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Sample records for assignments secondary structure

  1. Protein secondary structure: category assignment and predictability

    DEFF Research Database (Denmark)

    Andersen, Claus A.; Bohr, Henrik; Brunak, Søren

    2001-01-01

    structures. Single sequence prediction of the new three category assignment gives an overall prediction improvement of 3.1% and 5.1%, compared to the DSSP assignment and schemes where the helix category consists of a-helix and 3(10)-helix, respectively. These results were achieved using a standard feed...

  2. A New Secondary Structure Assignment Algorithm Using Cα Backbone Fragments.

    Science.gov (United States)

    Cao, Chen; Wang, Guishen; Liu, An; Xu, Shutan; Wang, Lincong; Zou, Shuxue

    2016-01-01

    The assignment of secondary structure elements in proteins is a key step in the analysis of their structures and functions. We have developed an algorithm, SACF (secondary structure assignment based on Cα fragments), for secondary structure element (SSE) assignment based on the alignment of Cα backbone fragments with central poses derived by clustering known SSE fragments. The assignment algorithm consists of three steps: First, the outlier fragments on known SSEs are detected. Next, the remaining fragments are clustered to obtain the central fragments for each cluster. Finally, the central fragments are used as a template to make assignments. Following a large-scale comparison of 11 secondary structure assignment methods, SACF, KAKSI and PROSS are found to have similar agreement with DSSP, while PCASSO agrees with DSSP best. SACF and PCASSO show preference to reducing residues in N and C cap regions, whereas KAKSI, P-SEA and SEGNO tend to add residues to the terminals when DSSP assignment is taken as standard. Moreover, our algorithm is able to assign subtle helices (310-helix, π-helix and left-handed helix) and make uniform assignments, as well as to detect rare SSEs in β-sheets or long helices as outlier fragments from other programs. The structural uniformity should be useful for protein structure classification and prediction, while outlier fragments underlie the structure-function relationship. PMID:26978354

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

    Directory of Open Access Journals (Sweden)

    de Brevern Alexandre G

    2005-09-01

    Full Text Available Abstract 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.

  4. Sequential 1H NMR assignments and secondary structure of hen egg white lysozyme in solution

    International Nuclear Information System (INIS)

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

  5. A proton nuclear magnetic resonance assignment and secondary structure determination of recombinant human thioredoxin

    International Nuclear Information System (INIS)

    Two-dimensional 1H NMR spectroscopy has been applied to a structural analysis of the reduced form of a recombinant human thioredoxin, a ubiquitous dithiol oxidoreductase recently isolated from an immunocompetent lymphoblastoid cell line. The sequential assignment of the spectrum, including all proline residues, has been accomplished by using experiments to demonstrate through-bond and through-space connectivities. The secondary structure has been determined by a qualitative interpretation of nuclear Overhauser effects, NH exchange data, and 3JHNα coupling constants. The secondary structure was found to be similar to that of the X-ray structure of Escherichia coli thioredoxin, consisting of a mixed five-stranded β-sheet surrounded by four α-helices. The assignment and structural characterization of human thioredoxin was facilitated by the increased resolution and sensitivity afforded by a magnetic field strength of 600 MHz and required the use of two temperatures and two pH conditions to resolve ambiguities caused by a duplication of resonances. This duplication, extending from Phe-41 to Val-59, and including Lys-3-Ile-5, Val-24, Val-25, Asn-39, and Ile-101-Glu-103, appears to be due to heterogeneity arising from the presence or absence of the N-terminal methionine

  6. Resonance assignments, secondary structure and topology of leukaemia inhibitory factor in solution

    International Nuclear Information System (INIS)

    The chemical shift assignments and secondary structure of a murine-human chimera,MH35, of leukaemia inhibitory factor (LIF), a 180-residue protein of molecular mass 20 kDa,have been determined from multidimensional heteronuclear NMR spectra acquired on a uniformly 13C,15N-labelled sample. Secondary structure elements were defined on the basis of chemical shifts, NH-CαH coupling constants, medium-range NOEs and the location of slowly exchanging amide protons. The protein contains four α-helices, the relative orientations of which were determined on the basis of long-range, interhelical NOEs. The four helices are arranged in an up-up-down-down orientation, as found in other four-helical bundle cytokines. The overall topology of MH35-LIF is similar to that of the X-ray crystallographic structure for murine LIF [Robinson et al. (1994) Cell, 77, 1101-1116]. Differences between the X-ray structure and the solution structure are evident in the N-terminal tail, where the solution structure has a trans-Pro17 compared with the cis-Pro17 found in the crystal structure and the small antiparallel β-sheet encompassing residues in the N-terminus and CD loop in the crystal structure is less stable

  7. Sequence-Specific Assignment and Secondary Structure of the Catalytic Domain of Protein from Ubiquitination Pathway

    International Nuclear Information System (INIS)

    Ubiquitination is a post-translational protein modification which plays an important role in a wide variety of cellular processes including cell cycle, DNA repair and cell apoptosis. It is well known, that the ubiquitination requires sequential activity of three enzymes with different functions: activation, conjugation and ligation. Unfortunately, the three-dimensional structures of all three proteins responsible for these processes are not available at present and the process of proteins ubiquitination still is not understood in detail. In our communication, we present first, preliminary NMR data for the sequence-specific assignments for 112 amino acid residues long domain of one of the proteins from the ubiquitination pathway. The NMR samples were prepared by dissolving 1 mm either 15N-labeled or 15N, 13C-double labeled protein in 90%/10% H2O/D2O, 50 mm TRIS buffer, and 50 mm NaCl. The ph was adjusted to 6.5 (uncorrected value). All NMR measurements were performed on the Varian Unity+ 500 NMR spectrometer (11.7 T) equipped with three channels, Performa II PFG unit and 5 mm 1H, 13C, 15N-triple resonance pro behead. The 1H, 15N, and 13C backbone resonances were assigned by standard methods using 3D heteronuclear HNCACB, CBCA(CO)NH, HNCA, HN(CO)CA, HNCO, (HCA)CO(CA)NH NMR spectra collected at 303 K. The aliphatic 1H and 13C resonances were assigned on the basis of C(CO)NH, HBHA(CO)NH, and H(CO)NH experiments. After finishing of assignment procedure, solution of secondary structure in studied protein has been performed. The exact position of the α-helices and β-strands were solved on base analysis of cross-peaks between HN and Hα protons in 3D 15N-edited NOESY-HSQC spectrum, 3JNHα coupling constants evaluated from 3D HNHA experiment, and chemical shifts of backbone nuclei (TALOS software). Obtained results will be used in future for solution of three-dimensional structure of catalytic domain with high resolution by means NMR methods. (author)

  8. 1H assignments and secondary structure determination of the soybean trypsin/chymotrypsin Bowman-Birk inhibitor

    International Nuclear Information System (INIS)

    The 1H resonance assignments and secondary structure of the trypsin/chymotrypsin Bowman-Birk inhibitor from soybeans were determined by nuclear magnetic resonance spectroscopy (NMR) at 600 MHz in an 18% acetonitrile-d3/aqueous cosolvent. Resonances from 69 to 71 amino acids were assigned sequence specifically. Residues Q11-T15 form an antiparallel β-sheet with residues Q21-S25 in the tryptic inhibitory domain and an analogous region of antiparallel sheet forms between residues S38-A42 and Q48-V52 in the chymotryptic inhibitory domain. The inhibitory sites of each fragment (K16-S17 for trypsin, L43-S44 for chymotrypsin) are each part of a type VI like turn at one end of their respective region of the antiparallel β-sheet. These structural elements are compared to those found in other Bowman-Birk inhibitors

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

    Czech Academy of Sciences Publication Activity Database

    Horničáková, M.; Kohoutová, Jaroslava; Schlagnitweit, J.; Wohlschlager, Ch.; Ettrich, Rüdiger; Fiala, R.; Schoefberger, W.; Müller, N.

    2011-01-01

    Roč. 5, č. 2 (2011), s. 169-175. ISSN 1874-2718 R&D Projects: GA MŠk(CZ) LC06010 Institutional research plan: CEZ:AV0Z60870520 Keywords : Photosystem II * PsbQ * Missing link * NMR resonance assignment * Protein-protein interaction Subject RIV: BO - Biophysics Impact factor: 0.720, year: 2011 http://www.springerlink.com/content/3n38075w5h1l1082/fulltext.pdf

  10. Sequence-specific Assignment of 1H-NMR Resonance and Determination of the Secondary Structure of Jingzhaotoxin-Ⅰ

    Institute of Scientific and Technical Information of China (English)

    Xiong-Zhi ZENG; Qi ZHU; Song-Ping LIANG

    2005-01-01

    Jingzhaotoxin-Ⅰ (JZTX-Ⅰ) purified from the venom of the spider Chilobrachys jingzhao is a novel neurotoxin preferentially inhibiting cardiac sodium channel inactivation by binding to receptor site 3.The structure of this toxin in aqueous solution was investigated using 2-D 1H-NMR techniques. The complete sequence-specific assignments of proton resonance in the 1H-NMR spectra of JZTX-Ⅰ were obtained by analyzing a series of 2-D spectra, including DQF-COSY, TOCSY and NOESY spectra, in H2O and D2O. All the backbone protons except for Gln4 and more than 95% of the side-chain protons were identified by dαN,dαδ, dβN and dNN connectivities in the NOESY spectrum. These studies provide a basis for the further determination of the solution conformation of JZTX-Ⅰ. Furthermore, the secondary structure of JZTX-Ⅰ was identified from NMR data. It consists mainly of a short triple-stranded antiparallel β-sheet with Trp7-Cys9, Phe20-Lys23 and Leu28-Trp31. The characteristics of the secondary structure of JZTX-Ⅰ are similar to those of huwentoxin-Ⅰ (HWTX-Ⅰ) and hainantoxin-Ⅳ (HNTX-Ⅳ), whose structures in solution have previously been reported.

  11. Practical use of chemical shift databases for protein solid-state NMR: 2D chemical shift maps and amino-acid assignment with secondary-structure information

    International Nuclear Information System (INIS)

    We introduce a Python-based program that utilizes the large database of 13C and 15N chemical shifts in the Biological Magnetic Resonance Bank to rapidly predict the amino acid type and secondary structure from correlated chemical shifts. The program, called PACSYlite Unified Query (PLUQ), is designed to help assign peaks obtained from 2D 13C–13C, 15N–13C, or 3D 15N–13C–13C magic-angle-spinning correlation spectra. We show secondary-structure specific 2D 13C–13C correlation maps of all twenty amino acids, constructed from a chemical shift database of 262,209 residues. The maps reveal interesting conformation-dependent chemical shift distributions and facilitate searching of correlation peaks during amino-acid type assignment. Based on these correlations, PLUQ outputs the most likely amino acid types and the associated secondary structures from inputs of experimental chemical shifts. We test the assignment accuracy using four high-quality protein structures. Based on only the Cα and Cβ chemical shifts, the highest-ranked PLUQ assignments were 40–60 % correct in both the amino-acid type and the secondary structure. For three input chemical shifts (CO–Cα–Cβ or N–Cα–Cβ), the first-ranked assignments were correct for 60 % of the residues, while within the top three predictions, the correct assignments were found for 80 % of the residues. PLUQ and the chemical shift maps are expected to be useful at the first stage of sequential assignment, for combination with automated sequential assignment programs, and for highly disordered proteins for which secondary structure analysis is the main goal of structure determination.

  12. Secondary structural analysis of proteins based on 13C chemical shift assignments in unresolved solid-state NMR spectra enhanced by fragmented structure database

    International Nuclear Information System (INIS)

    Magic-angle-spinning solid-state 13C NMR spectroscopy is useful for structural analysis of non-crystalline proteins. However, the signal assignments and structural analysis are often hampered by the signal overlaps primarily due to minor structural heterogeneities, especially for uniformly-13C,15N labeled samples. To overcome this problem, we present a method for assigning 13C chemical shifts and secondary structures from unresolved two-dimensional 13C–13C MAS NMR spectra by spectral fitting, named reconstruction of spectra using protein local structures (RESPLS). The spectral fitting was conducted using databases of protein fragmented structures related to 13Cα, 13Cβ, and 13C′ chemical shifts and cross-peak intensities. The experimental 13C–13C inter- and intra-residue correlation spectra of uniformly isotope-labeled ubiquitin in the lyophilized state had a few broad peaks. The fitting analysis for these spectra provided sequence-specific Cα, Cβ, and C′ chemical shifts with an accuracy of about 1.5 ppm, which enabled the assignment of the secondary structures with an accuracy of 79 %. The structural heterogeneity of the lyophilized ubiquitin is revealed from the results. Test of RESPLS analysis for simulated spectra of five different types of proteins indicated that the method allowed the secondary structure determination with accuracy of about 80 % for the 50–200 residue proteins. These results demonstrate that the RESPLS approach expands the applicability of the NMR to non-crystalline proteins exhibiting unresolved 13C NMR spectra, such as lyophilized proteins, amyloids, membrane proteins and proteins in living cells.

  13. NMR assignments, secondary structure, and global fold of calerythrin, an EF-hand calcium-binding protein from Saccharopolyspora erythraea.

    OpenAIRE

    Aitio, H.; Annila, A; Heikkinen, S.; Thulin, E.; Drakenberg, T; Kilpeläinen, I.

    1999-01-01

    Calerythrin is a 20 kDa calcium-binding protein isolated from gram-positive bacterium Saccharopolyspora erythraea. Based on amino acid sequence homology, it has been suggested that calerythrin belongs to the family of invertebrate sarcoplasmic EF-hand calcium-binding proteins (SCPs), and therefore it is expected to function as a calcium buffer. NMR spectroscopy was used to obtain structural information on the protein in solution. Backbone and side chain 1H, 13C, and 15N assignments were obtai...

  14. 1H, 15N and 13C NMR resonance assignment, secondary structure and global fold of the FMN-binding domain of human cytochrome P450

    International Nuclear Information System (INIS)

    The FMN-binding domain of human NADPH-cytochrome P450 reductase,corresponding to exons 3-;7, has been expressed at high level in an active form and labelled with 13C and 15N. Most of the backbone and aliphatic side-chain 1H, 15Nand 13C resonances have been assigned using heteronuclear double- and triple-resonance methods, together with a semiautomatic assignment strategy. The secondary structure as estimated from the chemical shift index and NOE connectivities consists of six α-helices and fiveβ-strands. The global fold was deduced from the long-range NOE sun ambiguously assigned in a 4D 13C-resolved HMQC-NOESY-HMQC spectrum. The fold is of the alternating α/β type, with the fiveβ-strands arranged into a parallel β-sheet. The secondary structure and global fold are very similar to those of the bacterial flavodoxins, but the FMN-binding domain has an extra short helix in place of a loop, and an extra helix at the N-terminus (leading to the membrane anchordomain in the intact P450 reductase). The experimental constraints were combined with homology modelling to obtain a structure of the FMN-bindingdomain satisfying the observed NOE constraints. Chemical shift comparisons showed that the effects of FMN binding and of FMN reduction are largely localised at the binding site

  15. Two- and three-dimensional sup 1 H NMR studies of a wheat phospholipid transfer protein: Sequential resonance assignments and secondary structure

    Energy Technology Data Exchange (ETDEWEB)

    Simorre, J.P.; Caille, A. (Centre National de la Recherche Scientifique, Orleans (France)); Marion, D. (Laboratoire de Resonance Magnetique en Biologie et Medecine, Grenoble (France)); Marion, D. (INRA, Nantes (France)); Ptak, M. (Centre National de la Recherche Scientifique, Orleans (France) Univ. d' Orleans (France))

    1991-12-10

    Two- and three-dimensional {sup 1}H NMR experiments have been used to sequentially assign nearly all proton resonances of the 90 residues of wheat phospholipid transfer protein. Only a few side-chain protons were not identified because of degeneracy or overlapping. The identification of spin systems and the sequential assignment were made at the same time by combining the data of the two- and three-dimensional experiments. The classical two-dimensional COSY, HOHAHA, and NOESY experiments benefit from both good resolution and high sensitivity, allowing the detection of long-range dipolar connectivities. The three-dimensional HOHAHA-NOESY experiment offers the advantage of a faster and unambiguous assignment. As a matter of fact, homonuclear three-dimensional NMR spectroscopy prove to be a very efficient method for resonance assignments of protein {sup 1}H NMR spectra which cannot be unraveled by 2D methods. An assignment strategy which overcomes most of the ambiguities has been proposed, in which each individual assignment toward the C-terminal end is supported by another in the opposite direction originating from a completely different part of the spectrum. Location of secondary structures of the phospholipid transfer protein was determined by using the method of analysis introduced here and was confirmed by {sup 3}J{sub {alpha}NH} coupling and NH exchange rates. Except for the C-terminal part, the polypeptide chain appears to be organized mainly as helical fragments connected by disulfide bridges. Further modeling will display the overall folding of the protein and should provide a better understanding of its interactions with lipids.

