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1

Determination of secondary structure in the initiation region of ovalbumin mRNA.  

PubMed Central

We have analyzed the secondary structure in the region surrounding the initiation codons of both cellular and synthetic versions of ovalbumin mRNA. RNase V1 cleavage sites and structure-dependent, chemically modified bases in cellular ovalbumin mRNA were determined by reverse transcription of hen poly A(+) RNA using ovalbumin-specific, synthetic DNA primers. These results indicate an extensive region of unpaired nucleotides preceding the initiation codon and a region of base-paired nucleotides including and following the initiation codon. A synthetic ovalbumin mRNA (SP65.OV) was prepared by run-off transcription of a cloned ovalbumin cDNA (pSP65.OV). Identical regions of hen ovalbumin and SP65.OV mRNAs gave identical patterns of structure-dependent base modifications. A computer program for determining RNA secondary structure was used to find a 5'-region structure for ovalbumin mRNA that is consistent with our data. Images PMID:3205742

Liarakos, C D; Maddox, R P; Hilscher, K A; Bishop, J R; McGuire, D K; Kopper, R A

1988-01-01

2

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

PubMed Central

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

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

2010-01-01

3

Secondary structure of splice sites in adenovirus mRNA precursors.  

PubMed Central

In order to investigate the possible role of RNA secondary structure in determining the efficiency and specificity of mRNA splicing, the structures of sequences at three acceptor splice sites in adenovirus were studied. Transcripts spanning intron-exon junctions were synthesized using SP6 RNA polymerase and analyzed using single and double-strand specific nucleases. Distinctive patterns of nuclease cleavage were observed for each of the 3 sites examined. At both sites in the E2a region sequences adjacent to the splice sites were particularly susceptible to digestion with T1 and S1 nucleases. In contrast, a splice site for hexon mRNA was largely resistant to these nucleases. The results obtained suggest that the conformation of the RNA at some, but not all, acceptor sites may enhance the accessibility of these sites to factors involved in splicing nuclear RNA and confirm the presence of a large, previously predicted hairpin structure centered on the acceptor site at 67 map units. Images PMID:6095200

Munroe, S H

1984-01-01

4

A MYLK variant regulates asthmatic inflammation via alterations in mRNA secondary structure.  

PubMed

Myosin light-chain kinase (MYLK) is a gene known to be significantly associated with severe asthma in African Americans. Here we further examine the molecular function of a single-nucleotide polymorphism (SNP), located in the non-muscle myosin light-chain kinase isoform (nmMLCK), in asthma susceptibility and pathobiology. We identified nmMLCK variant (reference SNP: rs9840993, NM_053025: 721C>T, c.439C>T) with a distinct mRNA secondary structure from the other variants. The nmMLCK variant (721C) secondary structure exhibits increased stability with an elongated half-life in the human endothelial cell, and greater efficiency in protein translation initiation owing to an increased accessibility to translation start site. Finally, nmMLCK expression of 721C- and 721T-containing MYLK transgenes were compared in nmMLCK(-/-) mice and confirmed deleterious effects of nmMLCK expression on asthmatic indices and implicated the augmented influence of MYLK 721C>T (c.439C>T) SNP on asthma severity. The confirmation of the novel mechanism of the regulation of asthmatic inflammation by a MYLK advances knowledge of the genetic basis for asthma disparities, and further suggests the potential of nmMLCK as a therapeutic target. Our study suggests that in addition to altering protein structure and function, non-synonymous SNPs may also lead to phenotypic disparity by altering protein expression.European Journal of Human Genetics advance online publication, 1 October 2014; doi:10.1038/ejhg.2014.201. PMID:25271083

Wang, Ting; Zhou, Tong; Saadat, Laleh; Garcia, Joe Gn

2014-10-01

5

Identification of Secondary Structure in the 5' Untranslated Region of the Human Adrenomedullin mRNA with Implications for the Regulation of mRNA Translation  

E-print Network

RNA with Implications for the Regulation of mRNA Translation Fabienne Brenet1,# , Nadège Dussault1,# , Christine Delfino' UTR, Translational control, Stem-loop structure, RNA-binding proteins. Abbreviated Title : Regulatory role of the stem-loop in translation of AM mRNA. Number of pages : 30 Number of figures : 6 Number

Paris-Sud XI, Université de

6

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

PubMed

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

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

2015-03-01

7

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

PubMed Central

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

2014-01-01

8

mRNA secondary structure at start AUG codon is a key limiting factor for human protein expression in Escherichia coli  

SciTech Connect

Codon usage and thermodynamic optimization of the 5'-end of mRNA have been applied to improve the efficiency of human protein production in Escherichia coli. However, high level expression of human protein in E. coli is still a challenge that virtually depends upon each individual target genes. Using human interleukin 10 (huIL-10) and interferon {alpha} (huIFN-{alpha}) coding sequences, we systematically analyzed the influence of several major factors on expression of human protein in E. coli. The results from huIL-10 and reinforced by huIFN-{alpha} showed that exposing AUG initiator codon from base-paired structure within mRNA itself significantly improved the translation of target protein, which resulted in a 10-fold higher protein expression than the wild-type genes. It was also noted that translation process was not affected by the retained short-range stem-loop structure at Shine-Dalgarno (SD) sequences. On the other hand, codon-optimized constructs of huIL-10 showed unimproved levels of protein expression, on the contrary, led to a remarkable RNA degradation. Our study demonstrates that exposure of AUG initiator codon from long-range intra-strand secondary structure at 5'-end of mRNA may be used as a general strategy for human protein production in E. coli.

Zhang Weici [Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027 (China); Xiao Weihua [Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027 (China) and School of Pharmaceutical Sciences, Shandong University, Jinan, Shandong 250012 (China)]. E-mail: xiaow@ustc.edu.cn; Wei Haiming [Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027 (China); Zhang Jian [School of Pharmaceutical Sciences, Shandong University, Jinan, Shandong 250012 (China); Tian Zhigang [Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027 (China) and School of Pharmaceutical Sciences, Shandong University, Jinan, Shandong 250012 (China)]. E-mail: tzg@ustc.edu.cn

2006-10-13

9

The secondary structure of the protein L1 binding region of ribosomal 23S RNA. Homologies with putative secondary structures of the L11 mRNA and of a region of mitochondrial 16S rRNA.  

PubMed Central

An heterologous complex was formed between E. coli protein L1 and P. vulgaris 23S RNA. We determined the primary structure of the RNA region which remained associated with protein L1 after RNase digestion of this complex. We also identified the loci of this RNA region which are highly susceptible to T1, S1 and Naja oxiana nuclease digestions respectively. By comparison of these results with those previously obtained with the homologous regions of E. coli and B. stearothermophilus 23S RNAs, we postulate a general structure for the protein L1 binding region of bacterial 23S RNA. Both mouse and human mit 16S rRNAs and Xenopus laevis and Tetrahymena 28S rRNAs contain a sequence similar to the E. coli 23s RNS region preceding the L1 binding site. The region of mit 16S rRNA which follows this sequence has a potential secondary structure bearing common features with the L1-associated region of bacterial 23S rRNA. The 5'-end region of the L11 mRNA also has several sequence potential secondary structures displaying striking homologies with the protein L1 binding region of 23S rRNA and this probably explains how protein L1 functions as a translational repressor. One of the L11 mRNA putative structures bears the features common to both the L1-associated region of bacterial 23S rRNA and the corresponding region of mit 16S rRNA. Images PMID:7010313

Branlant, C; Krol, A; Machatt, A; Ebel, J P

1981-01-01

10

CFTR mRNA expression is regulated by an upstream open reading frame and RNA secondary structure in its 5' untranslated region.  

PubMed

Post-transcriptional regulation of gene expression through 5' untranslated region (5'UTR)-encoded cis-acting elements is an important mechanism for the control of protein expression levels. Through controlling specific aspects of translation initiation, expression can be tightly regulated while remaining responsive to cellular requirements. With respect to cystic fibrosis (CF), the overexpression of cystic fibrosis transmembrane conductance regulator (CFTR) protein trafficking mutants, such as delta-F508, is of great biological and clinical interest. By understanding the post-transcriptional mechanisms that regulate CFTR expression, new procedures can be developed to enhance CFTR expression in homozygous delta-F508 CF patients. We have identified the key elements of a complex negative regulatory mechanism that is encoded within the human CFTR 5'UTR and show how these elements act in combination to restrict CFTR gene expression to a consistently low level in a transcript-specific manner. This study shows, for the first time, that endogenous human CFTR expression is post-transcriptionally regulated through a 5'UTR-mediated mechanism. We show that the very low levels of endogenous CFTR expression, compared with other low expression genes, are maintained through the co-operative inhibitory effects of an upstream open reading frame and a thermodynamically stable RNA secondary structure. PMID:25274779

Lukowski, Samuel W; Rothnagel, Joseph A; Trezise, Ann E O

2015-02-15

11

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

12

Secondary Structure Switch  

ERIC Educational Resources Information Center

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

King, Angela G.

2006-01-01

13

The genetic code as expressed through relationships between mRNA structure and protein function  

PubMed Central

Structured RNA elements within messenger RNA often direct or modulate the cellular production of active proteins. As reviewed here, RNA structures have been discovered that govern nearly every step in protein production: mRNA production and stability; translation initiation, elongation, and termination; protein folding; and cellular localization. Regulatory RNA elements are common within RNAs from every domain of life. This growing body of RNA-mediated mechanisms continues to reveal new ways in which mRNA structure regulates translation. We integrate examples from several different classes of RNA structure-mediated regulation to present a global perspective that suggests that the secondary and tertiary structure of RNA ultimately constitutes an additional level of the genetic code that both guides and regulates protein biosynthesis. PMID:23499436

Weeks, Kevin M.

2014-01-01

14

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

SciTech Connect

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

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

2011-09-27

15

mRNA structures influencing translation in the yeast Saccharomyces cerevisiae.  

PubMed Central

The mRNA sequence and structures that modify and are required for translation of iso-1-cytochrome c in the yeast Saccharomyces cerevisiae were investigated with sets of CYC1 alleles having alterations in the 5' leader region. Measurements of levels of CYC1 mRNA and iso-1-cytochrome c in strains having single copies of altered alleles with nested deletions led to the conclusion that there is no specific sequence adjacent to the AUG initiator codon required for efficient translation. However, the nucleotides preceding the AUG initiator codon at positions -1 and -3 slightly modified the efficiency of translation to an order of preference similar to that found in higher cells. In contrast to large effects observed in higher eucaryotes, the magnitude of this AUG context effect in S. cerevisiae was only two- to threefold. Furthermore, introduction of hairpin structures in the vicinity of the AUG initiator codon inhibited translation, with the degree of inhibition related to the stability and proximity of the hairpin. These results with S. cerevisiae and published findings on other organisms suggest that translation in S. cerevisiae is more sensitive to secondary structures than is translation in higher eucaryotes. Images PMID:2837649

Baim, S B; Sherman, F

1988-01-01

16

Current perspectives on RNA secondary structure probing  

PubMed Central

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

Kenyon, Julia; Prestwood, Liam; Lever, Andrew

2014-01-01

17

5'Terminal structure and mRNA stability  

Microsoft Academic Search

Reovirus mRNAs with 5'-terminal m7GpppGm or GpppG are more stable than mRNA containing unblocked ppG 5'-ends when injected into Xenopus laevis oocytes or incubated in cell-free protein synthesising extracts of wheat germ and mouse L cells. The greater stability of mRNA with blocked 5' termini is not dependent upon translation but seems to result from protection against 5'-exonucleolytic degradation.

Yasuhiro Furuichi; Alba Lafiandra; Aaron J. Shatkin

1977-01-01

18

Prediction of protein secondary structure by mining structural fragment database  

E-print Network

-sheet-rich structures, responsible for Alzheimer's and Parkinson's diseases [5]. Secondary structure prediction can vector machines (SVM) to improve the accuracy of predictions and found that SVM gave the best performance patterns like a-helices and b-sheets. Many have shown that predicting secondary structure can be a first

Margaritis, Dimitris

19

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

20

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

PubMed Central

Human ether--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.Sroubek, J., Krishnan, Y., McDonald, T V. Sequence- and structure-specific elements of HERG mRNA determine channel synthesis and trafficking efficiency. PMID:23608144

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

2013-01-01

21

PEGylated nanoparticles: protein corona and secondary structure  

NASA Astrophysics Data System (ADS)

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

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

2014-09-01

22

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

23

Structural perspectives on secondary active transporters  

PubMed Central

Secondary active transporters catalyze concentrative transport of substrates across lipid membranes by harnessing the energy of electrochemical ion gradients. These transporters bind their ligands on one side of the membrane, and undergo a global conformational change to release them on the other side of the membrane. Over the last few years, crystal structures have captured several bacterial secondary transporters in different states along their transport cycle, providing insight into possible molecular mechanisms. In this review, we will summarize recent findings focusing on the emerging structural and mechanistic similarities between evolutionary diverse transporters. We will also discuss the structural basis of substrate binding, ion coupling and inhibition viewed from the perspective of these similarities. PMID:20655602

Boudker, Olga; Verdon, Grgory

2010-01-01

24

Discrete breathers in protein secondary structure  

Microsoft Academic Search

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

A. E. Sitnitsky

2003-01-01

25

RNA secondary structure prediction using soft computing.  

PubMed

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

Ray, Shubhra Sankar; Pal, Sankar K

2013-01-01

26

Parsing nucleic acid pseudoknotted secondary structure: algorithm and applications  

E-print Network

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

Condon, Anne

27

Novel cis-active structures in the coding region mediate CRM1-dependent nuclear export of IFN-? 1 mRNA.  

PubMed

We recently reported the chromosome region maintenance 1 (CRM1)-dependent nuclear export of intron-less human interferon-?1 (IFN-?1) mRNA, which encodes a main effecter of host innate immunity. We show that the coding region of IFN-?1 mRNA forms novel secondary structures that are responsible for the CRM1-dependent export of the transcript. Deletion-mutagenesis, in vivo export assays, and computer analyses of the folding potentials of export-competent fragments revealed the presence of a domain, termed the conserved secondary structure (CSS), comprising two adjacent putative stable stem-loop structures (nt 208-452). Internal deletion-mutagenesis and constitutive export assays of each stem-loop structure demonstrated that subregions 308-322 and 352-434 act as a core element by conferring the export function on the CSS. Leptomycin B (LMB) inhibition of the CRM1 pathway decreased the export of core element RNA, implying that the principal site of CRM1 action for exporting IFN-?1 mRNA resides within the core element. An RNPS1 (RNA-binding protein S1, serine-rich domain) cDNA was isolated by yeast three-hybrid screening, using bait containing two CSS regions. We showed that RNPS1 might recognize IFN-?1 mRNP that includes CRM1. The data demonstrate that interaction between RNA structures in the coding region and CRM1 affects the nucleocytoplasmic translocation of IFN-?1 mRNA. PMID:20857263

Kimura, Tominori; Hashimoto, Iwao; Nishizawa, Mikio; Ito, Seiji; Yamada, Hisao

2010-09-01

28

Neural network definitions of highly predictable protein secondary structure classes  

Microsoft Academic Search

We use two co-evolving neural networks to determine new classes of protein secondary structure which are significantly more predictable from local amino sequence than the conventional secondary structure classification. Accurate prediction of the conventional secondary structure classes: alpha helix, beta strand, and coil, from primary sequence has long been an important problem in computational molecular biology. Neural networks have been

A. Lapedes; E. Steeg; R. Farber

1994-01-01

29

Expected degree for RNA secondary structure networks.  

PubMed

Consider the network of all secondary structures of a given RNA sequence, where nodes are connected when the corresponding structures have base pair distance one. The expected degree of the network is the average number of neighbors, where average may be computed with respect to the either the uniform or Boltzmann probability. Here, we describe the first algorithm, RNAexpNumNbors, that can compute the expected number of neighbors, or expected network degree, of an input sequence. For RNA sequences from the Rfam database, the expected degree is significantly less than the constrained minimum free energy structure, defined to have minimum free energy (MFE) over all structures consistent with the Rfam consensus structure. The expected degree of structural RNAs, such as purine riboswitches, paradoxically appears to be smaller than that of random RNA, yet the difference between the degree of the MFE structure and the expected degree is larger than that of random RNA. Expected degree does not seem to correlate with standard structural diversity measures of RNA, such as positional entropy and ensemble defect. The program RNAexpNumNbors is written in C, runs in cubic time and quadratic space, and is publicly available at http://bioinformatics.bc.edu/clotelab/RNAexpNumNbors. 2014 Wiley Periodicals, Inc. PMID:25382310

Clote, Peter

2015-01-15

30

Circumstances and mechanisms of inhibition of translation by secondary structure in eucaryotic mRNAs.  

PubMed Central

This paper describes in vitro experiments with two types of intramolecular duplex structures that inhibit translation in cis by preventing the formation of an initiation complex or by causing the complex to be abortive. One stem-loop structure (delta G = -30 kcal/mol) prevented mRNA from engaging 40S subunits when the hairpin occurred 12 nucleotides (nt) from the cap but had no deleterious effect when it was repositioned 52 nt from the cap. This result confirms prior in vivo evidence that the 40S subunit-factor complex, once bound to mRNA, has considerable ability to penetrate secondary structure. Consequently, translation is most sensitive to secondary structure at the entry site for ribosomes, i.e., the 5' end of the mRNA. The second stem-loop structure (hp7; delta G = -61 kcal/mol, located 72 nt from the cap) was too stable to be unwound by 40S ribosomes, hp7 did not prevent a 40S ribosomal subunit from binding but caused the 40S subunit to stall on the 5' side of the hairpin, exactly as the scanning model predicts. Control experiments revealed that 80S elongating ribosomes could disrupt duplex structures, such as hp7, that were too stable to be penetrated by the scanning 40S ribosome-factor complex. A third type of base-paired structure shown to inhibit translation in vivo involves a long-range interaction between the 5' and 3' noncoding sequences. Images PMID:2601712

Kozak, M

1989-01-01

31

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

PubMed Central

The protein-synthesizing ribosome undergoes large motions to effect the translocation of tRNAs and mRNA; here the domain motions of this system are explored with a coarse-grained elastic network model using normal mode analysis. Crystal structures are used to construct various model systems of the 70S complex with/without tRNA, elongation factor Tu and the ribosomal proteins. Computed motions reveal the well-known ratchet-like rotational motion of the large subunits, as well as the head rotation of the small subunit and the high flexibility of the L1 and L7/L12 stalks, even in the absence of ribosomal proteins. This result indicates that these experimentally observed motions during translocation are inherently controlled by the ribosomal shape and only partially dependent upon GTP hydrolysis. Normal mode analysis further reveals the mobility of A- and P-tRNAs to increase in the absence of the E-tRNA. In addition, the dynamics of the E-tRNA is affected by the absence of the ribosomal protein L1. The mRNA in the entrance tunnel interacts directly with helicase proteins S3 and S4, which constrain the mRNA in a clamp-like fashion, as well as with protein S5, which likely orients the mRNA to ensure correct translation. The ribosomal proteins S7, S11 and S18 may also be involved in assuring translation fidelity by constraining the mRNA at the exit site of the channel. The mRNA also interacts with the 16S 3 end forming the Shine-Dalgarno complex at the initiation step; the 3 end may act as a hook to reel in the mRNA to facilitate its exit. PACS: 87.10.Pq; 87.15.bk; 87.15.kj; 87.16.dj; 87.16.dr PMID:19029596

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

2009-01-01

32

Drawing and Editing the Secondary Structure(s) of RNA.  

PubMed

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

Ponty, Yann; Leclerc, Fabrice

2015-01-01

33

Protein Secondary Structure Prediction Method Based on Neural Networks  

Microsoft Academic Search

Protein secondary structure prediction remains an open and important problem in life sciences as a first step towards the crucial tertiary structure prediction. In [3], a protein secondary structure prediction algorithm called PSIPRED presents an innovative approach - feeding the neural network (NN) with a position specific scoring matrix as input data. Starting from this idea, in this paper we

Vasilka Dzikovska; M. Oreskovic; S. Kalajdziski; K. Trivodaliev; D. Davcev

2008-01-01

34

Structured mRNA induces the ribosome into a hyper-rotated state  

PubMed Central

During protein synthesis, mRNA and tRNA are moved through the ribosome by the process of translocation. The small diameter of the mRNA entrance tunnel only permits unstructured mRNA to pass through. However, there are structured elements within mRNA that present a barrier for translocation that must be unwound. The ribosome has been shown to unwind RNA in the absence of additional factors, but the mechanism remains unclear. Here, we show using single molecule Frster resonance energy transfer and small angle X-ray scattering experiments a new global conformational state of the ribosome. In the presence of the frameshift inducing dnaX hairpin, the ribosomal subunits are driven into a hyper-rotated state and the L1 stalk is predominantly in an open conformation. This previously unobserved conformational state provides structural insight into the helicase activity of the ribosome and may have important implications for understanding the mechanism of reading frame maintenance. PMID:24401932

Qin, Peiwu; Yu, Dongmei; Zuo, Xiaobing; Cornish, Peter V

2014-01-01

35

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

PubMed

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

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

2014-03-01

36

First structural evidence of sequestration of mRNA cap structures by type 1 ribosome inactivating protein from Momordica balsamina.  

PubMed

This is the first structural evidence of recognition of mRNA cap structures by a ribosome inactivating protein. It is well known that a unique cap structure is formed at the 5' end of mRNA for carrying out various processes including mRNA maturation, translation initiation, and RNA turnover. The binding studies and crystal structure determinations of type 1 ribosome inactivating protein (RIP-1) from Momordica balsamina (MbRIP-1) were carried out with mRNA cap structures including (i) N7-methyl guanine (m7G), (ii) N7-methyl guanosine diphosphate (m7GDP), and (iii) N7-methyl guanosine triphosphate (m7GTP). These compounds showed affinities to MbRIP-1 at nanomolar concentrations. The structure determinations of the complexes of MbRIP-1 with m7G, m7GDP, and m7GTP at 2.65, 1.77, and 1.75 resolutions revealed that all the three compounds bound to MbRIP-1 in the substrate binding site at the positions which are slightly shifted towards Glu85 as compared to those of rRNA substrates. In this position, Glu85 forms several hydrogen bonds with guanine moiety while N-7 methyl group forms van der Waals contacts. However, the guanine rings are poorly stacked in these complexes. Thus, the mode of binding by MbRIP-1 to mRNA cap structures is different which results in the inhibition of depurination. Since some viruses are known to exploit the capping property of the host, this action of MbRIP-1 may have implications for the antiviral activity of this protein in vivo. The understanding of the mode of binding of MbRIP-1 to cap structures may also assist in the design of anti-viral agents. PMID:23280611

Kushwaha, Gajraj Singh; Yamini, Shavait; Kumar, Mukesh; Sinha, Mau; Kaur, Punit; Sharma, Sujata; Singh, Tej P

2013-05-01

37

Neural network definitions of highly predictable protein secondary structure classes  

SciTech Connect

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

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

1994-02-01

38

Bayesian Model of Protein Primary Sequence for Secondary Structure Prediction  

E-print Network

into a protein's function in the cell. Understanding a protein's secondary structure is a first step towards of residues on the secondary structure determination, including those packed close in space but distant sequences relatively cheap, accurate and fast, in comparison to the costly and involved approaches

Dahl, David B.

39

Bayesian Model of Protein Primary Sequence for Secondary Structure Prediction  

E-print Network

into a protein's function in the cell. Understanding a protein's secondary structure is a first step towards influence of residues on the secondary structure determination, including those packed close in space made obtaining protein sequences relatively cheap, accurate and fast, in comparison to the costly

Vannucci, Marina

40

RNAstructure: software for RNA secondary structure prediction and analysis  

Microsoft Academic Search

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

Jessica S. Reuter; David H. Mathews

2010-01-01

41

Deleterious mutation prediction in the secondary structure of RNAs  

E-print Network

transcription termination in the thiamin pyrophosphate and S- adenosyl-methionine induced riboswitches. Ribo- switches are mRNA structures that have recently been found to regulate transcription termination or translation initiation in bacteria by conformation rearrangement in response to direct metabolite binding

Barash, Danny

42

Unified approach to partition functions of RNA secondary structures.  

PubMed

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

Bundschuh, Ralf

2014-11-01

43

PCI-SS: MISO dynamic nonlinear protein secondary structure prediction  

Microsoft Academic Search

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

James R. Green; Michael J. Korenberg; Mohammed O. Aboul-magd

2009-01-01

44

Enhanced protein fold recognition using secondary structure information from nmr  

Microsoft Academic Search

NMR offers the possibility of accurate secondary structure for proteins that would be too large for structure determi- nation. In the absence of an X-ray crystal structure, this information should be useful as an adjunct to protein fold recognition methods based on low resolution force fields. The value of this information has been tested by adding varying amounts of artificial

Daniel J. Ayers; Paul R. Gooley; Asaph Widmer-Cooper; Andrew E. Torda

1999-01-01

45

Description of protein secondary structure using dual quaternions  

NASA Astrophysics Data System (ADS)

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

Prokov, Jitka

2014-11-01

46

Hierarchical Protein Structure Superposition using both Secondary Structure and Atomic Representations  

E-print Network

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

Brutlag, Doug

47

Communication Secondary structure of dengue virus type 4  

E-print Network

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

Hanley, Kathryn A.

48

RNA Secondary Structures Adam Novak, Jotun Hein & Rune Lyngs  

E-print Network

dogma of molecular biology states that the flow of information is from DNA, through RNA, to proteinsRNA Secondary Structures Adam Novak, Jotun Hein & Rune Lyngsø July 23, 2010 Background The central are the molecules with functional and structural rôles. In this view, RNA is mostly considered a `supporting actor

Goldschmidt, Christina

49

An mRNA structure that controls gene expression by binding FMN.  

PubMed

The RFN element is a highly conserved domain that is found frequently in the 5'-untranslated regions of prokaryotic mRNAs that encode for flavin mononucleotide (FMN) biosynthesis and transport proteins. We report that this domain serves as the receptor for a metabolite-dependent riboswitch that directly binds FMN in the absence of proteins. Our results also indicate that in Bacillus subtilis, the riboswitch most likely controls gene expression by causing premature transcription termination of the ribDEAHT operon and precluding access to the ribosome-binding site of ypaA mRNA. Sequence and structural analyses indicate that the RFN element is a natural FMN-binding aptamer, the allosteric character of which is harnessed to control gene expression. PMID:12456892

Winkler, Wade C; Cohen-Chalamish, Smadar; Breaker, Ronald R

2002-12-10

50

Aligning Protein Sequences with Predicted Secondary Structure  

E-print Network

the amino acid sequence alone often does not provide enough information to obtain accurate alignments under in regions that may be in the structural core, and are employed by CLUSTAL W (Thompson et al., 1994), T-Coffee favors matches in the alignment that have high support, and is employed by T-Coffee, MAFFT, Prob

Wheeler, Travis

51

Aligning protein sequences with predicted secondary structure  

E-print Network

. Since the amino acid sequence alone often does not provide enough information to obtain accurate be in the structural core, and are employed by CLUSTAL W (Thompson et al. 1994), T-Coffee (Notredame et al. 2000 high support, and is employed by T-Coffee, MAFFT, ProbCons, SPEM (Zhou and Zhou 2005), PROMALS (Pei

Kececioglu, John

52

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

PubMed

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

Taverniti, Valerio; Sraphin, Bertrand

2014-11-28

53

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

PubMed Central

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

Taverniti, Valerio; Sraphin, Bertrand

2015-01-01

54

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

PubMed Central

T. brucei survival relies on the expression of mitochondrial genes, most of which require RNA editing to become translatable. In trypanosomes, RNA editing involves the insertion and deletion of uridylates, a developmentally regulated process directed by guide RNAs (gRNAs) and catalyzed by the editosome, a complex of proteins. The pathway for mRNA/gRNA complex formation and assembly with the editosome is still unknown. Work from our laboratory has suggested that distinct mRNA/gRNA complexes anneal to form a conserved core structure that may be important for editosome assembly. The secondary structure for the apocytochrome b (CYb) pair has been previously determined and is consistant with our model of a three-helical structure. Here, we used cross-linking and solution structure probing experiments to determine the structure of the ATPase subunit 6 (A6) mRNA hybridized to its cognate gA6-14 gRNA in different stages of editing. Our results indicate that both unedited and partially edited A6/gA6-14 pairs fold into a three-helical structure similar to the previously characterized CYb/gCYb-558 pair. These results lead us to conclude that at least two mRNA/gRNA pairs with distinct editing sites and distinct primary sequences fold to a three-helical secondary configuration that persists through the first few editing events. PMID:18772247

Reifur, Larissa; Koslowsky, Donna J.

2008-01-01

55

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

56

Application of expert networks for predicting proteins secondary structure  

Microsoft Academic Search

The present study utilizes expert neural networks for the prediction of proteins secondary structure. We use three independent networks, one for each structure (alpha, beta and coil) as the first-level processing unit; decision upon the chosen structure for each residue is carried out by a second-level, post-processing unit, which utilizes the Chou and Fasman frequency values F? and F? in

Sarit Sivan; Orna Filo; Hava Siegelmann

2007-01-01

57

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

PubMed Central

Caenorhabditis elegans fem-3 binding factor (FBF) is a founding member of the PUMILIO/FBF (PUF) family of mRNA regulatory proteins. It regulates multiple mRNAs critical for stem cell maintenance and germline development. Here, we report crystal structures of FBF in complex with 6 different 9-nt RNA sequences, including elements from 4 natural mRNAs. These structures reveal that FBF binds to conserved bases at positions 13 and 78. The key specificity determinant of FBF vs. other PUF proteins lies in positions 46. In FBF/RNA complexes, these bases stack directly with one another and turn away from the RNA-binding surface. A short region of FBF is sufficient to impart its unique specificity and lies directly opposite the flipped bases. We suggest that this region imposes a flattened curvature on the protein; hence, the requirement for the additional nucleotide. The principles of FBF/RNA recognition suggest a general mechanism by which PUF proteins recognize distinct families of RNAs yet exploit very nearly identical atomic contacts in doing so. PMID:19901328

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

2009-01-01

58

Asymptotic number of hairpins of saturated RNA secondary structures.  

