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1

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

PubMed Central

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

Chursov, Andrey; Frishman, Dmitrij; Shneider, Alexander

2013-01-01

2

mRNA secondary structure optimization using a correlated stem-loop prediction  

PubMed Central

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

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

2013-01-01

3

Deciphering the rules by which dynamics of mRNA secondary structure affect translation efficiency in Saccharomyces cerevisiae  

PubMed Central

Messenger RNA (mRNA) secondary structure decreases the elongation rate, as ribosomes must unwind every structure they encounter during translation. Therefore, the strength of mRNA secondary structure is assumed to be reduced in highly translated mRNAs. However, previous studies in vitro reported a positive correlation between mRNA folding strength and protein abundance. The counterintuitive finding suggests that mRNA secondary structure affects translation efficiency in an undetermined manner. Here, we analyzed the folding behavior of mRNA during translation and its effect on translation efficiency. We simulated translation process based on a novel computational model, taking into account the interactions among ribosomes, codon usage and mRNA secondary structures. We showed that mRNA secondary structure shortens ribosomal distance through the dynamics of folding strength. Notably, when adjacent ribosomes are close, mRNA secondary structures between them disappear, and codon usage determines the elongation rate. More importantly, our results showed that the combined effect of mRNA secondary structure and codon usage in highly translated mRNAs causes a short ribosomal distance in structural regions, which in turn eliminates the structures during translation, leading to a high elongation rate. Together, these findings reveal how the dynamics of mRNA secondary structure coupling with codon usage affect translation efficiency.

Mao, Yuanhui; Liu, HuiLing; Liu, Yanlin; Tao, Shiheng

2014-01-01

4

Dynamics of translation by single ribosomes through mRNA secondary structures.  

PubMed

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

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

2013-05-01

5

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.

1988-07-01

6

Dynamics of translation by single ribosomes through mRNA secondary structures  

PubMed Central

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

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

2013-01-01

7

Secondary structure of bacteriophage T4 gene 60 mRNA: Implications for translational bypassing  

PubMed Central

Translational bypassing is a unique phenomenon of bacteriophage T4 gene 60 mRNA wherein the bacterial ribosome produces a single polypeptide chain from a discontinuous open reading frame (ORF). Upon reaching the 50-nucleotide untranslated region, or coding gap, the ribosome either dissociates or bypasses the interruption to continue translating the remainder of the ORF, generating a subunit of a type II DNA topoisomerase. Mutational and computational analyses have suggested that a compact structure, including a stable hairpin, forms in the coding gap to induce bypassing, yet direct evidence is lacking. Here we have probed the secondary structure of gene 60 mRNA with both Tb3+ ions and the selective 2?-hydroxyl acylation analyzed by primer extension (SHAPE) reagent 1M7 under conditions where bypassing is observed. The resulting experimentally informed secondary structure models strongly support the presence of the predicted coding gap hairpin and highlight the benefits of using Tb3+ as a second, complementary probing reagent. Contrary to several previously proposed models, however, the rest of the coding gap is highly reactive with both probing reagents, suggesting that it forms only a short stem–loop. Mutational analyses coupled with functional assays reveal that two possible base-pairings of the coding gap with other regions of the mRNA are not required for bypassing. Such structural autonomy of the coding gap is consistent with its recently discovered role as a mobile genetic element inserted into gene 60 mRNA to inhibit cleavage by homing endonuclease MobA.

Todd, Gabrielle C.; Walter, Nils G.

2013-01-01

8

Influences of mRNA Secondary Structure on Initiation by Eukaryotic Ribosomes  

Microsoft Academic Search

Oligonucleotides designed to create hairpin structures were inserted upstream from the ATG initiator codon in several plasmids that encode preproinsulin, and the effects on translation were monitored in COS cells transfected by the vectors. Creation of a hairpin (Delta G= -30 kcal\\/mol) that directly involves the ATG triplet at the start of the preproinsulin coding sequence does not reduce the

Marilyn Kozak

1986-01-01

9

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

PubMed Central

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

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

2004-01-01

10

A Synonymous Single Nucleotide Polymorphism in ?F508 CFTR Alters the Secondary Structure of the mRNA and the Expression of the Mutant Protein*  

PubMed Central

Recent advances in our understanding of translational dynamics indicate that codon usage and mRNA secondary structure influence translation and protein folding. The most frequent cause of cystic fibrosis (CF) is the deletion of three nucleotides (CTT) from the cystic fibrosis transmembrane conductance regulator (CFTR) gene that includes the last cytosine (C) of isoleucine 507 (Ile507ATC) and the two thymidines (T) of phenylalanine 508 (Phe508TTT) codons. The consequences of the deletion are the loss of phenylalanine at the 508 position of the CFTR protein (?F508), a synonymous codon change for isoleucine 507 (Ile507ATT), and protein misfolding. Here we demonstrate that the ?F508 mutation alters the secondary structure of the CFTR mRNA. Molecular modeling predicts and RNase assays support the presence of two enlarged single stranded loops in the ?F508 CFTR mRNA in the vicinity of the mutation. The consequence of ?F508 CFTR mRNA “misfolding” is decreased translational rate. A synonymous single nucleotide variant of the ?F508 CFTR (Ile507ATC), that could exist naturally if Phe-508 was encoded by TTC, has wild type-like mRNA structure, and enhanced expression levels when compared with native ?F508 CFTR. Because CFTR folding is predominantly cotranslational, changes in translational dynamics may promote ?F508 CFTR misfolding. Therefore, we propose that mRNA “misfolding” contributes to ?F508 CFTR protein misfolding and consequently to the severity of the human ?F508 phenotype. Our studies suggest that in addition to modifier genes, SNPs may also contribute to the differences observed in the symptoms of various ?F508 homozygous CF patients.

Bartoszewski, Rafal A.; Jablonsky, Michael; Bartoszewska, Sylwia; Stevenson, Lauren; Dai, Qun; Kappes, John; Collawn, James F.; Bebok, Zsuzsa

2010-01-01

11

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

PubMed

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

2014-08-01

12

Availability of a second upstream AUG can completely overcome inhibition of protein synthesis initiation engendered by mRNA secondary structure encompassing the start codon.  

PubMed

Secondary structure analysis of the mRNA from a nonproductive construct carrying the nonstructural gene 3 (NS3) of Japanese Encephalitis Virus revealed the presence of a potential 28 nucleotide long stem and loop beginning with the guanine of the initiation codon AUG that had a calculated stabilization energy of -13 kcal/mol (delta Gfzero). Provision of an additional AUG along with three codons upstream resulted in complete relief of inhibition. N-terminal amino acid sequence of the recombinant protein was consistent with initiation of protein synthesis having occurred from the upstream AUG. Similar levels of NS3 specific RNA in E. coli cells carrying the expressing and nonexpressing constructs and restoration of recombinant protein expression following deletion of segments beginning with the stem and loop confirmed the role of this structure in blocking expression at the level of translation initiation. Our approach exploits the ability of a ribosome in motion to open up downstream secondary structural elements of considerable stability and represents a novel and widely applicable strategy to overcome a block in translation initiation caused by mRNA secondary structure around the translation start site. PMID:9322762

Satchidanandam, V; Shivashankar, Y

1997-09-01

13

Translation of chloroplast psbD mRNA in Chlamydomonas is controlled by a secondary RNA structure blocking the AUG start codon  

PubMed Central

Translation initiation represents a key step during regulation of gene expression in chloroplasts. Here, we report on the identification and characterization of three suppressor point mutations which overcome a translational defect caused by the deletion of a U-rich element in the 5?-untranslated region (5?-UTR) of the psbD mRNA in the green alga Chlamydomonas reinhardtii. All three suppressors affect a secondary RNA structure encompassing the psbD AUG initiation codon within a double-stranded region as judged by the analysis of site-directed chloroplast mutants as well as in vitro RNA mapping experiments using RNase H. In conclusion, the data suggest that these new element serves as a negative regulator which mediates a rapid shut-down of D2 synthesis.

Klinkert, Birgit; Elles, Ingolf; Nickelsen, Jorg

2006-01-01

14

Two Tunisian patients with Peters plus syndrome harbouring a novel splice site mutation in the B3GALTL gene that modulates the mRNA secondary structure.  

PubMed

Peters plus syndrome is an autosomal recessive rare disorder comprising ocular anterior segment dysgenesis, short stature, hand abnormalities, distinctive facial features, and often other major/minor additional defects. Peters plus syndrome is related to mutations in the B3GALTL gene with only seven recently reported mutations, leading to the inactivation of the B1, 3-glucosyltransferase. In this study, we screened the B3GALTL gene in two unrelated patients with typical Peters plus syndrome. A novel homozygous c.597-2A>G mutation was identified in both patients. Bioinformatic analyses showed that this mutation modulates the pre mRNA secondary structure of the gene, and decreases the score value related to the formation of splicing loops. Moreover, the c.597-2A>G mutation is located in a CpG Island of the B3GALTL gene, suggesting a potential epigenetic role of this position including gene's methylation and regulation. These data confirm an important role of the B3GALTL gene test that provides diagnosis confirmation and improves genetic counseling for the families. PMID:22759511

Siala, Olfa; Belguith, Neila; Kammoun, Hassen; Kammoun, Bourane; Hmida, Nedia; Chabchoub, Imen; Hchicha, Mongia; Fakhfakh, Faiza

2012-10-01

15

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

Microsoft Academic Search

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

Anna Nadal; Anna Coll; Nigel Cook; Maria Pla

2007-01-01

16

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

PubMed Central

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

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

2013-01-01

17

Inhibition of translation initiation on Escherichia coli gnd mRNA by formation of a long-range secondary structure involving the ribosome binding site and the internal complementary sequence.  

PubMed Central

Previous research has indicated that the growth rate-dependent regulation of Escherichia coli gnd expression involves the internal complementary sequence (ICS), a negative control site that lies within the 6-phosphogluconate dehydrogenase coding sequence. To determine whether the ICS acts as a transcriptional operator or attenuator, we measured beta-galactosidase-specific activities in strains carrying gnd-lac operon and protein fusions containing or lacking the ICS. Whereas the presence of the ICS repressed beta-galactosidase expression from a protein fusion by 5-fold during growth on acetate and by 2.5-fold during growth on glucose, it had no effect on beta-galactosidase expression from an operon fusion. In vitro ribosome binding experiments employing the primer extension inhibition (toeprint) assay demonstrated that the presence of the ICS in gnd mRNA reduces both the maximum extent and the rate of ternary complex formation. Moreover, the effects of deletions scanning the ICS on in vivo gene expression were highly correlated with the effects of the deletions on ribosome binding in vitro. In addition, the distal end of the ICS element was found to contribute more to ICS function than did the proximal portion, which contains the complement to the Shine-Dalgarno sequence. Finally, RNA structure mapping experiments indicated that the presence of the ICS in gnd mRNA reduces the access of the nucleotides of the ribosome binding site to the single-strand-specific chemical reagents dimethyl sulfate and kethoxal. Taken together, these data support the hypothesis that the role of the ICS in the growth rate-dependent regulation of gnd expression is to sequester the translation initiation region into a long-range mRNA secondary structure that blocks ribosome binding and thereby reduces the frequency of translation initiation.

Chang, J T; Green, C B; Wolf, R E

1995-01-01

18

Vienna RNA secondary structure server  

Microsoft Academic Search

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

Ivo L. Hofacker

2003-01-01

19

Combinatorics of RNA Secondary Structures  

Microsoft Academic Search

Secondary structures of polynucleotides can be viewed as a class of planar vertex-labeled graphs. We compute recursion formulae for enumerating a variety sub-classes of and classes of sub-graphs (structural elements) of secondary structure graphs. First order asymptotics are derived and their dependence on the composition of the underlying nucleic acid sequences is discussed.

Ivo L. Hofacker; Peter Schuster; Peter F. Stadler

1998-01-01

20

Extended secondary structures in proteins.  

PubMed

Super secondary structures of proteins have been systematically searched and classified, but not enough attention has been devoted to such large edifices beyond the basic identification of secondary structures. The objective of the present study is to show that the association of secondary structures that share some of their backbone residues is a commonplace in globular proteins, and that such deeper fusion of secondary structures, namely extended secondary structures (ESSs), helps stabilize the original secondary structures and the resulting tertiary structures. For statistical purposes, a set of 163 proteins from the protein databank was randomly selected and a few specific cases are structurally analyzed and characterized in more detail. The results point that about 30%of the residues from each protein, on average, participate in ESS. Alternatively, for the specific cases considered,our results were based on the secondary structures produced after extensive Molecular Dynamics simulation of a protein–aqueous solvent system. Based on the very small width of the time distribution of the root mean squared deviations, between the ESS taken along the simulation and the ESS from the mean structure of the protein, for each ESS, we conclude that the ESSs significantly increase the conformational stability by forming very stable aggregates.The ubiquity and specificity of the ESS suggest that the role they play in the structure of proteins, including the domains formation, deserves to be thoroughly investigated. PMID:24513313

Degrève, Léo; Fuzo, Carlos A; Caliri, Antonio

2014-02-01

21

A statistical sampling algorithm for RNA secondary structure prediction  

Microsoft Academic Search

An RNA molecule, particularly a long-chain mRNA, may exist as a population of structures. Further- more, multiple structures have been demonstrated to play important functional roles. Thus, a repre- sentation of the ensemble of probable structures is of interest. We present a statistical algorithm to sample rigorously and exactly from the Boltzmann ensemble of secondary structures. The forward step of

Ye Ding; Charles E. Lawrence

2003-01-01

22

Secondary structures of peptides  

Microsoft Academic Search

75.46 MHz 13C-NMR CP\\/MAS spectra of solid poly(1-alanines) with various degrees of polymerization were measured. The signals of all three carbons are split into two peaks. One peak presents the a-helix structure and one the pleated sheet form. Equimolar mixtures of helical poly(L-alanine) with poly(glycine) and poly(L-valine) were measured under various conditions. It was found that the peak areas are

Detlef Müller; Hans R. Kricheldorf

1981-01-01

23

Prediction of RNA Secondary Structure  

Microsoft Academic Search

Calculations of the free energy required to close single-strand loops by formation of a base pair in double-helical nucleic acids are reported. These results can be used to estimate the free energy of particular secondary structures for a given RNA molecule under conditions of high-salt concentration.

Charles Delisi; Donald M. Crothers

1971-01-01

24

Linear Trees and RNA Secondary Structure  

Microsoft Academic Search

The total number of RNA secondary structures of a given length with a fixed number of base pairs is computed, under the assumption that all base pairs can occur. This is done by establishing a one-to-one correspondence between secondary structures and trees. A duality operator on trees is presented, which explains a symmetry in the numbers counting secondary structures.

William R. Schmitt; Michael S. Waterman

1994-01-01

25

Structural and mechanistic diversity of secondary transporters.  

PubMed

Recent reports on the three-dimensional structure of secondary transporters have dramatically increased our knowledge of the translocation mechanism of ions and solutes. The structures of five transporters at atomic resolution have yielded four different folds and as many different translocation mechanisms. The structure of the glutamate transporter homologue GltPh confirmed the role of pore-loop structures as essential parts of the translocation mechanism in one family of secondary transporters. Biochemical evidence for pore-loop structures in several other families suggest that they might be common in secondary transporters, adding to the structural and mechanistic diversity of secondary transporters. PMID:15802247

Sobczak, Iwona; Lolkema, Juke S

2005-04-01

26

K-Partite RNA Secondary Structures  

NASA Astrophysics Data System (ADS)

RNA secondary structure prediction is a fundamental problem in structural bioinformatics. The prediction problem is difficult because RNA secondary structures may contain pseudoknots formed by crossing base pairs. We introduce k-partite secondary structures as a simple classification of RNA secondary structures with pseudoknots. An RNA secondary structure is k-partite if it is the union of k pseudoknot-free sub-structures. Most known RNA secondary structures are either bipartite or tripartite. We show that there exists a constant number k such that any secondary structure can be modified into a k-partite secondary structure with approximately the same free energy. This offers a partial explanation of the prevalence of k-partite secondary structures with small k. We give a complete characterization of the computational complexities of recognizing k-partite secondary structures for all k ? 2, and show that this recognition problem is essentially the same as the k-colorability problem on circle graphs. We present two simple heuristics, iterated peeling and first-fit packing, for finding k-partite RNA secondary structures. For maximizing the number of base pair stackings, our iterated peeling heuristic achieves a constant approximation ratio of at most k for 2 ? k ? 5, and at most frac6{1-(1-6/k)^k} le frac6{1-e^{-6}} < 6.01491 for k ? 6. Experiment on sequences from PseudoBase shows that our first-fit packing heuristic outperforms the leading method HotKnots in predicting RNA secondary structures with pseudoknots. Source code, data set, and experimental results are available at http://www.cs.usu.edu/ mjiang/rna/kpartite/.

Jiang, Minghui; Tejada, Pedro J.; Lasisi, Ramoni O.; Cheng, Shanhong; Fechser, D. Scott

27

K-partite RNA secondary structures.  

PubMed

RNA secondary structure prediction is a fundamental problem in structural bioinformatics. The prediction problem is difficult because RNA secondary structures may contain pseudoknots formed by crossing base pairs. We introduce k-partite secondary structures as a simple classification of RNA secondary structures with pseudoknots. An RNA secondary structure is k-partite if it is the union of k pseudoknot-free sub-structures. Most known RNA secondary structures are either bipartite or tripartite. We show that there exists a constant number k such that any secondary structure can be modified into a k-partite secondary structure with approximately the same free energy. This offers a partial explanation of the prevalence of k-partite secondary structures with small k. We give a complete characterization of the computational complexities of recognizing k-partite secondary structures for all k > or = 2, and show that this recognition problem is essentially the same as the k-colorability problem on circle graphs. We present two simple heuristics, iterated peeling and first-fit packing, for finding k-partite RNA secondary structures. For maximizing the number of base pair stackings, our iterated peeling heuristic achieves a constant approximation ratio of at most k for 2 < or = k < or = 5, and at most [Formula: see text] for k > or = 6. Experiment on sequences from PseudoBase shows that our first-fit packing heuristic outperforms the leading method HotKnots in predicting RNA secondary structures with pseudoknots. Supplementary Material can be found at www.libertonline.com. PMID:20632871

Jiang, Minghui; Tejada, Pedro J; Lasisi, Ramoni O; Cheng, Shanhong; Fechser, D Scott

2010-07-01

28

mRNA pseudoknot structures can act as ribosomal roadblocks.  

PubMed

Several viruses utilize programmed ribosomal frameshifting mediated by mRNA pseudoknots in combination with a slippery sequence to produce a well defined stochiometric ratio of the upstream encoded to the downstream-encoded protein. A correlation between the mechanical strength of mRNA pseudoknots and frameshifting efficiency has previously been found; however, the physical mechanism behind frameshifting still remains to be fully understood. In this study, we utilized synthetic sequences predicted to form mRNA pseudoknot-like structures. Surprisingly, the structures predicted to be strongest lead only to limited frameshifting. Two-dimensional gel electrophoresis of pulse labelled proteins revealed that a significant fraction of the ribosomes were frameshifted but unable to pass the pseudoknot-like structures. Hence, pseudoknots can act as ribosomal roadblocks, prohibiting a significant fraction of the frameshifted ribosomes from reaching the downstream stop codon. The stronger the pseudoknot the larger the frameshifting efficiency and the larger its roadblocking effect. The maximal amount of full-length frameshifted product is produced from a structure where those two effects are balanced. Taking ribosomal roadblocking into account is a prerequisite for formulating correct frameshifting hypotheses. PMID:21908395

Tholstrup, Jesper; Oddershede, Lene B; Sørensen, Michael A

2012-01-01

29

Computational prediction of RNA secondary structure.  

PubMed

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

Moss, Walter N

2013-01-01

30

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

SciTech Connect

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

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

2011-09-27

31

[Optimizing the expression of Mx gene in Escherichia coli based on rare codon and mRNA structure].  

PubMed

Rare codon and mRNA secondary structure of translation initiation region were analyzed. Four bioengineered bacterium BL21(DE3)/pET-Mx, Rosseta (DE3)/pET-Mx, BL21(DE3)/pGEX-Mx, and Rosseta (DE3)/pGEX-Mx were obtained. Through optimizing the rare codon and mRNA secondary structure of translation initiation region, Mx protein was expressed in Rosseta (DE3)/pET-Mx, and Rosseta (DE3)/pGEX-Mx. The specified product of 75 kDa was detected by means of Western blotting analysis. The result showed that Rosetta (DE3) strain expressing some rare codon used in our experiment can obtain Mx protein expression, and the lower energy of mRNA structure can improve the expression level of Mx protein. This is the first report on the expression of the full open reading frame of Mx gene. PMID:19138905

Yin, Chun-Guang; DU, Li-Xin; Zhao, Gui-Ping; Li, Hong-Bin

2009-01-01

32

A statistical sampling algorithm for RNA secondary structure prediction  

PubMed Central

An RNA molecule, particularly a long-chain mRNA, may exist as a population of structures. Further more, multiple structures have been demonstrated to play important functional roles. Thus, a representation of the ensemble of probable structures is of interest. We present a statistical algorithm to sample rigorously and exactly from the Boltzmann ensemble of secondary structures. The forward step of the algorithm computes the equilibrium partition functions of RNA secondary structures with recent thermodynamic parameters. Using conditional probabilities computed with the partition functions in a recursive sampling process, the backward step of the algorithm quickly generates a statistically representative sample of structures. With cubic run time for the forward step, quadratic run time in the worst case for the sampling step, and quadratic storage, the algorithm is efficient for broad applicability. We demonstrate that, by classifying sampled structures, the algorithm enables a statistical delineation and representation of the Boltzmann ensemble. Applications of the algorithm show that alternative biological structures are revealed through sampling. Statistical sampling provides a means to estimate the probability of any structural motif, with or without constraints. For example, the algorithm enables probability profiling of single-stranded regions in RNA secondary structure. Probability profiling for specific loop types is also illustrated. By overlaying probability profiles, a mutual accessibility plot can be displayed for predicting RNA:RNA interactions. Boltzmann probability-weighted density of states and free energy distributions of sampled structures can be readily computed. We show that a sample of moderate size from the ensemble of an enormous number of possible structures is sufficient to guarantee statistical reproducibility in the estimates of typical sampling statistics. Our applications suggest that the sampling algorithm may be well suited to prediction of mRNA structure and target accessibility. The algorithm is applicable to the rational design of small interfering RNAs (siRNAs), antisense oligonucleotides, and trans-cleaving ribozymes in gene knock-down studies.

Ding, Ye; Lawrence, Charles E.

2003-01-01

33

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.

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

2014-01-01

34

SHAPE-Directed RNA Secondary Structure Prediction  

PubMed Central

The diverse functional roles of RNA are determined by its underlying structure. Accurate and comprehensive knowledge of RNA structure would inform a broader understanding of RNA biology and facilitate exploiting RNA as a biotechnological tool and therapeutic target. Determining the pattern of base pairing, or secondary structure, of RNA is a first step in these endeavors. Advances in experimental, computational, and comparative analysis approaches for analyzing secondary structure have yielded accurate structures for many small RNAs, but only a few large (>500 nts) RNAs. In addition, most current methods for determining a secondary structure require considerable effort, analytical expertise, and technical ingenuity. In this review, we outline an efficient strategy for developing accurate secondary structure models for RNAs of arbitrary length. This approach melds structural information obtained using SHAPE chemistry with structure prediction using nearest-neighbor rules and the dynamic programming algorithm implemented in the RNAstructure program. Prediction accuracies reach ?95% for RNAs on the kilobase scale. This approach facilitates both development of new models and refinement of existing RNA structure models, which we illustrate using the Gag-Pol frameshift element in an HIV-1 M-group genome. Most promisingly, integrated experimental and computational refinement brings closer the ultimate goal of efficiently and accurately establishing the secondary structure for any RNA sequence.

Low, Justin T.; Weeks, Kevin M.

2010-01-01

35

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

PubMed

RNA has 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 computational and experimental 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 vivo. 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 sulphate (DMS), which reacts with unpaired adenine and cytosine residues, followed by deep sequencing to monitor modifications. Our data from yeast and mammalian cells are in excellent agreement with known messenger RNA structures and with the high-resolution crystal structure of the Saccharomyces cerevisiae ribosome. 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 shows 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 whereby the structure formed is the most thermodynamically favourable, thermodynamics have an incomplete role in determining mRNA structure in vivo. PMID:24336214

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

2014-01-30

36

Systematic Discovery of Structural Elements Governing Mammalian mRNA Stability  

PubMed Central

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

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

2012-01-01

37

Secondary structure-based assignment of the protein structural classes  

Microsoft Academic Search

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

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

2008-01-01

38

Data Mining for Protein Secondary Structure Prediction  

Microsoft Academic Search

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

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

39

RNA Secondary Structure Analysis Using RNAstructure.  

PubMed

RNAstructure is a user-friendly program for the prediction and analysis of RNA secondary structure. It is available as a Web server, as a program with a graphical user interface, or as a set of command-line tools. The programs are available for Microsoft Windows, Macintosh OS X, or Linux. This unit provides protocols for RNA secondary structure prediction (using the Web server or the graphical user interface) and prediction of high-affinity oligonucleotide biding sites to a structured RNA target (using the graphical user interface). Curr. Protoc. Bioinform. 46:12.6.1-12.6.25. © 2014 by John Wiley & Sons, Inc. PMID:24939127

Mathews, David H

2014-01-01

40

RNA Secondary Structure Analysis Using RNAstructure  

PubMed Central

RNAstructure is a user-friendly program for the prediction and analysis of RNA secondary structure. It is available as a web server, as a program with a graphical user interface, or as a set of command line tools. The programs are available for Microsoft Windows, Macintosh OS X, or Linux. This unit provides protocols for RNA secondary structure prediction (using the web server or the graphical user interface) and prediction of high affinity oligonucleotide biding sites to a structured RNA target (using the graphical user interface).

Mathews, David H.

2014-01-01

41

A conserved secondary structure for telomerase RNA.  

PubMed

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

Romero, D P; Blackburn, E H

1991-10-18

42

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

PubMed Central

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

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

1989-01-01

43

Protein secondary structure prediction using local alignments.  

PubMed

The accuracy of secondary structure prediction methods has been improved significantly by the use of aligned protein sequences. The PHD method and the NNSSP method reach 71 to 72% of sustained overall three-state accuracy when multiple sequence alignments are with neural networks and nearest-neighbor algorithms, respectively. We introduce a variant of the nearest-neighbor approach that can achieve similar accuracy using a single sequence as the query input. We compute the 50 best non-intersecting local alignments of the query sequence with each sequence from a set of proteins with known 3D structures. Each position of the query sequence is aligned with the database amino acids in alpha-helical, beta-strand or coil states. The prediction type of secondary structure is selected as the type of aligned position with the maximal total score. On the dataset of 124 non-membrane non-homologous proteins, used earlier as a benchmark for secondary structure predictions, our method reaches an overall three-state accuracy of 71.2%. The performance accuracy is verified by an additional test on 461 non-homologous proteins giving an accuracy of 71.0%. The main strength of the method is the high level of prediction accuracy for proteins without any known homolog. Using multiple sequence alignments as input the method has a prediction accuracy of 73.5%. Prediction of secondary structure by the SSPAL method is available via Baylor College of Medicine World Wide Web server. PMID:9149139

Salamov, A A; Solovyev, V V

1997-04-25

44

Local Similarity in RNA Secondary Structures  

Microsoft Academic Search

We present a systematic treatment of alignment distance and local similarity algorithms on trees and forests. We build upon the tree alignment algorithm for ordered trees given by Jiang et. al (1995) and extend it to calculate local forest alignments, which is essential for finding local similar regions in RNA secondary structures. The time complexity of our algorithm is O(jF1

Matthias Höchsmann; Thomas Töller; Robert Giegerich; Stefan Kurtz

2003-01-01

45

RNA secondary structure: a complete mathematical analysis  

Microsoft Academic Search

Using a rigorous mathematical analysis, the prediction of RNA secondary structure as a function of free energy is obtained. The iterative method effectively allows a search over the entire configuration space of the RNA molecule not possible by earlier methods. The approach also allows for the direct inclusion of the nearest neighbor or stacking energies.

M. S. Waterman; T. F. Smith

1978-01-01

46

RNA Folding Causes Secondary Structure Rearrangement  

Microsoft Academic Search

The secondary structure of the P5abc subdomain (a 56-nt RNA) of the Tetrahymena thermophila group I intron ribozyme has been determined by NMR. Its base pairing in aqueous solution in the absence of magnesium ions is significantly different from the RNA in a crystal but is consistent with thermodynamic predictions. On addition of magnesium ions, the RNA folds into a

Ming Wu; Ignacio Tinoco Jr.

1998-01-01

47

Accurate Prediction of Protein Secondary Structural Content  

Microsoft Academic Search

An improved multiple linear regression (MLR) method is proposed to predict a protein's secondary structural content based on its primary sequence. The amino acid composition, the autocorrelation function, and the interaction function of side-chain mass derived from the primary sequence are taken into account. The average absolute errors of prediction over 704 unrelated proteins with the jackknife test are 0.088,

Zong Lin; Xian-Ming Pan

2001-01-01

48

Secondary structure formation in peptide amphiphile micelles  

NASA Astrophysics Data System (ADS)

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

Tirrell, Matthew

2012-02-01

49

Synthetic mimetics of protein secondary structure domains  

PubMed Central

Proteins modulate the majority of all biological functions and are primarily composed of highly organized secondary structural elements such as helices, turns and sheets. Many of these functions are affected by a small number of key protein–protein contacts, often involving one or more of these well-defined structural elements. Given the ubiquitous nature of these protein recognition domains, their mimicry by peptidic and non-peptidic scaffolds has become a major focus of contemporary research. This review examines several key advances in secondary structure mimicry over the past several years, particularly focusing upon scaffolds that show not only promising projection of functional groups, but also a proven effect in biological systems.

Ross, Nathan T.; Katt, William P.; Hamilton, Andrew D.

2010-01-01

50

Neural networks for secondary structure and structural class predictions  

Microsoft Academic Search

A pair of neural network-based algorithms is presented for predicting the tertiary structural class and the second- ary structure of proteins. Each algorithm realizes improvements in accuracy based on information provided by the other. Structural class prediction of proteins nonhomologous to any in the training set is improved signifi- cantly, from 62.3% to 73.9%, and secondary structure prediction accuracy improves

JOHN-MARC CHANDONIA; MARTIN KARPLUS

1995-01-01

51

Levels of BMP-6 mRNA in goat ovarian follicles and in vitro effects of BMP-6 on secondary follicle development.  

