinelli, Sherry L; Childs, Jessica L; Eickbush, Thomas H; Turner, Douglas H

    2004-06-01

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

  13. Secondary structure models of the 3? untranslated regions of diverse R2 RNAs

    PubMed Central

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

    2004-01-01

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

  14. 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

  15. 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

  16. New charge-bearing amino acid residues that promote ?-sheet secondary structure.

    PubMed

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

    2014-11-26

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

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

    PubMed

    Mattei, Eugenio; Pietrosanto, Marco; Ferrč, 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

  18. Structural and functional analysis of the interaction between the nucleoporin Nup98 and the mRNA export factor Rae1

    SciTech Connect

    Ren, Yi; Seo, Hyuk-Soo; Blobel, Günter; Hoelz, André

    2010-07-23

    The export of mRNAs is a multistep process, involving the packaging of mRNAs into messenger ribonucleoprotein particles (mRNPs), their transport through nuclear pore complexes, and mRNP remodeling events prior to translation. Ribonucleic acid export 1 (Rae1) and Nup98 are evolutionarily conserved mRNA export factors that are targeted by the vesicular stomatitis virus matrix protein to inhibit host cell nuclear export. Here, we present the crystal structure of human Rae1 in complex with the Gle2-binding sequence (GLEBS) of Nup98 at 1.65 {angstrom} resolution. Rae1 forms a seven-bladed {beta}-propeller with several extensive surface loops. The Nup98 GLEBS motif forms an {approx} 50-{angstrom}-long hairpin that binds with its C-terminal arm to an essentially invariant hydrophobic surface that extends over the entire top face of the Rae1 {beta}-propeller. The C-terminal arm of the GLEBS hairpin is necessary and sufficient for Rae1 binding, and we identify a tandem glutamate element in this arm as critical for complex formation. The Rae1 {center_dot} Nup98{sup GLEBS} surface features an additional conserved patch with a positive electrostatic potential, and we demonstrate that the complex possesses single-stranded RNA-binding capability. Together, these data suggest that the Rae1 {center_dot} Nup98 complex directly binds to the mRNP at several stages of the mRNA export pathway.

  19. Crystal Structure of A. aeolicus Argonaute, a Site-Specific DNA-Guided Endoribonuclease, Provides Insights into RISC-Mediated mRNA Cleavage

    PubMed Central

    Yuan, Yu-Ren; Pei, Yi; Ma, Jin-Biao; Kuryavyi, Vitaly; Zhadina, Maria; Meister, Gunter; Chen, Hong-Ying; Dauter, Zbigniew; Tuschl, Thomas; Patel, Dinshaw J.

    2015-01-01

    Summary Argonaute (Ago) proteins constitute a key component of the RNA-induced silencing complex (RISC). We report the crystal structure of Aquifex aeolicus Ago (Aa-Ago) together with binding and cleavage studies, which establish this eubacterial Ago as a bona fide guide DNA strand-mediated site-specific RNA endonuclease. We have generated a stereochemically robust model of the complex, where the guide DNA-mRNA duplex is positioned within a basic channel spanning the bilobal interface, such that the 5? phosphate of the guide strand can be anchored in a basic pocket, and the mRNA can be positioned for site-specific cleavage by RNase H-type divalent cation-coordinated catalytic Asp residues of the PIWI domain. Domain swap experiments involving chimeras of human Ago (hAgo1) and cleavage-competent hAgo2 reinforce the role of the PIWI domain in “slicer” activity. We propose a four-step Ago-mediated catalytic cleavage cycle model, which provides distinct perspectives into the mechanism of guide strand-mediated mRNA cleavage within the RISC. PMID:16061186

  20. Structural and Functional Analysis of the Interaction Between the Nucleoporin Nup98 and the mRNA Export Facto Rae1

    SciTech Connect

    Y Ren; H Seo; G Blobel; A Hoelz

    2011-12-31

    The export of mRNAs is a multistep process, involving the packaging of mRNAs into messenger ribonucleoprotein particles (mRNPs), their transport through nuclear pore complexes, and mRNP remodeling events prior to translation. Ribonucleic acid export 1 (Rae1) and Nup98 are evolutionarily conserved mRNA export factors that are targeted by the vesicular stomatitis virus matrix protein to inhibit host cell nuclear export. Here, we present the crystal structure of human Rae1 in complex with the Gle2-binding sequence (GLEBS) of Nup98 at 1.65 {angstrom} resolution. Rae1 forms a seven-bladed {beta}-propeller with several extensive surface loops. The Nup98 GLEBS motif forms an {approx}50-{angstrom}-long hairpin that binds with its C-terminal arm to an essentially invariant hydrophobic surface that extends over the entire top face of the Rae1 {beta}-propeller. The C-terminal arm of the GLEBS hairpin is necessary and sufficient for Rae1 binding, and we identify a tandem glutamate element in this arm as critical for complex formation. The Rae1 {center_dot} Nup98{sup GLEBS} surface features an additional conserved patch with a positive electrostatic potential, and we demonstrate that the complex possesses single-stranded RNA-binding capability. Together, these data suggest that the Rae1 {center_dot} Nup98 complex directly binds to the mRNP at several stages of the mRNA export pathway.

  1. Crystal structure of A. aeolicus argonaute, a site-specific DNA-guided endoribonuclease, provides insights into RISC-mediated mRNA cleavage

    SciTech Connect

    Yuan,Y.; Pei, Y.; Ma, J.; Kuryavyi, V.; Zhadina, M.; Meister, G.; Chen, H.; Dauter, Z.; Tuschi, T.; Patel, D.

    2005-01-01

    Argonaute (Ago) proteins constitute a key component of the RNA-induced silencing complex (RISC). We report the crystal structure of Aquifex aeolicus Ago (Aa-Ago) together with binding and cleavage studies, which establish this eubacterial Ago as a bona fide guide DNA strand-mediated site-specific RNA endonuclease. We have generated a stereochemically robust model of the complex, where the guide DNA-mRNA duplex is positioned within a basic channel spanning the bilobal interface, such that the 5' phosphate of the guide strand can be anchored in a basic pocket, and the mRNA can be positioned for site-specific cleavage by RNase H-type divalent cation-coordinated catalytic Asp residues of the PIWI domain. Domain swap experiments involving chimeras of human Ago (hAgo1) and cleavage-competent hAgo2 reinforce the role of the PIWI domain in 'slicer' activity. We propose a four-step Ago-mediated catalytic cleavage cycle model, which provides distinct perspectives into the mechanism of guide strand-mediated mRNA cleavage within the RISC.

  2. Direct-Coupling Analysis of nucleotide coevolution facilitates RNA secondary and tertiary structure prediction

    PubMed Central

    De Leonardis, Eleonora; Lutz, Benjamin; Ratz, Sebastian; Cocco, Simona; Monasson, Rémi; Schug, Alexander; Weigt, Martin

    2015-01-01

    Despite the biological importance of non-coding RNA, their structural characterization remains challenging. Making use of the rapidly growing sequence databases, we analyze nucleotide coevolution across homologous sequences via Direct-Coupling Analysis to detect nucleotide-nucleotide contacts. For a representative set of riboswitches, we show that the results of Direct-Coupling Analysis in combination with a generalized Nussinov algorithm systematically improve the results of RNA secondary structure prediction beyond traditional covariance approaches based on mutual information. Even more importantly, we show that the results of Direct-Coupling Analysis are enriched in tertiary structure contacts. By integrating these predictions into molecular modeling tools, systematically improved tertiary structure predictions can be obtained, as compared to using secondary structure information alone. PMID:26420827

  3. Direct-Coupling Analysis of nucleotide coevolution facilitates RNA secondary and tertiary structure prediction.

    PubMed

    De Leonardis, Eleonora; Lutz, Benjamin; Ratz, Sebastian; Cocco, Simona; Monasson, Rémi; Schug, Alexander; Weigt, Martin

    2015-12-01

    Despite the biological importance of non-coding RNA, their structural characterization remains challenging. Making use of the rapidly growing sequence databases, we analyze nucleotide coevolution across homologous sequences via Direct-Coupling Analysis to detect nucleotide-nucleotide contacts. For a representative set of riboswitches, we show that the results of Direct-Coupling Analysis in combination with a generalized Nussinov algorithm systematically improve the results of RNA secondary structure prediction beyond traditional covariance approaches based on mutual information. Even more importantly, we show that the results of Direct-Coupling Analysis are enriched in tertiary structure contacts. By integrating these predictions into molecular modeling tools, systematically improved tertiary structure predictions can be obtained, as compared to using secondary structure information alone. PMID:26420827

  4. Direct-Coupling Analysis of nucleotide coevolution facilitates RNA secondary and tertiary structure prediction

    E-print Network

    De Leonardis, Eleonora; Ratz, Sebastian; Cocco, Simona; Monasson, Remi; Schug, Alexander; Weigt, Martin

    2015-01-01

    Despite the biological importance of non-coding RNA, their structural characterization remains challenging. Making use of the rapidly growing sequence databases, we analyze nucleotide coevolution across homologous sequences via Direct-Coupling Analysis to detect nucleotide-nucleotide contacts. For a representative set of riboswitches, we show that the results of Direct-Coupling Analysis in combination with a generalized Nussinov algorithm systematically improve the results of RNA secondary structure prediction beyond traditional covariance approaches based on mutual information. Even more importantly, we show that the results of Direct-Coupling Analysis are enriched in tertiary structure contacts. By integrating these predictions into molecular modeling tools, systematically improved tertiary structure predictions can be obtained, as compared to using secondary structure information alone.

  5. A critical assessment of the secondary structure alpha-helices and their termini in proteins.

    PubMed

    Wilson, Claire L; Hubbard, Simon J; Doig, Andrew J

    2002-07-01

    Secondary structure prediction from amino acid sequence is a key component of protein structure prediction, with current accuracy at approximately 75%. We analysed two state-of-the-art secondary structure prediction methods, PHD and JPRED, comparing predictions with secondary structure assigned by the algorithms DSSP and STRIDE. The specific focus of our study was alpha-helix N-termini, as empirical free energy scales are available for residue preferences at N-terminal positions. Although these prediction methods perform well in general at predicting the alpha-helical locations and length distributions in proteins, they perform less well at predicting the correct helical termini. For example, although most predicted alpha-helices overlap a real alpha-helix (with relatively few completely missed or extra predicted helices), only one-third of JPRED and PHD predictions correctly identify the N-terminus. Analysis of neighbouring N-terminal sequences to predicted helical N-termini shows that the correct N-terminus is often within one or two residues. More importantly, the true N-terminal motif is, on average, more favourable as judged by our experimentally measured free energies. This suggests a simple, but powerful, strategy to improve secondary structure prediction using empirically derived energies to adjust the predicted output to a more favourable N-terminal sequence. PMID:12200536

  6. 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

  7. Description and recognition of regular and distorted secondary structures in proteins using the automated protein structure analysis method.

    PubMed

    Ranganathan, Sushilee; Izotov, Dmitry; Kraka, Elfi; Cremer, Dieter

    2009-08-01

    The Automated Protein Structure Analysis (APSA) method, which describes the protein backbone as a smooth line in three-dimensional space and characterizes it by curvature kappa and torsion tau as a function of arc length s, was applied on 77 proteins to determine all secondary structural units via specific kappa(s) and tau(s) patterns. A total of 533 alpha-helices and 644 beta-strands were recognized by APSA, whereas DSSP gives 536 and 651 units, respectively. Kinks and distortions were quantified and the boundaries (entry and exit) of secondary structures were classified. Similarity between proteins can be easily quantified using APSA, as was demonstrated for the roll architecture of proteins ubiquitin and spinach ferridoxin. A twenty-by-twenty comparison of all alpha domains showed that the curvature-torsion patterns generated by APSA provide an accurate and meaningful similarity measurement for secondary, super secondary, and tertiary protein structure. APSA is shown to accurately reflect the conformation of the backbone effectively reducing three-dimensional structure information to two-dimensional representations that are easy to interpret and understand. PMID:19205025

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

    PubMed

    Sanchita; Singh, Swati; Sharma, Ashok

    2014-11-01

    Withania somnifera (Ashwagandha) is an affluent storehouse of large number of pharmacologically active secondary metabolites known as withanolides. These secondary metabolites are produced by withanolide biosynthetic pathway. Very less information is available on structural and functional aspects of enzymes involved in withanolides biosynthetic pathways of Withiana somnifera. We therefore performed a bioinformatics analysis to look at functional and structural properties of these important enzymes. The pathway enzymes taken for this study were 3-Hydroxy-3-methylglutaryl coenzyme A reductase, 1-Deoxy-D-xylulose-5-phosphate synthase, 1-Deoxy-D-xylulose-5-phosphate reductase, farnesyl pyrophosphate synthase, squalene synthase, squalene epoxidase, and cycloartenol synthase. The prediction of secondary structure was performed for basic structural information. Three-dimensional structures for these enzymes were predicted. The physico-chemical properties such as pI, AI, GRAVY and instability index were also studied. The current information will provide a platform to know the structural attributes responsible for the function of these protein until experimental structures become available. PMID:25085038

  9. Ribosomal RNA Secondary Structure: Compensatory Mutations and Implications for Phylogenetic Analysis '

    E-print Network

    Hillis, David

    Ribosomal RNA Secondary Structure: Compensatory Mutations and Implications for Phylogenetic Using sequence data from the 28s ribosomal RNA (rRNA) genes of selected ver- tebrates, we investigated Ribosomal RNA (rRNA) genes have become firmly established as a useful sys- tematic data base across

  10. Novel tree edit operations for RNA secondary structure Julien Allali1

    E-print Network

    Sagot, Marie-France

    Bernard, Lyon I, 43 Bd du 11 Novembre 1918, 69622 Villeurbanne cedex, France, Marie-FranceNovel tree edit operations for RNA secondary structure comparison Julien Allali1 and Marie-France-sur-Marne, 77454 Marne-la-Vall´ee Cedex 2, France, allali@univ-mlv.fr 2 Inria Rh^one-Alpes, Universit´e Claude

  11. Scan2S: increasing the precision of PROSITE pattern motifs using secondary structure constraints.

    PubMed

    Skrabanek, Lucy; Niv, Masha Y

    2008-09-01

    Sequence signature databases such as PROSITE, which include protein pattern motifs indicative of a protein's function, are widely used for function prediction studies, cellular localization annotation, and sequence classification. Correct annotation relies on high precision of the motifs. We present a new and general approach for increasing the precision of established protein pattern motifs by including secondary structure constraints (SSCs). We use Scan2S, the first sequence motif-scanning program to optionally include SSCs, to augment PROSITE pattern motifs. The constraints were derived from either the DSSP secondary structure assignment or the PSIPRED predictions for PROSITE-documented true positive hits. The secondary structure-augmented motifs were scanned against all SwissProt sequences, for which secondary structure predictions were precalculated. Against this dataset, motifs with PSIPRED-derived SSCs exhibited improved performance over motifs with DSSP-derived constraints. The precision of 763 of the 782 PSIPRED-augmented motifs remained unchanged or increased compared to the original motifs; 26 motifs showed an absolute precision increase of 10-30%. We provide the complete set of augmented motifs and the Scan2S program at http://physiology.med.cornell.edu/go/scan2s. Our results suggest a general protocol for increasing the precision of protein pattern detection via the inclusion of SSCs. PMID:18320586

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

    PubMed

    Cuff, J A; Barton, G J

    1999-03-01

    A new dataset of 396 protein domains is developed and used to evaluate the performance of the protein secondary structure prediction algorithms DSC, PHD, NNSSP, and PREDATOR. The maximum theoretical Q3 accuracy for combination of these methods is shown to be 78%. A simple consensus prediction on the 396 domains, with automatically 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 Accuracy (SOV) is 75.4% for the consensus method on the 396-protein set. The secondary structure definition method DSSP defines 8 states, but these are reduced by most authors to 3 for prediction. Application of the different published 8- to 3-state reduction methods shows variation of over 3% on apparent prediction accuracy. This suggests that care should be taken to compare methods by the same reduction method. Two new sequence datasets (CB513 and CB251) are derived which are suitable for cross-validation of secondary structure prediction methods without artifacts due to internal homology. A fully automatic World Wide Web service that predicts protein secondary structure by a combination of methods is available via http://barton.ebi.ac.uk/. PMID:10081963

  13. RNA UK 2010 1099 Secondary structure of U6 small nuclear RNA

    E-print Network

    Rader, Stephen

    to group II self- splicing introns have led to the proposal that, like self-splicing introns, pre-mRNARNA UK 2010 1099 Secondary structure of U6 small nuclear RNA: implications for spliceosome assembly, Prince George, British Columbia, Canada V2N 4Z9 Abstract U6 snRNA (small nuclear RNA), one of five RNA

  14. 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…

  15. Elastic properties and secondary structure formation of single-stranded DNA at

    E-print Network

    Ritort, Felix

    Elastic properties and secondary structure formation of single-stranded DNA at monovalent and divalent salt conditions Alessandro Bosco1,2 , Joan Camunas-Soler3,4 and Felix Ritort3,4, * 1 SISSA salt conditions, and obtain its elastic parameters by fitting the FECs to semiflexible models

  16. Amide I’-II’ 2D IR spectroscopy provides enhanced protein secondary structural sensitivity

    E-print Network

    DeFlores, Lauren P.

    We demonstrate how multimode 2D IR spectroscopy of the protein amide I? and II? vibrations can be used to distinguish protein secondary structure. Polarization-dependent amide I??II? 2D IR experiments on poly-l-lysine in ...

  17. Towards New Structures of Post-Secondary Education; A Preliminary Statement of Issues.

    ERIC Educational Resources Information Center

    Organisation for Economic Cooperation and Development, Paris (France).

    This report deals with some of the basic problems member countries of the Organization for Economic Cooperation and Development have to face as they approach the threshold of mass higher education. Part I deals with the issues in the planning of future overall structures of post-secondary education. Specifically, it discusses: (1) prospects of…

  18. Prevent and Cure: RPA Cooperates with Mre11-Sae2 in DNA Secondary Structure Repair.

    PubMed

    Leach, David R F

    2015-11-01

    DNA inversion duplications are genome rearrangements observed in cancer. In this issue, Deng et al. (2015) demonstrate that in S. cerevisiae RPA and Mre11-Sae2 cooperate to prevent the formation of inversion duplications initiated at short DNA secondary structures. PMID:26545073

  19. Training Set Reduction Methods for Protein Secondary Structure Prediction in Single-Sequence Condition

    E-print Network

    Erdogan, Hakan

    Training Set Reduction Methods for Protein Secondary Structure Prediction in Single accuracy. One way to improve the performance of a single-sequence algorithm is to perform re-training. In this approach, first, the models used by the algorithm are trained by a representative set of proteins

  20. EFFECT OF SOLVENT AND TEMPERATURE ON SECONDARY AND TERTIARY STRUCTURE OF ZEIN BY CIRCULAR DICHROISM

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Circular dichroism studies were performed on various samples of commercial zein to determine how the secondary and tertiary structure changes with different solvents, temperatures or pH. It was found that alcoholic solvent type and common denaturants, such as SDS and low amounts of urea, had little...

  1. 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'…

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

    PubMed

    Milyutina, I A; Ignatov, M S

    2015-01-01

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

  3. BCL::Score—Knowledge Based Energy Potentials for Ranking Protein Models Represented by Idealized Secondary Structure Elements

    PubMed Central

    Woetzel, Nils; Karaka?, Mert; Staritzbichler, Rene; Müller, Ralf; Weiner, Brian E.; Meiler, Jens

    2012-01-01

    The topology of most experimentally determined protein domains is defined by the relative arrangement of secondary structure elements, i.e. ?-helices and ?-strands, which make up 50–70% of the sequence. Pairing of ?-strands defines the topology of ?-sheets. The packing of side chains between ?-helices and ?-sheets defines the majority of the protein core. Often, limited experimental datasets restrain the position of secondary structure elements while lacking detail with respect to loop or side chain conformation. At the same time the regular structure and reduced flexibility of secondary structure elements make these interactions more predictable when compared to flexible loops and side chains. To determine the topology of the protein in such settings, we introduce a tailored knowledge-based energy function that evaluates arrangement of secondary structure elements only. Based on the amino acid C? atom coordinates within secondary structure elements, potentials for amino acid pair distance, amino acid environment, secondary structure element packing, ?-strand pairing, loop length, radius of gyration, contact order and secondary structure prediction agreement are defined. Separate penalty functions exclude conformations with clashes between amino acids or secondary structure elements and loops that cannot be closed. Each individual term discriminates for native-like protein structures. The composite potential significantly enriches for native-like models in three different databases of 10,000–12,000 protein models in 80–94% of the cases. The corresponding application, “BCL::ScoreProtein,” is available at www.meilerlab.org. PMID:23173051

  4. Structural basis for the regulatory function of a complex zinc-binding domain in a replicative arterivirus helicase resembling a nonsense-mediated mRNA decay helicase

    PubMed Central

    Deng, Zengqin; Lehmann, Kathleen C.; Li, Xiaorong; Feng, Chong; Wang, Guoqiang; Zhang, Qi; Qi, Xiaoxuan; Yu, Lin; Zhang, Xingliang; Feng, Wenhai; Wu, Wei; Gong, Peng; Tao, Ye; Posthuma, Clara C.; Snijder, Eric J.; Gorbalenya, Alexander E.; Chen, Zhongzhou

    2014-01-01

    All positive-stranded RNA viruses with genomes >?7 kb encode helicases, which generally are poorly characterized. The core of the nidovirus superfamily 1 helicase (HEL1) is associated with a unique N-terminal zinc-binding domain (ZBD) that was previously implicated in helicase regulation, genome replication and subgenomic mRNA synthesis. The high-resolution structure of the arterivirus helicase (nsp10), alone and in complex with a polynucleotide substrate, now provides first insights into the structural basis for nidovirus helicase function. A previously uncharacterized domain 1B connects HEL1 domains 1A and 2A to a long linker of ZBD, which further consists of a novel RING-like module and treble-clef zinc finger, together coordinating three Zn atoms. On substrate binding, major conformational changes were evident outside the HEL1 domains, notably in domain 1B. Structural characterization, mutagenesis and biochemistry revealed that helicase activity depends on the extensive relay of interactions between the ZBD and HEL1 domains. The arterivirus helicase structurally resembles the cellular Upf1 helicase, suggesting that nidoviruses may also use their helicases for post-transcriptional quality control of their large RNA genomes. PMID:24369429

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

    PubMed

    Kneller, Gerald R; Hinsen, Konrad

    2015-07-01

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

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

    PubMed

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

    2015-09-01

    The determination of secondary structure topology is a critical step in deriving the atomic structures from the protein density maps obtained from electron cryomicroscopy technique. This step often relies on matching the secondary structure traces detected from the protein density map to the secondary structure sequence segments predicted from the amino acid sequence. Due to inaccuracies in both sources of information, a pool of possible secondary structure positions needs to be sampled. One way to approach the problem is to first derive a small number of possible topologies using existing matching algorithms, and then find the optimal placement for each possible topology. We present a dynamic programming method of ?(Nq(2)h) to find the optimal placement for a secondary structure topology. We show that our algorithm requires significantly less computational time than the brute force method that is in the order of ?(q(N) h). PMID:26244416

  7. Phenotypic variation and spatial structure of secondary chemistry in a natural population of a tropical tree species

    E-print Network

    Coley, Phyllis

    Phenotypic variation and spatial structure of secondary chemistry in a natural population. Phenotypic variation and spatial structure of secondary chemistry in a natural population of a tropical tree chemistry of the tropical tree Quararibea asterolepis, Pitt. (Bombacaceae) in a natural population on Barro

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

    PubMed Central

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

    2015-01-01

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

  9. Investigation of Oxide Layer Structure on Niobium Surfaces using a Secondary Ion Mass Spectrometer

    SciTech Connect

    Andy T. Wu

    2005-07-10

    Oxide layer structure on the surfaces of niobium (Nb) can be studied by continuously monitoring peaks of the secondary ions of Nb and its relevant oxides as a function of time during depth profiling measurements employing a secondary ion mass spectrometer (SIMS). This is based on the fact that different oxides have different cracking patterns. This new approach is much simpler and easier for studying oxide layer structure on Nb surfaces than the conventional approach through deconvolution of oxide peaks obtained from an x-ray photoemission spectrometer. Eventually it can be developed into an in-situ tool for monitoring the oxide layer structure on Nb surfaces prepared by various procedures. Preliminary results of SIMS measurements on the surfaces of Nb samples treated by buffered electropolishing and buffered chemical polishing will be reported.

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

    PubMed Central

    Weber, K; Kabsch, W

    1994-01-01

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

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

    PubMed Central

    Berkhout, B; Schoneveld, I

    1993-01-01

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

  12. Rigidity of poly-L-glutamic acid scaffolds: Influence of secondary and supramolecular structure.

    PubMed

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

    2015-09-01

    Poly-l-glutamic acid (PGA) is a widely used biomaterial, with applications ranging from drug delivery and biological glues to food products and as a tissue engineering scaffold. A biodegradable material with flexible conjugation functional groups, tunable secondary structure, and mechanical properties, PGA has potential as a tunable matrix material in mechanobiology. Recent studies in proteins connecting dynamics, nanometer length scale rigidity, and secondary structure suggest a new point of view from which to analyze and develop this promising material. We have characterized the structure, topology, and rigidity properties of PGA prepared with different molecular weights and secondary structures through various techniques including scanning electron microscopy, FTIR, light, and neutron scattering spectroscopy. On the length scale of a few nanometers, rigidity is determined by hydrogen bonding interactions in the presence of neutral species and by electrostatic interactions when the polypeptide is negatively charged. When probed over hundreds of nanometers, the rigidity of these materials is modified by long range intermolecular interactions that are introduced by the supramolecular structure. PMID:25690698

  13. Assessing the influence of electrostatic schemes on molecular dynamics simulations of secondary structure forming peptides

    NASA Astrophysics Data System (ADS)

    Monticelli, Luca; Simőes, Carlos; Belvisi, Laura; Colombo, Giorgio

    2006-04-01

    Electrostatic interactions play a fundamental role in determining the structure and dynamics of biomolecules in solution. However the accurate representation of electrostatics in classical mechanics based simulation approaches such as molecular dynamics (MD) is a challenging task. Given the growing importance that MD simulation methods are taking on in the study of protein folding, protein stability and dynamics, and in structure prediction and design projects, it is important to evaluate the influence that different electrostatic schemes have on the results of MD simulations. In this paper we performed long timescale simulations (500 ns) of two peptides, beta3 and RN24 forming different secondary structures, using for each peptide four different electrostatic schemes (namely PME, reaction field correction, and cut-off schemes with and without neutralizing counterions) for a total of eight 500 ns long MD runs. The structural and conformational features of each peptide under the different conditions were evaluated in terms of the time dependence of the flexibility, secondary structure evolution, hydrogen-bonding patterns, and several other structural parameters. The degree of sampling for each simulation as a function of the electrostatic scheme was also critically evaluated. Our results suggest that, while in the case of the short peptide RN24 the performances of the four methods are comparable, PME and RF schemes perform better in maintaining the structure close to the native one for the ?-sheet peptide beta3, in which long range contacts are mostly responsible for the definition of the native structure.

  14. A secondary mirror adjustment system with hexapod structure for optical telescope application

    NASA Astrophysics Data System (ADS)

    Zhou, Nan; Li, Chuang; Gao, Wei; Song, ZongXi; Zhao, Chao; Ren, GuoRui; Jing, Nan

    2014-09-01

    Benefiting from low cost, light weight and reduced volume in launch, deployable optical telescopes will be extensively applied in microsatellites. As a result of manufactured tolerance and external disturbance, the secondary mirror can't arrive at designed position precisely after a deployable telescope is unfolded. We investigate an adjustment system with six degrees of freedom based on hexapod structure to solve this problem. There are mainly four parts in this paper. Firstly, the adjustment methods of deployable telescopes for microsatellites are introduced. Generally several kinds of optical components can be adjusted to align a deployed telescope: primary mirror, tip/tilt mirror and secondary mirror. Due to its high sensitivity and convenience, the secondary mirror is chosen to collimate the optical system of the telescope. Secondly, an adjustment system with hexapod structure is designed for a secondary mirror with 85 mm diameter. After comparing the characteristics of step motors, piezo actuators and voice coil motors (VCMs), VCMs are selected as the linear actuators. By using optical gratings as displacement sensors in the system, we can make closed-loop control come true. The hexapod structure mainly consists of 6 VCMs, 6 optical gratings and 6 oblique legs with flexible hinges. The secondary mirror adjustment system is 83 mm in diameter and 55 mm high. It has tip/tilt rotational ranges of +/-2.205° with resolution of better than +/-0.007°, and translational ranges of +/-1.545 mm with resolution of better than +/-0.966 ?m. Thirdly, the maximum stress and the maximum deformation in the adjustment system are computed with finite element method. At last, the kinematics problems of the adjustment system are discussed.

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

    NASA Astrophysics Data System (ADS)

    Schuster, Peter

    2006-05-01

    RNA secondary structures are derived from RNA sequences, which are strings built form the natural four letter nucleotide alphabet, {AUGC}. These coarse-grained structures, in turn, are tantamount to constrained strings over a three letter alphabet. Hence, the secondary structures are discrete objects and the number of sequences always exceeds the number of structures. The sequences built from two letter alphabets form perfect structures when the nucleotides can form a base pair, as is the case with {GC} or {AU}, but the relation between the sequences and structures differs strongly from the four letter alphabet. A comprehensive theory of RNA structure is presented, which is based on the concepts of sequence space and shape space, being a space of structures. It sets the stage for modelling processes in ensembles of RNA molecules like evolutionary optimization or kinetic folding as dynamical phenomena guided by mappings between the two spaces. The number of minimum free energy (mfe) structures is always smaller than the number of sequences, even for two letter alphabets. Folding of RNA molecules into mfe energy structures constitutes a non-invertible mapping from sequence space onto shape space. The preimage of a structure in sequence space is defined as its neutral network. Similarly the set of suboptimal structures is the preimage of a sequence in shape space. This set represents the conformation space of a given sequence. The evolutionary optimization of structures in populations is a process taking place in sequence space, whereas kinetic folding occurs in molecular ensembles that optimize free energy in conformation space. Efficient folding algorithms based on dynamic programming are available for the prediction of secondary structures for given sequences. The inverse problem, the computation of sequences for predefined structures, is an important tool for the design of RNA molecules with tailored properties. Simultaneous folding or cofolding of two or more RNA molecules can be modelled readily at the secondary structure level and allows prediction of the most stable (mfe) conformations of complexes together with suboptimal states. Cofolding algorithms are important tools for efficient and highly specific primer design in the polymerase chain reaction (PCR) and help to explain the mechanisms of small interference RNA (si-RNA) molecules in gene regulation. The evolutionary optimization of RNA structures is illustrated by the search for a target structure and mimics aptamer selection in evolutionary biotechnology. It occurs typically in steps consisting of short adaptive phases interrupted by long epochs of little or no obvious progress in optimization. During these quasi-stationary epochs the populations are essentially confined to neutral networks where they search for sequences that allow a continuation of the adaptive process. Modelling RNA evolution as a simultaneous process in sequence and shape space provides answers to questions of the optimal population size and mutation rates. Kinetic folding is a stochastic process in conformation space. Exact solutions are derived by direct simulation in the form of trajectory sampling or by solving the master equation. The exact solutions can be approximated straightforwardly by Arrhenius kinetics on barrier trees, which represent simplified versions of conformational energy landscapes. The existence of at least one sequence forming any arbitrarily chosen pair of structures is granted by the intersection theorem. Folding kinetics is the key to understanding and designing multistable RNA molecules or RNA switches. These RNAs form two or more long lived conformations, and conformational changes occur either spontaneously or are induced through binding of small molecules or other biopolymers. RNA switches are found in nature where they act as elements in genetic and metabolic regulation. The reliability of RNA secondary structure prediction is limited by the accuracy with which the empirical parameters can be determined and by principal deficiencies, for example by the lack o

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

    SciTech Connect

    Gunisova, Stanislava; Bartosova, Zdenka; Kramara, Juraj; Nosek, Jozef; Tomaska, Lubomir

    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.

  17. On the structure and dynamics of secondary n-alkyl cations

    NASA Astrophysics Data System (ADS)

    East, Allan L. L.; Bu?ko, Tomáš; Hafner, Jürgen

    2009-09-01

    A variety of computational studies was undertaken to examine and establish the relative importance of open versus closed structures for unbranched secondary n-alkyl cations. First, the PW91 level of density functional theory was used to optimize over 20 minimum-energy structures of sec-pentyl, sec-hexyl, and sec-heptyl ions, demonstrating that closed structures are more stable than open ones on the potential energy surface (PES). Second, PW91 was used with a theoretical Andersen thermostat to perform a molecular dynamics simulation (150 ps) of C9H19+ at a typical catalytic temperature of 800 K, demonstrating that the structure preference is inverted on the free-energy surface. Third, both quantum (rigid-rotor/harmonic oscillator) and classical partition functions were used to demonstrate that the simulated structure-opening at catalytic temperatures is due to the floppiness of the open forms, which improves its free energy by both lowering its zero-point vibrational energy and increasing its molecular entropy. The particular conformer of the preferred open form (at 800 K) is dependent on length of alkyl ion, with pentyl ions preferring syn/anti structures but longer ions preferring open-clinal ones. These results, plus an additional set of PES optimized structures from an alternative level of theory (MP2/6-31G(d,p)), are used to discuss the likely nature of secondary n-alkyl ions.

  18. Predicting protein secondary structure and solvent accessibility with an improved multiple linear regression method.

    PubMed

    Qin, Sanbo; He, Yun; Pan, Xian-Ming

    2005-11-15

    We have improved the multiple linear regression (MLR) algorithm for protein secondary structure prediction by combining it with the evolutionary information provided by multiple sequence alignment of PSI-BLAST. On the CB513 dataset, the three states average overall per-residue accuracy, Q(3), reached 76.4%, while segment overlap accuracy, SOV99, reached 73.2%, using a rigorous jackknife procedure and the strictest reduction of eight states DSSP definition to three states. This represents an improvement of approximately 5% on overall per-residue accuracy compared with previous work. The relative solvent accessibility prediction also benefited from this combination of methods. The system achieved 77.7% average jackknifed accuracy for two states prediction based on a 25% relative solvent accessibility mode, with a Mathews' correlation coefficient of 0.548. The improved MLR secondary structure and relative solvent accessibility prediction server is available at http://spg.biosci.tsinghua.edu.cn/. PMID:16152601

  19. SOPMA: significant improvements in protein secondary structure prediction by consensus prediction from multiple alignments.