PubMed

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

Clote, Peter; Kranakis, Evangelos; Krizanc, Danny

2013-12-01

59

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

60

Functional and Structural Analysis of the Internal Ribosome Entry Site Present in the mRNA of Natural Variants of the HIV-1  

PubMed Central

The 5?untranslated regions (UTR) of the full length mRNA of the HIV-1 proviral clones pNL4.3 and pLAI, harbor an internal ribosomal entry site (IRES). In this study we extend this finding by demonstrating that the mRNA 5?UTRs of natural variants of HIV-1 also exhibit IRES-activity. Cap-independent translational activity was demonstrated using bicistronic mRNAs in HeLa cells and in Xenopus laevis oocytes. The possibility that expression of the downstream cistron in these constructs was due to alternative splicing or to cryptic promoter activity was ruled out. The HIV-1 variants exhibited significant 5?UTR nucleotide diversity with respect to the control sequence recovered from pNL4.3. Interestingly, translational activity from the 5?UTR of some of the HIV-1 variants was enhanced relative to that observed for the 5?UTR of pNL4.3. In an attempt to explain these findings we probed the secondary structure of the variant HIV-1 5?UTRs using enzymatic and chemical approaches. Yet subsequent structural analyses did not reveal significant variations when compared to the pNL4.3-5?UTR. Thus, the increased IRES-activity observed for some of the HIV-1 variants cannot be ascribed to a specific structural modification. A model to explain these findings is proposed. PMID:22496887

Vallejos, Maricarmen; Carvajal, Felipe; Pino, Karla; Navarrete, Camilo; Ferres, Marcela; Huidobro-Toro, Juan Pablo; Sargueil, Bruno; Lpez-Lastra, Marcelo

2012-01-01

61

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

62

IMPORTANCE OF SECONDARY STRUCTURE ELEMENTS FOR PREDICTION OF GO ANNOTATIONS  

E-print Network

for the proteins of human, mouse, rat, arabidop- sis, zebra fish, chicken and cow. It also provides a Protein Data: bioinfo.ce.itu.edu.tr ABSTRACT Predicted or actual protein secondary structure, in addition to amino acid: loop) for protein function prediction is investi- gated. Smith-Waterman alignment similarity scores

Cataltepe, Zehra

63

Algorithm independent properties of RNA secondary structure predictions  

Microsoft Academic Search

Algorithms predicting RNA secondary structures based on different folding criteria minimum free energies (mfe), kinetic\\u000a folding (kin), maximum matching (mm) and different parameter sets are studied systematically. Two base pairing alphabets\\u000a were used: the binary GC and the natural four-letter AUGC alphabet. Computed structures and free energies depend strongly on both the algorithm and the parameter set. Statistical

Manfred Tacker; Peter F. Stadler; Erich G. Bornberg-Bauer; Ivo L. Hofacker; Peter Schuster

1996-01-01

64

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

PubMed

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

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

2014-04-01

65

Prion proteins: evolution and preservation of secondary structure.  

PubMed

Prions cause a variety of neurodegenerative disorders that seem to result from a conformational change in the prion protein (PrP). Thirty-two PrP sequences have been subjected to phylogenetic analysis followed by reconstruction of the most probable evolutionary spectrum of amino acid replacements. The replacement rates suggest that the protein does not seem to be very conservative, but in the course of evolution amino acids have only been substituted within the elements of the secondary structure by those with very similar physico-chemical properties. Analysis of the full spectrum of single-step amino acid substitutions in human PrP using secondary structure prediction algorithms shows an over-representation of substitutions that tend to destabilize alpha-helices. PMID:9276441

Kuznetsov, I B; Morozov, P S; Matushkin, Y G

1997-08-01

66

Using circular dichroism spectra to estimate protein secondary structure  

PubMed Central

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

Greenfield, Norma J.

2009-01-01

67

Random generation of RNA secondary structures according to native distributions  

PubMed Central

Background Random biological sequences are a topic of great interest in genome analysis since, according to a powerful paradigm, they represent the background noise from which the actual biological information must differentiate. Accordingly, the generation of random sequences has been investigated for a long time. Similarly, random object of a more complicated structure like RNA molecules or proteins are of interest. Results In this article, we present a new general framework for deriving algorithms for the non-uniform random generation of combinatorial objects according to the encoding and probability distribution implied by a stochastic context-free grammar. Briefly, the framework extends on the well-known recursive method for (uniform) random generation and uses the popular framework of admissible specifications of combinatorial classes, introducing weighted combinatorial classes to allow for the non-uniform generation by means of unranking. This framework is used to derive an algorithm for the generation of RNA secondary structures of a given fixed size. We address the random generation of these structures according to a realistic distribution obtained from real-life data by using a very detailed context-free grammar (that models the class of RNA secondary structures by distinguishing between all known motifs in RNA structure). Compared to well-known sampling approaches used in several structure prediction tools (such as SFold) ours has two major advantages: Firstly, after a preprocessing step in time O(n2) for the computation of all weighted class sizes needed, with our approach a set of m random secondary structures of a given structure size n can be computed in worst-case time complexity Om?n? log(n) while other algorithms typically have a runtime in O(m?n2). Secondly, our approach works with integer arithmetic only which is faster and saves us from all the discomforting details of using floating point arithmetic with logarithmized probabilities. Conclusion A number of experimental results shows that our random generation method produces realistic output, at least with respect to the appearance of the different structural motifs. The algorithm is available as a webservice at http://wwwagak.cs.uni-kl.de/NonUniRandGen and can be used for generating random secondary structures of any specified RNA type. A link to download an implementation of our method (in Wolfram Mathematica) can be found there, too. PMID:21992500

2011-01-01

68

Secondary structure of the Dictyostelium discoideum small subunit ribosomal RNA.  

PubMed Central

We have used comparative analyses of prokaryotic and eukaryotic small subunit ribosomal RNAs to deduce a secondary structure for the Dictyostelium discoideum 18S rRNA. Most of the duplex regions are evolutionarily conserved in all organisms. We have taken advantage of the variation to the D. discoideum sequence (relative to the yeast and frog 19S rRNAs) to identify additional helical regions which are common to the eukaryotic 18S rRNAs. PMID:6359065

Olsen, G J; McCarroll, R; Sogin, M L

1983-01-01

69

Predicting protein secondary structure by cascade-correlation neural networks  

Microsoft Academic Search

Summary: The back-propagation neural network algorithm is a commonly used method for predicting the secondary structure of proteins. Whilst popular, this method can be slow to learn and here we compare it with an alternative: the cascade-correlation architecture. Using a constructive algorithm, cascade-correlation achieves predictive accuracies comparable to those obtained by back-propagation, in shorter time. Availability: A web server is

Matthew J. Wood; Jonathan D. Hirst

2004-01-01

70

Distinct circular dichroism spectroscopic signatures of polyproline II and unordered secondary structures: applications in secondary structure analyses.  

PubMed

Circular dichroism (CD) spectroscopy is a valuable method for defining canonical secondary structure contents of proteins based on empirically-defined spectroscopic signatures derived from proteins with known three-dimensional structures. Many proteins identified as being "Intrinsically Disordered Proteins" have a significant amount of their structure that is neither sheet, helix, nor turn; this type of structure is often classified by CD as "other", "random coil", "unordered", or "disordered". However the "other" category can also include polyproline II (PPII)-type structures, whose spectral properties have not been well-distinguished from those of unordered structures. In this study, synchrotron radiation circular dichroism spectroscopy was used to investigate the spectral properties of collagen and polyproline, which both contain PPII-type structures. Their native spectra were compared as representatives of PPII structures. In addition, their spectra before and after treatment with various conditions to produce unfolded or denatured structures were also compared, with the aim of defining the differences between CD spectra of PPII and disordered structures. We conclude that the spectral features of collagen are more appropriate than those of polyproline for use as the representative spectrum for PPII structures present in typical amino acid-containing proteins, and that the single most characteristic spectroscopic feature distinguishing a PPII structure from a disordered structure is the presence of a positive peak around 220nm in the former but not in the latter. These spectra are now available for inclusion in new reference data sets used for CD analyses of the secondary structures of soluble proteins. PMID:25262612

Lopes, Jose L S; Miles, Andrew J; Whitmore, Lee; Wallace, B A

2014-12-01

71

Coating concrete secondary containment structures exposed to agrichemicals  

SciTech Connect

Concrete has traditionally been the material of choice for building secondary containment structures because it is relatively inexpensive and has structural properties which make it ideal for supporting the loads of vehicles and large tanks. However, concrete`s chemical properties make it susceptible to corrosion by some common fertilizers. Though fairly impervious to water movement, concrete is easily penetrated by vapors and solvents. It is also prone to cracking. For these reasons, the Environmental Protection Agency (EPA) believes that concrete alone may not provide an effective barrier to pesticide movement and has proposed that concrete in pesticide secondary containment structures be sealed or coated to reduce its permeability. Some state secondary containment regulations require that concrete exposed to fertilizers and pesticides be sealed or protected with a coating. Lacking guidelines, some retailers have used penetrating sealants to satisfy the law, even though these products provide little protection from chemical attack nor do they prevent pesticide egress. Other retailers who have applied thick film coatings which were properly selected have had disastrous results because the application was poorly done. Consequently, much skepticism exists regarding the performance and benefit of protective coatings.

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

1995-06-01

72

Improving the accuracy of protein secondary structure prediction using structural alignment  

PubMed Central

Background The accuracy of protein secondary structure prediction has steadily improved over the past 30 years. Now many secondary structure prediction methods routinely achieve an accuracy (Q3) of about 75%. We believe this accuracy could be further improved by including structure (as opposed to sequence) database comparisons as part of the prediction process. Indeed, given the large size of the Protein Data Bank (>35,000 sequences), the probability of a newly identified sequence having a structural homologue is actually quite high. Results We have developed a method that performs structure-based sequence alignments as part of the secondary structure prediction process. By mapping the structure of a known homologue (sequence ID >25%) onto the query protein's sequence, it is possible to predict at least a portion of that query protein's secondary structure. By integrating this structural alignment approach with conventional (sequence-based) secondary structure methods and then combining it with a "jury-of-experts" system to generate a consensus result, it is possible to attain very high prediction accuracy. Using a sequence-unique test set of 1644 proteins from EVA, this new method achieves an average Q3 score of 81.3%. Extensive testing indicates this is approximately 45% better than any other method currently available. Assessments using non sequence-unique test sets (typical of those used in proteome annotation or structural genomics) indicate that this new method can achieve a Q3 score approaching 88%. Conclusion By using both sequence and structure databases and by exploiting the latest techniques in machine learning it is possible to routinely predict protein secondary structure with an accuracy well above 80%. A program and web server, called PROTEUS, that performs these secondary structure predictions is accessible at . For high throughput or batch sequence analyses, the PROTEUS programs, databases (and server) can be downloaded and run locally. PMID:16774686

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

2006-01-01

73

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

PubMed Central

Messenger RNA export is mediated by the TAP-p15 heterodimer, which belongs to the family of NTF2-like export receptors. TAP-p15 heterodimers also bind to the constitutive transport element (CTE) present in simian type D retroviral RNAs, and mediate export of viral unspliced RNAs to the host cytoplasm. We have solved the crystal structure of the RNA recognition and leucine-rich repeat motifs of TAP bound to one symmetrical-half of CTE RNA. L-shaped conformations of protein and RNA are involved in a mutual molecular embrace on complex formation. We have monitored the impact of structure-guided mutations on binding affinities in vitro and transport assays in vivo. Our studies define the principles by which CTE RNA subverts the mRNA export receptor TAP, thereby facilitating nuclear export of viral genomic RNAs, and more generally, provide insights on cargo RNA recognition by mRNA export receptors. PMID:21822283

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

2011-01-01

74

Computational RNA secondary structure design: empirical complexity and improved methods  

PubMed Central

Background We investigate the empirical complexity of the RNA secondary structure design problem, that is, the scaling of the typical difficulty of the design task for various classes of RNA structures as the size of the target structure is increased. The purpose of this work is to understand better the factors that make RNA structures hard to design for existing, high-performance algorithms. Such understanding provides the basis for improving the performance of one of the best algorithms for this problem, RNA-SSD, and for characterising its limitations. Results To gain insights into the practical complexity of the problem, we present a scaling analysis on random and biologically motivated structures using an improved version of the RNA-SSD algorithm, and also the RNAinverse algorithm from the Vienna package. Since primary structure constraints are relevant for designing RNA structures, we also investigate the correlation between the number and the location of the primary structure constraints when designing structures and the performance of the RNA-SSD algorithm. The scaling analysis on random and biologically motivated structures supports the hypothesis that the running time of both algorithms scales polynomially with the size of the structure. We also found that the algorithms are in general faster when constraints are placed only on paired bases in the structure. Furthermore, we prove that, according to the standard thermodynamic model, for some structures that the RNA-SSD algorithm was unable to design, there exists no sequence whose minimum free energy structure is the target structure. Conclusion Our analysis helps to better understand the strengths and limitations of both the RNA-SSD and RNAinverse algorithms, and suggests ways in which the performance of these algorithms can be further improved. PMID:17266771

Aguirre-Hernndez, Rosala; Hoos, Holger H; Condon, Anne

2007-01-01

75

A seqlet-based maximum entropy Markov approach for protein secondary structure prediction  

Microsoft Academic Search

A novel method for predicting the secondary structures of proteins from amino acid sequence has been presented. The protein\\u000a secondary structure seqlets that are analogous to the words in natural language have been extracted. These seqlets will capture\\u000a the relationship between amino acid sequence and the secondary structures of proteins and further form the protein secondary\\u000a structure dictionary. To be

Qiwen Dong; Xiaolong Wang; Lei Lin; Yi Guan

2005-01-01

76

A protein structural classes prediction method based on predicted secondary structure and PSI-BLAST profile.  

PubMed

Knowledge of protein secondary structural classes plays an important role in understanding protein folding patterns. In this paper, 25 features based on position-specific scoring matrices are selected to reflect evolutionary information. In combination with other 11 rational features based on predicted protein secondary structure sequences proposed by the previous researchers, a 36-dimensional representation feature vector is presented to predict protein secondary structural classes for low-similarity sequences. ASTRALtraining dataset is used to train and design our method, other three low-similarity datasets ASTRALtest, 25PDB and 1189 are used to test the proposed method. Comparisons with other methods show that our method is effective to predict protein secondary structural classes. Stand alone version of the proposed method (PSSS-PSSM) is written in MATLAB language and it can be downloaded from http://letsgob.com/bioinfo_PSSS_PSSM/. PMID:24067326

Ding, Shuyan; Li, Yan; Shi, Zhuoxing; Yan, Shoujiang

2014-02-01

77

A water molecule participates in the secondary structure of hyaluronan.  

PubMed Central

The structure of hyaluronan was investigated in water/dimethyl sulphoxide mixtures by using high-field n.m.r. and space-filling molecular models. The secondary structure previously established in detail in 'dry' dimethyl sulphoxide [Heatley, Scott & Hull (1984) Biochem. J. 220, 197-205] undergoes changes on addition of water, compatible with the incorporation of a water bridge between the uronate carboxylate and acetamido NH groups. Molecular models show that such a configuration is highly probable, and saturation-transfer experiments yield rates of NH proton exchange that support this proposed structure. The existence of two distinct stable configurations for hyaluronan, in water-rich and water-poor conditions respectively, may have biological implications, e.g. during its biosynthesis in cell membranes. There are extensive hydrophobic regions in both forms, which may be important for interactions with e.g., membranes, proteins and itself. PMID:2845953

Heatley, F; Scott, J E

1988-01-01

78

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 PMID:6269091

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

1981-01-01

79

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

PubMed Central

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

Jani, Divyang; Valkov, Eugene; Stewart, Murray

2014-01-01

80

Quantitation of secondary structure in ATR infrared spectroscopy  

PubMed Central

Polarized attenuated total reflection infrared spectroscopy of aligned membranes provides essential information on the secondary structure content and orientation of the associated membrane proteins. Quantitation of the relative content of different secondary structures, however, requires allowance for geometric relations of the electric field components (E(x), E(y), E(z)) of the evanescent wave, and of the components of the infrared transition moments, in combining absorbances (A() and A( perpendicular)) measured with radiation polarized parallel with and perpendicular to, respectively, the plane of incidence. This has hitherto not been done. The appropriate combination for exact evaluation of relative integrated absorbances is A() + (2E(z)(2)/E(y)(2) - E(x)(2)/E(y)(2))A( perpendicular), where z is the axis of ordering that is normal to the membrane plane, and the x-axis lies in the membrane plane within the plane of incidence. This combination can take values in the range approximately from A() - 0.4A( perpendicular) to A() + 2.7A( perpendicular), depending on experimental conditions and the attenuated total reflection crystal used. With unpolarized radiation, this correction is not possible. Similar considerations apply to the dichroic ratios of multicomponent bands, which are also treated. PMID:10545362

Marsh, D

1999-01-01

81

[Self-association and secondary structure of beta-casein].  

PubMed

The secondary structure alterations, accompanying isothermal and temperature guided beta-casein micellization have been studied by dynamic light scattering, circular dichroism and Fourier transform infrared spectroscopy techniques. Micelle formation induced by increase of protein concentration at constant temperature is accompanied by the formation of scanty number of additional peptide hydrogen bonds, preliminary assigned to intraprotein beta-structure. Heating results in more pronounced but qualitatively different changes consisted in dehydration of peptide groups and disruption of polyproline II helix segments with subsequent conversion to random and beta-turns. Nevertheless, in both cases the total number of residues involved in transition is quite few and cannot be regarded as a decisive factor for casein micellization. PMID:24707721

Fa?zullin, D A; Konnova, T A; Haertle, T; Zuev, Iu F

2013-01-01

82

Mining overrepresented 3D patterns of secondary structures in proteins.  

PubMed

We consider the problem of finding overrepresented arrangements of secondary structure elements (SSEs) in a given dataset of representative protein structures. While most papers in the literature study the distribution of geometrical properties, in particular angles and distances, between pairs of interacting SSEs, in this paper we focus on the distribution of angles of all quartets of SSEs and on the extraction of overrepresented angular patterns. We propose a variant of the Apriori method that obtains overrepresented arrangements of quartets of SSEs by combining arrangements of triplets of SSEs. This specific case will pose the basis for a natural extension of the problem to any given number of SSEs. We analyze the results of our method on a dataset of 300 nonredundant proteins. Supplementary material is available at (http://www.dei.unipd.it/nciompin/papers/CGZ-jbcb-suppl.pdf/). PMID:19090018

Comin, Matteo; Guerra, Concettina; Zanotti, Giuseppe

2008-12-01

83

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

PubMed

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

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

2013-10-01

84

Secondary structure of Huntingtin amino-terminal region  

PubMed Central

Summary Huntington's disease (HD) is a genetic neurodegenerative disorder resulting from polyglutamine (polyQ) expansion (> 36Q) within first exon of Huntingtin (Htt) protein. Here we applied X-ray crystallography to determine the secondary structure of the first exon (EX1) of Htt-17Q. The structure of Htt17Q-EX1 consists of an amino-terminal ?-helix, a poly17Q region, and a polyproline helix formed by the proline-rich region. The poly17Q region adopts multiple conformations in the structure, including ?-helix, random coil and extended loop. The conformation of the poly17Q region is influenced by the conformation of neighbouring protein regions, demonstrating 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. PMID:19748341

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

2010-01-01

85

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

E-print Network

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

Erdogan, Hakan

86

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

87

Structural insights into the mechanism and evolution of the vaccinia virus mRNA cap N7 methyl-transferase  

PubMed Central

The vaccinia virus mRNA capping enzyme is a multifunctional heterodimeric protein associated with the viral polymerase that both catalyses the three steps of mRNA capping and regulates gene transcription. The structure of a subcomplex comprising the C-terminal N7-methyl-transferase (MT) domain of the large D1 subunit, the stimulatory D12 subunit and bound S-adenosyl-homocysteine (AdoHcy) has been determined at 2.7 resolution and reveals several novel features of the poxvirus capping enzyme. The structure shows for the first time the critical role played by the proteolytically sensitive N-terminus of the MT domain in binding the methyl donor and in catalysis. In addition, the poxvirus enzyme has a completely unique mode of binding of the adenosine moiety of AdoHcy, a feature that could be exploited for design of specific anti-poxviral compounds. The structure of the poxvirus-specific D12 subunit suggests that it was originally an RNA cap 2?O-MT that has evolved to a catalytically inactive form that has been retained for D1 stabilisation and MT activity enhancement through an allosteric mechanism. PMID:17989694

De la Pea, Marcos; Kyrieleis, Otto J P; Cusack, Stephen

2007-01-01

88

Strong Epistatic Selection on the RNA Secondary Structure of HIV  

PubMed Central

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

Assis, Raquel

2014-01-01

89

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

E-print Network

The low-lying level structure of the unbound neutron-rich nucleus $^{13}$Be has been investigated via breakup on a carbon target of secondary beams of $^{14,15}$B at 35 MeV/nucleon. The coincident detection of the beam velocity $^{12}$Be fragments and neutrons permitted the invariant mass of the $^{12}$Be+$n$ and $^{12}$Be+$n$+$n$ systems to be reconstructed. In the case of the breakup of $^{15}$B, a very narrow structure at threshold was observed in the $^{12}$Be+$n$ channel. Contrary to earlier stable beam fragmentation studies which identified this as a strongly interacting $s$-wave virtual state in $^{13}$Be, analysis here of the $^{12}$Be+$n$+$n$ events demonstrated that this was an artifact resulting from the sequential-decay of the $^{14}$Be(2$^+$) state. Single-proton removal from $^{14}$B was found to populate a broad low-lying structure some 0.70 MeV above the neutron-decay threshold in addition to a less prominent feature at around 2.4 MeV. Based on the selectivity of the reaction and a comparison ...

Randisi, G; Falou, H Al; Orr, N A; Marqus, F M; Achouri, N L; Anglique, J -C; Ashwood, N; Bastin, B; Bloxham, T; Brown, B A; Catford, W N; Curtis, N; Delaunay, F; Freer, M; Brennand, E de Ges; Haigh, P; Hanappe, F; Harlin, C; Laurent, B; Lecouey, J -L; Ninane, A; Patterson, N; Price, D; Stuttg, L; Thomas, J S

2013-01-01

90

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

PubMed Central

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

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

2000-01-01

91

Structure of 13Be probed via secondary-beam reactions  

NASA Astrophysics Data System (ADS)

The low-lying level structure of the unbound neutron-rich nucleus 13Be has been investigated via breakup on a carbon target of secondary beams of 14,15B at 35 MeV/nucleon. The coincident detection of the beam velocity 12Be fragments and neutrons permitted the invariant mass of the 12Be+n and 12Be+n+n systems to be reconstructed. In the case of the breakup of 15B, a very narrow structure at threshold was observed in the 12Be+n channel. Analysis of the 12Be+n+n events demonstrated that this resulted from the sequential decay of the unbound 14Be(2+) state rather than a strongly interacting s-wave virtual state in 13Be, as had been surmised in stable beam fragmentation studies. Single-proton removal from 14B was found to populate a broad low-lying structure some 0.7 MeV above the neutron-decay threshold, in addition to a less prominent feature at around 2.4 MeV. Based on the selectivity of the reaction and a comparison with (0-3)?? shell-model calculations, the low-lying structure is concluded to arise from closely spaced J?=1/2+ and 5/2+ resonances (Er=0.400.03 and 0.85-0.11+0.15 MeV), while the broad higher-lying feature is a second 5/2+ level (Er=2.350.14 MeV). Taken in conjunction with earlier studies, the results suggest that the lowest 1/2+ and 1/2- levels lie relatively close together below 1 MeV.

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

2014-03-01

92

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

E-print Network

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

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

2014-02-28

93

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

PubMed

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

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

1995-08-21

94

Structurally Coloured Secondary Particles Composed of Black and White Colloidal Particles  

PubMed Central

This study investigated the colourful secondary particles formed by controlling the aggregation states of colloidal silica particles and the enhancement of the structural colouration of the secondary particles caused by adding black particles. We obtained glossy, partially structurally coloured secondary particles in the absence of NaCl, but matte, whitish secondary particles were obtained in the presence of NaCl. When a small amount of carbon black was incorporated into both types of secondary particles, the incoherent multiple scattering of light from the amorphous region was considerably reduced. However, the peak intensities in the reflection spectra, caused by Bragg reflection and by coherent single wavelength scattering, were only slightly decreased. Consequently, a brighter structural colour of these secondary particles was observed with the naked eye. Furthermore, when magnetite was added as a black particle, the coloured secondary particles could be moved and collected by applying an external magnetic field. PMID:23917891

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

2013-01-01

95

Selection intensity against deleterious mutations in RNA secondary structures and rate of compensatory nucleotide substitutions.  

PubMed Central

A two-locus model of reversible mutations with compensatory fitness interactions is presented; single mutations are assumed to be deleterious but neutral in appropriate combinations. The expectation of the time of compensatory nucleotide substitutions is calculated analytically for the case of tight linkage between sites. It is shown that selection increases the substitution time dramatically when selection intensity Ns > 1, where N is the diploid population size and s the selection coefficient. Computer simulations demonstrate that recombination increases the substitution time, but the effect of recombination is small when selection is weak. The amount of linkage disequilibrium generated in the process of compensatory substitution is also investigated. It is shown that significant linkage disequilibrium is expected to be rare in natural populations. The model is applied to the mRNA secondary structure of the bicoid 3' untranslated region of Drosophila. It is concluded that average selection intensity Ns against single deleterious mutations is not likely to be much larger than 1. PMID:11560913

Innan, H; Stephan, W

2001-01-01

96

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

PubMed Central

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

Battelle, S. Saraswathi; Fernndez-Martnez, J. L.; Koli?ski, A.; Jernigan, R. L.; Battelle, A. Kloczkowski

2013-01-01

97

Structural reform in secondary school education-tendencies and strategies  

Microsoft Academic Search

Since the virtual abolition of the double-track system, secondary school education worldwide has carried a double task: to continue to provide general education for qualified students after they finish elementary schooling and to train mid-level professional personnel and technically skilled workers. These will continue to be the tasks of secondary school education until the realization of universalization of higher education.

Zhenye Gao; Mingan Xiong

1988-01-01

98

Secondary structures and structural fluctuation in a dimeric protein, Streptomyces subtilisin inhibitor.  

PubMed

Based on the nuclear magnetic resonance assignments of a dimeric protein, Streptomyces subtilisin inhibitor (SSI), microscopic details of secondary structures in solution have been elucidated. The chemical shift index of C(alpha) signals, together with information on the hydrogen exchange rates of the backbone amide protons, were used to identify secondary structures. The locations of these secondary structures were found to be different in some critical points from those determined earlier by X-ray crystallography of the crystal. Notably, the beta3 strand is completely missing and the alpha2 helix is extended toward the C-terminus. Furthermore, hydrogen exchange experiments of individual peptide NH protons under strongly folding conditions revealed mechanisms of global and local structural fluctuation within the dimeric structure. It has been suggested that the global fluctuation of the monomeric unit occurs without affecting the accompanying monomer, in contrast to the equilibrium thermal unfolding, which is cooperative. Higher protection against hydrogen exchange for residues in part of the beta4 strand implies that this region might serve as a folding core. PMID:10544278

Sasakawa, H; Tamura, A; Fujimaki, S; Taguchi, S; Akasaka, K

1999-11-01

99

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

PubMed Central

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

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

2013-01-01

100

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

Microsoft Academic Search

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

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

1999-01-01

101

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

E-print Network

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

Mag Washietl, Stefan

102

G-quadruplex RNA structure as a signal for neurite mRNA targeting.  

PubMed

Targeting of messenger RNAs (mRNAs) in neuron processes relies on cis-acting regulatory elements, the nature of which is poorly understood. Here, we report that approximately 30% of the best-known dendritic mRNAs contain a guanine (G)-quadruplex consensus in their 3'-untranslated region. Among these mRNAs, we show by using RNA structure probing that a G-quadruplex is present in the mRNAs of two key postsynaptic proteins: PSD-95 and CaMKIIa. The G-quadruplex structure is necessary and sufficient for the potent and fast localization of mRNAs in cortical neurites and this occurs in a metabotropic glutamate receptor-responsive manner. Thus, G-quadruplex seems to be a common neurite localization signal. PMID:21566646

Subramanian, Murugan; Rage, Florence; Tabet, Ricardos; Flatter, Eric; Mandel, Jean-Louis; Moine, Herv

2011-07-01

103

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

PubMed Central

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

Veo, Bethany L.; Krushel, Leslie A.

2012-01-01

104

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

PubMed Central

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

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

2014-01-01

105

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

PubMed

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

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

2014-01-01

106

Structure of the Saccharomyces cerevisiae Cet1-Ceg1 mRNA capping apparatus  

PubMed Central

SUMMARY The 5 guanine-N7 cap is the first co-transcriptional modification of messenger RNA. In Saccharomyces cerevisiae, the first two steps in capping are catalyzed by the RNA triphosphatase Cet1 and RNA guanylyltransferase Ceg1 which form a complex that is directly recruited to phosphorylated RNA polymerase II (RNAP IIo), primarily via contacts between RNAP IIo and Ceg1. A 3.0 crystal structure of Cet1-Ceg1 revealed a 176 kDa heterotetrameric complex composed of one Cet1 homodimer that associates with two Ceg1 molecules via interactions between the Ceg1 OB domain and an extended Cet1 WAQKW amino acid motif. The WAQKW motif is followed by a flexible linker that would allow Ceg1 to achieve conformational changes required for capping while maintaining interactions with both Cet1 and RNAP IIo. The impact of mutations as assessed through genetic analysis in S. cerevisiae are consonant with contacts observed in the Cet1-Ceg1 structure. PMID:20159466

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

2010-01-01

107

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

108

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

PubMed Central

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

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

1995-01-01

109

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

110

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

Microsoft Academic Search

BackgroundProtein 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

111

Protein secondary structure assignment revisited: a detailed analysis of different assignment methods  

PubMed Central

Background A number of methods are now available to perform automatic assignment of periodic secondary structures from atomic coordinates, based on different characteristics of the secondary structures. In general these methods exhibit a broad consensus as to the location of most helix and strand core segments in protein structures. However the termini of the segments are often ill-defined and it is difficult to decide unambiguously which residues at the edge of the segments have to be included. In addition, there is a "twilight zone" where secondary structure segments depart significantly from the idealized models of Pauling and Corey. For these segments, one has to decide whether the observed structural variations are merely distorsions or whether they constitute a break in the secondary structure. Methods To address these problems, we have developed a method for secondary structure assignment, called KAKSI. Assignments made by KAKSI are compared with assignments given by DSSP, STRIDE, XTLSSTR, PSEA and SECSTR, as well as secondary structures found in PDB files, on 4 datasets (X-ray structures with different resolution range, NMR structures). Results A detailed comparison of KAKSI assignments with those of STRIDE and PSEA reveals that KAKSI assigns slightly longer helices and strands than STRIDE in case of one-to-one correspondence between the segments. However, KAKSI tends also to favor the assignment of several short helices when STRIDE and PSEA assign longer, kinked, helices. Helices assigned by KAKSI have geometrical characteristics close to those described in the PDB. They are more linear than helices assigned by other methods. The same tendency to split long segments is observed for strands, although less systematically. We present a number of cases of secondary structure assignments that illustrate this behavior. Conclusion Our method provides valuable assignments which favor the regularity of secondary structure segments. PMID:16164759

Martin, Juliette; Letellier, Guillaume; Marin, Antoine; Taly, Jean-Franois; de Brevern, Alexandre G; Gibrat, Jean-Franois

2005-01-01

112

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

PubMed Central

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

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

2014-01-01

113

Secondary structures of the core histone N-terminal tails: their role in regulating chromatin structure.  