PubMed

Expression of BMP-6 mRNA was quantified by real-time polymerase chain reaction (PCR) and the BMP-6 protein was demonstrated by immunohistochemistry in the primordial, primary, secondary, small and large antral follicles of goat. Furthermore, the influence of BMP-6 on increase in diameter, antrum formation and expression of BMP-6 and FSH-R in in vitro cultured secondary follicles was studied. Therefore, goat primordial, primary and secondary follicles, as well as small and large antral follicles were obtained and the mRNA levels of BMP-6 were quantified by PCR in real time. Expression of BMP-6 protein in goat follicles was demonstrated by immunohistochemistry. The influence of BMP-6 in the presence or absence of follicle-stimulating hormone (FSH) on both the development of secondary follicles and the expression of mRNA for BMP-6 and FSH-R was evaluated after 6 days of culture. Furthermore, the follicular diameter and the formation of the antrum were evaluated before and after 6 days of culture and compared by Kruskal-Wallis and chi-squared tests (P < 0.05), respectively. The results show that the level of mRNA for BMP-6 in primary and secondary follicles was significantly higher than in the primordial follicles (P < 0.05). Similar levels of BMP-6 mRNA were observed in cumulus-oocyte complexes and mural granulosa/theca cells from small and large antral follicles, respectively. BMP-6 protein was expressed in oocytes of all categories of follicles and in granulosa cells from secondary follicles onwards. Addition of BMP-6 to the culture medium increased the diameter of secondary follicles mainly by antrum formation after 6 days' culture, in the presence or absence of FSH (P < 0.05). Furthermore, addition of FSH resulted in increased levels of BMP-6 mRNA in these follicles (P < 0.05). Simultaneous administration of FSH and BMP-6 enhanced the levels of FSH receptor (FSH-R) mRNA (P < 0.05). It is concluded that BMP-6 mRNA is increased during transition from primordial to primary/secondary follicles in the goat ovaries and that BMP-6 enhances the growth of cultured secondary follicles. PMID:22008252

Frota, Isana M A; Leitão, Cintia C F; Costa, José J N; van den Hurk, Robert; Saraiva, Márcia V A; Figueiredo, José R; Silva, José R V

2013-08-01

52

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

PubMed Central

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

Meyer, Irmtraud M.; Miklos, Istvan

2005-01-01

53

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

PubMed Central

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

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

2008-01-01

54

RNA-SSPT: RNA Secondary Structure Prediction Tools.  

PubMed

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

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

2013-01-01

55

Protein Secondary Structure Prediction with a Neural Network  

Microsoft Academic Search

A method is presented for protein secondary structure prediction based on a neural network. A training phase was used to teach the network to recognize the relation between secondary structure and amino acid sequences on a sample set of 48 proteins of known structure. On a separate test set of 14 proteins of known structure, the method achieved a maximum

L. Howard Holley; Martin Karplus

1989-01-01

56

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

PubMed

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

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

2013-08-01

57

Regulation of translation via mRNA structure in prokaryotes and eukaryotes  

Microsoft Academic Search

The mechanism of initiation of translation differs between prokaryotes and eukaryotes, and the strategies used for regulation differ accordingly. Translation in prokaryotes is usually regulated by blocking access to the initiation site. This is accomplished via base-paired structures (within the mRNA itself, or between the mRNA and a small trans-acting RNA) or via mRNA-binding proteins. Classic examples of each mechanism

Marilyn Kozak

2005-01-01

58

Protein secondary structure. Studies on the limits of prediction accuracy.  

PubMed

A secondary structure prediction technique is proposed which includes nucleation site determination through multiplication of conformational preference parameters as well as weighting factors to represent structurally stabilizing short range interactions. The prediction accuracy of the method is calculated using data bases categorized according to the four protein structural classes and with differing assignments of secondary structural regions. The results indicate that nearest neighbor prediction techniques (a) are insensitive to various assignment criteria for the secondary structural spans, (b) have nearly achieved their upper limit of prediction accuracy, and (c) can be somewhat improved through the use of stereochemical weighting factors and conformational parameters derived from the four structural groups. PMID:7118409

Palau, J; Argos, P; Puigdomenech, P

1982-04-01

59

A novel approach to represent and compare RNA secondary structures.  

PubMed

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

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

2014-06-01

60

A novel approach to represent and compare RNA secondary structures  

PubMed Central

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

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

2014-01-01

61

Insights into the structure, mechanism, and regulation of scavenger mRNA decapping activity.  

PubMed

Complete removal of residual N-7 guanine cap from degraded messenger RNA is necessary to prevent accumulation of intermediates that might interfere with RNA processing, export, and translation. The human scavenger decapping enzyme, DcpS, catalyzes residual cap hydrolysis following mRNA degradation, releasing N-7 methyl guanosine monophosphate and 5'-diphosphate terminated cap or mRNA products. DcpS structures bound to m(7)GpppG or m(7)GpppA reveal an asymmetric DcpS dimer that simultaneously creates an open nonproductive DcpS-cap complex and a closed productive DcpS-cap complex that alternate via 30 A domain movements. Structural and biochemical analysis suggests an autoregulatory mechanism whereby premature decapping mRNA is prevented by blocking the conformational changes that are required to form a closed productive active site capable of cap hydrolysis. PMID:15068804

Gu, Meigang; Fabrega, Carme; Liu, Shin-Wu; Liu, Hudan; Kiledjian, Megerditch; Lima, Christopher D

2004-04-01

62

Characterising RNA secondary structure space using information entropy.  

PubMed

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

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

2013-01-01

63

HFold: RNA Pseudoknotted Secondary Structure Prediction Using Hierarchical Folding  

Microsoft Academic Search

Improving the accuracy and efficiency of computational RNA secondary structure prediction is an important challenge, particularly\\u000a for pseudoknotted secondary structures. We propose a new approach for prediction of pseudoknotted structures, motivated by\\u000a the hypothesis that RNA structures fold hierarchically, with pseudoknot free pairs forming initially, and pseudoknots forming\\u000a later so as to minimize energy relative to the initial pseudoknot free

Hosna Jabbari; Anne Condon; Ana Pop; Cristina Pop; Yinglei Zhao

2007-01-01

64

hnRNP A1 and secondary structure coordinate alternative splicing of Mag.  

PubMed

Myelin-associated glycoprotein (MAG) is a major component of myelin in the vertebrate central nervous system. MAG is present in the periaxonal region of the myelin structure, where it interacts with neuronal proteins to inhibit axon outgrowth and protect neurons from degeneration. Two alternatively spliced isoforms of Mag mRNA have been identified. The mRNA encoding the shorter isoform, known as S-MAG, contains a termination codon in exon 12, while the mRNA encoding the longer isoform, known as L-MAG, skips exon 12 and produces a protein with a longer C-terminal region. L-MAG is required in the central nervous system. How inclusion of Mag exon 12 is regulated is not clear. In a previous study, we showed that heteronuclear ribonucleoprotein A1 (hnRNP A1) contributes to Mag exon 12 skipping. Here, we show that hnRNP A1 interacts with an element that overlaps the 5' splice site of Mag exon 12. The element has a reduced ability to interact with the U1 snRNP compared with a mutant that improves the splice site consensus. An evolutionarily conserved secondary structure is present surrounding the element. The structure modulates interaction with both hnRNP A1 and U1. Analysis of splice isoforms produced from a series of reporter constructs demonstrates that the hnRNP A1-binding site and the secondary structure both contribute to exclusion of Mag exon 12. PMID:23704325

Zearfoss, N Ruth; Johnson, Emily S; Ryder, Sean P

2013-07-01

65

ncRNA consensus secondary structure derivation using grammar strings.  

PubMed

Many noncoding RNAs (ncRNAs) function through both their sequences and secondary structures. Thus, secondary structure derivation is an important issue in today's RNA research. The state-of-the-art structure annotation tools are based on comparative analysis, which derives consensus structure of homologous ncRNAs. Despite promising results from existing ncRNA aligning and consensus structure derivation tools, there is a need for more efficient and accurate ncRNA secondary structure modeling and alignment methods. In this work, we introduce a consensus structure derivation approach based on grammar string, a novel ncRNA secondary structure representation that encodes an ncRNA's sequence and secondary structure in the parameter space of a context-free grammar (CFG) and a full RNA grammar including pseudoknots. Being a string defined on a special alphabet constructed from a grammar, grammar string converts ncRNA alignment into sequence alignment. We derive consensus secondary structures from hundreds of ncRNA families from BraliBase 2.1 and 25 families containing pseudoknots using grammar string alignment. Our experiments have shown that grammar string-based structure derivation competes favorably in consensus structure quality with Murlet and RNASampler. Source code and experimental data are available at http://www.cse.msu.edu/~yannisun/grammar-string. PMID:21523935

Achawanantakun, Rujira; Sun, Yanni; Takyar, Seyedeh Shohreh

2011-04-01

66

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

PubMed Central

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

Ellington, Roni; Wachira, James

2010-01-01

67

RNAMotif, an RNA secondary structure definition and search algorithm  

Microsoft Academic Search

RNA molecules fold into characteristic secondary and tertiary structures that account for their diverse functional activities. Many of these RNA structures are assembled from a collection of RNA structural motifs. These basic building blocks are used repeat- edly, and in various combinations, to form different RNA types and define their unique structural and functional properties. Identification of recurring RNA structural

Thomas J. Macke; David J. Ecker; Robin R. Gutell; Daniel Gautheret; David A. Case; Rangarajan Sampath

2001-01-01

68

Statistical analysis of SHAPE-directed RNA secondary structure modeling  

PubMed Central

The ability to predict RNA secondary structure is fundamental for understanding and manipulating RNA function. The structural information obtained from selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) experiments greatly improves the accuracy of RNA secondary structure prediction. Recently, Das and colleagues [Kladwang et al., Biochemistry 50:8049 (2011)] proposed a “bootstrapping” approach to estimate the variance and helix-by-helix confidence levels of predicted secondary structures based on resampling (randomizing and summing) the measured SHAPE data. We show that the specific resampling approach described by Kladwang et al. introduces systematic errors and underestimates confidence in secondary structure prediction using SHAPE data. Instead, a leave-data-out jackknife approach better estimates the influence of a given experimental dataset on SHAPE-directed secondary structure modeling. Even when 35% of the data were left out in the jackknife approach, the confidence levels of SHAPE-directed secondary structure prediction were significantly higher than those calculated by Das and colleagues using bootstrapping. Helix confidence levels were thus significantly underestimated in the recent study, and resampling approach implemented by Kladwang et al. is not an appropriate metric for assigning confidences in SHAPE-directed secondary structure modeling.

Ramachandran, Srinivas; Ding, Feng; Weeks, Kevin M.; Dokholyan, Nikolay V.

2013-01-01

69

Regulatory Impact of RNA Secondary Structure across the Arabidopsis Transcriptome[W][OA  

PubMed Central

The secondary structure of an RNA molecule plays an integral role in its maturation, regulation, and function. However, the global influence of this feature on plant gene expression is still largely unclear. Here, we use a high-throughput, sequencing-based, structure-mapping approach in conjunction with transcriptome-wide sequencing of rRNA-depleted (RNA sequencing), small RNA, and ribosome-bound RNA populations to investigate the impact of RNA secondary structure on gene expression regulation in Arabidopsis thaliana. From this analysis, we find that highly unpaired and paired RNAs are strongly correlated with euchromatic and heterochromatic epigenetic histone modifications, respectively, providing evidence that secondary structure is necessary for these RNA-mediated posttranscriptional regulatory pathways. Additionally, we uncover key structural patterns across protein-coding transcripts that indicate RNA folding demarcates regions of protein translation and likely affects microRNA-mediated regulation of mRNAs in this model plant. We further reveal that RNA folding is significantly anticorrelated with overall transcript abundance, which is often due to the increased propensity of highly structured mRNAs to be degraded and/or processed into small RNAs. Finally, we find that secondary structure affects mRNA translation, suggesting that this feature regulates plant gene expression at multiple levels. These findings provide a global assessment of RNA folding and its significant regulatory effects in a plant transcriptome.

Li, Fan; Zheng, Qi; Vandivier, Lee E.; Willmann, Matthew R.; Chen, Ying; Gregory, Brian D.

2012-01-01

70

Metabolism of DNA secondary structures at the eukaryotic replication fork.  

PubMed

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

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

2014-07-01

71

Amino acid propensities for secondary structures are influenced by the protein structural class  

Microsoft Academic Search

Amino acid propensities for secondary structures were used since the 1970s, when Chou and Fasman evaluated them within datasets of few tens of proteins and developed a method to predict secondary structure of proteins, still in use despite prediction methods having evolved to very different approaches and higher reliability. Propensity for secondary structures represents an intrinsic property of amino acid,

Susan Costantini; Giovanni Colonna; Angelo M. Facchiano

2006-01-01

72

Genetic Manipulation of Arterivirus Alternative mRNA Leader-Body Junction Sites Reveals Tight Regulation of Structural Protein Expression  

PubMed Central

To express its structural proteins, the arterivirus Equine arteritis virus (EAV) produces a nested set of six subgenomic (sg) RNA species. These RNA molecules are generated by a mechanism of discontinuous transcription, during which a common leader sequence, representing the 5? end of the genomic RNA, is attached to the bodies of the sg RNAs. The connection between the leader and body parts of an mRNA is formed by a short, conserved sequence element termed the transcription-regulating sequence (TRS), which is present at the 3? end of the leader as well as upstream of each of the structural protein genes. With the exception of RNA3, only one body TRS was previously assumed to be used to join the leader and body of each EAV sg RNA. Here we show that for the synthesis of two other sg RNAs, RNA4 and RNA5, alternative leader-body junction sites that differ substantially in transcriptional activity are used. By site-directed mutagenesis of an EAV infectious cDNA clone, the alternative TRSs used to generate RNA3, -4, and -5 were inactivated, which strongly influenced the corresponding RNA levels and the production of infectious progeny virus. The relative amounts of RNA produced from alternative TRSs differed significantly and corresponded to the relative infectivities of the virus mutants. This strongly suggested that the structural proteins that are expressed from these RNAs are limiting factors during the viral life cycle and that the discontinuous step in sg RNA synthesis is crucial for the regulation of their expression. On the basis of a theoretical analysis of the predicted RNA structure of the 3? end of the EAV genome, we propose that the local secondary RNA structure of the body TRS regions is an important factor in the regulation of the discontinuous step in EAV sg mRNA synthesis.

Pasternak, Alexander O.; Gultyaev, Alexander P.; Spaan, Willy J. M.; Snijder, Eric J.

2000-01-01

73

Light can transform the secondary structure of silk protein  

Microsoft Academic Search

.   Fibroin is the main component of silk and is expected to be used as a novel functional material in medicine and bioelectronics.\\u000a The main secondary structures of this protein are of the random-coil and the ?-sheet types. In this study, we carried out\\u000a laser-induced transformation of the secondary structure, from the random-coil type to the ?-sheettype, in solid fibroin

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

2001-01-01

74

Dynamic programming algorithms for RNA secondary structure prediction with pseudoknots  

Microsoft Academic Search

This paper shows simple dynamic programming algorithms for RNA secondary structure pre- diction with pseudoknots. For a basic version of the problem (i.e., maximizing the number of base pairs), this paper presents an O(n4) time exact algorithm and an O(n4 ) time approxima- tion algorithm. The latter one outputs, for most RNA sequences, a secondary structure in which the number

Tatsuya Akutsu

2000-01-01

75

A method for rapid similarity analysis of RNA secondary structures  

PubMed Central

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

Liu, Na; Wang, Tianming

2006-01-01

76

Crystal structure of Dcp1p and its functional implications in mRNA decapping  

Microsoft Academic Search

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

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

2004-01-01

77

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

NASA Astrophysics Data System (ADS)

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

Lin, Yi-Hsuan; Bundschuh, Ralf

2013-03-01

78

Computing the Partition Function for Kinetically Trapped RNA Secondary Structures  

PubMed Central

An RNA secondary structure is locally optimal if there is no lower energy structure that can be obtained by the addition or removal of a single base pair, where energy is defined according to the widely accepted Turner nearest neighbor model. Locally optimal structures form kinetic traps, since any evolution away from a locally optimal structure must involve energetically unfavorable folding steps. Here, we present a novel, efficient algorithm to compute the partition function over all locally optimal secondary structures of a given RNA sequence. Our software, RNAlocopt runs in time and space. Additionally, RNAlocopt samples a user-specified number of structures from the Boltzmann subensemble of all locally optimal structures. We apply RNAlocopt to show that (1) the number of locally optimal structures is far fewer than the total number of structures – indeed, the number of locally optimal structures approximately equal to the square root of the number of all structures, (2) the structural diversity of this subensemble may be either similar to or quite different from the structural diversity of the entire Boltzmann ensemble, a situation that depends on the type of input RNA, (3) the (modified) maximum expected accuracy structure, computed by taking into account base pairing frequencies of locally optimal structures, is a more accurate prediction of the native structure than other current thermodynamics-based methods. The software RNAlocopt constitutes a technical breakthrough in our study of the folding landscape for RNA secondary structures. For the first time, locally optimal structures (kinetic traps in the Turner energy model) can be rapidly generated for long RNA sequences, previously impossible with methods that involved exhaustive enumeration. Use of locally optimal structure leads to state-of-the-art secondary structure prediction, as benchmarked against methods involving the computation of minimum free energy and of maximum expected accuracy. Web server and source code available at http://bioinformatics.bc.edu/clotelab/RNAlocopt/.

Lorenz, William A.; Clote, Peter

2011-01-01

79

A new algorithm for RNA secondary structure design.  

PubMed

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

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

2004-02-20

80

Protein secondary structure prediction with a neural network  

SciTech Connect

A method is presented for protein secondary structure prediction based on a neural network. A training phase was used to teach the network to recognize the relation between secondary structure and amino acid sequences on a sample set of 48 proteins of known structure. On a separate test set of 14 proteins of known structure, the method achieved a maximum overall predictive accuracy of 63% for three states: helix, sheet, and coil. A numerical measure of helix and sheet tendency for each residue was obtained from the calculations. When predictions were filtered to include only the strongest 31% of predictions, the predictive accuracy rose to 79%.

Holley, L.H.; Karplus, M. (Harvard Univ., Cambridge, MA (United States))

1989-01-01

81

Characterization of the 5'-terminal capped structures of late simian virus 40-specific mRNA.  

PubMed

32P-labeled, late simian virus 40-specific RNA was isoalted from infected CV1 cells and completely degraded with RNase T2 and bacterial alkaline phosphatase. The RNase-resistant material was fractionated two dimensionally and further characterized with Penicillium nuclease and nucleotide pyrophosphatase. Two major 5' termini were identified in late simian virus 40 RNA, namely, 7-methyl Gppp 2',6-dimethyl ApUp and 7-methyl Gppp 2',6-dimethyl Ap 2'-methyl, UpUp. Both 5' termini are present in unfractionated viral RNA as well as in the separated 16S and 19S species. As both caps differ only in secondary modification, it is possible that they are derived from the same site on the DNA. The relatively higher cap II content of the 16S mRNA may be related to its slower rate of turnover. PMID:205672

Haegeman, G; Fiers, W

1978-03-01

82

Characterization of the 5'-terminal capped structures of late simian virus 40-specific mRNA.  

PubMed Central

32P-labeled, late simian virus 40-specific RNA was isoalted from infected CV1 cells and completely degraded with RNase T2 and bacterial alkaline phosphatase. The RNase-resistant material was fractionated two dimensionally and further characterized with Penicillium nuclease and nucleotide pyrophosphatase. Two major 5' termini were identified in late simian virus 40 RNA, namely, 7-methyl Gppp 2',6-dimethyl ApUp and 7-methyl Gppp 2',6-dimethyl Ap 2'-methyl, UpUp. Both 5' termini are present in unfractionated viral RNA as well as in the separated 16S and 19S species. As both caps differ only in secondary modification, it is possible that they are derived from the same site on the DNA. The relatively higher cap II content of the 16S mRNA may be related to its slower rate of turnover. Images

Haegeman, G; Fiers, W

1978-01-01

83

RNAstructure: software for RNA secondary structure prediction and analysis  

PubMed Central

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

2010-01-01

84

Structure and function of the selenium translation element in the 3'-untranslated region of human cellular glutathione peroxidase mRNA.  

PubMed Central

In eukaryotes, incorporation of selenocysteine into the polypeptide chain at a UGA codon requires a unique sequence motif, or "selenium translation element" (STE), located in the 3'-untranslated region of the mRNA. The present study examines structure-function relationships of conserved sequence elements and of the putative stem-loop secondary structure in the STE of human GPX1 mRNA, which encodes the important antioxidant enzyme cellular glutathione peroxidase (EC 1.11.1.9). Deletion of the basal stem, upper stem, or apical loop of the stem-loop structure eliminated the ability of the STE to direct selenocysteine incorporation at the UGA codon of an epitope-tagged GPX1 reporter construct transfected into COS1 cells. However, mutations that change the primary nucleotide sequence of nonconserved portions of the stem-loop, but preserve its overall secondary structure, by inversion of apical loop sequences or exchange of 5' and 3' sides of stem segments, had little or no effect on selenocysteine incorporation. Effects of single- and double-nucleotide substitutions in three short, highly conserved elements in the GPX1 STE depended in large part on their computer-predicted perturbation of the stem-loop and its midstem bulge. Only in the conserved "AAA" apical loop sequence did mutations show major effects on function without predicted changes in secondary structure. Our results demonstrate the critical role of the three short, highly conserved sequences. However, outside of these elements, the function of the human GPX1 STE appears to depend strongly on the stem-loop secondary structure. Images FIGURE 1 FIGURE 2 FIGURE 3

Shen, Q; Leonard, J L; Newburger, P E

1995-01-01

85

Secondary structural effects on protein NMR chemical shifts  

Microsoft Academic Search

For an amino acid in protein, its chemical shift, d(?, ?)s, is expressed as a function of its backbone torsion angles (? and ?) and secondary state (s): d(?, ?)s=d?, ?)_coil+?d(?, ?)_s, where d(?, ?)coil represents its chemical shift at coil state (s=coil); ? d(?, ?)s (s=sheet or helix) is herein defined as secondary structural effect correction factor, which are

Yunjun Wang

2004-01-01

86

CD spectroscopy has intrinsic limitations for protein secondary structure analysis  

PubMed Central

Secondary structure content (SSC) cannot be accurately calculated from circular dichroism (CD) spectra for the majority of proteins whose three dimensional structures have been solved. ‘Reliable’ SSC that is significantly different from random SSC can be calculated from CD spectra only for all-? proteins and all-? proteins with canonical ?-strand geometry.

Khrapunov, Sergei

2009-01-01

87

Fast folding and comparison of RNA secondary structures  

Microsoft Academic Search

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

I. L. Hofacker; W. Fontana; P. F. Stadler; L. S. Bonhoeffer; M. Tacker; P. Schuster

1994-01-01

88

SRP-RNA sequence alignment and secondary structure.  

PubMed Central

The secondary structures of the RNAs from the signal recognition particle, termed SRP-RNA, were derived buy comparative analyses of an alignment of 39 sequences. The models are minimal in that only base pairs are included for which there is comparative evidence. The structures represent refinements of earlier versions and include a new short helix.

Larsen, N; Zwieb, C

1991-01-01

89

Improved free energy parameters for RNA pseudoknotted secondary structure prediction.  

PubMed

Accurate prediction of RNA pseudoknotted secondary structures from the base sequence is a challenging computational problem. Since prediction algorithms rely on thermodynamic energy models to identify low-energy structures, prediction accuracy relies in large part on the quality of free energy change parameters. In this work, we use our earlier constraint generation and Boltzmann likelihood parameter estimation methods to obtain new energy parameters for two energy models for secondary structures with pseudoknots, namely, the Dirks-Pierce (DP) and the Cao-Chen (CC) models. To train our parameters, and also to test their accuracy, we create a large data set of both pseudoknotted and pseudoknot-free secondary structures. In addition to structural data our training data set also includes thermodynamic data, for which experimentally determined free energy changes are available for sequences and their reference structures. When incorporated into the HotKnots prediction algorithm, our new parameters result in significantly improved secondary structure prediction on our test data set. Specifically, the prediction accuracy when using our new parameters improves from 68% to 79% for the DP model, and from 70% to 77% for the CC model. PMID:19933322

Andronescu, Mirela S; Pop, Cristina; Condon, Anne E

2010-01-01

90

Nuclear fuel assembly incorporating primary and secondary structural support members  

SciTech Connect

A nuclear fuel assembly, comprising: (a) an upper end structure; (b) a lower end structure; (c) elongated primary structural members extending longitudinally between and rigidly interconnecting the upper and lower end structures, the upper and lower end structures and primary structural members together forming a rigid structural skeleton of the fuel assembly; (d) transverse grids supported on the primary structural members at axially spaced locations therealong between the upper and lower end structures; (e) fuel rods extending through and supported by the grids between the upper and lower end structures so as to extend in generally side-by-side spaced relation to one another and to the primary structural members; and (f) elongated secondary structural members extending longitudinally between but unconnected with the upper and lower end structures, the secondary structural members extending through and rigidly interconnected with the grids to extend in generally side-by-side spaced relation to one another, to the fuel rods and to the primary structural members so as to bolster the stiffness of the structural skeleton of the fuel assembly.

Carlson, W.R.; Gjertsen, R.K.; Miller, J.V.

1987-07-28

91

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

PubMed Central

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

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

2013-01-01

92

Quantifying variances in comparative RNA secondary structure prediction  

PubMed Central

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

2013-01-01

93

THE KINK-TURN: A NEW RNA SECONDARY STRUCTURE MOTIF  

Microsoft Academic Search

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

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

2001-01-01

94

Multistrand RNA secondary structure prediction and nanostructure design including pseudoknots.  

PubMed

We are presenting NanoFolder, a method for the prediction of the base pairing of potentially pseudoknotted multistrand RNA nanostructures. We show that the method outperforms several other structure prediction methods when applied to RNA complexes with non-nested base pairs. We extended this secondary structure prediction capability to allow RNA sequence design. Using native PAGE, we experimentally confirm that four in silico designed RNA strands corresponding to a triangular RNA structure form the expected stable complex. PMID:22067111

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

2011-12-27

95

Improving the accuracy of protein secondary structure prediction using structural alignment  

Microsoft Academic Search

Background: The accuracy of protein secondary structure prediction has steadily improved over the past 30 years. Now many secondary structure prediction methods routinely achieve an accuracy (Q3) of about 75%. We believe this accuracy could be further improved by including structure (as opposed to sequence) database comparisons as part of the prediction process. Indeed, given the large size of the

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

2006-01-01

96

Statistical mechanics of secondary structures formed by random RNA sequences  

NASA Astrophysics Data System (ADS)

In addition to its importance for the biological function of RNA molecules RNA secondary structure formation is an interesting system from the statistical physics point of view. The ensemble of secondary structures of random RNA sequences shows a rich phase diagram with distinct native, denatured, molten, and glassy phases separated by thermodynamical phase transitions. These phase transitions are driven by the competition between thermal fluctuations, the disorder frozen into the specific sequence of a given RNA molecule, and the evolutionary bias towards the formation of some biologically relevant structure. Yet, in contrast to the protein folding problem which is driven by very similar principles and shows a similar phase diagram RNA secondary structure formation can be represented by a simple diagrammatic language which allows the application of various analytical and numerical methods. This makes RNA secondary structure formation an ideal model system for heteropolymer folding. In the talk, I will characterize and explain the complex behaviour of RNA folding using several simple models and discuss possible implications to biological processes.

Bundschuh, Ralf

2003-03-01

97

Prediction of the secondary structure of HIV-1 gp120.  

PubMed

The secondary structure of HIV-1 gp120 was predicted using multiple alignment and a combination of two independent methods based on neural network and nearest-neighbor algorithms. The methods agreed on the secondary structure for 80% of the residues in BH10 gp120. Six helices were predicted in HIV strain BH10 gp120, as well as in 27 other HIV-1 strains examined. Two helical segments were predicted in regions displaying profound sequence variation, one in a region suggested to be critical for CD4 binding. The predicted content of helix, beta-strand, and coil was consistent with estimates from Fourier transform infrared spectroscopy. The predicted secondary structure of gp120 compared well with data from NMR analysis of synthetic peptides from the V3 loop and the C4 region. As a first step towards modeling the tertiary structure of gp120, the predicted secondary structure may guide the design of future HIV subunit vaccine candidates. PMID:8727315

Hansen, J E; Lund, O; Nielsen, J O; Brunak, S; Hansen, J E

1996-05-01

98

Ensemble-based prediction of RNA secondary structures  

PubMed Central

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

2013-01-01

99

RNA secondary structures: complex statics and glassy dynamics  

Microsoft Academic Search

Models for RNA secondary structures (the topology of folded RNA) without pseudo-knots are disordered systems with a complex state space below a critical temperature. Hence, a complex dynamical (glassy) behavior can be expected when performing Monte Carlo simulations. Interestingly, in contrast to most other complex systems, the ground states and the density of states can be computed in polynomial time

S. Wolfsheimer; B. Burghardt; A. Mann; A. K. Hartmann

2008-01-01

100

Fast evaluation of internal loops in RNA secondary structure prediction  

Microsoft Academic Search

Motivation: Though not as abundant in known biologicalprocesses as proteins, RNA molecules serve as morethan mere intermediaries between DNA and proteins.Research in the last 15 years demonstrates that RNAmolecules serve in many roles, including catalysis. Furthermore,RNA secondary structure prediction based onfree energy rules for stacking and loop formation remainsone of the few major breakthroughs in the eld of structureprediction, as

Rune B. Lyngsø; Michael Zuker; Christian N. S. Pedersen

1999-01-01

101

Using circular dichroism spectra to estimate protein secondary structure  

Microsoft Academic Search

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

Norma J Greenfield

2007-01-01

102

A comparative study on filtering protein secondary structure prediction.  

PubMed

Filtering of Protein Secondary Structure Prediction (PSSP) aims to provide physicochemically realistic results, while it usually improves the predictive performance. We performed a comparative study on this challenging problem, utilizing both machine learning techniques and empirical rules and we found that combinations of the two lead to the highest improvement. PMID:22291162

Kountouris, Petros; Agathocleous, Michalis; Promponas, Vasilis J; Christodoulou, Georgia; Hadjicostas, Simos; Vassiliades, Vassilis; Christodoulou, Chris

2012-01-01

103

RNA Movies 2: sequential animation of RNA secondary structures.  

