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1

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

PubMed

Recent reports indicate that mutations in viral genomes tend to preserve RNA secondary structure, and those mutations that disrupt secondary structural elements may reduce gene expression levels, thereby serving as a functional knockout. In this article, we explore the conservation of secondary structures of mRNA coding regions, a previously unknown factor in bacterial evolution, by comparing the structural consequences of mutations in essential and nonessential Escherichia coli genes accumulated over 40 000 generations in the course of the 'long-term evolution experiment'. We monitored the extent to which mutations influence minimum free energy (MFE) values, assuming that a substantial change in MFE is indicative of structural perturbation. Our principal finding is that purifying selection tends to eliminate those mutations in essential genes that lead to greater changes of MFE values and, therefore, may be more disruptive for the corresponding mRNA secondary structures. This effect implies that synonymous mutations disrupting mRNA secondary structures may directly affect the fitness of the organism. These results demonstrate that the need to maintain intact mRNA structures imposes additional evolutionary constraints on bacterial genomes, which go beyond preservation of structure and function of the encoded proteins. PMID:23783573

Chursov, Andrey; Frishman, Dmitrij; Shneider, Alexander

2013-06-19

2

mRNA secondary structure optimization using a correlated stem-loop prediction  

PubMed Central

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

Gaspar, Paulo; Moura, Gabriela; Santos, Manuel A. S.; Oliveira, Jose Luis

2013-01-01

3

Dynamics of translation by single ribosomes through mRNA secondary structures  

PubMed Central

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

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

2013-01-01

4

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

PubMed Central

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.

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

2010-01-01

5

mRNA Secondary Structures Fold Sequentially But Exchange Rapidly In Vivo  

PubMed Central

RNAs adopt defined structures to perform biological activities, and conformational transitions among alternative structures are critical to virtually all RNA-mediated processes ranging from metabolite-activation of bacterial riboswitches to pre-mRNA splicing and viral replication in eukaryotes. Mechanistic analysis of an RNA folding reaction in a biological context is challenging because many steps usually intervene between assembly of a functional RNA structure and execution of a biological function. We developed a system to probe mechanisms of secondary structure folding and exchange directly in vivo using self-cleavage to monitor competition between mutually exclusive structures that promote or inhibit ribozyme assembly. In previous work, upstream structures were more effective than downstream structures in blocking ribozyme assembly during transcription in vitro, consistent with a sequential folding mechanism. However, upstream and downstream structures blocked ribozyme assembly equally well in vivo, suggesting that intracellular folding outcomes reflect thermodynamic equilibration or that annealing of contiguous sequences is favored kinetically. We have extended these studies to learn when, if ever, thermodynamic stability becomes an impediment to rapid equilibration among alternative RNA structures in vivo. We find that a narrow thermodynamic threshold determines whether kinetics or thermodynamics govern RNA folding outcomes in vivo. mRNA secondary structures fold sequentially in vivo, but exchange between adjacent secondary structures is much faster in vivo than it is in vitro. Previous work showed that simple base-paired RNA helices dissociate at similar rates in vivo and in vitro so exchange between adjacent structures must occur through a different mechanism, one that likely involves facilitation of branch migration by proteins associated with nascent transcripts.

Mahen, Elisabeth M.; Watson, Peter Y.; Cottrell, Joseph W.; Fedor, Martha J.

2010-01-01

6

Volatility in mRNA secondary structure as a design principle for antisense  

PubMed Central

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.

Johnson, Erik; Srivastava, Ranjan

2013-01-01

7

Optimization of antisense drug design against conservative local motif in simulant secondary structures of HER2 mRNA and QSAR analysis 1  

Microsoft Academic Search

AIM: To study the role of mRNA secondary structure stability in antisense drug design and obtain better antisense candidates against neu\\/HER-2\\/erbB-2 mRNA than previous report. METHODS: Program RNAstructure was utilized to simulate the secondary structures of HER-2 mRNA. Then 21 antisense phosphorothioate oligodeoxynucleotides (S-ODN) targeting different parts of secondary structural motif were designed. HA4 was set as positive control. Mean

YANG Shuan-Ping; SONG San-Tai; TANG Zhong-Ming; SONG Hai-Feng

2003-01-01

8

Relationship between mRNA secondary structure and sequence variability in Chloroplast genes: possible life history implications  

PubMed Central

Background Synonymous sites are freer to vary because of redundancy in genetic code. Messenger RNA secondary structure restricts this freedom, as revealed by previous findings in mitochondrial genes that mutations at third codon position nucleotides in helices are more selected against than those in loops. This motivated us to explore the constraints imposed by mRNA secondary structure on evolutionary variability at all codon positions in general, in chloroplast systems. Results We found that the evolutionary variability and intrinsic secondary structure stability of these sequences share an inverse relationship. Simulations of most likely single nucleotide evolution in Psilotum nudum and Nephroselmis olivacea mRNAs, indicate that helix-forming propensities of mutated mRNAs are greater than those of the natural mRNAs for short sequences and vice-versa for long sequences. Moreover, helix-forming propensity estimated by the percentage of total mRNA in helices increases gradually with mRNA length, saturating beyond 1000 nucleotides. Protection levels of functionally important sites vary across plants and proteins: r-strategists minimize mutation costs in large genes; K-strategists do the opposite. Conclusion Mrna length presumably predisposes shorter mRNAs to evolve under different constraints than longer mRNAs. The positive correlation between secondary structure protection and functional importance of sites suggests that some sites might be conserved due to packing-protection constraints at the nucleic acid level in addition to protein level constraints. Consequently, nucleic acid secondary structure a priori biases mutations. The converse (exposure of conserved sites) apparently occurs in a smaller number of cases, indicating a different evolutionary adaptive strategy in these plants. The differences between the protection levels of functionally important sites for r- and K-strategists reflect their respective molecular adaptive strategies. These converge with increasing domestication levels of K-strategists, perhaps because domestication increases reproductive output.

Krishnan, Neeraja M; Seligmann, Herve; Rao, Basuthkar J

2008-01-01

9

mRNA secondary structure modulates the translation of organophosphate hydrolase (OPH) in E. coli  

Microsoft Academic Search

Organophosphate hydrolases (OPHs), involved in hydrolytic cleavage of structurally diverse organophosphates are coded by a\\u000a plasmid borne, highly conserved organophosphate degrading (opd) gene. An inverted repeat sequence found in the signal coding region of the opd gene was found to be responsible for inducing a stable stem loop structure with a ?G of ?23.1 kcal\\/mol. This stem loop structure has shown

Jay Prakash Pandey; Purushotham Gorla; Bramanandam Manavathi; Dayananda Siddavattam

2009-01-01

10

Heat induction of sigma 32 synthesis mediated by mRNA secondary structure: a primary step of the heat shock response in Escherichia coli.  

PubMed Central

Induction of heat shock proteins following transfer of E. coli cells from 30 degrees C to 42 degrees C depends on rapid accumulation of sigma 32, a minor sigma factor specifically required for transcription of heat shock genes. The synthesis of sigma 32 is induced by enhancing translation of its mRNA transcribed from the rpoH (htpR) gene. We previously showed that the translational control of rpoH-lacZ gene fusion is mediated by two cis-acting rpoH coding regions presumably involving mRNA secondary structure. To further examine this model, we constructed and analyzed a set of gene fusions carrying base substitution(s) or internal deletions within rpoH, including constitutive mutations predicted to destroy the mRNA secondary structure and compensatory second-site mutations that may restore the secondary structure. The results demonstrate that base pairings between the translation initiation region of some 20 nucleotides and part of the internal complementary sequences are critical for maintaining repression during steady-state growth and for modulating heat-induced synthesis of sigma 32-beta-galactosidase fusion protein upon temperature upshift. Furthermore, some of the compensatory mutations resulted in super-repressed (non-inducible) phenotypes, suggesting that the heat induction depends on a specific nucleotide sequence(s) as well as the mRNA secondary structure within the 5'-proximal regulatory segment of rpoH coding region. Images

Yuzawa, H; Nagai, H; Mori, H; Yura, T

1993-01-01

11

Regulation of protein synthesis by eIF4E phosphorylation in adult cardiocytes: the consequence of secondary structure in the 5'-untranslated region of mRNA.  

PubMed Central

In adult cardiocytes, eIF4E (eukaryotic initiation factor 4E) activity and protein synthesis are increased concomitantly in response to stimuli that induce hypertrophic growth. We tested the hypothesis that increases in eIF4E activity selectively improve the translational efficiency of mRNAs that have an excessive amount of secondary structure in the 5'-UTR (5'-untranslated region). The activity of eIF4E was modified in primary cultures of adult cardiocytes using adenoviral gene transfer to increase either the amount of eIF4E or the extent of endogenous eIF4E phosphorylation. Subsequently, the effects of eIF4E on translational efficiency were assayed following adenoviral-mediated expression of luciferase reporter mRNAs that were either 'stronger' (less structure in the 5'-UTR) or 'weaker' (more structure in the 5'-UTR) with respect to translational efficiency. The insertion of G+C-rich repeats into the 5'-UTR doubled the predicted amount of secondary structure and was sufficient to reduce translational efficiency of the reporter mRNA by 48+/-13%. Translational efficiency of the weaker reporter mRNA was not significantly improved by overexpression of wild-type eIF4E when compared with the stronger reporter mRNA. In contrast, overexpression of the eIF4E kinase Mnk1 [MAP (mitogen-activated protein) kinase signal-integrating kinase 1] was sufficient to increase the translational efficiency of either reporter mRNA, independent of the amount of secondary structure in their respective 5'-UTRs. The increases in translational efficiency produced by Mnk1 occurred in association with corresponding decreases in mRNA levels. These findings indicate that the positive effect of eIF4E phosphorylation on translational efficiency in adult cardiocytes is coupled with the stability of mRNA.

Tuxworth, William J; Saghir, Atif N; Spruill, Laura S; Menick, Donald R; McDermott, Paul J

2004-01-01

12

Photochemical cross-linking of cap binding proteins to eucaryotic mRNAs: effect of mRNA 5' secondary structure.  

PubMed Central

We used UV light-induced cross-linking to study the interactions of cap binding proteins with the 5' cap structure of eucaryotic mRNAs. Thymidine kinase gene (herpes simplex virus type 1) transcripts prepared in vitro using the SP6 RNA polymerase transcription system were capped and methylated posttranscriptionally with [alpha-32P]GTP and S-adenosyl-L-methionine to yield cap-labeled transcripts. Irradiation of capped transcripts with crude rabbit reticulocyte initiation factors in the presence of ATP-Mg2+ resulted in the cap-specific cross-linking of two polypeptides with molecular masses of 24 and 80 kilodaltons (kDa). The cross-linking characteristics of these polypeptides resemble those of the cap-binding proteins previously detected by a chemical cross-linking assay (N. Sonenberg, D. Guertin, D. Cleveland, and H. Trachsel, Cell 27:563-572, 1981). However, the relative efficiency of the cross-linking of these two polypeptides to the cap structure was different from that in previous studies, and there was no detectable cross-linking of the previously described 50-kDa polypeptide. In addition, we present data indicating that the insertion of secondary structure into the 5' noncoding region of tk mRNA, 6 nucleotides from the cap structure, decreases the cap-specific cross-linking of the 80-kDa but not the 24-kDa polypeptide. In contrast, the insertion of secondary structure 37 nucleotides from the cap structure had no significant effect on the cross-linking of either the 24- or the 80-kDa cap-specific polypeptide. These results demonstrate that the position of mRNA 5'-proximal secondary structure relative to the cap structure can influence the cap-specific interaction between the mRNA and a translation initiation factor. Images

Pelletier, J; Sonenberg, N

1985-01-01

13

Secondary Structure of a Conserved Domain in the Intron of Influenza A NS1 mRNA  

PubMed Central

Influenza A virus is a segmented single-stranded (?)RNA virus that causes substantial annual morbidity and mortality. The transcriptome of influenza A is predicted to have extensive RNA secondary structure. The smallest genome segment, segment 8, encodes two proteins, NS1 and NEP, via alternative splicing. A conserved RNA domain in the intron of segment 8 may be important for regulating production of NS1. Two different multi-branch loop structures have been proposed for this region. A combination of in vitro chemical mapping and isoenergetic microarray techniques demonstrate that the consensus sequence for this region folds into a hairpin conformation. These results provide an alternative folding for this region and a foundation for designing experiments to probe its functional role in the influenza life cycle.

Priore, Salvatore F.; Kierzek, Elzbieta; Kierzek, Ryszard; Baman, Jayson R.; Moss, Walter N.; Dela-Moss, Lumbini I.; Turner, Douglas H.

2013-01-01

14

Specific temperature-induced perturbations of secondary mRNA structures are associated with the cold-adapted temperature-sensitive phenotype of influenza A virus  

PubMed Central

For decades, cold-adapted, temperature-sensitive (ca/ts) strains of influenza A virus have been used as live attenuated vaccines. Due to their great public health importance it is crucial to understand the molecular mechanism(s) of cold adaptation and temperature sensitivity that are currently unknown. For instance, secondary RNA structures play important roles in influenza biology. Thus, we hypothesized that a relatively minor change in temperature (32–39°C) can lead to perturbations in influenza RNA structures and, that these structural perturbations may be different for mRNAs of the wild type (wt) and ca/ts strains. To test this hypothesis, we developed a novel in silico method that enables assessing whether two related RNA molecules would undergo (dis)similar structural perturbations upon temperature change. The proposed method allows identifying those areas within an RNA chain where dissimilarities of RNA secondary structures at two different temperatures are particularly pronounced, without knowing particular RNA shapes at either temperature. We identified such areas in the NS2, PA, PB2 and NP mRNAs. However, these areas are not identical for the wt and ca/ts mutants. Differences in temperature-induced structural changes of wt and ca/ts mRNA structures may constitute a yet unappreciated molecular mechanism of the cold adaptation/temperature sensitivity phenomena.

Chursov, Andrey; Kopetzky, Sebastian J.; Leshchiner, Ignaty; Kondofersky, Ivan; Theis, Fabian J.; Frishman, Dmitrij; Shneider, Alexander

2012-01-01

15

ASH1 mRNA localization in yeast involves multiple secondary structural elementsand Ash1 protein translation  

Microsoft Academic Search

Localization of ASH1 mRNA to the distal cortex of daughter but not mother cells at the end of anaphase is responsible for the two cell's differential mating-type switching during the subsequent cell cycle. This localization depends on actin filaments and a type V myosin (She1\\/Myo4). The 3? untranslated region (3? UTR) of ASH1 mRNA is reportedly capable of directing heterologous

Isabel Gonzalez; Sara B. C. Buonomo; Kim Nasmyth; Uwe von Ahsen

1999-01-01

16

Small cis-Acting Sequences That Specify Secondary Structures in a Chloroplast mRNA Are Essential for RNA Stability and Translation  

PubMed Central

Nucleus-encoded proteins interact with cis-acting elements in chloroplast transcripts to promote RNA stability and translation. We have analyzed the structure and function of three such elements within the Chlamydomonas petD 5? untranslated region; petD encodes subunit IV of the cytochrome b6/f complex. These elements were delineated by linker-scanning mutagenesis, and RNA secondary structures were investigated by mapping nuclease-sensitive sites in vitro and by in vivo dimethyl sulfate RNA modification. Element I spans a maximum of 8 nucleotides (nt) at the 5? end of the mRNA; it is essential for RNA stability and plays a role in translation. This element appears to form a small stem-loop that may interact with a previously described nucleus-encoded factor to block 5??3? exoribonucleolytic degradation. Elements II and III, located in the center and near the 3? end of the 5? untranslated region, respectively, are essential for translation, but mutations in these elements do not affect mRNA stability. Element II is a maximum of 16 nt in length, does not form an obvious secondary structure, and appears to bind proteins that protect it from dimethyl sulfate modification. Element III spans a maximum of 14 nt and appears to form a stem-loop in vivo, based on dimethyl sulfate modification and the sequences of intragenic suppressors of element III mutations. Furthermore, mutations in element II result in changes in the RNA structure near element III, consistent with a long-range interaction that may promote translation.

Higgs, David C.; Shapiro, Risa S.; Kindle, Karen L.; Stern, David B.

1999-01-01

17

A molecular beacon-based real time NASBA assay for detection of Listeria monocytogenes in food products: Role of target mRNA secondary structure on NASBA design  

Microsoft Academic Search

A molecular beacon-based real-time NASBA (QNASBA) assay for detection and identification of Listeria monocytogenes has been developed. A correlation between targeting highly accessible mRNA sequences and QNASBA efficiency and sensitivity was demonstrated. The assay targets a sequence from the mRNA transcript of the hly gene which is specific for this bacterium; and includes an internal amplification control to disclose failure

Anna Nadal; Anna Coll; Nigel Cook; Maria Pla

2007-01-01

18

RNA secondary structures located in the interchromosomal region of human ACAT1 chimeric mRNA are required to produce the 56-kDa isoform  

Microsoft Academic Search

We have previously reported that the human ACAT1 gene produces a chimeric mRNA through the interchromosomal processing of two discontinuous RNAs transcribed from chromosomes 1 and 7. The chimeric mRNA uses AUG1397-1399 and GGC1274-1276 as translation initiation codons to produce normal 50-kDa ACAT1 and a novel enzymatically active 56-kDa isoform, respectively, with the latter being authentically present in human cells,

Jia Chen; Xiao-Nan Zhao; Li Yang; Guang-Jing Hu; Ming Lu; Ying Xiong; Xin-Ying Yang; Catherine CY Chang; Bao-Liang Song; Ta-Yuan Chang; Bo-Liang Li

2008-01-01

19

Secondary Emission Multiplier Structure.  

National Technical Information Service (NTIS)

The secondary emission multiplier structure is for use in electron tubes wherein there is an electron-optical image, such as image intensifier tubes. The structure consists of a plurality of plates or sheets of material each having a number of tapered con...

E. W. Poor

1965-01-01

20

Vienna RNA secondary structure server  

Microsoft Academic Search

The Vienna RNA secondary structure server provides a web interface to the most frequently used functions of the Vienna RNA software package for the analysis of RNA secondary structures. It currently offers prediction of secondary structure from a single sequence, prediction of the consensus secondary structure for a set of aligned sequences, and the design of sequences that will fold

Ivo L. Hofacker

2003-01-01

21

Secondary Structure Switch  

ERIC Educational Resources Information Center

|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…

King, Angela G.

2006-01-01

22

Selection of antisense oligonucleotides based on multiple predicted target mRNA structures  

Microsoft Academic Search

Background: Local structures of target mRNAs play a significant role in determining the efficacies of antisense oligonucleotides (ODNs), but some structure-based target site selection methods are limited by uncertainties in RNA secondary structure prediction. If all the predicted structures of a given mRNA within a certain energy limit could be used simultaneously, target site selection would obviously be improved in

Xiaochen Bo; Shaoke Lou; Daochun Sun; Wenjie Shu; Jing Yang; Shengqi Wang

2006-01-01

23

Structure of the Rho transcription terminator: mechanism of mRNA recognition and helicase loading.  

PubMed

In bacteria, one of the major transcriptional termination mechanisms requires a RNA/DNA helicase known as the Rho factor. We have determined two structures of Rho complexed with nucleic acid recognition site mimics in both free and nucleotide bound states to 3.0 A resolution. Both structures show that Rho forms a hexameric ring in which two RNA binding sites--a primary one responsible for target mRNA recognition and a secondary one required for mRNA translocation and unwinding--point toward the center of the ring. Rather than forming a closed ring, the Rho hexamer is split open, resembling a "lock washer" in its global architecture. The distance between subunits at the opening is sufficiently wide (12 A) to accommodate single-stranded RNA. This open configuration most likely resembles a state poised to load onto mRNA and suggests how related ring-shaped enzymes may be breached to bind nucleic acids. PMID:12859904

Skordalakes, Emmanuel; Berger, James M

2003-07-11

24

Selection of antisense oligonucleotides based on multiple predicted target mRNA structures  

PubMed Central

Background Local structures of target mRNAs play a significant role in determining the efficacies of antisense oligonucleotides (ODNs), but some structure-based target site selection methods are limited by uncertainties in RNA secondary structure prediction. If all the predicted structures of a given mRNA within a certain energy limit could be used simultaneously, target site selection would obviously be improved in both reliability and efficiency. In this study, some key problems in ODN target selection on the basis of multiple predicted target mRNA structures are systematically discussed. Results Two methods were considered for merging topologically different RNA structures into integrated representations. Several parameters were derived to characterize local target site structures. Statistical analysis on a dataset with 448 ODNs against 28 different mRNAs revealed 9 features quantitatively associated with efficacy. Features of structural consistency seemed to be more highly correlated with efficacy than indices of the proportion of bases in single-stranded or double-stranded regions. The local structures of the target site 5' and 3' termini were also shown to be important in target selection. Neural network efficacy predictors using these features, defined on integrated structures as inputs, performed well in "minus-one-gene" cross-validation experiments. Conclusion Topologically different target mRNA structures can be merged into integrated representations and then used in computer-aided ODN design. The results of this paper imply that some features characterizing multiple predicted target site structures can be used to predict ODN efficacy.

Bo, Xiaochen; Lou, Shaoke; Sun, Daochun; Shu, Wenjie; Yang, Jing; Wang, Shengqi

2006-01-01

25

Synopsis of Research on RNA Secondary Structure.  

National Technical Information Service (NTIS)

This work concerns secondary structure of single-stranded nucleic acids, specifically that of RNA. The topics include graph theory of such structures, enumeration of structures, algorithms and programs for finding the optimal structures, and the partition...

M. S. Waterman

1978-01-01

26

Computational prediction of RNA secondary structure.  

PubMed

The purpose of this section is to detail methods for the computational prediction of RNA secondary structure. This protocol is intended to provide an easy entry into the field of RNA structure prediction for those wishing to utilize it in their research and to suggest 'best practices' for going from sequence to secondary structure depending on the available data. PMID:24034313

Moss, Walter N

2013-01-01

27

Structure of an RNA dimer of a regulatory element from human thymidylate synthase mRNA  

SciTech Connect

A sequence around the start codon of the mRNA of human thymidylate synthase (TS) folds into a secondary-structure motif in which the initiation site is sequestered in a metastable hairpin. Binding of the protein to its own mRNA at the hairpin prevents the production of TS through a translation-repression feedback mechanism. Stabilization of the mRNA hairpin by other ligands has been proposed as a strategy to reduce TS levels in anticancer therapy. Rapidly proliferating cells require high TS activity to maintain the production of thymidine as a building block for DNA synthesis. The crystal structure of a model oligonucleotide (TS1) that represents the TS-binding site of the mRNA has been determined. While fluorescence studies showed that the TS1 RNA preferentially adopts a hairpin structure in solution, even at high RNA concentrations, an asymmetric dimer of two hybridized TS1 strands was obtained in the crystal. The TS1 dimer contains an unusual S-turn motif that also occurs in the 'off' state of the human ribosomal decoding site RNA.

Dibrov, Sergey; McLean, Jaime; Hermann, Thomas (UCSD)

2011-09-27

28

Protein secondary structure pattern discovery and its application in secondary structure prediction  

Microsoft Academic Search

A method of protein secondary structure pattern discovery is presented. The TEIRESIAS algorithm has been improved to discover protein secondary structure patterns. Four protein secondary structure pattern dictionaries have been built for four organisms. The distribution of patterns and common patterns' structure in different dictionaries is different. Different organism's proteins represent different biological language. Based on the organism-specific dictionary, a

Ming-Hui Li; Xiao-Long Wang; Lei Lin; Yi Guan

2004-01-01

29

Specific inhibition of expression of a human collagen gene (COL1A1) with modified antisense oligonucleotides. The most effective target sites are clustered in double-stranded regions of the predicted secondary structure for the mRNA.  

PubMed

A series of antisense oligonucleotides (ASOs) were synthesized and tested to define the best target sites within an RNA transcript of collagen for effective inhibition of expression. The test system consisted of mouse NIH 3T3 fibroblasts that were stably transfected with a human minigene for procollagen I so that the cells simultaneously synthesized full-length mouse pro alpha 1 (I) chains and internally deleted human pro alpha 1 (I) chains. The sequences of the transcripts from both genes were compared, and a series of 28 ASOs were designed to target sites in which there were at least two base differences within a 20-nucleotide sequence between the human and mouse transcripts. Six of the ASOs specifically decreased the levels of pro alpha 1 (I) chain synthesized from the human gene without a decrease in the levels of pro alpha 1 (I) chains from the mouse endogenous gene. The most effective ASOs reduced the intracellular levels of human pro alpha 1 (I) chains relative to the mouse pro alpha 1 (I) chains to 37-67% of the control values. Combined addition of two effective ASOs or a second administration of the same effective ASO did not produce any additive effect. The results did not support previous suggestions that the best target sites for ASOs were sequences around initiation codons for translation, at intron-exon boundaries, or in single-stranded loops in hairpin structures. Also, the results did not support previous suggestions that the most effective ASOs are those with the highest affinities for their target sequences. Instead, the most consistent pattern in the data was that the most effective ASOs were those targeted to sequences that were predicted to form clustered double-stranded structures in RNA transcripts. PMID:8086420

Laptev, A V; Lu, Z; Colige, A; Prockop, D J

1994-09-13

30

Unorthodox mRNA start site to extend the highly structured leader of retrotransposon Tto1 mRNA increases transposition rate.  

PubMed

Retroelement RNAs serve as templates for both translation and reverse transcription into extrachromosomal DNA. DNA copies may be inserted into the host genome to multiply element sequences. This transpositional activity of retroelements is usually restricted to specific conditions, particularly to conditions that impose stress on the host organism. In this work, we examined how the mRNA initiation point, and features of primary and secondary structure, of tobacco retrotransposon Tto1 RNA influence its transpositional activity. We found that the most abundant Tto1 RNA is not a substrate for reverse transcription. It is poorly translated, and its 5'-end does not contain a region of redundancy with the most prominent 3'-end. In contrast, expression of an mRNA with the 5'-end extended by 28 nucleotides allows translation and gives rise to transposition events in the heterologous host, Arabidopsis thaliana. In addition, the presence of extended hairpins and of two short open reading frames in the 5'-leader sequence of Tto1 mRNA suggests that translation does not involve ribosome scanning from the mRNA 5'-end to the translation initiation site. PMID:16043504

Böhmdorfer, Gudrun; Hofacker, Ivo L; Garber, Karin; Jelenic, Srecko; Nizhynska, Viktoria; Hirochika, Hirohiko; Stadler, Peter F; Bachmair, Andreas

2005-08-01

31

Secondary structure-based assignment of the protein structural classes  

Microsoft Academic Search

Structural class categorizes proteins based on the amount and arrangement of the constituent secondary structures. The knowledge\\u000a of structural classes is applied in numerous important predictive tasks that address structural and functional features of\\u000a proteins. We propose novel structural class assignment methods that use one-dimensional (1D) secondary structure as the input.\\u000a The methods are designed based on a large set

Lukasz A. Kurgan; Tuo Zhang; Hua Zhang; Shiyi Shen; Jishou Ruan

2008-01-01

32

Computational prediction of secondary and supersecondary structures.  

PubMed

The sequence-based prediction of the secondary and supersecondary structures enjoys strong interest and finds applications in numerous areas related to the characterization and prediction of protein structure and function. Substantial efforts in these areas over the last three decades resulted in the development of accurate predictors, which take advantage of modern machine learning models and availability of evolutionary information extracted from multiple sequence alignment. In this chapter, we first introduce and motivate both prediction areas and introduce basic concepts related to the annotation and prediction of the secondary and supersecondary structures, focusing on the ? hairpin, coiled coil, and ?-turn-? motifs. Next, we overview state-of-the-art prediction methods, and we provide details for 12 modern secondary structure predictors and 4 representative supersecondary structure predictors. Finally, we provide several practical notes for the users of these prediction tools. PMID:22987347

Chen, Ke; Kurgan, Lukasz

2013-01-01

33

Systematic Discovery of Structural Elements Governing Mammalian mRNA Stability  

PubMed Central

Decoding post-transcriptional regulatory programs in RNA is a critical step in the larger goal to develop predictive dynamical models of cellular behavior. Despite recent efforts1–3, the vast landscape of RNA regulatory elements remain largely uncharacterized. A longstanding obstacle is the contribution of local RNA secondary structure in defining interaction partners in a variety of regulatory contexts, including but not limited to transcript stability3, alternative splicing4 and localization3. There are many documented instances where the presence of a structural regulatory element dictates alternative splicing patterns (e.g. human cardiac troponin T) or affects other aspects of RNA biology5. Thus, a full characterization of post-transcriptional regulatory programs requires capturing information provided by both local secondary structures and the underlying sequence3,6. We have developed a computational framework based on context-free grammars3,7 and mutual information2 that systematically explores the immense space of small structural elements and reveals motifs that are significantly informative of genome-wide measurements of RNA behavior. The application of this framework to genome-wide mammalian mRNA stability data revealed eight highly significant elements with substantial structural information, for the strongest of which we showed a major role in global mRNA regulation. Through biochemistry, mass-spectrometry, and in vivo binding studies, we identified HNRPA2B1 as the key regulator that binds this element and stabilizes a large number of its target genes. Ultimately, we created a global post-transcriptional regulatory map based on the identity of the discovered linear and structural cis-regulatory elements, their regulatory interactions and their target pathways. This approach can also be employed to reveal the structural elements that modulate other aspects of RNA behavior.

Goodarzi, Hani; Najafabadi, Hamed S.; Oikonomou, Panos; Greco, Todd M.; Fish, Lisa; Salavati, Reza; Cristea, Ileana M.; Tavazoie, Saeed

2012-01-01

34

Data Mining for Protein Secondary Structure Prediction  

Microsoft Academic Search

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

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

35

The Protein Secondary Structure Flexibility  

Microsoft Academic Search

Modeling protein flexibility is a long standing challenge in computational biology with a special impact to protein docking. Relating problems are protein structures alignment and identification of flexible and rigid protein regions, as well as a general definition of a region degree of flexibility. Determination of protein flexibility from a single protein conformation, so called apriori approach is still computationally

Kresimir Sikic; Branko Jeren; Sanja Tomic

2008-01-01

36

RNA secondary structure and in vitro translation efficiency.  

PubMed

Cell-free protein synthesis is a promising technology featuring many advantages compared to in vivo expression techniques. However, most proteins are still synthesized in vivo due to relatively low protein yields commonly achieved in vitro, especially in the batch mode of reaction. In Escherichia coli S30 extract-based cell-free systems protein yields are supposed to be partially limited by a secondary structure formation of the mRNA. In this study we checked promising members of various classes of RNA chaperones and several different RNA helicases on their ability to enhance in vitro translation. The data clearly show that the addition of none of these factors provides a general solution to the problem. However, protein yields can be increased in presence of a microRNA hybridizing with the 5' untranslated region of mRNAs, possibly by inducing structural changes improving accessibility of the Shine Dalgarno sequence for the ribosomes. PMID:22100525

Freischmidt, Axel; Liss, Michael; Wagner, Ralf; Kalbitzer, Hans Robert; Horn, Gudrun

2011-11-10

37

Hybrid system for protein secondary structure prediction.  

PubMed

We have developed a hybrid system to predict the secondary structures (alpha-helix, beta-sheet and coil) of proteins and achieved 66.4% accuracy, with correlation coefficients of C(coil) = 0.429, C alpha = 0.470 and C beta = 0.387. This system contains three subsystems ("experts"): a neural network module, a statistical module and a memory-based reasoning module. First, the three experts independently learn the mapping between amino acid sequences and secondary structures from the known protein structures, then a Combiner learns to combine automatically the outputs of the experts to make final predictions. The hybrid system was tested with 107 protein structures through k-way cross-validation. Its performance was better than each expert and all previously reported methods with greater than 0.99 statistical significance. It was observed that for 20% of the residues, all three experts produced the same but wrong predictions. This may suggest an upper bound on the accuracy of secondary structure predictions based on local information from the currently available protein structures, and indicate places where non-local interactions may play a dominant role in conformation. For 64% of the residues, at least two experts were the same and correct, which shows that the Combiner performed better than majority vote. For 77% of the residues, at least one expert was correct, thus there may still be room for improvement in this hybrid approach. Rigorous evaluation procedures were used in testing the hybrid system, and statistical significance measures were developed in analyzing the differences among different methods. When measured in terms of the number of secondary structures (rather than the number of residues) that were predicted correctly, the prediction produced by the hybrid system was also better than those of individual experts. PMID:1613789

Zhang, X; Mesirov, J P; Waltz, D L

1992-06-20

38

The terminal structures of feather keratin mRNA  

Microsoft Academic Search

Terminal labeling of embryonic feather keratin mRNA with [3H]KBH4 followed by digestion with ribonuclease T1 and T2, alkaline phosphatase, snake venom phosphodiesterase, and nucleotide pyrophosphatase and analysis of the products by high voltage paper electrophoresis, indicated the presence of the sequence m7G(5')ppp(5')N at the 5'-end of the mRNA. Ribonuclease T1 and A digests of the terminally labeled, and also of

C. Phillip Morris; George E. Rogers

1979-01-01

39

Conserved RNA Secondary Structures in Picornaviridae Genomes  

Microsoft Academic Search

The family Picornaviridae contains important pathogens including, for example, Hepatitis A virus and Foot-and-Mouth Disease Virus. The genome of these viruses is a single messenger-active (+)-RNA of 7200 to 8500nts. Besides coding for the viral proteins, it also contains functionally important RNA secondary structures, among them an IRES region toward the 5'end. This contribution provides a comprehensive computational survey of

Christina Witwer; Susanne Rauscher; Ivo L. Hofacker; Peter F. Stadler

2001-01-01

40

Conserved RNA Secondary Structures in Picornaviridae Genomes  

Microsoft Academic Search

The family Picornaviridae contains important pathogens including, for example, Hep- atitis A virus and Foot-and-Mouth Disease Virus. The genome of these viruses is a single messenger-active (+)-RNA of 7200 to 8500nts. Besides coding for the viral proteins, it also contains functionally important RNA secondary structures, among them an IRES region toward the 5'end. This contribution provides a comprehensive computational survey

Christina Witwer; Susanne Rauscher; Ivo L. Hofacker; Peter F. Stadler

41

Discrete breathers in protein secondary structure  

Microsoft Academic Search

The role of the rigidity of a peptide chain in its equilibrium dynamics is\\u000ainvestigated within a realistic model with stringent microscopically derived\\u000acoupling interaction potential and effective on-site potential. The coupling\\u000ainteraction characterizing the chain rigidity and the effective on-site\\u000apotentials are calculated for three main types of protein secondary structure.\\u000aThe coupling interaction is found to be surprisingly

A. E. Sitnitsky

2003-01-01

42

Quantification of PRV1 mRNA distinguishes polycythemia vera from secondary erythrocytosis  

Microsoft Academic Search

To date, the diagnosis of polycythemia vera (PV) relies on clinical criteria. We have recently described the overexpres- sion of a hematopoietic receptor, polycy- themia rubra vera-1 (PRV-1), in patients with PV. Here, we report a quantitative reverse transcriptase-polymerase chain reaction (RT-PCR) assay for the measure- ment of PRV-1 mRNA levels. We have determined PRV-1 expression in 71 pa- tients

Steffen Klippel; Elisabeth Strunck; Snezana Temerinac; Anthony J. Bench; Gerold Meinhardt; Ursula Mohr; Rosi Leichtle; Anthony R. Green; Martin Griesshammer; Hermann Heimpel; Heike L. Pahl; Klinikum Innenstadt; Robert Koch

2003-01-01

43

?-Turn Secondary Structure and Melanocortin Ligands  

PubMed Central

The melanocortin pathway has emerged during this past decade as an important target area for the discovery and development of therapeutic agents related to obesity and type 2 diabetes. This peptide-G-protein coupled receptor (GPCR) pathway has evolved from peptide based ligands to small molecules possessing a variety of different molecular scaffolds. Herein, we summarize the originating hypothesis of the importance of the reverse ?-turn secondary structure for agonist ligand potency at the melanocortin receptors and how that information was utilized for the discovery of small molecules based upon this type of turn structure.

Haslach, Erica M.; Schaub, Jay W.; Haskell-Luevano, Carrie

2009-01-01

44

RNA secondary structure prediction using soft computing.  

PubMed

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

Ray, Shubhra Sankar; Pal, Sankar K

45

Statistical evidence for conserved, local secondary structure in the coding regions of eukaryotic mRNAs and pre-mRNAs  

PubMed Central

Owing to the degeneracy of the genetic code, protein-coding regions of mRNA sequences can harbour more than only amino acid information. We search the mRNA sequences of 11 human protein-coding genes for evolutionarily conserved secondary structure elements using RNA-Decoder, a comparative secondary structure prediction program that is capable of explicitly taking the known protein-coding context of the mRNA sequences into account. We detect well-defined, conserved RNA secondary structure elements in the coding regions of the mRNA sequences and show that base-paired codons strongly correlate with sparse codons. We also investigate the role of repetitive elements in the formation of secondary structure and explain the use of alternate start codons in the caveolin-1 gene by a conserved secondary structure element overlapping the nominal start codon. We discuss the functional roles of our novel findings in regulating the gene expression on mRNA level. We also investigate the role of secondary structure on the correct splicing of the human CFTR gene. We study the wild-type version of the pre-mRNA as well as 29 variants with synonymous mutations in exon 12. By comparing our predicted secondary structures to the experimentally determined splicing efficiencies, we find with weak statistical significance that pre-mRNAs with high-splicing efficiencies have different predicted secondary structures than pre-mRNAs with low-splicing efficiencies.

Meyer, Irmtraud M.; Miklos, Istvan

2005-01-01

46

Neural network definitions of highly predictable protein secondary structure classes.  

National Technical Information Service (NTIS)

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 conventi...

A. Lapedes E. Steeg R. Farber

1994-01-01

47

Computing folding pathways between RNA secondary structures  

PubMed Central

Given an RNA sequence and two designated secondary structures A, B, we describe a new algorithm that computes a nearly optimal folding pathway from A to B. The algorithm, RNAtabupath, employs a tabu semi-greedy heuristic, known to be an effective search strategy in combinatorial optimization. Folding pathways, sometimes called routes or trajectories, are computed by RNAtabupath in a fraction of the time required by the barriers program of Vienna RNA Package. We benchmark RNAtabupath with other algorithms to compute low energy folding pathways between experimentally known structures of several conformational switches. The RNApathfinder web server, source code for algorithms to compute and analyze pathways and supplementary data are available at http://bioinformatics.bc.edu/clotelab/RNApathfinder.

Dotu, Ivan; Lorenz, William A.; Van Hentenryck, Pascal; Clote, Peter

2010-01-01

48

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

SciTech Connect

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.

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

1982-12-01

49

A folding algorithm for extended RNA secondary structures  

PubMed Central

Motivation: RNA secondary structure contains many non-canonical base pairs of different pair families. Successful prediction of these structural features leads to improved secondary structures with applications in tertiary structure prediction and simultaneous folding and alignment. Results: We present a theoretical model capturing both RNA pair families and extended secondary structure motifs with shared nucleotides using 2-diagrams. We accompany this model with a number of programs for parameter optimization and structure prediction. Availability: All sources (optimization routines, RNA folding, RNA evaluation, extended secondary structure visualization) are published under the GPLv3 and available at www.tbi.univie.ac.at/software/rnawolf/. Contact: choener@tbi.univie.ac.at

zu Siederdissen, Christian Honer; Bernhart, Stephan H.; Stadler, Peter F.; Hofacker, Ivo L.