    PubMed

    Geourjon, C; Deléage, G

    1995-12-01

    Recently a new method called the self-optimized prediction method (SOPM) has been described to improve the success rate in the prediction of the secondary structure of proteins. In this paper we report improvements brought about by predicting all the sequences of a set of aligned proteins belonging to the same family. This improved SOPM method (SOPMA) correctly predicts 69.5% of amino acids for a three-state description of the secondary structure (alpha-helix, beta-sheet and coil) in a whole database containing 126 chains of non-homologous (less than 25% identity) proteins. Joint prediction with SOPMA and a neural networks method (PHD) correctly predicts 82.2% of residues for 74% of co-predicted amino acids. Predictions are available by Email to deleage@ibcp.fr or on a Web page (http:@www.ibcp.fr/predict.html). PMID:8808585

  20. 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.

  1. Solution secondary structure of calcium-saturated troponin C monomer determined by multidimensional heteronuclear NMR spectroscopy.

    PubMed Central

    Slupsky, C. M.; Reinach, F. C.; Smillie, L. B.; Sykes, B. D.

    1995-01-01

    The solution secondary structure of calcium-saturated skeletal troponin C (TnC) in the presence of 15% (v/v) trifluoroethanol (TFE), which has been shown to exist predominantly as a monomer (Slupsky CM, Kay CM, Reinach FC, Smillie LB, Sykes BD, 1995, Biochemistry 34, forthcoming), has been investigated using multidimensional heteronuclear nuclear magnetic resonance spectroscopy. The 1H, 15N, and 13C NMR chemical shift values for TnC in the presence of TFE are very similar to values obtained for calcium-saturated NTnC (residues 1-90 of skeletal TnC), calmodulin, and synthetic peptide homodimers. Moreover, the secondary structure elements of TnC are virtually identical to those obtained for calcium-saturated NTnC, calmodulin, and the synthetic peptide homodimers, suggesting that 15% (v/v) TFE minimally perturbs the secondary and tertiary structure of this stably folded protein. Comparison of the solution structure of calcium-saturated TnC with the X-ray crystal structure of half-saturated TnC reveals differences in the phi/psi angles of residue Glu 41 and in the linker between the two domains. Glu 41 has irregular phi/psi angles in the crystal structure, producing a kink in the B helix, whereas in calcium-saturated TnC, Glu 41 has helical phi/psi angles, resulting in a straight B helix. The linker between the N and C domains of calcium-saturated TnC is flexible in the solution structure. PMID:7670371

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

    PubMed

    Avinash, M B; Govindaraju, T

    2013-02-21

    Serendipitously, we found that isoleucine methylester functionalized perylenediimide 1 undergoes an extremely slow supramolecular helical assembly over a day's time. Surprisingly, heating led to irreversible chiral denaturation. However, reversible helical assembly could be achieved only in the presence of nondenatured aggregates of 1, which act as seeds. The intriguing functional relevance deduced from 1 was employed to draw parallels with the secondary structure of proteins, envisaging its plausible implications. PMID:26281870

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

    PubMed Central

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

    2015-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2015-09-01

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

  5. SVM-PB-Pred: SVM based protein block prediction method using sequence profiles and secondary structures.

    PubMed

    Suresh, V; Parthasarathy, S

    2014-01-01

    We developed a support vector machine based web server called SVM-PB-Pred, to predict the Protein Block for any given amino acid sequence. The input features of SVM-PB-Pred include i) sequence profiles (PSSM) and ii) actual secondary structures (SS) from DSSP method or predicted secondary structures from NPS@ and GOR4 methods. There were three combined input features PSSM+SS(DSSP), PSSM+SS(NPS@) and PSSM+SS(GOR4) used to test and train the SVM models. Similarly, four datasets RS90, DB433, LI1264 and SP1577 were used to develop the SVM models. These four SVM models developed were tested using three different benchmarking tests namely; (i) self consistency, (ii) seven fold cross validation test and (iii) independent case test. The maximum possible prediction accuracy of ~70% was observed in self consistency test for the SVM models of both LI1264 and SP1577 datasets, where PSSM+SS(DSSP) input features was used to test. The prediction accuracies were reduced to ~53% for PSSM+SS(NPS@) and ~43% for PSSM+SS(GOR4) in independent case test, for the SVM models of above two same datasets. Using our method, it is possible to predict the protein block letters for any query protein sequence with ~53% accuracy, when the SP1577 dataset and predicted secondary structure from NPS@ server were used. The SVM-PB-Pred server can be freely accessed through http://bioinfo.bdu.ac.in/~svmpbpred. PMID:23855661

  6. Precursors linked via the zipper-like structure or the filopodium during the secondary fusion of osteoclasts

    PubMed Central

    Takito, Jiro; Nakamura, Masanori

    2012-01-01

    We previously reported the transient appearance of an actin superstructure, called the zipper-like structure, during the primary fusion (fusion of mononuclear precursors) and the secondary fusion (fusion of multinucleated cells) of osteoclasts. Here, we focus on the actin-based superstructures that link two precursor cells during the secondary fusion event. In one type of secondary fusion, the osteoclasts transformed the podosome belts into the zipper-like structure at the site of cell contact and the apposed plasma membranes in the zipper-like structure attached to each other via a discontinuous interface. In another type of secondary fusion, the osteoclasts used a filopodium-like protrusion that linked the two cells. Both types of cell fusion required a lag period between the adhesion of the cells and the fusion of cell bodies. Thus, the secondary fusion of osteoclasts uses actin-based superstructures for cell-cell interactions before the definitive fusion of the plasma membranes. PMID:23181159

  7. HYPROSP: a hybrid protein secondary structure prediction algorithm--a knowledge-based approach.

    PubMed

    Wu, Kuen-Pin; Lin, Hsin-Nan; Chang, Jia-Ming; Sung, Ting-Yi; Hsu, Wen-Lian

    2004-01-01

    We develop a knowledge-based approach (called PROSP) for protein secondary structure prediction. The knowledge base contains small peptide fragments together with their secondary structural information. A quantitative measure M, called match rate, is defined to measure the amount of structural information that a target protein can extract from the knowledge base. Our experimental results show that proteins with a higher match rate will likely be predicted more accurately based on PROSP. That is, there is roughly a monotone correlation between the prediction accuracy and the amount of structure matching with the knowledge base. To fully utilize the strength of our knowledge base, a hybrid prediction method is proposed as follows: if the match rate of a target protein is at least 80%, we use the extracted information to make the prediction; otherwise, we adopt a popular machine-learning approach. This comprises our hybrid protein structure prediction (HYPROSP) approach. We use the DSSP and EVA data as our datasets and PSIPRED as our underlying machine-learning algorithm. For target proteins with match rate at least 80%, the average Q3 of PROSP is 3.96 and 7.2 better than that of PSIPRED on DSSP and EVA data, respectively. PMID:15448186

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

    PubMed Central

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

    2015-01-01

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

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

    PubMed Central

    SEIF, ELIAS R.; FORGET, LISE; MARTIN, NANCY C.; LANG, B. FRANZ

    2003-01-01

    The RNA subunit of mitochondrial RNase P (mtP-RNA) is encoded by a mitochondrial gene (rnpB) in several ascomycete fungi and in the protists Reclinomonas americana and Nephroselmis olivacea. By searching for universally conserved structural elements, we have identified previously unknown rnpB genes in the mitochondrial DNAs (mtDNAs) of two fission yeasts, Schizosaccharomyces pombe and Schizosaccharomyces octosporus; in the budding yeast Pichia canadensis; and in the archiascomycete Taphrina deformans. The expression of mtP-RNAs of the predicted size was experimentally confirmed in the two fission yeasts, and their precise 5? and 3? ends were determined by sequencing of cDNAs generated from circularized mtP-RNAs. Comparative RNA secondary structure modeling shows that in contrast to mtP-RNAs of the two protists R. americana and N. olivacea, those of ascomycete fungi all have highly reduced secondary structures. In certain budding yeasts, such as Saccharomycopsis fibuligera, we find only the two most conserved pairings, P1 and P4. A P18 pairing is conserved in Saccharomyces cerevisiae and its close relatives, whereas nearly half of the minimum bacterial consensus structure is retained in the RNAs of fission yeasts, Aspergillus nidulans and Taphrina deformans. The evolutionary implications of the reduction of mtP-RNA structures in ascomycetes will be discussed. PMID:12923256

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

    PubMed

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

    2003-09-01

    The RNA subunit of mitochondrial RNase P (mtP-RNA) is encoded by a mitochondrial gene (rnpB) in several ascomycete fungi and in the protists Reclinomonas americana and Nephroselmis olivacea. By searching for universally conserved structural elements, we have identified previously unknown rnpB genes in the mitochondrial DNAs (mtDNAs) of two fission yeasts, Schizosaccharomyces pombe and Schizosaccharomyces octosporus; in the budding yeast Pichia canadensis; and in the archiascomycete Taphrina deformans. The expression of mtP-RNAs of the predicted size was experimentally confirmed in the two fission yeasts, and their precise 5' and 3' ends were determined by sequencing of cDNAs generated from circularized mtP-RNAs. Comparative RNA secondary structure modeling shows that in contrast to mtP-RNAs of the two protists R. americana and N. olivacea, those of ascomycete fungi all have highly reduced secondary structures. In certain budding yeasts, such as Saccharomycopsis fibuligera, we find only the two most conserved pairings, P1 and P4. A P18 pairing is conserved in Saccharomyces cerevisiae and its close relatives, whereas nearly half of the minimum bacterial consensus structure is retained in the RNAs of fission yeasts, Aspergillus nidulans and Taphrina deformans. The evolutionary implications of the reduction of mtP-RNA structures in ascomycetes will be discussed. PMID:12923256

  11. 3512 IEEE TRANSACTIONS ON SIGNAL PROCESSING, VOL. 55, NO. 7, JULY 2007 Bayesian Protein Secondary Structure Prediction

    E-print Network

    Erdogan, Hakan

    that contribute to the stabilization of a protein molecule. In this paper, we introduce an alternative decoding3512 IEEE TRANSACTIONS ON SIGNAL PROCESSING, VOL. 55, NO. 7, JULY 2007 Bayesian Protein Secondary is an invaluable tool in determining the 3-D structure and function of proteins. Typically, protein secondary

  12. Insight into the secondary structure of chloramphenicol acetyltransferase type I — computer analysis and FT-IR spectroscopic characterization of the protein structure

    NASA Astrophysics Data System (ADS)

    Andreeva, A. E.; Karamancheva, I. R.

    2001-05-01

    The secondary structure of chloramphenicol O-acetyltransferase type I (CAT I) and an N-terminal deleted mutant has been studied by Fourier transform infrared spectroscopy. The analysis of the amide I band of different samples (KBr, hydrated films and buffer solution) by Fourier self-deconvolution followed by a curve fitting was performed. The spectroscopic data have been utilized to determine the ?-helix and ?-structure % contents, which depend strongly on the protein sample preparation. Furthermore, the secondary structure of the enzyme-inhibitor Crystal Violet complex was analyzed. The observed difference in the secondary structural contents suggests that some conformational changes of the enzyme are induced by the inhibitor after binding.

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

    NASA Astrophysics Data System (ADS)

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

    2015-10-01

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

  14. Secondary structure transitions and aggregation induced in dynorphin neuropeptides by the detergent sodium dodecyl sulfate.

    PubMed

    Hugonin, Loďc; Barth, Andreas; Gräslund, Astrid; Perálvarez-Marín, Alex

    2008-11-01

    Dynorphins, endogeneous opioid neuropeptides, function as ligands to the opioid kappa receptors and also induce non-opioid effects in neurons, probably related to direct membrane interactions. We have characterized the structure transitions of dynorphins (big dynorphin, dynorphin A and dynorphin B) induced by the detergent sodium dodecyl sulfate (SDS). In SDS titrations monitored by circular dichroism, we observed secondary structure conversions of the peptides from random coil to alpha-helix with a highly aggregated intermediate. As determined by Fourier transform infrared spectroscopy, this intermediate exhibited beta-sheet structure for dynorphin B and big dynorphin. In contrast, aggregated dynorphin A was alpha-helical without considerable beta-sheet content. Hydrophobicity analysis indicates that the YGGFLRR motif present in all dynorphins is prone to be inserted in the membrane. Comparing big dynorphin with dynorphin A and dynorphin B, we suggest that the potent neurotoxicity of big dynorphin could be related to the combination of amino acid sequences and secondary structure propensities of dynorphin A and dynorphin B, which may generate a synergistic effect for big dynorphin membrane perturbing properties. The induced aggregated alpha-helix of dynorphin A is also correlated with membrane perturbations, whereas the beta-sheet of dynorphin B does not correlate with membrane perturbations. PMID:18694723

  15. 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

  16. RNA-d2: a computer program for editing and display of RNA secondary structures.

    PubMed

    Perochon-Dorisse, J; Chetouani, F; Aurel, S; Iscolo, N; Michot, B

    1995-02-01

    RNA-d2 is a user-friendly program developed for interactively generating aesthetic and non-overlapping drawings of RNA secondary structures. It designed so that the drawings can be edited in a very natural and intuitive way, in order to emphasize structural homologies between several molecules, as well as the foldings themselves to update the base-pair sets according to new data. The program automatically produces a polygonal display in which the unpaired nucleotides are regularly positioned on circles and the stems harmoniously distributed on their periphery. RNA secondary structures can be encoded via the keyboard, but the program also automatically draws output files from thermodynamic prediction programs. The user interacts directly on different screen displays according to the editing functions. Rotation/translation of any subdomain and deletion of stems are performed on a coloured backbone view to make easier the identification of structural features, whereas addition of new base-pairings and numbering manipulation are realized on a complete polygonal view. Each modification is displayed in real time on the screen. When the display is obscured by numerous overlaps despite the colour code of the backbone view, an automatic function progressively straightens the subdomains which are highly compacted by very dissymmetric internal loops. RNA-d2 allows easy untangling and editing of RNA molecules > 1000 nucleotides long. PMID:7540936

  17. Role of Backbone Dipole Interactions in the Formation of Secondary and Supersecondary Structures of Proteins

    PubMed Central

    2015-01-01

    We present a generic solvated coarse-grained protein model that can be used to characterize the driving forces behind protein folding. Each amino acid is coarse-grained with two beads, a backbone, and a side chain. Although the backbone beads are modeled as polar entities, side chains are hydrophobic, polar, or charged, thus allowing the exploration of how sequence patterning determines a protein fold. The change in orientation of the atoms of the coarse-grained unit is captured by the addition of two oppositely charged dummy particles inside the backbone coarse-grained bead. These two dummy charges represent a dipole that can fluctuate, thus introducing structural polarization into the coarse-grained model. Realistic ?/? content is achieved de novo without any biases in the force field toward a particular secondary structure. The dipoles created by the dummy particles interact with each other and drive the protein models to fold into unique structures depending on the amino acid patterning and presence of capping residues. We have also characterized the role of dipole–dipole and dipole–charge interactions in shaping the secondary and supersecondary structure of proteins. Formation of helix bundles and ?-strands are also discussed. PMID:24932137

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

    PubMed

    Kou, Gaoshan; Feng, Yonge

    2015-09-01

    The biological function of protein is largely determined by its spatial structure. The research on the relationship between structure and function is the basis of protein structure prediction. However, the prediction of super secondary structure is an important step in the prediction of protein spatial structure. Many algorithms have been proposed for the prediction of protein super secondary structure. However, the parameters used by these methods were primarily based on amino acid sequences. In this paper, we proposed a novel model for predicting five kinds of protein super secondary structures based on the chemical shifts (CSs). Firstly, we analyzed the statistical distribution of chemical shifts of six nuclei in five kinds of protein super secondary structures by using the analysis of variance (ANOVA). Secondly, we used chemical shifts of six nuclei as features, and combined with quadratic discriminant analysis (QDA) to predict five kinds of protein super secondary structures. Finally, we achieved the averaged sensitivity, specificity and the overall accuracy of 81.8%, 95.19%, 82.91%, respectively in seven-fold cross-validation. Moreover, we have performed the prediction by combining the five different chemical shifts as features, the maximum overall accuracy up to 89.87% by using the C,C?,C?,N,H? of H? chemical shifts, which are clearly superior to that of the quadratic discriminant analysis (QDA) algorithm by using 20 amino acid compositions (AAC) as feature in the seven-fold cross-validation. These results demonstrated that chemical shifts (CSs) are indeed an outstanding parameter for the prediction of five kinds of super secondary structures. In addition, we compared the prediction of the quadratic discriminant analysis (QDA) with that of support vector machine (SVM) by using the same six CSs as features. The result suggested that the quadratic discriminant analysis method by using chemical shifts as features is a good predictor for protein super secondary structures. PMID:26087283

  19. Structural model of human ceruloplasmin based on internal triplication, hydrophilic/hydrophobic character, and secondary structure of domains.

    PubMed Central

    Ortel, T L; Takahashi, N; Putnam, F W

    1984-01-01

    A molecular model for the structure of human ceruloplasmin is proposed that is based on the determination of the complete amino acid sequence, studies of the products of limited proteolytic cleavage, calculations of the hydrophilic/hydrophobic character (hydropathy profile), and predictions of the local secondary structure. This multicopper oxidase (Mr approximately 132,000) consists of a single polypeptide chain (1046 amino acid residues) with four attached glucosamine oligosaccharides. Computer-assisted statistical analysis of the internal repetition in the amino acid sequence confirms that the entire polypeptide chain is divided into three contiguous homology units, each containing about 350 amino acid residues. Each homology unit is subdivided into three domains, designated A1, A2, and B, that differ in structure and probably in function. Calculations of the hydropathy profile and predictions of the secondary structure support a molecular model based on internal repetition of three homology units and help to identify characteristic features of the interdomain junctions. The alignment scores for internal duplication of pairings of the three homology units of ceruloplasmin exceed the scores yet reported for contiguous internal duplication of any other protein. This highly significant evidence for intragenic repetition suggests that the ceruloplasmin molecule evolved by tandem triplication of ancestral genes coding for a primordial copper oxidase. Images PMID:6589622

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

    NASA Astrophysics Data System (ADS)

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

    2015-04-01

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

  1. 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

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

    NASA Astrophysics Data System (ADS)

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

    2015-06-01

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

  3. The secondary structure of the 7SL RNA in the signal recognition particle: functional implications.

    PubMed Central

    Zwieb, C

    1985-01-01

    The secondary structure of the 7SL RNA in the signal recognition particle was determined by applying both a theoretical and an experimental approach. The compensatory base change approach was taken comparing the published sequences of human, Drosophila and Xenopus 7SL RNA's. The deduced secondary structure was confirmed by post-labeling of an RNase V1-nicked dog SRP with P32-pCp and RNA-ligase and analysis of the labeled RNA-fragments by non-denaturing/denaturing 2D polyacrylamide gel electrophoresis. Two interesting features in the secondary structure were revealed: Firstly, bases at positions 122 to 127 of the human 7SL RNA are not only able to pair with bases at positions 167 to 170, but also with a single-stranded region of the bases at positions 223 to 228, suggesting an alternative base pairing scheme for the 7SL RNA in all three organisms. In agreement with this finding, four different conformations were identified after transcription of the 7SL RNA from the genomic human clone. The involvement of the particular basepairing interaction postulated was confirmed by the analysis of a 7SL RNA deletion mutant (Sma1-409). Secondly, a significant sequence homology of the paired bases at positions 236 to 255 and 104 to 109 in 7SL RNA with bases in 5S ribosomal RNA at the positions 84 to 110 was noticed, suggesting that 5S ribosomal and 7SL RNA interact with the same target during protein biosynthesis. These findings are summarized by proposing a mechanism for the translational arrest of protein synthesis by the signal recognition particle using specific sequences and an alternative configuration in the 7SL RNA. Images PMID:2413423

  4. Active structural acoustic control using active constrained layer damping system and secondary acoustic controller

    NASA Astrophysics Data System (ADS)

    Lee, Joshua Taekyoung

    The active structural acoustic control of a beam with classical boundary conditions using an active constrained layer damping and a secondary acoustic controller is investigated. The beam is placed on an infinite rigid baffle. It is excited by a plane wave acoustic load and radiates sound into an anechoic acoustic medium. The primary goal of the control mechanisms is to reduce the radiated sound in a wide frequency range. The active constrained layer damping is used to dissipate the vibration energy of the beam. Although a damping device is usually more effective in mid- to high frequency ranges than in low frequency range, this research has developed a methodology that makes the active constrained layer damping effective in controlling resonant responses in the low frequency range. The secondary acoustic controller complements the active constrained layer damping by minimizing the subsequent radiated sound power. This acoustic controller is highly effective in reducing the overall noise in the low to mid-frequency ranges. In conclusion, it is found that, for a tonal excitation, the combined application of the active constrained layer damping and the secondary acoustic controller is an effective means to control acoustic response of a vibrating beam. By using them together, an efficient control of radiating sound power of vibrating beams is achieved in a wide frequency range.

  5. The effect of coherent structures on the secondary flow in a square duct

    NASA Astrophysics Data System (ADS)

    Sekimoto, A.; Pinelli, A.; Uhlmann, M.; Kawahara, G.

    The appearance of secondary flow of Prandtl's second kind is a well-known phenomenon in fully developed turbulent rectangular duct flow. The intensity of the secondary flow is two orders of magnitude smaller than that of the mean streamwise velocity; however, it plays an important role in the crossstreamwise momentum, heat and mass transfer. Our recent study [1] revealed that the mean secondary flow is a statistical footprint of the turbulent flow structures, i.e. streamwise vortices and streaks which are observed in the nearwall region, whose cross-sectional positions are constrained by the presence of the side walls at marginal Reynolds number (approximately 1100, based on the bulk velocity and the duct half width, corresponding to a friction Reynolds number of about 80). In this marginal case, one low-speed streak associated with a pair of counter-rotating streamwise vortices can exist over each wall and they are self-sustained [2]. When considering the higher Reynolds numbers, the increment of duct width in wall unit allows the simultaneous presence of multiple low velocity streaks and pairs of streamwise vortices upon the wall.

  6. Sequential sup 1 H NMR assignments and secondary structure of aponeocarzinostatin in solution

    SciTech Connect

    Remerowski, M.L.; Glaser, S.J.; Drobny, G.P.; Sieker, L.C. ); Samy, T.S.A. )

    1990-09-11

    Sequential assignments and secondary structural analysis have been accomplished for the 113-residue apoprotein of the antitumor drug neocarzinostatin (NCS) from Streptomyces carzinostaticus. A total of 98% of the main-chain and 77% of the side-chain resonances have been sequence specifically assigned by use of information from coherence transfer experiments and by sequential and interstrand NOEs. Because of the complexity of the NCS spectrum, several sequential assignments strategies were employed to complete the analysis. Apo-NCS consists of three antiparallel {beta}-sheeted domains by NMR analysis. There is an extensive four-strand antiparallel {beta}-sheet, and two two-stranded domains. One of the two-strand domains is contiguous, S72-N87, with chain reversal occurring through the region L77-R82. The other two-stranded domain has the section G16-A24 antiparallel with respect to the region S62-R70. This secondary structure is consistent with the crystal structure of holo-NCS at 2.8-{angstrom} resolution.

  7. A global sampling approach to designing and reengineering RNA secondary structures

    PubMed Central

    Levin, Alex; Lis, Mieszko; Ponty, Yann; O’Donnell, Charles W.; Devadas, Srinivas; Berger, Bonnie; Waldispühl, Jérôme

    2012-01-01

    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

  8. MacSECPROT: two programs in BASIC to evaluate protein secondary structure.

    PubMed

    Luttke, A

    1989-12-01

    Two interactive programs in BASIC are described, which provide useful tools to evaluate protein secondary structure. Output is given in two formats: (1) graphics are displayed on screen, which can be printed immediately, and (2) textfiles are saved to disk as permanent records and can be printed with a word-processing program. The programs are fast and easy to use and could be a valuable teaching aid in biochemical and molecular biology courses. Program lists are written in Microsoft BASIC for the Apple Macintosh, but can be adapted to other machines accepting graphic commands. PMID:2606566

  9. Improved prediction of protein secondary structure by use of sequence profiles and neural networks.

    PubMed Central

    Rost, B; Sander, C

    1993-01-01

    The explosive accumulation of protein sequences in the wake of large-scale sequencing projects is in stark contrast to the much slower experimental determination of protein structures. Improved methods of structure prediction from the gene sequence alone are therefore needed. Here, we report a substantial increase in both the accuracy and quality of secondary-structure predictions, using a neural-network algorithm. The main improvements come from the use of multiple sequence alignments (better overall accuracy), from "balanced training" (better prediction of beta-strands), and from "structure context training" (better prediction of helix and strand lengths). This method, cross-validated on seven different test sets purged of sequence similarity to learning sets, achieves a three-state prediction accuracy of 69.7%, significantly better than previous methods. In addition, the predicted structures have a more realistic distribution of helix and strand segments. The predictions may be suitable for use in practice as a first estimate of the structural type of newly sequenced proteins. PMID:8356056

  10. Improving the prediction of protein secondary structure in three and eight classes using recurrent neural networks and profiles.

    PubMed

    Pollastri, Gianluca; Przybylski, Darisz; Rost, Burkhard; Baldi, Pierre

    2002-05-01

    Secondary structure predictions are increasingly becoming the workhorse for several methods aiming at predicting protein structure and function. Here we use ensembles of bidirectional recurrent neural network architectures, PSI-BLAST-derived profiles, and a large nonredundant training set to derive two new predictors: (a) the second version of the SSpro program for secondary structure classification into three categories and (b) the first version of the SSpro8 program for secondary structure classification into the eight classes produced by the DSSP program. We describe the results of three different test sets on which SSpro achieved a sustained performance of about 78% correct prediction. We report confusion matrices, compare PSI-BLAST to BLAST-derived profiles, and assess the corresponding performance improvements. SSpro and SSpro8 are implemented as web servers, available together with other structural feature predictors at: http://promoter.ics.uci.edu/BRNN-PRED/. PMID:11933069

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

    PubMed

    Cuff, J A; Barton, G J

    2000-08-15

    The effect of training a neural network secondary structure prediction algorithm with different types of multiple sequence alignment profiles 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% (Q(3)) and 4.4% (SOV2) better than the PHD algorithm run on the same set of 406 sequence non-redundant proteins that were not used to train either method. Residues predicted by the new method with a confidence value of 5 or greater, have an average Q(3) accuracy of 84%, and cover 68% of the residues. Relative solvent accessibility based on a two state model, for 25, 5, and 0% accessibility are predicted at 76.2, 79.8, and 86. 6% accuracy respectively. The source of the improvements obtained from training with different representations of the same alignment data are described in detail. The new Jnet prediction method resulting from this study is available in the Jpred secondary structure prediction server, and as a stand-alone computer program from: http://barton.ebi.ac.uk/. Proteins 2000;40:502-511. PMID:10861942

  12. 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

  13. 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.

  14. NNvPDB: Neural Network based Protein Secondary Structure Prediction with PDB Validation

    PubMed Central

    Sakthivel, Seethalakshmi; S.K.M, Habeeb

    2015-01-01

    The predicted secondary structural states are not cross validated by any of the existing servers. Hence, information on the level of accuracy for every sequence is not reported by the existing servers. This was overcome by NNvPDB, which not only reported greater Q3 but also validates every prediction with the homologous PDB entries. NNvPDB is based on the concept of Neural Network, with a new and different approach of training the network every time with five PDB structures that are similar to query sequence. The average accuracy for helix is 76%, beta sheet is 71% and overall (helix, sheet and coil) is 66%. Availability http://bit.srmuniv.ac.in/cgi-bin/bit/cfpdb/nnsecstruct.pl PMID:26420924

  15. 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

  16. PROSIGN: a method for protein secondary structure assignment based on three-dimensional coordinates of consecutive C(alpha) atoms.

    PubMed

    Hosseini, Sayed-Rzgar; Sadeghi, Mehdi; Pezeshk, Hamid; Eslahchi, Changiz; Habibi, Mahnaz

    2008-12-01

    The automatic assignment of secondary structure from three-dimensional atomic coordinates of proteins is an essential step for the analysis and modeling of protein structures. So different methods based on different criteria have been designed to perform this task. We introduce a new method for protein secondary structure assignment based solely on C(alpha) coordinates. We introduce four certain relations between C(alpha) three-dimensional coordinates of consecutive residues, each of which applies to one of the four regular secondary structure categories: alpha-helix, 3(10)-helix, pi-helix and beta-strand. In our approach, the deviation of the C(alpha) coordinates of each residue from each relation is calculated. Based on these deviation values, secondary structures are assigned to all residues of a protein. We show that our method agrees well with popular methods as DSSP, STRIDE and assignments in PDB files. It is shown that our method gives more information about helix geometry leading to more accurate secondary structure assignment. PMID:18789769

  17. Impact of Microscale and Pilot-Scale Freeze-Drying on Protein Secondary Structures: Sucrose Formulations of Lysozyme and Catalase.

    PubMed

    Peters, Björn-Hendrik; Leskinen, Jari T T; Molnár, Ferdinand; Ketolainen, Jarkko

    2015-11-01

    Microscale (MS) freeze-drying offers rapid process cycles for early-stage formulation development. The effects of the MS approach on the secondary structures of two model proteins, lysozyme and catalase, were compared with pilot-scale (PS) vial freeze-drying. The secondary structures were assessed by attenuated total reflection Fourier transformed infrared spectroscopy. Formulations were made with increasing sucrose-protein ratios. Freeze-drying protocols involved regular cooling without thermal treatment and annealing with MS and PS equipment, and cooling rate variations with the MS. Principal component analysis of smoothed second-derivative amide I spectra revealed sucrose-protein ratio-dependent shifts toward ?-helical structures. Transferability of sucrose-protein formulations from MS to PS vial freeze-drying was evidenced at regular cooling rates. Local differences in protein secondary structures between the bottom and top of sucrose-catalase samples could be detected at the sucrose-catalase ratios of 1 and 2, this being related to the initial filling height and ice crystal morphology. Annealing revealed temperature, protein, formulation, and sample location-dependent effects influencing surface morphology at the top, or causing protein secondary structure perturbation at the bottom. With the MS approach, protein secondary structure differences at different cooling rates could be detected for sucrose-lysozyme samples at the sucrose-lysozyme ratio of 1. © 2015 Wiley Periodicals, Inc. and the American Pharmacists Association J Pharm Sci 104:3710-3721, 2015. PMID:26305147

  18. Laser Raman evidence for new cloverleaf secondary structures for eukaryotic 5.8S RNA and prokaryotic 5S RNA.

    PubMed Central

    Luoma, G A; Marshall, A G

    1978-01-01

    Neither of the two previously proposed secondary structures for eukaryotic 5.8S RNA is consistent with the present laser Raman results. A new, highly stable "cloverleaf" secondary structure not only fits the Raman data but also accounts for previously determined enzymatic partial cleavage patterns, base sequence and pairing homologies, and G-C and A-U base pair numbers and ratios. The new cloverleaf model also conserves several structural features (constant loops, bulges, and stems) consistent with known 5.8S RNA functions. Finally, we propose a similar new cloverleaf secondary structure for Escherichia coli 5S RNA, consonant with many known properties of prokaryotic 5S RNA. PMID:368804

  19. Alignment editing and identification of consensus secondary structures for nucleic acid sequences: interactive use of dot matrix representations.

    PubMed Central

    Davis, J P; Janji?, N; Pribnow, D; Zichi, D A

    1995-01-01

    We present a computer-aided approach for identifying and aligning consensus secondary structure within a set of functionally related oligonucleotide sequences aligned by sequence. The method relies on visualization of secondary structure using a generalization of the dot matrix representation appropriate for consensus sequence data sets. An interactive computer program implementing such a visualization of consensus structure has been developed. The program allows for alignment editing, data and display filtering and various modes of base pair representation, including co-variation. The utility of this approach is demonstrated with four sample data sets derived from in vitro selection experiments and one data set comprising tRNA sequences. Images PMID:7501472

  20. The importance of secondary structure in determining CO2-protein binding patterns.

    PubMed

    Drummond, Michael L; Wilson, Angela K; Cundari, Thomas R

    2012-06-01

    One potential means to decrease the level of atmospheric carbon dioxide is through the utilization of protein-CO(2) interactions. A recent bioinformatics analysis [Cundari TR et al. (2009) J Chem Inf Model 49:2111-2115] of these interactions revealed a marked disparity in CO(2) affinity between ?-helices and ?-sheets. In order to understand this difference, a series of molecular dynamics simulations was performed on polypeptide model systems. Numerous factors that may influence CO(2) affinity were systematically investigated, including the specific location of the amino acids within the secondary structural elements (SSEs), the partial charges on CO(2), chemical modifications made to the protein backbone, the inclusion of singly, doubly, and many functionalized residues, and the effect of solvent water. The differing abilities of the secondary structure types to participate in hydrogen bonding along the backbone were identified as being a crucial influence on CO(2) affinity; the lesser role of polypeptide-CO(2) electrostatic interactions was also noted. The effect of incorporating functionalized amino acid side chains, such as those possessed by Arg and His, on the affinity differs between the two structure types, and also strongly depends on the number included and the distance between them. The inclusion of explicit water molecules was found to attenuate all interactions, but did not change the overall trends in CO(2) affinity. Collectively, these results highlight the role of the backbone atoms in binding the CO(2) ligand, which will have important implications for efforts to ameliorate atmospheric carbon dioxide through the use of natural, designed, and modified proteins. PMID:22038461

  1. 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

  2. Design and analysis of supporting structure between the primary mirror and the secondary mirror on a space telescope

    NASA Astrophysics Data System (ADS)

    Wang, Chenjie; Chai, Wenyi; Feng, Liangjie; Yang, Wengang; Wang, Wei; Fan, Xuewu

    2015-10-01

    Mechanical stability is a significant segment for an on-axis space telescope to assure its assembly accuracy as well as the image quality in the rigorous space environment, supporting structure between the primary mirror and the secondary mirror as a main structure of the on-axis space telescope must be designed reasonably to meet the mission requirements of the space telescope. Meanwhile, in view of the limitation of the satellite launching cost, it is necessary to reduce the weight and power compensation during the supporting structure design based on the satisfaction of telescope performance. Two types of supporting structure for a space telescope are designed, one is three-tripod structure which has three tripods located on the optical bench to support the secondary mirror assemblies and keep the distance between the primary mirror and the secondary mirror, the other is barrel supporting structure which includes a tube and a secondary mirror support with four spider struts. To compare the mechanical performance and launching cost of the two kinds of supporting structure, both structural and thermal analysis model are established. The analysis results indicates that the three-tripod support is lighter, has better mechanical performance and needs less power compensation than the barrel support.

  3. Improved sequence-based prediction of protein secondary structures by combining vacuum-ultraviolet circular dichroism spectroscopy with neural network.

