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1

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

PubMed Central

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

2013-01-01

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. PMID:23325845

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

2013-01-01

3

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

PubMed

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

Johnson, Erik; Srivastava, Ranjan

2013-02-01

4

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

PubMed Central

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

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

2015-01-01

5

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

PubMed

The structure of messenger RNA is important for post-transcriptional regulation, mainly because it affects binding of trans-acting factors. However, little is known about the in vivo structure of full-length mRNAs. Here we present hiCLIP, a biochemical technique for transcriptome-wide identification of RNA secondary structures interacting with RNA-binding proteins (RBPs). Using this technique to investigate RNA structures bound by Staufen 1 (STAU1) in human cells, we uncover a dominance of intra-molecular RNA duplexes, a depletion of duplexes from coding regions of highly translated mRNAs, an unexpected prevalence of long-range duplexes in 3' untranslated regions (UTRs), and a decreased incidence of single nucleotide polymorphisms in duplex-forming regions. We also discover a duplex spanning 858 nucleotides in the 3' UTR of the X-box binding protein 1 (XBP1) mRNA that regulates its cytoplasmic splicing and stability. Our study reveals the fundamental role of mRNA secondary structures in gene expression and introduces hiCLIP as a widely applicable method for discovering new, especially long-range, RNA duplexes. PMID:25799984

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

2015-03-26

6

mRNA secondary structure engineering of Thermobifida fusca endoglucanase (Cel6A) for enhanced expression in Escherichia coli.  

PubMed

The sequence and structure of mRNA plays an important role in solubility and expression of the translated protein. To divulge the role of mRNA secondary structure and its thermodynamics in the expression level of the recombinant endoglucanase in Escherichia coli, 5'-end of the mRNA was thermodynamically optimized. Molecular engineering was done by introducing two silent synonymous mutations at positions +5 (UCU with UCC) and +7 (UUC with UUU) of the 5'-end of mRNA to relieve hybridization with ribosomal binding site. Two variants of glycoside hydrolase family six endoglucanase, wild type (cel6A.wt) and mutant (cel6A.mut) from Thermobifida fusca were expressed and characterized in E. coli using T7 promoter-based expression vector; pET22b(+). Enhanced expression level of engineered construct (Cel6A.mut) with ?G = -2.7 kcal mol(-1)was observed. It showed up to ~45 % higher expression as compared to the wild type construct (Cel6A.wt) having ?G = -7.8 kcal mol(-1) and ~25 % expression to the total cell proteins. Heterologous protein was purified by heating the recombinant E. coli BL21 (DE3) CodonPlus at 60 °C. The optimum pH for enzyme activity was six and optimum temperature was 60 °C. Maximum activity was observed 4.5 Umg(-1) on CMC. Hydrolytic activity was also observed on insoluble substrates, i.e. RAC (2.8 Umg(-1)), alkali treated bagass (1.7 Umg(-1)), filter paper (1.2 Umg(-1)) and BMCC (0.3 Umg(-1)). Metal ions affect endoglucanase activity in different ways. Only Fe(2+) exhibited 20.8 % stimulatory effects on enzyme activity. Enzyme activity was profoundly inhibited by Hg2(+) (91.8 %). PMID:25617066

Ali, Imran; Asghar, Rehana; Ahmed, Sajjad; Sajjad, Muhammad; Tariq, Muhammad; Waheed Akhtar, M

2015-03-01

7

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

PubMed Central

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

2014-01-01

8

The stability of the Chlorella nitrate reductase mRNA is determined by the secondary structure of the 5'-UTR: implications for posttranscriptional regulation of nitrate reductase.  

PubMed

Nitrate reductase (NR; EC 1.6.1.1-3) can be controlled at both transcriptional and posttranscriptional levels. Here we describe stability of NR mRNA as a mechanism of control. The NR gene in Chlorella vulgaris (Warburg strain) transcribes a stable mRNA and an unstable mRNA. In-vitro-synthesized transcripts representing these mRNAs show the same stability characteristics. The unstable mRNA is 30 nucleotides longer at the 5'-UTR compared to the stable mRNA. Using an RNA-folding program the 5'-UTR of the longer unstable RNA showed a more extensive stem-loop structure compared to the more linear form of the shorter stable mRNA. Transcripts representing RNAs with intermediate 5'-UTRs folded similarly to the long form and were unstable, or similarly to the short form and were more stable. Thus the secondary structure of the 5'-UTR of NR mRNA is important in the stability of NR transcripts in Chlorella and allows the cell to respond to changes in nitrogen source in an energy-efficient manner. PMID:11855653

Cannons, Andrew C; Cannon, Jennifer

2002-01-01

9

Protein-specific prediction of mRNA binding using RNA sequences, binding motifs and predicted secondary structures  

PubMed Central

Background RNA-binding proteins interact with specific RNA molecules to regulate important cellular processes. It is therefore necessary to identify the RNA interaction partners in order to understand the precise functions of such proteins. Protein-RNA interactions are typically characterized using in vivo and in vitro experiments but these may not detect all binding partners. Therefore, computational methods that capture the protein-dependent nature of such binding interactions could help to predict potential binding partners in silico. Results We have developed three methods to predict whether an RNA can interact with a particular RNA-binding protein using support vector machines and different features based on the sequence (the Oli method), the motif score (the OliMo method) and the secondary structure (the OliMoSS method). We applied these approaches to different experimentally-derived datasets and compared the predictions with RNAcontext and RPISeq. Oli outperformed OliMoSS and RPISeq, confirming our protein-specific predictions and suggesting that tetranucleotide frequencies are appropriate discriminative features. Oli and RNAcontext were the most competitive methods in terms of the area under curve. A precision-recall curve analysis achieved higher precision values for Oli. On a second experimental dataset including real negative binding information, Oli outperformed RNAcontext with a precision of 0.73 vs. 0.59. Conclusions Our experiments showed that features based on primary sequence information are sufficiently discriminating to predict specific RNA-protein interactions. Sequence motifs and secondary structure information were not necessary to improve these predictions. Finally we confirmed that protein-specific experimental data concerning RNA-protein interactions are valuable sources of information that can be used for the efficient training of models for in silico predictions. The scripts are available upon request to the corresponding author. PMID:24780077

2014-01-01

10

The stability of the Chlorella nitrate reductase mRNA is determined by the secondary structure of the 5'-UTR: implications for posttranscriptional regulation of nitrate reductase  

Microsoft Academic Search

Nitrate reductase (NR; EC 1.6.1.1-3) can be controlled at both transcriptional and posttranscriptional levels. Here we describe stability of NR mRNA as a mechanism of control. The NR gene in Chlorella vulgaris (Warburg strain) transcribes a stable mRNA and an unstable mRNA. In-vitro-synthesized transcripts representing these mRNAs show the same stability characteristics. The unstable mRNA is 30 nucleotides longer at

Andrew C. Cannons; Jennifer Cannon

2002-01-01

11

Exon B of human surfactant protein A2 mRNA, alone or within its surrounding sequences, interacts with 14-3-3; role of cis-elements and secondary structure  

PubMed Central

Human surfactant protein A, an innate immunity molecule, is encoded by two genes: SFTPA1 (SP-A1) and SFTPA2 (SP-A2). The 5? untranslated (5?UTR) splice variant of SP-A2 (ABD), but not of SP-A1 (AD), contains exon B (eB), which is an enhancer for transcription and translation. We investigated whether eB contains cis-regulatory elements that bind trans-acting factors in a sequence-specific manner as well as the role of the eB mRNA secondary structure. Binding of cytoplasmic NCI-H441 proteins to wild-type eB, eB mutant, AD, and ABD 5?UTR mRNAs were studied by RNA electromobility shift assays (REMSAs). The bound proteins were identified by mass spectroscopy and specific antibodies (Abs). We found that 1) proteins bind eB mRNA in a sequence-specific manner, with two cis-elements identified within eB to be important; 2) eB secondary structure is necessary for binding; 3) mass spectroscopy and specific Abs in REMSAs identified 14-3-3 proteins to bind (directly or indirectly) eB and the natural SP-A2 (ABD) splice variant but not the SP-A1 (AD) splice variant; 4) other ribosomal and cytoskeletal proteins, and translation factors, are also present in the eB mRNA-protein complex; 5) knockdown of 14-3-3 ?/? isoform resulted in a downregulation of SP-A2 expression. In conclusion, proteins including the 14-3-3 family bind two cis-elements within eB of hSP-A2 mRNA in a sequence- and secondary structure-specific manner. Differential regulation of SP-A1 and SP-A2 is mediated by the 14-3-3 protein family as well as by a number of other proteins that bind UTRs with or without eB mRNA. PMID:23525782

Noutsios, Georgios T.; Silveyra, Patricia; Bhatti, Faizah

2013-01-01

12

Secondary Structure Prediction of Proposed RNAi  

E-print Network

, as they function to recruit translational machinery to the mRNA, are potential targets for RNAi. In addition, #12Secondary Structure Prediction of Proposed RNAi Targets: Can Current Energy Minimization Algorithms-dimensional shape of a protein can provide essential information in the determination of its function, the activity

13

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

14

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

15

Genetic analysis of bacteriophage lambda cIII gene: mRNA structural requirements for translation initiation.  

PubMed Central

The bacteriophage lambda cIII gene product regulates the lysogenic pathway. The cIII gene is located in the leftward operon, which is transcribed from the pL promoter. We have previously shown (S. Altuvia and A. B. Oppenheim, J. Bacteriol. 167:415-419, 1986) that mutations that show elevated expression lie within the cIII coding sequence. We isolated mutants that show decreased CIII activity. All the mutations were found to cause a drastic reduction in the rate of initiation of cIII translation. Several mutations were found to be scattered within the first 40 nucleotides of the cIII coding region. Additional mutations affected the AUG initiation codon, the Shine-Dalgarno sequence, and the upstream RNaseIII processing site. Computer folding of the cIII mRNA suggested the presence of two alternative RNA structures. All the mutations within the coding region that reduce expression reduce the stability of one specific mRNA structure (structure B). Mutations that increase expression lie in the loops of this structure and may in fact stabilize it by interfering with the formation of the alternative structure (structure A). Thus, it appears that a specific mRNA secondary structure at the beginning of the cIII coding region is essential for efficient translation, suggesting that changes in mRNA structure regulate cIII expression. Images PMID:2523380

Kornitzer, D; Teff, D; Altuvia, S; Oppenheim, A B

1989-01-01

16

Current perspectives on RNA secondary structure probing  

PubMed Central

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

Kenyon, Julia; Prestwood, Liam; Lever, Andrew

2014-01-01

17

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

Microsoft Academic Search

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 pro- gram that is capable of explicitly taking the known protein-coding context of the mRNA sequences

Irmtraud M. Meyer; Istvan Miklos

2005-01-01

18

Structure and stability correlation of an mRNA pseudoknot  

E-print Network

heptanucleotide sequence and a downstream pseudoknot are essential for mRNA frameshifting. The BWYV pseudoknot is a classical H-type pseudoknot containing two helical stems and two connecting loop regions. The loop-stem interactions have been proposed...

Suram, Saritha

2002-01-01

19

Improving RNA secondary structure prediction with structure mapping data.  

PubMed

Methods to probe RNA secondary structure, such as small molecule modifying agents, secondary structure-specific nucleases, inline probing, and SHAPE chemistry, are widely used to study the structure of functional RNA. Computational secondary structure prediction programs can incorporate probing data to predict structure with high accuracy. In this chapter, an overview of current methods for probing RNA secondary structure is provided, including modern high-throughput methods. Methods for guiding secondary structure prediction algorithms using these data are explained, and best practices for using these data are provided. This chapter concludes by listing a number of open questions about how to best use probing data, and what these data can provide. PMID:25726462

Sloma, Michael F; Mathews, David H

2015-01-01

20

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

21

Data Mining for Protein Secondary Structure Prediction  

Microsoft Academic Search

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 Sen; Robert Jernigan; Andrzej Kloczkowski

22

Deleterious mutation prediction in the secondary structure of RNAs  

PubMed Central

Methods for computationally predicting deleterious mutations have recently been investigated for proteins, mainly by probabilistic estimations in the context of genomic research for identifying single nucleotide polymorphisms that can potentially affect protein function. It has been demonstrated that in cases where a few homologs are available, ab initio predicted structures modeled by the Rosetta method can become useful for including structural information to improve the deleterious mutation prediction methods for proteins. In the field of RNAs where very few homologs are available at present, this analogy can serve as a precursor to investigate a deleterious mutation prediction approach that is based on RNA secondary structure. When attempting to develop models for the prediction of deleterious mutations in RNAs, useful structural information is available from folding algorithms that predict the secondary structure of RNAs, based on energy minimization. Detecting mutations with desired structural effects among all possible point mutations may then be valuable for the prediction of deleterious mutations that can be tested experimentally. Here, a method is introduced for the prediction of deleterious mutations in the secondary structure of RNAs. The mutation prediction method, based on subdivision of the initial structure into smaller substructures and construction of eigenvalue tables, is independent of the folding algorithms but relies on their success to predict the folding of small RNA structures. Application of this method to predict mutations that may cause structural rearrangements, thereby disrupting stable motifs, is given for prokaryotic transcription termination in the thiamin pyrophosphate and S-adenosyl-methionine induced riboswitches. Ribo switches are mRNA structures that have recently been found to regulate transcription termination or translation initiation in bacteria by conformation rearrangement in response to direct metabolite binding. Predicting deleterious mutations on riboswitches may succeed to systematically intervene in bacterial genetic control. PMID:14602917

Barash, Danny

2003-01-01

23

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

24

Multithreaded parsing for predicting RNA secondary structures.  

PubMed

Many computational approaches have been developed for modelling and analysing the RNA secondary structure. These approaches are based on diverse methods such as grammars, dynamic programming, matching and evolutionary algorithms. This paper proposes a new parsing algorithm for the prediction of RNA secondary structures. The proposed algorithm is based on the shift-reduce LR parsing algorithm for programming languages. It has two main contributions: it extends the LR parsing algorithm by using a Stochastic Context-Free Grammar (SCFG) instead of Context-Free Grammar (CFG) for parsing RNA secondary structures; it extends the LR parsing algorithm by using a multithreaded approach to handle the LR parsing conflicts resulting from the use of ambiguous grammars. PMID:21354966

Al-Mulhem, Muhammed S

2010-01-01

25

Structural and functional features of eukaryotic mRNA untranslated regions  

Microsoft Academic Search

The crucial role of the non-coding portion of genomes is now widely acknowledged. In particular, mRNA untranslated regions are involved in many post-transcriptional regulatory pathways that control mRNA localization, stability and translation efficiency. We review in this paper the major structural and compositional features of eukaryotic mRNA untranslated regions and provide some examples of bioinformatic analyses for their functional characterization.

Graziano Pesole; Flavio Mignone; Carmela Gissi; Giorgio Grillo; Flavio Licciulli; Sabino Liuni

2001-01-01

26

MPGAfold in dengue secondary structure prediction.  

PubMed

This chapter presents the computational prediction of the secondary structures within the 5' and 3' untranslated regions of the dengue virus serotype 2 (DENV2), with the focus on the conformational prediction of the two dumbbell-like structures, 5' DB and 3' DB, found in the core region of the 3' untranslated region of DENV2. For secondary structure prediction purposes we used a 719 nt-long subgenomic RNA construct from DENV2, which we refer to as the minigenome. The construct combines the 5'-most 226 nt from the 5' UTR and a fragment of the capsid coding region with the last 42 nt from the non-structural protein NS5 coding region and the 451 nt of the 3' UTR. This minigenome has been shown to contain the elements needed for translation, as well as negative strand RNA synthesis. We present the Massively Parallel Genetic Algorithm MPGAfold, a non-deterministic algorithm, that was used to predict the secondary structures of the DENV2 719 nt long minigenome construct, as well as our computational workbench called StructureLab that was used to interactively explore the solution spaces produced by MPGAfold. The MPGAfold algorithm is first introduced at the conceptual level. Then specific parameters guiding its performance are discussed and illustrated with a representative selection of the results from the study. Plots of the solution spaces generated by MPGAfold illustrate the algorithm, while selected secondary structures focus on variable formation of the dumbbell structures and other identified structural motifs. They also serve as illustrations of some of the capabilities of the StructureLab workbench. Results of the computational structure determination calculations are discussed and compared to the experimental data. PMID:24696339

Kasprzak, Wojciech K; Shapiro, Bruce A

2014-01-01

27

Knowledge-based protein secondary structure assignment  

Microsoft Academic Search

We have developed an auto- matic algorithm STRIDE for protein secondary structure assignment from atomic coordinates based on the combined use of hydrogen bond energy and statistically derived backbone tor- sional angle information. Parameters of the pattern recognition procedure were optimized using designations provided by the crystallog- raphers as a standard-of-truth. Comparison to the currently most widely used technique DSSP

Dmitrij Frishman; Patrick Argos

1995-01-01

28

PEGylated nanoparticles: protein corona and secondary structure  

NASA Astrophysics Data System (ADS)

Nanoparticles have important biological and biomedical applications ranging from drug and gene delivery to biosensing. In the presence of extracellular proteins, a "corona" of proteins adsorbs on the surface of the nanoparticles, altering their interaction with cells, including immune cells. Nanoparticles are often functionalized with polyethylene glycol (PEG) to reduce this non-specific adsorption of proteins. To understand the change in protein corona that occurs following PEGylation, we first quantified the adsorption of blood serum proteins on bare and PEGylated gold nanoparticles using gel electrophoresis. We find a threefold decrease in the amount of protein adsorbed on PEGylated gold nanoparticles compared to the bare gold nanoparticles, showing that PEG reduces, but does not prevent, corona formation. To determine if the secondary structure of corona proteins was altered upon adsorption onto the bare and PEGylated gold nanoparticles, we use CD spectroscopy to characterize the secondary structure of bovine serum albumin following incubation with the nanoparticles. Our results show no significant change in protein secondary structure following incubation with bare or PEGylated nanoparticles. Further examination of the secondary structure of bovine serum albumin, ?2-macroglobulin, and transferrin in the presence of free PEG showed similar results. These findings provide important insights for the use of PEGylated gold nanoparticles under physiological conditions.

Runa, Sabiha; Hill, Alexandra; Cochran, Victoria L.; Payne, Christine K.

2014-09-01

29

Protein secondary structural types are differentially coded on messenger RNA.  

PubMed Central

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

Thanaraj, T. A.; Argos, P.

1996-01-01

30

Secondary structure formation in peptide amphiphile micelles  

NASA Astrophysics Data System (ADS)

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

Tirrell, Matthew

2012-02-01

31

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

2013-01-01

32

Parsing nucleic acid pseudoknotted secondary structure: algorithm and applications  

E-print Network

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

Condon, Anne

33

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

E-print Network

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

Karplus, Kevin

34

Protein similarity search under mRNA structural constraints: application to selenocysteine incorporation  

E-print Network

acid sequence. We show that the problem can be solved in linear time when the structure doesProtein similarity search under mRNA structural constraints: application to selenocysteine the UGA-codon that forms a hairpin like structure (called Sec insertion sequence (SECIS)). We consider

Will, Sebastian

35

Structural organization of mRNA complexes with major core mRNP protein YB-1.  

PubMed

YB-1 is a universal major protein of cytoplasmic mRNPs, a member of the family of multifunctional cold shock domain proteins (CSD proteins). Depending on its amount on mRNA, YB-1 stimulates or inhibits mRNA translation. In this study, we have analyzed complexes formed in vitro at various YB-1 to mRNA ratios, including those typical for polysomal (translatable) and free (untranslatable) mRNPs. We have shown that at mRNA saturation with YB-1, this protein alone is sufficient to form mRNPs with the protein/RNA ratio and the sedimentation coefficient typical for natural mRNPs. These complexes are dynamic structures in which the protein can easily migrate from one mRNA molecule to another. Biochemical studies combined with atomic force microscopy and electron microscopy showed that mRNA-YB-1 complexes with a low YB-1/mRNA ratio typical for polysomal mRNPs are incompact; there, YB-1 binds to mRNA as a monomer with its both RNA-binding domains. At a high YB-1/mRNA ratio typical for untranslatable mRNPs, mRNA-bound YB-1 forms multimeric protein complexes where YB-1 binds to mRNA predominantly with its N-terminal part. A multimeric YB-1 comprises about twenty monomeric subunits; its molecular mass is about 700 kDa, and it packs a 600-700 nt mRNA segment on its surface. PMID:15494450

Skabkin, Maxim A; Kiselyova, Olga I; Chernov, Konstantin G; Sorokin, Alexey V; Dubrovin, Evgeniy V; Yaminsky, Igor V; Vasiliev, Victor D; Ovchinnikov, Lev P

2004-01-01

36

Linkers of secondary structures in proteins.  

PubMed Central

Linkers that connect repeating secondary structures fall into conformational classes based on distance and main-chain torsion clustering. A data set of 300 unique protein chains with low pairwise sequence identity was clustered into only a few groups representing the preferred motifs. The linkers of two to eight residues for the nonredundant data set are designated H-Ln-H, H-Ln-E, E-Ln-H, E-Ln-E, where n is the length, H stands for alpha-helices, and E for beta-strands. Most of the clusters identified here corroborate earlier findings. However, 19 new clusters are identified in this paper, with many of them having seven and eight residue linkers. In our first analysis, the secondary structures flanking the linkers are both interacting and noninteracting and there is no precise angle of orientation between them. A second analysis was performed on a set of proteins with restricted orientations for the flanking elements, namely, mainly alpha class of proteins with orthogonal architecture. Two definite clusters are identified, one corresponding to linkers of orthogonal helices and the other to linkers of antiparallel helices. Loops forming binding sites or involved in catalytic activity are important determinants of the function of proteins. Although the structural conservation of the residues around the catalytic triad of serine proteases has been studied widely, there has not been a systematic analysis of the conformation of the loops that contain them. Residues of the catalytic triad reside in the linkers of beta-strands, with varying lengths of more than eight residues. Here, we analyze the structural conservation of such linkers by superposition, and observe a conserved structural feature of the linkers incorporating each of the three residues of the catalytic triad. PMID:9416603

Geetha, V.; Munson, P. J.

1997-01-01

37

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

PubMed Central

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

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

2002-01-01

38

RNA-SSPT: RNA Secondary Structure Prediction Tools.  

PubMed

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

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

2013-01-01

39

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

PubMed

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

Ponty, Yann; Leclerc, Fabrice

2015-01-01

40

Secondary structure adventures with Carl Woese.  

PubMed

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

Noller, Harry F

2014-01-01

41

Secondary structure adventures with Carl Woese  

PubMed Central

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

Noller, Harry F

2014-01-01

42

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

PubMed Central

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

Ellington, Roni; Wachira, James

2010-01-01

43

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

44

A novel approach to represent and compare RNA secondary structures  

PubMed Central

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

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

2014-01-01

45

A dynamic programming algorithm for finding alternative RNA secondary structures.  

PubMed Central

Dynamic programming algorithms that predict RNA secondary structure by minimizing the free energy have had one important limitation. They were able to predict only one optimal structure. Given the uncertainties of the thermodynamic data and the effects of proteins and other environmental factors on structure, the optimal structure predicted by these methods may not have biological significance. We present a dynamic programming algorithm that can determine optimal and suboptimal secondary structures for an RNA. The power and utility of the method is demonstrated in the folding of the intervening sequence of the rRNA of Tetrahymena. By first identifying the major secondary structures corresponding to the lowest free energy minima, a secondary structure of possible biological significance is derived. Images PMID:3003675

Williams, A L; Tinoco, I

1986-01-01

46

Prediction of protein secondary structure by the hidden Markov model.  

PubMed

The purpose of this paper is to introduce a new method for analyzing the amino acid sequences of proteins using the hidden Markov model (HMM), which is a type of stochastic model. Secondary structures such as helix, sheet and turn are learned by HMMs, and these HMMs are applied to new sequences whose structures are unknown. The output probabilities from the HMMs are used to predict the secondary structures of the sequences. The authors tested this prediction system on approximately 100 sequences from a public database (Brookhaven PDB). Although the implementation is 'without grammar' (no rule for the appearance patterns of secondary structure) the result was reasonable. PMID:8481815

Asai, K; Hayamizu, S; Handa, K

1993-04-01

47

Phytoene desaturase is localized exclusively in the chloroplast and up-regulated at the mRNA level during accumulation of secondary carotenoids in Haematococcus pluvialis (Volvocales, chlorophyceae).  

PubMed

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

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

2000-04-01

48

Comparing RNA Secondary Structures Based on LZ Complexity  

NASA Astrophysics Data System (ADS)

In this paper, we propose a new similarity measure to compare RNA secondary structure. We first transform an RNA secondary structure into three characteristic sequences. Then, based on these characteristic sequences, we calculate their LZ complexity. Finally, we obtain the similarity/dissimilarity matrix based on the LZ complexity, and make a comparison for the secondary structures at the 3?-terminus belonging to nine different species. The proposed method does not require multiple alignments and is easy to operate. This method will also be useful to researchers who are interested in evolutionary analysis.

Liu, Liwei; Bai, Fenglan; Wang, Tianming

49

Sequence periodicity and secondary structure propensity in model proteins  

PubMed Central

We explore the question of whether local effects (originating from the amino acids intrinsic secondary structure propensities) or nonlocal effects (reflecting the sequence of amino acids as a whole) play a larger role in determining the fold of globular proteins. Earlier circular dichroism studies have shown that the pattern of polar, non polar amino acids (nonlocal effect) dominates over the amino acid intrinsic propensity (local effect) in determining the secondary structure of oligomeric peptides. In this article, we present a coarse grained computational model that allows us to quantitatively estimate the role of local and nonlocal factors in determining both the secondary and tertiary structure of small, globular proteins. The amino acid intrinsic secondary structure propensity is modeled by a dihedral potential term. This dihedral potential is parametrized to match with experimental measurements of secondary structure propensity. Similarly, the magnitude of the attraction between hydrophobic residues is parametrized to match the experimental transfer free energies of hydrophobic amino acids. Under these parametrization conditions, we systematically explore the degree of frustration a given polar, non polar pattern can tolerate when the secondary structure intrinsic propensities are in opposition to it. When the parameters are in the biophysically relevant range, we observe that the fold of small, globular proteins is determined by the pattern of polar, non polar amino acids regardless of their instrinsic secondary structure propensities. Our simulations shed new light on previous observations that tertiary interactions are more influential in determining protein structure than secondary structure propensity. The fact that this can be inferred using a simple polymer model that lacks most of the biochemical details points to the fundamental importance of binary patterning in governing folding. PMID:19937649

Bellesia, Giovanni; Jewett, Andrew Iain; Shea, Joan-Emma

2010-01-01

50

Multiple alignment through protein secondary-structure information  

Microsoft Academic Search

It is well known that protein secondary-structure information can help the process of performing multiple alignment, in particular when the amount of similarity among the involved sequences moves toward the \\

Giuliano Armano; Luciano Milanesi; Alessandro Orro

2005-01-01

51

Structural Reform in Secondary School Education--Tendencies and Strategies.  

ERIC Educational Resources Information Center

This article describes structural changes in China which have given secondary education a double task: to provide general education beyond elementary school, and to train mid-level professional personnel and technically skilled workers. (IAH)

Zhenye, Gao; Mingan, Xiong

1988-01-01

52

Bayesian Model of Protein Primary Sequence for Secondary Structure Prediction  

PubMed Central

Determining the primary structure (i.e., amino acid sequence) of a protein has become cheaper, faster, and more accurate. Higher order protein structure provides insight into a protein’s function in the cell. Understanding a protein’s secondary structure is a first step towards this goal. Therefore, a number of computational prediction methods have been developed to predict secondary structure from just the primary amino acid sequence. The most successful methods use machine learning approaches that are quite accurate, but do not directly incorporate structural information. As a step towards improving secondary structure reduction given the primary structure, we propose a Bayesian model based on the knob-socket model of protein packing in secondary structure. The method considers the packing influence of residues on the secondary structure determination, including those packed close in space but distant in sequence. By performing an assessment of our method on 2 test sets we show how incorporation of multiple sequence alignment data, similarly to PSIPRED, provides balance and improves the accuracy of the predictions. Software implementing the methods is provided as a web application and a stand-alone implementation. PMID:25314659

Li, Qiwei; Dahl, David B.; Vannucci, Marina; Hyun Joo; Tsai, Jerry W.

2014-01-01

53

PALSSE: A program to delineate linear secondary structural elements from protein structures  

Microsoft Academic Search

BACKGROUND: The majority of residues in protein structures are involved in the formation of ?-helices and ?-strands. These distinctive secondary structure patterns can be used to represent a protein for visual inspection and in vector-based protein structure comparison. Success of such structural comparison methods depends crucially on the accurate identification and delineation of secondary structure elements. RESULTS: We have developed

Indraneel Majumdar; S. Sri Krishna; Nick V. Grishin

2005-01-01

54

Description of protein secondary structure using dual quaternions  

NASA Astrophysics Data System (ADS)

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

Prošková, Jitka

2014-11-01

55

The structure of a ribosomal protein S8/spc operon mRNA complex  

PubMed Central

In bacteria, translation of all the ribosomal protein cistrons in the spc operon mRNA is repressed by the binding of the product of one of them, S8, to an internal sequence at the 5? end of the L5 cistron. The way in which the first two genes of the spc operon are regulated, retroregulation, is mechanistically distinct from translational repression by S8 of the genes from L5 onward. A 2.8 Å resolution crystal structure has been obtained of Escherichia coli S8 bound to this site. Despite sequence differences, the structure of this complex is almost identical to that of the S8/helix 21 complex seen in the small ribosomal subunit, consistent with the hypothesis that autogenous regulation of ribosomal protein synthesis results from conformational similarities between mRNAs and rRNAs. S8 binding must repress the translation of its own mRNA by inhibiting the formation of a ribosomal initiation complex at the start of the L5 cistron. PMID:15146079

MERIANOS, HELEN J.; WANG, JIMIN; MOORE, PETER B.

2004-01-01

56

The structure of a ribosomal protein S8/spc operon mRNA complex.  