2011-01-01

50

Maximum expected accuracy structural neighbors of an RNA secondary structure  

PubMed Central

Background Since RNA molecules regulate genes and control alternative splicing by allostery, it is important to develop algorithms to predict RNA conformational switches. Some tools, such as paRNAss, RNAshapes and RNAbor, can be used to predict potential conformational switches; nevertheless, no existent tool can detect general (i.e., not family specific) entire riboswitches (both aptamer and expression platform) with accuracy. Thus, the development of additional algorithms to detect conformational switches seems important, especially since the difference in free energy between the two metastable secondary structures may be as large as 15-20 kcal/mol. It has recently emerged that RNA secondary structure can be more accurately predicted by computing the maximum expected accuracy (MEA) structure, rather than the minimum free energy (MFE) structure. Results Given an arbitrary RNA secondary structure S0 for an RNA nucleotide sequence a = a1,..., an, we say that another secondary structure S of a is a k-neighbor of S0, if the base pair distance between S0 and S is k. In this paper, we prove that the Boltzmann probability of all k-neighbors of the minimum free energy structure S0 can be approximated with accuracy ? and confidence 1 - p, simultaneously for all 0 ? k < K, by a relative frequency count over N sampled structures, provided that N>N(?,p,K)=?-1p2K24?2, where ?(z) is the cumulative distribution function (CDF) for the standard normal distribution. We go on to describe the algorithm RNAborMEA, which for an arbitrary initial structure S0 and for all values 0 ? k < K, computes the secondary structure MEA(k), having maximum expected accuracy over all k-neighbors of S0. Computation time is O(n3 · K2), and memory requirements are O(n2 · K). We analyze a sample TPP riboswitch, and apply our algorithm to the class of purine riboswitches. Conclusions The approximation of RNAbor by sampling, with rigorous bound on accuracy, together with the computation of maximum expected accuracy k-neighbors by RNAborMEA, provide additional tools toward conformational switch detection. Results from RNAborMEA are quite distinct from other tools, such as RNAbor, RNAshapes and paRNAss, hence may provide orthogonal information when looking for suboptimal structures or conformational switches. Source code for RNAborMEA can be downloaded from http://sourceforge.net/projects/rnabormea/ or http://bioinformatics.bc.edu/clotelab/RNAborMEA/.

2012-01-01

51

Role for gene sequence, codon bias and mRNA folding energy in modulating structural symmetry of proteins.  

PubMed

Structural symmetry in proteins is commonly observed in the majority of fundamental protein folds. Meanwhile, nascent polypeptide chains of proteins have the potential to start the co-translational folding process and this process can have drastic effects on protein structure. Thus we are interested in understanding mechanisms that gene adopts in specifying structural symmetry in proteins. In the present paper, we reveal that for two representative symmetric proteins from (a?)8-barrel fold and beta-trefoil fold, intragenic symmetry is detected in the corresponding gene sequences. Codon bias and mRNA folding energy might be involved in mediating translation speed for the formation of structural symmetry: at least one major decrease in both codon bias and mRNA folding energy can be observed in the connecting region of the symmetric substructures along the codon sequence. Results suggest that gene duplication and fusion is responsible for structural symmetry in these proteins, and the usage of rare codons or higher order of secondary structure near the boundaries of symmetric substructures might be selected in order to slow down translation speed for effectively co-translational folding process of symmetric proteins. PMID:24109757

Shen, Xiaojuan; Chen, Shixiong; Li, Guanglin

2013-07-01

52

Structural basis for mRNA recognition by elongation factor SelB  

Microsoft Academic Search

In bacteria, incorporation of selenocysteine, the 21st amino acid, into proteins requires elongation factor SelB, which has the unusual property of binding to both transfer RNA (tRNA) and mRNA. SelB binds to an mRNA hairpin formed by the selenocysteine insertion sequence (SECIS) with extremely high specificity, the molecular basis of which has been unknown. We have determined the crystal structure

Linda Rasubala; Toyoyuki Ose; Daisuke Kohda; Dominique Fourmy; Satoko Yoshizawa; Katsumi Maenaka

2005-01-01

53

Peptide-chain secondary structure of bacteriorhodopsin  

SciTech Connect

Ultraviolet circular dichroism spectroscopy in the interval from 190 to 240 nm and infrared spectroscopy in the region of the amide I band (1600 cm/sup -1/ to 1700 cm/sup -1/) has been used to estimate the ..cap alpha..-helix content and the ..beta..-sheet content of bacteriorhodopsin. Circular dichroism spectroscopy strongly suggests that the ..cap 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 confirmation in bacteriorhodopsin. The presence of ..beta..-sheet secondary structure is further suggested by the presence of a 1639 cm/sup -1/ shoulder on the amide I band in the infrared spectrum. Although a structural model consisting of seven ..cap alpha..-helical rods has been generally accepted up to this point, the spectroscopic data are more consistent with a model consisting of five ..cap alpha..-helices and four strands of ..beta..-sheet. The primary amino acid sequence can be assigned to segments of ..cap 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.

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

1983-07-01

54

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

PubMed

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

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

2013-04-24

55

Neural network definitions of highly predictable protein secondary structure classes  

SciTech Connect

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.

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

1994-02-01

56

Characterising RNA secondary structure space using information entropy.  

PubMed

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

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

2013-01-21

57

Simultaneous prediction of protein secondary structure and transmembrane spans.  

PubMed

Prediction of transmembrane spans and secondary structure from the protein sequence is generally the first step in the structural characterization of (membrane) proteins. Preference of a stretch of amino acids in a protein to form secondary structure and being placed in the membrane are correlated. Nevertheless, current methods predict either secondary structure or individual transmembrane states. We introduce a method that simultaneously predicts the secondary structure and transmembrane spans from the protein sequence. This approach not only eliminates the necessity to create a consensus prediction from possibly contradicting outputs of several predictors but bears the potential to predict conformational switches, i.e., sequence regions that have a high probability to change for example from a coil conformation in solution to an ?-helical transmembrane state. An artificial neural network was trained on databases of 177 membrane proteins and 6048 soluble proteins. The output is a 3 × 3 dimensional probability matrix for each residue in the sequence that combines three secondary structure types (helix, strand, coil) and three environment types (membrane core, interface, solution). The prediction accuracies are 70.3% for nine possible states, 73.2% for three-state secondary structure prediction, and 94.8% for three-state transmembrane span prediction. These accuracies are comparable to state-of-the-art predictors of secondary structure (e.g., Psipred) or transmembrane placement (e.g., OCTOPUS). The method is available as web server and for download at www.meilerlab.org. PMID:23349002

Leman, Julia Koehler; Mueller, Ralf; Karakas, Mert; Woetzel, Nils; Meiler, Jens

2013-04-10

58

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

NASA Astrophysics Data System (ADS)

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.

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

2008-12-01

59

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

PubMed Central

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. PACS: 87.10.Pq; 87.15.bk; 87.15.kj; 87.16.dj; 87.16.dr

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

2009-01-01

60

Small changes in free energy assignments for unpaired bases do not affect predicted secondary structures in single stranded RNA.  

PubMed Central

We present extensive calculations of the secondary structure of mRNA which point to its insensitivity to small changes in the free energy assignments of single stranded regions. Truncating the free energies of hairpin loops, bulges, internal loops and multibranched junctions to two significant digits yields structures nearly identical to those generated using three digit values. The results show that one can safely use truncated values in RNA folding calculations. The implementation of these results enabled us to carry out secondary structure calculations on 2600 nucleotides in a single computer run.

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

1982-01-01

61

Structural basis of the PNRC2-mediated link between mrna surveillance and decapping.  

PubMed

Nonsense-mediated mRNA decay (NMD) is an important mRNA surveillance system, and human PNRC2 protein mediates the link between mRNA surveillance and decapping. However, the mechanism by which PNRC2 interacts with the mRNA surveillance machinery and stimulates NMD is unknown. Here, we present the crystal structure of Dcp1a in complex with PNRC2. The proline-rich region of PNRC2 is bound to the EVH1 domain of Dcp1a, while its NR-box mediates the interaction with the hyperphosphorylated Upf1. The mode of PNRC2 interaction with Dcp1a is distinct from those observed in other EVH1/proline-rich ligands interactions. Disruption of the interaction of PNRC2 with Dcp1a abolishes its P-body localization and ability to promote mRNA degradation when tethered to mRNAs. PNRC2 acts in synergy with Dcp1a to stimulate the decapping activity of Dcp2 by bridging the interaction between Dcp1a and Dcp2, suggesting that PNRC2 is a decapping coactivator in addition to its adaptor role in NMD. PMID:23085078

Lai, Tingfeng; Cho, Hana; Liu, Zhou; Bowler, Matthew W; Piao, Shunfu; Parker, Roy; Kim, Yoon Ki; Song, Haiwei

2012-10-18

62

Predicting RNA secondary structures with pseudoknots by MCMC sampling  

Microsoft Academic Search

The most probable secondary structure of an RNA molecule, given the nucleotide sequence, can be computed efficiently if a\\u000a stochastic context-free grammar (SCFG) is used as the prior distribution of the secondary structure. The structures of some\\u000a RNA molecules contain so-called pseudoknots. Allowing all possible configurations of pseudoknots is not compatible with context-free\\u000a grammar models and makes the search for

Dirk Metzler; Markus E. Nebel

2008-01-01

63

A 3' stem/loop structure of the Chlamydomonas chloroplast atpB gene regulates mRNA accumulation in vivo.  

PubMed

The Chlamydomonas reinhardtii chloroplast atpB mRNA contains sequences at its 3' end that can form a complex stem/loop structure. Deletions of part or all of this sequence in transformed C. reinhardtii cells led to decreased atpB mRNA accumulation, whereas transcription rates were unaffected. The reduction of mRNA to 20% to 35% of wild-type levels in transformants without 3' stem/loops was correlated with the accumulation of atpB mRNA that was heterogeneous in size. These results indicated that RNA secondary structures function both in mRNA stabilization and in 3' end formation in C. reinhardtii chloroplasts. Furthermore, deletion of the stem/loop resulted in a decrease in the steady-state level of the ATPase beta-subunit to approximately 60% of wild-type levels, suggesting that translational and/or post-translational mechanisms may influence the steady-state level of the atpB gene product. PMID:1840911

Stern, D B; Radwanski, E R; Kindle, K L

1991-03-01

64

A 3' stem/loop structure of the Chlamydomonas chloroplast atpB gene regulates mRNA accumulation in vivo.  

PubMed Central

The Chlamydomonas reinhardtii chloroplast atpB mRNA contains sequences at its 3' end that can form a complex stem/loop structure. Deletions of part or all of this sequence in transformed C. reinhardtii cells led to decreased atpB mRNA accumulation, whereas transcription rates were unaffected. The reduction of mRNA to 20% to 35% of wild-type levels in transformants without 3' stem/loops was correlated with the accumulation of atpB mRNA that was heterogeneous in size. These results indicated that RNA secondary structures function both in mRNA stabilization and in 3' end formation in C. reinhardtii chloroplasts. Furthermore, deletion of the stem/loop resulted in a decrease in the steady-state level of the ATPase beta-subunit to approximately 60% of wild-type levels, suggesting that translational and/or post-translational mechanisms may influence the steady-state level of the atpB gene product.

Stern, D B; Radwanski, E R; Kindle, K L

1991-01-01

65

The interplay between single-stranded binding proteins on RNA secondary structure  

NASA Astrophysics Data System (ADS)

RNA-protein interactions are critical for Biology because of their regulatory effects on mRNA and protein levels. There are typically several specific protein binding sites on an RNA molecule. A protein can bind one of these sites only if the RNA folds into a structure that leaves the entire binding site free of base pairs. Therefore, a protein binding to an RNA excludes some of the originally permitted RNA structures, causing a change in the structural ensemble. Thus, the probability of another protein to bind the same RNA at a different site will change upon binding of the first protein. To discover such effects, we combine methods of RNA secondary structure prediction with models of protein-RNA interaction. We focus on an RNA molecule with two protein binding sites. The ensemble of secondary structures of random RNA sequences is considered, and numerical calculations show the existence of a semi-long-range interaction between the protein binding sites mediated by the thermodynamics of the RNA structures. A brief analytic argument for this correlation is given, and a phase transition to a high-temperature phase, possibly related to the molten-glass phase transition of secondary RNA structures, is discussed.

Lin, Yi-Hsuan; Bundschuh, Ralf

2013-03-01

66

Pre-mRNA Secondary Structures Influence Exon Recognition  

Microsoft Academic Search

The secondary structure of a pre-mRNA influences a number of processing steps including alternative splicing. Since most splicing regulatory proteins bind to single-stranded RNA, the sequestration of RNA into double strands could prevent their binding. Here, we analyzed the secondary structure context of experimentally determined splicing enhancer and silencer motifs in their natural pre-mRNA context. We found that these splicing

Michael Hiller; Zhaiyi Zhang; Rolf Backofen; Stefan Stamm

2007-01-01

67

A method for rapid similarity analysis of RNA secondary structures  

PubMed Central

Background Owing to the rapid expansion of RNA structure databases in recent years, efficient methods for structure comparison are in demand for function prediction and evolutionary analysis. Usually, the similarity of RNA secondary structures is evaluated based on tree models and dynamic programming algorithms. We present here a new method for the similarity analysis of RNA secondary structures. Results Three sets of real data have been used as input for the example applications. Set I includes the structures from 5S rRNAs. Set II includes the secondary structures from RNase P and RNase MRP. Set III includes the structures from 16S rRNAs. Reasonable phylogenetic trees are derived for these three sets of data by using our method. Moreover, our program runs faster as compared to some existing ones. Conclusion The famous Lempel-Ziv algorithm can efficiently extract the information on repeated patterns encoded in RNA secondary structures and makes our method an alternative to analyze the similarity of RNA secondary structures. This method will also be useful to researchers who are interested in evolutionary analysis.

Liu, Na; Wang, Tianming

2006-01-01

68

The DNA secondary structure of the Bacillus subtilis genome  

Microsoft Academic Search

The entire genomic DNA sequence of the Gram-positive bacterium Bacillus subtilis reported in the SubtiList database has been subjected in this work to a complete bioinformatic analysis of the potential formation of secondary DNA structures such as hairpins and bending. The most significant of these structures have been mapped with respect to their genomic location and compared to those structures

Valentina Tosato; Kresimir Gjuracic; Kristian Vlahovicek; Sandor Pongor; Antoine Danchin; Carlo V. Bruschi

2003-01-01

69

Crystal structure of Dcp1p and its functional implications in mRNA decapping  

Microsoft Academic Search

A major pathway of eukaryotic mRNA turnover begins with deadenylation, followed by decapping and 5??3? exonucleolytic degradation. A critical step in this pathway is decapping, which is carried out by an enzyme composed of Dcp1p and Dcp2p. The crystal structure of Dcp1p shows that it markedly resembles the EVH1 family of protein domains. Comparison of the proline-rich sequence (PRS)-binding sites

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

2004-01-01

70

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

PubMed

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

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

2013-09-19

71

Computer simulation of tRNA secondary structure folding.  

PubMed

Computer simulation results of folding linear RNA molecules into secondary structures are presented. The structure is formed by two interacting processes: the RNA molecular chain growth (beginning from an initial length, L0), and the structuring (secondary structure sequential growth in the region of the existing molecular chain, based on the local free energy minimization by sequential addition of elementary substructures--stems). It was found that the final secondary structure formation is greatly influenced by the 'structuring period' T (the ratio of the molecular chain growth rate to the structuring rate), and the direction of RNA synthesis. The computer simulation has been performed for 219 and 906 tRNA genes from two published catalogues, on the whole two-dimensional domain (T,L0) parameters, by using four known free-energy models. Minimum stem length and molecular chain growth direction have been also varied. The calculated secondary structures have been compared to the natural tRNA structures given in the catalogues, and the region of best coincidence for the model parameters has been determined. It has been proved that, on average, > 86% of the paired bases of natural tRNA structures appear in the folding simulation. PMID:8324625

Kozlov, N N; Kugushev, E I

1993-06-01

72

Metastable structures and refolding kinetics in hok mRNA of plasmid R1.  

PubMed Central

Programmed cell death by hok/sok of plasmid R1 and pnd/pndB of R483 mediates plasmid maintenance by killing of plasmid-free cells. It has been previously suggested that premature translation of the plasmid-mediated toxin is prevented during transcription of the hok and pnd mRNAs by the formation of metastable hairpins in the mRNA at the 5' end. Here, experimental evidence is presented for the existence of metastable structures in the 5' leader of the hok and pnd mRNAs in vitro. The kinetics of refolding from the metastable to the stable structure in the isolated fragments of the 5' ends of both the hok and pnd mRNAs could be estimated, in agreement with the structural rearrangement in this region, as predicted to occur during transcription and mRNA activation. The refolding rates of hok and pnd structures are slow enough to allow for the formation of downstream hairpin structures during elongation of the mRNAs, which thereby helps to stabilize the metastable structures. Thus, the kinetic refolding parameters of the hok and pnd mRNAs are consistent with the proposal that the metastable structures prevent premature translation and/or antisense RNA binding during transcription.

Nagel, J H; Gultyaev, A P; Gerdes, K; Pleij, C W

1999-01-01

73

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

PubMed

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

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

2013-01-24

74

Flexibility in the site of exon junction complex deposition revealed by functional group and RNA secondary structure alterations in the splicing substrate  

Microsoft Academic Search

The exon junction complex (EJC) is critical for mammalian nonsense-mediated mRNA decay and translational regulation, but the mechanism of its stable deposition on mRNA is unknown. To examine requirements for EJC deposition, we created splicing substrates containing either DNA nucleotides or RNA secondary structure in the 59 exon. Using RNase H protection, toeprinting, and coimmunoprecipitation assays, we found that EJC

DENNIS M. MISHLER; ALEXANDER B. CHRIST; JOAN A. STEITZ

2008-01-01

75

RNAstructure: software for RNA secondary structure prediction and analysis  

PubMed Central

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

2010-01-01

76

Crystal Structure of the Lysine Riboswitch Regulatory mRNA Element  

Microsoft Academic Search

Riboswitches are metabolite-sensitive elements found in mRNAs that control gene expression through a regulatory secondary structural switch. Along with regulation of lysine biosynthetic genes, mutations within the lysine-responsive riboswitch (L-box) play a role in the acquisition of resistance to antimicrobial lysine analogs. To understand the structural basis for lysine binding, we have determined the 2.8 resolution crystal structure of lysine

Andrew D. Garst; Annie Heroux; Robert P. Rambo; Robert T. Batey

2008-01-01

77

Predicting Secondary Structural Folding Kinetics for Nucleic Acids  

PubMed Central

Abstract We report a new computational approach to the prediction of RNA secondary structure folding kinetics. In this approach, each elementary kinetic step is represented as the transformation between two secondary structures that differ by a helix. Based on the free energy landscape analysis, we identify three types of dominant pathways and the rate constants for the kinetic steps: 1), formation; 2), disruption of a helix stem; and 3), helix formation with concomitant partial melting of a competing (incompatible) helix. The third pathway, termed the tunneling pathway, is the low-barrier dominant pathway for the conversion between two incompatible helices. Comparisons with experimental data indicate that this new method is quite reliable in predicting the kinetics for RNA secondary structural folding and structural rearrangements. The approach presented here may provide a robust first step for further systematic development of a predictive theory for the folding kinetics for large RNAs.

Zhao, Peinan; Zhang, Wen-Bing; Chen, Shi-Jie

2010-01-01

78

Predicting secondary structural folding kinetics for nucleic acids.  

PubMed

We report a new computational approach to the prediction of RNA secondary structure folding kinetics. In this approach, each elementary kinetic step is represented as the transformation between two secondary structures that differ by a helix. Based on the free energy landscape analysis, we identify three types of dominant pathways and the rate constants for the kinetic steps: 1), formation; 2), disruption of a helix stem; and 3), helix formation with concomitant partial melting of a competing (incompatible) helix. The third pathway, termed the tunneling pathway, is the low-barrier dominant pathway for the conversion between two incompatible helices. Comparisons with experimental data indicate that this new method is quite reliable in predicting the kinetics for RNA secondary structural folding and structural rearrangements. The approach presented here may provide a robust first step for further systematic development of a predictive theory for the folding kinetics for large RNAs. PMID:20409482

Zhao, Peinan; Zhang, Wen-Bing; Chen, Shi-Jie

2010-04-21

79

A Bayesian Statistical Algorithm for RNA Secondary Structure Prediction  

Microsoft Academic Search

A Bayesian approach for predicting RNA secondary structure that addresses the following three open issues is described: (1) the need for a representation of the full ensemble of probable structures; (2) the need to specify a fixed set of energy parameters; (3) the desire to make statistical inferences on all variables in the problem. It has recently been shown that

Ye Ding; Charles E. Lawrence

1999-01-01

80

Coating concrete secondary containment structures exposed to agrichemicals  

Microsoft Academic Search

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

M. F. Broder; D. T. Nguyen

1995-01-01

81

Identification of consensus RNA secondary structures using suffix arrays  

Microsoft Academic Search

BACKGROUND: The identification of a consensus RNA motif often consists in finding a conserved secondary structure with minimum free energy in an ensemble of aligned sequences. However, an alignment is often difficult to obtain without prior structural information. Thus the need for tools to automate this process. RESULTS: We present an algorithm called Seed to identify all the conserved RNA

Mohammad Anwar; Truong Nguyen; Marcel Turcotte

2006-01-01

82

Automated Discovery of Active Motifs in Multiple RNA Secondary Structures  

Microsoft Academic Search

In this paper we present a method for discovering ap- proximately common motifs (also known as active mo- tifs) in multiple RNA secondary structures. The sec- ondary structures can be represented as ordered trees (i.e., the order among siblings matters). Motifs in these trees are connected subgraphs that can differ in both substitutions and deletions\\/insertions. The pro- posed method consists

Jason Tsong-li Wang; Bruce A. Shapiro; Dennis Shasha; Kaizhong Zhang; Chia-yo Chang

1996-01-01

83

Synthesis of 13C- and 14C-labeled dinucleotide mRNA cap analogues for structural and biochemical studies  

PubMed Central

Herein we describe the first simple and short method for specific labeling of mono- and trimethylated dinucleotide mRNA cap analogues with 13C and 14C isotopes. The labels were introduced within the cap structures either at the N7 for monomethylguanosine cap or N7 and N2 position for trimethylguanosine cap. The compounds designed for structural and biochemical studies will be useful tools for better understanding the role of the mRNA cap structures in pre-mRNA splicing, nucleocytoplasmic transport, translation initiation and mRNA degradation.

Piecyk, Karolina; Davis, Richard E.; Jankowska-Anyszka, Marzena

2013-01-01

84

Transitions between secondary structures in isolated polyalanines  

NASA Astrophysics Data System (ADS)

Monte Carlo simulations of gas-phase polyalanine peptides have been carried out with the Amber ff96 force field. A low-temperature structural transition takes place between the ?-helix stable conformation and ?-sheet structures, followed by the unfolding phase change. The transition state ensembles connecting the helix and sheet conformations are investigated by sampling the energy landscape along specific geometric order parameters as putative reaction coordinates, namely the electric dipole ?, the end-to-end distance d, and the gyration radius Rg. By performing series of shooting trajectories, the committor probabilities and their distributions are obtained, revealing that only the electric dipole provides a satisfactory transition coordinate for the ??? interconversion. The nucleus at the transition is found to have a high helical content.

Calvo, F.; Poulain, P.

2009-01-01

85

Quantifying variances in comparative RNA secondary structure prediction  

PubMed Central

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

2013-01-01

86

Improving the accuracy of protein secondary structure prediction using structural alignment  

Microsoft Academic Search

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

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

2006-01-01

87

Assessment of Gaussian Radial Basis Function Network on Protein Secondary Structures.  

National Technical Information Service (NTIS)

Studies of the radial basis function (RBF) network on protein secondary structures are presented. Secondary structure prediction is a useful first step in understanding how the amino acid sequence of protein determines the native state. If the secondary s...

T. Ibrikci M. Guler M. Acikkar

2001-01-01

88

Translation of the psbA mRNA of Chlamydomonas reinhardtii requires a structured RNA element contained within the 5' untranslated region  

PubMed Central

Translational regulation is a key modulator of gene expression in chloroplasts of higher plants and algae. Genetic analysis has shown that translation of chloroplast mRNAs requires nuclear-encoded factors that interact with chloroplastic mRNAs in a message-specific manner. Using site-specific mutations of the chloroplastic psbA mRNA, we show that RNA elements contained within the 5' untranslated region of the mRNA are required for translation. One of these elements is a Shine- Dalgarno consensus sequence, which is necessary for ribosome association and psbA translation. A second element required for high levels of psbA translation is located adjacent to and upstream of the Shine-Dalgarno sequence, and maps to the location on the RNA previously identified as the site of message-specific protein binding. This second element appears to act as a translational attenuator that must be overcome to activate translation. Mutations that affect the secondary structure of these RNA elements greatly reduce the level of psbA translation, suggesting that secondary structure of these RNA elements plays a role in psbA translation. These data suggest a mechanism for translational activation of the chloroplast psbA mRNA in which an RNA element containing the ribosome-binding site is bound by message- specific RNA binding proteins allowing for increased ribosome association and translation initiation. These elements may be involved in the light-regulated translation of the psbA mRNA.

1994-01-01

89

Improving protein secondary structure prediction with aligned homologous sequences.  

PubMed Central

Most recent protein secondary structure prediction methods use sequence alignments to improve the prediction quality. We investigate the relationship between the location of secondary structural elements, gaps, and variable residue positions in multiple sequence alignments. We further investigate how these relationships compare with those found in structurally aligned protein families. We show how such associations may be used to improve the quality of prediction of the secondary structure elements, using the Quadratic-Logistic method with profiles. Furthermore, we analyze the extent to which the number of homologous sequences influences the quality of prediction. The analysis of variable residue positions shows that surprisingly, helical regions exhibit greater variability than do coil regions, which are generally thought to be the most common secondary structure elements in loops. However, the correlation between variability and the presence of helices does not significantly improve prediction quality. Gaps are a distinct signal for coil regions. Increasing the coil propensity for those residues occurring in gap regions enhances the overall prediction quality. Prediction accuracy increases initially with the number of homologues, but changes negligibly as the number of homologues exceeds about 14. The alignment quality affects the prediction more than other factors, hence a careful selection and alignment of even a small number of homologues can lead to significant improvements in prediction accuracy.

Di Francesco, V.; Garnier, J.; Munson, P. J.

1996-01-01

90

Ensemble-based prediction of RNA secondary structures  

PubMed Central

Background Accurate structure prediction methods play an important role for the understanding of RNA function. Energy-based, pseudoknot-free secondary structure prediction is one of the most widely used and versatile approaches, and improved methods for this task have received much attention over the past five years. Despite the impressive progress that as been achieved in this area, existing evaluations of the prediction accuracy achieved by various algorithms do not provide a comprehensive, statistically sound assessment. Furthermore, while there is increasing evidence that no prediction algorithm consistently outperforms all others, no work has been done to exploit the complementary strengths of multiple approaches. Results In this work, we present two contributions to the area of RNA secondary structure prediction. Firstly, we use state-of-the-art, resampling-based statistical methods together with a previously published and increasingly widely used dataset of high-quality RNA structures to conduct a comprehensive evaluation of existing RNA secondary structure prediction procedures. The results from this evaluation clarify the performance relationship between ten well-known existing energy-based pseudoknot-free RNA secondary structure prediction methods and clearly demonstrate the progress that has been achieved in recent years. Secondly, we introduce AveRNA, a generic and powerful method for combining a set of existing secondary structure prediction procedures into an ensemble-based method that achieves significantly higher prediction accuracies than obtained from any of its component procedures. Conclusions Our new, ensemble-based method, AveRNA, improves the state of the art for energy-based, pseudoknot-free RNA secondary structure prediction by exploiting the complementary strengths of multiple existing prediction procedures, as demonstrated using a state-of-the-art statistical resampling approach. In addition, AveRNA allows an intuitive and effective control of the trade-off between false negative and false positive base pair predictions. Finally, AveRNA can make use of arbitrary sets of secondary structure prediction procedures and can therefore be used to leverage improvements in prediction accuracy offered by algorithms and energy models developed in the future. Our data, MATLAB software and a web-based version of AveRNA are publicly available at http://www.cs.ubc.ca/labs/beta/Software/AveRNA.

2013-01-01

91

Structural investigation of the proton-coupled secondary transporters.  

PubMed

Transmembrane proton gradients, known as Proton Motive Force (PMF), serve important physiological functions. In addition to driving ATP synthesis, PMF is harnessed by a large variety of secondary transporters to achieve 'uphill' translocation of specific substrates across the membrane. Proton-coupled secondary transporters, including both symporters and antiporters, are widely involved in nutrient uptake and metabolite expulsion, multidrug resistance, and the maintenance of electrolyte homeostasis. Structural studies have led to the identification of several new folds for proton co-transporters, and establish an important framework for the mechanistic understanding of proton-dependent substrate transport. This review focuses on recent advances in the structural elucidation of proton-coupled secondary transporters. PMID:23806360

Yan, Nieng

2013-06-24

92

Clustering to identify RNA conformations constrained by secondary structure  

PubMed Central

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

Sim, Adelene Y. L.; Levitt, Michael

2011-01-01

93

Using circular dichroism spectra to estimate protein secondary structure  

Microsoft Academic Search

Circular dichroism (CD) is an excellent tool for rapid determination of the secondary structure and folding properties of proteins that have been obtained using recombinant techniques or purified from tissues. The most widely used applications of protein CD are to determine whether an expressed, purified protein is folded, or if a mutation affects its conformation or stability. In addition, it

Norma J Greenfield

2007-01-01

94

RNALOSS: a web server for RNA locally optimal secondary structures  

Microsoft Academic Search

RNAomics, analogous to proteomics, concerns aspects of the secondary and tertiary structure, fold- ing pathway, kinetics, comparison, function and regulation of all RNA in a living organism. Given recently discovered roles played by micro RNA, small interfering RNA, riboswitches, ribozymes, etc., it is important to gain insight into the fold- ing process of RNA sequences. We describe the web server

P. Clote

2005-01-01

95

Thickness-dependent secondary structure formation of tubelike polymers  

NASA Astrophysics Data System (ADS)

By means of sophisticated Monte Carlo methods, we investigate the conformational phase diagram of a simple model for flexible polymers with explicit thickness. The thickness constraint, which is introduced geometrically via the global radius of curvature of a polymer conformation, accounts for the excluded volume of the polymer and induces cooperative effects supporting the formation of secondary structures. In our detailed analysis of the temperature and thickness dependence of the conformational behavior for classes of short tubelike polymers, we find that known secondary-structure segments like helices and turns, but also ringlike conformations and stiff rods are dominant intrinsic topologies governing the phase behavior of such cooperative tubelike objects. This shows that the thickness constraint is indeed a fundamental physical parameter that allows for a classification of generic polymer structures.

Vogel, T.; Neuhaus, T.; Bachmann, M.; Janke, W.

2009-01-01

96

Light can transform the secondary structure of silk protein  

NASA Astrophysics Data System (ADS)

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

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

97

A cytosolic Protein Binds to Structural Elements within the Iron Regulatory Region of the Transferrin Receptor mRNA  

Microsoft Academic Search

The level of mRNA encoding the transferrin receptor (TfR) is regulated by iron, and this regulation is mediated by a portion of the 3' untranslated region (UTR) of the TfR transcript. This portion of 3' UTR of the human TfR mRNA contains five RNA elements that have structural similarity to the iron-responsive element (IRE) found as a single copy in

David M. Koeller; John L. Casey; Matthias W. Hentze; Elizabeth M. Gerhardt; Lee-Nien L. Chan; Richard D. Klausner; Joe B. Harford

1989-01-01

98

Reduction of the secondary structure topological space through direct estimation of the contact energy formed by the secondary structures  

PubMed Central

Background Electron cryomicroscopy is a fast developing technique aiming at the determination of the 3-dimensional structures of large protein complexes. Using this technique, protein density maps can be generated with 6 to 10 Å resolution. At such resolutions, the secondary structure elements such as helices and ?-strands appear to be skeletons and can be computationally detected. However, it is not known which segment of the protein sequence corresponds to which of the skeletons. The topology in this paper refers to the linear order and the directionality of the secondary structures. For a protein with N helices and M strands, there are (N!2N)(M!2M) different topologies, each of which maps N helix segments and M strand segments on the protein sequence to N helix and M strand skeletons. Since the backbone position is not available in the skeleton, each topology of the skeletons corresponds to additional freedom to position the atoms in the skeletons. Results We have developed a method to construct the possible atomic structures for the helix skeletons by sampling the solution space of all the possible topologies of the skeletons. Our method also ranks the possible structures based on the contact energy formed by the secondary structures, rather than the entire chain. If we assume that the backbone atomic positions are known for the skeletons, then the native topology of the secondary structures can be found in the top 30% of the ranked list of all possible topologies for all the 30 proteins tested, and within the top 5% for most of the 30 proteins. Without assuming the backbone location of the skeletons, the possible atomic structures of the skeletons can be constructed using the axis of the skeleton and the sequence segments. The best constructed structure for the skeletons has RMSD to native between 4 and 5 Å for the four tested ?-proteins. These best constructed structures were ranked the 17th, 31st, 16th and 5th respectively for the four proteins out of 32066, 391833, 98755 and 192935 possible assignments in the pool. Conclusion Our work suggested that the direct estimation of the contact energy formed by the secondary structures is quite effective in reducing the topological space to a small subset that includes a near native structure for the skeletons.

Sun, Weitao; He, Jing

2009-01-01

99

Predicting secondary structures of membrane proteins with neural networks.  

PubMed

Back-propagation, feed-forward neural networks are used to predict the secondary structures of membrane proteins whose structures are known to atomic resolution. These networks are trained on globular proteins and can predict globular protein structures having no homology to those of the training set with correlation coefficients (Ci) of 0.45, 0.32 and 0.43 for alpha-helix, beta-strand and random coil structures, respectively. When tested on membrane proteins, neural networks trained on globular proteins do, on average, correctly predict (Qi) 62%, 38% and 69% of the residues in the alpha-helix, beta-strand and random coil structures. These scores rank higher than those obtained with the currently used statistical methods and are comparable to those obtained with the joint approaches tested so far on membrane proteins. The lower success score for beta-strand as compared to the other structures suggests that the sample of beta-strand patterns contained in the training set is less representative than those of alpha-helix and random coil. Our analysis, which includes the effects of the network parameters and of the structural composition of the training set on the prediction, shows that regular patterns of secondary structures can be successfully extrapolated from globular to membrane proteins. PMID:8513752

Fariselli, P; Compiani, M; Casadio, R

1993-01-01

100

Integrating Chemical Footprinting Data into RNA Secondary Structure Prediction  

PubMed Central

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

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

2012-01-01

101

Accurate SHAPE-directed RNA secondary structure modeling, including pseudoknots  

PubMed Central

A pseudoknot forms in an RNA when nucleotides in a loop pair with a region outside the helices that close the loop. Pseudoknots occur relatively rarely in RNA but are highly overrepresented in functionally critical motifs in large catalytic RNAs, in riboswitches, and in regulatory elements of viruses. Pseudoknots are usually excluded from RNA structure prediction algorithms. When included, these pairings are difficult to model accurately, especially in large RNAs, because allowing this structure dramatically increases the number of possible incorrect folds and because it is difficult to search the fold space for an optimal structure. We have developed a concise secondary structure modeling approach that combines SHAPE (selective 2?-hydroxyl acylation analyzed by primer extension) experimental chemical probing information and a simple, but robust, energy model for the entropic cost of single pseudoknot formation. Structures are predicted with iterative refinement, using a dynamic programming algorithm. This melded experimental and thermodynamic energy function predicted the secondary structures and the pseudoknots for a set of 21 challenging RNAs of known structure ranging in size from 34 to 530 nt. On average, 93% of known base pairs were predicted, and all pseudoknots in well-folded RNAs were identified.

Hajdin, Christine E.; Bellaousov, Stanislav; Huggins, Wayne; Leonard, Christopher W.; Mathews, David H.; Weeks, Kevin M.

2013-01-01

102

Random generation of RNA secondary structures according to native distributions  

PubMed Central

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

2011-01-01

103

Extracting physicochemical features to predict protein secondary structure.  

PubMed

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

Huang, Yin-Fu; Chen, Shu-Ying

2013-05-14

104

Extracting Physicochemical Features to Predict Protein Secondary Structure  

PubMed Central

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, Q3 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.

Chen, Shu-Ying

2013-01-01

105

Using circular dichroism spectra to estimate protein secondary structure  

PubMed Central

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

Greenfield, Norma J.

2009-01-01

106

Structure of secondary cast aluminum alloys obtained by granulation  

Microsoft Academic Search

1.After crystallization of secondary alloys AK5M2 and AK4M4 by granulation the size of dendritic cells is an order lower and that of excess phases 5–7 times smaller than in ingots of the alloys cast in chill molds. The structural components are evenly distributed; initial crystallization of brittle phases containing iron and manganese is suppressed.2.The concentration of alloying elements in the

P. A. Parkhutik; M. Z. Lubenskii; V. G. Badaev; L. P. Seleznev

1980-01-01

107

Coating concrete secondary containment structures exposed to agrichemicals  

SciTech Connect

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.

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

1995-06-01

108

Trypanosoma brucei ATPase subunit 6 mRNA bound to gA6-14 forms a conserved three-helical structure  

PubMed Central

T. brucei survival relies on the expression of mitochondrial genes, most of which require RNA editing to become translatable. In trypanosomes, RNA editing involves the insertion and deletion of uridylates, a developmentally regulated process directed by guide RNAs (gRNAs) and catalyzed by the editosome, a complex of proteins. The pathway for mRNA/gRNA complex formation and assembly with the editosome is still unknown. Work from our laboratory has suggested that distinct mRNA/gRNA complexes anneal to form a conserved core structure that may be important for editosome assembly. The secondary structure for the apocytochrome b (CYb) pair has been previously determined and is consistant with our model of a three-helical structure. Here, we used cross-linking and solution structure probing experiments to determine the structure of the ATPase subunit 6 (A6) mRNA hybridized to its cognate gA6-14 gRNA in different stages of editing. Our results indicate that both unedited and partially edited A6/gA6-14 pairs fold into a three-helical structure similar to the previously characterized CYb/gCYb-558 pair. These results lead us to conclude that at least two mRNA/gRNA pairs with distinct editing sites and distinct primary sequences fold to a three-helical secondary configuration that persists through the first few editing events.

Reifur, Larissa; Koslowsky, Donna J.

2008-01-01

109

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

Microsoft Academic Search

Comparative analysis is the preferred method of inferring RNA secondary structure, but its use requires considerable expertise and manual effort. As the importance of secondary structure for accurate sequence alignment and phylogenetic analysis becomes increasingly realised, the need for secondary structure models for diverse taxonomic groups becomes more pressing. The number of available structures bears little relation to the relative

Roderic D. M. Page

2000-01-01

110

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

PubMed

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

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

2013-09-30

111

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

PubMed Central

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

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

2013-01-01

112

Study of coal structure using secondary ion mass spectrometry  

SciTech Connect

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

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

1980-12-01

113

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

PubMed Central

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.