PubMed

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

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

2007-07-01

104

Reaction of psoralen with RNA: specificity and use as a probe for secondary-structure analysis  

SciTech Connect

A variety of techniques has been used to study how psoralen and its derivatives react with RNA. This information has then been used to analyze the secondary structure of different ribosomal RNAs. Paper electrophoresis at pH 3.5 and 8.8 and HPLC has been used to get high-resolution separation of RNA-psoralen adducts. The separated adducts have been analyzed and shown to be primarily uridine adducts with the psoralen reacted at the furan end. The stereochemistry of the major adducts was determined by NMR. The effect of structural transitions on the number and type of adducts was found for several polymers. The effect of psoralen structure on cross linking ability was analyzed. Charged derivatives formed monoadducts very efficiently but did not produce the level of crosslinking obtainable with lower levels of reaction with uncharged derivatives. Secondary structure analysis of D. melanogaster 5S RNA yielded two definite and two tentative crosslinks which support the generally accepted models for 5S structure. Analysis of E. coli 16S RNA by gel techniques yielded 13 cross-links. Evidence is also presented for an interaction between eukaryotic mRNA (5' cap structure) and 18S RNA (hypermodified base am psi) which serves a function analogous to the Shine-Dalgarno sequence in pro karyotes.

Thompson, J.F.

1982-09-01

105

CONTRAfold: RNA secondary structure prediction without physics-based models  

Microsoft Academic Search

Motivation: For several decades, free energy minimization methods have been the dominant strategy for single sequence RNA secondary structure prediction. More recently, stochastic context-free grammars (SCFGs)have emergedas an alternative probabilisticmethodology for modeling RNA structure. Unlike physics-based methods, which rely on thousands of experimentally-measured thermodynamic parameters, SCFGs use fully-automated statistical learning algorithms to derive model parameters. Despite this advantage, however, probabilistic

Chuong B. Do; Daniel A. Woods; Serafim Batzoglou

2006-01-01

106

Protein secondary structure prediction using nearest-neighbor methods.  

PubMed

We have studied the use of nearest-neighbor classifiers to predict the secondary structure of proteins. The nearest-neighbor rule states that a test instance is classified according to the classifications of "nearby" training examples from a database of known structures. In the context of secondary structure prediction, the test instances are windows of n consecutive residues, and the label is the secondary structure type (alpha-helix, beta-strand, or coil) of the center position of the window. To define the neighborhood of a test instance, we employed a novel similarity metric based on the local structural environment scoring scheme of Bowie et al. In this manner, we have attempted to exploit the underlying structural similarity between segments of different proteins to aid in the prediction of secondary structure. Furthermore, in addition to using neighborhoods of fixed radius, we explored a modification of the standard nearest-neighbor algorithm that involved defining an "effective radius" for each exemplar by measuring its performance on a training set. Using these ideas, we achieved a peak prediction accuracy of 68%. Finally, we sought to improve the biological utility of secondary structure prediction by identifying the subset of the predictions that are most likely to be correct. Toward this end, we developed a nearest-neighbor estimator that produced not the traditional "one-state" prediction (alpha-helix, beta-strand, or coil) but rather a probability distribution over the three states. It should be emphasized that this scheme estimates true probability values and that the resulting numbers are not pseudo-probability scores generated by simple normalization of the raw output of the predictor. Applying the mutual information statistic, we found that these probability triplets possess 58% more information than the one-state predictions. Furthermore, the probability estimates allow one to assign an a priori confidence level to the prediction at each residue. Using this approach, we found that the top 28% of the predictions were 86% accurate and the top 43% of the predictions were 81% accurate. These results indicate that, notwithstanding the limitations on overall accuracy of secondary structure prediction, a substantial proportion of a protein can be predicted with considerable accuracy. PMID:8371270

Yi, T M; Lander, E S

1993-08-20

107

PCI-SS: MISO dynamic nonlinear protein secondary structure prediction  

PubMed Central

Background Since the function of a protein is largely dictated by its three dimensional configuration, determining a protein's structure is of fundamental importance to biology. Here we report on a novel approach to determining the one dimensional secondary structure of proteins (distinguishing ?-helices, ?-strands, and non-regular structures) from primary sequence data which makes use of Parallel Cascade Identification (PCI), a powerful technique from the field of nonlinear system identification. Results Using PSI-BLAST divergent evolutionary profiles as input data, dynamic nonlinear systems are built through a black-box approach to model the process of protein folding. Genetic algorithms (GAs) are applied in order to optimize the architectural parameters of the PCI models. The three-state prediction problem is broken down into a combination of three binary sub-problems and protein structure classifiers are built using 2 layers of PCI classifiers. Careful construction of the optimization, training, and test datasets ensures that no homology exists between any training and testing data. A detailed comparison between PCI and 9 contemporary methods is provided over a set of 125 new protein chains guaranteed to be dissimilar to all training data. Unlike other secondary structure prediction methods, here a web service is developed to provide both human- and machine-readable interfaces to PCI-based protein secondary structure prediction. This server, called PCI-SS, is available at . In addition to a dynamic PHP-generated web interface for humans, a Simple Object Access Protocol (SOAP) interface is added to permit invocation of the PCI-SS service remotely. This machine-readable interface facilitates incorporation of PCI-SS into multi-faceted systems biology analysis pipelines requiring protein secondary structure information, and greatly simplifies high-throughput analyses. XML is used to represent the input protein sequence data and also to encode the resulting structure prediction in a machine-readable format. To our knowledge, this represents the only publicly available SOAP-interface for a protein secondary structure prediction service with published WSDL interface definition. Conclusion Relative to the 9 contemporary methods included in the comparison cascaded PCI classifiers perform well, however PCI finds greatest application as a consensus classifier. When PCI is used to combine a sequence-to-structure PCI-based classifier with the current leading ANN-based method, PSIPRED, the overall error rate (Q3) is maintained while the rate of occurrence of a particularly detrimental error is reduced by up to 25%. This improvement in BAD score, combined with the machine-readable SOAP web service interface makes PCI-SS particularly useful for inclusion in a tertiary structure prediction pipeline.

Green, James R; Korenberg, Michael J; Aboul-Magd, Mohammed O

2009-01-01

108

Detection and study of secondary structures in some planetary nebulae  

NASA Astrophysics Data System (ADS)

Results of long exposure plates, made at the Haute Provence Observatory, France, are presented for nine selected nebulae, using a large bandwidth interference filter coupled with an ITT image tube. Spectrophotometric observations have been made for one nebula, IC 418, and the contour map of the (N II)/H-alpha ratio is derived. It is found that this ratio increases toward the outer extended envelope of the nebula. Results show that one of the typical features of secondary structures is the enhancement of the N II line with respect to H-alpha. In addition, filamentary structures appear sharper in N II than in H-alpha, as shown for example in NGC 650-1. It is concluded that direct photography with long exposure time and modern spectrophotometry are complementary methods for detecting and studying secondary structures in planetary nebulae.

Louise, R.

1982-10-01

109

Improved Chou-Fasman method for protein secondary structure prediction  

PubMed Central

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

Chen, Hang; Gu, Fei; Huang, Zhengge

2006-01-01

110

CyloFold: secondary structure prediction including pseudoknots.  

PubMed

Computational RNA secondary structure prediction approaches differ by the way RNA pseudoknot interactions are handled. For reasons of computational efficiency, most approaches only allow a limited class of pseudoknot interactions or are not considering them at all. Here we present a computational method for RNA secondary structure prediction that is not restricted in terms of pseudoknot complexity. The approach is based on simulating a folding process in a coarse-grained manner by choosing helices based on established energy rules. The steric feasibility of the chosen set of helices is checked during the folding process using a highly coarse-grained 3D model of the RNA structures. Using two data sets of 26 and 241 RNA sequences we find that this approach is competitive compared to the existing RNA secondary structure prediction programs pknotsRG, HotKnots and UnaFold. The key advantages of the new method are that there is no algorithmic restriction in terms of pseudoknot complexity and a test is made for steric feasibility. Availability: The program is available as web server at the site: http://cylofold.abcc.ncifcrf.gov. PMID:20501603

Bindewald, Eckart; Kluth, Tanner; Shapiro, Bruce A

2010-07-01

111

Exploiting intrastructure information for secondary structure prediction with multifaceted pipelines.  

PubMed

Predicting the secondary structure of proteins is still a typical step in several bioinformatic tasks, in particular, for tertiary structure prediction. Notwithstanding the impressive results obtained so far, mostly due to the advent of sequence encoding schemes based on multiple alignment, in our view the problem should be studied from a novel perspective, in which understanding how available information sources are dealt with plays a central role. After revisiting a well-known secondary structure predictor viewed from this perspective (with the goal of identifying which sources of information have been considered and which have not), we propose a generic software architecture designed to account for all relevant information sources. To demonstrate the validity of the approach, a predictor compliant with the proposed generic architecture has been implemented and compared with several state-of-the-art secondary structure predictors. Experiments have been carried out on standard data sets, and the corresponding results confirm the validity of the approach. The predictor is available at http://iasc.diee.unica.it/ssp2/ through the corresponding web application or as downloadable stand-alone portable unpack-and-run bundle. PMID:22201070

Armano, Giuliano; Ledda, Filippo

2012-01-01

112

Integrating Chemical Footprinting Data into RNA Secondary Structure Prediction  

PubMed Central

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

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

2012-01-01

113

Accurate SHAPE-directed RNA secondary structure modeling, including pseudoknots.  

PubMed

A pseudoknot forms in an RNA when nucleotides in a loop pair with a region outside the helices that close the loop. Pseudoknots occur relatively rarely in RNA but are highly overrepresented in functionally critical motifs in large catalytic RNAs, in riboswitches, and in regulatory elements of viruses. Pseudoknots are usually excluded from RNA structure prediction algorithms. When included, these pairings are difficult to model accurately, especially in large RNAs, because allowing this structure dramatically increases the number of possible incorrect folds and because it is difficult to search the fold space for an optimal structure. We have developed a concise secondary structure modeling approach that combines SHAPE (selective 2'-hydroxyl acylation analyzed by primer extension) experimental chemical probing information and a simple, but robust, energy model for the entropic cost of single pseudoknot formation. Structures are predicted with iterative refinement, using a dynamic programming algorithm. This melded experimental and thermodynamic energy function predicted the secondary structures and the pseudoknots for a set of 21 challenging RNAs of known structure ranging in size from 34 to 530 nt. On average, 93% of known base pairs were predicted, and all pseudoknots in well-folded RNAs were identified. PMID:23503844

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

2013-04-01

114

Quinary lattice model of secondary structures of polymers  

NASA Astrophysics Data System (ADS)

In the standard approach to lattice proteins models based on nearest neighbor interaction are used. In this kind of model it is difficult to explain the existence of secondary structures-special preferred conformations of protein chains. In the present paper a new lattice model of proteins is proposed which is based on non-local cooperative interactions. In this model the energy of a conformation of a polymer is equal to the sum of energies of conformations of fragments of the polymer chain of length five. It is shown that this quinary lattice model is able to describe at a qualitative level secondary structures of proteins: for this model all conformations with minimal energy are combinations of lattice models of alpha-helix and beta-strand. Moreover for lattice polymers of length not longer that 38 monomers we can describe all conformations with minimal energy.

Kozyrev, S. V.; Volovich, I. V.

2014-01-01

115

Approximation algorithms for predicting RNA secondary structures with arbitrary pseudoknots.  

PubMed

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

Jiang, Minghui

2010-01-01

116

Extracting Physicochemical Features to Predict Protein Secondary Structure  

PubMed Central

We propose a protein secondary structure prediction method based on position-specific scoring matrix (PSSM) profiles and four physicochemical features including conformation parameters, net charges, hydrophobic, and side chain mass. First, the SVM with the optimal window size and the optimal parameters of the kernel function is found. Then, we train the SVM using the PSSM profiles generated from PSI-BLAST and the physicochemical features extracted from the CB513 data set. Finally, we use the filter to refine the predicted results from the trained SVM. For all the performance measures of our method, Q3 reaches 79.52, SOV94 reaches 86.10, and SOV99 reaches 74.60; all the measures are higher than those of the SVMpsi method and the SVMfreq method. This validates that considering these physicochemical features in predicting protein secondary structure would exhibit better performances.

Chen, Shu-Ying

2013-01-01

117

The response of mRNA expression upon secondary challenge with Vibrio anguillarum suggests the involvement of C-lectins in the immune priming of scallop Chlamys farreri.  

PubMed

The enhanced immunity against a second encounter with the particular pathogen has suggested the presence of "immune priming" in scallop. In the present study, the survival rate and expression patterns of five C-lectin isoforms from scallop Chlamys farreri were explored after "vaccination" of heat-killed Vibrio anguillarum or successively challenge with V. anguillarum and Micrococcus luteus. When scallops were challenged with live bacteria, the survival rate increased significantly only in the group firstly "vaccinated" with inactivated V. anguillarum and then challenged with live V. anguillarum compared with naive scallops (from 41% to 63.6%, P<0.05), showing enhanced protective effects of inactivated bacteria with "specificity". When scallops received the challenge with V. anguillarum, the mRNA expression level of five C-lectins in scallops which were immuned previously with heat-killed V. anguillarum peaked significantly higher (26.7-, 121.7-, 60.1-, 27.4-, 16.3-fold to 0h, respectively, P<0.01) than that in non-immuned scallops (7.6-fold, P<0.05; 6.4-, 3.9-fold, P>0.05; 5.7-fold, P<0.05; 11.7-fold, P<0.01, to 0h, respectively). A significantly higher peak and 3-9h earlier response of all C-lectins mRNA expression were observed after challenge with live V. anguillarum (26.7-, 121.7-, 60.1-, 26.4- and 16.3-fold to 0h, respectively, P<0.01), compared with those only received first injection with heat-killed V. anguillarum (1.6-fold, P>0.05; 8.3-fold, P<0.05; 5.2-fold, P>0.05; 14.5-fold, P<0.01; 4.3-fold, P>0.05, to 0h, respectively). The response of mRNA expression to the secondary encounter with the same bacteria was stronger than that of successively encounter with the different class of bacteria. It was obvious that the mRNA expression of C-lectins in scallops was significantly enhanced by the successive challenge of same species of bacteria with a certain degree of specificity. All the results suggested that C-lectins might be involved in some form of immune priming, and it might provide new insights into mechanism of invertebrate immune priming. PMID:23434464

Wang, Jingjing; Wang, Lingling; Yang, Chuanyan; Jiang, Qiufen; Zhang, Huan; Yue, Feng; Huang, Mengmeng; Sun, Zhibin; Song, Linsheng

2013-06-01

118

Dimeric structure of a human apolipoprotein B mRNA editing protein and cloning and chromosomal localization of its gene.  

PubMed Central

Apolipoprotein B (apoB) mRNA editing consists of a posttranscriptional C-->U conversion involving the first base of the codon CAA encoding glutamine-2153 to UAA, a stop codon, in apoB mRNA. Using a cloned rat cDNA as a probe, we cloned the cDNA and genomic sequences of the gene for a human apoB mRNA editing protein. Expression of the cDNA in HepG2 cells results in editing of the intracellular apoB mRNA. By fluorescence in situ hybridization, we localized the gene for the editing protein to chromosome band 12p13.1-p13.2. By Northern blot analysis, it was shown that the human editing protein mRNA is expressed exclusively in the small intestine. The cDNA sequence predicts a translation product of 236-aa residues. By attaching an epitope tag sequence to the C terminus of the editing protein, we examined the polymerization state of the editing protein synthesized in vitro. We found that the editing protein undergoes spontaneous polymerization. The migration of the human apoB mRNA editing protein on an HPLC column and the stoichiometry of polymeric epitope-tagged to untagged protein indicate that the protein exists as a dimer. Dimerization does not require glycosylation of a consensus N-linked glycosylation sequence present in the protein and is not mediated by disulfide bridge formation. The human apoB mRNA editing protein is a cytidine deaminase showing structural homology to some known mammalian and bacteriophage deoxycytidylate deaminases. The latter enzymes exist as homopolymers. The fact that the apoB mRNA editing protein also exists as a homodimer has important implications for the mechanism of apoB mRNA editing in humans. Images

Lau, P P; Zhu, H J; Baldini, A; Charnsangavej, C; Chan, L

1994-01-01

119

Determining ?-helical and ?-sheet Secondary Structures via Pulsed EPR Spectroscopy  

PubMed Central

A new method has been developed to determine ?-helical and ?-sheet secondary structural components of aqueous and membrane-bound proteins using pulsed electron paramagnetic resonance (EPR) spectroscopy. The threepulse electron spin echo envelope modulation (ESEEM) technique was used to detect weakly coupled 2H-labeled nuclei on side chains in the proximity of a strategically placed nitroxide spin-label up to 8 Å away. Changes in the ESEEM spectra for different samples correlate directly to periodic structural differences between ?-helical and ?-sheet motifs. These distinct trends were demonstrated with ?-helical (M2? subunit of the acetylcholine receptor) and ?-sheet (Ubiquitin) peptides in biologically relevant sample environments.

Zhou, Andy; Abu-Baker, Shadi; Sahu, Indra D.; Liu, Lishan; McCarrick, Robert M.; Dabney-Smith, Carole; Lorigan, Gary A.

2012-01-01

120

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

PubMed

To study local structures in proteins, we previously developed an autoassociative artificial neural network (autoANN) and clustering tool to discover intrinsic features of macromolecular structures. The hidden unit activations computed by the trained autoANN are a convenient low-dimensional encoding of the local protein backbone structure. Clustering these activation vectors results in a unique classification of protein local structural features called Structural Building Blocks (SBBs). Here we describe application of this method to a larger database of proteins, verification of the applicability of this method to structure classification, and subsequent analysis of amino acid frequencies and several commonly occurring patterns of SBBs. The SBB classification method has several interesting properties: 1) it identifies the regular secondary structures, alpha helix and beta strand; 2) it consistently identifies other local structure features (e.g., helix caps and strand caps); 3) strong amino acid preferences are revealed at some positions in some SBBs; and 4) distinct patterns of SBBs occur in the "random coil" regions of proteins. Analysis of these patterns identifies interesting structural motifs in the protein backbone structure, indicating that SBBs can be used as "building blocks" in the analysis of protein structure. This type of pattern analysis should increase our understanding of the relationship between protein sequence and local structure, especially in the prediction of protein structures. PMID:9061789

Fetrow, J S; Palumbo, M J; Berg, G

1997-02-01

121

RNA secondary structure prediction using high-throughput SHAPE.  

PubMed

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

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

2013-01-01

122

A stem-loop structure directs oskar mRNA to microtubule minus ends  

PubMed Central

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

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

2014-01-01

123

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

SciTech Connect

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

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

2011-12-31

124

Crystal structure of Dcp1p and its functional implications in mRNA decapping  

PubMed Central

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

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

2007-01-01

125

On the page number of RNA secondary structures with pseudoknots.  

PubMed

Let S denote the set of (possibly noncanonical) base pairs {i, j } of an RNA tertiary structure; i.e. {i, j} ? S if there is a hydrogen bond between the ith and jth nucleotide. The page number of S, denoted ?(S), is the minimum number k such that Scan be decomposed into a disjoint union of k secondary structures. Here, we show that computing the page number is NP-complete; we describe an exact computation of page number, using constraint programming, and determine the page number of a collection of RNA tertiary structures, for which the topological genus is known. We describe an approximation algorithm from which it follows that ?(S) ? ?(S) ? ?(S) ?log n,where the clique number of S, ?(S), denotes the maximum number of base pairs that pairwise cross each other. PMID:22159642

Clote, Peter; Dobrev, Stefan; Dotu, Ivan; Kranakis, Evangelos; Krizanc, Danny; Urrutia, Jorge

2012-12-01

126

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

Microsoft Academic Search

RNA secondary structures are important in many biological processes and efficient structure predic- tion can give vital directions for experimental investigations. Many available programs for RNA secondary structure prediction only use a single sequence at a time. This may be sufficient in some applications, but often it is possible to obtain related RNA sequences with conserved secondary struc- ture. These

Bjarne Knudsen; Jotun Hein

2003-01-01

127

The Coherent Structure of Turbulent Mixing Layers. I. Similarity of the Primary Vortex Structure. II. Secondary Streamwise Vortex Structure.  

National Technical Information Service (NTIS)

The primary spanwise organized vortex structure and the secondary streamwise vortex structure of turbulent mixing layers have been investigated. Flow visualization motion pictures of a constant density mixing layer were used to measure the properties of t...

L. P. Bernal

1981-01-01

128

Secondary structure conformations and long range electronic interactions in oligopeptides  

SciTech Connect

Combined quantum mechanical coupling calculations and molecular dynamics simulations were performed to examine the role of modest geometrical fluctuations of peptide secondary structures on long range electronic interactions in oligopeptides. Molecular dynamics simulations were performed to obtain typical relevent conformations of oligopeptides, and self-consistent Hartree-Fock calculations at the semiempirical quantum theory level were performed to extract the long range electronic propagation. Initial {alpha}-helical oligopeptides show dominant hole-mediated coupling over a large tunneling energy range, while the initial extended conformation oligopeptides have more nearly equal contributions from both hole and electron mechanisms. Modest geometrical fluctuations lead to changes in the character of long range electronic interactions. The computations highlight the danger of drawing conclusions from electronic structure calculations of electronic coupling in peptide model systems on the basis of computations on single geometries. 28 refs., 9 figs., 1 tab.

Wolfgang, J.; Risser, S.M. [Texas A& M Univ., Commerce, TX (United States)] [Texas A& M Univ., Commerce, TX (United States); Priyadarshy, S.; Beratan, D.N. [Univ. of Pittsburgh, PA (United States)] [Univ. of Pittsburgh, PA (United States)

1997-04-10

129

Predicting protein secondary structure with a nearest-neighbor algorithm.  

PubMed

We have developed a new method for protein secondary structure prediction that achieves accuracies as high as 71.0%, the highest value yet reported. The main component of our method is a nearest-neighbor algorithm that uses a more sophisticated treatment of the feature space than standard nearest-neighbor methods. It calculates distance tables that allow it to produce real-valued distances between amino acid residues, and attaches weights to the instances to further modify the the structure of feature space. The algorithm, which is closely related to the memory-based reasoning method of Zhang et al., is simple and easy to train, and has also been applied with excellent results to the problem of identifying DNA promoter sequences. PMID:1404357

Salzberg, S; Cost, S

1992-09-20

130

Protein secondary structure prediction using NMR chemical shift data.  

PubMed

Accurate determination of protein secondary structure from the chemical shift information is a key step for NMR tertiary structure determination. Relatively few work has been done on this subject. There needs to be a systematic investigation of algorithms that are (a) robust for large datasets; (b) easily extendable to (the dynamic) new databases; and (c) approaching to the limit of accuracy. We introduce new approaches using k-nearest neighbor algorithm to do the basic prediction and use the BCJR algorithm to smooth the predictions and combine different predictions from chemical shifts and based on sequence information only. Our new system, SUCCES, improves the accuracy of all existing methods on a large dataset of 805 proteins (at 86% Q(3) accuracy and at 92.6% accuracy when the boundary residues are ignored), and it is easily extendable to any new dataset without requiring any new training. The software is publicly available at http://monod.uwaterloo.ca/nmr/succes. PMID:20981892

Zhao, Yuzhong; Alipanahi, Babak; Li, Shuai Cheng; Li, Ming

2010-10-01

131

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

PubMed

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

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

2012-01-01

132

Secondary Structure of Huntingtin Amino-Terminal Region  

SciTech Connect

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

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

2010-09-21

133

Localizing the critical point of random RNA secondary structures  

NASA Astrophysics Data System (ADS)

Previous numerical studies have found that below the denaturation temperature random RNA secondary structures can exist in one of two phases: a strongly disordered, low-temperature glass phase and a weakly disordered, high-temperature molten phase. The probability of two bases pairing in these phases have been shown to scale with the distance between the two bases as -3/2 and -4/3 in the molten and glass phases, respectively. In this study, we characterize the scaling behavior of various sub-strand lengths within the molecule for a range of temperatures both far from and near the critical point. We anticipate that this approach allows to more accurately determine the critical point and to measure the critical exponents of the system right at the phase transition.

Baez, William; Bundschuh, Ralf

2013-03-01

134

The predictive accuracy of secondary chemical shifts is more affected by protein secondary structure than solvent environment  

Microsoft Academic Search

Biomolecular NMR spectroscopy frequently employs estimates of protein secondary structure using secondary chemical shift (??)\\u000a values, measured as the difference between experimental and random coil chemical shifts (RCCS). Most published random coil\\u000a data have been determined in aqueous conditions, reasonable for non-membrane proteins, but potentially less relevant for membrane\\u000a proteins. Two new RCCS sets are presented here, determined in dimethyl

Marie-Laurence Tremblay; Aaron W. Banks; Jan K. Rainey

2010-01-01

135

THE STRUCTURE OF A RIBOSOMAL PROTEIN S8\\/SPC OPERON MRNA COMPLEX  

Microsoft Academic Search

In bacteria, translation of all the ribosomal protein cistrons in the spc operon mRNA is repressed by the binding of the product of one of them, S8, to an internal sequence at the 5 end of the L5 cistron. The way in which the first two genes of the spc operon are regulated, retroregulation, is mechanistically distinct from translational repression

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

2004-01-01

136

Mutational Patterns in RNA Secondary Structure Evolution Examined in Three RNA Families  

Microsoft Academic Search

The goal of this work was to study mutational patterns in the evolution of RNA secondary structure. We analyzed bacterial tmRNA, RNaseP and eukaryotic telomerase RNA secondary structures, mapping structural variability onto phylogenetic trees constructed primarily from rRNA sequences. We found that secondary structures evolve both by whole stem insertion\\/deletion, and by mutations that create or disrupt stem base pairing.

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

2011-01-01

137

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

Microsoft Academic Search

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

Wolfgang Kabsch; Christian Sander

1983-01-01

138

Spliced mRNA Encoding the Murine Cytomegalovirus Chemokine Homolog Predicts a b Chemokine of Novel Structure  

Microsoft Academic Search

A viral mRNA of the late kinetic class expressed by murine cytomegalovirus (MCMV) contains an open reading frame (ORF) whose predicted protein, designated MCK-1, has homology to b chemokines (M. R. MacDonald, X.-Y. Li, and H. W. Virgin IV, J. Virol. 71:1671-1678, 1997). The present study analyzed further the structure of the transcript in infected fibroblast cells. A splicing event

MARGARET R. MACDONALD; MARY W. BURNEY; STUART B. RESNICK

1999-01-01

139

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

NASA Astrophysics Data System (ADS)

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

Rocha, L. F. O.

2014-04-01

140

Relating secondary structure to the mechanical properties of polypeptide hydrogels  

NASA Astrophysics Data System (ADS)

Biomimetic hydrogels are being developed for use in medicine as drug delivery devices and tissue engineering matrices, and the mechanical properties of the materials play an important role in their performance. For example, in tissue engineering, gene expression and cell adhesion have been closely linked to the mechanical properties of the surrounding hydrogel matrix. In poly-L-lysine hydrogels, a five-fold increase in storage modulus, a 50% increase in equilibrium modulus, and a 62% decrease in swelling degree are shown to occur as the hydrogel network chains transition from an alpha-helix to a beta-sheet conformation. The manipulation of the network's mechanical behavior through changes in the secondary structure of the polymer chains offers an additional design variable in the development of biosynthetic materials. Analogous to poly-L-lysine, elastin-mimetic proteins based on the consensus repeat sequence of elastin (VPGVG) undergo a temperature-dependent secondary structure transition from a random coil to a beta-spiral. In this research, chemically-crosslinked poly[(VPGVG)4(VPGKG)] hydrogels are shown to possess temperature- and pH-dependent swelling. Following scaling law predictions (G ˜ ?2n), the hydrogels have been shown to behave as ideal elastic networks when the crosslink density is varied at synthesis (theory: n = 9/4, experimental: n = 2.0 +/- 0.1), and behave as flexible networks above and below their structural transition temperature of 35°C (theory: n = 1/3, experimental: n = 0.45 +/- 0.06). Evaluation of published data on elastin-mimetic hydrogels shows that the hydrogels behave as ideal elastic networks for all crosslinking techniques, crosslink spacings, and crosslink functionalities reported. As a contrast to chemically-crosslinked hydrogels, a novel elastin-mimetic triblock (EMT) copolymer was evaluated because of its potential use in cell encapsulation without potentially harmful side reactions. Unlike other thermally gelling copolymers, the EMT hydrogel shrinks to approximately 50% of its original size when heated from 30°C to 50°C in water. This physically-crosslinked hydrogel exhibits reproducible swelling kinetics (Dp ˜ 4 x 10-7 cm2/s), similar to chemically-crosslinked, thermally-responsive hydrogels such as poly(N-isopropylacrylamide). The addition of salts to the synthesis solution of EMT hydrogels reduces the equilibrium swelling by 85% and increases the shear modulus 14- to 17-fold depending on the type of salt.

Hagan, Sharon Anne

141

Human growth hormone DNA sequence and mRNA structure: possible alternative splicing.  

PubMed Central

We have determined the complete sequence of the human growth hormone (hGH) gene and the position of the mature 5' end of the hGH mRNA within the sequence. Comparison of this sequence with that of a cloned hGH cDNA shows that the gene is interrupted by four intervening sequences. S1 mapping shows that one of these intervening sequences has two different 3' splice sites. These alternate splicing pathways generate hGH peptides of different sizes which are found in normal pituitaries. Comparison of sequences near the 5' end of the hGH mRNA with a similar region of the alpha subunit of the human glycoprotein hormones reveals an unexpected region of homology between these otherwise unrelated peptide hormones. Images

DeNoto, F M; Moore, D D; Goodman, H M

1981-01-01

142

Human Dcp2: a catalytically active mRNA decapping enzyme located in specific cytoplasmic structures  

PubMed Central

We have cloned cDNAs for the human homologues of the yeast Dcp1 and Dcp2 factors involved in the major (5?–3?) and NMD mRNA decay pathways. While yeast Dcp1 has been reported to be the decapping enzyme, we show that recombinant human Dcp2 (hDcp2) is enzymatically active. Dcp2 activity appears evolutionarily conserved. Mutational and biochemical analyses indicate that the hDcp2 MutT/Nudix domain mediates this activity. hDcp2 generates m7GDP and 5?-phosphorylated mRNAs that are 5?–3? exonuclease substrates. Corresponding decay intermediates are present in human cells showing the relevance of this activity. hDcp1 and hDcp2 co-localize in cell cytoplasm, consistent with a role in mRNA decay. Interestingly, these two proteins show a non-uniform distribution, accumulating in specific foci.

van Dijk, Erwin; Cougot, Nicolas; Meyer, Sylke; Babajko, Sylvie; Wahle, Elmar; Seraphin, Bertrand

2002-01-01

143

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.