PubMed

In bacteria, translation of all the ribosomal protein cistrons in the spc operon mRNA is repressed by the binding of the product of one of them, S8, to an internal sequence at the 5' end of the L5 cistron. The way in which the first two genes of the spc operon are regulated, retroregulation, is mechanistically distinct from translational repression by S8 of the genes from L5 onward. A 2.8 A resolution crystal structure has been obtained of Escherichia coli S8 bound to this site. Despite sequence differences, the structure of this complex is almost identical to that of the S8/helix 21 complex seen in the small ribosomal subunit, consistent with the hypothesis that autogenous regulation of ribosomal protein synthesis results from conformational similarities between mRNAs and rRNAs. S8 binding must repress the translation of its own mRNA by inhibiting the formation of a ribosomal initiation complex at the start of the L5 cistron. PMID:15146079

Merianos, Helen J; Wang, Jimin; Moore, Peter B

2004-06-01

57

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. PMID:20230624

2010-01-01

58

Hierarchical Protein Structure Superposition using both Secondary Structure and Atomic Representations  

E-print Network

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

Brutlag, Doug

59

De novo secondary structure motif discovery using RNAProfile.  

PubMed

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

Zambelli, Federico; Pavesi, Giulio

2015-01-01

60

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

61

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

PubMed

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

Taverniti, Valerio; Séraphin, Bertrand

2015-01-01

62

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

PubMed Central

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

Taverniti, Valerio; Séraphin, Bertrand

2015-01-01

63

Local Absence of Secondary Structure Permits Translation of mRNAs that Lack Ribosome-Binding Sites  

PubMed Central

The initiation of translation is a fundamental and highly regulated process in gene expression. Translation initiation in prokaryotic systems usually requires interaction between the ribosome and an mRNA sequence upstream of the initiation codon, the so-called ribosome-binding site (Shine-Dalgarno sequence). However, a large number of genes do not possess Shine-Dalgarno sequences, and it is unknown how start codon recognition occurs in these mRNAs. We have performed genome-wide searches in various groups of prokaryotes in order to identify sequence elements and/or RNA secondary structural motifs that could mediate translation initiation in mRNAs lacking Shine-Dalgarno sequences. We find that mRNAs without a Shine-Dalgarno sequence are generally less structured in their translation initiation region and show a minimum of mRNA folding at the start codon. Using reporter gene constructs in bacteria, we also provide experimental support for local RNA unfoldedness determining start codon recognition in Shine-Dalgarno–independent translation. Consistent with this, we show that AUG start codons reside in single-stranded regions, whereas internal AUG codons are usually in structured regions of the mRNA. Taken together, our bioinformatics analyses and experimental data suggest that local absence of RNA secondary structure is necessary and sufficient to initiate Shine-Dalgarno–independent translation. Thus, our results provide a plausible mechanism for how the correct translation initiation site is recognized in the absence of a ribosome-binding site. PMID:21731509

Walther, Dirk; Bock, Ralph

2011-01-01

64

Efficient alignment of RNA secondary structures using sparse dynamic programming  

PubMed Central

Background Current advances of the next-generation sequencing technology have revealed a large number of un-annotated RNA transcripts. Comparative study of the RNA structurome is an important approach to assess their biological functionalities. Due to the large sizes and abundance of the RNA transcripts, an efficient and accurate RNA structure-structure alignment algorithm is in urgent need to facilitate the comparative study. Despite the importance of the RNA secondary structure alignment problem, there are no computational tools available that provide high computational efficiency and accuracy. In this case, designing and implementing such an efficient and accurate RNA secondary structure alignment algorithm is highly desirable. Results In this work, through incorporating the sparse dynamic programming technique, we implemented an algorithm that has an O(n3) expected time complexity, where n is the average number of base pairs in the RNA structures. This complexity, which can be shown assuming the polymer-zeta property, is confirmed by our experiments. The resulting new RNA secondary structure alignment tool is called ERA. Benchmark results indicate that ERA can significantly speedup RNA structure-structure alignments compared to other state-of-the-art RNA alignment tools, while maintaining high alignment accuracy. Conclusions Using the sparse dynamic programming technique, we are able to develop a new RNA secondary structure alignment tool that is both efficient and accurate. We anticipate that the new alignment algorithm ERA will significantly promote comparative RNA structure studies. The program, ERA, is freely available at http://genome.ucf.edu/ERA. PMID:24011432

2013-01-01

65

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. PMID:21317361

Sim, Adelene Y. L.; Levitt, Michael

2011-01-01

66

A New Algorithm for RNA Secondary Structure Design  

E-print Network

A New Algorithm for RNA Secondary Structure Design Mirela Andronescu , Anthony P. Fejes , Frank Hutter , Anne Condon , Holger H. Hoos £ Department of Computer Science University of British Columbia beyond acting as interme- diaries in the translation of genomic DNA into proteins. For example, ribosomal

Hutter, Frank

67

Effect of target secondary structure on RNAi efficiency  

Microsoft Academic Search

RNA interference (RNAi) mediated by small interfering RNAs (siRNAs) or short hairpin RNAs (shRNAs) has become a powerful tool for gene knockdown studies. However, the levels of knockdown vary greatly. Here, we examine the effect of target disruption energy, a novel measure of target accessibility, along with other parameters that may affect RNAi efficiency. Based on target secondary structures predicted

YU SHAO; CHI YU CHAN; ANIL MALIYEKKEL; CHARLES E. LAWRENCE; IGOR B. RONINSON; YE DING

2007-01-01

68

RNA Movies 2: sequential animation of RNA secondary structures  

PubMed Central

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

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

2007-01-01

69

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

70

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

71

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

72

The structural basis of secondary active transport mechanisms.  

PubMed

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

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

2011-02-01

73

The crystal structure of the exon junction complex reveals how it maintains a stable grip on mRNA.  

PubMed

The exon junction complex (EJC) plays a major role in posttranscriptional regulation of mRNA in metazoa. The EJC is deposited onto mRNA during splicing and is transported to the cytoplasm where it influences translation, surveillance, and localization of the spliced mRNA. The complex is formed by the association of four proteins (eIF4AIII, Barentsz [Btz], Mago, and Y14), mRNA, and ATP. The 2.2 A resolution structure of the EJC reveals how it stably locks onto mRNA. The DEAD-box protein eIF4AIII encloses an ATP molecule and provides the binding sites for six ribonucleotides. Btz wraps around eIF4AIII and stacks against the 5' nucleotide. An intertwined network of interactions anchors Mago-Y14 and Btz at the interface between the two domains of eIF4AIII, effectively stabilizing the ATP bound state. Comparison with the structure of the eIF4AIII-Btz subcomplex that we have also determined reveals that large conformational changes are required upon EJC assembly and disassembly. PMID:16923391

Bono, Fulvia; Ebert, Judith; Lorentzen, Esben; Conti, Elena

2006-08-25

74

Improved Chou-Fasman method for protein secondary structure prediction  

PubMed Central

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

Chen, Hang; Gu, Fei; Huang, Zhengge

2006-01-01

75

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. PMID:23091593

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

2012-01-01

76

Accelerating calculations of RNA secondary structure partition functions using GPUs  

PubMed Central

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

2013-01-01

77

Control of mammalian translation by mRNA structure near caps  

PubMed Central

The scanning model of RNA translation proposes that highly stable secondary structures within mRNAs can inhibit translation, while structures of lower thermal stability also affect translation if close enough to the 5? methyl G cap. However, only fragmentary information is available about the dependence of translation efficiency in live mammalian cells on the thermodynamic stability, location, and GC content of RNA structures in the 5?-untranslated region. We devised a two-color fluorescence assay for translation efficiency in single live cells and compared a wide range of hairpins with predicted thermal stabilities ranging from ?10 to ?50 kcal/mol and 5? G cap-to-hairpin distances of 1–46 bases. Translation efficiency decreased abruptly as hairpin stabilities increased from ?G = ?25 to ?35 kcal/mol. Shifting a hairpin as little as nine bases relative to the 5? cap could modulate translation more than 50-fold. Increasing GC content diminished translation efficiency when predicted thermal stability and cap-to-hairpin distances were held constant. We additionally found naturally occurring 5?-untranslated regions affected translation differently in live cells compared with translation in in vitro lysates. Our study will assist scientists in designing experiments that deliberately modulate mammalian translation with designed 5? UTRs. PMID:16540693

Babendure, Jeremy R.; Babendure, Jennie L.; Ding, Jian-Hua; Tsien, Roger Y.

2006-01-01

78

Automatic RNA secondary structure determination stochastic context-free grammars  

SciTech Connect

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

Grate, L. [Univ. of California, Santa Cruz, CA (United States)

1995-12-31

79

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. PMID:21992500

2011-01-01

80

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

81

Reconstruction and stability of secondary structure elements in the context of protein structure prediction.  

PubMed

Efficient and accurate reconstruction of secondary structure elements in the context of protein structure prediction is the major focus of this work. We present a novel approach capable of reconstructing alpha-helices and beta-sheets in atomic detail. The method is based on Metropolis Monte Carlo simulations in a force field of empirical potentials that are designed to stabilize secondary structure elements in room-temperature simulations. Particular attention is paid to lateral side-chain interactions in beta-sheets and between the turns of alpha-helices, as well as backbone hydrogen bonding. The force constants are optimized using contrastive divergence, a novel machine learning technique, from a data set of known structures. Using this approach, we demonstrate the applicability of the framework to the problem of reconstructing the overall protein fold for a number of commonly studied small proteins, based on only predicted secondary structure and contact map. For protein G and chymotrypsin inhibitor 2, we are able to reconstruct the secondary structure elements in atomic detail and the overall protein folds with a root mean-square deviation of <10 A. For cold-shock protein and the SH3 domain, we accurately reproduce the secondary structure elements and the topology of the 5-stranded beta-sheets, but not the barrel structure. The importance of high-quality secondary structure and contact map prediction is discussed. PMID:19486664

Podtelezhnikov, Alexei A; Wild, David L

2009-06-01

82

Structure of a Complex between a Cap Analogue and mRNA Guanylyl Transferase Demonstrates the Structural Chemistry of RNA Capping  

Microsoft Academic Search

Paramecium bursaria Chlorella virus PBCV-1 mRNA guanylyl transferase (capping enzyme) has been complexed with an mRNA cap analogue G[5']ppp[5']G and crystallized. The crystals belong to space group C2221 with unit cell dimensions a = 78.4 angstrom, b = 164.1 angstrom, c = 103.3 angstrom, and diffraction data to 3.1 angstrom has been collected by using synchrotron radiation. The structure has

Kjell Hakansson; Dale B. Wigley

1998-01-01

83

Improving the accuracy of protein secondary structure prediction using structural alignment  

PubMed Central

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

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

2006-01-01

84

Detection of protein secondary structures via the discrete wavelet transform  

NASA Astrophysics Data System (ADS)

We subject the primary sequence of proteins gathered from the Structural Classification of Proteins (SCOP) database to a discrete wavelet transform (DWT) analysis to search for predictors of secondary structures. We use proteins with both alpha helices and beta sheets (the A/B , A+B databases from SCOP). The amino acids composing the protein are converted to their hydrophobicity values using three hydrophobicity scales. Results prove to be independent of the scale used. Using a DWT multiresolution decomposition, each protein is coarse grained, in effect, creating snapshots of each protein at multiple scales. For each protein, a control data set is formed by generating random realizations that remove the positional informational in the sequence but still contain the same amino acid frequencies. Regions of salient hydrophobicity in the protein sequence are identified by comparing the transforms of the original sequence with those of the control set, at each resolution. We find significant matching between regions of salient hydrophobicity and the locations of secondary structure along the amino acid chains. We calculate the sensitivity, specificity, and Matthews correlation to quantify the agreement between the wavelet detected structures and the real protein. In addition we are able to distinguish between the morphologically different subsets, A/B and A+B . We also construct a correlation function based on the DWT that correlates quasilocalized structures at lengths in wavelet space. Through a similar comparison to the control data sets, features in this space-scale correlation are identified that show correspondence to the typical lengths of the secondary structures.

Pando, Jesús; Sands, Luke; Shaheen, Sean E.

2009-11-01

85

Solving novel RNA structures using only secondary structural fragments  

Microsoft Academic Search

The crystallographic phase problem is the primary bottleneck encountered when attempting to solve macromolecular structures for which no close crystallographic structural homologues are known. Typically, isomorphous “heavy-atom” replacement and\\/or anomalous dispersion methods must be used in such cases to obtain experimentally-determined phases. Even three-dimensional NMR structures of the same macromolecule are often not sufficient to solve the crystallographic phase problem.

Michael P. Robertson; Young-In Chi; William G. Scott

2010-01-01

86

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. PMID:24124412

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

2013-01-01

87

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

88

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

89

Structural basis for binding the TREX2 complex to nuclear pores, GAL1 localisation and mRNA export.  

PubMed

The conserved Sac3:Thp1:Sem1:Sus1:Cdc31 (TREX2) complex binds to nuclear pore complexes (NPCs) and, in addition to integrating mRNA nuclear export with preceding steps in the gene expression pathway, facilitates re-positioning of highly regulated actively transcribing genes (such as GAL1) to NPCs. Although TREX2 is thought to bind NPC protein Nup1, defining the precise role of this interaction has been frustrated by the complex pleiotropic phenotype exhibited by nup1? strains. To provide a structural framework for understanding the binding of TREX2 to NPCs and its function in the gene expression pathway, we have determined the structure of the Nup1:TREX2 interaction interface and used this information to engineer a Sac3 variant that impairs NPC binding while not compromising TREX2 assembly. This variant inhibited the NPC association of both de-repressed and activated GAL1 and also produced mRNA export and growth defects. These results indicate that the TREX2:Nup1 interaction facilitates the efficient nuclear export of bulk mRNA together with the re-positioning of GAL1 to NPCs that is required for transcriptional control that is mediated by removal of SUMO from repressors by NPC-bound Ulp1. PMID:24705649

Jani, Divyang; Valkov, Eugene; Stewart, Murray

2014-06-01

90

Structural basis for binding the TREX2 complex to nuclear pores, GAL1 localisation and mRNA export  

PubMed Central

The conserved Sac3:Thp1:Sem1:Sus1:Cdc31 (TREX2) complex binds to nuclear pore complexes (NPCs) and, in addition to integrating mRNA nuclear export with preceding steps in the gene expression pathway, facilitates re-positioning of highly regulated actively transcribing genes (such as GAL1) to NPCs. Although TREX2 is thought to bind NPC protein Nup1, defining the precise role of this interaction has been frustrated by the complex pleiotropic phenotype exhibited by nup1? strains. To provide a structural framework for understanding the binding of TREX2 to NPCs and its function in the gene expression pathway, we have determined the structure of the Nup1:TREX2 interaction interface and used this information to engineer a Sac3 variant that impairs NPC binding while not compromising TREX2 assembly. This variant inhibited the NPC association of both de-repressed and activated GAL1 and also produced mRNA export and growth defects. These results indicate that the TREX2:Nup1 interaction facilitates the efficient nuclear export of bulk mRNA together with the re-positioning of GAL1 to NPCs that is required for transcriptional control that is mediated by removal of SUMO from repressors by NPC-bound Ulp1. PMID:24705649

Jani, Divyang; Valkov, Eugene; Stewart, Murray

2014-01-01

91

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

PubMed

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

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

2014-07-17

92

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

PubMed Central

We analyzed in detail the structure of the L-myc gene isolated from human placental DNA and characterized its expression in several small-cell lung cancer cell lines. The gene is composed of three exons and two introns spanning 6.6 kilobases in human DNA. Several distinct mRNA species are produced in all small-cell lung cancer cell lines that express L-myc. These transcripts are generated from a single gene by alternative splicing of introns 1 and 2 and by use of alternative polyadenylation signals. In some mRNAs there is a long open reading frame with a predicted translated protein of 364 residues. Amino acid sequence comparison with c-myc and N-myc demonstrated multiple discrete regions with extensive homology. In contrast, other mRNA transcripts, generated by alternative processing, could encode a truncated protein with a novel carboxy-terminal end. Images PMID:2827002

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

1988-01-01

93

The binding site for ribosomal protein S8 in 16S rRNA and spc mRNA from Escherichia coli: minimum structural requirements and the effects of single bulged bases on S8-RNA interaction.  

PubMed Central

Through specific interactions with rRNA and mRNA, ribosomal protein S8 of Escherichia coli plays a central role in both assembly of the 30S ribosomal subunit and translational regulation of spc operon expression. To better understand S8-RNA association, we have measured the affinity of S8 for a number of variants of its rRNA and mRNA binding sites prepared by in vitro transcription or chemical synthesis. With the aid of site-directed deletions, we demonstrate that an imperfect, 33-nucleotide helical stem encompassing nucleotides 588-603 and 635-651 possesses all of the structural information necessary for specific binding of S8 to the 16S rRNA. This segment consists of two short duplexes that enclose a conserved, asymmetric internal loop which contains features crucial for protein recognition. The S8 binding site in spc operon mRNA is very similar in both primary and secondary structure to that in 16S rRNA except for the presence of two single bulged bases in one of the duplex segments. In addition, the apparent association constant for the S8-mRNA interaction is approximately fivefold less than that for the S8-rRNA interaction. We show that the difference in affinity can be attributed to the effects of the bulged bases. Deletion of the bulged bases from the mRNA site increases its affinity for S8 to a level similar to that of the rRNA, whereas insertion of single-base bulges at equivalent positions within the rRNA site reduces its affinity for S8 to a value typical of the mRNA. Single-base bulges in the proximity of essential recognition features are therefore capable of modulating the strength of protein-RNA interactions. PMID:7515489

Wu, H; Jiang, L; Zimmermann, R A

1994-01-01

94

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

PubMed Central

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

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

2014-01-01

95

Regulation of secondary metabolism by chromatin structure and epigenetic codes  

PubMed Central

Chromatin, composed of DNA wrapped around an octamer of histones, is the relevant substrate for all genetic processes in eukaryotic nuclei. Changes in chromatin structure are associated with the activation and silencing of gene transcription and reversible post-translational modifications of histones are now known to direct chromatin structure transitions. Recent studies in several fungal species have identified a chromatin-based regulation of secondary metabolism (SM) gene clusters representing an upper-hierarchical level for the coordinated control of large chromosomal elements. Regulation by chromatin transition processes provides a mechanistic model to explain how different SM clusters located at dispersed genomic regions can be simultaneously silenced during primary metabolism. Activation of SM clusters has been shown to be associated with increased acetylation of histones H3 and H4 and, consequently, inhibition of histone de-acetylase activities also leads to increased production of secondary metabolites. New findings suggest that SM clusters are silenced by heterochromatic histone marks and that the “closed” heterochromatic structures are reversed during SM activation. This process is mediated by the conserved activator of SM, LaeA. Despite the increase in knowledge about these processes, much remains to be learned from chromatin-level regulation of SM. For example, which proteins “position” the chromatin restructuring signal onto SM clusters or how exactly LaeA works to mediate the low level of heterochromatic marks inside different clusters remain open questions. Answers to these and other chromatin-related questions would certainly complete our understanding of SM gene regulation and signaling and, because for many predicted SM clusters corresponding products have not been identified so far, anti-silencing strategies would open new ways for the identification of novel bioactive substances. PMID:20659575

Strauss, Joseph; Reyes-Dominguez, Yazmid

2012-01-01

96

On the Effectiveness of Rebuilding RNA Secondary Structures from Sequence Chunks  

E-print Network

Despite the computing power of emerging technologies, predicting long RNA secondary structures with thermodynamics-based methods is still infeasible, especially if the structures include complex motifs such as pseudoknots. This paper presents preliminary results on rebuilding RNA secondary structures by an extensive and systematic sampling of nucleotide chunks. The rebuilding approach merges the significant motifs found in the secondary structures of the single chunks. The extensive sampling and prediction of nucleotide chunks are supported by grid technology as part of the RNAVLab functionality. Significant motifs are identified in the chunk secondary structures and merged in a single structure based on their recurrences and other statistical insights. A critical analysis of the strengths,

Michela Taufer; Thamar Solorio; Abel Licon; David Mireles; Ming-ying Leung

97

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

98

Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features  

Microsoft Academic Search

For a successful analysis of the relation between amino acid sequence and protein structure, an unambiguous and physically meaningful definition of secondary structure is essential. We have developed a set of simple and physically motivated criteria for secondary structure, programmed as a pattern-recognition process of hydrogen-bonded and geometrical features extracted from x-ray coordinates. Cooperative secondary structure is recognized as repeats

Wolfgang Kabsch; Christian Sander

1983-01-01

99

Strong epistatic selection on the RNA secondary structure of HIV.  

PubMed

A key question in evolutionary genomics is how populations navigate the adaptive landscape in the presence of epistasis, or interactions among loci. This problem can be directly addressed by studying the evolution of RNA secondary structures, for which there is constraint to maintain pairing between Watson-Crick (WC) sites. Replacement of a nucleotide at one site of a WC pair reduces fitness by disrupting binding, which can be restored via a compensatory replacement at the interacting site. Here, I present the first genome-scale analysis of epistasis on the RNA secondary structure of human immunodeficiency virus type 1 (HIV-1). Comparison of polymorphism frequencies at ancestrally conserved sites reveals that selection against replacements is ? 2.7 times stronger at WC than at non-WC sites, such that nearly 50% of constraint can be attributed to epistasis. However, almost all epistatic constraint is due to selection against conversions of WC pairs to unpaired (UP) nucleotides, whereas conversions to GU wobbles are only slightly deleterious. This disparity is also evident in pairs with second-site compensatory replacements; conversions from UP nucleotides to WC pairs increase median fitness by ? 4.2%, whereas conversions from GU wobbles to WC pairs only increase median fitness by ? 0.3%. Moreover, second-site replacements that convert UP nucleotides to GU wobbles also increase median fitness by ? 4%, indicating that such replacements are nearly as compensatory as those that restore WC pairing. Thus, WC peaks of the HIV-1 epistatic adaptive landscape are connected by high GU ridges, enabling the viral population to rapidly explore distant peaks without traversing deep UP valleys. PMID:25210786

Assis, Raquel

2014-09-01

100

Structural and Functional Analysis of an mRNP Complex That Mediates the High Stability of Human  Globin mRNA  

Microsoft Academic Search

Human globins are encoded by mRNAs exhibiting high stabilities in transcriptionally silenced erythrocyte progenitors. Unlike a-globin mRNA, whose stability is enhanced by assembly of a specific messenger RNP (mRNP) a complex on its 3* untranslated region (UTR), neither the structure(s) nor the mechanism(s) that effects the high-level stability of human b-globin mRNA has been identified. The present work describes an

JIA YU; J. ERIC RUSSELL

2001-01-01

101

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

E-print Network

The low-lying level structure of the unbound neutron-rich nucleus $^{13}$Be has been investigated via breakup on a carbon target of secondary beams of $^{14,15}$B at 35 MeV/nucleon. The coincident detection of the beam velocity $^{12}$Be fragments and neutrons permitted the invariant mass of the $^{12}$Be+$n$ and $^{12}$Be+$n$+$n$ systems to be reconstructed. In the case of the breakup of $^{15}$B, a very narrow structure at threshold was observed in the $^{12}$Be+$n$ channel. Contrary to earlier stable beam fragmentation studies which identified this as a strongly interacting $s$-wave virtual state in $^{13}$Be, analysis here of the $^{12}$Be+$n$+$n$ events demonstrated that this was an artifact resulting from the sequential-decay of the $^{14}$Be(2$^+$) state. Single-proton removal from $^{14}$B was found to populate a broad low-lying structure some 0.70 MeV above the neutron-decay threshold in addition to a less prominent feature at around 2.4 MeV. Based on the selectivity of the reaction and a comparison with (0-3)$\\hbar\\omega$ shell-model calculations, the low-lying structure is concluded to most probably arise from closely spaced J$^\\pi$=1/2$^+$ and 5/2$^+$ resonances (E$_r$=0.40$\\pm$0.03 and 0.85$^{+0.15}_{-0.11}$ MeV), whilst the broad higher-lying feature is a second 5/2$^+$ level (E$_r$=2.35$\\pm$0.14 MeV). Taken in conjunction with earlier studies, it would appear that the lowest 1/2$^+$ and 1/2$^-$ levels lie relatively close together below 1 MeV.

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

2014-02-28

102

Expected distance between terminal nucleotides of RNA secondary structures.  

PubMed

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

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

2012-09-01

103

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

E-print Network

). The problem of finding the MFE structure given a certain sequence has been conceptually solved provided pursued. There is convincing evidence showing that, as in NMR protein structure prediction, the secondaryTT2NE: a novel algorithm to predict RNA secondary structures with pseudoknots Michae¨ l Bon

Paris-Sud XI, Université de

104

Predicting the secondary structure of globular proteins using neural network models  

Microsoft Academic Search

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

Ning Qian; Terrence J. Sejnowski

1988-01-01

105

Ovarian structure in cases of primary and secondary infertility.  

PubMed

The present study was carried out to assess the ovarian structure in cases of primary infertility (PI), and secondary infertility (SI). 40 patients were selected from the infertility clinic of Al Azhar University hospital from those suspected to have ovarian abnormalities with history of amenorrhea or oligomenorrhea or those having enlarged ovaries on pelvic examination. Their ages ranged from 17 to 40 years; their husbands were generally in good health and fertile. 28 were suffering from PI and 12 from SI. Ovarian biopsy was taken in 20 patients by laparoscopic technique and 20 patients by wedge resection. At the same time endometrial biopsy was taken with a specimen of cervical mucus and vaginal cells to detect the presence or absence of ovulation. Evidence of recent ovulation was present in 57.1% of the cases of PI and 50% of the cases of SI. However, the ovarian structure was abnormal in 92.9% of the cases of PI and 83.3% of the cases of SI. Polycystic ovary was present in 71.4% of PI cases and in 58.3% of SI cases and was considered the most common ovarian abnormality in both groups, followed by sclerotic ovary, which was detected in 14.3% of PI cases and no SI cases. Other findings in both groups included tubo-ovarian abscess, ovarian fibroma and a serous cystadenoma. PMID:12295113

Fakhr, M; Abou-salem, A M; El Sayed, L; El Hakim, S; El Sokkary, M B; El Sokkary, F

1986-01-01

106

Protein 8-class secondary structure prediction using conditional neural fields  

PubMed Central

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

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

2012-01-01

107

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

PubMed Central

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

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

2000-01-01

108

Structural insights into the targeting of mRNA GU-rich elements by the three RRMs of CELF1  

PubMed Central

The CUG-BP, Elav-like family (CELF) of RNA-binding proteins control gene expression at a number of different levels by regulating pre-mRNA splicing, deadenylation and mRNA stability. We present structural insights into the binding selectivity of CELF member 1 (CELF1) for GU-rich mRNA target sequences of the general form 5?-UGUNxUGUNyUGU and identify a high affinity interaction (Kd ? 100 nM for x = 2 and y = 4) with simultaneous binding of all three RNA recognition motifs within a single 15-nt binding element. RNA substrates spin-labelled at either the 3? or 5? terminus result in differential nuclear magnetic resonance paramagnetic relaxation enhancement effects, which are consistent with a non-sequential 2-1-3 arrangement of the three RNA recognition motifs on UGU sites in a 5? to 3? orientation along the RNA target. We further demonstrate that CELF1 binds to dispersed single-stranded UGU sites at the base of an RNA hairpin providing a structural rationale for recognition of CUG expansion repeats and splice site junctions in the regulation of alternative splicing. PMID:23748565

Edwards, John M.; Long, Jed; de Moor, Cornelia H.; Emsley, Jonas; Searle, Mark S.

2013-01-01

109

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

SciTech Connect

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, the authors 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. They 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.

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

1986-03-01

110

Teleost isotocin receptor: structure, functional expression, mRNA distribution and phylogeny.  

PubMed

A cDNA encoding a receptor for the oxytocin-related peptide isotocin has been identified by screening a lambda gt11 library constructed from poly(A)+ RNA of the hypothalamic region of the teleost Catostomus commersoni. The probe used was obtained by PCR amplification of white sucker genomic DNA using degenerate primers based on conserved sequences in the mammalian receptor counterparts. The full-length cDNA specifies a polypeptide of 390 amino acid residues that displays the typical hydrophobicity profile of a seven transmembrane domain receptor and which exhibits greatest similarity to mammalian oxytocin receptors. Oocytes that express the cloned receptor respond to the application of isotocin by an induction of membrane chloride currents indicating that it is coupled to the inositol phosphate/calcium pathway. The isotocin receptor (ITR) can also be activated by vasotocin, mesotocin, oxytocin and Arg-vasopressin, although these have lower potencies than isotocin. ITR-encoding mRNA has been detected in brain, intestine, bladder, skeletal muscle, lateral line, gills and kidney indicating that this receptor may mediate a variety of physiological functions. PMID:7656982

Hausmann, H; Meyerhof, W; Zwiers, H; Lederis, K; Richter, D

1995-08-21

111

Peptide Secondary Structures in the Gas Phase: Consensus Motif of N-Linked Glycoproteins  

E-print Network

Peptide Secondary Structures in the Gas Phase: Consensus Motif of N-Linked Glycoproteins Emilio J-linked glycoproteins, has been addressed by determining the intrinsic secondary structures of the capped oligopeptide-Linked glycoproteins found in eukaryotes are created by similar enzyme complexes, oligosac- charyltransferases (OSTs

Davis, Ben G.

112

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

113

Peptide Secondary Structure Determination by Three-Pulse Coherent Vibrational Spectroscopies: A Simulation Study  

E-print Network

and vibrational circular dichroism21,22 are complimentary methods for studying the same amide transitionsPeptide Secondary Structure Determination by Three-Pulse Coherent Vibrational Spectroscopies vibrational spectra of four ideal secondary structural motiffs of peptides, R helix, 310 helix, parallel sheet

Mukamel, Shaul

114

Evaluation and Improvement of Multiple Sequence Methods for Protein Secondary Structure Prediction  

E-print Network

Evaluation and Improvement of Multiple Sequence Methods for Protein Secondary Structure Prediction over PHD, which was the best single method evaluated. Segment Overlap Ac- curacy (SOV) is 75 is developed and used to evaluate the perfor- mance of the protein secondary structure predic- tion algorithms

Barton, Geoffrey J.