Wang, Yeming; Opperman, Laura; Wickens, Marvin; Hall, Traci M. Tanaka

2009-01-01

114

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

SciTech Connect

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.

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

2011-11-02

115

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

SciTech Connect

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.

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

2010-08-19

116

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

SciTech Connect

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.

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

2011-12-31

117

Hierarchical Protein Structure Superposition Using Both Secondary Structure and Atomic Representations  

Microsoft Academic Search

The structural comparison of proteins has become increasingly important as a means to identify protein motifs and fold families. In this paper we present a new algorithm for the comparison of proteins based on a hierarchy of structural representations, from the secondary structure level to the atomic level. Our technique represents ?-helices and ?-strands as vectors and uses a set

Amit Pal Singh; Douglas L. Brutlag

1997-01-01

118

Quantitative DMS mapping for automated RNA secondary structure inference  

PubMed Central

For decades, dimethyl sulfate (DMS) mapping has informed manual modeling of RNA structure in vitro and in vivo. Here, we incorporate DMS data into automated secondary structure inference using an energy minimization framework developed for 2?-OH acylation (SHAPE) map-ping. On six non-coding RNAs with crystallographic models, DMS-guided modeling achieves overall false negative and false discovery rates of 9.5% and 11.6%, comparable or better than SHAPE-guided modeling; and bootstrapping provides straightforward confidence estimates. Integrating DMS/SHAPE data and including CMCT reactivities give small additional improvements. These results establish DMS mapping – an already routine technique – as a quantitative tool for unbiased RNA structure modeling.

Cordero, Pablo; Kladwang, Wipapat; VanLang, Christopher C.; Das, Rhiju

2012-01-01

119

Novel scales based on hydrophobicity indices for secondary protein structure.  

PubMed

This paper is concerned with a branch of computational biology related to protein prediction and analysis of secondary structure of proteins. Although traditional methods use a simple amino acid composition to predict the secondary structure content, hydrophobicity has been recently found to improve the results in this and several related prediction tasks. To this end, we propose and analyze advantages of two new hydrophobicity index-based scales that incorporate information about long-range interactions along the protein sequence and contrast them with currently used raw hydrophobic index values. We also compare three leading hydrophobicity indices, i.e., Eisenberg's, Fauchere-Pliska's, and Cid's, using the proposed scales. The analysis is performed using fuzzy cognitive maps that quantify the strength of relation between the hydrophobicity scales/indices and the protein content values. A set of empirical tests that involve generation of fuzzy cognitive map models for a set of 200 low homology proteins have been performed. The results show that the secondary structure content along the protein sequence is characterized by about 2.5 times stronger relation with the two proposed hydrophobicity scales when compared with the currently used raw index values. The new scales exhibit stronger relation irrespective of the applied hydrobhobicity indices. Analysis of different scales shows superiority of the Eisenberg's hydrophobicity index, when used with the new scales. In contrast, the Fauchere-Pliska's index is found to perform better when compared with the two other indices when using raw hydrophobic index values that disregard the long-range interactions. PMID:17572446

Kurgan, Lukasz A; Stach, Wojciech; Ruan, Jishou

2007-05-18

120

[RNA secondary structure dynamics and genetic vector symmetry].  

PubMed

The sequence of nucleotides in a single-stranded RNA molecule is represented by a complex vector, whose k-th component corresponds to the k-th base of the sequence ordered in the 5'3' direction. An analysis of the proposed formalisms permits to predict a new type of reversible conformational transitions between the secondary structure patterns of RNA which may have an oscillatory character. A possible experimental approach based on the ESR technique for recording and time-scale estimation of these transitions is proposed. PMID:7682446

Magarshak, Iu; Benem, G; Malinski?, L; Bliumenfel'd, L A

121

Evolution of conserved secondary structures and their function in transcriptional regulation networks  

Microsoft Academic Search

BACKGROUND: Many conserved secondary structures have been identified within conserved elements in the human genome, but only a small fraction of them are known to be functional RNAs. The evolutionary variations of these conserved secondary structures in human populations and their biological functions have not been fully studied. RESULTS: We searched for polymorphisms within conserved secondary structures and identified a

Hai-Bing Xie; David M. Irwin; Ya-Ping Zhang

2008-01-01

122

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

ERIC Educational Resources Information Center

|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…

Ellington, Roni; Wachira, James; Nkwanta, Asamoah

2010-01-01

123

A phase transition in energy-filtered RNA secondary structures.  

PubMed

In this article we study the effect of energy parameters on minimum free energy (mfe) RNA secondary structures. Employing a simplified combinatorial energy model that is only dependent on the diagram representation and is not sequence-specific, we prove the following dichotomy result. Mfe structures derived via the Turner energy parameters contain only finitely many complex irreducible substructures, and just minor parameter changes produce a class of mfe structures that contain a large number of small irreducibles. We localize the exact point at which the distribution of irreducibles experiences this phase transition from a discrete limit to a central limit distribution and, subsequently, put our result into the context of quantifying the effect of sparsification of the folding of these respective mfe structures. We show that the sparsification of realistic mfe structures leads to a constant time and space reduction, and that the sparsification of the folding of structures with modified parameters leads to a linear time and space reduction. We, furthermore, identify the limit distribution at the phase transition as a Rayleigh distribution. PMID:23057821

Han, Hillary S W; Reidys, Christian M

2012-10-01

124

Expression, purification, and secondary structure characterization of recombinant KCTD1.  

PubMed

Potassium channel tetramerization domain containing 1 (KCTD1) contains a BTB domain, which can facilitate protein-protein interactions that may be involved in the regulation of signaling pathways. Here we describe an expression and purification system that can provide a significant amount of recombinant KCTD1 from Escherichia coli. The cDNA encoding human KCTD1 was amplified and cloned into the expression vector pET-30a(+). The recombinant protein was expressed in E. coli BL21(DE3) cells and subsequently purified using affinity chromatography. To confirm that KCTD1 was correctly expressed and folded, the molecular weight and conformation were analyzed using mass spectroscopy, Western blot, and circular dichroism. Optimizing KCTD1 expression and investigating its secondary structure will provide valuable information for future structural and functional studies of KCTD1 and KCTD family proteins. PMID:22860917

Mei, Fanghua; Xiang, Jin; Han, Song; He, Yuan; Lu, Yajing; Xu, Jian; Guo, Deyin; Xiao, Gengfu; Tien, Po; Sun, Guihong

2012-08-01

125

Performance of secondary structure prediction methods on proteins containing structurally ambivalent sequence fragments.  

PubMed

Several approaches for predicting secondary structures from sequences have been developed and reached a fair accuracy. One of the most rigorous tests for these prediction methods is their ability to correctly predict identical fragments of protein sequences adopting different secondary structures in unrelated proteins. In our previous work, we obtained 30 identical octapeptide sequence fragments adopting different backbone conformations. It is of interest to find whether the presence of structurally ambivalent fragments in proteins will affect the accuracy of secondary structure prediction methods or not. Hence, in this work, we have made a systematic comparative analysis on secondary structure prediction results of 30 identical octapeptide pairs and 52 identical heptapeptide pairs adopting different conformations with the aid of segment overlap measure. The results reveal the better performance of profile-based methods such as PSIpred and JPred and misprediction by classical rule-based methods such as Garnier Osguthorpe Robson Method and Double Prediction Method. The results discussed here insist that modern secondary structure prediction methods are able to better discriminate conformationally ambivalent peptide fragments. © 2012 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 100: 148-153, 2013. PMID:23616098

Saravanan, K Mani; Selvaraj, Samuel

2013-04-01

126

Rabbit milk protein genes: from mRNA identification to chromatin structure.  

PubMed

Milk protein genes are among the most intensively expressed and they are active only in epithelial mammary cells of lactating animals. They code for proteins which represent 30% of the proteins consumed by humans in developed countries. Mammary gland development occurs essentially during each pregnancy. This offers experimenters attractive models to study the expression mechanisms of genes controlled by known hormones and factors (prolactin, glucocorticoids, progesterone, insulin-like growth factor-1 and others) as well as extracellular matrix. In the mid-1970s, it became possible to identify and quantify mRNAs from higher living organisms using translation in reticulocyte lysate. A few years later, the use of radioactive cDNAs as probes made it possible for the quantification of mRNA in various physiological situations using hybridisation in the liquid phase. Gene cloning offered additional tools to measure milk protein mRNAs and also to identify transcription factors. Gene transfer in cultured mammary cells and in animals contributed greatly to these studies. It is now well established that most if not all genes of higher eukaryotes are under the control of multiple distal regulatory elements and that local modifications of the chromatin structure play an essential role in the mechanisms of differentiation from embryos to adults. The technique, known as ChIP (chromatin immunoprecipitation), is being implemented to identify the factors that modify chromatin structure at the milk protein gene level during embryo development, mammogenesis and lactogenesis, including the action of hormones and extracellular matrix. Transgenesis is not just a tool to study gene regulation and function, it is also currently used for various biotechnological applications including the preparation of pharmaceutical proteins in milk. This implies the design of efficient vectors capable of directing the secretion of recombinant proteins in milk at a high concentration. Milk protein gene promoters and long genomic-DNA fragments containing essentially all the regulatory elements of milk protein genes are used to optimise recombinant protein production in milk. PMID:22445034

Jolivet, G; Daniel-Carlier, N; Thépot, D; Rival-Gervier, S; Houdebine, L M

2008-03-01

127

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

PubMed

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

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

2011-11-29

128

Incorporating secondary structural features into sequence information for predicting protein structural class.  

PubMed

Knowledge of structural classes is applied in numerous important predictive tasks that address structural and functional features of proteins, although the prediction accuracy of the protein structural classes is not high. In this study, 45 different features were rationally designed to model the differences between protein structural classes, among which, 30 of them reflect the combined protein sequence information. In terms of correlation function, the protein sequence can be converted to a digital signal sequence, from which we can generate 20 discrete Fourier spectrum numbers. According to the segments of amino with different characteristics occurring in protein sequences, the frequencies of the 10 kinds of segments of amino acid (motifs) in protein are calculated. Other features include the secondary structural information :10 features were proposed to model the strong adjacent correlations in the secondary structural elements and capture the long-range spatial interactions between secondary structures, other 5 features were designed to differentiate ?/? from ?+? classes , which is a major problem of the existing algorithm. The methods were proposed based on a large set of low-identity sequences for which secondary structure is predicted from their sequence (based on PSI-PRED). By means of this method, the overall prediction accuracy of four benchmark datasets were all improved. Especially for the dataset FC699, 25PDB and D1189 which are 1.26%, 1% and 0.85% higher than the best previous method respectively. PMID:23688152

Liao, Bo; Peng, Ting; Chen, Haowen; Lin, Yaping

2013-10-01

129

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

PubMed

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

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

2012-10-03

130

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

PubMed Central

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

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

2013-01-01

131

Secondary Structure of Huntingtin Amino-Terminal Region  

SciTech Connect

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.

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

2010-09-21

132

Secondary structure of the r(CUUCGG) tetraloop.  

PubMed Central

The oligonucleotide r(GGACUUCGGUCC) has been observed to adopt a hairpin conformation by solution NMR and a double helical conformation by X-ray diffraction. In order to understand this apparent conflict, we used time-resolved fluorescence depolarization and 19fluorine NMR to follow the secondary structure of this dodecamer as the solution composition was changed stepwise from the NMR experimental conditions to those used for crystallization. Calculation of the dodecamer concentration in the crystal (180 mM strands) and the cation concentration needed for neutrality (>2 M) prompted investigation of a tethered species, in which two dodecamers are connected by a string of 4 nt, geometrically equivalent to approximately 100 mM strands, in 2.5 M NaCl. The RNA tetraloop and its DNA analog maintain a single-strand hairpin conformation in solution, even under the conditions used to grow the crystal. Under high salt conditions, the tethered RNA and DNA analogs of this sequence yield secondary components which could be the double helical conformation. Crystal contacts in addition to solvent changes and high RNA concentrations are needed to obtain the double helix as the predominant species.

Kanyo, J E; Duhamel, J; Lu, P

1996-01-01

133

A Feature Selection Algorithm Based on Graph Theory and Random Forests for Protein Secondary Structure Prediction  

Microsoft Academic Search

Protein secondary structure prediction problem is one of the widely studied problems in bioinformatics. Predicting the secondary\\u000a structure of a protein is an important step for determining its tertiary structure and thus its function. This paper explores\\u000a the protein secondary structure problem using a novel feature selection algorithm combined with a machine learning approach\\u000a based on random forests. For feature

Gulsah Altun; Hae-jin Hu; Stefan Gremalschi; Robert W. Harrison; Yi Pan

2007-01-01

134

Structure-function studies of nucleocytoplasmic transport of retroviral genomic RNA by mRNA export factor TAP  

PubMed Central

Messenger RNA 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 mediate 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 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 nuclear export of viral genomic RNAs, and more generally, provide insights on cargo RNA recognition by mRNA export receptors.

Teplova, Marianna; Wohlbold, Lara; Khin, Nyan W.; Izaurralde, Elisa; Patel, Dinshaw J.

2011-01-01

135

A 3' StemlLoop Structure of the Chkmydomonas Chloroplast atpB Gene Regulates mRNA Accumulation in Vivo  

Microsoft Academic Search

The Chlamydomonas reinhardfii chloroplast afp6 mRNA contains sequences at its 3' end that can form a complex stem\\/loop structure. Deletions of part or all of this sequence in transformed C. reinhardfii cells led to decreased atp6 mRNA accumulation, whereas transcription rates were unaffected. The reduction of mRNA to 20% to 35% of wild-type levels in transformants without 3' stem\\/loops was

David B. Stern; Elaine R. Radwanski; Karen L. Kindleb

1991-01-01

136

Structural Compartments within Neurons: Developmentally Regulated Organization of Microfilament Isoform mRNA and Protein  

Microsoft Academic Search

The microfilament system is thought to be a crucial cytoskeletal component regulating development and mature function of neurons. The intracellular distribution of the microfilament isoform components, actin and tropomyosin (Tm), in neurons primarilyin vivo,has been investigated at both the mRNA and the protein level using isoform specific riboprobes and antibodies. Ourin vivoandin vitrostudies have identified at least six neuronal compartments

Anthony J. Hannan; Peter Gunning; Peter L. Jeffrey; Ron P. Weinberger

1998-01-01

137

Synchrotron radiation circular dichroism spectroscopy of proteins: secondary structure, fold recognition and structural genomics  

Microsoft Academic Search

Recent developments in instrumentation and bioinformatics show that the technique of synchrotron radiation circular dichroism spectroscopy can provide novel information on protein secondary structures and folding motifs, and has the potential to play an important role in structural genomics studies, both as a means of target selection and as a high-throughput, low-sample-requiring screening method. This is possible because of the

B. A Wallace; Robert W Janes

2001-01-01

138

Synchronous visual analysis and editing of RNA sequence and secondary structure alignments using 4SALE  

Microsoft Academic Search

BACKGROUND: The function of a noncoding RNA sequence is mainly determined by its secondary structure and therefore a family of noncoding RNA sequences is much more conserved on the structural level than on the sequence level. Understanding the function of noncoding RNA sequence families requires two things: a hand-crafted or hand-improved alignment and detailed analyses of the secondary structures. There

Philipp N Seibel; Tobias Müller; Thomas Dandekar; Matthias Wolf

2008-01-01

139

Structure of the histone mRNA hairpin required for cell cycle regulation of histone gene expression.  

PubMed Central

Expression of replication-dependent histone genes requires a conserved hairpin RNA element in the 3' untranslated regions of poly(A)-less histone mRNAs. The 3' hairpin element is recognized by the hairpin-binding protein or stem-loop-binding protein (HBP/SLBP). This protein-RNA interaction is important for the endonucleolytic cleavage generating the mature mRNA 3' end. The 3' hairpin and presumably HBP/SLBP are also required for nucleocytoplasmic transport, translation, and stability of histone mRNAs. RNA 3' processing and mRNA stability are both regulated during the cell cycle. Here, we have determined the three-dimensional structure of a 24-mer RNA comprising a mammalian histone RNA hairpin using heteronuclear multidimensional NMR spectroscopy. The hairpin adopts a novel UUUC tetraloop conformation that is stabilized by base stacking involving the first and third loop uridines and a closing U-A base pair, and by hydrogen bonding between the first and third uridines in the tetraloop. The HBP interaction of hairpin RNA variants was analyzed in band shift experiments. Particularly important interactions for HBP recognition are mediated by the closing U-A base pair and the first and third loop uridines, whose Watson-Crick functional groups are exposed towards the major groove of the RNA hairpin. The results obtained provide novel structural insight into the interaction of the histone 3' hairpin with HBP, and thus the regulation of histone mRNA metabolism.

Zanier, Katia; Luyten, Ingrid; Crombie, Catriona; Muller, Berndt; Schumperli, Daniel; Linge, Jens P; Nilges, Michael; Sattler, Michael

2002-01-01

140

Probing translation initiation through ligand binding to the 5' mRNA coding region.  

PubMed

Secondary structure matters: We have constructed artificial intragenic riboswitches to probe ribosome accessibility to the 5' mRNA coding region at three-base resolution in Escherichia coli. We show that only mRNA folding stability in the +1 to +15 nt region affects the translation process. PMID:22927129

Jo, Joon-Jung; Kim, Joo-Hee; Shin, Jong-Shik

2012-08-24

141

Fast SCOP Classification of Structural Class and Fold Using Secondary Structure Mining in Distance Matrix  

NASA Astrophysics Data System (ADS)

It is an urgent need to understand the structure-function relationship in proteomic era. One of the important techniques to meet this demand is to analyze and represent the spatial structure of domain which is the functional unit of the whole protein, and perform fast domain classification. In this paper, we introduce a novel method of rapid domain classification. Instead of analyzing directly protein sequence or 3-D tertiary structure, the presented method maps firstly tertiary structure of protein domain into 2-D C?-C? distance matrix. Then, two distance functions for alpha helix and beta strand are modeled by considering their geometrical properties respectively. After that, the distance functions are further applied to mine secondary structure elements in such distance matrix with the way similar to image processing. Furthermore, composition feature and arrangement feature of secondary structure elements are presented to characterize domain structure for classification of structural class and fold in Structural Classification of Proteins (SCOP) database. Finally, the results compared with other methods show that the presented method can perform effectively and efficiently automatic classification of domain with the benefit of low dimension and meaningful features, but also no need of complicated classifier system.

Shi, Jian-Yu; Zhang, Yan-Ning

142

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

PubMed

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

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

1995-11-01

143

Structurally coloured secondary particles composed of black and white colloidal particles.  

PubMed

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

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

2013-08-01

144

Distributions of amino acids suggest that certain residue types more effectively determine protein secondary structure.  

PubMed

Exponential growth in the number of available protein sequences is unmatched by the slower growth in the number of structures. As a result, the development of efficient and fast protein secondary structure prediction methods is essential for the broad comprehension of protein structures. Computational methods that can efficiently determine secondary structure can in turn facilitate protein tertiary structure prediction, since most methods rely initially on secondary structure predictions. Recently, we have developed a fast learning optimized prediction methodology (FLOPRED) for predicting protein secondary structure (Saraswathi et al. in JMM 18:4275, 2012). Data are generated by using knowledge-based potentials combined with structure information from the CATH database. A neural network-based extreme learning machine (ELM) and advanced particle swarm optimization (PSO) are used with this data to obtain better and faster convergence to more accurate secondary structure predicted results. A five-fold cross-validated testing accuracy of 83.8 % and a segment overlap (SOV) score of 78.3 % are obtained in this study. Secondary structure predictions and their accuracy are usually presented for three secondary structure elements: ?-helix, ?-strand and coil but rarely have the results been analyzed with respect to their constituent amino acids. In this paper, we use the results obtained with FLOPRED to provide detailed behaviors for different amino acid types in the secondary structure prediction. We investigate the influence of the composition, physico-chemical properties and position specific occurrence preferences of amino acids within secondary structure elements. In addition, we identify the correlation between these properties and prediction accuracy. The present detailed results suggest several important ways that secondary structure predictions can be improved in the future that might lead to improved protein design and engineering. PMID:23907551

Saraswathi, S; Fernández-Martínez, J L; Koli?ski, A; Jernigan, R L; Kloczkowski, A

2013-08-02

145

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

PubMed Central

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

Page, Roderic D. M.

2000-01-01

146

Automated RNA Tertiary Structure Prediction from Secondary Structure and Low-Resolution Restraints  

PubMed Central

A novel protocol for all-atom RNA tertiary structure prediction is presented that employs restrained molecular mechanics and simulated annealing. The restraints are from secondary structure, co-variation analysis, coaxial stacking predictions for helices in junctions, and, when available, cross-linking data. Results are demonstrated on the Alu domain of the mammalian signal recognition particle RNA, the Saccharomyces cerevisiae phenylalanine tRNA, the hammerhead ribozyme, the hepatitis C virus internal ribosomal entry site, and the P4-P6 domain of the Tetrahymena thermophila group I intron. The predicted structure is selected from a pool of decoy structures with a score that maximizes radius of gyration and base-base contacts, which was empirically found to select higher quality decoys. This simple ab initio approach is sufficient to make good predictions of the structure of RNAs compared to current crystal structures using both root mean square deviation and the accuracy of base-base contacts.

Seetin, Matthew G.; Mathews, David H.

2011-01-01

147

Inferences from structural comparison: flexibility, secondary structure wobble and sequence alignment optimization  

PubMed Central

Background Work on protein structure prediction is very useful in biological research. To evaluate their accuracy, experimental protein structures or their derived data are used as the 'gold standard'. However, as proteins are dynamic molecular machines with structural flexibility such a standard may be unreliable. Results To investigate the influence of the structure flexibility, we analysed 3,652 protein structures of 137 unique sequences from 24 protein families. The results showed that (1) the three-dimensional (3D) protein structures were not rigid: the root-mean-square deviation (RMSD) of the backbone C? of structures with identical sequences was relatively large, with the average of the maximum RMSD from each of the 137 sequences being 1.06 Å; (2) the derived data of the 3D structure was not constant, e.g. the highest ratio of the secondary structure wobble site was 60.69%, with the sequence alignments from structural comparisons of two proteins in the same family sometimes being completely different. Conclusion Proteins may have several stable conformations and the data derived from resolved structures as a 'gold standard' should be optimized before being utilized as criteria to evaluate the prediction methods, e.g. sequence alignment from structural comparison. Helix/?-sheet transition exists in normal free proteins. The coil ratio of the 3D structure could affect its resolution as determined by X-ray crystallography.

2012-01-01

148

Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure1  

Microsoft Academic Search

An improved dynamic programming algorithm is reported for RNA secondary structure prediction by free energy minimization. Thermodyn- amic parameters for the stabilities of secondary structure motifs are revised to include expanded sequence dependence as revealed by recent experiments. Additional algorithmic improvements include reduced search time and storage for multibranch loop free energies and improved imposition of folding constraints. An extended

David H. Mathews; Jeffrey Sabina; Michael Zuker; Douglas H. Turner

1999-01-01

149

Estimation of protein secondary structure and error analysis from circular dichroism spectra  

Microsoft Academic Search

The estimation of protein secondary structure from circular dichroism spectra is described by a multivar- iate linear model with noise (Gauss-Markoff model). With this formalism the adequacy of the linear model is investigated, paying special attention to the estimation of the error in the secondary structure estimates. It is shown that the linear model is only adequate for the a-helix

I VANSTOKKUM; Hans J. W. Spoelder; Michael Bloemendal; R VANGRONDELLE; Frans C. A. Groen

1990-01-01

150

Secondary Structural Elements within the 3' Untranslated Region of Mouse Hepatitis Virus Strain JHM Genomic RNA  

Microsoft Academic Search

Previously, we characterized two host protein binding elements located within the 3-terminal 166 nucleo- tides of the mouse hepatitis virus (MHV) genome and assessed their functions in defective-interfering (DI) RNA replication. To determine the role of RNA secondary structures within these two host protein binding elements in viral replication, we explored the secondary structure of the 3-terminal 166 nucleotides of

QI LIU; REED F. JOHNSON; JULIAN L. LEIBOWITZ

2001-01-01

151

Structure and expression of Furin mRNA in the ovary of the medaka, Oryzias latipes.  

PubMed

A cDNA for furin was cloned from the ovary of the medaka, Oryzias latipes, by a combination of cDNA library screening, 5'-rapid amplification of cDNA ends (RACE), and 3'- RACE. The cDNA sequence codes for a protein of 814 amino acid residues highly homologous to other vertebrate furins, Ca(2+)-dependent serine proteases belonging to the subtilysin-like proprotein convertase family. The medaka preprofurin consists of a leader sequence, a propeptide with autoactivation sites, a Kex2-like catalytic domain, a P domain, a cysteine-rich domain, a putative transmembrane domain, and a cytoplasmic domain. The catalytic triad residues (Asp-164, His-205, and Ser-379) were all conserved. Furin mRNA was expressed in many tissues of this, including the ovary. In the ovary, the greatest expression of furin mRNA occurred in oocytes of small growing follicles, as demonstrated by Northern blotting, RT-PCR, and in situ hybridization analysis. Temporary and spatial expression patterns of the medaka fish furin were similar to those of stromelysin-3 and MT5-MMP during oocyte growth and postnatal development. PMID:15114652

Ogiwara, Katsueki; Shinohara, Masakazu; Takahashi, Takayuki

2004-05-01

152

CentroidHomfold-LAST: accurate prediction of RNA secondary structure using automatically collected homologous sequences  

PubMed Central

Although secondary structure predictions of an individual RNA sequence have been widely used in a number of sequence analyses of RNAs, accuracy is still limited. Recently, we proposed a method (called ‘CentroidHomfold’), which includes information about homologous sequences into the prediction of the secondary structure of the target sequence, and showed that it substantially improved the performance of secondary structure predictions. CentroidHomfold, however, forces users to prepare homologous sequences of the target sequence. We have developed a Web application (CentroidHomfold-LAST) that predicts the secondary structure of the target sequence using automatically collected homologous sequences. LAST, which is a fast and sensitive local aligner, and CentroidHomfold are employed in the Web application. Computational experiments with a commonly-used data set indicated that CentroidHomfold-LAST substantially outperformed conventional secondary structure predictions including CentroidFold and RNAfold.

Hamada, Michiaki; Yamada, Koichiro; Sato, Kengo; Frith, Martin C.; Asai, Kiyoshi

2011-01-01

153

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

PubMed Central

Structure mapping experiments (using probes such as dimethyl sulfate [DMS], kethoxal, and T1 and V1 RNases) are used to determine the secondary structures of RNA molecules. The process is iterative, combining the results of several probes with constrained minimum free-energy calculations to produce a model of the structure. We aim to evaluate whether particular probes provide more structural information, and specifically, how noise in the data affects the predictions. Our approach involves generating “decoy” RNA structures (using the sFold Boltzmann sampling procedure) and evaluating whether we are able to identify the correct structure from this ensemble of structures. We show that with perfect information, we are always able to identify the optimal structure for five RNAs of known structure. We then collected orthogonal structure mapping data (DMS and RNase T1 digest) under several solution conditions using our high-throughput capillary automated footprinting analysis (CAFA) technique on two group I introns of known structure. Analysis of these data reveals the error rates in the data under optimal (low salt) and suboptimal solution conditions (high MgCl2). We show that despite these errors, our computational approach is less sensitive to experimental noise than traditional constraint-based structure prediction algorithms. Finally, we propose a novel approach for visualizing the interaction of chemical and enzymatic mapping data with RNA structure. We project the data onto the first two dimensions of a multidimensional scaling of the sFold-generated decoy structures. We are able to directly visualize the structural information content of structure mapping data and reconcile multiple data sets.

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

2010-01-01

154

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

PubMed

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

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

2010-04-22

155

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

PubMed Central

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

2010-01-01

156

The structure of the Myo4p globular tail and its function in ASH1 mRNA localization.  

PubMed

Type V myosin (MyoV)-dependent transport of cargo is an essential process in eukaryotes. Studies on yeast and vertebrate MyoV showed that their globular tails mediate binding to the cargo complexes. In Saccharomyces cerevisiae, the MyoV motor Myo4p interacts with She3p to localize asymmetric synthesis of HO 1 (ASH1) mRNA into the bud of dividing cells. A recent study showed that localization of GFP-MS2-tethered ASH1 particles does not require the Myo4p globular tail, challenging the supposed role of this domain. We assessed ASH1 mRNA and Myo4p distribution more directly and found that their localization is impaired in cells expressing globular tail-lacking Myo4p. In vitro studies further show that the globular tail together with a more N-terminal linker region is required for efficient She3p binding. We also determined the x-ray structure of the Myo4p globular tail and identify a conserved surface patch important for She3p binding. The structure shows pronounced similarities to membrane-tethering complexes and indicates that Myo4p may not undergo auto-inhibition of its motor domain. PMID:20439999

Heuck, Alexander; Fetka, Ingrid; Brewer, Daniel N; Hüls, Daniela; Munson, Mary; Jansen, Ralf-Peter; Niessing, Dierk

2010-05-01

157

Primary structure of the human melanoma-associated antigen p97 (melanotransferrin) deduced from the mRNA sequence.  

PubMed Central

p97 is a cell-surface glycoprotein that is present in most human melanomas but only in trace amounts in normal adult tissues. To determine the structure of this tumor-associated antigen and to identify its functional domains, we have purified and cloned p97 mRNA and determined its nucleotide sequence. The mRNA encodes a 738-residue precursor, which contains the previously determined N-terminal amino acid sequence of p97. After removal of a 19-residue signal peptide, the mature p97 molecule comprises extracellular domains of 342 and 352 residues and a C-terminal 25-residue stretch of predominantly uncharged and hydrophobic amino acids, which we believe acts as a membrane anchor. Each extracellular domain contains 14 cysteine residues, which form seven intradomain disulfide bridges, and one or two potential N-glycosylation sites. Protease digestion studies show that the three major antigenic determinants of p97 are present on the N-terminal domain. The domains are strikingly homologous to each other (46% amino acid sequence homology) and to the corresponding domains of human serum transferrin (39% homology). Conservation of disulfide bridges and of amino acids thought to compose the iron binding pockets suggests that p97 is also related to transferrin in tertiary structure and function. We propose that p97 be renamed melanotransferrin to denote its original identification in melanoma cells and its evolutionary relationship to serotransferrin and lactotransferrin, the other members of the transferrin superfamily. Images

Rose, T M; Plowman, G D; Teplow, D B; Dreyer, W J; Hellstrom, K E; Brown, J P

1986-01-01

158

Stabilization of SMAR1 mRNA by PGA2 involves a stem-loop structure in the 5? UTR  

PubMed Central

Prostaglandins are anticancer agents known to inhibit tumor cell proliferation both in vitro and in vivo by affecting the mRNA stability. Here we report that a MAR-binding protein SMAR1 is a target of Prostaglandin A2 (PGA2) induced growth arrest. We identify a regulatory mechanism leading to stabilization of SMAR1 transcript. Our results show that a minor stem and loop structure present in the 5? UTR of SMAR1 (?1-UTR) is critical for nucleoprotein complex formation that leads to SMAR1 stabilization in response to PGA2. This results in an increased SMAR1 transcript and altered protein levels, that in turn causes downregulation of Cyclin D1 gene, essential for G1/S phase transition. We also provide evidence for the presence of a variant 5? UTR SMAR1 (?17-UTR) in breast cancer-derived cell lines. This form lacks the minor stem and loop structure required for mRNA stabilization in response to PGA2. As a consequence of this, there is a low level of endogenous tumor suppressor protein SMAR1 in breast cancer-derived cell lines. Our studies provide a mechanistic insight into the regulation of tumor suppressor protein SMAR1 by a cancer therapeutic PGA2, that leads to repression of Cyclin D1 gene.

Pavithra, Lakshminarasimhan; Rampalli, Shravanti; Sinha, Surajit; Sreenath, Kadreppa; Pestell, Richard G.; Chattopadhyay, Samit

2007-01-01

159

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

PubMed Central

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

2011-01-01

160

The turn of the screw: an exercise in protein secondary structure.  

PubMed

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 protein secondary structure and to complement the common computer-based structural portrayals often used in teaching biochemistry. As students fold these paper strips into model secondary structures, they will better grasp how intramolecular hydrogen bonds form in the folding of a polypeptide into secondary structure, and how these hydrogen bonds direct the overall shape of helical and sheet structures, including the handedness of the ?-helix and the difference between right- and the left-handed twist. PMID:21618388

Pikaart, Michael

161

Neotropical secondary forest succession: changes in structural and functional characteristics  

Microsoft Academic Search

In this review, we highlight the main biotic and abiotic factors that influence the patterns of Neotropical secondary forest successions, referred as the woody vegetation that regrows after complete forest clearance due to human activities. We focus on both patterns of species replacement and various processes that occur during succession, and suggest that the sequence of processes may be predictable

Manuel R Guariguata; Rebecca Ostertag

2001-01-01

162

Rapid degradation of AU-rich element (ARE) mRNAs is activated by ribosome transit and blocked by secondary structure at any position 5' to the ARE.  

PubMed

The 3' noncoding region (NCR) AU-rich element (ARE) selectively confers rapid degradation on many mRNAs via a process requiring translation of the message. The role of cotranslation in destabilization of ARE mRNAs was examined by insertion of translation-blocking stable secondary structure at different sites in test mRNAs containing either the granulocyte-macrophage colony-stimulating factor (GM-CSF) ARE or a control sequence. A strong (-80 kcal/mol [1 kcal = 4.184 kJ]) but not a moderate (-30 kcal/mol) secondary structure prevented destabilization of mRNAs when inserted at any position upstream of the ARE, including in the 3' NCR. Surprisingly, a strong secondary structure did not block rapid mRNA decay when placed immediately downstream of the ARE. Studies are also presented showing that the turnover of mRNAs containing control or ARE sequences is not altered by insertion of long (1,000-nucleotide) intervening segments between the stop codon and the ARE or between the ARE and poly(A) tail. Characterization of ARE-containing mRNAs in polyadenylated and whole cytoplasmic RNA fractions failed to find evidence for decay intermediates degraded to the site of strong secondary structure from either the 5' or 3' end. From these and other data presented, this study demonstrates that complete translation of the coding region is essential for activation of rapid mRNA decay controlled by the GM-CSF ARE and that the structure of the 3' NCR can strongly influence activation. The results are consistent with activation of ARE-mediated decay by possible entry of translation-linked decay factors into the 3' NCR or translation-coupled changes in 3' NCR ribonucleoprotein structure or composition. PMID:7565786

Curatola, A M; Nadal, M S; Schneider, R J

1995-11-01

163

Analysis of an optimal hidden Markov model for secondary structure prediction  

Microsoft Academic Search

Background  Secondary structure prediction is a useful first step toward 3D structure prediction. A number of successful secondary structure\\u000a prediction methods use neural networks, but unfortunately, neural networks are not intuitively interpretable. On the contrary,\\u000a hidden Markov models are graphical interpretable models. Moreover, they have been successfully used in many bioinformatic\\u000a applications. Because they offer a strong statistical background and allow

Juliette Martin; Jean-François Gibrat; François Rodolphe

2006-01-01

164

Evolved RNA Secondary Structure and the Rooting of the Universal Tree of Life  

Microsoft Academic Search

.   The origin and diversification of RNA secondary structure were traced using cladistic methods. Structural components were\\u000a coded as polarized and ordered multi-state characters, following a model of character state transformation outlined by considerations\\u000a in statistical mechanics. Several classes of functional RNA were analyzed, including ribosomal RNA (rRNA). Considerable phylogenetic\\u000a signal was present in their secondary structure. The intrinsically rooted

Gustavo Caetano-Anollés

2002-01-01

165

Protein secondary structure imaging with ultrabroadband multiplex coherent anti-Stokes Raman scattering (CARS) microspectroscopy.  

PubMed

Protein secondary structures in human hair have been studied with ultrabroadband multiplex coherent anti-Stokes Raman scattering (CARS) microspectroscopy. The CARS peak-shift mapping method has been developed and applied to hair samples with and without treatments by chemical reduction and mechanical extension. It clearly visualizes the treatment induced changes in protein secondary structures and their spatial distributions. Using the new imaging technique, we found a multilayered structure in the human hair cortex. PMID:22220757

Bito, Kotatsu; Okuno, Masanari; Kano, Hideaki; Tokuhara, Shihomi; Naito, Satoru; Masukawa, Yoshinori; Leproux, Philippe; Couderc, Vincent; Hamaguchi, Hiro-o

2012-01-24

166

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

PubMed

Ribosomal genes and their spacers have been extensively utilized to examine the biodiversity and phylogenetics of protists. Among these, the internal transcribed spacer regions 1 and 2 (ITS1 and ITS2) are known to form secondary structures that are critically important for proper processing of the pre-rRNA into mature ribosomes. Although the secondary structure of ITS2 has been widely investigated, considerably less is known about ITS1 and its secondary structure. Here, secondary structures of the ITS1 were modeled for 46 ITS "types" from Symbiodinium, a diverse dinoflagellate genus that forms symbioses with many protists and metazoans, using comparative phylogenetic and minimum free energy approaches. The predicted ITS1 secondary structures for each Symbiodinium "type" were highly stable (DeltaG=-46.40 to -85.30 kcal mol(-1) at 37 degrees C) and consisted of an open loop with five helices separated by single-stranded regions. Several structural characteristics were conserved within monophyletic sub-groups, providing additional support for the predicted structures and the relationships within this genus. Finally, the structures were applied to identify potential pseudogenes from five Symbiodinium ITS1 datasets. Consequently, ITS1 secondary structures are useful in understanding the biology and phylogenetics, as well as recognizing and excluding questionable sequences from datasets, of protists such as Symbiodinium. PMID:20106718

Thornhill, Daniel J; Lord, Jenna B

2010-01-27

167

HSRNAFold: A harmony search algorithm for RNA secondary structure prediction based on minimum free energy  

Microsoft Academic Search

Current physical methods for RNA structure determination are time consuming and expensive; thus the methods for the computational prediction of structure are necessary. Various algorithms have been used for RNA structure prediction including dynamic programming and meta-heuristic algorithms. This paper proposes a meta-heuristic harmony search algorithm (HSRNAFold) for finding RNA secondary structure with minimum free energy and similarity to the

Abdulqader M. Mohsen; Ahamad Tajudin Khader; Dhanesh Ramachandram

2008-01-01

168

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

PubMed

The supersecondary structure of amyloids and prions, proteins of intense clinical and biological interest, are difficult to determine by standard experimental or computational means. In addition, significant conformational heterogeneity is known or suspected to exist in many amyloid fibrils. Previous work has demonstrated that probability-based prediction of discrete ?-strand pairs can offer insight into these structures. Here, we devise a system of energetic rules that can be used to dynamically assemble these discrete ?-strand pairs into complete amyloid ?-structures. The STITCHER algorithm progressively 'stitches' strand-pairs into full ?-sheets based on a novel free-energy model, incorporating experimentally observed amino-acid side-chain stacking contributions, entropic estimates, and steric restrictions for amyloidal parallel ?-sheet construction. A dynamic program computes the top 50 structures and returns both the highest scoring structure and a consensus structure taken by polling this list for common discrete elements. Putative structural heterogeneity can be inferred from sequence regions that compose poorly. Predictions show agreement with experimental models of Alzheimer's amyloid beta peptide and the Podospora anserina Het-s prion. Predictions of the HET-s homolog HET-S also reflect experimental observations of poor amyloid formation. We put forward predicted structures for the yeast prion Sup35, suggesting N-terminal structural stability enabled by tyrosine ladders, and C-terminal heterogeneity. Predictions for the Rnq1 prion and alpha-synuclein are also given, identifying a similar mix of homogenous and heterogeneous secondary structure elements. STITCHER provides novel insight into the energetic basis of amyloid structure, provides accurate structure predictions, and can help guide future experimental studies. Proteins 2011. © 2011 Wiley Periodicals, Inc. PMID:22095906

Bryan, Allen W; O'Donnell, Charles W; Menke, Matthew; Cowen, Lenore J; Lindquist, Susan; Berger, Bonnie

2011-09-23

169

Protein secondary structure prediction using modular reciprocal bidirectional recurrent neural networks.  