  16. 1H NMR assignment and secondary structure of the Ca2+-free form of the amino-terminal epidermal growth factor like domain in coagulation factor X

    International Nuclear Information System (INIS)

    Blood coagulation factor X is composed of discrete domains, two of which are homologous to the epidermal growth factor (EGF). The N-terminal EGF like domain in factor X (fX-EGFN), residues 45-86 of the intact protein contains a β-hydroxylated asparatic acid and has one Ca2+-binding site. Using 2D NMR techniques, the authors have made a full assignment of the 500-MHz 1H NMR spectrum of Ca2+-free fX-EGFN. On the basis of this assignment and complementary NOESY experiments, they have also determined the secondary structure of Ca2+-free fX-EGFN in water solution. Residues 45-49 are comparatively mobile, whereas residues 5-56 are constrained by two disulfide bonds to one side of an antiparallel β-sheet involving residues 59-64 and 67-72. Another antiparallel β-sheet involves residues 76-77 and 83-84. A small, parallel β-sheet connects residues 80-81 and 55-56 and thereby orients the two antiparallel β-sheets relative to each other. Four β-turns are identified, involving residues 50-53, 56-59, 64-67, 73-76. Residues 78-82 adopt an extended bend structure. On the basis of secondary structure and the location of the three disulfide bonds, they find that Asp 46, Asp 48, and Hya 63 are sufficiently close to each other to form a Ca2+-binding site. However, the amino terminus of the Ca2+-free form of fX-EGFN is not part of a triple-stranded β-sheet as in other EGF like peptides. Differences and similarities between fX-EGFN and murine EGF with respect to secondary structure and conformational shifts are discussed

  17. Multinuclear NMR resonance assignments and the secondary structure of Escherichia coli thioesterase/protease I: A member of a new subclass of lipolytic enzymes

    International Nuclear Information System (INIS)

    Escherichia coli thioesterase/protease I is a 183 amino acid protein with a molecular mass of 20500. This protein belongs to a new subclass of lipolytic enzymes of the serine protease superfamily, but with a new GDSLS consensus motif, of which no structure has yet been determined. The protein forms a tetramer at pH values above 6.5 and exists as a monomer at lower pH values. Both monomer and tetramer are catalytically active. From analysis of a set of heteronuclear multidimensional NMR spectra with uniform and specific amino acid labeled protein samples, we have obtained near-complete resonance assignments of the backbone 1H,13 C and 15N nuclei (BMRB databank accession number 4060). The secondary structure of E. coli thioesterase/protease I was further deduced from the consensus chemical shift indices, backbone short- and medium-range NOEs, and amide proton exchange rates. The protein was found to consist of four β-strands and seven α-helices, arranged in alternate order. The four β-strands were shown to form a parallel β-sheet. The topological arrangement of the β-strands of -1x, +2x, +1x appears to resemble that of the core region of the αβ hydrolase superfamily, typically found in common lipases and esterases. However, substantial differences, such as the number of β-strands and the location of the catalytic triad residues, make it difficult to give a definitive classification of the structure of E. coli thioesterase/protease I at present

  18. 4-Oxalocrotonate tautomerase, a 41-kDa homohexamer: backbone and side-chain resonance assignments, solution secondary structure, and location of active site residues by heteronuclear NMR spectroscopy.

    OpenAIRE

    Stivers, J T; Abeygunawardana, C; Whitman, C. P.; Mildvan, A. S.

    1996-01-01

    4-Oxalocrotonate tautomerase (4-OT), a homohexamer consisting of 62 residues per subunit, catalyzes the isomerization of unsaturated alpha-keto acids using Pro-1 as a general base (Stivers et al., 1996a, 1996b). We report the backbone and side-chain 1H, 15N, and 13C NMR assignments and the solution secondary structure for 4-OT using 2D and 3D homonuclear and heteronuclear NMR methods. The subunit secondary structure consists of an alpha-helix (residues 13-30), two beta-strands (beta 1, residu...

  19. Towards Automated Structure-Based NMR Resonance Assignment

    Science.gov (United States)

    Jang, Richard; Gao, Xin; Li, Ming

    We propose a general framework for solving the structure-based NMR backbone resonance assignment problem. The core is a novel 0-1 integer programming model that can start from a complete or partial assignment, generate multiple assignments, and model not only the assignment of spins to residues, but also pairwise dependencies consisting of pairs of spins to pairs of residues. It is still a challenge for automated resonance assignment systems to perform the assignment directly from spectra without any manual intervention. To test the feasibility of this for structure-based assignment, we integrated our system with our automated peak picking and sequence-based resonance assignment system to obtain an assignment for the protein TM1112 with 91% recall and 99% precision without manual intervention. Since using a known structure has the potential to allow one to use only N-labeled NMR data and avoid the added expense of using C-labeled data, we work towards the goal of automated structure-based assignment using only such labeled data. Our system reduced the assignment error of Xiong-Pandurangan-Bailey-Kellogg's contact replacement (CR) method, which to our knowledge is the most error-tolerant method for this problem, by 5 folds on average. By using an iterative algorithm, our system has the added capability of using the NOESY data to correct assignment errors due to errors in predicting the amino acid and secondary structure type of each spin system. On a publicly available data set for Ubiquitin, where the type prediction accuracy is 83%, we achieved 91% assignment accuracy, compared to the 59% accuracy that was obtained without correcting for typing errors.

  20. Complete assignment of 1H, 13C and 15N chemical shifts for bovine β-lactoglobulin: Secondary structure and topology of the native state is retained in a partially unfolded form

    International Nuclear Information System (INIS)

    Although β-lactoglobulin (β-LG) has been studied extensively for more than 50 years, its physical properties in solution are not yet understood fully in terms of its three-dimensional (3D) structure. For example, despite a recent high-resolution crystal structure, it is still not clear why the two common variants of bovine β-LG which differ by just two residues have different aggregation properties during milk processing. We have conducted solution-state NMR studies on a recombinant form of the A variant of β-LG at low pH conditions where the protein is partially unfolded and exists as a monomer rather than a dimer. Using a13 C,15N-labelled sample, expressed in Pichia pastoris, we have employed the standard combination of 3D heteronuclear NMR techniques to obtain near complete assignments of proton, carbon and nitrogen resonances. Using a novel pulse sequence we were able to obtain additional assignments, in particular those of methyl groups in residues preceding proline within the sequence. From chemical shifts and on the basis of inter-residue NOEs, we have inferred the secondary structure and topology of monomeric β-LG A. It includes eight antiparallel β-strands arranged in a barrel, flanked by an α-helix, which is typical of a member of the lipocalin family. A detailed comparison with the crystal structure of the dimeric form (for a mixture of A and B variants) at pH 6.5 reveals a close resemblance in both secondary structure and overall topology. Both forms have a ninth β-strand which, at the higher pH, forms part of the dimer interface. These studies represent the first full NMR assignment of β-LG and will form the basis for a complete characterisation of the solution structure and dynamics of this protein and its variants

  1. On pole structure assignment in linear systems

    Czech Academy of Sciences Publication Activity Database

    Loiseau, J.-J.; Zagalak, Petr

    2009-01-01

    Roč. 82, č. 7 (2009), s. 1179-1192. ISSN 0020-7179 R&D Projects: GA ČR(CZ) GA102/07/1596 Institutional research plan: CEZ:AV0Z10750506 Keywords : linear systems * linear state feedback * pole structure assignment Subject RIV: BC - Control Systems Theory Impact factor: 1.124, year: 2009 http://library.utia.cas.cz/separaty/2009/AS/zagalak-on pole structure assignment in linear systems.pdf

  2. Monothiodibenzoylmethane: Structural and vibrational assignments

    DEFF Research Database (Denmark)

    Hansen, Bjarke Knud Vilster; Gorski, Alexander; Posokhov, Yevgen;

    2007-01-01

    The vibrational structure of the title compound (1,3-diphenyl-3-thioxopropane-1-one, TDBM) was studied by a variety of experimental and theoretical methods. The stable ground state configuration of TDBM was investigated by IR absorption measurements in different media, by LD polarization spectros...... to an “open”, non-chelated enethiol form (t-TCC), thereby supporting the previous conclusions by Posokhov et al. No obvious indications of the contribution of other forms to the observed spectra could be found....

  3. Unifying Temporal and Structural Credit Assignment Problems

    Science.gov (United States)

    Agogino, Adrian K.; Tumer, Kagan

    2004-01-01

    Single-agent reinforcement learners in time-extended domains and multi-agent systems share a common dilemma known as the credit assignment problem. Multi-agent systems have the structural credit assignment problem of determining the contributions of a particular agent to a common task. Instead, time-extended single-agent systems have the temporal credit assignment problem of determining the contribution of a particular action to the quality of the full sequence of actions. Traditionally these two problems are considered different and are handled in separate ways. In this article we show how these two forms of the credit assignment problem are equivalent. In this unified frame-work, a single-agent Markov decision process can be broken down into a single-time-step multi-agent process. Furthermore we show that Monte-Carlo estimation or Q-learning (depending on whether the values of resulting actions in the episode are known at the time of learning) are equivalent to different agent utility functions in a multi-agent system. This equivalence shows how an often neglected issue in multi-agent systems is equivalent to a well-known deficiency in multi-time-step learning and lays the basis for solving time-extended multi-agent problems, where both credit assignment problems are present.

  4. Sequence-specific 1H NMR assignments, secondary structure, and location of the calcium binding site in the first epidermal growth factor like domain of blood coagulation factor IX

    International Nuclear Information System (INIS)

    Factor IX is a blood clotting protein that contains three regions, including a γ-carboxyglutamic acid (Gla) domain, two tandemly connected epidermal growth factor like (EGF-like) domains, and a serine protease region. The protein exhibits a high-affinity calcium binding site in the first EGF0like domain, in addition to calcium binding in the Gla domain. The first EGF-like domain, factor IX (45-87), has been synthesized. Sequence-specific resonance assignment of the peptide has been made by using 2D NMR techniques, and its secondary structure has been determined. The protein is found to have two antiparallel β-sheets, and preliminary distance geometry calculations indicate that the protein has two domains, separated by Trp28, with the overall structure being similar to that of EGF. An NMR investigation of the calcium-bound first EGF-like domain indicates the presence and location of a calcium binding site involving residues on both strands of one of the β-sheets as well as the N-terminal region of the peptide. These results suggest that calcium binding in the first EGF-like domain could induce long-range (possibly interdomain) conformational changes in factor IX, rather than causing structural alterations in the EGF-like domain itself

  5. Sequential 1H NMR assignments and secondary structure of the B domain of staphylococcal protein A: Structural changes between the free B domain in solution and the Fc-bound B domain in crystal

    International Nuclear Information System (INIS)

    The recombinant B domain (FB) of staphylococcal protein A, which specifically binds to the Fc portion of immunoglobulin G (IgG), has been investigated with the use of two-dimensional proton nuclear magnetic resonance spectroscopy. All backbone and side-chain proton resonances of FB (60 amino acid residues), except the amide proton resonance of Ala2, were assigned by the sequential assignment procedures by using double-quantum-filtered correlated spectroscopy (DQF-COSY), homonuclear Hartmann-Hahn spectroscopy (HOHAHA), and nuclear Overhauser enhancement spectroscopy (NOESY). On the basis of the NOESY data, three helical regions, Glu9-His19, Glu25-Asp37, and Ser42-Ala55, were identified in the free FB in solution. Existence of two of the three helical regions, Glu9-His19 and Glu25-Asp37, is consistent with the X-ray crystallographic structure of the Fc-bound FB. By contrast, in the Fc-bound FB as revealed by the X-ray analysis, the Ser42-Glu48 segment and no structural information has been available in the Ala49-Ala55 segment. The authors suggest that a significant conformation change is induced in the C-terminal region of FB when it is bound to the Fc portion of IgG

  6. Chapter V: Secondary landscape structure

    International Nuclear Information System (INIS)

    This chapter deals with the secondary landscape structure of the Slovak Republic. It consists of next subchapters: (1) Land use pattern; (2) Special landscape structures; (3) Real vegetation. The secondary landscape structure consists of the elements influenced by man, created or recreated. They represent material elements with a particular spatial delimitation in the landscape. Vegetation, above all forest vegetation, is the indispensable part of the secondary landscape structure. Special space was given to the historical landscape structure

  7. Structure elucidation of secondary natural products

    International Nuclear Information System (INIS)

    The presented thesis deals with the structure elucidation of secondary natural products. Most of the compounds under investigation were terpenes, especially triterpenes, alkaloids and stilbenoids. Besides characterizing a multitude of already known and also new compounds, it was possible to detect and correct wrongly assigned literature data. The methodological aspect of this thesis lies - beside in the utilization of modern 2D NMR spectroscopy - in the evaluation of computer assisted structure elucidation (CASE) techniques in the course of spectroscopy supported structure elucidation processes. (author)

  8. The assignment of elementary school pupils to secondary school types: A correlational study.

    NARCIS (Netherlands)

    P. Groeneboom; J. Hoogstraten; G.J. Mellenbergh; J.P. van Santen

    1978-01-01

    Examined relationships between personality, intelligence, and achievement measures and the allocation to 1 of 6 secondary school types; Ss were 135 6th graders. Results of discriminant analyses indicated that personality scores predicted only a small portion of pupil assignment, whereas achievement

  9. Influence of assignment on the prediction of transmembrane helices in protein structures.

    Science.gov (United States)

    Pylouster, Jean; Bornot, Aurélie; Etchebest, Catherine; de Brevern, Alexandre G

    2010-11-01

    α-Helical transmembrane proteins (TMPα) are composed of a series of helices embedded in the lipid bilayer. Due to technical difficulties, few 3D structures are available. Therefore, the design of structural models of TMPα is of major interest. We study the secondary structures of TMPα by analyzing the influence of secondary structures assignment methods (SSAMs). For this purpose, a published and updated benchmark databank of TMPα is used and several SSAMs (9) are evaluated. The analysis of the results points to significant differences in SSA depending on the methods used. Pairwise comparisons between SSAMs led to more than 10% of disagreement. Helical regions corresponding to transmembrane zones are often correctly characterized. The study of the sequence-structure relationship shows very limited differences with regard to the structural disagreement. Secondary structure prediction based on Bayes' rule and using only a single sequence give correct prediction rates ranging from 78 to 81%. A structural alphabet approach gives a slightly better prediction, i.e., only 2% less than the best equivalent approach, whereas the prediction rate with a very different assignment bypasses 86%. This last result highlights the importance of the correct assignment choice to evaluate the prediction assessment. PMID:20349322

  10. Flexibility of Protein Secondary Structures

    Science.gov (United States)

    Emberly, Eldon; Mukhopadhyay, Ranjan; Tang, Chao; Wingreen, Ned

    2004-03-01

    Proteins consist of compact packings of secondary structural elements: helices and sheets comprised of strands. The deformations of these structures often play an important role in determining the final shape of the protein (i.e. coiled coils or beta-barrels). We have performed a principal component analysis on secondary structural elements extracted from the protein structure database to determine their flexible modes. For helices we find only two dominant internal modes: bend and twist. Sheets also only display two dominant modes: in-sheet bend and a spiral twist. We report on the scaling of these modes with secondary element size. For helices, the dynamic normal modes of a simple spring model are able to recapitulate the modes and scalings found. For sheets, we find different scaling behaviors for parallel and anti-parallel sheets and these differences can not be accounted for using a simple spring model.

  11. Combined automated NOE assignment and structure calculation with CYANA

    Energy Technology Data Exchange (ETDEWEB)

    Güntert, Peter, E-mail: guentert@em.uni-frankfurt.de; Buchner, Lena [Goethe University Frankfurt am Main, Center for Biomolecular Magnetic Resonance, Institute of Biophysical Chemistry (Germany)

    2015-08-15

    The automated assignment of NOESY cross peaks has become a fundamental technique for NMR protein structure analysis. A widely used algorithm for this purpose is implemented in the program CYANA. It has been used for a large number of structure determinations of proteins in solution but was so far not described in full detail. In this paper we present a complete description of the CYANA implementation of automated NOESY assignment, which differs extensively from its predecessor CANDID by the use of a consistent probabilistic treatment, and we discuss its performance in the second round of the critical assessment of structure determination by NMR.

  12. Combined automated NOE assignment and structure calculation with CYANA

    International Nuclear Information System (INIS)

    The automated assignment of NOESY cross peaks has become a fundamental technique for NMR protein structure analysis. A widely used algorithm for this purpose is implemented in the program CYANA. It has been used for a large number of structure determinations of proteins in solution but was so far not described in full detail. In this paper we present a complete description of the CYANA implementation of automated NOESY assignment, which differs extensively from its predecessor CANDID by the use of a consistent probabilistic treatment, and we discuss its performance in the second round of the critical assessment of structure determination by NMR

  13. Undergraduates Improve upon Published Crystal Structure in Class Assignment

    Science.gov (United States)

    Horowitz, Scott; Koldewey, Philipp; Bardwell, James C.

    2014-01-01

    Recently, 57 undergraduate students at the University of Michigan were assigned the task of solving a crystal structure, given only the electron density map of a 1.3 Å crystal structure from the electron density server, and the position of the N-terminal amino acid. To test their knowledge of amino acid chemistry, the students were not given the…

  14. Combinatorics of saturated secondary structures of RNA.

    Science.gov (United States)

    Clote, P

    2006-11-01

    Following Zuker (1986), a saturated secondary structure for a given RNA sequence is a secondary structure such that no base pair can be added without violating the definition of secondary structure, e.g., without introducing a pseudoknot. In the Nussinov-Jacobson energy model (Nussinov and Jacobson, 1980), where the energy of a secondary structure is -1 times the number of base pairs, saturated secondary structures are local minima in the energy landscape, hence form kinetic traps during the folding process. Here we present recurrence relations and closed form asymptotic limits for combinatorial problems related to the number of saturated secondary structures. In addition, Python source code to compute the number of saturated secondary structures having k base pairs can be found at the web servers link of bioinformatics.bc.edu/clotelab/. PMID:17147486

  15. 13C-NMR assignment, structure, and dynamics of deoxyoligonucleotides

    International Nuclear Information System (INIS)

    The unique spectral properties of 13C-NMR for studying nucleic acids and some of the important features of 13C-NMR in oligonucleotide studies are demostrated. The main difficulty in studying oligonucleotides by 13C-NMR and recent improvements in NMR instrumentation and advances in oligonucleotide synthesis are presented. The high resolution 13C-NMR spectra, T1 relaxation times and NOEs were measured for duplex of the self-complementary oligo-DNAs: d(CG)3 and d(GGTATACC) are studied. The target of this study is to developed a systematic 13C-NMR spectral assignment and to investigate the structure and dynamics of these two sequences by this techniques. (M.J.C.)