115

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

Microsoft Academic Search

We develop a knowledge-based approach (called PROSP) for protein secondary struc- ture prediction. The knowledge base contains small peptide fragments together with their secondary structural information. A quantitative measure M, called match rate, is defined to measure the amount of structural information that a target protein can ex- tract from the knowledge base. Our experimental results show that proteins with

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

2004-01-01

116

Effects of Template Sequence and Secondary Structure on DNA-Templated Reactivity  

E-print Network

Effects of Template Sequence and Secondary Structure on DNA-Templated Reactivity Thomas M. Snyder, we have systematically examined the effects of template sequence and secondary structure on DNA, and amplification of DNA sequences encoding synthetic small-molecule libraries. As the size of DNA

Liu, David R.

117

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

E-print Network

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

Mag Washietl, Stefan

118

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

PubMed Central

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

Veo, Bethany L.; Krushel, Leslie A.

2012-01-01

119

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

PubMed Central

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

2013-01-01

120

Secondary Impacts on Structures on the Lunar Surface  

NASA Technical Reports Server (NTRS)

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

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

2010-01-01

121

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 Central

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

1995-01-01

122

Decapping Scavenger (DcpS) enzyme: advances in its structure, activity and roles in the cap-dependent mRNA metabolism.  

PubMed

Decapping Scavenger (DcpS) enzyme rids eukaryotic cells of short mRNA fragments containing the 5' mRNA cap structure, which appear in the 3'?5' mRNA decay pathway, following deadenylation and exosome-mediated turnover. The unique structural properties of the cap, which consists of 7-methylguanosine attached to the first transcribed nucleoside by a triphosphate chain (m(7)GpppN), guarantee its resistance to non-specific exonucleases. DcpS enzymes are dimers belonging to the Histidine Triad (HIT) superfamily of pyrophosphatases. The specific hydrolysis of m(7)GpppN by DcpS yields m(7)GMP and NDP. By precluding inhibition of other cap-binding proteins by short m(7)GpppN-containing mRNA fragments, DcpS plays an important role in the cap-dependent mRNA metabolism. Over the past decade, lots of new structural, biochemical and biophysical data on DcpS has accumulated. We attempt to integrate these results, referring to DcpS enzymes from different species. Such a synergistic characteristic of the DcpS structure and activity might be useful for better understanding of the DcpS catalytic mechanism, its regulatory role in gene expression, as well as for designing DcpS inhibitors of potential therapeutic application, e.g. in spinal muscular atrophy. PMID:24742626

Milac, Adina L; Bojarska, Elzbieta; Wypijewska del Nogal, Anna

2014-06-01

123

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

PubMed

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

Mayr, Florian; Heinemann, Udo

2013-01-01

124

Mutational patterns in RNA secondary structure evolution examined in three RNA families.  

PubMed

The goal of this work was to study mutational patterns in the evolution of RNA secondary structure. We analyzed bacterial tmRNA, RNaseP and eukaryotic telomerase RNA secondary structures, mapping structural variability onto phylogenetic trees constructed primarily from rRNA sequences. We found that secondary structures evolve both by whole stem insertion/deletion, and by mutations that create or disrupt stem base pairing. We analyzed the evolution of stem lengths and constructed substitution matrices describing the changes responsible for the variation in the RNA stem length. In addition, we used principal component analysis of the stem length data to determine the most variable stems in different families of RNA. This data provides new insights into the evolution of RNA secondary structures and patterns of variation in the lengths of double helical regions of RNA molecules. Our findings will facilitate design of improved mutational models for RNA structure evolution. PMID:21698102

Srivastava, Anuj; Cai, Liming; Mrázek, Jan; Malmberg, Russell L

2011-01-01

125

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

PubMed Central

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

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

2014-01-01

126

Structure of the Saccharomyces cerevisiae Cet1-Ceg1 mRNA Capping Apparatus  

SciTech Connect

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

Gu, Meigang; Rajashankar, Kanagalaghatta R.; Lima, Christopher D. (Cornell); (SKI)

2010-05-04

127

[Species structure of natural secondary forest in the Wudaohe farm].  

PubMed

The analysis of soil thickness and slope gradient in natural secondary forest of the Wudaohe forest farm showed that the area of the secondary forest whose soil thickness was lower than 30 cm and slope gradient was higher than 25 degrees was 2390.1 hm2, covering 83.5% of its total area, while the area with soil thickness of higher than or equal to 30 cm and slope gradient of lower than or equal to 25 degrees was only 474.2 hm2, covering 16.5% of the total. It is suggested that the secondary forest is ecologically fragile, and this forest farm should develop a mulriple forest including waterhead-protection forest, lumber stand and economic forest. It was shown by analytic hierarchy process (AHP) that the suitable ratio of three forest types is 72.7%, 18.6%, 8.7%, respectively. PMID:12181887

Huang, Qingfeng; Kang, Xingang

2002-05-01

128

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. PMID:16954375

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

2006-01-01

129

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

130

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

131

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

ERIC Educational Resources Information Center

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…

Li, Spencer D.

2011-01-01

132

TileSoft: Sequence Optimization Software for Designing DNA Secondary Structures  

E-print Network

1 TileSoft: Sequence Optimization Software for Designing DNA Secondary Structures P. Yin*, B. Guo in constructing DNA objects is the design of DNA sequences that can correctly assemble into desired DNA secondary to be optimized #12;Prior work v.s. TileSoft 4 · DNA word design software: · Produce a pool of DNA sequences

Reif, John H.

133

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

E-print Network

with the associated anion. The enantioselectivities observed under base-rich reaction conditions follow directly from of these reactions is the enantioselective oxidation of secondary alcohols to ketones by a (-)-sparteine-PdX2A Computational Model Relating Structure and Reactivity in Enantioselective Oxidations of Secondary

Goddard III, William A.

134

The Structure of Secondary School Teacher Job Satisfaction and Its Relationship with Attrition and Work Enthusiasm  

ERIC Educational Resources Information Center

This study used the results of a questionnaire survey of 230 secondary school teachers to analyze the factors constituting job satisfaction and its effects on teacher attrition and work enthusiasm. The results show that (a) the structure of secondary school teacher job satisfaction is made up of ten components and is consistent with the model put…

Weiqi, Chen

2007-01-01

135

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

SciTech Connect

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

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

2008-01-01

136

Topological Constraints: Using RNA Secondary Structure to Model 3D Conformation, Folding Pathways, and Dynamic Adaptation  

PubMed Central

Summary Accompanying recent advances in determining RNA secondary structure is the growing appreciation for the importance of relatively simple topological constraints, encoded at the secondary structure level, in defining the overall architecture, folding pathways, and dynamic adaptability of RNA. A new view is emerging in which tertiary interactions do not define RNA 3D structure, but rather, help select specific conformers from an already narrow, topologically pre-defined conformational distribution. Studies are providing fundamental insights into the nature of these topological constraints, how they are encoded by the RNA secondary structure, and how they interplay with other interactions, breathing new meaning to RNA secondary structure. New approaches have been developed that take advantage of topological constraints in determining RNA backbone conformation based on secondary structure, and a limited set of other, easily accessible constraints. Topological constraints are also providing a much-needed framework for rationalizing and describing RNA dynamics and structural adaptation. Finally, studies suggest that topological constraints may play important roles steering RNA folding pathways. Here, we review recent advances in our understanding of topological constraints encoded by the RNA secondary structure. PMID:21497083

Bailor, Maximillian; Mustoe, Anthony M.

2012-01-01

137

Topological constraints: using RNA secondary structure to model 3D conformation, folding pathways, and dynamic adaptation.  

PubMed

Accompanying recent advances in determining RNA secondary structure is the growing appreciation for the importance of relatively simple topological constraints, encoded at the secondary structure level, in defining the overall architecture, folding pathways, and dynamic adaptability of RNA. A new view is emerging in which tertiary interactions do not define RNA 3D structure, but rather, help select specific conformers from an already narrow, topologically pre-defined conformational distribution. Studies are providing fundamental insights into the nature of these topological constraints, how they are encoded by the RNA secondary structure, and how they interplay with other interactions, breathing new meaning to RNA secondary structure. New approaches have been developed that take advantage of topological constraints in determining RNA backbone conformation based on secondary structure, and a limited set of other, easily accessible constraints. Topological constraints are also providing a much-needed framework for rationalizing and describing RNA dynamics and structural adaptation. Finally, studies suggest that topological constraints may play important roles in steering RNA folding pathways. Here, we review recent advances in our understanding of topological constraints encoded by the RNA secondary structure. PMID:21497083

Bailor, Maximillian H; Mustoe, Anthony M; Brooks, Charles L; Al-Hashimi, Hashim M

2011-06-01

138

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

PubMed Central

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

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

2014-01-01

139

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. PMID:22095906

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

2012-02-01

140

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) PMID:22689785

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

2012-01-01

141

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

E-print Network

. They concluded that bases from single- I. Key words:ribosomal RNA, secondary structure, phylogeny. Address eliminating these nu- cleotide positions or weighting them by one-half. In contrast, an analysis of echinoderm

Hillis, David

142

A global sampling approach to designing and reengineering RNA secondary structures  

E-print Network

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 ...

Levin, Alexander

143

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

144

Comparative analysis of mt LSU rRNA secondary structures of Odonates: structural variability and phylogenetic signal.  

PubMed

Secondary structures of the most conserved part of the mt 16S rRNA gene, domains IV and V, have been recently analysed in a comparative study. However, full secondary structures of the mt LSU rRNA molecule are published for only a few insect species. The present study presents full secondary structures of domains I, II, IV and V of Odonates and one representative of mayflies, Ephemera sp. The reconstructions are based on a comparative approach and minimal consensus structures derived from sequence alignments. The inferred structures exhibit remarkable similarities to the published Drosophila melanogaster model, which increases confidence in these structures. Structural variance within Odonates is homoplastic, and neighbour-joining trees based on tree edit distances do not correspond to any of the phylogenetically expected patterns. However, despite homoplastic quantitative structural variation, many similarities between Odonates and Ephemera sp. suggest promising character sets for higher order insect systematics that merit further investigations. PMID:14986915

Misof, B; Fleck, G

2003-12-01

145

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

146

G quadruplex RNA structures in PSD-95 mRNA: potential regulators of miR-125a seed binding site accessibility.  

PubMed

Fragile X syndrome (FXS) is the most common inherited form of intellectual disability caused by the CGG trinucleotide expansion in the 3'-untranslated region of the FMR1 gene on the X chromosome, that silences the expression of the Fragile X mental retardation protein (FMRP). FMRP has been shown to bind to a G-rich region within the PSD-95 mRNA which encodes for the postsynaptic density protein 95 (PSD-95), and together with the microRNA miR-125a, to play an important role in the reversible inhibition of the PSD-95 mRNA translation in neurons. The loss of FMRP in Fmr1 KO mice disables this translation control in the production of the PSD-95 protein. Interestingly, the miR-125a binding site on PSD-95 mRNA is embedded in the G-rich region bound by FMRP and postulated to adopt one or more G quadruplex structures. In this study, we have used different biophysical techniques to validate and characterize the formation of parallel G quadruplex structures and binding of miR-125a to its complementary sequence located within the 3' UTR of PSD-95 mRNA. Our results indicate that the PSD-95 mRNA G-rich region folds into alternate G quadruplex conformations that coexist in equilibrium. miR-125a forms a stable complex with PSD-95 mRNA, as evident by characteristic Watson-Crick base-pairing that coexists with one of the G quadruplex forms, suggesting a novel mechanism for G quadruplex structures to regulate the access of miR-125a to its binding site. PMID:25406362

Stefanovic, Snezana; Bassell, Gary J; Mihailescu, Mihaela Rita

2015-01-01

147

2005/12/11 15:16 1 A kernel for protein secondary structure  

E-print Network

problems in structural biology. In the sixties, An#12;nsen proposed his \\Thermody- namic Hypothesis" (An#12 to simplify the prediction problem by projecting the very complicated 3D structure onto one dimension, i2005/12/11 15:16 1 A kernel for protein secondary structure prediction Yann Guermeur LORIA - CNRS

Guermeur, Yann

148

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

Microsoft Academic Search

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

Yanga Byun; Kyungsook Han

2006-01-01

149

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

PubMed

Transcriptomics experiments and computational predictions both enable systematic discovery of new functional RNAs. However, many putative noncoding transcripts arise instead from artifacts and biological noise, and current computational prediction methods have high false positive rates. I discuss prospects for improving computational methods for analyzing and identifying functional RNAs, with a focus on detecting signatures of conserved RNA secondary structure. An interesting new front is the application of chemical and enzymatic experiments that probe RNA structure on a transcriptome-wide scale. I review several proposed approaches for incorporating structure probing data into the computational prediction of RNA secondary structure. Using probabilistic inference formalisms, I show how all these approaches can be unified in a well-principled framework, which in turn allows RNA probing data to be easily integrated into a wide range of analyses that depend on RNA secondary structure inference. Such analyses include homology search and genome-wide detection of new structural RNAs. PMID:24895857

Eddy, Sean R

2014-01-01

150

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

PubMed

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

Patel, Maulika S; Mazumdar, Himanshu S

2014-11-21

151

Probing Protein Secondary Structure using EPR: Investigating a Dynamic Region of Visual Arrestin  

PubMed Central

One key application of site-directed spin labeling (SDSL) electron paramagnetic resonance (EPR) spectroscopy is the determination of sequence-specific secondary structure in proteins. Regular secondary structure leads to a periodic variation in both side chain motion and solvent accessibility, two properties easily monitored by EPR techniques. Specifically, saturation recovery (SR) EPR spectroscopy has proven to be useful for making accessibility measurements for multiple protein structure populations by determining individual accessibilities and is therefore well suited to study the structure of proteins exhibiting multiple conformations in equilibrium. Here we employ both continuous wave and SR EPR spectroscopy in combination to examine the secondary structure of a short sequence showing conformational heterogeneity in visual rod arrestin. The EPR data presented here clearly distinguish between the unstructured loop and the helical structure formed in the crystallographic tetramer of visual arrestin and show that this region is unstructured in solution. PMID:25419051

Francis, Derek J.; Hubbell, Wayne L.; Klug, Candice S.

2014-01-01

152

Structure-function relationships in enzymes of the nucleotidyltransferase superfamily : RNA ligation and mRNA capping  

E-print Network

agent of African sleeping sickness, and the GTP-dependent mRNA cappingcapping enzyme from the Paramecium bursaria chlorella virus; and TbREL1, an ATP-dependent RNA ligase of Trypanosoma brucei, the causative agent

Swift, Robert

2009-01-01

153

Sheath structure transition controlled by secondary electron emission  

NASA Astrophysics Data System (ADS)

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

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

2015-04-01

154

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

NASA Astrophysics Data System (ADS)

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

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

2014-01-01

155

Structural analysis of human 2?-O-ribose methyltransferases involved in mRNA cap structure formation  

PubMed Central

The 5? cap of human messenger RNA contains 2?-O-methylation of the first and often second transcribed nucleotide that is important for its processing, translation and stability. Human enzymes that methylate these nucleotides, termed CMTr1 and CMTr2, respectively, have recently been identified. However, the structures of these enzymes and their mechanisms of action remain unknown. In the present study, we solve the crystal structures of the active CMTr1 catalytic domain in complex with a methyl group donor and a capped oligoribonucleotide, thereby revealing the mechanism of specific recognition of capped RNA. This mechanism differs significantly from viral enzymes, thus providing a framework for their specific targeting. Based on the crystal structure of CMTr1, a comparative model of the CMTr2 catalytic domain is generated. This model, together with mutational analysis, leads to the identification of residues involved in RNA and methyl group donor binding. PMID:24402442

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

2014-01-01

156

An evolutionary method for learning HMM structure: prediction of protein secondary structure  

PubMed Central

Background The prediction of the secondary structure of proteins is one of the most studied problems in bioinformatics. Despite their success in many problems of biological sequence analysis, Hidden Markov Models (HMMs) have not been used much for this problem, as the complexity of the task makes manual design of HMMs difficult. Therefore, we have developed a method for evolving the structure of HMMs automatically, using Genetic Algorithms (GAs). Results In the GA procedure, populations of HMMs are assembled from biologically meaningful building blocks. Mutation and crossover operators were designed to explore the space of such Block-HMMs. After each step of the GA, the standard HMM estimation algorithm (the Baum-Welch algorithm) was used to update model parameters. The final HMM captures several features of protein sequence and structure, with its own HMM grammar. In contrast to neural network based predictors, the evolved HMM also calculates the probabilities associated with the predictions. We carefully examined the performance of the HMM based predictor, both under the multiple- and single-sequence condition. Conclusion We have shown that the proposed evolutionary method can automatically design the topology of HMMs. The method reads the grammar of protein sequences and converts it into the grammar of an HMM. It improved previously suggested evolutionary methods and increased the prediction quality. Especially, it shows good performance under the single-sequence condition and provides probabilistic information on the prediction result. The protein secondary structure predictor using HMMs (P.S.HMM) is on-line available http://www.binf.ku.dk/~won/pshmm.htm. It runs under the single-sequence condition. PMID:17888163

Won, Kyoung-Jae; Hamelryck, Thomas; Prügel-Bennett, Adam; Krogh, Anders

2007-01-01

157

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

158

A manually curated database of tetrapod mitochondrially encoded tRNA sequences and secondary structures  

PubMed Central

Background Mitochondrial tRNAs have been the subject of study for structural biologists interested in their secondary structure characteristics, evolutionary biologists have researched patterns of compensatory and structural evolution and medical studies have been directed towards understanding the basis of human disease. However, an up to date, manually curated database of mitochondrially encoded tRNAs from higher animals is currently not available. Description We obtained the complete mitochondrial sequence for 277 tetrapod species from GenBank and re-annotated all of the tRNAs based on a multiple alignment of each tRNA gene and secondary structure prediction made independently for each tRNA. The mitochondrial (mt) tRNA sequences and the secondary structure based multiple alignments are freely available as Supplemental Information online. Conclusion We compiled a manually curated database of mitochondrially encoded tRNAs from tetrapods with completely sequenced genomes. In the course of our work, we reannotated more than 10% of all tetrapod mt-tRNAs and subsequently predicted the secondary structures of 6060 mitochondrial tRNAs. This carefully constructed database can be utilized to enhance our knowledge in several different fields including the evolution of mt-tRNA secondary structure and prediction of pathogenic mt-tRNA mutations. In addition, researchers reporting novel mitochondrial genome sequences should check their tRNA gene annotations against our database to ensure a higher level of fidelity of their annotation. PMID:17999775

Popadin, Konstantin Yu; Mamirova, Leila A; Kondrashov, Fyodor A

2007-01-01

159

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. PMID:20660479

Cevec, Mirko; Thibaudeau, Christophe; Plavec, Janez

2010-01-01

160

Efficient sampling of RNA secondary structures from the Boltzmann ensemble of low-energy: the boustrophedon method.  

PubMed

We adapt here a surprising technique, the boustrophedon method, to speed up the sampling of RNA secondary structures from the Boltzmann low-energy ensemble. This technique is simple and its implementation straight-forward, as it only requires a permutation in the order of some operations already performed in the stochastic traceback stage of these algorithms. It nevertheless greatly improves their worst-case complexity from O(n2)] to O(n log (n)), for n the size of the original sequence. Moreover the average-case complexity of the generation is shown to be improved from O(n square root n) to (O n log ((n)) in an Boltzmann-weighted homopolymer model based on the Nussinov-Jacobson free-energy model. These results are extended to the more realistic Turner free-energy model through experiments performed on both structured (Drosophilia melanogaster mRNA 5S) and hybrid (Staphylococcus aureus RNAIII) RNA sequences, using a boustrophedon modified version of the popular software UnaFold. This improvement allows for the sampling of greater and more significant sets of structures in a given time. PMID:17932676

Ponty, Yann

2008-01-01

161

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

PubMed Central

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

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

2006-01-01

162

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

PubMed

Determining the RNA secondary structure from sequence data by computational predictions is a long-standing problem. Its solution has been approached in two distinctive ways. If a multiple sequence alignment of a collection of homologous sequences is available, the comparative method uses phylogeny to determine conserved base pairs that are more likely to form as a result of billions of years of evolution than by chance. In the case of single sequences, recursive algorithms that compute free energy structures by using empirically derived energy parameters have been developed. This latter approach of RNA folding prediction by energy minimization is widely used to predict RNA secondary structure from sequence. For a significant number of RNA molecules, the secondary structure of the RNA molecule is indicative of its function and its computational prediction by minimizing its free energy is important for its functional analysis. A general method for free energy minimization to predict RNA secondary structures is dynamic programming, although other optimization methods have been developed as well along with empirically derived energy parameters. In this chapter, we introduce and illustrate by examples the approach of free energy minimization to predict RNA secondary structures. PMID:25577369

Churkin, Alexander; Weinbrand, Lina; Barash, Danny

2015-01-01

163

Efficient calculation of exact probability distributions of integer features on RNA secondary structures  

PubMed Central

Background Although the needs for analyses of secondary structures of RNAs are increasing, prediction of the secondary structures of RNAs are not always reliable. Because an RNA may have a complicated energy landscape, comprehensive representations of the whole ensemble of the secondary structures, such as the probability distributions of various features of RNA secondary structures are required. Results A general method to efficiently compute the distribution of any integer scalar/vector function on the secondary structure is proposed. We also show two concrete algorithms, for Hamming distance from a reference structure and for 5? ? 3? distance, which can be constructed by following our general method. These practical applications of this method show the effectiveness of the proposed method. Conclusions The proposed method provides a clear and comprehensive procedure to construct algorithms for distributions of various integer features. In addition, distributions of integer vectors, that is a combination of different integer scores, can be also described by applying our 2D expanding technique. PMID:25560710

2014-01-01

164

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

PubMed Central

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

2012-01-01

165

Structural Basis for the Recognition of Cellular mRNA Export Factor REF by Herpes Viral Proteins HSV-1 ICP27 and HVS ORF57  

PubMed Central

The herpesvirus proteins HSV-1 ICP27 and HVS ORF57 promote viral mRNA export by utilizing the cellular mRNA export machinery. This function is triggered by binding to proteins of the transcription-export (TREX) complex, in particular to REF/Aly which directs viral mRNA to the TAP/NFX1 pathway and, subsequently, to the nuclear pore for export to the cytoplasm. Here we have determined the structure of the REF-ICP27 interaction interface at atomic-resolution and provided a detailed comparison of the binding interfaces between ICP27, ORF57 and REF using solution-state NMR. Despite the absence of any obvious sequence similarity, both viral proteins bind on the same site of the folded RRM domain of REF, via short but specific recognition sites. The regions of ICP27 and ORF57 involved in binding by REF have been mapped as residues 104–112 and 103–120, respectively. We have identified the pattern of residues critical for REF/Aly recognition, common to both ICP27 and ORF57. The importance of the key amino acid residues within these binding sites was confirmed by site-directed mutagenesis. The functional significance of the ORF57-REF/Aly interaction was also probed using an ex vivo cytoplasmic viral mRNA accumulation assay and this revealed that mutants that reduce the protein-protein interaction dramatically decrease the ability of ORF57 to mediate the nuclear export of intronless viral mRNA. Together these data precisely map amino acid residues responsible for the direct interactions between viral adaptors and cellular REF/Aly and provide the first molecular details of how herpes viruses access the cellular mRNA export pathway. PMID:21253573

Tunnicliffe, Richard B.; Hautbergue, Guillaume M.; Kalra, Priti; Jackson, Brian R.; Whitehouse, Adrian; Wilson, Stuart A.; Golovanov, Alexander P.

2011-01-01

166

Secondary DNA structure formation for Hoxb9 promoter and identification of its specific binding protein  

Microsoft Academic Search

Hox genes determine anterior-posterior specificity of an animal body. In mammals, these genes map onto four chromosomal loci in a clustered manner, and their expression is regulated in a coordinated manner according to their chromosomal structure. In the present study, we analysed the Hoxb9 promoter and found that promoter activity in cultured cells is linked to secondary structure formation of

Takumi Yamagishi; Shigehisa Hirose; Takashi Kondo

2008-01-01

167

Protein and peptide secondary structure and conformational determination with vibrational circular dichroism  

Microsoft Academic Search

Vibrational circular dichroism (VCD) provides alternative views of protein and peptide conformation with advantages over electronic (UV) CD (ECD) or IR spectroscopy. VCD is sensitive to short-range order, allowing it to discriminate ?-sheet and various helices as well as disordered structure. Quantitative secondary structure analyses use protein VCD bandshapes, but are best combined with ECD and IR for balance. Much

Timothy A Keiderling

2002-01-01

168

SCFGs as Predictors of RNA's Secondary Structure Antonio F. Martnez-Alcntara  

E-print Network

SCFGs as Predictors of RNA's Secondary Structure Antonio F. Martínez-Alcántara Bioc218 Computational Molecular Biology, Final Paper antonio@colpos.mx Abstract The use of bioinformatics' tools Structure Source: [Mount] #12;Antonio F. Martínez-Alcántara 2 Their relevance has moved from the more

169

Predicting RNA secondary structure by the comparative approach: how to select the homologous sequences  

PubMed Central

Background The secondary structure of an RNA must be known before the relationship between its structure and function can be determined. One way to predict the secondary structure of an RNA is to identify covarying residues that maintain the pairings (Watson-Crick, Wobble and non-canonical pairings). This "comparative approach" consists of identifying mutations from homologous sequence alignments. The sequences must covary enough for compensatory mutations to be revealed, but comparison is difficult if they are too different. Thus the choice of homologous sequences is critical. While many possible combinations of homologous sequences may be used for prediction, only a few will give good structure predictions. This can be due to poor quality alignment in stems or to the variability of certain sequences. This problem of sequence selection is currently unsolved. Results This paper describes an algorithm, SSCA, which measures the suitability of sequences for the comparative approach. It is based on evolutionary models with structure constraints, particularly those on sequence variations and stem alignment. We propose three models, based on different constraints on sequence alignments. We show the results of the SSCA algorithm for predicting the secondary structure of several RNAs. SSCA enabled us to choose sets of homologous sequences that gave better predictions than arbitrarily chosen sets of homologous sequences. Conclusion SSCA is an algorithm for selecting combinations of RNA homologous sequences suitable for secondary structure predictions with the comparative approach. PMID:18045491

Engelen, Stéfan; Tahi, Fariza

2007-01-01

170

IMPORTANCE OF SECONDARY STRUCTURE ELEMENTS FOR PREDICTION OF GO ANNOTATIONS  

E-print Network

Bank (PDB) [22] association file, which contains only the assignments for the proteins present in the PDB database. To be able to fetch sequence and structure information from PDB, we used the PDB. To remove sequence homologs, PDB's scheme is applied. PDB provides several clusterings of proteins generated

Cataltepe, Zehra

171

Probabilistic Approaches to Predicting the Secondary Structure of Proteins  

Microsoft Academic Search

Today's increasingly unaffordable medical treatment forces genomic research to have far-reaching consequences. Most members of the public do not realize that the genetic sequence does not only encode information about hereditary make-up, but that it also contains the necessary blueprints for the structural formation of essential proteins. As the central dogma of molecular biology declares, DNA is transcribed into RNA,

Roopal Sampat

172

RNA secondary structure prediction from sequence alignments using a network of k-nearest neighbor classifiers  

PubMed Central

We present a machine learning method (a hierarchical network of k-nearest neighbor classifiers) that uses an RNA sequence alignment in order to predict a consensus RNA secondary structure. The input to the network is the mutual information, the fraction of complementary nucleotides, and a novel consensus RNAfold secondary structure prediction of a pair of alignment columns and its nearest neighbors. Given this input, the network computes a prediction as to whether a particular pair of alignment columns corresponds to a base pair. By using a comprehensive test set of 49 RFAM alignments, the program KNetFold achieves an average Matthews correlation coefficient of 0.81. This is a significant improvement compared with the secondary structure prediction methods PFOLD and RNAalifold. By using the example of archaeal RNase P, we show that the program can also predict pseudoknot interactions. PMID:16495232

BINDEWALD, ECKART; SHAPIRO, BRUCE A.

2006-01-01

173

The Regulation of mRNA Stability in Mammalian Cells: 2.0  

PubMed Central

Messenger RNA decay is an essential step in gene expression to set mRNA abundance in the cytoplasm. The binding of proteins and/or noncoding RNAs to specific recognition sequences or secondary structures within mRNAs dictates mRNA decay rates by recruiting specific enzyme complexes that perform the destruction processes. Often, the cell coordinates the degradation or stabilization of functional subsets of mRNAs encoding proteins collectively required for a biological process. As well, extrinsic or intrinsic stimuli activate signal transduction pathways that modify the mRNA decay machinery with consequent effects on decay rates and mRNA abundance. This review is an update to our 2001 Gene review on mRNA stability in mammalian cells, and we survey the enormous progress made over the past decade. PMID:22452843

Wu, Xiangyue; Brewer, Gary

2012-01-01

174

Macromolecular ab initio phasing enforcing secondary and tertiary structure.  

PubMed

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

Millán, Claudia; Sammito, Massimo; Usón, Isabel

2015-01-01

175

Macromolecular ab initio phasing enforcing secondary and tertiary structure  

PubMed Central

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

Millán, Claudia; Sammito, Massimo; Usón, Isabel

2015-01-01

176

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

PubMed Central

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

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

2014-01-01

177

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

NASA Technical Reports Server (NTRS)

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

Mishler, H. W.

1974-01-01

178

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

PubMed

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

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

2014-11-26

179

A novel protein structural classes prediction method based on predicted secondary structure.  

PubMed

Knowledge of structural classes plays an important role in understanding protein folding patterns. In this paper, features based on the predicted secondary structure sequence and the corresponding E-H sequence are extracted. Then, an 11-dimensional feature vector is selected based on a wrapper feature selection algorithm and a support vector machine (SVM). Among the 11 selected features, 4 novel features are newly designed to model the differences between ?/? class and ? + ? class, and other 7 rational features are proposed by previous researchers. To examine the performance of our method, a total of 5 datasets are used to design and test the proposed method. The results show that competitive prediction accuracies can be achieved by the proposed method compared to existing methods (SCPRED, RKS-PPSC and MODAS), and 4 new features are demonstrated essential to differentiate ?/? and ? + ? classes. Standalone version of the proposed method is written in JAVA language and it can be downloaded from http://web.xidian.edu.cn/slzhang/paper.html. PMID:22353242

Ding, Shuyan; Zhang, Shengli; Li, Yang; Wang, Tianming

2012-05-01

180

Multiple structurally distinct ER? mRNA variants in zebrafish are differentially expressed by tissue type, stage of development and estrogen exposure.  