PubMed

The supervised learning of recurrent neural networks well-suited for prediction of protein secondary structures from the underlying amino acids sequence is studied. Modular reciprocal recurrent neural networks (MRR-NN) are proposed to model the strong correlations between adjacent secondary structure elements. Besides, a multilayer bidirectional recurrent neural network (MBR-NN) is introduced to capture the long-range intramolecular interactions between amino acids in formation of the secondary structure. The final modular prediction system is devised based on the interactive integration of the MRR-NN and the MBR-NN structures to arbitrarily engage the neighboring effects of the secondary structure types concurrent with memorizing the sequential dependencies of amino acids along the protein chain. The advanced combined network augments the percentage accuracy (Q?) to 79.36% and boosts the segment overlap (SOV) up to 70.09% when tested on the PSIPRED dataset in three-fold cross-validation. PMID:20472322

Babaei, Sepideh; Geranmayeh, Amir; Seyyedsalehi, Seyyed Ali

2010-05-15

170

Feature extraction of protein folds based on secondary structure transformation  

Microsoft Academic Search

We propose a classification method of protein folds from the structural features of clusters that are extracted based on the cost of structural transformation from one protein to another. In the method, the feature to be extracted is defined as a pair of a delegate structure and a cluster region. The delegate structure is generated by estimating the center of

T. Maeda; K. Kamada; T. Ohkawa; N. Komoda; H. Nakamura; A. Kidera

1998-01-01

171

Floristic and structural patterns along a chronosequence of secondary forest succession in Argentinean subtropical montane forests  

Microsoft Academic Search

We studied forest structure and composition along a chronosequence of secondary forest succession in Northwest Argentina's montane forests (‘Yungas’) at 27°S, between 700 and 900 m. Early herbaceous stages, forested stages of 11, 25, 45, and 50 years after abandonment, and old-growth forests were surveyed. Secondary forests included stands that originated in abandoned herbaceous crops and in abandoned fruit orchards.

H. R. Grau; M. F. Arturi; A. D. Brown; P. G. Aceñolaza

1997-01-01

172

Changes in Forest Structure and Species Composition during Secondary Forest Succession in the Bolivian Amazon1  

Microsoft Academic Search

Changes in forest structure and species diversity throughout secondary succession were studied using a chronosequence at two sites in the Bolivian Amazon. Secondary forests ranging in age from 2 to 40 years as well as mature forests were included, making a total of 14 stands. Fifty plants per forest layer (understory, subcanopy, and canopy) were sampled using the transect of

Marielos Pena-Claros

2003-01-01

173

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

PubMed Central

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

Sharma, Sudha

2011-01-01

174

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

PubMed Central

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

Cybulsky, M I; Fries, J W; Williams, A J; Sultan, P; Eddy, R; Byers, M; Shows, T; Gimbrone, M A; Collins, T

1991-01-01

175

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

SciTech Connect

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

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

1991-09-01

176

Methylation of vesicular stomatitis virus (VSV) mRNA 5'-cap structures in vitro  

SciTech Connect

Monocistronic VSV mRNAs synthesized by subviral particles in vitro display the methylated 5'-cap structure m'G(5')ppp(5')Am. The authors have detected both monomethylated cap structures, m/sup 7/G(5')ppp(5')A and G(5')Am, in reactions containing suboptimal concentrations of AdoMet. To assess the putative precursor roles of these cap structures the authors devised dual label pulse-chase analyses employing S-(CH/sub 3/-/sup 3/H)-AdoMet and (..beta..-/sup 32/P)GTP. The labeled cap structures were analyzed by HPLC. The simultaneous chasing of both radiolabeled substrates allowed 1) the isolation of a specific set of caps labeled as (..beta..-/sup 32/P)-R/sup 7/G(5')ppp(5')AR (R=H or CH/sub 3/) and 2) the determination of the transcriptive fate of each intermediate cap structure within the set. The results demonstrated that both monomethylated cap structures serve as intermediates for the dimethylated cap and that the order of cap methylation is non-compulsory. These data, coupled with previous observations of hypomethylated cap structures in polyadenylated RNAs, have suggested that methylation occurs in a chain length dependent window.

Hammond, D.C.; Lesnaw, J.A.

1987-05-01

177

Minimum message length inference of secondary structure from protein coordinate data  

PubMed Central

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)

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

2012-01-01

178

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

PubMed

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

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

2008-11-01

179

A Non-parametric Bayesian Approach for Predicting RNA Secondary Structures  

NASA Astrophysics Data System (ADS)

Since many functional RNAs form stable secondary structures which are related to their functions, RNA secondary structure prediction is a crucial problem in bioinformatics. We propose a novel model for generating RNA secondary structures based on a non-parametric Bayesian approach, called hierarchical Dirichlet processes for stochastic context-free grammars (HDP-SCFGs). Here non-parametric means that some meta-parameters, such as the number of non-terminal symbols and production rules, do not have to be fixed. Instead their distributions are inferred in order to be adapted (in the Bayesian sense) to the training sequences provided. The results of our RNA secondary structure predictions show that HDP-SCFGs are more accurate than the MFE-based and other generative models.

Sato, Kengo; Hamada, Michiaki; Mituyama, Toutai; Asai, Kiyoshi; Sakakibara, Yasubumi

180

The Development of the Secondary Wing Structure for a Rigid Wing Hang Glider.  

National Technical Information Service (NTIS)

The design, construction and testing of a secondary wing structure using foam and glass fiber sandwich construction are described. Materials and construction techniques used were those readily available to the amateur. The wing section, an FX 72-MS-150B, ...

C. P. Blackman I. Grant

1980-01-01

181

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

Microsoft Academic Search

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

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

182

The Internal Transcribed Spacer 2 Exhibits a Common Secondary Structure in Green Algae and Flowering Plants  

Microsoft Academic Search

.   Sequences of the Internal Transcribed Spacer 2 (ITS-2) regions of the nuclear rDNA repeats from 111 organisms of the family\\u000a Volvocaceae (Chlorophyta) and unicellular organisms of the Volvocales, including Chlamydomonas reinhardtii, were determined. The use of thermodynamic energy optimization to generate secondary structures and phylogenetic comparative\\u000a analysis of the spacer regions revealed a common secondary structure that is conserved

Jeffrey C. Mai; Annette W. Coleman

1997-01-01

183

A secondary copulatory structure in a female insect: a clasp for a nuptial meal?  

NASA Astrophysics Data System (ADS)

Secondary copulatory structures are well-known in male dragonflies and spiders. Here I report a secondary copulatory organ in female ground weta, Hemiandrus pallitarsis (Ensifera, Orthoptera - crickets and allies). The organ, located on the underside of the abdomen, appears to secure the male's genitalia during the transfer of a spermatophylax nuptial meal to this location, an area quite separate from the female's primary copulatory structures, where the sperm ampulla is attached.

Gwynne, Darryl

2002-02-01

184

Predicting RNA Secondary Structure Using Profile Stochastic Context-Free Grammars and Phylogenic Analysis  

Microsoft Academic Search

Stochastic context-free grammars (SCFGs) have been applied to predicting RNA secondary structure. The prediction of RNA secondary\\u000a structure can be facilitated by incorporating with comparative sequence analysis. However, most of existing SCFG-based methods\\u000a lack explicit phylogenic analysis of homologous RNA sequences, which is probably the reason why these methods are not ideal\\u000a in practical application. Hence, we present a new

Xiao-Yong Fang; Zhi-Gang Luo; Zheng-hua Wang

2008-01-01

185

S6:S18 ribosomal protein complex interacts with a structural motif present in its own mRNA.  

PubMed

Prokaryotic ribosomal protein genes are typically grouped within highly conserved operons. In many cases, one or more of the encoded proteins not only bind to a specific site in the ribosomal RNA, but also to a motif localized within their own mRNA, and thereby regulate expression of the operon. In this study, we computationally predicted an RNA motif present in many bacterial phyla within the 5' untranslated region of operons encoding ribosomal proteins S6 and S18. We demonstrated that the S6:S18 complex binds to this motif, which we hereafter refer to as the S6:S18 complex-binding motif (S6S18CBM). This motif is a conserved CCG sequence presented in a bulge flanked by a stem and a hairpin structure. A similar structure containing a CCG trinucleotide forms the S6:S18 complex binding site in 16S ribosomal RNA. We have constructed a 3D structural model of a S6:S18 complex with S6S18CBM, which suggests that the CCG trinucleotide in a specific structural context may be specifically recognized by the S18 protein. This prediction was supported by site-directed mutagenesis of both RNA and protein components. These results provide a molecular basis for understanding protein-RNA recognition and suggest that the S6S18CBM is involved in an auto-regulatory mechanism. PMID:23980204

Matelska, Dorota; Purta, Elzbieta; Panek, Sylwia; Boniecki, Michal J; Bujnicki, Janusz M; Dunin-Horkawicz, Stanislaw

2013-08-26

186

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

PubMed Central

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/.

2010-01-01

187

Foldability of barnase mutants obtained by permutation of modules or secondary structure units.  

PubMed

Modules, defined as stable, compact structure units in a globular protein, are good candidates for the construction of novel foldable proteins by permutation. Here we decomposed barnase into six modules (M1-M6) and constructed 23 barnase mutants containing permutations of the internal four (M2-M5) out of six modules. Globular proteins can also be subdivided into secondary structure units based on the extended structures that control the mutual relationships of the modules. We also decomposed barnase into six secondary structure units (S1-S6) and constructed 21 barnase mutants containing permutations of the internal four (S2-S5) out of six secondary structure units. Foldability of these two types of mutants was assessed by means of circular dichroism, fluorescence, and 1H-NMR measurements. A total of 15 of 23 module mutants and 15 of 21 secondary structure unit mutants formed definite secondary structures, such as alpha-helix and beta-sheet, at 20 microM owing to intermolecular interactions, but most of them converted to random coil structures at a lower concentration (1 microM). Of the 44 mutants, only two, M3245 and S2543, gave distinct near-UV CD spectra. S2543 especially showed definite signal dispersion in the amide and methyl regions of the 1H-NMR spectrum, though M3245 did not. Furthermore, urea-induced unfolding of S2543 monitored by far-UV CD and fluorescence measurements showed a distinct cooperative transition. These results strongly suggest that S2543 takes partially folded conformations in aqueous solution. Our results also suggest that building blocks such as secondary structure units capable of taking different stable conformations by adapting themselves to the surrounding environment, rather than building blocks such as modules having a specified stable conformation, are required for the formation of foldable proteins. Therefore, the use of secondary structure units for the construction of novel globular proteins is likely to be an effective approach. PMID:10064693

Tsuji, T; Yoshida, K; Satoh, A; Kohno, T; Kobayashi, K; Yanagawa, H

1999-03-12

188

The structure of the C-terminal KH domains of KSRP reveals a noncanonical motif important for mRNA degradation.  

PubMed

The AU-rich element (ARE) RNA-binding protein KSRP (K-homology splicing regulator protein) contains four KH domains and promotes the degradation of specific mRNAs that encode proteins with functions in cellular proliferation and inflammatory response. The fourth KH domain (KH4) is essential for mRNA recognition and decay but requires the third KH domain (KH3) for its function. We show that KH3 and KH4 behave as independent binding modules and can interact with different regions of the AU-rich RNA targets of KSRP. This provides KSRP with the structural flexibility needed to recognize a set of different targets in the context of their 3'UTR structural settings. Surprisingly, we find that KH4 binds to its target AREs with lower affinity than KH3 and that KSRP's mRNA binding, and mRNA degradation activities are closely associated with a conserved structural element of KH4. PMID:17437720

García-Mayoral, María Flor; Hollingworth, David; Masino, Laura; Díaz-Moreno, Irene; Kelly, Geoff; Gherzi, Roberto; Chou, Chu-Fang; Chen, Ching-Yi; Ramos, Andres

2007-04-01

189

2D-RNA-coupling numbers: a new computational chemistry approach to link secondary structure topology with biological function.  

PubMed

Methods for prediction of proteins, DNA, or RNA function and mapping it onto sequence often rely on bioinformatics alignment approach instead of chemical structure. Consequently, it is interesting to develop computational chemistry approaches based on molecular descriptors. In this sense, many researchers used sequence-coupling numbers and our group extended them to 2D proteins representations. However, no coupling numbers have been reported for 2D-RNA topology graphs, which are highly branched and contain useful information. Here, we use a computational chemistry scheme: (a) transforming sequences into RNA secondary structures, (b) defining and calculating new 2D-RNA-coupling numbers, (c) seek a structure-function model, and (d) map biological function onto the folded RNA. We studied as example 1-aminocyclopropane-1-carboxylic acid (ACC) oxidases known as ACO, which control fruit ripening having importance for biotechnology industry. First, we calculated tau(k)(2D-RNA) values to a set of 90-folded RNAs, including 28 transcripts of ACO and control sequences. Afterwards, we compared the classification performance of 10 different classifiers implemented in the software WEKA. In particular, the logistic equation ACO = 23.8 . tau(1)(2D-RNA) + 41.4 predicts ACOs with 98.9%, 98.0%, and 97.8% of accuracy in training, leave-one-out and 10-fold cross-validation, respectively. Afterwards, with this equation we predict ACO function to a sequence isolated in this work from Coffea arabica (GenBank accession DQ218452). The tau(1)(2D-RNA) also favorably compare with other descriptors. This equation allows us to map the codification of ACO activity on different mRNA topology features. The present computational-chemistry approach is general and could be extended to connect RNA secondary structure topology to other functions. PMID:17279496

González-Díaz, Humberto; Agüero-Chapin, Guillermín; Varona, Javier; Molina, Reinaldo; Delogu, Giovanna; Santana, Lourdes; Uriarte, Eugenio; Podda, Gianni

2007-04-30

190

Mechanisms of Lin28-Mediated miRNA and mRNA Regulation--A Structural and Functional Perspective  

PubMed Central

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

Mayr, Florian; Heinemann, Udo

2013-01-01

191

Secondary structure content of the HDV ribozyme in 95% formamide.  

PubMed Central

The Hepatitis Delta Virus (HDV) ribozyme self-cleaving activity in 20 M formamide solutions is unique. Does this catalytic activity result from the conservation of its tertiary structure in 20 M formamide? We followed the ribozyme structure in formamide solutions by monitoring the amount of bound Ethidium Bromide (EB). We were able to measure the quantity of dye bound using time-resolved fluorescence spectroscopy, as an estimate of the ribozyme double helical content. This method, calibrated by using oligonucleotides with defined tertiary structure and denaturing solvents, parallels NMR and UV measurements as a function of temperature. Measurements with the HDV ribozyme lead to three conclusions: (a) both the precursor and product RNAs are structured to 24 M (95% w/w) formamide or 4 M H2O solutions which is equivalent to 4 M H2O; (b) the HDV ribozyme is the only RNA sequence investigated in this study that retains so much structure in formamide; and (c) DNA analogs of formamide resistant HDV ribozyme sequences lose their structure at less than 15 M formamide. Thus, the structural integrity of the HDV ribozyme is an intrinsic property of the RNA molecule and its sequence.

Duhamel, J; Liu, D M; Evilia, C; Fleysh, N; Dinter-Gottlieb, G; Lu, P

1996-01-01

192

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

PubMed

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

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

2012-10-16

193

A Comparative Taxonomy of Parallel Algorithms for RNA Secondary Structure Prediction  

PubMed Central

RNA molecules have been discovered playing crucial roles in numerous biological and medical procedures and processes. RNA structures determination have become a major problem in the biology context. Recently, computer scientists have empowered the biologists with RNA secondary structures that ease an understanding of the RNA functions and roles. Detecting RNA secondary structure is an NP-hard problem, especially in pseudoknotted RNA structures. The detection process is also time-consuming; as a result, an alternative approach such as using parallel architectures is a desirable option. The main goal in this paper is to do an intensive investigation of parallel methods used in the literature to solve the demanding issues, related to the RNA secondary structure prediction methods. Then, we introduce a new taxonomy for the parallel RNA folding methods. Based on this proposed taxonomy, a systematic and scientific comparison is performed among these existing methods.

Al-Khatib, Ra'ed M.; Abdullah, Rosni; Rashid, Nur'Aini Abdul

2010-01-01

194

Destabilization of interleukin-6 mRNA requires a putative RNA stem-loop structure, an AU-rich element, and the RNA-binding protein AUF1.  

PubMed

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

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

2006-09-05

195

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

PubMed Central

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

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

2006-01-01

196

RNA-protein hybrid ribozymes that efficiently cleave any mRNA independently of the structure of the target RNA  

PubMed Central

Ribozyme activity in vivo depends on achieving high-level expression, intracellular stability, target colocalization, and cleavage site access. At present, target site selection is problematic because of unforeseeable secondary and tertiary RNA structures that prevent cleavage. To overcome this design obstacle, we wished to engineer a ribozyme that could access any chosen site. To create this ribozyme, the constitutive transport element (CTE), an RNA motif that has the ability to interact with intracellular RNA helicases, was attached to our ribozymes so that the helicase-bound, hybrid ribozymes would be produced in cells. This modification significantly enhanced ribozyme activity in vivo, permitting cleavage of sites previously found to be inaccessible. To confer cleavage enhancement, the CTE must retain helicase-binding activity. Binding experiments demonstrated the likely involvement of RNA helicase(s). We found that attachment of the RNA motif to our tRNA ribozymes leads to cleavage in vivo at the chosen target site regardless of the local RNA secondary or tertiary structure.

Warashina, Masaki; Kuwabara, Tomoko; Kato, Yoshio; Sano, Masayuki; Taira, Kazunari

2001-01-01

197

PARTS: Probabilistic Alignment for RNA joinT Secondary structure prediction  

PubMed Central

A novel method is presented for joint prediction of alignment and common secondary structures of two RNA sequences. The joint consideration of common secondary structures and alignment is accomplished by structural alignment over a search space defined by the newly introduced motif called matched helical regions. The matched helical region formulation generalizes previously employed constraints for structural alignment and thereby better accommodates the structural variability within RNA families. A probabilistic model based on pseudo free energies obtained from precomputed base pairing and alignment probabilities is utilized for scoring structural alignments. Maximum a posteriori (MAP) common secondary structures, sequence alignment and joint posterior probabilities of base pairing are obtained from the model via a dynamic programming algorithm called PARTS. The advantage of the more general structural alignment of PARTS is seen in secondary structure predictions for the RNase P family. For this family, the PARTS MAP predictions of secondary structures and alignment perform significantly better than prior methods that utilize a more restrictive structural alignment model. For the tRNA and 5S rRNA families, the richer structural alignment model of PARTS does not offer a benefit and the method therefore performs comparably with existing alternatives. For all RNA families studied, the posterior probability estimates obtained from PARTS offer an improvement over posterior probability estimates from a single sequence prediction. When considering the base pairings predicted over a threshold value of confidence, the combination of sensitivity and positive predictive value is superior for PARTS than for the single sequence prediction. PARTS source code is available for download under the GNU public license at http://rna.urmc.rochester.edu.

Harmanci, Arif Ozgun; Sharma, Gaurav; Mathews, David H.

2008-01-01

198

A G-quadruplex structure within the 5?-UTR of TRF2 mRNA represses translation in human cells  

PubMed Central

Telomeres protect chromosome ends from being recognized as double-stranded breaks. Telomeric function is ensured by the shelterin complex in which TRF2 protein is an essential player. The G-rich strand of telomere DNA can fold into G-quadruplex (G4) structure. Small molecules stabilizing G4 structures, named G4 ligands, have been shown to alter telomeric functions in human cells. In this study, we show that a guanine-rich RNA sequence located in the 5?-UTR region of the TRF2 mRNA (hereafter 91TRF2G) is capable of forming a stable quadruplex that causes a 2.8-fold decrease in the translation of a reporter gene in human cells, as compared to a mutant 5?-UTR unable to fold into G4. We also demonstrate that several highly selective G4 ligands, the pyridine dicarboxamide derivative 360A and bisquinolinium compounds Phen-DC(3) and Phen-DC(6), are able to bind the 91TRF2G:RNA sequence and to modulate TRF2 protein translation in vitro. Since the naturally occurring 5?-UTR TRF2:RNA G4 element was used here, which is conserved in several vertebrate orthologs, the present data substantiate a potential translational mechanism mediated by a G4 RNA motif for the downregulation of TRF2 expression.

Gomez, Dennis; Guedin, Aurore; Mergny, Jean-Louis; Riou, Jean-Francois; Teulade-Fichou, Marie-Paule; Calsou, Patrick

2010-01-01

199

mRNA expression profiling of laser microbeam microdissected cells from slender embryonic structures.  

PubMed

Microarray hybridization has rapidly evolved as an important tool for genomic studies and studies of gene regulation at the transcriptome level. Expression profiles from homogenous samples such as yeast and mammalian cell cultures are currently extending our understanding of biology, whereas analyses of multicellular organisms are more difficult because of tissue complexity. The combination of laser microdissection, RNA amplification, and microarray hybridization has the potential to provide expression profiles from selected populations of cells in vivo. In this article, we present and evaluate an experimental procedure for global gene expression analysis of slender embryonic structures using laser microbeam microdissection and laser pressure catapulting. As a proof of principle, expression profiles from 1000 cells in the mouse embryonic (E9.5) dorsal aorta were generated and compared with profiles for captured mesenchymal cells located one cell diameter further away from the aortic lumen. A number of genes were overexpressed in the aorta, including 11 previously known markers for blood vessels. Among the blood vessel markers were endoglin, tie-2, PDGFB, and integrin-beta1, that are important regulators of blood vessel formation. This demonstrates that microarray analysis of laser microbeam micro-dissected cells is sufficiently sensitive for identifying genes with regulative functions. PMID:11891179

Scheidl, Stefan J; Nilsson, Sven; Kalén, Mattias; Hellström, Mats; Takemoto, Minoru; Håkansson, Joakim; Lindahl, Per

2002-03-01

200

Patterns, structures, and amino acid frequencies in structural building blocks, a protein secondary structure classification scheme  

Microsoft Academic Search

To study local structures in proteins, we previously developed an autoasso- ciative artificial neural network (autoANN) and clustering tool to discover intrinsic fea- tures of macromolecular structures. The hid- den unit activations computed by the trained autoANN are a convenient low-dimensional encoding of the local protein backbone struc- ture. Clustering these activation vectors re- sults in a unique classification of

Jacquelyn S. Fetrow; Michael J. Palumbo; George Berg

1997-01-01

201

Secondary Structure Analysis of Native Cellulose by Molecular Dynamics Simulations with Coarse Grained Model  

NASA Astrophysics Data System (ADS)

The secondary structure of different I? cellulose was analyzed by a molecular dynamics simulation with MARTINI coarse-grained force field, where each chain of the cellulose includes 40 D-glucoses units. Calculation gives a satisfied description about the secondary structure of the cellulose. As the chain number increasing, the cellulose becomes the form of a helix, with the diameter of screw growing and spiral rising. Interestingly, the celluloses with chain number N 4 of 6, 24 and 36 do show right-hand twisting. On the contrast, the celluloses with N 8 of 12, 16 chains are left-hand twisting. These simulations indicate that the cellulose with chain number larger than 36 will break down to two parts. Besides, the result indicates that 36-chains cellulose model is the most stable among all models. Furthermore, the Lennard-Jones potential determines the secondary structure. In addition, an equation was set up to analyze the twisting structure.

Wu, Shuai; Zhan, Hai-yi; Wang, Hong-ming; Ju, Yan

2012-04-01

202

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

PubMed

Protein structures and their complexes are formed and stabilized by interactions, both inside and outside of the protein. Analysis of such interactions helps in understanding different levels of structures (secondary, super-secondary, and oligomeric states). It can also assist molecular biologists in understanding structural consequences of modifying proteins and/or ligands. In this chapter, our definition of atom-atom and residue-residue contacts is described and applied to analysis of protein-protein interactions in dimeric ?-sandwich proteins. PMID:22987352

Potapov, Vladimir; Edelman, Marvin; Sobolev, Vladimir

2013-01-01

203

An algorithm for comparing RNA secondary structures and searching for similar substructures.  

PubMed

To access the functional informations carried by RNA molecules at the level of their secondary structure interactions, we propose a comparison method based on a tree edit algorithm which takes into account the tree structure of RNA foldings. Any secondary structure is translated into a tree involving all its elementary substructures; then a shorter condensed tree is built in which any unbranched helix interspersed with bulges and interior loops is taken as a single node. This method includes several parameters: a comparison matrix between structural units, gap penalties, and the scoring between nodes of the condensed trees. Their effects have been analysed using as a model a rapidly divergent domain of the large ribosomal RNA, for which structural variation during evolution is well known. This method allows one to recognize precisely, in large target molecules, definite substructures that present with the query molecules only a limited set of closely related secondary structure features; it is still efficient if intervening features, which can correspond to insertion/deletion of entire stem regions, separate such structural elements. When coupled with a hierarchical clustering algorithm, this method is suitable for classifying RNA molecules according to their secondary structure homologies. PMID:1378772

Chevalet, C; Michot, B

1992-06-01

204

Fast Folding and Comparison of RNA Secondary Structures (The Vienna RNA Package)  

Microsoft Academic Search

Computer codes for computation and comparison of RNA secondary structures, the Vienna RNA package, are presented, that are based on dynamic programming algorithms and aim at predictions of structures with minimum free energies as well as at computations of the equilibrium partition functions and base pairing probabilities. An efficient heuristic for the inverse folding problem of RNA is introduced. In

Ivo L. Hofacker; Walter Fontana; Peter F. Stadler; L. Sebastian Bonhoeffer; Manfred Tacker; Peter Schuster

1994-01-01

205

The importance of larger data sets for protein secondary structure prediction with neural networks  

Microsoft Academic Search

A neural network algorithm is applied to secondary structure and structural class prediction for a database of 318 nonhomologous protein chains. Significant improvement in accuracy is obtained as compared with performance on smaller databases. A systematic study of the effects of network topology shows that, for the larger database, better results are obtained with more units in the hidden layer.

John-Marc Chandonia; Martin Karplus

2008-01-01

206

Two Strategies for Sequence Comparison: Profile-preprocessed and Secondary Structure-induced Multiple Alignment  

Microsoft Academic Search

Multiple sequence alignment remains one of the most powerful tools for assessing sequence relateness and the identification of structurally and functionally important protein regions. In this work, two new techniques are introduced to increase the sensitivity of dynamic programming and to enable checks for alignment consistency: Profile-preprocessed and secondary structure-induced alignments. Both strategies are based upon the hierarchical dynamic programming

Jaap Heringa

1999-01-01

207

Secondary Structure Propensities in Peptide Folding Simulations: A Systematic Comparison of Molecular Mechanics Interaction Schemes  

Microsoft Academic Search

We present a systematic study directed toward the secondary structure propensity and sampling behavior in peptide folding simulations with eight different molecular dynamics force-field variants in explicit solvent. We report on the combinational result of force field, water model, and electrostatic interaction schemes and compare to available experimental characterization of five studied model peptides in terms of reproduced structure and

Dirk Matthes; Bert L. de Groot

2009-01-01

208

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

PubMed

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

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

2011-08-30

209

Influence of Algal Secondary Metabolites on Plankton Community Structure  

Microsoft Academic Search

Plankton chemical ecologists face numerous challenges in understanding the roles of chemical signalling and defence. They\\u000a have to deal with a community of diverse species living in high dilutions in the nearly homogenous environments of oceans\\u000a and lakes. During the annual cycle the community structure changes dramatically, but local influences, such as gradients in\\u000a light, nutrients, and temperature, also can

Georg Pohnert

210

The Role of Secondary Structure on the Mechanical Properties of Titin  

NASA Astrophysics Data System (ADS)

Elastomeric proteins are characterized by high resilience and low stiffness. Recent work suggests that charge interactions between the proteins and water have a large role in these mechanical properties. However, some elastomeric proteins are nonpolar, and, as such, do not have high charge interactions with the surrounding water. This indicates that there are also other factors at work. We consider the role of secondary structure (i.e. alpha helices and beta sheets) on the mechanical properties of one such elastomeric protein, titin. Molecular dynamics simulations are performed on four different configurations: (i) the PEVK domain of titin (little secondary structure in its natural state), (ii) an immunoglobulin-like domain of titin (high secondary structure in its natural state), (iii) the same immunoglobulin-like domain with all of its secondary structure artificially removed, and finally (iv) the PEVK domain linked to the immunoglobulin-like domain in its natural state. These simulations will provide key insight on the role of secondary structure on mechanical properties, which can be used to more efficiently design smart materials.

Kappiyoor, Ravi; Dudek, Daniel; Puri, Ishwar

2013-03-01

211

A method for discovering common patterns from two RNA secondary structures and its application to structural repeat detection.  

PubMed

We propose an ab initio method, named DiscoverR, for finding common patterns from two RNA secondary structures. The method works by representing RNA secondary structures as ordered labeled trees and performs tree pattern discovery using an efficient dynamic programming algorithm. DiscoverR is able to identify and extract the largest common substructures from two RNA molecules having different sizes without prior knowledge of the locations and topologies of these substructures. We also extend DiscoverR to find repeated regions in an RNA secondary structure, and apply this extended method to detect structural repeats in the 3'-untranslated region of a protein kinase gene. We describe the biological significance of a repeated hairpin found by our method, demonstrating the usefulness of the method. DiscoverR is implemented in Java; a jar file including the source code of the program is available for download at http://bioinformatics.njit.edu/DiscoverR. PMID:22809414

Hua, Lei; Wang, Jason T L; Ji, Xiang; Malhotra, Ankur; Khaladkar, Mugdha; Shapiro, Bruce A; Zhang, Kaizhong

2012-06-22

212

A Reference Database for Circular Dichroism Spectroscopy Covering Fold and Secondary Structure Space  

SciTech Connect

Circular Dichroism (CD) spectroscopy is a long-established technique for studying protein secondary structures in solution. Empirical analyses of CD data rely on the availability of reference datasets comprised of far-UV CD spectra of proteins whose crystal structures have been determined. This article reports on the creation of a new reference dataset which effectively covers both secondary structure and fold space, and uses the higher information content available in synchrotron radiation circular dichroism (SRCD) spectra to more accurately predict secondary structure than has been possible with existing reference datasets. It also examines the effects of wavelength range, structural redundancy and different means of categorizing secondary structures on the accuracy of the analyses. In addition, it describes a novel use of hierarchical cluster analyses to identify protein relatedness based on spectral properties alone. The databases are shown to be applicable in both conventional CD and SRCD spectroscopic analyses of proteins. Hence, by combining new bioinformatics and biophysical methods, a database has been produced that should have wide applicability as a tool for structural molecular biology.

Lees,J.; Miles, A.; Wien, F.; Wallace, B.

2006-01-01

213

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

Microsoft Academic Search

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

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

214

In vitro secondary structure of the genomic RNA of satellite tobacco mosaic virus.  

PubMed

Satellite tobacco mosaic virus (STMV) is a T = 1 icosahedral virus with a single-stranded RNA genome. It is widely accepted that the RNA genome plays an important structural role during assembly of the STMV virion. While the encapsidated form of the RNA has been extensively studied, less is known about the structure of the free RNA, aside from a purported tRNA-like structure at the 3' end. Here we use selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) analysis to examine the secondary structure of in vitro transcribed STMV RNA. The predicted secondary structure is unusual in the sense that it is highly extended, which could be significant for protecting the RNA from degradation. The SHAPE data are also consistent with the previously predicted tRNA-like fold at the 3' end of the molecule, which is also known to hinder degradation. Our data are not consistent with the secondary structure proposed for the encapsidated RNA by Schroeder et al., suggesting that, if the Schroeder structure is correct, either the RNA is packaged as it emerges from the replication complex, or the RNA undergoes extensive refolding upon encapsidation. We also consider the alternative, i.e., that the structure of the encapsidated STMV RNA might be the same as the in vitro structure presented here, and we examine how this structure might be organized in the virus. This possibility is not rigorously ruled out by the available data, so it remains open to examination by experiment. PMID:23349871

Athavale, Shreyas S; Gossett, J Jared; Bowman, Jessica C; Hud, Nicholas V; Williams, Loren Dean; Harvey, Stephen C

2013-01-22

215

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

PubMed

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

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

2004-06-01

216

A method for WD40 repeat detection and secondary structure prediction.  

PubMed

WD40-repeat proteins (WD40s), as one of the largest protein families in eukaryotes, play vital roles in assembling protein-protein/DNA/RNA complexes. WD40s fold into similar ?-propeller structures despite diversified sequences. A program WDSP (WD40 repeat protein Structure Predictor) has been developed to accurately identify WD40 repeats and predict their secondary structures. The method is designed specifically for WD40 proteins by incorporating both local residue information and non-local family-specific structural features. It overcomes the problem of highly diversified protein sequences and variable loops. In addition, WDSP achieves a better prediction in identifying multiple WD40-domain proteins by taking the global combination of repeats into consideration. In secondary structure prediction, the average Q3 accuracy of WDSP in jack-knife test reaches 93.7%. A disease related protein LRRK2 was used as a representive example to demonstrate the structure prediction. PMID:23776530

Wang, Yang; Jiang, Fan; Zhuo, Zhu; Wu, Xian-Hui; Wu, Yun-Dong

2013-06-11

217

Evaluating minimalist mimics by exploring key orientations on secondary structures (EKOS).  

PubMed

Peptide mimics that display amino acid side-chains on semi-rigid scaffolds (not peptide polyamides) can be referred to as minimalist mimics. Accessible conformations of these scaffolds may overlay with secondary structures giving, for example, "minimalist helical mimics". It is difficult for researchers who want to apply minimalist mimics to decide which one to use because there is no widely accepted protocol for calibrating how closely these compounds mimic secondary structures. Moreover, it is also difficult for potential practitioners to evaluate which ideal minimalist helical mimics are preferred for a particular set of side-chains. For instance, what mimic presents i, i + 4, i + 7 side-chains in orientations that best resemble an ideal ?-helix, and is a different mimic required for a i, i + 3, i + 7 helical combination? This article describes a protocol for fitting each member of an array of accessible scaffold conformations on secondary structures. The protocol involves: (i) use quenched molecular dynamics (QMD) to generate an ensemble consisting of hundreds of accessible, low energy conformers of the mimics; (ii) representation of each of these as a set of C? and C? coordinates corresponding to three amino acid side-chains displayed by the scaffolds; (iii) similar representation of each combination of three side-chains in each ideal secondary structure as a set of C? and C? coordinates corresponding to three amino acid side-chains displayed by the scaffolds; and, (iv) overlay C? and C? coordinates of all the conformers on all the sets of side-chain "triads" in the ideal secondary structures and express the goodness of fit in terms of root mean squared deviation (RMSD, Å) for each overlay. We refer to this process as Exploring Key Orientations on Secondary structures (EKOS). Application of this procedure reveals the relative bias of a scaffold to overlay on different secondary structures, the "side-chain correspondences" (e.g. i, i + 4, i + 7 or i, i + 3, i + 4) of those overlays, and the energy of this state relative to the minimum located. This protocol was tested on some of the most widely cited minimalist ?-helical mimics (1-8 in the text). The data obtained indicates several of these compounds preferentially exist in conformations that resemble other secondary structures as well as ?-helices, and many of the ?-helical conformations have unexpected side-chain correspondences. These observations imply the featured minimalist mimics have more scope for disrupting PPI interfaces than previously anticipated. Finally, the same simulation method was used to match preferred conformations of minimalist mimics with actual protein/peptide structures at interfaces providing quantitative comparisons of predicted fits of the test mimics at protein-protein interaction sites. PMID:24121516

Xin, Dongyue; Ko, Eunhwa; Perez, Lisa M; Ioerger, Thomas R; Burgess, Kevin

2013-10-14

218

Secondary structure of the nicotinic acetylcholine receptor: implications for structural models of a ligand-gated ion channel.  

PubMed

The secondary structure and effects of two ligands, carbamylcholine and tetracaine, on the secondary structure of affinity-purified nicotinic acetylcholine receptor (nAChR) from Torpedo has been studied using Fourier transform infrared spectroscopy (FTIR). FTIR spectra of the nAChR were acquired in both 1H2O and 2H2O buffer and exhibit spectral features indicative of a substantial alpha-helical content with lesser amounts of beta-sheet and random coil structures. The resolution enhancement techniques of Fourier self-deconvolution and Fourier derivation reveal seven component bands contributing to both the amide I band and amide I' band contours in 1H2O and 2H2O, respectively. Curve-fitting estimates of the nAChR secondary structure are consistent with the qualitative analysis of the FTIR spectra as follows: 39% alpha-helix, 35% beta-sheet, 6% turn, and 20% random coil. Of particular interest is the estimated alpha-helical content as this value places restrictions on models of the nAChR transmembrane topology and on the types of secondary structures that may contribute to functional domains, such as the ligand-binding site. The estimated alpha-helical content is sufficient to account for four transmembrane alpha-helices in each nAChR subunit as well as a substantial portion of the extracellular and/or the cytoplasmic domains. FTIR spectra were also acquired in the presence and absence of 1 mM carbamylcholine and 5 mM tetracaine to examine the effects of ligand binding on the secondary structure of the nAChR. The similarity of the spectra, even after spectral deconvolution, indicates that the secondary structure of the nAChR is essentially unaffected by desensitization.(ABSTRACT TRUNCATED AT 250 WORDS) PMID:7516704

Méthot, N; McCarthy, M P; Baenziger, J E

1994-06-21

219

Multi-Strand RNA Secondary Structure Prediction and Nanostructure Design including Pseudoknots  

PubMed Central

We are presenting NanoFolder, a method for the prediction of the base pairing of potentially pseudoknotted multi-strand RNA nanostructures. We show that the method outperforms several other structure prediction methods when applied to RNA complexes with non-nested base pairs. We extended this secondary structure prediction capability to allow RNA sequence design. Using native PAGE, we experimentally confirm that 4 in silico designed RNA strands corresponding to a triangular RNA structure form the expected stable complex.

Bindewald, Eckart; Afonin, Kirill; Jaeger, Luc; Shapiro, Bruce A.