2013-02-01

144

Primary structure of the human Met and Leuenkephalin precursor and its mRNA  

Microsoft Academic Search

The nucleotide sequence of a complete cDNA copy of enkephalin precursor mRNA from human phaeochromocytoma is reported. The corresponding amino acid sequence shows that the precursor is 267 amino acids long and contains six interspersed Met-enkephalin sequences and one Leu-enkephalin sequence. Five of the seven enkephalins are flanked on both sides by pairs of basic amino acid residues. The precursor

Michael Comb; Peter H. Seeburg; John Adelman; Lee Eiden; Edward Herbert

1982-01-01

145

Predicting the secondary structure of globular proteins using neural network models  

Microsoft Academic Search

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

Ning Qian; Terrence J. Sejnowski

1988-01-01

146

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

2003-01-01

147

Statistical properties of thermodynamically predicted RNA secondary structures in viral genomes  

NASA Astrophysics Data System (ADS)

By performing a comprehensive study on 1832 segments of 1212 complete genomes of viruses, we show that in viral genomes the hairpin structures of thermodynamically predicted RNA secondary structures are more abundant than expected under a simple random null hypothesis. The detected hairpin structures of RNA secondary structures are present both in coding and in noncoding regions for the four groups of viruses categorized as dsDNA, dsRNA, ssDNA and ssRNA. For all groups, hairpin structures of RNA secondary structures are detected more frequently than expected for a random null hypothesis in noncoding rather than in coding regions. However, potential RNA secondary structures are also present in coding regions of dsDNA group. In fact, we detect evolutionary conserved RNA secondary structures in conserved coding and noncoding regions of a large set of complete genomes of dsDNA herpesviruses.

Spanò, M.; Lillo, F.; Miccichè, S.; Mantegna, R. N.

2008-10-01

148

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

PubMed

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

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

2014-07-17

149

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

PubMed Central

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

Jani, Divyang; Valkov, Eugene; Stewart, Murray

2014-01-01

150

A 3D graphical representation of RNA secondary structures based on chaos game representation  

NASA Astrophysics Data System (ADS)

In this Letter, based on chaos game representation (CGR), we propose a 3D graphical representation for RNA secondary structures in terms of classifications of bases of nucleic acids. Some information on the base distribution and compositions of RNA secondary structure can be intuitively reflected by the graphical representation. Furthermore, the numerical characterization of the graphical representation is applied to compute the similarities of RNA secondary structures. As application, we make quantitative comparisons for two sets of RNA secondary structures based on the graphical representation.

Feng, Jie; Wang, Tian-ming

2008-03-01

151

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

PubMed Central

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

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

1988-01-01

152

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

PubMed

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

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

2013-10-01

153

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

PubMed Central

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

Page, Roderic D. M.

2000-01-01

154

Role of DNA secondary structures in fragile site breakage along human chromosome 10  

PubMed Central

The formation of alternative DNA secondary structures can result in DNA breakage leading to cancer and other diseases. Chromosomal fragile sites, which are regions of the genome that exhibit chromosomal breakage under conditions of mild replication stress, are predicted to form stable DNA secondary structures. DNA breakage at fragile sites is associated with regions that are deleted, amplified or rearranged in cancer. Despite the correlation, unbiased examination of the ability to form secondary structures has not been evaluated in fragile sites. Here, using the Mfold program, we predict potential DNA secondary structure formation on the human chromosome 10 sequence, and utilize this analysis to compare fragile and non-fragile DNA. We found that aphidicolin (APH)-induced common fragile sites contain more sequence segments with potential high secondary structure-forming ability, and these segments clustered more densely than those in non-fragile DNA. Additionally, using a threshold of secondary structure-forming ability, we refined legitimate fragile sites within the cytogenetically defined boundaries, and identified potential fragile regions within non-fragile DNA. In vitro detection of alternative DNA structure formation and a DNA breakage cell assay were used to validate the computational predictions. Many of the regions identified by our analysis coincide with genes mutated in various diseases and regions of copy number alteration in cancer. This study supports the role of DNA secondary structures in common fragile site instability, provides a systematic method for their identification and suggests a mechanism by which DNA secondary structures can lead to human disease.

Dillon, Laura W.; Pierce, Levi C. T.; Ng, Maggie C. Y.; Wang, Yuh-Hwa

2013-01-01

155

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

PubMed Central

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

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

1994-01-01

156

Accurate prediction of protein structural classes using functional domains and predicted secondary structure sequences.  

PubMed

Protein structural class prediction is one of the challenging problems in bioinformatics. Previous methods directly based on the similarity of amino acid (AA) sequences have been shown to be insufficient for low-similarity protein data-sets. To improve the prediction accuracy for such low-similarity proteins, different methods have been recently proposed that explore the novel feature sets based on predicted secondary structure propensities. In this paper, we focus on protein structural class prediction using combinations of the novel features including secondary structure propensities as well as functional domain (FD) features extracted from the InterPro signature database. Our comprehensive experimental results based on several benchmark data-sets have shown that the integration of new FD features substantially improves the accuracy of structural class prediction for low-similarity proteins as they capture meaningful relationships among AA residues that are far away in protein sequence. The proposed prediction method has also been tested to predict structural classes for partially disordered proteins with the reasonable prediction accuracy, which is a more difficult problem comparing to structural class prediction for commonly used benchmark data-sets and has never been done before to the best of our knowledge. In addition, to avoid overfitting with a large number of features, feature selection is applied to select discriminating features that contribute to achieve high prediction accuracy. The selected features have been shown to achieve stable prediction performance across different benchmark data-sets. PMID:22545993

Ahmadi Adl, Amin; Nowzari-Dalini, Abbas; Xue, Bin; Uversky, Vladimir N; Qian, Xiaoning

2012-01-01

157

PreSSAPro: A software for the prediction of secondary structure by amino acid properties  

Microsoft Academic Search

PreSSAPro is a software, available to the scientific community as a free web service designed to provide predictions of secondary structures starting from the amino acid sequence of a given protein. Predictions are based on our recently published work on the amino acid propensities for secondary structures in either large but not homogeneous protein data sets, as well as in

Susan Costantini; Giovanni Colonna; Angelo M. Facchiano

2007-01-01

158

Secondary Impacts on Structures on the Lunar Surface  

NASA Technical Reports Server (NTRS)

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

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

2010-01-01

159

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

PubMed Central

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

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

2011-01-01

160

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

PubMed Central

Background The function of a noncoding RNA sequence is mainly determined by its secondary structure and therefore a family of noncoding RNA sequences is much more conserved on the structural level than on the sequence level. Understanding the function of noncoding RNA sequence families requires two things: a hand-crafted or hand-improved alignment and detailed analyses of the secondary structures. There are several tools available that help performing these tasks, but all of them are specialized and focus on only one aspect, editing the alignment or plotting the secondary structure. The problem is both these tasks need to be performed simultaneously. Findings 4SALE is designed to handle sequence and secondary structure information of RNAs synchronously. By including a complete new method of simultaneous visualization and editing RNA sequences and secondary structure information, 4SALE enables to improve and understand RNA sequence and secondary structure evolution much more easily. Conclusion 4SALE is a step further for simultaneously handling RNA sequence and secondary structure information. It provides a complete new way of visual monitoring different structural aspects, while editing the alignment. The software is freely available and distributed from its website at

Seibel, Philipp N; Muller, Tobias; Dandekar, Thomas; Wolf, Matthias

2008-01-01

161

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.

2003-03-01

162

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

PubMed

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

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

2013-08-01

163

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

PubMed Central

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

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

2013-01-01

164

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

PubMed Central

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

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

2010-01-01

165

A probabilistic model for secondary structure prediction from protein chemical shifts.  

PubMed

Protein chemical shifts encode detailed structural information that is difficult and computationally costly to describe at a fundamental level. Statistical and machine learning approaches have been used to infer correlations between chemical shifts and secondary structure from experimental chemical shifts. These methods range from simple statistics such as the chemical shift index to complex methods using neural networks. Notwithstanding their higher accuracy, more complex approaches tend to obscure the relationship between secondary structure and chemical shift and often involve many parameters that need to be trained. We present hidden Markov models (HMMs) with Gaussian emission probabilities to model the dependence between protein chemical shifts and secondary structure. The continuous emission probabilities are modeled as conditional probabilities for a given amino acid and secondary structure type. Using these distributions as outputs of first- and second-order HMMs, we achieve a prediction accuracy of 82.3%, which is competitive with existing methods for predicting secondary structure from protein chemical shifts. Incorporation of sequence-based secondary structure prediction into our HMM improves the prediction accuracy to 84.0%. Our findings suggest that an HMM with correlated Gaussian distributions conditioned on the secondary structure provides an adequate generative model of chemical shifts. PMID:23292699

Mechelke, Martin; Habeck, Michael

2013-06-01

166

A novel predictor for protein structural class based on integrated information of the secondary structure sequence.  

PubMed

The structural class has become one of the most important features for characterizing the overall folding type of a protein and played important roles in many aspects of protein research. At present, it is still a challenging problem to accurately predict protein structural class for low-similarity sequences. In this study, an 18-dimensional integrated feature vector is proposed by fusing the information about content and position of the predicted secondary structure elements. The consistently high accuracies of jackknife and 10-fold cross-validation tests on different low-similarity benchmark datasets show that the proposed method is reliable and stable. Comparison of our results with other methods demonstrates that our method is an effective computational tool for protein structural class prediction, especially for low-similarity sequences. PMID:24859536

Zhang, Lichao; Zhao, Xiqiang; Kong, Liang; Liu, Shuxia

2014-08-01

167

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

PubMed

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

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

2011-01-01

168

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

PubMed

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

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

2012-07-01

169

Learning sparse models for a dynamic Bayesian network classifier of protein secondary structure  

Microsoft Academic Search

Background  Protein secondary structure prediction provides insight into protein function and is a valuable preliminary step for predicting\\u000a the 3D structure of a protein. Dynamic Bayesian networks (DBNs) and support vector machines (SVMs) have been shown to provide\\u000a state-of-the-art performance in secondary structure prediction. As the size of the protein database grows, it becomes feasible\\u000a to use a richer model in

Zafer Aydin; Ajit Singh; Jeff Bilmes; William Stafford Noble

2011-01-01

170

Hydrogen-Bonded Synthetic Mimics of Protein Secondary Structure as Disruptors of Protein-Protein Interactions  

Microsoft Academic Search

\\u000a Small molecules which can mimic the key structural facets of protein secondary structure, in particular the ?-helix, ?-strand,\\u000a and ?-sheet, have been shown to be potent disruptors of protein–protein interactions. Researchers have recently taken the\\u000a organizational imitation of protein secondary structure to a new level by using intramolecular hydrogen bonds as stabilizing\\u000a forces in these small molecule mimetics. The inclusion

Marc J. Adler; Andrew G. Jamieson; Andrew D. Hamilton

171

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

PubMed Central

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

Veo, Bethany L.; Krushel, Leslie A.

2012-01-01

172

Prediction of protein secondary structure using Large Margin Nearest Neighbour classification.  

PubMed

In this paper, we introduce a novel method for protein secondary structure prediction by using Position-Specific Scoring Matrices (PSSM) profiles and Large Margin Nearest Neighbour (LMNN) classification. Since the PSSM profiles are not specifically designed for protein secondary structure prediction, the traditional nearest neighbour method could not achieve satisfactory prediction accuracy. To address this problem, we first use a LMNN model to learn a Mahalanobis distance metric for nearest neighbour classification. Then, an energy-based rule is invoked to assign secondary structure. Tests show that the proposed method obtains better prediction accuracy when compared with previous nearest neighbour methods. PMID:23467064

Yang, Wei; Wang, Kuanquan; Zuo, Wangmeng

2013-01-01

173

Native disulfide bonds greatly accelerate secondary structure formation in the folding of lysozyme.  

PubMed Central

To assess the respective roles of local and long-range interactions during protein folding, the influence of the native disulfide bonds on the early formation of secondary structure was investigated using continuous-flow circular dichroism. Within the first 4 ms of folding, lysozyme with intact disulfide bonds already had a far-UV CD spectrum reflecting large amounts of secondary structure. Conversely, reduced lysozyme remained essentially unfolded at this early folding time. Thus, native disulfide bonds not only stabilize the cfinal conformation of lysozyme but also provide, in early folding intermediates, the necessary stabilization that favors the formation of secondary structure.

Goldberg, M. E.; Guillou, Y.

1994-01-01

174

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

PubMed Central

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

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

1991-01-01

175

Crystal structure of the UPF2-interacting domain of nonsense-mediated mRNA decay factor UPF1  

PubMed Central

UPF1 is an essential eukaryotic RNA helicase that plays a key role in various mRNA degradation pathways, notably nonsense-mediated mRNA decay (NMD). In combination with UPF2 and UPF3, it forms part of the surveillance complex that detects mRNAs containing premature stop codons and triggers their degradation in all organisms studied from yeast to human. We describe the 3 Å resolution crystal structure of the highly conserved cysteine–histidine-rich domain of human UPF1 and show that it is a unique combination of three zinc-binding motifs arranged into two tandem modules related to the RING-box and U-box domains of ubiquitin ligases. This UPF1 domain interacts with UPF2, and we identified by mutational analysis residues in two distinct conserved surface regions of UPF1 that mediate this interaction. UPF1 residues we identify as important for the interaction with UPF2 are not conserved in UPF1 homologs from certain unicellular parasites that also appear to lack UPF2 in their genomes.

Kadlec, Jan; Guilligay, Delphine; Ravelli, Raimond B.; Cusack, Stephen

2006-01-01

176

Effect of secondary elements on bridge structural system reliability considering moment capacity  

Microsoft Academic Search

Secondary elements such as barriers, sidewalks, and diaphragms may increase the load carrying capacity of girder bridges. This in turn affects reliability. The objective of this study is to evaluate the potential benefit of secondary elements on the system reliability of girder bridges, if these elements are designed with the structural system to participate resisting vehicular live loads. Simple span,

Christopher D. Eamon; Andrzej S. Nowak

2004-01-01

177

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

National Technical Information Service (NTIS)

Oxide layer structure on the surfaces of niobium (Nb) can be studied by continuously monitoring peaks of the secondary ions of Nb and its relevant oxides as a function of time during depth profiling measurements employing a secondary ion mass spectrometer...

A. T. Wu

2005-01-01

178

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

Microsoft Academic Search

Oxide layer structure on the surfaces of niobium (Nb) can be studied by continuously monitoring peaks of the secondary ions of Nb and its relevant oxides as a function of time during depth profiling measurements employing a secondary ion mass spectrometer (SIMS). This is based on the fact that different oxides have different cracking patterns. This new approach is much

Andy T. Wu

2005-01-01

179

Investigation of oxide layer structure on niobium surface using a secondary ion mass spectrometry  

Microsoft Academic Search

Oxide layer structure on the surfaces of niobium (Nb) can be studied by continuously monitoring peaks of the secondary ions of Nb and its relevant oxides as a function of time during depth profiling measurements employing a secondary ion mass spectrometry (SIMS). This is based on the fact that different oxides have different cracking patterns. This new approach is much

A. T. Wu

2006-01-01

180

A Parallel, Out-of-Core Algorithm for RNA Secondary Structure Prediction  

Microsoft Academic Search

RNA pseudoknot prediction is an algorithm for RNA se- quence search and alignment. An important building block towards pseudoknot prediction is RNA secondary structure prediction. The difculty of extending the secondary struc- ture prediction algorithm to a parallel program is (1) it has complicated data dependences, and (2) it has a large data set that typically cannot t completely in

Wenduo Zhou; David K. Lowenthal

2006-01-01

181

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

PubMed Central

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

Bailor, Maximillian; Mustoe, Anthony M.

2012-01-01

182

Constraint-based assembly of tertiary protein structures from secondary structure elements.  

PubMed Central

A challenge in computational protein folding is to assemble secondary structure elements-helices and strands-into well-packed tertiary structures. Particularly difficult is the formation of beta-sheets from strands, because they involve large conformational searches at the same time as precise packing and hydrogen bonding. Here we describe a method, called Geocore-2, that (1) grows chains one monomer or secondary structure at a time, then (2) disconnects the loops and performs a fast rigid-body docking step to achieve canonical packings, then (3) in the case of intrasheet strand packing, adjusts the side-chain rotamers; and finally (4) reattaches loops. Computational efficiency is enhanced by using a branch-and-bound search in which pruning rules aim to achieve a hydrophobic core and satisfactory hydrogen bonding patterns. We show that the pruning rules reduce computational time by 10(3)- to 10(5)-fold, and that this strategy is computationally practical at least for molecules up to about 100 amino acids long.

Yue, K.; Dill, K. A.

2000-01-01

183

The coherent structure of turbulent mixing layers. 1: Similarity of the primary vortex structure. 2: Secondary streamwise vortex structure  

NASA Astrophysics Data System (ADS)

The primary spanwise organized vortex structure and the secondary streamwise vortex structure of turbulent mixing layers have been investigated. Flow visualization motion pictures of a constant density mixing layer were used to measure the properties of the large scale vortices. It was found that after an initial transition region mean properties of the large scale vortices reach the expected linear growth with downstream distance required by similarity. In the self-similar region, the vortex core area and visual thickness increase continuously during its life-span. A theoretical model of probability distribution function for the large-scale vortex circulation was developed. This distribution is found to be lognormal and to have a standard deviation, normalized with the mean of 0.28. From this model the mean life-span of the vortices could also be obtained and was found to be 0.67 times the mean life-span position. The streamwise streak pattern observed by Konrad (1976) and Breidenthal (1978) in plan-view pictures of the mixing layer was investigated, using flow visualization and spanwise concentration measurements. It was confirmed that this pattern is the results of a secondary vortex structure dominated by streamwise, counter-rotating vortices. A detailed description of its spatial relation to the primary, spanwise vortex structure is presented. From time average flow pictures, the onset position and initial scale of the secondary structures were determined.

Bernal, L. P.

1981-06-01

184

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

PubMed

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

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

2014-06-01

185

Mutations that alter the higher-order structure of its 5' untranslated region affect the stability of chloroplast rps7 mRNA  

Microsoft Academic Search

In this paper, we examine the effects of mutations in the 5'UTR of the chloroplast rps7 transcript of Chlamydomonas reinhardtii that reduce the stability of the mRNA. Five point mutants in the rps7 5'UTR were selected on the basis of their failure to accumulate reporter mRNA in Escherichia coli. Each of these mutations produces alterations in the predicted higher-order structures

D. C. Fargo; E. Hu; J. E. Boynton; N. W. Gillham

2000-01-01

186

The coherent structure of turbulent mixing layers. I. Similarity of the primary vortex structure. II. Secondary streamwise vortex structure  

NASA Astrophysics Data System (ADS)

The primary spanwise organized vortex structure and the secondary streamwise vortex structure of turbulent mixing layers have been investigated. Flow visualization motion pictures of a constant density mixing layer were used to measure the properties of the large scale vortices. It was found that after an initial transition region mean properties of the large scale vortices reach the expected linear growth with downstream distance required by similarity. In the self-similar region, the vortex core area and visual thickness increase continuously during its life-span. A theoretical model of probability distribution function for the large-scale vortex circulation was developed. This distribution is found to be lognormal and to have a standard deviation, normalized with the mean of 0.28. From this model the mean life-span of the vortices could also be obtained and was found to be 0.67 times the mean life-span position. The streamwise streak pattern observed by Konrad (1976) and Breidenthal (1978) in plan-view pictures of the mixing layer was investigated, using flow visualization and spanwise concentration measurements. It was confirmed that this pattern is the result of a secondary vortex structure dominated by streamwise, counterrotating vortices. A detailed description of its spatial relation to the primary, spanwise vortex structure is presented. From time average flow pictures, the onset position and initial scale of the secondary structures were determined. From concentration measurements, spanwise variations in mean properties, resulting from the secondary structure, were found. This also showed an increase of the spanwise scale with downstream distance and the existence of the streamwise vortices in the fully developed turbulent region. In this region the mean spacing is found approximately equal to the vorticity thickness.

Bernal, Luis Paulino

187

Minimum message length inference of secondary structure from protein coordinate data  

PubMed Central

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

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

2012-01-01

188

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

189

STRIDE: a web server for secondary structure assignment from known atomic coordinates of proteins  

Microsoft Academic Search

STRIDE is a software tool for secondary structure assignment from atomic resolution protein struc- tures. It implements a knowledge-based algorithm that makes combined use of hydrogen bond energy and statistically derived backbone torsional angle information and is optimized to return resulting assignmentsinmaximalagreementwithcrystallogra- phers'designations.TheSTRIDEwebserverprovides access to this tool and allows visualization of the secondary structure, as well as contact and Ramachandran

Matthias Heinig; Dmitrij Frishman

2004-01-01

190

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

Microsoft Academic Search

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

Jeffrey C. Mai; Annette W. Coleman

1997-01-01

191

4SALE - A tool for synchronous RNA sequence and secondary structure alignment and editing  

PubMed Central

Background In sequence analysis the multiple alignment builds the fundament of all proceeding analyses. Errors in an alignment could strongly influence all succeeding analyses and therefore could lead to wrong predictions. Hand-crafted and hand-improved alignments are necessary and meanwhile good common practice. For RNA sequences often the primary sequence as well as a secondary structure consensus is well known, e.g., the cloverleaf structure of the t-RNA. Recently, some alignment editors are proposed that are able to include and model both kinds of information. However, with the advent of a large amount of reliable RNA sequences together with their solved secondary structures (available from e.g. the ITS2 Database), we are faced with the problem to handle sequences and their associated secondary structures synchronously. Results 4SALE fills this gap. The application allows a fast sequence and synchronous secondary structure alignment for large data sets and for the first time synchronous manual editing of aligned sequences and their secondary structures. This study describes an algorithm for the synchronous alignment of sequences and their associated secondary structures as well as the main features of 4SALE used for further analyses and editing. 4SALE builds an optimal and unique starting point for every RNA sequence and structure analysis. Conclusion 4SALE, which provides an user-friendly and intuitive interface, is a comprehensive toolbox for RNA analysis based on sequence and secondary structure information. The program connects sequence and structure databases like the ITS2 Database to phylogeny programs as for example the CBCAnalyzer. 4SALE is written in JAVA and therefore platform independent. The software is freely available and distributed from the website at

Seibel, Philipp N; Muller, Tobias; Dandekar, Thomas; Schultz, Jorg; Wolf, Matthias

2006-01-01

192

Sequences of a hairpin structure in the 3'-untranslated region mediate regulation of human pulmonary surfactant protein B mRNA stability.  

PubMed

The ability of pulmonary surfactant to reduce alveolar surface tension requires adequate expression of surfactant protein B (SP-B). Dexamethasone (DEX, 10(-7) M) increases human SP-B mRNA stability by a mechanism that requires a 126-nt-long segment (the 7.6S region) of the 3'-untranslated region (3'-UTR). The objective of this study was to identify sequences in the 7.6S region that mediate regulation of SP-B mRNA stability. The 7.6S region was found to be sufficient for DEX-mediated stabilization of mRNA. Sequential substitution mutagenesis of the 7.6S region indicates that a 90-nt region is required for DEX-mediated stabilization and maintenance of intrinsic stability. In this region, one 30-nt-long element (002), predicted to form a stem-loop structure, is sufficient for DEX-mediated stabilization of mRNA and intrinsic mRNA stability. Cytosolic proteins specifically bind element 002, and binding activity is unaffected whether proteins are isolated from cells incubated in the absence or presence of DEX. While loop sequences of element 002 have no role in regulation of SP-B mRNA stability, the proximal stem sequences are required for DEX-mediated stabilization and specific binding of proteins. Mutation of the sequences that comprise the proximal or distal arm of the stem negates the destabilizing activity of element 002 on intrinsic SP-B mRNA stability. These results indicate that cytosolic proteins bind a single hairpin structure that mediates intrinsic and hormonal regulation of SP-B mRNA stability via mechanisms that involve sequences of the stems of the hairpin structure. PMID:22367784

Huang, Helen W; Payne, David E; Bi, Weizhen; Pan, Su; Bruce, Shirley R; Alcorn, Joseph L

2012-05-15

193

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

PubMed Central

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

Mayr, Florian; Heinemann, Udo

2013-01-01

194

Generic properties of combinatory maps: Neutral networks of RNA secondary structures  

Microsoft Academic Search

Random graph theory is used to model and analyse the relationships between sequences and secondary structures of RNA molecules, which are understood as mappings from sequence space into shape space. These maps are non-invertible since there are always many orders of magnitude more sequences than structures. Sequences folding into identical structures form neutral networks. A neutral network is embedded in

Christian Reidys; Peter F. Stadler; Peter Schuster

1997-01-01

195

From Sequences to Shapes and Back: A Case Study in RNA Secondary Structures  

Microsoft Academic Search

RNA folding is viewed here as a map assigning secondary structures to sequences. At fixed chain length the number of sequences far exceeds the number of structures. Frequencies of structures are highly non-uniform and follow a generalized form of Zipf's law: we find relatively few common and many rare ones. By using an algorithm for inverse folding, we show that

Peter Schuster; Walter Fontana; Peter F. Stadler; Ivo L. Hofacker

1994-01-01

196

Generic Properties of Combinatory Maps: Neutral Networks of RNA Secondary Structures  

Microsoft Academic Search

Random graph theory is used to model relationships between sequences and secondary structure of RNA molecules. Sequences folding into identical structures form neutral networks which percolate sequence space if the fraction of neutral nearest neighbors exceeds a threshold value. The networks of any two different structures almost touch each other, and sequences folding into almost all \\

Christian Reidys; Peter F. Stadler; Peter Schuster

1995-01-01

197

An APL-programmed genetic algorithm for the prediction of RNA secondary structure  

Microsoft Academic Search

The possibilities of using a genetic algorithm for the prediction of RNA secondary structure were investigated. The algorithm, using the procedure of stepwise selection of the most fit structures (similarly to natural evolution), allows different models of fitness or driving forces determining RNA structure to be easily introduced. This can be used for simulation of the RNA folding process and

F. H. D. Van Batenburg; A. P. Gultyaev; C. W. A. Pleij

1995-01-01

198

A comparative method for finding and folding RNA secondary structures within protein-coding regions.  

PubMed

Existing computational methods for RNA secondary-structure prediction tacitly assume RNA to only encode functional RNA structures. However, experimental studies have revealed that some RNA sequences, e.g. compact viral genomes, can simultaneously encode functional RNA structures as well as proteins, and evidence is accumulating that this phenomenon may also be found in Eukaryotes. We here present the first comparative method, called RNA-DECODER, which explicitly takes the known protein-coding context of an RNA-sequence alignment into account in order to predict evolutionarily conserved secondary-structure elements, which may span both coding and non-coding regions. RNA-DECODER employs a stochastic context-free grammar together with a set of carefully devised phylogenetic substitution-models, which can disentangle and evaluate the different kinds of overlapping evolutionary constraints which arise. We show that RNA-DECODER's parameters can be automatically trained to successfully fold known secondary structures within the HCV genome. We scan the genomes of HCV and polio virus for conserved secondary-structure elements, and analyze performance as a function of available evolutionary information. On known secondary structures, RNA-DECODER shows a sensitivity similar to the programs MFOLD, PFOLD and RNAALIFOLD. When scanning the entire genomes of HCV and polio virus for structure elements, RNA-DECODER's results indicate a markedly higher specificity than MFOLD, PFOLD and RNAALIFOLD. PMID:15448187

Pedersen, Jakob Skou; Meyer, Irmtraud Margret; Forsberg, Roald; Simmonds, Peter; Hein, Jotun

2004-01-01

199

Organizational Structure and Student Behavior in Secondary School.  

ERIC Educational Resources Information Center

This report presents findings from four studies of adolescent behavior in high schools. A basic assumption was that organization structure has strong effects on behavior. The authors concluded that the large comprehensive high school's organization structure with emphasis on teacher initiated action, routine batch processing, and reliance on…

Cusick, Philip A.; And Others

1978-01-01

200

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

PubMed

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

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

2014-06-01

201

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

PubMed Central

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

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

2012-01-01

202

A Comparative Taxonomy of Parallel Algorithms for RNA Secondary Structure Prediction  

PubMed Central

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

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

2010-01-01

203

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

SciTech Connect

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

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

2008-01-01

204

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

PubMed Central

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

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

2006-01-01

205

Structural organization of the 16S ribosomal RNA from E. coli. Topography and secondary structure.  

PubMed Central

Extensive studies in our laboratory using different ribonucleases resulted in valuable data on the topography of the E.coli 16S ribosomal RNA within the native 30S subunit, within partially unfolded 30S subunits, in the free state, and in association with individual ribosomal proteins. Such studies have precise details on the accessibility of certain residues and delineated highly accessible RNA regions. Furthermore, they provided evidence that the 16S rRNA is organized in its subunit into four distinct domains. A secondary structure model of the E.coli 16S rRNA has been derived from these topographical data. Additional information from comparative sequence analyses of the small ribosomal subunit RNAs from other species sequenced so far has been used.