PubMed

The core histone N-terminal tails dissociate from their binding positions in nucleosomes at moderate salt concentrations, and appear unstructured in the crystal. This suggested that the tails contributed minimally to chromatin structure. However, in vitro studies have shown that the tails were involved in a range of intra- and inter-nucleosomal as well as inter-fibre contacts. The H4 tail, which is essential for chromatin compaction, was shown to contact an adjacent nucleosome in the crystal. Acetylation of H4K16 was shown to abolish the ability of a nucleosome array to fold into a 30 nm fibre. The application of secondary structure prediction software has suggested the presence of extended structured regions in the histone tails. Molecular Dynamics studies have further shown that sections of the H3 and H4 tails assumed ?-helical and ?-strand content that was enhanced by the presence of DNA, and that post-translational modifications of the tails had a major impact on these structures. Circular dichroism and NMR showed that the H3 and H4 tails exhibited significant ?-helical content, that was increased by acetylation of the tail. There is thus strong evidence, both from biophysical and from computational approaches, that the core histones tails, particularly that of H3 and H4, are structured, and that these structures are influenced by post-translational modifications. This chapter reviews studies on the position, binding sites and secondary structures of the core histone tails, and discusses the possible role of the histone tail structures in the regulation of chromatin organization, and its impact on human disease. PMID:23150245

du Preez, Louis L; Patterton, Hugh-G

2013-01-01

114

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. PMID:8069219

Goldberg, M. E.; Guillou, Y.

1994-01-01

115

Hormones, Sex Accessory Structures, and Secondary Sexual Characteristics  

E-print Network

gland secretions) and secondary sexual characteristics (e.g., genial glands and skin glands of newts pads of American newts (e.g., Notophthalmus viridescens), whereas oxytocin antagonizes the influence of prolactin. In the Japanese newt (Cynops pyrrhogaster), however, estrogens block the action of prolactin

Sever, David M.

116

PRT-HMM: A Novel Hidden Markov Model for Protein Secondary Structure Prediction  

Microsoft Academic Search

Protein secondary structure prediction is one of the most important and challenging problems in structural bioinformatics, which has been an essential task in determining the structure and function of the proteins. Despite significant progress made in recent years, protein structure prediction maintains its status as one of the prime unsolved problems in computational biology. A novel probability revise table based

Wang Ding; Dongbo Dai; Jiang Xie; Huiran Zhang; Wu Zhang; Hao Xie

2012-01-01

117

New Secondary Structure Prediction software package using automatically trained Bayesian Networks  

E-print Network

. · secondary structure: Local structure of linear segments of the polypeptide backbone atoms without regard structure: The three-dimensional arrangement of all atoms in a single polypeptide chain. · quaternary spectroscopy (NMR) techniques are capable of producing structures at atomic resolution. However, these methods

118

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

Microsoft Academic Search

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

Spencer D. Li

2011-01-01

119

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

ERIC Educational Resources Information Center

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

Weiqi, Chen

2007-01-01

120

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

ERIC Educational Resources Information Center

Mediation analysis in child and adolescent development research is possible using large secondary data sets. This article provides an overview of two statistical methods commonly used to test mediated effects in secondary analysis: multiple regression and structural equation modeling (SEM). Two empirical studies are presented to illustrate the

Li, Spencer D.

2011-01-01

121

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

PubMed

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

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

2015-01-01

122

Effect of peptide secondary structure on peptide amphiphile supramolecular structure and interactions  

PubMed Central

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

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

2011-01-01

123

CSSP2: an improved method for predicting contact-dependent secondary structure propensity.  

PubMed

The calculation of contact-dependent secondary structure propensity (CSSP) has been reported to sensitively detect non-native beta-strand propensities in the core sequences of amyloidogenic proteins. Here we describe a noble energy-based CSSP method implemented on dual artificial neural networks that rapidly and accurately estimate the potential for the non-native secondary structure formation in local regions of protein sequences. In this method, we attempted to quantify long-range interaction patterns in diverse secondary structures by potential energy calculations and decomposition on a pairwise per-residue basis. The calculated energy parameters and seven-residue sequence information were used as inputs for artificial neural networks (ANNs) to predict sequence potential for secondary structure conversion. The trained single ANN using the >(i, i+/-4) interaction energy parameter exhibited 74% accuracy in predicting the secondary structure of test sequences in their native energy state, while the dual ANN-based predictor using (i, i+/-4) and >(i, i+/-4) interaction energies showed 83% prediction accuracy. The present method provides a simple and accurate tool for predicting sequence potential for secondary structure conversions without using 3D structural information. PMID:17644485

Yoon, Sukjoon; Welsh, William J; Jung, Heeyoung; Yoo, Young Do

2007-10-01

124

Polyadenylation accelerates degradation of chloroplast mRNA.  

PubMed Central

The expression of chloroplast genes is regulated by several mechanisms, one of which is the modulation of RNA stability. To understand how this regulatory step is controlled during chloroplast development, we have begun to define the mechanism of plastid mRNA degradation. We show here that the degradation petD mRNA involves endonucleolytic cleavage at specific sites upstream of the 3' stem-loop structure. The endonucleolytic petD cleavage products can be polyadenylated in vitro, and similar polyadenylated RNA products are detectable in vivo. PCR analysis of the psbA and psaA-psaB-rps14 operons revealed other polyadenylated endonucleolytic cleavage products, indicating that poly(A) addition appears to be an integral modification during chloroplast mRNA degradation. Polyadenylation promotes efficient degradation of the cleaved petD RNAs by a 3'-5' exoribonuclease. Furthermore, polyadenylation also plays an important role in the degradation of the petD mRNA 3' end. Although the 3' end stem-loop is usually resistant to nucleases, adenylation renders the secondary structure susceptible to the 3'-5' exoribonuclease. Analysis of 3' ends confirms that polyadenylation occurs in vivo, and reveals that the extent of adenylation increases during the degradation of plastid mRNA in the dark. Based on these results, we propose a novel mechanism for polyadenylation in the regulation of plastid mRNA degradation. Images PMID:9003789

Kudla, J; Hayes, R; Gruissem, W

1996-01-01

125

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

PubMed

As ribonucleic acid (RNA) molecules play important roles in many biological processes including gene expression and regulation, their secondary structures have been the focus of many recent studies. Despite the computing power of supercomputers, computationally predicting secondary structures with thermodynamic methods is still not feasible when the RNA molecules have long nucleotide sequences and include complex motifs such as pseudoknots. This paper presents RNAVLab (RNA Virtual Laboratory), a virtual laboratory for studying RNA secondary structures including pseudoknots that allows scientists to address this challenge. Two important case studies show the versatility and functionalities of RNAVLab. The first study quantifies its capability to rebuild longer secondary structures from motifs found in systematically sampled nucleotide segments. The extensive sampling and predictions are made feasible in a short turnaround time because of the grid technology used. The second study shows how RNAVLab allows scientists to study the viral RNA genome replication mechanisms used by members of the virus family Nodaviridae. PMID:19885376

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

2008-11-01

126

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

PubMed Central

As ribonucleic acid (RNA) molecules play important roles in many biological processes including gene expression and regulation, their secondary structures have been the focus of many recent studies. Despite the computing power of supercomputers, computationally predicting secondary structures with thermodynamic methods is still not feasible when the RNA molecules have long nucleotide sequences and include complex motifs such as pseudoknots. This paper presents RNAVLab (RNA Virtual Laboratory), a virtual laboratory for studying RNA secondary structures including pseudoknots that allows scientists to address this challenge. Two important case studies show the versatility and functionalities of RNAVLab. The first study quantifies its capability to rebuild longer secondary structures from motifs found in systematically sampled nucleotide segments. The extensive sampling and predictions are made feasible in a short turnaround time because of the grid technology used. The second study shows how RNAVLab allows scientists to study the viral RNA genome replication mechanisms used by members of the virus family Nodaviridae. PMID:19885376

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

2009-01-01

127

Modeling k-Noncrossing Closed RNA Secondary Structures via Meandric Compression.  

PubMed

In this chapter we present the transformation of a meander to its compression and we apply this new formulation for the modeling of k-noncrossing closed RNA secondary structures. We obtain this by using curves which consist parts of their meandric curve. We prove basic properties and produce generating procedures. Two new types of meanders arise: the simple and the perpendicular, in order to be used as representatives of k-noncrossing closed RNA secondary structures. PMID:25417026

Panayotopoulos, Antonios; Vlamos, Panayiotis

2015-01-01

128

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

PubMed Central

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

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

2014-01-01

129

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

NASA Astrophysics Data System (ADS)

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

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

2014-01-01

130

Students' understanding of primary and secondary protein structure: drawing secondary protein structure reveals student understanding better than simple recognition of structures.  

PubMed

The interdisciplinary nature of biochemistry courses requires students to use both chemistry and biology knowledge to understand biochemical concepts. Research that has focused on external representations in biochemistry has uncovered student difficulties in comprehending and interpreting external representations in addition to a fragmented understanding of fundamental biochemistry concepts. This project focuses on students' understanding of primary and secondary protein structure and drawings (representations) of hydrogen-bonding in alpha helices and beta sheets. Analysis demonstrated that students can recognize and identify primary protein structure concepts when given a polypeptide. However, when asked to draw alpha helices and beta sheets and explain the role of hydrogen bonding their drawings students exhibited a fragmented understanding that lacked coherence. Faculty are encouraged to have students draw molecular level representations to make their mental models more explicit, complete, and coherent. This is in contrast to recognition and identification tasks, which do not adequately probe mental models and molecular level understanding. PMID:24019228

Harle, Marissa; Towns, Marcy H

2013-01-01

131

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

Microsoft Academic Search

Orphan proteins are characterized by the lack of significant sequence similarity to database proteins. To infer the functional properties of the orphans, more elaborate techniques that utilize structural information are required. In this regard, the protein structure prediction gains considerable importance. Secondary structure prediction algorithms designed for orphan proteins (also known as single-sequence algorithms) cannot utilize multiple alignments or alignment

Zafer Aydin; Yucel Altunbasak; Isa Kemal Pakatci; Hakan Erdogan

2007-01-01

132

Training Set Reduction Methods for Single Sequence Protein Secondary Structure Prediction  

Microsoft Academic Search

Orphan proteins are characterized by the lack of significant sequence similarity to almost all proteins in the database. To infer the functional properties of the orphans, more elaborate techniques that utilize structural information are required. In this regard, the protein structure prediction gains considerable importance. Secondary structure prediction algorithms designed for orphan proteins (also known as single-sequence algorithms) cannot utilize

I. K. Pakatci; Z. Aydin; H. Erdogan; Y. Altunbasak

2007-01-01

133

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

Microsoft Academic Search

Background: Mitochondrial tRNAs have been the subject of study for structural biologists interested in their secondary structure characteristics, evolutionary biologists have researched patterns of compensatory and structural evolution and medical studies have been directed towards understanding the basis of human disease. However, an up to date, manually curated database of mitochondrially encoded tRNAs from higher animals is currently not available.

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

2007-01-01

134

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

Microsoft Academic Search

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

Yanga Byun; Kyungsook Han

2006-01-01

135

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

PubMed

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

Eddy, Sean R

2014-01-01

136

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

Gonzlez-Daz, Humberto; Agero-Chapin, Guillermn; Varona, Javier; Molina, Reinaldo; Delogu, Giovanna; Santana, Lourdes; Uriarte, Eugenio; Podda, Gianni

2007-04-30

137

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

PubMed

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

Zhang, Yuan; Sagui, Celeste

2015-02-01

138

Secondary structure of Streptococcus downei GTF-I glucansucrase  

Microsoft Academic Search

Multiple sequence alignment and structure prediction of glucansucrases produced by oral streptococci and Leuconostoc mesenteroides showed that all have common structural features, with three major domains. There is no conservation of primary sequence or structure in the N-terminal variable region. Sequence-based structure prediction combined with circular dichroism spectrum analysis of purified truncated forms of Streptococcus downei GTF-I revealed that the

Vincent Monchois; Jeremy H. Lakey; Roy R. B. Russell

1999-01-01

139

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

PubMed

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

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

2013-02-01

140

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

PubMed

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

Churkin, Alexander; Weinbrand, Lina; Barash, Danny

2015-01-01

141

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

PubMed Central

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

2014-01-01

142

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

PubMed Central

The Hepatitis Delta Virus (HDV) ribozyme self-cleaving activity in 20 M formamide solutions is unique. Does this catalytic activity result from the conservation of its tertiary structure in 20 M formamide? We followed the ribozyme structure in formamide solutions by monitoring the amount of bound Ethidium Bromide (EB). We were able to measure the quantity of dye bound using time-resolved fluorescence spectroscopy, as an estimate of the ribozyme double helical content. This method, calibrated by using oligonucleotides with defined tertiary structure and denaturing solvents, parallels NMR and UV measurements as a function of temperature. Measurements with the HDV ribozyme lead to three conclusions: (a) both the precursor and product RNAs are structured to 24 M (95% w/w) formamide or 4 M H2O solutions which is equivalent to 4 M H2O; (b) the HDV ribozyme is the only RNA sequence investigated in this study that retains so much structure in formamide; and (c) DNA analogs of formamide resistant HDV ribozyme sequences lose their structure at less than 15 M formamide. Thus, the structural integrity of the HDV ribozyme is an intrinsic property of the RNA molecule and its sequence. PMID:8918791

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

1996-01-01

143

[Topography and structure of secondary brain damage in edema associated with supratentorial foci of encephalomalacia].  

PubMed

The paper comprises 70 cases of extensive supratentorial infarctions. The topography and structure of secondary lesions occurring in the region of herniation and displacements caused by the coexisting brain edema were analysed. The extent of edema served as criterion in the division of the material into three groups in dependence on the occurrence of herniations and displacements. Most frequent was herniation of hippocampal uncus and most rare that of the cerebellar vermis. In group I showing no herniations selective necrosis was noted of neurons particularly sensitive to ischemia and anoxia, especially in Sommer's sector of the hippocampus. In group II secondary necrosis was visible in the regions of herniae, and in the group III also in the translocated deep brain structures in the hemisphere contralateral to the infarct and in the brain stem where, moreover, secondary hemorrhages were present. Supratentorial secondary hemorrhages were less frequent. They were noted in the thalamus both on the side of the infarct and in the contralateral hemisphere. Supratentorial necroses were more frequent. Their intensity varied from selective necrosis to Jacob's edematous necrosis. Severe displacement of deep structures and of the brain stem was associated with development of secondary internal hydrocephalus, especially in the hemisphere contralateral to the herniation. To the most important pathogenetic factors causing development of secondary morphological lesions belong disturbances of blood supply occurring as the result of pressure differences between the supra- and infratentorial space, resulting from pressure and displacement of arterial vessels, damage of their walls and distrubances of venous flow and also development of secondary internal hydrocephalus. Extensive necroses and hemorrhages increase the area of primary necrosis. Lesions resulting from herniation, displacement and compression of vessels were superposed on the picture of brain edema both present or passed. Secondary necroses damaging bilaterally structures belonging to the limbic system and reticular formation may be an additional factor in the development of edematous encephalopathy and the development of a psychoorganic syndrome after stroke. PMID:2626177

Szpakowa, G M

1989-01-01

144

mRNA localisation during development.  

PubMed

Although there are many differences, mRNA localisations in the Xenopus oocyte show some tantalizing similarities to those occurring in Drosophila development. As in Drosophila, transcripts localise to opposite poles of the oocyte, this localisation is hierarchical and occurs in a multistep process in which localisation is followed by anchoring at the cortex. This distinction between initial transport and long-term maintenance reflects the dynamic nature of the cytoskeleton: the microtubule tracks form and reform according to the needs of the cell so that stable localisation must be mediated by a more constant structure--the cortex. A possible exception is the localisation of gurken mRNA where it is unknown whether there are separate mechanisms for transport to and maintenance at the oocyte nucleus. However, gurken is responsible for the transmission of a transitory signal; once this has been received, and the fate of the recipient follicle cells determined, there is no further need for localisation. It is possible that the time scale over which the localisation machinery is stable is sufficient for transmission of this signal without the need for a separate maintenance phase. The existence of a nanos homologue, Xcat-2 (Mosquera et al., 1993), associated with the Xenopus germ plasm is particularly interesting because of the morphological and functional similarities between Drosophila polar granules, Caenorhabditis P-granules, and Xenopus germ plasm. These electron-dense protein-RNA complexes are maternally supplied and in each case segregate with the germ line. These granules may represent a fundamental conserved pathway to germ-cell specification and it is now at least a possibility that they are also involved in establishing the embryonic axis through translational repression. In the case of Drosophila, this occurs through localised nanos acting (via Pumilio) on nanos response elements in hunchback mRNA. No such regulatory pair has yet been demonstrated in C. elegans or X. laevis, but each contains a candidate for one half of the interaction: glp-1 could be a target for an unidentified nanos-like protein; Xcat-2 may control translation of an unknown NRE-containing mRNA. Another common feature of mRNA localisation is that in every case where the targeting signal has been determined, it has been mapped to a region of the 3' UTR capable of forming an extensive secondary structure (e.g., David and Ish-Horowicz, 1991; Dalby and Glover, 1992; Gavis and Lehmann, 1992; Kim-Ha et al., 1993; Kislauskis et al., 1993, 1994; Lantz and Schedl, 1994). In several cases, translational control and transcript stability signals have also been mapped to these regions (Jackson and Standart, 1990; Standart et al., 1990; Standart and Hunt, 1990; Davis and Ish-Horowicz, 1991; Wharton and Struhl, 1991; Dalby and Glover, 1993; Evans et al., 1994; Kim-Ha et al., 1995). The large secondary structures may provide a means for stably exposing sequence-specific regions of RNA to proteins. Due to the ease with which RNA forms base pairs, it is likely that rather than remaining single-stranded, RNA within the cell forms some sort of secondary structure. The geometry of purely double-stranded RNA does not permit sequence specific interactions between proteins and the bases because the major groove is inaccessible to amino acid side chains (Weeks and Crothers, 1993). However, the distortions to the dsRNA helix provided by bulges, pseudoknots, and the single-strand loop regions in stem-loop structures do present sequence information that can be "read" by proteins. The extensive 3'UTRs may produce a stable secondary structure which ensures that regulatory elements remain exposed in such regions rather than hidden in double-stranded stems. (ABSTRACT TRUNCATED) PMID:8612958

Micklem, D R

1995-12-01

145

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

146

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

147

Aging of Dry Desiccation-Tolerant Pollen Does Not Affect Protein Secondary Structure.  

PubMed Central

Protein secondary structure and membrane phase behavior in aging Typha latifolia pollen were studied by means of Fourier transform infrared microspectroscopy (FTIR). Membranes isolated from fresh pollen occurred mainly in the liquid crystalline phase at room temperature, whereas the membrane fluidity of aged pollen was drastically decreased. This decrease did not result in large-scale irreversible protein aggregation, as was concluded from in situ FTIR assessment of the amide-1 bands. Curve-fitting on the infrared absorbance spectra enabled estimation of the proportion of different classes of protein secondary structure. Membrane proteins had a relatively large amount of [alpha]-helical structure (48%; band at 1658 cm-1), and turn-like structures (at 1637 and 1680 cm-1) were also detected. The secondary protein structure of isolated cytoplasmic proteins resembled that of proteins in whole pollen and was conserved upon drying in the absence of sucrose. The isolated cytoplasmic proteins had a large amount of [alpha]-helical structure (43%), and also [beta]-sheet (at 1637 and 1692 cm-1) and turn structures were detected. Heat-denaturing experiments with intact hydrated pollen showed low (1627 cm-1) and high (1692 cm-1) wave number bands indicating irreversible protein aggregates. The results presented in this paper show that FTIR is an extremely suitable technique to study protein secondary structure in intact plant cells of different hydration levels and developmental stages. PMID:12228641

Wolkers, W. F.; Hoekstra, F. A.

1995-01-01

148

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

Microsoft Academic Search

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

Takumi Yamagishi; Shigehisa Hirose; Takashi Kondo

2008-01-01

149

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

Microsoft Academic Search

BACKGROUND: Protein deformation has been extensively analysed through global methods based on RMSD, torsion angles and Principal Components Analysis calculations. Here we use a local approach, able to distinguish among the different backbone conformations within loops, ?-helices and ?-strands, to address the question of secondary structures' shape variation within proteins and deformation at interface upon complexation. RESULTS: Using a structural

Julie Baussand; Anne-Claude Camproux

2011-01-01

150

Probing the glycosidic linkage: secondary structures in the gas phase  

NASA Astrophysics Data System (ADS)

The functional importance of carbohydrates in biological processes, particularly those involving specific molecular recognition, is immense. Characterizing the three-dimensional (3D) structures of carbohydrates and glycoproteins, and their interactions with other molecules, not least the ubiquitous solvent, water, is a key starting point for understanding these processes. The combination of laser-based electronic and vibrational spectroscopy of mass-selected carbohydrate molecules and their hydrated complexes, conducted under molecular beam conditions, with ab initio computation is providing a uniquely powerful means of characterizing 3D carbohydrate conformations; the structures of their hydrated complexes, the hydrogen-bonded networks they support (or which support them); and the factors that determine their conformational and structural preferences.

Simons, John P.; Cristina Stanca-Kaposta, E.; Cocinero, Emilio J.; Liu, B.; Davis, Benjamin G.; Gamblin, David P.; Kroemer, Romano T.

2008-10-01

151

Thermodynamic and phylogenetic prediction of RNA secondary structures in the coding region of hepatitis C virus.  

PubMed Central

The existence and functional importance of RNA secondary structure in the replication of positive-stranded RNA viruses is increasingly recognized. We applied several computational methods to detect RNA secondary structure in the coding region of hepatitis C virus (HCV), including thermodynamic prediction, calculation of free energy on folding, and a newly developed method to scan sequences for covariant sites and associated secondary structures using a parsimony-based algorithm. Each of the prediction methods provided evidence for complex RNA folding in the core- and NS5B-encoding regions of the genome. The positioning of covariant sites and associated predicted stem-loop structures coincided with thermodynamic predictions of RNA base pairing, and localized precisely in parts of the genome with marked suppression of variability at synonymous sites. Combined, there was evidence for a total of six evolutionarily conserved stem-loop structures in the NS5B-encoding region and two in the core gene. The virus most closely related to HCV, GB virus-B (GBV-B) also showed evidence for similar internal base pairing in its coding region, although predictions of secondary structures were limited by the absence of comparative sequence data for this virus. While the role(s) of stem-loops in the coding region of HCV and GBV-B are currently unknown, the structure predictions in this study could provide the starting point for functional investigations using recently developed self-replicating clones of HCV. PMID:12088154

Tuplin, Andrew; Wood, Jonny; Evans, David J; Patel, Arvind H; Simmonds, Peter

2002-01-01

152

Learning models for aligning protein sequences with predicted secondary structure  

E-print Network

that may be in the structural core, and are employed by CLUSTAL W [34], T-Coffee [28], and MUSCLE [10]; (b in the alignment that have high support, and is employed by T-Coffee, MAFFT, ProbCons, SPEM [39], PROMALS [29 the input residues with profiles of amino acid exchanges from closely related sequences found through

Kececioglu, John

153

Genome-wide measurement of RNA secondary structure in yeast  

E-print Network

analysis of RNA structure (PARS), which is based on deep sequencing fragments of RNAs that were treated-stranded conformation (Fig. 1). We chose renatura- tionand enzymatic cleavage conditions underwhich thecleavagereac (Supplementary Fig. 2). As both enzymes leave a 59 phosphate at the cleavage point and because only 59 phosphoryl

154

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

PubMed Central

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

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

2013-01-01

155

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

156

Macromolecular ab initio phasing enforcing secondary and tertiary structure  

PubMed Central

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

Milln, Claudia; Sammito, Massimo; Usn, Isabel

2015-01-01

157

A Method for WD40 Repeat Detection and Secondary Structure Prediction  

PubMed Central

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

158

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

PubMed

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

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

2004-06-01

159

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

PubMed Central

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

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

2004-01-01

160

RNAmutants: a web server to explore the mutational landscape of RNA secondary structures  

PubMed Central

The history and mechanism of molecular evolution in DNA have been greatly elucidated by contributions from genetics, probability theory and bioinformaticsindeed, mathematical developments such as Kimura's neutral theory, Kingman's coalescent theory and efficient software such as BLAST, ClustalW, Phylip, etc., provide the foundation for modern population genetics. In contrast to DNA, the function of most noncoding RNA depends on tertiary structure, experimentally known to be largely determined by secondary structure, for which dynamic programming can efficiently compute the minimum free energy secondary structure. For this reason, understanding the effect of pointwise mutations in RNA secondary structure could reveal fundamental properties of structural RNA molecules and improve our understanding of molecular evolution of RNA. The web server RNAmutants provides several efficient tools to compute the ensemble of low-energy secondary structures for all k-mutants of a given RNA sequence, where k is bounded by a user-specified upper bound. As we have previously shown, these tools can be used to predict putative deleterious mutations and to analyze regulatory sequences from the hepatitis C and human immunodeficiency genomes. Web server is available at http://bioinformatics.bc.edu/clotelab/RNAmutants/, and downloadable binaries at http://rnamutants.csail.mit.edu/. PMID:19531740

Waldisphl, Jerome; Devadas, Srinivas; Berger, Bonnie; Clote, Peter

2009-01-01

161

A set of nearest neighbor parameters for predicting the enthalpy change of RNA secondary structure formation  

PubMed Central

A complete set of nearest neighbor parameters to predict the enthalpy change of RNA secondary structure formation was derived. These parameters can be used with available free energy nearest neighbor parameters to extend the secondary structure prediction of RNA sequences to temperatures other than 37C. The parameters were tested by predicting the secondary structures of sequences with known secondary structure that are from organisms with known optimal growth temperatures. Compared with the previous set of enthalpy nearest neighbor parameters, the sensitivity of base pair prediction improved from 65.2 to 68.9% at optimal growth temperatures ranging from 10 to 60C. Base pair probabilities were predicted with a partition function and the positive predictive value of structure prediction is 90.4% when considering the base pairs in the lowest free energy structure with pairing probability of 0.99 or above. Moreover, a strong correlation is found between the predicted melting temperatures of RNA sequences and the optimal growth temperatures of the host organism. This indicates that organisms that live at higher temperatures have evolved RNA sequences with higher melting temperatures. PMID:16982646

Lu, Zhi John; Turner, Douglas H.; Mathews, David H.

2006-01-01

162

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

PubMed

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

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

2014-11-26

163

Analysis of secondary structure in proteins by chemical cross-linking coupled to MS.  

PubMed

Chemical cross-linking is an attractive technique for the study of the structure of protein complexes due to its low sample consumption and short analysis time. Furthermore, distance constraints obtained from the identification of cross-linked peptides by MS can be used to construct and validate protein models. If a sufficient number of distance constraints are obtained, then determining the secondary structure of a protein can allow inference of the protein's fold. In this work, we show how the distance constraints obtained from cross-linking experiments can identify secondary structures within the protein sequence. Molecular modeling of alpha helices and beta sheets reveals that each secondary structure presents different cross-linking possibilities due to the topological distances between reactive residues. Cross-linking experiments performed with amine reactive cross-linkers with model alpha helix containing proteins corroborated the molecular modeling predictions. The cross-linking patterns established here can be extended to other cross-linkers with known lengths for the determination of secondary structures in proteins. PMID:22778071

Fioramonte, Mariana; dos Santos, Aline Mara; McIlwain, Sean; Noble, William S; Franchini, Kleber G; Gozzo, Fabio C

2012-08-01

164

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

PubMed Central

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

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

2009-01-01

165

First determination of the secondary structure of purified factor VIII light chain.  

PubMed

The first analysis of the secondary structure of human factor VIII light chain was performed by c.d. spectroscopy. The purification process described in this paper allowed us to obtain the large amounts of purified factor VIII light chains required for c.d. experiments. Since this 80 kDa protein is non-covalently associated with a heavy chain to form the active molecule, isolated factor VIII light chains were obtained after immunoadsorption and dissociation of the immobilized active complexes by EDTA. Furthermore, factor VIII light chains were discriminated from the residual active complexes and the free heavy chains by a final ion-exchange-chromatography step. This f.p.l.c. analysis showed that factor VIII light chains were less electronegative than the active complexes. The results of conformational analysis by c.d. show that the protein possesses a high degree of regular secondary structure (58%) with approx. 22% of alpha-helix and 36% of beta-strand structures. The protein was completely unfolded by 3 M-guanidine hydrochloride. The results obtained from the analysis of c.d. spectra were compared with those predicted from three different statistical methods based on amino-acid sequence. The secondary structure information obtained from these methods was in good agreement with the c.d. results. These results were comparable with the secondary structure prediction of ceruloplasmin, a protein known to show sequence identity to factor VIII. PMID:1445279

Bihoreau, N; Fontaine-Aupart, M P; Lehegarat, A; Desmadril, M; Yon, J M

1992-11-15

166

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. PMID:23695796

Rivas, Elena

2013-01-01

167

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

168

Prediction of protein secondary structure using probability based features and a hybrid system.  

