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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, Jose Luis



Conflicting selection pressures on synonymous codon use in yeast suggest selection on mRNA secondary structures  

Microsoft Academic Search

BACKGROUND: Eukaryotic mRNAs often contain secondary structures in their untranslated regions that are involved in expression regulation. Whether secondary structures in the protein coding regions are of functional importance remains unclear: laboratory studies suggest stable secondary structures within the protein coding sequence interfere with translation, while several bioinformatic studies indicate stable mRNA structures are more frequent than expected. RESULTS: In

Nina Stoletzki



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

SciTech Connect

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

Kozak, M.



Secondary structures involving the poly(A) tail and other 3? sequences are major determinants of mRNA isoform stability in yeast  

PubMed Central

In Saccharomyces cerevisiae, previous measurements of mRNA stabilities have been determined on a per-gene basis. We and others have recently shown that yeast genes give rise to a highly heterogeneous population of mRNAs thanks to extensive alternative 3? end formation. Typical genes can have fifty or more distinct mRNA isoforms with 3? endpoints differing by as little as one and as many as hundreds of nucleotides. In our recent paper [Geisberg et al. Cell (2014) 156: 812–824] we measured half-lives of individual mRNA isoforms in Saccharomyces cerevisiae by using the anchor away method for the rapid removal of Rpb1, the largest subunit of RNA Polymerase II, from the nucleus, followed by direct RNA sequencing of the cellular mRNA population over time. Combining these two methods allowed us to determine half-lives for more than 20,000 individual mRNA isoforms originating from nearly 5000 yeast genes. We discovered that different 3? mRNA isoforms arising from the same gene can have widely different stabilities, and that such half-life variability across mRNA isoforms from a single gene is highly prevalent in yeast cells. Determining half-lives for many different mRNA isoforms from the same genes allowed us to identify hundreds of RNA sequence elements involved in the stabilization and destabilization of individual isoforms. In many cases, the poly(A) tail is likely to participate in the formation of stability-enhancing secondary structures at mRNA 3? ends. Our results point to an important role for mRNA structure at 3? termini in governing transcript stability, likely by reducing the interaction of the mRNA with the degradation apparatus.

Moqtaderi, Zarmik; Geisberg, Joseph V.; Struhl, Kevin



The relationship between third-codon position nucleotide content, codon bias, mRNA secondary structure and gene expression in the drosophilid alcohol dehydrogenase genes Adh and Adhr.  


To gain insights into the relationship between codon bias, mRNA secondary structure, third-codon position nucleotide distribution, and gene expression, we predicted secondary structures in two related drosophilid genes, Adh and Adhr, which differ in degree of codon bias and level of gene expression. Individual structural elements (helices) were inferred using the comparative method. For each gene, four types of randomization simulations were performed to maintain/remove codon bias and/or to maintain or alter third-codon position nucleotide composition (N3). In the weakly expressed, weakly biased gene Adhr, the potential for secondary structure formation was found to be much stronger than in the highly expressed, highly biased gene Adh. This is consistent with the observation of approximately equal G and C percentages in Adhr ( approximately 31% across species), whereas in Adh the N3 distribution is shifted toward C (42% across species). Perturbing the N3 distribution to approximately equal amounts of A, G, C, and T increases the potential for secondary structure formation in Adh, but decreases it in Adhr. On the other hand, simulations that reduce codon bias without changing N3 content indicate that codon bias per se has only a weak effect on the formation of secondary structures. These results suggest that, for these two drosophilid genes, secondary structure is a relatively independent, negative regulator of gene expression. Whereas the degree of codon bias is positively correlated with level of gene expression, strong individual secondary structural elements may be selected for to retard mRNA translation and to decrease gene expression. PMID:11606539

Carlini, D B; Chen, Y; Stephan, W



Optimisation of the mRNA secondary structure to improve the expression of interleukin-24 (IL-24) in Escherichia coli.  


Interleukin-24 (IL-24) is a novel cytokine selectively inhibiting proliferation of cancer cells but with little effect on normal cells. However, IL-24 is difficult to express in Escherichia coli. In this study, we optimised the secondary structure of the translation initiation region using computational approach to obtain non-fusion recombinant IL-24 (nrIL-24). The Gibbs free energy of the region was decreased from -22 to -9.07 kcal mol(-1), potentially promoting a loose secondary structure formation and improving the translation initiation efficiency. As a result, the expression of nrIL-24 was increased to 26 % of the total cellular protein from being barely initially detectable. nrIL-24 showed a concentration-dependent inhibition of A375 cells but had little effect on normal human cells. These results demonstrate that this method in increasing nrIL-24 expression is effective and efficient. PMID:24752814

Bai, Chaogang; Wang, Xiaojuan; Zhang, Jian; Sun, Aiyou; Wei, Dongzhi; Yang, Shengli



Protein secondary structure prediction.  


While the prediction of a native protein structure from sequence continues to remain a challenging problem, over the past decades computational methods have become quite successful in exploiting the mechanisms behind secondary structure formation. The great effort expended in this area has resulted in the development of a vast number of secondary structure prediction methods. Especially the combination of well-optimized/sensitive machine-learning algorithms and inclusion of homologous sequence information has led to increased prediction accuracies of up to 80%. In this chapter, we will first introduce some basic notions and provide a brief history of secondary structure prediction advances. Then a comprehensive overview of state-of-the-art prediction methods will be given. Finally, we will discuss open questions and challenges in this field and provide some practical recommendations for the user. PMID:20221928

Pirovano, Walter; Heringa, Jaap



Differential accumulation of nif structural gene mRNA in Azotobacter vinelandii.  


Northern analysis was employed to investigate mRNA produced by mutant strains of Azotobacter vinelandii with defined deletions in the nif structural genes and in the intergenic noncoding regions. The results indicate that intergenic RNA secondary structures effect the differential accumulation of transcripts, supporting the high Fe protein-to-MoFe protein ratio required for optimal diazotrophic growth. PMID:21725008

Hamilton, Trinity L; Jacobson, Marty; Ludwig, Marcus; Boyd, Eric S; Bryant, Donald A; Dean, Dennis R; Peters, John W



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.



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)



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

PubMed Central

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

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



Secondary Structure Prediction of Proposed RNAi  

E-print Network

Secondary Structure Prediction of Proposed RNAi Targets: Can Current Energy Minimization Algorithms structures such as pseudoknots has proved a challenge, relatively recent advances in modeling algorithms have allowed for the development of several web-based secondary structure modeling programs. Until now, most


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



Current perspectives on RNA secondary structure probing.  


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



Network for Protein Secondary Structure Prediction  

Microsoft Academic Search

The formation of protein secondary structure especially the regions of fl-sheets involves long-range interactions between amino acids. We propose a novel recurrent neural network architecture called Segmented-Memory Recurrent Neural Network (SMRNN) and present experimental results showing that SMRNN outperforms conventional recurrent neu- ral networks on long-term dependency problems. In order to capture long-term dependencies in protein sequences for secondary structure

Jinmiao Chen; Narendra S. Chaudhari


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



Corticothalamic cells in layers 5 and 6 of primary and secondary sensory cortex express GAP-43 mRNA in the adult rat.  


The expression of a presynaptic phosphoprotein, growth-associated protein (GAP)-43, is associated with synaptogenesis during development and synaptic remodeling in the adult. This study examined GAP-43 mRNA expression and distribution in primary and secondary areas of visual, auditory, and somatosensory cortex of the adult rat, by in situ hybridization with a digoxigenin-coupled mRNA probe, focusing particularly on the corticothalamic cells in layers 5 and 6. In the six cortical areas studied, GAP-43 mRNA was expressed predominantly in layers 5 and 6 and was greater in secondary than primary areas. There were densely labeled cells in layers 5 and 6 of all areas, which showed a restricted sublaminar distribution in primary areas and more even distribution in secondary areas. Combining retrograde transport of rhodamine beads with in situ hybridization in visual and auditory cortex showed that corticothalamic cells in layers 5 and 6 express GAP-43 mRNA. There are more of these GAP-43 mRNA positive corticothalamic cells in layer 5 of secondary areas than in primary areas. The evidence suggests that in the adult rat, plasticity related to GAP-43 is present in primary and secondary sensory cortex and more so in secondary areas. PMID:14648693

Feig, Sherry L



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.



The Jpred 3 secondary structure prediction server  

PubMed Central

Jpred ( is a secondary structure prediction server powered by the Jnet algorithm. Jpred performs over 1000 predictions per week for users in more than 50 countries. The recently updated Jnet algorithm provides a three-state (?-helix, ?-strand and coil) prediction of secondary structure at an accuracy of 81.5%. Given either a single protein sequence or a multiple sequence alignment, Jpred derives alignment profiles from which predictions of secondary structure and solvent accessibility are made. The predictions are presented as coloured HTML, plain text, PostScript, PDF and via the Jalview alignment editor to allow flexibility in viewing and applying the data. The new Jpred 3 server includes significant usability improvements that include clearer feedback of the progress or failure of submitted requests. Functional improvements include batch submission of sequences, summary results via email and updates to the search databases. A new software pipeline will enable Jnet/Jpred to continue to be updated in sync with major updates to SCOP and UniProt and so ensures that Jpred 3 will maintain high-accuracy predictions. PMID:18463136

Cole, Christian; Barber, Jonathan D.; Barton, Geoffrey J.



Investigation of the number of possible secondary RNA structures  

E-print Network

Investigation of the number of possible secondary RNA structures with reference to theoretical of counting the number of possible RNA secondary structures is closely linked to predicting RNA secondary structures. In this project the formula given in Zuker and Sankoff [1984] is investigated and compared

Goldschmidt, Christina


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.



The Structural Basis for mRNA Recognition and Cleavage by the  

E-print Network

. coli RelE in isolation (2.5 A° ) and bound to pro- grammed Thermus thermophilus 70S ribosomes before (3; Pedersen et al., 2003). After the controlled degradation of RelB by Lon protease, RelE is able to bindThe Structural Basis for mRNA Recognition and Cleavage by the Ribosome-Dependent Endonuclease RelE

Ramakrishnan, Venki


Simplicity in RNA Secondary Structure Alignment: Towards biologically plausible alignments  

Microsoft Academic Search

Ribonucleic acid (RNA) molecules contain the genetic information that regulates the functions of organisms. Given two different molecules, a preserved function corresponds to a preserved secondary RNA structure. Hence, RNA secondary-structure comparison is essential in predicting the functions of a newly discovered molecule. In this paper, we discuss our SPRC method for RNA structure comparison. In this work, we developed,

Rimon Mikhaiel; Guohui Lin; Eleni Stroulia



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)



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


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

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



A classifier system for predicting RNA secondary structure.  


Finding the secondary structures of ribonucleic acid sequences is a very important task. The secondary structure helps determine their functionalities which in turn plays a role in the proteins production. Manual laboratory methods use X-ray diffraction to predict secondary structures but it is complex, slow and expensive. Therefore, different computational approaches are used to predict RNA secondary structure in order to reduce the time and cost associated with the manual process. We propose a system called IsRNA to predict a single element, internal loop, of the RNA secondary structure. IsRNA experiments with different classifiers such as SVM, KNN, Naive Bayes and Simple K means to find the most accurate classifier. We present a through experimental evaluation of 24 features, classified into five groups, to determine the most relevant feature groups. The system is evaluated using Rfam sequences and achieves an overall sensitivity, selectivity, and accuracy of 96.1%, 98%, and 96.1%, respectively. PMID:24794072

Aldwairi, Monther; Al-Hajasad, Bashar; Khamayseh, Yaser



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).  


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



Pure Multiple RNA Secondary Structure Alignments: A Progressive Profile Approach  

E-print Network

Pure Multiple RNA Secondary Structure Alignments: A Progressive Profile Approach Matthias Ho¨chsmann, Bjo¨rn Voss, and Robert Giegerich Abstract--In functional, noncoding RNA, structure is often essential to function. While the full 3D structure is very difficult to determine, the 2D structure of an RNA molecule

Moeller, Ralf


Unified approach to partition functions of RNA secondary structures.  


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

Bundschuh, Ralf



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



Hormones, Sex Accessory Structures, and Secondary Sexual Characteristics  

E-print Network

Chapter 5 Hormones, Sex Accessory Structures, and Secondary Sexual Characteristics in Amphibians University, Spokane, WA, USA SUMMARY Gonadal steroid hormones, particularly testosterone (T) and related hormones, such as prolactin, have been found to be necessary in conjunction with gonadal steroids

Sever, David M.


GTfold: A Scalable Multicore Code for RNA Secondary Structure Prediction  

E-print Network

, and the secondary structure of viruses like dengue [3], ebola [16], and HIV [17] is known to have functional significance. Thus, disrupting functionally significant base pairings in RNA viral genomes is one potential

Bader, David A.


Cascaded Bidirectional Recurrent Neural Networks for Protein Secondary Structure Prediction  

Microsoft Academic Search

Protein secondary structure (PSS) prediction is an important topic in bioinformatics. Our study on a large set of non-homologous proteins shows that long-range interactions commonly exist and negatively affect PSS prediction. Besides, we also reveal strong correlations between secondary structure (SS) elements. In order to take into account the long-range interactions and SS-SS correlations, we propose a novel prediction system

Jinmiao Chen; Narendra S. Chaudhari



Secondary structure assignment that accurately reflects physical and evolutionary characteristics  

E-print Network

, for example, left-handed helices. Cut-offs for all parameters used for assigning secondary structure were determined empirically. To do this, authors assigned secondary structure by visual inspection, and adjusted parameters until the automatic assignments... . In the majority of the cases the assignments provided by the various assignment programs are similar (more than 80%). However a further analysis of the results has revealed that this apparent agreement hides many differ- ences particularly in the definition...



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.



Spectrum of disease-causing mutations in protein secondary structures  

PubMed Central

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

Khan, Sofia; Vihinen, Mauno



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



Secondary Structure and Secondary Structure Dynamics of DNA Hairpins Complexed with HIV-1 NC Protein  

PubMed Central

Reverse transcription of the HIV-1 RNA genome involves several complex nucleic acid rearrangement steps that are catalyzed by the HIV-1 nucleocapsid protein (NC), including for example, the annealing of the transactivation response (TAR) region of the viral RNA to the complementary region (TAR DNA) in minus-strand strong-stop DNA. We report herein single-molecule fluorescence resonance energy transfer measurements on single immobilized TAR DNA hairpins and hairpin mutants complexed with NC (i.e., TAR DNA/NC). Using this approach we have explored the conformational distribution and dynamics of the hairpins in the presence and absence of NC protein. The data demonstrate that NC shifts the equilibrium secondary structure of TAR DNA hairpins from a fully “closed” conformation to essentially one specific “partially open” conformation. In this specific conformation, the two terminal stems are “open” or unwound and the other stems are closed. This partially open conformation is arguably a key TAR DNA intermediate in the NC-induced annealing mechanism of TAR DNA. PMID:15454467

Cosa, Gonzalo; Harbron, Elizabeth J.; Zeng, Yining; Liu, Hsiao-Wei; O'Connor, Donald B.; Eta-Hosokawa, Chie; Musier-Forsyth, Karin; Barbara, Paul F.



Predicting Secondary Structural Folding Kinetics for Nucleic Acids  

PubMed Central

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

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



Parsing nucleic acid pseudoknotted secondary structure: algorithm and applications  

E-print Network

Nucleic acids - that is, DNA and RNA molecules - play fundamental roles in the cell: in translation based on dynamic programming aim to find a structure with minimum free energy according to some to calculate the free en- ergy of a pseudoknotted secondary structure. This is useful for heuristic prediction

Condon, Anne


Coating concrete secondary containment structures exposed to agrichemicals  

Microsoft Academic Search

Concrete has traditionally been the material of choice for building secondary containment structures because it is relatively inexpensive and has structural properties which make it ideal for supporting the loads of vehicles and large tanks. However, concrete`s chemical properties make it susceptible to corrosion by some common fertilizers. Though fairly impervious to water movement, concrete is easily penetrated by vapors

M. F. Broder; D. T. Nguyen



Polyadenylation of the mRNA of hepatitis delta virus is dependent on the structure of the nascent RNA and regulated by the small or large delta antigen.  

PubMed Central

During the hepatitis delta virus (HDV) RNA replication, synthesis of either the mRNA for the delta antigen (HDAg) or the full-length antigenomic RNA is determined by selective usage of the potent poly(A) signal on the antigenome. To elucidate the regulatory mechanism, HDV cDNA cotransfection system was used to examine the potential effect of the secondary structure of the nascent RNA and that of the HDAg on HDV polyadenylation in transfected cells. We found that when the nascent RNA species could fold itself to form the rodlike structure, the HDV polyadenylation was suppressed 3 to 5 fold by the HDAg. In addition, we observed that the small and the large HDAg exerted a similar suppressive effect on the HDV polyadenylation, though they played different roles in HDV replication. We concluded that the HDV polyadenylation could be regulated by the structure of the nascent antigenomic RNA and by either the small or large HDAg. Images PMID:8127676

Hsieh, S Y; Yang, P Y; Ou, J T; Chu, C M; Liaw, Y F




Microsoft Academic Search

Hyderabad - 500019 Abstract: Biological systems function with the aid of large number of proteins involved in complex network of chemical reactions. Interfering with the expression of proteins native or foreign leads to overall changes in the functioning of the biological systems . Manipulating the expression of proteins responsible for the manifestation of diseases has therefore been an interesting area

D. Satyanarayana Rao


Asymptotic number of hairpins of saturated RNA secondary structures.  


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

Clote, Peter; Kranakis, Evangelos; Krizanc, Danny



Structure and expression of an ethylene-related mRNA from tomato.  

PubMed Central

Messenger RNAs homologous to a cDNA clone (pTOM 13) derived from a ripe-tomato-specific cDNA library are expressed during tomato fruit ripening and after the wounding of leaf and green fruit material. Both responses involve the synthesis of the hormone ethylene. Accumulation of the pTOM 13--homologous RNA during ripening is rapid and sustained, and reaches its maximum level in orange fruit. Following mechanical wounding of tomato leaves a pTOM 13--homologous RNA shows rapid induction within 30 minutes, which occurs before maximal ethylene evolution (2-3 h). This RNA also accumulates following the wounding of green tomato fruit. Northern blot analysis of poly(A)+ RNA indicates that the length of the mRNA is about 1400 nucleotides. Nucleotide sequence analysis showed the cDNA insert to contain the complete coding region of the pTOM 13 protein (33.5 kD) and an unusual 5' structure of ten dT-nucleotides. Hybridisation of the pTOM 13 cDNA insert to Southern blots of tomato DNA indicates the presence of only a small number of homologous sequences in the tomato genome. Images PMID:3029690

Holdsworth, M J; Bird, C R; Ray, J; Schuch, W; Grierson, D



Protein Secondary Structure Prediction Using Sigmoid Belief Networks to Parameterize  

E-print Network

of these methods have utilized neural networks. A major improvement in the prediction accuracy of these methodsProtein Secondary Structure Prediction Using Sigmoid Belief Networks to Parameterize Segmental Semi-Markov Models Wei Chu , Zoubin Ghahramani Gatsby Computational Neuroscience Unit, University College London

Ghahramani, Zoubin


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



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


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

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



ESSA: an integrated and interactive computer tool for analysing RNA secondary structure.  


With ESSA, we propose an approach of RNA secondary structure analysis based on extensive viewing within a friendly graphical interface. This computer program is organized around the display of folding models produced by two complementary methods suitable to draw long RNA molecules. Any feature of interest can be managed directly on the display and highlighted by a rich combination of colours and symbols with emphasis given to structural probe accessibilities. ESSA also includes a word searching procedure allowing easy visual identification of structural features even complex and degenerated. Analysis functions make it possible to calculate the thermodynamic stability of any part of a folding using several models and compare homologous aligned RNA both in primary and secondary structure. The predictive capacities of ESSA which brings together the experimental, thermodynamic and comparative methods, are increased by coupling it with a program dedicated to RNA folding prediction based on constraints management and propagation. The potentialities of ESSA are illustrated by the identification of a possible tertiary motif in the LSU rRNA and the visualization of a pseudoknot in S15 mRNA. PMID:9254713

Chetouani, F; Monestié, P; Thébault, P; Gaspin, C; Michot, B



ESSA: an integrated and interactive computer tool for analysing RNA secondary structure.  

PubMed Central

With ESSA, we propose an approach of RNA secondary structure analysis based on extensive viewing within a friendly graphical interface. This computer program is organized around the display of folding models produced by two complementary methods suitable to draw long RNA molecules. Any feature of interest can be managed directly on the display and highlighted by a rich combination of colours and symbols with emphasis given to structural probe accessibilities. ESSA also includes a word searching procedure allowing easy visual identification of structural features even complex and degenerated. Analysis functions make it possible to calculate the thermodynamic stability of any part of a folding using several models and compare homologous aligned RNA both in primary and secondary structure. The predictive capacities of ESSA which brings together the experimental, thermodynamic and comparative methods, are increased by coupling it with a program dedicated to RNA folding prediction based on constraints management and propagation. The potentialities of ESSA are illustrated by the identification of a possible tertiary motif in the LSU rRNA and the visualization of a pseudoknot in S15 mRNA. PMID:9254713

Chetouani, F; Monestie, P; Thebault, P; Gaspin, C; Michot, B



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 PMID:24180434



Using circular dichroism spectra to estimate protein secondary structure  

PubMed Central

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

Greenfield, Norma J.



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 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



Solving novel RNA structures using only secondary structural fragments  

PubMed Central

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. RNA crystal structures present additional challenges due to greater difficulty in obtaining suitable heavy-atom derivatives. We present a unique approach to solving the phase problem for novel RNA crystal structures that has enjoyed a reasonable degree of success. This approach involves modeling only those portions of the RNA sequence whose structure can be predicted readily, i.e., the individual A-form helical regions and well-known stem-loop sub-structures. We have found that no prior knowledge of how the helices and other structural elements are arranged with respect to one another in three-dimensional space, or in some cases, even the sequence, is required to obtain a useable solution to the phase problem, using simultaneous molecular replacement of a set of generic helical RNA fragments. PMID:20541014

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



Correlations of Amino Acids with Secondary Structure Types: Connection with Amino Acid Structure  

Microsoft Academic Search

The correlations of primary and secondary structures were analyzed using\\u000aproteins with known structure from Protein Data Bank. The correlation values of\\u000aamino acid type and the eight secondary structure types at distant position\\u000awere calculated for distances between -25 and 25. Shapes of the diagrams\\u000aindicate that amino acids polarity and capability for hydrogen bonding have\\u000ainfluence on the

Miodrag V. ivkovi?; V. Beljanski; Milos V. Beljanski; Snezana D. Zaric



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.



Patterns, Structures, and Amino Acid Frequencies in Structural Building Blocks, a Protein Secondary  

E-print Network

Patterns, Structures, and Amino Acid Frequencies in Structural Building Blocks, a Protein Secondary Structure Classification Scheme Jacquelyn S. Fetrow,1* Michael J. Palumbo,1 and George Berg2 Departments ABSTRACT To study local structures in proteins, we previously developed an autoasso- ciative artificial

Berg, George


Thermal Folding and Mechanical Unfolding Pathways of Protein Secondary Structures  

E-print Network

Mechanical stretching of secondary structures is studied through molecular dynamics simulations of a Go-like model. Force vs. displacement curves are studied as a function of the stiffness and velocity of the pulling device. The succession of stretching events, as measured by the order in which contacts are ruptured, is compared to the sequencing of events during thermal folding and unfolding. Opposite cross-correlations are found for an $\\alpha$-helix and a $\\beta$-hairpin structure. In a tandem of two $\\alpha$-helices, the two constituent helices unravel nearly simultaneously. A simple condition for simultaneous vs. sequential unraveling of repeat units is presented.

Marek Cieplak; Trinh Xuan Hoang; Mark O. Robbins



Deduced Primary Structure of Rat Hepatocyte Growth Factor and Expression of the mRNA in Rat Tissues  

Microsoft Academic Search

The primary structure of rat hepatocyte growth factor (HGF) was elucidated by determining the base sequence of the complementary DNA (cDNA) of HGF. The cDNA for rat HGF was isolated by screening a liver cDNA library with oligonucleotides based on the partial N-terminal amino acid sequence of the beta subunit of purified rat HGF. HGF is encoded in an mRNA

Kosuke Tashiro; Mitchio Hagiya; Tsutomu Nishizawa; Tatsuya Seki; Manabu Shimonishi; Shin Shimizu; Toshikazu Nakamura



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



Transcription of structural and intervening sequences in the ovalbumin gene and identification of potential ovalbumin mRNA precursors.  


Structural sequences that are extensively separated by nonstructural intervening sequences in the natural ovalbumin gene are coordinately expressed in target and nontarget tissue. The intervening sequences, which consist of unique sequences in the chick genome, are transcribed in their entirety. The amount of nuclear RNA corresponding to these sequences, however, is approximately 10 times less than that observed for structural sequences. The accumulation of RNA corresponding to structural and intervening sequences during acute estrogen stimulation suggests either that there are different rates of transcription for these regions of the ovalbumin gene or that RNA sequences corresponding to the intervening sequences are preferentially processed and degraded. Comparison of the in vitro expression of portions of the ovalbumin gene in nuclei isolated from chronically stimulated oviducts indicates that both structural and intervening sequences are preferentially transcribed in vitro at rates approximately 500 times greater than expected for random transcription of the haploid chick genome. In addition, electrophoresis of oviduct nuclear RNA on agarose gels containing methylmercury hydroxide reveals multiple species of RNA that are from 1.3 to over 4 times larger than ovalbumin mRNA and hybridize to both structural and intervening sequences of the ovalbumin gene. These results are consistent with transcription of the entire ovalbumin gene into a large precursor molecule followed by excision of the intervening sequences and appropriate ligation of the structural sequences to form the mature mRNA. PMID:719758

Roop, D R; Nordstrom, J L; Tsai, S Y; Tsai, M J; O'Malley, B W



Covalent bond symmetry breaking and protein secondary structure  

E-print Network

Both symmetry and organized breaking of symmetry have a pivotal r\\^ole in our understanding of structure and pattern formation in physical systems, including the origin of mass in the Universe and the chiral structure of biological macromolecules. Here we report on a new symmetry breaking phenomenon that takes place in all biologically active proteins, thus this symmetry breaking relates to the inception of life. The unbroken symmetry determines the covalent bond geometry of a sp3 hybridized carbon atom. It dictates the tetrahedral architecture of atoms around the central carbon of an amino acid. Here we show that in a biologically active protein this symmetry becomes broken. Moreover, we show that the pattern of symmetry breaking is in a direct correspondence with the local secondary structure of the folded protein.

Lundgren, Martin



Covalent bond symmetry breaking and protein secondary structure  

E-print Network

Both symmetry and organized breaking of symmetry have a pivotal r\\^ole in our understanding of structure and pattern formation in physical systems, including the origin of mass in the Universe and the chiral structure of biological macromolecules. Here we report on a new symmetry breaking phenomenon that takes place in all biologically active proteins, thus this symmetry breaking relates to the inception of life. The unbroken symmetry determines the covalent bond geometry of a sp3 hybridized carbon atom. It dictates the tetrahedral architecture of atoms around the central carbon of an amino acid. Here we show that in a biologically active protein this symmetry becomes broken. Moreover, we show that the pattern of symmetry breaking is in a direct correspondence with the local secondary structure of the folded protein.

Martin Lundgren; Antti J. Niemi



[Comparative analysis of spatial organization of myoglobins. II. Secondary structure].  


An analysis of probability of distribution curves of alpha-helical sites and bends of polypeptide chains of myoglobins in half-water mammals (beaver, nutria, muskrat, otter) carried out in comparison with those of myoglobins of the horse and Sperm whale (X-ray diffraction analysis has revealed their tertiary structure) has revealed a coincidence of the secondary structure sites end bends of the chain in the studied respiratory hemoproteins of muscles. Despite a considerable number of amino acid substitutions the profiles of alpha-helicity and B-bends of the compared proteins are practically identical. This indicates to the "resistance" of the probability curves to amino acid substitutions and to retention of the tertiary structure of myoglobins in evolutionary remote species of the animals. PMID:1413113

Korobov, V N; Nazarenko, V I; Radomski?, N F; Starodub, N F



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

SciTech Connect

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

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



Generating non-overlapping displays of nucleic acid secondary structure.  

PubMed Central

A new algorithm is presented which permits the display of nucleic acid secondary structure by computer. This algorithm circumvents the problem of overlapping portions of the molecule which is inherent in some other drawing programs. The results from this algorithm may also be used as input to the drawing algorithm previously reported in this journal [1] to untangle most of a drawing. The algorithm also represents the molecule in a form which makes visual comparisons for similarity quite easy since it guarantees that comparable features will reside in the same relative position in the drawings when the drawings are normalized. PMID:6694904

Shapiro, B A; Maizel, J; Lipkin, L E; Currey, K; Whitney, C



New Secondary Structure Prediction software package using automatically trained Bayesian Networks  

E-print Network

New Secondary Structure Prediction software package using automatically trained Bayesian Networks software package for prediction of secondary structure of proteins. Two main contribution are presented: A novel approach to protein secondary structure prediction based on the usage of Bayesian Networks whose


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



Interactions of mRNAs and gRNAs involved in trypanosome mitochondrial RNA editing: structure probing of an mRNA bound to its cognate gRNA.  

PubMed Central

Posttranscriptional editing of trypanosome mitochondrial messenger RNA is directed by small guide RNAs (gRNAs). Using crosslinking techniques, we have previously shown that the gRNA base pairs to the mRNA via a 5' anchor, whereas its 3' U-tail interacts with upstream purine-rich mRNA sequences. The incorporation of crosslinking data into RNA folding programs produced similar structure predictions for all gRNA/mRNA pairs examined. This suggests that gRNA/mRNA pairs can form common secondary structure motifs that may be important for recognition by the editing complex. In this study, the structure of CYb mRNA crosslinked to gCYb-558 was examined using solution-probing techniques. The mRNA/gRNA crosslinked molecules are efficient substrates for gRNA-directed cleavage. In addition, when the cleavage assay is performed in the presence or absence of additional UTP, the activities of both the U-specific exonuclease and terminal uridylyl transferase (tutase) can be detected. These results indicate that a partial editing complex can assemble and function on these substrates suggesting that the crosslink captured the molecules in a biologically relevant interaction. The structure probing data directly show that the U-tail protects several mRNA bases predicted to be involved in the U-tail-mRNA duplex. In combination with our previous studies, these new data provide additional support for the predicted secondary structure of interacting gRNA/mRNA pairs. PMID:11780636

Leung, S S; Koslowsky, D J



Role of the highly structured 5?-end region of MDR1 mRNA in P-glycoprotein expression  

PubMed Central

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

Randle, Rebecca A.; Raguz, Selina; Higgins, Christopher F.; Yague, Ernesto



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

PubMed Central

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

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



[RNA secondary structure prediction based on support vector machine classification].  


The comparative sequence analysis is the most reliable method for RNA secondary structure prediction, and many algorithms based on it have been developed in last several decades. This paper considers RNA structure prediction as a 2-classes classification problem: given a sequence alignment, to decide whether or not two columns of alignment form a base pair. We employed Support Vector Machine (SVM) to predict potential paired sites, and selected co-variation information, thermodynamic information and the fraction of complementary bases as feature vectors. Considering the effect of sequence similarity upon co-variation score, we introduced a similarity weight factor, which could adjust the contribution of co-variation and thermodynamic information toward prediction according to sequence similarity. The test on 49 Rfam-seed alignments showed the effectiveness of our method, and the accuracy was better than many similar algorithms. Furthermore, this method could predict simple pseudoknot. PMID:18837386

Zhao, Yingjie; Wang, Zhengzhi



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

PubMed Central

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

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



The secondary structure of guide RNA molecules from Trypanosoma brucei.  