  16. Towards fully automated structure-based NMR resonance assignment of 15N-labeled proteins from automatically picked peaks

    KAUST Repository

    Jang, Richard

    2011-03-01

    In NMR resonance assignment, an indispensable step in NMR protein studies, manually processed peaks from both N-labeled and C-labeled spectra are typically used as inputs. However, the use of homologous structures can allow one to use only N-labeled NMR data and avoid the added expense of using C-labeled data. We propose a novel integer programming framework for structure-based backbone resonance assignment using N-labeled data. The core consists of a pair of integer programming models: one for spin system forming and amino acid typing, and the other for backbone resonance assignment. The goal is to perform the assignment directly from spectra without any manual intervention via automatically picked peaks, which are much noisier than manually picked peaks, so methods must be error-tolerant. In the case of semi-automated/manually processed peak data, we compare our system with the Xiong-Pandurangan-Bailey- Kellogg\\'s contact replacement (CR) method, which is the most error-tolerant method for structure-based resonance assignment. Our system, on average, reduces the error rate of the CR method by five folds on their data set. In addition, by using an iterative algorithm, our system has the added capability of using the NOESY data to correct assignment errors due to errors in predicting the amino acid and secondary structure type of each spin system. On a publicly available data set for human ubiquitin, where the typing accuracy is 83%, we achieve 91% accuracy, compared to the 59% accuracy obtained without correcting for such errors. In the case of automatically picked peaks, using assignment information from yeast ubiquitin, we achieve a fully automatic assignment with 97% accuracy. To our knowledge, this is the first system that can achieve fully automatic structure-based assignment directly from spectra. This has implications in NMR protein mutant studies, where the assignment step is repeated for each mutant. © Copyright 2011, Mary Ann Liebert, Inc.

  17. NMR Analysis of RNA Bulged Structures: Tabu Search Application in NOE Signal Assignment

    International Nuclear Information System (INIS)

    Bulges are the most frequently occurring RNA secondary structural elements of high functional importance. At present, they are known to participate in the process of RNA folding, RNA-RNA and RNA-protein interactions. It has been shown that bulges can induce destabilization in RNA duplexes and the extent of the destabilization depends on many factors such as the size of the bulge, the nature of the bulge bases, and the flanking residues. However, relatively very little is known about these structural elements. Only several studies have been performed to address the preferred conformations of bulged residues in DNA and RNA duplexes. The knowledge of spatial structure of RNA bulges in solution requires application of NMR spectroscopy. A considerable part of NMR analytical process of RNA fragment is based on automatic methods. However, manual assistance is still essential in resonance assignment. Thus, there has been a great need to introduce automatic procedures also at this level. We propose a tabu search algorithm being a tool for an automatic resonance assignment. The assignment is determined by NOE pathways, which can be constructed in aromatic/anomeric region of 2D NOESY spectrum generated during NMR experiment. Computational tests demonstrate performance of the tabu search applied to the experimental spectra of RNA bulged duplexes. (author)

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

    Science.gov (United States)

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

    2014-10-20

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

  19. Secondary structure of synthetic oligopeptides

    CERN Document Server

    Martinez-Insua, M

    2000-01-01

    The secondary structure of three hydrophobic peptides P2, PRMo and P4 was studied by a combination of Circular Dichroism (CD), Fourier Transform InfraRed (FTIR) and Photoinduced Electron Transfer (PET). These peptides were fluorescence labelled in the central part of the backbone and contained two modified glutamic acid residues (relative positions i, i+4): one conjugated with the fluorescence methoxynapththalene electron donor (DON) and the other with the piperidone electron acceptor (ACC). The three peptides were synthesised to study the length dependence of the switch between alpha-helix and the 3 sub 1 sub 0 -helix conformations, previously observed for peptide PRM1 (Hungerford et al., Angew. Chem., Int. Ed. Engl., 1996, 35, 326-329). The CD and FTIR data indicated that peptides P2, PRMo and P4 adopt alpha-helical conformation in organic media in the temperature range studied and no conformational switch was detected. Furthermore, a mathematical correlation was observed in the PET data, questioning the ag...

  20. Gene3D: structural assignments for the biologist and bioinformaticist alike

    OpenAIRE

    Buchan, D. W. A.; Rison, S. C. G.; Bray, J.E.; Lee, D; Pearl, F.; Thornton, J M; Orengo, C. A.

    2003-01-01

    The Gene3D database ( http: / / www. biochem. ucl. ac. uk/ bsm/ cath_ new/ Gene3D/) provides structural assignments for genes within complete genomes. These are available via the internet from either the World Wide Web or FTP. Assignments are made using PSI- BLAST and subsequently processed using the DRange protocol. The DRange protocol is an empirically benchmarked method for assessing the validity of structural assignments made using sequence searching methods where appropriate assignment s...

  1. Combinatorics of locally optimal RNA secondary structures.

    Science.gov (United States)

    Fusy, Eric; Clote, Peter

    2014-01-01

    It is a classical result of Stein and Waterman that the asymptotic number of RNA secondary structures is 1.104366∙n-3/2∙2.618034n. Motivated by the kinetics of RNA secondary structure formation, we are interested in determining the asymptotic number of secondary structures that are locally optimal, with respect to a particular energy model. In the Nussinov energy model, where each base pair contributes -1 towards the energy of the structure, locally optimal structures are exactly the saturated structures, for which we have previously shown that asymptotically, there are 1.07427∙n-3/2∙2.35467n many saturated structures for a sequence of length n. In this paper, we consider the base stacking energy model, a mild variant of the Nussinov model, where each stacked base pair contributes -1 toward the energy of the structure. Locally optimal structures with respect to the base stacking energy model are exactly those secondary structures, whose stems cannot be extended. Such structures were first considered by Evers and Giegerich, who described a dynamic programming algorithm to enumerate all locally optimal structures. In this paper, we apply methods from enumerative combinatorics to compute the asymptotic number of such structures. Additionally, we consider analogous combinatorial problems for secondary structures with annotated single-stranded, stacking nucleotides (dangles). PMID:23263300

  2. Pairwise amino acid secondary structural propensities

    Science.gov (United States)

    Chemmama, Ilan E.; Chapagain, Prem P.; Gerstman, Bernard S.

    2015-04-01

    We investigate the propensities for amino acids to form a specific secondary structure when they are paired with other amino acids. Our investigations use molecular dynamics (MD) computer simulations, and we compare the results to those from the Protein Data Bank (PDB). Proper comparison requires weighting of the MD results in a manner consistent with the relative frequency of appearance in the PDB of each possible pair of amino acids. We find that the propensity for an amino acid to assume a secondary structure varies dramatically depending on the amino acid that is before or after it in the primary sequence. This cooperative effect means that when selecting amino acids to facilitate the formation of a secondary structure in peptide engineering experiments, the adjacent amino acids must be considered. We also examine the preference for a secondary structure in bacterial proteins and compare the results to those of human proteins.

  3. Current perspectives on RNA secondary structure probing.

    Science.gov (United States)

    Kenyon, Julia; Prestwood, Liam; Lever, Andrew

    2014-08-01

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

  4. Strong Eukaryotic IRESs Have Weak Secondary Structure

    OpenAIRE

    Xuhua Xia; Martin Holcik

    2009-01-01

    BACKGROUND: The objective of this work was to investigate the hypothesis that eukaryotic Internal Ribosome Entry Sites (IRES) lack secondary structure and to examine the generality of the hypothesis. METHODOLOGY/PRINCIPAL FINDINGS: IRESs of the yeast and the fruit fly are located in the 5'UTR immediately upstream of the initiation codon. The minimum folding energy (MFE) of 60 nt RNA segments immediately upstream of the initiation codons was calculated as a proxy of secondary structure stabili...

  5. Strong eukaryotic IRESs have weak secondary structure.

    Directory of Open Access Journals (Sweden)

    Xuhua Xia

    Full Text Available BACKGROUND: The objective of this work was to investigate the hypothesis that eukaryotic Internal Ribosome Entry Sites (IRES lack secondary structure and to examine the generality of the hypothesis. METHODOLOGY/PRINCIPAL FINDINGS: IRESs of the yeast and the fruit fly are located in the 5'UTR immediately upstream of the initiation codon. The minimum folding energy (MFE of 60 nt RNA segments immediately upstream of the initiation codons was calculated as a proxy of secondary structure stability. MFE of the reverse complements of these 60 nt segments was also calculated. The relationship between MFE and empirically determined IRES activity was investigated to test the hypothesis that strong IRES activity is associated with weak secondary structure. We show that IRES activity in the yeast and the fruit fly correlates strongly with the structural stability, with highest IRES activity found in RNA segments that exhibit the weakest secondary structure. CONCLUSIONS: We found that a subset of eukaryotic IRESs exhibits very low secondary structure in the 5'-UTR sequences immediately upstream of the initiation codon. The consistency in results between the yeast and the fruit fly suggests a possible shared mechanism of cap-independent translation initiation that relies on an unstructured RNA segment.

  6. Predicting Protein Secondary Structure with Markov Models

    DEFF Research Database (Denmark)

    Fischer, Paul; Larsen, Simon; Thomsen, Claus

    2004-01-01

    The primary structure of a protein is the sequence of its amino acids. The secondary structure describes structural properties of the molecule such as which parts of it form sheets, helices or coils. Spacial and other properties are described by the higher order structures. The classification tas...... Markov model for this task. Classifications that are purely based on statistical models might not always be biologically meaningful. We present combinatorial methods to incorporate biological background knowledge to enhance the prediction performance.......The primary structure of a protein is the sequence of its amino acids. The secondary structure describes structural properties of the molecule such as which parts of it form sheets, helices or coils. Spacial and other properties are described by the higher order structures. The classification task...

  7. Secondary structures in long compact polymers.

    Science.gov (United States)

    Oberdorf, Richard; Ferguson, Allison; Jacobsen, Jesper L; Kondev, Jané

    2006-11-01

    Compact polymers are self-avoiding random walks that visit every site on a lattice. This polymer model is used widely for studying statistical problems inspired by protein folding. One difficulty with using compact polymers to perform numerical calculations is generating a sufficiently large number of randomly sampled configurations. We present a Monte Carlo algorithm that uniformly samples compact polymer configurations in an efficient manner, allowing investigations of chains much longer than previously studied. Chain configurations generated by the algorithm are used to compute statistics of secondary structures in compact polymers. We determine the fraction of monomers participating in secondary structures, and show that it is self-averaging in the long-chain limit and strictly less than 1. Comparison with results for lattice models of open polymer chains shows that compact chains are significantly more likely to form secondary structure. PMID:17279930

  8. Enumerating secondary structures and structural moieties for circular RNAs

    CERN Document Server

    Cuesta, José A

    2016-01-01

    A quantitative characterization of the relationship between molecular sequence and structure is essential to improve our understanding of how function emerges. This particular genotype-phenotype map has been often studied in the context of RNA sequences, with the folded configurations standing as a proxy for the phenotype. Here, we count the secondary structures of circular RNAs of length $n$ and calculate the asymptotic distributions of different structural moieties, such as stems or hairpin loops, by means of symbolic combinatorics. Circular RNAs differ in essential ways from their linear counterparts. From the mathematical viewpoint, the enumeration of the corresponding secondary structures demands the use of combinatorial techniques additional to those used for linear RNAs. The asymptotic number of secondary structures for circular RNAs grows as $a^nn^{-5/2}$, with a depending on particular constraints applied to the secondary structure. The abundance of any structural moiety is normally distributed in th...

  9. Automated assignment of NMR chemical shifts based on a known structure and 4D spectra.

    Science.gov (United States)

    Trautwein, Matthias; Fredriksson, Kai; Möller, Heiko M; Exner, Thomas E

    2016-08-01

    Apart from their central role during 3D structure determination of proteins the backbone chemical shift assignment is the basis for a number of applications, like chemical shift perturbation mapping and studies on the dynamics of proteins. This assignment is not a trivial task even if a 3D protein structure is known and needs almost as much effort as the assignment for structure prediction if performed manually. We present here a new algorithm based solely on 4D [(1)H,(15)N]-HSQC-NOESY-[(1)H,(15)N]-HSQC spectra which is able to assign a large percentage of chemical shifts (73-82 %) unambiguously, demonstrated with proteins up to a size of 250 residues. For the remaining residues, a small number of possible assignments is filtered out. This is done by comparing distances in the 3D structure to restraints obtained from the peak volumes in the 4D spectrum. Using dead-end elimination, assignments are removed in which at least one of the restraints is violated. Including additional information from chemical shift predictions, a complete unambiguous assignment was obtained for Ubiquitin and 95 % of the residues were correctly assigned in the 251 residue-long N-terminal domain of enzyme I. The program including source code is available at https://github.com/thomasexner/4Dassign . PMID:27484442

  10. Secondary structure of fluorescence labelled synthetic peptides

    CERN Document Server

    Martin, A S

    2000-01-01

    A series of eight synthetic oligopeptides has been prepared and their secondary structures investigated using various techniques. The project represents a continuation of an investigation into thermally induced changes in secondary structure. Following the previously reported results, the change in structure was initially thought to represent a change from an alpha-helix at low temperature to 3 sub 1 sub 0 -helix at high temperature. However, the results reported herein suggest the peptides retain an alpha-helical configuration at all temperatures studied, but that this helix can adopt at least two related forms. The difference in the structures relates to the nature of the H-bonds which may or may not involve an additional interaction from water molecules or side-chains. The peptides were encouraged to adopt a helical configuration by the inclusion of alpha- aminoisobutyric acid (Aib) residues. Also, modified forms of glutamic acid were included in the sequences. These had pendant donor (4-methoxy naphthalen...

  11. Effects of Verbal Event Structure on Online Thematic Role Assignment

    Science.gov (United States)

    Malaia, Evie; Wilbur, Ronnie B.; Weber-Fox, Christine

    2012-01-01

    Event structure describes the relationships between general semantics ("Aktionsart") of the verb and its syntactic properties, separating verbs into two classes: telic verbs, which denote change of state events with an inherent end-point or boundary ("catch, rescue"), and atelic, which refer to homogenous activities ("tease, host"). As telic verbs…

  12. Efficient eigenvalue assignment by state and output feedback with applications for large space structures

    Science.gov (United States)

    Vannell, Eric C.; Kenny, Sean P.; Maghami, Peiman G.

    1995-01-01

    The erection and deployment of large flexible structures having thousands of degrees of freedom requires controllers based on new techniques of eigenvalue assignment that are computationally stable and more efficient. Scientists at NASA Langley Research Center have developed a novel and efficient algorithm for the eigenvalue assignment of large, time-invariant systems using full-state and output feedback. The objectives of this research were to improve upon the output feedback version of this algorithm, to produce a toolbox of MATLAB functions based on the efficient eigenvalue assignment algorithm, and to experimentally verify the algorithm and software by implementing controllers designed using the MATLAB toolbox on the phase 2 configuration of NASA Langley's controls-structures interaction evolutionary model, a laboratory model used to study space structures. Results from laboratory tests and computer simulations show that effective controllers can be designed using software based on the efficient eigenvalue assignment algorithm.

  13. Statistical mechanics of structural and temporal credit assignment effects on learning in neural networks

    Science.gov (United States)

    Saito, Hiroshi; Katahira, Kentaro; Okanoya, Kazuo; Okada, Masato

    2011-05-01

    Neural networks can learn flexible input-output associations by changing their synaptic weights. The representational performance and learning dynamics of neural networks are intensively studied in several fields. Neural networks face the “credit assignment problem” in situations in which only incomplete performance evaluations are available. The credit assignment problem is that a network should assign credit or blame for its behaviors according to the contribution to the network performance. In reinforcement learning, a scalar evaluation signal is delivered to a network. The two main types of credit assignment problems in reinforcement learning are structural and temporal, that is, which parameters of the network (structural) and which past network activities (temporal) are related to an evaluation signal given from an environment. In this study, we apply statistical mechanical analysis to the learning processes in a simple neural network model to clarify the effects of two kinds of credit assignments and their interactions. Our model is based on node perturbation learning with eligibility trace. Node perturbation is a stochastic gradient learning method that can solve structural credit assignment problems by introducing a perturbation into the system output. The eligibility trace preserves the past network activities with a temporal credit to deal with the delay of an instruction signal. We show that both credit assignment effects mutually interact and the optimal time constant of the eligibility trace varies not only for the evaluation delay but also the network size.

  14. RNA secondary structure prediction using soft computing.

    Science.gov (United States)

    Ray, Shubhra Sankar; Pal, Sankar K

    2013-01-01

    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

  15. On the Variability of Neural Network Classification Measures in the Protein Secondary Structure Prediction Problem

    Directory of Open Access Journals (Sweden)

    Eric Sakk

    2013-01-01

    Full Text Available We revisit the protein secondary structure prediction problem using linear and backpropagation neural network architectures commonly applied in the literature. In this context, neural network mappings are constructed between protein training set sequences and their assigned structure classes in order to analyze the class membership of test data and associated measures of significance. We present numerical results demonstrating that classifier performance measures can vary significantly depending upon the classifier architecture and the structure class encoding technique. Furthermore, an analytic formulation is introduced in order to substantiate the observed numerical data. Finally, we analyze and discuss the ability of the neural network to accurately model fundamental attributes of protein secondary structure.