PubMed

In this paper, we propose some co-occurrence probability-based features for prediction of protein secondary structure. The features are extracted using occurrence/nonoccurrence of secondary structures in the protein sequences. We explore two types of features: position-specific (based on position of amino acid on fragments of protein sequences) as well as position-independent (independent of amino acid position on fragments of protein sequences). We use a hybrid system, NEUROSVM, consisting of neural networks and support vector machines for classification of secondary structures. We propose two schemes NSVMps and NSVM for protein secondary structure prediction. The NSVMps uses position-specific probability-based features and NEUROSVM classifier whereas NSVM uses the same classifier with position-independent probability-based features. The proposed method falls in the single-sequence category of methods because it does not use any sequence profile information such as position specific scoring matrices (PSSM) derived from PSI-BLAST. Two widely used datasets RS126 and CB513 are used in the experiments. The results obtained using the proposed features and NEUROSVM classifier are better than most of the existing single-sequence prediction methods. Most importantly, the results using NSVMps that are obtained using lower dimensional features, are comparable to those by other existing methods. The NSVMps and NSVM are finally tested on target proteins of the critical assessment of protein structure prediction experiment-9 (CASP9). A larger dataset is used to compare the performance of the proposed methods with that of two recent single-sequence prediction methods. We also investigate the impact of presence of different amino acid residues (in protein sequences) that are responsible for the formation of different secondary structures. PMID:24131056

Ghanty, Pradip; Pal, Nikhil R; Mudi, Rajani K

2013-10-01

169

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

PubMed

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

Sanchita; Singh, Swati; Sharma, Ashok

2014-11-01

170

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. PMID:21788211

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

2011-01-01

171

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

PubMed

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

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

2014-11-21

172

Protein secondary structure prediction for a single-sequence using hidden semi-Markov models  

Microsoft Academic Search

Background: The accuracy of protein secondary structure prediction has been improving steadily towards the 88% estimated theoretical limit. There are two types of prediction algorithms: Single- sequence prediction algorithms imply that information about other (homologous) proteins is not available, while algorithms of the second type imply that information about homologous proteins is available, and use it intensively. The single-sequence algorithms

Zafer Aydin; Yucel Altunbasak; Mark Borodovsky

2006-01-01

173

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

E-print Network

Secondary Structure of Cell-Penetrating Peptides Controls Membrane Interaction and Insertion Emelía and Therapeutics, 1919 Route de Mende, 34293 Montpellier, France. c Laboratory of Molecular Technology, Institute.bbamem.2010.03.005 #12;Abstract The clinical use of efficient therapeutic agents is often limited by the poor

Boyer, Edmond

174

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

E-print Network

ABSTRACT The DICHROWEB web server enables on-line ana- lyses of circular dichroism (CD) spectroscopic data comple- tion of a registration form. The server facilitates ana- lyses using five popular algorithms technique that can be used to determine the secondary structural content of pro- teins. This is because

Wallace, Bonnie Ann

175

PROTEIN FUNCTION PREDICTION WITH AMINO ACID SEQUENCE AND SECONDARY STRUCTURE ALIGNMENT SCORES  

E-print Network

Aygün1 , Caner Kömürlü2 , Zafer Aydin3 and Zehra ?ataltepe1 1 Computer Engineering Department and 2 and Computer Engineering, Georgia Institute of Technology, Atlanta, GA 30332 eser.aygun@gmail.com, komurluc and showed that secondary structure informa- tion contributes to the accuracy of fold recognition. Aydin et

Cataltepe, Zehra

176

The Move to Faculty Middle Management Structures in Scottish Secondary Schools: A Case Study  

ERIC Educational Resources Information Center

This article looks at the move from a management structure based on discrete subject departments managed by subject specialist principal teachers within Scottish secondary schools towards groupings of subjects (faculties) with a single manager. This article examines the impact of this change upon the experiences of students and probationer

Anderson, Cherie; Nixon, Graeme

2010-01-01

177

Teachers Working in Collaborative Structures: A Case Study of a Secondary School in the USA  

ERIC Educational Resources Information Center

This article reports on a study that explores collaborative structures of shared decision-making in an urban secondary school in the USA. The data in the study came from unstructured interviews with 20 teachers, the principal, the assistant principal, a counsellor and 10 students. The interviews took place over a three-week period in June of 2001

Cameron, David Hagen

2005-01-01

178

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

E-print Network

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

Cheng, Jianlin Jack

179

Interplay between Secondary and Tertiary Structure Formation in Protein Folding Cooperativity  

E-print Network

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

Bachmann, Michael

180

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

Microsoft Academic Search

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

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

1976-01-01

181

The RNAmute web server for the mutational analysis of RNA secondary structures  

E-print Network

The RNAmute web server for the mutational analysis of RNA secondary structures Alexander Churkin and destabilize the optimal one are considered as candidates for being deleterious. The RNAmute web server for mu RNAmute web- server was performed on a TPP-riboswitch, and experi- mental results were able to verify

Barash, Danny

182

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, 1618 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

183

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

184

Assessing the impact of secondary structure and solvent accessibility on protein evolution.  

PubMed Central

Empirically derived models of amino acid replacement are employed to study the association between various physical features of proteins and evolution. The strengths of these associations are statistically evaluated by applying the models of protein evolution to 11 diverse sets of protein sequences. Parametric bootstrap tests indicate that the solvent accessibility status of a site has a particularly strong association with the process of amino acid replacement that it experiences. Significant association between secondary structure environment and the amino acid replacement process is also observed. Careful description of the length distribution of secondary structure elements and of the organization of secondary structure and solvent accessibility along a protein did not always significantly improve the fit of the evolutionary models to the data sets that were analyzed. As indicated by the strength of the association of both solvent accessibility and secondary structure with amino acid replacement, the process of protein evolution-both above and below the species level-will not be well understood until the physical constraints that affect protein evolution are identified and characterized. PMID:9584116

Goldman, N; Thorne, J L; Jones, D T

1998-01-01

185

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...

186

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

E-print Network

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

Erdogan, Hakan

187

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

PubMed Central

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

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

2014-01-01

188

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

189

DNA Secondary structures and their contribution to mutagenesis in B. subtilis stationary phase cells.  

E-print Network

DNA Secondary structures and their contribution to mutagenesis in B. subtilis stationary phase cells. Carmen Vallin, Katherine Ona, Chris Ross, Ronald E. Yasbin and Eduardo A. Robleto School of Life · In stationary phase cell division and replication are halted due to an environmental stress setting the stage

Walker, Lawrence R.

190

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

Microsoft Academic Search

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

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

2007-01-01

191

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

192

Function of RNA Secondary Structures in Transcriptional Attenuation of the Bacillus subtilis pyr Operon  

Microsoft Academic Search

The Bacillus subtilis pyr operon is regulated by exogenous pyrimidines by a transcriptional attenuation mechanism. Transcription in vitro from pyr DNA templates specifying attenuation regions yielded terminated and read-through transcripts of the expected lengths. Addition of the PyrR regulatory protein plus UMP led to greatly increased termination. Synthetic antisense deoxyoligonucleotides were used to probe possible secondary structures in the pyr

Yang Lu; Robert J. Turner; Robert L. Switzer

1996-01-01

193

Biomass and structure estimation of primary and secondary tropical rain forests using AirSAR data  

Microsoft Academic Search

Summary form only given, substantially as follows. During the 1993 South American AirSAR Deployment fully polarimetric C-, L-, and P-band data have been acquired over a settlement area in Guaviare at the edge of the Colombian Amazon. Preliminary analysis showed obvious (qualitative) relations between backscatter level, tropical rain forest structure and age of secondary forests and other types of vegetation.

D. H. Hoekman; F. Amar; M. J. Quinones

1995-01-01

194

Phylogenetic hypotheses of gorgoniid octocorals according to ITS2 and their predicted RNA secondary structures  

Microsoft Academic Search

Gorgoniid octocorals taxonomy (Cnidaria; Octocorallia; Gorgoniidae) includes diagnostic characters not well defined at the generic level, and based on the family diagnosis some species could be classified in either Gorgoniidae or Plexauridae. In this study, we used sequences from the Internal Transcribed Spacer 2 (ITS2) and their predicted RNA secondary structure to both correct the alignment and reconstruct phylogenies using

Catalina Aguilar; Juan Armando Snchez

2007-01-01

195

PolyprOnline: polyproline helix II and secondary structure assignment database  

PubMed Central

The polyproline helix type II (PPII) is a regular protein secondary structure with remarkable features. Many studies have highlighted different crucial biological roles supported by this local conformation, e.g. in the interactions between biological macromolecules. Although PPII is less frequently present than regular secondary structures such as canonical alpha helices and beta strands, it corresponds to 310% of residues. Up to now, PPII is not assigned by most popular assignment tools, and therefore, remains insufficiently studied. PolyprOnline database is, therefore, dedicated to PPII structure assignment and analysis to facilitate the study of PPII structure and functional roles. This database is freely accessible from www.dsimb.inserm.fr/dsimb_tools/polyproline. PMID:25380779

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

2014-01-01

196

Secondary structure of the entomocidal toxin from Bacillus thuringiensis subsp. kurstaki HD-73.  

PubMed

The secondary structure of the toxin from Bacillus thuringiensis subsp. kurstaki (Btk) HD-73 was estimated by Raman, infrared, and circular dichroism spectroscopy, and by predictive methods. Circular dichroism and infrared spectroscopy gave an estimate of 33-40% alpha-helix, whereas Raman and predictive methods gave approximately 20%. Raman and circular dichroism spectra, as well as predictive methods, indicated that the toxin contains 32-40% beta-sheet structure, whereas infrared spectroscopy gave a slightly lower estimate. Thus, all of these approaches are in agreement that the native conformation of Btk HD-73 toxin is highly folded and contains considerable amounts of both alpha-helical and beta-sheet structures. No significant differences were detected in the secondary structure of the toxin either in solution or as a hydrated pellet. PMID:2340079

Choma, C T; Surewicz, W K; Carey, P R; Pozsgay, M; Kaplan, H

1990-02-01

197

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

NASA Technical Reports Server (NTRS)

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

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

2001-01-01

198

RNApdbeea webserver to derive secondary structures from pdb files of knotted and unknotted RNAs  

PubMed Central

In RNA structural biology and bioinformatics an access to correct RNA secondary structure and its proper representation is of crucial importance. This is true especially in the field of secondary and 3D RNA structure prediction. Here, we introduce RNApdbeea new tool that allows to extract RNA secondary structure from the pdb file, and presents it in both textual and graphical form. RNApdbee supports processing of knotted and unknotted structures of large RNAs, also within protein complexes. The method works not only for first but also for high order pseudoknots, and gives an information about canonical and non-canonical base pairs. A combination of these features is unique among existing applications for RNA structure analysis. Additionally, a function of converting between the text notations, i.e. BPSEQ, CT and extended dot-bracket, is provided. In order to facilitate a more comprehensive study, the webserver integrates the functionality of RNAView, MC-Annotate and 3DNA/DSSR, being the most common tools used for automated identification and classification of RNA base pairs. RNApdbee is implemented as a publicly available webserver with an intuitive interface and can be freely accessed at http://rnapdbee.cs.put.poznan.pl/. PMID:24771339

Antczak, Maciej; Zok, Tomasz; Popenda, Mariusz; Lukasiak, Piotr; Adamiak, Ryszard W.; Blazewicz, Jacek; Szachniuk, Marta

2014-01-01

199

?-Casein terminates casein micelle build-up by its "soft" secondary structure.  

PubMed

In our previous paper (Nagy et al. in J Biol Chem 285:38811-38817, 2010) by using a multilayered model system, we showed that, from ?-casein, aggregates (similar to natural casein micelles) can be built up step by step if Ca-phosphate nanocluster incorporation is ensured between the protein adsorption steps. It remained, however, an open question whether the growth of the aggregates can be terminated, similarly to in nature with casein micelles. Here, we show that, in the presence of Ca-phosphate nanoclusters, upon adsorbing onto earlier ?-casein surfaces, the secondary structure of ?-casein remains practically unaffected, but ?-casein exhibits considerable changes in its secondary structure as manifested by a shift toward having more ?-structures. In the absence of Ca-phosphate, only ?-casein can still adsorb onto the underlying casein surface; this ?-casein also expresses considerable shift toward ?-structures. In addition, this ?-casein cover terminates casein aggregation; no further adsorption of either ?- or ?-casein can be achieved. These results, while obtained on a model system, may show that the Ca-insensitive ?-casein can, indeed, be the outer layer of the casein micelles, not only because of its "hairy" extrusion into the water phase, but because of its "softer" secondary structure, which can "occlude" the interacting motifs serving casein aggregation. We think that the revealed nature of the molecular interactions, and the growth mechanism found here, might be useful to understand the aggregation process of casein micelles also in vivo. PMID:23015063

Nagy, Krisztina; Vr, Gyrgy; Szalontai, Balzs

2012-11-01

200

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

PubMed

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

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

2000-04-01

201

Training set reduction methods for protein secondary structure prediction in single-sequence condition.  

PubMed

Orphan proteins are characterized by the lack of significant sequence similarity to database proteins. To infer the functional properties of the orphans, more elaborate techniques that utilize structural information are required. In this regard, the protein structure prediction gains considerable importance. Secondary structure prediction algorithms designed for orphan proteins (also known as single-sequence algorithms) cannot utilize multiple alignments or alignment profiles, which are derived from similar proteins. This is a limiting factor for the prediction accuracy. One way to improve the performance of a single-sequence algorithm is to perform re-training. In this approach, first, the models used by the algorithm are trained by a representative set of proteins and a secondary structure prediction is computed. Then, using a distance measure, the original training set is refined by removing proteins that are dissimilar to the given protein. This step is followed by the re-estimation of the model parameters and the prediction of the secondary structure. In this paper, we compare training set reduction methods that are used to re-train the hidden semi-Markov models employed by the IPSSP algorithm [1]. We found that the composition based reduction method has the highest performance compared to the alignment based and the Chou-Fasman based reduction methods. In addition, threshold-based reduction performed better than the reduction technique that selects the first 80% of the dataset proteins. PMID:18003135

Aydin, Zafer; Altunbasak, Yucel; Pakatci, Isa Kemal; Erdogan, Hakan

2007-01-01

202

Influence of MLS laser radiation on erythrocyte membrane fluidity and secondary structure of human serum albumin.  

PubMed

The biostimulating activity of low level laser radiation of various wavelengths and energy doses is widely documented in the literature, but the mechanisms of the intracellular reactions involved are not precisely known. The aim of this paper is to evaluate the influence of low level laser radiation from an multiwave locked system (MLS) of two wavelengths (wavelength=808nm in continuous emission and 905nm in pulsed emission) on the human erythrocyte membrane and on the secondary structure of human serum albumin (HSA). Human erythrocytes membranes and HSA were irradiated with laser light of low intensity with surface energy density ranging from 0.46 to 4.9Jcm(-2) and surface energy power density 195mWcm(-2) (1,000Hz) and 230mWcm(-2) (2,000Hz). Structural and functional changes in the erythrocyte membrane were characterized by its fluidity, while changes in the protein were monitored by its secondary structure. Dose-dependent changes in erythrocyte membrane fluidity were induced by near-infrared laser radiation. Slight changes in the secondary structure of HSA were also noted. MLS laser radiation influences the structure and function of the human erythrocyte membrane resulting in a change in fluidity. PMID:24357115

Pasternak, Kamila; Nowacka, Olga; Wrbel, Dominika; Pieszy?ski, Ireneusz; Bryszewska, Maria; Kujawa, Jolanta

2014-03-01

203

Obtaining information about protein secondary structures in aqueous solution using Fourier transform IR spectroscopy.  

PubMed

Fourier transform IR (FTIR) spectroscopy is a nondestructive technique for structural characterization of proteins and polypeptides. The IR spectral data of polymers are usually interpreted in terms of the vibrations of a structural repeat. The repeat units in proteins give rise to nine characteristic IR absorption bands (amides A, B and I-VII). Amide I bands (1,700-1,600 cm(-1)) are the most prominent and sensitive vibrational bands of the protein backbone, and they relate to protein secondary structural components. In this protocol, we have detailed the principles that underlie the determination of protein secondary structure by FTIR spectroscopy, as well as the basic steps involved in protein sample preparation, instrument operation, FTIR spectra collection and spectra analysis in order to estimate protein secondary-structural components in aqueous (both H2O and deuterium oxide (D2O)) solution using algorithms, such as second-derivative, deconvolution and curve fitting. Small amounts of high-purity (>95%) proteins at high concentrations (>3 mg ml(-1)) are needed in this protocol; typically, the procedure can be completed in 1-2 d. PMID:25654756

Yang, Huayan; Yang, Shouning; Kong, Jilie; Dong, Aichun; Yu, Shaoning

2015-03-01

204

Probing the secondary structure of bovine serum albumin during heat-induced denaturation using mid-infrared fiberoptic sensors.  

PubMed

Attenuated total reflection Fourier transform infrared (ATR-FTIR) spectroscopy using a special waveguide based on a silver halide fiber was used for probing the heat-induced secondary structure and conformation changes of bovine serum albumin (BSA). From the secondary derivative and the curve fitting of the obtained ATR-FTIR spectra, the changes of the BSA secondary structure with temperature were clearly identified. Two different thermal denaturation temperature ranges (i.e., 50-52 and 80-82 C, at which a change of the protein structure occurred) were determined, while only one denaturation temperature was previously identified via classical FTIR measurements. Additionally, taking advantage of two-dimensional correlation spectroscopy more detailed information on changes of the protein secondary structure was revealed. The developed method facilitates in situ, sensitive, and more in-depth probing of protein secondary structures, which represents a significant advancement compared to conventional characterization methods. PMID:25525641

Lu, Rui; Li, Wen-Wei; Katzir, Abraham; Raichlin, Yosef; Yu, Han-Qing; Mizaikoff, Boris

2015-01-20

205

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

NASA Astrophysics Data System (ADS)

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

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

2006-04-01

206

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

NASA Astrophysics Data System (ADS)

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

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

2014-09-01

207

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

208

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

PubMed Central

Computational methods are rapidly gaining importance in the field of structural biology, mostly due to the explosive progress in genome sequencing projects and the large disparity between the number of sequences and the number of structures. There has been an exponential growth in the number of available protein sequences and a slower growth in the number of structures. There is therefore an urgent need to develop computational methods to predict structures and identify their functions from the sequence. Developing methods that will satisfy these needs both efficiently and accurately is of paramount importance for advances in many biomedical fields, including drug development and discovery of biomarkers. A novel method called Fast Learning Optimized PREDiction Methodology (FLOPRED) is proposed for predicting protein secondary structure, using knowledge-based potentials combined with structure information from the CATH database. A Neural Network-based Extreme Learning Machine (ELM) and advanced Particle Swarm Optimization (PSO) are used with this data that yield better and faster convergence to produce more accurate results. Protein secondary structures are predicted efficiently, reliably, more efficiently and more accurately using FLOPRED. These techniques yield superior classification of secondary structure elements, with a training accuracy ranging between 83% and 87% over a wide range of hidden neurons and a cross-validated testing accuracy ranging between 81% and 84% and a Segment OVerlap (SOV) score of 78% that are obtained with different sets of proteins. These results are comparable to other recently published studies, but are obtained with greater efficiencies, in terms of time and cost. PMID:22562230

Saraswathi, Saras; Fernndez-Martnez, Juan Luis; Kolinski, Andrzej; Jernigan, Robert L.; Kloczkowski, Andrzej

2013-01-01

209

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

210

Effect of hexafluoroisopropanol on the thermodynamics of peptide secondary structure formation  

SciTech Connect

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

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

1999-10-27

211

Outer membrane proteins can be simply identified using secondary structure element alignment  

PubMed Central

Background Outer membrane proteins (OMPs) are frequently found in the outer membranes of gram-negative bacteria, mitochondria and chloroplasts and have been found to play diverse functional roles. Computational discrimination of OMPs from globular proteins and other types of membrane proteins is helpful to accelerate new genome annotation and drug discovery. Results Based on the observation that almost all OMPs consist of antiparallel ?-strands in a barrel shape and that their secondary structure arrangements differ from those of other types of proteins, we propose a simple method called SSEA-OMP to identify OMPs using secondary structure element alignment. Through intensive benchmark experiments, the proposed SSEA-OMP method is better than some well-established OMP detection methods. Conclusions The major advantage of SSEA-OMP is its good prediction performance considering its simplicity. The web server implements the method is freely accessible at http://protein.cau.edu.cn/SSEA-OMP/index.html. PMID:21414186

2011-01-01

212

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

213

Structure changes and succession dynamic of the natural secondary forest after severe fire interference  

Microsoft Academic Search

The structure and dynamic succession law of natural secondary forest after severe fire interference in recent 20 years were\\u000a studied by adopting the method of deducing time series from the spatial sequence of vegetation in Heihe region, Heilongjiang,\\u000a China. Two typical and widely distributed forest types in the study area, namely forest type A and forest type B, were selected

Bin-fan Liu; Guang-ju Liu; Zhi-cheng Wang

2009-01-01

214

Application of Multiple Sequence Alignment Profiles to Improve Protein Secondary Structure Prediction  

E-print Network

, and as a stand-alone computer program from: http://barton.ebi.ac.uk/. Proteins 2000; 40:502­511. © 2000 Wiley algorithms.1­5 Secondary structure predictions may also be used to guide the design of site directed,13 machine learning,14,15 neural networks,16 ­22 k-way nearest neighbors,23­28 evolutionary trees,29

Barton, Geoffrey J.

215

Effect of pressure on secondary structure of proteins under ultra high pressure liquid chromatographic conditions.  

PubMed

There are several spectroscopic techniques such as IR and CD, that allow for analyzing protein secondary structure in solution. However, a majority of these techniques require using purified protein, concentrated enough in the solution, to produce a relevant spectrum. Fundamental principles for the usage of reversed-phase ultra high pressure liquid chromatography (UHPLC) as an alternative technique to study protein secondary structures in solution were investigated. Several "model" proteins, as well as several small ionizable and neutral molecules, were used for these studies. The studies were conducted with UHPLC in isocratic mode, using premixed mobile phases at constant flow rate and temperature. The pressure was modified by a backpressure regulator from about 6000psi to about 12,000psi. It was found that when using a mobile phase composition at which proteins were fully denatured (loss of alpha-helix secondary structure), the retention factors of the proteins increased upon pressure increase in the same manner as non-proteins. When using a mobile phase composition in which proteins were not fully denatured, it was observed that the retention factors of the proteins displayed a much steeper (by one order of magnitude) increase in retention upon pressure increase. It was concluded that in a mobile phase in which the protein is not initially fully denatured, the increase of pressure may facilitate the folding back of the protein to its native state (alpha-helix secondary structure). The impact of different mobile phase compositions on the denaturation of the proteins was studied using CD (Circular Dichroism). Moreover, the effect of flow rate on retention of proteins and small molecules was studied at constant pressure on the different pore size silicas and the impact of internal frictional heating was evaluated. PMID:24140255

Makarov, Alexey; LoBrutto, Rosario; Karpinski, Paul

2013-11-29

216

SPEM: improving multiple sequence alignment with sequence profiles and predicted secondary structures  

Microsoft Academic Search

Motivation: Multiple sequence alignment is an essential part of bioinformatics tools for a genome-scale study of genes and their evolution relations. However, making an accurate alignment between remote homologs is challenging. Here, we develop a method, called SPEM, that aligns multiple sequences using pre-processed sequence profiles and predicted secondary structures for pairwise alignment, consistency-based scoring for refinement of the pairwise

Hongyi Zhou; Yaoqi Zhou

2005-01-01

217

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

E-print Network

. Computer Resources Partitioning of Secondary Structure . . . . . . . . . . ?. Contact Determination Defining a Motif with Energetic Potentials Clustering Contact Maps. . 5 5 8 8 11 12 15 RESULTS 16 Helix:Helix Helix:Hairpin Helix: Strand... Helix:Loop Hairpin:Hairpin Hairpin: Strand Hairpin:Loop . Strand: Strand Strand:Loop Loop:Loop 21 25 28 31 34 37 37 42 45 45 DISCUSSION REFERENCES 46 47 VITA 52 LIST OF FIGURES FIGURE I RMSD Cutoff Distribution for Clusters Page...

Hodges, Hamilton Courtney

2013-02-22

218

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

PubMed Central

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

2014-01-01

219

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

PubMed

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

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

2013-11-01

220

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

PubMed Central

Background Secondary structures prediction of proteins is important to many protein structure modeling applications. Correct prediction of secondary structures can significantly reduce the degrees of freedom in protein tertiary structure modeling and therefore reduces the difficulty of obtaining high resolution 3D models. Methods In this work, we investigate a template-based approach to enhance 8-state secondary structure prediction accuracy. We construct structural templates from known protein structures with certain sequence similarity. The structural templates are then incorporated as features with sequence and evolutionary information to train two-stage neural networks. In case of structural templates absence, heuristic structural information is incorporated instead. Results After applying the template-based 8-state secondary structure prediction method, the 7-fold cross-validated Q8 accuracy is 78.85%. Even templates from structures with only 20%~30% sequence similarity can help improve the 8-state prediction accuracy. More importantly, when good templates are available, the prediction accuracy of less frequent secondary structures, such as 3-10 helices, turns, and bends, are highly improved, which are useful for practical applications. Conclusions Our computational results show that the templates containing structural information are effective features to enhance 8-state secondary structure predictions. Our prediction algorithm is implemented on a web server named "C8-SCORPION" available at: http://hpcr.cs.odu.edu/c8scorpion. PMID:25080939

2014-01-01

221

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

PubMed Central

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

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

2014-01-01

222

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

PubMed Central

The investigation on the types of secondary structure (SS) of a protein is important. The evolution of secondary structures during molecular dynamics simulations is a useful parameter to analyze protein structures. Therefore, it is of interest to describe VMD-SS (a software program) for the identification of secondary structure elements and its trajectories during simulation for known structures available at the Protein Data Bank (PDB). The program helps to calculate (1) percentage SS, (2) SS occurrence in each residue, (3) percentage SS during simulation, and (4) percentage residues in all SS types during simulation. The VMD-SS plug-in was designed using TCL script and stride to calculate secondary structure features. Availability The database is available for free at http://science.scu.ac.ir/HomePage.aspx?TabID=13755 PMID:25258493

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

2014-01-01

223

Correlation between protein secondary structure, backbone bond angles, and side-chain orientations  

NASA Astrophysics Data System (ADS)

We investigate the fine structure of the sp3 hybridized covalent bond geometry that governs the tetrahedral architecture around the central C? carbon of a protein backbone, and for this we develop new visualization techniques to analyze high-resolution x-ray structures in the Protein Data Bank. We observe that there is a correlation between the deformations of the ideal tetrahedral symmetry and the local secondary structure of the protein. We propose a universal coarse-grained energy function to describe the ensuing side-chain geometry in terms of the C? carbon orientations. The energy function can model the side-chain geometry with a subatomic precision. As an example we construct the C?-C? structure of HP35 chicken villin headpiece. We obtain a configuration that deviates less than 0.4 in root-mean-square distance from the experimental x-ray structure.

Lundgren, Martin; Niemi, Antti J.

2012-08-01

224

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

Ren, Yi; Seo, Hyuk-Soo; Blobel, Gnter; Hoelz, Andr (Rockefeller)

2010-07-23

225

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

226

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

PubMed

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

Raja, Mobeen

2014-08-01

227

Regenerated silk fibroin films with controllable nanostructure size and secondary structure for drug delivery.  

PubMed

The ability of drug release from SF materials was governed largely by their secondary structure. It is known that the breakage degree of the peptide chain during the silk fibroin (SF) dissolution can affect the structure, property, and applications of SF materials. To deeply understand this effect, we designed a reaction system based on CaCl2/H2O/C2H5OH ternary solvent with different ethanol content to obtain the regenerated SF films with different morphologies and secondary structures. The results showed that the globule-like nanostructure was observed in all regenerated SF films, and their size decreased significantly with reducing the ethanol content in the solvent. Correspondingly, the ?-sheet structure content of the SF films increased. In addition, the contact angle and the elongation ratio increased, and water absorption decreased significantly with decreasing the ethanol content in the solvent. The accumulated release percents of doxorubicin from these SF films were significantly different with increasing the time. With smaller nanostructure size and more ?-sheet content, the SF films had a slower drug release at the beginning. This study indicated the importance of the ethanol content in the solvent in controlling the structure and properties of the regenerated SF films, which would improve the application of SF in drug delivery. PMID:25536875

Zhou, Juan; Zhang, Bin; Shi, Lijun; Zhong, Jian; Zhu, Jun; Yan, Juan; Wang, Ping; Cao, Chuanbao; He, Dannong

2014-12-24

228

Structural differences between a primary and a secondary forest in the Argentine Dry Chaco and management implications  

Microsoft Academic Search

We studied the structure of a primary and a secondary forest in the driest portion of the South American Chaco (average annual precipitation 400mm) and the forest evolution after exploitation. The work was conducted in Chancan Provincial Natural Park and Forest Reserve, Crdoba, Argentina, where the best preserved forests of the region are found. The secondary forest was subjected to

Emma E. Bonino; Publio Araujo

2005-01-01

229

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

PubMed

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

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

2012-02-14

230

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. PMID:20447823

Weeks, Kevin M.

2010-01-01

231

Initiation factor 3-induced structural changes in the 30 S ribosomal subunit and in complexes containing tRNA(f)(Met) and mRNA.  

PubMed

Initiation factor 3 (IF3) acts to switch the decoding preference of the small ribosomal subunit from elongator to initiator tRNA. The effects of IF3 on the 30 S ribosomal subunit and on the 30 S.mRNA. tRNA(f)(Met) complex were determined by UV-induced RNA crosslinking. Three intramolecular crosslinks in the 16 S rRNA (of the 14 that were monitored by gel electrophoresis) are affected by IF3. These are the crosslinks between C1402 and C1501 within the decoding region, between C967xC1400 joining the end loop of a helix of 16 S rRNA domain III and the decoding region, and between U793 and G1517 joining the 790 end loop of 16 S rRNA domain II and the end loop of the terminal helix. These changes occur even in the 30 S.IF3 complex, indicating they are not mediated through tRNA(f)(Met) or mRNA. UV-induced crosslinks occur between 16 S rRNA position C1400 and tRNA(f)(Met) position U34, in tRNA(f)(Met) the nucleotide adjacent to the 5' anticodon nucleotide, and between 16 S rRNA position C1397 and the mRNA at positions +9 and +10 (where A of the initiator AUG codon is +1). The presence of IF3 reduces both of these crosslinks by twofold and fourfold, respectively. The binding site for IF3 involves the 790 region, some other parts of the 16 S rRNA domain II and the terminal stem/loop region. These are located in the front bottom part of the platform structure in the 30 S subunit, a short distance from the decoding region. The changes that occur in the decoding region, even in the absence of mRNA and tRNA, may be induced by IF3 from a short distance or could be caused by the second IF3 structural domain. PMID:10835272

Shapkina, T G; Dolan, M A; Babin, P; Wollenzien, P

2000-06-01

232

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

PubMed

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

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

1995-02-01

233

Solution structure of a purine rich hexaloop hairpin belonging to PGY/MDR1 mRNA and targeted by antisense oligonucleotides  

PubMed Central

A preferential target of antisense oligonucleotides directed against human PGY/MDR1 mRNA is a hairpin containing a stem with a GU wobble pair, capped by the purine-rich 5?r(GGGAUG)3? hexaloop. This hairpin is studied by multidimensional NMR and restrained molecular dynamics, with special emphasis on the conformation of south sugars and non-standard phosphate linkages evidenced in both the stem and the loop. The hairpin is found to be highly structured. The GU wobble pair, a strong counterion binding site, displays structural particularities that are characteristic of this type of mismatch. The upper part of the stem undergoes distortions that optimize its interactions with the beginning of the loop. The loop adopts a new fold in which the single-stranded GGGA purine tract is structured in A-like conformation stacked in continuity of the stem and displays an extensive hydrogen bonding surface for recognition. The remarkable hairpin stability results from classical inter- and intra-strand interactions reinforced by numerous hydrogen bonds involving unusual backbone conformations and ribose 2?-hydroxyl groups. Overall, this work emphasizes numerous features that account for the well-ordered structure of the whole hairpin and highlights the loop properties that facilitate interaction with antisense oligonucleotides. PMID:17041234

Joli, Flore; Bouchemal, Nadia; Laigle, Alain; Hartmann, Brigitte; Hantz, Edith

2006-01-01

234

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. PMID:24369429

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

235

Prediction of protein structural classes for low-similarity sequences using reduced PSSM and position-based secondary structural features.  