Stiegler, P; Carbon, P; Zuker, M; Ebel, J P; Ehresmann, C

1981-01-01

206

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

PubMed

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

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

2007-04-30

207

RnaViz, a program for the visualisation of RNA secondary structure  

Microsoft Academic Search

RnaViz is a user-friendly, portable, windows-type program for producing publication-quality secondary structure drawings of RNA molecules. Drawings can be created starting from DCSE alignment files if they incorporate structure information or from mfold ct files. The layout of a structure can be changed easily. Display of special structural elements such as pseudo-knots or unformatted areas is possible. Sequences can be

Peter De Rijk; Rupert De Wachter

1997-01-01

208

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

PubMed Central

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

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

2014-01-01

209

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

2012-01-01

210

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

Microsoft Academic Search

BACKGROUND: RNA secondary structure prediction methods based on probabilistic modeling can be developed using stochastic context-free grammars (SCFGs). Such methods can readily combine different sources of information that can be expressed probabilistically, such as an evolutionary model of comparative RNA sequence analysis and a biophysical model of structure plausibility. However, the number of free parameters in an integrated model for

Robin D. Dowell; Sean R. Eddy

2004-01-01

211

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

Microsoft Academic Search

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

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

1994-01-01

212

Downstream Secondary Structure Facilitates Recognition of Initiator Codons by Eukaryotic Ribosomes  

Microsoft Academic Search

Recognition of an AUG initiator codon in a suboptimal context improves when a modest amount of secondary structure is introduced near the beginning of the protein-coding sequence. This facilitating effect depends on the position of the downstream stem-loop (hairpin) structure. The strongest facilitation is seen when the hairpin is separated from the preceding AUG codon by 14 nucleotides. Because 14

Marilyn Kozak

1990-01-01

213

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

Microsoft Academic Search

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

Jaap Heringa

1999-01-01

214

An application software for protein secondary structure prediction based on peptide triplet units and artificial neural networks: Protein secondary structure prediction from amino acid sequences  

Microsoft Academic Search

On the basis of a bank of tendentious factors of tripeptide units, a protein secondary structure prediction system (PSSP) was built. Our research results revealed that PSSP represents a higher prediction accuracy of alpha-helix up to 89.45% on average, even the mean correct rate of alpha-helix also achieved 67.78% for all-beta proteins. PSSP only achieved a whole prediction accuracy of

Jie Yang; Tong-Yang Zhu; Xian-Chi Dong

2010-01-01

215

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

PubMed

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

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

2012-08-01

216

The Eect of RNA Secondary Structures on RNA-Ligand Binding and the Modier RNA Mechanism: A Quantitative Model  

Microsoft Academic Search

RNA-ligand binding often depends crucially on the local RNA secondary structure at the binding site. We develop here a model that quantitatively predicts the eect of RNA secondary structure on eectiv e RNA-ligand binding activities based on equilibrium thermodynamics and the explicit computations of partition functions for the RNA structures. A statistical test for the impact of a particular structural

Jorg Hackermuller; Nicole-Claudia Meisner; Manfred Auer; Markus Jaritz; Peter F. Stadler

2004-01-01

217

IPknot: fast and accurate prediction of RNA secondary structures with pseudoknots using integer programming  

PubMed Central

Motivation: Pseudoknots found in secondary structures of a number of functional RNAs play various roles in biological processes. Recent methods for predicting RNA secondary structures cover certain classes of pseudoknotted structures, but only a few of them achieve satisfying predictions in terms of both speed and accuracy. Results: We propose IPknot, a novel computational method for predicting RNA secondary structures with pseudoknots based on maximizing expected accuracy of a predicted structure. IPknot decomposes a pseudoknotted structure into a set of pseudoknot-free substructures and approximates a base-pairing probability distribution that considers pseudoknots, leading to the capability of modeling a wide class of pseudoknots and running quite fast. In addition, we propose a heuristic algorithm for refining base-paring probabilities to improve the prediction accuracy of IPknot. The problem of maximizing expected accuracy is solved by using integer programming with threshold cut. We also extend IPknot so that it can predict the consensus secondary structure with pseudoknots when a multiple sequence alignment is given. IPknot is validated through extensive experiments on various datasets, showing that IPknot achieves better prediction accuracy and faster running time as compared with several competitive prediction methods. Availability: The program of IPknot is available at http://www.ncrna.org/software/ipknot/. IPknot is also available as a web server at http://rna.naist.jp/ipknot/. Contact: satoken@k.u-tokyo.ac.jp; ykato@is.naist.jp Supplementary information: Supplementary data are available at Bioinformatics online.

Sato, Kengo; Kato, Yuki; Hamada, Michiaki; Akutsu, Tatsuya; Asai, Kiyoshi

2011-01-01

218

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

PubMed

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

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

2014-06-01

219

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

PubMed

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

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

2012-05-01

220

The FT-IR spectrometric analysis of the changes of polyphenol oxidase II secondary structure  

NASA Astrophysics Data System (ADS)

Polyphenol oxidase II is a novel protein purified from tobacco, which acts as a key role in plant defense system. From the analysis of FT-IR spectrums, Fourier self-deconvolution (FSD) spectrums and second-derivative spectrums of PPO II at different pH and peroxide PPO II adduct, the secondary structure fractions are analyzed. PPO II at low pH (pH=3.0) and peroxide PPO II adduct almost keep the same secondary structure of native PPO II. The percentages of ?-turn and random coil increase rapidly and the percentages of ?-helix and anti-parallel ?-sheet decrease rapidly at high pH (pH=10.0) comparing with that of native PPO II. All these conclusions are proved by the secondary structure calculations of circular dichroism spectrums in different states.

Shi, Chunhua; Dai, Ya; Liu, Qingliang; Xie, Yongshu; Xu, Xiaolong

2003-01-01

221

Impacts of maintenance dredged material disposal on macrobenthic structure and secondary productivity.  

PubMed

The results of a monitoring programme to assess the spatial impacts associated with ongoing dredged material disposal activity at a dispersive, coastal disposal site (southwest UK) are described. Benthic impacts were assessed using benthic community structure and secondary productivity estimates. Analyses of univariate indices (including secondary production) and multivariate community structure revealed differences between stations inside and those outside the disposal site were minimal. Generally, stations within and outside the disposal site were characterised by the same species. Regression models indicated that the variability in biological structure and secondary production was predominantly accounted for by natural variables (e.g., depth, sediment granulometry) with only a small amount of residual variability being due to contaminant variables. Thus, the elevated levels of certain contaminants in the vicinity of the disposal area were not sufficient to result in significant ecological or ecotoxicological changes. We ascribe such findings partly to the dispersive nature of the disposal site. PMID:21868044

Bolam, S G; Barry, J; Bolam, T; Mason, C; Rumney, H S; Thain, J E; Law, R J

2011-10-01

222

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

PubMed

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

Bindewald, Eckart; Shapiro, Bruce A

2006-03-01

223

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

PubMed

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

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

2013-11-28

224

A method for WD40 repeat detection and secondary structure prediction.  

PubMed

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

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

2013-01-01

225

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

PubMed

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

2014-05-01

226

Artificial Intelligence in Prediction of Secondary Protein Structure Using CB513 Database  

PubMed Central

In this paper we describe CB513 a non-redundant dataset, suitable for development of algorithms for prediction of secondary protein structure. A program was made in Borland Delphi for transforming data from our dataset to make it suitable for learning of neural network for prediction of secondary protein structure implemented in MATLAB Neural-Network Toolbox. Learning (training and testing) of neural network is researched with different sizes of windows, different number of neurons in the hidden layer and different number of training epochs, while using dataset CB513.

Avdagic, Zikrija; Purisevic, Elvir; Omanovic, Samir; Coralic, Zlatan

2009-01-01

227

Interplay between single-stranded binding proteins on RNA secondary structure  

NASA Astrophysics Data System (ADS)

RNA-protein interactions control the fate of cellular RNAs and play an important role in gene regulation. An interdependency between such interactions allows for the implementation of logic functions in gene regulation. We investigate the interplay between RNA-binding partners in the context of the statistical physics of RNA secondary structure and define a linear correlation function between the two partners as a measurement of the interdependency of their binding events. We demonstrate the emergence of a long-range power-law behavior of this linear correlation function. This suggests RNA secondary structure driven interdependency between binding sites as a general mechanism for combinatorial post-transcriptional gene regulation.

Lin, Yi-Hsuan; Bundschuh, Ralf

2013-11-01

228

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

PubMed

Mediation analysis in child and adolescent development research is possible using large secondary data sets. This article provides an overview of two statistical methods commonly used to test mediated effects in secondary analysis: multiple regression and structural equation modeling (SEM). Two empirical studies are presented to illustrate the respective circumstances in which the two methods are most useful. One study examines the mediated effect of parents' social capital on parent involvement in Head Start programs through parent-child bond. The other study assesses the mediating effects of structured routine activities, delinquent association, and prosocial belief on the relationship between religiosity and juvenile delinquency. PMID:21917711

Li, Spencer D

2011-06-01

229

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

Microsoft Academic Search

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

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

2001-01-01

230

Tfold: efficient in silico prediction of non-coding RNA secondary structures.  

PubMed

Predicting RNA secondary structures is a very important task, and continues to be a challenging problem, even though several methods and algorithms are proposed in the literature. In this article, we propose an algorithm called Tfold, for predicting non-coding RNA secondary structures. Tfold takes as input a RNA sequence for which the secondary structure is searched and a set of aligned homologous sequences. It combines criteria of stability, conservation and covariation in order to search for stems and pseudoknots (whatever their type). Stems are searched recursively, from the most to the least stable. Tfold uses an algorithm called SSCA for selecting the most appropriate sequences from a large set of homologous sequences (taken from a database for example) to use for the prediction. Tfold can take into account one or several stems considered by the user as belonging to the secondary structure. Tfold can return several structures (if requested by the user) when 'rival' stems are found. Tfold has a complexity of O(n(2)), with n the sequence length. The developed software, which offers several different uses, is available on the web site: http://tfold.ibisc.univ-evry.fr/TFold. PMID:20047957

Engelen, Stéfan; Tahi, Fariza

2010-04-01

231

The four ingredients of single-sequence RNA secondary structure prediction. A unifying perspective  

PubMed Central

Any method for RNA secondary structure prediction is determined by four ingredients. The architecture is the choice of features implemented by the model (such as stacked basepairs, loop length distributions, etc.). The architecture determines the number of parameters in the model. The scoring scheme is the nature of those parameters (whether thermodynamic, probabilistic, or weights). The parameterization stands for the specific values assigned to the parameters. These three ingredients are referred to as “the model.” The fourth ingredient is the folding algorithms used to predict plausible secondary structures given the model and the sequence of a structural RNA. Here, I make several unifying observations drawn from looking at more than 40 years of methods for RNA secondary structure prediction in the light of this classification. As a final observation, there seems to be a performance ceiling that affects all methods with complex architectures, a ceiling that impacts all scoring schemes with remarkable similarity. This suggests that modeling RNA secondary structure by using intrinsic sequence-based plausible “foldability” will require the incorporation of other forms of information in order to constrain the folding space and to improve prediction accuracy. This could give an advantage to probabilistic scoring systems since a probabilistic framework is a natural platform to incorporate different sources of information into one single inference problem.

Rivas, Elena

2013-01-01

232

Backbone assignment and secondary structure of the PsbQ protein from photosystem II.  

PubMed

PsbQ is one of the extrinsic proteins situated on the lumenal surface of photosystem II (PSII) in the higher plants and green algae. Its three-dimensional structure was determined by X-ray crystallography with exception of the residues 14-33. To obtain further details about its structure and potentially its dynamics, we approached the problem by NMR. In this paper we report (1)H, (15)N, and (13)C NMR assignments for the PsbQ protein. The very challenging oligo-proline stretches could be assigned using (13)C-detected NMR experiments that enabled the assignments of twelve out of the thirteen proline residues of PsbQ. The identification of PsbQ secondary structure elements on the basis of our NMR data was accomplished with the programs TALOS+, web server CS23D and CS-Rosetta. To obtain additional secondary structure information, three-bond H(N)-H(?) J-coupling constants and deviation of experimental (13)C(?) and (13)C(?) chemical shifts from random coil values were determined. The resulting "consensus" secondary structure of PsbQ compares very well with the resolved regions of the published X-ray crystallographic structure and gives a first estimate of the structure of the "missing link" (i.e. residues 14-33), which will serve as the basis for the further investigation of the structure, dynamics and interactions. PMID:21259076

Horni?áková, Michaela; Kohoutová, Jaroslava; Schlagnitweit, Judith; Wohlschlager, Christian; Ettrich, Rüdiger; Fiala, Radovan; Schoefberger, Wolfgang; Müller, Norbert

2011-10-01

233

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

PubMed Central

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

2014-01-01

234

Evolutionary Change in 5S RNA Secondary Structure and a Phylogenic Tree of 54 5S RNA Species  

Microsoft Academic Search

Secondary structure models of 54 5S RNA species are constructed based on the comparative analyses of their primary structure. All 5S RNAs examined have essentially the same secondary structure. However, there are revealing characteristic differences between eukaryotic and prokaryotic types. The prokaryotic 5S RNAs may be further classified into two types, one having 120 nucleotides (120-N type) and another having

Hiroshi Hori; Syozo Osawa

1979-01-01

235

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

PubMed

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

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

2014-01-01

236

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

NASA Astrophysics Data System (ADS)

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

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

2011-12-01

237

Prediction of RNA secondary structure by maximizing pseudo-expected accuracy  

PubMed Central

Background Recent studies have revealed the importance of considering the entire distribution of possible secondary structures in RNA secondary structure predictions; therefore, a new type of estimator is proposed including the maximum expected accuracy (MEA) estimator. The MEA-based estimators have been designed to maximize the expected accuracy of the base-pairs and have achieved the highest level of accuracy. Those methods, however, do not give the single best prediction of the structure, but employ parameters to control the trade-off between the sensitivity and the positive predictive value (PPV). It is unclear what parameter value we should use, and even the well-trained default parameter value does not, in general, give the best result in popular accuracy measures to each RNA sequence. Results Instead of using the expected values of the popular accuracy measures for RNA secondary structure prediction, which is difficult to be calculated, the pseudo-expected accuracy, which can easily be computed from base-pairing probabilities, is introduced. It is shown that the pseudo-expected accuracy is a good approximation in terms of sensitivity, PPV, MCC, or F-score. The pseudo-expected accuracy can be approximately maximized for each RNA sequence by stochastic sampling. It is also shown that well-balanced secondary structures between sensitivity and PPV can be predicted with a small computational overhead by combining the pseudo-expected accuracy of MCC or F-score with the ?-centroid estimator. Conclusions This study gives not only a method for predicting the secondary structure that balances between sensitivity and PPV, but also a general method for approximately maximizing the (pseudo-)expected accuracy with respect to various evaluation measures including MCC and F-score.

2010-01-01

238

Reactivity of molybdovanadophosphoric acids: Influence of the presence of vanadium in the primary and secondary structure  

SciTech Connect

The catalytic behavior in butadiene and n-butane oxidation of molybdovanadophosphoric acids with vanadium localized inside the primary (oxoanion) and/or the secondary structure is reported. The samples are characterized by infrared, [sup 31]P-NMR, [sup 51]V-NMR, and UV-visible diffuse reflectance spectroscopies in order to obtain information on the nature and localization of vanadium in the samples before reaction and the possible changes occurring during the course of the catalytic reaction. In particular, it is shown that vanadium localized initially in the secondary structure can exchange with the molybdenum atoms of the oxoanion during the catalytic reaction. Introduction of vanadium in the molybdophosphoric acid structure enhances the selective formation of maleic anhydride from the butadiene when vanadium is present both inside the oxoanion or localized in the secondary structure (before the catalytic tests), but the maximum in catalytic performance is found for different amounts of vanadium, depending on where the vanadium is localized initially. However, when present in the secondary structure, vanadium also has a negative influence on the activity of the heteropoly acid. On the contrary, in n-butane oxidation, the presence of vanadium enhances the rate of alkane activation due to the different rate-determining step. The presence of V ions also affects the maximum selectivity and yield to maleic anhydride from butane. V ions in the secondary structure are more selective at low conversion, while V ions inside the oxoanion are more selective at higher conversions and thus allow better maximum yields to maleic anhydride. 40 refs., 11 figs., 2 tabs.

Casarini, D.; Centi, G.; Lena, V.; Tvaruzkova, Z. (Universita di Bologna (Italy)); Jiru, P. (J. Heyrovsky Institute of Physical Chemistry and Electrochemistry, Prague (Czech Republic))

1993-10-01

239

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

PubMed

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. ogic.ca/projects/k2d3. Proteins 2011. © 2011 Wiley Periodicals, Inc. PMID:22095872

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

2011-09-14

240

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

PubMed

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

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

2013-01-01

241

RNA secondary structure modeling at consistent high accuracy using differential SHAPE.  

PubMed

RNA secondary structure modeling is a challenging problem, and recent successes have raised the standards for accuracy, consistency, and tractability. Large increases in accuracy have been achieved by including data on reactivity toward chemical probes: Incorporation of 1M7 SHAPE reactivity data into an mfold-class algorithm results in median accuracies for base pair prediction that exceed 90%. However, a few RNA structures are modeled with significantly lower accuracy. Here, we show that incorporating differential reactivities from the NMIA and 1M6 reagents-which detect noncanonical and tertiary interactions-into prediction algorithms results in highly accurate secondary structure models for RNAs that were previously shown to be difficult to model. For these RNAs, 93% of accepted canonical base pairs were recovered in SHAPE-directed models. Discrepancies between accepted and modeled structures were small and appear to reflect genuine structural differences. Three-reagent SHAPE-directed modeling scales concisely to structurally complex RNAs to resolve the in-solution secondary structure analysis problem for many classes of RNA. PMID:24742934

Rice, Greggory M; Leonard, Christopher W; Weeks, Kevin M

2014-06-01

242

RNAG: a new Gibbs sampler for predicting RNA secondary structure for unaligned sequences  

PubMed Central

Motivation: RNA secondary structure plays an important role in the function of many RNAs, and structural features are often key to their interaction with other cellular components. Thus, there has been considerable interest in the prediction of secondary structures for RNA families. In this article, we present a new global structural alignment algorithm, RNAG, to predict consensus secondary structures for unaligned sequences. It uses a blocked Gibbs sampling algorithm, which has a theoretical advantage in convergence time. This algorithm iteratively samples from the conditional probability distributions P(Structure | Alignment) and P(Alignment | Structure). Not surprisingly, there is considerable uncertainly in the high-dimensional space of this difficult problem, which has so far received limited attention in this field. We show how the samples drawn from this algorithm can be used to more fully characterize the posterior space and to assess the uncertainty of predictions. Results: Our analysis of three publically available datasets showed a substantial improvement in RNA structure prediction by RNAG over extant prediction methods. Additionally, our analysis of 17 RNA families showed that the RNAG sampled structures were generally compact around their ensemble centroids, and at least 11 families had at least two well-separated clusters of predicted structures. In general, the distance between a reference structure and our predicted structure was large relative to the variation among structures within an ensemble. Availability: The Perl implementation of the RNAG algorithm and the data necessary to reproduce the results described in Sections 3.1 and 3.2 are available at http://ccmbweb.ccv.brown.edu/rnag.html Contact: charles_lawrence@brown.edu Supplementary information: Supplementary data are available at Bioinformatics online.

Wei, Donglai; Alpert, Lauren V.; Lawrence, Charles E.

2011-01-01

243

Impact of residue accessible surface area on the prediction of protein secondary structures  

PubMed Central

Background The problem of accurate prediction of protein secondary structure continues to be one of the challenging problems in Bioinformatics. It has been previously suggested that amino acid relative solvent accessibility (RSA) might be an effective factor for increasing the accuracy of protein secondary structure prediction. Previous studies have either used a single constant threshold to classify residues into discrete classes (buries vs. exposed), or used the real-value predicted RSAs in their prediction method. Results We studied the effect of applying different RSA threshold types (namely, fixed thresholds vs. residue-dependent thresholds) on a variety of secondary structure prediction methods. With the consideration of DSSP-assigned RSA values we realized that improvement in the accuracy of prediction strictly depends on the selected threshold(s). Furthermore, we showed that choosing a single threshold for all amino acids is not the best possible parameter. We therefore used residue-dependent thresholds and most of residues showed improvement in prediction. Next, we tried to consider predicted RSA values, since in the real-world problem, protein sequence is the only available information. We first predicted the RSA classes by RVP-net program and then used these data in our method. Using this approach, improvement in prediction was also obtained. Conclusion The success of applying the RSA information on different secondary structure prediction methods suggest that prediction accuracy can be improved independent of prediction approaches. Thus, solvent accessibility can be considered as a rich source of information to help the improvement of these methods.

Momen-Roknabadi, Amir; Sadeghi, Mehdi; Pezeshk, Hamid; Marashi, Sayed-Amir

2008-01-01

244

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

PubMed

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

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

1996-07-15

245

Protein Secondary Structure Prediction Based on Position-specific Scoring Matrices  

Microsoft Academic Search

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

David T. Jones

1999-01-01

246

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

ERIC Educational Resources Information Center

An exercise using simple paper strips to illustrate protein helical and sheet secondary structures is presented. Drawing on the rich historical context of the use of physical models in protein biochemistry by early practitioners, in particular Linus Pauling, the purpose of this activity is to cultivate in students a hands-on, intuitive sense of…

Pikaart, Michael

2011-01-01

247

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

Microsoft Academic Search

The conformation of peptide and protein drugs in various microenvironments and the interaction with drug carriers such as liposomes are of considerable interest. In this study the influence of microenvironments such as pH, salt concentration, and surface charge on the secondary structure of a model protein, lysozyme, either in solution or entrapped in liposomes with various molar ratios of phosphatidylcholine

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

2010-01-01

248

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

Microsoft Academic Search

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

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

1997-01-01

249

An Iterated loop matching approach to the prediction of RNA secondary structures with pseudoknots  

Microsoft Academic Search

Motivation: Pseudoknots have generally been excluded from the prediction of RNA secondary structures due to its diffi- culty in modeling. Although, several dynamic programming algorithms exist for the prediction of pseudoknots using thermodynamic approaches, they are neither reliable nor effi- cient. On the other hand, comparative methods are more reliable, but are often done in an ad hoc manner and

Jianhua Ruan; Gary D. Stormo; Weixiong Zhang

2004-01-01

250

Decision tree-based formation of consensus protein secondary structure prediction  

Microsoft Academic Search

Motivation: Prediction of protein secondary structure provides information that is useful for other prediction methods like fold recognition and ab initio 3D prediction. A consensus prediction constructed from the output of several methods should yield more reliable results than each of the individual methods. Method: We present an approach that reveals subtle but systematic differences in the output of different

Joachim Selbig; Heinz-theodor Mevissen; Thomas Lengauer

1999-01-01

251

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

EPA Science Inventory

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

252

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

Microsoft Academic Search

The active structural acoustic control of a beam with classical boundary conditions using an active constrained layer damping and a secondary acoustic controller is investigated. The beam is placed on an infinite rigid baffle. It is excited by a plane wave acoustic load and radiates sound into an anechoic acoustic medium. The primary goal of the control mechanisms is to

Joshua Taekyoung Lee

2003-01-01

253

A Study of Protein Secondary Structure Hydrogen Bonds under Oxidizing Conditions  

Microsoft Academic Search

Molecular simulations show that hydrogen bond energies are stable between oxidized and unoxidized variants of the same protein, and that, consequentially, the secondary-structure elements are stable. Whilst there is no change in the energy of hydrogen bonds, it is shown that oxidation increases the number of hydrogen bonds between the oxidized histone octamer and its solvation layer. This analysis shows

Christopher M. Wood; H. J. Kadim

2007-01-01

254

Determination of endosperm protein secondary structure in hard wheat breeding lines using synchrotron infrared microspectroscopy  

Microsoft Academic Search

One molecular aspect of mature hard wheat protein quality for breadmaking is the relative amount of endosperm protein in the ?-helix form compared with that in other secondary structure forms including ?-sheet. Modeling of ?-helix and ?-sheet absorption bands that contribute to the amide I band at 1650cm?1 was applied to more than 1500 spectra in this study. The microscopic

Emily S. Bonwell; Tiffany L. Fisher; Allan K. Fritz; David L. Wetzel

2008-01-01

255

Secondary Structure in Solution of the Hydrophobic Protein of Soybean (HPS) as Revealed by H NMR  

Microsoft Academic Search

COSY, TOCSY and NOESY experiments have been used to assign sequentially the H 500 MHz NMR spectra of the Hydrophobic Protein of Soybean (HPS). Spin systems identification combined with sequential assignment allowed to identify the proton resonances of this 80 residues protein. Analysis of medium range connectivities showed that its secondary structure involved four helical fragments similarly located as in

Patrick Sodano; Marius Ptak

1995-01-01

256

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

ERIC Educational Resources Information Center

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

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

2011-01-01

257

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

SciTech Connect

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

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

2002-09-28

258

Near identity of 3- RNA secondary structure in bromoviruses and cucumber mosaic virus.  

PubMed

The 3- terminal sequences of RNAs 1, 2, 3 and 4 from each of the three bromoviruses (brome mosaic, cowpea chlorotic mottle and broad bean mottle viruses) and also from cucumber mosaic virus display interviral sequence similarity in addition to strong intraviral homology. Interviral similarity is much more evident when RNA secondary, rather than primary, structures are compared. The last 190 bases of the various RNAs can fold into strikingly similar, extensively base-paired secondary structures whose common features are supported by RNA structure mapping. The extreme 3' end of each viral RNA can base-pair in two distinct configurations. Bromovirus RNA 3s each contain an unusually accessible internal oligo(A) sequence which, in brome mosaic virus at least, is located in the intercistronic noncoding region. Functional implications of these structural features are discussed. PMID:7214524

Ahlquist, P; Dasgupta, R; Kaesberg, P

1981-01-01

259

Secondary structures of proteins and peptides in amphiphilic environments. (A review).  

PubMed Central

Many peptides and proteins that act at lipid--water interfaces assume a unique amphiphilic secondary structure which is induced by the anisotropy of the interface. By using synthetic peptides in which these inducible amphiphilic structures have been optimized, one can show that the amphiphilic alpha helix is a functional determinant of representative apolipoproteins, peptide toxins, and peptide hormones. By increasing the amphiphilicity of the structurally important regions of the molecule, one can enhance the biological activity of the peptide even beyond that of the naturally occurring polypeptide. It is proposed that rigid amphiphilic secondary structures such as alpha helix, beta sheet, or pi helix will be found in most medium-sized peptides acting at membranes and lipid--water interfaces.

Kaiser, E T; Kezdy, F J

1983-01-01

260

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

PubMed Central

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

Bajaj, Chandrajit; Goswami, Samrat; Zhang, Qin

2012-01-01

261

Polypurine DNAs and RNAs form secondary structures which may be tetra-stranded.  

PubMed Central

Polypurine DNAs and RNAs containing at least 33% guanine form a stable secondary structure at neutral pH and moderate ionic strengths. The tm's of the polymers increase with increasing guanine content. To eliminate possible structures three novel polymers, d(Gn2A)n, d(Gm6A)n and d(IA)n, as well as the random copolymer rr(G,A)n were were studied. Both d(Gn2A)n and d(IA)n can form a secondary structure whereas d(Gm6A)n and r(G,A)n cannot. Model building suggested two possible structures, one a duplex and the other a tetra-stranded polymer. The latter is considered to be the more likely, since previous X-ray diffraction studies have shown that rGn and rIn are tetra-stranded. Circular dichroism spectra are also consistent with such an interpretation.

Lee, J S; Evans, D H; Morgan, A R

1980-01-01

262

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

PubMed

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

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

1997-04-01

263

Prediction of Protein Secondary Structure by Combining Nearest-neighbor Algorithms and Multiple Sequence Alignments  

Microsoft Academic Search

Recently Yi & Lander used a neural network and nearest and nearest-neighbor method with a scoring system that combined a sequence-similarity matrix with the local structural environment scoring scheme described by Bowie and co-workers for predicting protein secondary structure. We have improved their scoring system by taking into consideration N and C-terminal positions of ?-helices and ?-strands and also ?-turns

Asaf A. Salamov; Victor V. Solovyev

1995-01-01

264

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

Microsoft Academic Search

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

Gianfranco Menestrina; Veronique Cabiaux; Mayra Tejuca

1999-01-01

265

Neutron and secondary gamma-ray doses in concrete structures. Final report  

Microsoft Academic Search

Adjoint Monte Carlo calculations have been made to determine the neutron and secondary-gamma doses along the vertical center line of a one-room concrete structure with and without windows. The doses are given as a function of geometric origin within the structure walls and roof. The neutron source used was that calculated at 1200 m in air from a 30-degree elevated

Mooney

1976-01-01

266

Conformational analysis of protein secondary structure during spray-drying of antibody/mannitol formulations.  

PubMed

Inhalation of spray-dried particles is a promising delivery route for proteins as an alternative to injection. Changes in the protein structure and aggregation have to be avoided. The effect of mannitol, a stabilizing agent typically used in both liquid and lyophilized protein formulations, on an antibody (IgG1) in a spray-dried powder was studied using different biophysical and chromatographic techniques. At first, different solutions composed of antibody (IgG1) and mannitol at a ratio between 20/80 and 100/0 IgG1/mannitol (100 mg/ml total solid) were investigated for their stability. Protein solutions containing the IgG1 showed mannitol-dependent aggregation. High amounts of mannitol (50-80%) exerted a destabilizing effect on the antibody and the aggregate 9 level increased to 2.6-4.2%. In contrast, solutions with only 20-40% mannitol showed the same amount of aggregates as the pure antibody solution. The antibody mannitol solutions were investigated by circular dichroism (CD) and Fourier transform infrared spectroscopy (FTIR) to evaluate whether changes in the protein secondary structure can be correlated with aggregation. Considering the sensitivity of the used methods and data evaluation, FTIR spectra did not reveal structural changes in the IgG1/mannitol solutions compared to the pure antibody, despite varying aggregate levels. Thermal stress was reflected in perturbations of the secondary structure, but mannitol-dependent aggregation could not be correlated to detectable alterations in the FTIR spectra. Analyzing the CD spectra revealed no distinctive change in the shape of the CD curve, indicating that the protein secondary structure is mainly retained. This is in agreement with the infrared data. Subsequently, the IgG1/mannitol solutions were spray-dried at Tin/Tout of 90/50 degrees C. Using ATR-FTIR for the investigation of the protein amide I band in the spray-dried powder revealed changes in the sub-components of the amide I band. This indicates that the peptide groups (CO and NH) of the protein are found in a different environment in the solid state, compared to the liquid protein formulation. After redissolution of the powders, the native structure of the pure antibody solution was found identical to the protein secondary structure before spray-drying, indicating that the protein secondary structure is not strongly altered in the dry state, and not affected by the spray-drying process. Thus, from the presented study it can be concluded that the formation of antibody aggregates in mannitol formulations cannot be correlated with significant perturbations of the protein secondary structure elements. PMID:17034996

Schüle, Stefanie; Friess, Wolfgang; Bechtold-Peters, Karoline; Garidel, Patrick

2007-01-01

267

Learning sparse models for a dynamic Bayesian network classifier of protein secondary structure  

PubMed Central

Background Protein secondary structure prediction provides insight into protein function and is a valuable preliminary step for predicting the 3D structure of a protein. Dynamic Bayesian networks (DBNs) and support vector machines (SVMs) have been shown to provide state-of-the-art performance in secondary structure prediction. As the size of the protein database grows, it becomes feasible to use a richer model in an effort to capture subtle correlations among the amino acids and the predicted labels. In this context, it is beneficial to derive sparse models that discourage over-fitting and provide biological insight. Results In this paper, we first show that we are able to obtain accurate secondary structure predictions. Our per-residue accuracy on a well established and difficult benchmark (CB513) is 80.3%, which is comparable to the state-of-the-art evaluated on this dataset. We then introduce an algorithm for sparsifying the parameters of a DBN. Using this algorithm, we can automatically remove up to 70-95% of the parameters of a DBN while maintaining the same level of predictive accuracy on the SD576 set. At 90% sparsity, we are able to compute predictions three times faster than a fully dense model evaluated on the SD576 set. We also demonstrate, using simulated data, that the algorithm is able to recover true sparse structures with high accuracy, and using real data, that the sparse model identifies known correlation structure (local and non-local) related to different classes of secondary structure elements. Conclusions We present a secondary structure prediction method that employs dynamic Bayesian networks and support vector machines. We also introduce an algorithm for sparsifying the parameters of the dynamic Bayesian network. The sparsification approach yields a significant speed-up in generating predictions, and we demonstrate that the amino acid correlations identified by the algorithm correspond to several known features of protein secondary structure. Datasets and source code used in this study are available at http://noble.gs.washington.edu/proj/pssp.