PubMed Central

RNA editing in kinetoplastid organisms is a mitochondrial RNA processing phenomenon that is characterized by the insertion and deletion of uridine nucleotides into incomplete mRNAs. Key molecules in the process are guide RNAs which direct the editing reaction by virtue of their primary sequences in an RNA-RNA interaction with the pre-edited mRNAs. To understand the molecular details of this reaction, especially potential RNA folding and unfolding processes as well as assembly phenomena with mitochondrial proteins, we analyzed the secondary structure of four different guide RNAs from Trypanosoma brucei at physiological conditions. By using structure-sensitive chemical and enzymatic probes in combination with spectroscopic techniques we found that the four molecules despite their different primary sequences, fold into similar structures consisting of two imperfect hairpin loops of low thermodynamic stability. The molecules melt in two-state monomolecular transitions with Tms between 33 and 39 degrees C and transition enthalpies of -32 to -38 kcal/mol. Both terminal ends of the RNAs are single-stranded with the 3' ends possibly adopting a single-stranded, helical conformation. Thus, it appears that the gRNA structures are fine tuned to minimize stability for an optimal annealing reaction to the pre-mRNAs while at the same time maximizing higher order structural features to permit the assembly with other mitochondrial components into the editing machinery. Images PMID:7667084

Schmid, B; Riley, G R; Stuart, K; Goringer, H U



In Silico Sciences The RNA secondary structure dependence  

E-print Network

, TTP, ...) Quiescent AAAAA AAAAA NPC mRNA stability regulation by HuR deca y HuR HuR #12;AAAAA neg. regulators (AUF1, TTP, ...) Quiescent AAAAA AAAAA NPC mRNA stability regulation by HuR deca y Trigger

Wien, Universität


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


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

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



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

PubMed Central

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

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



Strong Epistatic Selection on the RNA Secondary Structure of HIV  

PubMed Central

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




E-print Network

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

Erdogan, Hakan


Global or local? Predicting secondary structure and accessibility in mRNAs  

E-print Network

RNA. This is surprising, since a vast number of cis-regulatory structures (4), e.g. riboswitches (5), iron response structure prediction is required to characterize RNA regulatory mechan- isms. Although various structure conformation. For example, local structures in messenger RNA (mRNA) can regulate protein gene expression

Will, Sebastian


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



Changes in secondary structure of gluten proteins due to emulsifiers  

NASA Astrophysics Data System (ADS)

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

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



Prediction of the secondary structure content of globular proteins based on structural classes  

Microsoft Academic Search

The prediction of the secondary structure content (a-helix and?-strand content) of a globular protein may play an important complementary role in the prediction of the protein's structure. We propose a new prediction algorithm based on Chou's database [Chou (1995),Proteins Struct. Fund Genet.21, 319]. The new algorithm is an improved multiple linear regression method, taking the nonlinear and coupling terms of

Chun-Ting Zhang; Ziding Zhang; Zhimin He



A Dynamic Programming Algorithm for Circular Single-stranded DNA Tiles Secondary Structure Prediction  

E-print Network

DNA computing, and PCR-based applications. DNA secondary structure prediction is the key part for these DNA nanotechnologies. In this paper, we present a dynamic programming algorithm to predict the secondary structure of single-stranded DNA tiles. The algorithm calculates all possible maximum matches based on the nearest-neighbour model and global energy minimization. Experimental results show that the algorithm performers significantly to predict secondary structures for single-stranded DNA tiles.

Zhang Kai; Huang Xinquan; Shi Xiaolong; Qiang Xiaoli; Song Tao; Shi Xinzhu; Chen Zhihua



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

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



A Combination of Support Vector Machines and Bidirectional Recurrent Neural Networks for Protein Secondary Structure Prediction  

Microsoft Academic Search

Predicting the secondary structure of a protein is a main topic in bioinformatics. A reliable predictor is needed by threading meth- ods to improve the prediction of tertiary structure. Moreover,the pre- dicted secondary structure content of a protein can be used to assign the protein to a specific folding class and thus estimate its function. We discuss here the use

Alessio Ceroni; Paolo Frasconi; Andrea Passerini; Alessandro Vullo



Structurally Coloured Secondary Particles Composed of Black and White Colloidal Particles  

NASA Astrophysics Data System (ADS)

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

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



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)



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


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

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



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

PubMed Central

Exponential growth in the number of available protein sequences is unmatched by the slower growth in the number of structures. As a result, the development of efficient and fast protein secondary structure prediction methods is essential for the broad comprehension of protein structures. Computational methods that can efficiently determine secondary structure can in turn facilitate protein tertiary structure prediction, since most methods rely initially on secondary structure predictions. Recently, we have developed a fast learning optimized prediction methodology (FLOPRED) for predicting protein secondary structure (S. Saraswathi, et al., [1]). Data are generated by using knowledge-based potentials combined with structure information from the CATH database. A neural network-based extreme learning machine (ELM) and advanced particle swarm optimization (PSO) are used with this data to obtain better and faster convergence to more accurate secondary structure predicted results. A five-fold cross-validated testing accuracy of 83.8 % and a segment overlap (SOV) score of 78.3 % are obtained in this study. Secondary structure predictions and their accuracy are usually presented for three secondary structure elements: ?-helix, ?-strand and coil but rarely have the results been analyzed with respect to their constituent amino acids. In this paper, we use the results obtained with FLOPRED to provide detailed behaviors for different amino acid types in the secondary structure prediction. We investigate the influence of the composition, physico-chemical properties and position specific occurrence preferences of amino acids within secondary structure elements. In addition, we identify the correlation between these properties and prediction accuracy. The present detailed results suggest several important ways that secondary structure predictions can be improved in the future that might lead to improved protein design and engineering. PMID:23907551

Battelle, S. Saraswathi; Fernandez-Martinez, J. L.; Kolinski, A.; Jernigan, R. L.; Battelle, A. Kloczkowski



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

PubMed Central

Comparative analysis is the preferred method of inferring RNA secondary structure, but its use requires considerable expertise and manual effort. As the importance of secondary structure for accurate sequence alignment and phylogenetic analysis becomes increasingly realised, the need for secondary structure models for diverse taxonomic groups becomes more pressing. The number of available structures bears little relation to the relative diversity or importance of the different taxonomic groups. Insects, for example, comprise the largest group of animals and yet are very poorly represented in secondary structure databases. This paper explores the utility of maximum weighted matching (MWM) to help automate the process of comparative analysis by inferring secondary structure for insect mitochondrial small subunit (12S) rRNA sequences. By combining information on correlated changes in substitutions and helix dot plots, MWM can rapidly generate plausible models of secondary structure. These models can be further refined using standard comparative techniques. This paper presents a secondary structure model for insect 12S rRNA based on an alignment of 225 insect sequences and an alignment for 16 exemplar insect sequences. This alignment is used as a template for a web server that automatically generates secondary structures for insect sequences. PMID:11024161

Page, Roderic D. M.



Discriminating acidic and alkaline enzymes using a random forest model with secondary structure amino acid composition  

Microsoft Academic Search

Understating the adaptation mechanism of enzymes to pH extremes and discriminating them is a challenging task and would help to design stable enzymes. In this work, we have systematically analyzed the secondary structure amino acid compositions of 105 acidic and 111 alkaline enzymes, respectively. We found that the propensity of the individual residues to participate in different secondary structures might

Guangya Zhang; Hongchun Li; Baishan Fang



Protein Secondary Structure Prediction using Bayesian Inference method on Decision fusion algorithms  

Microsoft Academic Search

Prediction of protein secondary structure (alpha-helix, beta-sheet, coil) from primary sequence of amino acids is a very challenging task, and the problem has been approached from several angles. Previously research was performed in this field using several techniques such as neural networks, simulated annealing (SA) and genetic algorithms (GA) for improving the protein secondary structure prediction accuracy. Decision fusion methods

Somasheker Akkaladevi; Ajay K. Katangur



UV Resonance Raman-Selective Amide Vibrational Enhancement: Quantitative Methodology for Determining Protein Secondary Structure  

E-print Network

UV Resonance Raman-Selective Amide Vibrational Enhancement: Quantitative Methodology secondary structures, using UV resonance Raman spectroscopy (UVRRS) excited with a 206.5-nm CW laser changes in secondary structure in the protein, such as R-helix melting, while changes in the aromatic

Asher, Sanford A.


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



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


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.



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


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

Rani, Pooja; Baruah, Anupaul; Biswas, Parbati



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

Microsoft Academic Search

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

Kay Grunewald; Manfred Eckert; Joseph Hirschberg; Christoph Hagen



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.



Structure of Secondary Crystals in Ethylene-Based Ionomers  

NASA Astrophysics Data System (ADS)

A typical DSC thermogram of an ethylene-(meth)acrylic acid ionomer displays two melting endotherms: one near 100^oC reflecting the melting of primary ethylene crystals, and one at 40-60^oC which we have shown via simultaneous SAXS/WAXS/DSC to arise from the melting of interlamellar secondary crystals. Dynamic DSC (DDSC) confirms that the two peaks reflect a bimodal crystal thickness distribution, rather than a superposition of melting and recrystallization events. The melting temperature of these secondary crystals, estimated to be 2.5-3.5 nm thick, is sensitive to annealing history. DDSC also indicates that these secondary crystals melt irreversibly, as expected if each must be individually nucleated. The 2-D SAXS patterns of highly-oriented blown films of such ionomers show intense peaks, arising from the polyethylene lamellar crystallites, along the direction of principal orientation. Comparing the azimuthal variation in SAXS peak intensity at temperatures below and above the low-temperature endotherm reveals that the secondary crystallites are significantly oriented, but less so than the primary lamellae. Thus, the secondary interlamellar crystals also have a lamellar (anisotropic) habit, rather than resembling fringed micelles (isotropic).

Wakabayashi, K.; Loo, Y.-L.; Huang, Y. E.; Lee, L.-B. W.; Register, R. A.



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.



Improvement of RNA secondary structure prediction using RNase H cleavage and randomized oligonucleotides  

PubMed Central

RNA secondary structure prediction using free energy minimization is one method to gain an approximation of structure. Constraints generated by enzymatic mapping or chemical modification can improve the accuracy of secondary structure prediction. We report a facile method that identifies single-stranded regions in RNA using short, randomized DNA oligonucleotides and RNase H cleavage. These regions are then used as constraints in secondary structure prediction. This method was used to improve the secondary structure prediction of Escherichia coli 5S rRNA. The lowest free energy structure without constraints has only 27% of the base pairs present in the phylogenetic structure. The addition of constraints from RNase H cleavage improves the prediction to 100% of base pairs. The same method was used to generate secondary structure constraints for yeast tRNAPhe, which is accurately predicted in the absence of constraints (95%). Although RNase H mapping does not improve secondary structure prediction, it does eliminate all other suboptimal structures predicted within 10% of the lowest free energy structure. The method is advantageous over other single-stranded nucleases since RNase H is functional in physiological conditions. Moreover, it can be used for any RNA to identify accessible binding sites for oligonucleotides or small molecules. PMID:19596816

Kauffmann, Andrew D.; Campagna, Ryan J.; Bartels, Chantal B.; Childs-Disney, Jessica L.



Prediction of Protein Secondary Structure Content by Using the Concept of Chou's Pseudo Amino Acid Composition and Support Vector Machine  

Microsoft Academic Search

Protein secondary structure carries information about local structural arrangements. Significant majority of suc- cessful methods for predicting the secondary structure is based on multiple sequence alignment. However, the multiple alignment fails to achieve accurate results when a protein sequence is characterized by low homology. To this end, we propose a novel method for prediction of secondary structure content through comprehensive

Chao Chen; Lixuan Chen; Xiaoyong Zou; Peixiang Cai



RNA secondary structure prediction using dynamic programming algorithm — A review and proposed work  

Microsoft Academic Search

Ribonucleic acid (RNA) plays a fundamental and important role in cellular life forms and their function is directly related to their structure. RNA secondary structure prediction is a significant area of study for many scientists seeking insights into potential drug interactions or innovative new treatment methodologies. Predicting structure can overcome many issues related with physical structure determination and their study

Mohd Nizam Osman; Rosni Abdullah; Nuraini AbdulRashid



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



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.



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

PubMed Central

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

Sharma, Sudha



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

E-print Network

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

Baiz, Carlos


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


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


Computer Science and Artificial Intelligence Laboratory Secondary Structure Prediction of All-Helical  

E-print Network

Computer Science and Artificial Intelligence Laboratory Secondary Structure Prediction of All Dijk, S. Devadas Technical Report massachusetts institute of technology, cambridge, ma 02139 usa -- www Dijk and S. Devadas Computer Science and Artificial Intelligence Laboratory (CSAIL) Massachusetts

Gifford, David K.


A Critical Review of Computational Methods for RNA Secondary Structure Prediction  

E-print Network

A Critical Review of Computational Methods for RNA Secondary Structure Prediction Adam Silverman Biochem218 Submitted June 6, 2003 Introduction The three-dimensional structure of RNA molecules is crucial to their function. The primary structure is determined by the sequence of G, A, C, and U bases in a strand


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


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



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

PubMed Central

Human globins are encoded by mRNAs exhibiting high stabilities in transcriptionally silenced erythrocyte progenitors. Unlike ?-globin mRNA, whose stability is enhanced by assembly of a specific messenger RNP (mRNP) ? complex on its 3? untranslated region (UTR), neither the structure(s) nor the mechanism(s) that effects the high-level stability of human ?-globin mRNA has been identified. The present work describes an mRNP complex assembling on the 3? UTR of the ?-globin mRNA that exhibits many of the properties of the stability-enhancing ? complex. The ?-globin mRNP complex is shown to contain one or more factors homologous to ?CP, a 39-kDa RNA-binding protein that is integral to ?-complex assembly. Sequence analysis implicates a specific 14-nucleotide pyrimidine-rich track within its 3? UTR as the site of ?-globin mRNP assembly. The importance of this track to mRNA stability is subsequently verified in vivo using mice expressing human ?-globin transgenes that contain informative mutations in this region. In combination, the in vitro and in vivo analyses indicate that the high stabilities of the ?- and ?-globin mRNAs are maintained through related mRNP complexes that may share a common regulatory pathway. PMID:11486027

Yu, Jia; Russell, J. Eric



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

PubMed Central

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



TRACES Centre Secondary structure of proteins and peptides1  

E-print Network

VCD (upper) and absorption (lower) spectra of hemoglobin (left), lysozyme (mid) and concanavalin while concanavalin A exists in a -sheet predominantly and lysozyme shares both structure elements that the VCD spectrum of lysozyme consists of both structure elements. VCD spectroscopy therefore provides

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


SUPPLEMENTARY MATERIAL FOR Predicting RNA Secondary Structures with Pseudoknots by  

E-print Network

Structures for Treponema Pallidum pre-tmRNA . . . . . . . . . . . . . . . . . 3 2.2 PPV and Sensitivity the evaluations shown below. 2 #12;2.1 Sampled Structures for Treponema Pallidum pre-tmRNA McQFold samples from of the following 20 panels show the samples for the pre-tmRNA sequence of Treponema Pallid

Metzler, Dirk


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


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

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



A Comparative Taxonomy of Parallel Algorithms for RNA Secondary Structure Prediction  

PubMed Central

RNA molecules have been discovered playing crucial roles in numerous biological and medical procedures and processes. RNA structures determination have become a major problem in the biology context. Recently, computer scientists have empowered the biologists with RNA secondary structures that ease an understanding of the RNA functions and roles. Detecting RNA secondary structure is an NP-hard problem, especially in pseudoknotted RNA structures. The detection process is also time-consuming; as a result, an alternative approach such as using parallel architectures is a desirable option. The main goal in this paper is to do an intensive investigation of parallel methods used in the literature to solve the demanding issues, related to the RNA secondary structure prediction methods. Then, we introduce a new taxonomy for the parallel RNA folding methods. Based on this proposed taxonomy, a systematic and scientific comparison is performed among these existing methods. PMID:20458364

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



Predicting Secondary Structure of All-Helical Proteins Using  

E-print Network

methods in use today [10,14], delivering a pointwise prediction accuracy (Q3) of about 77% and a segment structure pre- diction, it likely will be necessary to develop a cost model that mirrors the underlying

Gifford, David K.


Fourier transform infrared analysis of amide III bands of proteins for the secondary structure estimation  

NASA Astrophysics Data System (ADS)

Protein secondary structure has been analyzed using a Fourier transform infrared spectroscopic method in the amide III region. Although extensive work has been done on protein secondary structure using the amide I region (1700 - 1600 cm-1), the amide III region has not been utilized in the past for its potential in protein structural analysis. One of the major reasons for non-use of the amide III vibrations is perhaps the very weak signal in the amide III frequency region (1200 - 1350 cm-1). However, benefits of using the amide III region are substantial. For example, water vibrations do not interfere with the protein spectrum unlike in the amide I region. In the amide III region, the protein spectrum is better resolved into individual bands than in the amide I region. This feature allows for a greater ease in peak definement of the protein spectra. In the amide III region, the bands for the individual secondary structures ((alpha) -helix, (beta) -sheet and random coils) do not overlap as much as they do in the amide I region. This lack of overlapping allows for easier and a more reliable means of peak assignment, and secondary structure band positions are easier to determine. Amide III region of protein IR spectra appears to be a valuable tool in estimating the amount of secondary structure present in proteins.

Singh, Bal R.; DeOliveira, Daniel B.; Fu, Fen-Ni; Fuller, Michael P.



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


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



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

Microsoft Academic Search

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

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


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



mRNA Structural constraints on EBNA1 synthesis impact on in vivo antigen presentation and early priming of CD8+ T cells.  


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

Tellam, Judy T; Zhong, Jie; Lekieffre, Lea; Bhat, Purnima; Martinez, Michelle; Croft, Nathan P; Kaplan, Warren; Tellam, Ross L; Khanna, Rajiv



GTfold: A Scalable Multicore Code for RNA Secondary Structure Prediction  

E-print Network

our website. Keywords Computational Biology, Parallel Algorithms, Ribosomal and Viral RNA College structure of viruses like dengue [3], ebola [18], and HIV [19] is known to have func- tional significance. Thus, disrupting functionally significant base pairings in RNA viral genomes is one potential method

Bader, David A.


Argumentation in Secondary School Students' Structured and Unstructured Chat Discussions  

ERIC Educational Resources Information Center

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

Salminen, Timo; Marttunen, Miika; Laurinen, Leena



Inhibition of polyadenylation by stable RNA secondary structure.  

PubMed Central

The presence of a polyadenylation signal in the repeat (R) region of the HIV-1 genome, which is located at both the 5' and 3' ends of the viral transcripts, requires differential regulation of polyadenylation. The HIV-1 poly(A) site can fold in a stable stem-loop structure that is well-conserved among different human and simian immunodeficiency viruses. In this study, we tested the effect of this hairpin on polyadenylation by introducing mutations that either stabilize or destabilize the RNA structure. The HIV-1 sequences were inserted into the pSV2CAT reporter plasmid upstream of the SV40 early poly(A) site. These constructs were transfected into COS cells and transcripts were analyzed for the usage of the HIV-1 versus SV40 poly(A) site. The wild-type HIV-1 poly(A) site was used efficiently in this context and destabilization of the poly(A) hairpin did not affect the polyadenylation efficiency. In contrast, further stabilization of the hairpin severely inhibited HIV-1 polyadenylation. Additional mutations that repair the thermodynamic stability of this mutant hairpin restored the polyadenylation activity. These results indicate that the mechanism of polyadenylation can be repressed by stable RNA structure encompassing the poly(A) signal. Experiments performed at reduced temperatures also suggest an inverse correlation between the stability of the RNA structure and the efficiency of polyadenylation. PMID:9518478

Klasens, B I; Das, A T; Berkhout, B



Genome-wide mapping of conserved RNA Secondary Structures Reveals Evidence for Thousands of functional  

E-print Network

conserved RNAs in the human genome. Results Selection of conserved sequences and screening for structuralGenome-wide mapping of conserved RNA Secondary Structures Reveals Evidence for Thousands to the fairly reliable and complete annotation of the protein coding genes in the human genome, comparable

Stadler, Peter F.


Genomewide mapping of conserved RNA Secondary Structures Reveals Evidence for Thousands of functional  

E-print Network

conserved RNAs in the human genome. Results Selection of conserved sequences and screening for structuralGenome­wide mapping of conserved RNA Secondary Structures Reveals Evidence for Thousands to the fairly reliable and complete annotation of the protein coding genes in the human genome, comparable

Stadler, Peter F.


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

E-print Network

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

Simons, Jack


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

PubMed Central

The mechanisms of export of RNA from the nucleus are poorly understood; however, several viral proteins modulate nucleocytoplasmic transport of mRNA. Among these are the adenoviral proteins E1B-55kDa and E4-34kDa. Late in infection, these proteins inhibit export of host transcripts and promote export of viral mRNA. To investigate the mechanism by which these proteins act, we have expressed them in Saccharomyces cerevisiae. Overexpression of either or both proteins has no obvious effect on cell growth. By contrast, overexpression of E1B-55kDa bearing a nuclear localization signal (NLS) dramatically inhibits cell growth. In this situation, the NLS-E1B-55kDa protein is localized to the nuclear periphery, fibrous material is seen in the nucleoplasm, and poly(A)+ RNA accumulates in the nucleus. Simultaneous overexpression of E4-34kDa bearing or lacking an NLS does not modify these effects. We discuss the mechanisms of selective mRNA transport. Images Fig. 1 Fig. 2 Fig. 3 PMID:7638199

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



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


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

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



Structural Requirement in Clostridium perfringens Collagenase mRNA 5? Leader Sequence for Translational Induction through Small RNA-mRNA Base Pairing  

PubMed Central

The Gram-positive anaerobic bacterium Clostridium perfringens is pathogenic to humans and animals, and the production of its toxins is strictly regulated during the exponential phase. We recently found that the 5? leader sequence of the colA transcript encoding collagenase, which is a major toxin of this organism, is processed and stabilized in the presence of the small RNA VR-RNA. The primary colA 5?-untranslated region (5?UTR) forms a long stem-loop structure containing an internal bulge and masks its own ribosomal binding site. Here we found that VR-RNA directly regulates colA expression through base pairing with colA mRNA in vivo. However, when the internal bulge structure was closed by point mutations in colA mRNA, translation ceased despite the presence of VR-RNA. In addition, a mutation disrupting the colA stem-loop structure induced mRNA processing and ColA-FLAG translational activation in the absence of VR-RNA, indicating that the stem-loop and internal bulge structure of the colA 5? leader sequence is important for regulation by VR-RNA. On the other hand, processing was required for maximal ColA expression but was not essential for VR-RNA-dependent colA regulation. Finally, colA processing and translational activation were induced at a high temperature without VR-RNA. These results suggest that inhibition of the colA 5? leader structure through base pairing is the primary role of VR-RNA in colA regulation and that the colA 5? leader structure is a possible thermosensor. PMID:23585542

Nomura, Nobuhiko; Nakamura, Kouji



Computational study of protein secondary structure elements: Ramachandran plots revisited.  


Potential energy surface (PES) were built for nineteen amino acids using density functional theory (PW91 and DFT M062X/6-311**). Examining the energy as a function of the ?/? dihedral angles in the allowed regions of the Ramachandran plot, amino acid groups that share common patterns on their PES plots and global minima were identified. These patterns show partial correlation with their structural and pharmacophoric features. Differences between these computational results and the experimentally noted permitted conformations of each amino acid are rationalized on the basis of attractive intra- and inter-molecular non-covalent interactions. The present data are focused on the intrinsic properties of an amino acid - an element which to our knowledge is typically ignored, as larger models are always used for the sake of similarity to real biological polypeptides. PMID:24793053

Carrascoza, Francisco; Zaric, Snezana; Silaghi-Dumitrescu, Radu



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.



Evolving stochastic context--free grammars for RNA secondary structure prediction  

PubMed Central

Background Stochastic Context–Free Grammars (SCFGs) were applied successfully to RNA secondary structure prediction in the early 90s, and used in combination with comparative methods in the late 90s. The set of SCFGs potentially useful for RNA secondary structure prediction is very large, but a few intuitively designed grammars have remained dominant. In this paper we investigate two automatic search techniques for effective grammars – exhaustive search for very compact grammars and an evolutionary algorithm to find larger grammars. We also examine whether grammar ambiguity is as problematic to structure prediction as has been previously suggested. Results These search techniques were applied to predict RNA secondary structure on a maximal data set and revealed new and interesting grammars, though none are dramatically better than classic grammars. In general, results showed that many grammars with quite different structure could have very similar predictive ability. Many ambiguous grammars were found which were at least as effective as the best current unambiguous grammars. Conclusions Overall the method of evolving SCFGs for RNA secondary structure prediction proved effective in finding many grammars that had strong predictive accuracy, as good or slightly better than those designed manually. Furthermore, several of the best grammars found were ambiguous, demonstrating that such grammars should not be disregarded. PMID:22559985



New Charge-Bearing Amino Acid Residues That Promote ?-Sheet Secondary Structure.  


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



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.



Secondary structure analysis of proteins embedded in spherical polyelectrolyte brushes by FT-IR spectroscopy.  


The adsorption of bovine serum albumin (BSA), bovine beta-lactoglobulin, and bovine pancreatic ribonuclease A onto spherical polyelectrolyte brushes (SPB) is reported. The SPB consist of narrowly distributed poly(styrene) core particles (diameter approximately 100 nm) onto which linear chains of anionic polyelectrolytes are grafted. The polyelectrolyte shell consists of either the weak polyelectrolyte poly(acrylic acid) or the strong polyacid poly(styrenesulfonate). The SPB particles are dispersed in H(2)O at room temperature. The secondary structure of the proteins was investigated by Fourier transform infrared spectroscopy in transmission mode before and during adsorption to these colloidal brushes. The alpha-helix and beta-sheet content of the proteins was nearly fully retained in the adsorbed state for all systems. Only in the case of BSA interacting with poly(styrenesulfonic) brushes could a slight loss of alpha-helix structure be observed. As the interaction of SPB and proteins can be controlled by the ionic strength in the buffer, additional experiments were performed to release the adsorbed protein. The amount of released protein was quantified and was found to be strongly dependent on the kind of protein and brush used. The secondary structure of the released proteins could be analyzed as well. An almost full preservation of secondary structure was found. This demonstrates that SPB are well-suited to immobilize proteins. The SPB can be charged and decharged under retention of the secondary structure of the biomolecules. PMID:15144192

Wittemann, Alexander; Ballauff, Matthias



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


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



A statistical learning approach to the modeling of chromatographic retention of oligonucleotides incorporating sequence and secondary structure data  

PubMed Central

We propose a new model for predicting the retention time of oligonucleotides. The model is based on ? support vector regression using features derived from base sequence and predicted secondary structure of oligonucleotides. Because of the secondary structure information, the model is applicable even at relatively low temperatures where the secondary structure is not suppressed by thermal denaturing. This makes the prediction of oligonucleotide retention time for arbitrary temperatures possible, provided that the target temperature lies within the temperature range of the training data. We describe different possibilities of feature calculation from base sequence and secondary structure, present the results and compare our model to existing models. PMID:17567619

Sturm, Marc; Quinten, Sascha; Huber, Christian G.; Kohlbacher, Oliver



Prediction of protein secondary structure from circular dichroism using theoretically derived spectra.  


Circular dichroism (CD) is a spectroscopic technique commonly used to investigate the structure of proteins. Major secondary structure types, alpha-helices and beta-strands, produce distinctive CD spectra. Thus, by comparing the CD spectrum of a protein of interest to a reference set consisting of CD spectra of proteins of known structure, predictive methods can estimate the secondary structure of the protein. Currently available methods, including K2D2, use such experimental CD reference sets, which are very small in size when compared to the number of tertiary structures available in the Protein Data Bank (PDB). Conversely, given a PDB structure, it is possible to predict a theoretical CD spectrum from it. The methodological framework for this calculation was established long ago but only recently a convenient implementation called DichroCalc has been developed. In this study, we set to determine whether theoretically derived spectra could be used as reference set for accurate CD based predictions of secondary structure. We used DichroCalc to calculate the theoretical CD spectra of a nonredundant set of structures representing most proteins in the PDB, and applied a straightforward approach for predicting protein secondary structure content using these theoretical CD spectra as reference set. We show that this method improves the predictions, particularly for the wavelength interval between 200 and 240 nm and for beta-strand content. We have implemented this method, called K2D3, in a publicly accessible web server at http://www. Proteins 2011. © 2011 Wiley Periodicals, Inc. PMID:22095872

Louis-Jeune, Caroline; Andrade-Navarro, Miguel A; Perez-Iratxeta, Carol



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


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

Dohrmann, Martin



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


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

Sanchita; Singh, Swati; Sharma, Ashok



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

ERIC Educational Resources Information Center

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

Palla, Marina; Potari, Despina; Spyrou, Panagiotis



A Graphical Model for Protein Secondary Structure Prediction Wei Chu  

E-print Network

used in neural network prediction methods to achieve fur- ther improvements (Jones, 1999; Cuff & BartonA Graphical Model for Protein Secondary Structure Prediction Wei Chu Zoubin Ghahramani Gatsby Computational Neuroscience Unit, University College London, London

Ghahramani, Zoubin


A Graphical Model for Protein Secondary Structure Prediction Wei Chu  

E-print Network

in neural network prediction methods to achieve fur- ther improvements (Jones, 1999; Cuff & Barton, 2000A Graphical Model for Protein Secondary Structure Prediction Wei Chu Zoubin Ghahramani Gatsby Computational Neuroscience Unit, University College London, London

Wei, Chu


A Graphical Model for Protein Secondary Structure Prediction Wei Chu  

E-print Network

in neural network prediction methods to achieve fur­ ther improvements (Jones, 1999; Cu# & Barton, 2000A Graphical Model for Protein Secondary Structure Prediction Wei Chu Zoubin Ghahramani Gatsby Computational Neuroscience Unit, University College London, London

Wei, Chu


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

Microsoft Academic Search

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

Randy Moore; John Pasieniuk



Secondary Structure of Cell-Penetrating Peptides Controls Membrane Interaction and Insertion  

E-print Network

Secondary Structure of Cell-Penetrating Peptides Controls Membrane Interaction and Insertion Emelía permeability of the biological membranes. In order to enhance their cell delivery, short amphipathic peptides called cell-penetrating peptides (CPPs) have been intensively developed for the last two decades. CPPs

Boyer, Edmond


ESSA: an integrated and interactive computer tool for analysing RNA secondary structure  

Microsoft Academic Search

With ESSA, we propose an approach of RNA secondary structure analysis based on extensive viewing within a friendly graphical interface. This computer program is organized around the display of folding models produced by two complementary methods suitable to draw long RNA molecules. Any feature of interest can be managed directly on the display and highlighted by a rich combination of

F. Chetouani; P. Monestié; P. Thébault; C. Gaspin; B. Michot



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

ERIC Educational Resources Information Center

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

Pearce, Richard R.; Lin, Zeng



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



The Dependence of Secondary Structure in X-Ray Absorption on Crystal Form  

Microsoft Academic Search

An examination of the Ca K absorption edge in the x-ray absorption spectra of different compounds shows clearly that the secondary structure is not the same in different compounds, and is not even the same in the two crystals calcite and aragonite, which are the same chemically, but of different crystalline form. These facts are in accord with Kronig's theory

Vola P. Barton; Geo A. Lindsay



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

E-print Network

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

Erdogan, Hakan


MicroRNAfold: microRNA secondary structure prediction based on Modified NCM model with  

E-print Network

of a functional miRNA is largely dependent on the secondary structure of the miRNA precursor (pre) that are derived from larger hairpin RNA precursors and target their complementary gene tran- scripts for degradation or translational repression. MicroRNAs are found to play an important role in regulation of gene

Zhang, Jun


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



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


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.


PolyprOnline: polyproline helix II and secondary structure assignment database.  


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 PMID:25380779

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



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 PMID:25380779

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



Secondary structures of rRNAs from all three domains of life.  


Accurate secondary structures are important for understanding ribosomes, which are extremely large and highly complex. Using 3D structures of ribosomes as input, we have revised and corrected traditional secondary (2°) structures of rRNAs. We identify helices by specific geometric and molecular interaction criteria, not by co-variation. The structural approach allows us to incorporate non-canonical base pairs on parity with Watson-Crick base pairs. The resulting rRNA 2° structures are up-to-date and consistent with three-dimensional structures, and are information-rich. These 2° structures are relatively simple to understand and are amenable to reproduction and modification by end-users. The 2° structures made available here broadly sample the phylogenetic tree and are mapped with a variety of data related to molecular interactions and geometry, phylogeny and evolution. We have generated 2° structures for both large subunit (LSU) 23S/28S and small subunit (SSU) 16S/18S rRNAs of Escherichia coli, Thermus thermophilus, Haloarcula marismortui (LSU rRNA only), Saccharomyces cerevisiae, Drosophila melanogaster, and Homo sapiens. We provide high-resolution editable versions of the 2° structures in several file formats. For the SSU rRNA, the 2° structures use an intuitive representation of the central pseudoknot where base triples are presented as pairs of base pairs. Both LSU and SSU secondary maps are available ( Mapping of data onto 2° structures was performed on the RiboVision server ( PMID:24505437

Petrov, Anton S; Bernier, Chad R; Gulen, Burak; Waterbury, Chris C; Hershkovits, Eli; Hsiao, Chiaolong; Harvey, Stephen C; Hud, Nicholas V; Fox, George E; Wartell, Roger M; Williams, Loren Dean



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

Microsoft Academic Search

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

Gianfranco Menestrina; Veronique Cabiaux; Mayra Tejuca



Exploiting the past and the future in protein secondary structure prediction  

Microsoft Academic Search

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

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



Molecular dynamics of folding of secondary structures in Go-type models of proteins  

E-print Network

We consider six different secondary structures of proteins and construct two types of Go-type off-lattice models: with the steric constraints and without. The basic aminoacid-aminoacid potential is Lennard Jones for the native contacts and a soft repulsion for the non-native contacts. The interactions are chosen to make the target secondary structure be the native state of the system. We provide a thorough equilibrium and kinetic characterization of the sequences through the molecular dynamics simulations with the Langevin noise. Models with the steric constraints are found to be better folders and to be more stable, especially in the case of the $\\beta$-structures. Phononic spectra for vibrations around the native states have low frequency gaps that correlate with the thermodynamic stability. Folding of the secondary structures proceeds through a well defined sequence of events. For instance, $\\alpha$-helices fold from the ends first. The closer to the native state, the faster establishment of the contacts. Increasing the system size deteriorates the folding characteristics. We study the folding times as a function of viscous friction and find a regime of moderate friction with the linear dependence. We also consider folding when one end of a structure is pinned which imitates instantaneous conditions when a protein is being synthesized. We find that, under such circumstances, folding of helices is faster and of the $\\beta$-sequences slower.