PubMed

Many efficient methods have been proposed to advance protein structural class prediction, but there are still some challenges where additional insight or technology is needed for low-similarity sequences. In this work, we schemed out a new prediction method for low-similarity datasets using reduced PSSM and position-based secondary structural features. We evaluated the proposed method with four experiments and compared it with the available competing prediction methods. The results indicate that the proposed method achieved the best performance among the evaluated methods, with overall accuracy 3-5% higher than the existing best-performing method. This paper also found that the reduced alphabets with size 13 simplify PSSM structures efficiently while reserving its maximal information. This understanding can be used to design more powerful prediction methods for protein structural class. PMID:25445293

Wang, Junru; Wang, Cong; Cao, Jiajia; Liu, Xiaoqing; Yao, Yuhua; Dai, Qi

2015-01-10

236

Landscape and variation of RNA secondary structure across the human transcriptome.  

PubMed

In parallel to the genetic code for protein synthesis, a second layer of information is embedded in all RNA transcripts in the form of RNA structure. RNA structure influences practically every step in the gene expression program. However, the nature of most RNA structures or effects of sequence variation on structure are not known. Here we report the initial landscape and variation of RNA secondary structures (RSSs) in a human family trio (mother, father and their child). This provides a comprehensive RSS map of human coding and non-coding RNAs. We identify unique RSS signatures that demarcate open reading frames and splicing junctions, and define authentic microRNA-binding sites. Comparison of native deproteinized RNA isolated from cells versus refolded purified RNA suggests that the majority of the RSS information is encoded within RNA sequence. Over 1,900 transcribed single nucleotide variants (approximately 15% of all transcribed single nucleotide variants) alter local RNA structure. We discover simple sequence and spacing rules that determine the ability of point mutations to impact RSSs. Selective depletion of 'riboSNitches' versus structurally synonymous variants at precise locations suggests selection for specific RNA shapes at thousands of sites, including 3' untranslated regions, binding sites of microRNAs and RNA-binding proteins genome-wide. These results highlight the potentially broad contribution of RNA structure and its variation to gene regulation. PMID:24476892

Wan, Yue; Qu, Kun; Zhang, Qiangfeng Cliff; Flynn, Ryan A; Manor, Ohad; Ouyang, Zhengqing; Zhang, Jiajing; Spitale, Robert C; Snyder, Michael P; Segal, Eran; Chang, Howard Y

2014-01-30

237

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

238

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

Microsoft Academic Search

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

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

2004-01-01

239

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

PubMed Central

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

2013-01-01

240

Noncanonical DNA secondary structures as drug targets: the prospect of the i-motif.  

PubMed

Under certain conditions, specific DNA sequences have the potential to adopt noncanonical secondary structures, such as i-motifs. Interestingly, these DNA stretches are not randomly located throughout the genome but rather frequently clustered in regulatory regions of oncogenes and in telomeres, the terminal regions of chromosomes. Recent evidences suggest that i-motif DNA structures exist in living cells and could be involved in a variety of biological processes, such as replication, regulation of oncogene expression, and telomere functions. Therefore, the targeting of i-motif DNA is an emerging research area in medicinal chemistry. Bringing these noncanonical structures into focus as targets for anticancer drug design and gene regulation processes could be crucial for a better understanding of their biological functions and to open the way to new, effective strategies for cancer treatment. PMID:24962454

Amato, Jussara; Iaccarino, Nunzia; Randazzo, Antonio; Novellino, Ettore; Pagano, Bruno

2014-09-01

241

Nucleotide sequence and proposed secondary structure of Columnea latent viroid: a natural mosaic of viroid sequences.  

PubMed Central

The Columnea latent viroid (CLV) occurs latently in certain Columnea erythrophae plants grown commercially. In potato and tomato, CLV causes potato spindle tuber viroid (PSTV)-like symptoms. Its nucleotide sequence and proposed secondary structure reveal that CLV consists of a single-stranded circular RNA of 370 nucleotides which can assume a rod-like structure with extensive base-pairing characteristic of all known viroids. The electrophoretic mobility of circular CLV under nondenaturing conditions suggests a potential tertiary structure. CLV contains extensive sequence homologies to the PSTV group of viroids but contains a central conserved region identical to that of hop stunt viroid (HSV). CLV also shares some biological properties with each of the two types of viroids. Most probably, CLV is the result of intracellular RNA recombination between an HSV-type and one or more PSTV-type viroids replicating in the same plant. Images PMID:2602114

Hammond, R; Smith, D R; Diener, T O

1989-01-01

242

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

PubMed Central

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

Zwieb, C

1985-01-01

243

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

PubMed Central

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

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

2014-01-01

244

Pan-eukaryote ITS2 homologies revealed by RNA secondary structure  

PubMed Central

For evolutionary comparisons, phylogenetics and evaluation of potential interbreeding taxa of a species, various loci have served for animals and plants and protistans. One [second internal transcribed spacer (ITS2) of the nuclear ribosomal DNA] is highly suitable for all. Its sequence is species specific. It has already been used extensively and very successfully for plants and some protistans, and a few animals (where historically, the mitochondrial genes have dominated species studies). Despite initial impressions that ITS2 is too variable, it has proven to provide useful biological information at higher taxonomic levels, even across all eukaryotes, thanks to the conserved aspects of its transcript secondary structure. The review of all eukaryote groups reveals that ITS2 is expandable, but always retains in its RNA transcript a common core structure of two helices with hallmark characteristics important for ribosomal RNA processing. This aspect of its RNA transcript secondary structure can rescue difficult alignment problems, making the ITS2?a more powerful tool for phylogenetics. Equally important, the recognition of eukaryote-wide homology regions provides extensive and detailed information to test experimental studies of ribosomal rRNA processing. PMID:17459886

Coleman, Annette W.

2007-01-01

245

A consensus secondary structure of ITS2 in the chlorophyta identified by phylogenetic reconstruction.  

PubMed

The definition of species plays a pivotal role in biology. It has been proposed that Compensatory Base Changes (CBCs) in the fast-evolving Internal Transcribed Spacer 2 (ITS2) correlate with speciation and thus can be used to distinguish species. The applicability of CBC - based species concepts using ITS2, however, rests on the homology of the investigated ITS2 positions. We studied the ITS2 molecule of 147 strains of Chlorophyceae (Chlorophyta, Viridiplantae) including 26 new sequences in the order Chaetophorales, and compared their secondary structures to ITS2 in the sister class Ulvophyceae, represented by the order Ulvales. Using a phylogenetic/comparative approach, it was possible to identify 1) the first consensus structure model of the ITS2 molecule that can be applied to two classes of green algae [Ulvophyceae (Ulvales), Chlorophyceae] and 2) landmarks (the spacer regions separating the ITS2 Helices) for more robust prediction of the secondary structures in green algae. Moreover, we found that CBCs in homologous positions in these 147 strains (representing 115 validly described species) are either completely absent or mostly associated with internal branches representing higher order taxonomic levels (genera, families, orders). As reported for the Ulvales, CBCs are not diagnostic at the species level in the dataset used. PMID:23770573

Caisov, Lenka; Marin, Birger; Melkonian, Michael

2013-07-01

246

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

PubMed Central

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

Whitmore, Lee; Wallace, B. A.

2004-01-01

247

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

PubMed Central

In vitro selection can generate functional sequence variants of an RNA structural motif that are useful for comparative analysis. The technique is particularly valuable in cases where natural variation is unavailable or non-existent. We report the extension of this approach to a new extreme--the identification of a 112 nt ribozyme secondary structure imbedded within a 186 nt RNA. A pool of 10(14) variants of an RNA ligase ribozyme was generated using combinatorial chemical synthesis coupled with combinatorial enzymatic ligation such that 172 of the 186 relevant positions were partially mutagenized. Active variants of this pool were enriched using an in vitro selection scheme that retains the sequence variability at positions very close to the ligation junction. Ligases isolated after four rounds of selection catalyzed self-ligation up to 700 times faster than the starting sequence. Comparative analysis of the isolates indicated that when complexed with substrate RNAs the ligase forms a nested, double pseudo-knot secondary structure with seven stems and several important joining segments. Comparative analysis also suggested the identity of mutations that account for the increased activity of the selected ligase variants; designed constructs incorporating combinations of these changes were more active than any of the individual ligase isolates. Images PMID:7667099

Ekland, E H; Bartel, D P

1995-01-01

248

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. PMID:22936943

Cosgrove, Daniel J.; Jarvis, Michael C.

2012-01-01

249

Concentration Independent Estimation of Protein Secondary Structure by Circular Dichroism; A Comparison of Methods  

PubMed Central

Estimation of a protein's secondary structure from its circular dichroism spectrum usually requires accurate knowledge of the concentration and pathlength of the sample. Two recently described methods avoid this problem by analysis of g-factor spectra (McPhie, Anal. Bioch. 293, 109?119) or scaling of relative intensities (Raussens et al, ibid. 319, 114?121). Application of the two methods to the same samples shows that they can have similar efficacies. Calculation with the latter method is more rapid, but the performance of the former is maintained over reduced wavelength ranges. PMID:18294952

McPhie, Peter

2008-01-01

250

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

E-print Network

The supersecondary structure of amyloids and prions, proteins of intense clinical and biological interest, are difficult to determine by standard experimental or computational means. In addition, significant conformational ...

Bryan, Allen W.

251

Evolutionary conservation of sequence and secondary structures inCRISPR repeats  

SciTech Connect

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

Kunin, Victor; Sorek, Rotem; Hugenholtz, Philip

2006-09-01

252

Differential protein occupancy profiling of the mRNA transcriptome  

PubMed Central

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

2014-01-01

253

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

PubMed

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

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

2011-07-01

254

Nonrandom gene organization: structural arrangements of specific pre- mRNA transcription and splicing with SC-35 domains  

PubMed Central

This work demonstrates a highly nonrandom distribution of specific genes relative to nuclear domains enriched in splicing factors and poly(A)+ RNA, and provides evidence for the direct involvement of these in pre-mRNA metabolism. As investigated in hundreds of diploid fibroblasts, human collagen I alpha 1 and beta-actin DNA/RNA showed a very high degree of spatial association with SC-35 domains, whereas three nontranscribed genes, myosin heavy chain, neurotensin, and albumin, showed no such preferential association. Collagen I alpha 1 RNA accumulates within the more central region of the domain, whereas beta-actin RNA localizes at the periphery. A novel approach revealed that collagen RNA tracks are polarized, with the entire gene at one end, on the edge of the domain, and the RNA extending into the domain. Intron 26 is spliced within the RNA track at the domain periphery. Transcriptional inhibition studies show both the structure of the domain and the gene's relationship to it are not dependent upon the continued presence of accumulated collagen RNA, and that domains remaining after inhibition are not just storage sites. Results support a model reconciling light and electron microscopic observations which proposes that transcription of some specific genes occurs at the border of domains, which may also function in the assembly or distribution of RNA metabolic components. In contrast to the apparently random dispersal of total undefined hnRNA synthesis through interdomain space, transcription and splicing for some genes occurs preferentially at specific sites, and a high degree of individual pre-mRNA metabolism is compartmentalized with discrete SC-35 domains. PMID:8557734

1995-01-01

255

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

SciTech Connect

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

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

2010-02-12

256

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

257

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

PubMed Central

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

Born, K.; Freskgrd, P. O.; Carlsson, U.

1996-01-01

258

Secondary structure specificity of the nuclease activity of the 1,10-phenanthroline-copper complex.  

PubMed Central

The artificial DNase activity of the 1,10-phenanthroline-cuprous ion complex [(OP)2Cu+] and H2O2 cleaves the A, B, and Z forms of DNA at different rates. The B structure, formed by most DNAs including poly(dA-dT) and poly(dA) X poly(dT), is the most susceptible to cleavage. It is completely degraded within 1 min by 40 microM 1,10-phenanthroline/4 microM Cu2+/7 mM H2O2/7 mM 3-mercaptopropionic acid. The A structure, formed by RNA X DNA hybrids such as poly(rA) X poly(dT), is cleaved in both strands roughly 10-20% as rapidly as poly(dA-dT) under comparable conditions. In contrast, the left-handed Z structure, formed by poly(dG-dC) in 3.0 M NaCl, is completely resistant to cleavage even though the same copolymer in the B structure at 15 mM NaCl is readily degraded. Poly(dA-dT) is rendered acid soluble at both salt concentrations at similar rates. The basis for the secondary structure specificity of the DNA cleavage reaction most likely resides in the requisite formation of a productive complex between (OP)2Cu+ and DNA during the course of this reaction. Previous studies have suggested that strand scission is due to oxidative destruction of the deoxyribose by hydroxyl radicals produced by the oxidation of DNA-bound Cu+ by H2O2. Apparently, the Z and A structures are unable to form a stable noncovalent complex with the same optimal geometry for cleavage as the B structure and are less susceptible to degradation. This artificial DNase activity may provide an approach to assess the formation of non-B-DNA structures in solution. PMID:6320169

Pope, L E; Sigman, D S

1984-01-01

259

The efficacy of small interfering RNAs targeted to the type 1 insulin-like growth factor receptor (IGF1R) is influenced by secondary structure in the IGF1R transcript.  

PubMed

The type 1 insulin-like growth factor receptor (IGF1R) is often overexpressed by tumors and mediates growth and apoptosis protection. We previously showed that antisense reagents complementary to the IGF1R translation start site enhance radio- and chemosensitivity and impair Atm function. However these agents induce relatively modest IGF1R down-regulation and affect insulin receptor levels. To identify alternative sites for molecular targeting, we utilized scanning oligonucleotide arrays to probe the secondary structure of IGF1R mRNA. This strategy enabled selection of antisense oligonucleotides that generated high heteroduplex yield with IGF1R but not insulin receptor transcripts. Antisense oligonucleotides that hybridized strongly to IGF1R mRNA caused IGF1R down-regulation within intact tumor cells, whereas weakly hybridizing oligonucleotides were inactive. Furthermore, the ability of small interfering RNAs (siRNAs) to block IGF1R expression correlated with the accessibility of the target sequence within the transcript. Thus, siRNAs corresponding to weakly hybridizing oligonucleotides caused minor IGF1R down-regulation, whereas siRNAs homologous to accessible targets induced profound sequence-specific IGF1R gene silencing, blocked IGF signaling, and enhanced tumor cell radiosensitivity. This indicates that secondary structure in the target transcript has a major effect on siRNA efficacy. These findings have implications for siRNA design and suggest that IGF1R-targeting agents incorporating this mode of action have potential as anticancer therapy. PMID:12604614

Bohula, Erin A; Salisbury, Amanda J; Sohail, Muhammad; Playford, Martin P; Riedemann, Johann; Southern, Edwin M; Macaulay, Valentine M

2003-05-01

260

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. PMID:1373201

Pathak, V K; Temin, H M

1992-01-01

261

Hydrolysis of haemoglobin surveyed by infrared spectroscopy: I. solvent effect on the secondary structure of haemoglobin  

NASA Astrophysics Data System (ADS)

The hydrolysis of bovine haemoglobin in an acetic acid/sodium acetate buffer enables to produce peptides of major importance in biomedical research. The global objective is to survey this reaction by infrared spectroscopy. This article concerns the first step: the evaluation by spectroscopy of the effect on protein secondary structure of the addition of ethanol in the buffer.Conformational changes are related to solvent-protein interactions as the protein folding is driven by the entropy of removing hydrophobic groups from contact with the solvent. Therefore, the stability of haemoglobin in an ethanol-water mixture results in a competition between the water structure, which is strengthened by the presence of the alcohol, and the solubility of hydrophobic residues. Previous non infrared experiments, based on mass spectrometry for example, have been reported for the investigation of the denaturation of haemoglobin by an organic solvent.The use of vibrational spectroscopy for protein secondary structure determination has proved its efficiency. We focus here on the study of the denaturing of haemoglobin in a water medium by addition of ethanol. As our investigations deal with very low concentrated haemoglobin, we apply a technique that uses films dried from dilute solution. Although it is not generally accepted that the protein conformation is retained when the solvent evaporates off, we validate this method comparing some results to previous infrared study made at upper concentrations with liquid sampling. We observe that Fourier Transform Infrared (FTIR) Spectroscopy, combined with few mathematical treatments, permits to estimate that haemoglobin remains in a native form unless a concentration of more or less 20% of ethanol is reached. For greater values modifications are perceptible on the infrared spectra.

Ruckebusch, Cyril; Nedjar-Arroume, Naima; Magazzeni, Stephanie; Huvenne, Jean-Pierre; Legrand, Pierre

1999-03-01

262

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

PubMed Central

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

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

2014-01-01

263

Regulation of Dscam exon 17 alternative splicing by steric hindrance in combination with RNA secondary structures  

PubMed Central

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

2013-01-01

264

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

PubMed Central

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

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

2014-01-01

265

Effects of proline cis-trans isomerization on TB domain secondary structure.  

PubMed Central

The transforming growth factor beta (TGF-beta) binding protein-like (TB) domain is found principally in proteins localized to extracellular matrix fibrils, including human fibrillin-1, the defective protein in the Marfan syndrome. Analysis of the nuclear magnetic resonance (NMR) data for the sixth TB module from human fibrillin-1 has revealed the existence of two stable conformers that differ in the isomerization states of two proline residues. Unusually, the two isoforms do not readily interconvert and are stable on the time scale of milliseconds. We have computed independent structures of the major and minor conformers of TB6 to assess how the domain fold adjusts to incorporate alternatively cis- or trans-prolines. Based on previous observations, it has been suggested that multiple conformers can only be accommodated in flexible regions of protein structure. In contrast, P22, which exists in trans in the major form and cis in the minor form of TB6, is in a rigid region of the domain, which is confirmed by backbone dynamics measurements. Overall, the structures of the major and minor conformers are similar. However, the secondary structure topologies of the two forms differ as a direct consequence of the changes in proline conformation. PMID:9792099

Yuan, X.; Werner, J. M.; Knott, V.; Handford, P. A.; Campbell, I. D.; Downing, K.

1998-01-01

266

Suppression of secondary electron yield by micro-porous array structure  

SciTech Connect

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. [School of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an 710049 (China); Wang, R.; Hu, T. C.; Yang, J.; Cui, W. Z. [Science and Technology on Space Microwave Laboratory, China Academy of Space Technology, Xi'an 710100 (China)

2013-02-21

267

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

PubMed Central

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

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

2002-01-01

268

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

PubMed Central

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

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

2011-01-01

269

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

270

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

PubMed

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

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

2009-12-01

271

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

PubMed Central

Taking advantage of recent advances in polarized Raman microspectroscopy, and based on a rational decomposition of the amide I band, the conformation and orientation of proteins have been determined for cocoon silks of the silkworms Bombyx mori and Samia cynthia ricini and dragline silks of the spiders Nephila clavipes and Nephila edulis. This study distinguished between band components due to ?-sheets, ?-turns, 31-helices, and unordered structure for the four fibers. For B. mori, the ?-sheet content is 50%, which matches the proportion of residues that form the GAGAGS fibroin motifs. For the Nephila dragline and S. c. ricini cocoon, the ?-sheet content (3637% and 45%, respectively) is higher than the proportion of residues that belong to polyalanine blocks (18% and 42%, respectively), showing that adjacent GGA motifs are incorporated into the ?-sheets. Nephila spidroins contain fewer ?-sheets and more flexible secondary structures than silkworm fibroins. The amorphous polypeptide chains are preferentially aligned parallel to the fiber direction, although their level of orientation is much lower than that of ?-sheets. Overall, the results show that the four silks exhibit a common molecular organization, with mixtures of different amounts of ?-sheets and flexible structures, which are organized with specific orientation levels. PMID:17277183

Lefvre, Thierry; Rousseau, Marie-Eve; Pzolet, Michel

2007-01-01

272

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

PubMed

The mechanism of action on biomolecules of N? gas plasma, a novel sterilization technique, remains unclear. Here, the effect of N? gas plasma on protein structure was investigated. BSA, which was used as the model protein, was exposed to N? gas plasma generated by short-time high voltage pulses from a static induction thyristor power supply. N? gas plasma-treated BSA at 1.5?kilo pulses per second showed evidence of degradation and modification when assessed by Coomassie brilliant blue staining and ultraviolet spectroscopy at 280?nm. Fourier transform infrared spectroscopy analysis was used to determine the protein's secondary structure. When the amide I region was analyzed in the infrared spectra according to curve fitting and Fourier self-deconvolution, N? gas plasma-treated BSA showed increased ?-helix and decreased ?-turn content. Because heating decreased ?-helix and increased ?-sheet content, the structural changes induced by N? gas plasma-treatment of BSA were not caused by high temperatures. Thus, the present results suggest that conformational changes induced by N? gas plasma are mediated by mechanisms distinct from heat denaturation. PMID:23617321

Sakudo, Akikazu; Higa, Masato; Maeda, Kojiro; Shimizu, Naohiro; Imanishi, Yuichiro; Shintani, Hideharu

2013-07-01

273

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

NASA Technical Reports Server (NTRS)

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

Koenig, B.

1977-01-01

274

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

PubMed Central

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

Minami, Shintaro; Sawada, Kengo; Chikenji, George

2014-01-01

275

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

PubMed

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

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

2012-01-01

276

Identification of novel DNA repair proteins via primary sequence, secondary structure, and homology  

PubMed Central

Background DNA repair is the general term for the collection of critical mechanisms which repair many forms of DNA damage such as methylation or ionizing radiation. DNA repair has mainly been studied in experimental and clinical situations, and relatively few information-based approaches to new extracting DNA repair knowledge exist. As a first step, automatic detection of DNA repair proteins in genomes via informatics techniques is desirable; however, there are many forms of DNA repair and it is not a straightforward process to identify and classify repair proteins with a single optimal method. We perform a study of the ability of homology and machine learning-based methods to identify and classify DNA repair proteins, as well as scan vertebrate genomes for the presence of novel repair proteins. Combinations of primary sequence polypeptide frequency, secondary structure, and homology information are used as feature information for input to a Support Vector Machine (SVM). Results We identify that SVM techniques are capable of identifying portions of DNA repair protein datasets without admitting false positives; at low levels of false positive tolerance, homology can also identify and classify proteins with good performance. Secondary structure information provides improved performance compared to using primary structure alone. Furthermore, we observe that machine learning methods incorporating homology information perform best when data is filtered by some clustering technique. Analysis by applying these methodologies to the scanning of multiple vertebrate genomes confirms a positive correlation between the size of a genome and the number of DNA repair protein transcripts it is likely to contain, and simultaneously suggests that all organisms have a non-zero minimum number of repair genes. In addition, the scan result clusters several organisms' repair abilities in an evolutionarily consistent fashion. Analysis also identifies several functionally unconfirmed proteins that are highly likely to be involved in the repair process. A new web service, INTREPED, has been made available for the immediate search and annotation of DNA repair proteins in newly sequenced genomes. Conclusion Despite complexity due to a multitude of repair pathways, combinations of sequence, structure, and homology with Support Vector Machines offer good methods in addition to existing homology searches for DNA repair protein identification and functional annotation. Most importantly, this study has uncovered relationships between the size of a genome and a genome's available repair repetoire, and offers a number of new predictions as well as a prediction service, both which reduce the search time and cost for novel repair genes and proteins. PMID:19154573

Brown, JB; Akutsu, Tatsuya

2009-01-01

277

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

PubMed

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

Hall, Vincent; Sklepari, Meropi; Rodger, Alison

2014-09-01

278

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

NASA Technical Reports Server (NTRS)

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

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

1998-01-01

279

Implications of protein structure instability: from physiological to pathological secondary structure.  

PubMed

Proteins are folded during their synthesis; this process may be spontaneous or assisted. Both phenomena are carefully regulated by the "housekeeping" mechanism and molecular chaperones to avoid the appearance of misfolded proteins. Unfolding process generally occurs during physiological degradation of protein, but in some specific cases it results from genetic or environmental changes and does not correspond to metabolic needs. The main outcome of these phenomena is the appearance of nonfunctional pathologically unfolded proteins with a strong tendency to aggregation. Moreover, for some of these unfolded proteins, the agglomeration that follows initial proteins association may give rise to highly structured soluble aggregates. These aggregates have been identified as the main cause of the so-called amyloidosis or amyloid diseases, such as Alzheimer's, Parkinson's, and Creutzfeldt-Jakob diseases, and type II diabetes mellitus. Although some common mechanisms of amyloid protein aggregation have been identified, the roles of the environmental conditions inducing amyloidosis remain to be clarified. In this review, we will summarize recent studies identifying the origin of amyloid nucleation and will try to predict the therapeutic prospects that may be opened by elucidation of the amyloidosis mechanisms. PMID:22605549

Sukhanova, Alyona; Poly, Simon; Shemetov, Anton; Bronstein, Igor; Nabiev, Igor

2012-08-01

280

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

NASA Astrophysics Data System (ADS)

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

Matsushima, Norio; Enkhbayar, Purevjav

2012-09-01

281

UV resonance Raman examination of environmental effects on protein secondary structure  

NASA Astrophysics Data System (ADS)

This thesis discusses work which develops UV resonance Raman spectroscopy (UVRR) as a method for examining protein secondary structure. We demonstrated the utility of a novel continuous-wave (CW) 206.5 rim krypton ion laser to probe protein secondary structure and examine CVD diamond material properties. We utilized 206.5 nm excitation to selectively enhance the amide vibrations, and to examine environmental. effects that induce a-helical formation in two amphiphilic peptides, bombolitin I (BI) and bombolitin III (BIII). The presence of a salt-bridge in BIII (Lys2-Asp5) stabilizes an alpha-helix turn at neutral pH. We demonstrate that reduction in the intra and/or intermolecular repulsions, along with less polar solvating environments induce alpha-helical formation in BI and BIII. Furthermore, we show that the amphiphilic alpha-helix formation, which results from increasing ionic strengths, is accompanied by self-association. We also demonstrate that an increase in the angiotensin II (AII) beta-turn structure in the presence of sodium dodecylsulfate (SDS) mainly derives from the binding of two SDS molecules to the positively charged AII N-terminus and the Arg2 residue. This AII-SDS complexation may also account for the slight higher Tyr (AII) solvent accessibility in SDS micelles compared to DPC micelles. We also examined the cis-trans isomerization dynamics of Glycylglycine (Gly-Gly) and Gly-Gly derivatives. Utilizing Li et al.'s three state model, we determined the Gibbs free energy differences between the ground states of trans and cis Gly-Gly at pH 3.0, 5.7, and 10.5 of 3.6 +/- 0.4, 3.0 +/- 0.5 and 4.4 +/- 0.7 kcal/mol, respectively. We also found that the cis to trans activation barrier for the cationic, zwitterionic and anionic Gly-Gly species are essentially identical ( 9.7 +/- 0.8 kcal/mol). Our results suggest only a modest impact of the Gly-Gly charge state on cis-trans energy differences and activation barriers for Gly-Gly derivatives.

Holtz, Janet Shan-Mei Wang

1998-12-01

282

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

PubMed Central

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

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

2015-01-01

283

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

NASA Astrophysics Data System (ADS)

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

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

2003-06-01

284

The susceptibility of ?-helical secondary structure to steric strain: Coarse-grained simulation of dendronized polypeptides  

NASA Astrophysics Data System (ADS)

The propensity of a peptide chain for adopting helical secondary structure can be modulated not only through the solvation properties of its side chains but also through their size and shape. Here we examine a coarse-grained model for dendronized polypeptides that focuses on the susceptibility of ?-helical structure to the steric strain exerted by hydrophilic pendant groups. Undecorated molecules exhibit a pronounced transition from random coil to helix upon cooling [J. P. Kemp and J. Z. Y. Chen, Biomacromolecules 2, 389 (2001)]. As gauged by specific heat and by order parameters characterizing helicity at several length scales, this transition is quite robust to the introduction of first- and second-generation dendron side chains. More highly branched side chains, however, reduce the entropy of compact states so severely that helical ordering is undetectable over the entire temperature range accessible to our importance sampling methods. Consistent with experimental observations for side chains comparable to those of our model in volume-excluding size and shape, we find the backbone of these third-generation molecules to assume a distended rodlike state that is both stiff and achiral.

Browne, William; Geissler, Phillip L.

2010-10-01

285

Dietary fats affect rat plasma lipoprotein secondary structure as assessed by Fourier transform infrared spectroscopy.  

PubMed

This investigation was undertaken to determine by Fourier transform infrared spectroscopy the effects of diets enriched with fish, sunflower or olive oils on the secondary structure of plasma HDL and LDL from rats, as well as the effects on lipid unsaturation and acyl chain lengths. Controls were fed a commercial diet. In HDL, random coil conformation was relatively high in rats fed the fish diet, probably due to the irregular geometry of polyunsaturated fatty acids interacting with apoproteins. Parallel structural behaviors were observed for rats fed control and olive oil diets. The lowest lipid unsaturation level was found in HDL of rats fed olive oil, and acyl chain lengths were slightly increased by the three fats. Rats fed olive oil had the lowest percentage of LDL beta-sheets and these were more abundant in rats fed the fish oil diet. The least lipid unsaturation in LDL was in rats fed the olive oil diet. No significant differences in acyl chain lengths were observed. Certain protein conformational changes and/or apoprotein composition differences due to dietary fat may affect the binding between lipoproteins and their receptors in cells. PMID:11435504

Lpez, G; Martnez, R; Gallego, J; Tarancn, M J; Carmona, P; Fraile, M V

2001-07-01

286

Interplay between Secondary and Tertiary Structure Formation in Protein Folding Cooperativity  

E-print Network

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

Tristan Bereau; Michael Bachmann; Markus Deserno

2011-07-01

287

Including secondary structure, fossils and molecular dating in the centipede tree of life.  

PubMed

A well-corroborated morphological scheme of interrelationships for centipedes, once broadly accepted, has been in conflict with molecular data with respect to deep branching events. Expanded taxonomic coverage compared to previous analyses adds longer fragments for 28S rRNA and a structural alignment as part of a sample of four genes (two nuclear ribosomal and two mitochondrial) for 111 extant species; these sequence data are combined with morphology under parsimony and maximum likelihood, exploring both traditional multiple sequence alignment and direct optimization approaches. Novel automated procedures to incorporate secondary structure information are also explored. The molecular data in combination yield trees that are highly congruent with morphology as regards the monophyly of all centipede orders as well as the major groups within each of the large orders. Regardless of the optimality criterion or alignment strategy, the Tasmanian/New Zealand Craterostigmomorpha is resolved in a different position by the molecular data than by morphology. Addition of morphology overturns the placement of Craterostigmomorpha in favour of the traditional morphological resolution and eliminates the need to posit major character reversals with respect to developmental mode and maternal care. Calibration of the tree with Palaeozoic and Mesozoic fossils for a relaxed clock analysis corroborates the palaeontological signal that divergences between centipede orders date to the Silurian and earliest Devonian, and familial divergences are likewise almost wholly Palaeozoic. PMID:20601003

Murienne, Jerome; Edgecombe, Gregory D; Giribet, Gonzalo

2010-10-01

288

Understanding the effect of secondary structure on molecular interactions of poly-L-lysine with different substrates by SFA.  