2011-01-01

268

Electric field structure inside the secondary island in the reconnection diffusion region  

NASA Astrophysics Data System (ADS)

Secondary islands have recently been intensively studied because of their essential role in dissipating energy during reconnection. Secondary islands generally form by tearing instability in a stretched current sheet, with or without guide field. In this article, we study the electric field structure inside a secondary island in the diffusion region using large-scale two-and-half dimensional particle-in-cell (PIC) simulation. Intense in-plane electric fields, which point toward the center of the island, form inside the secondary island. The magnitudes of the in-plane electric fields Ex and Ez inside the island are much larger than those outside the island in the surrounding diffusion region. The maximum magnitudes of the fields are about three times the B0VA, where B0 is the asymptotic magnetic field strength and VA is the Alfvén speed based on B0 and the initial current sheet density. Our results could explain the intense electric field (~100 mV/m) inside the secondary island observed in the Earth's magnetosphere. The electric field Ex inside the secondary island is primarily balanced by the Hall term (j × B)/ne, while Ez is balanced by a combination of (j × B)/ne, -(vi × B), and the divergence of electron pressure tensor, with (j × B)/ne term being dominant. This large Hall electric field is due to the large out-of-plane current density jy inside the island, which consists mainly of accelerated electrons forming a strong bulk flow in the -y direction. The electric field Ey shows a bipolar structure across the island, with negative Ey corresponding to negative Bz and positive Ey corresponding to positive Bz. It is balanced by (j × B)/ne and the convective electric field. There are significant parallel electric fields, forming a quadrupolar structure inside the island, with maximum amplitude of about 0.3B0VA.

Zhou, M.; Deng, X. H.; Huang, S. Y.

2012-04-01

269

Targeting nucleic acid secondary structures by antisense oligonucleotides designed through in vitro selection.  

PubMed Central

Using an in vitro selection approach, we have isolated oligonucleotides that can bind to a DNA hairpin structure. Complex formation of these oligonucleotides with the target hairpin involves some type of triple-stranded structure with noncanonical interaction, as indicated by bandshift assays and footprinting studies. The selected oligomers can block restriction endonuclease cleavage of the target hairpin in a sequence-specific manner. We demonstrate that in vitro selection can extend the antisense approach to functional targeting of secondary structure motifs. This could provide a basis for interfering with regulatory processes mediated by a variety of nucleic acid structures. Images Fig. 1 Fig. 2 Fig. 3 Fig. 4

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

1996-01-01

270

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

PubMed Central

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

Dowell, Robin D; Eddy, Sean R

2004-01-01

271

Differential mRNA decay within the transfer operon of plasmid R1: identification and analysis of an intracistronic mRNA stabilizer.  

PubMed

Processing of the transfer operon mRNA of the conjugative resistance plasmid R1-19 results in the accumulation of stable traA mRNAs. The stable traA transcripts found in vivo have identical 3' ends within downstream traL sequences, but vary at their 5' ends. The 3' ends determined coincide with the 3' base of a predicted large clover-leaf-like RNA secondary structure. Here we demonstrate that this putative RNA structure, although part of a coding sequences, stabilizes the upstream traA mRNA very efficiently. We also show that the 3' ends of the stable mRNAs are formed posttranscriptionally and not by transcription termination. Half-life determinations reveal the same half-lives of 13 +/- 2 min for the traA mRNAs transcribed from hybrid lac-traAL-cat test plasmids, the R1-19 plasmid, and the F plasmid. Protein expression experiments demonstrate that the processed stable traA mRNA is translationally active. Partial deletions of sequences corresponding to the predicted secondary structure within the traL coding region drastically reduce the chemical and functional half-life of the traA mRNA. The results presented here unambiguously demonstrate that the proposed secondary structure acts as an efficient intracistronic mRNA stabilizer. PMID:8602164

Koraimann, G; Teferle, K; Mitteregger, R; Wagner, S; Högenauer, G

1996-03-01

272

Correlation between recombination junctions and RNA secondary structure elements in poliovirus Sabin strains.  

PubMed

In order to test the hypothesis that RNA structural elements promote the distribution of certain types of recombination junctions in each one of the 2C and 3D poliovirus genomic regions (Sabin 3/Sabin 2 or Sabin 1 in 2C and Sabin 2/Sabin 1 or Sabin 3 in 3D), we searched in 2C and 3D regions of reference Sabin strains for high probability RNA structural elements that could promote recombination. Recombination junctions that were identified in clinical strains of this study, as well as in clinical strains of previous studies, were superimposed on RNA secondary structure models of 2C and 3D genomic regions. Furthermore, we created an in vitro model, based on double infection of cell-culture with two poliovirus strains, for the production and identification of recombinant Sabin strains in 2C and 3D regions. Our intention was to compare the results that refer to the correlation of recombination junctions and RNA secondary structures in 2C and 3D regions of clinical strains, with the respective results of the in vitro model. Most of the recombination junctions of the clinical strains were correlated with RNA secondary structure elements, which were identical between recombining Sabin strains, and also presented high predictive value. In consensus were, the respective results originated from the in vitro model. We propose that the distribution of specific types of recombination junctions in certain regions of Sabin strains is not fortuitous and is correlated with RNA secondary structure elements identical to both recombination partners. Furthermore, results of this study highlight an important role for the stem region of the RNA structure elements in promoting recombination. PMID:20640496

Dedepsidis, Evaggelos; Kyriakopoulou, Zaharoula; Pliaka, Vaia; Markoulatos, Panayotis

2010-10-01

273

Protein secondary structure prediction using support vector machine with advanced encoding schemes  

NASA Astrophysics Data System (ADS)

Over the decades, many studies have been done for the prediction of the protein structure. Since the protein secondary structure is closely related to the protein tertiary structure, many approaches begin with the prediction of secondary structure and apply the results to predict the tertiary structure. The recent trend of secondary structure prediction studies is mostly based on the neural network or the support vector machine (SVM). In this study, SVM is used as a machine learning tool for the prediction of secondary structure and several new encoding schemes, including orthogonal matrix, hydrophobicity matrix, BLOSUM62 substitution matrix and combined matrix of these, are developed and optimized to improve the prediction accuracy. Based on the best encoding scheme, each protein sequence is expressed as consecutive sliding windows and each amino acid inside a window is represented with 20 different matrix values. Once the optimal window length for six SVM binary classifiers is chosen to be 13 through many experiments, the new encoding scheme is tested based on this optimal window size with the 7-fold cross validation tests. The results show 2% increase in the accuracy of the binary classifiers when compared with the instances in which the classical orthogonal matrix is used. For the training and testing of the SVM binary classifiers, RS126 data sets is used since this is the common set adopted by the previous research groups. Finally, to combine the results of the six SVM binary classifiers, several existing tertiary classifiers are applied and the efficiency of each tertiary classifier is compared.

Hu, Hae-Jin; Pan, Yi; Harrison, Robert; Tai, Phang C.

2004-04-01

274

Simplified RNA secondary structure mapping by automation of SHAPE data analysis  

PubMed Central

SHAPE (Selective 2?-hydroxyl acylation analysed by primer extension) technology has emerged as one of the leading methods of determining RNA secondary structure at the nucleotide level. A significant bottleneck in using SHAPE is the complex and time-consuming data processing that is required. We present here a modified data collection method and a series of algorithms, embodied in a program entitled Fast Analysis of SHAPE traces (FAST), which significantly reduces processing time. We have used this method to resolve the secondary structure of the first ?900?nt of the hepatitis C virus (HCV) genome, including the entire core gene. We have also demonstrated the ability of SHAPE/FAST to detect the binding of a small molecule inhibitor to the HCV internal ribosomal entry site (IRES). In conclusion, FAST allows for high-throughput data processing to match the current high-throughput generation of data possible with SHAPE, reducing the barrier to determining the structure of RNAs of interest.

Pang, Phillip S.; Elazar, Menashe; Pham, Edward A.; Glenn, Jeffrey S.

2011-01-01

275

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

SciTech Connect

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

Andy T. Wu

2005-07-10

276

Genetic code redundancy and the evolutionary stability of protein secondary structure.  

PubMed

The genetic code has an inherent bias towards some amino acids because of the variable number of synonymous codons per amino acid. The extent to which these biases are expressed in protein secondary structure is described through the analysis of the overall amino acid compositions of the alpha-helix, beta-sheet, beta-turn and random coil segments elucidated by X-ray crystallography. Given the concept of neutral mutation in proteins, the allocation of synonyms in the genetic code appears to protect secondary structures from amino acid changes and discourages the appearance of chemically complex residues. The level of protection is similar for each structural form, despite their clear preferences for certain amino acids. The organization of the code is therefore relevant to the preservation of conformation seen in the evolution of many protein families. PMID:4058024

Dufton, M J

1985-10-01

277

Investigation of oxide layer structure on niobium surface using a secondary ion mass spectrometry  

NASA Astrophysics Data System (ADS)

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

Wu, A. T.

2006-07-01

278

The Drosophila ankyrin repeat protein cactus has a predominantly alpha-helical secondary structure.  

PubMed

The cactus protein is the Drosophila homologue of the mammalian I kappa B family of cytoplasmic anchor proteins. We have expressed in E. coli and purified a cactus fusion protein, CACT-Bgl. CACT-Bgl protein contains the six ankyrin repeat sequences which are necessary for specific binding to the Drosophila rel family transcription factor dorsal. We show that the purified CACT-Bgl protein can bind specifically to dorsal and, using circular dichroism spectroscopy, that the protein adopts a largely alpha-helical secondary structure. A further analysis of the ankyrin repeat domains of cactus, using an improved secondary structure prediction program indicates that the N-terminal of the repeat will form into a loop structure and the C-terminal section into an interrupted, amphipathic alpha-helix. On the basis of these findings we propose that the ankyrin repeats of cactus fold together into helical bundles interconnected by diverged loops. PMID:8253187

Gay, N J; Ntwasa, M

1993-12-01

279

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

PubMed Central

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

Berkhout, B; Schoneveld, I

1993-01-01

280

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

ERIC Educational Resources Information Center

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

Betoret, Fernando Domenech

2009-01-01

281

Recognition of secondary structures in proteins by a diiron(III) complex via a hydrolytic pathway.  

PubMed

The diiron(III) complex Fe(2)(DTPB)(mu(2)-O)(mu(2)-OAc)Cl(BF(4))(2) [DTPB = 1,1,4,7,7-pentakis(2'-benzimidazol-2-yl-methyl)triazaheptane, OAc = acetate] exhibits a similar affinity for proteins belonging to different structural patterns. However, this diiron complex is sensitive to secondary structures in a protein when it is used to promote the protein hydrolysis, indicating that some metal complexes, such as artificial proteolytic agents, could become a new hydrolytic probe of protein structures. PMID:16411678

Pan, Qunhui; Jiang, Wei; Liao, Zhanru; Zhang, Tianle; Liu, Changlin

2006-01-23

282

Electric field structure inside the secondary island in reconnection diffusion region  

NASA Astrophysics Data System (ADS)

Secondary islands have recently been intensively studied because of its essential role in energy dissipation during reconnection. It is generally formed due to tearing instability in a stretched current sheet with or without guide field. In this presentation we study the electric field structure inside the secondary island in diffusion region by large scale two-and-half dimensional Particle-In-Cell (PIC) simulation. Intense in-plane electric fields, which point toward the center of island, are formed inside the secondary island. The magnitudes of in-plane electric field Ex and Ez inside the island are much larger than those outside the island in diffusion region. Their maximum magnitudes are about 3 times the B0VA, where B0 is the asymptotic magnetic field strength and VA is the Alfvén speed based on B0 and initial current sheet density. Our results could explain the intense electric field (~100mV/m) inside the secondary island observed in the Earth magnetosphere. Ex inside the secondary island is primarily balanced by the Hall term (j×B)/ne, while Ez is balanced by a combination of (j×B)/ne, -(vi×B) and divergence of electron pressure tensor with (j×B)/ne term dominates. This large Hall electric field is due to the large out-of-plane current density jy inside the island, which is mainly carried by accelerated electrons forming strong bulk flow in the -y direction. Ey shows bipolar structure across the island, with negative Ey corresponding to negative Bz and vice versa. It is balanced by (j×B)/ne and convective electric field. There are significant parallel electric fields, forming quadrupolar structure, inside the island with largest amplitude about 0.3B0VA.

Zhou, M.; Deng, X. H.; Huang, S. Y.

2012-04-01

283

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

NASA Astrophysics Data System (ADS)

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

Schuster, Peter

2006-05-01

284

3S: shotgun secondary structure determination of long non-coding RNAs.  

PubMed

Long non-coding RNAs (lncRNAs) have emerged as an important class of RNAs playing key roles in development, disease and epigenetics. Knowledge of lncRNA structure may be critical in understanding function for many lncRNA systems. Due to the enormous number of possible folds for these sequences, secondary structure determination presents a significant challenge, both experimentally and computationally. Here, we present a new strategy capable of determining the RNA secondary structure in the wet lab without significant reliance on computational predictions. First, we chemically probe the entire lncRNA. Next, using a shotgun approach, we divide the RNA into overlapping fragments and probe these fragments. We then compare probing profiles of fragments with the profiles of the full RNA and identify similarities. Sequence regions with profiles that are similar in the fragment and full-length transcript possess only base pairing partners within the fragment. Thus, by experimentally folding smaller and smaller fragments of the full RNA and probing these chemically, we are able to isolate modular sub-domains, dramatically reducing the number of possible folds. The method also eliminates the possibility of pseudoknots within a modular sub-domain. The 3S technique is ideally suited for lncRNAs because it is designed for long RNA sequences. The 3S-determined secondary structure of a specific lncRNA in one species (e.g., human) enables searches for instances of the same lncRNA in other species. PMID:23927838

Novikova, Irina V; Dharap, Ashutosh; Hennelly, Scott P; Sanbonmatsu, Karissa Y

2013-09-15

285

Improved estimation of the secondary structures of proteins by vacuum-ultraviolet circular dichroism spectroscopy.  

PubMed

The vacuum-ultraviolet circular dichroism (VUVCD) spectra of 16 globular proteins (insulin, lactate dehydrogenase, glucose isomerase, lipase, conalbumin, transferrin, catalase, subtilisin A, alpha-amylase, staphylococcal nuclease, papain, thioredoxin, carbonic anhydrase, elastase, avidin, and xylanase) were successfully measured in aqueous solutions at 25 degrees C from 260 to 160 nm under a high vacuum using a synchrotron-radiation VUVCD spectrophotometer. These proteins exhibited characteristic CD spectra below 190 nm that were related to their different secondary structures, which could not be detected with a conventional CD spectrophotometer. The component spectra of alpha-helices, beta-strands, turns, and unordered structures were obtained by deconvolution analysis of the VUVCD spectra of 31 reference proteins including the 15 proteins reported in our previous paper [Matsuo, K. et al. (2004) J. Biochem. 135, 405-411]. Prediction of the secondary-structure contents using the SELCON3 program was greatly improved, especially for alpha-helices, by extending the short-wavelength limit of CD spectra to 160 nm and by increasing the number of reference proteins. The numbers of alpha-helix and beta-strand segments, which were calculated from the distorted alpha-helix and beta-strand contents, were close to those obtained on X-ray crystallography. These results demonstrate the usefulness of synchrotron-radiation VUVCD spectroscopy for the secondary structure analysis of proteins. PMID:16046451

Matsuo, Koichi; Yonehara, Ryuta; Gekko, Kunihiko

2005-07-01

286

Structural and functional characterization of a Dictyostelium gene encoding a DIF inducible, prestalk-enriched mRNA sequence.  

PubMed Central

The pDd56 mRNA sequence is highly enriched in prestalk over prespore cells and is inducible by DIF, the putative Dictyostelium stalk-specific morphogen. We show that the pDd56 gene is composed of forty one copies of a twenty four amino acid, cysteine rich repeat. This is highly homologus to a repeat which we have previously shown to compose the major fraction of the pDd63 mRNA, another DIF inducible, prestalk-enriched sequence. The predicted pDd56 protein contains a putative signal peptide but does not appear to contain a transmembrane segment. In combination these features suggest it to be an extrinsic protein and we confirm this elsewhere by showing that the pDd56 gene encodes a known, extracellular protein of the stalk. The pDd56 mRNA is dependent upon exogenous DIF for its accumulation. We show that this control is exerted at the transcriptional level and that a restriction fragment containing 1.7Kb of upstream sequence directs temporally-regulated expression of the gene. Images

Ceccarelli, A; McRobbie, S J; Jermyn, K A; Duffy, K; Early, A; Williams, J G

1987-01-01

287

Prediction of alpha-turns in proteins using PSI-BLAST profiles and secondary structure information.  

PubMed

In this paper a systematic attempt has been made to develop a better method for predicting alpha-turns in proteins. Most of the commonly used approaches in the field of protein structure prediction have been tried in this study, which includes statistical approach "Sequence Coupled Model" and machine learning approaches; i) artificial neural network (ANN); ii) Weka (Waikato Environment for Knowledge Analysis) Classifiers and iii) Parallel Exemplar Based Learning (PEBLS). We have also used multiple sequence alignment obtained from PSIBLAST and secondary structure information predicted by PSIPRED. The training and testing of all methods has been performed on a data set of 193 non-homologous protein X-ray structures using five-fold cross-validation. It has been observed that ANN with multiple sequence alignment and predicted secondary structure information outperforms other methods. Based on our observations we have developed an ANN-based method for predicting alpha-turns in proteins. The main components of the method are two feed-forward back-propagation networks with a single hidden layer. The first sequence-structure network is trained with the multiple sequence alignment in the form of PSI-BLAST-generated position specific scoring matrices. The initial predictions obtained from the first network and PSIPRED predicted secondary structure are used as input to the second structure-structure network to refine the predictions obtained from the first net. The final network yields an overall prediction accuracy of 78.0% and MCC of 0.16. A web server AlphaPred (http://www.imtech.res.in/raghava/alphapred/) has been developed based on this approach. PMID:14997542

Kaur, Harpreet; Raghava, G P S

2004-04-01

288

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

Microsoft Academic Search

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

Dirk Krüger; Andrea GARGASz

2008-01-01

289

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

PubMed Central

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

2011-01-01

290

Pairwise covariance adds little to secondary structure prediction but improves the prediction of non-canonical local structure  

SciTech Connect

Amino acid sequence probability distributions, or profiles, have been used successfully to predict secondary structure and local structure in proteins. Profile models assume the statistical independence of each position in the sequence, but the energetics of protein folding is better captured in a scoring function that is based on pairwise interactions, like a force field. I-sites motifs are short sequence/structure motifs that populate the protein structure database due to energy-driven convergent evolution. Here we show that a pairwise covariant sequence model does not predict alpha helix or beta strand significantly better overall than a profile-based model, but it does improve the prediction of certain loop motifs. The finding is best explained by considering secondary structure profiles as multivariant, all-or-none models, which subsume covariant models. Pairwise covariance is nonetheless present and energetically rational. Examples of negative design are present, where the covariances disfavor non-native structures. Measured pairwise covariances are shown to be statistically robust in cross-validation tests, as long as the amino acid alphabet is reduced to nine classes. We present an updated I-sites local structure motif library and web server that provide sequence covariance information for all types of local structure in globular proteins.

Bystroff, Christopher; Webb-Robertson, Bobbie-Jo M.

2009-05-06

291

Analysis of the secondary structure of a protein's N-terminal  

NASA Astrophysics Data System (ADS)

The major protein component from aleurone cells of barley (Hordeum vulgare L.), PACB, is related to 7S globulins present in other cereals and to the vicilin-type 7S globulins of legumes and cotton seed. It contains 4 subunits of about 20, 25, 40 and 50 kDa molecular weights. The N-terminal sequence of 16 amino acids (over 260 atoms) in the protein was previously determined, and our aim is the prediction of its secondary structure. The empirical Chou-Fasman method was applied in an improved version as well as the empirical DSC method (discrimination of protein secondary structure class) with quite similar results. A molecular dynamics simulation was also performed, using the FF99SB forcefield within AMBER version 9.0. Solvation effects were incorporated using the Born model. The results are compared and a 3D model is proposed.

Floare, C. G.; Bogdan, M.; Horovitz, O.; Mocanu, A.; Tomoaia-Cotisel, M.

2009-08-01

292

Length-dependent stability and strand length limits in antiparallel ?-sheet secondary structure  

PubMed Central

Designed peptides that fold autonomously to specific conformations in aqueous solution are useful for elucidating protein secondary structural preferences. For example, autonomously folding model systems have been essential for establishing the relationship between ?-helix length and ?-helix stability, which would be impossible to probe with ?-helices embedded in folded proteins. Here, we use designed peptides to examine the effect of strand length on antiparallel ?-sheet stability. ?-Helices become more stable as they grow longer. Our data show that a two-stranded ?-sheet (“?-hairpin”) becomes more stable when the strands are lengthened from five to seven residues, but that further strand lengthening to nine residues does not lead to further ?-hairpin stabilization for several extension sequences examined. (In one case, all-threonine extension, there may be an additional stabilization on strand lengthening from seven to nine residues.) These results suggest that there may be an intrinsic limit to strand length for most sequences in antiparallel ?-sheet secondary structure.

Stanger, Heather E.; Syud, Faisal A.; Espinosa, Juan F.; Giriat, Izabela; Muir, Tom; Gellman, Samuel H.

2001-01-01

293

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

PubMed

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

Hamodrakas, S J

1988-11-01

294

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

PubMed Central

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

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

2012-01-01

295

Two-photon circular dichroism of molecular structures simulating L-tryptophan residues in proteins with secondary structures  

NASA Astrophysics Data System (ADS)

Herein, we report on the calculation and the comparative analysis of the theoretical two-photon circular dichroism (TPCD) spectra of L-tryptophan (Trp) residues in proteins with secondary structures (?-helix, ?-strand and random coil) conformation, down to the far-UV region (FUV). The examination of the TPCD spectra of the different conformers in each configuration reveals distinctive fingerprints in the FUV, a dark spectral region for electronic circular dichroism (ECD). Our results show the potential of FUV-TPCD to identify and study protein structures in a region never assessed before but filled with important structural information.

Vesga, Yuly; Diaz, Carlos; Higgs, Mary; Hernandez, Florencio E.

2014-05-01

296

Structural requirement in Clostridium perfringens collagenase mRNA 5' leader sequence for translational induction through small RNA-mRNA base pairing.  

PubMed

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

Obana, Nozomu; Nomura, Nobuhiko; Nakamura, Kouji

2013-06-01

297

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

2010-01-01

298

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

Microsoft Academic Search

Using sequence data from the 28s ribosomal RNA (rRNA) genes of selected ver- tebrates, we investigated the effects that constraints imposed by secondary structure have on the phylogenetic analysis of rRNA sequence data. Our analysis indicates that characters from both base-pairing regions (stems) and non-base-pairing regions (loops) contain phylogenetic information, as judged by the level of support of the phylogenetic

Michael T. Dixon; David M. Hillis

1993-01-01

299

Analysis of RNA secondary structure by photochemical reversal of psoralen crosslinks.  

PubMed Central

Aminomethyltrioxsalen (AMT), a psoralen, is known to cause interstrand crosslinks in double stranded nucleic acids. We have demonstrated the photochemical reversal of this reaction, and have used this result to develop a method for identification of specific sequences which are adjacent because of RNA secondary structure formation. E. coli 5S rRNA is used as a model system. We isolated and characterized a product that is derived from the stem region of 5S RNA. Images

Rabin, D; Crothers, D M

1979-01-01

300

Estimation of protein secondary structure from FTIR spectra using neural networks  

Microsoft Academic Search

Secondary structure of proteins have been predicted using neural networks (NN) from their Fourier transform infrared spectra. Leave-one-out approach has been used to demonstrate the applicability of the method. A form of cross-validation is used to train NN to prevent the overfitting problem. Multiple neural network outputs are averaged to reduce the variance of predictions. The networks realized have been

Mete Severcan; Feride Severcan; Parvez I Haris

2001-01-01

301

FTIR?ATR Study of pH Effects on Egg Albumin Secondary Structure  

Microsoft Academic Search

The pH effects on the secondary structures of egg albumin were investigated using Fourier transform infrared–attenuated total reflection (FTIR?ATR) technique with a single?bounce diamond crystal. The albumin was first denatured in a series of solutions with pH ranging from 1 to 12. The albumin film was then cast on the ATR crystal from the albumin solution for the IR spectrum

Ping Y. Furlan; Steven A. Scott; Margaret H. Peaslee

2007-01-01

302

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

Microsoft Academic Search

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

Libuse A. Bobek; Hongsa Situ

2003-01-01

303

Adsorption properties and secondary porous structure of adsorbents with a molecular sieve action  

Microsoft Academic Search

Summary 1.The adsorption properties of granulated industrial samples of Linde molecular sieves 4A and 5A with respect to the vapors of substances whose molecules penetrate through the windows into the elementary spaces of the zeolite crystals are described satisfactorily by the potential theory of adsorption.2.The secondary porous structure of the granules, which is formed by gaps and spaces between touching

M. M. Dubinin; M. M. Vishnyakova; E. D. Zaverina; E. G. Zhukovskaya; E. A. Leont'ev; V. M. Luk'yanovich; A. I. Sarakhov

1961-01-01

304

Xenopus laevis 28S ribosomal RNA: a secondary structure model and its evolutionary and functional implications.  

PubMed Central

Based upon the three experimentally derived models of E. coli 23S rRNA (1-3) and the partial model for yeast 26S rRNA (4), which was deduced by homology to E. coli, we derived a secondary structure model for Xenopus laevis 28S rRNA. This is the first complete model presented for eukaryotic 28S rRNA. Compensatory base changes support the general validity of our model and offer help to resolve which of the three E. coli models is correct in regions where they are different from one another. Eukaryotic rDNA is longer than prokaryotic rDNA by virtue of introns, expansion segments and transcribed spacers, all of which are discussed relative to our secondary structure model. Comments are made on the evolutionary origins of these three categories and the processing fates of their transcripts. Functionally important sites on our 28S rRNA secondary structure model are suggested by analogy for ribosomal protein binding, the GTPase center, the peptidyl transferase center, and for rRNA interaction with tRNA and 5S RNA. We discuss how RNA-RNA interactions may play a vital role in translocation.

Clark, C G; Tague, B W; Ware, V C; Gerbi, S A

1984-01-01

305

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

PubMed Central

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

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

2012-01-01

306

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

PubMed

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

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

1982-01-01

307

Thermodynamic heuristics with case-based reasoning: combined insights for RNA pseudoknot secondary structure.  

PubMed

The secondary structure of RNA pseudoknots has been extensively inferred and scrutinized by computational approaches. Experimental methods for determining RNA structure are time consuming and tedious; therefore, predictive computational approaches are required. Predicting the most accurate and energy-stable pseudoknot RNA secondary structure has been proven to be an NP-hard problem. In this paper, a new RNA folding approach, termed MSeeker, is presented; it includes KnotSeeker (a heuristic method) and Mfold (a thermodynamic algorithm). The global optimization of this thermodynamic heuristic approach was further enhanced by using a case-based reasoning technique as a local optimization method. MSeeker is a proposed algorithm for predicting RNA pseudoknot structure from individual sequences, especially long ones. This research demonstrates that MSeeker improves the sensitivity and specificity of existing RNA pseudoknot structure predictions. The performance and structural results from this proposed method were evaluated against seven other state-of-the-art pseudoknot prediction methods. The MSeeker method had better sensitivity than the DotKnot, FlexStem, HotKnots, pknotsRG, ILM, NUPACK and pknotsRE methods, with 79% of the predicted pseudoknot base-pairs being correct. PMID:21696223

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

2011-08-01

308

Peptide Length Determines Equilibrium Secondary Structure in Protein-Analogous Micelles  

NASA Astrophysics Data System (ADS)

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

Tirrell, Matthew; Marullo, Rachel; Kastantin, Mark

2013-03-01

309

Application of PRV-1 mRNA expression level and JAK2V617F mutation for the differentiating between polycytemia vera and secondary erythrocytosis and assessment of treatment by interferon or hydroxyurea.  