PubMed

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

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

2013-12-01

181

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

PubMed Central

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

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

2013-01-01

182

Identifying secondary structures in proteins using NMR chemical shift 3D correlation maps  

NASA Astrophysics Data System (ADS)

NMR chemical shifts are accurate indicators of molecular environment and have been extensively used as aids in protein structure determination. This work focuses on creating empirical 3D correlation maps of backbone chemical shift nuclei for use as identifiers of secondary structure elements in proteins. A correlated database of backbone nuclei chemical shifts was constructed from experimental structural data gathered from entries in the Protein Data Bank (PDB) as well as isotropic chemical shift values from the RefDB database. Rigorous statistical analysis of the maps led to the conclusion that specific correlations between triplets of backbone chemical shifts are best able to differentiate between different secondary structures such as ?-helices, ?-strands and turns. The method is compared with similar techniques that use NMR chemical shift information as aids in biomolecular structure determination and performs well in tests done on experimental data determined for different types of proteins, including large multi-domain proteins and membrane proteins.

Kumari, Amrita; Dorai, Kavita

2013-06-01

183

Using Neural Networks to Predict Secondary Structure by Integration of Amino Acid Conformational Preference and Multiple Sequence Alignment  

E-print Network

Using Neural Networks to Predict Secondary Structure by Integration of Amino Acid Conformational a protein sequence with amino acids {S1, S 2 ...S n}, the Secondary Structure Prediction (SSP) problem). The prediction of the protein structure from amino acid sequence is a key step to understand the relationship

Hefei Institute of Intelligent Machines

184

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

PubMed Central

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

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

2009-01-01

185

Secondary Blepharospasm Associated with Structural Lesions of the Brain  

PubMed Central

Background Blepharospasm is a form of focal dystonia that manifests as repetitive involuntary closure of the eyes. The pathogenesis of blepharospasm and the neuroanatomic substrates involved are not fully understood. Dysfunction of the basal ganglia traditionally is presumed to be the main cause of most forms of dystonia, but a growing body of evidence suggests that a network of additional cortical and subcortical structures may be involved. Methods The medical records of 1114 patients with blepharospasm seen over past 10 years at Emory University were reviewed to identify potentially contributing brain lesions. A systematic review of the published literature was also conducted to identify potentially contributing brain lesions. Results Among patients with blepharospasm at Emory University, 18 had focal lesions on imaging studies available for review. The literature review revealed 25 articles describing 30 additional cases of blepharospasm associated with focal lesions. Among all 48 cases, lesions were found in multiple regions including the thalamus (n=12), lower brainstem (n=11), basal ganglia (n=9), cerebellum (n=9), midbrain (n=7), and cortex (n=1). Conclusions These data in combination with functional imaging studies of primary blepharospasm support a model of dystonia in which a network of different regions plays a role in pathogenesis. PMID:23747003

Khooshnoodi, M. A.; Factor, S. A.; Jinnah, H. A.

2013-01-01

186

DNA secondary structures and epigenetic determinants of cancer genome evolution  

PubMed Central

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

De, Subhajyoti; Michor, Franziska

2014-01-01

187

Insights into mRNA export-linked molecular mechanisms of human disease through a Gle1 structure-function analysis.  

PubMed

A critical step during gene expression is the directional export of nuclear messenger (m)RNA through nuclear pore complexes (NPCs) to the cytoplasm. During export, Gle1 in conjunction with inositol hexakisphosphate (IP6) spatially regulates the activity of the DEAD-box protein Dbp5 at the NPC cytoplasmic face. GLE1 mutations are causally linked to the human diseases lethal congenital contracture syndrome 1 (LCCS-1) and lethal arthrogryposis with anterior horn cell disease (LAAHD). Here, structure prediction and functional analysis provide strong evidence to suggest that the LCCS-1 and LAAHD disease mutations disrupt the function of Gle1 in mRNA export. Strikingly, direct fluorescence microscopy in living cells reveals a dramatic loss of steady-state NPC localization for GFP-gle1 proteins expressed from human gle1 genes harboring LAAHD and LCCS-1 mutations. The potential significance of these residues is further clarified by analyses of sequence and predicted structural conservation. This work offers insights into the perturbed mechanisms underlying human LCCS-1 and LAAHD disease states and emphasizes the potential impact of altered mRNA transport and gene expression in human disease. PMID:24275432

Folkmann, Andrew W; Dawson, T Renee; Wente, Susan R

2014-01-01

188

In Vitro Secondary Structure of the Genomic RNA of Satellite Tobacco Mosaic Virus  

E-print Network

In Vitro Secondary Structure of the Genomic RNA of Satellite Tobacco Mosaic Virus Shreyas S, Atlanta, Georgia, United States of America Abstract 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

Williams, Loren

189

Interplay between Secondary and Tertiary Structure Formation in Protein Folding Cooperativity  

E-print Network

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

Bachmann, Michael

190

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

E-print Network

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

Cheng, Jianlin Jack

191

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...

192

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

E-print Network

PROTEIN SECONDARY STRUCTURE PREDICTION BASED ON THE AMINO ACIDS CONFORMATIONAL CLASSIFICATION from the Protein Data Bank (PDB), we group the 20 different amino acids into f (Former), b (Breaker, -sheets and Coil), which reflect the in- trinsic preference of that amino acid for a given type of sec

Hefei Institute of Intelligent Machines

193

Evolved Matrix Operations for Post-Processing Protein Secondary Structure Predictions  

E-print Network

of proteins is a hard problem, so many have opted instead to predict the secondary structural state (usually helix, strand or coil) of each amino acid residue. This should be an easier task, but it now seems probabilities produced by the popular, state-of-the-art neural network-based PSIPRED by David Jones. We show

MacCallum, Bob

194

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

Technology Transfer Automated Retrieval System (TEKTRAN)

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

195

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

196

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

ERIC Educational Resources Information Center

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

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

2011-01-01

197

Biomaterials 27 (2006) 38633874 Effect of RGD secondary structure and the synergy site PHSRN on  

E-print Network

Biomaterials 27 (2006) 3863­3874 Effect of RGD secondary structure and the synergy site PHSRN. Introduction Control of the microenvironment of the cell provides the biomaterials engineer- quently, a maturing theme in the biomaterials field is the design, synthesis, and modification

Kokkoli, Efie

198

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

PubMed Central

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

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

2014-01-01

199

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

SciTech Connect

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

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

2002-09-28

200

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

201

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

E-print Network

by McGuffin et al. [2]. We introduce a residue-based score function, which can incorporate amino acid similarity matrix is combined with the amino acid based BLOSUM30 matrix, the accuracy of our method imPROTEIN FOLD RECOGNITION USING RESIDUE-BASED ALIGNMENTS OF SEQUENCE AND SECONDARY STRUCTURE Zafer

Erdogan, Hakan

202

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

203

Protein Secondary Structure Prediction Based on Position-specific Scoring Matrices  

Microsoft Academic Search

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

David T. Jones

1999-01-01

204

Effects of surfactants on emulsification and secondary structure of lysozyme in aqueous solutions  

Microsoft Academic Search

This paper reports our investigations on the secondary structure of lysozyme in aqueous solution with D2O and comparing systems emulsified with ionic and non-ionic amphiphiles, respectively. The opposite effect of concentration of surfactants on the lysozyme aqueous system was studied and the activity of lysozyme by the turbidimetric assay with different kinds of surfactant was compared. The effect of different

Liu Huizhou; Yang Weijing; Chen Jiayong

1998-01-01

205

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

E-print Network

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

DeFlores, Lauren P.

206

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

PubMed

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

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

2014-12-16

207

PolyprOnline: polyproline helix II and secondary structure assignment database  

PubMed Central

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

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

2014-01-01

208

Computer simulation of secondary structure folding of random and ``edited'' RNA chains  

NASA Astrophysics Data System (ADS)

Computer simulation of secondary structure folding of RNA chains demonstrates that these chains under some temperature and solvent conditions find their native conformations much faster than by exhaustive sorting of all the possible chain conformations. This is true both for the random and the edited chains. However, for a random chain the native structure is thermodynamically stable in one region of temperature and solvent quality, while fast folding (and even faster unfolding) of the random chain occurs in another region. Some editing of a chain is necessary to make its native structure thermodynamically stable at the optimal for a fast folding range of conditions. Only for the edited chains can the thermodynamically stable native secondary structures fold fast. The dependence of folding time on the chain length is not an exponential one but much less steep.

Galzitskaya, Oxana V.; Finkelstein, Alexei V.

1996-07-01

209

Secondary structures of friction at the surface of bronze alloyed with tungsten disulfide  

Microsoft Academic Search

Methods of x-ray microprobe analysis, metallography, and continuous impression of an indentor are used to study secondary structures covering the friction surface of a bronze-tungsten disulfide (VAFC) composite-steel pair. Differences in the structure, composition, and properties of the friction track on a VAFC composite for four stages of testing in air, in a vacuum, in a vacuum with screen cooled

V. V. Gorskii; A. N. Gripachevskii; B. M. Krivitskii; V. A. Tsitovich

1993-01-01

210

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

PubMed Central

Previously, we characterized two host protein binding elements located within the 3?-terminal 166 nucleotides 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 the MHV strain JHM genome using limited RNase digestion assays. Our data indicate that multiple stem-loop and hairpin-loop structures exist within this region. Mutant and wild-type DIssEs were employed to test the function of secondary structure elements in DI RNA replication. Three stem structures were chosen as targets for the introduction of transversion mutations designed to destroy base pairing structures. Mutations predicted to destroy the base pairing of nucleotides 142 to 136 with nucleotides 68 to 74 exhibited a deleterious effect on DIssE replication. Destruction of base pairing between positions 96 to 99 and 116 to 113 also decreased DI RNA replication. Mutations interfering with the pairing of nucleotides 67 to 63 with nucleotides 52 to 56 had only minor effects on DIssE replication. The introduction of second complementary mutations which restored the predicted base pairing of positions 142 to 136 with 68 to 74 and nucleotides 96 to 99 with 116 to 113 largely ameliorated defects in replication ability, restoring DI RNA replication to levels comparable to that of wild-type DIssE RNA, suggesting that these secondary structures are important for efficient MHV replication. We also identified a conserved 23-nucleotide stem-loop structure involving nucleotides 142 to 132 and nucleotides 68 to 79. The upstream side of this conserved stem-loop is contained within a host protein binding element (nucleotides 166 to 129). PMID:11711601

Liu, Qi; Johnson, Reed F.; Leibowitz, Julian L.

2001-01-01

211

Non-protein amino acids in the design of secondary structure scaffolds.  

PubMed

The use of stereochemically constrained amino acids permits the design of short peptides as models for protein secondary structures. Amino acid residues that are restrained to a limited range of backbone torsion angles (phi-psi) may be used as folding nuclei in the design of helices and beta-hairpins. alpha-Amino-isobutyric acid (Aib) and related Calphaalpha dialkylated residues are strong promoters of helix formation, as exemplified by a large body of experimentally determined structures of helical peptides. DPro-Xxx sequences strongly favor type II' turn conformations, which serve to nucleate registered beta-hairpin formation. Appropriately positioned DPro-Xxx segments may be used to nucleate the formation of multistranded antiparallel beta-sheet structures. Mixed (alpha/beta) secondary structures can be generated by linking rigid modules of helices and beta-hairpins. The approach of using stereochemically constrained residues promotes folding by limiting the local structural space at specific residues. Several aspects of secondary structure design are outlined in this chapter, along with commonly used methods of spectroscopic characterization. PMID:16957333

Mahalakshmi, Radhakrishnan; Balaram, Padmanabhan

2006-01-01

212

Evaluation of several lightweight stochastic context-free grammars for RNA secondary structure prediction  

PubMed Central

Background RNA secondary structure prediction methods based on probabilistic modeling can be developed using stochastic context-free grammars (SCFGs). Such methods can readily combine different sources of information that can be expressed probabilistically, such as an evolutionary model of comparative RNA sequence analysis and a biophysical model of structure plausibility. However, the number of free parameters in an integrated model for consensus RNA structure prediction can become untenable if the underlying SCFG design is too complex. Thus a key question is, what small, simple SCFG designs perform best for RNA secondary structure prediction? Results Nine different small SCFGs were implemented to explore the tradeoffs between model complexity and prediction accuracy. Each model was tested for single sequence structure prediction accuracy on a benchmark set of RNA secondary structures. Conclusions Four SCFG designs had prediction accuracies near the performance of current energy minimization programs. One of these designs, introduced by Knudsen and Hein in their PFOLD algorithm, has only 21 free parameters and is significantly simpler than the others. PMID:15180907

Dowell, Robin D; Eddy, Sean R

2004-01-01

213

Secondary grain-boundary dislocations in (001) twist boundaries in MgO. II. Extrinsic structures  

SciTech Connect

Extrinsic secondary grain boundary dislocation (GBD) structures were observed by weak beam transmission electron microscopy in a variety of (001) twist boundaries in MgO. These structures were derived from segments of lattice dislocations embedded in the boundaries and could be interpreted as the result of the decomposition of the lattice dislocations into extrinsic GBDs and the subsequent interaction of the product GBDs with the intrinsic boundary structure. The results demonstrate that lattice dislocations in MgO are attracted to grain boundaries over a wide range of conditions and tend to remain embedded in the boundaries as extrinsic GBD structures.

Sun, C.P.; Balluffi, R.W.

1981-12-01

214

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

2010-02-01

215

Secondary DNA structure formation for Hoxb9 promoter and identification of its specific binding protein.  

PubMed

Hox genes determine anterior-posterior specificity of an animal body. In mammals, these genes map onto four chromosomal loci in a clustered manner, and their expression is regulated in a coordinated manner according to their chromosomal structure. In the present study, we analysed the Hoxb9 promoter and found that promoter activity in cultured cells is linked to secondary structure formation of promoter DNA. In nuclear extracts, we also detected binding activity specific for secondary-structured DNA. We successfully isolated a candidate gene encoding this specific DNA-binding protein, FBXL10, and demonstrated the effects of the gene product on Hoxb9 promoter activity. Our results suggest that DNA can regulate gene expression by other, non-sequence-specific modes of genetic coding. PMID:18276649

Yamagishi, Takumi; Hirose, Shigehisa; Kondo, Takashi

2008-04-01

216

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

PubMed Central

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

Kendrick, Samantha; Hurley, Laurence H.

2011-01-01

217

Use of electrophoretic mobility to determine the secondary structure of a small antisense RNA.  

PubMed Central

Natural antisense RNAs have stem-loop (hairpin) secondary structures that are important for their function. The sar antisense RNA of phage P22 is unusual: the 3' half of the molecule forms an extensive stem-loop, but potential structures for the 5' half are not predicted to be thermodynamically stable. We devised a novel method to determine the secondary structure of sar RNA by examining the electrophoretic mobility on non-denaturing gels of numerous sar mutants. The results show that the wild-type RNA forms a 5' stem-loop that enhances electrophoretic mobility. All mutations that disrupt the stem of this hairpin decrease mobility of the RNA. In contrast, mutations that change the sequence of the stem without disrupting it (e.g. change G.U to A.U) do not affect mobility. Nearly all mutations in single-stranded regions of the structure also have no effect on mobility. Confirmation of the proposed 5' stem-loop was obtained by constructing and analyzing compensatory double mutants. Combinations of mutations that restore a base-pair of the stem also restore mobility. The genetic phenotypes of sar mutants confirm that the proposed secondary structure is correct and is essential for optimal activity of the antisense RNA in vivo. Images PMID:2057355

Jacques, J P; Susskind, M M

1991-01-01

218

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

219

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

NASA Technical Reports Server (NTRS)

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

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

2001-01-01

220

Influence of secondary ion bombardment on the composition, structure and surface properties of platinum thin films  

NASA Astrophysics Data System (ADS)

Platinum (Pt) thin films were deposited by dual ion beam sputtering (DIBS) techniques on oxidized silicon substrates maintained at ambient temperature. Argon ions with energy of 1 keV and beam current of 15 mA were used to sputter the platinum target. The films during deposition were continuously bombarded by argon from a secondary argon ion source with ion energy of 150 eV and ion current density in the range 100-250 ?A/cm 2. The influence of the secondary ion beam parameters on the grain size, composition and surface morphology of the films were studied. X-ray diffraction (XRD) of all the films showed (1 1 1) orientation with other reflections being absent which is a stable structure for FCC crystals. The grain size of the Pt films prepared by DIBS at ambient temperature were found to be higher than those prepared at higher substrate temperature by low energy plasma sputtering. The presence of Ar impurities in the sputter deposited thin films is known to modify their properties. In this paper we report a method to control the Ar content in the films by secondary Ar ion bombardment of the growing films. The modification of the surface features by secondary ion beam current was studied by scanning tunneling microscope and is also presented in this paper. The surface analysis indicates a decrease in the surface roughness for the Pt films prepared at a secondary ion beam current density of 150 ?A/cm 2.

Balaji, S.; Satyam, P. V.; Lakshminarayanan, V.; Mohan, S.

2004-05-01

221

Hidden Markov models that use predicted secondary structures for fold recognition.  

PubMed

There are many proteins that share the same fold but have no clear sequence similarity. To predict the structure of these proteins, so called "protein fold recognition methods" have been developed. During the last few years, improvements of protein fold recognition methods have been achieved through the use of predicted secondary structures (Rice and Eisenberg, J Mol Biol 1997;267:1026-1038), as well as by using multiple sequence alignments in the form of hidden Markov models (HMM) (Karplus et al., Proteins Suppl 1997;1:134-139). To test the performance of different fold recognition methods, we have developed a rigorous benchmark where representatives for all proteins of known structure are matched against each other. Using this benchmark, we have compared the performance of automatically-created hidden Markov models with standard-sequence-search methods. Further, we combine the use of predicted secondary structures and multiple sequence alignments into a combined method that performs better than methods that do not use this combination of information. Using only single sequences, the correct fold of a protein was detected for 10% of the test cases in our benchmark. Including multiple sequence information increased this number to 16%, and when predicted secondary structure information was included as well, the fold was correctly identified in 20% of the cases. Moreover, if the correct secondary structure was used, 27% of the proteins could be correctly matched to a fold. For comparison, blast2, fasta, and ssearch identifies the fold correctly in 13-17% of the cases. Thus, standard pairwise sequence search methods perform almost as well as hidden Markov models in our benchmark. This is probably because the automatically-created multiple sequence alignments used in this study do not contain enough diversity and because the current generation of hidden Markov models do not perform very well when built from a few sequences. PMID:10373007

Hargbo, J; Elofsson, A

1999-07-01

222

Diffusion ordered NMR spectroscopy for analysis of DNA secondary structural elements  

PubMed Central

Structure determination of secondary DNA structural elements, such as G-quadruplexes, gains an increasing importance as fundamental physiological roles are being associated with the formation of such structures in vivo. A truncated native DNA sequence generally requires further optimization to obtain a candidate with desired NMR properties for structural analysis in solution. The optimum sequence is expected to form one dominant, stable molecular entity in solution with well-resolved NMR peaks. However, DNA sequences are prone to form structures composed of one, two, three or four strands depending on sequence and solution conditions. The thorough characterization of the molecularity (stoichiometry and molecular weight) and appropriate solution conditions for sequences with different modifications traditionally applies analytical techniques that generally do not represent the solution conditions for NMR structure determination. Here we present the application of diffusion ordered NMR spectroscopy as a useful analytical tool for the optimization and analysis of DNA secondary structural elements, specifically, the DNA G-quadruplex structures, including those formed in the human telomeric sequence and in the promoter regions of bcl-2 and c-myc genes. PMID:17570331

Ambrus, Attila; Yang, Danzhou

2007-01-01

223

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

NASA Astrophysics Data System (ADS)

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

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

2014-09-01

224

Sequence-specific sup 1 H NMR assignments and secondary structure of porcine motilin  

SciTech Connect

The solution structure of the 22-residue peptide hormone motilin has been studied by circular dichroism and two-dimensional {sup 1}H nuclear magnetic resonance spectroscopy. Circular dichroism spectra indicate the presence of {alpha}-helical secondary structure in aqueous solution, and the secondary structure can be stabilized with hexafluoro-2-propanol. Sequence-specific assignments of the proton NMR spectrum of porcine motilin in 30% hexafluoro-2-propanol have been made by using two-dimensional NMR techniques. All backbone proton resonances (NH and {alpha}CH) and most of the side-chain resonances have been assigned by using double-quantum-filtered COSY, RELAYED-COSY, and NOESY experiments. Simulations of NOESY cross-peak intensities as a function of mixing time indicate that spin diffusion has a relatively small effect in peptides the size of motilin, thereby allowing the use of long mixing times to confidently make assignments and delineate secondary structure. Sequential {alpha}CH-NH and NH-NH NOESY connectivities were observed over a significant portion of the length of the peptide. The intensities of selected NOESY cross-peaks relative to corresponding diagonal peaks were used to estimate a rotational correlation time of approximately 2.5 ns for the peptide, indicating that the peptide exists as a monomer in solution under the conditions used here.

Khan, N.; Graslund, A.; Shriver, J. (Southern Illinois Univ., Carbondale (USA)); Ehrenberg, A. (Univ. of Stockholm (Sweden))

1990-06-19

225

RDNAnalyzer: A tool for DNA secondary structure prediction and sequence analysis  

PubMed Central

RDNAnalyzer is an innovative computer based tool designed for DNA secondary structure prediction and sequence analysis. It can randomly generate the DNA sequence or user can upload the sequences of their own interest in RAW format. It uses and extends the Nussinov dynamic programming algorithm and has various application for the sequence analysis. It predicts the DNA secondary structure and base pairings. It also provides the tools for routinely performed sequence analysis by the biological scientists such as DNA replication, reverse compliment generation, transcription, translation, sequence specific information as total number of nucleotide bases, ATGC base contents along with their respective percentages and sequence cleaner. RDNAnalyzer is a unique tool developed in Microsoft Visual Studio 2008 using Microsoft Visual C# and Windows Presentation Foundation and provides user friendly environment for sequence analysis. It is freely available. Availability http://www.cemb.edu.pk/sw.html Abbreviations RDNAnalyzer - Random DNA Analyser, GUI - Graphical user interface, XAML - Extensible Application Markup Language. PMID:23055611

Afzal, Muhammad; Shahid, Ahmad Ali; Shehzadi, Abida; Nadeem, Shahid; Husnain, Tayyab

2012-01-01

226

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

PubMed

The complete DNA sequences and secondary structure of the mitochondrial (mt) 16S ribosomal (r) RNA gene were determined for six Ixodes scapularis adults. There were 44 variable nucleotide positions in the 1252 bp sequence alignment. Most (95%) nucleotide alterations did not affect the integrity of the secondary structure of the gene because they either occurred at unpaired positions or represented compensatory changes that maintained the base pairing in helices. A large proportion (75%) of the intraspecific variation in DNA sequence occurred within Domains I, II and VI of the 16S gene. Therefore, several regions within this gene may be highly informative for studies of the population genetics and phylogeography of I. scapularis, a major vector of pathogens of humans and domestic animals in North America. PMID:25444935

Krakowetz, Chantel N; Chilton, Neil B

2015-02-01

227

Efficient sampling of RNA secondary structures from the Boltzmann ensemble of low-energy  

Microsoft Academic Search

We adapt here a surprising technique, the boustrophedon method, to speed up the sampling of RNA secondary structures from\\u000a the Boltzmann low-energy ensemble. This technique is simple and its implementation straight-forward, as it only requires a\\u000a permutation in the order of some operations already performed in the stochastic traceback stage of these algorithms. It nevertheless\\u000a greatly improves their worst-case complexity

Yann Ponty

2007-01-01

228

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

Microsoft Academic Search

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

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

2007-01-01

229

A fast and robust iterative algorithm for prediction of RNA pseudoknotted secondary structures  

PubMed Central

Background Improving accuracy and efficiency of computational methods that predict pseudoknotted RNA secondary structures is an ongoing challenge. Existing methods based on free energy minimization tend to be very slow and are limited in the types of pseudoknots that they can predict. Incorporating known structural information can improve prediction accuracy; however, there are not many methods for prediction of pseudoknotted structures that can incorporate structural information as input. There is even less understanding of the relative robustness of these methods with respect to partial information. Results We present a new method, Iterative HFold, for pseudoknotted RNA secondary structure prediction. Iterative HFold takes as input a pseudoknot-free structure, and produces a possibly pseudoknotted structure whose energy is at least as low as that of any (density-2) pseudoknotted structure containing the input structure. Iterative HFold leverages strengths of earlier methods, namely the fast running time of HFold, a method that is based on the hierarchical folding hypothesis, and the energy parameters of HotKnots V2.0. Our experimental evaluation on a large data set shows that Iterative HFold is robust with respect to partial information, with average accuracy on pseudoknotted structures steadily increasing from roughly 54% to 79% as the user provides up to 40% of the input structure. Iterative HFold is much faster than HotKnots V2.0, while having comparable accuracy. Iterative HFold also has significantly better accuracy than IPknot on our HK-PK and IP-pk168 data sets. Conclusions Iterative HFold is a robust method for prediction of pseudoknotted RNA secondary structures, whose accuracy with more than 5% information about true pseudoknot-free structures is better than that of IPknot, and with about 35% information about true pseudoknot-free structures compares well with that of HotKnots V2.0 while being significantly faster. Iterative HFold and all data used in this work are freely available at http://www.cs.ubc.ca/~hjabbari/software.php. PMID:24884954

2014-01-01

230

Folding path of P5abc RNA involves direct coupling of secondary and tertiary structures  

PubMed Central

Folding mechanisms in which secondary structures are stabilized through the formation of tertiary interactions are well documented in protein folding but challenge the folding hierarchy normally assumed for RNA. However, it is increasingly clear that RNA could fold by a similar mechanism. P5abc, a small independently folding tertiary domain of the Tetrahymena thermophila group I ribozyme, is known to fold by a secondary structure rearrangement involving helix P5c. However, the extent of this rearrangement and the precise stage of folding that triggers it are unknown. We use experiments and simulations to show that the P5c helix switches to the native secondary structure late in the folding pathway and is directly coupled to the formation of tertiary interactions in the A-rich bulge. P5c mutations show that the switch in P5c is not rate-determining and suggest that non-native interactions in P5c aid folding rather than impede it. Our study illustrates that despite significant differences in the building blocks of proteins and RNA, there may be common ways in which they self-assemble. PMID:22641849

Koculi, Eda; Cho, Samuel S.; Desai, Ravi; Thirumalai, D.; Woodson, Sarah A.

2012-01-01

231

Multi-class support vector machines for protein secondary structure prediction.  

PubMed

The solution of binary classification problems using the Support Vector Machine (SVM) method has been well developed. Though multi-class classification is typically solved by combining several binary classifiers, recently, several multi-class methods that consider all classes at once have been proposed. However, these methods require resolving a much larger optimization problem and are applicable to small datasets. Three methods based on binary classifications: one-against-all (OAA), one-against-one (OAO), and directed acyclic graph (DAG), and two approaches for multi-class problem by solving one single optimization problem, are implemented to predict protein secondary structure. Our experiments indicate that multi-class SVM methods are more suitable for protein secondary structure (PSS) prediction than the other methods, including binary SVMs, because their capacity to solve an optimization problem in one step. Furthermore, in this paper, we argue that it is feasible to extend the prediction accuracy by adding a second-stage multi-class SVM to capture the contextual information among secondary structural elements and thereby further improving the accuracies. We demonstrate that two-stage SVMs perform better than single-stage SVM techniques for PSS prediction using two datasets and report a maximum accuracy of 79.5%. PMID:15706536

Nguyen, Minh N; Rajapakse, Jagath C

2003-01-01

232

Identifying the Tertiary Fold of Small Proteins with Different Topologies from Sequence and Secondary Structure using the Genetic Algorithm and Extended Criteria Specific for Strand Regions  

Microsoft Academic Search

Grid-free protein folding simulations based on sequence and secondary structure knowledge (using mostly experimentally determined secondary structure information but also analysing results from secondary structure predictions) were investigated using the genetic algorithm, a backbone representation, and standard dihedral angular conformations. Optimal structures are selected according to basic protein building principles. Having previously applied this approach to proteins with helical topology,

Thomas Dandekar; Patrick Argos

1996-01-01

233

[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

2011-01-01

234

Peptide Length Determines Equilibrium Secondary Structure in Protein-Analogous Micelles  

NASA Astrophysics Data System (ADS)

This work seeks improved bottom-up design of bioinspired materials built from peptide-amphiphiles, which are a class of bioconjugates whereby a biofunctional peptide is covalently attached to a hydrophobic moiety that drives self-assembly in aqueous solution. Specifically, this work highlights the importance of peptide length (i.e. molecular weight) in determining the equilibrium secondary structure of the peptide as well as the self-assembled (i.e. micelle) geometry. Peptides used here repeat a seven-amino acid sequence between one and four times to vary peptide length while maintaining similar peptide-peptide interactions. Without a hydrophobic tail, these peptides all exhibit a combination of random coil and ?-helical structure. Upon self-assembly, however, short peptides are prone to ?-sheet structure and cylindrical geometry while longer peptides remain helical in spheroidal micelles. The transition to ?-sheets in short peptides is kinetic, whereby amphiphiles first self-assemble with helical peptide structure, then overcome an activation barrier as they transition to their equilibrium ?-sheet structure at a rate that depends on both temperature and ionic strength. These results identify peptide length as an important control over equilibrium peptide secondary structure and micelle geometry. Furthermore, the kinetic nature of the helix-to-sheet transition opens the door for shape-changing bioinspired materials with tunable conversion rates.