PubMed

Nonspecific adsorption of proteins on biomaterial surfaces challenges the widespread application of engineered materials, and understanding the impact of secondary structure of proteins and peptides on their adsorption process is of both fundamental and practical importance in bioengineering. In this work, poly-L-lysine (PLL)-based ?-helices and ?-sheets were chosen as a model system to investigate the effect of secondary structure on peptide interactions with substrates of various surface chemistries. Circular dichroism (CD) was used to confirm the presence of both ?-helix and ?-sheet structured PLL in aqueous solutions and upon adsorption to quartz, where these secondary structures seemed to be preserved. Atomic force microscopy (AFM) imaging showed different surface patterns for adsorbed ?-helix and ?-sheet PLL. Interactions between PLL of different secondary structures and various substrates (i.e., PLL, Au, mica, and poly(ethylene glycol) (PEG)) were directly measured using a surface forces apparatus (SFA). It was found that ?-sheet PLL films showed higher adsorbed layer thicknesses in general. Adhesion energies of ?-sheet versus Au and ?-sheet versus ?-sheet were considerably higher than that of ?-helix versus Au and ?-helix versus ?-helix systems, respectively. Au and ?-sheet PLL interactions seemed to be more dependent on the salt concentration than that of ?-helix, while the presence of a grafted PEG layer greatly diminished any attraction with either PLL structure. The molecular interaction mechanism of peptide in different secondary structures is discussed in terms of Derjaguin-Landau-Verwey-Overbeek (DLVO) theory, Alexander-de Gennes (AdG) steric model and hydrogen bonding, which provides important insight into the fundamental understanding of the interaction mechanism between proteins and biomaterials. PMID:24032485

Binazadeh, Mojtaba; Faghihnejad, Ali; Unsworth, Larry D; Zeng, Hongbo

2013-10-14

289

mRNA  

NSDL National Science Digital Library

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

Darryl Leja (National Human Genome Research Institute REV)

2005-04-04

290

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

PubMed Central

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

2012-01-01

291

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

PubMed Central

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

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

2014-01-01

292

Characterization of a thermostable lipase showing loss of secondary structure at ambient temperature.  

PubMed

A gene encoding extracellular lipase was cloned and characterized from metagenomic DNA extracted from hot spring soil. The recombinant gene was expressed in E. coli and expressed protein was purified to homogeneity using hydrophobic interactions chromatography. The mature polypeptide consists of 388 amino acids with apparent molecular weight of 43 kDa. The enzyme displayed maximum activity at 50 C and pH 9.0. It showed thermal stability up to 40 C without any loss of enzyme activity. Nearly 80% enzyme activity was retained at 50 C even after incubation for 75 min. However above 50 C the enzyme displayed thermal instability. The half life of the enzyme was determined to be 5 min at 60 C. Interestingly the CD spectroscopic study carried out in the temperature range of 25-95 C revealed distortion in solution structure above 35 C. However the intrinsic tryptophan fluorescence spectroscopic study revealed that even with the loss of secondary structure at 35 C and above the tertiary structure was retained. With p-nitrophenyl laurate as a substrate, the enzyme exhibited a K ( m ), V ( max ) and K ( cat ) of 0.73 0.18 ?M, 239 16 ?mol/ml/min and 569 s(-1) respectively. Enzyme activity was strongly inhibited by CuCl(2), HgCl(2) and DEPC but not by PMSF, eserine and SDS. The protein retained significant activity (~70%) with Triton X-100. The enzyme displayed 100% activity in presence of 30% n-Hexane and acetone. PMID:21678056

Sharma, Pushpender Kumar; Singh, Kashmir; Singh, Ranvir; Capalash, Neena; Ali, Azmat; Mohammad, Owais; Kaur, Jagdeep

2012-03-01

293

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

ERIC Educational Resources Information Center

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

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

2007-01-01

294

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

ERIC Educational Resources Information Center

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

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

2012-01-01

295

Characterization of the secondary structure and thermostability of the extrinsic 16 kilodalton protein of spinach photosystem II by  

E-print Network

protein of spinach photosystem II by Fourier transform infrared spectroscopy H. Zhanga,1 , Y. Yamamotob of the extrinsic 16 kDa protein of the spinach photosystem II (OEC16) were characterized in solution between 25 Elsevier Science B.V. All rights reserved. Keywords: FTIR; OEC16; Secondary structure; Photosystem II 1

Carpentier, Robert

296

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

Microsoft Academic Search

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

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

2005-01-01

297

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

E-print Network

The overall structure of the human lens is one of succes- sive generations of secondary fiber cells stratified chrono- logically around the embryonic nucleus, with the primary fiber cells being formed by week six after fertilization [1,2]. Because all cells are retained, the lens grows continuously throughout

Hammock, Bruce D.

298

Secondary Structure of the rRNA ITS2 Region Reveals Key Evolutionary Patterns in Acroporid Corals  

Microsoft Academic Search

This study investigates the ribosomal RNA transcript secondary structure in corals as confirmed by compensatory base changes\\u000a in Isopora\\/Acropora species. These species are unique versus all other corals in the absence of a eukaryote-wide conserved structural component,\\u000a the helix III in internal transcriber spacer (ITS) 2, and their variability in the 5.8S-LSU helix basal to ITS2, a helix with\\u000a pairings

Annette W. Coleman; Madeleine J. H. van Oppen

2008-01-01

299

Ensembled support vector machines for human papillomavirus risk type prediction from protein secondary structures.  

PubMed

Infection by the human papillomavirus (HPV) is regarded as the major risk factor in the development of cervical cancer. Detection of high-risk HPV is important for understanding its oncogenic mechanisms and for developing novel clinical tools for its diagnosis, treatment, and prevention. Several methods are available to predict the risk types for HPV protein sequences. Nevertheless, no tools can achieve a universally good performance for all domains, including HPV and nor do they provide confidence levels for their decisions. Here, we describe ensembled support vector machines (SVMs) to classify HPV risk types, which assign given proteins into high-, possibly high-, or low-risk type based on their confidence level. Our approach uses protein secondary structures to obtain the differential contribution of subsequences for the risk type, and SVM classifiers are combined with a simple but efficient string kernel to handle HPV protein sequences. In the experiments, we compare our approach with previous methods in accuracy and F1-score, and present the predictions for unknown HPV types, which provides promising results. PMID:19185855

Kim, Sun; Kim, Jeongmi; Zhang, Byoung-Tak

2009-02-01

300

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

PubMed

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

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

2015-01-01

301

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

PubMed Central

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

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

2013-01-01

302

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

PubMed Central

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

Weber, Jeffrey K.; Pande, Vijay S.

2013-01-01

303

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

PubMed Central

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

Zou, Ye; Ma, Gang

2014-01-01

304

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

NASA Astrophysics Data System (ADS)

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

Weber, Jeffrey K.; Pande, Vijay S.

2013-09-01

305

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

SciTech Connect

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

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

2012-05-02

306

Global Analysis of the RNA-Protein Interaction and RNA Secondary Structure Landscapes of the Arabidopsis Nucleus.  

PubMed

Posttranscriptional regulation in eukaryotes requires cis- and trans-acting features and factors including RNA secondary structure and RNA-binding proteins (RBPs). However, a comprehensive view of the structural and RBP interaction landscape of nuclear RNAs has yet to be compiled for any organism. Here, we use our ribonuclease-mediated structure and RBP-binding site mapping approaches to globally profile these features in Arabidopsis seedling nuclei invivo. We reveal anticorrelated patterns of secondary structure and RBP binding throughout nuclear mRNAs that demarcate sites of alternative splicing and polyadenylation. We also uncover a collection of protein-bound sequence motifs, and identify their structural contexts, co-occurrences in transcripts encoding functionally related proteins, and interactions with putative RBPs. Finally, using these motifs, we find that the chloroplast RBP CP29A also interacts with nuclear mRNAs. In total, we provide a simultaneous view of the RNA secondary structure and RBP interaction landscapes in a eukaryotic nucleus. PMID:25557549

Gosai, Sager J; Foley, Shawn W; Wang, Dongxue; Silverman, Ian M; Selamoglu, Nur; Nelson, Andrew D L; Beilstein, Mark A; Daldal, Fevzi; Deal, Roger B; Gregory, Brian D

2015-01-22

307

Scoping the Duals: Structural Challenges of Combining Further and Higher Education in Post-Secondary Institutions  

ERIC Educational Resources Information Center

Dual sector universities (or duals) are a growing international phenomenon that cut across the divide that typically exists in post-secondary education. Duals combine "further" and "higher" education within a single institution providing enhanced opportunities for student transition between post-secondary sectors. This paper reports the results of

Garrod, Neil; Macfarlane, Bruce

2007-01-01

308

Characterization of the secondary structure of calmodulin in complex with a calmodulin-binding domain peptide  

SciTech Connect

The interaction between calcium-saturated chicken calmodulin and a peptide corresponding to the calmodulin-binding domain of the chicken smooth muscle myosin light chain kinase has been studied by multinuclear and multidimensional nuclear magnetic resonance methods. Extensive {sup 1}H and {sup 15}N resonance assignments of calmodulin in the complex have been obtained from the analysis of two- and three-dimensional nuclear magnetic resonance spectra. The assignment of calmodulin in the complex was facilitated by the use of selective labeling of the protein with {alpha}-{sup 15}N-labeled valine, alanine, lysine, leucine, and glycine. These provided reference points during the main-chain-directed analysis of three-dimensional spectra of complexes prepared with uniformly {sup 15}N-labeled calmodulin. The pattern of nuclear Overhauser effects (NOE) seen among main-chain amide NH, C{sub {alpha}}H, and C{sub {beta}}H hydrogens indicates that the secondary structure of the globular domains of calmodulin in the complex closely corresponds to that observed in the calcium-saturated state of the protein in the absence of bound peptide. However, the backbone conformation of residues 76-84 adopts an extended chain conformation upon binding of the peptide in contrast to its helical conformation in the absence of peptide. A sufficient number of NOEs between the globular domains of calmodulin and the bound peptide have been found to indicate that the N- and C-terminal regions of the peptide interact with the C- and N-terminal domains of calmodulin, respectively. The significance of these results are discussed in terms of recently proposed models for the structure of calmodulin-peptide complexes.

Roth, S.M.; Schneider, D.M.; Strobel, L.A.; Wand, A.J. (Inst. for Cancer Research, Philadelphia, PA (United States) Univ. of Illinois, Urbana (United States)); Van Berkum, M.F.A.; Means, A.R. (Baylor Coll., Houston, TX (United States))

1992-02-11

309

Carbon nanotubes induce secondary structure changes of bovine albumin in aqueous phase.  

PubMed

Interaction of nanomaterials to protein molecules is one of the most important issues to deeply understand the influences of the nanomaterials upon physiological processes and protein functions. So far most of investigations focused on the protein molecules adsorbed on the nanomaterials surface, less is known about those in the aqueous phase (not absorbed). In this work, luminescent spectroscopy analysis, circular dichroism measurement, atomic force microscopy, matrix-assisted laser desorption/ionization time of flight mass spectrometry, isoelectric focusing and sulfate polyacrylamide gel electrophoresis were used to investigate the influence of oxidized water-soluble multiwalled carbon nanotubes (CNT) dispersing in aqueous solution upon the structures of bovine serum albumin (BSA) through co-incubation. We focused on BSA molecules that stayed in the aqueous phase instead of those adsorbed by CNT. Experimental results show that the fractions of beta-sheet decreased from 33.3% to 29.8% and beta-turn increased from 2% to 5% in reference with native BSA. There was a slight increase of alpha-helix and a slight reduction of random coil. BSA molecules that had been encountered with CNT and were left in the solution formed a loose and flatten morphology on graphite substrates instead of their native tight and round morphology observed by AFM. The value of isoelectric point for BSA after exposed to CNT moved towards to a higher pH position compared with native BSA. All together, it was concluded that the oxidized water-soluble multiwalled carbon nanotubes not only adsorb bovine serum albumin molecules to their surface, but also induces albumin molecules in the aqueous solution undergo secondary structure changes, which lead to a conformation change. PMID:21137980

Yang, Man; Meng, Jie; Mao, Xiaobo; Yang, Yang; Cheng, Xuelian; Yuan, Hui; Wang, Chen; Xu, Haiyan

2010-11-01

310

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

SciTech Connect

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

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

2010-10-22

311

Formation of secondary Moir patterns for characterization of nanoporous alumina structures in multiple domains with different orientations  

NASA Astrophysics Data System (ADS)

We first report the formation of secondary Moir patterns from electron Moir fringes to characterize nanostructures in multiple domains with different orientations. The pitches and the orientations of the nanoporous alumina arrays in several domains are simultaneously measured using only one electron Moir image.We first report the formation of secondary Moir patterns from electron Moir fringes to characterize nanostructures in multiple domains with different orientations. The pitches and the orientations of the nanoporous alumina arrays in several domains are simultaneously measured using only one electron Moir image. Electronic supplementary information (ESI) available: Rotation directions of the secondary Moir fringes on the nanoporous alumina structure. See DOI: 10.1039/c3nr34042b

Wang, Qinghua; Kishimoto, Satoshi; Jiang, Xiangfen; Yamauchi, Yusuke

2013-02-01

312

Sequence based residue depth prediction using evolutionary information and predicted secondary structure  

PubMed Central

Background Residue depth allows determining how deeply a given residue is buried, in contrast to the solvent accessibility that differentiates between buried and solvent-exposed residues. When compared with the solvent accessibility, the depth allows studying deep-level structures and functional sites, and formation of the protein folding nucleus. Accurate prediction of residue depth would provide valuable information for fold recognition, prediction of functional sites, and protein design. Results A new method, RDPred, for the real-value depth prediction from protein sequence is proposed. RDPred combines information extracted from the sequence, PSI-BLAST scoring matrices, and secondary structure predicted with PSIPRED. Three-fold/ten-fold cross validation based tests performed on three independent, low-identity datasets show that the distance based depth (computed using MSMS) predicted by RDPred is characterized by 0.67/0.67, 0.66/0.67, and 0.64/0.65 correlation with the actual depth, by the mean absolute errors equal 0.56/0.56, 0.61/0.60, and 0.58/0.57, and by the mean relative errors equal 17.0%/16.9%, 18.2%/18.1%, and 17.7%/17.6%, respectively. The mean absolute and the mean relative errors are shown to be statistically significantly better when compared with a method recently proposed by Yuan and Wang [Proteins 2008; 70:509516]. The results show that three-fold cross validation underestimates the variability of the prediction quality when compared with the results based on the ten-fold cross validation. We also show that the hydrophilic and flexible residues are predicted more accurately than hydrophobic and rigid residues. Similarly, the charged residues that include Lys, Glu, Asp, and Arg are the most accurately predicted. Our analysis reveals that evolutionary information encoded using PSSM is characterized by stronger correlation with the depth for hydrophilic amino acids (AAs) and aliphatic AAs when compared with hydrophobic AAs and aromatic AAs. Finally, we show that the secondary structure of coils and strands is useful in depth prediction, in contrast to helices that have relatively uniform distribution over the protein depth. Application of the predicted residue depth to prediction of buried/exposed residues shows consistent improvements in detection rates of both buried and exposed residues when compared with the competing method. Finally, we contrasted the prediction performance among distance based (MSMS and DPX) and volume based (SADIC) depth definitions. We found that the distance based indices are harder to predict due to the more complex nature of the corresponding depth profiles. Conclusion The proposed method, RDPred, provides statistically significantly better predictions of residue depth when compared with the competing method. The predicted depth can be used to provide improved prediction of both buried and exposed residues. The prediction of exposed residues has implications in characterization/prediction of interactions with ligands and other proteins, while the prediction of buried residues could be used in the context of folding predictions and simulations. PMID:18803867

Zhang, Hua; Zhang, Tuo; Chen, Ke; Shen, Shiyi; Ruan, Jishou; Kurgan, Lukasz

2008-01-01

313

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

SciTech Connect

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

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

1991-11-19

314

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

Microsoft Academic Search

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

K. M. Kjer

1995-01-01

315

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

PubMed

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

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

2014-01-29

316

Identification and characterization of a sequence motif involved in nonsense-mediated mRNA decay.  

PubMed

In both prokaryotes and eukaryotes, nonsense mutations in a gene can enhance the decay rate or reduce the abundance of the mRNA transcribed from that gene, and we call this process nonsense-mediated mRNA decay. We have been investigating the cis-acting sequences involved in this decay pathway. Previous experiments have demonstrated that, in addition to a nonsense codon, specific sequences 3' of a nonsense mutation, which have been defined as downstream elements, are required for mRNA destabilization. The results presented here identify a sequence motif (TGYYGATGYYYYY, where Y stands for either T or C) that can predict regions in genes that, when positioned 3' of a nonsense codon, promote rapid decay of its mRNA. Sequences harboring two copies of the motif from five regions in the PGK1, ADE3, and HIS4 genes were able to function as downstream elements. In addition, four copies of this motif can function as an independent downstream element. The sequences flanking the motif played a more significant role in modulating its activity when fewer copies of the sequence motif were present. Our results indicate the sequences 5' of the motif can modulate its activity by maintaining a certain distance between the sequence motif and the termination codon. We also suggest that the sequences 3' of the motif modulate the activity of the downstream element by forming RNA secondary structures. Consistent with this view, a stem-loop structure positioned 3' of the sequence motif can enhance the activity of the downstream element. This sequence motif is one of the few elements that have been identified that can predict regions in genes that can be involved in mRNA turnover. The role of these sequences in mRNA decay is discussed. PMID:7891717

Zhang, S; Ruiz-Echevarria, M J; Quan, Y; Peltz, S W

1995-04-01

317

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

PubMed

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

Yan, Jing; Marcus, Max; Kurgan, Lukasz

2014-01-01

318

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

PubMed Central

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

2014-01-01

319

Bovine filensin possesses primary and secondary structure similarity to intermediate filament proteins  

PubMed Central

The cDNA coding for calf filensin, a membrane-associated protein of the lens fiber cells, has been cloned and sequenced. The predicted 755- amino acid-long open reading frame shows primary and secondary structure similarity to intermediate filament (IF) proteins. Filensin can be divided into an NH2-terminal domain (head) of 38 amino acids, a middle domain (rod) of 279 amino acids, and a COOH-terminal domain (tail) of 438 amino acids. The head domain contains a di- arginine/aromatic amino acid motif which is also found in the head domains of various intermediate filament proteins and includes a potential protein kinase A phosphorylation site. By multiple alignment to all known IF protein sequences, the filensin rod, which is the shortest among IF proteins, can be subdivided into three subdomains (coils 1a, 1b, and 2). A 29 amino acid truncation in the coil 2 region accounts for the smaller size of this domain. The filensin tail contains 6 1/2 tandem repeats which match analogous motifs of mammalian neurofilament M and H proteins. We suggest that filensin is a novel IF protein which does not conform to any of the previously described classes. Purified filensin fails to form regular filaments in vitro (Merdes, A., M. Brunkener, H. Horstmann, and S. D. Georgatos. 1991. J. Cell Biol. 115:397-410), probably due to the missing segment in the coil 2 region. Participation of filensin in a filamentous network in vivo may be facilitated by an assembly partner. PMID:8491777

1993-01-01

320

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

PubMed

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

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

2015-02-18

321

Characterizing the Secondary Protein Structure of Black Widow Dragline Silk Using Solid-State NMR & X-ray Diffraction  

PubMed Central

This study provides a detailed secondary structural characterization of major ampullate dragline silk from Latrodectus hesperus (black widow) spiders. X-ray diffraction results show that the structure of black widow major ampullate silk fibers is comprised of stacked ?-sheet nanocrystallites oriented parallel to the fiber axis and an amorphous region with oriented (anisotropic) and isotropic components. The combination of two-dimensional (2D) 13C-13C through-space and through-bond solid-state NMR experiments provide chemical shifts that are used to determine detailed information about amino acid motif secondary structure in black widow spider dragline silk. Individual amino acids are incorporated into different repetitive motifs that make up the majority of this protein-based biopolymer. From the solid-state NMR measurements, we assign distinct secondary conformations to each repetitive amino acid motif and hence to the amino acids that make up the motifs. Specifically, alanine is incorporated in ?-sheet (poly(Alan) and poly(Gly-Ala)), 31-helix (poly(Gly-Gly-Xaa), and ?-helix (poly(Gln-Gln-Ala-Tyr)) components. Glycine is determined to be in ?-sheet (poly(Gly-Ala)) and 31-helical (poly(Gly-Gly-Xaa)) regions, while serine is present in ?-sheet (poly(Gly-Ala-Ser)), 31-helix (poly(Gly-Gly-Ser)), and ?-turn (poly(Gly-Pro-Ser)) structures. These various motif-specific secondary structural elements are quantitatively correlated to the primary amino acid sequence of major ampullate spidroin 1 and 2 (MaSp1 and MaSp2) and are shown to form a self-consistent model for black widow dragline silk. PMID:24024617

Jenkins, Janelle E.; Sampath, Sujatha; Butler, Emily; Kim, Jihyun; Henning, Robert W.; Holland, Gregory P.; Yarger, Jeffery L.

2013-01-01

322

Characterizing the secondary protein structure of black widow dragline silk using solid-state NMR and X-ray diffraction.  

PubMed

This study provides a detailed secondary structural characterization of major ampullate dragline silk from Latrodectus hesperus (black widow) spiders. X-ray diffraction results show that the structure of black widow major ampullate silk fibers is comprised of stacked ?-sheet nanocrystallites oriented parallel to the fiber axis and an amorphous region with oriented (anisotropic) and isotropic components. The combination of two-dimensional (2D) (13)C-(13)C through-space and through-bond solid-state NMR experiments provide chemical shifts that are used to determine detailed information about the amino acid motif secondary structure in black widow spider dragline silk. Individual amino acids are incorporated into different repetitive motifs that make up the majority of this protein-based biopolymer. From the solid-state NMR measurements, we assign distinct secondary conformations to each repetitive amino acid motif and, hence, to the amino acids that make up the motifs. Specifically, alanine is incorporated in ?-sheet (poly(Alan) and poly(Gly-Ala)), 3(1)-helix (poly(Gly-Gly-Xaa), and ?-helix (poly(Gln-Gln-Ala-Tyr)) components. Glycine is determined to be in ?-sheet (poly(Gly-Ala)) and 3(1)-helical (poly(Gly-Gly-X(aa))) regions, while serine is present in ?-sheet (poly(Gly-Ala-Ser)), 3(1)-helix (poly(Gly-Gly-Ser)), and ?-turn (poly(Gly-Pro-Ser)) structures. These various motif-specific secondary structural elements are quantitatively correlated to the primary amino acid sequence of major ampullate spidroin 1 and 2 (MaSp1 and MaSp2) and are shown to form a self-consistent model for black widow dragline silk. PMID:24024617

Jenkins, Janelle E; Sampath, Sujatha; Butler, Emily; Kim, Jihyun; Henning, Robert W; Holland, Gregory P; Yarger, Jeffery L

2013-10-14

323

Structural characterization of genes corresponding to cotton fiber mRNA, E6: reduced E6 protein in transgenic plants by antisense gene  

Microsoft Academic Search

Two genes, each corresponding to fiber mRNA E6, were isolated from cotton cultivars Coker 312 (Gossypium hirsutum L.) and Sea Island (G. barbadense L.). E6 is one of the predominant fiber-specific mRNAs present during early fiber development. The distinguishing feature of the nucleotide-derived E6 protein is the presence of a motif where a dimer, Ser-Gly, is repeated several times. Two

Maliyakal E. John

1996-01-01

324

Secondary amenorrhea  

MedlinePLUS

Amenorrhea - secondary; No periods - secondary; Absent periods - secondary; Absent menses - secondary; Absence of periods - secondary ... In addition to having no menstrual periods, other symptoms can ... gain or weight loss Discharge from the breast ( galactorrhea ) or ...

325

STRUCTURAL AND GEOCHEMICAL CHARACTERISTICS OF SECONDARY DOLOMITIC BODIES OF CRETACEOUS COLIMA-JALISCO BASIN, WESTERN MEXICO  

NASA Astrophysics Data System (ADS)

The cretaceous Colima-Jalisco basin, at western Mexico, is characterized by the development of volcano sedimentary sequences belonging to the Late Jurassic-Early Cretaceous Alisitos-Teloloapan arc-island and the formation of volcanogenic massive sulphide deposits ("El Cuale", "La Minita", "Talpa de Allende"). Some bodies of dolomite have been described and have been classified into two groups in accordance with its secondary origin: sabkha (diagenetic) and hydrothermal. In both cases the primary dolomitized limestone belongs to the reef facies of the Tepalcatepec Formation (TF) of Albian-Cenomanian characterized by the next geochemical content: MgO (0.42%), CaO (53.7%), SiO2 (0.15%), Pb (140 ppm) and Zn (50 ppm). Diagenetical dolomite is characterized by an stratiform body and its contacts are consistent with the structural attitude of TF to which it belongs. In the dolomites formed by hydrothermal replacement process is limited by faults and fractures, thus its morphology is irregular and their contacts are discordant, adopting domic or columnar forms. Occasionally hydrothermal dolomite can be associated with concentrations of lead, zinc, silver and barite. The dolomitic body called "Cerro El Puro", (19 3.7' N; 103 36.7' W), located at 20 km SE 30 from Colima City, consists in a carbonate horizon of 300 m thick and over 5 km in length and is consistent with the structural attitude (N30W; NE50) of the southwestern flank of the syncline Tepames-Amarradero, in which southeast extreme an evaporitic stratiform deposits. The dolomite of this body is of ankeritic type, hence its typical light reddish brown. The geochemical content is shown on Table 1. After the structural and geochemical features of this dolomite, it is classified as sabkha with a diagenetic origin. The other dolomitic outcrop studied is called Cerro Bola (1854'N; 10347.5'W) which is located 40 km S10W from Colima City, and consists of a single dolomitic outcrop, black in color, that covers an area of 600 x 400 m, which in its northwest corner shows a remnant of limestone reef without dolomitization. It should be mentioned that the name of this outcrop is due to its characteristic rounded topographic profile. This outcrop is affected by a fracture system whose attitudes are: N6OE, vertical dip; N35W, NE50 to vertical dip; N7-20-33E; SE75 to vertical dip. Locally, quartz crystals (rock crystal), are observed hosted by millimetric druses, or covering the plans of some fractures. At least 400 m southeast of this outcrop, is located a deposit of baryte. Structurally Cerro Bola outcrop is located in a tilted block and the geochemical content is shown on Table 2. Due to their structural and geochemical characteristics, is considered formed by a hydrothermal process, which concentrated the metals existing in the limestone reef.Table 1. Geochemical content "Cerro El Puro" dolomite. Table 2. Geochemical content of "Cerro Bola" dolomite

Zarate, P. F.

2009-12-01

326

Phylogenetic conservation of RNA secondary and tertiary structure in the trpEDCFBA operon leader transcript in Bacillus.  

PubMed

Expression of the trpEDCFBA operon of Bacillus subtilis is regulated by transcription attenuation and translation control mechanisms. We recently determined that the B. subtilis trp leader readthrough transcript can adopt a Mg(2+)-dependent tertiary structure that appears to interfere with TRAP-mediated translation control of trpE. In the present study, sequence comparisons to trp leaders from three other Bacillus sp. were made, suggesting that RNA secondary and tertiary structures are phylogenetically conserved. To test this hypothesis, experiments were carried out with the trp leader transcript from Bacillus stearothermophilus. Structure mapping experiments confirmed the predicted secondary structure. Native gel experiments identified a faster mobility species in the presence of Mg(2+), suggesting that a Mg(2+)-dependent tertiary structure forms. Mg(2+)-dependent protection of residues within the first five triplet repeats of the TRAP binding target and a pyrimidine-rich internal loop were observed, consistent with tertiary structure formation between these regions. Structure mapping in the presence of a competitor DNA oligonucleotide allowed the interacting partners to be identified as a single-stranded portion of the purine-rich TRAP binding target and the large downstream pyrimidine-rich internal loop. Thermal denaturation experiments revealed a Mg(2+)- and pH-dependent unfolding transition that was absent for a transcript missing the first five triplet repeats. The stability of several mutant transcripts allowed a large portion of the base-pairing register for the tertiary interaction to be determined. These data indicate that RNA secondary and tertiary structures involved in TRAP-mediated translation control are conserved in at least four Bacillus species. PMID:14624006

Schaak, Janell E; Babitzke, Paul; Bevilacqua, Philip C

2003-12-01

327

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

PubMed Central

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

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

2013-01-01

328

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

SciTech Connect

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

Tsuboi, Yasuyuki; Goto, Masaharu; Itaya, Akira

2001-06-15

329

a High Efficiency Dye-Sensitized Solar Cell with NANO-TiO2 Secondary Structure in the Photoanode  

NASA Astrophysics Data System (ADS)

A high efficiency dye-sensitized solar cell (DSC) with nanocrystallite TiO2 (nano-TiO2) secondary structure in the photoanode was successfully fabricated via a simple one step doctor blade printing method with a special nano-TiO2 paste containing micro-sized nano-TiO2 aggregates formed in situ. The special secondary structure in the photoanode shows improved optical absorption, increased light scattering ability, and enhanced electron transport and collection efficiency, resulting in high power conversion efficiency of 7.30% with 6 ?m thin nano-TiO2 film in the photoanode, and the highest value of 9.28% by increasing the thickness of the nano-TiO2 film to 11 ?m.

Lan, Zhang; Wu, Jihuai; Lin, Jianming; Huang, Miaoliang

2013-04-01

330

Controlling nucleic acid secondary structure by intercalation: effects of DNA strand length on coralyne-driven duplex disproportionation  

PubMed Central

Small molecules that intercalate in DNA and RNA are powerful agents for controlling nucleic acid structural transitions. We recently demonstrated that coralyne, a small crescent-shaped molecule, can cause the complete and irreversible disproportionation of duplex poly(dA)poly(dT) into triplex poly(dA)poly(dT)poly(dT) and a poly(dA) self- structure. Both DNA secondary structures that result from duplex disproportionation are stabilized by coralyne intercalation. In the present study, we show that the kinetics and thermodynamics of coralyne-driven duplex disproportionation strongly depend on oligonucleotide length. For example, disproportionation of duplex (dA)16(dT)16 by coralyne reverts over the course of hours if the sample is maintained at 4C. Coralyne-disproportioned (dA)32 (dT)32, on the other hand, only partially reverts to the duplex state over the course of days at the same temperature. Furthermore, the equilibrium state of a (dA)16(dT)16 sample in the presence of coralyne at room temperature contains three different secondary structures [i.e. duplex, triplex and the (dA)16 self-structure]. Even the well-studied process of triplex stabilization by coralyne binding is found to be a length-dependent phenomenon and more complicated than previously appreciated. Together these observations indicate that at least one secondary structure in our nucleic acid system [i.e. duplex, triplex or (dA)n self-structure] binds coralyne in a length-dependent manner. PMID:12888521

Jain, Swapan S.; Polak, Matja; Hud, Nicholas V.