    PubMed

    Matsuo, Koichi; Watanabe, Hidenori; Gekko, Kunihiko

    2008-10-01

    Synchrotron-radiation vacuum-ultraviolet circular dichroism (VUVCD) spectroscopy can significantly improve the predictive accuracy of the contents and segment numbers of protein secondary structures by extending the short-wavelength limit of the spectra. In the present study, we combined VUVCD spectra down to 160 nm with neural-network (NN) method to improve the sequence-based prediction of protein secondary structures. The secondary structures of 30 target proteins (test set) were assigned into alpha-helices, beta-strands, and others by the DSSP program based on their X-ray crystal structures. Combining the alpha-helix and beta-strand contents estimated from the VUVCD spectra of the target proteins improved the overall sequence-based predictive accuracy Q(3) for three secondary-structure components from 59.5 to 60.7%. Incorporating the position-specific scoring matrix in the NN method improved the predictive accuracy from 70.9 to 72.1% when combining the secondary-structure contents, to 72.5% when combining the numbers of segments, and finally to 74.9% when filtering the VUVCD data. Improvement in the sequence-based prediction of secondary structures was also apparent in two other indices of the overall performance: the correlation coefficient (C) and the segment overlap value (SOV). These results suggest that VUVCD data could enhance the predictive accuracy to over 80% when combined with the currently best sequence-prediction algorithms, greatly expanding the applicability of VUVCD spectroscopy to protein structural biology. PMID:18395813

  4. McGenus: A Monte Carlo algorithm to predict RNA secondary structures with pseudoknots

    E-print Network

    M. Bon; C. Micheletti; H. Orland

    2013-02-14

    We present McGenus, an algorithm to predict RNA secondary structures with pseudoknots. The method is based on a classification of RNA structures according to their topological genus. McGenus can treat sequences of up to 1000 bases and performs an advanced stochastic search of their minimum free energy structure allowing for non trivial pseudoknot topologies. Specifically, McGenus employs a multiple Markov chain scheme for minimizing a general scoring function which includes not only free energy contributions for pair stacking, loop penalties, etc. but also a phenomenological penalty for the genus of the pairing graph. The good performance of the stochastic search strategy was successfully validated against TT2NE which uses the same free energy parametrization and performs exhaustive or partially exhaustive structure search, albeit for much shorter sequences (up to 200 bases). Next, the method was applied to other RNA sets, including an extensive tmRNA database, yielding results that are competitive with existing algorithms. Finally, it is shown that McGenus highlights possible limitations in the free energy scoring function. The algorithm is available as a web-server at http://ipht.cea.fr/rna/mcgenus.php .

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

    SciTech Connect

    Ye, M.; He, Y. N.; Hu, S. G.; Wang, R.; Hu, T. C.; Yang, J.; Cui, W. Z.

    2013-02-21

    We study secondary electron yield (SEY) suppression for metal materials using a roughened surface with a micro-porous array. First, we perform a Monte Carlo simulation of the electron trajectory in a single cylindrical well using a phenomenological model of secondary electron emission and the SEY suppression efficiency of a micro-porous array. The simulation results show that the SEY of a roughened surface is affected significantly by the aspect ratio of the micro-pores and the surface porosity of the metal plate. Then, to verify the simulation results, we produce a micro-porous array on metal plates using photolithography and measure their SEYs. We show that the micro-porous array structure can efficiently suppress the SEY of metal materials, and the measurements agree quantitatively with the corresponding simulation results. Finally, we derive an analytical formula to evaluate easily the SEY suppression efficiency of the Ag micro-porous array. In total, the micro-porous array proposed in this paper offers an alternative to SEY suppression in related areas such as multipactor effects in satellite payloads or electron cloud effects in accelerators.

  6. Innovative FT-IR imaging of protein film secondary structure before and after heat treatment.

    PubMed

    Bonwell, Emily S; Wetzel, David L

    2009-11-11

    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(-1)) to aggregated forms on either side of the original band. Seventy maxima were near 1625 cm(-1), and 40 shifted in the direction of 1670 cm(-1). The method developed was applied to films cast from two other commercial animal and plant protein sources. PMID:19835374

  7. Prot-2S: a new python web tool for protein secondary structure studies.

    PubMed

    Munteanu, Cristian R; Magalhăes, Alexandre L

    2009-01-01

    Prot-2S is a bioinformatics web application devised to analyse the protein chain secondary structures (2S) (http:/ /www.requimte.pt:8080/Prot-2S/). The tool is built on the RCSB Protein Data Bank PDB and DSSP application/files and includes calculation/graphical display of amino acid propensities in 2S motifs based on any user amino acid classification/code (for any particular protein chain list). The interface can calculate the 2S composition, display the 2S subsequences and search for DSSP non-standard residues and for pairs/triplets/quadruplets (amino acid patterns in 2S motifs). This work presents some Prot-2S applications showing its usefulness in protein research and as an e-learning tool as well. PMID:19640828

  8. Class Anxiety in Secondary Education: Exploring Structural Relations with Perceived Control, Engagement, Disaffection, and Performance.

    PubMed

    González, Antonio; Faílde Garrido, José María; Rodríguez Castro, Yolanda; Carrera Rodríguez, María Victoria

    2015-01-01

    The aim of this study was to assess the relationships between class-related anxiety with perceived control, teacher-reported behavioral engagement, behavioral disaffection, and academic performance. Participants were 355 compulsory secondary students (9th and 10th grades; Mean age = 15.2 years; SD = 1.8 years). Structural equation models revealed performance was predicted by perceived control, anxiety, disaffection, and engagement. Perceived control predicted anxiety, disaffection, and engagement. Anxiety predicted disaffection and engagement, and partially mediated the effects from control on disaffection (? = -.277, p < .005; CI = -.378, -.197) and engagement (? = .170, p < .002; CI = .103 .258). The negative association between anxiety and performance was mediated by engagement and disaffection (? = -.295, p < .002; CI = -.439, -.182). Anxiety, engagement, and disaffection mediated the effects of control on performance (? = .352, p < .003; CI = .279, .440). The implications of these results are discussed in the light of current theory and educational interventions. PMID:26364673

  9. An Efficient Multiple Alignment Method for RNA Secondary Structures Including Pseudoknots

    NASA Astrophysics Data System (ADS)

    Seki, Shinnosuke; Kobayashi, Satoshi

    Pseudoknots, one of the key components of RNA secondary structures, have been almost systematically intractable because of the difficulty in modeling them. Tree adjoining grammars have proved to be promising for this problem but the question of how to make TAG-based applications practical enough to analyze RNAs of thousands nucleotides remains open. This paper addresses this problem. It makes use of biological properties of pseudoknots, the scarcity and short-bp property. Experiments showed that our algorithm can align RNAs of the length up to about 2400 nucleotides with biologically meaningful outputs extremely fast on the standard workstation environment. An executable version of our implementation is available at http://www.csd.uwo.ca/~sseki/

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

    PubMed Central

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

    2011-01-01

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

  11. Improved prediction of RNA secondary structure by integrating the free energy model with restraints derived from experimental probing data.

    PubMed

    Wu, Yang; Shi, Binbin; Ding, Xinqiang; Liu, Tong; Hu, Xihao; Yip, Kevin Y; Yang, Zheng Rong; Mathews, David H; Lu, Zhi John

    2015-09-01

    Recently, several experimental techniques have emerged for probing RNA structures based on high-throughput sequencing. However, most secondary structure prediction tools that incorporate probing data are designed and optimized for particular types of experiments. For example, RNAstructure-Fold is optimized for SHAPE data, while SeqFold is optimized for PARS data. Here, we report a new RNA secondary structure prediction method, restrained MaxExpect (RME), which can incorporate multiple types of experimental probing data and is based on a free energy model and an MEA (maximizing expected accuracy) algorithm. We first demonstrated that RME substantially improved secondary structure prediction with perfect restraints (base pair information of known structures). Next, we collected structure-probing data from diverse experiments (e.g. SHAPE, PARS and DMS-seq) and transformed them into a unified set of pairing probabilities with a posterior probabilistic model. By using the probability scores as restraints in RME, we compared its secondary structure prediction performance with two other well-known tools, RNAstructure-Fold (based on a free energy minimization algorithm) and SeqFold (based on a sampling algorithm). For SHAPE data, RME and RNAstructure-Fold performed better than SeqFold, because they markedly altered the energy model with the experimental restraints. For high-throughput data (e.g. PARS and DMS-seq) with lower probing efficiency, the secondary structure prediction performances of the tested tools were comparable, with performance improvements for only a portion of the tested RNAs. However, when the effects of tertiary structure and protein interactions were removed, RME showed the highest prediction accuracy in the DMS-accessible regions by incorporating in vivo DMS-seq data. PMID:26170232

  12. Improved prediction of RNA secondary structure by integrating the free energy model with restraints derived from experimental probing data

    PubMed Central

    Wu, Yang; Shi, Binbin; Ding, Xinqiang; Liu, Tong; Hu, Xihao; Yip, Kevin Y.; Yang, Zheng Rong; Mathews, David H.; Lu, Zhi John

    2015-01-01

    Recently, several experimental techniques have emerged for probing RNA structures based on high-throughput sequencing. However, most secondary structure prediction tools that incorporate probing data are designed and optimized for particular types of experiments. For example, RNAstructure-Fold is optimized for SHAPE data, while SeqFold is optimized for PARS data. Here, we report a new RNA secondary structure prediction method, restrained MaxExpect (RME), which can incorporate multiple types of experimental probing data and is based on a free energy model and an MEA (maximizing expected accuracy) algorithm. We first demonstrated that RME substantially improved secondary structure prediction with perfect restraints (base pair information of known structures). Next, we collected structure-probing data from diverse experiments (e.g. SHAPE, PARS and DMS-seq) and transformed them into a unified set of pairing probabilities with a posterior probabilistic model. By using the probability scores as restraints in RME, we compared its secondary structure prediction performance with two other well-known tools, RNAstructure-Fold (based on a free energy minimization algorithm) and SeqFold (based on a sampling algorithm). For SHAPE data, RME and RNAstructure-Fold performed better than SeqFold, because they markedly altered the energy model with the experimental restraints. For high-throughput data (e.g. PARS and DMS-seq) with lower probing efficiency, the secondary structure prediction performances of the tested tools were comparable, with performance improvements for only a portion of the tested RNAs. However, when the effects of tertiary structure and protein interactions were removed, RME showed the highest prediction accuracy in the DMS-accessible regions by incorporating in vivo DMS-seq data. PMID:26170232

  13. Resonance assignments and secondary structure of a phytocystatin from Sesamum indicum.

    PubMed

    Hu, Yu-Jun; Irene, Deli; Lo, Chi-Jen; Cai, Yong-Liang; Tzen, T-C; Lin, Ta-Hsien; Chyan, Chia-Lin

    2015-10-01

    A cDNA encoding a cysteine protease inhibitor, cystatin was cloned from sesame (Sesamum indicum L.) seed. This clone was constructed into an expression vector and expressed in E. coli and purified to homogeneous. The recombinant sesame cystatin (SiCYS) showed effectively inhibitory activity toward C1 cysteine proteases. In order to unravel its inhibitory action from structural point of view, multidimensional heteronuclear NMR techniques were used to characterize the structure of SiCYS. The full (1)H, (15)N, and (13)C resonances of SiCYS were assigned. The secondary structure of SiCYS was identified by using the assigned chemical shifts of (1)H(?), (13)C(?), (13)C(?), and (13)CO through the consensus chemical shift index (CSI). The results of CSI analysis of SiCYS suggest eight ?-strands (residues 33-46, 51-61, 63-75, 80-87, 150-155, 157-169, 172-183, and 192-195) and two ?-helices (residues 16-30, and 120-135). PMID:25673506

  14. Resonance assignments and secondary structure of a phytocystatin from Ananas comosus.

    PubMed

    Irene, Deli; Chen, Bo-Jiun; Lo, Si-Hung; Liu, Ting-Hang; Tzen, Jason T-C; Chyan, Chia-Lin

    2012-04-01

    A cDNA encoding a cysteine protease inhibitor, cystatin was cloned from pineapple (Ananas comosus L.) stem. This clone was constructed into an expression vector and expressed in E. coli and purified to homogeneous. The recombinant pineapple cystatins (AcCYS) showed effectively inhibitory activity toward cysteine proteases including papain, bromelain, and cathepsin B. In order to unravel its inhibitory action from structural point of view, multidimensional heteronuclear NMR techniques were used to characterize the structure of AcCYS. The full (1)H, (15)N, and (13)C resonance assignments of AcCYS were determined. The secondary structure of AcCYS was identified by using the assigned chemical shift of (1)H?, (13)C?, (13)C?, and (13)CO through the consensus chemical shift index (CSI). The results of CSI analysis suggest 5 ?-strands (residues 45-47, 84-91, 94-104, 106-117, and 123-130) and one ?-helix (residues 55-73). PMID:21814766

  15. Linker histone partial phosphorylation: effects on secondary structure and chromatin condensation.

    PubMed

    Lopez, Rita; Sarg, Bettina; Lindner, Herbert; Bartolomé, Salvador; Ponte, Inma; Suau, Pedro; Roque, Alicia

    2015-05-19

    Linker histones are involved in chromatin higher-order structure and gene regulation. We have successfully achieved partial phosphorylation of linker histones in chicken erythrocyte soluble chromatin with CDK2, as indicated by HPCE, MALDI-TOF and Tandem MS. We have studied the effects of linker histone partial phosphorylation on secondary structure and chromatin condensation. Infrared spectroscopy analysis showed a gradual increase of ?-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

  16. The T-lymphocyte proliferative response to synthetic peptide antigens of defined secondary structure.

    PubMed

    Mouritsen, S; Meldal, M; Rubin, B; Holm, A; Werdelin, O

    1989-12-01

    Immunodominant sites in proteins recognized by T lymphocytes are segments consisting of at least 7-8 amino acids. It has previously been proposed that these sites in proteins are alpha-helical and amphipatic structures. We synthesized and investigated the immunogenicity of three synthetic peptides (MP7, MP8, and MP9), each consisting of the same 15 amino acids, but differing with respect to sequence. Based on information analysis and circular dichroism measurements, MP7 was shown to have an alpha-helical secondary structure and, based on previously assigned hydrophilicity indices, was also strongly longitudinally amphipatic. MP8 also was conformed as an alpha-helix, but was amphipatic in the sense that the N-terminal half of the molecule was hydrophilic and the C-terminal half hydrophobic. MP9 had neither an amphipatic nor alpha-helical structure. All three peptides were immunogenic in some strains of mice but none was immunogenic in all strains. This supports other studies concluding that amphipaticity per se is neither a necessary nor sufficient requirement for immunogenicity of a peptide. On the other hand, the present experimental data suggest that longitudinally amphipatic alpha-helical peptides may function better as T-cell determinants than the other peptides investigated. PMID:2481338

  17. FPGA accelerator for protein secondary structure prediction based on the GOR algorithm

    PubMed Central

    2011-01-01

    Background Protein is an important molecule that performs a wide range of functions in biological systems. Recently, the protein folding attracts much more attention since the function of protein can be generally derived from its molecular structure. The GOR algorithm is one of the most successful computational methods and has been widely used as an efficient analysis tool to predict secondary structure from protein sequence. However, the execution time is still intolerable with the steep growth in protein database. Recently, FPGA chips have emerged as one promising application accelerator to accelerate bioinformatics algorithms by exploiting fine-grained custom design. Results In this paper, we propose a complete fine-grained parallel hardware implementation on FPGA to accelerate the GOR-IV package for 2D protein structure prediction. To improve computing efficiency, we partition the parameter table into small segments and access them in parallel. We aggressively exploit data reuse schemes to minimize the need for loading data from external memory. The whole computation structure is carefully pipelined to overlap the sequence loading, computing and back-writing operations as much as possible. We implemented a complete GOR desktop system based on an FPGA chip XC5VLX330. Conclusions The experimental results show a speedup factor of more than 430x over the original GOR-IV version and 110x speedup over the optimized version with multi-thread SIMD implementation running on a PC platform with AMD Phenom 9650 Quad CPU for 2D protein structure prediction. However, the power consumption is only about 30% of that of current general-propose CPUs. PMID:21342582

  18. 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

  19. Investigating the secondary structures for long oligonucleotides using attenuated-total-reflection nanoplasmon-enhanced Raman scattering

    NASA Astrophysics Data System (ADS)

    Chiu, K.-C.; Yu, L.-Y.; Lin, C.-Y.; Chen, S.-J.

    2007-09-01

    This study utilizes a nanoplasmon-enhanced Raman scattering based on the attenuated-total-reflection (ATR) method to investigate the secondary structures of long oligonucleotides and their influence on the DNA hybridization. It is found that the ring-breathing modes of adenine, thymine, guanine, and cytosine in Raman fingerprint associated with three 60mer oligonucleotides with prominent secondary structures are lower than those observed for the two oligonucleotides with no obvious secondary structures. It is also determined that increasing the DNA hybridization temperature from 35 °C to 45 °C reduces secondary structure effects. The kinetics of biomolecular interaction analysis can be performed by using surface plasmons resonance biosensor, but the structural information of the oligonucleotides can not observed directly. The ATR-Raman spectrum can provide the structural information of the oligonucleotide monolayer on the sensing surface with the help of a silver patterned nanostructure film based on the finite-difference time-domain simulation and the e-beam lithography fabrication adapted as an ATR-Raman active substrate.

  20. RDC enhanced NMR spectroscopy in organic solvent media: the importance for the experimental determination of periodic hydrogen bonded secondary structures.

    PubMed

    Kiran, Marelli Udaya; Sudhakar, Ambadi; Klages, Jochen; Kummerlöwe, Grit; Luy, Burkhard; Jagadeesh, Bharatam

    2009-11-01

    Precise NMR structural determination of distinct hydrogen-bonded secondary folds in unnatural peptides is demonstrated by using residual dipolar couplings (RDCs), measured in organic solvent media. The results show that the conventional constraints, (3)J(HH) and NOE-derived distances alone do not allow the accurate structural elucidation even for rigid foldamers and emphasize the need of RDC-based structure validation and refinement for unnatural peptides in particular and small organic molecules in general. PMID:19860476

  1. Fine Structure in the Secondary Electron Emission Peak for Diamond Crystal with (100) Negative Electron Affinity Surface

    NASA Technical Reports Server (NTRS)

    Asnin, V. M.; Krainsky, I. L.

    1998-01-01

    A fine structure was discovered in the low-energy peak of the secondary electron emission spectra of the diamond surface with negative electron affinity. We studied this structure for the (100) surface of the natural type-IIb diamond crystal. We have found that the low-energy peak consists of a total of four maxima. The relative energy positions of three of them could be related to the electron energy minima near the bottom of the conduction band. The fourth peak, having the lowest energy, was attributed to the breakup of the bulk exciton at the surface during the process of secondary electron emission.

  2. 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.

  3. Residual Structure of Streptococcus mutans Biofilm following Complete Disinfection Favors Secondary Bacterial Adhesion and Biofilm Re-Development

    PubMed Central

    Ohsumi, Tatsuya; Takenaka, Shoji; Wakamatsu, Rika; Sakaue, Yuuki; Narisawa, Naoki; Senpuku, Hidenobu; Ohshima, Hayato; Terao, Yutaka; Okiji, Takashi

    2015-01-01

    Chemical disinfection of oral biofilms often leaves biofilm structures intact. This study aimed to examine whether the residual structure promotes secondary bacterial adhesion. Streptococcus mutans biofilms generated on resin-composite disks in a rotating disc reactor were disinfected completely with 70% isopropyl alcohol, and were again cultured in the same reactor after resupplying with the same bacterial solution. Specimens were subjected to fluorescence confocal laser scanning microscopy, viable cell counts and PCR-Invader assay in order to observe and quantify secondarily adhered cells. Fluorescence microscopic analysis, particularly after longitudinal cryosectioning, demonstrated stratified patterns of viable cells on the disinfected biofilm structure. Viable cell counts of test specimens were significantly higher than those of controls, and increased according to the amount of residual structure and culture period. Linear regression analysis exhibited a high correlation between viable and total cell counts. It was concluded that disinfected biofilm structures favored secondary bacterial adhesion. PMID:25635770

  4. A hairpin within YAP mRNA 3'UTR functions in regulation at post-transcription level.

    PubMed

    Gao, Yuen; Wang, Yuan; Feng, Jinyan; Feng, Guoxing; Zheng, Minying; Yang, Zhe; Xiao, Zelin; Lu, Zhanping; Ye, Lihong; Zhang, Xiaodong

    2015-04-01

    The central dogma of gene expression is that DNA is transcribed into messenger RNAs, which in turn serve as the template for protein synthesis. Recently, it has been reported that mRNAs display regulatory roles that rely on their ability to compete for microRNA binding, independent of their protein-coding function. However, the regulatory mechanism of mRNAs remains poorly understood. Here, we report that a hairpin within YAP mRNA 3'untranslated region (3'UTR) functions in regulation at post-transcription level through generating endogenous siRNAs (esiRNAs). Bioinformatics analysis for secondary structure showed that YAP mRNA displayed a hairpin structure (termed standard hairpin, S-hairpin) within its 3'UTR. Surprisingly, we observed that the overexpression of S-hairpin derived from YAP 3'UTR (YAP-sh) increased the luciferase reporter activities of transcriptional factor NF-?B and AP-1 in 293T cells. Moreover, we identified that a fragment from YAP-sh, an esiRNA, was able to target mRNA 3'UTR of NF2 (a member of Hippo-signaling pathway) and YAP mRNA 3'UTR itself in hepatoma cells. Thus, we conclude that the YAP-sh within YAP mRNA 3'UTR may serve as a novel regulatory element, which functions in regulation at post-transcription level. Our finding provides new insights into the mechanism of mRNAs in regulatory function. PMID:25727017

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

    PubMed

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

    2011-03-01

    Removing adsorbed protein from metals has significant health and industrial consequences. There are numerous protein-adsorption studies using model self-assembled monolayers or polymeric substrates but hardly any high-resolution measurements of adsorption and removal of proteins on industrially relevant transition metals. Surgeons and ship owners desire clean metal surfaces to reduce transmission of disease via surgical instruments and minimize surface fouling (to reduce friction and corrosion), respectively. A major finding of this work is that, besides hydrophobic interaction adhesion energy, water content in an adsorbed protein layer and secondary structure of proteins determined the access and hence ability to remove adsorbed proteins from metal surfaces with a strong alkaline-surfactant solution (NaOH and 5 mg/mL SDS in PBS at pH 11). This is demonstrated with three blood proteins (bovine serum albumin, immunoglobulin, and fibrinogen) and four transition metal substrates and stainless steel (platinum (Pt), gold (Au), tungsten (W), titanium (Ti), and 316 grade stainless steel (SS)). All the metallic substrates were checked for chemical contaminations like carbon and sulfur and were characterized using X-ray photoelectron spectroscopy (XPS). While Pt and Au surfaces were oxide-free (fairly inert elements), W, Ti, and SS substrates were associated with native oxide. Difference measurements between a quartz crystal microbalance with dissipation (QCM-D) and surface plasmon resonance spectroscopy (SPR) provided a measure of the water content in the protein-adsorbed layers. Hydrophobic adhesion forces, obtained with atomic force microscopy, between the proteins and the metals correlated with the amount of the adsorbed protein-water complex. Thus, the amount of protein adsorbed decreased with Pt, Au, W, Ti and SS, in this order. Neither sessile contact angle nor surface roughness of the metal substrates was useful as predictors here. All three globular proteins behaved similarly on addition of the alkaline-surfactant cleaning solution, in that platinum and gold exhibited an increase, while tungsten, titanium, and stainless steel showed a decrease in weight. According to dissipation measurements with the QCM-D, the adsorbed layer for platinum and gold was rigid, while that for the tungsten, titanium, and stainless steel was much more flexible. The removal efficiency of adsorbed-protein by alkaline solution of SDS depended on the water content of the adsorbed layers for W, Ti, and SS, while for Pt and Au, it depended on secondary structural content. When protein adsorption was high (Pt, Au), protein-protein interactions and protein-surface interactions were dominant and the removal of protein layers was limited. Water content of the adsorbed protein layer was the determining factor for how efficiently the layer was removed by alkaline SDS when protein adsorption was low. Hence, protein-protein and protein-surface interactions were minimal and protein structure was less perturbed in comparison with those for high protein adsorption. Secondary structural content determined the efficient removal of adsorbed protein for high adsorbed amount. PMID:21182242

  6. 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.

  7. 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.

  8. A Deep Learning Network Approach to ab initio Protein Secondary Structure Prediction

    PubMed Central

    Spencer, Matt; Eickholt, Jesse; Cheng, Jianlin

    2014-01-01

    Ab initio protein secondary structure (SS) predictions are utilized to generate tertiary structure predictions, which are increasingly demanded due to the rapid discovery of proteins. Although recent developments have slightly exceeded previous methods of SS prediction, accuracy has stagnated around 80% and many wonder if prediction cannot be advanced beyond this ceiling. Disciplines that have traditionally employed neural networks are experimenting with novel deep learning techniques in attempts to stimulate progress. Since neural networks have historically played an important role in SS prediction, we wanted to determine whether deep learning could contribute to the advancement of this field as well. We developed an SS predictor that makes use of the position-specific scoring matrix generated by PSI-BLAST and deep learning network architectures, which we call DNSS. Graphical processing units and CUDA software optimize the deep network architecture and efficiently train the deep networks. Optimal parameters for the training process were determined, and a workflow comprising three separately trained deep networks was constructed in order to make refined predictions. This deep learning network approach was used to predict SS for a fully independent test data set of 198 proteins, achieving a Q3 accuracy of 80.7% and a Sov accuracy of 74.2%. PMID:25750595

  9. 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

  10. DNA secondary structures are associated with recombination in major Plasmodium falciparum variable surface antigen gene families

    PubMed Central

    Sander, Adam F.; Lavstsen, Thomas; Rask, Thomas S.; Lisby, Michael; Salanti, Ali; Fordyce, Sarah L.; Jespersen, Jakob S.; Carter, Richard; Deitsch, Kirk W.; Theander, Thor G.; Pedersen, Anders Gorm; Arnot, David E.

    2014-01-01

    Many bacterial, viral and parasitic pathogens undergo antigenic variation to counter host immune defense mechanisms. In Plasmodium falciparum, the most lethal of human malaria parasites, switching of var gene expression results in alternating expression of the adhesion proteins of the Plasmodium falciparum-erythrocyte membrane protein 1 class on the infected erythrocyte surface. Recombination clearly generates var diversity, but the nature and control of the genetic exchanges involved remain unclear. By experimental and bioinformatic identification of recombination events and genome-wide recombination hotspots in var genes, we show that during the parasite’s sexual stages, ectopic recombination between isogenous var paralogs occurs near low folding free energy DNA 50-mers and that these sequences are heavily concentrated at the boundaries of regions encoding individual Plasmodium falciparum-erythrocyte membrane protein 1 structural domains. The recombinogenic potential of these 50-mers is not parasite-specific because these sequences also induce recombination when transferred to the yeast Saccharomyces cerevisiae. Genetic cross data suggest that DNA secondary structures (DSS) act as inducers of recombination during DNA replication in P. falciparum sexual stages, and that these DSS-regulated genetic exchanges generate functional and diverse P. falciparum adhesion antigens. DSS-induced recombination may represent a common mechanism for optimizing the evolvability of virulence gene families in pathogens. PMID:24253306

  11. Determination of the secondary structure of group II bulge loops using the fluorescent probe 2-aminopurine.

    PubMed

    Dishler, Abigael L; McMichael, Elizabeth L; Serra, Martin J

    2015-05-01

    Eleven RNA hairpins containing 2-aminopurine (2-AP) in either base-paired or single nucleotide bulge loop positions were optically melted in 1 M NaCl; and, the thermodynamic parameters ?H°, ?S°, ?G°37, and TM for each hairpin were determined. Substitution of 2-AP for an A (adenosine) at a bulge position (where either the 2-AP or A is the bulge) in the stem of a hairpin, does not affect the stability of the hairpin. For group II bulge loops such as AA/U, where there is ambiguity as to which of the A residues is paired with the U, hairpins with 2-AP substituted for either the 5' or 3' position in the hairpin stem have similar stability. Fluorescent melts were performed to monitor the environment of the 2-AP. When the 2-AP was located distal to the hairpin loop on either the 5' or 3' side of the hairpin stem, the change in fluorescent intensity upon heating was indicative of an unpaired nucleotide. A database of phylogenetically determined RNA secondary structures was examined to explore the presence of naturally occurring bulge loops embedded within a hairpin stem. The distribution of bulge loops is discussed and related to the stability of hairpin structures. PMID:25805856

  12. Determination of the secondary structure of group II bulge loops using the fluorescent probe 2-aminopurine

    PubMed Central

    Dishler, Abigael L.; McMichael, Elizabeth L.; Serra, Martin J.

    2015-01-01

    Eleven RNA hairpins containing 2-aminopurine (2-AP) in either base-paired or single nucleotide bulge loop positions were optically melted in 1 M NaCl; and, the thermodynamic parameters ?H°, ?S°, ?G°37, and TM for each hairpin were determined. Substitution of 2-AP for an A (adenosine) at a bulge position (where either the 2-AP or A is the bulge) in the stem of a hairpin, does not affect the stability of the hairpin. For group II bulge loops such as AA/U, where there is ambiguity as to which of the A residues is paired with the U, hairpins with 2-AP substituted for either the 5? or 3? position in the hairpin stem have similar stability. Fluorescent melts were performed to monitor the environment of the 2-AP. When the 2-AP was located distal to the hairpin loop on either the 5? or 3? side of the hairpin stem, the change in fluorescent intensity upon heating was indicative of an unpaired nucleotide. A database of phylogenetically determined RNA secondary structures was examined to explore the presence of naturally occurring bulge loops embedded within a hairpin stem. The distribution of bulge loops is discussed and related to the stability of hairpin structures. PMID:25805856

  13. Sheath structure transition controlled by secondary electron emission at low gas pressure

    NASA Astrophysics Data System (ADS)

    Schweigert, Irina; Langendorf, Samuel J.; Keidar, Michael; Walker, Mitchell L. R.

    2014-10-01

    Previously the experiments demonstrated that the growth of the electron temperature with power in the Hall thruster is restricted by plasma-wall interaction if the wall has an enhanced secondary electron emission (SEE) yield. It is known that the plasma and wall is separated by the sheath potential drop to provide the condition of zero-current on the surface with floating potential. The rearrangement of the sheath structure near the plate with enhanced SEE is the subject of our experimental and theoretical study. The experiment was carried out in multidipole plasma device, where plasma is maintained by the negatively-biased emissive filament. The plate with sapphire surface is placed 50 cm apart from the filament. The plasma parameters were measured for different negative biases Ub and discharge currents J at P = 10-4 Torr. In our PIC simulations the plasma was calculated for the experimental conditions. We solved self-consistently the Boltzmann equations for the electron and ion distribution functions and Poisson equation for electrical field. Both in the experiment and simulation we found non-monotonic change in sheath structure near the plate depending on Ub and J. The kinetic simulations allowed us to describe the sheath rearrangement in terms of the electron energy distribution function.

  14. Assessing secondary structure of a dyed wool fibre by means of FTIR and FTR spectroscopies

    NASA Astrophysics Data System (ADS)

    Pielesz, A.; Freeman, H. S.; Wese?ucha-Birczy?ska, A.; Wysocki, M.; W?ochowicz, A.

    2003-06-01

    The paper describes changes in the structure of a wool fibre dyed with model azo dyes. These were direct dyes, non-genotoxic derivatives of carcinogenic benzidine, synthesized specially for the purpose of the experiment. The non-mutagenic benzidine derivatives were: 2,2'-dimethyl-5,5'-dipropoxybenzidine and 5,5'-dipropoxybenzidine. Using FTIR, changes in secondary structure of fibres were assessed in three measuring ranges: 3600-3000, 1700-1400 and 1000-1300 cm -1. The dyes were found to distinctively affect wave-number shifts of amide A, amide I bands and in the fingerprint area around 1050 cm -1. It seems that these three areas are related to the sites in which dyes bind with wool fibre keratin. In FTR spectra, the focus was on assessing the changes of peptide bond configuration in the area of amide I, disulfide area of cystine and the area of the interaction between dyes and wool fibre keratin, i.e. 1250-1600 cm -1. For analysis, three kinds of materials were selected: (1) raw wool fibres, (2) fibres subjected to deuteration and treated with formic acid, (3) wool fabric. Each of them was dyed with the model azo dyes. The results obtained by both spectroscopies allow for identifying the functional groups responsible for the binding of dyes with keratin fibre.

  15. [Spatial structural characteristics of natural Populus davidiana - Betula platyphylla secondary forest].

    PubMed

    Shao, Fang-Li; Yu, Xin-Xiao; Song, Si-Ming; Zhao, Yang

    2011-11-01

    This paper analyzed the spatial structural characteristics of natural Populus davidiana - Betula platyphylla secondary forest in a 4 hm2 plot of Mulan Paddock, based on the diameter distribution and the spatial structure parameters mingling degree, neighborhood comparison, and angle index. In the forest, the diameter distribution of the stands presented as an inverse 'J' curve, the average mingling degree was 0.4, with the individuals at weak and zero mingling degree reached 51.6%, and the average mingling degree of P. davidiana and B. platyphylla was 0.25 and 0.39, respectively. The neighborhood comparison based on the diameter at breast height (DBH) and tree height was almost the same, suggesting that the P. davidiana and B. platyphylla were in the transition state from subdominant to middle. The horizontal distribution pattern had a close relation to the minimum measured DBH, being clustered when the DBH was > or = 1 cm and < 6 cm, and random when the DBH was > or = 6 cm. PMID:22303652

  16. Maintenance of Pdx1 mRNA Translation in Islet ?-Cells During the Unfolded Protein Response

    PubMed Central

    Templin, Andrew T.; Maier, Bernhard; Tersey, Sarah A.; Hatanaka, Masayuki

    2014-01-01

    In type 1 diabetes, proinflammatory cytokines secreted by infiltrating immune cells activate the unfolded protein response (UPR) in islet ?-cells, which leads to attenuation of global mRNA translation. Under such conditions, privileged mRNAs required for adaptation to the prevailing stress are maintained in an actively translated state. Pdx1 is a ?-cell transcription factor that is required for the adaptive UPR, but it is not known how translation of its mRNA is maintained under these conditions. To study translation, we established conditions in vitro with MIN6 cells and mouse islets and a mixture of proinflammatory cytokines (IL-1?, TNF-?, and IFN-?) that mimicked the UPR conditions seen in type 1 diabetes. Cell extracts were then subjected to polyribosome profiling to monitor changes to mRNA occupancy by ribosomes. Similar to other privileged mRNAs (Atf4 and Chop), Pdx1 mRNA remained partitioned in actively translating polyribosomes under the UPR, whereas the mRNA encoding a proinsulin-processing enzyme (Cpe) and others partitioned into inactively translating monoribosomes. Bicistronic luciferase reporter analyses revealed that the distal portion of the 5?-untranslated region of mouse Pdx1 (between bp ?105 to ?280) contained elements that promoted translation under both normal and UPR conditions, and this region exhibited conserved sequences and secondary structure similar to those of other known internal ribosome entry sites. Our findings suggest that Pdx1 protein levels are maintained in the setting of the UPR, in part, through elements in the 5?-untranslated region that confer privileged mRNA translation in a 5?-7-methylguanylate cap–independent manner. PMID:25251389

  17. Premature translation termination mediates triosephosphate isomerase mRNA degradation

    SciTech Connect

    Daar, I.O.; Maquat, L.E.