  16. Computing folding pathways between RNA secondary structures.

    Science.gov (United States)

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

    2010-03-01

    Given an RNA sequence and two designated secondary structures A, B, we describe a new algorithm that computes a nearly optimal folding pathway from A to B. The algorithm, RNAtabupath, employs a tabu semi-greedy heuristic, known to be an effective search strategy in combinatorial optimization. Folding pathways, sometimes called routes or trajectories, are computed by RNAtabupath in a fraction of the time required by the barriers program of Vienna RNA Package. We benchmark RNAtabupath with other algorithms to compute low energy folding pathways between experimentally known structures of several conformational switches. The RNApathfinder web server, source code for algorithms to compute and analyze pathways and supplementary data are available at http://bioinformatics.bc.edu/clotelab/RNApathfinder. PMID:20044352

  17. Structure of subcomplex Iβ of mammalian respiratory complex I leads to new supernumerary subunit assignments.

    Science.gov (United States)

    Zhu, Jiapeng; King, Martin S; Yu, Minmin; Klipcan, Liron; Leslie, Andrew G W; Hirst, Judy

    2015-09-29

    Mitochondrial complex I (proton-pumping NADH:ubiquinone oxidoreductase) is an essential respiratory enzyme. Mammalian complex I contains 45 subunits: 14 conserved "core" subunits and 31 "supernumerary" subunits. The structure of Bos taurus complex I, determined to 5-Å resolution by electron cryomicroscopy, described the structure of the mammalian core enzyme and allowed the assignment of 14 supernumerary subunits. Here, we describe the 6.8-Å resolution X-ray crystallography structure of subcomplex Iβ, a large portion of the membrane domain of B. taurus complex I that contains two core subunits and a cohort of supernumerary subunits. By comparing the structures and composition of subcomplex Iβ and complex I, supported by comparisons with Yarrowia lipolytica complex I, we propose assignments for eight further supernumerary subunits in the structure. Our new assignments include two CHCH-domain containing subunits that contain disulfide bridges between CX9C motifs; they are processed by the Mia40 oxidative-folding pathway in the intermembrane space and probably stabilize the membrane domain. We also assign subunit B22, an LYR protein, to the matrix face of the membrane domain. We reveal that subunit B22 anchors an acyl carrier protein (ACP) to the complex, replicating the LYR protein-ACP structural module that was identified previously in the hydrophilic domain. Thus, we significantly extend knowledge of how the mammalian supernumerary subunits are arranged around the core enzyme, and provide insights into their roles in biogenesis and regulation. PMID:26371297

  18. A folding algorithm for extended RNA secondary structures

    OpenAIRE

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

    2011-01-01

    Motivation: RNA secondary structure contains many non-canonical base pairs of different pair families. Successful prediction of these structural features leads to improved secondary structures with applications in tertiary structure prediction and simultaneous folding and alignment. Results: We present a theoretical model capturing both RNA pair families and extended secondary structure motifs with shared nucleotides using 2-diagrams. We accompany this model with a number of programs for para...

  19. RNA-SSPT: RNA Secondary Structure Prediction Tools.

    Science.gov (United States)

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

    2013-01-01

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

  20. Structural characterization of homogalacturonan by NMR spectroscopy - assignment of reference compounds

    DEFF Research Database (Denmark)

    Petersen, Bent O.; Meier, Sebastian; Duus, Jens Øllgaard;

    2008-01-01

    Complete assignment of 1H and 13C NMR of six hexagalactopyranuronic acids with varying degree and pattern of methyl esterification is reported. The NMR experiments were run at room temperature using approximately 2 mg of sample making this method convenient for studying the structure of...

  1. Structured Role Assignment and Other Techniques for Facilitating Process in Adolescent Psychotherapy Groups.

    Science.gov (United States)

    Corder, Billie F.; Whiteside, Reid

    1990-01-01

    Describes application of techniques for structuring interchange and feedback process in adolescent psychotherapy groups, including random assignment of "roles" for each member during sessions, "parent hot seat" exercises, group goal booklets, and negotiation exercises. Techniques discussed have proven helpful in ensuring effective group…

  2. Combining neural networks for protein secondary structure prediction

    DEFF Research Database (Denmark)

    Riis, Søren Kamaric

    1995-01-01

    In this paper structured neural networks are applied to the problem of predicting the secondary structure of proteins. A hierarchical approach is used where specialized neural networks are designed for each structural class and then combined using another neural network. The submodels are designe...... is better than most secondary structure prediction methods based on single sequences even though this model contains much fewer parameters...

  3. Systematic evaluation of combined automated NOE assignment and structure calculation with CYANA

    International Nuclear Information System (INIS)

    The automated assignment of NOESY cross peaks has become a fundamental technique for NMR protein structure analysis. A widely used algorithm for this purpose is implemented in the program CYANA. It has been used for a large number of structure determinations of proteins in solution but a systematic evaluation of its performance has not yet been reported. In this paper we systematically analyze the reliability of combined automated NOESY assignment and structure calculation with CYANA under a variety of conditions on the basis of the experimental NMR data sets of ten proteins. To evaluate the robustness of the algorithm, the original high-quality experimental data sets were modified in different ways to simulate the effect of data imperfections, i.e. incomplete or erroneous chemical shift assignments, missing NOESY cross peaks, inaccurate peak positions, inaccurate peak intensities, lower dimensionality NOESY spectra, and higher tolerances for the matching of chemical shifts and peak positions. The results show that the algorithm is remarkably robust with regard to imperfections of the NOESY peak lists and the chemical shift tolerances but susceptible to lacking or erroneous resonance assignments, in particular for nuclei that are involved in many NOESY cross peaks

  4. A novel strategy for NMR resonance assignment and protein structure determination

    International Nuclear Information System (INIS)

    The quality of protein structures determined by nuclear magnetic resonance (NMR) spectroscopy is contingent on the number and quality of experimentally-derived resonance assignments, distance and angular restraints. Two key features of protein NMR data have posed challenges for the routine and automated structure determination of small to medium sized proteins; (1) spectral resolution – especially of crowded nuclear Overhauser effect spectroscopy (NOESY) spectra, and (2) the reliance on a continuous network of weak scalar couplings as part of most common assignment protocols. In order to facilitate NMR structure determination, we developed a semi-automated strategy that utilizes non-uniform sampling (NUS) and multidimensional decomposition (MDD) for optimal data collection and processing of selected, high resolution multidimensional NMR experiments, combined it with an ABACUS protocol for sequential and side chain resonance assignments, and streamlined this procedure to execute structure and refinement calculations in CYANA and CNS, respectively. Two graphical user interfaces (GUIs) were developed to facilitate efficient analysis and compilation of the data and to guide automated structure determination. This integrated method was implemented and refined on over 30 high quality structures of proteins ranging from 5.5 to 16.5 kDa in size.

  5. Prediction of protein folding rates from simplified secondary structure alphabet.

    Science.gov (United States)

    Huang, Jitao T; Wang, Titi; Huang, Shanran R; Li, Xin

    2015-10-21

    Protein folding is a very complicated and highly cooperative dynamic process. However, the folding kinetics is likely to depend more on a few key structural features. Here we find that secondary structures can determine folding rates of only large, multi-state folding proteins and fails to predict those for small, two-state proteins. The importance of secondary structures for protein folding is ordered as: extended β strand > α helix > bend > turn > undefined secondary structure>310 helix > isolated β strand > π helix. Only the first three secondary structures, extended β strand, α helix and bend, can achieve a good correlation with folding rates. This suggests that the rate-limiting step of protein folding would depend upon the formation of regular secondary structures and the buckling of chain. The reduced secondary structure alphabet provides a simplified description for the machine learning applications in protein design. PMID:26247139

  6. APSY-NMR for protein backbone assignment in high-throughput structural biology

    Energy Technology Data Exchange (ETDEWEB)

    Dutta, Samit Kumar; Serrano, Pedro; Proudfoot, Andrew; Geralt, Michael [The Scripps Research Institute, Department of Integrative Structural and Computational Biology (United States); Pedrini, Bill [Paul Scherrer Institute (PSI), SwissFEL Project (Switzerland); Herrmann, Torsten [Université de Lyon, Institut des Sciences Analytiques, Centre de RMN à Très Hauts Champs, UMR 5280 CNRS, ENS Lyon, UCB Lyon 1 (France); Wüthrich, Kurt, E-mail: wuthrich@scripps.edu [The Scripps Research Institute, Department of Integrative Structural and Computational Biology (United States)

    2015-01-15

    A standard set of three APSY-NMR experiments has been used in daily practice to obtain polypeptide backbone NMR assignments in globular proteins with sizes up to about 150 residues, which had been identified as targets for structure determination by the Joint Center for Structural Genomics (JCSG) under the auspices of the Protein Structure Initiative (PSI). In a representative sample of 30 proteins, initial fully automated data analysis with the software UNIO-MATCH-2014 yielded complete or partial assignments for over 90 % of the residues. For most proteins the APSY data acquisition was completed in less than 30 h. The results of the automated procedure provided a basis for efficient interactive validation and extension to near-completion of the assignments by reference to the same 3D heteronuclear-resolved [{sup 1}H,{sup 1}H]-NOESY spectra that were subsequently used for the collection of conformational constraints. High-quality structures were obtained for all 30 proteins, using the J-UNIO protocol, which includes extensive automation of NMR structure determination.

  7. APSY-NMR for protein backbone assignment in high-throughput structural biology

    International Nuclear Information System (INIS)

    A standard set of three APSY-NMR experiments has been used in daily practice to obtain polypeptide backbone NMR assignments in globular proteins with sizes up to about 150 residues, which had been identified as targets for structure determination by the Joint Center for Structural Genomics (JCSG) under the auspices of the Protein Structure Initiative (PSI). In a representative sample of 30 proteins, initial fully automated data analysis with the software UNIO-MATCH-2014 yielded complete or partial assignments for over 90 % of the residues. For most proteins the APSY data acquisition was completed in less than 30 h. The results of the automated procedure provided a basis for efficient interactive validation and extension to near-completion of the assignments by reference to the same 3D heteronuclear-resolved [1H,1H]-NOESY spectra that were subsequently used for the collection of conformational constraints. High-quality structures were obtained for all 30 proteins, using the J-UNIO protocol, which includes extensive automation of NMR structure determination

  8. RNA secondary structure prediction from multi-aligned sequences

    OpenAIRE

    Hamada, Michiaki

    2013-01-01

    It has been well accepted that the RNA secondary structures of most functional non-coding RNAs (ncRNAs) are closely related to their functions and are conserved during evolution. Hence, prediction of conserved secondary structures from evolutionarily related sequences is one important task in RNA bioinformatics; the methods are useful not only to further functional analyses of ncRNAs but also to improve the accuracy of secondary structure predictions and to find novel functional RNAs from the...

  9. A tabu search approach for the NMR protein structure-based assignment problem.

    Science.gov (United States)

    Cavuşlar, Gizem; Çatay, Bülent; Apaydın, Mehmet Serkan

    2012-01-01

    Spectroscopy is an experimental technique which exploits the magnetic properties of specific nuclei and enables the study of proteins in solution. The key bottleneck of NMR studies is to map the NMR peaks to corresponding nuclei, also known as the assignment problem. Structure-Based Assignment (SBA) is an approach to solve this computationally challenging problem by using prior information about the protein obtained from a homologous structure. NVR-BIP used the Nuclear Vector Replacement (NVR) framework to model SBA as a binary integer programming problem. In this paper, we prove that this problem is NP-hard and propose a tabu search (TS) algorithm (NVR-TS) equipped with a guided perturbation mechanism to efficiently solve it. NVR-TS uses a quadratic penalty relaxation of NVR-BIP where the violations in the Nuclear Overhauser Effect constraints are penalized in the objective function. Experimental results indicate that our algorithm finds the optimal solution on NVRBIP’s data set which consists of seven proteins with 25 templates (31 to 126 residues). Furthermore, it achieves relatively high assignment accuracies on two additional large proteins, MBP and EIN (348 and 243 residues, respectively), which NVR-BIP failed to solve. The executable and the input files are available for download at http://people.sabanciuniv.edu/catay/NVR-TS/NVR-TS.html. PMID:23221084

  10. Fourier Transform Infrared Spectroscopic Analysis of Protein Secondary Structures

    Institute of Scientific and Technical Information of China (English)

    Jilie KONG; Shaoning YU

    2007-01-01

    Infrared spectroscopy is one of the oldest and well established experimental techniques for the analysis of secondary structure of polypeptides and proteins. It is convenient, non-destructive, requires less sample preparation, and can be used under a wide variety of conditions. This review introduces the recent developments in Fourier transform infrared (FTIR) spectroscopy technique and its applications to protein structural studies. The experimental skills, data analysis, and correlations between the FTIR spectroscopic bands and protein secondary structure components are discussed. The applications of FTIR to the secondary structure analysis, conformational changes, structural dynamics and stability studies of proteins are also discussed.

  11. Automating unambiguous NOE data usage in NVR for NMR protein structure-based assignments.

    Science.gov (United States)

    Akhmedov, Murodzhon; Çatay, Bülent; Apaydın, Mehmet Serkan

    2015-12-01

    Nuclear Magnetic Resonance (NMR) Spectroscopy is an important technique that allows determining protein structure in solution. An important problem in protein structure determination using NMR spectroscopy is the mapping of peaks to corresponding amino acids, also known as the assignment problem. Structure-Based Assignment (SBA) is an approach to solve this problem using a template structure that is homologous to the target. Our previously developed approach Nuclear Vector Replacement-Binary Integer Programming (NVR-BIP) computed the optimal solution for small proteins, but was unable to solve the assignments of large proteins. NVR-Ant Colony Optimization (ACO) extended the applicability of the NVR approach for such proteins. One of the input data utilized in these approaches is the Nuclear Overhauser Effect (NOE) data. NOE is an interaction observed between two protons if the protons are located close in space. These protons could be amide protons, protons attached to the alpha-carbon atom in the backbone of the protein, or side chain protons. NVR only uses backbone protons. In this paper, we reformulate the NVR-BIP model to distinguish the type of proton in NOE data and use the corresponding proton coordinates in the extended formulation. In addition, the threshold value over interproton distances is set in a standard manner for all proteins by extracting the NOE upper bound distance information from the data. We also convert NOE intensities into distance thresholds. Our new approach thus handles the NOE data correctly and without manually determined parameters. We accordingly adapt NVR-ACO solution methodology to these changes. Computational results show that our approaches obtain optimal solutions for small proteins. For the large proteins our ant colony optimization-based approach obtains promising results. PMID:26260854

  12. The architectural network for protein secondary structure prediction

    Directory of Open Access Journals (Sweden)

    Anindya Sundar Panja

    2016-07-01

    Full Text Available Over the past 25 years, the accuracy of proteins secondary structure prediction has improved substantially. Recently evolutionary information taken from the deviation of proteins in some structural family have again enhance prediction accuracy for all these residues predicted correctly is in one of the three sates helix, strands and others . The new methods developed over the past few years may be interesting in context of improvements which is achieved through combination of the existing methods. Evolutionary divergences profile posses’ adequate information to improve protein secondary structure prediction accuracy. These profiles can also able to correctly predict long stretches of identical residues in other secondary structure. This sequence structure relationship may help to help to developed tool which can efficiently predict the protein secondary structure from its amino acid sequence

  13. On some primary and secondary structures in combinatorics

    OpenAIRE

    Veljan, D.

    2001-01-01

    A possible upgrade of a curriculum in undergraduate course in combinatorics is presented by giving more bijective proofs in the standard (or primary) combinatorics and by adding some topics on more refined (or secondary) combinatorics, including Dyck and Motzkin paths, Catalan, Narayana and Motzkin numbers and secondary structures coming from biology. Some log-convexity properties and asymptotics of these numbers are also presented.

  14. Secondary Education in the European Union: Structures, Organisation and Administration.

    Science.gov (United States)

    EURYDICE European Unit, Brussels (Belgium).

    This study examines the existing secondary education structures of the European Union member nations, the organization of education, teacher training, and the way in which secondary education is managed in Europe today. The three European Free Trade Association/European Economic Area (EFTA/EEC) countries (Iceland, Liechtenstein, and Norway) also…

  15. Unified approach to partition functions of RNA secondary structures.

    Science.gov (United States)

    Bundschuh, Ralf

    2014-11-01

    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

  16. Combinatorics of RNA Secondary Structures with Base Triples.

    Science.gov (United States)

    Müller, Robert; Nebel, Markus E

    2015-07-01

    The structure of RNA has been the subject of intense research over the last decades due to its importance for the correct functioning of RNA molecules in biological processes. Hence, a large number of models for RNA folding and corresponding algorithms for structure prediction have been developed. However, previous models often only consider base pairs, although every base is capable of up to three edge-to-edge interactions with other bases. Recently, Höner zu Siederdissen et al. presented an extended model of RNA secondary structure, including base triples together with a folding algorithm-the first thermodynamics-based algorithm that allows the prediction of secondary structures with base triples. In this article, we investigate the search space processed by this new algorithm, that is, the combinatorics of extended RNA secondary structures with base triples. We present generalized definitions for structural motifs like hairpins, stems, bulges, or interior loops occurring in structures with base triples. Furthermore, we prove precise asymptotic results for the number of different structures (size of search space) and expectations for various parameters associated with structural motifs (typical shape of folding). Our analysis shows that the asymptotic number of secondary structures of size n increases exponentially to [Formula: see text] compared to the classic model by Stein and Waterman for which [Formula: see text] structures exist. A comparison with the classic model reveals large deviations in the expected structural appearance, too. The inclusion of base triples constitutes a significant refinement of the combinatorial model of RNA secondary structure, which, by our findings, is quantitatively characterized. Our results are of special theoretical interest, because a closer look at the numbers involved suggests that extended RNA secondary structures constitute a new combinatorial class not bijective with any other combinatorial objects studied so far. PMID

  17. BRASERO: A Resource for Benchmarking RNA Secondary Structure Comparison Algorithms

    OpenAIRE

    Chauve, Cedric; Allali, Julien; Saule, Cedric

    2012-01-01

    The pairwise comparison of RNA secondary structures is a fundamental problem, with direct application in mining databases for annotating putative noncoding RNA candidates in newly sequenced genomes. An increasing number of software tools are available for comparing RNA secondary structures, based on different models (such as ordered trees or forests, arc annotated sequences, and multilevel trees) and computational principles (edit distance, alignment). We describe here the website BRASERO tha...