Trinh Xuan Hoang; Marek Cieplak



Intergenic regions of Borrelia plasmids contain phylogenetically conserved RNA secondary structure motifs  

PubMed Central

Background Borrelia species are unusual in that they contain a large number of linear and circular plasmids. Many of these plasmids have long intergenic regions. These regions have many fragmented genes, repeated sequences and appear to be in a state of flux, but they may serve as reservoirs for evolutionary change and/or maintain stable motifs such as small RNA genes. Results In an in silico study, intergenic regions of Borrelia plasmids were scanned for phylogenetically conserved stem loop structures that may represent functional units at the RNA level. Five repeat sequences were found that could fold into stable RNA-type stem loop structures, three of which are closely linked to protein genes, one of which is a member of the Borrelia lipoprotein_1 super family genes and another is the complement regulator-acquiring surface protein_1 (CRASP-1) family. Modeled secondary structures of repeat sequences display numerous base-pair compensatory changes in stem regions, including C-G?A-U transversions when orthologous sequences are compared. Base-pair compensatory changes constitute strong evidence for phylogenetic conservation of secondary structure. Conclusion Intergenic regions of Borrelia species carry evolutionarily stable RNA secondary structure motifs. Of major interest is that some motifs are associated with protein genes that show large sequence variability. The cell may conserve these RNA motifs whereas allow a large flux in amino acid sequence, possibly to create new virulence factors but with associated RNA motifs intact. PMID:19267927

Delihas, Nicholas



Isolation and fine structure organisation of an avian vitellogenin gene coding for the major estrogen-inducible mRNA.  


Two phage lambda recombinant DNA clones covering the entire sequence of an avian vitellogenin gene, plus flanking regions, have been isolated from an erythrocyte DNA gene library and characterized by R-loop and restriction mapping. The total length of this avian vitellogenin gene is 23 kb. The cloned sequences flanking the gene at the 5' and 3' end are 7 and 3 kb, respectively. The total length of exons in the two clones is 6.7 kb (vitellogenin mRNA is 6.6 kb). The gene is interrupted by at least 25 introns with a mean intron length of 940 bp. Some 6--10 additional very small introns may also be present but they were not observed reproducibly. The mean exon length is 250 bp. Restriction endonuclease digests of total liver genomic DNA and lambda recombinant DNA were also analyzed by electrophoresis. Southern blotting and hybridization with cloned vitellogenin cDNA. The results show an identity of organisation of this vitellogenin in the DNA from the two sources, thus ruling out a possible cloning artifact. In contrast to Xenopus vitellogenin we have found no evidence to suggest that avian vitellogenin is encoded by a small family of related genes. PMID:6211392

Wilks, A; Cato, A C; Cozens, P J; Mattaj, I W; Jost, J P



Role of mRNA Stability during Bacterial Adaptation  

PubMed Central

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

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



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



Predicting the secondary structures and tertiary interactions of 211 group I introns in IE subgroup  

PubMed Central

The large number of currently available group I intron sequences in the public databases provides opportunity for studying this large family of structurally complex catalytic RNA by large-scale comparative sequence analysis. In this study, the detailed secondary structures of 211 group I introns in the IE subgroup were manually predicted. The secondary structure-favored alignments showed that IE introns contain 14 conserved stems. The P13 stem formed by long-range base-pairing between P2.1 and P9.1 is conserved among IE introns. Sequence variations in the conserved core divide IE introns into three distinct minor subgroups, namely IE1, IE2 and IE3. Co-variation of the peripheral structural motifs with core sequences supports that the peripheral elements function in assisting the core structure folding. Interestingly, host-specific structural motifs were found in IE2 introns inserted at S516 position. Competitive base-pairing is found to be conserved at the junctions of all long-range paired regions, suggesting a possible mechanism of establishing long-range base-pairing during large RNA folding. These findings extend our knowledge of IE introns, indicating that comparative analysis can be a very good complement for deepening our understanding of RNA structure and function in the genomic era. PMID:15843683

Li, Zhijie; Zhang, Yi



Thermal effects in stretching of Go-like models of titin and secondary structures  

E-print Network

The effect of temperature on mechanical unfolding of proteins is studied using a Go-like model with a realistic contact map and Lennard-Jones contact interactions. The behavior of the I27 domain of titin and its serial repeats is contrasted to that of simple secondary structures. In all cases thermal fluctuations accelerate the unraveling process, decreasing the unfolding force nearly linearly at low temperatures. However differences in bonding geometry lead to different sensitivity to temperature and different changes in the unfolding pattern. Due to its special native state geometry titin is much more thermally and elastically stable than the secondary structures. At low temperatures serial repeats of titin show a parallel unfolding of all domains to an intermediate state, followed by serial unfolding of the domains. At high temperatures all domains unfold simultaneously and the unfolding distance decreases monotonically with the contact order, that is the sequence distance between the amino acids that form the native contact.

Marek Cieplak; Trinh Xuan Hoang; Mark O. Robbins



A quantitative analysis of secondary RNA structure using domination based parameters on trees  

PubMed Central

Background It has become increasingly apparent that a comprehensive database of RNA motifs is essential in order to achieve new goals in genomic and proteomic research. Secondary RNA structures have frequently been represented by various modeling methods as graph-theoretic trees. Using graph theory as a modeling tool allows the vast resources of graphical invariants to be utilized to numerically identify secondary RNA motifs. The domination number of a graph is a graphical invariant that is sensitive to even a slight change in the structure of a tree. The invariants selected in this study are variations of the domination number of a graph. These graphical invariants are partitioned into two classes, and we define two parameters based on each of these classes. These parameters are calculated for all small order trees and a statistical analysis of the resulting data is conducted to determine if the values of these parameters can be utilized to identify which trees of orders seven and eight are RNA-like in structure. Results The statistical analysis shows that the domination based parameters correctly distinguish between the trees that represent native structures and those that are not likely candidates to represent RNA. Some of the trees previously identified as candidate structures are found to be "very" RNA like, while others are not, thereby refining the space of structures likely to be found as representing secondary RNA structure. Conclusion Search algorithms are available that mine nucleotide sequence databases. However, the number of motifs identified can be quite large, making a further search for similar motif computationally difficult. Much of the work in the bioinformatics arena is toward the development of better algorithms to address the computational problem. This work, on the other hand, uses mathematical descriptors to more clearly characterize the RNA motifs and thereby reduce the corresponding search space. These preliminary findings demonstrate that graph-theoretic quantifiers utilized in fields such as computer network design hold significant promise as an added tool for genomics and proteomics. PMID:16515683

Haynes, Teresa; Knisley, Debra; Seier, Edith; Zou, Yue



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 PMID:24884954



Understanding the Effect of Secondary Structures and Aggregation on Human Protein Folding Class Evolution  

Microsoft Academic Search

Using several model organisms it has been shown earlier that protein designability is related to contact density or fraction\\u000a of buried residues and influence protein evolutionary rates dramatically. Here, using Homo sapiens as a model organism, we have analyzed two main folding classes (all-? and all-?) to examine the factors affecting their evolutionary\\u000a rates. Since, secondary structures are the most

Tina BegumTapash; Tapash Chandra Ghosh



Preferential DNA secondary structure mutagenesis in the lagging strand of replication in E. coli  

Microsoft Academic Search

WHEN present in single-stranded DNA, palindromic or quasi-palindromic sequences have the potential to form complex secondary structures, including hairpins, which may facilitate inter-strand misalignment of direct repeats and be responsible for diverse types of replication-based mutations, including deletions, additions, frameshifts and duplications1-5. In regions of palindromic symmetry, specific deletion events may involve the formation of a hairpin or other DNA

Thuan Q. Trinh; Richard R. Sinden



TileSoft: Sequence Optimization Software For Designing DNA Secondary Structures  

Microsoft Academic Search

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

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



The HIV-2 Rev-response element: determining secondary structure and defining folding intermediates  

PubMed Central

Interaction between the viral protein Rev and the RNA motifs known as Rev response elements (RREs) is required for transport of unspliced and partially spliced human immunodeficiency virus (HIV)-1 and HIV-2 RNAs from the nucleus to the cytoplasm during the later stages of virus replication. A more detailed understanding of these nucleoprotein complexes and the host factors with which they interact should accelerate the development of new antiviral drugs targeting cis-acting RNA regulatory signals. In this communication, the secondary structures of the HIV-2 RRE and two RNA folding precursors have been identified using the SHAPE (selective 2?-hydroxyl acylation analyzed by primer extension) chemical probing methodology together with a novel mathematical approach for determining the secondary structures of RNA conformers present in a mixture. A complementary chemical probing technique was also used to support these secondary structure models, to confirm that the RRE2 RNA undergoes a folding transition and to obtain information about the relative positioning of RRE2 substructures in three dimensions. Our analysis collectively suggests that the HIV-2 RRE undergoes two conformational transitions before assuming the energetically most favorable conformer. The 3D models for the HIV-2 RRE and folding intermediates are also presented, wherein the Rev-binding stem–loops (IIB and I) are located coaxially in the former, which is in agreement with previous models for HIV-1 Rev-RRE binding. PMID:23640333

Lusvarghi, Sabrina; Sztuba-Solinska, Joanna; Purzycka, Katarzyna J.; Pauly, Gary T.; Rausch, Jason W.; Grice, Stuart F. J. Le



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

PubMed Central

We previously demonstrated an important role of the constant region in the pathogenicity of anti-DNA antibodies. To determine the mechanisms by which the constant region affects autoantibody binding, a panel of isotype–switch variants (IgG1, IgG2a, IgG2b) was generated from the murine PL9-11 IgG3 autoantibody. The affinity of the PL9-11 antibody panel for histone was measured by surface plasmon resonance (SPR). Tryptophan fluorescence was used to determine wavelength shifts of the antibody panel upon binding to DNA and histone. Finally, circular dichroism spectroscopy was used to measure changes in secondary structure. SPR analysis revealed significant differences in histone binding affinity between members of the PL9-11 panel. The wavelength shifts of tryptophan fluorescence emission were found to be dependent on the antibody isotype, while circular dichroism analysis determined that changes in antibody secondary structure content differed between isotypes upon antigen binding. Thus, the antigen binding affinity is dependent on the particular constant region expressed. Moreover, the effects of antibody binding to antigen were also constant region dependent. Alteration of secondary structures influenced by constant regions may explain differences in fine specificity of anti-DNA antibodies between antibodies with similar variable regions, as well as cross-reactivity of anti-DNA antibodies with non-DNA antigens. PMID:23665381

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



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

PubMed Central

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



Two distinct 18S rRNA secondary structures in Dipodascus (Hemiascomycetes).  


The nucleotide sequences of the 18S rRNA gene from ascomycetous yeast-like fungi in the genera Dipodascus, Galactomyces and Geotrichum were determined and the tested strains were separated into two groups by sequence length. In group 1, the length and secondary structure of 18S rRNA corresponded to those of typical eukaryotes. In group 2, the 18S rRNA gene sequences were about 150 nt shorter than those of most other eukaryotes and the predicted secondary structure lacked helices 10 and E21-5. Many substitutions and some deletions in group 2 18S rRNA gene were not only found in variable regions, but also in regions that are highly conserved among ascomycetes. Despite the considerable differences in 18S rRNA gene sequence and secondary structure between group 2 and other fungi, including group 1, phylogenetic analysis revealed that groups 1 and 2 are closely related. These findings suggest that a number of deletions occurred in the 18S rRNA of the common ancestor of group 2 strains. PMID:10832631

Ueda-Nishimura, K; Mikata, K



[Information about the protein secondary structure improves quality of an alignment of protein sequences].  


All popular algorithms of pair-wise alignment of protein primary structures (e.g. Smith-Waterman (SW), FASTA, BLAST, et al.) utilize only amino acid sequences. The SW-algorithm is the most accurate among them, i.e. it produces alignments that are most similar to the alignments obtained by superposition of protein 3D-structures. But even the SW-algorithm is unable to restore the 3D-based alignment if similarity of amino acid sequences (%id) is below 30%. We have proposed a novel alignment method that explicitly takes into account the secondary structure of the compared proteins. We have shown that it creates significantly more accurate alignments compared to SW-algorithm. In particular, for sequences with %id < 30% the average accuracy of the new method is 58% compared to 35% for SW-algorithm (the accuracy of an algorithmic sequence alignment is the part of restored position of a "golden standard" alignment obtained by superposition of corresponding 3D-structures). The accuracy of the proposed method is approximately identical both for experimental, and for theoretically predicted secondary structures. Thus the method can be applied for alignment of protein sequences even if protein 3D-structure is unknown. The program is available at PMID:16813172

Litvinov, I I; Lobanov, M Iu; Mironov, A A; Finkel'sht?n, M A



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


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

Chen, Ying; Stephan, Wolfgang



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



Peptide contour length determines equilibrium secondary structure in protein-analogous micelles.  


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. © 2013 Wiley Periodicals, Inc. Biopolymers 99: 573-581, 2013. PMID:23794370

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



Template-based C8-SCORPION: a protein 8-state secondary structure prediction method using structural information and context-based features  

PubMed Central

Background Secondary structures prediction of proteins is important to many protein structure modeling applications. Correct prediction of secondary structures can significantly reduce the degrees of freedom in protein tertiary structure modeling and therefore reduces the difficulty of obtaining high resolution 3D models. Methods In this work, we investigate a template-based approach to enhance 8-state secondary structure prediction accuracy. We construct structural templates from known protein structures with certain sequence similarity. The structural templates are then incorporated as features with sequence and evolutionary information to train two-stage neural networks. In case of structural templates absence, heuristic structural information is incorporated instead. Results After applying the template-based 8-state secondary structure prediction method, the 7-fold cross-validated Q8 accuracy is 78.85%. Even templates from structures with only 20%~30% sequence similarity can help improve the 8-state prediction accuracy. More importantly, when good templates are available, the prediction accuracy of less frequent secondary structures, such as 3-10 helices, turns, and bends, are highly improved, which are useful for practical applications. Conclusions Our computational results show that the templates containing structural information are effective features to enhance 8-state secondary structure predictions. Our prediction algorithm is implemented on a web server named "C8-SCORPION" available at: PMID:25080939



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

PubMed Central

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

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



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


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



Structural and Functional Insights into Dom34, a Key Component of No-Go mRNA Decay  

Microsoft Academic Search

SUMMARY The yeast protein Dom34 is a key component of no-go decay, by which mRNAs with transla- tional stalls are endonucleolytically cleaved and subsequently degraded. However, the identity of the endoribonuclease is unknown. Homologs of Dom34, called Pelota, are broadly conserved in eukaryotes and archaea. To gain insights into the structure and function of Dom34\\/Pelota, we have determined the struc-

Hyung Ho Lee; Youn-Sung Kim; Kyoung Hoon Kim; Inha Heo; Sang Kyu Kim; Olesya Kim; Hye Kyung Kim; Ji Young Yoon; Hyoun Sook Kim; Do Jin Kim; Sang Jae Lee; Hye Jin Yoon; Soon Jong Kim; Byung Gil Lee; Hyun Kyu Song; V. Narry Kim; Chung-Mo Park; Se Won Suh



Lysophosphatidic acid can support the formation of membranous structures and an increase in MBP mRNA levels in differentiating oligodendrocytes  

PubMed Central

During development, differentiating oligodendrocytes progress in distinct maturation steps from premyelinating to myelinating cells. Such maturing oligodendrocytes express both receptors mediating signaling via extracellular lysophosphatidic acid (LPA) and the major enzyme generating extracellular LPA, namely phosphodiesterase-I?/autotaxin (PD-I?/ATX). However, the biological role of extracellular LPA during the maturation of differentiating oligodendrocytes is currently unclear. Here, we demonstrate that application of exogenous LPA induced an increase in the area occupied by the oligodendrocytes’ process network, but only when PD-I?/ATX expression was down-regulated. This increase in network area was caused primarily by the formation of membranous structures. In addition, LPA increased the number of cells positive for myelin basic protein (MBP). This effect was associated by an increase in the mRNA levels coding for MBP but not myelin oligodendrocyte glycoprotein (MOG). Taken together, these data suggest that LPA may play a crucial role in regulating the later stages of oligodendrocyte maturation. PMID:18594965

Nogaroli, Luciana; Yuelling, Larra M.; Dennis, Jameel; Gorse, Karen; Payne, Shawn G.; Fuss, Babette



Secondary structure prediction of protein constructs using random incremental truncation and vacuum-ultraviolet CD spectroscopy  

E-print Network

A novel uracil-DNA degrading protein factor (termed UDE) was identified in Drosophila melanogaster with no significant structural and functional homology to other uracil-DNA binding or processing factors. Determination of the 3D structure of UDE will be a true breakthrough in description of the molecular mechanism of action of UDE catalysis, as well as in general uracil-recognition and nuclease action. The revolutionary ESPRIT technology was applied to the novel protein UDE to overcome problems in identifying soluble expressing constructs given the absence of precise information on domain content and arrangement. Nine specimen from the created numerous truncated constructs of UDE were choosen to dechiper structural and functional relationships. VUVCD with neural network was performed to define the secondary structure content and location of UDE and its truncated variants. The quantitative analysis demonstrated exclusive {\\alpha}-helical content for the full-length protein, which is preserved in the truncated ...

Pukáncsik, M; Matsuo, K; Gekko, K; Hart, D; Kézsmárki, I; Vértessy, B G



Secondary and tertiary structure of bacteriorhodopsin in the SDS denatured state.  


We characterized the structure of partially unfolded bacteriorhodopsin in sodium dodecyl sulfate (SDS) micelles and compared it with its in vitro refolded structure after reconstitution with dimyristoylphosphatidylcholine/3-[(3-cholamidopropyl)dimethylammonio]-1-propanesulfonate (DMPC/CHAPS). Intrahelical and interhelical distances were mapped in the protein using strategically located spin-label pairs at helical ends, assayed by pulsed electron paramagnetic resonance spectroscopy (double electron-electron spin resonance, DEER). We find that in SDS the intrahelical end-to-end distances exhibit broad distributions, suggesting a heterogeneous ensemble of conformations with differing secondary structures. Nevertheless, a majority of the denatured population retains end-to-end distances similar to those in the native state. In contrast, the observed greatly increased interhelical distances, in addition to their very broad distributions, suggest that in the SDS micelles very little of the native tertiary structure remains. PMID:22242919

Krishnamani, Venkatramanan; Hegde, Balachandra G; Langen, Ralf; Lanyi, Janos K



Effect of heat-induced structural perturbation of secondary and tertiary structures on the chaperone activity of alpha-crystallin.  


alpha-Crystallin, a major protein of the lens, is known to have chaperone activity to protect other proteins against thermal aggregation. Heat-induced structural change of alpha-crystallin was previously shown to increase its chaperone activity. In this report, we studied the thermal reversibility of alpha-crystallin and the effect of change in secondary structure on its chaperone function in vitro. The heat-induced conformational changes in the aromatic region of near-UV CD spectra showed only a small degree of reversibility. The structural transitions from 50 to 70 degrees C were largely reversible if the incubation time was short. However, the protective ability to inhibit thermal aggregation of alcohol dehydrogenase by alpha-crystallin was essentially similar at 48 and 70 degrees C. Under long-term heating at high temperatures, there was a time-dependent irreversibility of structural change in alpha-crystallin as revealed by CD spectroscopy. Such denatured alpha-crystallin by long-term heating can still preserve its ability to prevent UV-induced aggregation of gamma-crystallin at room temperature, indicating relatively little effect of heat-induced changes in secondary structure on the chaperone activity of alpha-crystallin. PMID:9268700

Lee, J S; Satoh, T; Shinoda, H; Samejima, T; Wu, S H; Chiou, S H



Selective inhibition of cell-free translation by oligonucleotides targeted to a mRNA hairpin structure.  

PubMed Central

Using an in vitro selection approach we have previously isolated oligodeoxy aptamers that can bind to a DNA hairpin structure without disrupting the double-stranded stem. We report here that these oligomers can bind to the RNA version of this hairpin, mostly through pairing with a designed 6 nt anchor. The part of the aptamer selected against the DNA hairpin did not increase stability of the RNA-aptamer complex. However, it contributed to the binding site for Escherichia coli RNase H, leading to very efficient cleavage of the target RNA. In addition, a 2'- O -methyloligoribonucleotide analogue of one selected sequence selectively blocked in vitro translation of luciferase in wheat germ extract by binding to the hairpin region inserted upstream of the initiation codon of the reporter gene. Therefore, non-complementary oligomers can exhibit antisense properties following hybridization with the target RNA. Our study also suggests that in vitro selection might provide a means to extend the repertoire of sequences that can be targetted by antisense oligonucleotides to structured RNA motifs of biological importance. PMID:9580674

Le Tinevez, R; Mishra, R K; Toulme, J J



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, Aurelie; Chane-Woon-Ming, Beatrice; Randrianjafy, Ramy; Vivet-Boudou, Valerie; Richer, Delphine; Pfeffer, Sebastien



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


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

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



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

NASA Astrophysics Data System (ADS)

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

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



Multilign: an algorithm to predict secondary structures conserved in multiple RNA sequences  

PubMed Central

Motivation: With recent advances in sequencing, structural and functional studies of RNA lag behind the discovery of sequences. Computational analysis of RNA is increasingly important to reveal structure–function relationships with low cost and speed. The purpose of this study is to use multiple homologous sequences to infer a conserved RNA structure. Results: A new algorithm, called Multilign, is presented to find the lowest free energy RNA secondary structure common to multiple sequences. Multilign is based on Dynalign, which is a program that simultaneously aligns and folds two sequences to find the lowest free energy conserved structure. For Multilign, Dynalign is used to progressively construct a conserved structure from multiple pairwise calculations, with one sequence used in all pairwise calculations. A base pair is predicted only if it is contained in the set of low free energy structures predicted by all Dynalign calculations. In this way, Multilign improves prediction accuracy by keeping the genuine base pairs and excluding competing false base pairs. Multilign has computational complexity that scales linearly in the number of sequences. Multilign was tested on extensive datasets of sequences with known structure and its prediction accuracy is among the best of available algorithms. Multilign can run on long sequences (> 1500 nt) and an arbitrarily large number of sequences. Availability: The algorithm is implemented in ANSI C++ and can be downloaded as part of the RNAstructure package at: Contact: Supplementary information: Supplementary data are available at Bioinformatics online. PMID:21193521

Xu, Zhenjiang; Mathews, David H.



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

PubMed Central

Summary A remaining challenge in protein modeling is to predict structures for sequences that do not share recognizable sequence similarity to any experimentally solved structure. This challenge can be addressed by hybrid algorithms that utilize easily obtainable experimental data and carry a limited amount of indirect structural information. Based on earlier observations, the library of protein super-secondary structure motifs (Smotifs) saturated about a decade ago, and new folds discovered since then are novel combinations of existing Smotifs. This observation suggests that it should be possible to build any structure, of either a known or yet to be discovered fold, from a combination of existing Smotifs derived from already known structures. In the absence of any sequence similarity signal, limited experimental data can be used to relate the backbone conformations of Smotifs between target proteins and known experimental structures. Here we present a modeling algorithm that relies on an exhaustive Smotif library and on NMR chemical shift patterns without any input of primary sequence information. In a test of 102 proteins with unique folds, the algorithm delivered 90 homology model quality models, among them 24 high quality ones, and a topologically correct solution for almost all cases. Detailed analysis of the method’s performance suggests that further improvement can be achieved by improving sampling algorithms and developing more precise tools that predict dihedral angle preferences from chemical shift assignments. The current approach opens a venue to address the modeling of larger protein structures for which chemical shifts are available. PMID:23685209

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



Abstract Secondary copulatory structures are well-known in male dragonflies and spiders. Here I report a second-  

E-print Network

Abstract Secondary copulatory structures are well-known in male dragonflies and spiders. Here I) and on the abdominal segments of male dragonflies (Odonata: Chapman 1998). The female ground weta, Hemiandrus

Gwynne, Darryl T.


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

E-print Network

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 ...

Bryan, Allen W.


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.



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

PubMed Central

Both increased temperature and moderate concentrations of fluorinated alcohols enhance aggregation of the Parkinson’s disease-associated protein ?–synuclein (?S). Here, we investigate the secondary structural rearrangements induced by heating and trifluoroethanol (TFE). At low TFE concentrations, CD spectra feature a negative peak characteristic of disordered polypeptides near 200 nm and a slight shoulder around 220 nm suggesting some polyproline-II content. Upon heating, these peaks weaken, while a weak negative signal develops at 222 nm. At high TFE concentrations, the spectra show distinct minima at 208 and 222 nm, indicative of considerable ?-helical structure, which diminish upon heating. We observe a crossover between the low-TFE and high-TFE behavior near 15% TFE, where we previously showed that a partially helical intermediate is populated. We postulate that the protein is well solvated by water at low TFE concentrations and by TFE at high TFE concentrations, but may become desolvated at the crossover point. We discuss the potential roles and interplay of desolvation and helical secondary structure in driving ?S aggregation. PMID:22932003

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



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

PubMed Central

?-D-Galactosidases (EC 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



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

NASA Astrophysics Data System (ADS)

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

Lee, Chang-Yong



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



Effect of neutral and acidic phospholipids on mitochondrial ATP synthase secondary structure.  


The secondary structure of delipidated and egg phosphatidylcholine or asolectin reconstituted mitochondrial ATP synthase complex from beef heart was investigated by Fourier transform infrared spectroscopy. Upon reconstitution, the infrared spectra of ATP synthase revealed an increase in turns and a concomitant decrease in beta-sheet content which occurred to a larger extent in the presence of asolectin rather than in the presence of egg phosphatidylcholine. These data correlate with kinetic data showing a higher ATPase activity of the asolectin reconstituted enzyme protein than the egg phosphatidylcholine reconstituted or delipidated enzyme complexes. PMID:8282114

Sala, F D; Loregian, A; Lippe, G; Bertoli, E; Tanfani, F



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



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

SciTech Connect

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

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



Evolutionary conservation of sequence and secondary structures inCRISPR repeats  

SciTech Connect

Clustered Regularly Interspaced Palindromic Repeats (CRISPRs) are a novel class of direct repeats, separated by unique spacer sequences of similar length, that are present in {approx}40% of bacterial and all archaeal genomes analyzed to date. More than 40 gene families, called CRISPR-associated sequences (CAS), appear in conjunction with these repeats and are thought to be involved in the propagation and functioning of CRISPRs. It has been proposed that the CRISPR/CAS system samples, maintains a record of, and inactivates invasive DNA that the cell has encountered, and therefore constitutes a prokaryotic analog of an immune system. Here we analyze CRISPR repeats identified in 195 microbial genomes and show that they can be organized into multiple clusters based on sequence similarity. All individual repeats in any given cluster were inferred to form characteristic RNA secondary structure, ranging from non-existent to pronounced. Stable secondary structures included G:U base pairs and exhibited multiple compensatory base changes in the stem region, indicating evolutionary conservation and functional importance. We also show that the repeat-based classification corresponds to, and expands upon, a previously reported CAS gene-based classification including specific relationships between CRISPR and CAS subtypes.

Kunin, Victor; Sorek, Rotem; Hugenholtz, Philip



Membrane Association and Destabilization by Aggregatibacter actinomycetemcomitans Leukotoxin Requires Changes in Secondary Structures  

PubMed Central

SUMMARY Aggregatibacter actinomycetemcomitans is a common inhabitant of the upper aerodigestive tract of humans and non-human primates and is associated with disseminated infections, including lung and brain abscesses, pediatric infective endocarditis in children, and localized aggressive periodontitis. A. actinomycetemcomitans secretes a repeats-in-toxin protein, leukotoxin, which exclusively kills lymphocyte function-associated antigen-1-bearing cells. The toxin's pathological mechanism is not fully understood; however, experimental evidence indicates that it involves the association with and subsequent destabilization of the target cell's plasma membrane. We have long hypothesized that leukotoxin secondary structure is strongly correlated with membrane association and/or destabilization. In this study, we tested this hypothesis by analyzing lipid-induced changes in leukotoxin conformation. Upon incubation of leukotoxin with lipids that favor leukotoxin-membrane association, we observed an increase in leukotoxin ?-helical content that was not observed with lipids that favor membrane destabilization. The change in leukotoxin conformation after incubation with these lipids suggests that membrane binding and membrane destabilization have distinct secondary structural requirements, suggesting that they are independent events. These studies thus provide insight into the mechanism of cell damage that leads to disease progression by A. actinomycetemcomitans. PMID:23678967

Walters, Michael J.; Brown, Angela C.; Edrington, Thomas C.; Baranwal, Somesh; Du, Yurong; Lally, Edward T.; Boesze-Battaglia, Kathleen



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))



Modeling the influence of alkane molecular structure on secondary organic aerosol formation.  


Secondary Organic Aerosols (SOA) production and ageing is a multigenerational oxidation process involving the formation of successive organic compounds with higher oxidation degree and lower vapor pressure. Intermediate Volatility Organic Compounds (IVOC) emitted to the atmosphere are expected to be a substantial source of SOA. These emitted IVOC constitute a complex mixture including linear, branched and cyclic alkanes. The explicit gas-phase oxidation mechanisms are here generated for various linear and branched C10-C22 alkanes using the GECKO-A (Generator for Explicit Chemistry and Kinetics of Organics in the Atmosphere) and SOA formation is investigated for various homologous series. Simulation results show that both the size and the branching of the carbon skeleton are dominant factors driving the SOA yield. However, branching appears to be of secondary importance for the particle oxidation state and composition. The effect of alkane molecular structure on SOA yields appears to be consistent with recent laboratory observations. The simulated SOA composition shows, however, an unexpected major contribution from multifunctional organic nitrates. Most SOA contributors simulated for the oxidation of the various homologous series are far too reduced to be categorized as highly oxygenated organic aerosols (OOA). On a carbon basis, the OOA yields never exceeded 10% regardless of carbon chain length, molecular structure or ageing time. This version of the model appears clearly unable to explain a large production of OOA from alkane precursors. PMID:24600999

Aumont, Bernard; Camredon, Marie; Mouchel-Vallon, Camille; La, Stéphanie; Ouzebidour, Farida; Valorso, Richard; Lee-Taylor, Julia; Madronich, Sasha



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


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

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



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

PubMed Central

The primary structure of the gene for 18 S rRNA of the crustacean Artemia salina was determined. The sequence has been aligned with 13 other small ribosomal subunit RNA sequences of eukaryotic, archaebacterial, eubacterial, chloroplastic and plant mitochondrial origin. Secondary structure models for these RNAs were derived on the basis of previously proposed models and additional comparative evidence found in the alignment. Although there is a general similarity in the secondary structure models for eukaryotes and prokaryotes, the evidence seems to indicate a different topology in a central area of the structures. Images PMID:6514572

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



In solution cation-induced secondary and tertiary structure alterations of human calprotectin.  


Calprotectin (CP) is widely considered to have diverse roles including growth inhibitory and apoptosis induction in a number of tumor cell lines and antimicrobial activities. As CP has been proposed to bind metal ions with high affinity, we have studied its functional and primarily its structural behavior upon Zn(2+) and Mn(2+) chelation solely and along with Ca(2+). We employed fluorescence spectroscopy and circular dichroism to determine the resulting modifications. Based upon our findings it is clear that treating CP with ions effectively weakened its natural growth inhibitory activity. Moreover, structural analysis of Zn(2+) and Mn(2+)-treated CPs indicated remarkable alterations in the regular secondary structures in favor of irregular structures while Zn(2+) and Mn(2+) treatment of CP after incubation with Ca(2+) displayed no remarkable shifts. Tertiary structure investigation using fluorescence spectroscopy showed that CP undergoes conformational changes upon Zn(2+) and Mn(2+) treatment whereby Trp residues of protein is slightly exposed to the hydrophilic environment, compactness of CP is compromised, whereas in Ca(2+)-treated CP, the tertiary structure integrity is intact upon Zn(2+) and Mn(2+) chelation. Interestingly, CP structural modifications upon Zn(2+) and Mn(2+) treatment was significantly comparable, probably due to similar radii and charges of ions. Taken all together, we have concluded that CP maintains its normal nature in Ca(2+)-loaded state when treated with Zn(2+) and Mn(2+) ions. It can be suggested that Ca(2+) not only stabilize CP structure but also helps CP to keep its structure upon metal ions chelation which is involved in host organism defense system. PMID:25213023

Imani, Mehdi; Bahrami, Yaser; Jaliani, Hossein Zarei; Ardestani, Sussan Kaboudanian



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

NASA Astrophysics Data System (ADS)

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

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



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



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.