PubMed

Increased PRV-1 mRNA expression and the presence of Jak2(V617F) mutation in peripheral blood granulocytes are specific markers for chronic myeloproliferative disorders (MPD), which facilitate the differential diagnosis between polycythemia vera (PV) and secondary erythrocytosis (SE) and may be helpful for monitoring treatment efficacy in MPD patients. We evaluated the presence of the Jak2V617F mutation and increased PRV-1 mRNA expression along with previously established markers - erythropoietin (EPO) independent colony formation (EEC) and erythropoietin level for diagnosis of PV and assessment of treatment efficiency. Increased PRV-1 expression was found in 37 out of 46 patients diagnosed with PV (80%), in 4 out of 15 patients diagnosed with essential thrombocythemia (ET) (27%) and in 4 out of 8 patients with chronic idiopathic myelofibrosis (CIMF) (50%), and increased PRV-1 expression plus EEC formation was observed in 19 of 36 examined MPD patients indicating the superiority of PVSG and WHO bone marrow criteria for the diagnosis of ET, PV and CIMF. We could confirm a very high sensitivity, specificity and utility of the Jak2(V617F) mutation for differential diagnosis between PV and SE. Spontaneous EEC, serum EPO levels, PRV-1 expression was evaluated in 22 PV patients who carried the Jak2(V617F) mutation. A concordance of increased PRV-1 expression and presence of Jak2(V617F) mutation in 19/22 (85%); of increased PRV-1/Jak2/EEC in 14/22 (63%); and of Jak2/PRV-1/EEC/low Epo level in 10/22 (45%) patients was found indicating the superiority of the presence of Jak2(V617F) mutation for the diagnosis of PV. IFN-alpha therapy in patients with PV was more effective then hydroxyurea treatment and significantly reduced increased PRV-1 expression together with higher levels of Jak2(V617F) mutation (50-100%) in PV patients treated with hydroxy urea (HU) and lower levels of Jak2(V617F) mutation (35-90%) in PV patients treated with IFN-alpha. Normal PRV-1 expression level was observed in 44% of PV patients who achieved clinical remission and only in 3% of patient who did not. These preliminary observations indicate that the Jak2(V617F) mutation in particular and PRV-1 overexpression appear to be suitable markers for monitoring treatment efficiency in prospective randomised clinical studies comparing pegylated interferon and hydroxyurea in well defined PV patients with a clear indication for cytoreductive therapy. PMID:17852451

Tutaeva, V; Misurin, A V; Michiels, J J; Rozenberg, J M; Sokolova, M A; Ivanova, V L; Kolosheinova, T I; Manakova, T E; Levina, A A; Semenova, E A; Khoroshko, N D

2007-12-01

310

ProbKnot: fast prediction of RNA secondary structure including pseudoknots.  

PubMed

It is a significant challenge to predict RNA secondary structures including pseudoknots. Here, a new algorithm capable of predicting pseudoknots of any topology, ProbKnot, is reported. ProbKnot assembles maximum expected accuracy structures from computed base-pairing probabilities in O(N(2)) time, where N is the length of the sequence. The performance of ProbKnot was measured by comparing predicted structures with known structures for a large database of RNA sequences with fewer than 700 nucleotides. The percentage of known pairs correctly predicted was 69.3%. Additionally, the percentage of predicted pairs in the known structure was 61.3%. This performance is the highest of four tested algorithms that are capable of pseudoknot prediction. The program is available for download at: http://rna.urmc.rochester.edu/RNAstructure.html. PMID:20699301

Bellaousov, Stanislav; Mathews, David H

2010-10-01

311

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

PubMed Central

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

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

2008-01-01

312

Secondary structure of protamine in sperm nuclei: an infrared spectroscopy study  

PubMed Central

Background Protamines are small basic proteins that condense the DNA in mature spermatozoa. Typical protamines are of simple composition and very arginine-rich, usually in the range of 60-80%. Arginine residues are distributed in a number of stretches separated by neutral amino acids. We have used Fourier transform infrared spectroscopy (FTIR) to gain access for the first time to the secondary structure of protamines in sperm nuclei. This technique is particularly well suited to the study of DNA-bound protamine in whole nuclei since it is not affected by turbidity. Results We show that DNA -bound salmon (salmine) and squid protamines contain ?-helix, ?-turns and a proportion of other structures not stabilized by intramolecular hydrogen bonding. No ?-sheet was observed. In salmine, the ?-helix amounted to ~20%, while in squid protamine it reached ~40%. In contrast, the structure not stabilized by intermolecular hydrogen bonding was more abundant in salmine (~40%) than in squid protamine (~20%). Both protamines contained ~40% ?-turns. The different helical potential of salmine and squid protamine was confirmed by structure predictions and CD in the presence of trifluoroethanol. Conclusion DNA-bound protamine in sperm nuclei contains large amounts of defined secondary structure stabilized by intramolecular hydrogen bonding. Both salmine and squid protamine contain similar amounts of ?-turns, but differ in the proportions of ?-helix and non-hydrogen bonded conformations. In spite of the large differences in the proportions of secondary structure motifs between salmon and squid protamines, they appear to be equally efficient in promoting tight hexagonal packing of the DNA molecules in sperm nuclei.

2011-01-01

313

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

PubMed

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

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

2014-01-01

314

The influence of the secondary relaxation processes on the structural relaxation in glass-forming materials  

NASA Astrophysics Data System (ADS)

In the frame of fractional-kinetic approach, the model of the structural ?-relaxation in the presence of the secondary ?-relaxation processes is suggested. The model is based on the rigorous bond between ?-processes with ?-process and leads to the generalized and justified expression for the complex dielectric permittivity (CDP). It allows to form a new sight on the problem of the fitting of multi-peak structure of the dielectric loss spectra in glass-forming materials. The consistency of the CDP expressions obtained is based on a good fit of experimental data for binary methanol-water mixtures.

Khamzin, A. A.; Popov, I. I.; Nigmatullin, R. R.

2013-06-01

315

Two metallothionein genes from mud loach Misgurnus mizolepis (Teleostei; Cypriniformes): gene structure, genomic organization, and mRNA expression analysis.  

PubMed

Two metallothionein genes, MLMT-IA and MLMT-IB, were isolated and characterized from the mud loach Misgurnus mizolepis (Teleostei; Cypriniformes). For these MTs, we determined a tandem "tail-to-head" genomic organizational pattern, identified conserved genomic features, showed high sequence identities in the coding regions, and examined the closest phylogenetic affiliation, suggesting their divergence by a recent gene duplication event. However, the 5'-flanking upstream regions in MLMT-IA and MLMT-IB exposed large differences in the composition and distribution patterns of various transcription factor binding motifs, especially regarding the organization of the metal response element clusters. Real-time RT-PCR assays showed that mRNA levels of both MLMT-IA and MLMT-IB isoforms were variable among tissues and the ratios between them were also variable across tissues, although the MLMT-IA was always predominant in every adult tissue tested. We also found that the MLMT-IA and MLMT-IB mRNA expression levels were regulated dynamically during embryonic and larval development stages, in which the basal expression level of MLMT-IA was also consistently higher than that of MLMT-IB. Upon acute in vivo metal exposure to cadmium, chromium, copper, iron, manganese, nickel, or zinc at 5 microM for 48 h, the transcriptional modulations of MLMT-IA and MLMT-IB were quite different from each other and the type of response was affected significantly by the kind of metals and tissues. PMID:19383548

Cho, Young Sun; Lee, Sang Yoon; Kim, Keun-Yong; Nam, Yoon Kwon

2009-08-01

316

RNA folding with soft constraints: reconciliation of probing data and thermodynamic secondary structure prediction  

PubMed Central

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 and probing experiments. The thermodynamic energy parameters are adjusted using ‘pseudo-energies’ to minimize the discrepancy between prediction and experiment. Our framework differs from related approaches that used pseudo-energies in several key aspects. (i) The energy model is only changed when necessary and no adjustments are made if prediction and experiment are consistent. (ii) Pseudo-energies remain biophysically interpretable and hold positional information where experiment and model disagree. (iii) The whole thermodynamic ensemble of structures is considered thus allowing to reconstruct mixtures of suboptimal structures from seemingly contradicting data. (iv) The noise of the energy model and the experimental data is explicitly modeled leading to an intuitive weighting factor through which the problem can be seen as folding with ‘soft’ constraints of different strength. We present an efficient algorithm to iteratively calculate pseudo-energies within this framework and demonstrate how this approach can be used in combination with SHAPE chemical probing data to improve secondary structure prediction. We further demonstrate that the pseudo-energies correlate with biophysical effects that are known to affect RNA folding such as chemical nucleotide modifications and protein binding.

Washietl, Stefan; Hofacker, Ivo L.; Stadler, Peter F.; Kellis, Manolis

2012-01-01

317

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

PubMed Central

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

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

2003-01-01

318

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

PubMed Central

We present a de novo re-determination of the secondary (2°) structure and domain architecture of the 23S and 5S rRNAs, using 3D structures, determined by X-ray diffraction, as input. In the traditional 2° structure, the center of the 23S rRNA is an extended single strand, which in 3D is seen to be compact and double helical. Accurately assigning nucleotides to helices compels a revision of the 23S rRNA 2° structure. Unlike the traditional 2° structure, the revised 2° structure of the 23S rRNA shows architectural similarity with the 16S rRNA. The revised 2° structure also reveals a clear relationship with the 3D structure and is generalizable to rRNAs of other species from all three domains of life. The 2° structure revision required us to reconsider the domain architecture. We partitioned the 23S rRNA into domains through analysis of molecular interactions, calculations of 2D folding propensities and compactness. The best domain model for the 23S rRNA contains seven domains, not six as previously ascribed. Domain 0 forms the core of the 23S rRNA, to which the other six domains are rooted. Editable 2° structures mapped with various data are provided (http://apollo.chemistry.gatech.edu/RibosomeGallery).

Petrov, Anton S.; Bernier, Chad R.; Hershkovits, Eli; Xue, Yuzhen; Waterbury, Chris C.; Hsiao, Chiaolong; Stepanov, Victor G.; Gaucher, Eric A.; Grover, Martha A.; Harvey, Stephen C.; Hud, Nicholas V.; Wartell, Roger M.; Fox, George E.; Williams, Loren Dean

2013-01-01

319

Crystal structures of human DcpS in ligand-free and m7GDP-bound forms suggest a dynamic mechanism for scavenger mRNA decapping.  

PubMed

Eukaryotic cells utilize DcpS, a scavenger decapping enzyme, to degrade the residual cap structure following 3'-5' mRNA decay, thereby preventing the premature decapping of the capped long mRNA and misincorporation of methylated nucleotides in nucleic acids. We report the structures of DcpS in ligand-free form and in a complex with m7GDP. apo-DcpS is a symmetric dimer, strikingly different from the asymmetric dimer observed in the structures of DcpS with bound cap analogues. In contrast, and similar to the m7GpppG-DcpS complex, DcpS with bound m7GDP is an asymmetric dimer in which the closed state appears to be the substrate-bound complex, whereas the open state mimics the product-bound complex. Comparisons of these structures revealed conformational changes of both the N-terminal swapped-dimeric domain and the cap-binding pocket upon cap binding. Moreover, Tyr273 in the cap-binding pocket displays remarkable conformational changes upon cap binding. Mutagenesis and biochemical analysis suggest that Tyr273 seems to play an important role in cap binding and product release. Examination of the crystallographic B-factors indicates that the N-terminal domain in apo-DcpS is inherently flexible, and in a dynamic state ready for substrate binding and product release. PMID:15769464

Chen, Nan; Walsh, Martin A; Liu, Yuying; Parker, Roy; Song, Haiwei

2005-04-01

320

The regulation of mRNA stability in mammalian cells: 2.0.  

PubMed

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

Wu, Xiangyue; Brewer, Gary

2012-05-25

321

The Regulation of mRNA Stability in Mammalian Cells: 2.0  

PubMed Central

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

Wu, Xiangyue; Brewer, Gary

2012-01-01

322

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

PubMed

We present TT2NE, a new algorithm to predict RNA secondary structures with pseudoknots. The method is based on a classification of RNA structures according to their topological genus. TT2NE is guaranteed to find the minimum free energy structure regardless of pseudoknot topology. This unique proficiency is obtained at the expense of the maximum length of sequences that can be treated, but comparison with state-of-the-art algorithms shows that TT2NE significantly improves the quality of predictions. Analysis of TT2NE's incorrect predictions sheds light on the need to study how sterical constraints limit the range of pseudoknotted structures that can be formed from a given sequence. An implementation of TT2NE on a public server can be found at http://ipht.cea.fr/rna/tt2ne.php. PMID:21593129

Bon, Michaël; Orland, Henri

2011-08-01

323

Advances in RNA Secondary and Tertiary Structure Analysis by Chemical Probing  

PubMed Central

RNA is arguably the most versatile biological macromolecule due to its ability both to encode and to manipulate genetic information. The diverse roles of RNA depend on its ability to fold back on itself to form biologically functional structures that bind small molecules and large protein ligands, to change conformation, and to affect the cellular regulatory state. These features of RNA biology can be structurally interrogated using chemical mapping experiments. The usefulness and applications of RNA chemical probing technologies have expanded dramatically over the past five years due to several critical advances. These innovations include new sequence-independent RNA chemistries, algorithmic tools for high-throughput analysis of complex data sets composed of thousands of measurements, new approaches for interpreting chemical probing data for both secondary and tertiary structure prediction, facile methods for following time-dependent processes, and the willingness of individual research groups to tackle increasingly bold problems in RNA structural biology.

Weeks, Kevin M.

2010-01-01

324

Conformational properties of phospholipases A2. Secondary-structure prediction, circular dichroism and relative interface hydrophobicity.  

PubMed

The sequences of 32 phospholipases A2 (EC 3.1.1.4) were analysed by secondary-structure prediction and the results were compared with the available crystallographic data. Good agreement is evident between prediction and experiment, especially for helical structure. Circular dichroic spectra were also determined for six enzymes from Elapid snake venom and these, in association with previously published spectra, confirm the main implication of the predictions, namely that all the homologues have qualitatively similar tertiary structures. Consideration was then given to possible structure/activity relationships in the light of the above findings. The relative hydrophobicity/hydrophilicity of the area of the enzyme thought to interact with lipid/water interfaces was predicted and certain correlations were noted with relative penetrating power, species of origin and the presence of beta-neurotoxic properties. PMID:6662109

Dufton, M J; Eaker, D; Hider, R C

1983-12-15

325

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

PubMed

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

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

2010-02-01

326

In situ protein secondary structure determination in ice: Raman spectroscopy-based process analytical tool for frozen storage of biopharmaceuticals.  

PubMed

A Raman spectroscopy-based method for in situ monitoring of secondary structural composition of proteins during frozen and thawed storage was developed. A set of reference proteins with different ?-helix and ?-sheet compositions was used for calibration and validation in a chemometric approach. Reference secondary structures were quantified with circular dichroism spectroscopy in the liquid state. Partial least squares regression models were established that enable estimation of secondary structure content from Raman spectra. Quantitative secondary structure determination in ice was accomplished for the first time and correlation with existing (qualitative) protein structural data from the frozen state was achieved. The method can be used in the presence of common stabilizing agents and is applicable in an industrial freezer setup. Raman spectroscopy represents a powerful, noninvasive, and flexibly applicable tool for protein stability monitoring during frozen storage. © 2014 Wiley Periodicals, Inc. and the American Pharmacists Association J Pharm Sci 103:2287-2295, 2014. PMID:24985932

Roessl, Ulrich; Leitgeb, Stefan; Pieters, Sigrid; De Beer, Thomas; Nidetzky, Bernd

2014-08-01

327

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

ERIC Educational Resources Information Center

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

Ellerbrock, Cheryl R.; Kiefer, Sarah M.

2013-01-01

328

Rapid protein domain assignment from amino acid sequence using predicted secondary structure  

PubMed Central

The elucidation of the domain content of a given protein sequence in the absence of determined structure or significant sequence homology to known domains is an important problem in structural biology. Here we address how successfully the delineation of continuous domains can be accomplished in the absence of sequence homology using simple baseline methods, an existing prediction algorithm (Domain Guess by Size), and a newly developed method (DomSSEA). The study was undertaken with a view to measuring the usefulness of these prediction methods in terms of their application to fully automatic domain assignment. Thus, the sensitivity of each domain assignment method was measured by calculating the number of correctly assigned top scoring predictions. We have implemented a new continuous domain identification method using the alignment of predicted secondary structures of target sequences against observed secondary structures of chains with known domain boundaries as assigned by Class Architecture Topology Homology (CATH). Taking top predictions only, the success rate of the method in correctly assigning domain number to the representative chain set is 73.3%. The top prediction for domain number and location of domain boundaries was correct for 24% of the multidomain set (±20 residues). These results have been put into context in relation to the results obtained from the other prediction methods assessed.

Marsden, Russell L.; McGuffin, Liam J.; Jones, David T.

2002-01-01

329

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

PubMed

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

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

2014-08-01

330

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

NASA Astrophysics Data System (ADS)

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

Yoda, Takao; Sugita, Yuji; Okamoto, Yuko

2004-12-01

331

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.

2006-12-01

332

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

SciTech Connect

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

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

1986-03-15

333

Linear optimization of predictors for secondary structure. Application to transbilayer segments of membrane proteins.  

PubMed

Sliding-window averaging of amino acid properties is a standard method for predicting protein secondary structure. For example, transmembrane segments are predicted to occur near the peaks in a hydropathy plot of a membrane protein. Such a scheme (linear convolutional recognizer, LCR) assigns a number (weight) to each type of monomer, and then convolutes some window function with the sequence of weights. The window has commonly been rectangular, and the weights derived from singlet amino acid frequencies in proteins of known secondary structure or from physical properties of amino acids. The accuracy of the windows and weights have remained unknown. We use linear optimization theory to develop a general method for approximating the optimal window and weights for a LCR. The method assumes that one knows the sequences of one or more chains and the locations of their "features", regions having the secondary structure of interest. We present formulae for quantifying the accuracy of predictors. We show why the optimal LCR is more accurate than methods based on the differences between singlet monomer frequencies inside and outside features. The advantage of an optimal LCR is that its weights inherently include correlations between nearby monomer positions. The optimal predictor is not perfect though. We argue that its inaccuracy is an intrinsic limitation of linear predictors based on monomer weights. As a practical example, we study predictors for transbilayer segments of membrane proteins. We estimate the optimal weights and windows for the two bacterial photosynthetic reaction centers whose three-dimensional structures are known. The resultant LCR, which is more accurate than previous ones, is still inexact. We apply it to bacteriorhodopsin and halorhodopsin. Several non-linear generalizations are examined as possible improvements to the LCR method: non-linear combinations of linear predictors and windowed Fourier transforms of the weight sequences. The former do not significantly increase the accuracy, while the latter reveal a weak negative correlation between the segments and periodic variations of the weights. PMID:2685329

Edelman, J; White, S H

1989-11-01

334

The structural basis of Edc3- and Scd6-mediated activation of the Dcp1:Dcp2 mRNA decapping complex  

PubMed Central

The Dcp1:Dcp2 decapping complex catalyses the removal of the mRNA 5? cap structure. Activator proteins, including Edc3 (enhancer of decapping 3), modulate its activity. Here, we solved the structure of the yeast Edc3 LSm domain in complex with a short helical leucine-rich motif (HLM) from Dcp2. The motif interacts with the monomeric Edc3 LSm domain in an unprecedented manner and recognizes a noncanonical binding surface. Based on the structure, we identified additional HLMs in the disordered C-terminal extension of Dcp2 that can interact with Edc3. Moreover, the LSm domain of the Edc3-related protein Scd6 competes with Edc3 for the interaction with these HLMs. We show that both Edc3 and Scd6 stimulate decapping in vitro, presumably by preventing the Dcp1:Dcp2 complex from adopting an inactive conformation. In addition, we show that the C-terminal HLMs in Dcp2 are necessary for the localization of the Dcp1:Dcp2 decapping complex to P-bodies in vivo. Unexpectedly, in contrast to yeast, in metazoans the HLM is found in Dcp1, suggesting that details underlying the regulation of mRNA decapping changed throughout evolution.

Fromm, Simon A; Truffault, Vincent; Kamenz, Julia; Braun, Joerg E; Hoffmann, Niklas A; Izaurralde, Elisa; Sprangers, Remco

2012-01-01

335

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.

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

2013-01-01

336

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

PubMed Central

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

Zhong, Cuncong; Tang, Haixu; Zhang, Shaojie

2010-01-01

337

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

PubMed

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

Zhong, Cuncong; Tang, Haixu; Zhang, Shaojie

2010-10-01

338

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

PubMed Central

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

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

1984-01-01

339

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

PubMed

Complementary neutron- and light-scattering results on nine proteins and amino acids reveal the role of rigidity and secondary structure in determining the time- and lengthscales of low-frequency collective vibrational dynamics in proteins. These dynamics manifest in a spectral feature, known as the boson peak (BP), which is common to all disordered materials. We demonstrate that BP position scales systematically with structural motifs, reflecting local rigidity: disordered proteins appear softer than ?-helical proteins; which are softer than ?-sheet proteins. Our analysis also reveals a universal spectral shape of the BP in proteins and amino acid mixtures; superimposable on the shape observed in typical glasses. Uniformity in the underlying physical mechanism, independent of the specific chemical composition, connects the BP vibrations to nanometer-scale heterogeneities, providing an experimental benchmark for coarse-grained simulations, structure/rigidity relationships, and engineering of proteins for novel applications. PMID:24940784

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

2014-06-17

340

Neural-network design applied to protein-secondary-structure predictions  

NASA Astrophysics Data System (ADS)

The success of neural networks is often limited by a sparse database of training examples, deficient neural-network architectures, and nonglobal optimization of the network variables. The convolution of these three problems has curtailed the application of network models to protein-structure predictions, where homology modeling or information theory approaches are considered better controlled alternatives. This paper introduces our broad objective of disentangling the three degrading features of neural networks cited above, beginning with improved designs of network architectures used in the prediction of protein secondary structure. This work demonstrates that network architecture design considerations greatly improve generalization and more efficiently extract complex sequence-structure relationships from the existing database, as compared to arbitrary architectures with the same size input window.

Yu, Richard C.; Head-Gordon, Teresa

1995-04-01

341

Prediction of Long Loops with Embedded Secondary Structure using the Protein Local Optimization Program  

PubMed Central

Robust homology modeling to atomic-level accuracy requires in the general case successful prediction of protein loops containing small segments of secondary structure. Further, as loop prediction advances to success with larger loops, the exclusion of loops containing secondary structure becomes awkward. Here, we extend the applicability of the Protein Local Optimization Program (PLOP) to loops up to 17 residues in length that contain either helical or hairpin segments. In general, PLOP hierarchically samples conformational space and ranks candidate loops with a high-quality molecular mechanics force field. For loops identified to possess ?-helical segments, we employ an alternative dihedral library composed of (?,?) angles commonly found in helices. The alternative library is searched over a user-specified range of residues that define the helical bounds. The source of these helical bounds can be from popular secondary structure prediction software or from analysis of past loop predictions where a propensity to form a helix is observed. Due to the maturity of our energy model, the lowest energy loop across all experiments can be selected with an accuracy of sub-Ångström RMSD in 80% of cases, 1.0 to 1.5 Å RMSD in 14% of cases, and poorer than 1.5 Å RMSD in 6% of cases. The effectiveness of our current methods in predicting hairpin-containing loops is explored with hairpins up to 13 residues in length and again reaching an accuracy of sub-Ångström RMSD in 83% of cases, 1.0 to 1.5 Å RMSD in 10% of cases, and poorer than 1.5 Å RMSD in 7% of cases. Finally, we explore the effect of an imprecise surrounding environment, in which side chains, but not the backbone, are initially in perturbed geometries. In these cases, loops perturbed to 3Å RMSD from the native environment were restored to their native conformation with sub-Ångström RMSD.

Miller, Edward B.; Murrett, Colleen S.; Zhu, Kai; Zhao, Suwen; Goldfeld, Dahlia A.; Bylund, Joseph H.; Friesner, Richard A.

2013-01-01

342

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

SciTech Connect

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

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

1998-01-01

343

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

PubMed Central

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

Bouziane, Hafida; Messabih, Belhadri; Chouarfia, Abdallah

2011-01-01

344

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

NASA Astrophysics Data System (ADS)

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

Lee, Chang-Yong

2013-10-01

345

Prediction of protein secondary structure by combining nearest-neighbor algorithms and multiple sequence alignments.  

PubMed

Recently Yi & Lander used a neural network and nearest-neighbor method with a scoring system that combined a sequence-similarity matrix with the local structural environment scoring scheme described by Bowie and co-workers for predicting protein secondary structure. We have improved their scoring system by taking into consideration N and C-terminal positions of alpha-helices and beta-strands and also beta-turns as distinctive types of secondary structure. Another improvement, which also decreases the time of computation, is performed by restricting a data base with a smaller subset of proteins that are similar with a query sequence. Using multiple sequence alignments rather than single sequences and a simple jury decision procedure our method reaches a sustained overall three-state accuracy of 72.2%, which is better than that observed for the most accurate multilayered neural-network approach, tested on the same data set of 126 non-homologous protein chains. PMID:7897654

Salamov, A A; Solovyev, V V

1995-03-17

346

Prediction of protein secondary structure with a reliability score estimated by local sequence clustering.  

PubMed

Most algorithms for protein secondary structure prediction are based on machine learning techniques, e.g. neural networks. Good architectures and learning methods have improved the performance continuously. The introduction of profile methods, e.g. PSI-BLAST, has been a major breakthrough in increasing the prediction accuracy to close to 80%. In this paper, a brute-force algorithm is proposed and the reliability of each prediction is estimated by a z-score based on local sequence clustering. This algorithm is intended to perform well for those secondary structures in a protein whose formation is mainly dominated by the neighboring sequences and short-range interactions. A reliability z-score has been defined to estimate the goodness of a putative cluster found for a query sequence in a database. The database for prediction was constructed by experimentally determined, non-redundant protein structures with <25% sequence homology, a list maintained by PDBSELECT. Our test results have shown that this new algorithm, belonging to what is known as nearest neighbor methods, performed very well within the expectation of previous methods and that the reliability z-score as defined was correlated with the reliability of prediction. This led to the possibility of making very accurate predictions for a few selected residues in a protein with an accuracy measure of Q3 > 80%. The further development of this algorithm, and a nucleation mechanism for protein folding are suggested. PMID:14560050

Jiang, Fan

2003-09-01

347

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

NASA Astrophysics Data System (ADS)

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

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

2012-10-01

348

Secondary Structure and Hybridization Accessibility of Hepatitis C Virus 3?-Terminal Sequences  

PubMed Central

The 3?-terminal sequences of hepatitis C virus (HCV) positive- and negative-strand RNAs contribute cis-acting functions essential for viral replication. The secondary structure and protein-binding properties of these highly conserved regions are of interest not only for the further elucidation of HCV molecular biology, but also for the design of antisense therapeutic constructs. The RNA structure of the positive-strand 3? untranslated region has been shown previously to influence binding by various host and viral proteins and is thus thought to promote HCV RNA synthesis and genome stability. Recent studies have attributed analogous functions to the negative-strand 3? terminus. We evaluated the HCV negative-strand secondary structure by enzymatic probing with single-strand-specific RNases and thermodynamic modeling of RNA folding. The accessibility of both 3?-terminal sequences to hybridization by antisense constructs was evaluated by RNase H cleavage mapping in the presence of combinatorial oligodeoxynucleotide libraries. The mapping results facilitated identification of antisense oligodeoxynucleotides and a 10-23 deoxyribozyme active against the positive-strand 3?-X region RNA in vitro.

Smith, Robert M.; Walton, Cherie M.; Wu, Catherine H.; Wu, George Y.

2002-01-01

349

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

PubMed Central

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

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

2014-01-01

350

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

SciTech Connect

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

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

1990-09-11

351

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.

Khrustaleva, Tatyana Aleksandrovna

2014-01-01

352

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

PubMed

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

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

2014-01-01

353

SARNA-Predict: accuracy improvement of RNA secondary structure prediction using permutation-based simulated annealing.  

PubMed

Ribonucleic acid (RNA), a single-stranded linear molecule, is essential to all biological systems. Different regions of the same RNA strand will fold together via base pair interactions to make intricate secondary and tertiary structures that guide crucial homeostatic processes in living organisms. Since the structure of RNA molecules is the key to their function, algorithms for the prediction of RNA structure are of great value. In this article, we demonstrate the usefulness of SARNA-Predict, an RNA secondary structure prediction algorithm based on Simulated Annealing (SA). A performance evaluation of SARNA-Predict in terms of prediction accuracy is made via comparison with eight state-of-the-art RNA prediction algorithms: mfold, Pseudoknot (pknotsRE), NUPACK, pknotsRG-mfe, Sfold, HotKnots, ILM, and STAR. These algorithms are from three different classes: heuristic, dynamic programming, and statistical sampling techniques. An evaluation for the performance of SARNA-Predict in terms of prediction accuracy was verified with native structures. Experiments on 33 individual known structures from eleven RNA classes (tRNA, viral RNA, antigenomic HDV, telomerase RNA, tmRNA, rRNA, RNaseP, 5S rRNA, Group I intron 23S rRNA, Group I intron 16S rRNA, and 16S rRNA) were performed. The results presented in this paper demonstrate that SARNA-Predict can out-perform other state-of-the-art algorithms in terms of prediction accuracy. Furthermore, there is substantial improvement of prediction accuracy by incorporating a more sophisticated thermodynamic model (efn2). PMID:21030739

Tsang, Herbert H; Wiese, Kay C

2010-01-01

354

Comparative structure and biomechanics of plant primary and secondary cell walls  

PubMed Central

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

Cosgrove, Daniel J.; Jarvis, Michael C.

2012-01-01

355

Secondary structure and patterns of evolution among mammalian mitochondrial 12S rRNA molecules  

Microsoft Academic Search

Forty-nine complete 12S ribosomal RNA (rRNA) gene sequences from a diverse assortment of mammals (one monotreme, 11 marsupials,\\u000a 37 placentals), including 11 new sequences, were employed to establish a “core” secondary structure model for mammalian 12S\\u000a rRNA. Base-pairing interactions were assessed according to the criteria of potential base-pairing as well as evidence for\\u000a base-pairing in the form of compensatory mutations.

Mark S. Springer; Emmanuel Douzery

1996-01-01

356

Topology of the secondary structure elements of ribosomal protein L7\\/L12 from E. coli in solution  

Microsoft Academic Search

Topology of the secondary structure elements of ribosomal protein L7\\/L12 has been studied. The sequential assignment was obtained for main and side chain resonances. This allows the overall secondary structure to be described. The results of high resolution NMR studies show that dimer of the ribosomal protein L7\\/L12 from Escherichia coli has a parallel (head-to-head) orientation of subunits, and N-terminal

E. V. Bocharov; A. T. Gudkov; A. S. Arseniev

1996-01-01

357

Automatic Self-Commissioning for Secondary-Saliencies Decoupling in Sensorless-Controlled AC Machines Using Structured Neural Networks  

Microsoft Academic Search

The focus of this paper is secondary-saliency decoupling in carrier signal injection-based sensorless control of AC machines using structured neural networks. Structured neural networks are utilized for automatic commissioning and decoupling of secondary saliencies including saturation-induced saliencies. Automatic commissioning process is necessary for easy implementation and for acceptance of the carrier signal injection-based sensorless control by drives industry. In comparison

Pablo Garcia; David Reigosa; Fernando Briz; Dejan Raca; Robert D. Lorenz

2007-01-01

358

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

NASA Astrophysics Data System (ADS)

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

Sinha, Sudipta Kumar; Bandyopadhyay, Sanjoy

2011-03-01

359

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

PubMed Central

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

Kretzner, L; Krol, A; Rosbash, M

1990-01-01

360

Ambient modal identification of a primary-secondary structure by Fast Bayesian FFT method  

NASA Astrophysics Data System (ADS)

The Mong Man Wai Building is a seven-storied reinforced concrete structure situated on the campus of the City University of Hong Kong. On its roof a two-storied steel frame has been recently constructed to host a new wind tunnel laboratory. The roof frame and the main building form a primary-secondary structure. The dynamic characteristics of the resulting system are of interest from a structural dynamics point of view. This paper presents work on modal identification of the structure using ambient vibration measurement. An array of tri-axial acceleration data has been obtained using a number of setups to cover all locations of interest with a limited number of sensors. Modal identification is performed using a recently developed Fast Bayesian FFT method. In addition to the most probable modal properties, their posterior uncertainties can also be assessed using the method. The posterior uncertainty of mode shape is assessed by the expected value of the Modal Assurance Criteria (MAC) of the most probable mode shape with a random mode shape consistent with the posterior distribution. The mode shapes of the overall structural system are obtained by assembling those from individual setups using a recently developed least-square method. The identification results reveal a number of interesting features about the structural system and provide important information defining the baseline modal properties of the building. Practical interpretation of the statistics of modal parameters calculated from frequentist and Bayesian context is also discussed.