2011-01-01

220

Secondary structure models of the 3 untranslated regions of diverse R2 RNAs  

Microsoft Academic Search

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,

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

2008-01-01

221

Determination method of the balance of the secondary-structure-forming tendencies of force fields  

Microsoft Academic Search

We propose a new method of optimisation of backbone torsion-energy parameters in the force field for molecular simulations of protein systems. This method is based on the idea of balancing the secondary-structure-forming tendencies, namely, those of ?-helix and ?-sheet structures. We perform a minimisation of the backbone dihedral angle-based root-mean-square deviation of the helix and ? structure regions in many

Yoshitake Sakae; Yuko Okamoto

2010-01-01

222

Global or local? Predicting secondary structure and accessibility in mRNAs  

PubMed Central

Determining the structural properties of mRNA is key to understanding vital post-transcriptional processes. As experimental data on mRNA structure are scarce, accurate structure prediction is required to characterize RNA regulatory mechanisms. Although various structure prediction approaches are available, it is often unclear which to choose and how to set their parameters. Furthermore, no standard measure to compare predictions of local structure exists. We assessed the performance of different methods using two types of data: transcriptome-wide enzymatic probing information and a large, curated set of cis-regulatory elements. To compare the approaches, we introduced structure accuracy, a measure that is applicable to both global and local methods. Our results showed that local folding was more accurate than the classic global approach. We investigated how the locality parameters, maximum base pair span and window size, influenced the prediction performance. A span of 150 provided a reasonable balance between maximizing the number of accurately predicted base pairs, while minimizing effects of incorrect long-range predictions. We characterized the error at artificial sequence ends, which we reduced by setting the window size sufficiently greater than the maximum span. Our method, LocalFold, diminished all border effects and produced the most robust performance.

Lange, Sita J.; Maticzka, Daniel; Mohl, Mathias; Gagnon, Joshua N.; Brown, Chris M.; Backofen, Rolf

2012-01-01

223

Global or local? Predicting secondary structure and accessibility in mRNAs.  

PubMed

Determining the structural properties of mRNA is key to understanding vital post-transcriptional processes. As experimental data on mRNA structure are scarce, accurate structure prediction is required to characterize RNA regulatory mechanisms. Although various structure prediction approaches are available, it is often unclear which to choose and how to set their parameters. Furthermore, no standard measure to compare predictions of local structure exists. We assessed the performance of different methods using two types of data: transcriptome-wide enzymatic probing information and a large, curated set of cis-regulatory elements. To compare the approaches, we introduced structure accuracy, a measure that is applicable to both global and local methods. Our results showed that local folding was more accurate than the classic global approach. We investigated how the locality parameters, maximum base pair span and window size, influenced the prediction performance. A span of 150 provided a reasonable balance between maximizing the number of accurately predicted base pairs, while minimizing effects of incorrect long-range predictions. We characterized the error at artificial sequence ends, which we reduced by setting the window size sufficiently greater than the maximum span. Our method, LocalFold, diminished all border effects and produced the most robust performance. PMID:22373926

Lange, Sita J; Maticzka, Daniel; Möhl, Mathias; Gagnon, Joshua N; Brown, Chris M; Backofen, Rolf

2012-02-28

224

Aging of the Secondary Relaxation to Probe Structural Relaxation in the Glassy State  

SciTech Connect

The importance of glass formation and the glass transition is linked to their universality, embracing many classes of materials: metallic, inorganic, and organic. There is no agreement on what drives this phenomenon; moreover, experiments are challenging due to the nonequilibrium nature of the glassy state. We present a new approach that provides information about the very slow structural relaxation in the glassy state and reveals the important role of the secondary relaxation. Structural ({alpha}) relaxation times for glassy polyvinylethylene were determined from changes in the properties of the secondary process during physical aging. These {alpha}-relaxation times exceed 3 years, making them inaccessible via direct measurement.

Casalini, R. [George Mason University, Department of Chemistry, Fairfax, Virginia 22030 (United States); Naval Research Laboratory, Chemistry Division, Washington D.C. 20375-5342 (United States); Roland, C. M. [Naval Research Laboratory, Chemistry Division, Washington D.C. 20375-5342 (United States)

2009-01-23

225

Lyophilization-induced reversible changes in the secondary structure of proteins.  

PubMed Central

Changes in the secondary structure of some dozen different proteins upon lyophilization of their aqueous solutions have been investigated by means of Fourier-transform infrared spectroscopy in the amide III band region. Dehydration markedly (but reversibly) alters the secondary structure of all the proteins studied, as revealed by both the quantitative analysis of the second derivative spectra and the Gaussian curve fitting of the original infrared spectra. Lyophilization substantially increases the beta-sheet content and lowers the alpha-helix content of all proteins. In all but one case, proteins become more ordered upon lyophilization.

Griebenow, K; Klibanov, A M

1995-01-01

226

Testing mediation using multiple regression and structural equation modeling analyses in secondary data.  

PubMed

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 respective circumstances in which the two methods are most useful. One study examines the mediated effect of parents' social capital on parent involvement in Head Start programs through parent-child bond. The other study assesses the mediating effects of structured routine activities, delinquent association, and prosocial belief on the relationship between religiosity and juvenile delinquency. PMID:21917711

Li, Spencer D

2011-06-01

227

Secondary Interactions Involving Zinc-Bound Ligands: Roles in Structural Stabilization and Macromolecular Interactions  

PubMed Central

A large number of proteins contain bound zinc ions. These zinc ions are frequently coordinated by a combination of histidine and cysteine residues. In addition to atoms that coordinate directly to the zinc ions, these side chains have groups that can donate or accept hydrogen bonds from other groups. These secondary interactions can help stabilize the zinc-binding sites, can contribute to protein folding and stability, and, on occasion, can participate in interactions with other macromolecules. Five examples of these secondary interactions are discussed: carbonic anhydrase (where secondary interactions involving histidine residues stabilize the zinc-binding site thermodynamically and kinetically), retroviral nucleocapsid proteins and TRAF proteins (where cysteinate sulfur to peptide NH hydrogen bonds contribute to the structural relationships between adjacent domains), and zinc finger proteins and TIS11 where secondary interactions participate in protein-nucleic acid interactions.

Namuswe, Frances; Berg, Jeremy M.

2012-01-01

228

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

PubMed Central

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

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

2008-01-01

229

Fast and accurate determination of sites along the FUT2 in vitro transcript that are accessible to antisense oligonucleotides by application of secondary structure predictions and RNase H in combination with MALDI-TOF mass spectrometry  

PubMed Central

Alteration of gene expression by use of antisense oligonucleotides has considerable potential for therapeutic purposes and scientific studies. Although applied for almost 25 years, this technique is still associated with difficulties in finding antisense-effective regions along the target mRNA. This is mainly due to strong secondary structures preventing binding of antisense oligonucleotides and RNase H, playing a major role in antisense-mediated degradation of the mRNA. These difficulties make empirical testing of a large number of sequences complementary to various sites in the target mRNA a very lengthy and troublesome procedure. To overcome this problem, more recent strategies to find efficient antisense sites are based on secondary structure prediction and RNase H-dependent mechanisms. We were the first who directly combined these two strategies; antisense oligonucleotides complementary to predicted unpaired target mRNA regions were designed and hybridized to the corresponding RNAs. Incubation with RNase H led to cleavage of the RNA at the respective hybridization sites. Analysis of the RNA fragments by matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry, which has not been used in this context before, allowed exact determination of the cleavage site. Thus the technique described here is very promising when searching for effective antisense sites.

Gabler, Angelika; Krebs, Stefan; Seichter, Doris; Forster, Martin

2003-01-01

230

mRNA: guanine-N7 cap methyltransferases: identification of novel members of the family, evolutionary analysis, homology modeling, and analysis of sequence-structure-function relationships  

Microsoft Academic Search

BACKGROUND: The 5'-terminal cap structure plays an important role in many aspects of mRNA metabolism. Capping enzymes encoded by viruses and pathogenic fungi are attractive targets for specific inhibitors. There is a large body of experimental data on viral and cellular methyltransferases (MTases) that carry out guanine-N7 (cap 0) methylation, including results of extensive mutagenesis. However, a crystal structure is

Janusz M. Bujnicki; Marcin Feder; Monika Radlinska; Leszek Rychlewski

2001-01-01

231

COFOLD: an RNA secondary structure prediction method that takes co-transcriptional folding into account.  

PubMed

Existing state-of-the-art methods that take a single RNA sequence and predict the corresponding RNA secondary structure are thermodynamic methods. These aim to predict the most stable RNA structure. There exists by now ample experimental and theoretical evidence that the process of structure formation matters and that sequences in vivo fold while they are being transcribed. None of the thermodynamic methods, however, consider the process of structure formation. Here, we present a conceptually new method for predicting RNA secondary structure, called CoFold, that takes effects of co-transcriptional folding explicitly into account. Our method significantly improves the state-of-art in terms of prediction accuracy, especially for long sequences of >1000 nt in length. PMID:23511969

Proctor, Jeff R; Meyer, Irmtraud M

2013-03-19

232

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

PubMed

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

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

2010-01-11

233

NMR structure of the let-7 miRNA interacting with the site LCS1 of lin-41 mRNA from Caenorhabditis elegans  

PubMed Central

We have determined the 3D structure of a 34-nt RNA construct, herein named LCS1co, which mimics the interaction of let-7 microRNA (miRNA) to one of its complementary binding sites, LCS1, in the 3?-untranslated region of lin-41 mRNA by solution-state NMR spectroscopy. let-7 miRNAs control the timing of development of the nematode Caenorhabditis elegans and are highly conserved in mammals. The sequence and structure of the two conserved let-7 complementary sites, LCS1 and LCS2, in the 3?-untranslated region of lin-41 mRNA are important for a proper downregulation of lin-41. The high-resolution NMR structure reveals details of the binding of let-7 miRNA to lin-41 mRNA which involves formation of a complex with non-canonical structural elements within the seed region. LCS1co exhibits a stem-loop structure with two stems, an asymmetric internal loop and an adenine bulge. Comparison with the NMR solution-state structure of the let-7:lin-41 complex involving the LCS2-binding site shows that conformational freedom of the asymmetric internal loop of LCS1co correlates with a smaller bend between the upper and lower stems in comparison to the well-defined asymmetric loop of LCS2co.

Cevec, Mirko; Thibaudeau, Christophe; Plavec, Janez

2010-01-01

234

Fast learning optimized prediction methodology (FLOPRED) for protein secondary structure prediction  

PubMed Central

Computational methods are rapidly gaining importance in the field of structural biology, mostly due to the explosive progress in genome sequencing projects and the large disparity between the number of sequences and the number of structures. There has been an exponential growth in the number of available protein sequences and a slower growth in the number of structures. There is therefore an urgent need to develop computational methods to predict structures and identify their functions from the sequence. Developing methods that will satisfy these needs both efficiently and accurately is of paramount importance for advances in many biomedical fields, including drug development and discovery of biomarkers. A novel method called Fast Learning Optimized PREDiction Methodology (FLOPRED) is proposed for predicting protein secondary structure, using knowledge-based potentials combined with structure information from the CATH database. A Neural Network-based Extreme Learning Machine (ELM) and advanced Particle Swarm Optimization (PSO) are used with this data that yield better and faster convergence to produce more accurate results. Protein secondary structures are predicted efficiently, reliably, more efficiently and more accurately using FLOPRED. These techniques yield superior classification of secondary structure elements, with a training accuracy ranging between 83% and 87% over a wide range of hidden neurons and a cross-validated testing accuracy ranging between 81% and 84% and a Segment OVerlap (SOV) score of 78% that are obtained with different sets of proteins. These results are comparable to other recently published studies, but are obtained with greater efficiencies, in terms of time and cost.

Saraswathi, Saras; Fernandez-Martinez, Juan Luis; Kolinski, Andrzej; Jernigan, Robert L.; Kloczkowski, Andrzej

2013-01-01

235

Polyadenylation accelerates degradation of chloroplast mRNA.  

PubMed Central

The expression of chloroplast genes is regulated by several mechanisms, one of which is the modulation of RNA stability. To understand how this regulatory step is controlled during chloroplast development, we have begun to define the mechanism of plastid mRNA degradation. We show here that the degradation petD mRNA involves endonucleolytic cleavage at specific sites upstream of the 3' stem-loop structure. The endonucleolytic petD cleavage products can be polyadenylated in vitro, and similar polyadenylated RNA products are detectable in vivo. PCR analysis of the psbA and psaA-psaB-rps14 operons revealed other polyadenylated endonucleolytic cleavage products, indicating that poly(A) addition appears to be an integral modification during chloroplast mRNA degradation. Polyadenylation promotes efficient degradation of the cleaved petD RNAs by a 3'-5' exoribonuclease. Furthermore, polyadenylation also plays an important role in the degradation of the petD mRNA 3' end. Although the 3' end stem-loop is usually resistant to nucleases, adenylation renders the secondary structure susceptible to the 3'-5' exoribonuclease. Analysis of 3' ends confirms that polyadenylation occurs in vivo, and reveals that the extent of adenylation increases during the degradation of plastid mRNA in the dark. Based on these results, we propose a novel mechanism for polyadenylation in the regulation of plastid mRNA degradation. Images

Kudla, J; Hayes, R; Gruissem, W

1996-01-01

236

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

NASA Astrophysics Data System (ADS)

The understanding of the flow structure in deep-sea turbidity currents is important for the formation of submarine meandering channels. Similarly to the case of subaerial channels, several types of secondary flows include turbulence-, curvature- and bed morphodynamic-driven flow structures that modulate sediment transport and channel bed morphodynamics. This study focuses on [1] a review of long-time research effort (Abad et al., 2011) that tackles the description of the secondary flow associated with a subaqueous bottom current (saline) in a high-curvature meandering channel and [2] ongoing numerical simulations of similar settings as the experiments to describe the entire flow structure. In the case of subaerial channels, the classical Rozovskiian paradigm is often invoked which indicates that the near-bottom secondary flow in a bend is directed inward. It has recently been suggested based on experimental and theoretical considerations, however, that this pattern is reversed (near-bottom secondary flow is directed outward) in the case of submarine meandering channels. Experimental results presented here, on the other hand, indicate near-bottom secondary flows that have the same direction as observed in a river (normal secondary flow). The implication is an apparent contradiction between experimental results. This study combines theory, experiments, reconstructions of field flows and ongoing simulations to resolve this apparent contradiction based on the flow densimetric Froude number. Three ranges of densimetric Froude number are found, such that a) in an upper regime, secondary flow is reversed, b) in a middle regime, it is normal and c) in a lower regime, it is reversed. These results are applied to field scale channel-forming turbidity currents in the Amazon submarine canyon-fan system (Amazon Channel) and the Monterey canyon and a saline underflow in the Black Sea flowing from the Bosphorus. Our analysis indicates that secondary flow should be normal throughout most of the Amazon submarine fan reach, lower-regime reversed in the case of the Black Sea underflow, and upper-regime reversed in the case of the Monterey canyon. The analysis predicts both normal and reversed regimes in the Amazon submarine canyon reach. This research presents insights on the importance of flow structure not only to describe subaqueous bed morphodynamics, but also to understand evolution of submarine meandering channels, therefore its importance for developing accurate morphodynamic models. Reference: Abad, J. D., Sequeiros, O. E., Spinewine, B., Pirmez, C., Garcia, M. H., Parker, G. (2011). SECONDARY CURRENT OF SALINE UNDERFLOW IN A HIGHLY MEANDERING CHANNEL: EXPERIMENTS AND THEORY. In press, Journal of Sedimentary Research

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

2011-12-01

237

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

ERIC Educational Resources Information Center

|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'…

Palla, Marina; Potari, Despina; Spyrou, Panagiotis

2012-01-01

238

Exploring protein fold space by secondary structure prediction using data distribution method on Grid platform  

Microsoft Academic Search

Motivation: Since the newly developed Grid platform has been considered as a powerful tool to share resources in the Internet environment, it is of interest to demonstrate an efficient methodology to process massive biological data on the Grid environments at a low cost. This paper presents an efficient and economical method based on a Grid platform to predict secondary structures

Soojin Lee; Min-kyu Cho; Jin-won Jung; Jai-hoon Kim; Weontae Lee

2004-01-01

239

Complete nucleotide sequence of bacteriophage MS2 RNA: primary and secondary structure of the replicase gene  

Microsoft Academic Search

Bacteriophage MS2 RNA is 3,569 nucleotides long. The nucleotide sequence has been established for the third and last gene, which codes for the replicase protein. A secondary structure model has also been proposed. Biological properties, such as ribosome binding and codon interactions can now be discussed on a molecular basis. As the sequences for the other regions of this RNA

W. Fiers; R. Contreras; F. Duerinck; G. Haegeman; D. Iserentant; J. Merregaert; W. Min Jou; F. Molemans; A. Raeymaekers; A. van den Berghe; G. Volckaert; M. Ysebaert

1976-01-01

240

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...

241

Incorporating Knowledge of Secondary Structures in a L-System-Based Encoding for Protein Folding  

Microsoft Academic Search

An encoding scheme for protein folding on lattice models, inspired by parametric L-systems, was proposed. The encoding incorpo- rates problem domain knowledge in the form of predesigned production rules that capture commonly known secondary structures: ?-helices and ?-sheets. The ability of this encoding to capture protein native con- formations was tested using an evolutionary algorithm as the inference procedure for

Gabriela Ochoa; Natalio Krasnogor

2005-01-01

242

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

Microsoft Academic Search

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

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

1997-01-01

243

Inclusion in Secondary Schools: An Analysis of School Structure Based on Teachers' Images of Change  

Microsoft Academic Search

The practice of providing totally inclusive schools to meet the needs of all learners is one of the emerging service delivery options gaining widespread support in public education in Canada and the United States. While many elementary schools have taken the initiative and established successful models of full inclusion, secondary schools, in part because of the historical-structural characteristics of these

J. David MacKinnon; Margaret E. Brown

1994-01-01

244

Use of tiling array data and RNA secondary structure predictions to identify noncoding RNA genes  

Microsoft Academic Search

BACKGROUND: Within the last decade a large number of noncoding RNA genes have been identified, but this may only be the tip of the iceberg. Using comparative genomics a large number of sequences that have signals concordant with conserved RNA secondary structures have been discovered in the human genome. Moreover, genome wide transcription profiling with tiling arrays indicate that the

Christian Weile; Paul P Gardner; Mads M Hedegaard; Jeppe Vinther

2007-01-01

245

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

EPA Science Inventory

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

246

Composite structure composed of overlapped fibre bundles, thermoplastic resin and metal plate for secondary forming process  

Microsoft Academic Search

A simple shape of a composite is preferable in mass production, while a curved or stretched shape is sometimes preferable for final products. High formability would enable the composite to deform into a preferable shape by secondary forming. In this paper, a structure for a composite is proposed to enhance formability. The composite is composed of reinforcing fibre bundles, thermoplastic

Takashi Kuboki; Shun-ichi Uematsu; Makoto Murata

2010-01-01

247

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

ERIC Educational Resources Information Center

|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…

Pikaart, Michael

2011-01-01

248

A parallel algorithm for estimating the secondary structure in ribonucleic acids  

Microsoft Academic Search

A parallel algorithm for estimating the secondary structure of an RNA molecule is presented in this paper. The mathematical problem to compute an optimal folding based on free-energy minimization is mapped onto a graph planarization problem. In the planarization problem we want to maximize the number of edges in a plane with no two edges crossing each other. To solve

Y. Takefuji; C. W. Lin; K. C. Lee

1990-01-01

249

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

PubMed Central

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

2013-01-01

250

PPfold 3.0: fast RNA secondary structure prediction using phylogeny and auxiliary data.  

PubMed

PPfold is a multi-threaded implementation of the Pfold algorithm for RNA secondary structure prediction. Here we present a new version of PPfold, which extends the evolutionary analysis with a flexible probabilistic model for incorporating auxiliary data, such as data from structure probing experiments. Our tests show that the accuracy of single-sequence secondary structure prediction using experimental data in PPfold 3.0 is comparable to RNAstructure. Furthermore, alignment structure prediction quality is improved even further by the addition of experimental data. PPfold 3.0 therefore has the potential of producing more accurate predictions than it was previously possible. Availability and implementation: PPfold 3.0 is available as a platform-independent Java application and can be downloaded from http://birc.au.dk/software/ppfold. PMID:22877864

Sükösd, Zsuzsanna; Knudsen, Bjarne; Kjems, Jørgen; Pedersen, Christian N S

2012-08-09

251

Secondary structure of T4 gene 33 protein. Fourier transform infrared and circular dichroic spectroscopic studies.  

PubMed

The secondary structure of bacteriophage T4 gene 33 protein (gp33) has been quantitatively examined by using Fourier transform infrared (FT-IR) and circular dichroism (CD) spectroscopy. Resolution enhancement techniques, including Fourier deconvolution and derivative spectroscopy were used to quantitate the spectral information from the amide I bands. The relative areas of these component bands indicate 21% alpha-helix, 25% beta-sheet, 34% turn, 12% random coil and 8% other undefined structures in gp33. An analysis of the CD spectrum of gp33 at the same pH and temperature revealed 19% alpha-helix, 25% beta-sheet, 13% turn and 43% random coil structures. The possible reasons for the discrepancies in estimates of the contributions to the secondary structure from turns and random coils are discussed. PMID:9184943

Shao, W; Kearns, D R; Sanders, G M

1997-04-01

252

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

Microsoft Academic Search

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

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

1998-01-01

253

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

Microsoft Academic Search

We have synthesized and characterized a family of structured oligo-N-substituted-glycines (peptoids) up to 36 residues in length by using an efficient solid-phase protocol to incorporate chemically diverse side chains in a sequence-specific fashion. We investigated polypeptoids containing side chains with a chiral center adjacent to the main chain nitrogen. Some of these sequences have stable secondary structure, despite the achirality

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

1998-01-01

254

Exploiting the past and the future in protein secondary structure prediction  

Microsoft Academic Search

Motivation: Predicting the secondary structure of a protein (alpha-helix, beta-sheet, coil) is an important step towards elucidating its three-dimensional structure, as well as its function. Presently, the best predictors are based on machine learning approaches, in particular neural network architectures with a fixed, and relatively short, input window of amino acids, centered at the prediction site. Although a fixed small

Pierre Baldi; Søren Brunak; Paolo Frasconi; Giovanni Soda; Gianluca Pollastri

1999-01-01

255

Secondary Structure of Sea Anemone Cytolysins in Soluble and Membrane Bound Form by Infrared Spectroscopy  

Microsoft Academic Search

Attenuated total reflection (ATR) Fourier transform infrared spectroscopy (FTIR) was used to investigate the secondary structure of two pore-forming cytolysins from the sea anemoneStichodactyla helianthusand their interaction with lipid membranes. Frequency component analysis of the amide I' band indicated that these peptides are composed predominantly of beta structure, comprising 44–50% ?-sheet, 18–20% ?-turn, 12–15% ?-helix, and 19–22% random coil. Upon

Gianfranco Menestrina; Veronique Cabiaux; Mayra Tejuca

1999-01-01

256

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

NASA Astrophysics Data System (ADS)

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

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

1996-10-01

257

A theoretical reappraisal of polylysine in the investigation of secondary structure sensitivity of infrared spectra.  

PubMed

Infrared spectroscopy has long provided a means to estimate the secondary structure of proteins and peptides. In particular, the vibrational spectra of the amide I' band have been widely used for this purpose as the frequency positions of the amide I' bands are related to the presence of specific secondary structures. Here, we calculate the amide I' IR spectra of polylysine in aqueous solution in its three secondary structure states, i.e., ?-helix, ?-sheet, and random coil, by means of a mixed quantum mechanics/molecular dynamics (QM/MD) theoretical-computational methodology based on the perturbed matrix method (PMM). The computed spectra show a good agreement with the experimental ones. Although our calculations confirm the importance of the excitonic coupling in reproducing important spectral features (e.g., the width of the absorption band), the frequency shift due to secondary-structure changes is also well reproduced without the inclusion of the excitonic coupling, pointing to a role played by the local environment. Concerning the ?-conformation spectrum, which is characterized by a double-peak amide I' band due to excitonic coupling, our results indicate that it does not correspond to a generic antiparallel ?-sheet (e.g., of the typical size present in native proteins) but is rather representative of extended ?-structures, which are common in ?-aggregates. Moreover, we also show that the solvent has a crucial role in the shape determination of the ?-conformation amide I' band and in particular in the disappearance of the high-frequency secondary peak in the case of small sheets (e.g., 6-stranded). PMID:22397736

Polzi, Laura Zanetti; Daidone, Isabella; Amadei, Andrea

2012-03-07

258

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

PubMed

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

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

1988-02-01

259

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

PubMed Central

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.

Woetzel, Nils; Karakas, Mert; Staritzbichler, Rene; Muller, Ralf; Weiner, Brian E.; Meiler, Jens

2012-01-01

260

Translational halt during elongation caused by G-quadruplex formed by mRNA.  

PubMed

mRNA forms various secondary and tertiary structures that affect gene expression. Although structures formed in the untranslated regions (UTRs) of mRNAs that inhibit translation have been characterized, stable mRNA structures in open reading frames (ORFs) may also cause translational halt or slow translation elongation. We previously established a method, termed a synchronized translation assay, that enables time course analysis of single turnover translation elongation. In this method, translation initiation, which is a rate determining step of the translation procedure, can be ignored because all ribosomes are synchronized on a specific position of mRNA before translation elongation is restarted from this position. In this paper, we used the synchronized translation assay to evaluate the effects of a G-quadruplex structure located at various positions within the mRNA ORF on translational halt. PMID:23747335

Endoh, Tamaki; Kawasaki, Yu; Sugimoto, Naoki

2013-06-07

261

Structural Model of Human Ceruloplasmin Based on Internal Triplication, Hydrophilic\\/Hydrophobic Character, and Secondary Structure of Domains  

Microsoft Academic Search

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≈ 132,000) consists of a single polypeptide chain (1046 amino acid residues)

Thomas L. Ortel; Nobuhiro Takahashi; Frank W. Putnam

1984-01-01

262

Dynamics of Secondary Large-Scale Structures in ETG Turbulence Simulations  

NASA Astrophysics Data System (ADS)

The dynamics of secondary large-scale structures in electron-temperature-gradient (ETG) turbulence is investigated based on gyrofluid simulations in sheared slab geometry. It is found that structural bifurcation to zonal flow dominated or streamer-like states depends on the spectral anisotropy of turbulent ETG fluctuation, which is governed by the magnetic shear. The turbulent electron transport is suppressed by enhanced zonal flows. However, it is still low even if the streamer is formed in ETG turbulence with strong shears. It is shown that the low transport may be related to the secondary excitation of poloidal long-wavelength mode due to the beat wave of the most unstable components or a modulation instability. This large-scale structure with a low frequency and a long wavelength may saturate, or at least contribute to the saturation of ETG fluctuations through a poloidal mode coupling. The result suggests a low fluctuation level in ETG turbulence.

Li, Jiquan; Y, Kishimoto; Dong, Jiaqi; N, Miyato; T, Matsumoto

2006-01-01

263

Analysis of Secondary Structure in Proteins by Chemical Cross-Linking Coupled to Mass Spectrometry  

PubMed Central

Chemical cross-linking is an attractive technique for the study of the structure of protein complexes due to its low sample consumption and short analysis time. Furthermore, distance constraints obtained from the identification of cross-linked peptides by mass spectrometry can be used to construct and validate protein models. If a sufficient number of distance constraints are obtained, then determining the secondary structure of a protein can allow inference of the protein’s fold. In this work, we show how the distance constraints obtained from cross-linking experiments can identify secondary structures within the protein sequence. Molecular modeling of alpha helices and beta sheets indicate cross-linking patterns based on the topological distances between reactive residues. DSS[1] cross-linking experiments with model alpha helix containing proteins corroborated the molecular modeling predictions. The patterns established here can be extended to other cross-linkers with known spacing lengths.

Fioramonte, Mariana; dos Santos, Aline Mara; McIlwain, Sean; Noble, William S.; Franchini, Kleber Gomes; Gozzo, Fabio Cesar

2013-01-01

264

Secondary Structure Propensities in Peptide Folding Simulations: A Systematic Comparison of Molecular Mechanics Interaction Schemes  

PubMed Central

Abstract We present a systematic study directed toward the secondary structure propensity and sampling behavior in peptide folding simulations with eight different molecular dynamics force-field variants in explicit solvent. We report on the combinational result of force field, water model, and electrostatic interaction schemes and compare to available experimental characterization of five studied model peptides in terms of reproduced structure and dynamics. The total simulation time exceeded 18 ?s and included simulations that started from both folded and extended conformations. Despite remaining sampling issues, a number of distinct trends in the folding behavior of the peptides emerged. Pronounced differences in the propensity of finding prominent secondary structure motifs in the different applied force fields suggest that problems point in particular to the balance of the relative stabilities of helical and extended conformations.

Matthes, Dirk; de Groot, Bert L.

2009-01-01

265

HotKnots: Heuristic prediction of RNA secondary structures including pseudoknots  

PubMed Central

We present HotKnots, a new heuristic algorithm for the prediction of RNA secondary structures including pseudoknots. Based on the simple idea of iteratively forming stable stems, our algorithm explores many alternative secondary structures, using a free energy minimization algorithm for pseudoknot free secondary structures to identify promising candidate stems. In an empirical evaluation of the algorithm with 43 sequences taken from the Pseudobase database and from the literature on pseudoknotted structures, we found that overall, in terms of the sensitivity and specificity of predictions, HotKnots outperforms the well-known Pseudoknots algorithm of Rivas and Eddy and the NUPACK algorithm of Dirks and Pierce, both based on dynamic programming approaches for limited classes of pseudoknotted structures. It also outperforms the heuristic Iterated Loop Matching algorithm of Ruan and colleagues, and in many cases gives better results than the genetic algorithm from the STAR package of van Batenburg and colleagues and the recent pknotsRG-mfe algorithm of Reeder and Giegerich. The HotKnots algorithm has been implemented in C/C++ and is available from http://www.cs.ubc.ca/labs/beta/Software/HotKnots.

REN, JIHONG; RASTEGARI, BAHARAK; CONDON, ANNE; HOOS, HOLGER H.

2005-01-01

266

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

PubMed Central

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

Berkhout, B; Schoneveld, I

1993-01-01

267

Phylogenetic analysis of molluscan mitochondrial LSU rDNA sequences and secondary structures.  

PubMed

Mollusks are an extraordinarily diverse group of animals with an estimated 200,000 species, second only to the phylum Arthropoda. We conducted a comparative analysis of complete mitochondrial ribosomal large subunit sequences (LSU) of a chiton, two bivalves, six gastropods, and a cephalopod. In addition, we determined secondary structure models for each of them. Comparative analyses of nucleotide variation revealed substantial length variation among the taxa, with stylommatophoran gastropods possessing the shortest lengths. Phylogenetic analyses of the nucleotide sequence data supported the monophyly of Albinaria, Euhadra herklotsi + Cepaea nemoralis, Stylommatophora, Cerithioidea, and when only transversions are included, the Bivalvia. The phylogenetic limits of the mitochondrial LSU rRNA gene within mollusks appear to be up to 400 million years, although this estimate will have to be tested further with additional taxa. Our most novel finding was the discovery of phylogenetic signal in the secondary structure of rRNA of mollusks. The absence of entire stem/loop structures in Domains II, III, and V can be viewed as three shared derived characters uniting the stylommatophoran gastropods. The absence of the aforementioned stem/loop structure explains much of the observed length variation of the mitochondrial LSU rRNA found within mollusks. The distribution of these unique secondary structure characters within mollusks should be examined. PMID:10764537

Lydeard, C; Holznagel, W E; Schnare, M N; Gutell, R R

2000-04-01

268

VH gene transcription creates stabilized secondary structures for coordinated mutagenesis during somatic hypermutation  

PubMed Central

During the adaptive immune response, antigen challenge triggers a million-fold increase in mutation rates in the variable region antibody genes. The frequency of mutation is causally and directly linked to transcription, which provides ssDNA and drives supercoiling that stabilizes secondary structures containing unpaired, intrinsically mutable bases. Simulation analysis of transcription in VH5 reveals a dominant 65 nt secondary structure in the non-transcribed strand containing six sites of mutable ssDNA that have also been identified independently in human B cell lines and in primary mouse B cells. This dominant structure inter-converts briefly with less stable structures and is formed repeatedly during transcription, due to periodic pauses and backtracking. In effect, this creates a stable yet dynamic “mutability platform” consisting of ever-changing patterns of unpaired bases that are simultaneously exposed and therefore able to coordinate mutagenesis. Such a complex of secondary structures may be the source of ssDNA for enzyme-based diversification, which ultimately results in high affinity antibodies.

Wright, Barbara E.; Schmidt, Karen H.; Minnick, Michael F.; Davis, Nick

2008-01-01

269

Up, down, and around: identifying recurrent interactions within and between super-secondary structures in ?-propellers.  

PubMed

The examination and analysis of super-secondary structures or other specific structural patterns associated with particular functions, sequence motifs, or structural contexts require that the set of structures examined shares the same feature. This seems obvious but in practice this may often present problems such as identifying complete sets of data avoiding false positives. In the case of the ?-propeller structures the symmetry of the propeller creates problems for many structure similarity search programs. Here we present a procedure that will identify propeller structures in PDB and assign them to the different N-propeller types. In addition we outline methods to examine similarities and differences within and between the four stranded up-and-down blades of the ?-propeller. PMID:22987345

Thirup, Søren; Gupta, Vikas; Quistgaard, Esben M

2013-01-01

270

Mutational analysis of apolipoprotein B mRNA editing enzyme (APOBEC1): structure-function relationships of RNA editing and dimerization  

Microsoft Academic Search

APOBEC1 is the catalytic subunit of an enzyme complex that mediates apolipoprotein (apo) B mRNA edit- ing. It dimerizes in vitro and requires complementation fac- tor(s) for its editing activity. We have performed a system- atic analysis of the structure-functional relationship of APOBEC1 by targeted mutagenesis of various sequence motifs within the protein. Using in vitro RNA editing assay, we

Ba-Bie Teng; Scott Ochsner; Qian Zhang; Kizhake V. Soman; Paul P. Lau; Lawrence Chan

271

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

PubMed Central

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

Zuker, M; Jacobson, A B

1995-01-01

272

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

ERIC Educational Resources Information Center

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

Betoret, Fernando Domenech

2009-01-01

273

Conserved Sequence Motifs, Alignment, and Secondary Structure for the Third Domain of Animal 12s rRNA  

Microsoft Academic Search

Secondary structure models are an important step for aligning sequences, understanding probabilities of nucleotide substitutions, and evaluating the reliability of phylogenetic reconstructions. A set of conserved sequence motifs is derived from comparative sequence analysis of 184 invertebrate and vertebrate taxa (including many taxa from the same genera, families, and orders) with reference to a secondary structure model for domain III

Robert E. Hickson; I Chris Simon; Alan Cooper; Greg S. Spicer; Jack Sullivan; David Penny

274

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

NASA Astrophysics Data System (ADS)

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

Wolfsheimer, S.; Hartmann, A. K.

2010-08-01

275

Secondary structure of ITS2 rRNA provides taxonomic characters for systematic studies — a case in Lycoperdaceae ( Basidiomycota)  

Microsoft Academic Search

The secondary structure of the ITS2 rDNA transcript (pre-rRNA) could provide information for identifying homologous nucleotide characters useful for cladistic inference of relationships. Such structure data could become taxonomic characters. This work compares the effect of several modern nucleotide alignment strategies, including those making use of structure data, on phylogenetic inference. From both the phylogenetic analyses and comparative secondary structure,

Dirk Krüger; Andrea GARGASz

2008-01-01

276

eIF4E-binding protein regulation of mRNAs with differential 5?-UTR secondary structure: a polyelectrostatic model for a component of protein-mRNA interactions  

PubMed Central

Control of translation in eukaryotes is complex, depending on the binding of various factors to mRNAs. Available data for subsets of mRNAs that are translationally up- and down-regulated in yeast eIF4E-binding protein (4E-BP) deletion mutants are coupled with reported mRNA secondary structure measurements to investigate whether 5?-UTR secondary structure varies between the subsets. Genes with up-regulated translational efficiencies in the caf20? mutant have relatively high averaged 5?-UTR secondary structure. There is no apparent wide-scale correlation of RNA-binding protein preferences with the increased 5?-UTR secondary structure, leading us to speculate that the secondary structure itself may play a role in differential partitioning of mRNAs between eIF4E/4E-BP repression and eIF4E/eIF4G translation initiation. Both Caf20p and Eap1p contain stretches of positive charge in regions of predicted disorder. Such regions are also present in eIF4G and have been reported to associate with mRNA binding. The pattern of these segments, around the canonical eIF4E-binding motif, varies between each 4E-BP and eIF4G. Analysis of gene ontology shows that yeast proteins containing predicted disordered segments, with positive charge runs, are enriched for nucleic acid binding. We propose that the 4E-BPs act, in part, as differential, flexible, polyelectrostatic scaffolds for mRNAs.

Cawley, Andrew; Warwicker, Jim

2012-01-01

277

eIF4E-binding protein regulation of mRNAs with differential 5'-UTR secondary structure: a polyelectrostatic model for a component of protein-mRNA interactions.  

PubMed

Control of translation in eukaryotes is complex, depending on the binding of various factors to mRNAs. Available data for subsets of mRNAs that are translationally up- and down-regulated in yeast eIF4E-binding protein (4E-BP) deletion mutants are coupled with reported mRNA secondary structure measurements to investigate whether 5'-UTR secondary structure varies between the subsets. Genes with up-regulated translational efficiencies in the caf20? mutant have relatively high averaged 5'-UTR secondary structure. There is no apparent wide-scale correlation of RNA-binding protein preferences with the increased 5'-UTR secondary structure, leading us to speculate that the secondary structure itself may play a role in differential partitioning of mRNAs between eIF4E/4E-BP repression and eIF4E/eIF4G translation initiation. Both Caf20p and Eap1p contain stretches of positive charge in regions of predicted disorder. Such regions are also present in eIF4G and have been reported to associate with mRNA binding. The pattern of these segments, around the canonical eIF4E-binding motif, varies between each 4E-BP and eIF4G. Analysis of gene ontology shows that yeast proteins containing predicted disordered segments, with positive charge runs, are enriched for nucleic acid binding. We propose that the 4E-BPs act, in part, as differential, flexible, polyelectrostatic scaffolds for mRNAs. PMID:22718971

Cawley, Andrew; Warwicker, Jim

2012-06-20

278

On the structure and dynamics of secondary n-alkyl cations  

NASA Astrophysics Data System (ADS)

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.

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

2009-09-01

279

TurboFold: Iterative probabilistic estimation of secondary structures for multiple RNA sequences  

PubMed Central

Background The prediction of secondary structure, i.e. the set of canonical base pairs between nucleotides, is a first step in developing an understanding of the function of an RNA sequence. The most accurate computational methods predict conserved structures for a set of homologous RNA sequences. These methods usually suffer from high computational complexity. In this paper, TurboFold, a novel and efficient method for secondary structure prediction for multiple RNA sequences, is presented. Results TurboFold takes, as input, a set of homologous RNA sequences and outputs estimates of the base pairing probabilities for each sequence. The base pairing probabilities for a sequence are estimated by combining intrinsic information, derived from the sequence itself via the nearest neighbor thermodynamic model, with extrinsic information, derived from the other sequences in the input set. For a given sequence, the extrinsic information is computed by using pairwise-sequence-alignment-based probabilities for co-incidence with each of the other sequences, along with estimated base pairing probabilities, from the previous iteration, for the other sequences. The extrinsic information is introduced as free energy modifications for base pairing in a partition function computation based on the nearest neighbor thermodynamic model. This process yields updated estimates of base pairing probability. The updated base pairing probabilities in turn are used to recompute extrinsic information, resulting in the overall iterative estimation procedure that defines TurboFold. TurboFold is benchmarked on a number of ncRNA datasets and compared against alternative secondary structure prediction methods. The iterative procedure in TurboFold is shown to improve estimates of base pairing probability with each iteration, though only small gains are obtained beyond three iterations. Secondary structures composed of base pairs with estimated probabilities higher than a significance threshold are shown to be more accurate for TurboFold than for alternative methods that estimate base pairing probabilities. TurboFold-MEA, which uses base pairing probabilities from TurboFold in a maximum expected accuracy algorithm for secondary structure prediction, has accuracy comparable to the best performing secondary structure prediction methods. The computational and memory requirements for TurboFold are modest and, in terms of sequence length and number of sequences, scale much more favorably than joint alignment and folding algorithms. Conclusions TurboFold is an iterative probabilistic method for predicting secondary structures for multiple RNA sequences that efficiently and accurately combines the information from the comparative analysis between sequences with the thermodynamic folding model. Unlike most other multi-sequence structure prediction methods, TurboFold does not enforce strict commonality of structures and is therefore useful for predicting structures for homologous sequences that have diverged significantly. TurboFold can be downloaded as part of the RNAstructure package at http://rna.urmc.rochester.edu.