    1988-02-01

    The authors characterized an anemia-inducing mutation in the human gene for triosephosphate isomerase (TPI) that resulted in the production of prematurely terminated protein and mRNA with a reduced cytoplasmic half-life. The mutation converted a CGA arginine codon to a TGA nonsense condon and generated a protein of 188 amino acids, instead of the usual 248 amino acids. To determine how mRNA primary structure and translation and influence mRNA stability, in vitro-mutagenized TPI alleles were introduced into cultured L cells and analyzed for their effect on TPI RNA metabolism. Results indicated that mRNA stability is decreased by all nonsense and frameshift mutations. To determine the relative contribution of the changes in mRNA structure and translation to the altered half-life, the effects of individual mutations were compared with the effects of second-site reversions that restored translation termination to normal. All mutations that resulted in premature translation termination reduced the mRNA half-life solely or mainly by altering the length of the mRNA that was translated. The only mutation that altered translation termination and that reduced the mRNA half-life mainly by affecting the mRNA structure was an insertion that shifted termination to a position downstream of the normal stop codon.

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

    PubMed

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

    2014-04-01

    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-Ĺ 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

  19. Chemometric tools for classification and elucidation of protein secondary structure from infrared and circular dichroism spectroscopic measurements.

    PubMed

    Navea, Susana; Tauler, Romá; Goormaghtigh, Erik; de Juan, Anna

    2006-05-15

    Protein classification and characterization often rely on the information contained in the protein secondary structure. Protein class assignment is usually based on X-ray diffraction measurements, which need the protein in a crystallized form, or on NMR spectra, to obtain the structure of a protein in solution. Simple spectroscopic techniques, such as circular dichroism (CD) and infrared (IR) spectroscopies, are also known to be related to protein secondary structure, but they have seldom been used for protein classification. To see the potential of CD, IR, and combined CD/IR measurements for protein classification, unsupervised pattern recognition methods, Principal Component Analysis (PCA) and cluster analysis, are proposed first to check for natural grouping tendencies of proteins according to their measured spectra. Partial Least Squares Discriminant Analysis (PLS-DA), a supervised pattern recognition method, is used afterwards to test the possibility to model explicitly each protein class and to test these models in class assignment of unknown proteins. Determination of the protein secondary structure, understood as the prediction of the abundance of the different secondary structure motifs in the biomolecule, was carried out with the local regression method interval Partial Least Squares (iPLS). CD, IR, and CD/IR measurements were correlated to the fraction of the motif to be predicted, determined from X-ray measurements. iPLS builds models extracting the spectral information most correlated to a specific secondary motif and avoids the use of irrelevant spectral regions. Spectral intervals chosen by iPLS models provide structural information which can be used to confirm previous biochemical assignments or identify new motif-related spectral features. The predictive ability of the models built with the selected spectral regions has a quality similar to previous classical approaches. PMID:16456850

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

    E-print Network

    Olins, Ada L.

    Raman spectroscopy is a valu- able tool for determining the secondary structures of nucleic acids in which the Raman frequencies and intensities are used to detect and quantify nucleic acid and protein con core of the nu body has a high a-helix content. The nucleohistone component of eukaryotic chromatin

  1. Biochemistry 1989, 28, 508 1-5089 5081 Determination of the Secondary Structure of the DNA Binding Protein Ner from

    E-print Network

    Clore, G. Marius

    at providingenough purified protein for our work. In this paper we describe the use of a combination of two spectrum of Ner and to delineate its secondary structure. Sample Preparation. Ner protein was purified from Protein Ner from Phage Mu Using 'H Homonuclear and 15N-'H Heteronuclear NMR Spectroscopy+ Angela M

  2. DNA secondary structure of the released strand stimulates WRN helicase action on forked duplexes without coordinate action of WRN exonuclease

    SciTech Connect

    Ahn, Byungchan; Bohr, Vilhelm A.

    2011-08-12

    Highlights: {yields} In this study, we investigated the effect of a DNA secondary structure on the two WRN activities. {yields} We found that a DNA secondary structure of the displaced strand during unwinding stimulates WRN helicase without coordinate action of WRN exonuclease. {yields} These results imply that WRN helicase and exonuclease activities can act independently. -- Abstract: Werner syndrome (WS) is an autosomal recessive premature aging disorder characterized by aging-related phenotypes and genomic instability. WS is caused by mutations in a gene encoding a nuclear protein, Werner syndrome protein (WRN), a member of the RecQ helicase family, that interestingly possesses both helicase and exonuclease activities. Previous studies have shown that the two activities act in concert on a single substrate. We investigated the effect of a DNA secondary structure on the two WRN activities and found that a DNA secondary structure of the displaced strand during unwinding stimulates WRN helicase without coordinate action of WRN exonuclease. These results imply that WRN helicase and exonuclease activities can act independently, and we propose that the uncoordinated action may be relevant to the in vivo activity of WRN.

  3. 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.

    Purpose: Human eye lenses contain cells that persist from embryonic development. These unique, highlyThe overall structure of the human lens is one of succes- sive generations of secondary fiber cells turnover in the water-soluble protein of the adult human lens Daniel N. Stewart,1 Jozsef Lango,1 Krishnan P

  4. Decentralization and Structural Change in Secondary Education in Argentina: The Case of the Province of Buenos Aires

    ERIC Educational Resources Information Center

    Acedo, Clementina; Gorostiaga, Jorge M.; Senen-Gonzalez, Silvia

    2007-01-01

    Over the past decade, Argentina created and implemented a compulsory lower-secondary education level, within an ambitious educational reform programme. This article addresses the reform at the national level, diverse provincial responses, and the particular way that the powerful province of Buenos Aires appropriated the structural change. The…

  5. Effects of the alternating backbone configuration on the secondary structure and self-assembly of beta-peptides.

    PubMed

    Martinek, Tamás A; Mándity, István M; Fülöp, Lívia; Tóth, Gábor K; Vass, Elemér; Hollósi, Miklós; Forró, Eniko; Fülöp, Ferenc

    2006-10-18

    Heterochiral homo-oligomers with alternating backbone configurations were constructed by using the different enantiomers of the cis- and trans-2-aminocyclopentanecarboxylic acid (ACPC) monomers. Molecular modeling and the spectroscopic techniques (NMR, ECD, and VCD) unequivocally proved that the alternating heterochiral cis-ACPC sequences form an H10/12 helix, where extra stabilization can be achieved via the cyclic side chains. The ECD and TEM measurements, together with molecular modeling, revealed that the alternating heterochiral trans-ACPC oligomers tend to attain a polar-strand secondary structure in solution, which can self-assemble into nanostructured fibrils. The observations indicate that coverage of all the possible secondary structures (various helix types and strand-mimicking conformations) can be attained with the help of cyclic beta-amino acid diastereomers. A relationship has been established between the backbone chirality pattern and the prevailing secondary structure, which underlines the role of stereochemical control in the beta-peptide secondary structure design and may contribute to future biological applications. PMID:17031967

  6. 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…

  7. Evaluation of the authenticity of a highly novel environmental sequence from boreal forest soil using ribosomal RNA secondary structure modeling

    E-print Network

    Taylor, Lee

    Evaluation of the authenticity of a highly novel environmental sequence from boreal forest soil using ribosomal RNA secondary structure modeling Daniel J. Glass a , Naoki Takebayashi a , Link E. Olson but does not fall unambiguously within any known phylum. We have evaluated this sequence type using

  8. Conformational analysis of peptides corresponding to all the secondary structure elements of protein L B1 domain: secondary structure propensities are not conserved in proteins with the same fold.

    PubMed Central

    Ramírez-Alvarado, M.; Serrano, L.; Blanco, F. J.

    1997-01-01

    The solution conformation of three peptides corresponding to the two beta-hairpins and the alpha-helix of the protein L B1 domain have been analyzed by circular dichroism (CD) and nuclear magnetic resonance spectroscopy (NMR). In aqueous solution, the three peptides show low populations of native and non-native locally folded structures, but no well-defined hairpin or helix structures are formed. In 30% aqueous trifluoroethanol (TFE), the peptide corresponding to the alpha-helix adopts a high populated helical conformation three residues longer than in the protein. The hairpin peptides aggregate in TFE, and no significant conformational change occurs in the NMR observable fraction of molecules. These results indicate that the helical peptide has a significant intrinsic tendency to adopt its native structure and that the hairpin sequences seem to be selected as non-helical. This suggests that these sequences favor the structure finally attained in the protein, but the contribution of the local interactions alone is not enough to drive the formation of a detectable population of native secondary structures. This pattern of secondary structure tendencies is different to those observed in two structurally related proteins: ubiquitin and the protein G B1 domain. The only common feature is a certain propensity of the helical segments to form the native structure. These results indicate that for a protein to fold, there is no need for large native-like secondary structure propensities, although a minimum tendency to avoid non-native structures and to favor native ones could be required. PMID:9007989

  9. 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

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

    SciTech Connect

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

    2012-05-02

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

  11. 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

  12. Ribosomal ITS sequences allow resolution of freshwater sponge phylogeny with alignments guided by secondary structure prediction.

    PubMed

    Itskovich, Valeria; Gontcharov, Andrey; Masuda, Yoshiki; Nohno, Tsutomu; Belikov, Sergey; Efremova, Sofia; Meixner, Martin; Janussen, Dorte

    2008-12-01

    Freshwater sponges include six extant families which belong to the suborder Spongillina (Porifera). The taxonomy of freshwater sponges is problematic and their phylogeny and evolution are not well understood. Sequences of the ribosomal internal transcribed spacers (ITS1 and ITS2) of 11 species from the family Lubomirskiidae, 13 species from the family Spongillidae, and 1 species from the family Potamolepidae were obtained to study the phylogenetic relationships between endemic and cosmopolitan freshwater sponges and the evolution of sponges in Lake Baikal. The present study is the first one where ITS1 sequences were successfully aligned using verified secondary structure models and, in combination with ITS2, used to infer relationships between the freshwater sponges. Phylogenetic trees inferred using maximum likelihood, neighbor-joining, and parsimony methods and Bayesian inference revealed that the endemic family Lubomirskiidae was monophyletic. Our results do not support the monophyly of Spongillidae because Lubomirskiidae formed a robust clade with E. muelleri, and Trochospongilla latouchiana formed a robust clade with the outgroup Echinospongilla brichardi (Potamolepidae). Within the cosmopolitan family Spongillidae the genera Radiospongilla and Eunapius were found to be monophyletic, while Ephydatia muelleri was basal to the family Lubomirskiidae. The genetic distances between Lubomirskiidae species being much lower than those between Spongillidae species are indicative of their relatively recent radiation from a common ancestor. These results indicated that rDNA spacers sequences can be useful in the study of phylogenetic relationships of and the identification of species of freshwater sponges. PMID:19009316

  13. Polymorphism, population structure, and multivariate relationships among secondary traits in open-pollinated corn heterotic groups

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Plant, ear and kernel traits directly or indirectly associated with grain yield in corn (Zea mays) were suggested as "secondary" traits to select for larger grain yield, especially in open-pollinated corn varieties (OPVs) and their hybrids (OPVhs). Thirty-four secondary traits, besides grain yield, ...

  14. 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

  15. Secondary structure and membrane interaction of PR-39, a Pro+Arg-rich antibacterial peptide.

    PubMed

    Cabiaux, V; Agerberth, B; Johansson, J; Homblé, F; Goormaghtigh, E; Ruysschaert, J M

    1994-09-15

    PR-39 is a 4719-Da peptide isolated from pig intestine and belonging to the recently discovered family of Pro+Arg-rich antibacterial peptides. PR-39 does not lyse Escherichia coli, instead the lethal action is probably linked to the termination of DNA and protein synthesis [Boman, H. G., Agerberth, B. & Boman, A. (1993) Infect. Immun. 61, 2978-2984]. Circular dichroism and Fourier-transform infrared spectroscopy have been used to investigate the secondary structure of PR-39 in the absence or presence of lipids. According to the circular dichroic data, this structure is not altered upon incubation of PR-39 with negatively charged vesicles, although the infrared spectra suggest that the hydrogen bond pattern is modified upon the peptide-lipid interaction. This is detected by a shift in the maximum wavelength of absorption of PR-39 from 1636 cm-1 in the absence of lipids to 1645 cm-1 in the presence of lipids. We have further addressed the question of the possible mechanism of interaction of PR-39 with model membranes (liposomes and planar lipid bilayers) whose lipid compositions mimick that of the E. coli inner membrane. PR-39 induced a calcein release from large unilamellar vesicles, which is dependent upon the peptide concentration and upon the presence of negatively charged lipid (glycerophosphoglycerol) in the membrane. The binding study of PR-39 to dioleoylglycerophosphoglycerol vesicles suggests that nearly 100% of the added peptide is membrane-bound. Addition of PR-39 to a planar lipid bilayer induced a linear increase in the current but no channel formation was observed since no discrete steps of conductance occurred. PMID:7925399

  16. Crystal Structure of a Bacterial Topoisomerase IB in Complex with DNA Reveals a Secondary DNA Binding Site

    SciTech Connect

    Patel, Asmita; Yakovleva, Lyudmila; Shuman, Stewart; Mondragón, Alfonso

    2010-10-22

    Type IB DNA topoisomerases (TopIB) are monomeric enzymes that relax supercoils by cleaving and resealing one strand of duplex DNA within a protein clamp that embraces a {approx}21 DNA segment. A longstanding conundrum concerns the capacity of TopIB enzymes to stabilize intramolecular duplex DNA crossovers and form protein-DNA synaptic filaments. Here we report a structure of Deinococcus radiodurans TopIB in complex with a 12 bp duplex DNA that demonstrates a secondary DNA binding site located on the surface of the C-terminal domain. It comprises a distinctive interface with one strand of the DNA duplex and is conserved in all TopIB enzymes. Modeling of a TopIB with both DNA sites suggests that the secondary site could account for DNA crossover binding, nucleation of DNA synapsis, and generation of a filamentous plectoneme. Mutations of the secondary site eliminate synaptic plectoneme formation without affecting DNA cleavage or supercoil relaxation.

  17. 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. ); Hengstenberg, W. )

    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.

  18. Accurate determination of interfacial protein secondary structure by combining interfacial-sensitive amide I and amide III spectral signals.

    PubMed

    Ye, Shuji; Li, Hongchun; Yang, Weilai; Luo, Yi

    2014-01-29

    Accurate determination of protein structures at the interface is essential to understand the nature of interfacial protein interactions, but it can only be done with a few, very limited experimental methods. Here, we demonstrate for the first time that sum frequency generation vibrational spectroscopy can unambiguously differentiate the interfacial protein secondary structures by combining surface-sensitive amide I and amide III spectral signals. This combination offers a powerful tool to directly distinguish random-coil (disordered) and ?-helical structures in proteins. From a systematic study on the interactions between several antimicrobial peptides (including LK?14, mastoparan X, cecropin P1, melittin, and pardaxin) and lipid bilayers, it is found that the spectral profiles of the random-coil and ?-helical structures are well separated in the amide III spectra, appearing below and above 1260 cm(-1), respectively. For the peptides with a straight backbone chain, the strength ratio for the peaks of the random-coil and ?-helical structures shows a distinct linear relationship with the fraction of the disordered structure deduced from independent NMR experiments reported in the literature. It is revealed that increasing the fraction of negatively charged lipids can induce a conformational change of pardaxin from random-coil to ?-helical structures. This experimental protocol can be employed for determining the interfacial protein secondary structures and dynamics in situ and in real time without extraneous labels. PMID:24384041

  19. BCL::Fold - De Novo Prediction of Complex and Large Protein Topologies by Assembly of Secondary Structure Elements

    PubMed Central

    Karaka?, Mert; Woetzel, Nils; Staritzbichler, Rene; Alexander, Nathan; Weiner, Brian E.; Meiler, Jens

    2012-01-01

    Computational de novo protein structure prediction is limited to small proteins of simple topology. The present work explores an approach to extend beyond the current limitations through assembling protein topologies from idealized ?-helices and ?-strands. The algorithm performs a Monte Carlo Metropolis simulated annealing folding simulation. It optimizes a knowledge-based potential that analyzes radius of gyration, ?-strand pairing, secondary structure element (SSE) packing, amino acid pair distance, amino acid environment, contact order, secondary structure prediction agreement and loop closure. Discontinuation of the protein chain favors sampling of non-local contacts and thereby creation of complex protein topologies. The folding simulation is accelerated through exclusion of flexible loop regions further reducing the size of the conformational search space. The algorithm is benchmarked on 66 proteins with lengths between 83 and 293 amino acids. For 61 out of these proteins, the best SSE-only models obtained have an RMSD100 below 8.0 Ĺ and recover more than 20% of the native contacts. The algorithm assembles protein topologies with up to 215 residues and a relative contact order of 0.46. The method is tailored to be used in conjunction with low-resolution or sparse experimental data sets which often provide restraints for regions of defined secondary structure. PMID:23173050

  20. 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 naďve 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

  1. Comprehensively designed consensus of standalone secondary structure predictors improves Q3 by over 3%.

    PubMed

    Yan, Jing; Marcus, Max; Kurgan, Lukasz

    2014-01-01

    Protein fold is defined by a spatial arrangement of three types of secondary structures (SSs) including helices, sheets, and coils/loops. Current methods that predict SS from sequences rely on complex machine learning-derived models and provide the three-state accuracy (Q3) at about 82%. Further improvements in predictive quality could be obtained with a consensus-based approach, which so far received limited attention. We perform first-of-its-kind comprehensive design of a SS consensus predictor (SScon), in which we consider 12 modern standalone SS predictors and utilize Support Vector Machine (SVM) to combine their predictions. Using a large benchmark data-set with 10 random training-test splits, we show that a simple, voting-based consensus of carefully selected base methods improves Q3 by 1.9% when compared to the best single predictor. Use of SVM provides additional 1.4% improvement with the overall Q3 at 85.6% and segment overlap (SOV3) at 83.7%, when compared to 82.3 and 80.9%, respectively, obtained by the best individual methods. We also show strong improvements when the consensus is based on ab-initio methods, with Q3 = 82.3% and SOV3 = 80.7% that match the results from the best template-based approaches. Our consensus reduces the number of significant errors where helix is confused with a strand, provides particularly good results for short helices and strands, and gives the most accurate estimates of the content of individual SSs in the chain. Case studies are used to visualize the improvements offered by the consensus at the residue level. A web-server and a standalone implementation of SScon are available at http://biomine.ece.ualberta.ca/SSCon/ . PMID:23298369

  2. [Skeleton or mummy: practices and structures for secondary burial in southern Italy in modern and contemporary age].

    PubMed

    Fornaciari, Antonio

    2013-01-01

    The ancient concepts of death as duration and the practices of secondary burial,first analysed by Robert Hertz, still survive in many areas of southern Italy. According to these beliefs death was perceived not as a sudden event, but as a long-lasting process, during which the deceased person had to go through a transitory phase, passing from one state of existence to another. Recent archeological research documents the persistence of secondary burial rites in Southern Italy during the Modern Age. A survey conducted in the province of Messina in Eastern Sicily has identified two surviving architectural structures appointed for the treatment of the bodies: the 'sitting colatoio' aimed at favoring the skeletonisation and the 'horizontal colatoio' used to obtain mummification by dehydration. Both these structures controlled the corpse's decay and transformed the body in a stable and durable simulacra of the dead. PMID:25807706

  3. 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

  4. Intrusive growth of primary and secondary phloem fibres in hemp stem determines fibre-bundle formation and structure

    PubMed Central

    Snegireva, Anastasia; Chernova, Tatyana; Ageeva, Marina; Lev-Yadun, Simcha; Gorshkova, Tatyana

    2015-01-01

    Plant fibres—cells with important mechanical functions and a widely used raw material—are usually identified in microscopic sections only after reaching a significant length or after developing a thickened cell wall. We characterized the early developmental stages of hemp (Cannabis sativa) stem phloem fibres, both primary (originating from the procambium) and secondary (originating in the cambium), when they still had only a primary cell wall. We gave a major emphasis to the role of intrusive elongation, the specific type of plant cell growth by which fibres commonly attain large cell length. We could identify primary phloem fibres at a distance of only 1.2–1.5 mm from the shoot apical meristem when they grew symplastically with the surrounding tissues. Half a millimeter further downwards along the stem, fibres began their intrusive elongation, which led to a sharp increase in fibre numbers visible within the stem cross-sections. The intrusive elongation of primary phloem fibres was completed within the several distal centimetres of the growing stem, before the onset of their secondary cell wall formation. The formation of secondary phloem fibres started long after the beginning of secondary xylem formation. Our data indicate that only a small portion of the fusiform cambial initials (<10 %) give rise directly or via their derivatives to secondary phloem fibres. The key determinant of final bundle structure, both for primary and secondary phloem fibres, is intrusive growth. Through bi-directional elongation, fibres join other fibres initiated individually in other stem levels, thus forming the bundles. Our results provide the specific developmental basis for further biochemical and molecular-genetic studies of phloem fibre development in hemp, but may be applied to many other species. PMID:26019229

  5. Generation of deviation parameters for amino acid singlets, doublets and triplets from three-dimentional structures of proteins and its implications for secondary structure prediction from amino acid sequences.

    PubMed

    Mugilan, S A; Veluraja, K

    2000-03-01

    We present a new method, secondary structure prediction by deviation parameter (SSPDP) for predicting the secondary structure of proteins from amino acid sequence. Deviation parameters (DP) for amino acid singlets, doublets and triplets were computed with respect to secondary structural elements of proteins based on the dictionary of secondary structure prediction (DSSP)-generated secondary structure for 408 selected non-homologous proteins. To the amino acid triplets which are not found in the selected dataset, a DP value of zero is assigned with respect to the secondary structural elements of proteins. The total number of parameters generated is 15,432, in the possible parameters of 25,260. Deviation parameter is complete with respect to amino acid singlets, doublets, and partially complete with respect to amino acid triplets. These generated parameters were used to predict secondary structural elements from amino acid sequence. The secondary structure predicted by our method (SSPDP) was compared with that of single sequence (NNPREDICT) and multiple sequence (PHD) methods. The average value of the percentage of prediction accuracy for a helix by SSPDP, NNPREDICT and PHD methods was found to be 57%, 44% and 69% respectively for the proteins in the selected dataset. For b-strand the prediction accuracy is found to be 69%, 21% and 53% respectively by SSPDP, NNPREDICT and PHD methods. This clearly indicates that the secondary structure prediction by our method is as good as PHD method but much better than NNPREDICT method. PMID:10824202

  6. The secondary structure of a messenger RNA precursor probed with psoralen is melted in an in vitro splicing reaction.

    PubMed Central

    Wollenzien, P L; Goswami, P; Teare, J; Szeberenyi, J; Goldenberg, C J

    1987-01-01

    The secondary structure of the SP6/mouse insulin precursor RNA was determined by psoralen cross-linking experiments. A series of long-range contacts occur within the left half of the pre-mRNA that contains the intervening sequence. Multiple secondary structures for the pre-mRNA exist since some of the interactions share common sites. In splicing buffer but without the splicing extract added, many of these interactions are stable up to at least 50 degrees C. These interactions, however, are dissociated during the in vitro splicing reaction. This dissociation requires ATP and it occurs during the first 30 min. of the splicing reaction. Pre-mRNAs containing psoralen cross-links in different locations within the RNA molecule were purified and used as substrates for in vitro splicing. Psoralen cross-links at any of the double-stranded regions resulted in complete inhibition of the splicing reaction. This indicates that destabilization of the secondary structure of the SP6/mouse insulin pre-mRNA is necessary for in vitro splicing. Images PMID:3317279

  7. Nuclear Magnetic Resonance-Assisted Prediction of Secondary Structure for RNA: Incorporation of Direction-Dependent Chemical Shift Constraints.

    PubMed

    Chen, Jonathan L; Bellaousov, Stanislav; Tubbs, Jason D; Kennedy, Scott D; Lopez, Michael J; Mathews, David H; Turner, Douglas H

    2015-11-17

    Knowledge of RNA structure is necessary to determine structure-function relationships and to facilitate design of potential therapeutics. RNA secondary structure prediction can be improved by applying constraints from nuclear magnetic resonance (NMR) experiments to a dynamic programming algorithm. Imino proton walks from NOESY spectra reveal double-stranded regions. Chemical shifts of protons in GH1, UH3, and UH5 of GU pairs, UH3, UH5, and AH2 of AU pairs, and GH1 of GC pairs were analyzed to identify constraints for the 5' to 3' directionality of base pairs in helices. The 5' to 3' directionality constraints were incorporated into an NMR-assisted prediction of secondary structure (NAPSS-CS) program. When it was tested on 18 structures, including nine pseudoknots, the sensitivity and positive predictive value were improved relative to those of three unrestrained programs. The prediction accuracy for the pseudoknots improved the most. The program also facilitates assignment of chemical shifts to individual nucleotides, a necessary step for determining three-dimensional structure. PMID:26451676

  8. High-Resolution NMR Reveals Secondary Structure and Folding of Amino Acid Transporter from Outer Chloroplast Membrane

    PubMed Central

    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 13C, 15N, 2H-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 T1Z 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. Nuclear Magnetic Resonance-Assisted Prediction of Secondary Structure for RNA: Incorporation of Direction-Dependent Chemical Shift Constraints

    PubMed Central

    2015-01-01

    Knowledge of RNA structure is necessary to determine structure–function relationships and to facilitate design of potential therapeutics. RNA secondary structure prediction can be improved by applying constraints from nuclear magnetic resonance (NMR) experiments to a dynamic programming algorithm. Imino proton walks from NOESY spectra reveal double-stranded regions. Chemical shifts of protons in GH1, UH3, and UH5 of GU pairs, UH3, UH5, and AH2 of AU pairs, and GH1 of GC pairs were analyzed to identify constraints for the 5? to 3? directionality of base pairs in helices. The 5? to 3? directionality constraints were incorporated into an NMR-assisted prediction of secondary structure (NAPSS-CS) program. When it was tested on 18 structures, including nine pseudoknots, the sensitivity and positive predictive value were improved relative to those of three unrestrained programs. The prediction accuracy for the pseudoknots improved the most. The program also facilitates assignment of chemical shifts to individual nucleotides, a necessary step for determining three-dimensional structure. PMID:26451676

  10. ąH, ą?N, ąłC assignment and secondary structure determination of two domains of La protein from D. discoideum.

    PubMed

    Apostolidi, Maria; Vourtsis, Dionysios J; Chasapis, Christos T; Stathopoulos, Constantinos; Bentrop, Detlef; Spyroulias, Georgios A

    2014-04-01

    Biosynthesis of RNA polymerase III transcripts requires binding of the La protein at their 3' end. La is an abundant nuclear RNA-binding protein which protects the nascent transcripts from 3' exonuclease degradation. Here, we report the high yield expression and preliminary structural analysis through NMR spectroscopy of two recombinant RNA binding domains (La motif and NRRM) from the La protein of Dictyostelium discoideum. Both recombinant protein constructs were well-folded and allowed for an almost complete sequence-specific assignment of the (15)N and (13)C labeled domains and their secondary structure prediction using PECAN online tool. PMID:23239108

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

    PubMed Central

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

    2014-01-01

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

  12. Factor Structure of the Test Anxiety Inventory for Children and Adolescents (TAICA) Scores across Gender among Students in Elementary and Secondary School Settings

    ERIC Educational Resources Information Center

    Lowe, Patricia A.; Lee, Steven W.

    2008-01-01

    The factor structure of the Test Anxiety Inventory for Children and Adolescents, a new multidimensional measure used to assess test anxiety in elementary and secondary school students, is examined across gender. The sample consisted of 696 elementary and secondary school students (391 girls and 305 boys). Coefficient of congruence and salient…

  13. 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...

  14. A Computational Model Relating Structure and Reactivity in Enantioselective Oxidations of Secondary Alcohols by

    E-print Network

    Goddard III, William A.

    Alcohols by (-)-Sparteine-PdII Complexes Robert J. Nielsen, Jason M. Keith, Brian M. Stoltz,*, and William oxidation of secondary alcohols have been elucidated using quantum mechanics (B3LYP DFT with the PBF: (1) substitution of the alcohol in place of an X-group, (2) deprotonation of the bound alcohol

  15. Simulation of the backscattered electron intensity of multi layer structure for the explanation of secondary electron contrast.

    PubMed

    Sulyok, A; Toth, A L; Zommer, L; Menyhard, M; Jablonski, A

    2013-01-01

    The intensities of the secondary electrons (SE) and of the backscattered electrons (BSE) at energy 100 eV have been measured on a Ni/C/Ni/C/Ni/C/(Si substrate) multilayer structure by exciting it with primary electrons of 5, 2.5 and 1.25 keV energies. It has been found that both intensities similarly vary while thinning the specimen. The difference as small as 4 nm in the underlying layer thicknesses resulted in visible intensity change. Utilizing this intensity change, the thickness difference of neighboring regions could be revealed from the SE image. No simple phenomenological model was found to interpret the change of intensity, thus the intensity of the BSE electrons has been calculated by means of a newly developed Monte Carlo simulation. This code also considers the secondary electron generation and transport through the solid. The calculated and measured intensities agree well supporting the validity of the model. PMID:23142749

  16. 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 <...

  17. Analysis of the relation between the sequence and secondary and three-dimensional structures of immunoglobulin molecules.

    PubMed Central

    Gelfand, I M; Kister, A E

    1995-01-01

    Methods of structural and statistical analysis of the relation between the sequence and secondary and three-dimensional structures are developed. About 5000 secondary structures of immunoglobulin molecules from the Kabat data base were predicted. Two statistical analyses of amino acids reveal 47 universal positions in strands and loops. Eight universally conservative positions out of the 47 are singled out because they contain the same amino acid in > 90% of all chains. The remaining 39 positions, which we term universally alternative positions, were divided into five groups: hydrophobic, charged and polar, aromatic, hydrophilic, and Gly-Ala, corresponding to the residues that occupied them in almost all chains. The analysis of residue-residue contacts shows that the 47 universal positions can be distinguished by the number and types of contacts. The calculations of contact maps in the 29 antibody structures revealed that residues in 24 of these 47 positions have contacts only with residues of antiparallel beta-strands in the same beta-sheet and residues in the remaining 23 positions always have far-away contacts with residues from other beta-sheets as well. In addition, residues in 6 of the 47 universal positions are also involved in interactions with residues of the other variable or constant domains. PMID:7479903

  18. Secondary structures comparison of aquaporin-1 and bacteriorhodopsin: a Fourier transform infrared spectroscopy study of two-dimensional membrane crystals.

    PubMed Central

    Cabiaux, V; Oberg, K A; Pancoska, P; Walz, T; Agre, P; Engel, A

    1997-01-01

    Aquaporins are integral membrane proteins found in diverse animal and plant tissues that mediate the permeability of plasma membranes to water molecules. Projection maps of two-dimensional crystals of aquaporin-1 (AQP1) reconstituted in lipid membranes suggested the presence of six to eight transmembrane helices in the protein. However, data from other sequence and spectroscopic analyses indicate that this protein may adopt a porin-like beta-barrel fold. In this paper, we use Fourier transform infrared spectroscopy to characterize the secondary structure of highly purified native and proteolyzed AQP1 reconstituted in membrane crystalline arrays and compare it to bacteriorhodopsin. For this analysis the fractional secondary structure contents have been determined by using several different algorithms. In addition, a neural network-based evaluation of the Fourier transform infrared spectra in terms of numbers of secondary structure segments and their interconnections [sij] has been performed. The following conclusions were reached: 1) AQP1 is a highly helical protein (42-48% alpha-helix) with little or no beta-sheet content. 2) The alpha-helices have a transmembrane orientation, but are more tilted (21 degrees or 27 degrees, depending on the considered refractive index) than the bacteriorhodopsin helices. 3) The helices in AQP1 undergo limited hydrogen/deuterium exchange and thus are not readily accessible to solvent. Our data support the AQP1 structural model derived from sequence prediction and epitope insertion experiments: AQP1 is a protein with at least six closely associated alpha-helices that span the lipid membrane. PMID:9199804

  19. Effects of Very Low Dose Fast Neutrons on Cell Membrane And Secondary Protein Structure in Rat Erythrocytes

    PubMed Central

    Nafee, Sherif S.; Shaheen, Salem A.; Al-Hadeethi, Y.

    2015-01-01

    The effects of ionizing radiation on biological cells have been reported in several literatures. Most of them were mainly concerned with doses greater than 0.01 Gy and were also concerned with gamma rays. On the other hand, the studies on very low dose fast neutrons (VLDFN) are rare. In this study, we have investigated the effects of VLDFN on cell membrane and protein secondary structure of rat erythrocytes. Twelve female Wistar rats were irradiated with neutrons of total dose 0.009 Gy (241Am-Be, 0.2 mGy/h) and twelve others were used as control. Blood samples were taken at the 0, 4th, 8th, and 12th days postirradiation. Fourier transform infrared (FTIR) spectra of rat erythrocytes were recorded. Second derivative and curve fitting were used to analysis FTIR spectra. Hierarchical cluster analysis (HCA) was used to classify group spectra. The second derivative and curve fitting of FTIR spectra revealed that the most significant alterations in the cell membrane and protein secondary structure upon neutron irradiation were detected after 4 days postirradiation. The increase in membrane polarity, phospholipids chain length, packing, and unsaturation were noticed from the corresponding measured FTIR area ratios. This may be due to the membrane lipid peroxidation. The observed band shift in the CH2 stretching bands toward the lower frequencies may be associated with the decrease in membrane fluidity. The curve fitting of the amide I revealed an increase in the percentage area of ?-helix opposing a decrease in the ?-structure protein secondary structure, which may be attributed to protein denaturation. The results provide detailed insights into the VLDFN effects on erythrocytes. VLDFN can cause an oxidative stress to the irradiated erythrocytes, which appears clearly after 4 days postirradiation. PMID:26436416

  20. Secondary Plant Products Causing Photosensitization in Grazing Herbivores: Their Structure, Activity and Regulation

    PubMed Central

    Quinn, Jane C.; Kessell, Allan; Weston, Leslie A.