  18. BRASERO: A Resource for Benchmarking RNA Secondary Structure Comparison Algorithms.

    Science.gov (United States)

    Allali, Julien; Saule, Cédric; Chauve, Cédric; d'Aubenton-Carafa, Yves; Denise, Alain; Drevet, Christine; Ferraro, Pascal; Gautheret, Daniel; Herrbach, Claire; Leclerc, Fabrice; de Monte, Antoine; Ouangraoua, Aida; Sagot, Marie-France; Termier, Michel; Thermes, Claude; Touzet, Hélène

    2012-01-01

    The pairwise comparison of RNA secondary structures is a fundamental problem, with direct application in mining databases for annotating putative noncoding RNA candidates in newly sequenced genomes. An increasing number of software tools are available for comparing RNA secondary structures, based on different models (such as ordered trees or forests, arc annotated sequences, and multilevel trees) and computational principles (edit distance, alignment). We describe here the website BRASERO that offers tools for evaluating such software tools on real and synthetic datasets. PMID:22675348

  19. Prediction of Protein Secondary Structures From Conformational Biases

    OpenAIRE

    Hoang, Trinh Xuan; Cieplak, Marek; Banavar, Jayanth R.; Maritan, Amos

    2002-01-01

    We use LINUS, a procedure developed by Srinivasan and Rose, to provide a physical interpretation of and to predict the secondary structures of proteins. The secondary structure type at a given site is identified by the largest conformational bias during short time simulations. We examine the rate of successful prediction as a function of temperature and the interaction window. At high temperatures, there is a large propensity for the establishment of $\\beta$-strands whereas $\\alpha$-helices a...

  20. A method for rapid similarity analysis of RNA secondary structures

    Directory of Open Access Journals (Sweden)

    Liu Na

    2006-11-01

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

  1. Material properties assignment to finite element models of bone structures: a new method.

    Science.gov (United States)

    Zannoni, C; Mantovani, R; Viceconti, M

    1998-12-01

    Finite element analysis (FEA) is widely adopted to investigate the mechanical behaviour of bone structures. Computed tomography (CT) data are frequently used to generate FE models of bone. If properly calibrated, CT images are capable of providing accurate information about the bone morphology and tissue density. The aim of this work was to develop a special program able to read a CT data set as well as the FEA mesh generated from it, and to assign to each element of the mesh the material properties derived from the bone tissue density at the element location. The program was tested on phantom data sets and was adopted to evaluate the effects of the discrete description of the bone material properties. A three-dimensional FE model was generated automatically from a 16 bit CT data set of a distal femur acquired in vivo. The strain energy density (SED) was evaluated for each model element for increasing model complexity (number of different material cards assigned to the model). The computed SED were strongly dependent on the material mapping strategy. PMID:10223642

  2. Protein structural alphabets: beyond the secondary structure description : Structural alphabet : A review

    OpenAIRE

    De Brevern, Alexandre; Camproux, Anne-Claude; Hazout, Serge,; Etchebest, Catherine; Tufféry, Pierre

    2001-01-01

    The considerable increase of the protein structural database allows to cross the line from the classical secondary structure description of proteins. While still confronted with numerous problems, defining structural alphabets is an emerging concept in the field of protein structure analysis. It is an attempt to objectively classify the whole set of conformations occurring in protein structures described by small overlapping fragments. It is expected to lead to a better understanding of prote...

  3. Transitions between secondary structures in isolated polyalanines

    OpenAIRE

    Calvo, Florent; Poulain, Pierre

    2009-01-01

    Monte Carlo simulations of gas-phase polyalanine peptides have been carried out with the Amber ff96 force field. A low-temperature structural transition takes place between the α-helix stable conformation and β-sheet structures, followed by the unfolding phase change. The transition state ensembles connect- ing the helix and sheet conformations are investigated by sampling the energy landscape along specific geometric order parameters as putative reaction coordinates, namely the electric dipo...

  4. Protein secondary-structure description with a coarse-grained model.

    Science.gov (United States)

    Kneller, Gerald R; Hinsen, Konrad

    2015-07-01

    A coarse-grained geometrical model for protein secondary-structure description and analysis is presented which uses only the positions of the C(α) atoms. A space curve connecting these positions by piecewise polynomial interpolation is constructed and the folding of the protein backbone is described by a succession of screw motions linking the Frenet frames at consecutive C(α) positions. Using the ASTRAL subset of the SCOPe database of protein structures, thresholds are derived for the screw parameters of secondary-structure elements and demonstrate that the latter can be reliably assigned on the basis of a C(α) model. For this purpose, a comparative study with the widely used DSSP (Define Secondary Structure of Proteins) algorithm was performed and it was shown that the parameter distribution corresponding to the ensemble of all pure C(α) structures in the RCSB Protein Data Bank matches that of the ASTRAL database. It is expected that this approach will be useful in the development of structure-refinement techniques for low-resolution data. PMID:26143913

  5. Predicting the Secondary Structure of Proteins by Cascading Neural Networks

    Directory of Open Access Journals (Sweden)

    Maryam Alirezaee

    2012-11-01

    Full Text Available Protein Secondary Structure Prediction (PSSP is considered as a challenging task in bioinformatics and so many approaches have been proposed in the literature to solve this problem via achieving more accurate prediction results. Accurate prediction of secondary structure is a critical role in deducing tertiary structure of proteins and their functions. Among the proposed approaches to tackle this problem, Artificial Neural Networks (ANNs are considered as one of the successful tools that are widely used in this field. Recently, many efforts have been devoted to modify, improve and combine this methodology with other machine learning methods in order to get better results. In this work, we have proposed a two-stage feed forward neural network for prediction of protein secondary structures. To evaluate our approach, it is applied on RS126 dataset and its results are compared with some other NN-based methods.

  6. A Model for Folding and Aggregation in RNA Secondary Structures

    CERN Document Server

    Guttal, V; Guttal, Vishwesha; Bundschuh, Ralf

    2006-01-01

    We study the statistical mechanics of RNA secondary structures designed to have an attraction between two different types of structures as a model system for heteropolymer aggregation. The competition between the branching entropy of the secondary structure and the energy gained by pairing drives the RNA to undergo a `temperature independent' second order phase transition from a molten to an aggregated phase'. The aggregated phase thus obtained has a macroscopically large number of contacts between different RNAs. The partition function scaling exponent for this phase is \\theta ~ 1/2 and the crossover exponent of the phase transition is \

  7. RNA secondary structure diagrams for very large molecules: RNAfdl

    DEFF Research Database (Denmark)

    Hecker, Nikolai; Wiegels, Tim; Torda, Andrew E.

    2013-01-01

    There are many programs that can read the secondary structure of an RNA molecule and draw a diagram, but hardly any that can cope with 10 3 bases. RNAfdl is slow but capable of producing intersection-free diagrams for ribosome-sized structures, has a graphical user interface for adjustments and...... produces output in common formats....

  8. Structuring asynchronous discussion groups by introducing roles: do students act in line with assigned roles?

    OpenAIRE

    Wever, Bram De; Schellens, Tammy; Van Keer, Hilde; Valcke, Martin

    2008-01-01

    This study focused on the introduction of roles as a scripting tool in asynchronous text-based discussion groups. Five roles were selected: source searcher, theoretician, summarizer, moderator, and starter. Because existing research on role assignment often neglects to check whether the role assignment is successful, the main goal was to examine to what extent the participants enacted assigned roles. The study took place in the 1st year of a university course in Instructional Sciences (N = 20...

  9. Microwave, r0 structural parameters, conformational stability and vibrational assignment of cyclopropylcyanosilane

    International Nuclear Information System (INIS)

    Highlights: • The most stable cis conformer has been identified from microwave spectra. • Enthalpy difference has been determined between the two forms. • Adjusted r0 structures were obtained for cis and gauche form. • Ab initio calculations were performed for the two conformers. - Abstract: The FT-microwave spectrum (6000–19,800 MHz) of cyclopropylcyanosilane, c-C3H5SiH2CN has been recorded and 773 transitions for the 28Si, 29Si, 30Si, 13C and 15N isotopomers have been assigned for cis and gauche conformers. Infrared spectra (3200–220 cm−1) of gas and Raman spectra (3200–40 cm−1) of the liquid have been recorded as well as the variable temperature (−60 to −100 °C) studies of the infrared spectra of the sample dissolved in liquid xenon. The enthalpy difference between the conformers in xenon solutions has been determined to be 123 ± 13 cm−1 (1.47 ± 0.16 kJ mol−1) with the cis conformer as the more stable form. Approximately 48 ± 2% of the cis form is present at ambient temperature. By utilizing the microwave rotational constants of six isotopomers for cis and seven isotopomers for gauche combined with the structural parameters predicted from MP2(full)/6-311+G(d,p) calculations, adjusted r0 parameters have been obtained for both conformers

  10. Collisional Line Assignments and Hyperfine Structure Interpretation in Cs2 23△1g State

    Institute of Scientific and Technical Information of China (English)

    Dan Li; Feng Xie; Li Li; Ergin H.Ahmed; A.Marjatta Lyyra

    2013-01-01

    Accurately known energy level structure of the Cs2 A1Σu+-b3IIu complex of states from a recent global de-perturbation of these states has enabled additional assignments of 140 perturbation facilitated infrared-infrared double resonance (PFIIDR) transitions to the 23/1g state from collisionally populated intermediate A1Σu+levels.Together with the 221 previously observed 23△1g←A1∑u+←X1∑g+ double resonance lines [J.Chem.Phys.128,204313(2008)],molecular constants and the Rydberg-Klein-Rees potential energy curve of the 23△1g state have been recalculated (excluding 54 perturbed levels).The centrifugal distortion constant has been determined and agrees well with the value calculated based on standard empirical formulas.The hyperfine structure of the 23/g state,which has not resolved in our sub-Doppler excitation spectra of the 23/1g state,has been interpreted with a preliminary simulation.

  11. Prediction algorithm for amino acid types with their secondary structure in proteins (PLATON) using chemical shifts

    Energy Technology Data Exchange (ETDEWEB)

    Labudde, D.; Leitner, D.; Krueger, M.; Oschkinat, H. [Forschungsinstitut fuer Molekulare Pharmakologie (Germany)], E-mail: oschkinat@fmp-berlin.de

    2003-01-15

    The algorithm PLATON is able to assign sets of chemical shifts derived from a single residue to amino acid types with its secondary structure (amino acid species). A subsequent ranking procedure using optionally two different penalty functions yields predictions for possible amino acid species for the given set of chemical shifts. This was demonstrated in the case of the {alpha}-spectrin SH3 domain and applied to 9 further protein data sets taken from the BioMagRes database. A database consisting of reference chemical shift patterns (reference CSPs) was generated from assigned chemical shifts of proteins with known 3D-structure. This reference CSP database is used in our approach for extracting distributions of amino acid types with their most likely secondary structure elements (namely {alpha}-helix, {beta}-sheet, and coil) for single amino acids by comparison with query CSPs. Results obtained for the 10 investigated proteins indicates that the percentage of correct amino acid species in the first three positions in the ranking list, ranges from 71.4% to 93.2% for the more favorable penalty function. Where only the top result of the ranking list for these 10 proteins is considered, 36.5% to 83.1% of the amino acid species are correctly predicted. The main advantage of our approach, over other methods that rely on average chemical shift values is the ability to increase database content by incorporating newly derived CSPs, and therefore to improve PLATON's performance over time.

  12. Prediction algorithm for amino acid types with their secondary structure in proteins (PLATON) using chemical shifts

    International Nuclear Information System (INIS)

    The algorithm PLATON is able to assign sets of chemical shifts derived from a single residue to amino acid types with its secondary structure (amino acid species). A subsequent ranking procedure using optionally two different penalty functions yields predictions for possible amino acid species for the given set of chemical shifts. This was demonstrated in the case of the α-spectrin SH3 domain and applied to 9 further protein data sets taken from the BioMagRes database. A database consisting of reference chemical shift patterns (reference CSPs) was generated from assigned chemical shifts of proteins with known 3D-structure. This reference CSP database is used in our approach for extracting distributions of amino acid types with their most likely secondary structure elements (namely α-helix, β-sheet, and coil) for single amino acids by comparison with query CSPs. Results obtained for the 10 investigated proteins indicates that the percentage of correct amino acid species in the first three positions in the ranking list, ranges from 71.4% to 93.2% for the more favorable penalty function. Where only the top result of the ranking list for these 10 proteins is considered, 36.5% to 83.1% of the amino acid species are correctly predicted. The main advantage of our approach, over other methods that rely on average chemical shift values is the ability to increase database content by incorporating newly derived CSPs, and therefore to improve PLATON's performance over time

  13. Protein Secondary Structure Prediction using Pattern Recognition Neural Network

    Directory of Open Access Journals (Sweden)

    P.V. Nageswara Rao

    2010-06-01

    Full Text Available Proteins are key biological molecules with diverse functions. With newer technologies producing more data (genomics, proteomics than can be annotated manually, in silico methods of predicting their structure and thereafter their function has been christened the Holy Grail of structural bioinformatics. Successful secondary structureprediction provides a starting point for direct tertiary structure modeling; in addition it improves sequence analysis and sequence-structure binding for structure and function determination. Using machine learning and data mining process, we developed a pattern recognition technique based on statistical for predicting protein secondary structure from the component amino acid sequence. By applying this technique, a performance score of Q8=72.3% was achieved. This compares well with other established techniques, such as NN-I and GOR IV which achieved Q3 scores of 64.05% and 63.19% respectively when predictions are made on single sequence alone.

  14. A phase transition in energy-filtered RNA secondary structures

    OpenAIRE

    Han, Hillary Siwei; Reidys, Christian

    2012-01-01

    In this paper we study the effect of energy parameters on minimum free energy (mfe) RNA secondary structures. Employing a simplified combinatorial energy model, that is only dependent on the diagram representation and that is not sequence specific, we prove the following dichotomy result. Mfe structures derived via the Turner energy parameters contain only finitely many complex irreducible substructures and just minor parameter changes produce a class of mfe-structures that contain a large nu...

  15. Asymptotic connectivity for the network of RNA secondary structures

    OpenAIRE

    Clote, Peter

    2015-01-01

    Given an RNA sequence a, consider the network G = (V;E), where the set V of nodes consists of all secondary structures of a, and whose edge set E consists of all edges connecting two secondary structures whose base pair distance is 1. De?ne the network connectivity, or expected network degree, as the average number of edges incident to vertices of G. Using algebraic combinatorial methods, we prove that the asymptotic connectivity of length n homopolymer sequences is 0:473418 ? n. This raises ...

  16. Approaches to link RNA secondary structures with splicing regulation

    DEFF Research Database (Denmark)

    Plass, Mireya; Eyras, Eduardo

    2014-01-01

    facilitating or hindering the interaction with factors and small nuclear ribonucleoproteins (snRNPs) that regulate splicing. Moreover, the secondary structure could play a fundamental role in the splicing of yeast species, which lack many of the regulatory splicing factors present in metazoans. This chapter......In higher eukaryotes, alternative splicing is usually regulated by protein factors, which bind to the pre-mRNA and affect the recognition of splicing signals. There is recent evidence that the secondary structure of the pre-mRNA may also play an important role in this process, either by...

  17. {sup 1}H and {sup 15}N NMR assignment and solution structure of the SH3 domain of spectrin: Comparison of unrefined and refined structure sets with the crystal structure

    Energy Technology Data Exchange (ETDEWEB)

    Blanco, Francisco J.; Ortiz, Angel R.; Serrano, Luis [European Molecular Biology Laboratory (Germany)

    1997-06-15

    The assignment of the {sup 1}H and {sup 15}Nnuclear magnetic resonance spectra of the Src-homology region 3 domain of chicken brain {alpha}-spectrin has been obtained. A set of solution structures has been determined from distance and dihedral angle restraints,which provide a reasonable representation of the protein structure in solution, as evaluated by a principal component analysis of the global pairwise root-mean-square deviation (rmsd) in a large set of structures consisting of the refined and unrefined solution structures and the crystal structure. The solution structure is well defined, with a lower degree of convergence between the structures in the loop regions than in the secondary structure elements. The average pairwise rmsd between the 15 refined solution structures is 0.71 {+-} 0.13 A for the backbone atoms and 1.43 {+-} 0.14 A for all heavy atoms. The solution structure is basically the same as the crystal structure. The average rmsd between the 15 refined solution structures and the crystal structure is 0.76 A for the backbone atoms and 1.45 {+-} 0.09 A for all heavy atoms. There are, however, small differences probably caused by intermolecular contacts in the crystal structure.

  18. Statistical mechanics of secondary structures formed by random RNA sequences

    Science.gov (United States)

    Bundschuh, Ralf

    2003-03-01

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

  19. The 5'-3' Distance of RNA Secondary Structures

    DEFF Research Database (Denmark)

    Han, Hillary S W; Reidys, Christian

    2012-01-01

    this article, we compute the exact distribution of 5'-3' distances of RNA secondary structures for any finite n. Furthermore, we compute the limit distribution and show that for n = 30 the exact distribution and the limit distribution are very close. Our results show that the distances of random RNA...