2011-01-01

280

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

PubMed

The king cobra neurotoxin CM-11 is a small protein with 72 amino acid residues. After its complete assignments of (1)H-NMR resonance's were obtained using various 2D-NMR technologies, including DQF-COSY, clean-TOCSY and NOESY, the secondary structure was analysed by studying the various NOEs extracted from the NOESY spectra and the distribution of chemical shifts. The secondary structure was finally determined by MCD as follows: a triple-strand antiparallel beta sheet with I20-W26, R37-A43 and V53-S59 as its beta strands, a short alpha helix formed by W30-G35 and four turns formed by P7-K1O, C14-G17, K50-V53 and D61-N64. PMID:12215791

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

1997-01-01

281

Effect of hexafluoroisopropanol on the thermodynamics of peptide secondary structure formation  

SciTech Connect

This report provides additional evidence for the importance of hydrophobic interactions in peptide secondary structure formation. For the hydrophobically driven {beta} hairpin formation examined, the addition of HFIP to the 8% level increases hairpin formation and increases {Delta}C{sub p} by nearly a factor of 3. Surprisingly, {alpha} helices bearing a few non-interacting hydrophobic residues can display even larger {Delta}C{sub p} values. The initial phase of secondary structure induction during fluoroalcohol titrations of peptides appears to be largely the result of these effects rather than differential stabilization (or destabilization) of the folded versus coil conformation by alcohol/peptide binding interactions, as the latter would be reflected predominantly in the enthalpy term. The addition of limited quantities of fluoroalcohol may mimic the early hydrophobic collapse stage of protein folding.

Andersen, N.H.; Dyer, R.B.; Fesinmeyer, R.M.; Gai, F.; Liu, Z.; Neidigh, J.W.; Tong, H.

1999-10-27

282

A protein secondary structure prediction scheme for the IBM PC and compatibles.  

PubMed

A prediction scheme has been developed for the IBM PC and compatibles containing computer programs which make use of the protein secondary structure prediction algorithms of Nagano (1977a,b), Garnier et al. (1978), Burgess et al. (1974), Chou and Fasman (1974a,b), Lim (1974) and Dufton and Hider (1977). The results of the individual prediction methods are combined as described by Hamodrakas et al. (1982) by the program PLOTPROG to produce joint prediction histograms for a protein, for three types of secondary structure: alpha-helix, beta-sheet and beta-turns. The scheme requires uniform input for the prediction programs, produced by any word processor, spreadsheet, editor or database program and produces uniform output on a printer, a graphics screen or a file. The scheme is independent of any additional software and runs under DOS 2.0 or later releases. PMID:3208182

Hamodrakas, S J

1988-11-01

283

Effects of heat treatment on the protein secondary structure and pigment microenvironment in photosystem 1 complex  

Microsoft Academic Search

The protein secondary structure and pigments' microenvironment in photosystem 1 (PS1) complexes were studied in the temperature range of 25–80 °C using Fourier transform infrared (FT-IR) and circular dichroism (CD) spectroscopy, respectively. Quantitative analysis of the component bands of the amide I band (1 700–1 600 cm?1) showed no significant change below 50 °C. However, apparent conformational changes occurred at

Z.-H. Hu; Y.-N. Xu; Y.-D. Gong; T.-Y. Kuang

2005-01-01

284

Profiles and fuzzy K-nearest neighbor algorithm for protein secondary structure prediction  

Microsoft Academic Search

We introduce a new approach for predicting the secondary structure of proteins using profiles and the Fuzzy K-Nearest Neighbor algorithm. K-Nearest Neighbor methods give relatively better performance than Neural Networks or Hidden Markov models when the query protein has few homologs in the sequence database to build sequence profile. Although the traditional K-Nearest Neighbor algorithms are a good choice for

Rajkumar Bondugula; Ognen Duzlevski; Dong Xu

2005-01-01

285

NNDB: the nearest neighbor parameter database for predicting stability of nucleic acid secondary structure  

Microsoft Academic Search

The Nearest Neighbor Database (NNDB, http:\\/\\/ rna.urmc.rochester.edu\\/NNDB) is a web-based resource for disseminating parameter sets for pre- dicting nucleic acid secondary structure stabilities. For each set of parameters, the database includes the set of rules with descriptive text, sequence- dependent parameters in plain text and html, literature references to experiments and usage tutorials. The initial release covers parameters for predicting

Douglas H. Turner; David H. Mathews

2010-01-01

286

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

Microsoft Academic Search

The community structure of beta-subclass Proteobacteria ammonia-oxidizing bacteria was determined in semi-natural chalk grassland soils at different stages of secondary succession. Both culture-mediated (most probable number; MPN) and direct nucleic acid-based approaches targeting genes encoding 16S rRNA and the AmoA subunit of ammonia monooxygenase were used. Similar shifts were detected in the composition of the ammonia oxidizer communities by both

George A. Kowalchuk; Atie W. Stienstra; Heilig H. J. G; John R. Stephen; Jan W. Woldendorp

2000-01-01

287

Evolution of secondary structure in the family of 7SL-like RNAs  

Microsoft Academic Search

Primate and rodent genomes are populated with hundreds of thousands copies of Alu and B1 elements dispersed by retroposition, i.e., by genomic reintegration of their reverse transcribed RNAs. These, as well as primate BC200 and rodent 4.5S RNAs, are ancestrally related to the terminal portions of 7SL RNA sequence. The secondary structure of 7SL RNA (an integral component of the

Damian Labuda; Ewa Zigtkiewicz

1994-01-01

288

TileSoft: Sequence Optimization Software For Designing DNA Secondary Structures  

Microsoft Academic Search

DNA is a crucial construction material for molecular scale objects with nano-scale fea- tures. Diverse synthetic DNA objects hold great potential for applications such as nano- fabrication, nano-robotics, nano-computing, and nano-electronics. The construction of DNA objects is generally carried out via self-assembly. During self-assembly, DNA strands are guided by their sequence information into secondary structures to maximize Watson- Crick pairing

Peng Yin; Bo Guo; Christina Belmore; Will Palmeri; Erik Winfree; Thomas H. LaBean; John H. Reif

2004-01-01

289

High-resolution proton magnetic resonance study of the secondary structure of the 3'-terminal 49-nucleotide fragment of 16S rRNA from Escherichia coli.  

PubMed Central

The 3' terminus of 16S rRNA has been implicated in the recognition of mRNA's by the ribosome. A fragment containing the 3'-terminal 49 nucleotides cleaved from the rRNA by cloacin DF13 was isolated in a pure form. The secondary structure of this fragment has been studied by measuring the high-resolution proton magnetic resonance spectra. The resonances observed at low field can be assigned to hydrogen-bonded iminoprotons of base-pairs present in the fragment. From the data we conclude that the rRNA fragment, under the conditions used, exists as a hairpin consisting of eight intramolecular base-pairs, the 3'-terminal dodecanucleotide being unpaired. The implications of these findings with respect to the function of the ribosomal protein S1 are discussed.

Baan, R A; Hilbers, C W; Van Charldorp, R; Van Leerdam, E; Van Knippenberg, P H; Bosch, L

1977-01-01

290

Assembly mechanisms of RNA pseudoknots are determined by the stabilities of constituent secondary structures  

PubMed Central

Understanding how RNA molecules navigate their rugged folding landscapes holds the key to describing their roles in a variety of cellular functions. To dissect RNA folding at the molecular level, we performed simulations of three pseudoknots (MMTV and SRV-1 from viral genomes and the hTR pseudoknot from human telomerase) using coarse-grained models. The melting temperatures from the specific heat profiles are in good agreement with the available experimental data for MMTV and hTR. The equilibrium free energy profiles, which predict the structural transitions that occur at each melting temperature, are used to propose that the relative stabilities of the isolated helices control their folding mechanisms. Kinetic simulations, which corroborate the inferences drawn from the free energy profiles, show that MMTV folds by a hierarchical mechanism with parallel paths, i.e., formation of one of the helices nucleates the assembly of the rest of the structure. The SRV-1 pseudoknot, which folds in a highly cooperative manner, assembles in a single step in which the preformed helices coalesce nearly simultaneously to form the tertiary structure. Folding occurs by multiple pathways in the hTR pseudoknot, the isolated structural elements of which have similar stabilities. In one of the paths, tertiary interactions are established before the formation of the secondary structures. Our work shows that there are significant sequence-dependent variations in the folding landscapes of RNA molecules with similar fold. We also establish that assembly mechanisms can be predicted using the stabilities of the isolated secondary structures.

Cho, Samuel S.; Pincus, David L.; Thirumalai, D.

2009-01-01

291

[Peculiarities of secondary structure of serum albumin of some representatives of the animal kingdom].  

PubMed

Methods of infrared (IR) spectroscopy and circular dichroism (CD) are suitable techniques for detection of proteins structural changes. These methods were used for determinating peculiarities of the secondary structure of serum albumins in some representatives of two classes of reptiles: Horsfield's tortoise (Testudo horsfieldi), water snake (Natrix tessellata) and grass snake (Natrix natrix) and birds: domestic goose (Anser anser), domestic chicken (Gallus domesticus), domestic duck (Anas platyrhyncha) and dove colored (Columba livia). An analysis of IR spectra and spectra obtained by the method of CD of serum albumins of both classes representatives revealed that beta-folding structure and alpha-helical sections that form the alpha-conformation play an important role in conformational structure formation of polypeptide chain and also disordered sites of molecules of these proteins. It was observed that certain redistribution depending on animals species exists, in the formation of secondary structure of serum albumins of the investigated representatives of reptiles and birds classes between the content of beta-folding structure, alpha-helical sections and disordered sites in molecules of these proteins. PMID:21888056

Pekhymenko, G V; Kuchmerovskaia, T M

292

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

PubMed Central

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

Chen, Ying; Stephan, Wolfgang

2003-01-01

293

Nucleotide sequence and secondary structure of citrus exocortis and chrysanthemum stunt viroid.  

PubMed

The complete nucleotide sequence of citrus exocortis viroid (CEV, propagated in Gymura) and chrysanthemum stunt viroid (CSV, propagated in Cineraria) has been established, using labelling in vitro and direct RNA sequencing methods and a new screening procedure for the rapid selection of suitable RNA fragments from limited digests. The covalently closed circular single-stranded viroid RNAs consist of 371 (CEV) and 354 (CSV) nucleotides, respectively. As previously shown for potato spindle tuber viroid (PSTV, 359 nucleotides), CEV and CSV also contain a long polypurine sequence. Maximal base-pairing of the established CEV and CSV sequences results in an extended rod-like secondary structure similar to that previously established for PSTV and as predicted from detailed physicochemical studies of all these viroids. Although the three viroid species sequenced to date differ in size and nucleotide sequence, there is 60--73% homology between them. As PSTV, CEV and CSV also contain conserved complementary sequences which are separated from each other in the native secondary structure. We postulate that the resulting 'secondary' hairpins, being formed and observed in vitro during the complex process of thermal denaturation of viroid RNA, must have a vital, although yet unknown, function in vivo. The possible origin and function of viroids are discussed on the basis of the characteristic structural features and of a considerable homology with U1a RNA found for a region highly conserved in the three viroids. PMID:7060550

Gross, H J; Krupp, G; Domdey, H; Raba, M; Jank, P; Lossow, C; Alberty, H; Ramm, K; Sänger, H L

1982-01-01

294

An analysis of intron positions in relation to nucleotides, amino acids, and protein secondary structure.  

PubMed

We present an analysis of intron positions in relation to nucleotides, amino acid residues, and protein secondary structure. Previous work has shown that intron sites in proteins are not randomly distributed with respect to secondary structures. Here we show that this preference can be almost totally explained by the nucleotide bias of splice site machinery, and may well not relate to protein stability or conformation at all. Each intron phase is preferentially associated with its own set of residues: phase 0 introns with lysine, glutamine, and glutamic acid before the intron, and valine after; phase 1 introns with glycine, alanine, valine, aspartic acid, and glutamic acid; and phase 2 introns with arginine, serine, lysine, and tryptophan. These preferences can be explained principally on the basis of nucleotide bias at intron locations, which is in accordance with previous literature. Although this work does not prove that introns are inserted into genomes at specific proto-splice sites, it shows that the nucleotide bias surrounding introns, however it originally occurred, explains the observed correlations between introns and protein secondary structure. PMID:16616935

Whamond, Gordon S; Thornton, Janet M

2006-03-29

295

CMD: A Database to Store the Bonding States of Cysteine Motifs with Secondary Structures  

PubMed Central

Computational approaches to the disulphide bonding state and its connectivity pattern prediction are based on various descriptors. One descriptor is the amino acid sequence motifs flanking the cysteine residue motifs. Despite the existence of disulphide bonding information in many databases and applications, there is no complete reference and motif query available at the moment. Cysteine motif database (CMD) is the first online resource that stores all cysteine residues, their flanking motifs with their secondary structure, and propensity values assignment derived from the laboratory data. We extracted more than 3 million cysteine motifs from PDB and UniProt data, annotated with secondary structure assignment, propensity value assignment, and frequency of occurrence and coefficiency of their bonding status. Removal of redundancies generated 15875 unique flanking motifs that are always bonded and 41577 unique patterns that are always nonbonded. Queries are based on the protein ID, FASTA sequence, sequence motif, and secondary structure individually or in batch format using the provided APIs that allow remote users to query our database via third party software and/or high throughput screening/querying. The CMD offers extensive information about the bonded, free cysteine residues, and their motifs that allows in-depth characterization of the sequence motif composition.

Bostan, Hamed; Salim, Naomie; Hussein, Zeti Azura; Klappa, Peter; Shamsir, Mohd Shahir

2012-01-01

296

Sequence and secondary structure variation in the Gyrodactylus (Platyhelminthes: Monogenea) ribosomal RNA gene array.  

PubMed

Nucleotide sequences were determined for the rRNA internal transcribed spacers 1 and 2 (ITS1 and 2) and the 5' terminus of the large subunit rRNA in selected Gyrodactylus species. Examination of primary sequence variation and secondary structure models in ITS2 and variable region V4 of the small subunit rRNA revealed that structure was largely conserved despite significant variation in sequence. ITS1 sequences were highly variable, and models of structure were unreliable but, despite this, show some resemblance to structures predicted in Digenea. ITS2 models demonstrated binding of the 3' end of 5.8S rRNA to the 5' end of the large subunit rRNA and enabled the termini of these genes to be defined with greater confidence than previously. The structure model shown here may prove useful in future phylogenetic analyses. PMID:10864256

Cunningham, C O; Aliesky, H; Collins, C M

2000-06-01

297

Gene structure and multiple mRNA species of Drosophila melanogaster aldolase generating three isozymes with different enzymatic properties.  

PubMed

Genomic clones encoding the Drosophila aldolase gene were isolated and the organization of the gene was determined. The protein-coding region spanning nearly 3.5 kb consists of five coding exons (exon 2, 3, 4 alpha, 4 beta, and 4 gamma). The insect exon 2 corresponds to exons 2 to 7 of vertebrate aldolase genes and thus appears to have been formed by the fusion of these 6 exons into a single exon during evolution. The Drosophila aldolase gene is predicted to generate mRNAs for three isozymes (alpha-, beta-, and gamma-types) from the primary transcripts by alternative usage of the final three exons. The reverse transcriptase-PCR assay revealed the occurrence of mRNAs for the three isozymic forms at different developmental stages, and tissue-specific expression was also found to occur in adult flies. In addition to the usual type mRNA species for the alpha-, beta-, and gamma-isozymes, two novel forms of mRNAs, alpha beta- and beta gamma-type mRNAs, were detected tissue-specifically in adult flies, although their functions are unpredictable. The alpha beta-mRNA is an alpha-type mRNA in which exon 4 beta remains unspliced, while the beta gamma-mRNA is a beta-type mRNA with the exon 4 gamma remaining unspliced. Recombinant enzymes expressed in Escherichia coli were all active and exhibited different enzymatic properties. PMID:1339430

Kai, T; Sugimoto, Y; Kusakabe, T; Zhang, R; Koga, K; Hori, K

1992-11-01

298

Adenoviral E1B-55kDa protein inhibits yeast mRNA export and perturbs nuclear structure.  

PubMed Central

The mechanisms of export of RNA from the nucleus are poorly understood; however, several viral proteins modulate nucleocytoplasmic transport of mRNA. Among these are the adenoviral proteins E1B-55kDa and E4-34kDa. Late in infection, these proteins inhibit export of host transcripts and promote export of viral mRNA. To investigate the mechanism by which these proteins act, we have expressed them in Saccharomyces cerevisiae. Overexpression of either or both proteins has no obvious effect on cell growth. By contrast, overexpression of E1B-55kDa bearing a nuclear localization signal (NLS) dramatically inhibits cell growth. In this situation, the NLS-E1B-55kDa protein is localized to the nuclear periphery, fibrous material is seen in the nucleoplasm, and poly(A)+ RNA accumulates in the nucleus. Simultaneous overexpression of E4-34kDa bearing or lacking an NLS does not modify these effects. We discuss the mechanisms of selective mRNA transport. Images Fig. 1 Fig. 2 Fig. 3

Liang, S; Hitomi, M; Tartakoff, A M

1995-01-01

299

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

PubMed

We present an energy model that combines information from the amino acid sequence of a protein and available NMR chemical shifts for the purposes of identifying low energy conformations and determining elements of secondary structure. The model ("PECAN", Protein Energetic Conformational Analysis from NMR chemical shifts) optimizes a combination of sequence information and residue-specific statistical energy function to yield energetic descriptions most favorable to predicting secondary structure. Compared to prior methods for secondary structure determination, PECAN provides increased accuracy and range, particularly in regions of extended structure. Moreover, PECAN uses the energetics to identify residues located at the boundaries between regions of predicted secondary structure that may not fit the stringent secondary structure class definitions. The energy model offers insights into the local energetic patterns that underlie conformational preferences. For example, it shows that the information content for defining secondary structure is localized about a residue and reaches a maximum when two residues on either side are considered. The current release of the PECAN software determines the well-defined regions of secondary structure in novel proteins with assigned chemical shifts with an overall accuracy of 90%, which is close to the practical limit of achievable accuracy in classifying the states. PMID:16041485

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

2005-05-01

300

CompaRNA: a server for continuous benchmarking of automated methods for RNA secondary structure prediction  

PubMed Central

We present a continuous benchmarking approach for the assessment of RNA secondary structure prediction methods implemented in the CompaRNA web server. As of 3 October 2012, the performance of 28 single-sequence and 13 comparative methods has been evaluated on RNA sequences/structures released weekly by the Protein Data Bank. We also provide a static benchmark generated on RNA 2D structures derived from the RNAstrand database. Benchmarks on both data sets offer insight into the relative performance of RNA secondary structure prediction methods on RNAs of different size and with respect to different types of structure. According to our tests, on the average, the most accurate predictions obtained by a comparative approach are generated by CentroidAlifold, MXScarna, RNAalifold and TurboFold. On the average, the most accurate predictions obtained by single-sequence analyses are generated by CentroidFold, ContextFold and IPknot. The best comparative methods typically outperform the best single-sequence methods if an alignment of homologous RNA sequences is available. This article presents the results of our benchmarks as of 3 October 2012, whereas the rankings presented online are continuously updated. We will gladly include new prediction methods and new measures of accuracy in the new editions of CompaRNA benchmarks.

Puton, Tomasz; Kozlowski, Lukasz P.; Rother, Kristian M.; Bujnicki, Janusz M.

2013-01-01

301

Dynamic secondary structural changes in Ca²?-saturated calmodulin upon interaction with the antagonist, W-7.  

PubMed

Although the 3D structure of the Ca(2+)-bound CaM (Ca(2+)/CaM) complex with the antagonist, N-(6-aminohexyl)-5-chloro-1-naphthalenesulphonamide (W-7), has been resolved, the dynamic changes in Ca(2+)/CaM structure upon interaction with W-7 are still unknown. We investigated time- and temperature-dependent dynamic changes in Ca(2+)/CaM interaction with W-7 in physiological conditions using one- and two-dimensional Fourier-transformed infrared spectroscopy (2D-IR). We observed changes in the ?-helix secondary structure of Ca(2+)/CaM when complexed with W-7 at a molar ratio of 1:2, but not at higher molar ratios (between 1:2 and 1:5). Kinetic studies revealed that, during the initial 125s at 25°C, Ca(2+)/CaM underwent formation of secondary coil and turn structures upon binding to W-7. Variations in temperature that induced significant changes in the structure of the Ca(2+)/CaM complex failed to do so when Ca(2+)/CaM was complexed with W-7. We concluded that W-7 induced stepwise conformational changes in Ca(2+)/CaM that resulted in a rigidification of the complex and its inability to interact with target proteins and/or polypeptides. PMID:22664109

Sasakura, Daisuke; Nunomura, Wataru; Takakuwa, Yuichi

2012-06-01

302

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

PubMed

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

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

2012-10-01

303

Secondary and Tertiary Structure Elasticity of Titin Z1Z2 and a Titin Chain Model  

PubMed Central

The giant protein titin, which is responsible for passive elasticity in muscle fibers, is built from ?300 regular immunoglobulin-like (Ig) domains and FN-III repeats. While the soft elasticity derived from its entropic regions, as well as the stiff mechanical resistance derived from the unfolding of the secondary structure elements of Ig- and FN-III domains have been studied extensively, less is known about the mechanical elasticity stemming from the orientation of neighboring domains relative to each other. Here we address the dynamics and energetics of interdomain arrangement of two adjacent Ig-domains of titin, Z1, and Z2, using molecular dynamics (MD) simulations. The simulations reveal conformational flexibility, due to the domain-domain geometry, that lends an intermediate force elasticity to titin. We employ adaptive biasing force MD simulations to calculate the energy required to bend the Z1Z2 tandem open to identify energetically feasible interdomain arrangements of the Z1 and Z2 domains. The finding is cast into a stochastic model for Z1Z2 interdomain elasticity that is generalized to a multiple domain chain replicating many Z1Z2-like units and representing a long titin segment. The elastic properties of this chain suggest that titin derives so-called tertiary structure elasticity from bending and twisting of its domains. Finally, we employ steered molecular dynamics simulations to stretch individual Z1 and Z2 domains and characterize the so-called secondary structure elasticity of the two domains. Our study suggests that titin's overall elastic response at weak force stems from a soft entropic spring behavior (not described here), from tertiary structure elasticity with an elastic spring constant of ?0.001–1 pN/Å and, at strong forces, from secondary structure elasticity.

Lee, Eric H.; Hsin, Jen; Mayans, Olga; Schulten, Klaus

2007-01-01

304

A Universal Trend of Reduced mRNA Stability near the Translation-Initiation Site in Prokaryotes and Eukaryotes  

PubMed Central

Recent studies have suggested that the thermodynamic stability of mRNA secondary structure near the start codon can regulate translation efficiency in Escherichia coli, and that translation is more efficient the less stable the secondary structure. We survey the complete genomes of 340 species for signals of reduced mRNA secondary structure near the start codon. Our analysis includes bacteria, archaea, fungi, plants, insects, fishes, birds, and mammals. We find that nearly all species show evidence for reduced mRNA stability near the start codon. The reduction in stability generally increases with increasing genomic GC content. In prokaryotes, the reduction also increases with decreasing optimal growth temperature. Within genomes, there is variation in the stability among genes, and this variation correlates with gene GC content, codon bias, and gene expression level. For birds and mammals, however, we do not find a genome-wide trend of reduced mRNA stability near the start codon. Yet the most GC rich genes in these organisms do show such a signal. We conclude that reduced stability of the mRNA secondary structure near the start codon is a universal feature of all cellular life. We suggest that the origin of this reduction is selection for efficient recognition of the start codon by initiator-tRNA.

Wilke, Claus O.

2010-01-01

305

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

PubMed

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

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

2009-12-11

306

Crumple: a method for complete enumeration of all possible pseudoknot-free RNA secondary structures.  

PubMed

The diverse landscape of RNA conformational space includes many canyons and crevices that are distant from the lowest minimum free energy valley and remain unexplored by traditional RNA structure prediction methods. A complete description of the entire RNA folding landscape can facilitate identification of biologically important conformations. The Crumple algorithm rapidly enumerates all possible non-pseudoknotted structures for an RNA sequence without consideration of thermodynamics while filtering the output with experimental data. The Crumple algorithm provides an alternative approach to traditional free energy minimization programs for RNA secondary structure prediction. A complete computation of all non-pseudoknotted secondary structures can reveal structures that would not be predicted by methods that sample the RNA folding landscape based on thermodynamic predictions. The free energy minimization approach is often successful but is limited by not considering RNA tertiary and protein interactions and the possibility that kinetics rather than thermodynamics determines the functional RNA fold. Efficient parallel computing and filters based on experimental data make practical the complete enumeration of all non-pseudoknotted structures. Efficient parallel computing for Crumple is implemented in a ring graph approach. Filters for experimental data include constraints from chemical probing of solvent accessibility, enzymatic cleavage of paired or unpaired nucleotides, phylogenetic covariation, and the minimum number and lengths of helices determined from crystallography or cryo-electron microscopy. The minimum number and length of helices has a significant effect on reducing conformational space. Pairing constraints reduce conformational space more than single nucleotide constraints. Examples with Alfalfa Mosaic Virus RNA and Trypanosome brucei guide RNA demonstrate the importance of evaluating all possible structures when pseduoknots, RNA-protein interactions, and metastable structures are important for biological function. Crumple software is freely available at http://adenosine.chem.ou.edu/software.html. PMID:23300665

Bleckley, Samuel; Stone, Jonathan W; Schroeder, Susan J

2012-12-27

307

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

NASA Astrophysics Data System (ADS)

Structural relations between secondary tungsten minerals with general composition Ax[(W,Fe)(O,OH)3]·yH2O are described. Phyllotungstite (A=predominantly Ca) is hexagonal, a=7.31(3)Å, c=19.55(1)Å, space group P63/mmc. Pittongite, a new secondary tungsten mineral from a wolframite deposit near Pittong in Victoria, southeastern Australia (A=predominantly Na) is hexagonal, a=7.286(1)Å, c=50.49(1)Å, space group P-6m2. The structures of both minerals can be described as unit-cell scale intergrowths of (111)py pyrochlore slabs with pairs of hexagonal tungsten bronze (HTB) layers. In phyllotungstite, the (111)py blocks have the same thickness, 6 Å, whereas pittongite contains pyrochlore blocks of two different thicknesses, 6 and 12 Å. The structures can alternatively be described in terms of chemical twinning of the pyrochlore structure on (111)py oxygen planes. At the chemical twin planes, pairs of HTB layers are corner connected as in hexagonal WO3.

Grey, Ian E.; Birch, William D.; Bougerol, Catherine; Mills, Stuart J.

2006-12-01

308

Computer method for predicting the secondary structure of single-stranded RNA.  

PubMed Central

We present a computer method utilizing published values for base pairing energies to compute the most energetically favorable secondary structure of an RNA from its primary nucleotide sequence. After listing all possible double-helical regions, every pair of mutally incompatible regions (whose nucleotides overlap) is examined to determine whether parts of those two regions can be combined by branch migration to form a pair of compatible new subregions which together are more stable than either of the original regions separately. These subregions are added to the list of base pairing regions which will compete to form the best overall structure. Then, a 'hyperstructure matrix' is generated, containing the unique topological relationship between every pair of regions. We have shown that the best structure can be chosen directly from this matrix, without the necessity of creating and examing every possible secondary structure. We have included the results from our solution of the 5S rRNA of the cyanobacterium Anacystis nidulans as an example of our program's capabilities.

Studnicka, G M; Rahn, G M; Cummings, I W; Salser, W A

1978-01-01

309

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

SciTech Connect

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

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

2006-12-15

310

Infrared spectroscopic study of photoreceptor membrane and purple membrane. Protein secondary structure and hydrogen deuterium exchange  

SciTech Connect

Infrared spectroscopy in the interval from 1800 to 1300 cm-1 has been used to investigate the secondary structure and the hydrogen/deuterium exchange behavior of bacteriorhodopsin and bovine rhodopsin in their respective native membranes. The amide I' and amide II' regions from spectra of membrane suspensions in D2O were decomposed into constituent bands by use of a curve-fitting procedure. The amide I' bands could be fit with a minimum of three theoretical components having peak positions at 1664, 1638, and 1625 cm-1 for bacteriorhodopsin and 1657, 1639, and 1625 cm-1 for rhodopsin. For both of these membrane proteins, the amide I' spectrum suggests that alpha-helix is the predominant form of peptide chain secondary structure, but that a substantial amount of beta-sheet conformation is present as well. The shape of the amide I' band was pH-sensitive for photoreceptor membranes, but not for purple membrane, indicating that membrane-bound rhodopsin undergoes a conformation change at acidic pH. Peptide hydrogen exchange of bacteriorhodopsin and rhodopsin was monitored by observing the change in the ratio of integrated absorbance (Aamide II'/Aamide I') during the interval from 1.5 to 25 h after membranes were introduced into buffered D2O. The fraction of peptide groups in a very slowly exchanging secondary structure was estimated to be 0.71 for bacteriorhodopsin at pD 7. The corresponding fraction in vertebrate rhodopsin was estimated to be less than or equal to 0.60. These findings are discussed in relationship to previous studies of hydrogen exchange behavior and to structural models for both proteins.

Downer, N.W.; Bruchman, T.J.; Hazzard, J.H.

1986-03-15

311

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

PubMed Central

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

Zhong, Cuncong; Tang, Haixu; Zhang, Shaojie

2010-01-01

312

Rapid increase of Nurr1 mRNA expression in limbic and cortical brain structures related to coping with depression-like behavior in mice.  

PubMed

The immediate-early gene Nurr1 is a member of the inducible orphan nuclear receptor family. Nurr1 is essential to the differentiation, maturation, and maintenance of midbrain dopaminergic neurons and is expressed in different brain regions. We have reported that adult mice with reduced Nurr1 expression displayed an increase in immobility response to acute stress. These mice were also deficient in the retention of emotional memory. Thus, Nurr1 expression seems to be relevant to normal cognitive processes. To investigate the response of Nurr1 to a stress stimulus, Nurr1 mRNA expression was examined by in situ hybridization in adult mice using a depression-like behavior paradigm, the forced swim test. The Nurr1 gene was rapidly and widely up-regulated throughout the brain, including cortical areas (i.e., prefrontal cortex, primary and secondary visual cortex, primary auditory cortex, and secondary somatosensory cortex), hippocampus (dentate gyrus, CA1, CA2, and CA3), and midbrain (substantia nigra pars compacta and ventral tegmental area) at 30 min and 3 hr after the forced swim test. Dopamine content was reduced in prefrontal cortex and midbrain following swim stress. These results suggest that the increase in Nurr1 expression might be a compensatory mechanism to counteract the changes in forebrain dopamine transmission in coping with acute stress. PMID:20175204

Rojas, Patricia; Joodmardi, Eliza; Perlmann, Thomas; Ogren, Sven Ove

2010-08-01

313

Analysis of the secondary structure of expansion segment 39 in ribosomes from fungi, plants and mammals.  

PubMed

The structure of expansion segment 39, ES39, in eukaryotic 23 S-like ribosomal RNA was analysed using a combination of chemical and enzymic reagents. Ribosomes were isolated from yeast, wheat, mouse, rat and rabbit, five organisms representing three different eukaryotic kingdoms. The isolated ribosomes were treated with structure-sensitive chemical and enzymic reagents and the modification patterns analysed by primer extension and gel electrophoresis on an ABI 377 automated DNA sequencer. The expansion segment was relatively accessible to modification by both enzymic and chemical probes, suggesting that ES39 was exposed on the surface of the ribosomes. The collected modification data were used in secondary structure modelling of the expansion segment. Despite considerable variation in both sequence and length between organisms from different kingdoms, the structure analysis of the expansion segment gave rise to structural fingerprints that allowed identification of homologous structures in ES39 from fungi, plants and mammals. The homologous structures formed an initial helix and an invariant hairpin connected to the initial helix via a long single-stranded loop. The remaining part of the ES39 sequences accounted for most of the length variation seen between the analysed species. This part could form additional, albeit less similar, hairpins. A comparison of ES39 sequences from other fungi, plants and mammals showed that identical structures could be formed in these organisms. PMID:16473366

Nygård, Odd; Alkemar, Gunnar; Larsson, Sofia L

2006-01-30

314

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

PubMed Central

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

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

1984-01-01

315

Structural and functional studies of RegB, a new member of a family of sequence-specific ribonucleases involved in mRNA inactivation on the ribosome.  

PubMed

The RegB endoribonuclease participates in the bacteriophage T4 life cycle by favoring early messenger RNA breakdown. RegB specifically cleaves GGAG sequences found in intergenic regions, mainly in translation initiation sites. Its activity is very low but can be enhanced up to 100-fold by the ribosomal 30 S subunit or by ribosomal protein S1. RegB has no significant sequence homology to any known protein. Here we used NMR to solve the structure of RegB and map its interactions with two RNA substrates. We also generated a collection of mutants affected in RegB function. Our results show that, despite the absence of any sequence homology, RegB has structural similarities with two Escherichia coli ribonucleases involved in mRNA inactivation on translating ribosomes: YoeB and RelE. Although these ribonucleases have different catalytic sites, we propose that RegB is a new member of the RelE/YoeB structural and functional family of ribonucleases specialized in mRNA inactivation within the ribosome. PMID:17046813

Odaert, Benoît; Saïda, Fakhri; Aliprandi, Pascale; Durand, Sylvain; Créchet, Jean-Bernard; Guerois, Raphaël; Laalami, Soumaya; Uzan, Marc; Bontems, François

2006-10-17

316

Protein secondary structure templates derived from bioactive natural products – Combinatorial chemistry meets structure-based design  

Microsoft Academic Search

Lead finding strategies in pharmaceutical research comprise structure-based drug design as well as screening efforts of natural product pools or large chemical libraries. In this context we propose a combined approach by utilizing natural product-derived structure information on receptor- or enzyme-complementarity for designing unique core structures that can be employed as privileged template molecules underlying combinatorial libraries. A set of

Gerhard Müller; Henry Giera

1998-01-01

317

Secondary Structure Analysis of a Minimal Avian Leukosis-Sarcoma Virus Packaging Signal  

PubMed Central

We previously identified a 160-nucleotide packaging signal, M?, from the 5? end of the Rous sarcoma virus genome. In this study, we determine the secondary structure of M? by using phylogenetic analysis with computer modeling and heterologous packaging assays of point mutants. The results of the in vivo studies are in good agreement with the computer model. Additionally, the packaging studies indicate several structures which are important for efficient packaging, including a single-stranded bulge containing the initiation codon for the short open reading frame, uORF3, as well as adjacent stem structures. Finally, we show that the L3 stem-loop at the 3? end of M? is dispensable for packaging, thus identifying an 82-nucleotide minimal packaging signal, ??, composed of the O3 stem-loop.

Banks, Jennifer D.; Linial, Maxine L.

2000-01-01

318

Secondary structure and hydrogen bonding of crambin in solution. A two-dimensional NMR study.  

PubMed

The secondary structure of crambin in solution has been determined using two-dimensional NMR and is found to be essentially identical to that of the crystal structure. The H-D exchange of most amide protons can be accounted for in terms of the hydrogen bonds found in the X-ray structure. Exceptions are the amide protons of Cys-4 and Ser-6, which exchange more slowly than expected, and of Asn-46 for which the exchange is faster. These results might be explained by a slightly different conformation of the C-terminal region of the protein in solution. The slow exchange of the amides of Cys-32 and Glu-23 might be due to aggregation involving an extremely hydrophobic part of the protein in solution. PMID:3338468

Lamerichs, R M; Berliner, L J; Boelens, R; De Marco, A; Llinàs, M; Kaptein, R

1988-01-15

319

Sequence-specific sup 1 H NMR assignments and secondary structure of eglin c  

SciTech Connect

Sequence-specific nuclear magnetic resonance assignments were obtained for eglin c, a polypeptide inhibitor of the granulocytic proteinases elastase and cathepsin G and some other proteinases. The protein consists of a single polypeptide chain of 70 residues. All proton resonances were assigned except for some labile protons of arginine side chains. The patterns of nuclear Overhauser enhancements and coupling constants and the observation of slow hydrogen exchange were used to characterize the secondary structure of the protein. The results indicate that the solution structure of the free inhibitor is very similar to the crystal structure reported for the same protein in the complex with subtilisin Carlsberg. However, a part of the binding loop seems to have a significantly different conformation in the free protein.

Hyberts, S.G.; Wagner, G. (Univ. of Michigan, Ann Arbor (USA))

1990-02-13

320

Structural Elucidation of the Nonclassical Secondary Cell Wall Polysaccharide from Bacillus cereus ATCC 10987  

PubMed Central

Nonclassical secondary cell wall polysaccharides constitute a major cell wall structure in the Bacillus cereus group of bacteria. The structure of the secondary cell wall polysaccharide from Bacillus cereus ATCC 10987, a strain that is closely related to Bacillus anthracis, was determined. This polysaccharide was released from the cell wall with aqueous hydrogen fluoride (HF) and purified by gel filtration chromatography. The purified polysaccharide, HF-PS, was characterized by glycosyl composition and linkage analyses, mass spectrometry, and one- and two-dimensional NMR analysis. The results showed that the B. cereus ATCC 10987 HF-PS has a repeating oligosaccharide consisting of a ?6)-?-GalNAc-(1?4)-?-ManNAc-(1?4)-?-GlcNAc-(1? trisaccharide that is substituted with ?-Gal at O3 of the ?-GalNAc residue and nonstoichiometrically acetylated at O3 of the N-acetylmannosamine (ManNAc) residue. Comparison of this structure with that of the B. anthracis HF-PS and with structural data obtained for the HF-PS from B. cereus type strain ATCC 14579 revealed that each HF-PS had the same general structural theme consisting of three HexNAc and one Hex residues. A common structural feature in the HF-PSs from B. cereus ATCC 10987 and B. anthracis was the presence of a repeating unit consisting of a HexNAc3 trisaccharide backbone in which two of the three HexNAc residues are GlcNAc and ManNAc and the third can be either GlcNAc or GalNAc. The implications of these results with regard to the possible functions of the HF-PSs are discussed.

Leoff, Christine; Choudhury, Biswa; Saile, Elke; Quinn, Conrad P.; Carlson, Russell W.; Kannenberg, Elmar L.

2008-01-01

321

Transforming growth factor beta 1: secondary structure as determined by heteronuclear magnetic resonance spectroscopy.  