    2014-01-01

    Photosensitivity in animals is defined as a severe dermatitis that results from a heightened reactivity of skin cells and associated dermal tissues upon their exposure to sunlight, following ingestion or contact with UV reactive secondary plant products. Photosensitivity occurs in animal cells as a reaction that is mediated by a light absorbing molecule, specifically in this case a plant-produced metabolite that is heterocyclic or polyphenolic. In sensitive animals, this reaction is most severe in non-pigmented skin which has the least protection from UV or visible light exposure. Photosensitization in a biological system such as the epidermis is an oxidative or other chemical change in a molecule in response to light-induced excitation of endogenous or exogenously-delivered molecules within the tissue. Photo-oxidation can also occur in the plant itself, resulting in the generation of reactive oxygen species, free radical damage and eventual DNA degradation. Similar cellular changes occur in affected herbivores and are associated with an accumulation of photodynamic molecules in the affected dermal tissues or circulatory system of the herbivore. Recent advances in our ability to identify and detect secondary products at trace levels in the plant and surrounding environment, or in organisms that ingest plants, have provided additional evidence for the role of secondary metabolites in photosensitization of grazing herbivores. This review outlines the role of unique secondary products produced by higher plants in the animal photosensitization process, describes their chemistry and localization in the plant as well as impacts of the environment upon their production, discusses their direct and indirect effects on associated animal systems and presents several examples of well-characterized plant photosensitization in animal systems. PMID:24451131

  1. Gene regulation by mRNA editing

    SciTech Connect

    Ashkenas, J.

    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.

  2. Structure of the Interstellar Boundary Explorer Ribbon from Secondary Charge-exchange at the Solar-Interstellar Interface

    NASA Astrophysics Data System (ADS)

    Zirnstein, E. J.; Heerikhuisen, J.; McComas, D. J.

    2015-05-01

    In 2009, the Interstellar Boundary Explorer discovered a bright “ribbon” of energetic neutral atom (ENA) flux in the energy range ?0.4-6 keV, encircling a large portion of the sky. This observation was not previously predicted by any models or theories, and since its discovery, it has been the subject of numerous studies of its origin and properties. One of the most studied mechanisms for its creation is the “secondary ENA” process. Here, solar wind ions, neutralized by charge-exchange with interstellar atoms, propagate outside the heliopause; experience two charge-exchange events in the dense outer heliosheath; and then propagate back inside the heliosphere, preferentially in the direction perpendicular to the local interstellar magnetic field. This process has been extensively analyzed using state-of-the-art modeling and simulation techniques, but it has been difficult to visualize. In this Letter, we show the three-dimensional structure of the source of the ribbon, providing a physical picture of the spatial and energy scales over which the secondary ENA process occurs. These results help us understand how the ribbon is generated and further supports a secondary ENA process as the leading ribbon source mechanism.

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

    SciTech Connect

    Cheng Guoxin; Liu Lie

    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.

  4. Responses of five small mammal species to micro-scale variations in vegetation structure in secondary Atlantic Forest remnants, Brazil

    PubMed Central

    Püttker, Thomas; Pardini, Renata; Meyer-Lucht, Yvonne; Sommer, Simone

    2008-01-01

    Background The Brazilian Atlantic Forest is highly endangered and only about 7% of the original forest remains, most of which consists of fragments of secondary forest. Small mammals in the Atlantic Forest have differential responses to this process of fragmentation and conversion of forest into anthropogenic habitats, and have varying abilities to occupy the surrounding altered habitats. We investigated the influence of vegetation structure on the micro-scale distribution of five small mammal species in six secondary forest remnants in a landscape of fragmented Atlantic Forest. We tested whether the occurrence of small mammal species is influenced by vegetation structure, aiming to ascertain whether species with different degrees of vulnerability to forest fragmentation (not vulnerable: A. montensis, O. nigripes and G. microtarsus; vulnerable: M. incanus and D. sublineatus; classification of vulnerability was based on the results of previous studies) are associated with distinct vegetation characteristics. Results Although vegetation structure differed among fragments, micro-scale distribution of most of the species was influenced by vegetation structure in a similar way in different fragments. Among the three species that were previously shown not to be vulnerable to forest fragmentation, A. montensis and G. microtarsus were present at locations with an open canopy and the occurrence of O. nigripes was associated to a low canopy and a dense understory. On the other hand, from the two species that were shown to be vulnerable to fragmentation, M. incanus was captured most often at locations with a closed canopy while the distribution of D. sublineatus was not clearly influenced by micro-scale variation in vegetation structure. Conclusion Results indicate the importance of micro-scale variation in vegetation structure for the distribution of small mammal species in secondary forest fragments. Species that are not vulnerable to fragmentation occurred at locations with vegetation characteristics of more disturbed forest, while one of the species vulnerable to fragmentation was found at locations with older forest characteristics. Results suggest that micro-habitat preferences may be an important factor influencing the capacity of small mammals to occupy altered habitats and, consequently, their vulnerability to forest fragmentation at a larger spatial scale. PMID:18457587

  5. Population Structure and Spatial Pattern of Main Tree Species in Secondary Betula platyphylla Forest in Ziwuling Mountains, China

    PubMed Central

    Kang, Di; Guo, Yaoxin; Ren, Chengjie; Zhao, Fazhu; Feng, Yongzhong; Han, Xinhui; Yang, Gaihe

    2014-01-01

    This study investigated a typical secondary Betula platyphylla forest in the Ziwuling Mountains, Loess Plateau, China. In the sample plot, the DBH (diameter at breast height) class structure of B. platyphylla was bimodal. Individuals with small and large DBH values were abundant. The DBH structures of Quercus wutaishanica and Pinus tabulaeformis were close to that of the logistic model, thus suggesting the increasing population of these species. B. platyphylla and Populus davidiana showed random spatial distributions at almost all scales. However, Q. wutaishanica and P. tabulaeformis were significantly clumped at small scales. B. platyphylla had a negative spatial relation with Q. wutaishanica at small spatial scales. P. tabulaeformis and Q. wutaishanica showed negative spatial correlations at small scales, but they had positive correlations at large scales. These results suggest that P. tabulaeformis and Q. wutaishanica shared habitat preferences at these scales. In the future, the secondary B. platyphylla forest in the Ziwuling Mountains in the Loess Plateau will probably change into a multi-species mixed forest (Quercus–Pinus mixed forest). Assisted restoration strategies must be employed to improve the regeneration dynamics of the forest in the long term. PMID:25362993

  6. Time-Resolved Fourier Transform Infrared Study on Photoadduct Formation and Secondary Structural Changes within the Phototropin LOV Domain

    PubMed Central

    Pfeifer, Anna; Majerus, Teresa; Zikihara, Kazunori; Matsuoka, Daisuke; Tokutomi, Satoru; Heberle, Joachim; Kottke, Tilman

    2009-01-01

    Phototropins are plant blue-light photoreceptors containing two light-, oxygen-, or voltage-sensitive (LOV) domains and a C-terminal kinase domain. The two LOV domains bind noncovalently flavin mononucleotide as a chromophore. We investigated the photocycle of fast-recovery mutant LOV2-I403V from Arabidopsis phototropin 2 by step-scan Fourier transform infrared spectroscopy. The reaction of the triplet excited state of flavin with cysteine takes place with a time constant of 3 ?s to yield the covalent adduct. Our data provide evidence that the flavin is unprotonated in the productive triplet state, disfavoring an ionic mechanism of bond formation. An intermediate adduct species was evident that displayed changes in secondary structure in the helix or loop region, and relaxed with a time constant of 120 ?s. In milliseconds, the final adduct state is formed by further alterations of secondary structure, including ?-sheets. A comparison with wild-type adduct spectra shows that the mutation does not interfere with the functionality of the domain. All signals originate from within the LOV domain, because the construct does not comprise the adjacent J? helix required for signal transduction. The contribution of early and late adduct intermediates to signal transfer to the J? helix outside of the domain is discussed. PMID:19217862

  7. 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

  8. Proton nuclear magnetic resonance assignments and secondary structure determination of the Co1E1 rop (rom) protein

    SciTech Connect

    Eberle, W. European Molecular Biology Lab., Heidelberg ); Klaus, W. ); Cesareni, G. ); Sander, C. ); Roesch, P. )

    1990-08-14

    The complete resonance assignment of the Co1E1 rop (rom) protein at pH 2.3 was obtained by two-dimensional (2D) proton nuclear magnetic resonance spectroscopy ({sup 1}H NMR) at 500 and 600 MHz using through-bond and through-space connectivities. Sequential assignments and elements of regular secondary structure were deduced by analysis of nuclear Overhauser enhancement spectroscopy (NOESY) experiments and {sup 3}J{sub HN{alpha}} coupling constants. One 7.2-kDa monomer of the homodimer consists of two antiparallel helices connected by a hairpin loop at residue 31. The C-terminal peptide consisting of amino acids 59-63 shows no stable conformation. The dimer forms a four-helix bundle with opposite polarization of neighboring elements in agreement with the x-ray structure.

  9. Optimal Estimation Retrievals of the Atmospheric Structure and Composition of HD 189733b from Secondary Eclipse Spectroscopy

    E-print Network

    Lee, Jae-Min; Irwin, Patrick G J

    2011-01-01

    Recent spectroscopic observations of transiting hot Jupiters have permitted the derivation of the thermal structure and molecular abundances of H2O, CO2, CO, and CH4 in these extreme atmospheres. Here, for the first time, we apply the technique of optimal estimation to determine the thermal structure and composition of an exoplanet by solving the inverse problem. The development of a suite of radiative transfer and retrieval tools for exoplanet atmospheres is described, building upon a retrieval algorithm which is extensively used in the study of our own solar system. First, we discuss the plausibility of detection of different molecules in the dayside atmosphere of HD 189733b and the best-fitting spectrum retrieved from all publicly available sets of secondary eclipse observations between 1.45 and 24 {\\mu}m. Additionally, we use contribution functions to assess the vertical sensitivity of the emission spectrum to temperatures and molecular composition. Over the altitudes probed by the contribution functions,...

  10. Modeling proteins using a super-secondary structure library and NMR chemical shift information.

    PubMed

    Menon, Vilas; Vallat, Brinda K; Dybas, Joseph M; Fiser, Andras

    2013-06-01

    A remaining challenge in protein modeling is to predict structures for sequences with no sequence similarity to any experimentally solved structure. Based on earlier observations, the library of protein backbone supersecondary structure motifs (Smotifs) saturated about a decade ago. Therefore, it should be possible to build any structure from a combination of existing Smotifs with the help of limited experimental data that are sufficient to relate the backbone conformations of Smotifs between target proteins and known structures. Here, we present a hybrid modeling algorithm that relies on an exhaustive Smotif library and on nuclear magnetic resonance chemical shift patterns without any input of primary sequence information. In a test of 102 proteins, the algorithm delivered 90 homology-model-quality models, among them 24 high-quality ones, and a topologically correct solution for almost all cases. The current approach opens a venue to address the modeling of larger protein structures for which chemical shifts are available. PMID:23685209

  11. A weighted sampling algorithm for the design of RNA sequences with targeted secondary structure and nucleotide distribution

    PubMed Central

    Reinharz, Vladimir; Ponty, Yann; Waldispühl, Jérôme

    2013-01-01

    Motivations: The design of RNA sequences folding into predefined secondary structures is a milestone for many synthetic biology and gene therapy studies. Most of the current software uses similar local search strategies (i.e. a random seed is progressively adapted to acquire the desired folding properties) and more importantly do not allow the user to control explicitly the nucleotide distribution such as the GC-content in their sequences. However, the latter is an important criterion for large-scale applications as it could presumably be used to design sequences with better transcription rates and/or structural plasticity. Results: In this article, we introduce IncaRNAtion, a novel algorithm to design RNA sequences folding into target secondary structures with a predefined nucleotide distribution. IncaRNAtion uses a global sampling approach and weighted sampling techniques. We show that our approach is fast (i.e. running time comparable or better than local search methods), seedless (we remove the bias of the seed in local search heuristics) and successfully generates high-quality sequences (i.e. thermodynamically stable) for any GC-content. To complete this study, we develop a hybrid method combining our global sampling approach with local search strategies. Remarkably, our glocal methodology overcomes both local and global approaches for sampling sequences with a specific GC-content and target structure. Availability: IncaRNAtion is available at csb.cs.mcgill.ca/incarnation/ Contact: jeromew@cs.mcgill.ca or yann.ponty@lix.polytechnique.fr Supplementary Information: Supplementary data are available at Bioinformatics online. PMID:23812999

  12. 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.

  13. Mineral Association Changes the Secondary Structure and Dynamics of Murine Amelogenin

    SciTech Connect

    Lu, Junxia; Xu, Yimin; Buchko, Garry W.; Shaw, Wendy J.

    2013-12-18

    Biomineralization proteins, present during the formation of hard tissues including bones, teeth, egg shells and nacre, result in the exquisite structures and properties of the resulting materials.[1] The structure of these proteins is often implicated in the control of the mineral properties, however very little structural data is available for the bulk of these proteins due to the difficulty in determining structures of immobilized proteins. Solid-state NMR is uniquely suited to the study of the structure of proteins bound to surfaces, demonstrated with the structural and orientation insights provided for the hydroxyapatite mineralization proteins statherin and the amelogenin, LRAP.[2] While these data are some of the only structural data available for this important class of protein, the experiments are often expensive and time consuming, due to the need to prepare and measure samples with isolated spin pairs, and are limited to a size of ~60 residues. In this work, we utilized a combination of 1D and recent 2D[3] solid-state NMR techniques along with a sparsely labelled sample to characterize the structure and dynamics of potential HAP binding residues of the 180 residue enamel protein, amelogenin. Amelogenin nanospheres and mineral bound amelogenin were investigated and a shift from unstructured to ?-sheet structure was observed, along with a decrease in protein flexibility. This work provides the first molecular level structure and dynamic information of full-length amelogenin on the surface of hydroxyapatite (HAP) and within nanospheres, and demonstrates the ability to evaluate structural characteristics of large biomineralization proteins bound to their physiologically relevant surface. The research was performed at the Pacific Northwest National Laboratory (PNNL), a facility operated by Battelle for the U.S. Department of Energy, with a portion of it performed at the W.R. Wiley Environmental Molecular Sciences Laboratory (EMSL), a national scientific user facility sponsored by the U.S. DOE Biological and Environmental Research program.

  14. New Secondary Structure Prediction software package using automatically trained Bayesian Networks

    E-print Network

    to protein structure A protein is a string of amino acids (or residues). The catalytic, binding this hierarchy should be. #12;One commonly accepted hierarchy is: · primary structure: The linear amino acid). Predicting the three-dimensional shape of proteins from their amino acid sequence is widely believed

  15. Novel Evolutionary Lineages Revealed in the Chaetothyriales (Fungi) Based on Multigene Phylogenetic Analyses and Comparison of ITS Secondary Structure

    PubMed Central

    Réblová, Martina; Untereiner, Wendy A.; Réblová, Kamila

    2013-01-01

    Cyphellophora and Phialophora (Chaetothyriales, Pezizomycota) comprise species known from skin infections of humans and animals and from a variety of environmental sources. These fungi were studied based on the comparison of cultural and morphological features and phylogenetic analyses of five nuclear loci, i.e., internal transcribed spacer rDNA operon (ITS), large and small subunit nuclear ribosomal DNA (nuc28S rDNA, nuc18S rDNA), ?-tubulin, DNA replication licensing factor (mcm7) and second largest subunit of RNA polymerase II (rpb2). Phylogenetic results were supported by comparative analysis of ITS1 and ITS2 secondary structure of representatives of the Chaetothyriales and the identification of substitutions among the taxa analyzed. Base pairs with non-conserved, co-evolving nucleotides that maintain base pairing in the RNA transcript and unique evolutionary motifs in the ITS2 that characterize whole clades or individual taxa were mapped on predicted secondary structure models. Morphological characteristics, structural data and phylogenetic analyses of three datasets, i.e., ITS, ITS-?-tubulin and 28S-18S-rpb2-mcm7, define a robust clade containing eight species of Cyphellophora (including the type) and six species of Phialophora. These taxa are now accommodated in the Cyphellophoraceae, a novel evolutionary lineage within the Chaetothyriales. Cyphellophora is emended and expanded to encompass species with both septate and nonseptate conidia formed on discrete, intercalary, terminal or lateral phialides. Six new combinations in Cyphellophora are proposed and a dichotomous key to species accepted in the genus is provided. Cyphellophora eugeniae and C. hylomeconis, which grouped in the Chaetothyriaceae, represent another novel lineage and are introduced as the type species of separate genera. PMID:23723988

  16. Secondary structure of the rRNA ITS2 region reveals key evolutionary patterns in acroporid corals.

    PubMed

    Coleman, Annette W; van Oppen, Madeleine J H

    2008-10-01

    This study investigates the ribosomal RNA transcript secondary structure in corals as confirmed by compensatory base changes in Isopora/Acropora species. These species are unique versus all other corals in the absence of a eukaryote-wide conserved structural component, the helix III in internal transcriber spacer (ITS) 2, and their variability in the 5.8S-LSU helix basal to ITS2, a helix with pairings identical among all other scleractinian corals. Furthermore, Isopora/Acropora individuals display at least two, and as many as three, ITS sequence isotypes in their genome which appear to be capable of function. From consideration of the conserved elements in ITS2 and flanking regions, it appears that there are three major groups within the IsoporaAcropora lineage: the Isopora + Acropora "longi" group, the large group including Caribbean Acropora + the Acropora "carib" types plus the bulk of the Indo-Pacific Acropora species, and the remaining enigmatic "pseudo" group found in the Pacific. Interbreeding is possible among Caribbean A. palmata and A. cervicornis and among some species of Indo-Pacific Acropora. Recombinant ITS sequences are obvious among these latter, such that morphology (as represented by species name) does not correlate with common ITS sequence. The combination of characters revealed by RNA secondary structure analyses suggests a recent past/current history of interbreeding among the Indo-Pacific Acropora species and a shared ancestry of some of these with the Caribbean Acropora. The unusual absence of helix III of ITS2 of Isopora/Acropora species may have some causative role in the equally unusual instability in the 5.8S-LSU helix basal to ITS2 of this species complex. PMID:18781354

  17. Synthesis, Characterization, and Secondary Structure Determination of a Silk-Inspired, Self-Assembling Peptide: A Laboratory Exercise for Organic and Biochemistry Courses

    ERIC Educational Resources Information Center

    Albin, Tyler J.; Fry, Melany M.; Murphy, Amanda R.

    2014-01-01

    This laboratory experiment gives upper-division organic or biochemistry undergraduate students a comprehensive look at the synthesis, chemical characterization, self-assembly, and secondary structure determination of small, N-acylated peptides inspired by the protein structure of silkworm silk. All experiments can be completed in one 4 h lab…

  18. Secondary structure and thermal stability of the extrinsic 23 kDa protein of photosystem II studied by Fourier transform infrared spectroscopy

    E-print Network

    Carpentier, Robert

    structure and has been increasingly applied to many water soluble as well as membrane proteins (for de protein; Fourier transform infrared; Oxygen evolving complex 23; Photosystem II; Secondary structure 1 association with the oxygen evolving complex, these OEC subunits are required for the maximal oxygen evolution

  19. Secondary structure of component 8c-1 of alpha-keratin. An analysis of the amino acid sequence.

    PubMed Central

    Dowling, L M; Crewther, W G; Parry, D A

    1986-01-01

    The amino acid sequence of component 8c-1 from alpha-keratin was analysed by using secondary-structure prediction techniques, homology search methods, fast Fourier-transform techniques to detect regularities in the linear disposition of amino acids, interaction counts to assess possible modes of chain aggregation and assessment of hydrophilicity distribution. The analyses show the following. The molecule has two lengths of coiled-coil structure, each about 20 nm long, one from residues 56-202 with a discontinuity from about residue 91 to residue 101, and the other from residues 219-366 with discontinuities from about residue 238 to residue 245 and at about residue 306. The acidic and basic residues in the coiled-coil segment between residues 102 and 202 show a 9,4-residue structural period in their linear disposition, whereas between residues 246 and 366 a period of 9.9 residues is observed in the positioning of ionic residues. Acidic and basic residues are out of phase by 180 degrees. Similar repeats occur in corresponding regions of other intermediate-filament proteins. The overall mean values for the repeats are 9.55 residues in the N-terminal region and 9.85 residues in the C-terminal region. The regions at each end of the protein chain (residues 1-55 and 367-412) are not alpha-helical and contain many potential beta-bends. The regions specified in have a significant degree of homology mainly due to a semi-regular disposition of proline and half-cystine residues on a three-residue grid; this is especially apparent in the C-terminal segment, in which short (Pro-Cys-Xaa)n regions occur. The coiled-coil segments of component 8c-1 bear a striking similarity to corresponding segments of other intermediate-filament proteins as regards sequence homology, structural periodicity of ionic residues and secondary/tertiary-structure predictions. The assessments of the probabilities that these homologies occurred by chance indicate that there are two populations of keratin filament proteins. The non-coiled-coil regions at each end of the chain are less hydrophilic than the coiled-coil regions. Ionic interactions between the heptad regions of components 8c-1 and 7c from the microfibrils of alpha-keratin are optimized when a coiled-coil structure is formed with the heptad regions of the constituent chains both parallel and in register. PMID:2431680

  20. An experimental and numerical study of the modifications of mixed-layer structure by inhomogeneous surface fluxes and secondary circulations

    SciTech Connect

    Zhong, S.; Doran, J.C.

    1994-07-01

    The problem of scale interactions in the planetary boundary layer (PBL), i.e., how forcing mechanisms of differing spatial and temporal scales affect the properties of the PBL, has been a subject of considerable interest for some time. One aspect of this problem that has received increasing attention in recent years is the representation, in mesoscale and general circulation models. of the effects of subgrid-scale inhomogeneities in surface properties. Differences in sensible and latent heat fluxes between adjacent areas can result in secondary circulations. modifications to the boundary layer structure, and the transport of heat and moisture from one area to another. Despite their potential included on local PBL properties, such effects can not be resolved by numerical models whose scale is too coarse; thus, suitable parameterizations that account for these phenomena are needed. In this paper the authors present some results of wind and temperature measurements over an area with significant variations in surface fluxes on scales of O(10 km). They then use fine resolution numerical simulations to show how synoptic, topographical, and thermal forcing combine to affect the properties of the PBL in the region. Specifically, they consider the relative importance of topography and land-use differences on the generation of secondary circulations and on the depth of the mixed layer, and they show how these effects are modified by synoptic wind fields. Implications for coarser resolution models are also discussed.

  1. Protective spin-labeled fluorenes maintain amyloid beta peptide in small oligomers and limit transitions in secondary structure.

    PubMed

    Altman, Robin; Ly, Sonny; Hilt, Silvia; Petrlova, Jitka; Maezawa, Izumi; Kálai, Tamás; Hideg, Kálmán; Jin, Lee-Way; Laurence, Ted A; Voss, John C

    2015-12-01

    Alzheimer's disease is characterized by the presence of extracellular plaques comprised of amyloid beta (A?) peptides. Soluble oligomers of the A? peptide underlie a cascade of neuronal loss and dysfunction associated with Alzheimer's disease. Single particle analyses of A? oligomers in solution by fluorescence correlation spectroscopy (FCS) were used to provide real-time descriptions of how spin-labeled fluorenes (SLFs; bi-functional small molecules that block the toxicity of A?) prevent and disrupt oligomeric assemblies of A? in solution. Furthermore, the circular dichroism (CD) spectrum of untreated A? shows a continuous, progressive change over a 24-hour period, while the spectrum of A? treated with SLF remains relatively constant following initial incubation. These findings suggest the conformation of A? within the oligomer provides a complementary determinant of A? toxicity in addition to oligomer growth and size. Although SLF does not produce a dominant state of secondary structure in A?, it does induce a net reduction in beta secondary content compared to untreated samples of A?. The FCS results, combined with electron paramagnetic resonance spectroscopy and CD spectroscopy, demonstrate SLFs can inhibit the growth of A? oligomers and disrupt existing oligomers, while retaining A? as a population of smaller, yet largely disordered oligomers. PMID:26374940

  2. 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

  3. Secondary Structure, a Missing Component of Sequence-Based Minimotif Definitions

    PubMed Central

    Sargeant, David P.; Gryk, Michael R.; Maciejewski, Mark W.; Thapar, Vishal; Kundeti, Vamsi; Rajasekaran, Sanguthevar; Romero, Pedro; Dunker, Keith; Li, Shun-Cheng; Kaneko, Tomonori; Schiller, Martin R.

    2012-01-01

    Minimotifs are short contiguous segments of proteins that have a known biological function. The hundreds of thousands of minimotifs discovered thus far are an important part of the theoretical understanding of the specificity of protein-protein interactions, posttranslational modifications, and signal transduction that occur in cells. However, a longstanding problem is that the different abstractions of the sequence definitions do not accurately capture the specificity, despite decades of effort by many labs. We present evidence that structure is an essential component of minimotif specificity, yet is not used in minimotif definitions. Our analysis of several known minimotifs as case studies, analysis of occurrences of minimotifs in structured and disordered regions of proteins, and review of the literature support a new model for minimotif definitions that includes sequence, structure, and function. PMID:23236358

  4. The inviscid secondary instability of fully nonlinear longitudinal vortex structures in growing boundary layers

    NASA Technical Reports Server (NTRS)

    Hall, Philip; Horseman, Nicola J.

    1990-01-01

    The inviscid instability of a longitudinal vortex structure within a steady boundary layer is investigated. The instability has a wavelength comparable with the boundary layer thickness so that a quasi-parallel approach to the instability problem can be justified. The generalization of the Rayleigh equation to such a flow is obtained and solved for the case when the vortex structure is induced by curvature. Two distinct modes of instability are found; these modes correspond with experimental observations on the breakdown process for Goertler vortices.

  5. Structural and Functional Characterization of BaiA, An Enzyme Involved in Secondary Bile Acid Synthesis in Human Gut Microbe

    PubMed Central

    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.

    2014-01-01

    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 co-factor 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 co-factor specificity and mechanism of proton relay. A conformational restriction involving Glu42 located in the co-factor binding site seems crucial in determining co-factor 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 towards NADP+ by 10- fold compared to wild type. The co-factor 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 Ĺ) and Lys161 (4.5 Ĺ). 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

  6. Characterization of mRNA for a proline-rich protein of cotton fiber.

    PubMed Central

    John, M E; Keller, G

    1995-01-01

    Cotton (Gossypium hirsutum L.) mRNA (H6) is expressed predominantly in fiber cells and is present during early primary cell wall formation. However, H6 protein is found to accumulate during later stages, when active secondary cell wall formation occurs, indicating possible regulation at the translational level and function in the secondary cell wall assembly. The nucleotide-derived amino acid sequence of pCK-H6 is proline rich (35 mol %) with a calculated molecular mass of 21 kD. Cotton protein H6 contains a repetitive pentameric motif (17) of alanine (serine)-threonine (serine)-proline-proline-proline. Its amino acid composition and solubility indicate that it may belong to the group of arabinogalactan proteins. Both sodium dodecyl sulfate-polyacrylamide gel electrophoresis (55 kD) and size-exclusion chromatography (77-83 kD) overestimated the size of in vitro synthesized H6 protein compared to the molecular mass derived from the nucleotide sequence (21 kD). The conformation of the molecule determined by its unusual primary structure may be the cause of its anomalous mobility. The presence of a proline-rich, arabinogalactan-type protein in cotton fiber raises the interesting possibility that it may be an integral part of the plasmalemma taking part in the development and architecture of the secondary wall of cotton fiber. PMID:7610164

  7. Dopamine agonist suppression of rapid-eye-movement sleep is secondary to sleep suppression mediated via limbic structures

    SciTech Connect

    Miletich, R.S.

    1985-01-01

    The effects of pergolide, a direct dopamine receptor agonist, on sleep and wakefulness, motor behavior and /sup 3/H-spiperone specific binding in limbic structures and striatum in rats was studied. The results show that pergolide induced a biphasic dose effect, with high doses increasing wakefulness and suppressing sleep while low dose decreased wakefulness, but increased sleep. It was shown that pergolide-induced sleep suppression was blocked by ..cap alpha..-glupenthixol and pimozide, two dopamine receptor antagonists. It was further shown that pergolide merely delayed the rebound resulting from rapid-eye-movement (REM) sleep deprivation, that dopamine receptors stimulation had no direct effect on the period, phase or amplitude of the circadian rhythm of REM sleep propensity and that there was no alteration in the coupling of REM sleep episodes with S/sub 2/ episodes. Rapid-eye-movement sleep deprivation resulted in increased sensitivity to the pergolide-induced wakefulness stimulation and sleep suppression and pergolide-induced motor behaviors of locomotion and head bobbing. /sup 3/H-spiperone specific binding to dopamine receptors was shown to be altered by REM sleep deprivation in the subcortical limbic structures. It is concluded that the REM sleep suppressing action of dopamine receptor stimulation is secondary to sleep suppression per se and not secondary to a unique effect on the REM sleep. Further, it is suggested that the wakefulness stimulating action of dopamine receptor agonists is mediated by activation of the dopamine receptors in the terminal areas of the mesolimbocortical dopamine projection system.

  8. Trapping a translocating protein within the anthrax toxin channel: implications for the secondary structure of permeating proteins

    PubMed Central

    Jennings-Antipov, Laura D.; Jakes, Karen S.; Finkelstein, Alan

    2011-01-01

    Anthrax toxin consists of three proteins: lethal factor (LF), edema factor (EF), and protective antigen (PA). This last forms a heptameric channel, (PA63)7, in the host cell’s endosomal membrane, allowing the former two (which are enzymes) to be translocated into the cytosol. (PA63)7 incorporated into planar bilayer membranes forms a channel that translocates LF and EF, with the N terminus leading the way. The channel is mushroom-shaped with a cap containing the binding sites for EF and LF, and an ?100 Ĺ–long, 15 Ĺ–wide stem. For proteins to pass through the stem they clearly must unfold, but is secondary structure preserved? To answer this question, we developed a method of trapping the polypeptide chain of a translocating protein within the channel and determined the minimum number of residues that could traverse it. We attached a biotin to the N terminus of LFN (the 263-residue N-terminal portion of LF) and a molecular stopper elsewhere. If the distance from the N terminus to the stopper was long enough to traverse the channel, streptavidin added to the trans side bound the N-terminal biotin, trapping the protein within the channel; if this distance was not long enough, streptavidin did not bind the N-terminal biotin and the protein was not trapped. The trapping rate was dependent on the driving force (voltage), the length of time it was applied, and the number of residues between the N terminus and the stopper. By varying the position of the stopper, we determined the minimum number of residues required to span the channel. We conclude that LFN adopts an extended-chain configuration as it translocates; i.e., the channel unfolds the secondary structure of the protein. We also show that the channel not only can translocate LFN in the normal direction but also can, at least partially, translocate LFN in the opposite direction. PMID:21402886

  9. A Multiple Graph Layers Model with Application to RNA Secondary Structures

    E-print Network

    Sagot, Marie-France

    of the comparison at a given step is communicated to the next step using a special colouring scheme. Mi or source codes. MiGaL is a more general structure in that it can model graphs besides trees, and edges can to the next step using a special colouring scheme. We then present an application of MiGaL to the analysis

  10. The Relationship between Professional Preparation and Class Structure on Health Instruction in the Secondary Classroom

    ERIC Educational Resources Information Center

    Hammig, Bart; Ogletree, Roberta; Wycoff-Horn, Marcie R.

    2011-01-01

    Background: The aim of the present study was to examine the impact of professional preparation and class structure on health content delivery and time spent delivering content among required health education classes in the United States. Methods: Data from the classroom-level file of the 2006 School Health Policies and Programs Study were…

  11. HYPROSP: A Hybrid Protein Secondary Structure Prediction Algorithm --A Knowledge-Based Approach*

    E-print Network

    Chu, Hao-hua

    . This comprises our hybrid protein structure prediction (HYPROSP) approach. We use the DSSP and EVA data as our at least 80%, the average Q3 of PROSP is 3.96 and 7.2 better than that of PSIPRED on DSSP and EVA data

  12. Determination of the Secondary Structure and Conformation of Puroindolines by Infrared and Raman Spectroscopy

    E-print Network

    Pezolet, Michel

    -transfer protein and some amylase-protease inhibitors. These proteins could form a homogeneous structural family Spectroscopy Thierry Le Bihan, Jean-EÄ rik Blochet, Andre´ De´sormeaux, Didier Marion,§ and Michel Pe Prote´ines, Institut National de la Recherche Agronomique, Rue de la Ge´raudie`re, B.P. 1627, 316 Nantes

  13. The Use of Structural Behavioral Assessment to Develop Interventions for Secondary Students Exhibiting Challenging Behaviors

    ERIC Educational Resources Information Center

    Losinski, Mickey; Maag, John W.; Katsiyannis, Antonis; Ryan, Joseph B.

    2015-01-01

    Structural behavioral assessment (SBA) involves a series of heuristic approaches similar to those used with functional behavioral assessment (FBA). It involves assessing contextual variables that precede the occurrence of a behavior. These variables have also been termed antecedents, setting events, or establishing operations. Once these variables…

  14. Comparison of the DNA sequences and secondary structure of the mitochondrial 16S rRNA gene of Ixodes kingi, Ixodes sculptus and Ixodes angustus.

    PubMed

    Anstead, Clare A; Chilton, Neil B

    2014-08-01

    The DNA sequences and predicted secondary structure of domains IV and V of the mitochondrial (mt) 16S rRNA gene were compared for three species of Ixodes: Ixodes kingi, Ixodes sculptus and Ixodes angustus. Each species had a unique set of DNA sequences for the 16S gene. Many of the differences in DNA sequence within and among species occurred in a "hypervariable" region of domain V, and either represented partial or full compensatory base pair changes that maintained the helices within the secondary structure, or nucleotide alterations at unpaired positions that had no effect on the secondary structure. The results of the phylogenetic analyses revealed that I. kingi, I. sculptus and I. angustus were placed in a clade with some other species of the subgenera Pholeoixodes and Ixodiopsis. In addition, individuals of I. sculptus from Saskatchewan (Canada) and Colorado (USA) did not form a monophyletic clade, suggesting the possible existence of cryptic species. PMID:24556375

  15. What an rRNA Secondary Structure Tells about Phylogeny of Fungi in Ascomycota with Emphasis on Evolution of Major Types of Ascus

    PubMed Central

    Zhuang, Wen-Ying; Liu, Chao-Yang

    2012-01-01

    Background RNA secondary structure is highly conserved throughout evolution. The higher order structure is fundamental in establishing important structure-function relationships. Nucleotide sequences from ribosomal RNA (rRNA) genes have made a great contribution to our understanding of Ascomycota phylogeny. However, filling the gaps between molecular phylogeny and morphological assumptions based on ascus dehiscence modes and type of fruitbodies at the higher level classification of the phylum remains an unfulfilled task faced by mycologists. Methodology/Principal Findings We selected some major groups of Ascomycota to view their phylogenetic relationships based on analyses of rRNA secondary structure. Using rRNA secondary structural information, here, we converted nucleotide sequences into the structure ones over a 20-symbol code. Our structural analyses together with ancestral character state reconstruction produced reasonable phylogenetic position for the class Geoglossomycetes as opposed to the classic nucleotide analyses. Judging from the secondary structure analyses with consideration of mode of ascus dehiscence and the ability of forming fruitbodies, we draw a clear picture of a possible evolutionary route for fungal asci and some major groups of fungi in Ascomycota. The secondary structure trees show a more reasonable phylogenetic position for the class Geoglossomycetes. Conclusions Our results illustrate that asci lacking of any dehiscence mechanism represent the most primitive type. Passing through the operculate and Orbilia-type asci, bitunicate asci occurred. The evolution came to the most advanced inoperculate type. The ascus-producing fungi might be derived from groups lacking of the capacity to form fruitbodies, and then evolved multiple times. The apothecial type of fruitbodies represents the ancestral state, and the ostiolar type is advanced. The class Geoglossomycetes is closely related to Leotiomycetes and Sordariomycetes having a similar ascus type other than it was originally placed based on nucleotide sequence analyses. PMID:23110078

  16. First-principles investigation of the structural characteristics of LiMO2 cathode materials for lithium secondary batteries

    NASA Astrophysics Data System (ADS)

    Kim, Yongseon

    2015-11-01

    The structural features related to the defects of LiMO2 (M = Ni, Co, Mn) cathode materials for lithium secondary batteries were investigated by a simulation of phase diagrams based on first-principle calculations. Crystal models with various types of point defects were designed and dealt with as independent phases, which enabled an examination of the thermodynamic stability of the defects. A perfect phase without defects appeared to be the most stable for LiCoO2, whereas the formation of Li vacancies, O vacancies, and antisites between Li and Ni was thermodynamically unavoidable for LiNiO2. The introduction of both Co and Mn in LiNiO2 was effective in reducing the formation of point defects, but increasing the relative amount of Mn was undesirable because the antisite defect remained stable with Mn doping. The simulation showed good agreement with the experimental data and previous reports. Therefore, the method and the results of this study are expected to be useful for examining the synthesis, structure and related properties of layer-structured cathode materials.