Au, Siu-Kui; Zhang, Feng-Liang

2012-04-01

361

Population genetic structure and secondary endosymbionts of Q Bemisia tabaci (Hemiptera: Aleyrodidae) from Greece.  

PubMed

We investigated the molecular diversity of the major agricultural pest Bemisia tabaci and of its associated secondary endosymbionts in Greece. Analyzing mitochondrial DNA, we found that the Q1 (=Q west) is predominant. We used eight microsatellite polymorphic markers to study the genetic structure of 37 populations from mainland and insular Greece, collected on different host species from outdoor and protected crops as well as from non-cultivated plants. In some cases, gene flow was found to be low even between populations separated by just a few kilometres. Bayesian analysis identified two main genetic groups, the first encompassing populations from south Crete and the second composed of populations from north Crete, two other Aegean islands and mainland Greece. Genetic differentiation was not correlated with different host plant species or habitat, or greenhouse versus open environment populations. Gene flow significantly decreased with geographic distance, but no isolation by distance existed when only the samples from mainland Greece or only the samples from Crete were considered. The secondary symbionts Wolbachia and Hamiltonella were present at high frequencies while Arsenophonus, Cardinium and Rickettsia were absent from Greek populations. Multilocus sequence typing of Wolbachia identified two Wolbachia strains. These two strains were found together in most of the populations studied but never in the same host individual. Their role on the observed population structure is discussed. PMID:22280837

Tsagkarakou, A; Mouton, L; Kristoffersen, J B; Dokianakis, E; Grispou, M; Bourtzis, K

2012-06-01

362

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

PubMed Central

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

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

1999-01-01

363

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

PubMed

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

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

1999-06-01

364

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

PubMed Central

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

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

2013-01-01

365

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

SciTech Connect

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

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

1991-12-17

366

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

PubMed Central

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

Rose, Dominic; Backofen, Rolf

2012-01-01

367

Structure of histone mRNA stem-loop, human stem-loop binding protein and 3?hExo ternary complex*  

PubMed Central

Metazoan replication-dependent histone mRNAs have a conserved stem-loop (SL) at their 3?-end. The stem–loop binding protein (SLBP) specifically recognizes the SL to regulate histone mRNA metabolism, and the 3?-5? exonuclease 3?hExo trims its 3?-end after processing. We report the crystal structure of a ternary complex of human SLBP RNA binding domain, human 3?hExo, and a 26-nucleotide SL RNA. Only one base of the SL is recognized specifically by SLBP, and the two proteins primarily recognize the shape of the RNA. SLBP and 3?hExo have no direct contact with each other, and induced structural changes in the loop of the SL mediate their cooperative binding. The 3? flanking sequence is positioned in the 3?hExo active site, but the ternary complex limits the extent of trimming.

Tan, Dazhi; Marzluff, William F.; Dominski, Zbigniew; Tong, Liang

2012-01-01

368

Dissecting coherent vibrational spectra of small proteins into secondary structural elements by sensitivity analysis  

PubMed Central

The response of proteins to sequences of femtosecond infrared pulses provides a multidimensional view into their equilibrium distribution of structures and snapshot pictures of fast-triggered dynamical events. Analyzing these experiments requires advanced computational tools for assigning regions in the resulting multi-dimensional correlation plots to specific secondary-structure elements and their couplings. A differential sensitivity analysis technique based on a perturbation of the local (real space) Hamiltonian is developed to achieve that goal. Application to the amide I region of a small globular protein reveals regions associated with the ?-helix, ?-sheet, and their coupling. Comparison of signals generated in different directions shows that the double-quantum-coherence signal has a higher sensitivity to the couplings compared with the single-quantum-coherence (photon echo) technique.

Zhuang, Wei; Abramavicius, Darius; Mukamel, Shaul

2005-01-01

369

Secondary structure of streptokinase in aqueous solution: a Fourier transform infrared spectroscopic study.  

PubMed

The secondary structure of streptokinase (Sk) in aqueous solution was quantitatively examined by using Fourier transform infrared (FT-IR) spectroscopy. Resolution enhancement techniques, including Fourier deconvolution and derivative spectroscopy, were combined with band curve-fitting procedures to quantitate the spectral information from the amide I bands. Nine component bands were found under the broad, nearly featureless amide I bands which reflect the presence of various substructures. The relative areas of these component bands indicate an amount of beta-sheet between 30 and 37% and an alpha-helix content of only 12-13% in Sk. Further conformational substructures are assigned to turns (25-26%) and to "random" structures (15-16%). Additionally, the correlation of a pronounced component band near 1640 cm-1 (10-16% fractional area) with the possible presence of 3(10)-helices is discussed. PMID:1633164

Fabian, H; Naumann, D; Misselwitz, R; Ristau, O; Gerlach, D; Welfle, H

1992-07-21

370

Secondary structure determination by FTIR of an archaeal ubiquitin-like polypeptide from Natrialba magadii.  

PubMed

The ubiquitin protein belongs to the ?-grasp fold family, characterized by four or five ?-sheets with a single ?-helical middle region. Ubiquitin-like proteins (Ubls) are structural homologues with low sequence identity to ubiquitin and are widespread among both eukaryotes and prokaryotes. We previously demonstrated by bioinformatics that P400, a polypeptide from the haloalkaliphilic archaeon Natrialba magadii, has structural homology with both ubiquitin and Ubls. This work examines the secondary structure of P400 by Fourier transform infrared spectroscopy (FTIR). After expression in Escherichia coli, recombinant P400 (rP400) was separated by PAGE and eluted pure from zinc-imidazole reversely stained gels. The requirement of high salt concentration of this polypeptide to be folded was corroborated by intrinsic fluorescence spectrum. Our results show that fluorescence spectra of rP400 in 1.5 M KCl buffer shifts and decreases after thermal denaturation as well as after chemical treatment. rP400 was lyophilized and rehydrated in buffer containing 1.5 M KCl before both immunochemical and FTIR tests were performed. It was found that rP400 reacts with anti-ubiquitin antibody after rehydration in the presence of high salt concentrations. On the other hand, like ubiquitin and Ubls, the amide I' band for rP400 shows 10% more of its sequence to be involved in ?-sheet structures than in ?-helix. These findings suggest that P400 is a structural homologue of the ubiquitin family proteins. PMID:21701865

Ordóñez, M V; Guillén, J; Nercessian, D; Villalaín, J; Conde, R D

2011-09-01

371

Secondary-Structure Analysis of Denatured Proteins by Vacuum-Ultraviolet Circular Dichroism Spectroscopy  

PubMed Central

To elucidate the structure of denatured proteins, we measured the vacuum-ultraviolet circular dichroism (VUVCD) spectra from 260 to 172 nm of three proteins (metmyoglobin, staphylococcal nuclease, and thioredoxin) in the native and the acid-, cold-, and heat-denatured states, using a synchrotron-radiation VUVCD spectrophotometer. The circular dichroism spectra of proteins fully unfolded by guanidine hydrochloride (GdnHCl) were also measured down to 197 nm for comparison. These denatured proteins exhibited characteristic VUVCD spectra that reflected a considerable amount of residual secondary structures. The contents of ?-helices, ?-strands, turns, poly-L-proline type II (PPII), and unordered structures were estimated for each denatured state of the three proteins using the SELCON3 program with Protein Data Bank data and the VUVCD spectra of 31 reference proteins reported in our previous study. Based on these contents, the characteristics of the four types of denaturation were discussed for each protein. In all types of denaturation, a decrease in ?-helices was accompanied by increases in ?-strands, PPII, and unordered structures. About 20% ?-strands were present even in the proteins fully unfolded by GdnHCl in which ?-sheets should be broken. From these results, we propose that denatured proteins constitute an ensemble of residual ?-helices and ?-sheets, partly unfolded (or distorted) ?-helices and ?-strands, PPII, and unordered structures.

Matsuo, Koichi; Sakurada, Yoshie; Yonehara, Ryuta; Kataoka, Mikio; Gekko, Kunihiko

2007-01-01

372

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.

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

2013-01-01

373

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

PubMed

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

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

2013-02-01

374

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

SciTech Connect

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

Y Ren; H Seo; G Blobel; A Hoelz

2011-12-31

375

5-Azacytidine and RNA secondary structure increase the retrovirus mutation rate.  

PubMed Central

A broad spectrum of mutations occurs at a high rate during a single round of retrovirus replication (V.K. Pathak and H. M. Temin, Proc. Natl. Acad. Sci. USA 87:6019-6023, 1990). We have now determined that this high rate of spontaneous mutation can be further increased by 5-azacytidine (AZC) treatment or by regions of potential RNA secondary structure. We found a 13-fold increase in the mutation rate after AZC treatment of retrovirus-producing cells and target cells. The AZC-induced substitutions were located at the same target sites as previously identified spontaneous substitutions. The concordance of the AZC-induced and spontaneous substitutions indicates the presence of reverse transcription "pause sites," where the growing point is error prone. An analysis of nucleotides that neighbored substitutions revealed that transversions occur primarily by transient template misalignment, whereas transitions occur primarily by misincorporation. We also introduced a 34-bp potential stem-loop structure as an in-frame insertion within a lacZ alpha gene that was inserted in the long terminal repeat (LTR) U3 region and determined whether this potential secondary structure increased the rate of retrovirus mutations. We found a threefold increase in the retrovirus mutation rate. Fifty-seven of 96 mutations were deletions associated with the potential stem-loop. We also determined that these deletion mutations occurred primarily during minus-strand DNA synthesis by comparing the frequencies of mutations in recovered provirus plasmids containing both LTRs and in provirus plasmids containing only one LTR.

Pathak, V K; Temin, H M

1992-01-01

376

'Y'Scenedesmus (Chlorophyta, Chlorophyceae): the internal transcribed spacer 2 rRNA secondary structure re-revisited.  

PubMed

Including RNA secondary structures improves accuracy and robustness in reconstruction of phylogenetic trees. It is possible to simultaneously infer alignments and phylogenies on the primary sequence and the secondary structure information. For the internal transcribed spacer 2 (ITS2), a phylogenetic RNA transcript marker, two different structure conformations (I or Y shape for helix I) were published for Scenedesmaceae, and a third appeared in the ITS2 database. We contrast the effects on phylogenetic tree reconstruction of different structure sets for a small scenedesmacean subset, using neighbour-joining, maximum parsimony and, for the first time, maximum likelihood, on sequence-structure alignments. Generally our study supports inclusion of secondary structure information. However, we found that any of the three structure conformations is equally fit for phylogenetic studies, but prefer the I shape for helix I. Moreover, our results enable us to give general recommendations on how to build a phylogenetic tree using ITS2 sequence-structure alignments, including different methods to obtain the secondary structures. Thus, we hope to provide a valuable contribution not only for scenedesmacean ITS2 phylogeny, but also for other approaches using RNA transcript markers. PMID:22639929

Markert, S M; Müller, T; Koetschan, C; Friedl, T; Wolf, M

2012-11-01

377

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.

Boren, K.; Freskgard, P. O.; Carlsson, U.

1996-01-01

378

R2R - software to speed the depiction of aesthetic consensus RNA secondary structures  

PubMed Central

Background With continuing identification of novel structured noncoding RNAs, there is an increasing need to create schematic diagrams showing the consensus features of these molecules. RNA structural diagrams are typically made either with general-purpose drawing programs like Adobe Illustrator, or with automated or interactive programs specific to RNA. Unfortunately, the use of applications like Illustrator is extremely time consuming, while existing RNA-specific programs produce figures that are useful, but usually not of the same aesthetic quality as those produced at great cost in Illustrator. Additionally, most existing RNA-specific applications are designed for drawing single RNA molecules, not consensus diagrams. Results We created R2R, a computer program that facilitates the generation of aesthetic and readable drawings of RNA consensus diagrams in a fraction of the time required with general-purpose drawing programs. Since the inference of a consensus RNA structure typically requires a multiple-sequence alignment, the R2R user annotates the alignment with commands directing the layout and annotation of the RNA. R2R creates SVG or PDF output that can be imported into Adobe Illustrator, Inkscape or CorelDRAW. R2R can be used to create consensus sequence and secondary structure models for novel RNA structures or to revise models when new representatives for known RNA classes become available. Although R2R does not currently have a graphical user interface, it has proven useful in our efforts to create 100 schematic models of distinct noncoding RNA classes. Conclusions R2R makes it possible to obtain high-quality drawings of the consensus sequence and structural models of many diverse RNA structures with a more practical amount of effort. R2R software is available at http://breaker.research.yale.edu/R2R and as an Additional file.

2011-01-01

379

Unique secondary and tertiary structural features of the eucaryotic selenocysteine tRNA(Sec).  

PubMed Central

Cotranslational insertion of selenocysteine into selenoenzymes is mediated by a specialized transfer RNA, the tRNA(Sec). We have carried out the determination of the solution structure of the eucaryotic tRNA(Sec). Based on the enzymatic and chemical probing approach, we show that the secondary structure bears a few unprecedented features like a 9 bp aminoacid-, a 4 bp thymine- and a 6 bp dihydrouridine-stems. Surprisingly, the eighth nucleotide, although being a uridine, is base-paired and cannot therefore correspond to the single-stranded invariant U8 found in all tRNAs. Rather, experimental evidence led us to propose that the role of the invariant U8 is actually played by the tenth nucleotide which is an A, numbered A8 to indicate this fact. The experimental data therefore demonstrate that the cloverleaf structure we derived experimentally resembles the hand-folded model proposed by Böck et al (ref. 3). Using the solution data and computer modelling, we derived a three-dimensional structure model which shows some unique aspects. Basically, A8, A14, U21 form a novel type of tertiary interaction in which A8 interacts with the Hoogsteen sites of A14 which itself forms a Watson-Crick pair with U21. No coherent model containing the canonical 15-48 interaction could be derived. Thus, the number of tertiary interactions appear to be limited, leading to an uncoupling of the variable stem from the rest of the molecule. Images

Sturchler, C; Westhof, E; Carbon, P; Krol, A

1993-01-01

380

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

PubMed Central

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

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

2014-01-01

381

Regulation of Dscam exon 17 alternative splicing by steric hindrance in combination with RNA secondary structures.  

PubMed

The gene Down syndrome cell adhesion molecule (Dscam) potentially encodes 38 016 distinct isoforms in Drosophila melanogaster via mutually exclusive splicing. Here we reveal a combinatorial mechanism of regulation of Dscam exon 17 mutually exclusive splicing through steric hindrance in combination with RNA secondary structure. This mutually exclusive behavior is enforced by steric hindrance, due to the close proximity of the exon 17.2 branch point to exon 17.1 in Diptera, and the interval size constraint in non-Dipteran species. Moreover, intron-exon RNA structures are evolutionarily conserved in 36 non-Drosophila species of six distantly related orders (Diptera, Lepidoptera, Coleoptera, Hymenoptera, Hemiptera, and Phthiraptera), which regulates the selection of exon 17 variants via masking the splice site. By contrast, a previously uncharacterized RNA structure specifically activated exon 17.1 by bringing splice sites closer together in Drosophila, while the other moderately suppressed exon 17.1 selection by hindering the accessibility of polypyrimidine sequences. Taken together, these data suggest a phylogeny of increased complexity in regulating alternative splicing of Dscam exon 17 spanning more than 300 million years of insect evolution. These results also provide models of the regulation of alternative splicing through steric hindrance in combination with dynamic structural codes. PMID:24448213

Yue, Yuan; Li, Guoli; Yang, Yun; Zhang, Wenjing; Pan, Huawei; Chen, Ran; Shi, Feng; Jin, Yongfeng

2013-12-01

382

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

PubMed

We present McGenus, an algorithm to predict RNA secondary structures with pseudoknots. The method is based on a classification of RNA structures according to their topological genus. McGenus can treat sequences of up to 1000 bases and performs an advanced stochastic search of their minimum free energy structure allowing for non-trivial pseudoknot topologies. Specifically, McGenus uses a Monte Carlo algorithm with replica exchange for minimizing a general scoring function which includes not only free energy contributions for pair stacking, loop penalties, etc. but also a phenomenological penalty for the genus of the pairing graph. The good performance of the stochastic search strategy was successfully validated against TT2NE which uses the same free energy parametrization and performs exhaustive or partially exhaustive structure search, albeit for much shorter sequences (up to 200 bases). Next, the method was applied to other RNA sets, including an extensive tmRNA database, yielding results that are competitive with existing algorithms. Finally, it is shown that McGenus highlights possible limitations in the free energy scoring function. The algorithm is available as a web server at http://ipht.cea.fr/rna/mcgenus.php. PMID:23248008

Bon, Michaël; Micheletti, Cristian; Orland, Henri

2013-02-01

383

Secondary structure of rabbit 18S ribosomal RNA determined from biochemical and phylogenetic data  

SciTech Connect

To understand the functional role of 18S rRNA in the eukaryotic 40S subunit, its higher order structure must first be determined. Native deproteinized 18S rRNA was isolated from purified rabbit 40S subunits, fractionated on SDS-sucrose density gradients and concentrated using centricon-30 microconcentrators. The structure of native 18S rRNA was probed chemically with both diethylpyrocarbonate (DEPC) and dimethyl sulfate (DMS) which react with unpaired adenosine and guanosine residues, respectively. After /sup 32/P-end-labeling of intact and fragmented RNA, the modified nucleotides were identified by polyacrylamide sequencing gel electrophoresis upon aniline induced strand scission. On the basis of both the biochemical and phylogenetic data, a secondary structure model is proposed which includes the two major G + C rich insertion elements. A comparison of the structure data with previously published phylogenetic models suggests an instability of certain predicted helices. These unstable helices may normally be stabilized by ribosomal proteins and could represent the flexible elements involved in biologically significant conformational switches within 40S subunit.

Rairkar, A.; Rubino, H.; Lockard, R.E.

1986-05-01

384

Role of secondary long wavelength structures in the saturation of electron temperature gradient driven turbulence  

SciTech Connect

The dynamics of secondary long wavelength structures (LWSs) in electron temperature gradient (ETG) driven turbulence are investigated by performing gyrofluid simulations and modeling analyses in a slab geometry with an emphasis of the underlying nonlinear interaction processes. It is shown that the back-reaction of the secondary LWS on the ambient fluctuations essentially contributes to saturating ETG instability and limiting the electron transport. The LWS is nonlinearly generated mainly through the beating of the most unstable ETG modes, even a weak modulation instability. The back-reaction is identified as the enhanced stabilization of the ETG modes due to the streamer-type feature of the LWS, which dominantly produces a local poloidal mode coupling among unstable and highly damped spectral components to form a global mode, besides the suppression effect of the LWS due to the radial shearing decorrelation and/or the radial mode coupling. Finally, the correspondence between the LWS in the slab model and the quasimode observed in toroidal ETG simulation [Z. Lin et al., Phys. Plasmas 12, 056125 (2005)] and the importance of the nonlinear mode coupling in the multiscale turbulence interaction are discussed.

Li Jiquan [Department of Fundamental Energy, Kyoto University, 611-0011 Gokasho, Uji (Japan); Institute for Fusion Theory and Simulation, Zhejiang University, Hangzhou (China); Kishimoto, Y. [Department of Fundamental Energy, Kyoto University, 611-0011 Gokasho, Uji (Japan)

2008-11-15

385

Suppression of secondary electron yield by micro-porous array structure  

NASA Astrophysics Data System (ADS)

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

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

2013-02-01

386

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

PubMed Central

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

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

2014-01-01

387

Secondary Structure of the Mature Ex Virio Moloney Murine Leukemia Virus Genomic RNA Dimerization Domain ?  

PubMed Central

Retroviral genomes are dimeric, comprised of two sense-strand RNAs linked at their 5? ends by noncovalent base pairing and tertiary interactions. Viral maturation involves large-scale morphological changes in viral proteins and in genomic RNA dimer structures to yield infectious virions. Structural studies have largely focused on simplified in vitro models of genomic RNA dimers even though the relationship between these models and authentic viral RNA is unknown. We evaluate the secondary structure of the minimal dimerization domain in genomes isolated from Moloney murine leukemia virions using a quantitative and single nucleotide resolution RNA structure analysis technology (selective 2?-hydroxyl acylation analyzed by primer extension, or SHAPE). Results are consistent with an architecture in which the RNA dimer is stabilized by four primary interactions involving two sets of intermolecular base pairs and two loop-loop interactions. The dimerization domain can independently direct its own folding since heating and refolding reproduce the same structure as visualized in genomic RNA isolated from virions. Authentic ex virio RNA has a SHAPE reactivity profile similar to that of a simplified transcript dimer generated in vitro, with the important exception of a region that appears to form a compact stem-loop only in the virion-isolated RNA. Finally, we analyze the conformational changes that accompany folding of monomers into dimers in vitro. These experiments support well-defined structural models for an authentic dimerization domain and also emphasize that many features of mature genomic RNA dimers can be reproduced in vitro using properly designed, simplified RNAs.

Gherghe, Cristina; Leonard, Christopher W.; Gorelick, Robert J.; Weeks, Kevin M.

2010-01-01

388

Innovative FT-IR Imaging of Protein Film Secondary Structure Before and After Heat Treatment  

SciTech Connect

Changes in the secondary structure of globular protein occur during thermal processing. An infrared reflecting mirrored optical substrate that is unaffected by heat allows recording infrared spectra of protein films in a reflection absorption mode on the stage of an FT-IR microspectrometer. Hydrated films of myoglobin protein cast from solution on the mirrored substrate are interrogated before and after thermal denaturation to allow a direct comparison. Focal plane array imaging of 280 protein films allowed selection of the same area in the image from which to extract spectra. After treatment, 110 of 140 spectra from multiple films showed a dramatic shift from the {alpha}-helix form (1650 {+-} 5 cm{sup -1}) to aggregated forms on either side of the original band. Seventy maxima were near 1625 cm{sup -1}, and 40 shifted in the direction of 1670 cm{sup -1}. The method developed was applied to films cast from two other commercial animal and plant protein sources.

Bonwell, E.; Wetzel, D

2009-01-01

389

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

PubMed Central

Mechanical aspects of the cellular environment can influence cell function, and in this context hydrogels can serve as an instructive matrix. Here we report that physicochemical properties of hydrogels derived from polysaccharides (agarose, ?-carrageenan) having an ?-helical backbone can be tailored by inducing a switch in the secondary structure from ?-helix to ?-sheet through carboxylation. This enables the gel modulus to be tuned over four orders of magnitude (G? 6 Pa–3.6 × 104 Pa) independently of polymer concentration and molecular weight. Using carboxylated agarose gels as a screening platform, we demonstrate that soft-carboxylated agarose provides a unique environment for the polarization of endothelial cells in the presence of soluble and bound signals, which notably does not occur in fibrin and collagen gels. Furthermore, endothelial cells organize into freestanding lumens over 100 ?m in length. The finding that a biomaterial can modulate soluble and bound signals provides impetus for exploring mechanobiology paradigms in regenerative therapies.

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

2013-01-01

390

Phylogenetic study of nine species of freshwater monogeneans using secondary structure and motif prediction from India.  

PubMed

The present study was performed to identify and validate monogenean species from different piscine hosts using molecular tools. Nine species of freshwater monogeneans were collected from gills and skin of freshwater fishes at Hastinapur, Meerut, India. After microscopic examination, molecular analysis was performed utilizing 28S gene marker. Phylogenetic analysis indicated the validation and systematic position of these nine different monogeneans belongs to the Dactylogyridae and Gyrodactylidae families. The findings also confirm that the 28S rDNA sequence is highly conserved and may prove to be useful in taxonomic studies of parasitic platyhelminthes. Besides this, the study is also supplemented by molecular morphometrics that is based on 28S secondary structure homologies of nine monogenean species. The data indicate that 28S motifs i.e., ? 50bp in size can also be considered a promising tool for monogenean species identification and their validation. PMID:23144541

Chaudhary, Anshu; Singh, Hridaya Shanker

2012-01-01

391

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

2010-10-01

392

[Study on secondary structure and properties of alpha- and gamma-forms of human thrombin].  

PubMed

Secondary structure and enzymatic properties of human a-thrombin and its gamma-form (obtaining during autolysis of the native enzyme) have been studied by differential scanning calorimetry (DSC) and circular dichroism (CD). According to DSC-data both alpha-thrombin and gamma-thrombin contained only one thermal transition peak at 58.5 and 53.3 degrees C, respectively. A comparison of these values suggested that gamma-form is less stable than initial a-thrombin. In contrast to that the thermogram of DIP-a-thrombin had two peaks (57.5 and 64.5 degrees C). CD spectra showed that conversion a- to gamma-thrombin influenced the secondary structure of the enzyme slightly. The study of the inhibitory effect of such polyanions as ATP and dextran sulfate (DS) upon thrombin-catalyzed cleavages of fibrinogen has shown that the growth of the negative charge of the polyanion molecule resulted in the increase of its inhibitory activity. The catalytically non-active DIP-alpha-thrombin, which retained the native anion-binding exosite 1, was shown to decrease the inhibitory power of the dextran sulfate. It was explained by competition of DS with the exosite 1 of both alpha- and DIP-alpha -thrombin. In contrast to that DIP-gamma-thrombin having exosite 1 destroyed neither competed nor influenced the anticoagulant capacity of dextran sulfate toward the native alpha-thrombin. In accordance with our data thrombin consists of two rather strong interacting domains. It was shown further that its anion-binding exosite 1 may play a significant role in the interaction of the enzyme with dextran sulfate. PMID:17147270

Shvachko, L P; Litvinovich, S V; Kibirev, V K

2006-01-01

393

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

PubMed Central

This study was aimed at examining the spectrum of antimicrobial activity of MUC7 20-mer (N-LAHQKPFIRKSYKCLHKRCR-C; residues 32 to 51 of MUC7, the low-molecular-weight human salivary mucin, comprised of 357 residues) and comparing its antifungal properties to those of salivary histatin 5 (Hsn-5). We also examined the secondary structure of the 20-mer and the possible mechanism of its antifungal action. Our results showed that MUC7 20-mer displays potent killing activity against a variety of fungi and both gram-positive and gram-negative bacteria at micromolar concentrations. Time-dependent killing of Candida albicans and Cryptococcus neoformans by MUC7 20-mer and Hsn-5 indicated differences in killing rates between MUC7 20-mer and Hsn-5. The secondary structure prediction showed that MUC7 20-mer adopts an amphiphilic helix with distinguishable hydrophilic and hydrophobic faces (a characteristic that is associated with antimicrobial activity). In comparison to that of Hsn-5, the fungicidal activity of MUC7 20-mer against C. albicans seems to be independent of fungal cellular metabolic activity, as evidenced by its killing potency at a low temperature (4°C) and in the presence of inhibitors of oxidative phosphorylation in the mitochondrial system. Fluorescence microscopy showed the ability of MUC7 20-mer to cross the fungal cell membrane and to accumulate inside the cells. The internalization of MUC7 20-mer was inhibited by divalent cations. Confocal microscopy of cells doubly labeled with MUC7 20-mer and a mitochondrion-specific dye indicated that mitochondria are not the target of MUC7 20-mer for either C. albicans or C. neoformans.

Bobek, Libuse A.; Situ, Hongsa

2003-01-01

394

Correlation of secondary structures of bradykinin B1 receptor antagonists with their activity.  

PubMed

The secondary structure of a bradykinin B(1)receptor antagonist B-10324 (F5C-Lys-(1)- Lys(0)-Arg(1)-Pro(2)- Hyp(3)-Gly(4)-CpG(5)- Ser(6)-DTic(7)-CpG(8)) was determined by NMR at 800MHz. The conformational data are compared with those obtained previously for two bradykinin B(1) receptor antagonists, namely B-9858 (Lys-(1)- Lys(0)-Arg(1)-Pro(2)- Hyp(3)-Gly(4)-Igl(5)- Ser(6)-DIgl(7)-Oic(8)) and B-10148 (Lys-(1)-Lys(0)-Arg(1)- Pro(2)-Hyp(3)-Gly(4)- Igl(5)-Ser(6)-DF5F(7)- Oic(8)). The abnormal amino acids are: Hyp, trans-4- hydroxyproline; Tic, 1, 2, 3, 4-tetrahydroisoquinoline-3-carboxylic acid; Oic, (2S, 3aS, 7aS)-octahydroindole-2-carboxylic acid; Igl, alpha(2- indanyl)glycine; F5F, 2,3,4,5,6-pentafluorophenylalanine; CpG, alpha- cyclopentylglycine. F5C, pentafluorocinnamoyl, is the N-terminal protecting group and is not involved in the peptide secondary structure. B-10324 contains an N-terminal Pro(2)- CpG(5) distorted type II beta-turn whereas the rest of the peptide is random. A salt bridge is not observed between the carboxylate group at the C-terminal end and the Arg(1) side chain, in contrast to that previously observed for B-9858 and B- 10148. The conformations are correlated with the measured B(1) receptor antagonist activities (J.-F. Larrivée, L. Gera, S. Houle, J. Bouthillier, D. R. Bachvarov, J. M. Stewart and F. Marc au, Br. J. Pharmacol. 131, 885-892 (2000)). The importance of the N-terminal beta-turn is highlighted. PMID:11843620

Miskolzie, Mark; Gera, Lajos; Stewart, John M; Kotovych, George

2002-02-01