PubMed

Virtually complete backbone NMR signal assignments have been reported for transforming growth factor beta 1 (TGF-beta 1) [Archer et al. (1993) Biochemistry (preceding paper in this issue)]. Herein we report the secondary structure of the protein in solution on the basis of these assignments and proton NOE's observed in a variety of 2D and 3D heteronuclear NMR spectra. Regular elements of secondary structure derived from the NOE data consist of (a) three helices spanning residues Y58-H68, F24-G29, and N5-F8 and (b) several pairs of two-stranded antiparallel beta-sheets. The longest two-stranded sheet runs from residue L83 to V106 with a type II reverse turn at G93-R94 and a chain twist at residue N103-M104. These elements of regular structure were confirmed by hydrogen exchange, chemical shift, and coupling constant data. With the exception of residues G46-S53, which exhibit relatively few and weak intraresidue NOE's, residues in the rest of the protein adopt an irregular but well-defined structure. All peptide bonds are trans except for a cis peptide bond between Glu35 and Pro36. The structural characteristics observed for TGF-beta 1 in solution generally agree closely with the recently derived crystal structures of TGF-beta 2 [Daopin et al. (1992) Science 257, 369-374; Schlunegger & Grütter (1992) Nature 358, 430-434]. Several noteworthy differences were observed that may be related to function. PMID:8424943

Archer, S J; Bax, A; Roberts, A B; Sporn, M B; Ogawa, Y; Piez, K A; Weatherbee, J A; Tsang, M L; Lucas, R; Zheng, B L

1993-02-01

322

Interdependence between DNA template secondary structure and priming efficiencies of short primers.  

SciTech Connect

Here we analyze the effect of DNA folding on the performance of short primers and describe a simple technique for assessing hitherto uncertain values of thermodynamic parameters that determine the folding of single-stranded DNA into secondary structure. An 8mer with two degenerate positions is extended simultaneously at several complementary sites on a known template (M13mp18) using one, two or three (but never all four) of the possible dNTPs. The length of the extension is site specific because it is limited by the first occurrence in the downstream template sequence of a base whose complementary dNTP is not present. The relative priming efficiencies of different sites are then ranked by comparing their band brightnesses on a gel. The priming efficiency of a short primer (unlike conventional long primers) depends dramatically on the secondary structure of the template at and around the priming site. We calculated the secondary structure and its effect on priming using a simple model with relatively few parameters which were then optimized to achieve the best match between the predictions and the actual rankings of the sites in terms of priming efficiency. This work introduces an efficient and conceptually novel approach that in the future can make use of more data to optimize a larger set of DNA folding parameters in a more refined model. The model we used, however crude it may be, significantly improved the prediction of priming efficiencies of 8mer primers and appreciably raised the success rate of our DNA sequencing technique (from 67 to 91% with a significance of P < 7 x 10(-5)), which uses such primers.

Lvovsky, L.; Ioshikhes, I.; Raja, M. C.; Zevin-Sonkin, D.; Sobolev, I. A.; Shwartzburd, J.; Ulanovsky, L. E.; Center for Mechanistic Biology and Biotechnology; Weizmann Inst. of Science; Weizmann Inst. of Science

1998-01-01

323

Enzyme activity inhibition and secondary structure disruption of nano-TiO2 on pepsin.  

PubMed

In this study, the binding and enzyme activity inhibitory effect of nano-TiO(2) on pepsin was explored compared with micro-TiO(2). Nano-TiO(2) was about 60 nm and micro-TiO(2) was about 200 nm, both round in shape. The activity of pepsin was depressed significantly by nano-TiO(2) comparing to micro-ones. The results of UV spectrometry, HPLC, SDS-PAGE and CD assay proved that micro-TiO(2) has only physical absorption effect on pepsin, but no impairment on primary sequences or secondary structure. However, nano-TiO(2) had coordination interaction with pepsin besides physical binding effect. The secondary structure of pepsin was unfolded with the treatment of nano-TiO(2) at pH 6.5 and pH 3.53, which might consequently affect the beta-hairpin loop that protects the active center of pepsin, and then reduce the enzyme activity. Furthermore, the thermodynamic mechanisms of interaction between nano-TiO(2) and pepsin were explored by fluorescence spectrum and ITC analysis. According to the results of thermodynamic analysis, the K value was 3.64x10(6), stoichiometry (N(pepsin:nano-TiO2)) was 3.04x10(3), the total DeltaH was -2277 cal/mol, DeltaS was 22.7 cal/(K mol), therefore the nano-TiO(2)-pepsin interaction is spontaneous. The depression of activity and the unfolding of secondary structure of pepsin were resulted from non-covalent reactions, including electrostatic force and hydrophobic binding. This work studied the different inhibitory effects and revealed mechanisms of the interaction between micro/nano-TiO(2) and pepsin, and provided a useful approach for evaluating the health risk of nano-materials on level of proteins. PMID:20541600

Zhu, Rong-Rong; Wang, Wen-Rui; Sun, Xiao-Yu; Liu, Hui; Wang, Shi-Long

2010-06-10

324

Profiles and Majority Voting-Based Ensemble Method for Protein Secondary Structure Prediction  

PubMed Central

Machine learning techniques have been widely applied to solve the problem of predicting protein secondary structure from the amino acid sequence. They have gained substantial success in this research area. Many methods have been used including k-Nearest Neighbors (k-NNs), Hidden Markov Models (HMMs), Artificial Neural Networks (ANNs) and Support Vector Machines (SVMs), which have attracted attention recently. Today, the main goal remains to improve the prediction quality of the secondary structure elements. The prediction accuracy has been continuously improved over the years, especially by using hybrid or ensemble methods and incorporating evolutionary information in the form of profiles extracted from alignments of multiple homologous sequences. In this paper, we investigate how best to combine k-NNs, ANNs and Multi-class SVMs (M-SVMs) to improve secondary structure prediction of globular proteins. An ensemble method which combines the outputs of two feed-forward ANNs, k-NN and three M-SVM classifiers has been applied. Ensemble members are combined using two variants of majority voting rule. An heuristic based filter has also been applied to refine the prediction. To investigate how much improvement the general ensemble method can give rather than the individual classifiers that make up the ensemble, we have experimented with the proposed system on the two widely used benchmark datasets RS126 and CB513 using cross-validation tests by including PSI-BLAST position-specific scoring matrix (PSSM) profiles as inputs. The experimental results reveal that the proposed system yields significant performance gains when compared with the best individual classifier.

Bouziane, Hafida; Messabih, Belhadri; Chouarfia, Abdallah

2011-01-01

325

DICHROWEB, an online server for protein secondary structure analyses from circular dichroism spectroscopic data.  

PubMed

The DICHROWEB web server enables on-line analyses of circular dichroism (CD) spectroscopic data, providing calculated secondary structure content and graphical analyses comparing calculated structures and experimental data. The server is located at http://www.cryst.bbk.ac.uk/cdweb and may be accessed via a password-limited user ID, available upon completion of a registration form. The server facilitates analyses using five popular algorithms and (currently) seven different reference databases by accepting data in a user-friendly manner in a wide range of formats, including those output by both commercial CD instruments and synchrotron radiation-based circular dichroism beamlines, as well as those produced by spectral processing software packages. It produces as output calculated secondary structures, a goodness-of-fit parameter for the analyses, and tabular and graphical displays of experimental, calculated and difference spectra. The web pages associated with the server provide information on CD spectroscopic methods and terms, literature references and aids for interpreting the analysis results. PMID:15215473

Whitmore, Lee; Wallace, B A

2004-07-01

326

Role of aromatic residues in stabilizing the secondary and tertiary structure of avian pancreatic polypeptide  

NASA Astrophysics Data System (ADS)

Avian pancreatic polypeptide (aPP) is a 36 residue protein that exhibits a tertiary fold. Results of previous experimental and computational studies indicate that the structure of aPP is stabilized more by nonbonded interactions than by the hydrophobic effect. Aromatic residues are known to participate in a variety of long-range nonbonded interactions, with both backbone atoms and the atoms of other side-chains, which could be responsible, in part, for the stability of both the local secondary structure and the tertiary fold. The effect of these aromatic interactions on the stability of aPP was calculated using BHandHLYP/cc-pVTZ. Aromatic residues were shown to participate in multiple hydrogen bonded and weakly polar interactions in the secondary structure. The energies of the weakly polar interactions are comparable with those of hydrogen bonds. Aromatic residues were also shown to participate in multiple weakly polar interactions across the tertiary fold, again with energies similar to those of hydrogen bonds.0

Palermo, Nicholas Y.; Csontos, József; Murphy, Richard F.; Lovas, Sándor

327

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

PubMed

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

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

2012-08-31

328

Self-similarity of rRNA secondary structures: A clue to RNA folding  

NASA Astrophysics Data System (ADS)

In this paper, we analyze helices in the secondary structures of the 16S and 23S rRNAs from the statistical physics perspective. The results of the analysis lead to propose a possible mechanism of the RNA folding based on the premise that the structure of RNA may bear a trace of its folding. We show that the frequency distribution of the helix contact order approximately follows a power-law, which implies that helices of large contact orders should inevitably exist. Furthermore, the frequencies of helix contact orders can be characterized by the multifractal. Comprehending the multifractality and the power-law of the distribution of the helix contact orders, we suggest a nearest-preferred helix formation as a mechanism for RNA folding via a random binary multiplicative process. The proposed process was supported by reconstructing the multifractal spectrum based on the transfer matrix theory and the binary tree representation of helices in the secondary structures. This justifies, at least partially if not entirely, the relevance of the proposed process as the kinetics of RNA folding.

Lee, Chang-Yong

2013-10-01

329

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

PubMed Central

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

Ekland, E H; Bartel, D P

1995-01-01

330

A global sampling approach to designing and reengineering RNA secondary structures  

PubMed Central

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.

Levin, Alex; Lis, Mieszko; Ponty, Yann; O'Donnell, Charles W.; Devadas, Srinivas; Berger, Bonnie; Waldispuhl, Jerome

2012-01-01

331

Interplay between desolvation and secondary structure in mediating cosolvent and temperature induced alpha-synuclein aggregation  

PubMed Central

Both increased temperature and moderate concentrations of fluorinated alcohols enhance aggregation of the Parkinson’s disease-associated protein ?–synuclein (?S). Here, we investigate the secondary structural rearrangements induced by heating and trifluoroethanol (TFE). At low TFE concentrations, CD spectra feature a negative peak characteristic of disordered polypeptides near 200 nm and a slight shoulder around 220 nm suggesting some polyproline-II content. Upon heating, these peaks weaken, while a weak negative signal develops at 222 nm. At high TFE concentrations, the spectra show distinct minima at 208 and 222 nm, indicative of considerable ?-helical structure, which diminish upon heating. We observe a crossover between the low-TFE and high-TFE behavior near 15% TFE, where we previously showed that a partially helical intermediate is populated. We postulate that the protein is well solvated by water at low TFE concentrations and by TFE at high TFE concentrations, but may become desolvated at the crossover point. We discuss the potential roles and interplay of desolvation and helical secondary structure in driving ?S aggregation.

Anderson, V L; Webb, W W; Eliezer, D

2013-01-01

332

Pan-eukaryote ITS2 homologies revealed by RNA secondary structure  

PubMed Central

For evolutionary comparisons, phylogenetics and evaluation of potential interbreeding taxa of a species, various loci have served for animals and plants and protistans. One [second internal transcribed spacer (ITS2) of the nuclear ribosomal DNA] is highly suitable for all. Its sequence is species specific. It has already been used extensively and very successfully for plants and some protistans, and a few animals (where historically, the mitochondrial genes have dominated species studies). Despite initial impressions that ITS2 is too variable, it has proven to provide useful biological information at higher taxonomic levels, even across all eukaryotes, thanks to the conserved aspects of its transcript secondary structure. The review of all eukaryote groups reveals that ITS2 is expandable, but always retains in its RNA transcript a common core structure of two helices with hallmark characteristics important for ribosomal RNA processing. This aspect of its RNA transcript secondary structure can rescue difficult alignment problems, making the ITS2?a more powerful tool for phylogenetics. Equally important, the recognition of eukaryote-wide homology regions provides extensive and detailed information to test experimental studies of ribosomal rRNA processing.

Coleman, Annette W.

2007-01-01

333

Discovering Sequence-Structure Patterns in Proteins with Variable Secondary Structure  

Microsoft Academic Search

Abstract. Proteins that share a similar ,function often exhibit conserved ,se- quence patterns. Sequence patterns help to classify proteins into families where the exact function may ,or may ,not be known. Research has shown ,that these domain,signatures often exhibit specific three-dimensional structures. We have previously shown that sequence patterns combined with structural information, ingeneral, have superior discrimination ability than those

Tom Milledge; Gaolin Zheng; Giri Narasimhan

2006-01-01

334

Mineral association changes the secondary structure and dynamics of murine amelogenin.  

PubMed

Amelogenin is one of the key protein constituents responsible for the exquisite organization of the calcium phosphate crystals in enamel. Amelogenin forms into nanospheres in solution, while its association with hydroxyapatite is also essential to enamel development. Structural information of full-length amelogenin in either of these physiologically important forms has the potential to provide mechanistic information; however, these data are limited because of the difficulty of determining the structure of large protein complexes and proteins bound to surfaces. To obtain structural insights into amelogenin during these early stages of enamel development, we used a lysine-specific (13)C-, (15)N-labeled sample of murine amelogenin to provide insight into the structure of the hydroxyapatite (HAP)-binding domains of the protein. A combination of one-and two-dimensional solid-state NMR experiments was used to obtain molecular-level insights into the secondary structure and dynamics of full-length amelogenin within a nanosphere-gel and on the surface of HAP. Regions of amelogenin that appear to be primarily random coil in the nanosphere-gel adopt a ?-strand structure and are less mobile with HAP binding, indicative of a structural switch upon binding that may be important in the role of amelogenin in enamel development. PMID:24130249

Lu, J X; Xu, Y S; Buchko, G W; Shaw, W J

2013-11-01

335

RNA secondary structure of the feline immunodeficiency virus 5?UTR and Gag coding region  

PubMed Central

The 5? untranslated region (5?UTR) of lentiviral genomic RNA is highly structured, and is the site of multiple RNA–RNA and RNA–protein interactions throughout the viral life cycle. The 5?UTR plays a critical role during transcription, translational regulation, genome dimerization, reverse transcription priming and encapsidation. The 5?UTR structures of human lentiviruses have been extensively studied, yet the respective role and conformation of each domain is still controversial. To gain insight into the structure-function relationship of lentiviral 5?UTRs, we modelled the RNA structure of the feline immunodeficiency virus (FIV), a virus that is evolutionarily distant from the primate viruses. Through combined chemical and enzymatic structure probing and a thorough phylogenetic study, we establish a model for the secondary structure of the 5?UTR and Gag coding region. This work highlights properties common to all lentiviruses, like the primer binding site structure and the presence of a stable stem-loop at the 5? extremity. We find that FIV has also evolved specific features, including a long stem loop overlapping the end of the 5?UTR and the beginning of the coding region. In addition, we observed footprints of Gag protein on each side of the initiation codon, this sheds light on the role of the sequences required for encapsidation.

James, Laurie; Sargueil, Bruno

2008-01-01

336

Assignments, secondary structure and dynamics of the inhibitor-free catalytic fragment of human fibroblast collagenase  

Microsoft Academic Search

Fibroblast collagenase (MMP-1), a 169-residue protein with amolecular mass of 18.7 kDa, is a matrix metalloproteinase which\\u000a has beenassociated with pathologies such as arthritis and cancer. The assignments ofthe 1H, 15N, 13CO and13C resonances, determination of the secondary structure andanalysis of 15N relaxation data of the inhibitor-freecatalytic fragment of recombinant human fibroblast collagenase (MMP-1) arepresented.\\u000a It is shown that MMP-1

Franklin J. Moy; Michael R. Pisano; Pranab K. Chanda; Charlotte Urbano; Loran M. Killar; Mei-Li Sung; Robert Powers

1997-01-01

337

Maintenance of secondary power and structural systems for electric arc furnaces  

SciTech Connect

Key components and assemblies utilized on the secondary side of electric arc melting (or refining furnaces) have been discussed with emphasis on maintenance, design and modification of current-carrying and structural equipment. Common causes of failure for electrode holders and pads, water-cooled furnace cables and mast arm assemblies have been reviewed, and the cause and effect relationship of production demands with equipment life evaluated. Normal and expected wear vs excessive and premature damage are discussed, and recommendations made on how to prolong equipment life leading to a reduction in production delays due to unscheduled maintenance downtime.

Surgeon, D.A. [Erie Copper Works, Inc., Medina, OH (United States)

1997-05-01

338

Comparative structure and biomechanics of plant primary and secondary cell walls  

PubMed Central

Recent insights into the physical biology of plant cell walls are reviewed, summarizing the essential differences between primary and secondary cell walls and identifying crucial gaps in our knowledge of their structure and biomechanics. Unexpected parallels are identified between the mechanism of expansion of primary cell walls during growth and the mechanisms by which hydrated wood deforms under external tension. There is a particular need to revise current “cartoons” of plant cell walls to be more consistent with data from diverse approaches and to go beyond summarizing limited aspects of cell walls, serving instead as guides for future experiments and for the application of new techniques.

Cosgrove, Daniel J.; Jarvis, Michael C.

2012-01-01

339

Influence of secondary structure on recovery from pauses during early stages of RNA transcription  

NASA Astrophysics Data System (ADS)

The initial stages of transcription by RNA polymerase are frequently marked by pausing and stalling events. These events have been linked to an inactive backtracked state in which the polymerase diffuses along the template DNA. We investigate theoretically the influence of RNA secondary structure in confining this diffusion. The effective confinement length peaks at transcript lengths commensurate with early stalling. This finite-size effect accounts for slow progress at the beginning of transcription, which we illustrate via stochastic hopping models for backtracking polymerases.

Klopper, A. V.; Bois, J. S.; Grill, S. W.

2010-03-01

340

Secondary Structure and Phylogenetic Utility of the Ribosomal Internal Transcribed Spacer 2 (ITS2) in Scleractinian Corals  

Microsoft Academic Search

Chaolun Allen Chen, Chau-Ching Chang, Nuwei Vivian Wei, Chien-Hsun Chen, Yi-Ting Lein, Ho-E Lin, Chang-Feng Dai and Carden C. Wallace (2004) Secondary structure and phylogenetic utility of the ribosomal internal transcribed spacer 2 (ITS2) in scleractinian corals. Zoological Studies 43(4): 759-771. In this study, we examined the nucleotide characteristics, the secondary structure, and phylogenetic utility of the ribosomal internal spacer

Chaolun Allen Chen; Chau-Ching Chang; Nuwei Vivian Wei; Chien-Hsun Chen; Yi-Ting Lein; Ho-E Lin; Chang-Feng Dai; Carden C. Wallace

2004-01-01

341

Promoter Region of the Escherichia coli O7-Specific Lipopolysaccharide Gene Cluster: Structural and Functional Characterization of an Upstream Untranslated mRNA Sequence  

PubMed Central

We report the identification of the promoter region of the Escherichia coli O7-specific lipopolysaccharide (LPS) gene cluster (wbEcO7). Typical ?10 and ?35 sequences were found to be located in the intervening region between galF and rlmB, the first gene of the wbEcO7 cluster. Data from RNase protection experiments revealed the existence of an untranslated leader mRNA segment of 173 bp, including the JUMPStart and two ops sequences. We characterized the structure of this leader mRNA by using the program Mfold and a combination of nested and internal deletions transcriptionally fused to a promoterless lac operon. Our results indicated that the leader mRNA may fold into a series of complex stem-loop structures, one of which includes the JUMPStart element. We have also found that one of the ops sequences resides on the predicted stem and the other resides on the loop region, and we confirmed that these sequences are essential for the RfaH-mediated regulation of the O polysaccharide cluster. A very similar stem-loop structure could be predicted in the promoter region of the LPS core operon encoding the waaQGPSBIJYZK genes. We observed another predicted stem-loop, located immediately downstream from the wbEcO7 transcription initiation site, which appeared to be involved in premature termination of transcription. This putative stem-loop is common to many other O polysaccharide gene clusters but is not present in core oligosaccharide genes. wbEcO7-lac transcriptional fusions in single copy numbers were also used to determine the effects of various environmental cues in the transcriptional regulation of O polysaccharide synthesis. No effects were detected with temperature, osmolarity, Mg2+ concentration, and drugs inducing changes in DNA supercoiling. We therefore conclude that the wbEcO7 promoter activity may be constitutive and that regulation takes place at the level of elongation of the mRNA in a RfaH-mediated manner.

Marolda, Cristina L.; Valvano, Miguel A.

1998-01-01

342

Differential flexibility of the secondary structures of lysozyme and the structure and ordering of surrounding water molecules  

NASA Astrophysics Data System (ADS)

We have performed an atomistic molecular dynamics simulation of an aqueous solution of hen egg-white lysozyme at room temperature with explicit water molecules. Several analyses have been carried out to explore the differential flexibility of the secondary structural segments of the protein and the structure and ordering of water around them. It is found that the overall flexibility of the protein molecule is primarily controlled by few large-amplitude bistable motions exhibited by two coils; one connecting two ?-helical segments in domain-1 and the other connecting a 310 helix and a ?-sheet in domain-2 of the protein. The heterogeneous structuring of water around the segments of the protein has been found to depend on the degree of exposure of the segments to water. The ordering of water molecules around the protein segments and their tagged potential energies have been found to be anticorrelated with each other. Some of these findings can be verified by suitable experimental studies.

Sinha, Sudipta Kumar; Bandyopadhyay, Sanjoy

2011-03-01

343

Characterization of the human NTAK gene structure and distribution of the isoforms for rat NTAK mRNA.  

PubMed

NTAK (neural- and thymus-derived activator for the ErbB kinase, neuregulin-2) is a novel member of the epidermal growth factor (EGF) family. We have isolated and characterized the human NTAK gene, comprising 12 exons spanning in excess of 55 kilobases (kb). The 7. 0kb long mRNA of the human NTAK gene was expressed in the human neuroblastoma SK-N-SH cell line with two alternative isoforms detected. Furthermore, six isoforms have been identified from rat brain and PC-12 cells. Although the alpha isoform of the NTAK gene was found to be expressed in all tissues including brain, the beta isoform was expressed only in rat brain tissues. Potential regulatory regions included consensus binding sites for AP-2, TF-IIIA, Sp-1, and YY-1 located in the 5'-flanking region of the NTAK gene. PMID:10974560

Yamada, K; Ichino, N; Nishii, K; Sawada, H; Higashiyama, S; Ishiguro, H; Nagatsu, T

2000-09-01

344

Kinetic assembling of the biologically active secondary structure for CAR, the target sequence for the Rev protein of HIV-1.  

PubMed

We predict the metastable secondary structure for the CAR (cis anti-repressor sequence) which is active in the regulation of the interaction with the Rev protein of HIV-1. We prove that the active structure sustained between nts 7364 and 7559 of the env RNA is the most probable metastable structure whose formation is kinetically governed and not thermodynamically determined. The structure is obtained by means of a Monte Carlo simulation which computes refolding events which occur as the CAR portion of the viral RNA is being assembled. Thus, the regulatory role of the secondary structure is determined as soon as the new RNA has been synthesized and it is preserved for further recognition by the Rev protein. In analogy with previous work by the author, it is shown that the destabilization by site-directed mutagenesis of the secondary structure for a non-chain-specific recognition site enhances the Rev response. PMID:2195997

Fernández, A

1990-08-01

345

GraphClust: alignment-free structural clustering of local RNA secondary structures  

PubMed Central

Motivation: Clustering according to sequence–structure similarity has now become a generally accepted scheme for ncRNA annotation. Its application to complete genomic sequences as well as whole transcriptomes is therefore desirable but hindered by extremely high computational costs. Results: We present a novel linear-time, alignment-free method for comparing and clustering RNAs according to sequence and structure. The approach scales to datasets of hundreds of thousands of sequences. The quality of the retrieved clusters has been benchmarked against known ncRNA datasets and is comparable to state-of-the-art sequence–structure methods although achieving speedups of several orders of magnitude. A selection of applications aiming at the detection of novel structural ncRNAs are presented. Exemplarily, we predicted local structural elements specific to lincRNAs likely functionally associating involved transcripts to vital processes of the human nervous system. In total, we predicted 349 local structural RNA elements. Availability: The GraphClust pipeline is available on request. Contact: backofen@informatik.uni-freiburg.de Supplementary information: Supplementary data are available at Bioinformatics online.

Rose, Dominic; Backofen, Rolf

2012-01-01

346

RNA sequence and secondary structure requirements for rho-dependent transcription termination.  

PubMed Central

The interaction of E. coli termination factor rho with the nascent RNA transcript appears to be a central feature of the rho-dependent transcription termination process. Based on in vitro studies of the rho-dependent termination of the transcript initiated at the PR promoter of bacteriophage lambda, and on earlier studies, Morgan, Bear and von Hippel (J. Biol. Chem. 258, 9565-9574, 1983) proposed a model defining the features of a potential binding site for rho protein on transcripts subject to rho-dependent termination. This model suggested that an effective rho binding site on a nascent RNA transcript should be: (i) greater than 70-80 nucleotide residues in length; (ii) essentially unencumbered with stable secondary structure; (iii) relatively sequence non-specific; and (iv) located within a few hundred nucleotide residues upstream of the potential rho-dependent terminus. In this paper we examine the sequences and secondary structures of several transcripts that exhibit rho-dependent termination to test this hypothesis further. Unstructured regions of approximately the expected size and location were found on all the transcripts examined. Though several short specific sequence elements were found to occur in a very similar arrangement on the lambda PR- and lambda PL-initiated transcripts of lambda phage, no such elements of sequence regularity were found on any of the other rho-dependent transcripts. The results of the sequence comparisons reported here strongly support the generality of the "unstructured binding site" hypothesis for rho-dependent termination.

Morgan, W D; Bear, D G; Litchman, B L; von Hippel, P H

1985-01-01

347

Primary and secondary structure of dinoflagellate U5 small nuclear RNA.  

PubMed Central

U5 RNA is one of the six capped small nuclear RNAs present in most eukaryotic cells. Like U1, U2, U4 and U6 RNAs, U5 RNA is associated with hnRNP particles and is thus probably involved in some, as yet undefined, aspects of pre-messenger RNA processing. In this study, the complete nucleotide sequence of U5 RNA of a dinoflagellate, Crypthecodinium cohnii was determined. The analysis of this dinoflagellate U5 RNA sequence showed that a) the sequence homology between human, rat and chicken U5 RNA sequences and dinoflagellate U5 RNA sequence is 64%; b) the extent and the position of post-transcriptional modifications are similar to those found in U5 RNA of higher eukaryotes; c) although the dinoflagellate U5 RNA is shorter in length (108 nucleotides long vs 117 long in human, rat and chicken cells), the RNA fits well into the same secondary structure proposed for U5 RNA of higher eukaryotes (Krol et al. (1981) Nucl. Acids Res. 9, 769); and d) the AUn nucleotide sequence protected by the Sm-antigen and the tight secondary structure found near the 3'-end of other U-RNAs was also found in dinoflagellate U5 RNA. The high order of homology observed between dinoflagellate U5 RNA and U5 RNA of higher eukaryotes indicates that dinoflagellates are more closely related to metazoans than to early eukaryotes. Images

Liu, M H; Reddy, R; Henning, D; Spector, D; Busch, H

1984-01-01

348

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

PubMed

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

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

2013-04-14

349

Proton NMR assignments and secondary structure of the snake venom protein echistatin  

SciTech Connect

The snake venom protein echistatin is a potent inhibitor of platelet aggregation. The inhibitory properties of echistatin have been attributed to the Arg-Gly-Asp sequence at residues 24-26. In this paper, sequence-specific nuclear magnetic resonance assignments are presented for the proton resonances of echistatin in water. The single-chain protein contains 49 amino acids and 4 cystine bridges. All of the backbone amide, C{sub alpha}H, and side-chain resonances, except for the {eta}-NH of the arginines, have been assigned. The secondary structure of the protein was characterized from the pattern of nuclear Overhauser enhancements, from the identification of slowly exchanging amide protons, from {sup 3}J{sub c{alpha}H-NH} coupling constants, and from circular dichroism studies. The data suggest that the secondary structure consists of a type I {beta}-turn, a short {beta}-hairpin, and a short-, irregular, antiparallel {beta}-sheet and that the Arg-Gly-Asp sequence is in a flexible loop connecting two strands of the distorted antiparallel {beta}-sheet.

Yuan Chen; Baum, J. (Rutgers-the State Univ., Piscataway, NJ (United States)); Pitzenberger, S.M.; Garsky, V.M.; Lumma, P.K.; Sanyal, G. (Merck Sharp and Dohme Research Labs., West Point, PA (United States))

1991-12-17

350

Minimising the secondary structure of DNA targets by incorporation of a modified deoxynucleoside: implications for nucleic acid analysis by hybridisation  

PubMed Central

Some regions of nucleic acid targets are not accessible to heteroduplex formation with complementary oligonucleotide probes because they are involved in secondary structure through intramolecular Watson–Crick pairing. The secondary conformation of the target may be destabilised to assist its interaction with oligonucleotide probes. To achieve this, we modified a DNA target, which has self-complementary sequence able to form a hairpin loop, by replacing dC with N4-ethyldeoxycytidine (d4EtC), which hybridises specifically with natural dG to give a G:4EtC base pair with reduced stability compared to the natural G:C base pair. Substitution by d4EtC greatly reduced formation of the target secondary structure. The lower level of secondary structure allowed hybridisation with complementary probes made with natural bases. We confirmed that hybridisation could be further enhanced by modifying the probes with intercalating groups which stabilise the duplex.

Nguyen, Hong-Khanh; Southern, Edwin M.

2000-01-01

351

Viruses and Raman spectroscopy: determination of secondary structures of viral capsids and chromosomes by difference methods  

NASA Astrophysics Data System (ADS)

Vibrational spectra of the double-stranded DNA genome of an icosahedral virus (P22) in packaged and unpackaged states have been accurately compared by digital difference Raman spectroscopy. The difference Raman spectrum, which is sensitive to structural changes at the level of < 2% of a given nucleotide type, reveals the effects of packaging upon sugar pucker, glycosyl orientation, phosphodiester geometry, base pairing, base stacking and the electrostatic environment of DNA phosphate groups. At the experimental conditions employed, the B form secondary structure of unpackaged P22 DNA is minimally perturbed by packaging the viral genome in the virion capsid. However, the electrostatic environment of DNA phosphates is dramatically altered with packaging. The present results suggest a simple model for organization of the condensed dsDNA chromosomes of icosahedral viruses.

Aubrey, Kelly L.; Towse, Stacy A.; Thomas, George J.

1993-06-01

352

Isoprenyl diphosphate synthases: protein sequence comparisons, a phylogenetic tree, and predictions of secondary structure.  

PubMed Central

Isoprenyl diphosphate synthases are ubiquitous enzymes that catalyze the basic chain-elongation reaction in the isoprene biosynthetic pathway. Pairwise sequence comparisons were made for 6 farnesyl diphosphate synthases, 6 geranylgeranyl diphosphate synthases, and a hexaprenyl diphosphate synthase. Five regions with highly conserved residues, two of which contain aspartate-rich DDXX(XX)D motifs found in many prenyltransferases, were identified. A consensus secondary structure for the group, consisting mostly of alpha-helices, was predicted for the multiply aligned sequences from amino acid compositions, computer assignments of local structure, and hydropathy indices. Progressive sequence alignments suggest that the 13 isoprenyl diphosphate synthases evolved from a common ancestor into 3 distinct clusters. The most distant separation is between yeast hexaprenyl diphosphate synthetase and the other enzymes. Except for the chromoplastic geranylgeranyl diphosphate synthase from Capsicum annuum, the remaining farnesyl and geranylgeranyl diphosphate synthases segregate into prokaryotic/archaebacterial and eukaryotic families.

Chen, A.; Kroon, P. A.; Poulter, C. D.

1994-01-01

353

Isoprenyl diphosphate synthases: protein sequence comparisons, a phylogenetic tree, and predictions of secondary structure.  

PubMed

Isoprenyl diphosphate synthases are ubiquitous enzymes that catalyze the basic chain-elongation reaction in the isoprene biosynthetic pathway. Pairwise sequence comparisons were made for 6 farnesyl diphosphate synthases, 6 geranylgeranyl diphosphate synthases, and a hexaprenyl diphosphate synthase. Five regions with highly conserved residues, two of which contain aspartate-rich DDXX(XX)D motifs found in many prenyltransferases, were identified. A consensus secondary structure for the group, consisting mostly of alpha-helices, was predicted for the multiply aligned sequences from amino acid compositions, computer assignments of local structure, and hydropathy indices. Progressive sequence alignments suggest that the 13 isoprenyl diphosphate synthases evolved from a common ancestor into 3 distinct clusters. The most distant separation is between yeast hexaprenyl diphosphate synthetase and the other enzymes. Except for the chromoplastic geranylgeranyl diphosphate synthase from Capsicum annuum, the remaining farnesyl and geranylgeranyl diphosphate synthases segregate into prokaryotic/archaebacterial and eukaryotic families. PMID:8003978

Chen, A; Kroon, P A; Poulter, C D

1994-04-01

354

Selective cleavages of tRNAPhe with secondary and tertiary structures by enediyne antitumor antibiotics.  

PubMed

Some enediyne antitumor antibiotics induce site-selective cleavages for yeast tRNA(Phe) with three-dimensional structure. Of special interest is the fact that tRNA(Phe) is specifically cleaved at the anticodon arm regions by C-1027 and esperamicin A1 in the presence of Mg2+ ions. Although neocarzinostatin strongly breaks tRNA(Phe) at 5'-GPu steps in the absence of magnesium ions, its cleavage ability is completely lost in the presence of 100 microM Mg2+ ions. Dynemicin A, which favors an intercalative binding, causes no strand scissions for the RNA with secondary and tertiary structures. This cutting of tRNA(Phe) may reveal that RNA as well as DNA constitutes a therapeutically relevant target for certain enediyne antitumor antibiotics. PMID:9222516

Sugiura, Y; Totsuka, R; Araki, M; Okuno, Y

1997-06-01

355

Evaluation of a sophisticated SCFG design for RNA secondary structure prediction.  

PubMed

Predicting secondary structures of RNA molecules is one of the fundamental problems of and thus a challenging task in computational structural biology. Over the past decades, mainly two different approaches have been considered to compute predictions of RNA secondary structures from a single sequence: the first one relies on physics-based and the other on probabilistic RNA models. Particularly, the free energy minimization (MFE) approach is usually considered the most popular and successful method. Moreover, based on the paradigm-shifting work by McCaskill which proposes the computation of partition functions (PFs) and base pair probabilities based on thermodynamics, several extended partition function algorithms, statistical sampling methods and clustering techniques have been invented over the last years. However, the accuracy of the corresponding algorithms is limited by the quality of underlying physics-based models, which include a vast number of thermodynamic parameters and are still incomplete. The competing probabilistic approach is based on stochastic context-free grammars (SCFGs) or corresponding generalizations, like conditional log-linear models (CLLMs). These methods abstract from free energies and instead try to learn about the structural behavior of the molecules by learning (a manageable number of) probabilistic parameters from trusted RNA structure databases. In this work, we introduce and evaluate a sophisticated SCFG design that mirrors state-of-the-art physics-based RNA structure prediction procedures by distinguishing between all features of RNA that imply different energy rules. This SCFG actually serves as the foundation for a statistical sampling algorithm for RNA secondary structures of a single sequence that represents a probabilistic counterpart to the sampling extension of the PF approach. Furthermore, some new ways to derive meaningful structure predictions from generated sample sets are presented. They are used to compare the predictive accuracy of our model to that of other probabilistic and energy-based prediction methods. Particularly, comparisons to lightweight SCFGs and corresponding CLLMs for RNA structure prediction indicate that more complex SCFG designs might yield higher accuracy but eventually require more comprehensive and pure training sets. Investigations on both the accuracies of predicted foldings and the overall quality of generated sample sets (especially on an abstraction level, called abstract shapes of generated structures, that is relevant for biologists) yield the conclusion that the Boltzmann distribution of the PF sampling approach is more centered than the ensemble distribution induced by the sophisticated SCFG model, which implies a greater structural diversity within generated samples. In general, neither of the two distinct ensemble distributions is more adequate than the other and the corresponding results obtained by statistical sampling can be expected to bare fundamental differences, such that the method to be preferred for a particular input sequence strongly depends on the considered RNA type. PMID:22135038

Nebel, Markus E; Scheid, Anika

2011-12-02

356

Networks of interactions in the secondary and tertiary structure of ribosomal RNA  

NASA Astrophysics Data System (ADS)

We construct four different structural networks for both the secondary and tertiary structures of the 16S and 23S ribosomal RNAs (rRNAs) in the high-resolution crystal structures of the Thermus thermophilus 30S and Haloarcula marismortui 50S ribosomal subunits, and investigate topological characteristics of the rRNA structures by determining relevant measures, such as the characteristic path length, the clustering coefficient, and the helix betweenness. This study reveals that the 23S rRNA network is more compact than the 16S rRNA networks, reflecting the more globular overall structure of the 23S rRNA relative to the 16S rRNA. In particular, the large number of tertiary interactions in the 23S rRNA tends to cluster, accounting for its small-world network properties. In addition, although the rRNA networks are not the scale-free network, their helix betweenness has a power-law distribution and is correlated with the phylogenetic conservation of helices. The higher the helix betweenness, the more conserved the helix. These results suggest a potential role of the rRNA network as a new quantitative approach in rRNA research.

Lee, Chang-Yong; Lee, Jung C.; Gutell, Robin R.

2007-12-01

357

Interpreting oligonucleotide microarray data to determine RNA secondary structure: application to the 3' end of Bombyx mori R2 RNA.  

PubMed

A method to deduce RNA secondary structure on the basis of data from microarrays of 2'-O-methyl RNA 9-mers immobilized in agarose film on glass slides is tested with a 249 nucleotide RNA from the 3' end of the R2 retrotransposon from Bombyx mori. Various algorithms incorporating binding data and free-energy minimization calculations were compared for interpreting the data to provide possible secondary structures. Two different methods give structures with 100 and 87% of the base pairs determined by sequence comparison. In contrast, structures predicted by free-energy minimization alone by Mfold and RNAstructure contain 52 and 72% of the known base pairs, respectively. This combination of high throughput microarray techniques with algorithms using free-energy calculations has potential to allow for fast determination of RNA secondary structure. It should also facilitate the design of antisense and siRNA oligonucleotides. PMID:16893182

Duan, Shenghua; Mathews, David H; Turner, Douglas H

2006-08-15

358

Isolation and characterization of human glycophorin A cDNA clones by a synthetic oligonucleotide approach: nucleotide sequence and mRNA structure  

SciTech Connect

In an effort to understand the relationships among and the regulation of human glycophorins, the authors have isolated and characterized several glycophorin A-specific cDNA clones obtained from a human erythroleukemic K562 cell cDNA library. This was accomplished by using mixed synthetic oligonucleotides, corresponding to various regions of the known amino acid sequence, to prime the synthesis of the cDNA as well as to screen the cDNA library. They also used synthetic oligonucleotides to sequence the largest of the glycophorin cDNAs. The nucleotide sequence obtained suggests the presence of a potential leader peptide, consistent with the membrane localization of this glycoprotein. Examination of the structure of glycophorin mRNA by blot hybridization revealed the existence of several electrophoretically distinct mRNAs numbering three or four, depending on the size of the glycophorin cDNA used as a hybridization probe. The smaller cDNA hybridized to three mRNAs of approximately 2.8, 1.7, and 1.0 kilobases. In contrast, the larger cDNA hybridized to an additional mRNA of approximately 0.6 kilobases. Further examination of the relationships between these multiple mRNAs by blot hybridization was conducted with the use of exact-sequence oligonucleotide probes constructed from various regions of the cDNA representing portions of the amino acid sequence of glycophorin A with or without known homology with glycophorin B. In total, the results obtained are consistent with the hypothesis that the three larger mRNAs represent glycophorin A gene transcripts and that the smallest (0.6 kilobase) mRNA may be specific for glycophorin B.