The structure of the lentil (Lens culinaris) lectin. Amino acid sequence determination and prediction of the secondary structure.  


The subunit structure and complete amino acid sequence of the lectin extracted from Lens culinaris (LcL) seeds was determined. In previous studies, the primary structure of the alpha-chain (Mr = 5,710) was shown to be homologous to the alpha-chain of the lectin from Pisum sativum, the Vicia cracca glucose-specific lectin, and a region in the middle of the concanavalin A sequence (residues 70-121). The complete amino acid sequence of the beta-chain (Mr = 17,572) has been determined from 11 tryptic peptides, 4 peptides derived by chemical cleavage of the beta-chain at its three tryptophan residues, 11 peptides obtained after digestion with Staphylococcus aureus protease, and 5 tryptic peptides from the succinylated polypeptide chain. The extensive homologies by alignment of the alpha- and beta-chains of the L. culinaris lectin with portions of concanavalin A situated between 1 to 45 and 70 to 237, suggest that the L. culinaris and Canavalia ensiformis lectins have evolved from each other. A comparison was made between the secondary structure of the C. ensiformis lectin and the probable secondary structure of the L. culinaris lectin as predicted by two different methods. The results indicate that the folding of these two polypeptides has been particularly well conserved during evolution. It is suggested that the L. culinaris lectin is synthesized as a single polypeptide chain and cleaved subsequently into two or possibly three fragments, two of which would be alpha and beta and the third a fragment homologous to portion 46 to 69 in concanavalin A. As in favin, the amino acids postulated to be involved in the formation of the hydrophobic cavity and the sugar and metal binding sites are highly conserved in L. culinaris lectin. PMID:7240155

Foriers, A; Lebrun, E; Van Rapenbusch, R; de Neve, R; Strosberg, A D



MicroRNA-directed cleavage of Nicotiana sylvestris PHAVOLUTA mRNA regulates the vascular cambium and structure of apical meristems.  


Leaf initiation in the peripheral zone of the shoot apical meristem involves a transition to determinate cell fate, but indeterminacy is maintained in the vascular cambium, a tissue critical to the continuous growth of vascular tissue in leaves and stems. We show that the orientation of cambial growth is regulated by microRNA (miRNA)-directed cleavage of mRNA from the Nicotiana sylvestris ortholog of PHAVOLUTA (NsPHAV). Loss of miRNA regulation in semidominant phv1 mutants misdirects lateral growth of leaf midveins and stem vasculature away from the shoot, disrupting vascular connections in stem nodes. The phv1 mutation also expands the central zone in vegetative and inflorescence meristems, implicating miRNA and NsPHAV in regulation of meristem structure. In flowers, phv1 causes reiteration of carpel initiation, a phenocopy for loss of CARPEL FACTORY/DICER LIKE1, indicating that miRNA is critical to the termination of indeterminacy in floral meristems. Results point to a common role for miRNA in spatial and temporal restriction of HD-ZIPIII mediated indeterminacy in apical and vascular meristems. PMID:15194817

McHale, Neil A; Koning, Ross E



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


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



Plant secondary metabolite-induced shifts in bacterial community structure and degradative ability in contaminated soil.  


The aim of the study was to investigate how selected natural compounds (naringin, caffeic acid, and limonene) induce shifts in both bacterial community structure and degradative activity in long-term polychlorinated biphenyl (PCB)-contaminated soil and how these changes correlate with changes in chlorobiphenyl degradation capacity. In order to address this issue, we have integrated analytical methods of determining PCB degradation with pyrosequencing of 16S rRNA gene tag-encoded amplicons and DNA-stable isotope probing (SIP). Our model system was set in laboratory microcosms with PCB-contaminated soil, which was enriched for 8 weeks with the suspensions of flavonoid naringin, terpene limonene, and phenolic caffeic acid. Our results show that application of selected plant secondary metabolites resulted in bacterial community structure far different from the control one (no natural compound amendment). The community in soil treated with caffeic acid is almost solely represented by Proteobacteria, Acidobacteria, and Verrucomicrobia (together over 99 %). Treatment with naringin resulted in an enrichment of Firmicutes to the exclusion of Acidobacteria and Verrucomicrobia. SIP was applied in order to identify populations actively participating in 4-chlorobiphenyl catabolism. We observed that naringin and limonene in soil foster mainly populations of Hydrogenophaga spp., caffeic acid Burkholderia spp. and Pseudoxanthomonas spp. None of these populations were detected among 4-chlorobiphenyl utilizers in non-amended soil. Similarly, the degradation of individual PCB congeners was influenced by the addition of different plant compounds. Residual content of PCBs was lowest after treating the soil with naringin. Addition of caffeic acid resulted in comparable decrease of total PCBs with non-amended soil; however, higher substituted congeners were more degraded after caffeic acid treatment compared to all other treatments. Finally, it appears that plant secondary metabolites have a strong effect on the bacterial community structure, activity, and associated degradative ability. PMID:23250224

Uhlik, Ondrej; Musilova, Lucie; Ridl, Jakub; Hroudova, Miluse; Vlcek, Cestmir; Koubek, Jiri; Holeckova, Marcela; Mackova, Martina; Macek, Tomas



A comparative CD study of carbonic anhydrase isoenzymes with different number of tryptophans: impact on calculation of secondary structure content.  

PubMed Central

The CD spectra of human carbonic anhydrase I and II and bovine carbonic anhydrase III were recorded and analyzed. The 3D structures of these isoenzymes are known, showing very similar secondary structure and polypeptide-chain fold. The tryptophan content, however, differs between the isoenzymes, i.e., isoenzymes I, II, and III possess 6, 7, and 8 tryptophans, respectively. All of the tryptophans except the additional tryptophans in isoenzymes II and III, i.e., W245 and W47, are conserved. Despite the fact that X-ray structure determinations showed that the isoenzymes had highly similar secondary structure, the contents of alpha-helix and beta-sheet structure differed considerably when using different CD algorithms for estimation of the fractions of various secondary structural elements. This shows that aromatic amino acids also interfere in the wavelength region (far-UV) used to calculate the amount of secondary structure. Such interference is especially problematic when analyzing proteins like carbonic anhydrase, which consist mainly of beta-structure that gives rise to weak ellipticity bands, compared to the bands arising from alpha-helical structure. PMID:8976556

Borén, K.; Freskgård, P. O.; Carlsson, U.



Conformational analysis and clustering of short and medium size loops connecting regular secondary structures: a database for modeling and prediction.  

PubMed Central

Loops are regions of nonrepetitive conformation connecting regular secondary structures. We identified 2,024 loops of one to eight residues in length, with acceptable main-chain bond lengths and peptide bond angles, from a database of 223 protein and protein-domain structures. Each loop is characterized by its sequence, main-chain conformation, and relative disposition of its bounding secondary structures as described by the separation between the tips of their axes and the angle between them. Loops, grouped according to their length and type of their bounding secondary structures, were superposed and clustered into 161 conformational classes, corresponding to 63% of all loops. Of these, 109 (51% of the loops) were populated by at least four nonhomologous loops or four loops sharing a low sequence identity. Another 52 classes, including 12% of the loops, were populated by at least three loops of low sequence similarity from three or fewer nonhomologous groups. Loop class suprafamilies resulting from variations in the termini of secondary structures are discussed in this article. Most previously described loop conformations were found among the classes. New classes included a 2:4 type IV hairpin, a helix-capping loop, and a loop that mediates dinucleotide-binding. The relative disposition of bounding secondary structures varies among loop classes, with some classes such as beta-hairpins being very restrictive. For each class, sequence preferences as key residues were identified; those most frequently at these conserved positions than in proteins were Gly, Asp, Pro, Phe, and Cys. Most of these residues are involved in stabilizing loop conformation, often through a positive phi conformation or secondary structure capping. Identification of helix-capping residues and beta-breakers among the highly conserved positions supported our decision to group loops according to their bounding secondary structures. Several of the identified loop classes were associated with specific functions, and all of the member loops had the same function; key residues were conserved for this purpose, as is the case for the parvalbumin-like calcium-binding loops. A significant number, but not all, of the member loops of other loop classes had the same function, as is the case for the helix-turn-helix DNA-binding loops. This article provides a systematic and coherent conformational classification of loops, covering a broad range of lengths and all four combinations of bounding secondary structure types, and supplies a useful basis for modelling of loop conformations where the bounding secondary structures are known or reliably predicted. PMID:8976569

Donate, L. E.; Rufino, S. D.; Canard, L. H.; Blundell, T. L.



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.



Using flexible loop mimetics to extend ?-value analysis to secondary structure interactions  

PubMed Central

Chemical synthesis allows the incorporation of nonnatural amino acids into proteins that may provide previously untried probes of their folding pathway and thermodynamic stability. We have used a flexible thioether linker as a loop mimetic in the human yes kinase-associated protein (YAP 65) WW domain, a three-stranded, 44-residue, ?-sheet protein. This linkage avoids problems of incorporating sequences that constrain loops to the extent that they significantly change the nature of the denatured state with concomitant effects on the folding kinetics. An NMR solution structure shows that the thioether linker had little effect on the global fold of the domain, although the loop is apparently more dynamic. The thioether variants are destabilized by up to 1.4 kcal/mol (1 cal = 4.18 J). Preliminary ?-value analysis showed that the first loop is highly structured in the folding transition state, and the second loop is essentially unstructured. These data are consistent with results from simulated unfolding and detailed protein-engineering studies of structurally homologous WW domains. Previously, ?-value analysis was limited to studying side-chain interactions. The linkers used here extend the protein engineering method directly to secondary-structure interactions. PMID:11687614

Ferguson, Neil; Pires, José Ricardo; Toepert, Florian; Johnson, Christopher M.; Pan, Yong Ping; Volkmer-Engert, Rudolf; Schneider-Mergener, Jens; Daggett, Valerie; Oschkinat, Hartmut; Fersht, Alan



A possible method for characterizing the secondary structure of ribonucleic acids  

PubMed Central

The E280/E260 ratio was found to be suitable for following the ionization of cytosine residues of polynucleotides on the basis of studies with model compounds such as oligoguanylic acid, oligocytidylic acid, a complex formed between polyadenylic acid and polyuridylic acid, and a copolymer of guanylic acid and cytidylic acid, provided that changes in secondary structure were taken into account. The pK of cytosine residues of a polynucleotide in the amorphous form was found to be 4·70 at 25° in 0·1m-sodium phosphate on the basis of titration at 75–85° and on the assumption that the heat of ionization was the same as the value (5·2kcal./mole) found for CMP. In contrast, the pK of cytosine residues in the double-helical form of DNA was found to be about 3·25. These observations were utilized in estimating the fraction of cytosine residues in helical segments of ribosomal RNA, a copolymer of guanylic acid and cytidylic acid, and a copolymer of adenylic acid, guanylic acid, uridylic acid and cytidylic acid. The ionization of guanine and uracil residues was estimated from changes in the E270/E260 ratio and E230/E260 ratio respectively. In the amorphous form of RNA both residues had the same pK, whereas in the double-helical form ionization was suppressed. The fraction of guanine and uracil residues in amorphous segments may be estimated from the titration curves. The difference in the denaturation spectrum of adenine--uracil and guanine--cytosine base pairs at 280m? was enhanced in acidic solutions whereas E260 was hardly affected. Hence a comparison of the increments in E280 and E260 obtained on increasing the temperature at constant pH may be used to distinguish the melting ranges of helical domains differing in nucleotide composition. In alkaline solutions comparison of the increments in E260 and E270 yields similar information. In acidic solutions the fraction of cytosine residues involved in helical secondary structure, the degree of ionization of cytosine residues and the fraction of adenine--uracil base pairs denatured may be estimated from ?E265 and ?E280. In alkaline solutions the fractions of guanine and uracil residues involved in secondary structure and the degrees of ionization of these residues may be estimated from ?E230, ?E245, ?E260 and ?E280. PMID:5338275

Cox, R. A.



Periodicity in DNA primary structure is defined by secondary structure of the coded protein.  

PubMed Central

A 10.5-base periodicity found earlier is inherent in both eu- and prokaryotic coding nucleotide sequences. In the case of noncoding eukaryotic sequences no periodicity is found, so the 10.5-base oscillation seemingly does not correlate with the nucleosomal organization of DNA. It is shown that the DNA fragments, coding the alpha-helical protein segments, manifest the pronounced 10.5-base periodicity, while those regions of DNA which code the beta-structure have a 6-base oscillation. The repeating pattern of nucleotide sequences can be used for comparison of the DNA segments with low degree of homology. PMID:7243595

Zhurkin, V B



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


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



The Binding Effect Of Metal On The Secondary Structure Of Albumin  

NASA Astrophysics Data System (ADS)

On the basis of vibrational analysis, the deconvolution and derivative procedures of amide bands in IR spectra has stimulated the interests in the study on the secondary structure of protein [1, 2]. The inter-relationships between metal ions and binding substances such as protein are important in the living system. However, the influnce of metal ions on the secondary stucture of protein has not been studied in details by this technique. In this investigation, NaC1, KC1,ZnC12, MgC12, CaC12, AlC13, NaNO3, AI (NO3)3, PrC13,NdC13,EuC13,DyC13, TbBr3, Ce(NO3)3, andGd(NO3)3 were reacted with bovine albumin in aqueons solutions for 4-5 hours respectively. The albumin complexes were formed both in supernatants and precipitates. Their FTIR spectra were measured with BaF2 pellet for the precipitates and cast film on BaF2 windows for the supernatants, utilizing a Nicolet 7199B spectrometer.

Li, Ly; Guo, Hai; Liu, Wentian; Wu, Jin-Guang; Xu, Guang-Xian



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



Ensemble of Secondary Structures for Encapsidated Satellite Tobacco Mosaic Virus RNA Consistent with Chemical Probing and Crystallography Constraints  

PubMed Central

Viral genomic RNA adopts many conformations during its life cycle as the genome is replicated, translated, and encapsidated. The high-resolution crystallographic structure of the satellite tobacco mosaic virus (STMV) particle reveals 30 helices of well-ordered RNA. The crystallographic data provide global constraints on the possible secondary structures for the encapsidated RNA. Traditional free energy minimization methods of RNA secondary structure prediction do not generate structures consistent with the crystallographic data, and to date no complete STMV RNA basepaired secondary structure has been generated. RNA-protein interactions and tertiary interactions may contribute a significant degree of stability, and the kinetics of viral assembly may dominate the folding process. The computational tools, Helix Find & Combine, Crumple, and Sliding Windows and Assembly, evaluate and explore the possible secondary structures for encapsidated STMV RNA. All possible hairpins consistent with the experimental data and a cotranscriptional folding and assembly hypothesis were generated, and the combination of hairpins that was most consistent with experimental data is presented as the best representative structure of the ensemble. Multiple solutions to the genome packaging problem could be an evolutionary advantage for viruses. In such cases, an ensemble of structures that share favorable global features best represents the RNA fold. PMID:21723827

Schroeder, Susan J.; Stone, Jonathan W.; Bleckley, Samuel; Gibbons, Theodore; Mathews, Deborah M.



Metal binding properties and secondary structure of the zinc-binding domain of Nup475.  


Nup475 is a nuclear zinc-binding protein of unknown function that is induced in mammalian cells by growth factor mitogens. Nup475 contains two tandemly repeated sequences YKTELCX8CX5CX3H (Cys3His repeats) that are thought to be zinc-bindin domains. Similar sequences have been found in a number of proteins from various species of eukaryotes. To determine the metal binding properties and secondary structure of the putative zinc-binding domains of Nup475, we have used synthetic or recombinant peptides that contain one or two domain sequences. The peptide with a single domain bound 1.0 +/- 0.1 equivalents of Co2+, and the peptide with two domains bound 1.7 +/- 0.4 equivalents of Co2+. Both peptides bound Co2+ and Zn2+ with affinities similar to those of classical zinc finger peptides. In each case, the Co2+ complex exhibited strong d-d transitions characteristic of tetrahedral coordination. For structural studies by nuclear magnetic resonance spectroscopy, we used a more soluble two-domain peptide that had a single amino acid substitution in a nonconserved amino acid residue in the second Cys3His repeat. The mutant peptide unexpectedly showed loss of one of its metal binding sites and displayed ordered structure for only the first Cys3His sequence. On the basis of the nuclear magnetic resonance data, we propose a structure for the Nup475 metal-binding domain in which the zinc ion is coordinated by the conserved cysteines and histidine, and the conserved YKTEL motif forms a parallel sheet-like structure with the C terminus of this domain. This structure is unlike that of any previously described class of metal binding domain. PMID:8943007

Worthington, M T; Amann, B T; Nathans, D; Berg, J M



Effect of the surface on the secondary structure of soft landed peptide ions  

SciTech Connect

Ion soft landing (SL) enables highly selective modification of substrates for applications in materials science, nanotechnology and biology. Our previous study showed that SL can be used for preparation of conformation-selected peptide arrays. Here we present a first study of the effect of the surface on the secondary structures of peptides soft-landed onto self-assembled monolayer surfaces (SAMs). Conformations of soft-landed peptide ions were examined using the newly constructed instrument that enables in situ infrared reflection absorption spectroscopy (IRRAS) characterization of surfaces during and after ion deposition. Polyalanine peptides, Ac-AnK and Ac-KAn (n=7, 15), that have been extensively studied both in solution and in the gas phase were used as model systems in this study. We demonstrate that physical and chemical properties of SAM surfaces have a strong effect on the conformations of soft-landed peptides ions. For example, deposition of the ?-helical [Ac-A15K+H]+ ion on the CH3-terminated (HSAM) surface results in immobilization of both the ?- and 310-helical conformations. In contrast, a significant fraction of Ac-A15K molecules are present in the ?-sheet conformation on the CF3- (FSAM) and COOH-terminated (COOH-SAM) surfaces. We show that the kinetic energy of the polyalanine ion, the charge, and the initial conformation have only a minor effect on the conformation of deposited species suggesting that the interaction between the molecule and the surface plays a major role in determining the secondary structures of immobilized polyalanines. This study demonstrates that SL of mass-selected ions can be utilized for obtaining fundamental understanding of the intrinsic properties of biomolecules and surfaces responsible for conformational changes upon adsorption.

Hu, Qichi; Wang, Peng; Laskin, Julia



Sequential /sup 1/H NMR assignments and secondary structure of hen egg white lysozyme in solution  

SciTech Connect

Assignments of /sup 1/H NMR resonances of 121 of the 129 residues of hen egg white lysozyme have been obtained by sequence-specific methods. Spin systems were identified with phase-sensitive two-dimensional (2-D) correlated spectroscopy and single and double relayed coherence transfer spectroscopy. For key types of amino acid residues, particularly alanine, threonine, valine, and glycine, complete spin systems were identified. For other residues a less complete definition of the spin system was found to be adequate for the purpose of sequential assignment. Sequence-specific assignments were achieved by phase-sensitive 2-D nuclear Overhauser enhancement spectroscopy (NOESY). Exploitation of the wide range of hydrogen exchange rates found in lysozyme was a useful approach to overcoming the problem of spectral overlap. The sequential assignment was built up from 21 peptide segments ranging in length from 2 to 13 residues. The NOESY spectra were also used to provide information about the secondary structure of the protein in solution. Three helical regions and two regions of ..beta..-sheet were identified from the NOESY data; these regions are identical with those found in the X-ray structure of hen lysozyme. Slowly exchanging amides are generally correlated with hydrogen bonding identified in the X-ray structure; a number of exceptions to this general trend were, however, found. The results presented in this paper indicate that highly detailed information can be obtained from 2-D NMR spectra of a protein that is significantly larger than those studies previously.

Redfield, C.; Dobson, C.M.



Protein Secondary Structure and Orientation in Silk as Revealed by Raman Spectromicroscopy  

PubMed Central

Taking advantage of recent advances in polarized Raman microspectroscopy, and based on a rational decomposition of the amide I band, the conformation and orientation of proteins have been determined for cocoon silks of the silkworms Bombyx mori and Samia cynthia ricini and dragline silks of the spiders Nephila clavipes and Nephila edulis. This study distinguished between band components due to ?-sheets, ?-turns, 31-helices, and unordered structure for the four fibers. For B. mori, the ?-sheet content is 50%, which matches the proportion of residues that form the GAGAGS fibroin motifs. For the Nephila dragline and S. c. ricini cocoon, the ?-sheet content (36–37% and 45%, respectively) is higher than the proportion of residues that belong to polyalanine blocks (18% and 42%, respectively), showing that adjacent GGA motifs are incorporated into the ?-sheets. Nephila spidroins contain fewer ?-sheets and more flexible secondary structures than silkworm fibroins. The amorphous polypeptide chains are preferentially aligned parallel to the fiber direction, although their level of orientation is much lower than that of ?-sheets. Overall, the results show that the four silks exhibit a common molecular organization, with mixtures of different amounts of ?-sheets and flexible structures, which are organized with specific orientation levels. PMID:17277183

Lefevre, Thierry; Rousseau, Marie-Eve; Pezolet, Michel



Protein secondary structure and orientation in silk as revealed by Raman spectromicroscopy.  


Taking advantage of recent advances in polarized Raman microspectroscopy, and based on a rational decomposition of the amide I band, the conformation and orientation of proteins have been determined for cocoon silks of the silkworms Bombyx mori and Samia cynthia ricini and dragline silks of the spiders Nephila clavipes and Nephila edulis. This study distinguished between band components due to beta-sheets, beta-turns, 3(1)-helices, and unordered structure for the four fibers. For B. mori, the beta-sheet content is 50%, which matches the proportion of residues that form the GAGAGS fibroin motifs. For the Nephila dragline and S. c. ricini cocoon, the beta-sheet content (36-37% and 45%, respectively) is higher than the proportion of residues that belong to polyalanine blocks (18% and 42%, respectively), showing that adjacent GGA motifs are incorporated into the beta-sheets. Nephila spidroins contain fewer beta-sheets and more flexible secondary structures than silkworm fibroins. The amorphous polypeptide chains are preferentially aligned parallel to the fiber direction, although their level of orientation is much lower than that of beta-sheets. Overall, the results show that the four silks exhibit a common molecular organization, with mixtures of different amounts of beta-sheets and flexible structures, which are organized with specific orientation levels. PMID:17277183

Lefèvre, Thierry; Rousseau, Marie-Eve; Pézolet, Michel



On The Dissolution Kinetics Of Positive Photoresists: The Secondary Structure Model  

NASA Astrophysics Data System (ADS)

Dissolution kinetics of several model resins with well defined molecular structures were studied extensively. These include a pure m-cresol formaldehyde novolac resin and an alternating m,R-cresol novolac. Other phenolic materials, such as poly(4-hydroxy-styrene), were also examined. Secondary structures of these materials were predicted by molecular mechanics energy minimization techniques and corroborated by comparison with existing experimentally determined X-ray crystallographic data, where available. The excellent agreement between theory and experiment for simple systems lends credence to structural predictions for our model systems. The salient conformational features of these molecules are manifested in the variety of inter- and intramolecular hydrogen bonding interactions which influence strongly the dissolution properties of a given resin. Dissolution kinetics were studied as a function of cation type, developer ionic strength, normality and temperature. The results are explained in terms of the inter- and intramolecular interactions predicted for these resins. Finally we show results which indicate the utility of our model to the design of resist/developer systems.

Templeton, Michael K.; Szmanda, Charles R.; Zampini, Anthony



Direct observation of protein secondary structure in gas vesicles by atomic force microscopy.  


The protein that forms the gas vesicle in the cyanobacterium Anabaena flos-aquae has been imaged by atomic force microscopy (AFM) under liquid at room temperature. The protein constitutes "ribs" which, stacked together, form the hollow cylindrical tube and conical end caps of the gas vesicle. By operating the microscope in deflection mode, it has been possible to achieve sub-nanometer resolution of the rib structure. The lateral spacing of the ribs was found to be 4.6 +/- 0.1 nm. At higher resolution the ribs are observed to consist of pairs of lines at an angle of approximately 55 degrees to the rib axis, with a repeat distance between each line of 0.57 +/- 0.05 nm along the rib axis. These observed dimensions and periodicities are consistent with those determined from previous x-ray diffraction studies, indicating that the protein is arranged in beta-chains crossing the rib at an angle of 55 degrees to the rib axis. The AFM results confirm the x-ray data and represent the first direct images of a beta-sheet protein secondary structure using this technique. The orientation of the GvpA protein component of the structure and the extent of this protein across the ribs have been established for the first time. PMID:9172769

McMaster, T J; Miles, M J; Walsby, A E



Sterilization mechanism of nitrogen gas plasma: induction of secondary structural change in protein.  


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



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



Secondary structure of Src homology 2 domain of c-Abl by heteronuclear NMR spectroscopy in solution.  

PubMed Central

The Src homology 2 (SH2) domain is a recognition motif thought to mediate the association of the cytoplasmic proteins involved in signal transduction by binding to phosphotyrosyl-containing sequences in proteins. Assignments of nearly all 1H and 15N resonances of the SH2 domain from the c-Abl protein-tyrosine kinase have been obtained from homonuclear and heteronuclear NMR experiments. The secondary structure has been elucidated from the pattern of nuclear Overhauser effects, from vicinal coupling constants, and from observation of slowly exchanging amino hydrogens. The secondary structure contains two alpha-helices and eight beta-strands, six of which are arranged in two contiguous, antiparallel beta-sheets. Residues believed to be involved in phosphotyrosyl ligand binding are on a face of one beta-sheet. The alignment of homologous sequences on the basis of secondary structure suggests a conserved global fold in a family of SH2 domains. Images PMID:1281542

Overduin, M; Mayer, B; Rios, C B; Baltimore, D; Cowburn, D



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.



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.



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.



Incorporating global features of RNA motifs in predictions for an ensemble of secondary structures for encapsidated MS2 bacteriophage RNA  

PubMed Central

The secondary structure of encapsidated MS2 genomic RNA poses an interesting RNA folding challenge. Cryoelectron microscopy has demonstrated that encapsidated MS2 RNA is well-ordered. Models of MS2 assembly suggest that the RNA hairpin–protein interactions and the appropriate placement of hairpins in the MS2 RNA secondary structure can guide the formation of the correct icosahedral particle. The RNA hairpin motif that is recognized by the MS2 capsid protein dimers, however, is energetically unfavorable, and thus free energy predictions are biased against this motif. Computer programs called Crumple, Sliding Windows, and Assembly provide useful tools for prediction of viral RNA secondary structures when the traditional assumptions of RNA structure prediction by free energy minimization may not apply. These methods allow incorporation of global features of the RNA fold and motifs that are difficult to include directly in minimum free energy predictions. For example, with MS2 RNA the experimental data from SELEX experiments, crystallography, and theoretical calculations of the path for the series of hairpins can be incorporated in the RNA structure prediction, and thus the influence of free energy considerations can be modulated. This approach thoroughly explores conformational space and generates an ensemble of secondary structures. The predictions from this new approach can test hypotheses and models of viral assembly and guide construction of complete three-dimensional models of virus particles. PMID:22645379

Bleckley, Samuel; Schroeder, Susan J.



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.



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


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

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



The secondary structure of heated whey protein and its hydrolysates antigenicity.  


Fourier transform infrared spectroscopy (FTIR) and circular dichroism (CD) were used to investigate the conformational changes of heated whey protein (WP) and the corresponding changes in the hydrolysates immunoreactivity were determined by competitive enzyme-linked immunosorbent assay (ELISA). Results showed that the contents of alpha- helix and beta-sheet of WP did not decrease much under mild heating conditions and the antigenicity was relatively high; when the heating intensity increased (70 degrees for 25 min or 75 degrees C for 20 min), the content of alpha- helix and beta-sheet decreased to the minimum, so was the antigenicity; However, when the WP was heated at even higher temperature and for a longer time, the beta-sheet associated with protein aggregation begun to increase and the antigenicity increased correspondingly. It was concluded that the conformations of heated WP and the antigenicity of its hydrolysates are related and the optimum structure for decreasing the hydrolysates antigeniity is the least content of alpha-helix and beta-sheet. Establishing the relationship between the WP secondary structure and WP hydrolysates antigenicity is significant to supply the reference for antigenicity reduction by enzymolysis. PMID:22242516

Pang, Zhi-Hua; Zhu, Jun; Wu, Wei-Jing; Wang, Fang; Ren, Fa-Zheng; Zhang, Lu-Da; Guo, Hui-Yuan



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

NASA Astrophysics Data System (ADS)

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

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



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



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




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)



Evaluating the effect of disturbed ensemble distributions on SCFG based statistical sampling of RNA secondary structures  

PubMed Central

Background Over the past years, statistical and Bayesian approaches have become increasingly appreciated to address the long-standing problem of computational RNA structure prediction. Recently, a novel probabilistic method for the prediction of RNA secondary structures from a single sequence has been studied which is based on generating statistically representative and reproducible samples of the entire ensemble of feasible structures for a particular input sequence. This method samples the possible foldings from a distribution implied by a sophisticated (traditional or length-dependent) stochastic context-free grammar (SCFG) that mirrors the standard thermodynamic model applied in modern physics-based prediction algorithms. Specifically, that grammar represents an exact probabilistic counterpart to the energy model underlying the Sfold software, which employs a sampling extension of the partition function (PF) approach to produce statistically representative subsets of the Boltzmann-weighted ensemble. Although both sampling approaches have the same worst-case time and space complexities, it has been indicated that they differ in performance (both with respect to prediction accuracy and quality of generated samples), where neither of these two competing approaches generally outperforms the other. Results In this work, we will consider the SCFG based approach in order to perform an analysis on how the quality of generated sample sets and the corresponding prediction accuracy changes when different degrees of disturbances are incorporated into the needed sampling probabilities. This is motivated by the fact that if the results prove to be resistant to large errors on the distinct sampling probabilities (compared to the exact ones), then it will be an indication that these probabilities do not need to be computed exactly, but it may be sufficient and more efficient to approximate them. Thus, it might then be possible to decrease the worst-case time requirements of such an SCFG based sampling method without significant accuracy losses. If, on the other hand, the quality of sampled structures can be observed to strongly react to slight disturbances, there is little hope for improving the complexity by heuristic procedures. We hence provide a reliable test for the hypothesis that a heuristic method could be implemented to improve the time scaling of RNA secondary structure prediction in the worst-case – without sacrificing much of the accuracy of the results. Conclusions Our experiments indicate that absolute errors generally lead to the generation of useless sample sets, whereas relative errors seem to have only small negative impact on both the predictive accuracy and the overall quality of resulting structure samples. Based on these observations, we present some useful ideas for developing a time-reduced sampling method guaranteeing an acceptable predictive accuracy. We also discuss some inherent drawbacks that arise in the context of approximation. The key results of this paper are crucial for the design of an efficient and competitive heuristic prediction method based on the increasingly accepted and attractive statistical sampling approach. This has indeed been indicated by the construction of prototype algorithms. PMID:22776037



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



mRNA degradation in bacteria  

Microsoft Academic Search

Messenger RNAs in prokaryotes exhibit short half-lives when compared with eukaryotic mRNAs. Considerable progress has been made during recent years in our understanding of mRNA degradation in bacteria. Two major aspects determine the life span of a messenger in the bacterial cell. On the side of the substrate, the structural features of mRNA have a profound influence on the stability

Reinhard Rauhut; Gabriele Klug



Protein kinase A stimulates binding of multiple proteins to a U-rich domain in the 3'-untranslated region of lactate dehydrogenase A mRNA that is required for the regulation of mRNA stability.  


We have explored the molecular basis of the cAMP-induced stabilization of lactate dehydrogenase A (LDH-A) mRNA and identified four cytoplasmic proteins of 96, 67, 52, and 50 kDa that specifically bind to a 30-nucleotide uridine-rich sequence in the LDH 3'-untranslated region with a predicted stem-loop structure. Mutational analysis revealed that specific protein binding is dependent upon an intact primary nucleotide sequence in the loop as well as integrity of the adjoining double-stranded stem structure, thus indicating a high degree of primary and secondary structure specificity. The critical stem-loop region is located between nucleotides 1473 and 1502 relative to the mRNA cap site and contains a previously identified cAMP-stabilizing region (CSR) required for LDH-A mRNA stability regulation by the protein kinase A pathway. The 3'-untranslated region binding activity of the proteins is up-regulated after protein kinase A activation, whereas protein dephosphorylation is associated with a loss of binding activity. These results imply a cause and effect relationship between LDH-A mRNA stabilization and CSR-phosphoprotein binding activity. We propose that the U-rich CSR is a recognition signal for CSR-binding proteins and for an mRNA processing pathway that specifically stabilizes LDH mRNA in response to activation of the protein kinase A signal transduction pathway. PMID:9774474

Tian, D; Huang, D; Brown, R C; Jungmann, R A



Inducible expression of Pisum sativum xyloglucan fucosyltransferase in the pea root cap meristem, and effects of antisense mRNA expression on root cap cell wall structural integrity.  