  20. JPred4: a protein secondary structure prediction server.

    Science.gov (United States)

    Drozdetskiy, Alexey; Cole, Christian; Procter, James; Barton, Geoffrey J

    2015-07-01

    JPred4 (http://www.compbio.dundee.ac.uk/jpred4) is the latest version of the popular JPred protein secondary structure prediction server which provides predictions by the JNet algorithm, one of the most accurate methods for secondary structure prediction. In addition to protein secondary structure, JPred also makes predictions of solvent accessibility and coiled-coil regions. The JPred service runs up to 94 000 jobs per month and has carried out over 1.5 million predictions in total for users in 179 countries. The JPred4 web server has been re-implemented in the Bootstrap framework and JavaScript to improve its design, usability and accessibility from mobile devices. JPred4 features higher accuracy, with a blind three-state (α-helix, β-strand and coil) secondary structure prediction accuracy of 82.0% while solvent accessibility prediction accuracy has been raised to 90% for residues <5% accessible. Reporting of results is enhanced both on the website and through the optional email summaries and batch submission results. Predictions are now presented in SVG format with options to view full multiple sequence alignments with and without gaps and insertions. Finally, the help-pages have been updated and tool-tips added as well as step-by-step tutorials. PMID:25883141

  1. Assignments and structure determination of the catalytic domain of human fibroblast collagenase using 3D double and triple resonance NMR spectroscopy

    International Nuclear Information System (INIS)

    We report here the backbone 1HN, 15N, 13Cα, 13CO, and 1Hα NMR assignments for the catalytic domain of human fibroblast collagenase (HFC). Three independent assignment pathways (matching 1H, 13Cα, and 13CO resonances) were used to establish sequential connections. The connections using 13Cα resonances were obtained from HNCOCA and HNCA experiments; 13CO connections were obtained from HNCO and HNCACO experiments. The sequential proton assignment pathway was established from a 3D(1H/15N) NOESY-HSQC experiment. Amino acid typing was accomplished using 13C and 15N chemical shifts, specific labeling of 15N-Leu, and spin pattern recognition from DQF-COSY. The secondary structure was determined by analyzing the 3D (1H/15N) NOESY-HSQC. A preliminary NMR structure calculation of HFC was found to be in agreement with recent X-ray structures of human fibroblast collagenase and human neutrophil collagenase as well as similar to recent NMR structures of a highly homologous protein, stromelysin. All three helices were located; a five-stranded β-sheet (four parallel strands, one antiparallel strand) was also determined. β-Sheet regions were identified by cross-strand dαN and dNN connections and by strong intraresidue dαN correlations, and were corroborated by observing slow amide proton exchange. Chemical shift changes in a selectively 15N-labeled sample suggest that substantial structural changes occur in the active site cleft on the binding of an inhibitor

  2. Ensemble-based prediction of RNA secondary structures

    OpenAIRE

    Aghaeepour, Nima; Hoos, Holger H

    2013-01-01

    Background Accurate structure prediction methods play an important role for the understanding of RNA function. Energy-based, pseudoknot-free secondary structure prediction is one of the most widely used and versatile approaches, and improved methods for this task have received much attention over the past five years. Despite the impressive progress that as been achieved in this area, existing evaluations of the prediction accuracy achieved by various algorithms do not provide a comprehensive,...

  3. Protein secondary structure prediction using deep convolutional neural fields

    OpenAIRE

    Sheng Wang; Jian Peng; Jianzhu Ma; Jinbo Xu

    2015-01-01

    Protein secondary structure (SS) prediction is important for studying protein structure and function. When only the sequence (profile) information is used as input feature, currently the best predictors can obtain ~80% Q3 accuracy, which has not been improved in the past decade. Here we present DeepCNF (Deep Convolutional Neural Fields) for protein SS prediction. DeepCNF is a Deep Learning extension of Conditional Neural Fields (CNF), which is an integration of Conditional Random Fields (CRF)...

  4. Quantitative DMS mapping for automated RNA secondary structure inference

    OpenAIRE

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

    2012-01-01

    For decades, dimethyl sulfate (DMS) mapping has informed manual modeling of RNA structure in vitro and in vivo. Here, we incorporate DMS data into automated secondary structure inference using a pseudo-energy framework developed for 2'-OH acylation (SHAPE) mapping. On six non-coding RNAs with crystallographic models, DMS- guided modeling achieves overall false negative and false discovery rates of 9.5% and 11.6%, comparable or better than SHAPE-guided modeling; and non-parametric bootstrappin...

  5. Thermal Folding and Mechanical Unfolding Pathways of Protein Secondary Structures

    OpenAIRE

    Cieplak, Marek; Hoang, Trinh Xuan; Robbins, Mark O.

    2001-01-01

    Mechanical stretching of secondary structures is studied through molecular dynamics simulations of a Go-like model. Force vs. displacement curves are studied as a function of the stiffness and velocity of the pulling device. The succession of stretching events, as measured by the order in which contacts are ruptured, is compared to the sequencing of events during thermal folding and unfolding. Opposite cross-correlations are found for an $\\alpha$-helix and a $\\beta$-hairpin structure. In a ta...

  6. Studies on solution NMR structure of brazzein——Secondary structure and molecular scaffold

    Institute of Scientific and Technical Information of China (English)

    高广华; 戴继勋; 丁鸣; 王金凤; 王大成

    1999-01-01

    Brazzein is a sweet-tasting protein isolated from the fruit of West African plant Pentadiplandra brazzeana Baillon. It is the smallest and the most water-soluble sweet protein discovered so far and is highly thermostable. The proton NMR study of brazzein at 600 MHz (pH 3.5, 300 K) is presented. The complete sequence specific assignments of the individual backbone and sideehain proton resonances were achieved using through-bond and through-space eonneetivities obtained from standard two-dimensional NMR techniques. The secondary structure of brazzein contains one α-helix (residues 21—29), one short 310-helix (residues 14—17), two strands of antiparallel β-sheet (residues 34—39, 44—50) and probably a third strand (residues 5—7) near the N-terminus. A comparative analysis found that brazzein shares a so-called ’eysteine-stabilized alpha-beta’ (CSαβ) motif with scorpion neurotoxins, insect defensins and plant γ-thionins. The significance of this multi-function motif, the possible active sites an

  7. STUDY ON THE SEQUENCE STRUCTURE OF SBR BY 13C- NMR METHOD Ⅰ. ASSIGNMENT FOR UNSATURATED CARBONS SPECTRA

    Institute of Scientific and Technical Information of China (English)

    JIAO Shuke; CHEN Xiaonong; HU Liping; YAN Baozhen

    1990-01-01

    The sequence structures of emulsion- processed SBR and solution- processed ( by lithium catalyst )SBR were investigated by 13C- NMR spectroscopy. Seventeen peaks within unsaturated carbon region were recorded under the adopted experimental conditions. Assignments for these peaks were made by empirical- parameter- evaluation method.

  8. Investigations of Protein Structure and Function Using the Scientific Literature: An Assignment for an Undergraduate Cell Physiology Course

    Science.gov (United States)

    Mulnix, Amy B.

    2003-01-01

    Undergraduate biology curricula are being modified to model and teach the activities of scientists better. The assignment described here, one that investigates protein structure and function, was designed for use in a sophomore-level cell physiology course at Earlham College. Students work in small groups to read and present in poster format on…

  9. The 5'-3' distance of RNA secondary structures

    CERN Document Server

    Han, Hillary S W

    2011-01-01

    Recently Yoffe {\\it et al.} \\citep{Yoffe} observed that the average distances between 5'-3' ends of RNA molecules are very small and largely independent of sequence length. This observation is based on numerical computations as well as theoretical arguments maximizing certain entropy functionals. In this paper we compute the exact distribution of 5'-3' distances of RNA secondary structures for any finite $n$. We furthermore compute the limit distribution and show that already for $n=30$ the exact distribution and the limit distribution are very close. Our results show that the distances of random RNA secondary structures are distinctively lower than those of minimum free energy structures of random RNA sequences.

  10. Electronic structures, vibrational spectra, and revised assignment of aniline and its radical cation: Theoretical study

    Science.gov (United States)

    Wojciechowski, Piotr M.; Zierkiewicz, Wiktor; Michalska, Danuta; Hobza, Pavel

    2003-06-01

    Comprehensive studies of the molecular and electronic structures, vibrational frequencies, and infrared and Raman intensities of the aniline radical cation, C6H5NH2+ have been performed by using the unrestricted density functional (UB3LYP) and second-order Møller-Plesset (UMP2) methods with the extended 6-311++G(df,pd) basis set. For comparison, analogous calculations were carried out for the closed-shell neutral aniline. The studies provided detailed insight into the bonding changes that take place in aniline upon ionization. The natural bond orbital (NBO) analysis has revealed that the pπ-radical conjugative interactions are of prime importance in stabilizing the planar, quinoid-type structure of the aniline radical cation. It is shown that the natural charges calculated for aniline are consistent with the chemical properties of this molecule (an ortho- and para-directing power of the NH2 group in electrophilic substitutions), whereas Mulliken charges are not reliable. The theoretical vibrational frequencies of aniline, calculated by the B3LYP method, show excellent agreement with the available experimental data. In contrast, the MP2 method is deficient in predicting the frequencies of several modes in aniline, despite the use of the extended basis set in calculations. The frequencies of aniline radical cation, calculated at the UB3LYP/6-311++G(df,pd) level, are in very good agreement with the recently reported experimental data from zero kinetic energy photoelectron and infrared depletion spectroscopic studies. The clear- cut assignment of the IR and Raman spectra of the investigated molecules has been made on the basis of the calculated potential energy distributions. Several bands in the spectra have been reassigned. It is shown that ionization of aniline can be easily identified by the appearance of the very strong band at about 1490 cm-1, in the Raman spectrum. The redshift of the N-H stretching frequencies and the blueshift of the C-H stretching

  11. Complete {sup 1}H and {sup 13}C NMR structural assignments for a group of four goyazensolide-type furanoheliangolides

    Energy Technology Data Exchange (ETDEWEB)

    Soares, Ana Carolina Ferreira; Silva, Aline Nazare; Matos, Priscilla Mendonca; Silva, Eder Henrique da; Heleno, Vladimir Constantino Gomes [Universidade de Franca, Franca, SP (Brazil). Nucleo de Pesquisas em Ciencias Exatas e Tecnologicas; Lopes, Norberto Peporine; Lopes, Joao Luis Callegari [Universidade de Sao Paulo (FCFRP/USP), Ribeirao Preto, SP (Brazil). Fac. de Ciencias Farmaceuticas de Ribeirao Preto. Dept. de Quimica e Fisica; Sass, Daiane Cristina, E-mail: vheleno_05@yahoo.com.br [Universidade de Sao Paulo (FFCLRP/USP), Ribeirao Preto, SP (Brazil). Fac. de Filosofia, Ciencias e Letras de Ribeirao Preto. Dept. de Quimica

    2012-07-01

    Four goyazensolide-type sesquiterpene lactones - lychnofolide, centratherin, goyazensolide and goyazensolide acetate - were thoroughly studied by NMR experimental techniques. {sup 1}H NMR, {sup 13}C NMR {l_brace}{sup 1}H{r_brace}, COSY, HMQC, HMBC, J-res. and NOE experiments were performed to provide the needed structural information. Complete and unequivocal assignment, including the determination of all multiplicities, was obtained for each structure and the data collections are presented in tables (author)

  12. Complete 1H and 13C NMR structural assignments for a group of four goyazensolide-type furanoheliangolides

    International Nuclear Information System (INIS)

    Four goyazensolide-type sesquiterpene lactones - lychnofolide, centratherin, goyazensolide and goyazensolide acetate - were thoroughly studied by NMR experimental techniques. 1H NMR, 13C NMR {1H}, COSY, HMQC, HMBC, J-res. and NOE experiments were performed to provide the needed structural information. Complete and unequivocal assignment, including the determination of all multiplicities, was obtained for each structure and the data collections are presented in tables (author)

  13. Integrating chemical footprinting data into RNA secondary structure prediction.

    Directory of Open Access Journals (Sweden)

    Kourosh Zarringhalam

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

  14. A phase transition in energy-filtered RNA secondary structures

    CERN Document Server

    Han, Hillary S W

    2012-01-01

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

  15. Random generation of RNA secondary structures according to native distributions

    Directory of Open Access Journals (Sweden)

    Nebel Markus E

    2011-10-01

    Full Text Available Abstract 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

  16. Large finite size effects in RNA secondary structures

    CERN Document Server

    Liu, T; Liu, Tsunglin; Bundschuh, Ralf

    2003-01-01

    The ensemble of RNA secondary structures of uniform sequences is studied analytically. We calculate the partition function for very long sequences and discuss how the cross-over length, beyond which asymptotic scaling laws apply, depends on thermodynamic parameters. For realistic choices of parameters this length can be much longer than natural RNA molecules. This has to be taken into account when applying asymptotic theory to interpret experiments or numerical results.

  17. Coating concrete secondary containment structures exposed to agrichemicals

    Energy Technology Data Exchange (ETDEWEB)

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

    1995-06-01

    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.

  18. A phase transition in energy-filtered RNA secondary structures

    DEFF Research Database (Denmark)

    Han, Hillary Siwei; reidys, Christian

    2012-01-01

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

  19. Gene-associated markers can assign origin in a weakly structured fish, Atlantic herring

    DEFF Research Database (Denmark)

    Bekkevold, Dorte; Helyar, Sarah J.; Limborg, Morten T.;

    2015-01-01

    Regulations on the exploitation of populations of commercially important fish species and the ensuing consumer interest in sustainable products have increased the need to accurately identify the population of origin of fish and fish products. Although genomics-based tools have proven highly useful......, there are relatively few examples in marine fish displaying accurate origin assignment. We synthesize data for 156 single-nucleotide polymorphisms typed in 1039 herring, Clupea harengus L., spanning the Northeast Atlantic to develop a tool that allows assignment of individual herring to their regional...... origin. We show the method's suitability to address specific biological questions, as well as management applications. We analyse temporally replicated collections from two areas, the Skagerrak (n = 81, 84, 66) and the western Baltic (n = 52, 52). Both areas harbour heavily fished mixed-origin stocks...

  20. Computational RNA secondary structure design: empirical complexity and improved methods

    Directory of Open Access Journals (Sweden)

    Condon Anne

    2007-01-01

    Full Text Available Abstract 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.

  1. On the NMR structure determination of a 44n RNA pseudoknot: Assignment strategies and derivation of torsion angle restraints

    Energy Technology Data Exchange (ETDEWEB)

    Kolk, Michael H. [University of Nijmegen, Toernooiveld, NSR Center for Molecular Structure, Design and Synthesis, Laboratory of Biophysical Chemistry (Netherlands); Wijmenga, Sybren S. [University of Umea, Department of Medical Biochemistry and Biophysics (Sweden); Heus, Hans A.; Hilbers, Cornelis W. [University of Nijmegen, Toernooiveld, NSR Center for Molecular Structure, Design and Synthesis, Laboratory of Biophysical Chemistry (Netherlands)

    1998-10-15

    The complete T- and pseudoknotted acceptor arm of the tRNA-like structure of turnip yellow mosaic virus (TYMV) genomic RNA has been studied by NMR spectroscopy. Resonance assignment and the gathering of restraints of the 44-mer are impeded by spectral complexity as well as by line broadening. The latter is caused by local dynamical effects in the pseudoknot domain in the molecule. These specific problems could be solved by using different field strengths and selectively {sup 13}C/{sup 15} labeled samples. Experiments for assigning the sugar spin systems were adjusted to satisfy the requirements of this system. Furthermore, the quality of the structure could be improved by determining the backbone torsion angles {beta}, {gamma} and {epsilon}, using new approaches that were tailored for use in large RNA molecules.

  2. PCI-SS: MISO dynamic nonlinear protein secondary structure prediction

    Directory of Open Access Journals (Sweden)

    Aboul-Magd Mohammed O

    2009-07-01

    Full Text Available Abstract 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 α-helices, β-strands, and non-regular structures from primary sequence data which makes use of Parallel Cascade Identification (PCI, a powerful technique from the field of nonlinear system identification. Results Using PSI-BLAST divergent evolutionary profiles as input data, dynamic nonlinear systems are built through a black-box approach to model the process of protein folding. Genetic algorithms (GAs are applied in order to optimize the architectural parameters of the PCI models. The three-state prediction problem is broken down into a combination of three binary sub-problems and protein structure classifiers are built using 2 layers of PCI classifiers. Careful construction of the optimization, training, and test datasets ensures that no homology exists between any training and testing data. A detailed comparison between PCI and 9 contemporary methods is provided over a set of 125 new protein chains guaranteed to be dissimilar to all training data. Unlike other secondary structure prediction methods, here a web service is developed to provide both human- and machine-readable interfaces to PCI-based protein secondary structure prediction. This server, called PCI-SS, is available at http://bioinf.sce.carleton.ca/PCISS. In addition to a dynamic PHP-generated web interface for humans, a Simple Object Access Protocol (SOAP interface is added to permit invocation of the PCI-SS service remotely. This machine-readable interface facilitates incorporation of PCI-SS into multi-faceted systems biology analysis pipelines requiring protein secondary structure information, and greatly simplifies high-throughput analyses. XML is used to represent the input

  3. Strategies for measuring evolutionary conservation of RNA secondary structures

    Directory of Open Access Journals (Sweden)

    Hofacker Ivo L

    2008-02-01

    Full Text Available Abstract Background Evolutionary conservation of RNA secondary structure is a typical feature of many functional non-coding RNAs. Since almost all of the available methods used for prediction and annotation of non-coding RNA genes rely on this evolutionary signature, accurate measures for structural conservation are essential. Results We systematically assessed the ability of various measures to detect conserved RNA structures in multiple sequence alignments. We tested three existing and eight novel strategies that are based on metrics of folding energies, metrics of single optimal structure predictions, and metrics of structure ensembles. We find that the folding energy based SCI score used in the RNAz program and a simple base-pair distance metric are by far the most accurate. The use of more complex metrics like for example tree editing does not improve performance. A variant of the SCI performed particularly well on highly conserved alignments and is thus a viable alternative when only little evolutionary information is available. Surprisingly, ensemble based methods that, in principle, could benefit from the additional information contained in sub-optimal structures, perform particularly poorly. As a general trend, we observed that methods that include a consensus structure prediction outperformed equivalent methods that only consider pairwise comparisons. Conclusion Structural conservation can be measured accurately with relatively simple and intuitive metrics. They have the potential to form the basis of future RNA gene finders, that face new challenges like finding lineage specific structures or detecting mis-aligned sequences.