  17. Formation of higher-order secondary and tertiary chromatin structures by genomic mouse mammary tumor virus promoters

    PubMed Central

    Georgel, Philippe T.; Fletcher, Terace M.; Hager, Gordon L.; Hansen, Jeffrey C.

    2003-01-01

    Agarose multigel electrophoresis has been used to characterize the structural features of isolated genomic mouse mammary tumor virus (MMTV) promoters. The mouse 3134cells used for these studies contain ?200 stably integrated tandem repeats of a 2.4-kb MMTV promoter fragment. Inactive, basally active, and hormonally activated genomic promoters were liberated by restriction digestion of isolated nuclei, recovered in low-salt nuclear extracts, and electrophoresed in multigels consisting of nine individual agarose running gels. Specific bands were detected and characterized by Southern and Western blotting. We find that transcriptionally inactive promoters contain TBP and high levels of histone H1, and are present to varying extents in both untreated and dexamethasone (DEX)-treated 3134cells. In contrast, the basally active promoter, present in untreated cells, is bound to RNA Pol II, TBP, and Oct1, contains acetylated H3 tail domains, and is depleted of histone H1. The DEX-activated promoter possessed similar composition as the basal promoter, but also contains stably bound Brg1. Strikingly, all forms of the MMTV promoter condense into higher-order secondary and/or tertiary chromatin structures in vitro in the presence of Mg2+. Thus, genomic MMTV promoter chromatin retains the ability to form classical higher-order structures under physiological salt conditions, even after dissociation of H1 and binding of several transcription factors and multiprotein complexes. These results suggest that transcriptionally active eukaryotic promoters may function in a locally folded chromatin environment in vivo. PMID:12842912

  18. Efficient sequence-specific purification of Listeria innocua mRNA species by triplex affinity capture with parallel tail-clamps.

    PubMed

    Nadal, Anna; Coll, Anna; Avińó, Anna; Esteve, Teresa; Eritja, Ramon; Pla, Maria

    2006-07-01

    Parallel clamps can interact in a sequence-specific manner with homopyrimidine DNA and RNA oligonucleotides to form triplexes. For longer nucleic acids, we have previously demonstrated the inhibitory effect of DNA-target secondary structures on triplex formation. We further designed a modification of these molecules-that is, tail-clamps formed by addition of a tail sequence to the parallel clamp-and proved efficient binding of the molecules with structured single-stranded DNA targets. Here we explore the possible application of the tail-clamp strategy for triplex formation with RNA targets, which are typically found as strongly folded single-stranded molecules. Efficient and specific binding of a tail-clamp designed to form a parallel triplex with Listeria innocua iap mRNA sequences has been verified by UV melting curves and triplex affinity capture techniques. Furthermore, we show for the first time the formation of stable complexes of mRNA with tail-clamps not only under acidic but also under neutral and slightly basic pH conditions. These results signify a further step towards the possible applications of triplexes with mRNA molecules; research, analytical, and therapeutic uses can be envisaged. As an example, our tail-clamp-based triplex affinity capture assay allowed the specific capture and recovery of iap mRNA molecules from an L. innocua total RNA solution with 45 % yield. PMID:16729343

  19. 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

  20. Protein Structure Analysis Iosif Vaisman

    E-print Network

    Vaisman, Iosif

    Protein Structure Analysis Iosif Vaisman 2015 BINF 731 Secondary Structure: Computational Problems Secondary structure characterization Secondary structure assignment Secondary structure prediction Protein structure classification Structural classes of proteins all a all b a/b Protein Structure Classification

  1. Site-directed Mutagenesis of Apolipoprotein CII to Probe the Role of Its Secondary Structure for Activation of Lipoprotein Lipase*

    PubMed Central

    Shen, Yan; Lookene, Aivar; Zhang, Liyang; Olivecrona, Gunilla

    2010-01-01

    Apolipoprotein CII (apoCII) is a necessary activator for lipoprotein lipase (LPL). We had identified four residues (Tyr-63, Ile-66, Asp-69, and Gln-70), presumably contained in an ?-helix, as a potential binding site for LPL. We have now used structure prediction, mutagenesis, and functional assays to explore the functional role of the secondary structure in this part of apoCII. First, mutants were generated by replacements with proline residues to disturb the helical structure. Activation by mutant G65P was reduced by 30%, whereas mutant S54P retained activation ability. Mutants V71P and L72P should be located outside the LPL-binding site, but V71P was totally inactive, whereas activation by L72P was reduced by 65%. Insertion of alanine after Tyr-63, changing the position of the putative LPL-binding site in relation to the hydrophobic face of the ?-helix, also severely impeded the activation ability, and a double mutant (Y63A/I66A) was completely inactive. Next, to investigate the importance of conserved hydrophobic residues in the C-terminal end of apoCII, Phe-67, Val-71, Leu-72, and Leu-75 were exchanged for polar residues. Only F67S showed dramatic loss of function. Finally, fragment 39–62, previously claimed to activate LPL, was found to be completely inactive. Our data support the view that the helical structure close to the C-terminal end of apoCII is important for activation of LPL, probably by placing residues 63, 66, 69, and 70 in an optimal steric position. The structural requirements for the hydrophobic face on the back side of this helix and further out toward the C terminus were less stringent. PMID:20042600

  2. 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.

  3. Structural characterization of 2-hydroxyterpenylic acid, an abundant oxygenated marker compound for ?-pinene secondary organic aerosol in ambient fine aerosol

    NASA Astrophysics Data System (ADS)

    Kahnt, Ariane; Iinuma, Yoshiteru; Blockhuys, Frank; van Alsenoy, Christian; Mutzel, Anke; Vermeylen, Reinhilde; Offenberg, John; Lewandowski, Michael; Jaoui, Mohammed; Kleindienst, Tadeusz; Böge, Olaf; Herrmann, Hartmut; Maenhaut, Willy; Claeys, Magda

    2014-05-01

    A highly hydrophilic and oxygenated MW 188 compound is commonly observed in substantial abundance in atmospheric aerosol samples and was proposed in previous studies as an ?-pinene-related marker compound that is associated with ageing processes (1). Paradoxically, the MW 188 compound is usually observed at low abundance in chamber-generated ?-pinene-secondary organic aerosol (SOA) (2), pointing to a non-achievement in crucial reaction conditions. Furthermore, the occurrence of several isobaric isomers did not lead to a complete assignment for individual MW 188 compounds from laboratory generated SOA samples in former studies. For the most abundant MW 188 compound two structures have been proposed, i.e., a C8-monohydroxycarboxylic acid structure (2-hydroxyterpenylic acid) (3), and a C8-hydroxydicarboxylic acid structure (hydroxynorpinic acid) (4). Results will be presented here from a comprehensive mass spectrometric analysis of the most abundant MW 188 compound as 2-hydroxyterpenylic acid. The application of liquid chromatographic/electrospray ionization - ion trap mass spectrometry in both negative and positive ion modes in combination with collision-induced dissociation, as well as the utilisation of a soft derivatisation technique followed by analysis of the formed methyl ester derivatives using the latter technique and gas chromatography/electron ionization mass spectrometry enabled a comprehensive characterization of MW 188 isomers. Theoretical calculations were performed to support the assignment of 2-hydroxyterpenylic acid diastereoisomers. In addition, a positional isomer of 2-hydroxyterpenylic acid, the 4-hydroxyterpenylic acid, was tentatively identified, which is also of atmospheric relevance as it could be detected in ambient fine aerosol. Results from a time-resolved ?-pinene photooxidation experiment do not support that the 2 hydroxyterpenylic acid is a marker compound for aged SOA. Compared to terpenylic acid it should rather be regarded as a higher-generation product of the ?-pinene oxidation cascade. This study presents a comprehensive chemical data set for a more complete structural characterization of hydroxyterpenylic acids in ambient fine aerosol, which sets the foundation to better understand the atmospheric fate of ?-pinene in future studies. This work was supported by the Belgian Federal Science Policy Office through the network project "Biogenic Influence on Oxidants and Secondary Organic Aerosol: theoretical, laboratory and modeling investigations (BIOSOA)", the Research Foundation - Flanders (FWO), and the European Commission through the EUROCHAMP-2 project (228335). References: (1) Gómez-González et al., Atmos. Chem. Phys, 2012, 12, (1), 125-138. (2) Vogel et al., Atmos. Chem. Phys. Discuss., 2013, 13, (7), 17901-17952. (3) Claeys et al., Environ. Sci. & Technol., 2009, 43, (18), 6976-6982. (4) Yasmeen et al., J. Mass Spectrom., 2011, 46, (4), 425-442.

  4. The Effect of Cholesterol on the Solution Structure of Proteins of Photosystem II. Protein Secondary Structure and

    E-print Network

    Carpentier, Robert

    The Effect of Cholesterol on the Solution Structure of Proteins of Photosystem II. Protein, 1998 Cholesterol induces large perturbations in the physical proper- ties of membranes, especially at physiological temperatures. This study was designed to examine the interaction of cholesterol with lipid

  5. 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

  6. Secondary structure of a general multiloop amplitude in open-bosonic-string theory

    SciTech Connect

    Konno, H.; Suzuki, T. )

    1990-05-15

    We investigate the structure of a general multiloop amplitude in open-bosonic-string theory. We show that any connected part of the {ital S} matrix can be constructed from three kinds of multiloop tadpole, one-loop nonplanar self-energy, and trees due to duality. A separate discussion for the unconnected part is also given. Some rules for calculating a general multiloop amplitude and explicit results for the nonorientable and nonplanar multiloop amplitudes are given in the framework of the Becchi-Rouet-Stora-Tyutin-invariant operator formalism.

  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. Secondary structure in the core of amyloid fibrils formed from human ??m and its truncated variant ?N6.

    PubMed

    Su, Yongchao; Sarell, Claire J; Eddy, Matthew T; Debelouchina, Galia T; Andreas, Loren B; Pashley, Clare L; Radford, Sheena E; Griffin, Robert G

    2014-04-30

    Amyloid fibrils formed from initially soluble proteins with diverse sequences are associated with an array of human diseases. In the human disorder, dialysis-related amyloidosis (DRA), fibrils contain two major constituents, full-length human ?2-microglobulin (h?2m) and a truncation variant, ?N6 which lacks the N-terminal six amino acids. These fibrils are assembled from initially natively folded proteins with an all antiparallel ?-stranded structure. Here, backbone conformations of wild-type h?2m and ?N6 in their amyloid forms have been determined using a combination of dilute isotopic labeling strategies and multidimensional magic angle spinning (MAS) NMR techniques at high magnetic fields, providing valuable structural information at the atomic-level about the fibril architecture. The secondary structures of both fibril types, determined by the assignment of ~80% of the backbone resonances of these 100- and 94-residue proteins, respectively, reveal substantial backbone rearrangement compared with the location of ?-strands in their native immunoglobulin folds. The identification of seven ?-strands in h?2m fibrils indicates that approximately 70 residues are in a ?-strand conformation in the fibril core. By contrast, nine ?-strands comprise the fibrils formed from ?N6, indicating a more extensive core. The precise location and length of ?-strands in the two fibril forms also differ. The results indicate fibrils of ?N6 and h?2m have an extensive core architecture involving the majority of residues in the polypeptide sequence. The common elements of the backbone structure of the two proteins likely facilitates their ability to copolymerize during amyloid fibril assembly. PMID:24679070

  9. Directing the secondary structure of polypeptides at will: from helices to amyloids and back again?

    PubMed

    Pagel, Kevin; Vagt, Toni; Koksch, Beate

    2005-11-01

    An ageing society faces an increasing number of neurodegenerative diseases such as Alzheimer's, Parkinson's, and Creutzfeld-Jacob disease. The deposition of amyloid fibrils is a pathogenic factor causing the destruction of neuronal tissue. Amyloid-forming proteins are mainly alpha-helical in their native conformation, but undergo an alpha-helix to beta-strand conversion before or during fibril formation. Partially unfolded or misfolded beta-sheet fragments are discussed as direct precursors of amyloids. To potentially cure neurodegenerative diseases we need to understand the complex folding mechanisms that shift the equilibrium from the functional to the pathological isoform of the proteins involved. This paper describes a novel approach that allows us to study the interplay between peptide primary structure and environmental conditions for peptide and protein folding in its whole complexity on a molecular level. This de novo designed peptide system may achieve selective inhibition of fibril formation. PMID:16239998

  10. Secondary structure of double-stranded DNA under stretching: Elucidation of the stretched form

    SciTech Connect

    Maaloum, M.; Muller, P.; Beker, A-F.

    2011-03-15

    Almost two decades ago, measurements of force versus extension on isolated double-stranded DNA molecules revealed a force plateau. This unusual stretching phenomenon in DNA suggests that the long molecules may be extended from the usual B form into a new conformation. Different models have been proposed to describe the nature of DNA in its stretched form, S-DNA. Using atomic force microscopy combined with a molecular combing method, we identified the structure of {lambda}-phage DNA for different stretching values. We provide strong evidence for the existence of a first-order transition between B form and S form. Beyond a certain extension of the natural length, DNA molecules adopt a new double-helix conformation characterized by a diameter of 1.2 nm and a helical pitch of18 nm.

  11. Assembling Ag nanoparticles into morphology controlled secondary structures on loosely packed self-assembled monolayers.

    PubMed

    Jiang, Jianwei; Chae, Byungjoon; Jeong, Soon Kwan; Min, Byoung Koun; Kim, Sang-Ho; Piao, Longhai; Yoon, Sungho

    2013-03-15

    An efficient route for the assembling of Ag nanoparticles (NPs) onto solution phase Ag(palmitate) bilayer structure has been developed. Two dimension (2D) arrays of Ag NPs on Ag(palmitate) were prepared by treating palmitate stabilized Ag NPs with the as-synthesized Ag(palmitate) or ribbon-shaped Ag(palmitate) templates. The interaction between long chain carboxylate surfactants of Ag NPs and the protruding aliphatic chains of the loosely packed self-assembled monolayer may play a role in directing the self-assembly of NPs in monolayer fashion. In addition, facile method to control morphology of Ag(carboxylates) from micro-flakes to micro-ribbons was also demonstrated. PMID:23261331

  12. 1H and 15N nuclear magnetic resonance assignment and secondary structure of the cytotoxic ribonuclease alpha-Sarcin.

    PubMed Central

    Campos-Olivas, R.; Bruix, M.; Santoro, J.; Martínez del Pozo, A.; Lacadena, J.; Gavilanes, J. G.; Rico, M.

    1996-01-01

    The ribosome-inactivating protein alpha-Sarcin (alpha S) is a 150-residue fungal ribonuclease that, after entering sensitive cells, selectively cleaves a single phosphodiester bond in an universally conserved sequence of the major rRNA to inactivate the ribosome and thus exert its cytotoxic action. As a first step toward establishing the structure-dynamics-function relationships in this system, we have carried out the assignment of the 1H and 15N NMR spectrum of alpha S on the basis of homonuclear (1H-1H) and heteronuclear (1H-15N) two-dimensional correlation spectra of a uniformly 15N-labeled sample, and two selectively 15N-labeled (Tyr and Phe) samples, as well as a single three-dimensional experiment. The secondary structure of alpha S, as derived from the characteristic patterns of dipolar connectivities between backbone protons, conformational chemical shifts, and the protection of backbone amide protons against exchange, consists of a long N-terminal beta-hairpin, a short alpha-helical segment, and a C-terminal beta-sheet of five short strands arranged in a + 1, + 1, + 1, + 1 topology, connected by long loops in which the 13 Pro residues are located. PMID:8732769

  13. Secondary and tertiary structure modeling reveals effects of novel mutations in polycystic liver disease genes PRKCSH and SEC63.

    PubMed

    Waanders, E; Venselaar, H; te Morsche, R H M; de Koning, D B; Kamath, P S; Torres, V E; Somlo, S; Drenth, J P H

    2010-07-01

    Polycystic liver disease (PCLD) is characterized by intralobular bile duct cysts in the liver. It is caused by mutations in PRKCSH, encoding hepatocystin, and SEC63, encoding Sec63p. The main goals of this study were to screen for novel mutations and to analyze mutations for effects on protein structure and function. We screened 464 subjects including 76 probands by direct sequencing or conformation-sensitive capillary electrophoresis. We analyzed the effects of all known and novel mutations using a combination of splice site recognition, evolutionary conservation, secondary and tertiary structure predictions, PolyPhen, and pMut and sift. We identified a total of 26 novel mutations in PRKCSH (n = 14) and SEC63 (n = 12), including four splice site mutations, eight insertions/ deletions, six non-sense mutations, and eight missense mutations. Out of 48 PCLD mutations, 13 were predicted to affect splicing. Most mutations were located in highly conserved regions and homology modeling for two domains of Sec63p showed severe effects of the residue substitutions. In conclusion, we identified 26 novel mutations associated with PCLD and we provide in silico analysis in order to delineate the role of these mutations. PMID:20095989

  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. Protein secondary structure of Green Lynx spider dragline silk investigated by solid-state NMR and X-ray diffraction.

    PubMed

    Xu, Dian; Shi, Xiangyan; Thompson, Forrest; Weber, Warner S; Mou, Qiushi; Yarger, Jeffery L

    2015-11-01

    In this study, the secondary structure of the major ampullate silk from Peucetia viridans (Green Lynx) spiders is characterized by X-ray diffraction and solid-state NMR spectroscopy. From X-ray diffraction measurement, ?-sheet nanocrystallites were observed and found to be highly oriented along the fiber axis, with an orientational order, fc?0.98. The size of the nanocrystallites was determined to be on average 2.5nm×3.3nm×3.8nm. Besides a prominent nanocrystalline region, a partially oriented amorphous region was also observed with an fa?0.89. Two-dimensional (13)C-(13)C through-space and through-bond solid-state NMR experiments were employed to elucidate structure details of P. viridans silk proteins. It reveals that ?-sheet nanocrystallites constitutes 40.0±1.2% of the protein and are dominated by alanine-rich repetitive motifs. Furthermore, based upon the NMR data, 18±1% of alanine, 60±2% glycine and 54±2% serine are incorporated into helical conformations. PMID:26226457

  16. Disruption of secondary structure by oxidative stress alters the cross-linking pattern of myosin by microbial transglutaminase.

    PubMed

    Li, Chunqiang; Xiong, Youling L

    2015-10-01

    Porcine myofibrillar protein (MP) was oxidatively stressed in an iron-H2O2 radical-producing system then subjected to microbial transglutaminase (TGase, E:S=1:20) at 4°C. Changes in the MP secondary structure and cross-linking site on myosin (subfragments S1, S2, rod, light meromyosin, and heavy meromyosin) after TGase treatment were investigated. Circular dichroism and FTIR recorded unraveling of helixes caused by both oxidation and TGase. The loss of ?-helix due to TGase treatment was oxidation-dependent, namely, mild oxidation (0.1-1mM H2O2)>non-oxidation>moderate oxidation (5-20mM H2O2). Moreover, oxidation altered the myosin cross-linking pattern: TGase-initiated S1 cross-linking (which dominated non-oxidized MP) partially shifted to the rod under 0.1-0.5mM H2O2 and extensively to the S2 site with 20mM H2O2. Unraveling of the helical structure and formation of disulfide bonds due to oxidation were implicated in the altered myosin cross-linking pattern during subsequent TGase reactions. PMID:26068405

  17. VITAL NMR: Using Chemical Shift Derived Secondary Structure Information for a Limited Set of Amino Acids to Assess Homology Model Accuracy

    SciTech Connect

    Brothers, Michael C; Nesbitt, Anna E; Hallock, Michael J; Rupasinghe, Sanjeewa; Tang, Ming; Harris, Jason B; Baudry, Jerome Y; Schuler, Mary A; Rienstra, Chad M

    2011-01-01

    Homology modeling is a powerful tool for predicting protein structures, whose success depends on obtaining a reasonable alignment between a given structural template and the protein sequence being analyzed. In order to leverage greater predictive power for proteins with few structural templates, we have developed a method to rank homology models based upon their compliance to secondary structure derived from experimental solid-state NMR (SSNMR) data. Such data is obtainable in a rapid manner by simple SSNMR experiments (e.g., (13)C-(13)C 2D correlation spectra). To test our homology model scoring procedure for various amino acid labeling schemes, we generated a library of 7,474 homology models for 22 protein targets culled from the TALOS+/SPARTA+ training set of protein structures. Using subsets of amino acids that are plausibly assigned by SSNMR, we discovered that pairs of the residues Val, Ile, Thr, Ala and Leu (VITAL) emulate an ideal dataset where all residues are site specifically assigned. Scoring the models with a predicted VITAL site-specific dataset and calculating secondary structure with the Chemical Shift Index resulted in a Pearson correlation coefficient (-0.75) commensurate to the control (-0.77), where secondary structure was scored site specifically for all amino acids (ALL 20) using STRIDE. This method promises to accelerate structure procurement by SSNMR for proteins with unknown folds through guiding the selection of remotely homologous protein templates and assessing model quality.

  18. A novel Multi-Agent Ada-Boost algorithm for predicting protein structural class with the information of protein secondary structure.

    PubMed

    Fan, Ming; Zheng, Bin; Li, Lihua

    2015-10-01

    Knowledge of the structural class of a given protein is important for understanding its folding patterns. Although a lot of efforts have been made, it still remains a challenging problem for prediction of protein structural class solely from protein sequences. The feature extraction and classification of proteins are the main problems in prediction. In this research, we extended our earlier work regarding these two aspects. In protein feature extraction, we proposed a scheme by calculating the word frequency and word position from sequences of amino acid, reduced amino acid, and secondary structure. For an accurate classification of the structural class of protein, we developed a novel Multi-Agent Ada-Boost (MA-Ada) method by integrating the features of Multi-Agent system into Ada-Boost algorithm. Extensive experiments were taken to test and compare the proposed method using four benchmark datasets in low homology. The results showed classification accuracies of 88.5%, 96.0%, 88.4%, and 85.5%, respectively, which are much better compared with the existing methods. The source code and dataset are available on request. PMID:26350693

  19. Protein Secondary Structures (alpha-helix and beta-sheet) at a Cellular Levle and Protein Fractions in Relation to Rumen Degradation Behaviours of Protein: A New Approach

    SciTech Connect

    Yu,P.

    2007-01-01

    Studying the secondary structure of proteins leads to an understanding of the components that make up a whole protein, and such an understanding of the structure of the whole protein is often vital to understanding its digestive behaviour and nutritive value in animals. The main protein secondary structures are the {alpha}-helix and {beta}-sheet. The percentage of these two structures in protein secondary structures influences protein nutritive value, quality and digestive behaviour. A high percentage of {beta}-sheet structure may partly cause a low access to gastrointestinal digestive enzymes, which results in a low protein value. The objectives of the present study were to use advanced synchrotron-based Fourier transform IR (S-FTIR) microspectroscopy as a new approach to reveal the molecular chemistry of the protein secondary structures of feed tissues affected by heat-processing within intact tissue at a cellular level, and to quantify protein secondary structures using multicomponent peak modelling Gaussian and Lorentzian methods, in relation to protein digestive behaviours and nutritive value in the rumen, which was determined using the Cornell Net Carbohydrate Protein System. The synchrotron-based molecular chemistry research experiment was performed at the National Synchrotron Light Source at Brookhaven National Laboratory, US Department of Energy. The results showed that, with S-FTIR microspectroscopy, the molecular chemistry, ultrastructural chemical make-up and nutritive characteristics could be revealed at a high ultraspatial resolution ({approx}10 {mu}m). S-FTIR microspectroscopy revealed that the secondary structure of protein differed between raw and roasted golden flaxseeds in terms of the percentages and ratio of {alpha}-helixes and {beta}-sheets in the mid-IR range at the cellular level. By using multicomponent peak modelling, the results show that the roasting reduced (P <0.05) the percentage of {alpha}-helixes (from 47.1% to 36.1%: S-FTIR absorption intensity), increased the percentage of {beta}-sheets (from 37.2% to 49.8%: S-FTIR absorption intensity) and reduced the {alpha}-helix to {beta}-sheet ratio (from 0.3 to 0.7) in the golden flaxseeds, which indicated a negative effect of the roasting on protein values, utilisation and bioavailability. These results were proved by the Cornell Net Carbohydrate Protein System in situ animal trial, which also revealed that roasting increased the amount of protein bound to lignin, and well as of the Maillard reaction protein (both of which are poorly used by ruminants), and increased the level of indigestible and undegradable protein in ruminants. The present results demonstrate the potential of highly spatially resolved synchrotron-based infrared microspectroscopy to locate 'pure' protein in feed tissues, and reveal protein secondary structures and digestive behaviour, making a significant step forward in and an important contribution to protein nutritional research. Further study is needed to determine the sensitivities of protein secondary structures to various heat-processing conditions, and to quantify the relationship between protein secondary structures and the nutrient availability and digestive behaviour of various protein sources. Information from the present study arising from the synchrotron-based IR probing of the protein secondary structures of protein sources at the cellular level will be valuable as a guide to maintaining protein quality and predicting digestive behaviours.

  20. Species-specific factors mediate extensive heterogeneity of mRNA 3' ends in yeasts.

    PubMed

    Moqtaderi, Zarmik; Geisberg, Joseph V; Jin, Yi; Fan, Xiaochun; Struhl, Kevin

    2013-07-01

    Most eukaryotic genes express mRNAs with alternative polyadenylation sites at their 3' ends. Here we show that polyadenylated 3' termini in three yeast species (Saccharomyces cerevisiae, Kluyveromyces lactis, and Debaryomyces hansenii) are remarkably heterogeneous. Instead of a few discrete 3' ends, the average yeast gene has an "end zone," a >200 bp window with >60 distinct poly(A) sites, the most used of which represents only 20% of the mRNA molecules. The pattern of polyadenylation within this zone varies across species, with D. hansenii possessing a higher focus on a single dominant point closer to the ORF terminus. Some polyadenylation occurs within mRNA coding regions with a strong bias toward the promoter. The polyadenylation pattern is determined by a highly degenerate sequence over a broad region and by a local sequence that relies on A residues after the cleavage point. Many dominant poly(A) sites are predicted to adopt a common secondary structure that may be recognized by the cleavage/polyadenylation machinery. We suggest that the end zone reflects a region permissive for polyadenylation, within which cleavage occurs preferentially at the A-rich sequence. In S. cerevisiae strains, D. hansenii genes adopt the S. cerevisiae polyadenylation profile, indicating that the polyadenylation pattern is mediated primarily by species-specific factors. PMID:23776204

  1. Identification and Classification of Conserved RNA Secondary Structures in the Human Genome

    PubMed Central

    Pedersen, Jakob Skou; Bejerano, Gill; Siepel, Adam; Rosenbloom, Kate; Lindblad-Toh, Kerstin; Lander, Eric S; Kent, Jim; Miller, Webb; Haussler, David

    2006-01-01

    The discoveries of microRNAs and riboswitches, among others, have shown functional RNAs to be biologically more important and genomically more prevalent than previously anticipated. We have developed a general comparative genomics method based on phylogenetic stochastic context-free grammars for identifying functional RNAs encoded in the human genome and used it to survey an eight-way genome-wide alignment of the human, chimpanzee, mouse, rat, dog, chicken, zebra-fish, and puffer-fish genomes for deeply conserved functional RNAs. At a loose threshold for acceptance, this search resulted in a set of 48,479 candidate RNA structures. This screen finds a large number of known functional RNAs, including 195 miRNAs, 62 histone 3?UTR stem loops, and various types of known genetic recoding elements. Among the highest-scoring new predictions are 169 new miRNA candidates, as well as new candidate selenocysteine insertion sites, RNA editing hairpins, RNAs involved in transcript auto regulation, and many folds that form singletons or small functional RNA families of completely unknown function. While the rate of false positives in the overall set is difficult to estimate and is likely to be substantial, the results nevertheless provide evidence for many new human functional RNAs and present specific predictions to facilitate their further characterization. PMID:16628248

  2. Effect of resonant magnetic perturbations on secondary structures in drift-wave turbulence

    SciTech Connect

    Leconte, M.; Diamond, P. H.

    2011-08-15

    Recent experiments showed a decrease of long range correlations during the application of resonant magnetic perturbations (RMPs) [Y. Xu et al., Nucl. Fusion 51, 063020 (2011)]. This finding suggests that RMPs damp zonal flows. To elucidate the effect of the RMPs on zonal structures in drift wave turbulence, we construct a generalized Hasegawa-Wakatani model including RMP fields. The effect of the RMPs is to induce a linear coupling between the zonal electric field and the zonal density gradient, which drives the system to a state of electron radial force balance for large RMP amplitude. A predator-prey model coupling the primary drift wave dynamics to the zonal modes evolution is derived. This model has both turbulence drive and RMP amplitude as control parameters and predicts a novel type of transport bifurcation in the presence of RMPs. The novel regime has a power threshold which increases with RMP amplitude as {gamma}{sub c}{approx}[({delta}B{sub r}/B)]{sup 2}.

  3. 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

  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. Proton NMR studies of human C3a anaphylatoxin in solution: Sequential resonance assignments, secondary structure, and global fold

    SciTech Connect

    Chazin, W.J.; Hugli, T.E.; Wright, P.E. )

    1988-12-27

    The spin systems that comprise the {sup 1}H nuclear magnetic resonance (NMR) spectrum of the complement fragment C3a (M{sub r} 8,900) have been completely identified by an approach which integrates data from a wide range of two-dimensional NMR experiments. Both relayed and multiple quantum experiments play an essential role in the analysis. After the first stage of analysis the spin systems of 60 of the 77 residues were assigned to the appropriate residue type, providing an ample basis for subsequent sequence-specific assignments. Elements of secondary structure were identified on the basis of networks of characteristic sequential and medium-range nuclear Overhauser effects (NOEs), values of {sup 3}J{sub HN{alpha}}, and locations of slowly exchanging backbone amide protons. Three well-defined helical segments are found. Gradients of increasing mobility in distinct segments of the C3a polypeptide are observed, with very high mobilities for several residues near the C- and N-termini, including the complete C-terminal receptor binding site pentapeptide LGLAR. The NMR data, combined with known disulfide linkages and a small number of critical long-range NOEs, provide the global folding pattern of C3a in solution. Identical solution structures were found for both the intact active protein and the largely inactive physiologic product des-Arg{sup 77}-C3a. Differences between the solution and crystal structures of C3a are observed, particularly in the N-terminal region. The relevance of these new observations is discussed with respect to physiologic responses that are elicited by the local hormone-like anaphylatoxin molecule.

  6. 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

  7. 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…

  8. Secondary flow structures in the presence of Type-IV stent fractures through a bent tube model for curved arteries: Effect of circulation thresholding

    NASA Astrophysics Data System (ADS)

    Hussain, Shadman; Bulusu, Kartik V.; Plesniak, Michael W.

    2013-11-01

    A common treatment for atherosclerosis is the opening of narrowed arteries resulting from obstructive lesions by angioplasty and stent implantation to restore unrestricted blood flow. ``Type-IV'' stent fractures involve complete transverse, linear fracture of stent struts, along with displacement of the stent fragments. Experimental data pertaining to secondary flows in the presence of stents that underwent ``Type-IV'' fractures in a bent artery model under physiological inflow conditions were obtained through a two-component, two-dimensional (2C-2D) PIV technique. Concomitant stent-induced flow perturbations result in secondary flow structures with complex, multi-scale morphologies and varying size-strength characteristics. Ultimately, these flow structures may have a role to play in restenosis and progression of atherosclerotic plaque. Vortex circulation thresholds were established with the goal of resolving and tracking iso-circulation secondary flow vortical structures and their morphological changes. This allowed for a parametric evaluation and quantitative representation of secondary flow structures undergoing deformation and spatial reorganization. Supported by NSF Grant No. CBET- 0828903 and GW Center for Biomimetics and Bioinspired Engineering.

  9. Structure of the velocity distribution of sheath-accelerated secondary electrons in an asymmetric RF-dc discharge

    NASA Astrophysics Data System (ADS)

    Khrabrov, Alexander V.; Kaganovich, Igor D.; Ventzek, Peter L. G.; Ranjan, Alok; Chen, Lee

    2015-10-01

    Low-pressure capacitively-coupled discharges with additional dc bias applied to a separate electrode are utilized in plasma-assisted etching for semiconductor device manufacturing. Measurements of the electron velocity distribution function (EVDF) of the flux impinging on the wafer, as well as in the plasma bulk, show a thermal population and additional peaks within a broad range of energies. That range extends from the thermal level up to the value for the ‘ballistic’ peak, corresponding to the bias potential. The non-thermal electron flux has been correlated to alleviating the electron shading effect and providing etch-resistance properties to masking photoresist layers. ‘Middle-energy peak electrons’ at energies of several hundred eV may provide an additional sustaining mechanism for the discharge. These features in the electron velocity (or energy) distribution functions are possibly caused by secondary electrons emitted from the electrodes and interacting with two high-voltage sheaths: a stationary sheath at the dc electrode and an oscillating self-biased sheath at the powered electrode. Since at those energies the mean free path for large-angle scattering (momentum relaxation length) is comparable to, or exceeds the size of the discharge gap, these ‘ballistic’ electrons will not be fully scattered by the background gas as they traverse the inter-electrode space. We have performed test-particle simulations in which the features in the EVDF of electrons impacting the RF electrode are fully resolved at all energies. An analytical model has been developed to predict existence of peaked and step-like structures in the EVDF. Those features can be explained by analyzing the kinematics of electron trajectories in the discharge gap. Step-like structures in the EVDF near the powered electrode appear due to accumulation of electrons emitted from the dc electrode within a portion of the RF cycle, and their subsequent release. Trapping occurs when the RF sheath voltage exceeds the applied bias, and is decreasing. The secondary electrons originating from the dc-biased surface also form a peak near the energy equal to the bias potential. Additional peaks, at lower energies, are formed by the electrons emitted from the RF electrode and eventually escaping to it. The latter can be grouped according to the number of bounces between the sheaths during their residence time in the discharge. Each of such groups may give rise to an individual peak in the distribution. The trap-and-release theory developed in this paper provides a convincing explanation for the observations of the ballistic and ‘middle energy peak’ electrons detected in experiments.