Mitosis and cell wall synthesis in the legume root cap meristem can be induced and synchronized by the nondestructive removal of border cells from the cap periphery. Newly synthesized cells can be examined microscopically as they differentiate progressively during cap development, and ultimately detach as a new population of border cells. This system was used to demonstrate that Pisum sativum L. fucosyl transferase (PsFut1) mRNA expression is strongly expressed in root meristematic tissues, and is induced >2-fold during a 5-h period when mitosis in the root cap meristem is increased. Expression of PsFut1 antisense mRNA in pea hairy roots under the control of the CaMV35S promoter, which exhibits meristem localized expression in pea root caps, resulted in a 50-60% reduction in meristem localized endogenous PsFut1 mRNA expression measured using whole mount in situ hybridization. Changes in gross levels of cell wall fucosylated xyloglucan were not detected, but altered surface localization patterns were detected using whole mount immunolocalization with CCRC-M1, an antibody that recognizes fucosylated xyloglucan. Emerging hairy roots expressing antisense PsFut1 mRNA appeared normal macroscopically but scanning electron microscopy of tissues with altered CCRC-M1 localization patterns revealed wrinkled, collapsed cell surfaces. As individual border cells separated from the cap periphery, cell death occurred in correlation with extrusion of cellular contents through breaks in the wall. PMID:18347802

Wen, Fushi; Celoy, Rhodesia M; Nguyen, Trang; Zeng, Weiqing; Keegstra, Kenneth; Immerzeel, Peter; Pauly, Markus; Hawes, Martha C



Orientation determination of protein helical secondary structures using linear and nonlinear vibrational spectroscopy.  


In this paper, we systematically presented the orientation determination of protein helical secondary structures using vibrational spectroscopic methods, particularly, nonlinear sum frequency generation (SFG) vibrational spectroscopy, along with linear vibrational spectroscopic techniques such as infrared spectroscopy and Raman scattering. SFG amide I signals can be collected using different polarization combinations of the input laser beams and output signal beam to measure the second-order nonlinear optical susceptibility components of the helical amide I modes, which are related to their molecular hyperpolarizability elements through the orientation distribution of these helices. The molecular hyperpolarizability elements of amide I modes of a helix can be calculated based on the infrared transition dipole moment and Raman polarizability tensor of the helix; these quantities are determined by using the bond additivity model to sum over the individual infrared transition dipole moments and Raman polarizability tensors, respectively, of the peptide units (or the amino acid residues). The computed overall infrared transition dipole moment and Raman polarizability tensor of a helix can be validated by experimental data using polarized infrared and polarized Raman spectroscopy on samples with well-aligned helical structures. From the deduced SFG hyperpolarizability elements and measured SFG second-order nonlinear susceptibility components, orientation information regarding helical structures can be determined. Even though such orientation information can also be measured using polarized infrared or polarized Raman amide I signals, SFG has a much lower detection limit, which can be used to study the orientation of a helix when its surface coverage is much lower than a monolayer. In addition, the combination of different vibrational spectroscopic techniques, for example, SFG and attenuated total reflectance Fourier transform infrared spectroscopy, provides more measured parameters for orientation determination, aiding in the deduction of more complicated orientation distributions. In this paper, we discussed two types of helices, the alpha-helix and 3-10 helix. However, the orientation determination method presented here is general and thus can be applied to study other helices as well. The calculations of SFG amide I hyperpolarizability components for alpha-helical and 3-10 helical structures with different chain lengths have also been performed. It was found that when the helices reached a certain length, the number of peptide units in the helix should not alter the data analysis substantially. It was shown in the calculation, however, that when the helix chain is short, the SFG hyperpolarizability component ratios can vary substantially when the chain length is changed. Because 3-10 helical structures can be quite short in proteins, the orientation determination for a short 3-10 helix needs to take into account the number of peptide units in the helix. PMID:19650636

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



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: [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)



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 fiber cells [1,3,4,11,12]. The lens must support the functionality of all of its constituent cells function of transporting water across cell membranes. Mutations in AQP0 have been shown to play a role

Hammock, Bruce D.


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



A ?-Amino Acid That Favors 12/10-Helical Secondary Structure in ?/?-Peptides.  


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



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



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


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



Circular-dichroic properties and secondary structure of Pseudomonas aeruginosa soluble cytochrome c oxidase.  

PubMed Central

The c.d. spectra of Pseudomonas aeruginosa cytochrome c oxidase in the oxidized state and the reduced state are reported in the visible- and u.v. absorption regions. In the visible region the comparison between the spectra of reduced cytochrome c oxidase and ferrocytochrome c-551 allows the identification of the c.d. bands mainly due to the d1 haem chromophore in cytochrome c oxidase. In the near-u.v. region the assignment of some of the observed peaks to the haem groups and to the aromatic amino acid residues is proposed. A careful analysis of the data in the far-u.v. region leads to the determination of the relative amounts of alpha-helix and beta-sheet in the enzyme, giving for the first time a picture of its secondary structure. A significant difference in this respect between the reduced and the oxidized species is observed and discussed in the light of similar conclusions reported by other workers. PMID:6326749

Tordi, M G; Silvestrini, M C; Colosimo, A; Provencher, S; Brunori, M



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



Secondary structure, dynamics, and architecture of the p7 membrane protein from hepatitis C virus by NMR spectroscopy  

Microsoft Academic Search

P7 is a small membrane protein that is essential for the infectivity of hepatitis C virus. Solution-state NMR experiments on p7 in DHPC micelles, including hydrogen\\/deuterium exchange, paramagnetic relaxation enhancement and bicelle ‘q-titration,’ demonstrate that the protein has a range of dynamic properties and distinct structural segments. These data along with residual dipolar couplings yield a secondary structure model of

Gabriel A. Cook



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

Microsoft Academic Search

Plasmodesmata (PD) structure and function vary temporally and spatially during all stages of plant development. PD that originate\\u000a during, or post, cell division are designated as primary or secondary according to classical terminology. PD structure may\\u000a be simple, twinned, or branched. Studies of PD during leaf, root, and embryo development have lead to the generalization that\\u000a cells in less mature

Tessa M. Burch-Smith; Solomon Stonebloom; Min Xu; Patricia C. Zambryski



miRNA sensitivity to Drosha levels correlates with pre-miRNA secondary structure.  


microRNAs (miRNAs) are crucial for cellular development and homeostasis. In order to better understand regulation of miRNA biosynthesis, we studied cleavage of primary miRNAs by Drosha. While Drosha knockdown triggers an expected decrease of many mature miRNAs in human embryonic stem cells (hESC), a subset of miRNAs are not reduced. Statistical analysis of miRNA secondary structure and fold change of expression in response to Drosha knockdown showed that absence of mismatches in the central region of the hairpin, 5 and 9-12 nt from the Drosha cutting site conferred decreased sensitivity to Drosha knockdown. This suggests that, when limiting, Drosha processes miRNAs without mismatches more efficiently than mismatched miRNAs. This is important because Drosha expression changes over cellular development and the fold change of expression for miRNAs with mismatches in the central region correlates with Drosha levels. To examine the biochemical relationship directly, we overexpressed structural variants of miRNA-145, miRNA-137, miRNA-9, and miRNA-200b in HeLa cells with and without Drosha knockdown; for these miRNAs, elimination of mismatches in the central region increased, and addition of mismatches decreased their expression in an in vitro assay and in cells with low Drosha expression. Change in Drosha expression can be a biologically relevant mechanism by which eukaryotic cells control miRNA profiles. This phenomenon may explain the impact of point mutations outside the seed region of certain miRNAs. PMID:24677349

Sperber, Henrik; Beem, Alan; Shannon, Sandra; Jones, Ross; Banik, Pratyusha; Chen, Yu; Ku, Sherman; Varani, Gabriele; Yao, Shuyuan; Ruohola-Baker, Hannele



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


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



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



MicroRNA-Directed Cleavage of Nicotiana sylvestris PHAVOLUTA mRNA Regulates the Vascular Cambium and Structure of Apical Meristems  

Microsoft Academic Search

Leaf initiation in the peripheral zone of the shoot apical meristem involves a transition to determinate cell fate, but indeterminacy is maintained in the vascular cambium, a tissue critical to the continuous growth of vascular tissue in leaves and stems. We show that the orientation of cambial growth is regulated by microRNA (miRNA)-directed cleavage of mRNA from the Nicotiana sylvestris

Neil A. Mchale; Ross E. Koning



Promoter Region of the Escherichia coli O7Specific Lipopolysaccharide Gene Cluster: Structural and Functional Characterization of an Upstream Untranslated mRNA Sequence  

Microsoft Academic Search

We report the identification of the promoter region of the Escherichia coli O7-specific lipopolysaccharide (LPS) gene cluster (wbEcO7). Typical 210 and 235 sequences were found to be located in the intervening region between galF and rlmB, the first gene of the wbEcO7 cluster. Data from RNase protection experiments revealed the existence of an untranslated leader mRNA segment of 173 bp,




Structure of the no-go mRNA decay complex Dom34–Hbs1 bound to a stalled 80S ribosome  

Microsoft Academic Search

No-go decay (NGD) is a mRNA quality-control mechanism in eukaryotic cells that leads to degradation of mRNAs stalled during translational elongation. The key factors triggering NGD are Dom34 and Hbs1. We used cryo-EM to visualize NGD intermediates resulting from binding of the Dom34–Hbs1 complex to stalled ribosomes. At subnanometer resolution, all domains of Dom34 and Hbs1 were identified, allowing the

Jean-Paul Armache; Alexander Jarasch; Andreas M Anger; Elizabeth Villa; Heidemarie Sieber; Basma Abdel Motaal; Thorsten Mielke; Otto Berninghausen; Thomas Becker; Roland Beckmann



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

Microsoft Academic Search

Translational regulation is a key modulator of gene expression in chloroplasts of higher plants and algae. Genetic analysis has shown that translation of chloroplast mRNAs requires nuclear-encoded factors that interact with chloroplastic mRNAs in a message- specific manner. Using site-specific mutations of the chloroplastic psbA mRNA, we show that RNA ele- ments contained within the 5' untranslated region of the

Stephen P. Mayfield; Amybeth Cohen; Avihai Danon; Christopher B. Yolm



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)



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))



Structure and hibernation-associated expression of the transient receptor potential vanilloid 4 channel (TRPV4) mRNA in the Japanese grass lizard (Takydromus tachydromoides).  


Animals possess systems for sensing environmental temperature using temperature-sensitive ion channels called transient receptor potential channels (TRPs). Various TRPs have been identified and characterized in mammals. However, those of ectotherms, such as reptiles, are less well studied. Here, we identify the V subfamily of TRP (TRPV) in two reptile species: Japanese grass lizard (Takydromus tachydromoides) and Japanese four-lined ratsnake (Elaphe quadrivirgata). Phylogenetic analysis of TRPVs indicated that ectothermic reptilian TRPVs are more similar to those of endothermic chicken and mammals, than to other ectotherms, such as frog and fish. Expression analysis of TRPV4 mRNA in the lizard showed that its expression in tissues and organs is specifically controlled in cold environments and hibernation. The mRNA was ubiquitously expressed in seven tissues/organs examined. Both cold-treatment and hibernation lowered TRPV4 expression, but in a tissue/organ-specific manner. Cold-treatment reduced TRPV4 expression in tongue and muscle, while in hibernation it was reduced more widely in brain, tongue, heart, lung, and muscle. Interestingly, however, levels of TRPV4 mRNA in the skin remained unaffected after entering hibernation and cold-treatment, implying that TRPV4 in the skin may act as an environmental temperature sensor throughout the reptilian life cycle, including hibernation. This is the first report, to our knowledge, to describe reptilian TRPV4 in relation to hibernation. PMID:22379986

Nagai, Kazuya; Saitoh, Yasushi; Saito, Shigeru; Tsutsumi, Ken-ichi



Sequence comparison and secondary structure analysis of the 3' noncoding region of flavivirus genomes reveals multiple pseudoknots.  

PubMed Central

Sequences of 191 flavivirus RNAs belonging to four sero-groups were used to predict the secondary structure of the 3' noncoding region (3' NCR) directly upstream of the conserved terminal hairpin. In mosquito-borne flavivirus RNAs (n = 164) a characteristic structure element was identified that includes a phylogenetically well-supported pseudoknot. This element is repeated in the dengue and Japanese encephalitis RNAs and centers around the conserved sequences CS2 and RCS2. In yellow fever virus RNAs that contain one CS2 motif, only one copy of this pseudoknotted structure was found. The conserved pseudoknotted element is absent from the 3' NCR of tick-borne virus RNAs, which altogether adopt a secondary structure that is very different from that of mosquito-borne virus RNAs. The strong conservation of the pseudoknot in mosquito-borne flavivirus RNAs implies a stronger relationship between these viruses than concluded from previous secondary structure analyses. The role of the (tandem) pseudoknots in flavivirus replication is discussed. PMID:11680841

Olsthoorn, R C; Bol, J F



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



Lanthanide(III) complexes with two hexapeptides incorporating unnatural chelating amino acids: secondary structure and stability.  


Unnatural metal-chelating amino acids bearing aminodiacetate side-chains have been introduced into two hexapeptides to obtain efficient lanthanide-binding peptides. The synthesis of the enantiopure Fmoc-Ada(n)(tBu)2-OH synthons is described with overall yields of 32 and 50% for n=2 and n=3 side-chain carbon atoms, respectively. The two peptides AcWAda(n)PGAda(n)GNH2 (Pn) were synthesized from the protected synthons by standard solid-phase peptide synthesis. Studies of the lanthanide complexes of the two peptides Pn by luminescence titrations, mass spectrometry, circular dichroism, and solution NMR spectroscopy demonstrate that the Ada(n) chain length has a dramatic effect on the complexation properties. Indeed, the flexible compound P3 forms a mononuclear complex of moderate stability (beta11=10(9.9)), which tends to transform into a binuclear species in the presence of excess of the metal ion. Interestingly, the more compact peptide P2 provides stable Ln3+ complexes with the exclusive formation of the mononuclear LnP2 adduct. The stability constant of TbP2 is two orders of magnitude higher (beta11=10(12.1)) than that measured for P3. The 800 MHz NMR spectrum of the La3+ complex of P2 evidences a well-defined type II beta-turn as well as a hydrophobic Trp(indole)-Pro interaction. These interactions exemplify the non-innocent character of the peptide spacer in the complex LaP2 as well as the role of a peptide secondary structure in the stabilization of metal complexes. PMID:19562785

Cisnetti, Federico; Gateau, Christelle; Lebrun, Colette; Delangle, Pascale



Secondary N-nitrosocarbamate anions: Structure and alkylation reactions. A DFT study  

E-print Network

carcinogenicity [1]. At the same time, some of them have proved to be very effective anti-tumor agents. Both and greater reactivity. The best-known representative of secondary N-nitrosocarbamates is N-nitro- sourethane

Benin, Vladimir


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




NASA Astrophysics Data System (ADS)

The cretaceous Colima-Jalisco basin, at western Mexico, is characterized by the development of volcano sedimentary sequences belonging to the Late Jurassic-Early Cretaceous Alisitos-Teloloapan arc-island and the formation of volcanogenic massive sulphide deposits ("El Cuale", "La Minita", "Talpa de Allende"). Some bodies of dolomite have been described and have been classified into two groups in accordance with its secondary origin: sabkha (diagenetic) and hydrothermal. In both cases the primary dolomitized limestone belongs to the reef facies of the Tepalcatepec Formation (TF) of Albian-Cenomanian characterized by the next geochemical content: MgO (0.42%), CaO (53.7%), SiO2 (0.15%), Pb (140 ppm) and Zn (50 ppm). Diagenetical dolomite is characterized by an stratiform body and its contacts are consistent with the structural attitude of TF to which it belongs. In the dolomites formed by hydrothermal replacement process is limited by faults and fractures, thus its morphology is irregular and their contacts are discordant, adopting domic or columnar forms. Occasionally hydrothermal dolomite can be associated with concentrations of lead, zinc, silver and barite. The dolomitic body called "Cerro El Puro", (19° 3.7' N; 103° 36.7' W), located at 20 km SE 30° from Colima City, consists in a carbonate horizon of 300 m thick and over 5 km in length and is consistent with the structural attitude (N30°W; NE50°) of the southwestern flank of the syncline Tepames-Amarradero, in which southeast extreme an evaporitic stratiform deposits. The dolomite of this body is of ankeritic type, hence its typical light reddish brown. The geochemical content is shown on Table 1. After the structural and geochemical features of this dolomite, it is classified as sabkha with a diagenetic origin. The other dolomitic outcrop studied is called “Cerro Bola” (18°54'N; 103°47.5'W) which is located 40 km S10°W from Colima City, and consists of a single dolomitic outcrop, black in color, that covers an area of 600 x 400 m, which in its northwest corner shows a remnant of limestone reef without dolomitization. It should be mentioned that the name of this outcrop is due to its characteristic rounded topographic profile. This outcrop is affected by a fracture system whose attitudes are: N6O°E, vertical dip; N35°W, NE50° to vertical dip; N7°-20°-33°E; SE75° to vertical dip. Locally, quartz crystals (rock crystal), are observed hosted by millimetric druses, or covering the plans of some fractures. At least 400 m southeast of this outcrop, is located a deposit of baryte. Structurally “Cerro Bola” outcrop is located in a tilted block and the geochemical content is shown on Table 2. Due to their structural and geochemical characteristics, is considered formed by a hydrothermal process, which concentrated the metals existing in the limestone reef.Table 1. Geochemical content "Cerro El Puro" dolomite. Table 2. Geochemical content of "Cerro Bola" dolomite

Zarate, P. F.



Exploring Cross-Species-Related miRNAs Based on Sequence and Secondary Structure  

Microsoft Academic Search

MicroRNA (miRNA) plays an important role as a regulator of mRNA. But how miRNAs relate with each other in gene regulation network is still remaining. Understanding the reactions between miRNAs can be very significant for exploring miRNA target, gene regulation mechanism, and gene conservation in evolution process. We explore cross-species-related miRNAs to find out how miRNAs regulate each other by

Feng Chen; Yi-Ping Phoebe Chen



Hybrid host-guest complexes: directing the supramolecular structure through secondary host-guest interactions.  


A set of four hybrid host-guest complexes based on the inorganic crown ether analogue [H12W36O120]12- ({W36}) have been isolated and characterised. The cluster anion features a central rigid binding site made up of six terminal oxygen ligands and this motif allows the selective binding of a range of alkali and alkali-earth-metal cations. Here, the binding site was utilised to functionalise the metal oxide-based cavity by complexing a range of protonated primary amines within the recognition site. As a result, a set of four hybrid organic-inorganic host-guest complexes were obtained whereby the interactions are highly directed specifically within this cavity. The guest cations in these molecular assemblies range from the aromatic 2-phenethylamine (1) and 4-phenylbutylamine (2) to the bifunctional aromatic p-xylylene diamine (3) and the aliphatic, bifunctional 1,6-diaminohexane (4). Compounds 1-4 were structurally characterised by single-crystal X-ray diffraction, elemental analysis, flame atomic absorption spectroscopy, FTIR and bond valence sum calculations. This comparative study focuses on the supramolecular effects of the amine guest cations and investigates their structure-directing effects on the framework arrangement arising by locking the protonated amines within the cavity of the {W36} cluster. It was shown that parts of the organic guest cation protrude from the central binding cavity and the nature of this protruding organic "tail" directs the solid-state arrangement of compounds 1-4. Guest cations with a hydrophobic phenyl tail result in an antiparallel assembly of {W36} complexes arranged in a series of pillared layers. As a consequence, no direct supramolecular interactions between {W36} clusters are observed. In contrast, bifunctional guest cations with a secondary amino binding site act as molecular connectors and directly link two cluster units thus locking the supramolecular assembly in a tilted arrangement. This direct linking of {W36} anions results in the formation of an infinite supramolecular scaffold. PMID:18780383

Streb, Carsten; McGlone, Thomas; Brücher, Oliver; Long, De-Liang; Cronin, Leroy




PubMed Central

Prion diseases are neurodegenerative disorders associated with the accumulation of an abnormal isoform of the mammalian prion protein (PrP). Fourier transform infrared spectroscopy (FTIR) has previously been used to show that the conformation of aggregated, infectious PrP (PrPSc) varies between prion strains and these unique conformations may determine strain-specific disease phenotypes. However, the relative amounts of ?-helix, ?-sheet and other secondary structures have not always been consistent between studies suggesting that other proteins might be confounding the analysis of PrPSc secondary structure. We have used FTIR and tandem mass spectrometry to analyze enriched PrPSc from mouse and hamster prion strains both before and after the removal of protein contaminants that commonly co-purify with PrPSc. Our data show that non-PrP proteins do contribute to absorbances that have been associated with ?-helical, loop, turn, and ?-sheet structures attributed to PrPSc. The major contaminant, the ?-helical protein ferritin, absorbs strongly at 1652cm?1 in the FTIR spectrum associated with PrPSc. However, even the removal of greater than 99% of the ferritin from PrPSc did not completely abolish absorbance at 1652cm?1. Our results show that contaminating proteins alter the FTIR spectrum attributed to PrPSc and suggest that the ?-helical, loop/turn, and ?-sheet secondary structure that remains following their removal are derived from PrPSc itself. PMID:21805638

Moore, Roger A.; Timmes, Andrew; Wilmarth, Phillip A.; Safronetz, David; Priola, Suzette A.



Interactions between MUR10/CesA7-Dependent Secondary Cellulose Biosynthesis and Primary Cell Wall Structure1[OA  

PubMed Central

Primary cell walls are deposited and remodeled during cell division and expansion. Secondary cell walls are deposited in specialized cells after the expansion phase. It is presently unknown whether and how these processes are interrelated. The Arabidopsis (Arabidopsis thaliana) MUR10 gene is required for normal primary cell wall carbohydrate composition in mature leaves as well as for normal plant growth, hypocotyl strength, and fertility. The overall sugar composition of young mur10 seedlings is not significantly altered; however, the relative proportion of pectin side chains is shifted toward an increase in 1 ? 5-?-arabinan relative to 1 ? 4-?-galactan. mur10 seedlings display reduced fucogalactosylation of tightly cell wall-bound xyloglucan. Expression levels of genes encoding either nucleotide sugar interconversion enzymes or glycosyl transferases, known to be involved in primary and secondary cell wall biosynthesis, are generally unaffected; however, the CesA7 transcript is specifically suppressed in the mur10-1 allele. The MUR10 locus is identical with the CesA7 gene, which encodes a cellulose catalytic subunit previously thought to be specifically involved in secondary cell wall formation. The xylem vessels in young mur10 hypocotyls are collapsed and their birefringence is lost. Moreover, a fucogalactosylated xyloglucan epitope is reduced and a 1 ? 5-?-arabinan epitope increased in every cell type in mur10 hypocotyls, including cells that do not deposit secondary walls. mur10 also displays altered distribution of an arabinogalactan-protein epitope previously associated with xylem differentiation and secondary wall thickening. This work indicates the existence of a mechanism that senses secondary cell wall integrity and controls biosynthesis or structural remodeling of primary cell walls and cellular differentiation. PMID:17041031

Bosca, Sonia; Barton, Christopher J.; Taylor, Neil G.; Ryden, Peter; Neumetzler, Lutz; Pauly, Markus; Roberts, Keith; Seifert, Georg J.



Chromophore topography and secondary structure of 124-kilodalton Avena phytochrome probed by Zn2(+)-induced chromophore modification  

Microsoft Academic Search

The relative extent of chromophore exposure of the red-absorbing (Pr) and far-red-absorbing (Pfr) forms of 124-kDa oat phytochrome and the secondary structure of the phytochrome apoprotein have been investigated by using zinc-induced modification of the phytochrome chromophore. The absence of bleaching of Pr in the presence of a 1:1 stoichiometric ratio of zinc ions, in contrast to extensive spectral bleaching

Debbie Sommer; Pill Soon Song



Time-of-flight secondary ion mass spectrometry with energetic cluster ion impact ionization for highly sensitive chemical structure characterization  

NASA Astrophysics Data System (ADS)

Energetic cluster ions with energies of the order of sub MeV or greater were applied to time-of-flight (TOF) secondary ion (SI) mass spectrometry. This gave various advantages including enhancement of SIs required for chemical structure characterization and prevention of charging effects in SI mass spectra for organic targets. We report some characteristic features of TOF SI mass spectrometry using energetic cluster ion impact ionization and discuss two future applications of it.

Hirata, K.; Saitoh, Y.; Chiba, A.; Yamada, K.; Narumi, K.



The effects of various alcohols on the secondary structural integrity of melittin, TH-10Aox, and Tc1 by molecular dynamics simulations  

NASA Astrophysics Data System (ADS)

In this study, molecular dynamics simulations were conducted to investigate the effects of various alcohols on the structural integrity of three peptides: melittin with 2 ?-helices, TH-10Aox with 3 ?-strands, and Tc1 with 1 ?-helix and 2 ?-strands. The results reveal that the secondary structural integrity of these peptides increased with decreasing dielectric constant of the solvent, indicating that there is a positive correlation between the number of carbon atoms in alcohols and the stability of the secondary structures. In addition, TFE enhanced the secondary structural stability of these peptides to a greater extent than the other alcohols.

Zhao, Jian-Hua; Liu, Hsuan-Liang



5-Fluoro pyrimidines: labels to probe DNA and RNA secondary structures by 1D 19F NMR spectroscopy  

PubMed Central

19F NMR spectroscopy has proved to be a valuable tool to monitor functionally important conformational transitions of nucleic acids. Here, we present a systematic investigation on the application of 5-fluoro pyrimidines to probe DNA and RNA secondary structures. Oligonucleotides with the propensity to adapt secondary structure equilibria were chosen as model systems and analyzed by 1D 19F and 1H NMR spectroscopy. A comparison with the unmodified analogs revealed that the equilibrium characteristics of the bistable DNA and RNA oligonucleotides were hardly affected upon fluorine substitution at C5 of pyrimidines. This observation was in accordance with UV spectroscopic melting experiments which demonstrated that single 5-fluoro substitutions in double helices lead to comparable thermodynamic stabilities. Thus, 5-fluoro pyrimidine labeling of DNA and RNA can be reliably applied for NMR based nucleic acid secondary structure evaluation. Furthermore, we developed a facile synthetic route towards 5-fluoro cytidine phosphoramidites that enables their convenient site-specific incorporation into oligonucleotides by solid-phase synthesis. PMID:19843610

Puffer, Barbara; Kreutz, Christoph; Rieder, Ulrike; Ebert, Marc-Olivier; Konrat, Robert; Micura, Ronald



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, Jurgen; Cherry, Brian R.; Brown, Michael F.; Fromme, Petra



One antitoxin--two functions: SR4 controls toxin mRNA decay and translation  

PubMed Central

Type I toxin–antitoxin systems encoded on bacterial chromosomes became the focus of research during the past years. However, little is known in terms of structural requirements, kinetics of interaction with their targets and regulatory mechanisms of the antitoxin RNAs. Here, we present a combined in vitro and in vivo analysis of the bsrG/SR4 type I toxin–antitoxin system from Bacillus subtilis. The secondary structures of SR4 and bsrG mRNA and of the SR4/bsrG RNA complex were determined, apparent binding rate constants calculated and functional segments required for complex formation narrowed down. The initial contact between SR4 and its target was shown to involve the SR4 terminator loop and loop 3 of bsrG mRNA. Additionally, a contribution of the stem of SR4 stem-loop 3 to target binding was found. On SR4/bsrG complex formation, a 4 bp double-stranded region sequestering the bsrG Shine Dalgarno (SD) sequence was extended to 8 bp. Experimental evidence was obtained that this extended region caused translation inhibition of bsrG mRNA. Therefore, we conclude that SR4 does not only promote degradation of the toxin mRNA but also additionally inhibit its translation. This is the first case of a dual-acting antitoxin RNA. PMID:23969414

Jahn, Natalie; Brantl, Sabine



Translational Attenuation and mRNA Stabilization as Mechanisms of erm(B) Induction by Erythromycin?  

PubMed Central

Translational attenuation has been proposed to be the mechanism by which the erm(B) gene is induced. Here, we report genetic and biochemical evidence, obtained by using erythromycin as the inducing antibiotic, that supports this hypothesis. We also show that erythromycin increases the level of the erm(B) transcript by stalling the ribosome on the leader mRNA and thereby facilitating the stabilization and processing of the mRNA. Erythromycin-induced mRNA stabilization and processing were observed with an ochre stop at codons 11 to 13 of the leader but not with an ochre stop at codon 10. This suggests that erythromycin does not stall the ribosome before codon 11 of the leader reaches the aminoacyl site. Secondary structure analyses of the erm(B) transcripts by in vitro and in vivo chemical probing techniques identified conformational changes in the transcripts that result from induction by erythromycin. These findings demonstrate that stalling of erythromycin-bound ribosomes at leader codon 11 causes the refolding of mRNA into a conformation in which the translational initiation site for the structural gene is unmasked and renders erm(B) translationally active. PMID:18299414

Min, Yu-Hong; Kwon, Ae-Ran; Yoon, Eun-Jeong; Shim, Mi-Ja; Choi, Eung-Chil



The origin of vibrational mode couplings in various secondary structural motifs of polypeptides  

E-print Network

(received for review May 23, 2003) Electrostatic (through-space) and covalent (through-bond) contri- butions) and through-bond covalent contributions. The latter were shown to be important for amide I modes in adjacent transition densities are delocalized, and covalent contributions to the coupling are significant. Secondary

Mukamel, Shaul


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



Characterization and prediction of mRNA polyadenylation sites in human genes.  


The accurate identification of potential poly(A) sites has contributed to all many studies with regard to alternative polyadenylation. The aim of this study was the development of a machine-learning methodology that will help to discriminate real polyadenylation signals from randomly occurring signals in genomic sequence. Since previous studies have revealed that RNA secondary structure in certain genes has significant impact, the authors tried to computationally pinpoint common structural patterns around the poly(A) sites and to investigate how RNA secondary structure may influence polyadenylation. This involved an initial study on the impact of RNA structure and it was found using motif search tools that hairpin structures might be important. Thus, it was propose that, in addition to the sequence pattern around poly(A) sites, there exists a widespread structural pattern that is also employed during human mRNA polyadenylation. In this study, the authors present a computational model that uses support vector machines to predict human poly(A) sites. The results show that this predictive model has a comparable performance to the current prediction tool. In addition, it was identified common structural patterns associated with polyadenylation using several motif finding programs and this provides new insight into the role of RNA secondary structure plays in polyadenylation. PMID:21286831

Chang, Tzu-Hao; Wu, Li-Ching; Chen, Yu-Ting; Huang, Hsien-Da; Liu, Baw-Jhiune; Cheng, Kuang-Fu; Horng, Jorng-Tzong



Vaccination with messenger RNA (mRNA).  


Both DNA and mRNA can be used as vehicles for gene therapy. Because the immune system is naturally activated by foreign nucleic acids thanks to the presence of Toll-like Receptors (TLR) in endosomes (TLR3, 7, and 8 detect exogenous RNA, while TLR9 can detect exogenous DNA), the delivery of foreign nucleic acids usually induces an immune response directed against the encoded protein. Many preclinical and clinical studies were performed using DNA-based experimental vaccines. However, no such products are yet approved for the human population. Meanwhile, the naturally transient and cytosolically active mRNA molecules are seen as a possibly safer and more potent alternative to DNA for gene vaccination. Optimized mRNA (improved for codon usage, stability, antigen-processing characteristics of the encoded protein, etc.) were demonstrated to be potent gene vaccination vehicles when delivered naked, in liposomes, coated on particles or transfected in dendritic cells in vitro. Human clinical trials indicate that the delivery of mRNA naked or transfected in dendritic cells induces the expected antigen-specific immune response. Follow-up efficacy studies are on the way. Meanwhile, mRNA can be produced in large amounts and GMP quality, allowing the further development of mRNA-based therapies. This chapter describes the structure of mRNA, its possible optimizations for immunization purposes, the different methods of delivery used in preclinical studies, and finally the results of clinical trial where mRNA is the active pharmaceutical ingredient of new innovative vaccines. PMID:18071662

Pascolo, Steve



Comparing secondary structures of RNA and calculating the free energy of an interior loop using a novel method for calculating free energy  

E-print Network

The thesis consists of two projects. In the first project, we present a software that analyses RNA secondary structures and compares them. The goal of this software is to find the differences between two secondary structures (experimental or predicted) in order to improve or compare algorithms for predicting secondary structures. Then, a comparison between secondary structures predicted by the Vienna package to those found experimentally is presented and cases in which there exists a difference between the prediction and the experimental structure are identified. As the differences originate mainly from faces and hydrogen bonds that are not allowed by the Vienna package, it is suggested that prediction may be improved by integrating them into the software. In the second project we calculate the free energy of an interior loop using Monte-Carlo simulation. We first present a semi-coarse grained model for interior loops of RNA, and the energy model for the different interactions. We then introduce the Monte-Car...