Tirrell, Matthew; Marullo, Rachel; Kastantin, Mark

2013-03-01

235

Peptide Contour Length Determines Equilibrium Secondary Structure in Protein-Analogous Micelles  

PubMed Central

This work advances bottom-up design of bioinspired materials built from peptide-amphiphiles, which are a class of bioconjugates in which a biofunctional peptide is covalently attached to a hydrophobic moiety that drives self-assembly in aqueous solution. Specifically, this work highlights the importance of peptide contour length in determining the equilibrium secondary structure of the peptide as well as the self-assembled (i.e. micelle) geometry. Peptides used here repeat a seven-amino acid sequence between one and four times to vary peptide contour length while maintaining similar peptide-peptide interactions. Without a hydrophobic tail, these peptides all exhibit a combination of random coil and ?-helical structure. Upon self-assembly in the crowded environment of a micellar corona, however, short peptides are prone to ?-sheet structure and cylindrical micelle geometry while longer peptides remain helical in spheroidal micelles. The transition to ?-sheets in short peptides is rapid, whereby amphiphiles first self-assemble with ?-helical peptide structure, then transition to their equilibrium ?-sheet structure at a rate that depends on both temperature and ionic strength. These results identify peptide contour length as an important control over equilibrium peptide secondary structure and micelle geometry. Furthermore, the time-dependent nature of the helix-to-sheet transition opens the door for shape-changing bioinspired materials with tunable conversion rates. PMID:23794370

Marullo, Rachel; Kastantin, Mark; Drews, Laurie B.; Tirrell, Matthew

2014-01-01

236

An automatic method involving cluster analysis of secondary structures for the identification of domains in proteins.  

PubMed Central

With a growing number of structures available in the Brookhaven Protein Data Bank, automatic methods for domain identification are required for the construction of databases. Domains are considered to be clusters of secondary structure elements. Thus, helices and strands are first clustered using intersecondary structural distances between C alpha positions, and dendrograms based on this distance measure are used to identify domains. Individual domains are recognized by a disjoint factor, which enables the automatic identification and classification into disjoint, interacting, and conjoint domains. Application to a database of 83 protein families and 18 unique structures shows that the approach provides an effective delineation of boundaries and identifies those proteins that can be considered as a single domain. A quantitative estimate of the interaction between domains has been proposed. The database of protein domains is a useful tool for understanding protein folding, for recognizing protein folds, and for understanding structure-activity relationships. PMID:7795532

Sowdhamini, R.; Blundell, T. L.

1995-01-01

237

Using compensatory base change analysis of internal transcribed spacer 2 secondary structures to identify three new species in Paramacrobiotus (Tardigrada)  

Microsoft Academic Search

Species within the tardigrade genus Paramacrobiotus could be distinguished via an analysis of internal transcribed spacer 2 (ITS2) secondary structures. Sequences of P. richtersi and four populations previously treated under provisional names (Paramacrobiotus ‘richtersi group’ 1 to 4) from different continents were determined and annotated, and their secondary structures were predicted. A\\u000a tree based on a combined sequence-structure alignment was

Ralph O. Schill; Frank Förster; Thomas Dandekar; Matthias Wolf

2010-01-01

238

Super-secondary structure of oligopeptide aggregates in an organic solvent  

NASA Astrophysics Data System (ADS)

For N-acetyl-L-glutamic acid hexamer ?,?-benzyl ester (A6Z), synthesized by a stepwise procedure, the shape and size of an aggregate formed in dioxane has been investigated in connection with the super-secondary structure of oligopeptides by the SANS method. The results are summarized as follows. An A6Z aggregate in dioxane has a cylinder-like shape having a radius of 13 Å and a height of 135 Å, and the aggregation number is 36. Probably, the cylinder aggregate has a stacking structure of the A6Z ?-sheets.

Hirata, H.; Yuuki, H.; Ogasawara, T.; Taga, K.; Yoshida, T.; Okabayashi, H.; Furusaka, M.; Kawasaki, K.; Kawakatsu, T.; Hirai, M.

1995-02-01

239

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. PMID:23435231

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

2013-01-01

240

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

2012-11-12

241

Ebola virus VP30-mediated transcription is regulated by RNA secondary structure formation.  

PubMed

The nucleocapsid protein VP30 of Ebola virus (EBOV), a member of the Filovirus family, is known to act as a transcription activator. By using a reconstituted minigenome system, the role of VP30 during transcription was investigated. We could show that VP30-mediated transcription activation is dependent on formation of a stem-loop structure at the first gene start site. Destruction of this secondary structure led to VP30-independent transcription. Analysis of the transcription products of bicistronic minigenomes with and without the ability to form the secondary structure at the first transcription start signal revealed that transcription initiation at the first gene start site is a prerequisite for transcription of the second gene, independent of the presence of VP30. When the transcription start signal of the second gene was exchanged with the transcription start signal of the first gene, transcription of the second gene also was regulated by VP30, indicating that the stem-loop structure of the first transcription start site acts autonomously and independently of its localization on the RNA genome. Our results suggest that VP30 regulates a very early step of EBOV transcription, most likely by inhibiting pausing of the transcription complex at the RNA structure of the first transcription start site. PMID:12163572

Weik, Michael; Modrof, Jens; Klenk, Hans-Dieter; Becker, Stephan; Mühlberger, Elke

2002-09-01

242

Special interaction of anionic phosphatidic acid promotes high secondary structure in tetrameric potassium channel.  

PubMed

Anionic phosphatidic acid (PA) has been shown to stabilize and bind stronger than phosphatidylglycerol via electrostatic and hydrogen bond interaction with the positively charged residues of potassium channel KcsA. However, the effects of these lipids on KcsA folding or secondary structure are not clear. In this study, the secondary structure analyses of KcsA potassium channel was carried out using circular dichroism spectroscopy. It was found that PA interaction leads to increases in ?-helical and ?-sheet content of KcsA protein. In PA, KcsA ?-helical structure was further stabilized by classical membrane-active cosolvent trifluoroethanol followed by reduction in the ?-sheet content indicating cooperative transformation from the ?-sheet to an ?-helical structure. The data further uncover the role of anionic PA in KcsA folding and provide mechanism by which strong hydrogen bonds/electrostatic interaction among PA headgroup and basic residues on lipid binding domains may induce high helical structure thereby altering the protein folding and increasing the stability of tetrameric assembly. PMID:25024119

Raja, Mobeen

2014-08-01

243

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

ERIC Educational Resources Information Center

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

Ellerbrock, Cheryl R.; Kiefer, Sarah M.

2013-01-01

244

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

SciTech Connect

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

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

2005-01-01

245

Secondary structure spatial conformation footprint: a novel method for fast protein structure comparison and classification  

Microsoft Academic Search

BACKGROUND: Recently a new class of methods for fast protein structure comparison has emerged. We call the methods in this class projection methods as they rely on a mapping of protein structure into a high-dimensional vector space. Once the mapping is done, the structure comparison is reduced to distance computation between corresponding vectors. As structural similarity is approximated by distance

Elena Zotenko; Dianne P O'Leary; Teresa M Przytycka

2006-01-01

246

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

PubMed Central

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

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

2004-01-01

247

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

PubMed Central

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

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

2014-01-01

248

Secondary-structure preferences of force fields for proteins evaluated by generalized-ensemble simulations  

NASA Astrophysics Data System (ADS)

Secondary-structure forming tendencies are examined for six well-known protein force fields: AMBER94, AMBER96, AMBER99, CHARMM22, OPLS-AA/L, and GROMOS96. We performed generalized-ensemble molecular dynamics simulations of two peptides. One of these peptides is C-peptide of ribonuclease A, and the other is the C-terminal fragment from the B1 domain of streptococcal protein G. The former is known to form ?-helix structure and the latter ?-hairpin structure by experiments. The simulation results revealed significant differences of the secondary-structure forming tendencies among the force fields. Of the six force fields, the results of AMBER99 and CHARMM22 were in accord with experiments for C-peptide. For G-peptide, on the other hand, the results of OPLS-AA/L and GROMOS96 were most consistent with experiments. Therefore, further improvements on the force fields are necessary for studying the protein folding problem from the first principles, in which a single force field can be used for all cases.

Yoda, Takao; Sugita, Yuji; Okamoto, Yuko

2004-12-01

249

Secondary structures of proteins adsorbed onto aluminum hydroxide: Infrared spectroscopic analysis of proteins from low solution concentrations  

Microsoft Academic Search

Comparative studies of the secondary structures of six model proteins, adsorbed onto aluminum hydroxide gel (Alhydrogel) or in aqueous solution, were carried out by Fourier transform infrared (FTIR) spectroscopy. The analysis of high-quality spectra of all six model proteins, with a broad range of secondary structure compositions, obtained at 15mg\\/ml by the conventional method and at 0.5 and 1.0mg\\/ml adsorbed

Aichun Dong; LaToya S. Jones; Bruce A. Kerwin; Sampath Krishnan; John F. Carpenter

2006-01-01

250

Enhancement of accuracy and efficiency for RNA secondary structure prediction by sequence segmentation and MapReduce  

PubMed Central

Background Ribonucleic acid (RNA) molecules play important roles in many biological processes including gene expression and regulation. Their secondary structures are crucial for the RNA functionality, and the prediction of the secondary structures is widely studied. Our previous research shows that cutting long sequences into shorter chunks, predicting secondary structures of the chunks independently using thermodynamic methods, and reconstructing the entire secondary structure from the predicted chunk structures can yield better accuracy than predicting the secondary structure using the RNA sequence as a whole. The chunking, prediction, and reconstruction processes can use different methods and parameters, some of which produce more accurate predictions than others. In this paper, we study the prediction accuracy and efficiency of three different chunking methods using seven popular secondary structure prediction programs that apply to two datasets of RNA with known secondary structures, which include both pseudoknotted and non-pseudoknotted sequences, as well as a family of viral genome RNAs whose structures have not been predicted before. Our modularized MapReduce framework based on Hadoop allows us to study the problem in a parallel and robust environment. Results On average, the maximum accuracy retention values are larger than one for our chunking methods and the seven prediction programs over 50 non-pseudoknotted sequences, meaning that the secondary structure predicted using chunking is more similar to the real structure than the secondary structure predicted by using the whole sequence. We observe similar results for the 23 pseudoknotted sequences, except for the NUPACK program using the centered chunking method. The performance analysis for 14 long RNA sequences from the Nodaviridae virus family outlines how the coarse-grained mapping of chunking and predictions in the MapReduce framework exhibits shorter turnaround times for short RNA sequences. However, as the lengths of the RNA sequences increase, the fine-grained mapping can surpass the coarse-grained mapping in performance. Conclusions By using our MapReduce framework together with statistical analysis on the accuracy retention results, we observe how the inversion-based chunking methods can outperform predictions using the whole sequence. Our chunk-based approach also enables us to predict secondary structures for very long RNA sequences, which is not feasible with traditional methods alone. PMID:24564983

2013-01-01

251

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

252

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 PMID:6589622

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

1984-01-01

253

Secondary Structure Preferences of Mn2+ Binding Sites in Bacterial Proteins  

PubMed Central

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

Khrustaleva, Tatyana Aleksandrovna

2014-01-01

254

In Silico Analysis of ?-Galactosidases Primary and Secondary Structure in relation to Temperature Adaptation  

PubMed Central

?-D-Galactosidases (EC 3.2.1.23) hydrolyze the terminal nonreducing ?-D-galactose residues in ?-D-galactosides and are ubiquitously present in all life forms including extremophiles. Eighteen microbial ?-galactosidase protein sequences, six each from psychrophilic, mesophilic, and thermophilic microbes, were analyzed. Primary structure reveals alanine, glycine, serine, and arginine to be higher in psychrophilic ?-galactosidases whereas valine, glutamine, glutamic acid, phenylalanine, threonine, and tyrosine are found to be statistically preferred by thermophilic ?-galactosidases. Cold active ?-galactosidase has a strong preference towards tiny and small amino acids, whereas high temperature inhabitants had higher content of basic and aromatic amino acids. Thermophilic ?-galactosidases have higher percentage of ?-helix region responsible for temperature tolerance while cold loving ?-galactosidases had higher percentage of sheet and coil region. Secondary structure analysis revealed that charged and aromatic amino acids were significant for sheet region of thermophiles. Alanine was found to be significant and high in the helix region of psychrophiles and valine counters in thermophilic ?-galactosidase. Coil region of cold active ?-galactosidase has higher content of tiny amino acids which explains their high catalytic efficiency over their counterparts from thermal habitat. The present study has revealed the preference or prevalence of certain amino acids in primary and secondary structure of psychrophilic, mesophilic, and thermophilic ?-galactosidase. PMID:24790757

Kumar, Vijay; Sharma, Nikhil; Bhalla, Tek Chand

2014-01-01

255

Secondary structure of corona proteins determines the cell surface receptors used by nanoparticles.  

PubMed

Nanoparticles used for biological and biomedical applications encounter a host of extracellular proteins. These proteins rapidly adsorb onto the nanoparticle surface, creating a protein corona. Poly(ethylene glycol) can reduce, but not eliminate, the nonspecific adsorption of proteins. As a result, the adsorbed proteins, rather than the nanoparticle itself, determine the cellular receptors used for binding, the internalization mechanism, the intracellular transport pathway, and the subsequent immune response. Using fluorescence microscopy and flow cytometry, we first characterize a set of polystyrene nanoparticles in which the same adsorbed protein, bovine serum albumin, leads to binding to two different cell surface receptors: native albumin receptors and scavenger receptors. Using a combination of circular dichroism spectroscopy, isothermal titration calorimetry, and fluorescence spectroscopy, we demonstrate that the secondary structure of the adsorbed bovine serum albumin protein controls the cellular receptors used by the protein-nanoparticle complexes. These results show that protein secondary structure is a key parameter in determining the cell surface receptor used by a protein-nanoparticle complex. We expect this link between protein structure and cellular outcomes will provide a molecular basis for the design of nanoparticles for use in biological and biomedical applications. PMID:24779411

Fleischer, Candace C; Payne, Christine K

2014-12-11

256

Secondary structure preferences of mn (2+) binding sites in bacterial proteins.  

PubMed

3D structures of proteins with coordinated Mn(2+) ions from bacteria with low, average, and high genomic GC-content have been analyzed (149 PDB files were used). Major Mn(2+) binders are aspartic acid (6.82% of Asp residues), histidine (14.76% of His residues), and glutamic acid (3.51% of Glu residues). We found out that the motif of secondary structure "beta strand-major binder-random coil" is overrepresented around all the three major Mn(2+) binders. That motif may be followed by either alpha helix or beta strand. Beta strands near Mn(2+) binding residues should be stable because they are enriched by such beta formers as valine and isoleucine, as well as by specific combinations of hydrophobic and hydrophilic amino acid residues characteristic to beta sheet. In the group of proteins from GC-rich bacteria glutamic acid residues situated in alpha helices frequently coordinate Mn(2+) ions, probably, because of the decrease of Lys usage under the influence of mutational GC-pressure. On the other hand, the percentage of Mn(2+) sites with at least one amino acid in the "beta strand-major binder-random coil" motif of secondary structure (77.88%) does not depend on genomic GC-content. PMID:24778647

Khrustaleva, Tatyana Aleksandrovna

2014-01-01

257

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

NASA Astrophysics Data System (ADS)

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.

2012-10-01

258

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

2012-11-01

259

5' and 3' untranslated regions of pestivirus genome: primary and secondary structure analyses.  

PubMed Central

Within the conserved 5' untranslated region (UTR) of the pestivirus genome three highly variable regions were identified. Preceding the polyprotein start codon, multiple cryptic AUG codons and several small open reading frames are characteristic for all the five pestiviruses. Inspection of the context of AUGs revealed that the polyprotein initiation AUG of pestivirus has a weak context for efficient translation initiation. The most favorable context was found in two of the cryptic AUGs. Two oligopyrimidine-rich tracts upstream to the conserved either cryptic or authentic AUG in the 5'-UTR of pestivirus were identified and 83.3% of their nucleotide sequences are complementary to the consensus sequence at the 3' terminus of eucaryotic 18S rRNA. A secondary structure model for the 5'-UTR of pestivirus was predicted. Nucleotide sequence comparison among five pestiviruses led to the identification of a variable region and a conserved region in the 3'-UTR. A deletion of 41 nucleotides was found within the variable region in Osloss. A secondary structure model for the 3'-UTR was also predicted. The structural similarity of the 5'-UTR between pestiviruses and picornaviruses and hepatitis C viruses was demonstrated and the possible implications of features of the 5' and 3'-UTR of pestiviruses are discussed. PMID:8388102

Deng, R; Brock, K V

1993-01-01

260

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

SciTech Connect

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

Remerowski, M.L.; Glaser, S.J.; Drobny, G.P.; Sieker, L.C. (Univ. of Washington, Seattle (USA)); Samy, T.S.A. (Univ. of Miami, FL (USA))

1990-09-11

261

Structures of RNA Complexes with the Escherichia coli RNA Pyrophosphohydrolase RppH Unveil the Basis for Specific 5'-End-dependent mRNA Decay.  

PubMed

5'-End-dependent RNA degradation impacts virulence, stress responses, and DNA repair in bacteria by controlling the decay of hundreds of mRNAs. The RNA pyrophosphohydrolase RppH, a member of the Nudix hydrolase superfamily, triggers this degradation pathway by removing pyrophosphate from the triphosphorylated RNA 5' terminus. Here, we report the x-ray structures of Escherichia coli RppH (EcRppH) in apo- and RNA-bound forms. These structures show distinct conformations of EcRppH·RNA complexes on the catalytic pathway and suggest a common catalytic mechanism for Nudix hydrolases. EcRppH interacts with RNA by a bipartite mechanism involving specific recognition of the 5'-terminal triphosphate and the second nucleotide, thus enabling discrimination against mononucleotides as substrates. The structures also reveal the molecular basis for the preference of the enzyme for RNA substrates bearing guanine in the second position by identifying a protein cleft in which guanine interacts with EcRppH side chains via cation-? contacts and hydrogen bonds. These interactions explain the modest specificity of EcRppH at the 5' terminus and distinguish the enzyme from the highly selective RppH present in Bacillus subtilis. The divergent means by which RNA is recognized by these two functionally and structurally analogous enzymes have important implications for mRNA decay and the regulation of protein biosynthesis in bacteria. PMID:25657011

Vasilyev, Nikita; Serganov, Alexander

2015-04-10

262

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

PubMed Central

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

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

2014-01-01

263

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

264

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

PubMed

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. PMID:18625613

James, Laurie; Sargueil, Bruno

2008-08-01

265

Saccharomyces cerevisiae U1 small nuclear RNA secondary structure contains both universal and yeast-specific domains.  

PubMed Central

The five small nuclear RNAs (snRNAs) involved in mammalian pre-mRNA splicing (U1, U2, U4, U5, and U6) are well conserved in length, sequence, and especially secondary structure. These five snRNAs from Saccharomyces cerevisiae show notable size and sequence differences from their metazoan counterparts. This is most striking for the large S. cerevisiae U1 and U2 snRNAs, for which no secondary structure models currently exist. Because of the importance of U1 snRNA in the early steps of "spliceosome" assembly, we wanted to compare the highly conserved secondary structure of metazoan U1 snRNA (approximately 165 nucleotides) with that of S. cerevisiae U1 snRNA (568 nucleotides). To this end, we have cloned and sequenced the U1 gene from two other yeast species possessing large U1 RNAs. Using computer-derived structure predictions, phylogenetic comparisons, and structure probing, we have arrived at a secondary structure model for S. cerevisiae U1 snRNA. The results show that most elements of higher eukaryotic U1 snRNA secondary structure are conserved in S. cerevisiae. The hundreds of "extra" nucleotides of yeast U1 RNA, also highly structured, suggest that large insertions and/or deletions have occurred during the evolution of the U1 gene. Images PMID:2405391

Kretzner, L; Krol, A; Rosbash, M

1990-01-01

266

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

PubMed

Laser Raman spectroscopy of the cowpea chlorotic mottle virus (CCMV) in native (pH 5.0) and partially swollen (pH 7.5) states reveals the presence of small percentages of protonated adenine (less than 15%) and cytosine (less than 7%) bases in the encapsidated RNA molecule of the native virion. The protonated bases are titrated with pH-induced swelling of the virus. Titration of putative COOH groups of aspartic and glutamic side chains of the virion subunit cannot be detected over the same pH range, which suggests that carboxyl anions (CO-2) and protonated bases are both available at pH 5 to stabilize the ribonucleoprotein particles by electrostatic interactions. The highly (95%) ordered secondary structure of encapsidated RNA may undergo a small additional increase (less than 3%) in ordered structure with release from the virion, suggesting at most a marginal structure-distorting influence from protein contacts in the native particle. The Raman spectra of the virion are also compared by difference spectroscopy with spectra of capsids (empty shells devoid of RNA), subunit dimers, and protein-free RNA. The results indicate that the subunit structure is altered by the release of RNA from the virion, as well as by the swelling of the virion. Amino acid residues and protein secondary structures that are affected in these in vitro assembly and disassembly processes are identified from their characteristic Raman lines. Two classes of cysteinyl SH groups, solvent exposed and solvent protected, are revealed for the capsid and virion subunit.(ABSTRACT TRUNCATED AT 250 WORDS) PMID:6487602

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

1984-09-11

267

Accounting for solvent accessibility and secondary structure in protein phylogenetics is clearly beneficial.  

PubMed

Amino acid substitution models are essential to most methods to infer phylogenies from protein data. These models represent the ways in which proteins evolve and substitutions accumulate along the course of time. It is widely accepted that the substitution processes vary depending on the structural configuration of the protein residues. However, this information is very rarely used in phylogenetic studies, though the 3-dimensional structure of dozens of thousands of proteins has been elucidated. Here, we reinvestigate the question in order to fill this gap. We use an improved estimation methodology and a very large database comprising 1471 nonredundant globular protein alignments with structural annotations to estimate new amino acid substitution models accounting for the secondary structure and solvent accessibility of the residues. These models incorporate a confidence coefficient that is estimated from the data and reflects the reliability and usefulness of structural annotations in the analyzed sequences. Our results with 300 independent test alignments show an impressive likelihood gain compared with standard models such as JTT or WAG. Moreover, the use of these models induces significant topological changes in the inferred trees, which should be of primary interest to phylogeneticists. Our data, models, and software are available for download from http://atgc.lirmm.fr/phyml-structure/. PMID:20525635

Le, Si Quang; Gascuel, Olivier

2010-05-01

268

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

2013-01-01

269

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

270

Determination of penetratin secondary structure in live cells with Raman microscopy.  

PubMed

Cell penetrating peptides (CPPs) have attracted recent interest as drug delivery tools, although the mechanisms by which CPPs are internalized by cells are not well-defined. Here, we report a new experimental approach for the detection and secondary structure determination of CPPs in live cells using Raman microscopy with heavy isotope labeling of the peptide. As a first demonstration of principle, penetratin, a 16-residue CPP derived from the Antennapedia homeodomain protein of Drosophila, was measured in single, living melanoma cells. Carbon-13 labeling of the Phe residue of penetratin was used to shift the intense aromatic ring-breathing vibrational mode from 1003 to 967 cm(-1), thereby enabling the peptide to be traced in cells. Difference spectroscopy and principal components analysis (PCA) were used independently to resolve the Raman spectrum of the peptide from the background cellular Raman signals. On the basis of the position of the amide I vibrational band in the Raman spectra, the secondary structure of the peptide was found to be mainly random coil and beta-strand in the cytoplasm, and possibly assembling as beta-sheets in the nucleus. The rapid entry and almost uniform cellular distribution of the peptide, as well as the lack of correlation between peptide and lipid Raman signatures, indicated that the mechanism of internalization under the conditions of study was probably nonendocytotic. This experimental approach can be used to study a wide variety of CPPs as well as other classes of peptides in living cells. PMID:20041639

Ye, Jing; Fox, Sara A; Cudic, Mare; Rezler, Evonne M; Lauer, Janelle L; Fields, Gregg B; Terentis, Andrew C

2010-01-27

271

Influence of microenvironment and liposomal formulation on secondary structure and bilayer interaction of lysozyme.  

PubMed

The conformation of peptide and protein drugs in various microenvironments and the interaction with drug carriers such as liposomes are of considerable interest. In this study the influence of microenvironments such as pH, salt concentration, and surface charge on the secondary structure of a model protein, lysozyme, either in solution or entrapped in liposomes with various molar ratios of phosphatidylcholine (PC):cholesterol (Chol) was investigated. It was found that entrapment efficiency was more pronounced in negatively charged liposomes than in non-charged liposomes, which was independent of Chol content and pH of hydration medium. The occurrence of aggregation, decrease in zeta potential, and alteration of 31P NMR chemical shift of negatively charged lysozyme liposomes compared to blank liposomes suggested that the electrostatic interaction plays a major role in protein-lipid binding. Addition of sodium chloride could impair the neutralizing ability of positively charged lysozyme on negatively charged membrane via chloride counterion binding. Neither lysozyme in various buffer solutions with sodium chloride nor that entrapped in liposomes showed any significant change in their secondary structures. However, significant decrease in alpha-helical content of lysozyme in non-charged liposomes at higher pH and salt concentrations was discovered. PMID:19880295

Witoonsaridsilp, Wasu; Panyarachun, Busaba; Sarisuta, Narong; Müller-Goymann, Christel C

2010-02-01

272

Valence band structure in boron-zinc oxide films characterized by secondary electron emission  

NASA Astrophysics Data System (ADS)

Properties of the valence band structure in boron-zinc oxide (BZO) films were investigated using the secondary electron emission due to the Auger neutralization of helium ions, with respect to the application of BZO films to the development of solar cells, in which the conductivity of the BZO films plays a critical role in improving cell performance. The characteristic energy ?0 corresponding to the peak density of states in the valence band showed that BZO film prepared with a 3000 SCCM B2H6 gas flow rate (SCCM denotes cubic centimeters per minute at standard temperature and pressure) had a shallow characteristic energy ?0 = 5 eV, whereas film without boron doping had a deep characteristic energy ?0 = 8.2 eV, suggesting that a high concentration of boron impurity in BZO films might enhance the transition of electrons and holes through the bandgap from the valence to the conduction band in zinc oxide crystals, thereby improving the conductivity of the film. The measurement method developed here demonstrates that the secondary electron emission is very useful in the determination of the band structure in various synthetic films.

Uhm, Han S.; Choi, Joon H.; Yoo, Ha J.; Kwon, Gi C.; Choi, Eun H.

2012-03-01

273

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

E-print Network

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

Claus O Wilke; Richard E Lenski; Christoph Adami

2003-02-18

274

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

PubMed

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

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

2015-04-30

275

Secondary-Structure Design of Proteins by a Backbone Torsion Energy  

NASA Astrophysics Data System (ADS)

We propose a new backbone-torsion-energy term in the force field for protein systems. This torsion-energy term is represented by a double Fourier series in two variables, the backbone dihedral angles ? and \\psi. It gives a natural representation of the torsion energy in the Ramachandran space in the sense that any two-dimensional energy surface periodic in both ? and \\psi can be expanded by the double Fourier series. We can then easily control secondary-structure-forming tendencies by modifying the torsion-energy surface. For instance, we can increase/decrease the ?-helix-forming tendencies by lowering/raising the torsion-energy surface in the ?-helix region and likewise increase/decrease the ?-sheet-forming tendencies by lowering/raising the surface in the ?-sheet region in the Ramachandran space. We applied our approach to AMBER parm94 and AMBER parm96 force fields and demonstrated that our modifications of the torsion-energy terms resulted in the expected changes of secondary-structure-forming tendencies by performing folding simulations of ?-helical and ?-hairpin peptides.

Sakae, Yoshitake; Okamoto, Yuko

2006-05-01

276

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., Jr.

1993-06-01

277

SeqFold: Genome-scale reconstruction of RNA secondary structure integrating high-throughput sequencing data  

PubMed Central

We present an integrative approach, SeqFold, that combines high-throughput RNA structure profiling data with computational prediction for genome-scale reconstruction of RNA secondary structures. SeqFold transforms experimental RNA structure information into a structure preference profile (SPP) and uses it to select stable RNA structure candidates representing the structure ensemble. Under a high-dimensional classification framework, SeqFold efficiently matches a given SPP to the most likely cluster of structures sampled from the Boltzmann-weighted ensemble. SeqFold is able to incorporate diverse types of RNA structure profiling data, including parallel analysis of RNA structure (PARS), selective 2?-hydroxyl acylation analyzed by primer extension sequencing (SHAPE-Seq), fragmentation sequencing (FragSeq) data generated by deep sequencing, and conventional SHAPE data. Using the known structures of a wide range of mRNAs and noncoding RNAs as benchmarks, we demonstrate that SeqFold outperforms or matches existing approaches in accuracy and is more robust to noise in experimental data. Application of SeqFold to reconstruct the secondary structures of the yeast transcriptome reveals the diverse impact of RNA secondary structure on gene regulation, including translation efficiency, transcription initiation, and protein-RNA interactions. SeqFold can be easily adapted to incorporate any new types of high-throughput RNA structure profiling data and is widely applicable to analyze RNA structures in any transcriptome. PMID:23064747

Ouyang, Zhengqing; Snyder, Michael P.; Chang, Howard Y.

2013-01-01

278

Structural changes of eIF4E upon binding to the mRNA 5' monomethylguanosine and trimethylguanosine Cap.  

PubMed

Recognition of the 5' cap by the eukaryotic initiation factor 4E (eIF4E) is the rate-limiting step in the ribosome recruitment to mRNAs. The regular cap consists of 7-monomethylguanosine (MMG) linked by a 5'-5' triphosphate bridge to the first transcribed nucleoside, while some primitive eukaryotes possess a N (2), N (2),7-trimethylguanosine (TMG) cap structure as a result of trans splicing. Mammalian eIF4E is highly specific to the MMG form of the cap in terms of association constants and thermodynamic driving force. We have investigated conformational changes of eIF4E induced by interaction with two cap analogues, 7-methyl-GTP and N (2), N (2),7-trimethyl-GTP. Hydrogen-deuterium exchange and electrospray mass spectrometry were applied to probe local dynamics of murine eIF4E in the apo and cap-bound forms. The data show that the cap binding induces long-range conformational changes in the protein, not only in the cap-binding pocket but also in a distant region of the 4E-BP/eIF4G binding site. Formation of the complex with 7-methyl-GTP makes the eIF4E structure more compact, while binding of N (2), N (2),7-trimethyl-GTP leads to higher solvent accessibility of the protein backbone in comparison with the apo form. The results suggest that the additional double methylation at the N (2)-amino group of the cap causes sterical effects upon binding to mammalian eIF4E which influence the overall solution dynamics of the protein, thus precluding formation of a tight complex. PMID:18220364

Rutkowska-Wlodarczyk, Izabela; Stepinski, Janusz; Dadlez, Michal; Darzynkiewicz, Edward; Stolarski, Ryszard; Niedzwiecka, Anna

2008-03-01

279

Graphical exploratory data analysis of RNA secondary structure dynamics predicted by the massively parallel genetic algorithm.  