  10. 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

  11. Effect of thermal treatment on secondary structure and conformational change of mushroom polyphenol oxidase (PPO) as food quality related enzyme: A FTIR study.

    PubMed

    Baltac?o?lu, Hande; Bay?nd?rl?, Alev; Severcan, Mete; Severcan, Feride

    2015-11-15

    In order to understand the conformational changes of polyphenol oxidase (PPO), which is a food quality related enzyme, after thermal treatment, secondary structure changes of the enzyme were analyzed by using Fourier Transform Infrared (FTIR) spectroscopy and compared with the change in enzyme activity in the temperature range of 25-80 °C. Fourier self-deconvolution, neural network (NN) and curve-fitting analysis were applied to the amide I band of FTIR spectra for detail analysis of secondary structure elements. FTIR analysis indicated that PPO is an ?-helix dominating enzyme. Detail analysis revealed that, as temperature increased, ?-helix and ?-sheet decreased, but aggregated ?-sheet, turns and random coil increased. The marked changes were noted at 40 °C with the occurrence of new bands due to aggregated ?-sheet structures, all of which indicate protein denaturation. These aggregation bands were still observed when the temperature was reduced back to 25 °C, from 70 °C, demonstrating an irreversible change in the structure. PMID:25977025

  12. Effects of Oligomerization and Secondary Structure on the Surface Behavior of Pulmonary Surfactant Proteins SP-B and SP-C

    PubMed Central

    Wüstneck, N.; Wüstneck, R.; Perez-Gil, J.; Pison, U.

    2003-01-01

    The relationship among protein oligomerization, secondary structure at the interface, and the interfacial behavior was investigated for spread layers of native pulmonary surfactant associated proteins B and C. SP-B and SP-C were isolated either from butanol or chloroform/methanol lipid extracts that were obtained from sheep lung washings. The proteins were separated from other components by gel exclusion chromatography or by high performance liquid chromatography. SDS gel electrophoresis data indicate that the SP-B samples obtained using different solvents showed different oligomerization states of the protein. The CD and FTIR spectra of SP-B isolated from all extracts were consistent with a secondary structure dominated by ?-helix. The CD and FTIR spectra of the first SP-C corresponded to an ?-helical secondary structure and the spectra of the second SP-C corresponded to a mixture of ?-helical and ?-sheet conformation. In contrast, the spectra of the third SP-C corresponded to antiparallel ?-sheets. The interfacial behavior was characterized by surface pressure/area (?-A) isotherms. Differences in the oligomerization state of SP-B as well as in the secondary structure of SP-C all produce significant differences in the surface pressure/area isotherms. The molecular cross sections determined from the ?-A isotherms and from dynamic cycling experiments were 6 nm2/dimer molecule for SP-B and 1.15 nm2/molecule for SP-C in ?-helical conformation and 1.05 nm2/molecule for SP-C in ?-sheet conformation. Both the oligomer ratio of SP-B and the secondary structure of SP-C strongly influence organization and behavior of these proteins in monolayer assemblies. In addition, ?-helix ? ?-sheet conversion of SP-C occurs simply by an increase of the summary protein/lipid concentration in solution. PMID:12609896

  13. Impact of size, secondary structure, and counterions on the binding of small ribonucleic acids to layered double hydroxide nanoparticles.

    PubMed

    Rodriguez, Blanca V; Pescador, Jorge; Pollok, Nicole; Beall, Gary W; Maeder, Corina; Lewis, L Kevin

    2015-01-01

    Use of ribonucleic acid (RNA) interference to regulate protein expression has become an important research topic and gene therapy tool, and therefore, finding suitable vehicles for delivery of small RNAs into cells is of crucial importance. Layered double metal hydroxides such as hydrotalcite (HT) have shown great promise as nonviral vectors for transport of deoxyribose nucleic acid (DNA), proteins, and drugs into cells, but the adsorption of RNAs to these materials has been little explored. In this study, the binding of small RNAs with different lengths and levels of secondary structure to HT nanoparticles has been analyzed and compared to results obtained with small DNAs in concurrent experiments. Initial experiments established the spectrophotometric properties of HT in aqueous solutions and determined that HT particles could be readily sedimented with near 100% efficiencies. Use of RNA+HT cosedimentation experiments as well as electrophoretic mobility shift assays demonstrated strong adsorption of RNA 25mers to HT, with twofold greater binding of single-stranded RNAs relative to double-stranded molecules. Strong affinities were also observed with ssRNA and dsRNA 54mers and with more complex transfer RNA molecules. Competition binding and RNA displacement experiments indicated that RNA-HT associations were strong and were only modestly affected by the presence of high concentrations of inorganic anions. PMID:26620852

  14. 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. ); Roberts, G.C.K. )

    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.

  15. Lipid structural effects of oral administration of methylphenidate in Drosophila brain by secondary ion mass spectrometry imaging.

    PubMed

    Phan, Nhu T N; Fletcher, John S; Ewing, Andrew G

    2015-04-21

    We use time-of-flight secondary ion mass spectrometry (TOF-SIMS) imaging to investigate the effects of orally administrated methylphenidate on lipids in the brain of Drosophila melanogaster (fruit fly), a major invertebrate model system in biological study and neuroscience. TOF-SIMS imaging was carried out using a recently designed high energy 40 keV Ar4000(+) gas cluster ion gun which demonstrated improved sensitivity for intact lipids in the fly brain compared to the 40 keV C60(+) primary ion gun. In addition, correlation of TOF-SIMS and SEM imaging on the same fly brain showed that there is specific localization that is related to biological functions of various biomolecules. Different lipids distribute in different parts of the brain, central brain, optical lobes, and proboscis, depending on the length of the carbon chain and saturation level of fatty acid (FA) branches. Furthermore, data analysis using image principal components analysis (PCA) showed that methylphenidate dramatically affected both the distribution and abundance of lipids and their derivatives, particularly fatty acids, diacylglycerides, phosphatidylcholine, phosphatidylethanolamine, and phosphatidylinositol in the fly brains. Our approach using TOF-SIMS imaging successfully visualizes the effects of methylphenidate on the chemical structure of the fly brain. PMID:25856152

  16. Small RNA-induced mRNA degradation achieved through both translation block and activated cleavage.

    PubMed

    Prévost, Karine; Desnoyers, Guillaume; Jacques, Jean-François; Lavoie, François; Massé, Eric

    2011-02-15

    Small RNA (sRNA)-induced mRNA degradation occurs through binding of an sRNA to a target mRNA with the concomitant action of the RNA degradosome, which induces an endoribonuclease E (RNase E)-dependent cleavage and degradation of the targeted mRNA. Because many sRNAs bind at the ribosome-binding site (RBS), it is possible that the resulting translation block is sufficient to promote the rapid degradation of the targeted mRNA. Contrary to this mechanism, we report here that the pairing of the sRNA RyhB to the target mRNA sodB initiates mRNA degradation even in the absence of translation on the mRNA target. Remarkably, even though it pairs at the RBS, the sRNA RyhB induces mRNA cleavage in vivo at a distal site located >350 nucleotides (nt) downstream from the RBS, ruling out local cleavage near the pairing site. Both the RNA chaperone Hfq and the RNA degradosome are required for efficient cleavage at the distal site. Thus, beyond translation initiation block, sRNA-induced mRNA cleavage requires several unexpected steps, many of which are determined by structural features of the target mRNA. PMID:21289064

  17. Analysis of submicron CuTaSiO2 structures by highly charged ion secondary ion mass spectroscopy

    E-print Network

    that they produce up to three orders of magnitude more secondary ions than singly charge projectiles. Detection. The number of mo- lecular species in the area of a 1 m 1 m pixel is about 5 106 , and the number of secondary to 50%, ionization probabilities are generally smaller than 10 3 and limit detection sensitivities

  18. SPINE X: improving protein secondary structure prediction by multistep learning coupled with prediction of solvent accessible surface area and backbone torsion angles.

    PubMed

    Faraggi, Eshel; Zhang, Tuo; Yang, Yuedong; Kurgan, Lukasz; Zhou, Yaoqi

    2012-01-30

    Accurate prediction of protein secondary structure is essential for accurate sequence alignment, three-dimensional structure modeling, and function prediction. The accuracy of ab initio secondary structure prediction from sequence, however, has only increased from around 77 to 80% over the past decade. Here, we developed a multistep neural-network algorithm by coupling secondary structure prediction with prediction of solvent accessibility and backbone torsion angles in an iterative manner. Our method called SPINE X was applied to a dataset of 2640 proteins (25% sequence identity cutoff) previously built for the first version of SPINE and achieved a 82.0% accuracy based on 10-fold cross validation (Q(3)). Surpassing 81% accuracy by SPINE X is further confirmed by employing an independently built test dataset of 1833 protein chains, a recently built dataset of 1975 proteins and 117 CASP 9 targets (critical assessment of structure prediction techniques) with an accuracy of 81.3%, 82.3% and 81.8%, respectively. The prediction accuracy is further improved to 83.8% for the dataset of 2640 proteins if the DSSP assignment used above is replaced by a more consistent consensus secondary structure assignment method. Comparison to the popular PSIPRED and CASP-winning structure-prediction techniques is made. SPINE X predicts number of helices and sheets correctly for 21.0% of 1833 proteins, compared to 17.6% by PSIPRED. It further shows that SPINE X consistently makes more accurate prediction in helical residues (6%) without over prediction while PSIPRED makes more accurate prediction in coil residues (3-5%) and over predicts them by 7%. SPINE X Server and its training/test datasets are available at http://sparks.informatics.iupui.edu/ PMID:22045506

  19. Only one of four possible secondary structures of the central conserved region of potato spindle tuber viroid is a substrate for processing in a potato nuclear extract.

    PubMed Central

    Baumstark, T; Riesner, D

    1995-01-01

    The influence of RNA secondary structure on the substrate activity of a longer-than-unit length transcript for processing to circular viroids was studied in a nuclear extract from potato suspension cells. The nuclear extract was prepared according to a modified procedure for a plant transcription extract. The transcript of the potato spindle tuber viroid (PSTVd) consists of a monomeric molecule with 17 additional nucleotides, thus doubling most of the central conserved region of viroids of the PSTVd-class. The transcript can assume four different secondary structures, which either co-exist as conformers in solution or can be kept as metastable structures after different treatments by temperature and/or ionic strength. The structures were analysed by thermodynamic calculations and temperature-gradient gel electrophoresis and were confirmed by oligonucleotide mapping. Only the so-called extended middle structure was processed to exact viroid circles. In this structure the 5'- and 3'-ends are branching out from the rod-like viroid structure at the loop starting with nucleotide 87. The other structures were processed only if they could be rearranged into the active structure. Images PMID:7501442

  20. Messenger RNAs bearing tRNA-like features exemplified by interferon alfa 5 mRNA.

    PubMed

    Díaz-Toledano, Rosa; Gómez, Jordi

    2015-10-01

    The purpose of this work was to ascertain whether liver mRNA species share common structural features with hepatitis C virus (HCV) mRNA that allow them to support the RNase-P (pre-tRNA/processing enzyme) cleavage reaction in vitro. The presence of RNase-P competitive elements in the liver mRNA population was determined by means of biochemical techniques, and a set of sensitive mRNA species were identified through microarray screening. Cleavage specificity and substrate length requirement of around 200 nts, were determined for three mRNA species. One of these cleavage sites was found in interferon-alpha 5 (IFNA5) mRNA between specific base positions and with the characteristic RNase-P chemistry of cleavage. It was mapped within a cloverleaf-like structure revealed by a comparative structural analysis based on several direct enzymes and chemical probing methods of three RNA fragments of increasing size, and subsequently contrasted against site-directed mutants. The core region was coincident with the reported signal for the cytoplasmic accumulation region (CAR) in IFNAs. Striking similarities with the tRNA-like element of the antagonist HCV mRNA were found. In general, this study provides a new way of looking at a variety of viral tRNA-like motifs as this type of structural mimicry might be related to specific host mRNA species rather than, or in addition to, tRNA itself. PMID:25900662

  1. 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.

  2. 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.; Kaminska, E.

    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.

  3. Internal transcribed spacer (ITS) evolution in populations of the hyperparasitic European mistletoe pathogen fungus, Sphaeropsis visci (Botryosphaeriaceae): The utility of ITS2 secondary structures.

    PubMed

    Poczai, Péter; Varga, Ildikó; Hyvönen, Jaakko

    2015-03-01

    We investigated patterns of nucleotide polymorphism in the internal transcribed spacer (ITS) region for Sphaeropsis visci, a hyperparasitic fungus that causes the leaf spot disease of the hemiparasite European mistletoe (Viscum album). Samples of S. visci were obtained from Hungary covering all major infected forest areas. For obtaining PCR products we used a fast and efficient direct PCR approach based on a high fidelity DNA polymerase. A total of 140 ITS sequences were subjected to an array of complementary sequence analyses, which included analyses of secondary structure stability, nucleotide polymorphism patterns, GC content, and presence of conserved motifs. Analysed sequences exhibited features of functional rRNAs. Overall, polymorphism was observed within less conserved motifs, such as loops and bulges, or, alternatively, as non-canonical G-U pairs within conserved regions of double stranded helices. The secondary structure of ITS2 provides new opportunities for obtaining further valuable information, which could be used in phylogenetic analyses, or at population level as demonstrated in our study. This is due to additional information provided by secondary structures and their models. The combined score matrix was used with the methods implemented in the programme 4SALE. Besides the pseudoprotein coding method of 4SALE, the molecular morphometric character coding also has potential for gaining further information for phylogenetic analyses based on the geometric features of the sub-structural elements of the ITS2 RNA transcript. PMID:25536165

  4. Influence of high-molecular-weight glutenin subunit composition at Glu-B1 locus on secondary and micro structures of gluten in wheat (Triticum aestivum L.).

    PubMed

    Gao, Xin; Liu, Tianhong; Yu, Jing; Li, Liqun; Feng, Yi; Li, Xuejun

    2016-04-15

    Glutenin is one of the critical gluten proteins that affect the processing quality of wheat dough. High-molecular-weight glutenin subunits (HMW-GS) affect rheological behavior of wheat dough. This research demonstrated the effects of four variations of HMW-GS composition at the Glu-B1 locus on secondary and micro structures of gluten and rheological properties of wheat dough, using the bread wheat Xinong 1330 and its three near-isogenic lines (NILs). Results indicated that the Amide I bands of the four wheat lines shifted slightly, but the secondary structure, such as content of ?-helices, ?-sheets, disulfide bands, tryptophan bands and tyrosine bands, differed significantly among the four NILs. The micro structure of gluten in NIL 2 (Bx14+By15) and NIL 3 (Bx17+By18) showed more cross linkage, with two contrasting patterns. Correlation analysis demonstrated that the content of ?-sheets and disulfide bonds has a significant relationship with dough stability, which suggests that the secondary structures could be used as predictors of wheat quality. PMID:26675856

  5. Estimation of protein secondary structure from circular dichroism spectra: comparison of CONTIN, SELCON, and CDSSTR methods with an expanded reference set.

    PubMed

    Sreerama, N; Woody, R W

    2000-12-15

    We have expanded the reference set of proteins used in SELCON3 by including 11 additional proteins (selected from the reference sets of Yang and co-workers and Keiderling and co-workers). Depending on the wavelength range and whether or not denatured proteins are included in the reference set, five reference sets were constructed with the number of reference proteins varying from 29 to 48. The performance of three popular methods for estimating protein secondary structure fractions from CD spectra (implemented in software packages CONTIN, SELCON3, and CDSSTR) and a variant of CONTIN, CONTIN/LL, that incorporates the variable selection method in the locally linearized model in CONTIN, were examined using the five reference sets described here, and a 22-protein reference set. Secondary structure assignments from DSSP were used in the analysis. The performances of all three methods were comparable, in spite of the differences in the algorithms used in the three software packages. While CDSSTR performed the best with a smaller reference set and larger wavelength range, and CONTIN/LL performed the best with a larger reference set and smaller wavelength range, the performances for individual secondary structures were mixed. Analyzing protein CD spectra using all three methods should improve the reliability of predicted secondary structural fractions. The three programs are provided in CDPro software package and have been modified for easier use with the different reference sets described in this paper. CDPro software is available at the website: http://lamar.colostate.edu/ approximately sreeram/CDPro. PMID:11112271

  6. Biomaterials for mRNA delivery.

    PubMed

    Islam, Mohammad Ariful; Reesor, Emma K G; Xu, Yingjie; Zope, Harshal R; Zetter, Bruce R; Shi, Jinjun

    2015-12-10

    Messenger RNA (mRNA) has recently emerged with remarkable potential as an effective alternative to DNA-based therapies because of several unique advantages. mRNA does not require nuclear entry for transfection activity and has a negligible chance of integrating into the host genome which excludes the possibility of potentially detrimental genomic alternations. Chemical modification of mRNA has further enhanced its stability and decreased its activation of innate immune responses. Additionally, mRNA has been found to have rapid expression and predictable kinetics. Nevertheless, the ubiquitous application of mRNA remains challenging given its unfavorable attributes, such as large size, negative charge and susceptibility to enzymatic degradation. Further refinement of mRNA delivery modalities is therefore essential for its development as a therapeutic tool. This review provides an exclusive overview of current state-of-the-art biomaterials and nanotechnology platforms for mRNA delivery, and discusses future prospects to bring these exciting technologies into clinical practice. PMID:26280625

  7. Biomaterials for mRNA Delivery

    PubMed Central

    Islam, Mohammad Ariful; Reesor, Emma K. G.; Xu, Yingjie; Zope, Harshal R.; Zetter, Bruce R.; Shi, Jinjun

    2015-01-01

    Messenger RNA (mRNA) has recently emerged with remarkable potential as an effective alternative to DNA-based therapies because of several unique advantages. mRNA does not require nuclear entry for transfection activity and has a negligible chance of integrating into the host genome which excludes the possibility of potentially detrimental genomic alternations. Chemical modification of mRNA has further enhanced its stability and decreased its activation of innate immune responses. Additionally, mRNA has been found to have rapid expression and predictable kinetics. Nevertheless, the ubiquitous application of mRNA remains challenging given its unfavorable attributes, such as large size, negative charge and susceptibility to enzymatic degradation. Further refinement of mRNA delivery modalities is therefore essential for its development as a therapeutic tool. This review provides an exclusive overview of current state-of-the-art biomaterials and nanotechnology platforms for mRNA delivery, and discusses future prospects to bring these exciting technologies into clinical practice. PMID:26280625

  8. 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

  9. Secondary Structure Analyses of the Nuclear rRNA Internal Transcribed Spacers and Assessment of Its Phylogenetic Utility across the Brassicaceae (Mustards)

    PubMed Central

    Bird, Kevin A.; Mayfield, Dustin R.; Conant, Gavin; Mummenhoff, Klaus; Koch, Marcus A.; Pires, J. Chris

    2014-01-01

    The internal transcribed spacers of the nuclear ribosomal RNA gene cluster, termed ITS1 and ITS2, are the most frequently used nuclear markers for phylogenetic analyses across many eukaryotic groups including most plant families. The reasons for the popularity of these markers include: 1.) Ease of amplification due to high copy number of the gene clusters, 2.) Available cost-effective methods and highly conserved primers, 3.) Rapidly evolving markers (i.e. variable between closely related species), and 4.) The assumption (and/or treatment) that these sequences are non-functional, neutrally evolving phylogenetic markers. Here, our analyses of ITS1 and ITS2 for 50 species suggest that both sequences are instead under selective constraints to preserve proper secondary structure, likely to maintain complete self-splicing functions, and thus are not neutrally-evolving phylogenetic markers. Our results indicate the majority of sequence sites are co-evolving with other positions to form proper secondary structure, which has implications for phylogenetic inference. We also found that the lowest energy state and total number of possible alternate secondary structures are highly significantly different between ITS regions and random sequences with an identical overall length and Guanine-Cytosine (GC) content. Lastly, we review recent evidence highlighting some additional problematic issues with using these regions as the sole markers for phylogenetic studies, and thus strongly recommend additional markers and cost-effective approaches for future studies to estimate phylogenetic relationships. PMID:24984034

  10. Secondary structure analyses of the nuclear rRNA internal transcribed spacers and assessment of its phylogenetic utility across the Brassicaceae (mustards).

    PubMed

    Edger, Patrick P; Tang, Michelle; Bird, Kevin A; Mayfield, Dustin R; Conant, Gavin; Mummenhoff, Klaus; Koch, Marcus A; Pires, J Chris

    2014-01-01

    The internal transcribed spacers of the nuclear ribosomal RNA gene cluster, termed ITS1 and ITS2, are the most frequently used nuclear markers for phylogenetic analyses across many eukaryotic groups including most plant families. The reasons for the popularity of these markers include: 1.) Ease of amplification due to high copy number of the gene clusters, 2.) Available cost-effective methods and highly conserved primers, 3.) Rapidly evolving markers (i.e. variable between closely related species), and 4.) The assumption (and/or treatment) that these sequences are non-functional, neutrally evolving phylogenetic markers. Here, our analyses of ITS1 and ITS2 for 50 species suggest that both sequences are instead under selective constraints to preserve proper secondary structure, likely to maintain complete self-splicing functions, and thus are not neutrally-evolving phylogenetic markers. Our results indicate the majority of sequence sites are co-evolving with other positions to form proper secondary structure, which has implications for phylogenetic inference. We also found that the lowest energy state and total number of possible alternate secondary structures are highly significantly different between ITS regions and random sequences with an identical overall length and Guanine-Cytosine (GC) content. Lastly, we review recent evidence highlighting some additional problematic issues with using these regions as the sole markers for phylogenetic studies, and thus strongly recommend additional markers and cost-effective approaches for future studies to estimate phylogenetic relationships. PMID:24984034

  11. Changes in the protein secondary structure of hen's egg yolk determined by Fourier transform infrared spectroscopy during the first eight days of incubation.

    PubMed

    Lilienthal, Sabrina; Drotleff, Astrid M; Ternes, Waldemar

    2015-01-01

    In this study, incubation-induced alterations in the protein secondary structures of egg yolk and its major fractions (granules, plasma, and low-density lipoproteins [LDL]) were monitored during the first 8 d of embryogenesis using Fourier transform infrared spectroscopy (FTIR) and isoelectric focusing (IEF). Two factors potentially connected with egg yolk protein secondary structure changes were evaluated, i.e., the pH value of incubated egg yolk, and phosvitin, an important egg yolk protein assumed to play an important role in hematopoiesis as the iron carrier during early embryogenesis. However, neither the significant increase in pH value (6.07 to 6.92) of egg yolk during incubation of fertilized eggs, nor the release of iron from phosvitin were found to be directly related to the changes in protein secondary structure in egg yolk and its fractions. FTIR showed that the protein conformation in whole egg yolk, granules, and LDL was stable during incubation, but separate evaluation of the plasma fraction revealed considerable changes in secondary structure. However, it is unlikely that these changes were provoked by structure changes of the proteins originally present in plasma; instead, the physiological influx of albumen into the yolk sac was expected to play an important role in the protein modifications of egg yolk, as was shown both by FTIR and IEF of the water-soluble egg yolk proteins. Moreover, FTIR was used to determine the naturally occurring proportions (%) of the secondary structure elements in egg yolk and its 3 fractions on d 0 of incubation. The granules fraction mainly consisted of a mixture of inter- and intramolecular ?-sheets (57.04%±0.39%). The plasma fraction was found to consist mainly of ?-helices (43.23%±0.27%), whereas LDL was composed almost exclusively of intramolecular ?-sheets (67.36%±0.56%) or ?-turns, or both. On the other hand, whole egg yolk was mainly composed of intermolecular ?-sheets (39.77%±0.48%), potentially indicating molecular interchanges between the individual fractions. PMID:25577795

  12. Secondary Procedures in Replantation

    PubMed Central

    Sabapathy, S. Raja; Bhardwaj, Praveen

    2013-01-01

    The success of replantation surgery is not judged by survival of the replanted part, but by the functional outcome attained. Hence, primary repair of all injured structures is the preferred aim. At times, constraints induced by the ischemia time and nature of injury preclude primary repair. In such situations, secondary procedures are inevitable. Secondary procedures are also frequently required to improve the function and appearance of the replanted extremity. The incidence of secondary procedures will vary with the level of replantation and the type of patient population. Secondary procedures are difficult because they carry risk of injury to the vital neurovascular structures that now lay at nonanatomical locations. Nevertheless, when indicated and performed with caution they could significantly raise the functional status of the individuals. PMID:24872769

  13. ITS1, 5.8S and ITS2 secondary structure modelling for intra-specific differentiation among species of the Colletotrichum gloeosporioides sensu lato species complex.

    PubMed

    Rampersad, Sephra N

    2014-01-01

    The Colletotrichum gloeosporioides species complex is among the most destructive fungal plant pathogens in the world, however, identification of member species which are of quarantine importance is impacted by a number of factors that negatively affect species identification. Structural information of the rRNA marker may be considered to be a conserved marker which can be used as supplementary information for possible species identification. The difficulty in using ITS rDNA sequences for identification lies in the low level of sequence variation at the intra-specific level and the generation of artificially-induced sequence variation due to errors in polymerization of the ITS array during DNA replication. Type and query ITS sequences were subjected to sequence analyses prior to generation of predicted consensus secondary structures, including the pattern of nucleotide polymorphisms and number of indel haplotypes, GC content, and detection of artificially-induced sequence variation. Data pertaining to structure stability, the presence of conserved motifs in secondary structures and mapping of all sequences onto the consensus C. gloeosporioides sensu stricto secondary structure for ITS1, 5.8S and ITS2 markers was then carried out. Motifs that are evolutionarily conserved among eukaryotes were found for all ITS1, 5.8S and ITS2 sequences. The sequences exhibited conserved features typical of functional rRNAs. Generally, polymorphisms occurred within less conserved regions and were seen as bulges, internal and terminal loops or non-canonical G-U base-pairs within regions of the double stranded helices. Importantly, there were also taxonomic motifs and base changes that were unique to specific taxa and which may be used to support intra-specific identification of members of the C. gloeosporioides sensu lato species complex. PMID:25512885

  14. Primary and secondary structures of chicken, rat and man nuclear U4 RNAs. Homologies with U1 and U5 RNAs.

    PubMed Central

    Krol, A; Branlant, C; Lazar, E; Gallinaro, H; Jacob, M

    1981-01-01

    U4 RNA from chicken, rat and man was examined for nucleotide sequence and secondary structure. Three molecular species, U4A, U4B and U4C were detected in the three animal species. U4A is 146 nucleotide long and U4B RNA only lacks the 3' terminal G. four nucleotides are missing at the 3'-end of U4C RNA which, in addition, differs from U4A and U4B RNAs at two internal positions. Thus, U4C RNA is encoded by another gene as U4A and U4B RNAs. Only one nucleotide substitution occurred between chicken and man showing that U4A, U4B and U4C RNAs have been extremely conserved throughout evolution. The three molecular species are capped, they contain three psi, a 2'-P methyl A and a m6A. An additional post-transcriptional modification close to the cap structure is observed in man. On the basis on an experimental study, two models of secondary structure may be proposed for U4 RNA. The 3'domain is the same in both models and is homologous to that of U1 and U5 RNAs. It consists of a single-stranded region, containing the sequence Py-(A)2-(U)n-Gp flanked by two stable hairpins probably involved in tertiary interactions. The 5' domain is less stable than the 3' domain and its structure is different in the two models. However, a long single-stranded pyrimidine region containing modified nucleotides is found in both models as in U1 and U5 RNAs. Several other nucleotide sequence homologies related to specific features of secondary structure suggest that U1, U4 and U5 RNAs derive from a common ancestor and may have common function. Images PMID:6169000

  15. 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

  16. Analysis of secondary structure predictions of dengue virus type 2 NS2B/NS3 against crystal structure to evaluate the predictive power of the in silico methods.

    PubMed

    Othman, Rozana; Wahab, Habibah Abdul; Yusof, Rohana; Rahman, Noorsaadah Abd

    2007-01-01

    Multiple sequence alignment was performed against eight proteases from the Flaviviridae family using ClustalW to illustrate conserved domains. Two sets of prediction approaches were applied and the results compared. Firstly, secondary structure prediction was performed using available structure prediction servers. The second approach made use of the information on the secondary structures extracted from structure prediction servers, threading techniques and DSSP database of some of the templates used in the threading techniques. Consensus on the one-dimensional secondary structure of Den2 protease was obtained from each approach and evaluated against data from the recently crystallised Den2 NS2B/NS3 obtained from the Protein Data Bank (PDB). Results indicated the second approach to show higher accuracy compared to the use of prediction servers only. Thus, it is plausible that this approach is applicable to the initial stage of structural studies of proteins with low amino acid sequence homology against other available proteins in the PDB. PMID:17688447

  17. Cellular biopolymers and molecular structure of a secondary pulp and paper mill sludge verified by spectroscopy and chemical extraction techniques.

    PubMed

    Edalatmanesh, Maryam; Sain, Mohini; Liss, Steven N

    2010-01-01

    For proper treatment, recycling, or disposal of the pulp and paper mill secondary sludge qualitative and quantitative determination of its characteristics are necessary. Chemical extraction, quantitative characterization, and spectroscopic experiments have been performed to determine the molecular composition and chemical functionality of a pulp and paper mill secondary sludge. In order to extract the low-molecular-weight substances, soxhlet extraction with polar and non-polar solvents was performed where most of the target substances (17±1.3%.) were extracted after 2 hours. Over time, this extraction followed a first-order kinetics. Fiber analyses have shown 12±3% lignin, 28±3% cellulose, and 12±4% hemicelluloses content. The ash content was about 17±0.5%. In this work, 7 and 16% intra- and extracellular polymeric substances, respectively, were extracted from the secondary sludge. EPS and mixture of intra- and extracellular biopolymers have shown similar chemical functionalities. These analyses confirmed that the paper secondary sludge consisted mainly of wood fiber, i.e. lignocellulosic substances, along with proteins and polysaccharides originated from microorganisms. PMID:21123914

  18. 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

  19. Secondary structure analysis of swine pasivirus (family Picornaviridae) RNA reveals a type-IV IRES and a parechovirus-like 3' UTR organization.

    PubMed

    Boros, Ákos; Fenyvesi, Hajnalka; Pankovics, Péter; Biró, Hunor; Phan, Tung Gia; Delwart, Eric; Reuter, Gábor

    2015-05-01

    The potential RNA structures of the 5' and 3' untranslated regions (UTRs) and cis-acting replication elements (CREs) of a novel pasivirus (PaV) genotype (family Picornaviridae) were analysed. PaV-A3 (KM259923) was identified in a faecal sample from a domestic pig in Hungary with posterior paraplegia of unknown etiology. Based on likely structural features of the 5' UTR, the pasiviruses were inferred to possess Hepacivirus/Pestivirus-like type-IV IRES. The pasivirus CRE was mapped to the 2B genome region, similar to Ljungan virus. The secondary RNA structure of the pasivirus 3' UTR was structurally similar to that of human parechoviruses. The genome, CRE, and 3' UTR of pasiviruses provide further evidence of the common origin of the members of the genera Parechovirus and Pasivirus, although their different 5' UTR IRES types suggest that a recombination event occurred during the divergence these viruses. PMID:25716922

  20. Structural roles of the active site iron(III) ions in catechol 1,2-dioxygenases and differential secondary structure changes in isoenzymes A and B from Acinetobacter radioresistens S13.

    PubMed

    Di Nardo, Giovanna; Tilli, Silvia; Pessione, Enrica; Cavaletto, Maria; Giunta, Carlo; Briganti, Fabrizio

    2004-11-01

    The reversible active site metal ion removal process for two catechol 1,2-dioxygenase isoenzymes (IsoA and IsoB) isolated from Acinetobacter radioresistens S13 has been monitored using circular dichroism and fluorescence spectroscopic techniques. IsoA and IsoB are homodimers, containing one iron(III) ion per subunit. Their amino acid sequence identity is 48.4%. Previous experiments suggested that structural diversities could be responsible for the differential thermal and pH stabilities of the two isoenzymes and of their distinct demetallation kinetics. The far-UV CD spectra of IsoA and IsoB catechol 1,2-dioxygenases from A. radioresistens S13 provide information on their secondary structures. IsoB appears to have a content of alpha-helices higher than IsoA. Upon metal ion removal, both proteins reversibly lose part of their secondary structure following distinct pathways. CD spectra simulations allowed us to estimate the content of alpha-helices, beta-sheets, and turns for each isoenzyme and to monitor the secondary structure rearrangements. The metal ion withdrawal has large influence on the secondary structure: in particular a significant reduction of alpha-helices content is observed for both isoenzymes. Intrinsic fluorescence emission spectra clearly support such results, adding information on the local environment changes of the tryptophan residues. The positioning of Trp250 in IsoB has been shown to be of particular interest for monitoring the local structure changes occurring upon metal ion removal. For the first time these studies allow to underline the role of active site iron ions on dioxygenases folding and stability, further evidencing the differences in structural assembling between the two isoenzymes from A. radioresistens S13. PMID:15464729

  1. Probing of structural relaxation times in the glassy state of sucrose and trehalose based on dynamical properties of two secondary relaxation processes

    NASA Astrophysics Data System (ADS)

    Kaminski, K.; Adrjanowicz, K.; Kaminska, E.; Paluch, M.

    2011-06-01

    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 ? process is the Johari-Goldstein (JG) relaxation coupled to motions of the glycosidic linkage, while the ? 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.PRLTAO0031-900710.1103/PhysRevLett.102.035701 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. SolidsJNCSBJ0022-309310.1016/j.jnoncrysol.2010.07.067 357, 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. Tryptophan environment, secondary structure and thermal unfolding of the galactose-specific seed lectin from Dolichos lablab: fluorescence and circular dichroism spectroscopic studies.