Farhi, Asaf



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


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



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



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

PubMed Central

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

Gelfand, I M; Kister, A E



Treatment of Mycobacterium tuberculosis with antisense oligonucleotides to glutamine synthetase mRNA inhibits glutamine synthetase activity, formation of the poly-l-glutamate/glutamine cell wall structure, and bacterial replication  

PubMed Central

New antibiotics to combat the emerging pandemic of drug-resistant strains of Mycobacterium tuberculosis are urgently needed. We have investigated the effects on M. tuberculosis of phosphorothioate-modified antisense oligodeoxyribonucleotides (PS-ODNs) against the mRNA of glutamine synthetase, an enzyme whose export is associated with pathogenicity and with the formation of a poly-l-glutamate/glutamine cell wall structure. Treatment of virulent M. tuberculosis with 10 ?M antisense PS-ODNs reduced glutamine synthetase activity and expression by 25–50% depending on whether one, two, or three different PS-ODNs were used and the PS-ODNs' specific target sites on the mRNA. Treatment with PS-ODNs of a recombinant strain of Mycobacterium smegmatis expressing M. tuberculosis glutamine synthetase selectively inhibited the recombinant enzyme but not the endogenous enzyme for which the mRNA transcript was mismatched by 2–4 nt. Treatment of M. tuberculosis with the antisense PS-ODNs also reduced the amount of poly-l-glutamate/glutamine in the cell wall by 24%. Finally, treatment with antisense PS-ODNs reduced M. tuberculosis growth by 0.7 logs (1 PS-ODN) to 1.25 logs (3 PS-ODNs) but had no effect on the growth of M. smegmatis, which does not export glutamine synthetase nor possess the poly-l-glutamate/glutamine (P-l-glx) cell wall structure. The experiments indicate that the antisense PS-ODNs enter the cytoplasm of M. tuberculosis and bind to their cognate targets. Although more potent ODN technology is needed, this study demonstrates the feasibility of using antisense ODNs in the antibiotic armamentarium against M. tuberculosis. PMID:10618433

Harth, Gunter; Zamecnik, Paul C.; Tang, Jin-Yan; Tabatadze, David; Horwitz, Marcus A.



Identification of conserved secondary structures and expansion segments in enod40 RNAs reveals new enod40 homologues in plants  

PubMed Central

enod40 is a plant gene that participates in the regulation of symbiotic interaction between leguminous plants and bacteria or fungi. Furthermore, it has been suggested to play a general role in non-symbiotic plant development. Although enod40 seems to have multiple functions, being present in many land plants, the molecular mechanisms of its activity are unclear; they may be determined though, by short peptides and/or RNA structures encoded in the enod40 genes. We utilized conserved RNA structures in enod40 sequences to search nucleotide sequence databases and identified a number of new enod40 homologues in plant species that belong to known, but also, to yet unknown enod40-containing plant families. RNA secondary structure predictions and comparative sequence analysis of enod40 RNAs allowed us to determine the most conserved structural features, present in all known enod40 genes. Remarkably, the topology and evolution of one of the conserved structural domains are similar to those of the expansion segments found in structural RNAs such as rRNAs, RNase P and SRP RNAs. Surprisingly, the enod40 RNA structural elements are much more stronger conserved than the encoded peptides. This finding suggests that some general functions of enod40 gene could be determined by the encoded RNA structure, whereas short peptides may be responsible for more diverse functions found only in certain plant families. PMID:17452360

Gultyaev, Alexander P.; Roussis, Andreas



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



Premature translation termination mediates triosephosphate isomerase mRNA degradation.  

PubMed Central

We characterized an anemia-inducing mutation in the human gene for triosephosphate isomerase (TPI) that resulted in the production of prematurely terminated protein and mRNA with a reduced cytoplasmic half-life. The mutation converted a CGA arginine codon to a TGA nonsense codon and generated a protein of 188 amino acids, instead of the usual 248 amino acids. To determine how mRNA primary structure and translation influence mRNA stability, in vitro-mutagenized TPI alleles were introduced into cultured L cells and analyzed for their effect on TPI RNA metabolism. Results indicated that mRNA stability is decreased by all nonsense and frameshift mutations. To determine the relative contribution of the changes in mRNA structure and translation to the altered half-life, the effects of individual mutations were compared with the effects of second-site reversions that restored translation termination to normal. All mutations that resulted in premature translation termination reduced the mRNA half-life solely or mainly by altering the length of the mRNA that was translated. The only mutation that altered translation termination and that reduced the mRNA half-life mainly by affecting the mRNA structure was an insertion that shifted termination to a position downstream of the normal stop codon. Images PMID:2832737

Daar, I O; Maquat, L E



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

NASA Astrophysics Data System (ADS)

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

Cheng, Guoxin; Liu, Lie



Molecular-level secondary structure, polymorphism, and dynamics of full-length -synuclein fibrils studied by solid-state NMR  

NASA Astrophysics Data System (ADS)

The 140-residue protein -synuclein (AS) is able to form amyloid fibrils and as such is the main component of protein inclusions involved in Parkinson's disease. We have investigated the structure and dynamics of full-length AS fibrils by high-resolution solid-state NMR spectroscopy. Homonuclear and heteronuclear 2D and 3D spectra of fibrils grown from uniformly 13C/15N-labeled AS and AS reverse-labeled for two of the most abundant amino acids, K and V, were analyzed. 13C and 15N signals exhibited linewidths of <0.7 ppm. Sequential assignments were obtained for 48 residues in the hydrophobic core region. We identified two different types of fibrils displaying chemical-shift differences of up to 13 ppm in the 15N dimension and up to 5 ppm for backbone and side-chain 13C chemical shifts. EM studies suggested that molecular structure is correlated with fibril morphology. Investigation of the secondary structure revealed that most amino acids of the core region belong to -strands with similar torsion angles in both conformations. Selection of regions with different mobility indicated the existence of monomers in the sample and allowed the identification of mobile segments of the protein within the fibril in the presence of monomeric protein. At least 35 C-terminal residues were mobile and lacked a defined secondary structure, whereas the N terminus was rigid starting from residue 22. Our findings agree well with the overall picture obtained with other methods and provide insight into the amyloid fibril structure and dynamics with residue-specific resolution. EM | protein structure | amyloid | Parkinson's disease | protein aggregation

Heise, Henrike; Hoyer, Wolfgang; Becker, Stefan; Andronesi, Ovidiu C.; Riedel, Dietmar; Baldus, Marc



Population structure and secondary production of Siriella clausii, a dominant detritus feeding mysid in Posidonia oceanica meadows (W Mediterranean Sea)  

NASA Astrophysics Data System (ADS)

Temporal trends in abundance, demographic structure of the population and secondary production of Siriella clausii were studied at three different sectors of Posidonia oceanica meadows in the SE Iberian Peninsula, with different levels of habitat complexity. Secondary production was calculated through three methods widely employed in marine invertebrates: the Hynes method (based on demographic structure data) and models by Morin-Bourassa and Brey (based on biomass data). This filter/grazer and detritus feeder is the most abundant mysid in P. oceanica seagrass meadows in the Mediterranean. The population structure was similar in the three sectors, but the temporal pattern of abundance was different, at times even opposite. This pattern may be related to the aggregated spatial distribution, metapopulation dynamics or stochastic factors, but other potential factors could be involved, such as habitat features or predation rates. The values of production oscillated between 25 and 60 mgAFDW/m2/year, depending on the calculation method that was applied, and showed differences between sites and seagrass complexity. The present values are intermediate between those characterising highly productive systems, such as estuaries, and systems of limited productivity (bathyal habitats). Compared to other peracarids, mysid production is greater than that of isopods and less than amphipod production. This is possibly related to the life cycle and reproductive strategies. Detritus feeders such as S. clausii may play an important trophic role due their capacity to use as food the biomass associated to detritus, which constitutes larges reservoirs of carbon derived from seagrass primary production.

Barberá, Carmen; Sanchez-Jerez, Pablo; Sorbe, Jean Claude



ITS2 secondary structure improves phylogeny estimation in a radiation of blue butterflies of the subgenus Agrodiaetus (Lepidoptera: Lycaenidae: Polyommatus )  

PubMed Central

Background Current molecular phylogenetic studies of Lepidoptera and most other arthropods are predominantly based on mitochondrial genes and a limited number of nuclear genes. The nuclear genes, however, generally do not provide sufficient information for young radiations. ITS2 , which has proven to be an excellent nuclear marker for similarly aged radiations in other organisms like fungi and plants, is only rarely used for phylogeny estimation in arthropods, although universal primers exist. This is partly due to difficulties in the alignment of ITS2 sequences in more distant taxa. The present study uses ITS2 secondary structure information to elucidate the phylogeny of a species-rich young radiation of arthropods, the butterfly subgenus Agrodiaetus. One aim is to evaluate the efficiency of ITS2 to resolve the phylogeny of the subgenus in comparison with COI , the most important mitochondrial marker in arthropods. Furthermore, we assess the use of compensatory base changes in ITS2 for the delimitation of species and discuss the prospects of ITS2 as a nuclear marker for barcoding studies. Results In the butterfly family Lycaenidae, ITS2 secondary structure enabled us to successfully align sequences of different subtribes in Polyommatini and produce a Profile Neighbour Joining tree of this tribe, the resolution of which is comparable to phylogenetic trees obtained with COI+COII . The subgenus Agrodiaetus comprises 6 major clades which are in agreement with COI analyses. A dispersal-vicariance analysis (DIVA) traced the origin of most Agrodiaetus clades to separate biogeographical areas in the region encompassing Eastern Anatolia, Transcaucasia and Iran. Conclusions With the inclusion of secondary structure information, ITS2 appears to be a suitable nuclear marker to infer the phylogeny of young radiations, as well as more distantly related genera within a diverse arthropod family. Its phylogenetic signal is comparable to the mitochondrial marker COI . Compensatory base changes are very rare within Polyommatini and cannot be used for species delimitation. The implementation of secondary structure information into character-based phylogenetic methods is suggested to further improve the versatility of this marker in phylogenetic studies. PMID:20035628



A common core of secondary structure of the internal transcribed spacer 2 (ITS2) throughout the Eukaryota  

PubMed Central

The ongoing characterization of novel species creates the need for a molecular marker which can be used for species- and, simultaneously, for mega-systematics. Recently, the use of the internal transcribed spacer 2 (ITS2) sequence was suggested, as it shows a high divergence in sequence with an assumed conservation in structure. This hypothesis was mainly based on small-scale analyses, comparing a limited number of sequences. Here, we report a large-scale analysis of more than 54,000 currently known ITS2 sequences with the goal to evaluate the hypothesis of a conserved structural core and to assess its use for automated large-scale phylogenetics. Structure prediction revealed that the previously described core structure can be found for more than 5000 sequences in a wide variety of taxa within the eukaryotes, indicating that the core secondary structure is indeed conserved. This conserved structure allowed an automated alignment of extremely divergent sequences as exemplified for the ITS2 sequences of a ctenophorean eumetazoon and a volvocalean green alga. All classified sequences, together with their structures can be accessed at Furthermore, we found that, although sample sequences are known for most major taxa, there exists a profound divergence in coverage, which might become a hindrance for general usage. In summary, our analysis strengthens the potential of ITS2 as a general phylogenetic marker and provides a data source for further ITS2-based analyses. PMID:15769870




Insertion Mutagenesis as a Tool to Predict the Secondary Structure of a Muscarinic Receptor Domain Determining Specificity of G-Protein Coupling  

Microsoft Academic Search

The N-terminal segment of the third intracellular loop (i3) of muscarinic acetylcholine receptors and other G protein-coupled receptors has been shown to largely determine the G-protein coupling selectivity displayed by a given receptor subtype. Based on secondary-structure prediction algorithms, we have tested the hypothesis that this region adopts an alpha-helical secondary structure. Using the rat m3 muscarinic receptor as a

Klaus Bluml; Ernst Mutschler; Jurgen Wess



Two duplicated chicken-type lysozyme genes in disc abalone Haliotis discus discus: molecular aspects in relevance to structure, genomic organization, mRNA expression and bacteriolytic function.  


Lysozymes are crucial antibacterial proteins that are associated with catalytic cleavage of peptidoglycan and subsequent bacteriolysis. The present study describes the identification of two lysozyme genes from disc abalone Haliotis discus discus and their characterization at sequence-, genomic-, transcriptional- and functional-levels. Two cDNAs and BAC clones bearing lysozyme genes were isolated from abalone transcriptome and BAC genomic libraries, respectively and sequences were determined. Corresponding deduced amino acid sequences harbored a chicken-type lysozyme (LysC) family profile and exhibited conserved characteristics of LysC family members including active residues (Glu and Asp) and GS(S/T)DYGIFQINS motif suggested that they are LysC counterparts in disc abalone and designated as abLysC1 and abLysC2. While abLysC1 represented the homolog recently reported in Ezo abalone [1], abLysC2 shared significant identity with LysC homologs. Unlike other vertebrate LysCs, coding sequence of abLysCs were distributed within five exons interrupted by four introns. Both abLysCs revealed a broader mRNA distribution with highest levels in mantle (abLysC1) and hepatopancreas (abLysC2) suggesting their likely main role in defense and digestion, respectively. Investigation of temporal transcriptional profiles post-LPS and -pathogen challenges revealed induced-responses of abLysCs in gills and hemocytes. The in vitro muramidase activity of purified recombinant (r) abLysCs proteins was evaluated, and findings indicated that they are active in acidic pH range (3.5-6.5) and over a broad temperature range (20-60 °C) and influenced by ionic strength. When the antibacterial spectra of (r)abLysCs were examined, they displayed differential activities against both Gram positive and Gram negative strains providing evidence for their involvement in bacteriolytic function in abalone physiology. PMID:23664908

Umasuthan, Navaneethaiyer; Bathige, S D N K; Kasthuri, Saranya Revathy; Wan, Qiang; Whang, Ilson; Lee, Jehee



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

PubMed Central

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

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



Transcriptional Elongation and mRNA Export Are Coregulated Processes  

PubMed Central

Chromatin structure complexity requires the interaction and coordinated work of a multiplicity of factors at different transcriptional regulation stages. Transcription control comprises a set of processes that ensures proper balance in the gene expression under different conditions, such as signals, metabolic states, or development. We could frame those steps from epigenetic marks to mRNA stability to support the holistic view of a fine-tune balance of final mRNA levels through mRNA transcription, export, stability, translation, and degradation. Transport of mRNA from the nucleus to the cytoplasm is a key process in regulated gene expression. Transcriptional elongation and mRNA export are coregulated steps that determine the mature mRNA levels in the cytoplasm. In this paper, recent insights into the coordination of these processes in eukaryotes will be summarised. PMID:22567364

Molina-Navarro, Maria Micaela; Martinez-Jimenez, Celia Pilar; Rodriguez-Navarro, Susana



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

PubMed Central

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

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



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


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

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



Exciton annihilation and energy transfer in self-assembled peptide-porphyrin complexes depends on peptide secondary structure.  


We used picosecond transient absorption and fluorescence lifetime spectroscopy to study singlet exciton annihilation and depolarization in self-assembled aggregates of meso-tetra(4-sulfonatophenyl)porphine (TPPS(4)) and a synthetic 22-residue polypeptide. The polypeptide was designed and previously shown to bind three TPPS(4) monomers via electrostatic interactions between the sulfonate groups and cationic lysine residues. Additionally, the peptide induces formation of TPPS(4) J-aggregates in acidic solutions when the peptide secondary structure is disordered. In neutral solutions, the peptide adopts an ?-helical secondary structure that can bind TPPS(4) with high affinity but J-aggregate formation is inhibited. Detailed analysis of excitation-power dependent transient absorption kinetics was used to obtain rate constants describing the energy transfer between TPPS(4) molecules in an aggregate under acidic and neutral conditions. Independently, such analysis was confirmed by picosecond fluorescence emission depolarization measurements. We find that energy transfer between TPPS(4) monomers in a peptide-TPPS(4) complex is more than 30 times faster in acidic aqueous solution than in neutral solutions (9 vs 279 ps). This result was attributed to a conformational change of the peptide backbone from disordered at low pH to ?-helical at neutral pH and suggests a new approach to control intermolecular energy transfer with possible applications in fluorescent sensors or biomimetic light harvesting antennas. PMID:21069973

Kuciauskas, Darius; Kiskis, Juris; Caputo, Gregory A; Gulbinas, Vidmantas



Enhancement of Electron Spin Echo Envelope Modulation Spectroscopic Methods to Investigate the Secondary Structure of Membrane Proteins  

PubMed Central

This paper reports on a significant improvement of a new structural biology approach designed to probe the secondary structure of membrane proteins using the pulsed EPR technique of Electron Spin Echo Envelope Modulation (ESEEM) spectroscopy. Previously, we showed that we could characterize an ?-helical secondary structure with ESEEM spectroscopy using a 2H-labeled Val side chain coupled with site-directed spin-labeling (SDSL). In order to further develop this new approach, molecular dynamic (MD) simulations were conducted on several different hydrophobic residues that are commonly found in membrane proteins. 2H-SL distance distributions from the MD results indicated that 2H-labeled Leu was a very strong candidate to significantly improve this ESEEM approach. In order to test this hypothesis, the secondary structure of the ?-helical M2? peptide of the acetylcholine receptor (AChR) incorporated into a bicelle was investigated with 2H-labeled Leu d10 at position 10 (i) and nitroxide spin labels positioned 1, 2, 3 and 4 residues away (denoted i+1 to i+4) with ESEEM spectroscopy. The ESEEM data reveal a unique pattern that is characteristic of an ?-helix (3.6 residues per turn). Strong 2H modulation was detected for the i+3 and i+4 samples, but not for the i+2 sample. The 2H modulation depth observed for 2H-labeled d10 Leu was significantly enhanced (x4) when compared to previous ESEEM measurements that used 2H-labeled d8 Val. Computational studies indicate that deuterium nuclei on the Leu sidechain are closer to the spin label when compared to Val. The enhancement of 2H modulation and the corresponding Fourier Transform (FT) peak intensity for 2H-labeled Leu significantly reduces the ESEEM data acquisition time for Leu when compared to Val. This research demonstrates that a different 2H-labeled amino acid residue can be used as an efficient ESEEM probe further substantiating this important biophysical technique. Finally, this new method can provide pertinent qualitative structural information on membrane proteins in a short time (few minutes) at low sample concentrations (~50 ?M). PMID:22908896

Liu, Lishan; Sahu, Indra D.; Mayo, Daniel J.; McCarrick, Robert M.; Troxel, Kaylee; Zhou, Andy; Shockley, Erin; Lorigan, Gary A.



Mapping of conserved RNA secondary structures predicts thousands of functional noncoding RNAs in the human genome  

Microsoft Academic Search

In contrast to the fairly reliable and complete annotation of the protein coding genes in the human genome, comparable information is lacking for noncoding RNAs (ncRNAs). We present a comparative screen of vertebrate genomes for structural noncoding RNAs, which evaluates conserved genomic DNA sequences for signatures of structural conservation of base-pairing patterns and exceptional thermodynamic stability. We predict more than

Stefan Washietl; Ivo L Hofacker; Melanie Lukasser; Alexander Hüttenhofer; Peter F Stadler



Analysis of the role of predicted RNA secondary structures in Ebola virus replication  

Microsoft Academic Search

Thermodynamic modeling of Ebola viral RNA predicts the formation of RNA stem-loop structures at the 3? and 5? termini and panhandle structures between the termini of the genomic (or antigenomic) RNAs. Sequence analysis showed a high degree of identity among Ebola Zaire, Sudan, Reston, and Cote d’Ivoire subtype viruses in their 3? and 5? termini (18 nucleotides in length) and

Sharon M Crary; Jonathan S Towner; Jessica E Honig; Trevor R Shoemaker; Stuart T Nichol



An Architecture Combining Bayesian segmentation and Neural Network Ensembles for Protein Secondary Structure Prediction  

Microsoft Academic Search

A combined architecture of Bayesian segmentation along with ensembles of two layered feedforward network has been built and tested on widely studied two non membrane, non homologous databases comprising of 480 and 608 protein sequences respectively. In the first stage, Bayesian segmentation is used to infer sequence\\/structure relationship in terms of structural segments which is well suited to model non-local

Niranjan P. Bidargaddi; Madhu Chetty; Joarder Kamruzzaman



In-Cell NMR Characterization of the Secondary Structure Populations of a Disordered Conformation of ?-Synuclein within E. coli Cells  

PubMed Central

?-Synuclein is a small protein strongly implicated in the pathogenesis of Parkinson’s disease and related neurodegenerative disorders. We report here the use of in-cell NMR spectroscopy to observe directly the structure and dynamics of this protein within E. coli cells. To improve the accuracy in the measurement of backbone chemical shifts within crowded in-cell NMR spectra, we have developed a deconvolution method to reduce inhomogeneous line broadening within cellular samples. The resulting chemical shift values were then used to evaluate the distribution of secondary structure populations which, in the absence of stable tertiary contacts, are a most effective way to describe the conformational fluctuations of disordered proteins. The results indicate that, at least within the bacterial cytosol, ?-synuclein populates a highly dynamic state that, despite the highly crowded environment, has the same characteristics as the disordered monomeric form observed in aqueous solution. PMID:23991082

Waudby, Christopher A.; Camilloni, Carlo; Fitzpatrick, Anthony W. P.; Cabrita, Lisa D.; Dobson, Christopher M.; Vendruscolo, Michele; Christodoulou, John



Isolation and nucleotide sequence of the cDNA for rat liver serine dehydratase mRNA and structures of the 5' and 3' flanking regions of the serine dehydratase gene.  

PubMed Central

Rat serine dehydratase cDNA clones were isolated from a lambda gt11 cDNA library on the basis of their reactivity with monospecific immunoglobulin to the purified enzyme. Using the cDNA insert from a clone that encoded the serine dehydratase subunit as a probe, additional clones were isolated from the same library by plaque hybridization. Nucleotide sequence analysis of the largest clone obtained showed that it has 1444 base pairs with an open reading frame consisting of 1089 base pairs. The deduced amino acid sequence contained sequences of several portions of the serine dehydratase protein, as determined by Edman degradation. Rat liver serine dehydratase mRNA virtually disappeared from livers of rats fed a protein-free diet for 5 days. Several genomic clones were isolated from two libraries. Determinations of the transcription start site and the structure of the 3' flanking region of the gene indicated that the coded mRNA is 1504 nucleotides long. The 5' promoter region contained a variety of sequences similar to several consensus sequences believed to be important for the regulation of specific gene expression. Images PMID:3413060

Ogawa, H; Miller, D A; Dunn, T; Su, Y; Burcham, J M; Peraino, C; Fujioka, M; Babcock, K; Pitot, H C



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

E-print Network

Proteins are the molecular machines that drive the processes of the cell; they carry out the functional and structural instructions outlined in an organism's genome. At their simplest, these biological catalysts are comprised of linear chains...

Hodges, Hamilton Courtney



Dynamic changes in the secondary structure of ECE-1 and XCE account for their different substrate specificities  

PubMed Central

Background X-converting enzyme (XCE) involved in nervous control of respiration, is a member of the M13 family of zinc peptidases, for which no natural substrate has been identified yet. In contrast, it’s well characterized homologue endothelin-converting enzyme-1 (ECE-1) showed broad substrate specificity and acts as endopeptidase as well as dipeptidase. To explore the structural differences between XCE and ECE-1, homology model of XCE was built using the complex structure of ECE-1 with phosphoramidon (pdb-id: 3DWB) as template. Phosphoramidon was docked into the binding site of XCE whereas phosphate oxygen of the inhibitor was used as water molecule to design the apo forms of both enzymes. Molecular dynamics simulation of both enzymes was performed to analyze the dynamic nature of their active site residues in the absence and presence of the inhibitor. Results Homology model of XCE explained the role of non-conserved residues of its S2’ subsite. Molecular dynamics (MD) simulations identified the flexible transitions of F149/I150, N566/N571, W714/W719, and R145/R723 residues of ECE-1/XCE for the strong binding of the inhibitor. Secondary structure calculations using DSSP method reveals the folding of R145/R723 residue of ECE-1/XCE into ?-sheet structure while unfolding of the S2’ subsite residues in aECE-1 and sustained compact folding of that of aXCE. The results evaluated are in good agreement with available experimental data, thus providing detailed molecular models which can explain the structural and specificities differences between both zinc peptidases. Conclusions Secondary structure changes of both enzymes during the simulation time revealed the importance of ?-sheet structure of R145/R723 for its binding with the terminal carboxylate group of the inhibitor. Unfolding of the ?-helix comprising the S2’ subsite residues in aECE-1 correlate well with its endopeptidase activity while their compact folding in aXCE may account for the inactivity of the enzyme towards large C-terminal containing substrates. PMID:23113990



Alternative secondary structures of leader RNAs and the regulation of the trp, phe, his, thr, and leu operons.  

PubMed Central

The trp, phe, his, thr, and leu operons of enteric bacteria are regulated by a transcriptional attenuation mechanism. Under conditions of amino acid sufficiency, transcription terminates at an attenuator site after a leader of about 150 nucleotides has been synthesized. Under conditions of limitation of a controlling amino acid, transcription continues past the attenuator into adjacent structural genes. As demonstrated by others, each of the five leader RNAs contains two regions of potential secondary structure which are partially overlapping. One of these regions occurs at the 3' terminus of the leader and is named the "terminator." The other region, which potentially can preclude the formation of the terminator, is named the "preemptor." Conditions that allow the preemptor to form result in derepression. We report here that the five published leader RNA sequences contain an additional potential region of secondary structure, which we call the "protector." The protector partially overlaps the preemptor in such a way that pairing of the former precludes pairing of the latter. For derepression to occur, a ribosome that is translating the leader must block the protector without blocking the preemptor, a condition that is met when the ribosome is arrested at the 3' end of a set of control codons. Including the protector in the model for attenuation explains why derepression of the operon does not result from the arrest of a ribosome at a codon preceding the control set. It also explains why termination is the outcome when transcription occurs in the absence of ribosomes. Finally, termination is the predicted outcome when unfettered translation of the leader RNA occurs, resulting in release of the ribosome at the translational stop signal. PMID:392514

Keller, E B; Calvo, J M



Analysis of the role of predicted RNA secondary structures in Ebola virus replication.  


Thermodynamic modeling of Ebola viral RNA predicts the formation of RNA stem-loop structures at the 3' and 5' termini and panhandle structures between the termini of the genomic (or antigenomic) RNAs. Sequence analysis showed a high degree of identity among Ebola Zaire, Sudan, Reston, and Cote d'Ivoire subtype viruses in their 3' and 5' termini (18 nucleotides in length) and within a second region (internal by approximately 20 nucleotides). While base pairing of the two conserved regions could lead to the formation of the base of the putative stem-loop or panhandle structures, the intervening sequence variation altered the predictions for the rest of the structures. Using an in vivo minigenome replication system, we engineered mutations designed to disrupt potential base pairing in the viral RNA termini. Analysis of these variants by screening for enhanced green fluorescent protein reporter expression and by quantitation of minigenomic RNA levels demonstrated that the upper portions of the putative panhandle and 3' genomic structures can be destabilized without affecting virus replication. PMID:12642094

Crary, Sharon M; Towner, Jonathan S; Honig, Jessica E; Shoemaker, Trevor R; Nichol, Stuart T



Comprehensive Secondary Structure Elucidation of Four Genera of the Family Pospiviroidae  

PubMed Central

Viroids are small, circular, single stranded RNA molecules that infect plants. Since they are non-coding, their structures play a critical role in their life cycles. To date, little effort has been spend on elucidating viroid structures in solution due to both the experimental difficulties and the time-consuming nature of the methodologies implicated. Recently, the technique of high-throughput selective 2?-hydroxyl acylation analyzed by primer extension (SHAPE) was adapted for the probing of the members of family Avsunviroidae, all of whom replicate in the chloroplast and demonstrate ribozyme activity. In the present work, twelve viroid species belonging to four different genera of the family Pospiviroidae, whose members are characterized by the presence of a central conserved region (CCR) and who replicate in nucleus of the host, were probed. Given that the structures of five distinct viroid species from the family Pospiviroidae have been previously reported, an overview of the different structural characteristics for all genera and the beginning of a manual classification of the different viroids based on their structural features are presented here. PMID:24897295

Giguere, Tamara; Raj Adkar-Purushothama, Charith; Perreault, Jean-Pierre



The crystal structure and mutational analysis of a novel RNA-binding domain found in the human Tap nuclear mRNA export factor  

PubMed Central

The Tap protein mediates the sequence nonspecific nuclear export of cellular mRNAs as well as the sequence-specific export of retroviral mRNAs bearing the constitutive transport element (CTE). Previously, the structures of individual Tap subdomains, including ribonucleoprotein and leucine-rich repeat domains, have been described. Here, we report the crystal structure of a functional CTE RNA-binding domain of human Tap, including the N-terminal arm of the ribonucleoprotein domain and interdomain linking polypeptide. To identify residues that interact with the CTE, we have introduced 38 alanine substitutions for surface residues in the Tap CTE-binding domain and tested these mutants for their ability to support CTE-dependent nuclear RNA export and CTE binding. Four residues that cluster on a concave surface in the leucine-rich repeat domain were found to be critical for CTE binding and define a CTE-interacting surface on this domain. The second critical CTE-interacting surface on Tap is defined by three previously identified residues on the surface of the ribonucleoprotein domain. The structural and mutational data define a novel RNA-binding site on the Tap protein. PMID:11854490

Ho, Dona N.; Coburn, Glen A.; Kang, Yibin; Cullen, Bryan R.; Georgiadis, Millie M.



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

PubMed Central

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

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



Induction of Secondary Structure in Model Protein Fragments by Synthetic Lipidation  

NASA Astrophysics Data System (ADS)

Peptide-amphiphiles with collagen-model head groups and mono- or dialkyl chain tails have been synthesized and shown to self-assemble into highly ordered like triple-helical structures when dissolved in aqueous subphases. Evidence for this self-assembly process has been obtained from circular dichroism spectra and melting curves characteristic of triple-helices, and two-dimensional NMR spectra indicative of stable triple-helical structure at low temperatures and melted triple-helices at high temperatures. The thermal stability of the collagen-like structure in the peptide-amphiphile is substantially higher (? Tm = 15 - 20 ^circ C) than that of peptides without lipidation. The assembly process driven by the hydrophobic tail may provide a general method for creating protein molecular architecture using a minimalist peptide-based approach.

Tirrell, Matthew; Yu, Y.-C.; Berndt, Peter; Fields, Gregg B.



Secondary structure of short ?-peptides as the chiral expression of monomeric building units: a rational and predictive model.  


Chirality of the monomeric residues controls and determines the prevalent folding of small oligopeptides (from di- to tetramers) composed of 2-aminocyclobutane-1-carboxylic acid (ACBA) derivatives with the same or different absolute and relative configuration. The cis-form of the monomeric ACBA gives rise to two conformers, namely, Z6 and Z8, while the trans-form manifests uniquely as an H8 structure. By combining these subunits in oligo- and polypeptides, their local structural preference remains, thus allowing the rational design of new short foldamers. A lego-type molecular architecture evolves; the overall look depends only on the conformational properties of the structural building units. A versatile and efficient method to predict the backbone folds of designed cyclobutane ?-peptides is based on QM calculations. Predictions are corroborated by high-resolution NMR studies on selected stereoisomers, most of them being new foldamers that have been synthesized and characterized for the first time. Thus, the chiral expression of monomeric building units results in the defined secondary structures of small oligomers. As a result of this study, a new set of chirality controlled foldamers is provided to probe as biocompatible biopolymers. PMID:23030251

Gorrea, Esther; Pohl, Gábor; Nolis, Pau; Celis, Sergio; Burusco, Kepa K; Branchadell, Vicenç; Perczel, András; Ortuño, Rosa M



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

NASA Astrophysics Data System (ADS)

This article describes and discusses an example of how atomic structure can be taught in lower secondary chemistry using a modified jigsaw-classroom method. The lesson was taught in grades 9 and 10 (age range 15 17 years) chemistry in 13 learning groups with a total of 313 students in various grammar, middle, and comprehensive schools in Germany. The written evaluation of the lesson focused on determining the students’ opinions on the teaching methods that were used. Emphasis was on gathering information from the students’ viewpoint. Did the students think that these methods could make science lessons more attractive? Could these methods help to promote more active student learning, cooperative learning, or communicative and social abilities? Additional data that were derived from a cognitive test and teacher feedback are also presented. The results of the study show that teaching methods like the jigsaw classroom have potential to improve students’ attitude towards science. The results may also indicate that it is appropriate to demand that student-oriented and cooperative-learning methods be used more often in secondary level science education.