PubMed

Studies indicate that RNA may enter intermediate and multiple conformational states, which may impact gene expression and molecular function. It is known that the biologically functional states of RNA molecules may not correspond to their minimum energy conformations, that kinetic barriers may trap the molecule in a local minimum, that folding often occurs during transcription, and that cases exist in which a molecule will transition between one or more functional conformations. Thus, methods for simulating the folding pathway and dynamic behavior of an RNA molecule are important for the prediction of RNA structure and its associated functions. We have developed several data mining techniques guided by interactive visualization tools associated with our massively parallel genetic algorithm for RNA/DNA secondary structure prediction, MPGAfold, and StructureLab analysis workbench. Most of the methods and tools are also applicable to dynamic programming algorithm (DPA) folding data analysis. When applied to MPGAfold results these methodologies are used to determine the significant intermediate and final structures associated with co-transcriptional and full length RNA folding. Since the genetic algorithm is essentially stochastic, multiple runs are required to develop a consensus understanding of an RNA structure. The interactive visualizations facilitate interpretation of results from sequential or full length individual MPGAfold runs, final results of multiple folding runs, including multiple population sizes, and the results from multiple RNA sequences of one family. This paper describes several of these techniques and shows how they are used to help solve this highly combinatoric problem. PMID:16725358

Shapiro, Bruce A; Kasprzak, Wojciech; Grunewald, Calvin; Aman, Javed

2006-12-01

280

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. PMID:22689765

Rose, Dominic; Backofen, Rolf

2012-01-01

281

Silencing efficacy prediction: a retrospective study on target mRNA features  

PubMed Central

Post-transcriptional gene silencing is a widely used method to suppress gene expression. Unfortunately only a portion of siRNAs do successfully reduce gene expression. Target mRNA secondary structures and siRNA-mRNA thermodynamic features are believed to contribute to the silencing activity. However, there is still an open discussion as to what determines siRNA efficacy. In this retrospective study, we analysed the target accessibility comparing very high (VH) compared with low (L) efficacy siRNA sequences obtained from the siRecords Database. We determined the contribution of mRNA target local secondary structures on silencing efficacy. Both the univariable and the multivariable logistic regression evidenced no relationship between siRNA efficacy and mRNA target secondary structures. Moreover, none of the thermodynamic and sequence-base parameters taken into consideration (H-b index, ?G°overall, ?G°duplex, ?G°break-target and GC%) was associated with siRNA efficacy. We found that features believed to be predictive of silencing efficacy are not confirmed to be so when externally evaluated in a large heterogeneous sample. Although it was proposed that silencing efficacy could be influenced by local target accessibility we show that this could be not generalizable because of the diversity of experimental setting that may not be representative of biological systems especially in view of the many local protein factors, usually not taken into consideration, which could hamper the silencing process. PMID:25702798

Pascut, Devis; Bedogni, Giorgio; Tiribelli, Claudio

2015-01-01

282

Differential protein occupancy profiling of the mRNA transcriptome  

PubMed Central

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

2014-01-01

283

Identification of miRNA-Mediated Core Gene Module for Glioma Patient Prediction by Integrating High-Throughput miRNA, mRNA Expression and Pathway Structure  

PubMed Central

The prognosis of glioma patients is usually poor, especially in patients with glioblastoma (World Health Organization (WHO) grade IV). The regulatory functions of microRNA (miRNA) on genes have important implications in glioma cell survival. However, there are not many studies that have investigated glioma survival by integrating miRNAs and genes while also considering pathway structure. In this study, we performed sample-matched miRNA and mRNA expression profilings to systematically analyze glioma patient survival. During this analytical process, we developed pathway-based random walk to identify a glioma core miRNA-gene module, simultaneously considering pathway structure information and multi-level involvement of miRNAs and genes. The core miRNA-gene module we identified was comprised of four apparent sub-modules; all four sub-modules displayed a significant correlation with patient survival in the testing set (P-values?0.001). Notably, one sub-module that consisted of 6 miRNAs and 26 genes also correlated with survival time in the high-grade subgroup (WHO grade III and IV), P-value?=?0.0062. Furthermore, the 26-gene expression signature from this sub-module had robust predictive power in four independent, publicly available glioma datasets. Our findings suggested that the expression signatures, which were identified by integration of miRNA and gene level, were closely associated with overall survival among the glioma patients with various grades. PMID:24809850

Han, Junwei; Shang, Desi; Zhang, Yunpeng; Zhang, Wei; Yao, Qianlan; Han, Lei; Xu, Yanjun; Yan, Wei; Bao, Zhaoshi; You, Gan; Jiang, Tao; Kang, Chunsheng; Li, Xia

2014-01-01

284

The importance of a single G in the hairpin loop of the iron responsive element (IRE) in ferritin mRNA for structure: an NMR spectroscopy study.  

PubMed

Noncoding sequences regulate the function of mRNA and DNA. In animal mRNAs, iron responsive elements (IREs) regulate the synthesis of proteins for iron storage, uptake and red cell heme formation. Folding of the IRE was indicated previously by reactivity with chemical and enzymatic probes. 1H- and 31P-NMR spectra now confirm the IRE folding; an atypical 31P-spectrum, differential accessibility of imino protons to solvents, multiple long-range NOEs and heat stable subdomains were observed. Biphasic hyperchromic transitions occurred (52 and 73 degrees C). A G-C base pair occurs in the hairpin loop (HL) (based on dimethylsulfate, RNAse T1 previously used, and changes in NMR imino proton resonances typical of G-C base pairs after G/A substitution). Mutation of the hairpin loop also decreased temperature stability and changed the 31P-NMR spectrum; regulation and protein (IRP) binding were previously shown to change. Alteration of IRE structure shown by NMR spectroscopy, occurred at temperatures used in studies of IRE function, explaining loss of IRP binding. The effect of the HL mutation on the IRE emphasizes the importance of HL structure in other mRNAs, viral RNAs (e.g. HIV-TAR), and ribozymes. PMID:7870579

Sierzputowska-Gracz, H; McKenzie, R A; Theil, E C

1995-01-11

285

A Dynamic Programming Algorithm for Finding the Optimal Segmentation of an RNA Sequence in Secondary Structure Predictions  

PubMed Central

In this paper, we present a dynamic programming algorithm that runs in polynomial time and allows us to achieve the optimal, non-overlapping segmentation of a long RNA sequence into segments (chunks). The secondary structure of each chunk is predicted independently, then combined with the structures predicted for the other chunks, to generate a complete secondary structure prediction that is thus a combination of local energy minima. The proposed approach not only is more efficient and accurate than other traditionally used methods that are based on global energy minimizations, but it also allows scientists to overcome computing and storage constraints when trying to predict the secondary structure of long RNA sequences. PMID:25705724

Licon, Abel; Taufer, Michela; Leung, Ming-Ying; Johnson, Kyle L.

2013-01-01

286

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

287

Mamit-tRNA, a database of mammalian mitochondrial tRNA primary and secondary structures  

PubMed Central

Mamit-tRNA (http://mamit-tRNA.u-strasbg.fr), a database for mammalian mitochondrial genomes, has been developed for deciphering structural features of mammalian mitochondrial tRNAs and as a helpful tool in the frame of human diseases linked to point mutations in mitochondrial tRNA genes. To accommodate the rapid growing availability of fully sequenced mammalian mitochondrial genomes, Mamit-tRNA has implemented a relational database, and all annotated tRNA genes have been curated and aligned manually. System administrative tools have been integrated to improve efficiency and to allow real-time update (from GenBank Database at NCBI) of available mammalian mitochondrial genomes. More than 3000 tRNA gene sequences from 150 organisms are classified into 22 families according to the amino acid specificity as defined by the anticodon triplets and organized according to phylogeny. Each sequence is displayed linearly with color codes indicating secondary structural domains and can be converted into a printable two-dimensional (2D) cloverleaf structure. Consensus and typical 2D structures can be extracted for any combination of primary sequences within a given tRNA specificity on the basis of phylogenetic relationships or on the basis of structural peculiarities. Mamit-tRNA further displays static individual 2D structures of human mitochondrial tRNA genes with location of polymorphisms and pathology-related point mutations. The site offers also a table allowing for an easy conversion of human mitochondrial genome nucleotide numbering into conventional tRNA numbering. The database is expected to facilitate exploration of structure/function relationships of mitochondrial tRNAs and to assist clinicians in the frame of pathology-related mutation assignments. PMID:17585048

Pütz, Joern; Dupuis, Bruno; Sissler, Marie; Florentz, Catherine

2007-01-01

288

The NOESY Jigsaw: Automated Protein Secondary Structure and Main-Chain Assignment from Sparse, Unassigned NMR Data  

E-print Network

The NOESY Jigsaw: Automated Protein Secondary Structure and Main-Chain Assignment from Sparse presents the Jigsaw algorithm, a novel high-throughput, auto- mated approach to protein structure characterization with nuclear magnetic resonance (NMR). Jigsaw ap- plies graph algorithms and probabilistic

Richardson, David

289

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

PubMed

The internal transcribed spacer (ITS) is a popular barcode marker for fungi and in particular the ITS1 has been widely used for the anaerobic fungi (phylum Neocallimastigomycota). A good number of validated reference sequences of isolates as well as a large number of environmental sequences are available in public databases. Its highly variable nature predisposes the ITS1 for low level phylogenetics; however, it complicates the establishment of reproducible alignments and the reconstruction of stable phylogenetic trees at higher taxonomic levels (genus and above). Here, we overcame these problems by proposing a common core secondary structure of the ITS1 of the anaerobic fungi employing a Hidden Markov Model-based ITS1 sequence annotation and a helix-wise folding approach. We integrated the additional structural information into phylogenetic analyses and present for the first time an automated sequence-structure-based taxonomy of the ITS1 of the anaerobic fungi. The methodology developed is transferable to the ITS1 of other fungal groups, and the robust taxonomy will facilitate and improve high-throughput anaerobic fungal community structure analysis of samples from various environments. PMID:24663345

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

2014-01-01

290

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

PubMed Central

The internal transcribed spacer (ITS) is a popular barcode marker for fungi and in particular the ITS1 has been widely used for the anaerobic fungi (phylum Neocallimastigomycota). A good number of validated reference sequences of isolates as well as a large number of environmental sequences are available in public databases. Its highly variable nature predisposes the ITS1 for low level phylogenetics; however, it complicates the establishment of reproducible alignments and the reconstruction of stable phylogenetic trees at higher taxonomic levels (genus and above). Here, we overcame these problems by proposing a common core secondary structure of the ITS1 of the anaerobic fungi employing a Hidden Markov Model-based ITS1 sequence annotation and a helix-wise folding approach. We integrated the additional structural information into phylogenetic analyses and present for the first time an automated sequence-structure-based taxonomy of the ITS1 of the anaerobic fungi. The methodology developed is transferable to the ITS1 of other fungal groups, and the robust taxonomy will facilitate and improve high-throughput anaerobic fungal community structure analysis of samples from various environments. PMID:24663345

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

2014-01-01

291

Effect of chemical structure on secondary organic aerosol formation from C12 alkanes  

NASA Astrophysics Data System (ADS)

The secondary organic aerosol (SOA) formation from four C12 alkanes (n-dodecane, 2-methylundecane, hexylcyclohexane, and cyclododecane) is studied in the Caltech Environmental Chamber under low-NOx conditions, in which the principal fate of the peroxy radical formed in the initial OH reaction is reaction with HO2. Simultaneous gas- and particle-phase measurements elucidate the effect of alkane structure on the chemical mechanisms underlying SOA growth. Reaction of branched structures leads to fragmentation and more volatile products, while cyclic structures are subject to faster oxidation and lead to less volatile products. Product identifications reveal that particle-phase reactions involving peroxyhemiacetal formation from several multifunctional hydroperoxide species are key components of initial SOA growth in all four systems. The continued chemical evolution of the particle-phase is structure-dependent, with 2-methylundecane SOA formation exhibiting the least extent of chemical processing and cyclododecane SOA achieving sustained growth with the greatest variety of chemical pathways. The extent of chemical development is not necessarily reflected in the oxygen to carbon (O : C) ratio of the aerosol as cyclododecane achieves the lowest O : C, just above 0.2, by the end of the experiment and hexylcyclohexane the highest, approaching 0.35.

Yee, L. D.; Craven, J. S.; Loza, C. L.; Schilling, K. A.; Ng, N. L.; Canagaratna, M. R.; Ziemann, P. J.; Flagan, R. C.; Seinfeld, J. H.

2013-11-01

292

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

E-print Network

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

293

[Establishment of prescription research technology system in Chinese medicine secondary exploitation based on "component structure" theory].  

PubMed

Chinese medicine prescriptions are the wisdom outcomes of traditional Chinese medicine (TCM) clinical treatment determinations which based on differentiation of symptoms and signs. Chinese medicine prescriptions are also the basis of secondary exploitation of TCM. The study on prescription helps to understand the material basis of its efficacy, pharmacological mechanism, which is an important guarantee for the modernization of traditional Chinese medicine. Currently, there is not yet dissertation n the method and technology system of basic research on the prescription of Chinese medicine. This paper focuses on how to build an effective system of prescription research technology. Based on "component structure" theory, a technology system contained four-step method that "prescription analysis, the material basis screening, the material basis of analysis and optimization and verify" was proposed. The technology system analyzes the material basis of the three levels such as Chinese medicine pieces, constituents and the compounds which could respect the overall efficacy of Chinese medicine. Ideas of prescription optimization, remodeling are introduced into the system. The technology system is the combination of the existing research and associates with new techniques and methods, which used for explore the research thought suitable for material basis research and prescription remodeling. The system provides a reference for the secondary development of traditional Chinese medicine, and industrial upgrading. PMID:25775807

Cheng, Xu-Dong; Feng, Liang; Gu, Jun-Fei; Zhang, Ming-Hua; Jia, Xiao-Bin

2014-11-01

294

[Isolation and structural elucidation of secondary metabolites from marine Streptomyces sp. SCSIO 1934].  

PubMed

Marine Actinobacteria are emerging as new resources for bioactive natural products with promise in novel drug discovery. In recent years, the richness and diversity of marine Actinobacteria from the South China Sea and their ability in producing bioactive products have been investigated. The objective of this work is to isolate and identify bioactive secondary metabolites from a marine actinobacterium SCSIO 1934 derived from sediments of South China Sea. The strain was identified as a Streptomyces spieces by analyzing its 16S rDNA sequence. Streptomyces sp. SCSIO 1934 was fermented under optimized conditions and seven bioactive secondary metabolites were isolated and purified by chromatographic methods including colum chromatography over silica gel and Sephadex LH-20. Their structures were elucidated as 17-O-demethylgeldanamycin (1), lebstatin (2), 17-O-demethyllebstatin (3), nigericin (4), nigericin sodium salt (5), abierixin (6), respectively, by detailed NMR spectroscopic data (1H, 13C, COSY, HSQC and HMBC). This work provided a new marine actinobacterium Streptomyces sp. SCSIO 1934, capable of producing diverse bioactive natural products. PMID:22032140

Niu, Siwen; Li, Sumei; Tian, Xinpeng; Hu, Tao; Ju, Jianhua; Ynag, Xiaohong; Zhang, Si; Zhang, Changsheng

2011-07-01

295

Secondary structure conversions of Alzheimer's Abeta(1-40) peptide induced by membrane-mimicking detergents.  

PubMed

The amyloid beta peptide (Abeta) with 39-42 residues is the major component of amyloid plaques found in brains of Alzheimer's disease patients, and soluble oligomeric peptide aggregates mediate toxic effects on neurons. The Abeta aggregation involves a conformational change of the peptide structure to beta-sheet. In the present study, we report on the effect of detergents on the structure transitions of Abeta, to mimic the effects that biomembranes may have. In vitro, monomeric Abeta(1-40) in a dilute aqueous solution is weakly structured. By gradually adding small amounts of sodium dodecyl sulfate (SDS) or lithium dodecyl sulfate to a dilute aqueous solution, Abeta(1-40) is converted to beta-sheet, as observed by CD at 3 degrees C and 20 degrees C. The transition is mainly a two-state process, as revealed by approximately isodichroic points in the titrations. Abeta(1-40) loses almost all NMR signals at dodecyl sulfate concentrations giving rise to the optimal beta-sheet content (approximate detergent/peptide ratio = 20). Under these conditions, thioflavin T fluorescence measurements indicate a maximum of aggregated amyloid-like structures. The loss of NMR signals suggests that these are also involved in intermediate chemical exchange. Transverse relaxation optimized spectroscopy NMR spectra indicate that the C-terminal residues are more dynamic than the others. By further addition of SDS or lithium dodecyl sulfate reaching concentrations close to the critical micellar concentration, CD, NMR and FTIR spectra show that the peptide rearranges to form a micelle-bound structure with alpha-helical segments, similar to the secondary structures formed when a high concentration of detergent is added directly to the peptide solution. PMID:18786140

Wahlström, Anna; Hugonin, Loïc; Perálvarez-Marín, Alex; Jarvet, Jüri; Gräslund, Astrid

2008-10-01

296

Secondary grain-boundary dislocations in (001) twist boundaries in MgO. I. Intrinsic structures  

SciTech Connect

Intrinsic secondary grain boundary dislocation (GBD) structures were observed by weak beam transmission electron microscopy in a variety of (001) twist boundaries in MgO prepared by a welding technique. Square networks of intrinsic screw GBDs were found in boundaries possessing twist deviations from the exact = 1, 5, 13, 17, 25, 29 and 53 Coincidence Site Lattice (CSL) misorientations. ( = fraction of lattice sites in coincidence). These GBDs were all perfect GBDs with Burgers vectors given by the primitive vectors of the corresponding DSC-Lattice except in the case of = 13 where a square array of partial screw GBDs was observed. Arrays of screw GBDs were not detected in a number of high boundaries. Super-imposed arrays of edge type intrinsic GBDs were observed in all boundaries when a small tilt component was present.

Sun, C.P.; Balluffi, R.W.

1981-12-01

297

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

2010-11-01

298

An Efficient Multiple Alignment Method for RNA Secondary Structures Including Pseudoknots  

NASA Astrophysics Data System (ADS)

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

Seki, Shinnosuke; Kobayashi, Satoshi

299

Evolution of primary and secondary structures in 5S and 5. 8S rRNA. [Bombyx mori  

SciTech Connect

The secondary structure of Bombyx mori 5S rRNA was studied using the sing-strand specific S1 nuclease and the base pair specific cobra venom ribonuclease. The RNA was end-labeled with (/sup 32/P) at either the 5' or 3' end and sequenced using enzymatic digestion techniques. These enzymatic data coupled with thermodynamic structure prediction were used to generate a secondary structure for 5S rRNA. A computer algorithm has been implemented to aid in the comparison of a large set of homologous RNAs. Eukaryotic 5S rRNA sequences from thirty four diverse species were compared by (1) alignment or the sequences, (2) the positions of substitutions were located with respect to the aligned sequence and secondary structure, and (3) the R-Y model of base stacking was used to study stacking pattern relationships in the structure. Eukaryotic 5S rRNA was found to have significant sequence variation throughout much of the molecule while maintaining a relatively constant secondary structure. A detailed analysis of the sequence and structure variability in each region of the molecule is presented.

Curtiss, W.C.

1986-01-01

300

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

PubMed Central

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

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

2014-01-01

301

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

302

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

PubMed

The function of many non-coding RNA genes and cis-regulatory elements of messenger RNA largely depends on the structure, which is in turn determined by their sequence. Single nucleotide polymorphisms (SNPs) and other mutations may disrupt the RNA structure, interfere with the molecular function and hence cause a phenotypic effect. RNAsnp is an efficient method to predict the effect of SNPs on local RNA secondary structure based on the RNA folding algorithms implemented in the Vienna RNA package. The SNP effects are quantified in terms of empirical P-values, which, for computational efficiency, are derived from extensive pre-computed tables of distributions of substitution effects as a function of gene length and GC content. Here, we present a web service that not only provides an interface for RNAsnp but also features a graphical output representation. In addition, the web server is connected to a local mirror of the UCSC genome browser database that enables the users to select the genomic sequences for analysis and visualize the results directly in the UCSC genome browser. The RNAsnp web server is freely available at: http://rth.dk/resources/rnasnp/. PMID:23630321

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

2013-07-01

303

Computing the partition function and sampling for saturated secondary structures of RNA, with respect to the Turner energy model.  

PubMed

An RNA secondary structure is saturated if no base pairs can be added without violating the definition of secondary structure. Here we describe a new algorithm, RNAsat, which for a given RNA sequence a, an integral temperature 0 secondary structures of a which have exactly k base pairs, R is the universal gas constant and E(S) denotes the free energy with respect to the Turner nearest neighbor energy model. By dynamic programming, we compute Z(k)(T)simultaneously for all values of k in time O(n(5)) and space O(n(3)).Additionally, RNAsat computes the partition function Q(k)(T)(a) = SigmaSepsilonS(k)(a) exp(-E(S)/RT), where the sum is over all secondary structures of a which have k base pairs; the latter computation is performed simultaneously for all values of k in O(n(4)) time and O(n(3)) space. Lastly, using the partition function Z(k)(T) [resp. Q(k)(T)] with stochastic backtracking, RNAsat rigorously samples the collection of saturated secondary structures [resp. secondary structures] having k base pairs; for Q(k)(T) this provides a parametrized form of Sfold sampling (Ding and Lawrence, 2003). Using RNAsat, (i) we compute the ensemble free energy for saturated secondary structures having k base pairs, (ii) show cooperativity of the Turner model, (iii) demonstrate a temperature-dependent phase transition, (iv) illustrate the predictive advantage of RNAsat for precursor microRNA cel-mir-72 of C. elegans and for the pseudoknot PKB 00152 of Pseudobase (van Batenburg et al., 2001), (v) illustrate the RNA shapes (Giegerich et al., 2004) of sampled secondary structures [resp. saturated structures] having exactly k base pairs. A web server for RNAsat is under construction at bioinformatics.bc.edu/clotelab/RNAsat/. PMID:17456015

Waldispühl, J; Clote, P

2007-03-01

304

Investigations of primary and secondary impact structures on the moon and laboratory experiments to study the ejecta of secondary particles. Ph.D. Thesis - Ruprecht Karl Univ.  

NASA Technical Reports Server (NTRS)

Young lunar impact structures were investigated by using lunar orbiter, Apollo Metric and panorama photographs. Measurements on particularly homogeneous areas low in secondary craters made possible an expansion of primary crater distribution to small diameters. This is now sure for a range between 20m or = D or = 20km and this indicates that the size and velocity distribution of the impacting bodies in the last 3 billion years has been constant. A numerical approximation in the form of a 7th degree polynomial was obtained for the distribution.

Koenig, B.

1977-01-01

305

Structure of the ribosomal protein L1-mRNA complex at 2.1 A resolution: common features of crystal packing of L1-RNA complexes.  

PubMed

The crystal structure of a hybrid complex between the bacterial ribosomal protein L1 from Thermus thermophilus and a Methanococcus vannielii mRNA fragment containing an L1-binding site was determined at 2.1 A resolution. It was found that all polar atoms involved in conserved protein-RNA hydrogen bonds have high values of density in the electron-density map and that their hydrogen-bonding capacity is fully realised through interactions with protein atoms, water molecules and K(+) ions. Intermolecular contacts were thoroughly analyzed in the present crystals and in crystals of previously determined L1-RNA complexes. It was shown that extension of the RNA helices providing canonical helix stacking between open-open or open-closed ends of RNA fragments is a common feature of these and all known crystals of complexes between ribosomal proteins and RNAs. In addition, the overwhelming majority of complexes between ribosomal proteins and RNA molecules display crystal contacts formed by the central parts of the RNA fragments. These contacts are often very extensive and strong and it is proposed that they are formed in the saturated solution prior to crystal formation. PMID:17139090

Tishchenko, S; Nikonova, E; Nikulin, A; Nevskaya, N; Volchkov, S; Piendl, W; Garber, M; Nikonov, S

2006-12-01

306

NMR structure and dynamics of the RNA-binding site for the histone mRNA stem-loop binding protein.  

PubMed Central

The 3' end of replication-dependent histone mRNAs terminate in a conserved sequence containing a stem-loop. This 26-nt sequence is the binding site for a protein, stem-loop binding protein (SLBP), that is involved in multiple aspects of histone mRNA metabolism and regulation. We have determined the structure of the 26-nt sequence by multidimensional NMR spectroscopy. There is a 16-nt stem-loop motif, with a conserved 6-bp stem and a 4-nt loop. The loop is closed by a conserved U.A base pair that terminates the canonical A-form stem. The pyrimidine-rich 4-nt loop, UUUC, is well organized with the three uridines stacking on the helix, and the fourth base extending across the major groove into the solvent. The flanking nucleotides at the base of the hairpin stem do not assume a unique conformation, despite the fact that the 5' flanking nucleotides are a critical component of the SLBP binding site. PMID:11871662

DeJong, Eric S; Marzluff, William F; Nikonowicz, Edward P

2002-01-01

307

Secondary-structure analysis of alcohol-denatured proteins by vacuum-ultraviolet circular dichroism spectroscopy.  

PubMed

To elucidate the structural characteristics of alcohol-denatured proteins, we measured the vacuum-ultraviolet circular dichroism (VUVCD) spectra of six proteins-myoglobin, human serum albumin, ?-lactalbumin, thioredoxin, ?-lactoglobulin, and ?-chymotrypsinogen A-down to 170 nm in trifluoroethanol solutions (TFE: 0-50%) and down to 175 nm in methanol solutions (MeOH: 0-70%) at pH 2.0 and 25°C, using a synchrotron-radiation VUVCD spectrophotometer. The contents of ?-helices, ?-strands, turns, poly-L-proline type II helices (PPIIs), and unordered structures of these proteins were estimated using the SELCON3 program, including the numbers of ?-helix and ?-strand segments. Furthermore, the positions of ?-helices and ?-strands on amino acid sequences were predicted by combining these secondary-structure data with a neural-network method. All alcohol-denatured proteins showed higher ?-helix contents (up to ~ 90%) compared with the native states, and they consisted of several long helical segments. The helix-forming ability was higher in TFE than in MeOH, whereas small amounts of ?-strands without sheets were formed in the MeOH solution. The produced ?-helices were transformed dominantly from the ?-strands and unordered structures, and slightly from the turns. The content and mean length of ?-helix segments decreased as the number of disulfide bonds in the proteins increased, suggesting that disulfide bonds suppress helix formation by alcohols. These results demonstrate that alcohol-denatured proteins constitute an ensemble of many long ?-helices, a few ?-strands and PPIIs, turns, and unordered structures, depending on the types of proteins and alcohols involved. PMID:22076921

Matsuo, Koichi; Sakurada, Yoshie; Tate, Shin-ichi; Namatame, Hirofumi; Taniguchi, Masaki; Gekko, Kunihiko

2012-01-01

308

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

PubMed Central

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

2011-01-01

309

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

PubMed Central

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

Minami, Shintaro; Sawada, Kengo; Chikenji, George

2014-01-01

310

Investigating the secondary structures of long oligonucleotides using attenuated-total-reflection surface-enhanced Raman spectroscopy  

NASA Astrophysics Data System (ADS)

This study utilizes a surface-enhanced Raman spectroscopy (SERS) based on the attenuated-total-reflection method to investigate the secondary structures of long oligonucleotides and their influence on the DNA hybridization. It is found that the ring-breathing modes of adenine, thymine, guanine, and cytosine in Raman fingerprint associated with three 60mer oligonucleotides with prominent secondary structures are lower than those observed for the two oligonucleotides with no obvious secondary structures. It is also determined that increasing the DNA hybridization temperature from 35°C to 45°C reduces secondary structure effects. The kinetics of biomolecular interaction analysis can be performed by using surface plasmons resonance biosensor, but the structural information of the oligonucleotides can not observed directly. The SERS spectrum provides the structural information of the oligonucleotides with the help of a silver colloidal nanoparticle monolayer by control of the size and distribution of the nanoparticles adapted as a Raman active substrate. Also, the detection limit of the DNA Raman signal has been successfully improved to reach sub-micro molarity of DNA concentration.

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

2006-08-01

311

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

NASA Astrophysics Data System (ADS)

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

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

2007-09-01

312

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

PubMed

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

Hall, Vincent; Sklepari, Meropi; Rodger, Alison

2014-09-01

313

The NOESY Jigsaw: Automated Protein Secondary Structure and Main-Chain Assignment from Sparse, Unassigned NMR Data  

Microsoft Academic Search

High-throughput, data-directed computational protocols for Structural Genomics (or Proteomics) are required in order to evaluate the protein products of genes for structure and function at rates comparable to current gene-sequencing technology. This paper presents the JIGSAW algorithm, a novel high-throughput, automated approach to protein structure characterization with nuclear magnetic resonance (NMR). JIGSAW consists of two main components: (1) graphbased secondary

Chris Bailey-kellogg; Marcelo J. Berardi; Alik Widge; John H. Bushweller; John J. Kelley; Bruce Randall Donald

1999-01-01

314

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

NASA Technical Reports Server (NTRS)

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

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

1998-01-01

315

Common sequence variation in FLNB regulates bone structure in women in the general population and FLNB mRNA expression in osteoblasts in vitro.  