2003-01-01

331

Thermal denaturation of yeast alcohol dehydrogenase and protection of secondary and tertiary structural changes by sugars: CD and fluorescence studies  

Microsoft Academic Search

The present communication reports on changes in the secondary and tertiary structures of native and apo-yeast alcohol dehydrogenase upon heating at 50C, as evident from circular dichroism (CD) studies. The presence of sugars provided significant protection with trehalose being the most effective. Exposure of hydrophobic clusters in the protein molecule upon heat denaturation was confirmed by fluorescence studies using 1-anilinonaphthalene-8-sulfonate

Mehran Miroliaei; B. Ranjbar; H. Naderi-Manesh; Mohsen Nemat-Gorgani

2007-01-01

332

Primary and secondary structure analyses of the rDNA group-I introns of the Zygnematales (Charophyta)  

Microsoft Academic Search

The Zygnematales (Charophyta) contain a group-I intron (subgroup ICl) within their nuclear-encoded small subunit ribosomal DNA (SSU rDNA) coding region. This intron, which is inserted after position 1506 (relative to the SSU rDNA ofEscherichia coli), is proposed to have been vertically inherited since the origin of the Zygnematales approximately 350400 million years ago. Primary and secondary structure analyses were carried

Debashish Bhattacharya; Simon Damberger; Barbara Surek; Michael Melkonian

1996-01-01

333

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

Microsoft Academic Search

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

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

1992-01-01

334

Secondary structure models of D2-D3 expansion segments of 28S rRNA for Hoplolaiminae species  

PubMed Central

The D2-D3 expansion segments of the 28S ribosomal RNA (rRNA) were sequenced and compared to predict secondary structures for Hoplolaiminae species based on free energy minimization and comparative sequence analysis. The free energy based prediction method provides putative stem regions within primary structure and these base pairings in stems were confirmed manually by compensatory base changes among closely and distantly related species. Sequence differences ranged from identical between Hoplolaimus columbus and H. seinhorsti to 20.8% between Scutellonema brachyurum and H. concaudajuvencus. The comparative sequence analysis and energy minimization method yielded 9 stems in the D2 and 6 stems in the D3 which showed complete or partial compensatory base changes. At least 75% of nucleotides in the D2 and 68% of nucleotides in the D3 were related with formation of base pairings to maintain secondary structure. GC contents in stems ranged from 61 to 73% for the D2 and from 64 to 71% for the D3 region. These ranges are higher than G-C contents in loops which ranged from 37 to 48% in the D2 and 33-45% in the D3. In stems, G-C/C-G base pairings were the most common in the D2 and the D3 and also non-canonical base pairs including AA and UU, CU/UC, and GA/AG occurred in stems. The predicted secondary model and new sequence alignment based on predicted secondary structures for the D2 and D3 expansion segments provide useful information to assign positional nucleotide homology and reconstruction of more reliable phylogenetic trees. PMID:22736859

C. H, Bae; Robbins, R. T.; Szalanski, A. L.

2010-01-01

335

Genomic HIV RNA Induces Innate Immune Responses through RIG-I-Dependent Sensing of Secondary-Structured RNA  

PubMed Central

Background Innate immune responses have recently been appreciated to play an important role in the pathogenesis of HIV infection. Whereas inadequate innate immune sensing of HIV during acute infection may contribute to failure to control and eradicate infection, persistent inflammatory responses later during infection contribute in driving chronic immune activation and development of immunodeficiency. However, knowledge on specific HIV PAMPs and cellular PRRs responsible for inducing innate immune responses remains sparse. Methods/Principal Findings Here we demonstrate a major role for RIG-I and the adaptor protein MAVS in induction of innate immune responses to HIV genomic RNA. We found that secondary structured HIV-derived RNAs induced a response similar to genomic RNA. In primary human peripheral blood mononuclear cells and primary human macrophages, HIV RNA induced expression of IFN-stimulated genes, whereas only low levels of type I IFN and tumor necrosis factor ? were produced. Furthermore, secondary structured HIV-derived RNA activated pathways to NF-?B, MAP kinases, and IRF3 and co-localized with peroxisomes, suggesting a role for this organelle in RIG-I-mediated innate immune sensing of HIV RNA. Conclusions/Significance These results establish RIG-I as an innate immune sensor of cytosolic HIV genomic RNA with secondary structure, thereby expanding current knowledge on HIV molecules capable of stimulating the innate immune system. PMID:22235281

Berg, Randi K.; Melchjorsen, Jesper; Rintahaka, Johanna; Diget, Elisabeth; Sby, Stine; Horan, Kristy A.; Gorelick, Robert J.; Matikainen, Sampsa; Larsen, Carsten S.; Ostergaard, Lars; Paludan, Sren R.; Mogensen, Trine H.

2012-01-01

336

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

SciTech Connect

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

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

1991-06-04

337

Secondary structure determination by NMR spectroscopy of an immunoglobulin-like domain from the giant muscle protein titin.  

PubMed

We present the complete 15N and 1H NMR assignment and the secondary structure of an immunoglobulin-like domain from the giant muscle protein titin. The assignment was obtained using homonuclear and 15N heteronuclear 2D and 3D experiments. The complementarity of 3D TOCSY-NOESY and 3D 15N NOESY-HSQC experiments, using WATERGATE for water suppression, allowed an efficient assignment of otherwise ambiguous cross peaks and was helpful in overcoming poor TOCSY transfer for some amino acids. The secondary structure is derived from specific NOEs between backbone alpha- and amide protons, secondary chemical shifts of alpha-protons and chemical exchange for the backbone amide protons. It consists of eight beta-strands, forming two beta-sheets with four strands each, similar to the classical beta-sandwich of the immunoglobulin superfamily, as previously predicted by sequence analysis. Two of the beta-strands are connected by type II beta-turns; the first beta-strand forms a beta-bulge. The whole topology is very similar to the only intracellular immunoglobulin-like domain for which a structure has been determined so far, i.e., telokin. PMID:7663142

Pfuhl, M; Gautel, M; Politou, A S; Joseph, C; Pastore, A

1995-07-01

338

Disruptive mRNA folding increases translational efficiency of catechol-O-methyltransferase variant  

PubMed Central

Catechol-O-methyltransferase (COMT) is a major enzyme controlling catecholamine levels that plays a central role in cognition, affective mood and pain perception. There are three common COMT haplotypes in the human population reported to have functional effects, divergent in two synonymous and one nonsynonymous position. We demonstrate that one of the haplotypes, carrying the non-synonymous variation known to code for a less stable protein, exhibits increased protein expression in vitro. This increased protein expression, which would compensate for lower protein stability, is solely produced by a synonymous variation (C166T) situated within the haplotype and located in the 5? region of the RNA transcript. Based on mRNA secondary structure predictions, we suggest that structural destabilization near the start codon caused by the T allele could be related to the observed increase in COMT expression. Our folding simulations of the tertiary mRNA structures demonstrate that destabilization by the T allele lowers the folding transition barrier, thus decreasing the probability of occupying its native state. These data suggest a novel structural mechanism whereby functional synonymous variations near the translation initiation codon affect the translation efficiency via entropy-driven changes in mRNA dynamics and present another example of stable compensatory genetic variations in the human population. PMID:21486747

Tsao, Douglas; Shabalina, Svetlana A.; Gauthier, Jose; Dokholyan, Nikolay V.; Diatchenko, Luda

2011-01-01

339

Sequences of three molluscan 5 S ribosomal RNAs confirm the validity of a dynamic secondary structure model.  

PubMed Central

The collection of known 5 S rRNA primary structures is enriched with the sequences from three mollusca, the snails Helix pomatia and Arion rufus, and the mussel Mytilus edulis. The three sequences can be fitted in a five-helix secondary structure model previously shown (De Wachter et al. (1982) Biochimie 64, 311-329) to apply to all 5 S RNAs regardless of their origin. One of the helices in this model can undergo a bulge-internal loop transition. Within the metazoan kingdom, the dimensions of each helix and loop are rigidly conserved, except for one helix which can comprise either 6 or 7 base pairs. PMID:7133995

Fang, B L; De Baere, R; Vandenberghe, A; De Wachter, R

1982-01-01

340

Sequences of three molluscan 5 S ribosomal RNAs confirm the validity of a dynamic secondary structure model.  

PubMed

The collection of known 5 S rRNA primary structures is enriched with the sequences from three mollusca, the snails Helix pomatia and Arion rufus, and the mussel Mytilus edulis. The three sequences can be fitted in a five-helix secondary structure model previously shown (De Wachter et al. (1982) Biochimie 64, 311-329) to apply to all 5 S RNAs regardless of their origin. One of the helices in this model can undergo a bulge-internal loop transition. Within the metazoan kingdom, the dimensions of each helix and loop are rigidly conserved, except for one helix which can comprise either 6 or 7 base pairs. PMID:7133995

Fang, B L; De Baere, R; Vandenberghe, A; De Wachter, R

1982-08-11

341

Towards 3D structure prediction of large RNA molecules: an integer programming framework to insert local 3D motifs in RNA secondary structure  

PubMed Central

Motivation: The prediction of RNA 3D structures from its sequence only is a milestone to RNA function analysis and prediction. In recent years, many methods addressed this challenge, ranging from cycle decomposition and fragment assembly to molecular dynamics simulations. However, their predictions remain fragile and limited to small RNAs. To expand the range and accuracy of these techniques, we need to develop algorithms that will enable to use all the structural information available. In particular, the energetic contribution of secondary structure interactions is now well documented, but the quantification of non-canonical interactionsthose shaping the tertiary structureis poorly understood. Nonetheless, even if a complete RNA tertiary structure energy model is currently unavailable, we now have catalogues of local 3D structural motifs including non-canonical base pairings. A practical objective is thus to develop techniques enabling us to use this knowledge for robust RNA tertiary structure predictors. Results: In this work, we introduce RNA-MoIP, a program that benefits from the progresses made over the last 30 years in the field of RNA secondary structure prediction and expands these methods to incorporate the novel local motif information available in databases. Using an integer programming framework, our method refines predicted secondary structures (i.e. removes incorrect canonical base pairs) to accommodate the insertion of RNA 3D motifs (i.e. hairpins, internal loops and k-way junctions). Then, we use predictions as templates to generate complete 3D structures with the MC-Sym program. We benchmarked RNA-MoIP on a set of 9 RNAs with sizes varying from 53 to 128 nucleotides. We show that our approach (i) improves the accuracy of canonical base pair predictions; (ii) identifies the best secondary structures in a pool of suboptimal structures; and (iii) predicts accurate 3D structures of large RNA molecules. Availability: RNA-MoIP is publicly available at: http://csb.cs.mcgill.ca/RNAMoIP. Contact: jeromew@cs.mcgill.ca PMID:22689763

Reinharz, Vladimir; Major, Franois; Waldisphl, Jrme

2012-01-01

342

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

PubMed Central

Transfer of genetic information from genes into proteins is mediated by messenger RNA (mRNA) that must be first recruited to ribosomal pre-initiation complexes (PICs) by a mechanism that is still poorly understood. Recent studies showed that besides eIF4F and poly(A)-binding protein, eIF3 also plays a critical role in this process, yet the molecular mechanism of its action is unknown. We showed previously that the PCI domain of the eIF3c/NIP1 subunit of yeast eIF3 is involved in RNA binding. To assess the role of the second PCI domain of eIF3 present in eIF3a/TIF32, we performed its mutational analysis and identified a 10-Ala-substitution (Box37) that severely reduces amounts of model mRNA in the 4348S PICs in vivo as the major, if not the only, detectable defect. Crystal structure analysis of the a/TIF32-PCI domain at 2.65- resolution showed that it is required for integrity of the eIF3 core and, similarly to the c/NIP1-PCI, is capable of RNA binding. The putative RNA-binding surface defined by positively charged areas contains two Box37 residues, R363 and K364. Their substitutions with alanines severely impair the mRNA recruitment step in vivo suggesting that a/TIF32-PCI represents one of the key domains ensuring stable and efficient mRNA delivery to the PICs. PMID:24423867

Khoshnevis, Sohail; Guniov, Stanislava; Vl?kov, Vladislava; Kouba, Tom; Neumann, Piotr; Beznoskov, Petra; Ficner, Ralf; Valek, Leo Shivaya

2014-01-01

343

STRUCTURAL CHARACTERIZATION OF REACTIVE DYES USING SECONDARY ION MASS SPECTROMETRY/TANDEM MASS SPECTROMETRY  

EPA Science Inventory

Reactive Blue 19 (RB 19), its reactive form (RB 19-VS) and its hydrolyzed form, (RB 19-OH) were examined using liquid secondary ion mass spectrometry/tandem mass spectrometry (LSIMS/MS/MS) in the negative-ion mode under low-energy collision conditions (240-300 eV). tructurally ch...

344

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

PubMed Central

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

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

2014-01-01

345

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

ERIC Educational Resources Information Center

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

Lowe, Patricia A.; Lee, Steven W.

2008-01-01

346

Premature translation termination mediates triosephosphate isomerase mRNA degradation  

SciTech Connect

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

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

1988-02-01

347

Premature translation termination mediates triosephosphate isomerase mRNA degradation.  

PubMed Central

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

Daar, I O; Maquat, L E

1988-01-01

348

Complete sequence and secondary structure of the large subunit ribosomal RNA from the harmful unarmored dinoflagellate Akashiwo sanguinea.  

PubMed

This is the first report of the complete DNA sequence of the gene encoding the ribosomal large subunit (LSU rDNA, 3336 bp) from the naked gymnodinioid dinoflagellate Akashiwo sanguinea. No introns were found in the LSU rDNA coding region and secondary structures were predicted for both the LSU and 5.8S rRNAs. The predicted LSU structure showed most of the features seen in the consensus secondary structure model proposed for the eukaryotic nuclear LSU rRNAs. However, six helices (C1_1, C1_2, C1_3, D10, D20_1 and H1_2) are not present in the A. sanguinea LSU structure. Particularly, the C branch area (or D2 domain), was extremely reduced compared to the eukaryotic consensus sequence due to nucleotide deletion. Phylogenetic resolution against 12 divergent (D) domains and cores in LSU rDNA showed that the D1, D2 and D12 domains were highly variable and could be used as genetic markers within low taxonomic levels, particularly in the gymnodinioid complex. PMID:17364809

Ki, Jang-Seu; Han, Myung-Soo

2007-02-01

349

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

E-print Network

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

Einert, Thomas R; Netz, Roland R

2011-01-01

350

Neighboring residue effects in terminally blocked dipeptides: implications for residual secondary structures in intrinsically unfolded/disordered proteins.  

PubMed

For nuclear magnetic resonance (NMR)-based protein structure determinations, the random coil chemical shifts are very important because the secondary and tertiary protein structure predictions become possible by examining deviations of measured chemical shifts from those reference chemical shift values. In addition, neighboring residue effects on chemical shifts and J-coupling constants are crucial in understanding the nature of conformational propensities exhibited by unfolded or intrinsically disordered proteins. We recently reported the 1D NMR results for a complete set of terminally blocked dipeptides (Oh KI, Jung YS, Hwang GS, Cho M. J Biomol NMR 2012;53:25-41), but the NMR resonance assignments were not possible so that the average chemical shifts and J-coupling constants were only considered. In the present work, to thoroughly investigate the neighboring residue effects and random coil chemical shifts we extend the previous studies with 2D NMR, and measured all the (3) J(HNH?) values and H(?) and H(N) chemical shifts of the same set of terminally blocked dipeptides that are free from structural effects like secondary structure, hydrogen-bond, long-range backbone, and side-chain interactions. In particular, the preceding and following residue effects on amino-acid backbone conformational propensities are revealed and directly compared with previous works on either short peptides or empirical chemical shift database. PMID:24453185

Jung, Young-Sang; Oh, Kwang-Im; Hwang, Geum-Sook; Cho, Minhaeng

2014-09-01

351

Flow Structure and Secondary Flows in Fine-grained Bifurcate Channels  

NASA Astrophysics Data System (ADS)

Bifurcations form vital nodes within many fluvio\\-deltaic channels and their stability is critical in determining long- term channel behavior. Although there are an increasing number of laboratory and numerical models detailing flow and morphology within such bifurcations, relatively few field studies exist on the nature of flow within such sites by which to test and validate these models. In particular, the presence and nature of any secondary flow cells is seen as central in controlling fluid and sediment partitioning within the bifurcation, and contributing to long term stability or instability. Here we present results of a field study in the Cumberland Marshes, Saskatchewan, Canada, which sought to document the mean flow fields and patterns of secondary flow at two asymmetric bifurcations within the Mossy River delta. The study used a Teledyne RDI 1200 kHz acoustic Doppler profiler to record three\\-dimensional flow velocities along a series of flow\\-transverse cross\\-sections within these bifurcations. These surveys document the partitioning of main downstream flow through the bifurcation and reveal that bed topographic forcing and secondary flows can be important processes as the flows divide at the bifurcation. These results will be discussed in relation to the functioning of bifurcations and their sediment transport pathways.

Best, J. L.; Parsons, D. R.; Bridge, J. S.; Edmonds, D. A.; Janesko, D.; Klein, F. E.; Slingerland, R. L.; Smith, N. D.

2007-12-01

352

Phylogenetic reconstruction using secondary structures of Internal Transcribed Spacer 2 (ITS2, rDNA): finding the molecular and morphological gap in Caribbean gorgonian corals  

Microsoft Academic Search

BACKGROUND: Most phylogenetic studies using current methods have focused on primary DNA sequence information. However, RNA secondary structures are particularly useful in systematics because they include characteristics, not found in the primary sequence, that give \\

Alejandro Grajales; Catalina Aguilar; Juan A Snchez

2007-01-01

353

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

NASA Astrophysics Data System (ADS)

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

Cheng, Guoxin; Liu, Lie

2011-03-01

354

Structure and mechanism of an inverting alkylsulfatase from Pseudomonas sp. DSM6611 specific for secondary alkyl sulfates.  

PubMed

A highly enantioselective and stereoselective secondary alkylsulfatase from Pseudomonas sp. DSM6611 (Pisa1) was heterologously expressed in Escherichia coli BL21, and purified to homogeneity for kinetic and structural studies. Structure determination of Pisa1 by X-ray crystallography showed that the protein belongs to the family of metallo-?-lactamases with a conserved binuclear Zn(2+) cluster in the active site. In contrast to a closely related alkylsulfatase from Pseudomonas aeruginosa (SdsA1), Pisa1 showed a preference for secondary rather than primary alkyl sulfates, and enantioselectively hydrolyzed the (R)-enantiomer of rac-2-octyl sulfate, yielding (S)-2-octanol with inversion of absolute configuration as a result of C-O bond cleavage. In order to elucidate the mechanism of inverting sulfate ester hydrolysis, for which no counterpart in chemical catalysis exists, we designed variants of Pisa1 guided by three-dimensional structure and docking experiments. In the course of these studies, we identified an invariant histidine (His317) near the sulfate-binding site as the general acid for crucial protonation of the sulfate leaving group. Additionally, amino acid replacements in the alkyl chain-binding pocket generated an enzyme variant that lost its stereoselectivity towards rac-2-octyl sulfate. These findings are discussed in light of the potential use of this enzyme family for applications in biocatalysis. PMID:23061549

Knaus, Tanja; Schober, Markus; Kepplinger, Bernhard; Faccinelli, Martin; Pitzer, Julia; Faber, Kurt; Macheroux, Peter; Wagner, Ulrike

2012-12-01

355

The compositional transition of vertebrate genomes: an analysis of the secondary structure of the proteins encoded by human genes.  

PubMed

Fluctuations and increments of both C(3) and G(3) levels along the human coding sequences were investigated comparing two sets of Xenopus/human orthologous genes. The first set of genes shows minor differences of the GC(3) levels, the second shows considerable increments of the GC(3) levels in the human genes. In both data sets, the fluctuations of C(3) and G(3) levels along the coding sequences correlated with the secondary structures of the encoded proteins. The human genes that underwent the compositional transition showed a different increment of the C(3) and G(3) levels within and among the structural units of the proteins. The relative synonymous codon usage (RSCU) of several amino acids were also affected during the compositional transition, showing that there exists a correlation between RSCU and protein secondary structures in human genes. The importance of natural selection for the formation of isochore organization of the human genome has been discussed on the basis of these results. PMID:15716110

D'Onofrio, Giuseppe; Ghosh, Tapash Chandra

2005-01-17

356

An overview of the secondary structure of the V4 region of eukaryotic small-subunit ribosomal RNA.  

PubMed Central

The V4 region of the small subunit (18S) ribosomal RNA was examined in 72 different sequences representing a broad sample eukaryotic diversity. This domain is the most variable region of the 18S rRNA molecule and ranges in length from ca. 230 to over 500 bases. Based upon comparative analysis, secondary structural models were constructed for all sequences and the resulting generalized model shows that most organisms possess seven helices for this region. The protists and two insects show from one to as many as four helices in addition to the above seven. In this report, we summarize secondary structure information presented elsewhere for the V4 region, describe the general features for helical and apical regions, and identify signature sequences useful in helix identification. Our model generally agrees with other current concepts; however, we propose modifications or alternative structures for the start of the V4 region, the large protist inserts, and the sector that may possibly contain a pseudoknot. PMID:2014163

Nickrent, D L; Sargent, M L

1991-01-01

357

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

NASA Astrophysics Data System (ADS)

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


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

2005-11-01

358

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

PubMed Central

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

2009-01-01

359

Structural characterization of the acid-degraded secondary cell wall polymer of Geobacillus stearothermophilus PV72\\/p2  

Microsoft Academic Search

The secondary cell wall polymer (SCWP) from Geobacillus stearothermophilus PV72\\/p2, which is involved in the anchoring of the surface-layer protein to the bacterial cell wall layer, is composed of 2-amino-2-deoxy- and 2-acetamido-2-deoxy-d-glucose, 2-acetamido-2-deoxy-d-mannose, and 2-acetamido-2-deoxy-d-mannuronic acid. The primary structure of the acid-degraded polysaccharideliberated by HF-treatment from the cell wallwas determined by high-field NMR spectroscopy and mass spectrometry using N-acetylated and

Bent O. Petersen; Margit Sra; Christoph Mader; Harald F. Mayer; Uwe B. Sleytr; Martin Pabst; Michael Puchberger; Eberhard Krause; Andreas Hofinger; Jens . Duus; Paul Kosma

2008-01-01

360

Fine structure of secondary granule inclusions in fowl heterophils after ruthenium tetroxide fixation.  

PubMed

Bone marrow from domestic fowls was initially fixed for electron microscopy in glutaraldehyde and post-fixed with either ruthenium tetroxide or osmium tetroxide. Inclusions with distinct outlines were revealed in the secondary granules of heterophil leucocytes after ruthenium tetroxide but not with osmium tetroxide fixation. In longitudinal orientation, these inclusions were rod-shaped and composed of microfilaments measuring 3.7 nm in diameter. In transverse section, the outline of some of these inclusions was hexagonal and therefore the inclusions may be crystalline in nature. PMID:2047586

Robertson, G W; Maxwell, M H

1991-01-01

361

Primary and secondary structural determinants in the receptor binding sequence. beta. -(38-57) from human luteinizing hormone  

SciTech Connect

The intercysteine loop sequence 38-57 in the ..beta.. subunit has been shown to be a determinant for expression of biological activity in human lutropin (hLH) and choriogonadotropin (hCG). Together with other sequences, the 38-57 region may contribute to a multicomponent receptor binding domain in hLH/hCG. Because the structural features influencing activity in this important region are not easy to evaluate in the full-length subunit, the authors have used analogues of hLH..beta..-(38-57) prepared by solid-phase synthesis. The peptides were tested for inhibition of /sup 125/I-labeled hCG binding to rat ovarian membrane receptors. Secondary structure was analyzed by circular dichroism (CD) and by reactivity with antibodies to the native 38-57 peptide. An analogue lacking the 38-57 disulfide linkage retained 20% receptor binding and full immunoreactivity. Far-ultraviolet CD profiles were essentially identical with those of the disulfide-intact peptide; a transition from 10% to 30% ..cap alpha..-helix in 90% trifluoroethanol was characteristic of both. The peptide thus appears not to require the disulfide bridge to retain a looped conformation with amphipathic secondary structure. An essential positive charge at position 43 was shown by complete loss of activity upon substitution of Asp or Ala for the Arg found in all known species of LH. These results indicate that the 38-57 sequence is a relatively rigid and structurally autonomous region, not merely a series of residues constrained passively into a loop by a disulfide linkage. It includes segments of ordered structure, probably including both amphipathic helical and turn sequences. Evidence from studies of other hormones suggests that this region may be important to binding and specificity in the glycoprotein hormones as a group.

Keutmann, H.T.; Charlesworth, M.C.; Kitzmann, K.; Mason, K.A.; Johnson, L.; Ryan, R.J.

1988-12-13

362

Prediction and Fourier-transform infrared-spectroscopy estimation of the secondary structure of a recombinant beta-glucosidase from Streptomyces sp. (ATCC 11238).  

PubMed Central

The secondary structure of a recombinant beta-glucosidase (EC 3.2.1.21) from Streptomyces sp. (ATCC 11238) has been predicted by computer algorithms and also estimated by Fourier-transform IR spectroscopy. From curve fitting of the deconvoluted IR spectra, the most probable distribution of the secondary-structural classes appears to be about 34% alpha-helix, 30% beta-sheet, 25% reverse turns and 11% non-ordered structures. These data showed a good agreement with data from computer prediction (35% alpha-helix, 23% beta-sheet, 31% reverse turns and 11% non-ordered structures). PMID:8948434

Perez-Pons, J A; Padros, E; Querol, E

1995-01-01

363

Cyclization of the Intrinsically Disordered ?1S Dihydropyridine Receptor II-III Loop Enhances Secondary Structure and in Vitro Function*  

PubMed Central

A key component of excitation contraction (EC) coupling in skeletal muscle is the cytoplasmic linker (II-III loop) between the second and third transmembrane repeats of the ?1S subunit of the dihydropyridine receptor (DHPR). The II-III loop has been previously examined in vitro using a linear II-III loop with unrestrained N- and C-terminal ends. To better reproduce the loop structure in its native environment (tethered to the DHPR transmembrane domains), we have joined the N and C termini using intein-mediated technology. Circular dichroism and NMR spectroscopy revealed a structural shift in the cyclized loop toward a protein with increased ?-helical and ?-strand structure in a region of the loop implicated in its in vitro function and also in a critical region for EC coupling. The affinity of binding of the II-III loop binding to the SPRY2 domain of the skeletal ryanodine receptor (RyR1) increased 4-fold, and its ability to activate RyR1 channels in lipid bilayers was enhanced 3-fold by cyclization. These functional changes were predicted consequences of the structural enhancement. We suggest that tethering the N and C termini stabilized secondary structural elements in the DHPR II-III loop and may reflect structural and dynamic characteristics of the loop that are inherent in EC coupling. PMID:21525002

Tae, Han-Shen; Cui, Yanfang; Karunasekara, Yamuna; Board, Philip G.; Dulhunty, Angela F.; Casarotto, Marco G.

2011-01-01

364

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

PubMed Central

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

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

2009-01-01

365

Time-resolved Fourier transform infrared study on photoadduct formation and secondary structural changes within the phototropin LOV domain.  

PubMed

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

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

2009-02-18

366

The ITS2 of the genus Bulinus: novel secondary structure among freshwater snails and potential new taxonomic markers.  

PubMed

The freshwater snail genus Bulinus has been intensively investigated due to its role as intermediate host for trematode blood flukes that cause the debilitating disease schistosomiasis in man and livestock. Owing to taxonomic ambiguities within Bulinus, attention has often focused upon species delineation and several molecular methods have recently been used for identification and characterization purposes. Inspection of compensatory base changes (CBCs) in the secondary structure of the nuclear ribosomal internal transcribed spacer (ITS) has been used to differentiate species in other genera, and here we present a study investigating the presence of CBCs between species in the species groups within Bulinus. CBCs were present within B. forskalii and B. globosus indicating that these widely distributed taxa might constitute cryptic species complexes. However, other currently recognized species could not be distinguished by CBC analysis. The putative secondary structure of the very long ITS2 sequence of the B. reticulatus species group had an additional helix (DIIa) between DII and DIII not seen in other species groups of Bulinus. The accumulation and inspection of further ITS2 sequences will no doubt reveal additional variation between Bulinus populations, and CBCs should be incorporated in future taxonomic work in this group. PMID:22677601

Jrgensen, Aslak; Stothard, J R; Madsen, Henry; Nalugwa, Allen; Nyakaana, Silvester; Rollinson, David

2013-11-01

367

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

PubMed Central

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

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

2014-01-01

368

Secondary structure determination of the conserved 98-base sequence at the 3' terminus of hepatitis C virus genome RNA.  

PubMed Central

The RNA genome of hepatitis C virus (HCV) terminates with a highly conserved 98-base sequence. Enzymatic and chemical approaches were used to define the secondary structure of this 3'-terminal element in RNA transcribed in vitro from cloned cDNA. Both approaches yielded data consistent with a stable stem-loop structure within the 3'-terminal 46 bases. In contrast, the 5' 52 nucleotides of this 98-base element appear to be less ordered and may exist in multiple conformations. Under the experimental conditions tested, interaction between the 3' 98 bases and upstream HCV sequences was not detected. These data provide valuable information for future experiments aimed at identifying host and/or viral proteins which interact with this highly conserved RNA element. PMID:9311812

Blight, K J; Rice, C M

1997-01-01

369

Secondary structure of the Irf7 5'-UTR, analyzed using SHAPE (selective 2'-hydroxyl acylation analyzed by primer extension).  