  4. Generation of deviation parameters for amino acid singlets, doublets and triplets from three-dimensional structures of proteins and its implications for secondary structure prediction from amino acid sequences

    Indian Academy of Sciences (India)

    S A Mugilan; K Veluraja

    2000-03-01

    We present a new method, secondary structure prediction by deviation parameter (SSPDP) for predicting the secondary structure of proteins from amino acid sequence. Deviation parameters (DP) for amino acid singlets, doublets and triplets were computed with respect to secondary structural elements of proteins based on the dictionary of secondary structure prediction (DSSP)-generated secondary structure for 408 selected non-homologous proteins. To the amino acid triplets which are not found in the selected dataset, a DP value of zero is assigned with respect to the secondary structural elements of proteins. The total number of parameters generated is 15,432, in the possible parameters of 25,260. Deviation parameter is complete with respect to amino acid singlets, doublets, and partially complete with respect to amino acid triplets. These generated parameters were used to predict secondary structural elements from amino acid sequence. The secondary structure predicted by our method (SSPDP) was compared with that of single sequence (NNPREDICT) and multiple sequence (PHD) methods. The average value of the percentage of prediction accuracy for α-helix by SSPDP, NNPREDICT and PHD methods was found to be 57%, 44% and 69% respectively for the proteins in the selected dataset. For -strand the prediction accuracy is found to be 69%, 21% and 53% respectively by SSPDP, NNPREDICT and PHD methods. This clearly indicates that the secondary structure prediction by our method is as good as PHD method but much better than NNPREDICT method.

  5. Structural Analysis of Char by Raman Spectroscopy: Improving Band Assignments through Computational Calculations from First Principles

    Energy Technology Data Exchange (ETDEWEB)

    Smith, Matthew W.; Dallmeyer, Ian; Johnson, Timothy J.; Brauer, Carolyn S.; McEwen, Jean-Sabin; Espinal, Juan F.; Garcia-Perez, Manuel

    2016-04-01

    Raman spectroscopy is a powerful tool for the characterization of many carbon 27 species. The complex heterogeneous nature of chars and activated carbons has confounded 28 complete analysis due to the additional shoulders observed on the D-band and high intensity 29 valley between the D and G-bands. In this paper the effects of various vacancy and substitution 30 defects have been systematically analyzed via molecular modeling using density functional 31 theory (DFT) and how this is manifested in the calculated gas-phase Raman spectra. The 32 accuracy of these calculations was validated by comparison with (solid-phase) experimental 33 spectra, with a small correction factor being applied to improve the accuracy of frequency 34 predictions. The spectroscopic effects on the char species are best understood in terms of a 35 reduced symmetry as compared to a “parent” coronene molecule. Based upon the simulation 36 results, the shoulder observed in chars near 1200 cm-1 has been assigned to the totally symmetric 37 A1g vibrations of various small polyaromatic hydrocarbons (PAH) as well as those containing 38 rings of seven or more carbons. Intensity between 1400 cm-1 and 1450 cm-1 is assigned to A1g 39 type vibrations present in small PAHs and especially those containing cyclopentane rings. 40 Finally, band intensity between 1500 cm-1 and 1550 cm-1 is ascribed to predominately E2g 41 vibrational modes in strained PAH systems. A total of ten potential bands have been assigned 42 between 1000 cm-1 and 1800 cm-1. These fitting parameters have been used to deconvolute a 43 thermoseries of cellulose chars produced by pyrolysis at 300-700 °C. The results of the 44 deconvolution show consistent growth of PAH clusters with temperature, development of non-45 benzyl rings as temperature increases and loss of oxygenated features between 400 °C and 46 600 °C

  6. Secondary fast magnetoacoustic waves trapped in randomly structured plasmas

    CERN Document Server

    Yuan, Ding; Walsh, Robert W

    2016-01-01

    Fast magnetoacoustic wave is an important tool for inferring solar atmospheric parameters. We numerically simulate the propagation of fast wave pulses in randomly structured plasmas mimicking the highly inhomogeneous solar corona. A network of secondary waves is formed by a series of partial reflections and transmissions. These secondary waves exhibit quasi-periodicities in both time and space. Since the temporal and spatial periods are related simply through the fast wave speed, we quantify the properties of secondary waves by examining the dependence of the average temporal period ($\\bar{p}$) on the initial pulse width ($w_0$) as well as the density contrast ($\\delta_\\rho$) and correlation length ($L_c$) that characterize the randomness of the equilibrium density profiles. For small-amplitude pulses, $\\delta_\\rho$ does not alter $\\bar{p}$ significantly. Large-amplitude pulses, on the other hand, enhance the density contrast when $\\delta_\\rho$ is small but have a smoothing effect when $\\delta_\\rho$ is suffic...

  7. Secondary Structure of Rat and Human Amylin across Force Fields.

    Directory of Open Access Journals (Sweden)

    Kyle Quynn Hoffmann

    Full Text Available The aggregation of human amylin has been strongly implicated in the progression of Type II diabetes. This 37-residue peptide forms a variety of secondary structures, including random coils, α-helices, and β-hairpins. The balance between these structures depends on the chemical environment, making amylin an ideal candidate to examine inherent biases in force fields. Rat amylin differs from human amylin by only 6 residues; however, it does not form fibrils. Therefore it provides a useful complement to human amylin in studies of the key events along the aggregation pathway. In this work, the free energy of rat and human amylin was determined as a function of α-helix and β-hairpin content for the Gromos96 53a6, OPLS-AA/L, CHARMM22/CMAP, CHARMM22*, Amberff99sb*-ILDN, and Amberff03w force fields using advanced sampling techniques, specifically bias exchange metadynamics. This work represents a first systematic attempt to evaluate the conformations and the corresponding free energy of a large, clinically relevant disordered peptide in solution across force fields. The NMR chemical shifts of rIAPP were calculated for each of the force fields using their respective free energy maps, allowing us to quantitatively assess their predictions. We show that the predicted distribution of secondary structures is sensitive to the choice of force-field: Gromos53a6 is biased towards β-hairpins, while CHARMM22/CMAP predicts structures that are overly α-helical. OPLS-AA/L favors disordered structures. Amberff99sb*-ILDN, AmberFF03w and CHARMM22* provide the balance between secondary structures that is most consistent with available experimental data. In contrast to previous reports, our findings suggest that the equilibrium conformations of human and rat amylin are remarkably similar, but that subtle differences arise in transient alpha-helical and beta-strand containing structures that the human peptide can more readily adopt. We hypothesize that these transient

  8. Secondary Structure of Rat and Human Amylin across Force Fields.

    Science.gov (United States)

    Hoffmann, Kyle Quynn; McGovern, Michael; Chiu, Chi-Cheng; de Pablo, Juan J

    2015-01-01

    The aggregation of human amylin has been strongly implicated in the progression of Type II diabetes. This 37-residue peptide forms a variety of secondary structures, including random coils, α-helices, and β-hairpins. The balance between these structures depends on the chemical environment, making amylin an ideal candidate to examine inherent biases in force fields. Rat amylin differs from human amylin by only 6 residues; however, it does not form fibrils. Therefore it provides a useful complement to human amylin in studies of the key events along the aggregation pathway. In this work, the free energy of rat and human amylin was determined as a function of α-helix and β-hairpin content for the Gromos96 53a6, OPLS-AA/L, CHARMM22/CMAP, CHARMM22*, Amberff99sb*-ILDN, and Amberff03w force fields using advanced sampling techniques, specifically bias exchange metadynamics. This work represents a first systematic attempt to evaluate the conformations and the corresponding free energy of a large, clinically relevant disordered peptide in solution across force fields. The NMR chemical shifts of rIAPP were calculated for each of the force fields using their respective free energy maps, allowing us to quantitatively assess their predictions. We show that the predicted distribution of secondary structures is sensitive to the choice of force-field: Gromos53a6 is biased towards β-hairpins, while CHARMM22/CMAP predicts structures that are overly α-helical. OPLS-AA/L favors disordered structures. Amberff99sb*-ILDN, AmberFF03w and CHARMM22* provide the balance between secondary structures that is most consistent with available experimental data. In contrast to previous reports, our findings suggest that the equilibrium conformations of human and rat amylin are remarkably similar, but that subtle differences arise in transient alpha-helical and beta-strand containing structures that the human peptide can more readily adopt. We hypothesize that these transient states enable

  9. Combining automated peak tracking in SAR by NMR with structure-based backbone assignment from 15N-NOESY

    KAUST Repository

    Jang, Richard

    2012-03-21

    Background: Chemical shift mapping is an important technique in NMR-based drug screening for identifying the atoms of a target protein that potentially bind to a drug molecule upon the molecule\\'s introduction in increasing concentrations. The goal is to obtain a mapping of peaks with known residue assignment from the reference spectrum of the unbound protein to peaks with unknown assignment in the target spectrum of the bound protein. Although a series of perturbed spectra help to trace a path from reference peaks to target peaks, a one-to-one mapping generally is not possible, especially for large proteins, due to errors, such as noise peaks, missing peaks, missing but then reappearing, overlapped, and new peaks not associated with any peaks in the reference. Due to these difficulties, the mapping is typically done manually or semi-automatically, which is not efficient for high-throughput drug screening.Results: We present PeakWalker, a novel peak walking algorithm for fast-exchange systems that models the errors explicitly and performs many-to-one mapping. On the proteins: hBclXL, UbcH5B, and histone H1, it achieves an average accuracy of over 95% with less than 1.5 residues predicted per target peak. Given these mappings as input, we present PeakAssigner, a novel combined structure-based backbone resonance and NOE assignment algorithm that uses just 15N-NOESY, while avoiding TOCSY experiments and 13C-labeling, to resolve the ambiguities for a one-to-one mapping. On the three proteins, it achieves an average accuracy of 94% or better.Conclusions: Our mathematical programming approach for modeling chemical shift mapping as a graph problem, while modeling the errors directly, is potentially a time- and cost-effective first step for high-throughput drug screening based on limited NMR data and homologous 3D structures. 2012 Jang et al.; licensee BioMed Central Ltd.

  10. Mining overrepresented 3D patterns of secondary structures in proteins.

    Science.gov (United States)

    Comin, Matteo; Guerra, Concettina; Zanotti, Giuseppe

    2008-12-01

    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

  11. Combining ambiguous chemical shift mapping with structure-based backbone and NOE assignment from 15N-NOESY

    KAUST Repository

    Jang, Richard

    2011-01-01

    Chemical shift mapping is an important technique in NMRbased drug screening for identifying the atoms of a target protein that potentially bind to a drug molecule upon the molecule\\'s introduction in increasing concentrations. The goal is to obtain a mapping of peaks with known residue assignment from the reference spectrum of the unbound protein to peaks with unknown assignment in the target spectrum of the bound protein. Although a series of perturbed spectra help to trace a path from reference peaks to target peaks, a one-to-one mapping generally is not possible, especially for large proteins, due to errors, such as noise peaks, missing peaks, missing but then reappearing, overlapped, and new peaks not associated with any peaks in the reference. Due to these difficulties, the mapping is typically done manually or semi-automatically. However, automated methods are necessary for high-throughput drug screening. We present PeakWalker, a novel peak walking algorithm for fast-exchange systems that models the errors explicitly and performs many-to-one mapping. On the proteins: hBclXL, UbcH5B, and histone H1, it achieves an average accuracy of over 95% with less than 1.5 residues predicted per target peak. Given these mappings as input, we present PeakAssigner, a novel combined structure-based backbone resonance and NOE assignment algorithm that uses just 15N-NOESY, while avoiding TOCSY experiments and 13C- labeling, to resolve the ambiguities for a one-toone mapping. On the three proteins, it achieves an average accuracy of 94% or better. Copyright © 2011 ACM.

  12. Simultaneous structural and control optimization via linear quadratic regulator eigenstructure assignment

    Science.gov (United States)

    Becus, G. A.; Lui, C. Y.; Venkayya, V. B.; Tischler, V. A.

    1987-01-01

    A method for simultaneous structural and control design of large flexible space structures (LFSS) to reduce vibration generated by disturbances is presented. Desired natural frequencies and damping ratios for the closed loop system are achieved by using a combination of linear quadratic regulator (LQR) synthesis and numerical optimization techniques. The state and control weighing matrices (Q and R) are expressed in terms of structural parameters such as mass and stiffness. The design parameters are selected by numerical optimization so as to minimize the weight of the structure and to achieve the desired closed-loop eigenvalues. An illustrative example of the design of a two bar truss is presented.

  13. Complete assignment of lysine resonances in 1H NMR spectra of proteins as probes of surface structure and dynamics

    International Nuclear Information System (INIS)

    A strategy is presented for complete identification of 1H spin systems of lysine residues using sophisticated 2D NMR experiments. Relayed and remote connectivities within each spin system are determined for spin subsystems based at the backbone amide and Cε proton resonances. When complete spin system identification is combined with sequence-specific assignment, protein surface structure and dynamics can be probed in a site-specific manner. The interaction between the five lysine residues of French bean plastocyanin and a model redox partner Cr(CN)63- has been examined using this approach. 12 refs.; 3 figs.; 1 table

  14. Protein Secondary Structure Prediction Using Deep Convolutional Neural Fields

    Science.gov (United States)

    Wang, Sheng; Peng, Jian; Ma, Jianzhu; Xu, Jinbo

    2016-01-01

    Protein secondary structure (SS) prediction is important for studying protein structure and function. When only the sequence (profile) information is used as input feature, currently the best predictors can obtain ~80% Q3 accuracy, which has not been improved in the past decade. Here we present DeepCNF (Deep Convolutional Neural Fields) for protein SS prediction. DeepCNF is a Deep Learning extension of Conditional Neural Fields (CNF), which is an integration of Conditional Random Fields (CRF) and shallow neural networks. DeepCNF can model not only complex sequence-structure relationship by a deep hierarchical architecture, but also interdependency between adjacent SS labels, so it is much more powerful than CNF. Experimental results show that DeepCNF can obtain ~84% Q3 accuracy, ~85% SOV score, and ~72% Q8 accuracy, respectively, on the CASP and CAMEO test proteins, greatly outperforming currently popular predictors. As a general framework, DeepCNF can be used to predict other protein structure properties such as contact number, disorder regions, and solvent accessibility.

  15. Assessing Students' Structured Programming Skills with Java: The "Blue, Berry, and Blueberry" Assignment

    Science.gov (United States)

    Zhang, Xihui

    2010-01-01

    Java is an object-oriented programming language. From a software engineering perspective, object-oriented design and programming is used at the architectural design, and structured design and programming is used at the detailed design within methods. As such, structured programming skills are fundamental to more advanced object-oriented…

  16. An RNA secondary structure prediction method based on minimum and suboptimal free energy structures.

    Science.gov (United States)

    Fu, Haoyue; Yang, Lianping; Zhang, Xiangde

    2015-09-01

    The function of an RNA-molecule is mainly determined by its tertiary structures. And its secondary structure is an important determinant of its tertiary structure. The comparative methods usually give better results than the single-sequence methods. Based on minimum and suboptimal free energy structures, the paper presents a novel method for predicting conserved secondary structure of a group of related RNAs. In the method, the information from the known RNA structures is used as training data in a SVM (Support Vector Machine) classifier. Our method has been tested on the benchmark dataset given by Puton et al. The results show that the average sensitivity of our method is higher than that of other comparative methods such as CentroidAlifold, MXScrana, RNAalifold, and TurboFold. PMID:26100179

  17. Structural assignment and catagenetic behavior of macromolecular constituents of recent and fossil natural resins. Doctoral thesis

    Energy Technology Data Exchange (ETDEWEB)

    van Aarssen, B.G.K.

    1992-12-10

    The thesis describes the results obtained by molecular organic geochemical investigations of fossil and recent natural resins. A major constituent of these plant exudates is a polymeric substance which is resistant to degradation and is thus likely to fossilize. Time and the rise of temperature and pressure upon burial may lead to a disintegration of the polymeric structures into smaller molecules which can contribute to oil formation. The aim of the study was to assess the mechanisms of depolymerization by investigating in detail the chemical structures of resin polymers and their catagenetic products. In nature two major types of resinous polymers are known to occur: polysesquiterpenoids and polyditerpenoids. The first part of the thesis, chapters 2-8, contains the results of investigations concerning the sesquiterpenoid type polymer. Chemical structures, occurrence and origin of both the polymer and its catagenetic products are described. The second part of the thesis, chapters 9-11, deals with the structures of diterpenoid polymers.

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

    OpenAIRE

    Chursov, Andrey; Frishman, Dmitrij; Shneider, Alexander

    2013-01-01

    Recent reports indicate that mutations in viral genomes tend to preserve RNA secondary structure, and those mutations that disrupt secondary structural elements may reduce gene expression levels, thereby serving as a functional knockout. In this article, we explore the conservation of secondary structures of mRNA coding regions, a previously unknown factor in bacterial evolution, by comparing the structural consequences of mutations in essential and nonessential Escherichia coli genes accumul...

  19. Structure and molecular assignment of lactococcal phage TP901-1 baseplate

    DEFF Research Database (Denmark)

    Bebeacua, Cecilia; Bron, Patrick; Lai, Livia;

    2010-01-01

    lactococcal phage p2 BP, bearing only 6 RBPs, and which needs a conformational change to reach its activated state. The comparison of several Siphoviridae structures uncovers a close organization of their central BP core whereas striking differences occur at the periphery, leading to diverse mechanisms of...