Eilks, Ingo



Transcription of the genome of adenovirus type 12. I. Viral mRNA in abortively infected and transformed cells.  

PubMed Central

In baby hamster kidney (BKH-21) cells abortively infected with adenovirus type 12, polysome-associated, virus-specific RNA could be detected starting 5 to 7 h after infection. The amount of this RNA reached a maximum between 10 to 12 h after infection and continued to be synthesized at a reduced level until late in infection (48 to 50 h.). In BHK-21 cells transformed by adenovirus type 12 (HB cells), 0.26% of the polysome-associated mRNA was virus specific. The size of the virus-specific mRNA isolated from polysomes of BHK-21 cells abortively infected with, or transformed by adenovirus type 12 was determined by electrophoresis in polyacrylamide gels in 98% formamide, i.e., under conditions which eliminated secondary structure or aggregation of RNA. In abortively infected hamster cells viral mRNA size classes of molecular weights 0.9 times 10-6 and 0.65 times 10-6 to 0.67 times 10-6 were predominant. A minor fraction of 1.5 times 10-6 daltons was consistently found and increased with time after infection. Late after infection (24 to 26 h), viral mRNA of 1.9 times 10-6 daltons was also observed. The size distribution of adenovirus type 12-specific mRNA from transformed hamster cells (HB line) was very similar to that in abortively infected cells, except that the relative amount of the viral mRNA fraction of 1.5 times 10-6 daltons was much higher. It is uncertain whether the viral mRNA of high-molecular-weight represents mixed transcripts derived from integrated viral genomes and adjacent host genes. PMID:1167602

Ortin, J; Doerfler, W



Changes in the spatial structure of oak carbon-based secondary compounds after pine harvesting  

Microsoft Academic Search

In natural plant populations, leaf polyphenols show high intraspecific variation that occurs both temporally and spatially. Leaf phenolics may be induced by diverse ecological factors such as light, nitrogen availability or herbivory attack. Both light and nitrogen availability can show spatial structure in forested stands, meaning that they each have a high degree of autocorrelation, which can determine the appearance

Felisa Covelo; Antonio Gallardo



Improving the Keyboarding Composition Skills of Secondary Business Education Students through a Structured Approach.  

ERIC Educational Resources Information Center

A practicum was designed to improve students' manual keyboarding composition skill. A program was developed to integrate the other requisite skills of well-written composition, accurate punctuation and grammar, and fastidious proofreading in a structured, progressive plan. The 25 students in the Typing I Business Fundamentals class, a keyboarding…

Parker, Gay E.


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

ERIC Educational Resources Information Center

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

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



Improved Method for Prediction of Protein Backbone U-Turn Positions and Major Secondary Structural  

E-print Network

information for 3-D pro- tein model building. Additionally, the positions of U-turns provide invaluable structures the protein back- bone adopts in the transglobular blocks with rather high accuracy. The results obtained from this method are potentially very useful in protein model building and fold recognition

Skolnick, Jeff


A unique secondary-structure switch controls constitutive gene repression by retinoic acid receptor  

Microsoft Academic Search

In the absence of ligand, some nuclear receptors, including retinoic acid receptor (RAR), act as transcriptional repressors by recruiting corepressor complexes to target genes. This constitutive repression is crucial in metazoan reproduction, development and homeostasis. However, its specific molecular determinants had remained obscure. Using structural, biochemical and cell-based assays, we show that the basal repressive activity of RAR is conferred

Albane le Maire; Catherine Teyssier; Cathie Erb; Marina Grimaldi; Susana Alvarez; Angel R de Lera; Patrick Balaguer; Hinrich Gronemeyer; Catherine A Royer; Pierre Germain; William Bourguet



The Relationship between Professional Preparation and Class Structure on Health Instruction in the Secondary Classroom  

ERIC Educational Resources Information Center

Background: The aim of the present study was to examine the impact of professional preparation and class structure on health content delivery and time spent delivering content among required health education classes in the United States. Methods: Data from the classroom-level file of the 2006 School Health Policies and Programs Study were…

Hammig, Bart; Ogletree, Roberta; Wycoff-Horn, Marcie R.



Protein Structure Analysis Iosif Vaisman  

E-print Network

Protein Structure Analysis Iosif Vaisman 2013 BINF 731 Secondary Structure: Computational Problems Secondary structure characterization Secondary structure assignment Secondary structure prediction Protein structure classification Secondary Structure Conformations

Vaisman, Iosif


Protein Structure Analysis Iosif Vaisman  

E-print Network

Protein Structure Analysis Iosif Vaisman 2012 BINF 731 Secondary Structure: Computational Problems Secondary structure characterization Secondary structure assignment Secondary structure prediction Protein structure classification Secondary Structure Conformations

Vaisman, Iosif


Evaluating the accuracy of SHAPE-directed RNA secondary structure predictions  

PubMed Central

Recent advances in RNA structure determination include using data from high-throughput probing experiments to improve thermodynamic prediction accuracy. We evaluate the extent and nature of improvements in data-directed predictions for a diverse set of 16S/18S ribosomal sequences using a stochastic model of experimental SHAPE data. The average accuracy for 1000 data-directed predictions always improves over the original minimum free energy (MFE) structure. However, the amount of improvement varies with the sequence, exhibiting a correlation with MFE accuracy. Further analysis of this correlation shows that accurate MFE base pairs are typically preserved in a data-directed prediction, whereas inaccurate ones are not. Thus, the positive predictive value of common base pairs is consistently higher than the directed prediction accuracy. Finally, we confirm sequence dependencies in the directability of thermodynamic predictions and investigate the potential for greater accuracy improvements in the worst performing test sequence. PMID:23325843

Sukosd, Zsuzsanna; Swenson, M. Shel; Kjems, J?rgen; Heitsch, Christine E.



NMR-driven secondary and tertiary structure model of Ca 2+-loaded calexcitin  

Microsoft Academic Search

Calexcitin (CE) is a Ca2+-binding protein which is expressed in neuronal cells and is a member of the sarcoplasmic Ca2+-binding protein subfamily. The peptide backbone of Ca2+-CE has been assigned by NMR and it shows that CE is composed of nine ?-helices—forming four EF-hands and an additional helix near the C-terminus. A structural model of CE suggests the presence of

Zoltan Gombos; Kyoko L. Yap; Mitsuhiko Ikura; Avijit Chakrabartty



Ebola Virus VP30-Mediated Transcription Is Regulated by RNA Secondary Structure Formation  

Microsoft Academic Search

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

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



Controlling Secondary Structures of Bio-Polymers with Hydrogen-Like Bonding  

E-print Network

We present results for a lattice model of bio-polymers where the type of $\\beta$-sheet formation can be controlled by different types of hydrogen bonds depending on the relative orientation of close segments of the polymer. Tuning these different interaction strengths leads to low-temperature structures with different types of orientational order. We perform simulations of this model and so present the phase diagram, ascertaining the nature of the phases and the order of the transitions between these phases.

J. Krawczyk; A. L. Owczarek; T. Prellberg; A. Rechnitzer



Detection and alignment of 3D domain swapping proteins using angle-distance image-based secondary structural matching techniques.  


This work presents a novel detection method for three-dimensional domain swapping (DS), a mechanism for forming protein quaternary structures that can be visualized as if monomers had "opened" their "closed" structures and exchanged the opened portion to form intertwined oligomers. Since the first report of DS in the mid 1990s, an increasing number of identified cases has led to the postulation that DS might occur in a protein with an unconstrained terminus under appropriate conditions. DS may play important roles in the molecular evolution and functional regulation of proteins and the formation of depositions in Alzheimer's and prion diseases. Moreover, it is promising for designing auto-assembling biomaterials. Despite the increasing interest in DS, related bioinformatics methods are rarely available. Owing to a dramatic conformational difference between the monomeric/closed and oligomeric/open forms, conventional structural comparison methods are inadequate for detecting DS. Hence, there is also a lack of comprehensive datasets for studying DS. Based on angle-distance (A-D) image transformations of secondary structural elements (SSEs), specific patterns within A-D images can be recognized and classified for structural similarities. In this work, a matching algorithm to extract corresponding SSE pairs from A-D images and a novel DS score have been designed and demonstrated to be applicable to the detection of DS relationships. The Matthews correlation coefficient (MCC) and sensitivity of the proposed DS-detecting method were higher than 0.81 even when the sequence identities of the proteins examined were lower than 10%. On average, the alignment percentage and root-mean-square distance (RMSD) computed by the proposed method were 90% and 1.8Å for a set of 1,211 DS-related pairs of proteins. The performances of structural alignments remain high and stable for DS-related homologs with less than 10% sequence identities. In addition, the quality of its hinge loop determination is comparable to that of manual inspection. This method has been implemented as a web-based tool, which requires two protein structures as the input and then the type and/or existence of DS relationships between the input structures are determined according to the A-D image-based structural alignments and the DS score. The proposed method is expected to trigger large-scale studies of this interesting structural phenomenon and facilitate related applications. PMID:20976204

Chu, Chia-Han; Lo, Wei-Cheng; Wang, Hsin-Wei; Hsu, Yen-Chu; Hwang, Jenn-Kang; Lyu, Ping-Chiang; Pai, Tun-Wen; Tang, Chuan Yi



Variability in Secondary Structure of 18S Ribosomal RNA as Topological Marker for Identification of Paramecium species.  


Besides cytological and molecular applications, Paramecium is being used in water quality assessment and for determination of saprobic levels. An unambiguous identification of these unicellular eukaryotes is not only essential, but its ecological diversity must also be explored in the local environment. 18SrRNA genes of all the strains of Paramecium species isolated from waste water were amplified, cloned and sequenced. Phylogenetic comparison of the nucleotide sequences of these strains with 23 closely related Paramecium species from GenBank Database enabled identification of Paramecium multimicronucleatum and Paramecium jenningsi. Some isolates did not show significant close association with other Paramecium species, and because of their unique position in the phylogenetic tree, they were considered new to the field. In the present report, these isolates are being designated as Paramecium caudatum pakistanicus. In this article, secondary structure of 18SrRNA has also been analyzed as an additional and perhaps more reliable topological marker for species discrimination and for determining possible phylogenetic relationship between the ciliate species. On the basis of comparison of secondary structure of 18SrRNA of various isolated Paramacium strains, and among Paramecium caudatum pakistanicus, Tetrahymena thermophila, Drosophila melanogaster, and Homo sapiens, it can be deduced that variable regions are more helpful in differentiating the species at interspecific level rather than at intraspecific level. It was concluded that V3 was the least variable region in all the organisms, V2 and V7 were the longest expansion segments of D. melanogaster and there was continuous mutational bias towards G.C base pairing in H. sapiens. J. Cell. Biochem. 115: 2077-2088, 2014. © 2014 Wiley Periodicals, Inc. PMID:25043709

Shakoori, Farah R; Tasneem, Fareeda; Al-Ghanim, K; Mahboob, S; Al-Misned, F; Jahan, Nusrat; Shakoori, Abdul Rauf



The Effect of Cholesterol on the Solution Structure of Proteins of Photosystem II. Protein Secondary Structure and  

E-print Network

The Effect of Cholesterol on the Solution Structure of Proteins of Photosystem II. Protein, 1998 Cholesterol induces large perturbations in the physical proper- ties of membranes, especially at physiological temperatures. This study was designed to examine the interaction of cholesterol with lipid

Carpentier, Robert


[Spectroscopic study on the effect of crystallization of the hydroxyapatite on the secondary structure of bovine serum albumin].  


The effect of crystallization of hydroxyapatite on the secondary structure of bovine serum albumin (BSA) was studied by circular dichroism spectrum, Fourier transform infrared spectroscopy, derivative, deconvolution and curve-fitting techniques in the present paper. The CD results show that pure bovine serum albumin is composed of 56.8% alpha-helices, 5.8% beta-sheets, 14.1% beta-turns and 23.9% random structures, while the bovine serum albumin in the Ca10(PO4)6(OH)2/bovine serum albumin solution is composed of 25.4% alpha-helices, 25.0% beta-sheets, 20.0% beta-turns and 29.7% random structures. The results of Fourier transform infrared spectroscopy are in good agreement with those from the CD spectra. From these results it can be seen that the percentage of alpha-helix decreased, while that of the beta-sheet increased with the formation of the crystal of hydroxyapatite, and with the reaction time increasing, the percentages of alpha-helix obviously dropped and those of beta-sheet markedly rose. These results showed that alpha-helix transformed into beta-sheet. Furthermore the essence of these changes is discussed. PMID:17514966

Ye, Feng; An, Ying-ge; Qin, De-zhi; Yang, Lin; She, Lan; Xing, Rui-min



Detecting secondary structure and surface orientation of helical peptide monolayers from resonant hybridization signals  

PubMed Central

Hybridization of dominant vibrational modes with meta-surface resonance allows detection of both structural changes and surface orientations of bound helical peptides. Depending on the resonance frequency of meta-molecules, a red- or blue- shift in peptide Amide-I frequency is observed. The underlying coupling mechanism is described by using a temporal coupled mode theory that is in very good agreement with the experimental results. This hybridization phenomenon constitutes the basis of many nanophotonic systems such as tunable coupled mode bio-sensors and dynamic peptide systems driven by infrared signals. PMID:24129763

Alici, Kamil Boratay; Gallardo, Ignacio F.



Secondary Structural and Functional Studies of Rotavirus NSP4 and Caveolin-1 Peptide-Peptide Interactions  

E-print Network

binding domain of NSP4 (aa112-140) and to the N- (aa2-20 and 19-40) and C- (161-178) termini of caveolin-1, and were utilized in structural and functional studies. Fluorescence binding assays revealed that NSP4 (aa112-140) binds to the N-terminus (aa19...-L-serine] dsRNA Double-Stranded RNA eIF4G Eukaryotic Initiation Factor 4G ELISA Enzyme-Linked Immunosorbent Assay ER Endoplasmic Reticulum EU Endotoxin Units ix Fmax Maximum Fluorescence Fmoc Fluorenylmethoxycarbonyl FRET...

Schroeder, Megan Elizabeth



Distinct Secondary Structures of the Leucine-Rich Repeat Proteoglycans Decorin and Biglycan: Glycosylation-Dependent Conformational Stability  

NASA Technical Reports Server (NTRS)

Biglycan and decorin, closely related small leucine-rich repeat proteoglycans, have been overexpressed in eukaryotic cers and two major glycoforms isolated under native conditions: a proteoglycan substituted with glycosaminoglycan chains; and a core protein form secreted devoid of glycosaminoglycans. A comparative biophysical study of these glycoforms has revealed that the overall secondary structures of biglycan and decorin are different. Far-UV Circular Dichroism (CD) spectroscopy of decorin and biglycan proteoglycans indicates that, although they are predominantly Beta-sheet, biglycan has a significantly higher content of alpha-helical structure. Decorin proteoglycan and core protein are very similar, whereas the biglycan core protein exhibits closer similarity to the decorin glycoforms than to. the biglycan proteoglycan form. However, enzymatic removal of the chondroitin sulfate chains from biglycan proteoglycan does not induce a shift to the core protein structure, suggesting that the fmal form is influenced by polysaccharide addition only during biosynthesis. Fluorescence emission spectroscopy demonstrated that the single tryptophan residue, which is at a conserved position at the C-terminal domain of both biglycan and decorin, is found in similar microenvironments. This indicates that at least in this specific domain, the different glycoforms do exhibit apparent conservation of structure. Exposure of decorin and biglycan to 10 M urea resulted in an increase in fluorescent intensity, which indicates that the emission from tryptophan in the native state is quenched. Comparison of urea-induced protein unfolding curves provided further evidence that decorin and biglycan assume different structures in solution. Decorin proteoglycan and core protein unfold in a manner similar to a classic two-state model, in which there is a steep transition to an unfolded state between 1-2 M urea. The biglycan core protein also shows a similar steep transition. However, biglycan proteoglycan shows a broad unfolding transition between 1-6 M urea, probably indicating the presence of stable unfolding intermediates.

Krishnan, Priya; Hocking, Anne M.; Scholtz, J. Martin; Pace, C. Nick; Holik, Kimberly K.; McQuillan, David J.



Binding Specificity of Philyra pisum Lectin to Pathogen-Associated Molecular Patterns, and Its Secondary Structure  

PubMed Central

We recently reported a Philyra pisum lectin (PPL) that exerts mitogenic effects on human lymphocytes, and its molecular characterization. The present study provides a more detailed characterization of PPL based on the results from a monosaccharide analysis indicating that PPL is a glycoprotein, and circular dichroism spectra revealing its estimated ?-helix, ?-sheet, ?-turn, and random coil contents to be 14.0%, 39.6%, 15.8%, and 30.6%, respectively. These contents are quite similar to those of deglycosylated PPL, indicating that glycans do not affect its intact structure. The binding properties to different pathogen-associated molecular patterns were investigated with hemagglutination inhibition assays using lipoteichoic acid from Gram-positive bacteria, lipopolysaccharide from Gram-negative bacteria, and both mannan and ?-1,3-glucan from fungi. PPL binds to lipoteichoic acids and mannan, but not to lipopolysaccharides or ?-1,3-glucan. PPL exerted no significant antiproliferative effects against human breast or bladder cancer cells. These results indicate that PPL is a glycoprotein with a lipoteichoic acid or mannan-binding specificity and which contains low and high proportions of ?-helix and ?-structures, respectively. These properties are inherent to the innate immune system of P. pisum and indicate that PPL could be involved in signal transmission into Gram-positive bacteria or fungi. PMID:24381505

Park, Byung Tae; Kim, Byung Sun; Park, Heajin; Jeong, Jaehoon; Hyun, Hanbit; Hwang, Hye Seong



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


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

Loewen, P C; Switala, J



Membrane-induced alteration of the secondary structure in the SWAP-70 pleckstrin homology domain.  


Differences in the conformation of the pleckstrin homology (PH) domain of switch-associated protein-70 (SWAP-70) in solution and at the lipid bilayer membrane surface were examined using CD, fluorescence and NMR spectroscopy. Intracellular relocalization of SWAP-70 from the cytoplasm to the plasma membrane and then to the nucleus is associated with its cellular functions. The PH domain of SWAP-70 contains a phosphoinositide-binding site and a nuclear localization signal, which localize SWAP-70 to the plasma membrane and nucleus, respectively. CD and fluorescence spectra showed that a significant conformational alteration involving formation of disordered structure occurs when the PH domain binds to D-myo-phosphatidylinositol 3,4,5-trisphosphate or D-myo-phosphatidylinositol 4,5-bisphosphate embedded in lipid bilayer vesicles. NMR spectra indicate that Ala and Trp residues located in the C-terminal ?-helix of the PH domain undergo conformational alterations to form a disordered structure at the vesicle surface. These conformational alterations were not induced by association with inositol 1,3,4,5-tetrakisphosphate in solution or coexistence of phosphatidylcholine vesicles. Interaction with the plane of the lipid bilayer via association with the phosphoinositides is required for the unfolding of the C-terminal ?-helix of the PH domain. The unwinding of the C-terminal ?-helix could regulate the functions of SWAP-70 at the plasma membrane surface. PMID:22247562

Tokuda, Naomi; Kawai, Katsuhisa; Lee, Young-Ho; Ikegami, Takahisa; Yamaguchi, Satoru; Yagisawa, Hitoshi; Fukui, Yasuhisa; Tuzi, Satoru



Primary structure of human nuclear ribonucleoprotein particle C proteins: conservation of sequence and domain structures in heterogeneous nuclear RNA, mRNA, and pre-rRNA-binding proteins.  

PubMed Central

In the eucaryotic nucleus, heterogeneous nuclear RNAs exist in a complex with a specific set of proteins to form heterogeneous nuclear ribonucleoprotein particles (hnRNPs). The C proteins, C1 and C2, are major constituents of hnRNPs and appear to play a role in RNA splicing as suggested by antibody inhibition and immunodepletion experiments. With the use of a previously described partial cDNA clone as a hybridization probe, full-length cDNAs for the human C proteins were isolated. All of the cDNAs isolated hybridized to two poly(A)+ RNAs of 1.9 and 1.4 kilobases (kb). DNA sequencing of a cDNA clone for the 1.9-kb mRNA (pHC12) revealed a single open reading frame of 290 amino acids coding for a protein of 31,931 daltons and two polyadenylation signals, AAUAAA, approximately 400 base pairs apart in the 3' untranslated region of the mRNA. DNA sequencing of a clone corresponding to the 1.4-kb mRNA (pHC5) indicated that the sequence of this mRNA is identical to that of the 1.9-kb mRNA up to the first polyadenylation signal which it uses. Both mRNAs therefore have the same coding capacity and are probably transcribed from a single gene. Translation in vitro of the 1.9-kb mRNA selected by hybridization with a 3'-end subfragment of pHC12 demonstrated that it by itself can direct the synthesis of both C1 and C2. The difference between the C1 and C2 proteins which results in their electrophoretic separation is not known, but most likely one of them is generated from the other posttranslationally. Since several hnRNP proteins appeared by sodium dodecyl sulfate-polyacrylamide gel electrophoresis as multiple antigenically related polypeptides, this raises the possibility that some of these other groups of hnRNP proteins are also each produced from a single mRNA. The predicted amino acid sequence of the protein indicates that it is composed of two distinct domains: an amino terminus that contains what we have recently described as a RNP consensus sequence, which is the putative RNA-binding site, and a carboxy terminus that is very negatively charged, contains no aromatic amino acids or prolines, and contains a putative nucleoside triphosphate-binding fold, as well as a phosphorylation site for casein kinase type II. The RNP consensus sequence was also found in the yeast poly(A)-binding protein (PABP), the heterogeneous nuclear RNA-binding proteins A1 and A2, and the pre-rRNA binding protein C23. All of these proteins are also composed of at least two distinct domains: an amino terminus, which possesses one or more RNP consensus sequences, and a carboxy terminus, which is unique to each protein, being very acidic in the C proteins and rich in glycine in A1, and C23 and rich in proline in the poly(A)-binding protein. These findings suggest that the amino terminus of these proteins possesses a highly conserved RNA-binding domain, whereas the carboxy terminus contains a region essential to the unique function and interactions of each of the RNA-binding proteins. Images PMID:3110598

Swanson, M S; Nakagawa, T Y; LeVan, K; Dreyfuss, G



What an rRNA Secondary Structure Tells about Phylogeny of Fungi in Ascomycota with Emphasis on Evolution of Major Types of Ascus  

PubMed Central

Background RNA secondary structure is highly conserved throughout evolution. The higher order structure is fundamental in establishing important structure-function relationships. Nucleotide sequences from ribosomal RNA (rRNA) genes have made a great contribution to our understanding of Ascomycota phylogeny. However, filling the gaps between molecular phylogeny and morphological assumptions based on ascus dehiscence modes and type of fruitbodies at the higher level classification of the phylum remains an unfulfilled task faced by mycologists. Methodology/Principal Findings We selected some major groups of Ascomycota to view their phylogenetic relationships based on analyses of rRNA secondary structure. Using rRNA secondary structural information, here, we converted nucleotide sequences into the structure ones over a 20-symbol code. Our structural analyses together with ancestral character state reconstruction produced reasonable phylogenetic position for the class Geoglossomycetes as opposed to the classic nucleotide analyses. Judging from the secondary structure analyses with consideration of mode of ascus dehiscence and the ability of forming fruitbodies, we draw a clear picture of a possible evolutionary route for fungal asci and some major groups of fungi in Ascomycota. The secondary structure trees show a more reasonable phylogenetic position for the class Geoglossomycetes. Conclusions Our results illustrate that asci lacking of any dehiscence mechanism represent the most primitive type. Passing through the operculate and Orbilia-type asci, bitunicate asci occurred. The evolution came to the most advanced inoperculate type. The ascus-producing fungi might be derived from groups lacking of the capacity to form fruitbodies, and then evolved multiple times. The apothecial type of fruitbodies represents the ancestral state, and the ostiolar type is advanced. The class Geoglossomycetes is closely related to Leotiomycetes and Sordariomycetes having a similar ascus type other than it was originally placed based on nucleotide sequence analyses. PMID:23110078

Zhuang, Wen-Ying; Liu, Chao-Yang



Secondary structure of double-stranded DNA under stretching: Elucidation of the stretched form  

SciTech Connect

Almost two decades ago, measurements of force versus extension on isolated double-stranded DNA molecules revealed a force plateau. This unusual stretching phenomenon in DNA suggests that the long molecules may be extended from the usual B form into a new conformation. Different models have been proposed to describe the nature of DNA in its stretched form, S-DNA. Using atomic force microscopy combined with a molecular combing method, we identified the structure of {lambda}-phage DNA for different stretching values. We provide strong evidence for the existence of a first-order transition between B form and S form. Beyond a certain extension of the natural length, DNA molecules adopt a new double-helix conformation characterized by a diameter of 1.2 nm and a helical pitch of18 nm.

Maaloum, M.; Muller, P. [Institut Charles Sadron, CNRS, University of Strasbourg, 23 rue du Loess, BP 84087, F-67034 Strasbourg cedex 2 (France); Beker, A-F. [Institut Charles Sadron, CNRS, University of Strasbourg, 23 rue du Loess, BP 84087, F-67034 Strasbourg cedex 2 (France); Leiden Institute of Physics, Leiden University, Niels Bohrweg 2, NL-2333 CA Leiden (Netherlands)



Structural, chemical and magnetic properties of secondary phases in Co-doped ZnO  

NASA Astrophysics Data System (ADS)

We have utilized a comprehensive set of experimental techniques such as transmission electron microscopy (TEM) and synchrotron-based x-ray absorption spectroscopy (XAS) and the respective x-ray linear dichroism and x-ray magnetic circular dichroism to characterize the correlation of structural, chemical and magnetic properties of Co-doped ZnO samples. It can be established on a quantitative basis that the superparamagnetic (SPM) behavior observed by integral superconducting quantum interference device magnetometry is not an intrinsic property of the material but stems from precipitations of metallic Co. Their presence is revealed by TEM as well as XAS. Annealing procedures for these SPM samples were also studied, and the observed changes in the magnetic properties found to be due to a chemical reduction or oxidation of the metallic Co species.

Ney, A.; Kovács, A.; Ney, V.; Ye, S.; Ollefs, K.; Kammermeier, T.; Wilhelm, F.; Rogalev, A.; Dunin-Borkowski, R. E.



Free energy determinants of secondary structure formation: II. Antiparallel beta-sheets.  


The factors that determine the stability of antiparallel beta-sheets are considered via a theoretical analysis of conformational free energies. A series of idealized model polyalanine beta-sheets are built with constraints such that the angular geometry of hydrogen bonding varies in the range observed in proteins while hydrogen bonding distance remains fixed. The conformations of the sheets generated in this way have a broad distribution of twist angles ranging from highly twisted left-handed to highly twisted right-handed orientations. The association free energies of the sheets are calculated with a gas phase CHARMM potential and FDPB/gamma solvation models. Left-handed structures are found to be less stable than right handed structures due to intrachain steric hindrance in isolated left-handed strands. This explains why antiparallel beta-sheets in proteins are invariably twisted in the right-handed direction. The free energy surface for right-handed sheets shows particular preference for conformations ranging from flat to those that exhibit a pronounced right-handed twist. This suggests that antiparallel beta-sheets can adopt a variety of right-handed conformations, a result that is consistent with observations on known proteins. In parallel with our study of alpha-helices we find that van der Waals and hydrophobic interactions are the primary factor stabilizing polyalanine beta-sheets, while electrostatic interactions including hydrogen bonding are found to be destabilizing. However, in contrast to helices, the net change in conformational free energy involving only backbone-backbone interactions (including beta-carbons) is not sufficient to overcome the loss in configurational entropy that accompanies sheet formation. Rather we suggest that cross-strand non-polar side-chain-side-chain interactions are essential for sheet formation, explaining why large non-polar amino acids have the greatest sheet forming propensities. Thus, sheet propensities involve pairwise interactions and are expected to be context dependent, as has been observed in recent experiments. PMID:7563057

Yang, A S; Honig, B



Biophysical Analysis of Progressive C-Terminal Truncations of Human Apolipoprotein E4: Insights into Secondary Structure and Unfolding Properties  

PubMed Central

Apolipoprotein E4 (apoE4) is a risk factor for Alzheimer’s disease and has been associated with a variety of neuropathological processes. ApoE4 C-terminally truncated forms have been found in brains of Alzheimer’s disease patients. Structural rearrangements in apoE4 are known to be key to its physiological functions. To understand the effect of C-terminal truncations on apoE4 lipid-free structure, we produced a series of recombinant apoE4 forms with progressive C-terminal deletions between residues 166 and 299. Circular dichroism measurements show a dramatic loss in helicity upon removal of the last 40 C-terminal residues, whereas further truncations of residues 203–259 lead to recovery of helical content. Further deletion of residues 186–202 leads to a small increase in helical content. Thermal denaturation indicated that removal of residues 260–299 leads to an increase in melting temperature but truncations down to residue 186 did not further affect the melting temperature. The progressive C-terminal truncations, however, gradually increased the cooperativity of thermal unfolding. Chemical denaturation of the apoE4 forms revealed a two-step process with a clear intermediate stage that is progressively lost as the C-terminus is truncated down to residue 230. Hydrophobic fluorescent probe binding suggested that regions 260–299 and 186–202 contain hydrophobic sites, the former being solvent accessible in the wild-type molecule and the latter being accessible only upon truncation. Taken together, our results show an important but complex role of apoE4 C-terminal segments in secondary structure stability and unfolding and suggest that interactions mediated by the C-terminal segments are important for the structural integrity and conformational changes of apoE4. PMID:18690708

Chroni, Angeliki; Pyrpassopoulos, Serapion; Thanassoulas, Angelos; Nounesis, George; Zannis, Vassilis I.; Stratikos, Efstratios



Secondary structure, orientation, and oligomerization of phospholemman, a cardiac transmembrane protein.  


Human phospholemman (PLM) is a 72-residue protein, which is expressed at high density in the cardiac plasma membrane and in various other tissues. It forms ion channels selective for K+, Cl-, and taurine in lipid bilayers and colocalizes with the Na+/K+-ATPase and the Na+/Ca2+-exchanger, which may suggest a role in the regulation of cell volume. Here we present the first structural data based on synthetic peptides representing the transmembrane domain of PLM. Perfluoro-octaneoate-PAGE of reconstituted proteoliposomes containing PLM reveals a tetrameric homo-oligomerization. Infrared spectroscopy of proteoliposomes shows that the PLM peptide is completely alpha-helical, even beyond the hydrophobic core residues. Hydrogen/deuterium exchange experiments reveal that a core of 20-22 residues is not accessible to water, thus embedded in the lipid membrane. The maximum helix tilt is 17 degrees +/- 2 degrees obtained by attenuated total reflection infrared spectroscopy. Thus, our data support the idea of ion channel formation by the PLM transmembrane domain. PMID:16597826

Beevers, Andrew J; Kukol, Andreas



Sequence-specific H NMR assignments and secondary structure in the sea anemone polypeptide Stichodactyla helianthus neurotoxin I  

SciTech Connect

Sequence-specific assignments are reported for the 500-MHz H nuclear magnetic resonance (NMR) spectrum of the 48-residue polypeptide neurotoxin I from the sea anemone Stichodactyla helianthus (Sh I). Spin systems were first identified by using two-dimensional relayed or multiple quantum filtered correlation spectroscopy, double quantum spectroscopy, and spin lock experiments. Specific resonance assignments were then obtained from nuclear Overhauser enhancement (NOE) connectivities between protons from residues adjacent in the amino acid sequence. Of a total of 265 potentially observable resonances, 248 (i.e., 94%) were assigned, arising from 39 completely and 9 partially assigned amino acid spin systems. The secondary structure of Sh I was defined on the basis of the pattern of sequential NOE connectivities. NOEs between protons on separate strands of the polypeptide backbone, and backbone amide exchange rates. Sh I contains a four-stranded antiparallel {beta}-sheet encompassing residues 1-5, 16-24, 30-33, and 40-46, with a {beta}-bulge at residues 17 and 18 and a reverse turn, probably a type II {beta}-turn, involving residues 27-30. No evidence of {alpha}-helical structure was found.

Fogh, R.H.; Mabbutt, B.C.; Kem, W.R.; Norton, R.S. (Univ. of New South Wales, Kensington (Australia))



Secondary Structure-Induced Micro- and Macro-Phase Separation in Polypeptide Diblock, Triblock and Star-Block Copolymers  

NASA Astrophysics Data System (ADS)

Self-organized polypeptide block copolymers are of great interest due to their potential uses as materials for nano-devices and bio-engineering. In order to explore the effect of block copolymer topologies on their structures, a series of di-, tri- and tetra-block copolymers has been synthesized. A coil-like soft block based on poly(propylene oxide) chemistry was chosen due to its low glass transition temperature, amorphous nature and immiscibility with biological systems. On the other hand, rod-like block polypeptide based on poly(L-glutamic acid ?-benzyl ester) was selected and grown from the coil soft macroinitiator by ring opening polymerization. Because of the mono-, bi-, or tri-functionality of the coiled blocks, linear di-block, tri-block and star-like tetra-block copolymers could be successfully synthesized. The resulting materials show micro-phase separated liquid-crystalline morphologies, in which the architecture or connectivity of the blocks, the molecular weight of the coil segment, the volume fraction and the secondary structure of the polypeptide blocks all contribute to their micro-phase separated features. These materials can be seen as model reference systems towards the design of biocompatible scaffolds and artificial muscles.