Siebert, P.D.; Fukuda, M.

1986-03-01

359

Structural Insights into Parasite eIF4E Binding Specificity for m7G and m2,2,7G mRNA Caps*  

PubMed Central

The eukaryotic translation initiation factor eIF4E recognizes the mRNA cap, a key step in translation initiation. Here we have characterized eIF4E from the human parasite Schistosoma mansoni. Schistosome mRNAs have either the typical monomethylguanosine (m7G) or a trimethylguanosine (m2,2,7G) cap derived from spliced leader trans-splicing. Quantitative fluorescence titration analyses demonstrated that schistosome eIF4E has similar binding specificity for both caps. We present the first crystal structure of an eIF4E with similar binding specificity for m7G and m2,2,7G caps. The eIF4E·m7GpppG structure demonstrates that the schistosome protein binds monomethyl cap in a manner similar to that of single specificity eIF4Es and exhibits a structure similar to other known eIF4Es. The structure suggests an alternate orientation of a conserved, key Glu-90 in the cap-binding pocket that may contribute to dual binding specificity and a position for mRNA bound to eIF4E consistent with biochemical data. Comparison of NMR chemical shift perturbations in schistosome eIF4E on binding m7GpppG and m2,2,7GpppG identified key differences between the two complexes. Isothermal titration calorimetry demonstrated significant thermodynamics differences for the binding process with the two caps (m7G versus m2,2,7G). Overall the NMR and isothermal titration calorimetry data suggest the importance of intrinsic conformational flexibility in the schistosome eIF4E that enables binding to m2,2,7G cap.

Liu, Weizhi; Zhao, Rui; McFarland, Craig; Kieft, Jeffrey; Niedzwiecka, Anna; Jankowska-Anyszka, Marzena; Stepinski, Janusz; Darzynkiewicz, Edward; Jones, David N. M.; Davis, Richard E.

2009-01-01

360

Structural insights into parasite eIF4E binding specificity for m7G and m2,2,7G mRNA caps.  

PubMed

The eukaryotic translation initiation factor eIF4E recognizes the mRNA cap, a key step in translation initiation. Here we have characterized eIF4E from the human parasite Schistosoma mansoni. Schistosome mRNAs have either the typical monomethylguanosine (m(7)G) or a trimethylguanosine (m(2,2,7)G) cap derived from spliced leader trans-splicing. Quantitative fluorescence titration analyses demonstrated that schistosome eIF4E has similar binding specificity for both caps. We present the first crystal structure of an eIF4E with similar binding specificity for m(7)G and m(2,2,7)G caps. The eIF4E.m(7)GpppG structure demonstrates that the schistosome protein binds monomethyl cap in a manner similar to that of single specificity eIF4Es and exhibits a structure similar to other known eIF4Es. The structure suggests an alternate orientation of a conserved, key Glu-90 in the cap-binding pocket that may contribute to dual binding specificity and a position for mRNA bound to eIF4E consistent with biochemical data. Comparison of NMR chemical shift perturbations in schistosome eIF4E on binding m(7)GpppG and m(2,2,7)GpppG identified key differences between the two complexes. Isothermal titration calorimetry demonstrated significant thermodynamics differences for the binding process with the two caps (m(7)G versus m(2,2,7)G). Overall the NMR and isothermal titration calorimetry data suggest the importance of intrinsic conformational flexibility in the schistosome eIF4E that enables binding to m(2,2,7)G cap. PMID:19710013

Liu, Weizhi; Zhao, Rui; McFarland, Craig; Kieft, Jeffrey; Niedzwiecka, Anna; Jankowska-Anyszka, Marzena; Stepinski, Janusz; Darzynkiewicz, Edward; Jones, David N M; Davis, Richard E

2009-08-26

361

The secondary structure of calcineurin regulatory region and conformational change induced by calcium/calmodulin binding.  

PubMed

The protein serine/threonine phosphatase calcineurin (CN) is activated by calmodulin (CaM) in response to intracellular calcium mobilization. A widely accepted model for CN activation involves displacement of the CN autoinhibitory peptide (CN(467-486)) from the active site upon binding of CaM. However, CN activation requires calcium binding both to the low affinity sites of CNB and to CaM, and previous studies did not dissect the individual contributions of CNB and CaM to displacement of the autoinhibitory peptide from the active site. In this work we have produced separate CN fragments corresponding to the CNA regulatory region (CNRR(381-521), residues 381-521), the CNA catalytic domain truncated at residue 341, and the CNA-CNB heterodimer with CNA truncated at residue 380 immediately after the CNB binding helix. We show that the separately expressed regulatory region retains its ability to inhibit CN phosphatase activity of the truncated CN341 and CN380 and that the inhibition can be reversed by calcium/CaM binding. Tryptophan fluorescence quenching measurements further indicate that the isolated regulatory region inhibits CN activity by occluding the catalytic site and that CaM binding exposes the catalytic site. The results provide new support for a model in which calcium binding to CNB enables CaM binding to the CNA regulatory region, and CaM binding then instructs an activating conformational change of the regulatory region that does not depend further on CNB. Moreover, the secondary structural content of the CNRR(381-521) was tentatively addressed by Fourier transform infrared spectroscopy. The results indicate that the secondary structure of CNRR(381-521) fragment is predominantly random coil, but with significant amount of beta-strand and alpha-helix structures. PMID:18296442

Shen, Xianrong; Li, Huiming; Ou, Yan; Tao, Wenbing; Dong, Aichun; Kong, Jilie; Ji, Chaoneng; Yu, Shaoning

2008-02-22

362

Plant secondary metabolite-induced shifts in bacterial community structure and degradative ability in contaminated soil.  

PubMed

The aim of the study was to investigate how selected natural compounds (naringin, caffeic acid, and limonene) induce shifts in both bacterial community structure and degradative activity in long-term polychlorinated biphenyl (PCB)-contaminated soil and how these changes correlate with changes in chlorobiphenyl degradation capacity. In order to address this issue, we have integrated analytical methods of determining PCB degradation with pyrosequencing of 16S rRNA gene tag-encoded amplicons and DNA-stable isotope probing (SIP). Our model system was set in laboratory microcosms with PCB-contaminated soil, which was enriched for 8 weeks with the suspensions of flavonoid naringin, terpene limonene, and phenolic caffeic acid. Our results show that application of selected plant secondary metabolites resulted in bacterial community structure far different from the control one (no natural compound amendment). The community in soil treated with caffeic acid is almost solely represented by Proteobacteria, Acidobacteria, and Verrucomicrobia (together over 99 %). Treatment with naringin resulted in an enrichment of Firmicutes to the exclusion of Acidobacteria and Verrucomicrobia. SIP was applied in order to identify populations actively participating in 4-chlorobiphenyl catabolism. We observed that naringin and limonene in soil foster mainly populations of Hydrogenophaga spp., caffeic acid Burkholderia spp. and Pseudoxanthomonas spp. None of these populations were detected among 4-chlorobiphenyl utilizers in non-amended soil. Similarly, the degradation of individual PCB congeners was influenced by the addition of different plant compounds. Residual content of PCBs was lowest after treating the soil with naringin. Addition of caffeic acid resulted in comparable decrease of total PCBs with non-amended soil; however, higher substituted congeners were more degraded after caffeic acid treatment compared to all other treatments. Finally, it appears that plant secondary metabolites have a strong effect on the bacterial community structure, activity, and associated degradative ability. PMID:23250224

Uhlik, Ondrej; Musilova, Lucie; Ridl, Jakub; Hroudova, Miluse; Vlcek, Cestmir; Koubek, Jiri; Holeckova, Marcela; Mackova, Martina; Macek, Tomas

2012-12-19

363

DCL4 targets Cucumber mosaic virus satellite RNA at novel secondary structures.  

PubMed

It has been reported that plant virus-derived small interfering RNAs (vsiRNAs) originated predominantly from structured single-stranded viral RNA of a positive single-stranded RNA virus replicating in the cytoplasm and from the nuclear stem-loop 35S leader RNA of a double-stranded DNA (dsDNA) virus. Increasing lines of evidence have also shown that hierarchical actions of plant Dicer-like (DCL) proteins are required in the biogenesis process of small RNAs, and DCL4 is the primary producer of vsiRNAs. However, the structures of such single-stranded viral RNA that can be recognized by DCLs remain unknown. In an attempt to determine these structures, we have cloned siRNAs derived from the satellite RNA (satRNA) of Cucumber mosaic virus (CMV-satRNA) and studied the relationship between satRNA-derived siRNAs (satsiRNAs) and satRNA secondary structure. satsiRNAs were confirmed to be derived from single-stranded satRNA and are primarily 21 (64.7%) or 22 (22%) nucleotides (nt) in length. The most frequently cloned positive-strand satsiRNAs were found to derive from novel hairpins that differ from the structure of known DCL substrates, miRNA and siRNA precursors, which are prevalent stem-loop-shaped or dsRNAs. DCL4 was shown to be the primary producer of satsiRNAs. In the absence of DCL4, only 22-nt satsiRNAs were detected. Our results suggest that DCL4 is capable of accessing flexibly structured single-stranded RNA substrates (preferably T-shaped hairpins) to produce satsiRNAs. This result reveals that viral RNA of diverse structures may stimulate antiviral DCL activities in plant cells. PMID:17609283

Du, Quan-Sheng; Duan, Cheng-Guo; Zhang, Zhong-Hui; Fang, Yuan-Yuan; Fang, Rong-Xiang; Xie, Qi; Guo, Hui-Shan

2007-07-03

364

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

SciTech Connect

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.

Y Ren; H Seo; G Blobel; A Hoelz

2011-12-31

365

Correlation between the secondary structure of pre-mRNA introns and the efficiency of splicing in Saccharomyces cerevisiae  

PubMed Central

Background Secondary structure interactions within introns have been shown to be essential for efficient splicing of several yeast genes. The nature of these base-pairing interactions and their effect on splicing efficiency were most extensively studied in ribosomal protein gene RPS17B (previously known as RP51B). It was determined that complementary pairing between two sequence segments located downstream of the 5' splice site and upstream of the branchpoint sequence promotes efficient splicing of the RPS17B pre-mRNA, presumably by shortening the branchpoint distance. However, no attempts were made to compute a shortened, 'structural' branchpoint distance and thus the functional relationship between this distance and the splicing efficiency remains unknown. Results In this paper we use computational RNA secondary structure prediction to analyze the secondary structure of the RPS17B intron. We show that it is necessary to consider suboptimal structure predictions and to compute the structural branchpoint distances in order to explain previously published splicing efficiency results. Our study reveals that there is a tight correlation between this distance and splicing efficiency levels of intron mutants described in the literature. We experimentally test this correlation on additional RPS17B mutants and intron mutants within two other yeast genes. Conclusion The proposed model of secondary structure requirements for efficient splicing is the first attempt to specify the functional relationship between pre-mRNA secondary structure and splicing. Our findings provide further insights into the role of pre-mRNA secondary structure in gene splicing in yeast and also offer basis for improvement of computational methods for splice site identification and gene-finding.

Rogic, Sanja; Montpetit, Ben; Hoos, Holger H; Mackworth, Alan K; Ouellette, BF Francis; Hieter, Philip

2008-01-01

366

Effects of physicochemical factors on the secondary structure of beta-lactoglobulin.  

PubMed

Fourier transform infrared spectroscopy and differential scanning calorimetry were used as complementary techniques to study changes in the secondary structure of beta-lactoglobulin under various physicochemical conditions. The effects of pH (3-9), NaCl (0-2 M), and lactose, glucose and sucrose (100-500 g/l) in the temperature range 25-100 degrees C on the conformation sensitive amide I band in the i.r. spectrum of beta-lactoglobulin in D2O solution were examined. The 1692 cm-1 band in the amide I band profile had not been definitively assigned in previous studies of the i.r. spectrum of beta-lactoglobulin. The decrease in this band at ambient temperature with time or upon mild heating was attributed to slow H-D exchange, indicating that it was due to a structure buried deep within the protein. The disappearance of the 1692 cm-1 band on heating was accompanied by the appearance of two bands at 1684 and 1629 cm-1, assigned to beta-sheets. The 1692 cm-1 band was therefore attributed to a beta-type structure. beta-Lactoglobulin showed maximum thermal stability at pH 3 and was easily denatured at pH 9. On denaturation, the protein unfolded into more extensive random coil structures at pH 9 than at pH 3. After 10 h at pH 9 (25 degrees C), beta-lactoglobulin was partly denatured. Heating to 60-80 degrees C generally resulted in the loss of secondary structure. At all pH values studied, two new bands at 1618 and 1684 cm-1, characteristic of intermolecular beta-sheet structure and associated with aggregation, were observed after the initial denaturation. Differential scanning calorimetry studies indicated that the thermal stability of beta-lactoglobulin was enhanced in the presence of sugars. The Fourier transform i.r. results obtained provide evidence that sugars promoted the unfolding of beta-lactoglobulin via multiple transition pathways leading to a transition state resisting aggregation. PMID:8655744

Boye, J I; Ismail, A A; Alli, I

1996-02-01

367

[Study on the effect of high hydrostatic pressure treatment on the secondary structure of mushroom polyphenoloxidase by SRCD and FTIR].  

PubMed

The secondary structure of the mushroom polyphenoloxidase treated by the high hydrostatic pressure (HHP) was analyzed by the synchrotron radiation circular dichroism (SRCD) and Fourier transform infrared spectroscopy (FTIR). The alpha-helix content of mushroom PPO was decreased after HHP treatment, which indicated that the secondary structure of PPO was changed. There was a discrepancy of the result of the secondary structure content between untreated or HHP-treated mushroom PPO analyzed by SRCD and FTIR spectra, and this discrepancy may be due to the different determination temperature, the concentration of the PPO solution and the spectra analysis method etc. The fluorescence spectra showed that the fluorescence intensity of the mushroom PPO was decreased after HHP treatment, and a red shift was observed after HHP treatment, which indicated that the tertiary structure of the enzyme molecule has been modified. PMID:22512160

Yi, Jian-yong; Dong, Peng; Wang, Yong-tao; Jiang, Bin; Liao, Xiao-jun; Hu, Xiao-song; Zhang, Yan

2012-02-01

368

Poly(L-lysine) and Clay Nanocomposite with Desired Matrix Secondary Structure: Effects of Polypeptide Molecular Weight  

SciTech Connect

Nanocomposites (NC) were formed using cationic poly(L-lysine) (PLL), a semicrystalline polypeptide, that was reinforced by sodium montmorillonite (MMT) clay via solution intercalation technique. By varying solution conditions such as pH, temperature, and polypeptide concentration in the presence of clay platelets, the secondary structure of PLL was controllably altered into {alpha}-helical, {beta}-sheet, and random coil. The high molecular weight polypeptide shows a strong propensity to fold into the {beta}-sheet structure when cast as films, irrespective of the initial secondary structure in solution. Nanocomposite local morphology confirms intercalated MMT platelets with PLL over a wide range of compositions.

Hule,R.; Pochan, D.

2007-01-01

369

Secondary-structure characterization by far-UV CD of highly purified uncoupling protein 1 expressed in yeast.  

PubMed Central

The rat UCP1 (uncoupling protein 1) is a mitochondrial inner-membrane carrier involved in energy dissipation and heat production. We expressed UCP1 carrying a His6 epitope at its C-terminus in Saccharomyces cerevisiae mitochondria. The recombinant-tagged UCP1 was purified by immobilized metal-ion affinity chromatography to homogeneity (>95%). This made it suitable for subsequent biophysical characterization. Fluorescence resonance energy transfer experiments showed that n-dodecyl-beta-D-maltoside-solubilized UCP1-His6 retained its PN (purine nucleotide)-binding capacity. The far-UV CD spectrum of the functional protein clearly indicated the predominance of alpha-helices in the UCP1 secondary structure. The UCP1 secondary structure exhibited an alpha-helical degree of approx. 68%, which is at least 25% higher than the previously reported estimations based on computational predictions. Moreover, the helical content remained unchanged in free and PN-loaded UCP1. A homology model of the first repeat of UCP1, built on the basis of X-ray-solved close parent, the ADP/ATP carrier, strengthened the CD experimental results. Our experimental and computational results indicate that (i) alpha-helices are the major component of UCP1 secondary structure; (ii) PN-binding mechanism does not involve significant secondary-structure rearrangement; and (iii) UCP1 shares similar secondary-structure characteristics with the ADP/ATP carrier, at least for the first repeat.

Douette, Pierre; Navet, Rachel; Bouillenne, Fabrice; Brans, Alain; Sluse-Goffart, Claudine; Matagne, Andre; Sluse, Francis E

2004-01-01

370

Potential secondary and tertiary structure in the genomic RNA of foot and mouth disease virus.  

PubMed Central

The nucleotide sequence of the 5' untranslated region of foot and mouth disease virus (FMDV), serotype A10 has been determined. This completes the first total genomic sequence for any one serotype of FMDV. Analysis of the sequence to the 3' side of the poly (C) tract reveals the presence of a 24 nucleotide repeated motif which has homologies with a sequence located upstream of the transcriptional initiation site from several mammalian fibrinogen genes. The function of this element in FMDV is unclear. However, computer analysis of this region predicts the presence of a high degree of secondary and tertiary structure in which these repeats form an important part. The implications of these predictions are discussed.

Clarke, B E; Brown, A L; Currey, K M; Newton, S E; Rowlands, D J; Carroll, A R

1987-01-01

371

Nucleotide sequence determination and secondary structure of Xenopus U3 snRNA.  

PubMed

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

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

1988-03-25

372

Aging and Memory Effects in the Primary and Secondary Relaxations of a Structural Glass  

NASA Astrophysics Data System (ADS)

We report frequency-dependent dielectric susceptibility measurements of aging in the glass forming liquid sorbitol for a variety of thermal histories. Temporary interruptions in the cooling of the liquid below the glass transition lead to distinctive temperature dependence for the susceptibility that can later be recovered on subsequent heating. This "memory", which has also been observed in previous studies of spin glasses(K. Jonason et al., Phys. Rev. Lett.) 81, 3243 (1998)., an orientational glass(P. Doussineau et al., Europhys. Lett.) 46, 401 (1999). and a polymer (L. Bellon et al., Europhys. Lett.) 51, 551 (2000), appears to be a general feature of aging systems. We characterize quantitatively this behavior in the structural glass, making comparisons with the other aging systems and with recent theory. We further report the influence of aging on the secondary, Johari-Goldstein relaxation in sorbitol.

Yardimci, Hasan; Leheny, Robert L.

2002-03-01

373

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

PubMed

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

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

2010-06-17

374

Innovative FT-IR Imaging of Protein Film Secondary Structure Before and After Heat Treatment  

SciTech Connect

Changes in the secondary structure of globular protein occur during thermal processing. An infrared reflecting mirrored optical substrate that is unaffected by heat allows recording infrared spectra of protein films in a reflection absorption mode on the stage of an FT-IR microspectrometer. Hydrated films of myoglobin protein cast from solution on the mirrored substrate are interrogated before and after thermal denaturation to allow a direct comparison. Focal plane array imaging of 280 protein films allowed selection of the same area in the image from which to extract spectra. After treatment, 110 of 140 spectra from multiple films showed a dramatic shift from the {alpha}-helix form (1650 {+-} 5 cm{sup -1}) to aggregated forms on either side of the original band. Seventy maxima were near 1625 cm{sup -1}, and 40 shifted in the direction of 1670 cm{sup -1}. The method developed was applied to films cast from two other commercial animal and plant protein sources.

Bonwell, E.; Wetzel, D

2009-01-01

375

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

PubMed Central

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.

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

376

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

PubMed

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

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

2013-07-25

377

Stem-loop structures in prokaryotic genomes  

Microsoft Academic Search

BACKGROUND: Prediction of secondary structures in the expressed sequences of bacterial genomes allows to investigate spontaneous folding of the corresponding RNA. This is particularly relevant in untranslated mRNA regions, where base pairing is less affected by interactions with the translation machinery. Relatively large stem-loops significantly contribute to the formation of more complex secondary structures, often important for the activity of

Mauro Petrillo; Giustina Silvestro; Pier Paolo Di Nocera; Angelo Boccia; Giovanni Paolella

2006-01-01

378

Interaction of cisplatin drug with Na,K-ATPase: drug binding mode and protein secondary structure.  

PubMed

cis-Pt(NH(3))(2)Cl(2) (cisplatin) is an antitumor drug with many severe toxic side effects including enzymatic changes associated with its mechanism of action. This study was designed to examine the interaction of cisplatin drug with the Na(+), K(+)-dependent adenosine triphosphatase (Na,K-ATPase) in H(2)O and D(2)O solutions at physiological pH, using drug concentrations of 0.1 microM to 1 mM. UV absorption spectra and Fourier transform infrared difference spectroscopy with its self-deconvolution, second derivative resolution enhancement and curve-fitting procedures were applied to characterize the drug binding mode, the drug binding constant and the protein secondary structure in the cisplatin-ATPase complexes. Spectroscopic evidence showed that at low drug concentration (0.1 microM), cisplatin binds mainly to the lipid portion of the enzyme, whereas at higher drug contents, the Pt cation interaction is through the polypeptide C==O and C-N groups with overall binding constant of K=1.93 x 10(4) M(-1). At high cisplatin concentration (1 mM), drug binding results in protein secondary structural changes from that of the alpha-helix 19.8%; beta-pleated 25.6%; turn 9.1%; beta-antiparallel 7.5% and random 38%, in the free Na,K-ATPase to that of the alpha-helix 22.2%; beta-pleated 23.2%; turn 9.4%; beta-antiparallel 2.2% and random 43%, in the cis-Pt-ATPase complexes. PMID:11566333

Neault, J F; Benkirane, A; Malonga, H; Tajmir-Riahi, H A

2001-09-01

379

Sterilization mechanism of nitrogen gas plasma: induction of secondary structural change in protein.  

PubMed

The mechanism of action on biomolecules of N? gas plasma, a novel sterilization technique, remains unclear. Here, the effect of N? gas plasma on protein structure was investigated. BSA, which was used as the model protein, was exposed to N? gas plasma generated by short-time high voltage pulses from a static induction thyristor power supply. N? gas plasma-treated BSA at 1.5?kilo pulses per second showed evidence of degradation and modification when assessed by Coomassie brilliant blue staining and ultraviolet spectroscopy at 280?nm. Fourier transform infrared spectroscopy analysis was used to determine the protein's secondary structure. When the amide I region was analyzed in the infrared spectra according to curve fitting and Fourier self-deconvolution, N? gas plasma-treated BSA showed increased ?-helix and decreased ?-turn content. Because heating decreased ?-helix and increased ?-sheet content, the structural changes induced by N? gas plasma-treatment of BSA were not caused by high temperatures. Thus, the present results suggest that conformational changes induced by N? gas plasma are mediated by mechanisms distinct from heat denaturation. PMID:23617321

Sakudo, Akikazu; Higa, Masato; Maeda, Kojiro; Shimizu, Naohiro; Imanishi, Yuichiro; Shintani, Hideharu

2013-07-01

380

Study on silk sericin and chitosan blend film: morphology and secondary structure characterizations.  

PubMed

This study aimed to prepare and characterize silk sericin and chitosan blend film as well as the native silk sericin and chitosan films. The films were observed their morphology using Scanning Electron Microscope (SEM). The secondary structures of the films were analyzed using Fourier Transform Infrared (FTIR) spectroscopy. Transparency of the films was investigated with UV-visible spectroscopy. The results found that all of silk films were smooth throughout the film surfaces, including blend film. This showed that silk sericin and chitosan very well compatible. However, phase separation is also being observed. It is show that the interaction between two materials might be miscible together. The FTIR results indicated that the most of films were composed both in random coil and beta-sheet forms which predominantly of the random coil structures. The results suggesting the blend film between sericin and chitosan did not change the intramolecular structure when compared to the native films. The silk sericin and blend films were slightly yellowish color and were higher transparent than chitosan film. However, % transmittance at lamda max of 660 nm showed that all of films have similar values. The result suggested that the transparency of the film did not change even blend together. It is a promising that both silk sericin and chitosan would be blended into many forms for applications in specifically fields. PMID:20180324

Srihanam, P; Simcheur, W; Srisuwan, Y

2009-11-15

381

Secondary structure conservation of the U3 small nucleolar RNA introns in Saccharomyces.  

PubMed

Using a strategy based on PCR amplification of DNA and sequence analysis, we showed that the presence of introns with the characteristic features of introns spliced in a spliceosome, in the U3A and U3B snoRNA genes that code for the U3 small nucleolar RNA, is not a property restricted to Saccharomyces cerevisiae. It is probably an ancient property of yeasts from the genus Saccharomyces. We detected the U3A and U3B snoRNA genes in Saccharomyces bayanus and in a lager brewing yeast strain. The U3A and U3B intronic sequences are highly conserved. Two additional "U3B-like" snoRNA genes were detected in the lager brewing yeast. Their intronic sequences show several differences, when compared to the U3B intronic sequence. However, despite the numerous mutations, the intron secondary structure is conserved, especially, the central structure. This strongly suggests an important role of this central stem/loop structure for spliceosome assembly and efficient splicing. PMID:8745634

Brulé, F; Grégoire, A; Ségault, V; Mougin, A; Branlant, C

1995-12-01

382

Solution structure of a purine rich hexaloop hairpin belonging to PGY/MDR1 mRNA and targeted by antisense oligonucleotides  

PubMed Central

A preferential target of antisense oligonucleotides directed against human PGY/MDR1 mRNA is a hairpin containing a stem with a G•U wobble pair, capped by the purine-rich 5?r(GGGAUG)3? hexaloop. This hairpin is studied by multidimensional NMR and restrained molecular dynamics, with special emphasis on the conformation of south sugars and non-standard phosphate linkages evidenced in both the stem and the loop. The hairpin is found to be highly structured. The G•U wobble pair, a strong counterion binding site, displays structural particularities that are characteristic of this type of mismatch. The upper part of the stem undergoes distortions that optimize its interactions with the beginning of the loop. The loop adopts a new fold in which the single-stranded GGGA purine tract is structured in A-like conformation stacked in continuity of the stem and displays an extensive hydrogen bonding surface for recognition. The remarkable hairpin stability results from classical inter- and intra-strand interactions reinforced by numerous hydrogen bonds involving unusual backbone conformations and ribose 2?-hydroxyl groups. Overall, this work emphasizes numerous features that account for the well-ordered structure of the whole hairpin and highlights the loop properties that facilitate interaction with antisense oligonucleotides.

Joli, Flore; Bouchemal, Nadia; Laigle, Alain; Hartmann, Brigitte; Hantz, Edith

2006-01-01

383

Structure of the cytosine-cytosine mismatch in the thymidylate synthase mRNA binding site and analysis of its interaction with the aminoglycoside paromomycin  

PubMed Central

The structure of a cytosine–cytosine (CC) mismatch-containing RNA molecule derived from a hairpin structure in the thymidylate synthase mRNA that binds the aminoglycoside paromomycin with high affinity was determined using nuclear magnetic resonance (NMR) spectroscopy. The cytosines in the mismatch form a noncanonical base pair where both cytosines are uncharged and stack within the stem of the RNA structure. Binding to paromomycin was analyzed using isothermal titration calorimetry (ITC) to demonstrate the necessity of the CC mismatch and to determine the affinity dissociation constant of this RNA to paromomycin to be 0.5 ± 0.3 ?M. The CC mismatch, and the neighboring GC base pairs experienced the highest degree of chemical shift changes in their H6 and H5 resonances indicating that paromomycin binds in the major groove at the CC mismatch site. In comparing the structure of CC mismatch RNA with a fully Watson–Crick GC base paired stem, the CC mismatch is shown to confer a widening of the major groove. This widening, combined with the dynamic nature of the CC mismatch, enables binding of paromomycin to this RNA molecule.

Tavares, Tony J.; Beribisky, Alexander V.; Johnson, Philip E.

2009-01-01

384

Fructose-1,6-bisphosphate aldolase from Drosophila melanogaster: primary structure analysis, secondary structure prediction, and comparison with vertebrate aldolases.  

PubMed

The amino acid sequence of fructose-1,6-bisphosphate aldolase from Drosophila melanogaster was determined and was compared with those of five vertebrate aldolases on record. The four identical polypeptide chains of the insect enzyme, acetylated at the N-terminus and three residues shorter than the vertebrate chains, contain 360 amino acid residues. Of these 190 (or 53%) are identical in all six enzymes and in addition 33 positions (or 9%) are occupied by homologous residues. Comparison with the muscle-type isoaldolases from man and rabbit and the liver-type isoaldolases from man, rat, and chicken indicates an average sequence identity of 70 and 63%, respectively. Thus, the insect and the vertebrate muscle aldolases are probably coded by orthologous genes. On this basis an average rate of evolution of 3.0 PAM per 10(8) years is calculated, documenting an evolutional divergence slower than that of cytochrome c (4.2 PAM/10(8) years). The rate is also lower than that of the liver isoform (3.6 PAM/10(8) years). Secondary structure prediction analysis for Drosophila aldolase suggests the occurrence of 11-12 helical segments and 8-9 beta-strands. The conspicuous alternation of these structures in all six aldolases, especially in the C-terminal 200 residues, is consistant with the formation of an alpha beta-barrel supersecondary structure as documented for several other glycolytic enzymes. PMID:3140728

Malek, A A; Hy, M; Honegger, A; Rose, K; Brenner-Holzach, O

1988-10-01

385

Incorporating global features of RNA motifs in predictions for an ensemble of secondary structures for encapsidated MS2 bacteriophage RNA.  

PubMed

The secondary structure of encapsidated MS2 genomic RNA poses an interesting RNA folding challenge. Cryoelectron microscopy has demonstrated that encapsidated MS2 RNA is well-ordered. Models of MS2 assembly suggest that the RNA hairpin-protein interactions and the appropriate placement of hairpins in the MS2 RNA secondary structure can guide the formation of the correct icosahedral particle. The RNA hairpin motif that is recognized by the MS2 capsid protein dimers, however, is energetically unfavorable, and thus free energy predictions are biased against this motif. Computer programs called Crumple, Sliding Windows, and Assembly provide useful tools for prediction of viral RNA secondary structures when the traditional assumptions of RNA structure prediction by free energy minimization may not apply. These methods allow incorporation of global features of the RNA fold and motifs that are difficult to include directly in minimum free energy predictions. For example, with MS2 RNA the experimental data from SELEX experiments, crystallography, and theoretical calculations of the path for the series of hairpins can be incorporated in the RNA structure prediction, and thus the influence of free energy considerations can be modulated. This approach thoroughly explores conformational space and generates an ensemble of secondary structures. The predictions from this new approach can test hypotheses and models of viral assembly and guide construction of complete three-dimensional models of virus particles. PMID:22645379

Bleckley, Samuel; Schroeder, Susan J

2012-05-29

386

Secondary structure and stability of the selenocysteine insertion sequences (SECIS) for human thioredoxin reductase and glutathione peroxidase.  

PubMed

We have used high resolution NMR and thermodynamics to characterize the secondary structure and stability of the selenocysteine insertion sequences (SECIS) of human glutathione peroxidase (58 nt) and thioredoxin reductase (51 nt). These sequences are members of the two classes of SECIS recently identified with two distinct structures capable of directing selenocysteine incorporation into proteins in eukaryotes. UV melting experiments showed a single cooperative and reversible transition for each RNA, which indicates the presence of stable secondary structures. Despite their large size, the RNAs gave well resolved NMR spectra for the exchangeable protons. Using NOESY, the imino protons as well as the cytosine amino protons of all of the Watson-Crick base pairs were assigned. In addition, a number of non-canonical base pairs including the wobble G.U pairs were identified. The interbase-pair NOEs allowed definition of the hydrogen-bonded structure of the oligonucleotides, providing an experimental model of the secondary structure of these elements. The derived secondary structures are consistent with several features of the predicted models, but with some important differences, especially regarding the conserved sequence motifs. PMID:15026534

Ramos, Andres; Lane, Andrew N; Hollingworth, David; Fan, Teresa W-M

2004-03-16

387

Secondary structure model for the ITS-2 precursor rRNA of strongyloid nematodes of equids: implications for phylogenetic inference.  

PubMed

In order to maximise the positional homology in the primary sequence alignment of the second internal transcribed spacer for 30 species of equine strongyloid nematodes, the secondary structures of the precursor ribosomal RNA were predicted using an approach combining an energy minimisation method and comparative sequence analysis. The results indicated that a common secondary structure model of the second internal transcribed spacer of these nematodes was maintained despite significant interspecific differences (2-56%) in primary sequences. The secondary structure model was then used to refine the primary second internal transcribed spacer sequence alignment. The 'manual' and 'structure' alignments were both subjected to phylogenetic analysis to compare the effect of using different sequence alignments on phylogenetic inference. The topologies of the phylogenetic trees inferred from the manual second internal transcribed spacer alignment were usually different to those derived from the structure second internal transcribed spacer alignment. The results suggested that the positional homology in the second internal transcribed spacer primary sequence alignment was maximised when the secondary structure model was taken into consideration. PMID:10961851

Hung, G C; Chilton, N B; Beveridge, I; Gasser, R B

1999-12-01

388

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

PubMed

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

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

2010-12-23

389

Determination of Endosperm Protein Secondary Structure in Hard Wheat Breeding Lines using Synchrotron Infrared Microspectroscopy  

SciTech Connect

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.

Bonwell,E.; Fisher, T.; Fritz, A.; Wetzel, D.

2008-01-01

390

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

PubMed Central

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.

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

2009-01-01

391

The susceptibility of ?-helical secondary structure to steric strain: Coarse-grained simulation of dendronized polypeptides  

NASA Astrophysics Data System (ADS)

The propensity of a peptide chain for adopting helical secondary structure can be modulated not only through the solvation properties of its side chains but also through their size and shape. Here we examine a coarse-grained model for dendronized polypeptides that focuses on the susceptibility of ?-helical structure to the steric strain exerted by hydrophilic pendant groups. Undecorated molecules exhibit a pronounced transition from random coil to helix upon cooling [J. P. Kemp and J. Z. Y. Chen, Biomacromolecules 2, 389 (2001)]. As gauged by specific heat and by order parameters characterizing helicity at several length scales, this transition is quite robust to the introduction of first- and second-generation dendron side chains. More highly branched side chains, however, reduce the entropy of compact states so severely that helical ordering is undetectable over the entire temperature range accessible to our importance sampling methods. Consistent with experimental observations for side chains comparable to those of our model in volume-excluding size and shape, we find the backbone of these third-generation molecules to assume a distended rodlike state that is both stiff and achiral.

Browne, William; Geissler, Phillip L.

2010-10-01

392

Multiple determinants of functional mRNA stability: sequence alterations at either end of the lacZ gene affect the rate of mRNA inactivation.  

PubMed Central

The Escherichia coli lacZ gene was used as a model system to identify specific sequence elements affecting mRNA stability. Various insertions and substitutions at the ribosome-binding site increased or decreased the rate of mRNA inactivation by up to fourfold. Deletion of a dyad symmetry, which may give rise to a very stable secondary structure in the mRNA immediately downstream of the gene, decreased the functional stability of the lacZ message. The magnitude of the latter effect was strongly dependent on the sequences at the ribosome-binding site, ranging from practically no effect for the most labile transcripts to a threefold decrease in stability for the most stable one. The results suggest that the wild-type lacZ message is inactivated predominantly by attacks near the ribosome-binding site, presumably in part because the putative secondary structure downstream of the gene protects against 3'-exonucleolytic attack. Taken together, the data for all of the modified variants of lacZ were shown to be quantitatively compatible with a general model of mRNA inactivation involving multiple independent target sites. Images

Petersen, C

1991-01-01

393

Imaging the 3D structure of secondary osteons in human cortical bone using phase-retrieval tomography  

NASA Astrophysics Data System (ADS)

By applying a phase-retrieval step before carrying out standard filtered back-projection reconstructions in tomographic imaging, we were able to resolve structures with small differences in density within a densely absorbing sample. This phase-retrieval tomography is particularly suited for the three-dimensional segmentation of secondary osteons (roughly cylindrical structures) which are superimposed upon an existing cortical bone structure through the process of turnover known as remodelling. The resulting images make possible the analysis of the secondary osteon structure and the relationship between an osteon and the surrounding tissue. Our observations have revealed many different and complex 3D structures of osteons that could not be studied using previous methods. This work was carried out using a laboratory-based x-ray source, which makes obtaining these sorts of images readily accessible.

Arhatari, B. D.; Cooper, D. M. L.; Thomas, C. D. L.; Clement, J. G.; Peele, A. G.

2011-08-01

394

Secondary Structural Studies of Bovine Caseins: Structure and Temperature Dependence of ?-Casein Phosphopeptide (1-25) as Analyzed by Circular Dichroism, FTIR Spectroscopy, and Analytical Ultracentrifugation  

Microsoft Academic Search

The defining structural feature of all of the caseins is their common phosphorylation sequence. In milk, these phosphoserine residues combine with inorganic calcium and phosphate to form colloidal complexes. In addition, nutritional benefits have been ascribed to the phosphopeptides from casein. To obtain a molecular basis for the functional, chemical, and biochemical properties of these casein peptides, the secondary structure

H. M. Farrell; P. X. Qi; E. D. Wickham; J. J. Unruh

2002-01-01

395

Lost in folding space? Comparing four variants of the thermodynamic model for RNA secondary structure prediction  

PubMed Central

Background Many bioinformatics tools for RNA secondary structure analysis are based on a thermodynamic model of RNA folding. They predict a single, "optimal" structure by free energy minimization, they enumerate near-optimal structures, they compute base pair probabilities and dot plots, representative structures of different abstract shapes, or Boltzmann probabilities of structures and shapes. Although all programs refer to the same physical model, they implement it with considerable variation for different tasks, and little is known about the effects of heuristic assumptions and model simplifications used by the programs on the outcome of the analysis. Results We extract four different models of the thermodynamic folding space which underlie the programs RNAFOLD, RNASHAPES, and RNASUBOPT. Their differences lie within the details of the energy model and the granularity of the folding space. We implement probabilistic shape analysis for all models, and introduce the shape probability shift as a robust measure of model similarity. Using four data sets derived from experimentally solved structures, we provide a quantitative evaluation of the model differences. Conclusions We find that search space granularity affects the computed shape probabilities less than the over- or underapproximation of free energy by a simplified energy model. Still, the approximations perform similar enough to implementations of the full model to justify their continued use in settings where computational constraints call for simpler algorithms. On the side, we observe that the rarely used level 2 shapes, which predict the complete arrangement of helices, multiloops, internal loops and bulges, include the "true" shape in a rather small number of predicted high probability shapes. This calls for an investigation of new strategies to extract high probability members from the (very large) level 2 shape space of an RNA sequence. We provide implementations of all fo