PubMed

OASL1 is a member of the 2'-5'-oligoadenylate synthetase (OAS) family and promotes viral clearance by activating RNase L. OASL1 interacts with the 5'-untranslated region (UTR) of interferon regulatory factor 7 (Irf7) and inhibits its translation. To identify the secondary structure required for OASL1 binding, we examined the 5'-UTR of the Irf7 transcript using "selective 2'-hydroxyl acylation analyzed by primer extension" (SHAPE). SHAPE takes advantage of the selective acylation of residues in single-stranded regions by 1-methyl-7-nitroisatoic anhydride (1M7). We found five major acylation sites located in, or next to, predicted single-stranded regions of the Irf7 5'-UTR. These results demonstrate the involvement of the stem structure of the Irf7 5'-UTR in the regulation of Irf7 translation, mediated by OASL1. PMID:24393529

Kim, Yun-Mi; Choi, Won-Young; Oh, Chang-Mok; Han, Gyoon-Hee; Kim, Young-Joon

2014-10-01

370

Multiple secondary interaction arrangement in the crystal structure of cis-dichlorobis(thioureaS)-zinc(II)  

Microsoft Academic Search

In our series of investigations into the structural and thermal behaviour of metal thiourea (tu) complexes, the single-crystal X-ray structure of dichlorobis(thiourea-S)-zinc(II) is redetermined at higher accuracy to R?=?0.0315 proving the space group Pnma. Half of the complex molecule is in the asymmetric unit, the Zn and the two Cl atoms lie on the mirror plane. The structure analysis shows

Petra Bombicz; Jnos Madarsz; Malle Krunks; Lauri Niinist; Gyrgy Pokol

2007-01-01

371

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

PubMed Central

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

Reinharz, Vladimir; Ponty, Yann; Waldisphl, Jrme

2013-01-01

372

Secondary structure and molecular evolution of the mitochondrial small subunit ribosomal RNA in Agaricales (Euagarics clade, Homobasidiomycota).  

PubMed

The complete sequences and secondary structures of the mitochondrial small subunit (SSU) ribosomal RNAs of both mostly cultivated mushrooms Agaricus bisporus (1930 nt) and Lentinula edodes (2164 nt) were achieved. These secondary structures and that of Schizophyllum commune (1872 nt) were compared to that previously established for Agrocybe aegerita. The four structures are near the model established for Archae, Bacteria, plastids, and mitochondria; particularly the helices 23 and 37, described as specific to bacteria, are present. Within the four Agaricales (Homobasidiomycota), the SSU-rRNA "core" is conserved in size (966 to 1009 nt) with the exception of an unusual extension of 40 nt in the H17 helix of S. commune. The four core sequences possess 76% of conserved positions and a cluster of C in their 3' end, which could constitute a signal involved in the RNA maturation process. Among the nine putative variable domains, three (V3, V5, V7) do not show significant length variations and possess similar percentages of conserved positions (69%) than the core. The other six variable domains show important length variations, due to independent large size inserted/deleted sequences, and higher rates of nucleotide substitutions than the core (only 31% of conserved positions between the four species). Interestingly, the inserted/deleted sequences are located in few preferential sites (hot spots for insertion/deletion) where they seem to arise or disappear haphazardly during evolution. These sites are located on the surface of the tertiary structure of the 30S ribosomal subunit, at the beginning of hairpin loops; the insertions lead to a lengthening of existing hairpins or to branching loops bearing up to five additional helices. PMID:14708572

Barroso, Grard; Sirand-Pugnet, Pascal; Mouhamadou, Bello; Labarre, Jacques

2003-10-01

373

Design of 11-Residue Peptides with Unusual Biophysical Properties: Induced Secondary Structure in the Absence of Water?  

PubMed Central

A series of oligopeptides with ?-forming and adhesive properties, were synthesized and analyzed for adhesion shear strength, secondary structure, and association properties. The sequences contained related hydrophobic core segments varying in length from 5 to 12 residues and flanked by di- or tri-lysine segments. Three remarkable peptides consisting of just 11 residues with hydrophobic core sequences of FLIVI, IGSII, and IVIGS flanked by three lysine residues gave the highest dry adhesion shear strength and displayed unusual biophysical properties in the presence and absence of water. KKKFLIVIKKK had its highest adhesion strength at 2% (w/v) at pH 12.0 and showed the highest adhesion strength after exposure to water (water resistance). Both KKKIGSIIKKK and KKKIVIGSKKK, at 4% (w/v) at pH 12.0, displayed nearly identical dry shear strength values to that with the FLIVI core sequence. The peptide with IGSII core, however, displayed a lower water resistance and the latter, IVIGS, showed no water resistance, completely delaminating upon soaking in water. These are the smallest peptides with adhesive properties reported to date and show remarkable adhesion strength even at lower concentrations of 0.2% (w/v), which corresponds to 1.6mM. The FLIVI containing peptide adopted a ?-sheet secondary structure in water while the IGSII- and IVIGS-containing sequences folded similarly only in the absence of water. Analytical ultracentrifugation studies showed that when the FLIVI sequence adopts ?-structure in aqueous solution, it associates into a large molecular weight assembly. The random coils of IGSII and IVIGS showed no tendency to associate at any pH. PMID:18024497

Mo, Xiaoqun; Hiromasa, Yasuaki; Warner, Matt; Al-Rawi, Ahlam N.; Iwamoto, Takeo; Rahman, Talat S.; Sun, Xiuzhi; Tomich, John M.

2008-01-01

374

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

PubMed Central

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

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

2013-01-01

375

mRNA transcript therapy.  

PubMed

mRNA is the central molecule of all forms of life. It is generally accepted that current life on Earth descended from an RNA world. mRNA, after its first therapeutic description in 1992, has recently come into increased focus as a method to deliver genetic information. The recent solution to the two main difficulties in using mRNA as a therapeutic, immune stimulation and potency, has provided the basis for a wide range of applications. While mRNA-based cancer immunotherapies have been in clinical trials for a few years, novel approaches; including, in vivo delivery of mRNA to replace or supplement proteins, mRNA-based generation of pluripotent stem cells, or genome engineering using mRNA-encoded meganucleases are beginning to be realized. This review presents the current state of mRNA drug technologies and potential applications, as well as discussing the challenges and prospects in mRNA development and drug discovery. PMID:25359562

Weissman, Drew

2015-02-01

376

An updated 18S rRNA phylogeny of tunicates based on mixture and secondary structure models  

PubMed Central

Background Tunicates have been recently revealed to be the closest living relatives of vertebrates. Yet, with more than 2500 described species, details of their evolutionary history are still obscure. From a molecular point of view, tunicate phylogenetic relationships have been mostly studied based on analyses of 18S rRNA sequences, which indicate several major clades at odds with the traditional class-level arrangements. Nonetheless, substantial uncertainty remains about the phylogenetic relationships and taxonomic status of key groups such as the Aplousobranchia, Appendicularia, and Thaliacea. Results Thirty new complete 18S rRNA sequences were acquired from previously unsampled tunicate species, with special focus on groups presenting high evolutionary rate. The updated 18S rRNA dataset has been aligned with respect to the constraint on homology imposed by the rRNA secondary structure. A probabilistic framework of phylogenetic reconstruction was adopted to accommodate the particular evolutionary dynamics of this ribosomal marker. Detailed Bayesian analyses were conducted under the non-parametric CAT mixture model accounting for site-specific heterogeneity of the evolutionary process, and under RNA-specific doublet models accommodating the occurrence of compensatory substitutions in stem regions. Our results support the division of tunicates into three major clades: 1) Phlebobranchia + Thaliacea + Aplousobranchia, 2) Appendicularia, and 3) Stolidobranchia, but the position of Appendicularia could not be firmly resolved. Our study additionally reveals that most Aplousobranchia evolve at extremely high rates involving changes in secondary structure of their 18S rRNA, with the exception of the family Clavelinidae, which appears to be slowly evolving. This extreme rate heterogeneity precluded resolving with certainty the exact phylogenetic placement of Aplousobranchia. Finally, the best fitting secondary-structure and CAT-mixture models suggest a sister-group relationship between Salpida and Pyrosomatida within Thaliacea. Conclusion An updated phylogenetic framework for tunicates is provided based on phylogenetic analyses using the most realistic evolutionary models currently available for ribosomal molecules and an unprecedented taxonomic sampling. Detailed analyses of the 18S rRNA gene allowed a clear definition of the major tunicate groups and revealed contrasting evolutionary dynamics among major lineages. The resolving power of this gene nevertheless appears limited within the clades composed of Phlebobranchia + Thaliacea + Aplousobranchia and Pyuridae + Styelidae, which were delineated as spots of low resolution. These limitations underline the need to develop new nuclear markers in order to further resolve the phylogeny of this keystone group in chordate evolution. PMID:19656395

Tsagkogeorga, Georgia; Turon, Xavier; Hopcroft, Russell R; Tilak, Marie-Ka; Feldstein, Tamar; Shenkar, Noa; Loya, Yossi; Huchon, Dorothe; Douzery, Emmanuel JP; Delsuc, Frdric

2009-01-01

377

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

ERIC Educational Resources Information Center

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

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

2014-01-01

378

Secondary contact and changes in coastal habitat availability influence the nonequilibrium population structure of a salmonid (Oncorhynchus keta).  

PubMed

Numerous empirical studies have reported lack of migration-drift equilibrium in wild populations. Determining the causes of nonequilibrium population structure is challenging because different evolutionary processes acting at a variety of spatiotemporal scales can produce similar patterns. Studies of contemporary populations in northern latitudes suggest that nonequilibrium population structure is probably caused by recent colonization of the region after the last Pleistocene ice age ended ~13,000 years ago. The chum salmon's (Oncorhynchus keta) range was fragmented by dramatic environmental changes during the Pleistocene. We investigated the population structure of chum salmon on the North Alaska Peninsula (NAP) and, using both empirical data and simulations, evaluated the effects of colonization timing and founder population heterogeneity on patterns of genetic differentiation. We screened 161 single nucleotide polymorphisms and found evidence of nonequilibrium population structure when the slope of the isolation-by-distance relationship was examined at incremental spatial scales. In addition, simulations suggested that this pattern closely matched models of recent colonization of the NAP by secondary contact. Our results agree with geological and archaeological data indicating that the NAP was a dynamic landscape that may have been more recently colonized than during the last deglaciation because of dramatic changes in coastal hydrology over the last several thousand years. PMID:24118255

Petrou, E L; Hauser, L; Waples, R S; Seeb, J E; Templin, W D; Gomez-Uchida, D; Seeb, L W

2013-12-01

379

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

PubMed

P7 is a small membrane protein that is essential for the infectivity of hepatitis C virus. Solution-state NMR experiments on p7 in DHPC micelles, including hydrogen/deuterium exchange, paramagnetic relaxation enhancement and bicelle 'q-titration,' demonstrate that the protein has a range of dynamic properties and distinct structural segments. These data along with residual dipolar couplings yield a secondary structure model of p7. We were able to confirm previous proposals that the protein has two transmembrane segments with a short interhelical loop containing the two basic residues K33 and R35. The 63-amino acid protein has a remarkably complex structure made up of seven identifiable sections, four of which are helical segments with different tilt angles and dynamics. A solid-state NMR two-dimensional separated local field spectrum of p7 aligned in phospholipid bilayers provided the tilt angles of two of these segments. A preliminary structural model of p7 derived from these NMR data is presented. PMID:20727850

Cook, Gabriel A; Opella, Stanley J

2011-06-01

380

Secondary contact and changes in coastal habitat availability influence the nonequilibrium population structure of a salmonid (Oncorhynchus keta)  

PubMed Central

Numerous empirical studies have reported lack of migrationdrift equilibrium in wild populations. Determining the causes of nonequilibrium population structure is challenging because different evolutionary processes acting at a variety of spatiotemporal scales can produce similar patterns. Studies of contemporary populations in northern latitudes suggest that nonequilibrium population structure is probably caused by recent colonization of the region after the last Pleistocene ice age ended ?13000years ago. The chum salmon's (Oncorhynchus keta) range was fragmented by dramatic environmental changes during the Pleistocene. We investigated the population structure of chum salmon on the North Alaska Peninsula (NAP) and, using both empirical data and simulations, evaluated the effects of colonization timing and founder population heterogeneity on patterns of genetic differentiation. We screened 161 single nucleotide polymorphisms and found evidence of nonequilibrium population structure when the slope of the isolation-by-distance relationship was examined at incremental spatial scales. In addition, simulations suggested that this pattern closely matched models of recent colonization of the NAP by secondary contact. Our results agree with geological and archaeological data indicating that the NAP was a dynamic landscape that may have been more recently colonized than during the last deglaciation because of dramatic changes in coastal hydrology over the last several thousand years. PMID:24118255

Petrou, E L; Hauser, L; Waples, R S; Seeb, J E; Templin, W D; Gomez-Uchida, D; Seeb, L W

2013-01-01

381

Comprehensive Secondary Structure Elucidation of Four Genera of the Family Pospiviroidae  

PubMed Central

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

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

2014-01-01

382

Rationally selected basis proteins: A new approach to selecting proteins for spectroscopic secondary structure analysis  

PubMed Central

Protein basis sets have been extensively used as reference data for the determination of protein structure with optical methods such as circular dichroism and infrared spectroscopies. We have taken a new approach to basis protein selection by utilizing three crystal structure classification databases: CATH, SCOP, and PDB_SELECT. Through the use of the information available in these and other online resources, we identified 115 commercially available proteins as potential basis set candidates. By carefully screening the quality of the crystal structures and commercial protein preparations, we obtained a final set of 50 rationally selected proteins (RaSP50) that has been optimized for use in spectroscopic protein structure determination studies. These proteins span the full range of known protein folds as well as ?-helix and ?-sheet contents, and they represent a more comprehensive variety of fold types than any previous reference set. This report includes a detailed presentation of the reasoning behind the rational protein selection process, a description of the properties of the RaSP50 set, and a discussion of the types of structural and spectral variations that are represented in the set. PMID:12931000

Oberg, Keith A.; Ruysschaert, Jean-Marie; Goormaghtigh, Erik

2003-01-01

383

Structural basis for polyadenosine-RNA binding by Nab2 Zn fingers and its function in mRNA nuclear export.  

PubMed

Polyadenylation regulation and efficient nuclear export of mature mRNPs both require the polyadenosine-RNA-binding protein, Nab2, which contains seven CCCH Zn fingers. We describe here the solution structure of fingers 5-7, which are necessary and sufficient for high-affinity polyadenosine-RNA binding, and identify key residues involved. These Zn fingers form a single structural unit. Structural coherence is lost in the RNA-binding compromised Nab2-C437S mutant, which also suppresses the rat8-2 allele of RNA helicase Dbp5. Structure-guided Nab2 variants indicate that dbp5(rat8-2) suppression is more closely linked to hyperadenylation and suppression of mutant alleles of the nuclear RNA export adaptor, Yra1, than to affinity for polyadenosine-RNA. These results indicate that, in addition to modulating polyA tail length, Nab2 has an unanticipated function associated with generating export-competent mRNPs, and that changes within fingers 5-7 lead to suboptimal assembly of mRNP export complexes that are more easily disassembled by Dbp5 upon reaching the cytoplasm. PMID:22560733

Brockmann, Christoph; Soucek, Sharon; Kuhlmann, Sonja I; Mills-Lujan, Katherine; Kelly, Seth M; Yang, Ji-Chun; Iglesias, Nahid; Stutz, Francoise; Corbett, Anita H; Neuhaus, David; Stewart, Murray

2012-06-01

384

Two-dimensional self-assembly of amphiphilic peptides; adsorption-induced secondary structural transition on hydrophilic substrate.  

PubMed

Adsorption of sequential amphiphilic peptides on solid substrates triggered the spontaneous construction of nanoscaled architecture. An amphiphilic peptide designed with a cationic amino acid as a hydrophilic residue turned an anionic mica substrate into a water-repellent surface, simply by adsorbing it on the substrate surface. In contrast, an amphiphilic peptide designed with an anionic amino-acid residue formed a precisely controlled fiber array comprising a ?-sheet fiber monolayer at the anionic substrate/water interface. This phenomenon was based on the secondary structural transition from random-coil to ?-sheet, which occurred specifically when amphiphilic peptide adsorbed on the substrate surface. Such surface-specific nonorder/order transition was implemented by exploiting the strength of adsorption between the peptide and the substrate. A strategic design exploiting weak bonding such as hydrophobic interactions is essential for constructing precisely controlled nano-architectures in two dimensions. PMID:25521553

Tanaka, Masayoshi; Abiko, Souhei; Himeiwa, Takahiro; Kinoshita, Takatoshi

2015-03-15

385

Intrinsically disordered ?-subunit of cGMP phosphodiesterase encodes functionally relevant transient secondary and tertiary structure  

PubMed Central

The retinal phosphodiesterase (PDE6) inhibitory ?-subunit (PDE?) plays a central role in vertebrate phototransduction through alternate interactions with the catalytic ??-subunits of PDE6 and the ?-subunit of transducin (?t). Detailed structural analysis of PDE? has been hampered by its intrinsic disorder. We present here the NMR solution structure of PDE?, which reveals a loose fold with transient structural features resembling those seen previously in the x-ray structure of PDE?4687 when bound to ?t in the transition-state complex. NMR mapping of the interaction between PDE?4687 and the chimeric PDE5/6 catalytic domain confirmed that C-terminal residues 7487 of PDE? are involved in the association and demonstrated that its W70 indole group, which is critical for subsequent binding to ?t, is left free at this stage. These results indicate that the interaction between PDE? and ?t during the phototransduction cascade involves the selection of preconfigured transient conformations. PMID:18230733

Song, Jikui; Guo, Lian-Wang; Muradov, Hakim; Artemyev, Nikolai O.; Ruoho, Arnold E.; Markley, John L.

2008-01-01

386

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

ERIC Educational Resources Information Center

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

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

2007-01-01

387

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

ERIC Educational Resources Information Center

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

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

2011-01-01

388

Deletion of ?-Strand and ?-Helix Secondary Structure in Normal Prion Protein Inhibits Formation of Its Protease-Resistant Isoform  

PubMed Central

A fundamental event in the pathogenesis of transmissible spongiform encephalopathies (TSE) is the conversion of a normal, proteinase K-sensitive, host-encoded protein, PrP-sen, into its protease-resistant isoform, PrP-res. During the formation of PrP-res, PrP-sen undergoes conformational changes that involve an increase of ?-sheet secondary structure. While previous studies in which PrP-sen deletion mutants were expressed in transgenic mice or scrapie-infected cell cultures have identified regions in PrP-sen that are important in the formation of PrP-res, the exact role of PrP-sen secondary structures in the conformational transition of PrP-sen to PrP-res has not yet been defined. We constructed PrP-sen mutants with deletions of the first ?-strand, the second ?-strand, or the first ?-helix and tested whether these mutants could be converted to PrP-res in both scrapie-infected neuroblastoma cells (Sc+-MNB cells) and a cell-free conversion assay. Removal of the second ?-strand or the first ?-helix significantly altered both processing and the cellular localization of PrP-sen, while deletion of the first ?-strand had no effect on these events. However, all of the mutants significantly inhibited the formation of PrP-res in Sc+-MNB cells and had a greatly reduced ability to form protease-resistant PrP in a cell-free assay system. Thus, our results demonstrate that deletion of the ?-strands and the first ?-helix of PrP-sen can fundamentally affect PrP-res formation and/or PrP-sen processing. PMID:11581371

Vorberg, Ina; Chan, Kaman; Priola, Suzette A.

2001-01-01

389

Detection and Alignment of 3D Domain Swapping Proteins Using Angle-Distance Image-Based Secondary Structural Matching Techniques  

PubMed Central

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

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

2010-01-01

390

NMR assignment and secondary structure of coiled coil domain of C-terminal myosin binding subunit of myosin phosphatase.  

PubMed

Protein-protein interactions between the C-terminal domain of Myosin Binding Subunit (MBS) of MLC Phosphatase (MBS(CT180); C-terminal 180 aa) and the N-terminal coiled coil (CC) leucine zipper (LZ) domain of PKGI?, PKG-I?(1-159) play an important role in the process of Smooth Muscle Cell relaxation. The paucity of three-dimensional structural information for MBS(CT180) prevents an atomic level understanding of the MBS-PKG contractile complex. MBS(CT180) is comprised of three structurally different sub-domains including a non-canonical CC, a CC, and a LZ. Recently we reported polypeptide purification and biophysical characterization of the CC domain and the LZ domain of MBS(CT180) (Sharma et al, Prot Expr Purif 2012). Here we report (1)H, (13)C, (15)N chemical shift assignments of homodimeric CC MBS domain encompassing amino acid residues Asp931-Leu980 using 2D and 3D heteronuclear NMR spectroscopy. Secondary structure analyses deduced from these NMR chemical shift data have identified a contiguous stretch of 36 residues from Phe932 to Ala967 that is involved in the formation of coiled coil ?-helical region within CC MBS domain. The N-terminal residue Asp931 and the C-terminally positioned residues Thr968-Ala975, Arg977, and Ser978 adopt nonhelical loop conformations. PMID:24693955

Sharma, Alok K; Rigby, Alan C

2014-07-01

391

Changes in earthworm density and community structure during secondary succession in abandoned tropical pastures  

Microsoft Academic Search

Plant community succession alters the quantity and chemistry of organic inputs to soils. These differences in organic input may trigger changes in soil fertility and faunal activity. We examined earthworm density and community structure along a successional sequence of plant communities in abandoned tropical pastures in Puerto Rico. The chronological sequence of these plant communities were pasture, grass-vine-fern, shrub-small tree,

Xiaoming Zou; Grizelle Gonzalez

1997-01-01

392

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

Microsoft Academic Search

The DICHROWEB web server enables on-line ana- lyses of circular dichroism (CD) spectroscopic data, providingcalculatedsecondarystructurecontentand graphical analyses comparing calculated structures and experimental data. The server is located at http:\\/\\/ www.cryst.bbk.ac.uk\\/cdwebandmaybeaccessedvia a password-limited user ID, available upon comple- tion of a registration form. The server facilitates ana- lyses using five popular algorithms and (currently) sevendifferentreferencedatabasesbyacceptingdata in a user-friendly manner in a

Lee Whitmore; B. A. Wallace

2004-01-01

393

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

NASA Technical Reports Server (NTRS)

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

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

1998-01-01

394

Site-directed Mutagenesis of Apolipoprotein CII to Probe the Role of Its Secondary Structure for Activation of Lipoprotein Lipase*  

PubMed Central

Apolipoprotein CII (apoCII) is a necessary activator for lipoprotein lipase (LPL). We had identified four residues (Tyr-63, Ile-66, Asp-69, and Gln-70), presumably contained in an ?-helix, as a potential binding site for LPL. We have now used structure prediction, mutagenesis, and functional assays to explore the functional role of the secondary structure in this part of apoCII. First, mutants were generated by replacements with proline residues to disturb the helical structure. Activation by mutant G65P was reduced by 30%, whereas mutant S54P retained activation ability. Mutants V71P and L72P should be located outside the LPL-binding site, but V71P was totally inactive, whereas activation by L72P was reduced by 65%. Insertion of alanine after Tyr-63, changing the position of the putative LPL-binding site in relation to the hydrophobic face of the ?-helix, also severely impeded the activation ability, and a double mutant (Y63A/I66A) was completely inactive. Next, to investigate the importance of conserved hydrophobic residues in the C-terminal end of apoCII, Phe-67, Val-71, Leu-72, and Leu-75 were exchanged for polar residues. Only F67S showed dramatic loss of function. Finally, fragment 3962, previously claimed to activate LPL, was found to be completely inactive. Our data support the view that the helical structure close to the C-terminal end of apoCII is important for activation of LPL, probably by placing residues 63, 66, 69, and 70 in an optimal steric position. The structural requirements for the hydrophobic face on the back side of this helix and further out toward the C terminus were less stringent. PMID:20042600

Shen, Yan; Lookene, Aivar; Zhang, Liyang; Olivecrona, Gunilla

2010-01-01

395

The structurally distinct form of pp60/sup c-src/ detected in neuronal cells is encoded by a unique c-src mRNA  

SciTech Connect

A cellular scr (c-src) cDNA clone was isolated from a chicken embryonic brain cDNA library and characterized by DNA sequence analysis. Comparison with the published sequence of a chicken genomic c-src clone indicated that the brain cDNA clone contained an 18-base-pair insertion located between exons 3 and 4 of the c-src gene. The six amino acids encoded by the insertion caused an alteration in the electrophoretic mobility of the c-src gene product similar to that of the structurally distinct form of the src protein detected in neuronal cultures.

Levy, J.B.; Dorai, T.; Wang, L.H.; Brugge, J.S.

1987-11-01

396

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

PubMed Central

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

Alici, Kamil Boratay; Gallardo, Ignacio F.

2013-01-01

397

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

E-print Network

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

Carpentier, Robert

398

Secondary, tertiary, and quaternary structure of T-cell-specific immunoglobulin-like polypeptide chains.  

PubMed Central

To explore the possibility that the difference in antigen recognition between B and T cells derives from a structural difference in their respective antigen-specific receptors (immunoglobulins on B cells and immunoglobulin-like molecules on T cells), we compared the extracellular segments of the T-cell receptor alpha, beta, and gamma polypeptide chains and the N-terminal segment of the T-cell T8 (Lyt-2) antigen chain with the corresponding regions of immunoglobulins whose three-dimensional structures are known. The results indicate that the four T-cell polypeptide chains are organized into immunoglobulin-like domains consisting of multistranded antiparallel beta-sheet bilayers. Invariant amino acid side chains that are conserved in diverse immunoglobulins, including those that mediate domain-domain interactions and form a constant scaffold for antibody binding sites, are also conserved in the chains encoded by the T-cell receptor genes and in the N-terminal domain of T8 (Lyt-2). It appears that the binding sites of the antigen-specific T-cell alpha beta-chain receptors and of antibodies are very similar in their overall dimensions and geometry: a T-cell alpha beta receptor molecule probably has an antigen-specific binding site that is fundamentally no different than the conventional binding site of an antibody. PMID:3484824

Novotn, J; Tonegawa, S; Saito, H; Kranz, D M; Eisen, H N

1986-01-01

399

The effect of Berberine on the secondary structure of human serum albumin  

NASA Astrophysics Data System (ADS)

The presence of several high affinity binding sites on human serum albumin (HSA) makes it a possible target for many drugs. This study is designed to examine the effect of Berberine (an ancient Chinese drug used for antimicrobial, antiplasmodial, antidiarrheal and cardiovascular) on the solution structure of HSA using fluorescence, Fourier transform infrared (FT-IR), circular dichroism (CD) spectroscopic methods. The fluorescence spectroscopic results show that the fluorescence intensity of HSA was significantly decreased in the presence of Berberine. The Scatchard's plots indicated that the binding of Berberine to HSA at 296, 303, 318 K is characterized by one binding site with the binding constant is 4.071(0.128)10 4, 3.741(0.089)10 4, 3.454(0.110)10 4 M -1, respectively. The protein conformation is altered (FT-IR and CD data) with reductions of ?-helices from 54 to 47% for free HSA to 45-32% and with increases of turn structure5% for free HSA to 18% in the presence of Berberine. The binding process was exothermic, enthalpy driven and spontaneous, as indicated by the thermodynamic analyses, Berberine bound to HSA was mainly based on hydrophobic interaction and electrostatic interaction cannot be excluded from the binding. Furthermore, the displace experiments indicate that Berberine can bind to the subdomain IIA, that is, high affinity site (site II).

Li, Ying; He, WenYing; Tian, Jianniao; Tang, Jianghong; Hu, Zhide; Chen, Xingguo

2005-05-01

400

Secondary Structure in the Core of Amyloid Fibrils Formed from Human ?2m and its Truncated Variant ?N6  

PubMed Central

Amyloid fibrils formed from initially soluble proteins with diverse sequences are associated with an array of human diseases. In the human disorder, dialysis-related amyloidosis (DRA), fibrils contain two major constituents, full-length human ?2-microglobulin (h?2m) and a truncation variant, ?N6 which lacks the N-terminal six amino acids. These fibrils are assembled from initially natively folded proteins with an all antiparallel ?-stranded structure. Here, backbone conformations of wild-type h?2m and ?N6 in their amyloid forms have been determined using a combination of dilute isotopic labeling strategies and multidimensional magic angle spinning (MAS) NMR techniques at high magnetic fields, providing valuable structural information at the atomic-level about the fibril architecture. The secondary structures of both fibril types, determined by the assignment of ?80% of the backbone resonances of these 100- and 94-residue proteins, respectively, reveal substantial backbone rearrangement compared with the location of ?-strands in their native immunoglobulin folds. The identification of seven ?-strands in h?2m fibrils indicates that approximately 70 residues are in a ?-strand conformation in the fibril core. By contrast, nine ?-strands comprise the fibrils formed from ?N6, indicating a more extensive core. The precise location and length of ?-strands in the two fibril forms also differ. The results indicate fibrils of ?N6 and h?2m have an extensive core architecture involving the majority of residues in the polypeptide sequence. The common elements of the backbone structure of the two proteins likely facilitates their ability to copolymerize during amyloid fibril assembly. PMID:24679070

2014-01-01

401

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

SciTech Connect

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

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

2011-03-15

402

Influence of Secondary Structure on In-Source Decay of Protein in Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry  

PubMed Central

The susceptibility of the NC? bond of the peptide backbone to specific cleavage by in-source decay (ISD) in matrix-assisted laser desorption/ionization mass spectrometry (MALDI MS) was studied from the standpoint of the secondary structure of three proteins. A naphthalene derivative, 5-amino-1-naphtol (5,1-ANL), was used as the matrix. The resulting c?-ions, which originate from the cleavage at NC? bonds in flexible secondary structures such as turn and bend, and are free from intra-molecular hydrogen-bonded ?-helix structure, gave relatively intense peaks. Furthermore, ISD spectra of the proteins showed that the NC? bonds of specific amino acid residues, namely GlyXxx, XxxAsp, and XxxAsn, were more susceptible to MALDI-ISD than other amino acid residues. This is in agreement with the observation that Gly, Asp and Asn residues usually located in turns, rather than ?-helix. The results obtained indicate that protein molecules embedded into the matrix crystal in the MALDI experiments maintain their secondary structures as determined by X-ray crystallography, and that MALDI-ISD has the capability for providing information concerning the secondary structure of protein. PMID:24349902

Takayama, Mitsuo; Osaka, Issey; Sakakura, Motoshi

2012-01-01

403

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

NASA Astrophysics Data System (ADS)

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

Sanchez-Ferrer, Antoni; Mezzenga, Raffaele

2010-03-01

404

Poly(2-methylthio-7-deazainosinic acid)--hydrophobic stabilization of polynucleotide secondary structure by the 2-methylthio group.  

PubMed Central

Poly(2-methylthio-7-deazainosinic acid) [poly(ms2c7I)] was enzymatically synthesized by polymerization of 2-methylthio-7-deazainosine 5'-diphosphate with polynucleotide phosphorylase from Micrococcus luteus in high yield. The homopolymer shows much higher thermal stability than its parent polynucleotides poly(7-deazainosinic acid) [poly(c7I)] and poly(I). Its sigmoidal melting curve and pronounced hypochromicity imply a rigid, ordered structure. Poly(ms2c7I), like poly(2-methylthio-inosinic acid) [poly(ms2I)], does not form a complex with poly(C) because of the bulky 2-methylthio substituent. On the other hand, two poly(ms2c7I) strands form very rigid triple strands with poly(A). Different from poly(I) and poly(c7I) the homopolymer poly(ms2c7I) is very stable against cleavage by nuclease S1 and ribonuclease T2 as expected from its rigid secondary structure. PMID:6889137

Seela, F; Ott, J; Franzen, D

1983-01-01

405