PubMed

Previous data from our group indicate that BMD is linked to chromosome 3p14-p21. Because the filamin B (FLNB gene resides in this region, is the cause of skeletal dysplasias, and was identified among the top genes in our bioinformatics analysis, we hypothesized a role for FLNB in the regulation of bone structure in the general population. Using a tag single nucleotide polymorphism (SNP) approach, a family study of 767 female sibs in which the 3p14-p21 linkage with BMD was previously shown was examined. FLNB variants showing a BMD association were tested in two additional data sets, a study of 1085 UK female twins and a population study (CAIFOS) of 1315 Australian women. Genotype-expression studies were performed in 96 human osteoblast lines to examine the variants in vitro. rs7637505, rs9822918, rs2177153, and rs2001972 showed association with femoral neck (p = 0.0002-0.02) in the family-based study. The twin study provided further support for an association between rs7637505 and femoral neck and spine BMD (p = 0.02-0.03). The CAIFOS study further suggested an association between rs2177153 and rs9822918 and femoral neck BMD (p = 0.004-0.03). Prevalent fractures were increased in carriers of the A allele of rs2177153 (p = 0.009). In vitro studies showed association between rs11130605, itself in strong LD with rs7637505, and FLNB mRNA expression. These findings suggest common variants in FLNB have effects on bone structure in women. Although the location of variants having effects is not entirely consistent, variation at the 5' end of the gene may reflect effects on levels of FLNB transcription efficiency. PMID:19453265

Wilson, Scott G; Jones, Michelle R; Mullin, Ben H; Dick, Ian M; Richards, J Brent; Pastinen, Tomi M; Grundberg, Elin; Ljunggren, Osten; Surdulescu, Gabriela L; Dudbridge, Frank; Elliott, Katherine S; Cervino, Alessandra C L; Spector, Timothy D; Prince, Richard L

2009-12-01

316

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

NASA Astrophysics Data System (ADS)

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

Matsushima, Norio; Enkhbayar, Purevjav

2012-09-01

317

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 {alpha}-helix form compared with that in other secondary structure forms including {beta}-sheet. Modeling of {alpha}-helix and {beta}-sheet absorption bands that contribute to the amide I band at 1650 cm{sup -1} was applied to more than 1500 spectra in this study. The microscopic view of wheat endosperm is dominated by many large starch granules with protein in between. The spectrum produced from in situ microspectroscopy of this mixture is dominated by carbohydrate bands from the large starch granules that fill up the field. The high spatial resolution achievable with synchrotron infrared microspectroscopy enables revealing good in situ spectra of the protein located interstitially. Synchrotron infrared microspectroscopic mapping of 4 {mu}m thick frozen sections of endosperm in the subaleurone region provides spectra from a large number of pixels. Pixels with protein-dominated spectra are sorted out from among adjacent pixels to minimize the starch absorption and scattering contributions. Subsequent data treatment to extract information from the amide I band requires a high signal to noise ratio. Although spectral interference of the carbohydrate band on the amide band is not a problem, the scattering produced by the large starch granules diminishes the signal to noise ratio throughout the spectrum. High density mapping was done on beamlines U2B and U10B at the National Synchrotron Light Source at Brookhaven National Laboratory, Upton, NY. Mapping with a single masked spot size of 5.5 {mu}m diameter or confocal 5 {mu}mX5{mu}m spot size, respectively, on the two beamlines used produced spectra for new breeding lines under current consideration. Appropriate data treatment allows calculation of a numerical estimate of the {alpha}-helix population relative to other secondary protein structures from the position and shape of the amide I absorption band. Current breeding lines show a substantial variance in this feature and its determination allows the prediction of relative quality for breadmaking to be taken into consideration for subsequent steps in the wheat breeding process. Data treatments include deconvolution, modeling of the individual resulting bands that contribute to the amide I band to enable measurement of the relative amounts of both forms. Results with specimens representing multiple crop years of hard winter wheat breeding are reported. It is evident that a range is available for the breeder to choose from, that allows including this protein molecular structural attribute in the selection process.

Wetzel, D.; Bonwell, E; Fritz, T; Fritz, A

2008-01-01

318

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

319

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

PubMed Central

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.

2013-01-01

320

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

PubMed Central

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

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

2015-01-01

321

Linking secondary structure of individual size distribution with nonlinear size-trophic level relationship in food webs.  

PubMed

Existing individual size distribution (ISD) theories assume that the trophic level (TL) of an organism varies as a linear function of its log-transformed body size. This assumption predicts a power-law distribution of the ISD, i.e., a linear relationship between size and abundance in log space. However, the secondary structure of ISD (nonlinear dome shape structures deviating from a power-law distribution) is often observed. We propose a model that extends the metabolic theory to link the secondary structure of ISD to the nonlinear size-TL relationship. This model is tested with empirical data collected from a subtropical reservoir. The empirical ISD and size-TL relationships were constructed by FlowCAM imaging analysis and stable isotope analyses, respectively. Our results demonstrate that the secondary structure of ISD can be predicted from the nonlinear function of size-TL relationship and vice versa. Moreover, these secondary structures arise due to (1) zooplankton omnivory and (2) the trophic interactions within microbial food webs. PMID:24933809

Chang, Chun-Wei; Miki, Takeshi; Shiah, Fuh-Kwo; Kao, Shuh-Ji; Wu, Jiunn-Tzong; Sastri, Akash R; Hsieh, Chih-Hao

2014-04-01

322

The influence of viral RNA secondary structure on interactions with innate host cell defences  

PubMed Central

RNA viruses infecting vertebrates differ fundamentally in their ability to establish persistent infections with markedly different patterns of transmission, disease mechanisms and evolutionary relationships with their hosts. Although interactions with host innate and adaptive responses are complex and persistence mechanisms likely multi-factorial, we previously observed associations between bioinformatically predicted RNA secondary formation in genomes of positive-stranded RNA viruses with their in vivo fitness and persistence. To analyse this interactions functionally, we transfected fibroblasts with non-replicating, non-translated RNA transcripts from RNA viral genomes with differing degrees of genome-scale ordered RNA structure (GORS). Single-stranded RNA transcripts induced interferon-? mediated though RIG-I and PKR activation, the latter associated with rapid induction of antiviral stress granules. A striking inverse correlation was observed between induction of both cellular responses with transcript RNA structure formation that was independent of both nucleotide composition and sequence length. The consistent inability of cells to recognize RNA transcripts possessing GORS extended to downstream differences from unstructured transcripts in expression of TNF-?, other interferon-stimulated genes and induction of apoptosis. This functional association provides novel insights into interactions between virus and host early after infection and provides evidence for a novel mechanism for evading intrinsic and innate immune responses. PMID:24335283

Witteveldt, Jeroen; Blundell, Richard; Maarleveld, Joris J.; McFadden, Nora; Evans, David J.; Simmonds, Peter

2014-01-01

323

Effect of Macromolecular Crowding on Protein Folding Dynamics at the Secondary Structure Level  

PubMed Central

Macromolecular crowding is one of the key characteristics of the cellular environment and therefore, is intimately coupled to the process of protein folding in vivo. While previous studies have provided invaluable insight into the effect of crowding on the stability and folding rate of protein tertiary structures, very little is known about how crowding affects protein folding dynamics at the secondary structure level. Herein, we examine the thermal stability and folding-unfolding kinetics of three small folding motifs, i.e., a 34-residue ?-helix, a 34-residue cross-linked helix-turn-helix, and a 16-residue ? hairpin, in the presence of two commonly used crowding agents, Dextran 70 (200 g/L) and Ficoll 70 (200 g/L). We find that these polymers do not induce any appreciable changes in the folding kinetics of the two helical peptides, which is somewhat surprising as the helix-coil transition kinetics have been shown to depend on viscosity. Also to our surprise and in contrast to what has been observed for larger proteins, we find that crowding leads to an appreciable decrease in the folding rate of the shortest ?-hairpin peptide, indicating that besides the excluded volume effect, other factors also need to be considered when evaluating the net effect of crowding on protein folding kinetics. A model considering both the static and dynamic effects arising from the presence of the crowding agent is proposed to rationalize these results. PMID:19682997

Mukherjee, Smita; Waegele, Matthias M.; Chowdhury, Pramit; Guo, Lin; Gai, Feng

2009-01-01

324

Interplay between Secondary and Tertiary Structure Formation in Protein Folding Cooperativity  

E-print Network

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

Tristan Bereau; Michael Bachmann; Markus Deserno

2011-07-01

325

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

PubMed

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

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

2011-11-01

326

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

NASA Astrophysics Data System (ADS)

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

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

1989-12-01

327

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

PubMed

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

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

2015-05-01

328

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. PMID:19208138

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

2009-01-01

329

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

PubMed Central

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

Spencer, Matt; Eickholt, Jesse; Cheng, Jianlin

2014-01-01

330

Secondary organic aerosol formation via the isolation of individual reactive intermediates: role of alkoxy radical structure.  

PubMed

The study of the chemistry underlying secondary organic aerosol (SOA) formation is complicated by the large number of reaction pathways and oxidation generations available to a given precursor species. Here we simplify such complexity to that of a single alkoxy radical (RO), by forming SOA via the direct photolysis of alkyl nitrite (RONO) isomers. Chamber experiments were conducted with 11 C10 RONO isomers to determine how the position of the radical center and branching of the carbon skeleton influences SOA formation. SOA yields served as a probe of RO reactivity, with lower yields indicating that fragmentation reactions dominate and higher yields suggesting the predominance of RO isomerization. The largest yields were from straight-chain isomers, particularly those with radical centers located toward the terminus of the molecule. Trends in SOA yields can be explained in terms of two major effects: (1) the relative importance of isomerization and fragmentation reactions, which control the distribution of products, and (2) differences in volatility among the various isomeric products formed. Yields from branched isomers, which were low but variable, provide insight into the degree of fragmentation of the alkoxy radicals; in the case of the two ?-substituted alkoxy radicals, fragmentation appears to occur to a greater extent than predicted by structure-activity relationships. Our results highlight how subtle differences in alkoxy radical structure can have major impacts on product yields and SOA formation. PMID:25148415

Carrasquillo, Anthony J; Hunter, James F; Daumit, Kelly E; Kroll, Jesse H

2014-09-25

331

mRNA  

PubMed Central

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

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

2013-01-01

332

The Pekin duck IL-10R2 common chain: cDNA cloning, genomic structure, molecular characterization and mRNA expression analysis.  

PubMed

The interleukin-10 receptor 2 (IL-10R2, IL-10R?) is required for the signalling of the class 2 cytokines IL-10, IL-22, IL-26 and IFN-?1-3 . Here, we describe the identification of the Pekin duck IL-10R2 (duIL-10R2) common chain and its gene structure. The duIL-10R2 cDNA encodes a 343 amino acid protein that has an amino acid identity of 76% and 42% with chicken and human IL-10R2, respectively. Binding residues of human IL-10R2 for IL-10 and IL-22 were mostly conserved in the avian IL-10R2 proteins within loops L3 and L5, but not within loops L2 and L6. Homology modelling of the duIL-10R2 extracellular domain structure using soluble human IL-10R2 (shIL-10R2, PDB ID: 3LQM) as a template revealed a protruding loop L5 and two distinct clefts between loops L2/L3 and L3/L5, similar to shIL-10R2. However, in contrast to the three amino acid ?-hairpin loop L2 of shIL-10R2, loop L2 of duIL-10R2 is five residues longer. Residues within a putative Tyk2 binding site were highly conserved across all vertebrate IL-10R2 proteins examined. The duIL-10R2 gene shares a seven exon-six intron structure with chicken and human IL-10R2 genes, but avian genes are more compact. DuIL-10R2 mRNA was constitutively expressed in all tissues. Mitogen stimulation of duck peripheral blood mononuclear cells (PBMC) did not alter transcript levels. Our observations suggest that genomic organization and structural features implicated in multiple cytokine-binding properties of human IL-10R2 are conserved in duck IL-10R2, but the evolutionary changes that appear to have lead to low-affinity cytokine interaction within loop L2 are distinct to mammalian species. PMID:23331509

Yao, Q; Fischer, K P; Arnesen, K; Lorne Tyrrell, D; Gutfreund, K S

2013-10-01

333

Conventional and unconventional mechanisms for capping viral mRNA  

Microsoft Academic Search

In the eukaryotic cell, capping of mRNA 5? ends is an essential structural modification that allows efficient mRNA translation, directs pre-mRNA splicing and mRNA export from the nucleus, limits mRNA degradation by cellular 5?–3? exonucleases and allows recognition of foreign RNAs (including viral transcripts) as 'non-self'. However, viruses have evolved mechanisms to protect their RNA 5? ends with either a

Etienne Decroly; François Ferron; Julien Lescar; Bruno Canard

2011-01-01

334

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 four models, written in a declarative style that makes them easy to be modified. Based on our study, future work on thermodynamic RNA folding may make a choice of model based on our empirical data. It can take our implementations as a starting point for further program development. PMID:22051375

2011-01-01

335

[Effect of temperature on the secondary structure of fish scale collagen].  

PubMed

Pepsin-soluble collagen (PSC) was extracted from fish scale of grass carp and was analyzed by SDS-PAGE, which confirmed that PSC are typical type I collagen and reach electrophoretic purity. Effect of temperature on the secondary structure of collagen was studied by FTIR, Raman and CD. FTIR indicated that the fish scale PSC had typically characteristic absorptions of collagen, and 1659, 1552 and 1238 cm(-1) were assigned to be amide I, II and III respectively. When the temperature increased, amide A and amide B shifted to low frequency, the absorption of 1658 cm(-1) split into several absorption peaks, the absorption at 1552 cm(-1) had a slight red-shift followed by a distinct blue-shift, and the frequency of 1238 cm(-1) declined. Raman spectra showed that the absorptions of amide I, amide II and amide III appeared at 1669, 1557 and 1245 cm(-1) respectively, which were higher than those in FTIR spectra. Furthermore, the characteristic absorptions of proline at 921 and 855 cm(-1) only appeared in Raman spectra. CD spectra demonstrated a rotatory maximum at 221.6 nm and a negative peak at 204.4 nm of PSC solution, which were typical spectral characteristics of the collagen triple helix structure. The structure changes of the lyophilized PSC appeared mainly between 35 and 60 degrees C in FTIR and Raman spectra, yet CD spectra demonstrated that the configurational changes of PSC in acidic solution appeared in the range of 20 to 35 degrees C, indicating that the lyophilized PSC was more stable than the acidic solution of PSC. PMID:18306775

Zhong, Zhao-hui; Li, Chun-mei; Gu, Hai-feng; Dou, Hong-liang; Zhou, Li-ming

2007-10-01

336

eIF4AIII enhances translation of nuclear cap-binding complex–bound mRNAs by promoting disruption of secondary structures in 5?UTR  

PubMed Central

It has long been considered that intron-containing (spliced) mRNAs are translationally more active than intronless mRNAs (identical mRNA not produced by splicing). The splicing-dependent translational enhancement is mediated, in part, by the exon junction complex (EJC). Nonetheless, the molecular mechanism by which each EJC component contributes to the translational enhancement remains unclear. Here, we demonstrate the previously unappreciated role of eukaryotic translation initiation factor 4AIII (eIF4AIII), a component of EJC, in the translation of mRNAs bound by the nuclear cap-binding complex (CBC), a heterodimer of cap-binding protein 80 (CBP80) and CBP20. eIF4AIII is recruited to the 5?-end of mRNAs bound by the CBC by direct interaction with the CBC-dependent translation initiation factor (CTIF); this recruitment of eIF4AIII is independent of the presence of introns (deposited EJCs after splicing). Polysome fractionation, tethering experiments, and in vitro reconstitution experiments using recombinant proteins show that eIF4AIII promotes efficient unwinding of secondary structures in 5?UTR, and consequently enhances CBC-dependent translation in vivo and in vitro. Therefore, our data provide evidence that eIF4AIII is a specific translation initiation factor for CBC-dependent translation. PMID:25313076

Choe, Junho; Ryu, Incheol; Park, Ok Hyun; Park, Joori; Cho, Hana; Yoo, Jin Seon; Chi, Sung Wook; Kim, Min Kyung; Song, Hyun Kyu; Kim, Yoon Ki

2014-01-01

337

Development of Forest Structure and Leaf Area in Secondary Forests Regenerating on Abandoned Pastures in Central Amazônia  

Microsoft Academic Search

The area of secondary forest (SF) regenerating from pastures is increasing in the Amazon basin; however, the return of forest and canopy structure following abandonment is not well understood. This study examined the development of leaf area index (LAI), canopy cover, aboveground biomass,

Ted R. Feldpausch; Susan J. Riha; Erick C. M. Fernandes; Elisa V. Wandelli

2005-01-01

338

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

ERIC Educational Resources Information Center

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

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

2007-01-01

339

Administration and Evaluation Structures for Primary and Secondary Schools in the Twelve Member States of the European Community.  

ERIC Educational Resources Information Center

This comparative analysis deals with the administration and evaluation structures for primary and secondary schools in the member states of the European Community. It addresses four major issues: (1) how to hand over large amounts of autonomy to schools without upsetting the unity of the national education system; (2) what role parents and others…

Barroso, Joao; And Others

340

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

E-print Network

The overall structure of the human lens is one of succes- sive generations of secondary fiber cells Department of Cell Biology and Human Anatomy, School of Medicine, University of California, Davis, CA; 4 Purpose: Human eye lenses contain cells that persist from embryonic development. These unique, highly

Hammock, Bruce D.

341

Using Neural Networks to Predict Secondary Structure by Integration of Amino Acid Conformational Preference and Multiple Sequence Alignment  

E-print Network

a novel approach, based on the conformational preference of various amino acids and the information of MSAUsing Neural Networks to Predict Secondary Structure by Integration of Amino Acid Conformational: In this paper, we propose a new prediction method based on Feedforward Neural Network (FNN) by integrating Amino

Hefei Institute of Intelligent Machines

342

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

SciTech Connect

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

Ahn, Byungchan, E-mail: bbccahn@mail.ulsan.ac.kr [Department of Life Sciences, University of Ulsan, Ulsan (Korea, Republic of)] [Department of Life Sciences, University of Ulsan, Ulsan (Korea, Republic of); Bohr, Vilhelm A. [Laboratory of Molecular Gerontology, Biomedical Research Center, National Institute on Aging, Baltimore, MD (United States)] [Laboratory of Molecular Gerontology, Biomedical Research Center, National Institute on Aging, Baltimore, MD (United States)

2011-08-12

343

Observed Lesson Structure during the First Year of Secondary Education: Exploration of Change and Link with Academic Engagement  

ERIC Educational Resources Information Center

This study investigates whether lesson structure (LS) matters and which components are important for academic engagement during the first grade of secondary education. Data from videoed lessons of 10 Dutch and 12 Indonesian teachers analyzed using an observation protocol show that six LS components are found, that between class and over…

Maulana, Ridwan; Opdenakker, Marie-Christine; Stroet, Kim; Bosker, Roel

2012-01-01

344

Experiences and Reflections about Teaching Atomic Structure in a Jigsaw Classroom in Lower Secondary School Chemistry Lessons  

Microsoft Academic Search

This article describes and discusses an example of how atomic structure can be taught in lower secondary chemistry using a modified jigsaw-classroom method. The lesson was taught in grades 9 and 10 (age range 15 17 years) chemistry in 13 learning groups with a total of 313 students in various grammar, middle, and comprehensive schools in Germany. The written evaluation

Ingo Eilks

2005-01-01

345

Control of guanine-rich DNA secondary structures depending on the protease activity using a designed PNA peptide.  

PubMed

We constructed a regulation system for DNA secondary structure formation of G-rich sequences using a designed PNA peptide exhibiting an on-to-off switching functionality, depending on the protease activity. This study introduces the new concept of a simple and powerful system for regulating quadruplex-related important biological events. PMID:25519192

Usui, Kenji; Okada, Arisa; Kobayashi, Keita; Sugimoto, Naoki

2015-02-21

346

High pressure FT-IR spectroscopic study on the secondary structure changes in insulin amyloid fibril and aggregate  

Microsoft Academic Search

The pressure-induced changes in the secondary structure of two kinds of insulin aggregates, amyloid fibril and reduction-induced aggregate, were studied by using Fourier transform infrared (FT-IR) spectroscopy. The parallel ?-sheet for the amyloid fibril is not unfolded, but dramatically distorted with increasing pressure up to 1.0 GPa. This structural rearrangement is elastic and does not cause the backbone amide protons involved

Y. Taniguchi; N. Takeda; K. Ado; R. Maeda

2009-01-01

347

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

PubMed Central

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

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

1997-01-01

348

mRNA  

NSDL National Science Digital Library

Template for protein synthesis. Each set of three bases, called codons, specifies a certain protein in the sequence of amino acids that comprise the protein. The sequence of a strand of mRNA is based on the sequence of a complementary strand of DNA.

Darryl Leja (National Human Genome Research Institute REV)

2005-04-04

349

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

PubMed

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

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

2015-01-01

350

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

PubMed

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

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

2008-12-01

351

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

PubMed Central

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

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

2013-01-01

352

Fine-grained parallelism accelerating for RNA secondary structure prediction with pseudoknots based on FPGA.  

PubMed

PKNOTS is a most famous benchmark program and has been widely used to predict RNA secondary structure including pseudoknots. It adopts the standard four-dimensional (4D) dynamic programming (DP) method and is the basis of many variants and improved algorithms. Unfortunately, the O(N(6)) computing requirements and complicated data dependency greatly limits the usefulness of PKNOTS package with the explosion in gene database size. In this paper, we present a fine-grained parallel PKNOTS package and prototype system for accelerating RNA folding application based on FPGA chip. We adopted a series of storage optimization strategies to resolve the "Memory Wall" problem. We aggressively exploit parallel computing strategies to improve computational efficiency. We also propose several methods that collectively reduce the storage requirements for FPGA on-chip memory. To the best of our knowledge, our design is the first FPGA implementation for accelerating 4D DP problem for RNA folding application including pseudoknots. The experimental results show a factor of more than 50x average speedup over the PKNOTS-1.08 software running on a PC platform with Intel Core2 Q9400 Quad CPU for input RNA sequences. However, the power consumption of our FPGA accelerator is only about 50% of the general-purpose micro-processors. PMID:24969746

Xia, Fei; Jin, Guoqing

2014-06-01

353

Inclusion of persistence length-based secondary structure in replica field theoretic models of heteropolymer freezing  

NASA Astrophysics Data System (ADS)

The protein folding problem has long represented a "holy grail" in statistical physics due to its physical complexity and its relevance to many human diseases. While past theoretical work has yielded apt descriptions of protein folding landscapes, recent large-scale simulations have provided insights into protein folding that were impractical to obtain from early theories. In particular, the role that non-native contacts play in protein folding, and their relation to the existence of misfolded, ?-sheet rich trap states on folding landscapes, has emerged as a topic of interest in the field. In this paper, we present a modified model of heteropolymer freezing that includes explicit secondary structural characteristics which allow observations of "intramolecular amyloid" states to be probed from a theoretical perspective. We introduce a variable persistence length-based energy penalty to a model Hamiltonian, and we illustrate how this modification alters the phase transitions present in the theory. We find, in particular, that inclusion of this variable persistence length increases both generic freezing and folding temperatures in the model, allowing both folding and glass transitions to occur in a more highly optimized fashion. We go on to discuss how these changes might relate to protein evolution, misfolding, and the emergence of intramolecular amyloid states.

Weber, Jeffrey K.; Pande, Vijay S.

2013-09-01

354

Inclusion of persistence length-based secondary structure in replica field theoretic models of heteropolymer freezing.  

PubMed

The protein folding problem has long represented a "holy grail" in statistical physics due to its physical complexity and its relevance to many human diseases. While past theoretical work has yielded apt descriptions of protein folding landscapes, recent large-scale simulations have provided insights into protein folding that were impractical to obtain from early theories. In particular, the role that non-native contacts play in protein folding, and their relation to the existence of misfolded, ?-sheet rich trap states on folding landscapes, has emerged as a topic of interest in the field. In this paper, we present a modified model of heteropolymer freezing that includes explicit secondary structural characteristics which allow observations of "intramolecular amyloid" states to be probed from a theoretical perspective. We introduce a variable persistence length-based energy penalty to a model Hamiltonian, and we illustrate how this modification alters the phase transitions present in the theory. We find, in particular, that inclusion of this variable persistence length increases both generic freezing and folding temperatures in the model, allowing both folding and glass transitions to occur in a more highly optimized fashion. We go on to discuss how these changes might relate to protein evolution, misfolding, and the emergence of intramolecular amyloid states. PMID:24089729

Weber, Jeffrey K; Pande, Vijay S

2013-09-28

355

Inclusion of persistence length-based secondary structure in replica field theoretic models of heteropolymer freezing  

PubMed Central

The protein folding problem has long represented a “holy grail” in statistical physics due to its physical complexity and its relevance to many human diseases. While past theoretical work has yielded apt descriptions of protein folding landscapes, recent large-scale simulations have provided insights into protein folding that were impractical to obtain from early theories. In particular, the role that non-native contacts play in protein folding, and their relation to the existence of misfolded, ?-sheet rich trap states on folding landscapes, has emerged as a topic of interest in the field. In this paper, we present a modified model of heteropolymer freezing that includes explicit secondary structural characteristics which allow observations of “intramolecular amyloid” states to be probed from a theoretical perspective. We introduce a variable persistence length-based energy penalty to a model Hamiltonian, and we illustrate how this modification alters the phase transitions present in the theory. We find, in particular, that inclusion of this variable persistence length increases both generic freezing and folding temperatures in the model, allowing both folding and glass transitions to occur in a more highly optimized fashion. We go on to discuss how these changes might relate to protein evolution, misfolding, and the emergence of intramolecular amyloid states. PMID:24089729

Weber, Jeffrey K.; Pande, Vijay S.

2013-01-01

356

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

SciTech Connect

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

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

2012-05-02

357

A ?-amino acid that favors 12/10-helical secondary structure in ?/?-peptides.  

PubMed

H-bonded helices in conventional peptides (containing exclusively homochiral ?-amino acid residues) feature a uniform H-bonding directionality, N-terminal side C?O to C-terminal side NH. In contrast, heterochiral ?-peptides can form helices in which the H-bond directionality alternates along the backbone because neighboring amide groups are oriented in opposite directions. Alternating H-bond directions are seen also in helices formed by unnatural peptidic backbones, e.g., those containing ?- or ?-amino acid residues. In the present study, we used NMR spectroscopy and crystallography to evaluate the conformational preferences of the novel ?-amino acid (1R,2R,3S)-2-(1-aminopropyl)-cyclohexanecarboxylic acid (APCH), which is constrained by a six-membered ring across its C?-C? bond. These studies were made possible by the development of a stereoselective synthesis of N-protected APCH. APCH strongly enforces the ?/?-peptide 12/10-helical secondary structure, which features alternating H-bond directionality. Thus, APCH residues appear to have a conformational propensity distinct from those of other cyclically constrained ?-amino acid residues. PMID:25301259

Giuliano, Michael W; Maynard, Stacy J; Almeida, Aaron M; Guo, Li; Guzei, Ilia A; Spencer, Lara C; Gellman, Samuel H

2014-10-22

358

A new criterion to evaluate water vapor interference in protein secondary structural analysis by FTIR spectroscopy.  

PubMed

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

Zou, Ye; Ma, Gang

2014-01-01

359

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

PubMed Central

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

Zou, Ye; Ma, Gang

2014-01-01

360

A range of complex probabilistic models for RNA secondary structure prediction that includes the nearest-neighbor model and more.  

PubMed

The standard approach for single-sequence RNA secondary structure prediction uses a nearest-neighbor thermodynamic model with several thousand experimentally determined energy parameters. An attractive alternative is to use statistical approaches with parameters estimated from growing databases of structural RNAs. Good results have been reported for discriminative statistical methods using complex nearest-neighbor models, including CONTRAfold, Simfold, and ContextFold. Little work has been reported on generative probabilistic models (stochastic context-free grammars [SCFGs]) of comparable complexity, although probabilistic models are generally easier to train and to use. To explore a range of probabilistic models of increasing complexity, and to directly compare probabilistic, thermodynamic, and discriminative approaches, we created TORNADO, a computational tool that can parse a wide spectrum of RNA grammar architectures (including the standard nearest-neighbor model and more) using a generalized super-grammar that can be parameterized with probabilities, energies, or arbitrary scores. By using TORNADO, we find that probabilistic nearest-neighbor models perform comparably to (but not significantly better than) discriminative methods. We find that complex statistical models are prone to overfitting RNA structure and that evaluations should use structurally nonhomologous training and test data sets. Overfitting has affected at least one published method (ContextFold). The most important barrier to improving statistical approaches for RNA secondary structure prediction is the lack of diversity of well-curated single-sequence RNA secondary structures in current RNA databases. PMID:22194308

Rivas, Elena; Lang, Raymond; Eddy, Sean R

2012-02-01

361

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

Technology Transfer Automated Retrieval System (TEKTRAN)

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

362

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

PubMed Central

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

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

2013-01-01

363

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

PubMed Central

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

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

2014-01-01

364

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

PubMed

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

Di Liegro, Carlo Maria; Schiera, Gabriella; Di Liegro, Italia

2014-04-01

365

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

PubMed Central

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

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

2012-01-01

366

Inhibition of protein synthesis stabilizes histone mRNA  

SciTech Connect

The inhibition of protein synthesis in exponentially growing S49 cells leads to a specific fivefold increase in histone mRNA in 30 min. The rate of transcription of histone mRNA, measured in intact or digitonin-permeabilized cells, is increased slightly, if at all, by cycloheximide inhibition of protein synthesis. Both approach-to-equilibrium labeling and pulse-chase experiments show that cycloheximide prolongs histone mRNA half-life from approximately 30 min to > 2 h. Histone mRNA made before the addition of cycloheximide becomes stable after the inhibition of protein synthesis, whereas removal of the inhibitor is followed by rapid degradation of histone mRNA. This suggests that the increased stability of histone mRNA during inhibition of protein synthesis results not from alteration of the structure of the mRNA, but from the loss of an activity in the cell which regulates histone mRNA turnover.

Stimac, E.; Groppi, V.E. Jr.; Coffino, P.

1984-10-01

367

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

SciTech Connect

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

Patel, Asmita; Yakovleva, Lyudmila; Shuman, Stewart; Mondragón, Alfonso (NWU); (SKI)

2010-10-22

368

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

SciTech Connect

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

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

1991-11-19

369

Use of rRNA Secondary Structure in Phylogenetic Studies to Identify Homologous Positions: An Example of Alignment and Data Presentation from the Frogs  

Microsoft Academic Search

The alignment of ribosomal RNA (rRNA) by computer requires assumptions about the evolutionary costs for gaps in the alignment that are undefinable when uniformly applied across the entire molecule. The conservation of rRNA secondary structures exceeds that of its nucleotides, and therefore it is recommended that secondary structures guide decisions about the assignment of homologous positions for phylogenetic studies. Suggestions

K. M. Kjer

1995-01-01

370

RNase footprinting of protein binding sites on an mRNA target of small RNAs  

PubMed Central

Summary Endoribonuclease footprinting is an important technique for probing RNA•protein interactions with single nucleotide resolution. The susceptibility of RNA residues to enzymatic digestion gives information about the RNA secondary structure, the location of protein binding sites, and the effects of protein binding on the RNA structure. Here we present a detailed protocol for using RNase T2, which cleaves single stranded RNA with a preference for A nucleotides, to footprint the protein Hfq on the rpoS mRNA leader. This protocol covers how to form the RNP complex, determine the correct dose of enzyme, footprint the protein, and analyze the cleavage pattern using primer extension. PMID:22736006

Yi, Peng; Soper, Toby J.; Woodson, Sarah A.