    PubMed

    Sultan, Nabil Ali Mohammed; Rao, Rameshwaram Nagender; Nadimpalli, Siva Kumar; Swamy, Musti J

    2006-07-01

    Fluorescence and circular dichroism spectroscopic studies were carried out on the galactose-specific lectin from Dolichos lablab seeds (DLL-II). The microenvironment of the tryptophan residues in the lectin under native and denaturing conditions were investigated by quenching of the intrinsic fluorescence of the protein by a neutral quencher (acrylamide), an anionic quencher (iodide ion) and a cationic quencher (cesium ion). The results obtained indicate that the tryptophan residues of DLL-II are largely buried in the hydrophobic core of the protein matrix, with positively charged side chains residing close to at least some of the tryptophan residues under the experimental conditions. Analysis of the far UV CD spectrum of DLL-II revealed that the secondary structure of the lectin consists of 57% alpha-helix, 21% beta-sheet, 7% beta-turns and 15% unordered structures. Carbohydrate binding did not significantly alter the secondary and tertiary structures of the lectin. Thermal unfolding of DLL-II, investigated by monitoring CD signals, showed a sharp transition around 75 degrees C both in the far UV region (205 nm) and the near UV region (289 nm), which shifted to ca. 77-78 degrees C in the presence of 0.1 M methyl-beta-D-galactopyranoside, indicating that ligand binding leads to a moderate stabilization of the lectin structure. PMID:16650937

  3. 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 ...

  4. Long-Lasting Impact of Neonatal Exposure to Total Body Gamma Radiation on Secondary Lymphoid Organ Structure and Function.

    PubMed

    Rangel-Moreno, Javier; de la Luz Garcia-Hernandez, Maria; Ramos-Payan, Rosalio; Biear, Jamie; Hernady, Eric; Sangster, Mark Y; Randall, Troy D; Johnston, Carl J; Finkelstein, Jacob N; Williams, Jacqueline P

    2015-10-01

    The acute period after total body irradiation (TBI) is associated with an increased risk of infection, principally resulting from the loss of hematopoietic stem cells, as well as disruption of mucosal epithelial barriers. Although there is a return to baseline infection control coinciding with the apparent progressive recovery of hematopoietic cell populations, late susceptibility to infection in radiation-sensitive organs such as lung and kidney is known to occur. Indeed, pulmonary infections are particularly prevalent in hematopoietic cell transplant (HCT) survivors, in both adult and pediatric patient populations. Preclinical studies investigating late outcomes from localized thoracic irradiation have indicated that the mechanisms underlying pulmonary delayed effects are multifactorial, including exacerbated and persistent production of pro-inflammatory molecules and abnormal cross-talk among parenchymal and infiltrating immune and inflammatory cell populations. However, in the context of low-dose TBI, it is not clear whether the observed exacerbated response to infection remains contingent on these same mechanisms. It is possible instead, that after systemic radiation-induced injury, the susceptibility to infection may be independently related to defects in alternative organs that are revealed only through the challenge itself; indeed, we have hypothesized that this defect may be due to radiation-induced chronic effects in the structure and function of secondary lymphoid organs (SLO). In this study, we investigated the molecular and cellular alterations in SLO (i.e., spleen, mediastinal, inguinal and mesenteric lymph nodes) after TBI, and the time points when there appears to be immune competence. Furthermore, due to the high incidence of pulmonary infections in the late post-transplantation period of bone marrow transplant survivors, particularly in children, we focused on outcomes in mice irradiated as neonates, which served as a model for a pediatric population, and used the induction of adaptive immunity against influenza virus as a functional end point. We demonstrated that, in adult animals irradiated as neonates, high endothelial venule (HEV) expansion, generation of follicular helper T cells (TFH) and formation of splenic germinal centers (GC) were rapidly and, more importantly, persistently impaired in SLO, suggesting that the early-life exposure to sublethal radiation had long-lasting effects on the induction of humoral immunity. Although the neonatal TBI did not affect the overall outcome from influenza infection in the adults at the earlier time points assessed, we believe that they nonetheless contribute significantly to the increased mortality observed at subsequent late time points. Furthermore, we speculate that the detrimental and persistent impact on the induction of CD4 T- and B-cell responses in the mediastinal lymph nodes will decrease the animals' ability to respond to other aerial pathogens. Since many of these pathogens are normally cleared by antibodies, our findings provide an explanation for the susceptibility of survivors of childhood HCT to life-threatening respiratory tract infections. These findings have implications regarding the need for increased monitoring in pediatric hematopoietic cell transplant patients, since they indicate that there are ongoing and cumulative defects in SLO, which, importantly, develop during the immediate and early postirradiation period when patients may appear immunologically competent. The identification of changes in immune-related signals may offer bioindicators of progressive dysfunction, and of potential mechanisms that could be targeted so as to reduce the risk of infection from extracellular pathogens. Furthermore, these results support the potential susceptibility of the pediatric population to infection after sublethal irradiation in the context of a nuclear or radiological event. PMID:26397175

  5. A Nascent Peptide Signal Responsive to Endogenous Levels of Polyamines Acts to Stimulate Regulatory Frameshifting on Antizyme mRNA*

    PubMed Central

    Yordanova, Martina M.; Wu, Cheng; Andreev, Dmitry E.; Sachs, Matthew S.; Atkins, John F.

    2015-01-01

    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

  6. Staphylococcus aureus MazF specifically cleaves a pentad sequence, UACAU, which is unusually abundant in the mRNA for pathogenic adhesive factor SraP.

    PubMed

    Zhu, Ling; Inoue, Koichi; Yoshizumi, Satoshi; Kobayashi, Hiroshi; Zhang, Yonglong; Ouyang, Ming; Kato, Fuminori; Sugai, Motoyuki; Inouye, Masayori

    2009-05-01

    Escherichia coli mRNA interferases, such as MazF and ChpBK, are sequence-specific endoribonucleases encoded by toxin-antitoxin (TA) systems present in its genome. A MazF homologue in Staphylococcus aureus (MazF(Sa)) has been shown to inhibit cell growth when induced in E. coli. Here, we determined the cleavage site for MazF(Sa) with the use of phage MS2 RNA as a substrate and CspA, an RNA chaperone, which prevents the formation of secondary structures in the RNA substrate. MazF(Sa) specifically cleaves the RNA at a pentad sequence, U downward arrow ACAU. Bioinformatics analysis revealed that this pentad sequence is significantly abundant in several genes, including the sraP gene in the S. aureus N315 strain. This gene encodes a serine-rich protein, which is known to play an important role in adhesion of the pathogen to human tissues and thus in endovascular infection. We demonstrated that the sraP mRNA became extremely unstable in comparison with the ompA mRNA only when MazF(Sa) was induced in E. coli. Further bioinformatics analysis indicated that the pentad sequence is also significantly abundant in the mRNAs for all the pathogenic factors in S. aureus. This observation suggests a possible regulatory relationship between the MazEF(Sa) TA module and the pathogenicity in S. aureus. PMID:19251861

  7. Influences of incidence angle on 2D-flow and secondary flow structure in ultra-highly loaded turbine cascade

    NASA Astrophysics Data System (ADS)

    Tsujita, Hoshio; Yamamoto, Atsumasa

    2014-02-01

    An increase of turbine blade loading can reduce the numbers of blade and stage of gas turbines. However, an increase of blade loading makes the secondary flow much stronger because of the steep pitch-wise pressure gradient in the cascade passage, and consequently deteriorates the turbine efficiency. In this study, the computations were performed for the flow in an ultra-highly loaded turbine cascade with high turning angle in order to clarify the effects of the incidence angle on the two dimensional flow and the secondary flow in the cascade passage, which cause the profile loss and the secondary loss, respectively. The computed results showed good agreement with the experimental surface oil flow visualizations and the blade surface static pressure at mid-span of the blade. The profile loss was strongly increased by the increase of incidence angle especially in the positive range. Moreover, the positive incidences not only strengthened the horseshoe vortex and the passage vortex but also induced a new vortex on the end-wall. Moreover, the newly formed vortex influenced the formation of the pressure side leg of horseshoe vortex.

  8. In vitro Splicing of Influenza Viral NS1 mRNA and NS1-? -globin Chimeras: Possible Mechanisms for the Control of Viral mRNA Splicing

    NASA Astrophysics Data System (ADS)

    Plotch, Stephen J.; Krug, Robert M.

    1986-08-01

    In influenza virus-infected cells, the splicing of the viral NS1 mRNA catalyzed by host nuclear enzymes is controlled so that the steady-state amount of the spliced NS2 mRNA is only 5-10% of that of the unspliced NS1 mRNA. Here we examine the splicing of NS1 mRNA in vitro, using nuclear extracts from HeLa cells. We show that in addition to its consensus 5' and 3' splice sites, NS1 mRNA has an intron branch-point adenosine residue that was functional in lariat formation. Nonetheless, this RNA was not detectably spliced in vitro under conditions in which a human ? -globin precursor was efficiently spliced. Using chimeric RNA precursors containing both NS1 and ? -globin sequences, we show that the NS1 5' splice site was effectively utilized by the ? -globin branch-point sequence and 3' splice site to form a spliced RNA, whereas the NS1 3' splice site did not function in detectable splicing in vitro, even in the presence of the ? -globin branch-point sequence or in the presence of both the branch-point sequence and 5' exon and splice site from ? -globin With the chimeric precursors that were not detectably spliced, as with NS1 mRNA itself, a low level of a lariat structure containing only intron and not 3' exon sequences was formed. The inability of the consensus 3' splice site of NS1 mRNA to function effectively in in vitro splicing suggests that this site is structurally inaccessible to components of the splicing machinery. Based on these results, we propose two mechanisms whereby NS1 mRNA splicing in infected cells is controlled via the accessibility of its 3' splice site.

  9. 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

  10. Transatlantic secondary contact in Atlantic Salmon, comparing microsatellites, a single nucleotide polymorphism array and restriction-site associated DNA sequencing for the resolution of complex spatial structure.

    PubMed

    Bradbury, Ian R; Hamilton, Lorraine C; Dempson, Brian; Robertson, Martha J; Bourret, Vincent; Bernatchez, Louis; Verspoor, Eric

    2015-10-01

    Identification of discrete and unique assemblages of individuals or populations is central to the management of exploited species. Advances in population genomics provide new opportunities for re-evaluating existing conservation units but comparisons among approaches remain rare. We compare the utility of RAD-seq, a single nucleotide polymorphism (SNP) array and a microsatellite panel to resolve spatial structuring under a scenario of possible trans-Atlantic secondary contact in a threatened Atlantic Salmon, Salmo salar, population in southern Newfoundland. Bayesian clustering indentified two large groups subdividing the existing conservation unit and multivariate analyses indicated significant similarity in spatial structuring among the three data sets. mtDNA alleles diagnostic for European ancestry displayed increased frequency in southeastern Newfoundland and were correlated with spatial structure in all marker types. Evidence consistent with introgression among these two groups was present in both SNP data sets but not the microsatellite data. Asymmetry in the degree of introgression was also apparent in SNP data sets with evidence of gene flow towards the east or European type. This work highlights the utility of RAD-seq based approaches for the resolution of complex spatial patterns, resolves a region of trans-Atlantic secondary contact in Atlantic Salmon in Newfoundland and demonstrates the utility of multiple marker comparisons in identifying dynamics of introgression. PMID:26407171

  11. Secondary structure in solution of two anti-HIV-1 hammerhead ribozymes as investigated by two-dimensional 1H 500 MHz NMR spectroscopy in water

    NASA Technical Reports Server (NTRS)

    Sarma, R. H.; Sarma, M. H.; Rein, R.; Shibata, M.; Setlik, R. S.; Ornstein, R. L.; Kazim, A. L.; Cairo, A.; Tomasi, T. B.

    1995-01-01

    Two hammerhead chimeric RNA/DNA ribozymes (HRz) were synthesized in pure form. Both were 30 nucleotides long, and the sequences were such that they could be targeted to cleave the HIV-1 gag RNA. Named HRz-W and HRz-M, the former had its invariable core region conserved, the latter had a uridine in the invariable region replaced by a guanine. Their secodary structures were determined by 2D NOESY 1H 500 MHz NMR spectroscopy in 90% water and 10% D2(0), following the imino protons. The data show that both HRz-M and HRz-W form identical secondary structures with stem regions consisting of continuous stacks of AT and GT pairs. An energy minimized computer model of this stem region is provided. The results suggest that the loss of catalytic activity that is known to result when an invariant core residue is replaced is not related to the secondary structure of the ribozymes in the absence of substrate.

  12. Improved secondary structure predictions for a nicotinic receptor subunit: incorporation of solvent accessibility and experimental data into a two-dimensional representation.

    PubMed

    Le Novčre, N; Corringer, P J; Changeux, J P

    1999-05-01

    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 receptors. A consensus prediction was computed for the nAChR subunits through a "winner takes all" method. By integrating the probabilities obtained with PHD, DSC, and NNSSP, this prediction was filtered in order to eliminate the singletons and to more precisely establish the structure limits (only 4% of the residues were modified). The final consensus secondary structure includes nine alpha-helices (24.2% of the residues, with an average length of 13.9 residues) and 17 beta-strands (22.5% of the residues, with an average length of 6.6 residues). The large extracellular domain is predicted to be mainly composed of beta-strands, with only two helices at the amino-terminal end. The transmembrane segments are predicted to be in a mixed alpha/beta topology (with a predominance of alpha-helices), with no known equivalent in the current protein database. The cytoplasmic domain is predicted to consist of two well-conserved amphipathic helices joined together by an unfolded stretch of variable length and sequence. In general, the segments predicted to occur in a periodic structure correspond to the more conserved regions, as defined by an analysis of sequence conservation per position performed on 152 superfamily members. The solvent accessibility of each residue was predicted from the multiple alignments with PHDacc. Each segment with more than three exposed residues was assumed to be external to the core protein. Overall, these data constitute an envelope of structural constraints. In a subsequent step, experimental data relative to the extracellular portion of the complete receptor were incorporated into the model. This led to a proposed two-dimensional representation of the secondary structure in which the peptide chain of the extracellular domain winds alternatively between the two interfaces of the subunit. Although this representation is not a tertiary structure and does not lead to predictions of specific beta-beta interaction, it should provide a basic framework for further mutagenesis investigations and for fold recognition (threading) searches. PMID:10233052

  13. Mutation of genes controlling mRNA metabolism and protein synthesis predisposes to neurodevelopmental disorders.

    PubMed

    Sartor, Francesca; Anderson, Jihan; McCaig, Colin; Miedzybrodzka, Zosia; Müller, Berndt

    2015-12-01

    Brain development is a tightly controlled process that depends upon differentiation and function of neurons to allow for the formation of functional neural networks. Mutation of genes encoding structural proteins is well recognized as causal for neurodevelopmental disorders (NDDs). Recent studies have shown that aberrant gene expression can also lead to disorders of neural development. Here we summarize recent evidence implicating in the aetiology of NDDs mutation of factors acting at the level of mRNA splicing, mRNA nuclear export, translation and mRNA degradation. This highlights the importance of these fundamental processes for human health and affords new strategies and targets for therapeutic intervention. PMID:26614670

  14. Sequence and expression of ferredoxin mRNA in barley

    SciTech Connect

    Zielinski, R.; Funder, P.M.; Ling, V. )

    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.

  15. 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

  16. [Secondary dyslipidemias].

    PubMed

    Vargová, V; Pytliak, M; Mechírová, V

    2012-03-01

    Dyslipidemias rank among the most important preventabile factors of atherogenesis and its progression. This topic is increasingly being discussed as e.g. more than 50% of Slovak population die on atherosclerotic complications. According to etiology we distinguish primary dyslipidemias with strictly genetic background and secondary ones with origin in other disease or pathological state. Secondary dyslipidemias accompany various diseases, from common (endocrinopathies, renal diseases etc) to rare ones (thesaurismosis etc.) and represents one of symptoms of these diseases. Apart from particular clinical follow up of diagnosed dysipidemias, basic screening and secondary causes as well as treatment due to updated guidelines is recuired. In this review we present the most frequent dyslipidemias of clinical practice. PMID:22486289

  17. Secondary alkaline batteries

    SciTech Connect

    McBreen, J.

    1984-03-01

    This report on secondary alkaline batteries covers the overall reactions (charge/discharge characteristics), electrode structures and materials, and cell construction. The following batteries are studied, nickel oxide-cadmium, nickel oxide-iron, nickel oxide-hydrogen, nickel oxide-zinc, silver oxide-zinc, and silver oxide-cadmium, silver oxide-iron, and manganese dioxide-zinc batteries.

  18. Ferritin mRNA: interactions of iron regulatory element with translational regulator protein P-90 and the effect on base-paired flanking regions.

    PubMed Central

    Harrell, C M; McKenzie, A R; Patino, M M; Walden, W E; Theil, E C

    1991-01-01

    The ferritin iron regulatory element (IRE), a conserved sequence of 28 nucleotides in a hairpin loop, is a conserved mRNA-specific translational regulatory element; flanking the IRE are regions of varying sequence, which form 9-17 base pairs close to the 5' cap. P-90 is a ferritin mRNA-specific translation regulatory protein purified from animal liver and reticulocytes. To study the P-90-RNA interaction, protein nucleases (RNase S1 and T1) and chemical nucleases FeEDTA and/or 1,10-phenanthroline-Cu were used as probes of an oligonucleotide (n = 55), containing the IRE and flanking regions (FL), and natural ferritin mRNA. Footprints and "toeprints" showed that P-90 binding was confined to the stem and loop of the IRE itself. However, P-90 altered the structure of the flanking region by increasing base stacking or helicity (RNase V1 sensitivity). Comparison of the reactivity of the IRE and flanking regions in natural mRNA and the 55-mer showed that long-range interactions included protecting bulges, single-stranded, and stacked regions from protein nucleases as well as stabilizing the P-90-RNA interaction. Structural integration of the IRE with the base-paired flanking regions was indicated by common features of reactivity (periodic hypersensitivity to FeEDTA) and changes in the FL region caused by P-90. The increased secondary structure of the IRE flanking regions caused by P-90 binding to the IRE provides a likely mechanism for blocking initiation of ferritin mRNA translation, since the combined structure (IRE + FL) is so close (8-17 nucleotides) to the cap. Images PMID:1903535

  19. Improvement in fold recognition accuracy of a reduced-state-space Hidden Markov Model by using secondary structure information in scoring.

    PubMed

    Lampros, Christos; Papaloukas, Costas; Exarchos, Kostas; Fotiadis, Dimitrios I

    2007-01-01

    Fold recognition is a challenging field strongly related with function determination which is of high interest for the biologists and the pharmaceutical industry. Hidden Markov Models (HMMs) have been largely applied for this purpose. In this work, the fold recognition accuracy of a recently introduced Hidden Markov Model with a reduced state-space topology is improved. This model employs an efficient architecture and a low complexity training algorithm based on likelihood maximization. Currently we further improve the fold recognition accuracy of the proposed model in two steps. In the first step we adopt a smaller model architecture based on {E,H,L} alphabet instead of DSSP secondary structure alphabet. In the second step we additionally use the predicted and the correct secondary structure information in scoring of the test set sequences. The dataset, used for the evaluation of the proposed methodology, comes from the SCOP and PDB databases. The results show that the fold recognition performance increases significantly in both steps. PMID:18003132

  20. Effect of secondary structure on the potential of mean force for poly-L-lysine in the alpha-Helix and beta-sheet conformations

    SciTech Connect

    Grigsby, J.J.; Blanch, H.W.; Prausnitz, J.M.

    2001-10-30

    Because poly-L-lysine (PLL) can exist in the {alpha}-helix or {beta}-sheet conformation depending on solution preparation and solution conditions, PLL is a suitable candidate to probe the dependence of protein interactions on secondary structure. The osmotic second virial coefficient and weight-average molecular weight are reported from low-angle laser-light scattering measurements for PLL as a function of NaCl concentration, pH, and {alpha}-helix or {beta}-sheet content. Interactions between PLL molecules become more attractive as salt concentration increases due to screening of PLL charge by salt ions and at low salt concentration become more attractive as pH increases due to decreased net charge on PLL. The experimental results show that interactions are stronger for the {beta}-sheet conformation than for the {alpha}-helix conformation. A spherically-symmetric model for the potential of mean force is used to account for specific interactions not described by DLVO theory and to show how differences in secondary structure affect PLL interactions.

  1. Secondary structure of expansion segment D1 in LSU rDNA from Arachnida and its phylogenetic application in Eriophyoid mites and in Acari.

    PubMed

    Wang, Zheng-Hang; Zhao, Ya-E; Xu, Yang; Hu, Li; Chen, Yi-Meng

    2015-12-01

    An increasing number of researchers have applied secondary-structure based multiple alignments of rDNA genes in phylogeny. These studies mostly depended on a few valuable divergent domains in LSU and SSU rDNA. Yet other divergent domains, e.g. D1, were poorly investigated and rarely used. However, these domains might contain additional evolutionary data and play a vital role in DNA-based phylogenetic study. Here, we investigated all available D1 sequences of Arachnida taxa and predicted corresponding secondary structures to help identify homologous positions in the D1 region. Long insertions were found exclusive to Eriophyoidea and folded into three newly proposed helices. Non-Acari taxa were all GC rich. In Acari, most Trombidiformes and all Mesostigmata (Parasitiformes) taxa were AT rich and Ixodida (Parasitiformes) GC rich; however there was no consistent base bias in Sarcoptiformes sequences. For Eriophyoid mites, genera Cecidophyopsis and Aceria were both well supported in MP, NJ, ME and ML tress based on D1 sequences, and clusters of Cecidophyopsis species were identical with former study. This demonstrated that the D1 region could act as a valuable molecular marker in phylogenetic reconstruction of Eriophyoidea. Additionally, D1 has been proven suitable in phylogenetic analysis at the family and genus level in Acari, but not in Opiliones. PMID:26420464

  2. 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

  3. Enzyme IIBcellobiose of the phosphoenol-pyruvate-dependent phosphotransferase system of Escherichia coli: backbone assignment and secondary structure determined by three-dimensional NMR spectroscopy.

    PubMed Central

    Ab, E.; Schuurman-Wolters, G. K.; Saier, M. H.; Reizer, J.; Jacuinod, M.; Roepstorff, P.; Dijkstra, K.; Scheek, R. M.; Robillard, G. T.

    1994-01-01

    The assignment of backbone resonances and the secondary structure determination of the Cys 10 Ser mutant of enzyme IIBcellobiose of the Escherichia coli cellobiose-specific phosphoenol-pyruvate-dependent phosphotransferase system are presented. The backbone resonances were assigned using 4 triple resonance experiments, the HNCA and HN(CO)CA experiments, correlating backbone 1H, 15N, and 13C alpha resonances, and the HN(CA)CO and HNCO experiments, correlating backbone 1H,15N and 13CO resonances. Heteronuclear 1H-NOE 1H-15N single quantum coherence (15N-NOESY-HSQC) spectroscopy and heteronuclear 1H total correlation 1H-15N single quantum coherence (15N-TOCSY-HSQC) spectroscopy were used to resolve ambiguities arising from overlapping 13C alpha and 13CO frequencies and to check the assignments from the triple resonance experiments. This procedure, together with a 3-dimensional 1H alpha-13C alpha-13CO experiment (COCAH), yielded the assignment for all observed backbone resonances. The secondary structure was determined using information both from the deviation of observed 1H alpha and 13C alpha chemical shifts from their random coil values and 1H-NOE information from the 15N-NOESY-HSQC. These data show that enzyme IIBcellobiose consists of a 4-stranded parallel beta-sheet and 5 alpha-helices. In the wild-type enzyme IIBcellobiose, the catalytic residue appears to be located at the end of a beta-strand. PMID:8003964

  4. Enzyme IIBcellobiose of the phosphoenol-pyruvate-dependent phosphotransferase system of Escherichia coli: backbone assignment and secondary structure determined by three-dimensional NMR spectroscopy.

    PubMed

    Ab, E; Schuurman-Wolters, G K; Saier, M H; Reizer, J; Jacuinod, M; Roepstorff, P; Dijkstra, K; Scheek, R M; Robillard, G T

    1994-02-01

    The assignment of backbone resonances and the secondary structure determination of the Cys 10 Ser mutant of enzyme IIBcellobiose of the Escherichia coli cellobiose-specific phosphoenol-pyruvate-dependent phosphotransferase system are presented. The backbone resonances were assigned using 4 triple resonance experiments, the HNCA and HN(CO)CA experiments, correlating backbone 1H, 15N, and 13C alpha resonances, and the HN(CA)CO and HNCO experiments, correlating backbone 1H,15N and 13CO resonances. Heteronuclear 1H-NOE 1H-15N single quantum coherence (15N-NOESY-HSQC) spectroscopy and heteronuclear 1H total correlation 1H-15N single quantum coherence (15N-TOCSY-HSQC) spectroscopy were used to resolve ambiguities arising from overlapping 13C alpha and 13CO frequencies and to check the assignments from the triple resonance experiments. This procedure, together with a 3-dimensional 1H alpha-13C alpha-13CO experiment (COCAH), yielded the assignment for all observed backbone resonances. The secondary structure was determined using information both from the deviation of observed 1H alpha and 13C alpha chemical shifts from their random coil values and 1H-NOE information from the 15N-NOESY-HSQC. These data show that enzyme IIBcellobiose consists of a 4-stranded parallel beta-sheet and 5 alpha-helices. In the wild-type enzyme IIBcellobiose, the catalytic residue appears to be located at the end of a beta-strand. PMID:8003964

  5. Effect of secondary structure on the interactions of peptide T4 LYS (11-36) in mixtures of aqueous sodium chloride and 2,2,2,-Trifluoroethanol

    SciTech Connect

    Anderson, Camille O.; Spiegelberg, Susanne; Prausnitz, John M.; Blanch, Harvey W.

    2001-10-01

    The potential of mean force for protein-protein interactions is key to the development of a statistical-mechanical model for salt-induced protein precipitation and crystallization, and for understanding certain disease states, including cataract formation and {beta}-amyloid pathology in Alzheimer's disease. Fluorescence anisotropy provides a method for quantitative characterization of intermolecular interactions due to reversible association. Monomer-dimer equilibria for the peptide T4 LYS(11-36) were studied by fluorescence anisotropy. This peptide, derived from the {beta}-sheet region of the T4 lysozyme molecule, has the potential to form amyloid fibrils. 2,2,2-trifluoroethanol (TFE) induces a change in peptide secondary structure, and was used in aqueous solutions at concentrations from 0 to 50% (v/v) at 25 and 37 C to examine the role of peptide conformation on peptide-peptide interactions. The association constant for dimerization increased with rising TFE concentration and with falling temperature. The peptide-peptide potential of mean force was computed from these association constants. Circular-dichroism measurements showed that the secondary structure of the peptide plays an important role in these strong attractive interactions due to intermolecular hydrogen-bond formation and hydrophobic interactions.

  6. Identification of a gene family (kat) encoding kinesin-like proteins in Arabidopsis thaliana and the characterization of secondary structure of KatA.

    PubMed

    Mitsui, H; Yamaguchi-Shinozaki, K; Shinozaki, K; Nishikawa, K; Takahashi, H

    1993-04-01

    A gene family, designated kat, has been characterized in Arabidopsis thaliana by genomic Southern hybridization and nucleotide sequencing analysis. The kat gene family includes at least five members, named katA, katB, katC, katD and katE, whose products share appreciable sequence similarities in their presumptive ATP-binding and microtubule-binding motifs with known kinesin-like proteins. The carboxyl-terminal region of the KatA protein deduced from the nucleotide sequence of the cDNA clone has considerable homology with the mechanochemical motor domain of the kinesin heavy chain. The predicted secondary structure of the KatA protein indicates two globular domains separated by a long alpha helical coiled coil with heptad repeat structures, such as are commonly found in kinesin-like proteins. PMID:8492804

  7. Sensitivity of mRNA Translation

    PubMed Central

    Poker, Gilad; Margaliot, Michael; Tuller, Tamir

    2015-01-01

    Using the dynamic mean-field approximation of the totally asymmetric simple exclusion process (TASEP), we investigate the effect of small changes in the initiation, elongation, and termination rates along the mRNA strand on the steady-state protein translation rate. We show that the sensitivity of mRNA translation is equal to the sensitivity of the maximal eigenvalue of a symmetric, nonnegative, tridiagonal, and irreducible matrix. This leads to new analytical results as well as efficient numerical schemes that are applicable for large-scale models. Our results show that in the usual endogenous case, when initiation is more rate-limiting than elongation, the sensitivity of the translation rate to small mutations rapidly increases towards the 5? end of the ORF. When the initiation rate is high, as may be the case for highly expressed and/or heterologous optimized genes, the maximal sensitivity is with respect to the elongation rates at the middle of the mRNA strand. We also show that the maximal possible effect of a small increase/decrease in any of the rates along the mRNA is an increase/decrease of the same magnitude in the translation rate. These results are in agreement with previous molecular evolutionary and synthetic biology experimental studies. PMID:26238363

  8. 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.

  9. The DHX33 RNA Helicase Promotes mRNA Translation Initiation

    PubMed Central

    You, Jin; Wang, Xingshun

    2015-01-01

    DEAD/DEAH box RNA helicases play essential roles in numerous RNA metabolic processes, such as mRNA translation, pre-mRNA splicing, ribosome biogenesis, and double-stranded RNA sensing. Herein we show that a recently characterized DEAD/DEAH box RNA helicase, DHX33, promotes mRNA translation initiation. We isolated intact DHX33 protein/RNA complexes in cells and identified several ribosomal proteins, translation factors, and mRNAs. Reduction of DHX33 protein levels markedly reduced polyribosome formation and caused the global inhibition of mRNA translation that was rescued with wild-type DHX33 but not helicase-defective DHX33. Moreover, we observed an accumulation of mRNA complexes with the 80S ribosome in the absence of functional DHX33, consistent with a stalling in initiation, and DHX33 more preferentially promoted structured mRNA translation. We conclude that DHX33 functions to promote elongation-competent 80S ribosome assembly at the late stage of mRNA translation initiation. Our results reveal a newly recognized function of DHX33 in mRNA translation initiation, further solidifying its central role in promoting cell growth and proliferation. PMID:26100019

  10. 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

  11. Hierarchical structure of cascade of primary and secondary periodicities in Fourier power spectrum of alphoid higher order repeats

    PubMed Central

    Paar, Vladimir; Pavin, Nenad; Basar, Ivan; Rosandi?, Marija; Glun?i?, Matko; Paar, Nils

    2008-01-01

    Background Identification of approximate tandem repeats is an important task of broad significance and still remains a challenging problem of computational genomics. Often there is no single best approach to periodicity detection and a combination of different methods may improve the prediction accuracy. Discrete Fourier transform (DFT) has been extensively used to study primary periodicities in DNA sequences. Here we investigate the application of DFT method to identify and study alphoid higher order repeats. Results We used method based on DFT with mapping of symbolic into numerical sequence to identify and study alphoid higher order repeats (HOR). For HORs the power spectrum shows equidistant frequency pattern, with characteristic two-level hierarchical organization as signature of HOR. Our case study was the 16 mer HOR tandem in AC017075.8 from human chromosome 7. Very long array of equidistant peaks at multiple frequencies (more than a thousand higher harmonics) is based on fundamental frequency of 16 mer HOR. Pronounced subset of equidistant peaks is based on multiples of the fundamental HOR frequency (multiplication factor n for nmer) and higher harmonics. In general, nmer HOR-pattern contains equidistant secondary periodicity peaks, having a pronounced subset of equidistant primary periodicity peaks. This hierarchical pattern as signature for HOR detection is robust with respect to monomer insertions and deletions, random sequence insertions etc. For a monomeric alphoid sequence only primary periodicity peaks are present. The 1/f? – noise and periodicity three pattern are missing from power spectra in alphoid regions, in accordance with expectations. Conclusion DFT provides a robust detection method for higher order periodicity. Easily recognizable HOR power spectrum is characterized by hierarchical two-level equidistant pattern: higher harmonics of the fundamental HOR-frequency (secondary periodicity) and a subset of pronounced peaks corresponding to constituent monomers (primary periodicity). The number of lower frequency peaks (secondary periodicity) below the frequency of the first primary periodicity peak reveals the size of nmer HOR, i.e., the number n of monomers contained in consensus HOR. PMID:18980673

  12. Phylogenetic Reconstruction of the Calosphaeriales and Togniniales Using Five Genes and Predicted RNA Secondary Structures of ITS, and Flabellascus tenuirostris gen. et sp. nov.

    PubMed Central

    Réblová, Martina; Jaklitsch, Walter M.; Réblová, Kamila; Št?pánek, Václav

    2015-01-01

    The Calosphaeriales is revisited with new collection data, living cultures, morphological studies of ascoma centrum, secondary structures of the internal transcribed spacer (ITS) rDNA and phylogeny based on novel DNA sequences of five nuclear ribosomal and protein-coding loci. Morphological features, molecular evidence and information from predicted RNA secondary structures of ITS converged upon robust phylogenies of the Calosphaeriales and Togniniales. The current concept of the Calosphaeriales includes the Calosphaeriaceae and Pleurostomataceae encompassing five monophyletic genera, Calosphaeria, Flabellascus gen. nov., Jattaea, Pleurostoma and Togniniella, strongly supported by Bayesian and Maximum Likelihood methods. The structural elements of ITS1 form characteristic patterns that are phylogenetically conserved, corroborate observations based on morphology and have a high predictive value at the generic level. Three major clades containing 44 species of Phaeoacremonium were recovered in the closely related Togniniales based on ITS, actin and ?-tubulin sequences. They are newly characterized by sexual and RNA structural characters and ecology. This approach is a first step towards understanding of the molecular systematics of Phaeoacremonium and possibly its new classification. In the Calosphaeriales, Jattaea aphanospora sp. nov. and J. ribicola sp. nov. are introduced, Calosphaeria taediosa is combined in Jattaea and epitypified. The sexual morph of Phaeoacremonium cinereum was encountered for the first time on decaying wood and obtained in vitro. In order to achieve a single nomenclature, the genera of asexual morphs linked with the Calosphaeriales are transferred to synonymy of their sexual morphs following the principle of priority, i.e. Calosphaeriophora to Calosphaeria, Phaeocrella to Togniniella and Pleurostomophora to Pleurostoma. Three new combinations are proposed, i.e. Pleurostoma ochraceum comb. nov., P. repens comb. nov. and P. richardsiae comb. nov. The morphology-based key is provided to facilitate identification of genera accepted in the Calosphaeriales. PMID:26699541

  13. 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...

  14. 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.

  15. SPARCS: a web server to analyze (un)structured regions in coding RNA sequences

    PubMed Central

    Zhang, Yang; Ponty, Yann; Blanchette, Mathieu; Lécuyer, Eric; Waldispühl, Jérôme

    2013-01-01

    More than a simple carrier of the genetic information,