Sanchez-Ferrer, Antoni; Mezzenga, Raffaele



1H and 15N nuclear magnetic resonance assignment and secondary structure of the cytotoxic ribonuclease alpha-Sarcin.  

PubMed Central

The ribosome-inactivating protein alpha-Sarcin (alpha S) is a 150-residue fungal ribonuclease that, after entering sensitive cells, selectively cleaves a single phosphodiester bond in an universally conserved sequence of the major rRNA to inactivate the ribosome and thus exert its cytotoxic action. As a first step toward establishing the structure-dynamics-function relationships in this system, we have carried out the assignment of the 1H and 15N NMR spectrum of alpha S on the basis of homonuclear (1H-1H) and heteronuclear (1H-15N) two-dimensional correlation spectra of a uniformly 15N-labeled sample, and two selectively 15N-labeled (Tyr and Phe) samples, as well as a single three-dimensional experiment. The secondary structure of alpha S, as derived from the characteristic patterns of dipolar connectivities between backbone protons, conformational chemical shifts, and the protection of backbone amide protons against exchange, consists of a long N-terminal beta-hairpin, a short alpha-helical segment, and a C-terminal beta-sheet of five short strands arranged in a + 1, + 1, + 1, + 1 topology, connected by long loops in which the 13 Pro residues are located. PMID:8732769

Campos-Olivas, R.; Bruix, M.; Santoro, J.; Martínez del Pozo, A.; Lacadena, J.; Gavilanes, J. G.; Rico, M.



1H and 15N nuclear magnetic resonance assignment and secondary structure of the cytotoxic ribonuclease alpha-Sarcin.  


The ribosome-inactivating protein alpha-Sarcin (alpha S) is a 150-residue fungal ribonuclease that, after entering sensitive cells, selectively cleaves a single phosphodiester bond in an universally conserved sequence of the major rRNA to inactivate the ribosome and thus exert its cytotoxic action. As a first step toward establishing the structure-dynamics-function relationships in this system, we have carried out the assignment of the 1H and 15N NMR spectrum of alpha S on the basis of homonuclear (1H-1H) and heteronuclear (1H-15N) two-dimensional correlation spectra of a uniformly 15N-labeled sample, and two selectively 15N-labeled (Tyr and Phe) samples, as well as a single three-dimensional experiment. The secondary structure of alpha S, as derived from the characteristic patterns of dipolar connectivities between backbone protons, conformational chemical shifts, and the protection of backbone amide protons against exchange, consists of a long N-terminal beta-hairpin, a short alpha-helical segment, and a C-terminal beta-sheet of five short strands arranged in a + 1, + 1, + 1, + 1 topology, connected by long loops in which the 13 Pro residues are located. PMID:8732769

Campos-Olivas, R; Bruix, M; Santoro, J; Martínez del Pozo, A; Lacadena, J; Gavilanes, J G; Rico, M



The Influence of Flanking Secondary Structures on Amino Acid Content and Typical Lengths of 3/10 Helices  

PubMed Central

We used 3D structures of a highly redundant set of bacterial proteins encoded by genes of high, average, and low GC-content. Four types of connecting bridges—regions situated between any of two major elements of secondary structure (alpha helices and beta strands)—containing a pure random coil were compared with connecting bridges containing 3/10 helices. We included discovered trends in the original “VVTAK Connecting Bridges” algorithm, which is able to predict more probable conformation for a given connecting bridge. The highest number of significant differences in amino acid usage was found between 3/10 helices containing bridges connecting two beta strands (they have increased Phe, Tyr, Met, Ile, Leu, Val, and His usages but decreased usages of Asp, Asn, Gly, and Pro) and those without 3/10 helices. The typical (most common) length of 3/10 helices situated between two beta strands and between beta strand and alpha helix is equal to 5 amino acid residues. The preferred length of 3/10 helices situated between alpha helix and beta strand is equal to 3 residues. For 3/10 helices situated between two alpha helices, both lengths (3 and 5 amino acid residues) are typical. PMID:25371821

Khrustalev, Vladislav Victorovich; Barkovsky, Eugene Victorovich; Khrustaleva, Tatyana Aleksandrovna



Imposing function down a (cupin)-barrel: secondary structure and metal stereochemistry in the ?KG-dependent oxygenases.  


The Fe(ii)/?ketoglutarate (?KG) dependent oxygenases catalyze a diverse range of reactions significant in biological processes such as antibiotic biosynthesis, lipid metabolism, oxygen sensing, and DNA and RNA repair. Although functionally diverse, the eight-stranded ?-barrel (cupin) and HX(D/E)XnH facial triad motifs are conserved in this super-family of enzymes. Crystal structure analysis of 25 ?KG oxygenases reveals two stereoisomers of the Fe cofactor, Anti and Clock, which differ in the relative position of the exchangeable ligand position and the primary substrate. Herein, we discuss the relationship between the chemical mechanism and the secondary coordination sphere of the ?KG oxygenases, within the constraints of the stereochemistry of the Fe cofactor. Sequence analysis of the cupin barrel indicates that a small subset of positions constitute the second coordination sphere, which has significant ramifications for the structure of the ferryl intermediate. The competence of both Anti and Clock stereoisomers of Fe points to a ferryl intermediate that is 5 coordinate. The small number of conserved close contacts within the active sites of ?KG oxygenases can be extended to chemically related enzymes, such as the ?KG-dependent halogenases SyrB2 and CytC3, and the non-?KG dependent dioxygenases isopenicillin N synthase (IPNS) and cysteine dioxygenase (CDO). PMID:23446356

Hangasky, John A; Taabazuing, Cornelius Y; Valliere, Meaghan A; Knapp, Michael J



Relationship between the levels of calbindin synthesis and calbindin mRNA in chick intestine. Quantitation of calbindin mRNA.  


An RNA-excess filter hybridization assay was established to measure the absolute amount of calbindin mRNA in chick tissues. The tissue with the highest level of mRNA is intestine, followed by kidney and cerebellum; the mRNA was not detected in liver and skin. Calbindin mRNA in intestine and kidney is vitamin D-dependent. The maximum concentration of calbindin and its mRNA found after dosing vitamin D-deficient chicks with dihydroxyvitamin D3 (1,25-(OH)2D3) is less than 5% of that found with vitamin D dosing. Secondary 1,25-(OH)2D3 stimulation produced greatly increased amounts of both calbindin mRNA and the protein, at least reaching levels similar to those found after vitamin D dosing. In this last case, each mucosal cell contains about 2000 calbindin mRNA molecules which are translated at a rate sufficient to account for the levels of calbindin found. Calbindin mRNA is translated most rapidly in the very short time periods after its release into the cytoplasm. 1,25-(OH)2D3 has two effects on calbindin mRNA formation: first, to permit the expression of the calbindin gene and a second effect, of slower onset but more persistent, which increases either the rate of calbindin gene transcription or the stability of calbindin mRNA. PMID:3346251

Mayel-Afshar, S; Lane, S M; Lawson, D E



Staufen-mediated mRNA decay  

PubMed Central

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

Park, Eonyoung; Maquat, Lynne E.



VITAL NMR: using chemical shift derived secondary structure information for a limited set of amino acids to assess homology model accuracy.  


Homology modeling is a powerful tool for predicting protein structures, whose success depends on obtaining a reasonable alignment between a given structural template and the protein sequence being analyzed. In order to leverage greater predictive power for proteins with few structural templates, we have developed a method to rank homology models based upon their compliance to secondary structure derived from experimental solid-state NMR (SSNMR) data. Such data is obtainable in a rapid manner by simple SSNMR experiments (e.g., (13)C-(13)C 2D correlation spectra). To test our homology model scoring procedure for various amino acid labeling schemes, we generated a library of 7,474 homology models for 22 protein targets culled from the TALOS+/SPARTA+ training set of protein structures. Using subsets of amino acids that are plausibly assigned by SSNMR, we discovered that pairs of the residues Val, Ile, Thr, Ala and Leu (VITAL) emulate an ideal dataset where all residues are site specifically assigned. Scoring the models with a predicted VITAL site-specific dataset and calculating secondary structure with the Chemical Shift Index resulted in a Pearson correlation coefficient (-0.75) commensurate to the control (-0.77), where secondary structure was scored site specifically for all amino acids (ALL 20) using STRIDE. This method promises to accelerate structure procurement by SSNMR for proteins with unknown folds through guiding the selection of remotely homologous protein templates and assessing model quality. PMID:22183804

Brothers, Michael C; Nesbitt, Anna E; Hallock, Michael J; Rupasinghe, Sanjeewa G; Tang, Ming; Harris, Jason; Baudry, Jerome; Schuler, Mary A; Rienstra, Chad M



Protein Secondary Structures (alpha-helix and beta-sheet) at a Cellular Levle and Protein Fractions in Relation to Rumen Degradation Behaviours of Protein: A New Approach  

SciTech Connect

Studying the secondary structure of proteins leads to an understanding of the components that make up a whole protein, and such an understanding of the structure of the whole protein is often vital to understanding its digestive behaviour and nutritive value in animals. The main protein secondary structures are the {alpha}-helix and {beta}-sheet. The percentage of these two structures in protein secondary structures influences protein nutritive value, quality and digestive behaviour. A high percentage of {beta}-sheet structure may partly cause a low access to gastrointestinal digestive enzymes, which results in a low protein value. The objectives of the present study were to use advanced synchrotron-based Fourier transform IR (S-FTIR) microspectroscopy as a new approach to reveal the molecular chemistry of the protein secondary structures of feed tissues affected by heat-processing within intact tissue at a cellular level, and to quantify protein secondary structures using multicomponent peak modelling Gaussian and Lorentzian methods, in relation to protein digestive behaviours and nutritive value in the rumen, which was determined using the Cornell Net Carbohydrate Protein System. The synchrotron-based molecular chemistry research experiment was performed at the National Synchrotron Light Source at Brookhaven National Laboratory, US Department of Energy. The results showed that, with S-FTIR microspectroscopy, the molecular chemistry, ultrastructural chemical make-up and nutritive characteristics could be revealed at a high ultraspatial resolution ({approx}10 {mu}m). S-FTIR microspectroscopy revealed that the secondary structure of protein differed between raw and roasted golden flaxseeds in terms of the percentages and ratio of {alpha}-helixes and {beta}-sheets in the mid-IR range at the cellular level. By using multicomponent peak modelling, the results show that the roasting reduced (P <0.05) the percentage of {alpha}-helixes (from 47.1% to 36.1%: S-FTIR absorption intensity), increased the percentage of {beta}-sheets (from 37.2% to 49.8%: S-FTIR absorption intensity) and reduced the {alpha}-helix to {beta}-sheet ratio (from 0.3 to 0.7) in the golden flaxseeds, which indicated a negative effect of the roasting on protein values, utilisation and bioavailability. These results were proved by the Cornell Net Carbohydrate Protein System in situ animal trial, which also revealed that roasting increased the amount of protein bound to lignin, and well as of the Maillard reaction protein (both of which are poorly used by ruminants), and increased the level of indigestible and undegradable protein in ruminants. The present results demonstrate the potential of highly spatially resolved synchrotron-based infrared microspectroscopy to locate 'pure' protein in feed tissues, and reveal protein secondary structures and digestive behaviour, making a significant step forward in and an important contribution to protein nutritional research. Further study is needed to determine the sensitivities of protein secondary structures to various heat-processing conditions, and to quantify the relationship between protein secondary structures and the nutrient availability and digestive behaviour of various protein sources. Information from the present study arising from the synchrotron-based IR probing of the protein secondary structures of protein sources at the cellular level will be valuable as a guide to maintaining protein quality and predicting digestive behaviours.




Solution structure of neuronal bungarotoxin determined by two-dimensional NMR spectroscopy: Sequence-specific assignments, secondary structure, and dimer formation  

SciTech Connect

The solution structure of neuronal bungarotoxin (nBgt) has been studied by using two-dimensional {sup 1}H NMR spectroscopy. Sequence-specific assignments for over 95% of the backbone resonances and 85% of the side-chain resonances have been made by using a series of two-dimensional spectra at four temperatures. From these assignments over 75% of the NOESY spectrum has been assigned, which has in turn provided 582 distance constraints. Twenty-seven coupling constants (NH-{alpha}CH) were determined from the COSY spectra, which have provided dihedral angle constraints. In addition, hydrogen exchange experiments have suggested the probable position of hydrogen bonds. The NOE constraints, dihedral angle constraints, and the rates of amide proton exchange suggest that a triple-stranded antiparallel {beta} sheet is the major component of secondary structure, which includes 25% of the amino acid residues. A number of NOE peaks were observed that were inconsistent with the antiparallel {beta}-sheet structure. Because the authors have confirmed by sedimentation equilibrium that nBgt exists as a dimer, the authors have reinterpreted these NOE constraints as intermolecular interactions. These constraints suggest that the dimer consists of a six-stranded antiparallel {beta} sheet (three from each monomer), with residues 55-59 forming the dimer interface.

Oswald, R.E.; Bamberger, M. (Cornell Univ., Ithaca, NY (United States) Univ. of Oxford (England)); Sutcliffe, M.J. (Univ. of Oxford (England) Univ. of Leicester (England)); Loring, R. H. (Northeastern Univ., Boston, MA (United States)); Braswell, E. (Univ. of Connecticut, Storrs (United States)); Dobson, C.M. (Univ. of Oxford (England))



Fate and effects of the insecticide Dursban 4E in indoor Elodea-dominated and macrophyte-free freshwater model ecosystems: II. Secondary effects on community structure.  


Secondary effects of a single dose of the insecticide Dursban 4E (active ingredient chlorpyrifos) were studied in indoor experimental freshwater ecosystems intended to mimic drainage ditches. Two experiments were performed, one in which all model ecosystems were dominated by the macrophyte Elodea muttallii, and one using systems devoid of macrophytes. In the Elodea-dominated and macrophyte-free model ecosystems, populations of primary producers, herbivores, carnivores and detritivores were indirectly affected via the loss of populations of Arthropoda as a direct result of insecticide application. However, the taxa in which secondary effects were observed differed considerably between these two types of model ecosystem. In macrophyte-dominated systems secondary effects were observed on populations of periphytic algae, the macrophyte Elodea nuttallii, the gastropod Bithynia tentaculata, Turbellaria, and sediment dwelling Oligochaeta. In open water systems it were populations of phytoplankton, the rotators Polyarthra and Asplanchna, bivalves (Sphaeriidae), Hirudinea, sediment dwelling Oligochaeta, and that of the isopod Proasellus coxalis in which secondary effects were observed. In aquatic ecosystems the presence or absence of a well-developed macrophyte vegetation may be a very important characteristic that determines the nature and route of secondary effects induced by pesticides. The differences in secondary effects observed between Elodea-dominated and macrophyte-free model ecosystems indicate that the system's structure and trophic dynamics should be taken into account when predicting ecological effects. PMID:1280070

Brock, T C; van den Bogaert, M; Bos, A R; van Breukelen, S W; Reiche, R; Terwoert, J; Suykerbuyk, R E; Roijackers, R M



The impact of rRNA secondary structure consideration in alignment and tree reconstruction: simulated data and a case study on the phylogeny of hexapods.  


The use of secondary structures has been advocated to improve both the alignment and the tree reconstruction processes of ribosomal RNA (rRNA) data sets. We used simulated and empirical rRNA data to test the impact of secondary structure consideration in both steps of molecular phylogenetic analyses. A simulation approach was used to generate realistic rRNA data sets based on real 16S, 18S, and 28S sequences and structures in combination with different branch length and topologies. Alignment and tree reconstruction performance of four recent structural alignment methods was compared with exclusively sequence-based approaches. As empirical data, we used a hexapod rRNA data set to study the influence of nucleotide interdependencies in sequence alignment and tree reconstruction. Structural alignment methods delivered significantly better sequence alignments compared with pure sequence-based methods. Also, structural alignment methods delivered better trees judged by topological congruence to simulation base trees. However, the advantage of structural alignments was less pronounced and even vanished in several instances. For simulated data, application of mixed RNA/DNA models to stems and loops, respectively, led to significantly shorter branches. The application of mixed RNA/DNA models in the hexapod analyses delivered partly implausible relationships. This can be interpreted as a stronger sensitivity of mixed model setups to nonphylogenetic signal. Secondary structure consideration clearly influenced sequence alignment and tree reconstruction of ribosomal genes. Although sequence alignment quality can considerably be improved by the use of secondary structure information, the application of mixed models in tree reconstructions needs further studies to understand the observed effects. PMID:20530152

Letsch, Harald O; Kück, Patrick; Stocsits, Roman R; Misof, Bernhard



Discovery of a mRNA mitochondrial localization element in Saccharomyces cerevisiae by nonhomologous random recombination and in vivo selection.  


In budding yeast, over 100 nuclear-encoded mRNAs are localized to the mitochondria. The determinants of mRNA localization to the mitochondria are not well understood, and protein factors involved in this process have not yet been identified. To reveal the sequence determinants for mitochondrial localization in a comprehensive and unbiased manner, we generated highly diversified libraries of 3' UTR regions from a known mitochondrially localized mRNA by nonhomologous random recombination (NRR) and subjected the resulting sequences to an in vivo selection that links cell survival to mitochondrial mRNA localization. When applied to the yeast ATP2 mRNA, this approach rapidly identified a 50-nt consensus motif, designated Min2, as well as two Min2-homologous regions naturally present downstream of the ATP2 stop codon, which are sufficient when appended to the 3' end of various reporter mRNAs to induce mitochondrial localization. Site-directed mutagenesis of Min2 revealed primary and secondary structure elements that contribute to localization activity. In addition, the Min2 motif may facilitate the identification of proteins involved in this mode of establishing cellular asymmetry. PMID:17916575

Liu, Jane M; Liu, David R



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

E-print Network

by Fourier transform infrared spectroscopy Haoming Zhang , Yasuo Ishikawa , Yasusi Yamamoto , Robert characterized in solution between 25 and 75³C using Fourier transform infrared spectroscopy. Quantitative protein; Fourier transform infrared; Oxygen evolving complex 23; Photosystem II; Secondary structure 1

Carpentier, Robert


Structural Complexity, Differential Response to Infection, and Tissue Specificity of Indolic and Phenylpropanoid Secondary Metabolism in Arabidopsis Roots1[w  

PubMed Central

Levels of indolic and phenylpropanoid secondary metabolites in Arabidopsis (Arabidopsis thaliana) leaves undergo rapid and drastic changes during pathogen defense, yet little is known about this process in roots. Using Arabidopsis wild-type and mutant root cultures as an experimental system, and the root-pathogenic oomycete, Pythium sylvaticum, for infections, we analyzed the aromatic metabolite profiles in soluble extracts from uninfected and infected roots, as well as from the surrounding medium. A total of 16 indolic, one heterocyclic, and three phenylpropanoid compounds were structurally identified by mass spectrometry and nuclear magnetic resonance analyses. Most of the indolics increased strongly upon infection, whereas the three phenylpropanoids decreased. Concomitant increases in both indolic and phenylpropanoid biosynthetic mRNAs suggested that phenylpropanoids other than those examined here in “soluble extracts” were coinduced with the indolics. These and previous results indicate that roots differ greatly from leaves with regard to the nature and relative abundance of all major soluble phenylpropanoid constituents. For indolics, by contrast, our data reveal far-reaching similarities between roots and leaves and, beyond this comparative aspect, provide an insight into this highly diversified yet under-explored metabolic realm. The data point to metabolic interconnections among the compounds identified and suggest a partial revision of the previously proposed camalexin pathway. PMID:15923335

Bednarek, Pawel; Schneider, Bernd; Svatos, Ales; Oldham, Neil J.; Hahlbrock, Klaus



Robust Translation of the Nucleoid Protein Fis Requires a Remote Upstream AU Element and Is Enhanced by RNA Secondary Structure  

PubMed Central

Synthesis of the Fis nucleoid protein rapidly increases in response to nutrient upshifts, and Fis is one of the most abundant DNA binding proteins in Escherichia coli under nutrient-rich growth conditions. Previous work has shown that control of Fis synthesis occurs at transcription initiation of the dusB-fis operon. We show here that while translation of the dihydrouridine synthase gene dusB is low, unusual mechanisms operate to enable robust translation of fis. At least two RNA sequence elements located within the dusB coding region are responsible for high fis translation. The most important is an AU element centered 35 nucleotides (nt) upstream of the fis AUG, which may function as a binding site for ribosomal protein S1. In addition, a 44-nt segment located upstream of the AU element and predicted to form a stem-loop secondary structure plays a prominent role in enhancing fis translation. On the other hand, mutations close to the AUG, including over a potential Shine-Dalgarno sequence, have little effect on Fis protein levels. The AU element and stem-loop regions are phylogenetically conserved within dusB-fis operons of representative enteric bacteria. PMID:22389479

Nafissi, Maryam; Chau, Jeannette; Xu, Jimin



Proofreading and Secondary Structure Processing Determine the Orientation Dependence of CAG?CTG Trinucleotide Repeat Instability in Escherichia coli  

PubMed Central

Expanded CAG·CTG trinucleotide repeat tracts are associated with several human inherited diseases, including Huntington's disease, myotonic dystrophy, and spinocerebellar ataxias. Here we describe a new model system to investigate repeat instability in the Escherichia coli chromosome. Using this system, we reveal patterns of deletion instability consistent with secondary structure formation in vivo and address the molecular basis of orientation-dependent instability. We demonstrate that the orientation dependence of CAG·CTG trinucleotide repeat deletion is determined by the proofreading subunit of DNA polymerase III (DnaQ) in the presence of the hairpin nuclease SbcCD (Rad50/Mre11). Our results suggest that, although initiation of slippage can occur independently of CAG·CTG orientation, the folding of the intermediate affects its processing and this results in orientation dependence. We propose that proofreading is inefficient on the CTG-containing strand because of its ability to misfold and that SbcCD contributes to processing in a manner that is dependent on proofreading and repeat tract orientation. Furthermore, we demonstrate that transcription and recombination do not influence instability in this system. PMID:17339223

Zahra, Rabaab; Blackwood, John K.; Sales, Jill; Leach, David R. F.



Protein Structure Analysis Iosif Vaisman  

E-print Network

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

Vaisman, Iosif


Protein Structure Analysis Iosif Vaisman  

E-print Network

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

Vaisman, Iosif


Protein Structure Analysis Iosif Vaisman  

E-print Network

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

Vaisman, Iosif


Relation between the secondary structure of carbohydrate residues of alpha1-acid glycoprotein (orosomucoid) and the fluorescence of the protein.  


We studied in this work the relation that exists between the secondary structure of the glycans of alpha(1)-acid glycoprotein and the fluorescence of the Trp residues of the protein. We calculated for that the efficiency of quenching and the radiative and non-radiative constants. Our results indicate that the glycans display a spatial structure that is modified upon asialylation. The asialylated conformation is closer to the protein matrix than the sialylated form, inducing by that a decrease in the fluorescence parameters of the Trp residues. In fact, the mean quantum yield of Trp residues in sialylated and asialylated alpha(1)-acid glycoprotein are 0.0645 and 0.0385, respectively. Analysis of the fluorescence emission of alpha(1)-acid glycoprotein as the result of two contributions (surface and hydrophobic domains) indicates that quantum yields of both classes of Trp residues are lower when the protein is in the asialylated form. Also, the mean fluorescence lifetime of Trp residues decreases from 2.285 ns in the sialylated protein to 1.948 ns in the asialylated one. The radiative rate constant k(r) of the Trp residues in the sialylated alpha(1)-acid glycoprotein is higher than that in the asialylated protein. Thus, the carbohydrate residues are closer to the Trp residues in the absence of sialic acid. The modification of the spatial conformation of the glycans upon asialylation is confirmed by the decrease of the fluorescence lifetimes of Calcofluor, a fluorophore that binds to the carbohydrate residues. Finally, thermal intensity quenching of Calcofluor bound to alpha(1)-acid glycoprotein shows that the carbohydrate residues have slower residual motions in the absence of sialic acid residues. PMID:12706975

Albani, Jihad R



Testing secondary organic aerosol models using smog chamber data for complex precursor mixtures: influence of precursor volatility and molecular structure  

NASA Astrophysics Data System (ADS)

We use secondary organic aerosol (SOA) production data from an ensemble of unburned fuels measured in a smog chamber to test various SOA formation models. The evaluation considered data from 11 different fuels including gasoline, multiple diesels, and various jet fuels. The fuels are complex mixtures of species; they span a wide range of volatility and molecular structure to provide a challenging test for the SOA models. We evaluated three different versions of the SOA model used in the Community Multiscale Air Quality (CMAQ) model. The simplest and most widely used version of that model only accounts for the volatile species (species with less than or equal to 12 carbons) in the fuels. It had very little skill in predicting the observed SOA formation (R2 = 0.04, fractional error = 108%). Incorporating all of the lower-volatility fuel species (species with more than 12 carbons) into the standard CMAQ SOA model did not improve model performance significantly. Both versions of the CMAQ SOA model over-predicted SOA formation from a synthetic jet fuel and under-predicted SOA formation from diesels because of an overly simplistic representation of the SOA formation from alkanes that did not account for the effects of molecular size and structure. An extended version of the CMAQ SOA model that accounted for all organics and the influence of molecular size and structure of alkanes reproduced the experimental data. This underscores the importance of accounting for all low-volatility organics and information on alkane molecular size and structure in SOA models. We also investigated fitting an SOA model based solely on the volatility of the precursor mixture to the experimental data. This model could describe the observed SOA formation with relatively few free parameters, demonstrating the importance of precursor volatility for SOA formation. The exceptions were exotic fuels such as synthetic jet fuel that expose the central assumption of the volatility-dependent model that most emissions consist of complex mixtures with similar distribution of molecular classes. Despite its shortcomings, SOA formation as a function of volatility may be sufficient for modeling SOA formation in chemical transport models.

Jathar, S. H.; Donahue, N. M.; Adams, P. J.; Robinson, A. L.



Secondary parkinsonism  


Parkinsonism - secondary; Atypical Parkinson disease ... to be less responsive to medical therapy than Parkinson's disease. ... Unlike Parkinson disease, secondary parkinsonism may stabilize or even improve if the underlying cause is treated. Brain problems, such ...


Effect of freeze-drying, cryoprotectants and storage conditions on the stability of secondary structure of insulin-loaded solid lipid nanoparticles.  


This study aims to monitor the secondary structure behaviour of insulin when it is encapsulated into solid lipid nanoparticles (SLN), under the influence of several critical processing parameters. Insulin was used as a therapeutic protein model. Physicochemical properties of insulin-loaded SLN (Ins-SLN) were assessed, with special focus on the insulin secondary structure after its encapsulation into SLN and after freeze-drying using different cryoprotectants (glucose, fructose and sorbitol). Additionally, a 6-month stability study was performed to evaluate the maintenance of insulin secondary structure over time at different storage conditions (4 °C/60% RH, 25 °C/60% RH, 40 °C/75% RH). Ins-SLN were successfully produced with a mean and narrow particle size around 400 nm, zeta potential around -13 mV, an insulin association efficiency of 84%. Physical-chemical properties of SLN were maintained after freeze-drying. FTIR results showed that encapsulated insulin maintained a native-like structure in a degree of similarity around 92% after production, and 84% after freeze-drying. After 6 months, freeze-dried Ins-SLN without cryoprotectant stored at 40 °C/75% RH presented the same degree of structure preservation and morphology. Results revealed that insulin structure can be significantly protected by SLN matrix itself, without a cryoprotectant agent, even using a non-optimized freeze-drying process, and under the harsher storage conditions. Multivariable experimental settled the process parameters to fit with the desired product quality attributes regarding protein and nanoparticle stability. PMID:24036086

Soares, Sandra; Fonte, Pedro; Costa, Ana; Andrade, José; Seabra, Vítor; Ferreira, Domingos; Reis, Salette; Sarmento, Bruno



Secondary Alkaline Batteries.  

National Technical Information Service (NTIS)

This report on secondary alkaline batteries covers the overall reactions (charge/discharge characteristics), electrode structures and materials, and cell construction. The following batteries are studied, nickel oxide-cadmium, nickel oxide-iron, nickel ox...

J. McBreen



Only one of four possible secondary structures of the central conserved region of potato spindle tuber viroid is a substrate for processing in a potato nuclear extract.  

PubMed Central

The influence of RNA secondary structure on the substrate activity of a longer-than-unit length transcript for processing to circular viroids was studied in a nuclear extract from potato suspension cells. The nuclear extract was prepared according to a modified procedure for a plant transcription extract. The transcript of the potato spindle tuber viroid (PSTVd) consists of a monomeric molecule with 17 additional nucleotides, thus doubling most of the central conserved region of viroids of the PSTVd-class. The transcript can assume four different secondary structures, which either co-exist as conformers in solution or can be kept as metastable structures after different treatments by temperature and/or ionic strength. The structures were analysed by thermodynamic calculations and temperature-gradient gel electrophoresis and were confirmed by oligonucleotide mapping. Only the so-called extended middle structure was processed to exact viroid circles. In this structure the 5'- and 3'-ends are branching out from the rod-like viroid structure at the loop starting with nucleotide 87. The other structures were processed only if they could be rearranged into the active structure. Images PMID:7501442

Baumstark, T; Riesner, D



CNGA3 Deficiency Affects Cone Synaptic Terminal Structure and Function and Leads to Secondary Rod Dysfunction and Degeneration  

PubMed Central

Purpose. To investigate rod function and survival after cone dysfunction and degeneration in a mouse model of cone cyclic nucleotide-gated (CNG) channel deficiency. Methods. Rod function and survival in mice with cone CNG channel subunit CNGA3 deficiency (CNGA3?/? mice) were evaluated by electroretinographic (ERG), morphometric, and Western blot analyses. The arrangement, integrity, and ultrastructure of photoreceptor terminals were investigated by immunohistochemistry and electron microscopy. Results. The authors found loss of cone function and cone death accompanied by impairment of rods and rod-driven signaling in CNGA3?/? mice. Scotopic ERG b-wave amplitudes were reduced by 15% at 1 month, 30% at 6 months, and 40% at 9 months and older, while scotopic a-wave amplitudes were decreased by 20% at 9 months, compared with ERGs of age-matched wild-type mice. Outer nuclear layer thickness in CNGA3?/? retina was reduced by 15% at 12 months compared with age-matched wild-type controls. This was accompanied by a 30%–40% reduction in expression of rod-specific proteins, including rhodopsin, rod transducin ?-subunit, and glutamic acid-rich protein (GARP). Cone terminals in the CNGA3?/? retina showed a progressive loss of neurochemical and ultrastructural integrity. Abnormalities were observed as early as 1 month. Disorganized rod terminal ultrastructure was noted by 12 months. Conclusions. These findings demonstrate secondary rod impairment and degeneration after cone degeneration in mice with cone CNG channel deficiency. Loss of cone phototransduction accompanies the compromised integrity of cone terminals. With time, rod synaptic structure, function, and viability also become compromised. PMID:22247469

Xu, Jianhua; Morris, Lynsie M.; Michalakis, Stylianos; Biel, Martin; Fliesler, Steven J.; Sherry, David M.



Experiments and simulations show how long-range contacts can form in expanded unfolded proteins with negligible secondary structure.  


The sizes of unfolded proteins under highly denaturing conditions scale as N(0.59) with chain length. This suggests that denaturing conditions mimic good solvents, whereby the preference for favorable chain-solvent interactions causes intrachain interactions to be repulsive, on average. Beyond this generic inference, the broader implications of N(0.59) scaling for quantitative descriptions of denatured state ensembles (DSEs) remain unresolved. Of particular interest is the degree to which N(0.59) scaling can simultaneously accommodate intrachain attractions and detectable long-range contacts. Here we present data showing that the DSE of the N-terminal domain of the L9 (NTL9) ribosomal protein in 8.3 M urea lacks detectable secondary structure and forms expanded conformations in accord with the expected N(0.59) scaling behavior. Paramagnetic relaxation enhancements, however, indicate the presence of detectable long-range contacts in the denatured-state ensemble of NTL9. To explain these observations we used atomistic thermal unfolding simulations to identify ensembles whose properties are consistent with all of the experimental observations, thus serving as useful proxies for the DSE of NTL9 in 8.3 M urea. Analysis of these ensembles shows that residual attractions are present under mimics of good solvent conditions, and for NTL9 they result from low-likelihood, medium/long-range contacts between