2013-01-01

371

Counterion dependent variation of DNA secondary structure in (A . T) clusters: evidence by use of netropsin as a structural probe.  

PubMed Central

The interaction of the oligopeptide antibiotic netropsin (Nt) with (A . T) regions of DNA is characterized by a spectrum of discrete modes. This has been revealed by viscometric analysis, at 20 degrees C and 0.2 M "counterions", for NaDNA in a preceding and for NH4DNA in this paper. The increase of DNA contour length as induced by one Nt molecule was found to depend on the special mode only, while the respective stiffening is generally higher for NH4DNA. The latter property is interpreted in terms of an enhanced flexibility, relative to that of NaDNA, of the (A . T) cluster segments before complex formation. For some of the interaction modes of the DNA-Nt systems a difference in the number of corresponding binding sites has been observed. This phenomenon is understood by assuming an influence of the counterion species upon existing equilibria between different forms of the (A . T) cluster secondary structure. Not less than 5 to 10% of the total DNA are effected in this manner. Upper limits for the local differences in the axial rise per base pair are 0.04 nm and 0.02 nm. PMID:6258145

Reinert, K E; Thrum, H; Sarfert, E

1980-01-01

372

Folding of an mRNA Pseudoknot Required for Stop Codon Readthrough:  Effects of Mono and Divalent Ions on Stability †  

Microsoft Academic Search

Unfolding of an mRNA pseudoknot that induces ribosome suppression of the gag gene stop codon in Moloney murine leukemia virus has been studied by UV hyperchromicity and calorimetry. The pseudoknot melts in two steps, corresponding to its two helical stems. The total enthalpy of denaturation is170 kcal\\/mol, approximately the value expected for the secondary structure. At low salt concentrations (<50

Thomas C. Gluick; Norma M. Wills; Raymond F. Gesteland; David E. Draper

1997-01-01

373

Structural Variation in Human Apolipoprotein E3 and E4: Secondary Structure, Tertiary Structure, and Size Distribution  

PubMed Central

Human apolipoprotein E (apoE) is a 299-amino-acid protein with a molecular weight of 34 kDa. The difference between the apoE3 and apoE4 isoforms is a single residue substitution involving a Cys-Arg replacement at residue 112. ApoE4 is positively associated with atherosclerosis and late-onset and sporadic Alzheimer's disease (AD). ApoE4 and its C-terminal truncated fragments have been found in the senile plaques and neurofibrillary tangles in the brain of AD patients. However, detail structural information regarding isoform and domain interaction remains poorly understood. We prepared full-length, N-, and C-terminal truncated apoE3 and apoE4 proteins and studied their structural variation. Sedimentation velocity and continuous size distribution analysis using analytical ultracentrifugation revealed apoE372-299 as consisting of a major species with a sedimentation coefficient of 5.9. ApoE472-299 showed a wider and more complicated species distribution. Both apoE3 and E4 N-terminal domain (1–191) existed with monomers as the major component together with some tetramer. The oligomerization and aggregation of apoE protein increased when the C-terminal domain (192–271) was incorporated. The structural influence of the C-terminal domain on apoE is to assist self-association with no significant isoform preference. Circular dichroism and fluorescence studies demonstrated that apoE472-299 possessed a more ?-helical structure with more hydrophobic residue exposure. The structural variation of the N-terminal truncated apoE3 and apoE4 protein provides useful information that helps to explain the greater aggregation of the apoE4 isoform and thus has implication for the involvement of apoE4 in AD. PMID:15475580

Chou, Chi-Yuan; Lin, Yi-Ling; Huang, Yu-Chyi; Sheu, Sheh-Yi; Lin, Ta-Hsien; Tsay, Huey-Jen; Chang, Gu-Gang; Shiao, Ming-Shi

2005-01-01

374

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

PubMed Central

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

2014-01-01

375

Perturbed Amelogenin Secondary Structure Leads to Uncontrolled Aggregation in Amelogenesis Imperfecta Mutant Proteins*  

PubMed Central

Mutations in amelogenin sequence result in defective enamel, and the diverse group of genetically altered conditions is collectively known as amelogenesis imperfecta (AI). Despite numerous studies, the detailed molecular mechanism of defective enamel formation is still unknown. In this study, we have examined the biophysical properties of a recombinant murine amelogenin (rM180) and two point mutations identified from human DNA sequences in two cases of AI (T21I and P41T). At pH 5.8 and 25 °C, wild type (WT) rM180 and mutant P41T existed as monomers, and mutant T21I formed lower order oligomers. CD, dynamic light scattering, and fluorescence studies indicated that rM180 and P41T can be classified as a premolten globule-like subclass protein at 25 °C. Thermal denaturation and refolding monitored by CD ellipticity at 224 nm indicated the presence of a strong hysteresis in mutants compared with WT. Variable temperature tryptophan fluorescence and dynamic light scattering studies showed that WT transformed to a partially folded conformation upon heating and remained stable. The partially folded conformation formed by P41T, however, readily converted into a heterogeneous population of aggregates. T21I existed in an oligomeric state at room temperature and, upon heating, rapidly formed large aggregates over a very narrow temperature range. Thermal denaturation and refolding studies indicated that the mutants are less stable and exhibit poor refolding ability compared with WT rM180. Our results suggest that alterations in self-assembly of amelogenin are a consequence of destabilization of the intrinsic disorder. Therefore, we propose that, like a number of other human diseases, AI appears to be due to the destabilization of the secondary structure as a result of amelogenin mutations. PMID:20929860

Lakshminarayanan, Rajamani; Bromley, Keith M.; Lei, Ya-Ping; Snead, Malcolm L.; Moradian-Oldak, Janet

2010-01-01

376

Genomic mid-range inhomogeneity correlates with an abundance of RNA secondary structures  

PubMed Central

Background Genomes possess different levels of non-randomness, in particular, an inhomogeneity in their nucleotide composition. Inhomogeneity is manifest from the short-range where neighboring nucleotides influence the choice of base at a site, to the long-range, commonly known as isochores, where a particular base composition can span millions of nucleotides. A separate genomic issue that has yet to be thoroughly elucidated is the role that RNA secondary structure (SS) plays in gene expression. Results We present novel data and approaches that show that a mid-range inhomogeneity (~30 to 1000 nt) not only exists in mammalian genomes but is also significantly associated with strong RNA SS. A whole-genome bioinformatics investigation of local SS in a set of 11,315 non-redundant human pre-mRNA sequences has been carried out. Four distinct components of these molecules (5'-UTRs, exons, introns and 3'-UTRs) were considered separately, since they differ in overall nucleotide composition, sequence motifs and periodicities. For each pre-mRNA component, the abundance of strong local SS (< -25 kcal/mol) was a factor of two to ten greater than a random expectation model. The randomization process preserves the short-range inhomogeneity of the corresponding natural sequences, thus, eliminating short-range signals as possible contributors to any observed phenomena. Conclusion We demonstrate that the excess of strong local SS in pre-mRNAs is linked to the little explored phenomenon of genomic mid-range inhomogeneity (MRI). MRI is an interdependence between nucleotide choice and base composition over a distance of 20–1000 nt. Additionally, we have created a public computational resource to support further study of genomic MRI. PMID:18549495

Bechtel, Jason M; Wittenschlaeger, Thomas; Dwyer, Trisha; Song, Jun; Arunachalam, Sasi; Ramakrishnan, Sadeesh K; Shepard, Samuel; Fedorov, Alexei

2008-01-01

377

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

PubMed

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

Yan, Jing; Marcus, Max; Kurgan, Lukasz

2014-01-01

378

Tunable Loading of Oligonucleotides with Secondary Structure on Gold Nanoparticles through a pH-Driven Method.  

PubMed

This paper describes how pH can be used to control covalent attachment of oligonucleotides with secondary structure on gold nanoparticles (AuNPs). The highest loading of thiolated nucleic acids occurred at low pH (pH = 1.7) due to reduced repulsion between the negatively charged oligonucleotides and the AuNP surface. The packing of oligonucleotides at low pH decreased (single-stranded ? duplex > quadruplex) as the spatial footprint of secondary structure increased. As the pH increased, a decrease in the number of DNA strands grafted to the AuNPs was observed. Notably, the loading density depended on the flexibility and spatial organization of the secondary structures at all pH conditions. At the lowest pH tested, circular dichroism analysis revealed that G-quadruplex aptamers underwent a structural change (from parallel to antiparallel or vice versa), although the biological activity of the aptamer-loaded AuNPs was still maintained. We anticipate that pH-tuning can result in quantitative loading of oligonucleotides on various types of AuNPs with different shapes and surface capping layers. PMID:25564799

Dam, Duncan Hieu M; Lee, Hyojin; Lee, Raymond C; Kim, Ki Hun; Kelleher, Neil L; Odom, Teri W

2015-02-18

379

Far upstream element-binding protein 1 and RNA secondary structure both mediate second-step splicing repression  

PubMed Central

Splicing of mRNA precursors consists of two steps that are almost invariably tightly coupled to facilitate efficient generation of spliced mRNA. However, we described previously a splicing substrate that is completely blocked after the first step. We have now investigated the basis for this unusual second-step inhibition and unexpectedly elucidated two independent mechanisms. One involves a stem–loop structure located downstream of the 3?splice site, and the other involves an exonic splicing silencer (ESS) situated 3? to the structure. Both elements contribute to the second-step block in vitro and also cause exon skipping in vivo. Importantly, we identified far upstream element-binding protein 1 (FUBP1), a single-stranded DNA- and RNA-binding protein not previously implicated in splicing, as a strong ESS binding protein, and several assays implicate it in ESS function. We demonstrate using depletion/add-back experiments that FUBP1 acts as a second-step repressor in vitro and show by siRNA-mediated knockdown and overexpression assays that it modulates exon inclusion in vivo. Together, our results provide additional insights into splicing control, and identify FUBP1 as a splicing regulator. PMID:23818605

Li, Huang; Wang, Zhijia; Zhou, Xuexia; Cheng, Yuanming; Xie, Zhiqin; Manley, James L.; Feng, Ying

2013-01-01

380

Far upstream element-binding protein 1 and RNA secondary structure both mediate second-step splicing repression.  

PubMed

Splicing of mRNA precursors consists of two steps that are almost invariably tightly coupled to facilitate efficient generation of spliced mRNA. However, we described previously a splicing substrate that is completely blocked after the first step. We have now investigated the basis for this unusual second-step inhibition and unexpectedly elucidated two independent mechanisms. One involves a stem-loop structure located downstream of the 3'splice site, and the other involves an exonic splicing silencer (ESS) situated 3' to the structure. Both elements contribute to the second-step block in vitro and also cause exon skipping in vivo. Importantly, we identified far upstream element-binding protein 1 (FUBP1), a single-stranded DNA- and RNA-binding protein not previously implicated in splicing, as a strong ESS binding protein, and several assays implicate it in ESS function. We demonstrate using depletion/add-back experiments that FUBP1 acts as a second-step repressor in vitro and show by siRNA-mediated knockdown and overexpression assays that it modulates exon inclusion in vivo. Together, our results provide additional insights into splicing control, and identify FUBP1 as a splicing regulator. PMID:23818605

Li, Huang; Wang, Zhijia; Zhou, Xuexia; Cheng, Yuanming; Xie, Zhiqin; Manley, James L; Feng, Ying

2013-07-16

381

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

SciTech Connect

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

Tsuboi, Yasuyuki; Goto, Masaharu; Itaya, Akira

2001-06-15

382

The secondary structure of human 28S rRNA: The structure and evolution of a mosaic rRNA gene  

Microsoft Academic Search

Summary We have determined the secondary structure of the human 28S rRNA molecule based on comparative analysis of available eukaryotic cytoplasmic and prokaryotic large-rRNA gene sequences. Examination of large-rRNA sequences of both distantly and closely related species has enabled us to derive a structure that accounts both for highly conserved sequence tracts and for previously unanalyzed variable-sequence tracts that account

Jerome L. Gorski; Iris L. Gonzalez; Roy D. Schmickel

1987-01-01

383

Vibrational Circular Dichroism Spectra of Proteins in the Amide III Region: Measurement and Correlation of Bandshape to Secondary Structure  

Microsoft Academic Search

Vibrational circular dichroism (VCD) spectra have been measured for 23 globular proteins dissolved in H2O\\/phosphate buffer over the 1400 to 1100 cm?1region which encompasses the amide III mode. Spectral responses characteristic of the dominant secondary structure type were found as broad features at ?1300 cm?1, with the extreme forms having positive VCD for highly helical proteins and negative VCD for

Bernoli I. Baello; Petr Pancoska; Timothy A. Keiderling

1997-01-01

384

The chemical shift index: A fast and simple method for the assignment of protein secondary structure through NMR spectroscopy  

Microsoft Academic Search

Previous studies by Wishart et al. have demonstrated that ¹H NMR chemical shifts are strongly dependent on the character and nature of protein secondary structure. In particular, it has been found that the ¹H NMR chemical shift of the α-CH proton of all 20 naturally occurring amino acids experiences an upfield shift (with respect to the random coil value) when

D. S. Wishart; B. D. Sykes; F. M. Richards

1992-01-01

385

Acorn barnacle Megabalanus rosa lectin (BRA-3): cDNA cloning, gene structure and seasonal changes of mRNA and protein levels.  

PubMed

We have isolated cDNA clones coding for a lectin (BRA-3) from the acorn barnacle, Megabalanus rosa. Sequence comparison of the cDNA clones has revealed polymorphism in the BRA-3 mRNA, which results from single-nucleotide (nt) differences at three positions. All three differences are within the coding region and cause conservative amino acid (aa) changes. The BRA-3 gene is composed of four exons, and the three single-nt differences are located on different exons. In addition, the BRA-3 mRNA and BRA-3 protein levels increased during early summer in a similar fashion, indicating that BRA-3 production is regulated mainly at the level of transcription. PMID:8514190

Takamatsu, N; Takeda, T; Kojima, M; Heishi, M; Muramoto, K; Kamiya, H; Shiba, T

1993-06-30

386

Sensitive and label-free biosensing of RNA with predicted secondary structures by a triplex affinity capture method  

PubMed Central

A novel biosensing approach for the label-free detection of nucleic acid sequences of short and large lengths has been implemented, with special emphasis on targeting RNA sequences with secondary structures. The approach is based on selecting 8-aminoadenine-modified parallel-stranded DNA tail-clamps as affinity bioreceptors. These receptors have the ability of creating a stable triplex-stranded helix at neutral pH upon hybridization with the nucleic acid target. A surface plasmon resonance biosensor has been used for the detection. With this strategy, we have detected short DNA sequences (32-mer) and purified RNA (103-mer) at the femtomol level in a few minutes in an easy and level-free way. This approach is particularly suitable for the detection of RNA molecules with predicted secondary structures, reaching a limit of detection of 50?fmol without any label or amplification steps. Our methodology has shown a marked enhancement for the detection (18% for short DNA and 54% for RNA), when compared with the conventional duplex approach, highlighting the large difficulty of the duplex approach to detect nucleic acid sequences, especially those exhibiting stable secondary structures. We believe that our strategy could be of great interest to the RNA field. PMID:22241768

Carrascosa, Laura G.; Gómez-Montes, S.; Aviñó, A.; Nadal, A.; Pla, M.; Eritja, R.; Lechuga, L. M.

2012-01-01

387

Sequential sup 1 H NMR assignments and secondary structure of an IgG-binding domain from protein G  

SciTech Connect

Protein G is a member of a class of cell surface bacterial proteins from Streptococcus that bind IgG with high affinity. A fragment of molecular mass 6,988, which retains IgG-binding activity, has been generated by proteolytic digestion and analyzed by {sup 1}H NMR. Two-dimenstional DQF-COSY, TOCSY, and NOESY spectra have been employed to assign the {sup 1}H NMR spectrum of the peptide. Elements of regular secondary structure have been identified by using nuclear Overhauser enhancement, coupling constant, and amide proton exchange data. The secondary structure consists of a central {alpha}-helix (Ala28-Val44), flanked by two portions of {beta}-sheet (Val5-Val26 and Asp45-Lys62). This is a fundamentally different arrangement of secondary structure from that of protein A, which is made up of three consecutive {alpha}-helics in free solution. The authors conclude that the molecular mechanisms underlying the association of protein A and protein G with IgG are different.

Lian, L.Y.; Yang, J.C.; Derrick, J.P.; Sutcliffe, M.J.; Roberts, G.C.K. (Univ. of Leicester (England)); Murphy, J.P.; Goward, C.R.; Atkinson, T. (PHLS Center for Applied Microbiology and Research, Porton Down, Salisbury (England))

1991-06-04

388

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

PubMed Central

Solving high-resolution structures for membrane proteins continues to be a daunting challenge in the structural biology community. In this study we report our high-resolution NMR results for a transmembrane protein, outer envelope protein of molar mass 16 kDa (OEP16), an amino acid transporter from the outer membrane of chloroplasts. Three-dimensional, high-resolution NMR experiments on the 13C, 15N, 2H-triply-labeled protein were used to assign protein backbone resonances and to obtain secondary structure information. The results yield over 95% assignment of N, HN, CO, C?, and C? chemical shifts, which is essential for obtaining a high resolution structure from NMR data. Chemical shift analysis from the assignment data reveals experimental evidence for the first time on the location of the secondary structure elements on a per residue basis. In addition T1Z and T2 relaxation experiments were performed in order to better understand the protein dynamics. Arginine titration experiments yield an insight into the amino acid residues responsible for protein transporter function. The results provide the necessary basis for high-resolution structural determination of this important plant membrane protein. PMID:24205117

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

2013-01-01

389

Tri- to be mono- for bacterial mRNA decay.  

PubMed

Messing et al. (2009) report the homodimeric structure of the Bdellovibrio bacteriovorus RppH pyrophosphohydrolase, which hydrolyzes the mRNA 5' triphosphate to initiate bacterial mRNA decay. These structures reveal insights into BdRppH substrate recognition and analogies to eukaryotic decapping enzymes. PMID:19278643

Bail, Sophie; Kiledjian, Megerditch

2009-03-11

390

[Study of the secondary and tertiary structure of phage MS2 RNA using nucleases and fluorescent dyes specific for secondary structure].  

PubMed

The binding of ethidium bromide (EtBr) and acridine orange (AO) to RNA in native state or after hydrolysis by S1 and SV nucleases that specifically split single-stranded and double-stranded segments was studied. Nuclease S1 hydrolysis of RNA does not increase the number of EtBr strong binding sites, Tm and hyperchromic effect being also unchanged. Hydrolysis by double-stranded segments accessible to EtBr is followed by the diminishing of Tm and hyperchromism. A supposition is put forward that the main role in stabilization of the RNA tertiary structure is played by double-stranded segments arranged so that some of them are hidden and do not interact with dyes. One of the possible models may be parallel oriented intramolecular "hair-pins" forming compact "rod-like" structures. PMID:6097815

Borisova, O F; Grechko, V V; Aleshkina, L A; Kuznetsova, N V

1984-01-01

391

The Structure of Scientific Arguments by Secondary Science Teachers: Comparison of experimental and historical science topics  

Microsoft Academic Search

Just as scientific knowledge is constructed using distinct modes of inquiry (e.g. experimental or historical), arguments constructed during science instruction may vary depending on the mode of inquiry underlying the topic. The purpose of this study was to examine whether and how secondary science teachers construct scientific arguments during instruction differently for topics that rely on experimental or historical modes

Ron Gray; Nam-Hwa Kang

2012-01-01

392

Combining evolutionary information and neural networks to predict protein secondary structure  

Microsoft Academic Search

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

Burkhard Rost; Chris Sander

1994-01-01

393

The Structure of Scientific Arguments by Secondary Science Teachers: Comparison of Experimental and Historical Science Topics  

ERIC Educational Resources Information Center

Just as scientific knowledge is constructed using distinct modes of inquiry (e.g. experimental or historical), arguments constructed during science instruction may vary depending on the mode of inquiry underlying the topic. The purpose of this study was to examine whether and how secondary science teachers construct scientific arguments during…

Gray, Ron; Kang, Nam-Hwa

2014-01-01

394

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

PubMed Central

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

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

2014-01-01

395

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

ERIC Educational Resources Information Center

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

Lowe, Patricia A.; Lee, Steven W.

2008-01-01

396

Predictions of Secondary Structure using Statistical Analyses of Electronic and Vibrational Circular Dichroism and Fourier Transform Infrared Spectra of Proteins in H 2O  

Microsoft Academic Search

Vibrational circular dichroism (VCD) and Fourier transform IR (FTIR) methods for prediction of protein secondary structure are systematically compared using selective regression analysis. VCD and FTIR spectra over the amide I and II bands of 23 proteins dissolved in H2O were analyzed using the principal component method of factor analysis (PC\\/FA) and regression fits to fractional components (FC) of secondary

Vladimir Baumruk; Petr Pancoska; Timothy A. Keiderling

1996-01-01

397

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

PubMed

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

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

2015-04-01

398

Maintenance of Pdx1 mRNA translation in islet ?-cells during the unfolded protein response.  

PubMed

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

Templin, Andrew T; Maier, Bernhard; Tersey, Sarah A; Hatanaka, Masayuki; Mirmira, Raghavendra G

2014-11-01

399

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

E-print Network

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

Einert, Thomas R; Netz, Roland R

2011-01-01

400

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

PubMed Central

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

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

2014-01-01

401

Termination of transcription by Escherichia coli RNA polymerase: Influence of secondary structure of RNA transcripts on ?-independent and ?-dependent termination  

PubMed Central

The effect of RNA secondary structure on ?-independent and ?-dependent termination of transcription of T3 DNA by Escherichia coli RNA polymerase has been studied by incorporating, into nascent transcripts, base analogs that lead to altered base-pairing properties. A guanine ? hypoxanthine substitution, with attendant weakening of secondary structure, abolished the ?-independent termination at 20% of the genome; in contrast, replacement of cytosine with 5-bromocytosine, which forms stronger pairs with guanine, enhanced termination at this site. ?-Independent termination was not altered by replacing uracil with 5-bromouracil. There are two major ?-dependent termination sites on the T3 DNA—at 8 and 15%. The termination activity of ? in this system also depended on RNA secondary structure. The incorporation of 5-bromouracil instead of uracil into RNA did not alter the site specificity of ? action but ? was rendered inactive when cytosine was replaced by 5-bromocytosine. In contrast, replacement of GTP with ITP in the reaction increased ?-dependent inhibition of RNA synthesis, caused production of heterogeneous-sized transcripts, and stimulated ?-mediated ATP hydrolysis. The ?-associated ATPase activity, in the presence of isolated T3 RNA, was also stimulated by inosine substitution. Furthermore, the temperature-sensitive ? isolated from rho 15 mutant of E. coli, which does not terminate transcription in the presence of the common rNTPs, was active when GTP was replaced with ITP. These results suggest that strongly paired G·C-rich regions in RNA stem-loop structures or RNA·DNA hybrids are essential for ?-independent termination, whereas ?-dependent termination requires weakly paired cytosine residues for its action. Images PMID:156360

Adhya, Samit; Sarkar, Probir; Valenzuela, David; Maitra, Umadas

1979-01-01

402

Secondary plant products causing photosensitization in grazing herbivores: their structure, activity and regulation.  

PubMed

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

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

2014-01-01

403

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

PubMed Central

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

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

2014-01-01

404

Structural and kinetic characterization of lithium intercalation into carbon anodes for secondary lithium batteries  

Microsoft Academic Search

Electrochemical intercalation of lithium into carbons has been studied using mesophase-pitch-based carbon fibers with different heat-treatment temperatures, coke, and graphites as anodes for secondary lithium batteries. The variations in the average layer spacing and the voltage profile for the carbons with intercalating depend on the degree of graphitization. The intercalation into a more disordered carbon fiber heated at 900 C

Norio Takami; Asako Satoh; Michikazu Hara; Takahisa Ohsaki

1995-01-01

405

Fourier transform infrared spectroscopic studies of the secondary structure and thermal denaturation of CaATPase from rabbit skeletal muscle  

NASA Astrophysics Data System (ADS)

Fourier transform i.r. spectroscopy has been used to monitor structural alterations induced by thermal denaturation of the intrinsic membrane protein CaATPase in aqueous media. The protein has been isolated, purified and studied in five forms: (i) In its native lipid environment after isolation from rabbit sarcoplasmic reticulum, both in H 2O and D 2O suspensions. (ii) After both mild and extensive tryptic digestion has cleaved those residues external to the membrane bilayer. (iii) Reconstituted in vesicle form with bovine brain sphingomyelin. Fourier deconvolution techniques have been used to enhance the resolution of the intrinsically overlapped Amide I and Amide II spectral regions. Large spectral alterations apparent in the deconvoluted spectra occur in these regions upon thermal denaturation of the protein which are consistent with the formation of a large proportion of ?-antiparallel sheet form. The alteration parallels the loss in ATPase activity. A mild tryptic digestion increases slightly the proportion of ?-helix and/or random coil secondary structure. A thermal transition to a form containing a high proportion of ? structure is still evident. Extensive tryptic digestion nearly abolishes the alpha helical plus random coil secondary structure, while producing a high proportion of ? form which is resistant to further thermally induced structural alterations. Studies of CaATPase reconstituted into vesicles with bovine brain sphingomyelin reveal a higher proportion of ? structure than the native enzyme, with further introduction of ? structure on thermal denaturation. Both the utility of deconvolution techniques and the necessity for caution in their application are apparent from the current experiments.

Jaworsky, Mark; Brauner, Joseph W.; Mendelsohn, Richard

406

Induced Secondary Structure and Polymorphism in an Intrinsically Disordered Structural Linker of the CNS: Solid-State NMR and FTIR Spectroscopy of Myelin Basic Protein Bound to Actin  

PubMed Central

Abstract The 18.5 kDa isoform of myelin basic protein (MBP) is a peripheral membrane protein that maintains the structural integrity of the myelin sheath of the central nervous system by conjoining the cytoplasmic leaflets of oligodendrocytes and by linking the myelin membrane to the underlying cytoskeleton whose assembly it strongly promotes. It is a multifunctional, intrinsically disordered protein that behaves primarily as a structural stabilizer, but with elements of a transient or induced secondary structure that represent binding sites for calmodulin or SH3-domain-containing proteins, inter alia. In this study we used solid-state NMR (SSNMR) and Fourier transform infrared (FTIR) spectroscopy to study the conformation of 18.5 kDa MBP in association with actin microfilaments and bundles. FTIR spectroscopy of fully 13C,15N-labeled MBP complexed with unlabeled F-actin showed induced folding of both protein partners, viz., some increase in ?-sheet content in actin, and increases in both ?-helix and ?-sheet content in MBP, albeit with considerable extended structure remaining. Solid-state NMR spectroscopy revealed that MBP in MBP-actin assemblies is structurally heterogeneous but gains ordered secondary structure elements (both ?-helical and ?-sheet), particularly in the terminal fragments and in a central immunodominant epitope. The overall conformational polymorphism of MBP is consistent with its in vivo roles as both a linker (membranes and cytoskeleton) and a putative signaling hub. PMID:19134474

Ahmed, Mumdooh A.M.; Bamm, Vladimir V.; Shi, Lichi; Steiner-Mosonyi, Marta; Dawson, John F.; Brown, Leonid; Harauz, George; Ladizhansky, Vladimir

2009-01-01

407

Induced secondary structure and polymorphism in an intrinsically disordered structural linker of the CNS: solid-state NMR and FTIR spectroscopy of myelin basic protein bound to actin.  

PubMed

The 18.5 kDa isoform of myelin basic protein (MBP) is a peripheral membrane protein that maintains the structural integrity of the myelin sheath of the central nervous system by conjoining the cytoplasmic leaflets of oligodendrocytes and by linking the myelin membrane to the underlying cytoskeleton whose assembly it strongly promotes. It is a multifunctional, intrinsically disordered protein that behaves primarily as a structural stabilizer, but with elements of a transient or induced secondary structure that represent binding sites for calmodulin or SH3-domain-containing proteins, inter alia. In this study we used solid-state NMR (SSNMR) and Fourier transform infrared (FTIR) spectroscopy to study the conformation of 18.5 kDa MBP in association with actin microfilaments and bundles. FTIR spectroscopy of fully (13)C,(15)N-labeled MBP complexed with unlabeled F-actin showed induced folding of both protein partners, viz., some increase in beta-sheet content in actin, and increases in both alpha-helix and beta-sheet content in MBP, albeit with considerable extended structure remaining. Solid-state NMR spectroscopy revealed that MBP in MBP-actin assemblies is structurally heterogeneous but gains ordered secondary structure elements (both alpha-helical and beta-sheet), particularly in the terminal fragments and in a central immunodominant epitope. The overall conformational polymorphism of MBP is consistent with its in vivo roles as both a linker (membranes and cytoskeleton) and a putative signaling hub. PMID:19134474

Ahmed, Mumdooh A M; Bamm, Vladimir V; Shi, Lichi; Steiner-Mosonyi, Marta; Dawson, John F; Brown, Leonid; Harauz, George; Ladizhansky, Vladimir

2009-01-01

408

Expression of bacteriophage T4 gene 25 is regulated via RNA secondary structure in the translational initiation region.  

PubMed

Analysis of the nucleotide sequence in the 5' flanking region of bacteriophage T4 gene 25 revealed three potential Shine and Dalgarno sequences, SD1, SD2 and SD3, with a spacing of 8, 17 and 27 nucleotides from the initiation codon of this gene, respectively. Results of our experiments in the bacteriophage T7 expression system clearly demonstrate that the SD3 sequence is required for efficient expression of gene 25. We propose the existence of a stem-loop structure that includes SD1 and SD2 sequences and brings the SD3 sequence to a favourable spacing with the initiation codon of gene 25. Since the predicted secondary structure in the translational initiation region of gene 25 is relatively unstable and the SD3 sequence, GAGG, is more typical than the SD1 sequence, GAG, we suggest that this structure could control the level of gene expression. PMID:8478927

Nivinskas, R; Vaiskunaite, R; Raudonikiene, A

1993-04-01