  20. Structure and chromosome assignment of the murine p36 (calpactin I heavy chain) gene

    DEFF Research Database (Denmark)

    Amiquel, P; Kristensen, Torsten; D'Eustachio, P; Wetsel, R A; Saris, C J; Hunter, T; Chaplin, D D; Tack, B F

    1990-01-01

    determined from analysis of cloned cDNA. The protein contains 338 amino acids, has an approximate molecular weight of 39,000, and is comprised of several distinct domains, including four 75 amino acid repeats. From two overlapping cosmid clones isolated from different mouse genomic liver libraries, the...... complete intron/exon structure of the p36 gene was determined and the 5' and 3' noncoding regions of the gene were analyzed. The coding and 3' untranslated region of the p36 gene contains 12 exons which range in size from 48 to 322 base pairs (bp) with an average size of 107 bp. The repeat structures found...... range in size from 600 to 3600 bp with an average size of 1650 bp. The p36 gene is at least 22 kb in length and has a coding sequence of approximately 1 kb, representing only 4.5% of the gene...

  1. Investigating Resuscitation Code Assignment in the Intensive Care Unit using Structured and Unstructured Data

    OpenAIRE

    Lojun, Sharon L.; Sauper, Christina J.; Medow, Mitchell; Long, William J.; Mark, Roger G.; Barzilay, Regina

    2010-01-01

    This study investigates the feasibility of using structured data (age, gender, and medical condition), and unstructured medical notes on classification accuracy for resuscitation code status. Data was extracted from the MIMICII database. Natural language processing (NLP) was used to evaluate the social section of the nurses’ progress notes. BoosTexter was used to predict the code-status using notes, age, gender, and Simplified Acute Physiology Score (SAPS). The relative impact of features was...

  2. Structure elucidation and complete NMR spectral assignments of four new diterpenoids from Smallantus sonchifolius.

    Science.gov (United States)

    Dou, De-Qiang; Tian, Fang; Qiu, Ying-Kun; Kang, Ting-Guo; Dong, Feng

    2008-08-01

    Four new diterpenoids, named smaditerpenic acid A-D, together with five known compounds, were isolated from the H(2)O extract of the leaves of Smallantus sonchifolius (yacon) cultivated in Liaoning, China and their structures were elucidated on the basis of one- and two-dimensional NMR (including (1)H, (13)C-NMR, (1)H-(1)H COSY, HSQC, TOCSY, HMBC, and ROESY), electrospray ionization mass spectrometry (ESI-MS), and chemical methods. PMID:18470882

  3. Expected distance between terminal nucleotides of RNA secondary structures.

    Science.gov (United States)

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

    2012-09-01

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

  4. Assignment of fingerprint vibrations in the resonance Raman spectra of rhodopsin, isorhodopsin, and bathorhodopsin: implications for chromophore structure and environment

    International Nuclear Information System (INIS)

    13C- and 2H-labeled retinal derivatives have been used to assign normal modes in the 1100-1300-cm-1 fingerprint region of the resonance Raman spectra of rhodopsin, isorhodopsin, and bathorhodopsin. On the basis of the 13C shifts, C8-C9 stretching character is assigned at 1217 cm-1 in rhodopsin, at 1206 cm-1 in isorhodopsin, and at 1214 cm-1 in bathorhodopsin. C10-C11 stretching character is localized at 1098 cm-1 in rhodopsin, at 1154 cm-1 in isorhodopsin, and at 1166 cm-1 in bathorhodopsin. C14-C15 stretching character is found at 1190 cm-1 in rhodopsin, at 1206 cm-1 in isorhodopsin, and at 1210 cm-1 in bathorhodopsin. C12-C13 stretching character is much more delocalized, but the characteristic coupling with the C14H rock allows the authors to assign the C12-C13 stretch at ∼1240 cm-1 in rhodopsin, isorhodopsin, and bathorhodopsin. The insensitivity of the C14-C15 stretching mode to N-deuteriation in all three pigments demonstrates that each contains a trans (anti) protonated Schiff base bond. The relatively high frequency of the C10-C11 mode of bathorhodopsin demonstrates that bathorhodopsin is s-trans about the C10-C11 single bond. This provides strong evidence against the model of bathorhodopsin proposed by Liu and Asato, which suggests a C10-C11 s-cis structure. Comparison of the fingerprint modes of rhodopsin with those of the 11-cis-retinal protonated Schiff base in methanol shows that the frequencies of the C-C stretching modes are largely unperturbed by protein binding. The implications of these observations for the mechanism of wavelength regulation in visual pigments and energy storage in bathorhodopsin are discussed

  5. Changes in secondary structure of gluten proteins due to emulsifiers

    Science.gov (United States)

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

    2013-02-01

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

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

    OpenAIRE

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

    2007-01-01

    Abstract Background The prediction of the secondary structure of proteins is one of the most studied problems in bioinformatics. Despite their success in many problems of biological sequence analysis, Hidden Markov Models (HMMs) have not been used much for this problem, as the complexity of the task makes manual design of HMMs difficult. Therefore, we have developed a method for evolving the structure of HMMs automatically, using Genetic Algorithms (GAs). Results In the GA procedure, populati...

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

    OpenAIRE

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

    2011-01-01

    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...

  8. Amino Acid Molecular Units: Building Primary and Secondary Protein Structures

    Directory of Open Access Journals (Sweden)

    Aparecido R. Silva

    2008-05-01

    Full Text Available In order to guarantee the learning quality and suitable knowledge  use  about structural biology, it is fundamental to  exist, since the beginning of  students’ formation, the possibility of clear visualization of biomolecule structures. Nevertheless, the didactic books can only bring  schematic  drawings; even more elaborated figures and graphic computation  do not permit the necessary interaction.  The representation of three-dimensional molecular structures with ludic models, built with representative units, have supplied to the students and teachers a successfully experience to  visualize such structures and correlate them to the real molecules.  The design and applicability of the representative units were discussed with researchers and teachers before mould implementation.  In this stage  it  will be presented the  developed  kit  containing the  representative  plastic parts of the main amino acids.  The kit can demonstrate the interaction among the amino acids  functional groups  (represented by colors, shapes,  sizes and  the peptidic bonds between them  facilitating the assembly and visuali zation of the primary and secondary protein structure.  The models were designed for  Ca,  amino,  carboxyl groups  and  hydrogen. The  lateral chains have  well defined models that represent their geometrical shape.  The completed kit set  will be presented in this meeting (patent requested.  In the last phase of the project will be realized  an effective evaluation  of the kit  as a facilitative didactic tool of the teaching/learning process in the Structural Molecular Biology area.

  9. Spectral assignments and structural studies of a warfarin derivative stereoselectively formed by tandem cyclization

    Science.gov (United States)

    Velayutham Pillai, M.; Rajeswari, K.; Vidhyasagar, T.

    2015-11-01

    The structural elucidation of a Mannich condensation product of rac-Warfarin with benzaldehyde and methyl amine was carried out using IR, Mass, 1H NMR, 13C NMR, 1H-1H COSY, 1H-13C COSY, DEPT-135, HMBC, NOESY spectra and single crystal X-ray diffraction. Formation of a new pyran ring via a tandem cyclization in the presence of methyl amine was observed. The optimized geometry and HOMO-LUMO energy gap along with other important physical parameters were found by Gaussian 09 program using HF 6-31G (d, p) and B3YLP/DFT 6-31G (d, p) level of theory. The preferred conformation of the piperidine ring in solution state was found to be chair from the NMR spectra. Single crystal X-ray diffraction and optimized geometry (by theoretical study) also confirms the chair conformation in the solid state.

  10. Polynomial Assignments

    OpenAIRE

    Guillemin, Victor; Sabatini, Silvia; Zara, Catalin

    2013-01-01

    The concept of assignments was introduced in [GGK99] as a method for extracting geometric information about group actions on manifolds from combinatorial data encoded in the infinitesimal orbit-type stratification. In this paper we will answer in the affirmative a question posed in [GGK99] by showing that the equivariant cohomology ring of $M$ is to a large extent determined by this data.

  11. Enhanced functional and structural domain assignments using remote similarity detection procedures for proteins encoded in the genome of Mycobacterium tuberculosis H37Rv

    Indian Academy of Sciences (India)

    Seema Namboori; Natasha Mhatre; Sentivel Sujatha; Narayanaswamy Srinivasan; Shashi Bhushan Pandit

    2004-09-01

    The sequencing of the Mycobacterium tuberculosis (MTB) H37Rv genome has facilitated deeper insights into the biology of MTB, yet the functions of many MTB proteins are unknown. We have used sensitive profile-based search procedures to assign functional and structural domains to infer functions of gene products encoded in MTB. These domain assignments have been made using a compendium of sequence and structural domain families. Functions are predicted for 78% of the encoded gene products. For 69% of these, functions can be inferred by domain assignments. The functions for the rest are deduced from their homology to proteins of known function. Superfamily relationships between families of unknown and known structures have increased structural information by ∼ 11%. Remote similarity detection methods have enabled domain assignments for 1325 ‘hypothetical proteins’. The most populated families in MTB are involved in lipid metabolism, entry and survival of the bacillus in host. Interestingly, for 353 proteins, which we refer to as MTB-specific, no homologues have been identified. Numerous, previously unannotated, hypothetical proteins have been assigned domains and some of these could perhaps be the possible chemotherapeutic targets. MTB-specific proteins might include factors responsible for virulence. Importantly, these assignments could be valuable for experimental endeavors. The detailed results are publicly available at http://hodgkin.mbu.iisc.ernet.in/∼dots.

  12. New in silico approach to assessing RNA secondary structures with non-canonical base pairs

    OpenAIRE

    Rybarczyk, Agnieszka; Szostak, Natalia; Antczak, Maciej; Zok, Tomasz; Popenda, Mariusz; Adamiak, Ryszard; Blazewicz, Jacek; Szachniuk, Marta

    2015-01-01

    Background The function of RNA is strongly dependent on its structure, so an appropriate recognition of this structure, on every level of organization, is of great importance. One particular concern is the assessment of base-base interactions, described as the secondary structure, the knowledge of which greatly facilitates an interpretation of RNA function and allows for structure analysis on the tertiary level. The RNA secondary structure can be predicted from a sequence using in silico meth...

  13. 英语作业设计对英语学习动机影响的实证研究%The Motivating Function of English Assignment for the English Learning of the Students in Secondary Vocational Schools

    Institute of Scientific and Technical Information of China (English)

    钟义清

    2014-01-01

    With an empirical method, the writer, from the perspective of English assignment, explored the possibilities and effectiveness of improving the English learning motivation of the students in secondary vocational schools. The results showed that well-designed assignment according to some theories and principles could improve the students’ extrinsic and intrinsic motivations and their English learning autonomy as well.%本文采取实证的方法,从英语作业设计的角度,探索提高中职生英语学习动机的可能性和有效性。研究结果表明,依据一定的理论、原则,精心为学生设计的作业,可以提高中职生英语学习的外在动机、内在动机和努力学习的程度。

  14. Institutional structures of the flexible assignment of personnel between enterprises: An economic comparison of Temporary Agency Work, Interim Management and Consulting

    OpenAIRE

    Alewell, Dorothea; Bähring, Katrin; Thommes, Kirsten

    2005-01-01

    Temporary Agency Work, Interim Management and Consulting are three versions of the flexible assignment of personnel between enterprises, which are - with regard to their basic economic structure - more or less similar, but which are organised under thoroughly different contractual and legal regulations in Germany and in three more or less differentiated segments of the market. The paper aims at comparing these forms of flexible personnel assignment under empirical and institutional aspects fr...

  15. TurboKnot: rapid prediction of conserved RNA secondary structures including pseudoknots

    OpenAIRE

    Seetin, Matthew G.; Mathews, David H.

    2012-01-01

    Motivation: Many RNA molecules function without being translated into proteins, and function depends on structure. Pseudoknots are motifs in RNA secondary structures that are difficult to predict but are also often functionally important.

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

    Science.gov (United States)

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

    2010-06-01

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

  17. Mathematical and Biological Modelling of RNA Secondary Structure and Its Effects on Gene Expression

    Directory of Open Access Journals (Sweden)

    T. A. Hughes

    2006-01-01

    Full Text Available Secondary structures within the 5′ untranslated regions of messenger RNAs can have profound effects on the efficiency of translation of their messages and thereby on gene expression. Consequently they can act as important regulatory motifs in both physiological and pathological settings. Current approaches to predicting the secondary structure of these RNA sequences find the structure with the global-minimum free energy. However, since RNA folds progressively from the 5′ end when synthesised or released from the translational machinery, this may not be the most probable structure. We discuss secondary structure prediction based on local-minimisation of free energy with thermodynamic fluctuations as nucleotides are added to the 3′ end and show that these can result in different secondary structures. We also discuss approaches for studying the extent of the translational inhibition specified by structures within the 5′ untranslated region.

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

    DEFF Research Database (Denmark)

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

    2004-01-01

    Existing computational methods for RNA secondary-structure prediction tacitly assume RNA to only encode functional RNA structures. However, experimental studies have revealed that some RNA sequences, e.g. compact viral genomes, can simultaneously encode functional RNA structures as well as proteins...... that RNA-DECODER's parameters can be automatically trained to successfully fold known secondary structures within the HCV genome. We scan the genomes of HCV and polio virus for conserved secondary-structure elements, and analyze performance as a function of available evolutionary information. On known...... secondary structures, RNA-DECODER shows a sensitivity similar to the programs MFOLD, PFOLD and RNAALIFOLD. When scanning the entire genomes of HCV and polio virus for structure elements, RNA-DECODER's results indicate a markedly higher specificity than MFOLD, PFOLD and RNAALIFOLD....

  19. Structure-Based Alignment and Consensus Secondary Structures for Three HIV-Related RNA Genomes.

    Directory of Open Access Journals (Sweden)

    Christopher A Lavender

    2015-05-01

    Full Text Available HIV and related primate lentiviruses possess single-stranded RNA genomes. Multiple regions of these genomes participate in critical steps in the viral replication cycle, and the functions of many RNA elements are dependent on the formation of defined structures. The structures of these elements are still not fully understood, and additional functional elements likely exist that have not been identified. In this work, we compared three full-length HIV-related viral genomes: HIV-1NL4-3, SIVcpz, and SIVmac (the latter two strains are progenitors for all HIV-1 and HIV-2 strains, respectively. Model-free RNA structure comparisons were performed using whole-genome structure information experimentally derived from nucleotide-resolution SHAPE reactivities. Consensus secondary structures were constructed for strongly correlated regions by taking into account both SHAPE probing structural data and nucleotide covariation information from structure-based alignments. In these consensus models, all known functional RNA elements were recapitulated with high accuracy. In addition, we identified multiple previously unannotated structural elements in the HIV-1 genome likely to function in translation, splicing and other replication cycle processes; these are compelling targets for future functional analyses. The structure-informed alignment strategy developed here will be broadly useful for efficient RNA motif discovery.

  20. Molecular structure and vibrational bands and 13C chemical shift assignments of both enmein-type diterpenoids by DFT study

    Science.gov (United States)

    Wang, Tao; Wu, Yi fang; Wang, Xue liang

    2014-01-01

    We report here theoretical and experimental studies on the molecular structure and vibrational and NMR spectra of both natural enmein type diterpenoids molecule (6, 7-seco-ent-kaurenes enmein type), isolated from the leaves of Isodon japonica (Burm.f.) Hara var. galaucocalyx (maxin) Hara. The optimized geometry, total energy, NMR chemical shifts and vibrational wavenumbers of epinodosinol and epinodosin have been determined using B3LYP method with 6-311G (d,p) basis set. A complete vibrational assignment is provided for the observed IR spectra of studied compounds. The calculated wavenumbers and 13C c.s. are in an excellent agreement with the experimental values. Quantum chemical calculations at the B3LYP/6-311G (d,p) level of theory have been carried out on studied compounds to obtain a set of molecular electronic properties (MEP,HOMO, LUMO and gap energies ΔEg). Electrostatic potential surfaces have been mapped over the electron density isosurfaces to obtain information about the size, shape, charge density distribution and chemical reactivity of the molecules.

  1. cDNA, deduced polypeptide structure and chromosomal assignment of human pulmonary surfactant proteolipid, SPL(pVal)

    International Nuclear Information System (INIS)

    In hyaline membrane disease of premature infants, lack of surfactant leads to pulmonary atelectasis and respiratory distress. Hydrophobic surfactant proteins of M/sub r/ = 5000-14,000 have been isolated from mammalian surfactants which enhance the rate of spreading and the surface tension lowering properties of phospholipids during dynamic compression. The authors have characterized the amino-terminal amino acid sequence of pulmonary proteolipids from ether/ethanol extracts of bovine, canine, and human surfactant. Two distinct peptides were identified and termed SPL(pVal) and SPL(Phe). An oligonucleotide probe based on the valine-rich amino-terminal amino acid sequence of SPL(pVal) was utilized to isolate cDNA and genomic DNA encoding the human protein, termed surfactant proteolipid SPL(pVal) on the basis of its unique polyvaline domain. The primary structure of a precursor protein of 20,870 daltons, containing the SPL(pVal) peptide, was deduced from the nucleotide sequence of the cDNAs. Hybrid-arrested translation and immunoprecipitation of labeled translation products of human mRNA demonstrated a precursor protein, the active hydrophobic peptide being produced by proteolytic processing. Two classes of cDNAs encoding SPL(pVal) were identified. Human SPL(pVal) mRNA was more abundant in the adult than in fetal lung. The SPL(pVal) gene locus was assigned to chromosome 8

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

    Directory of Open Access Journals (Sweden)

    Camproux Anne-Claude

    2011-02-01

    Full Text Available Abstract 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, α-helices and β-strands, to address the question of secondary structures' shape variation within proteins and deformation at interface upon complexation. Results Using a structural alphabet, we translated the 3 D structures of large sets of protein-protein complexes into sequences of structural letters. The shape of the secondary structures can be assessed by the structural letters that modeled them in the structural sequences. The distribution analysis of the structural letters in the three protein compartments (surface, core and interface reveals that secondary structures tend to adopt preferential conformations that differ among the compartments. The local description of secondary structures highlights that curved conformations are preferred on the surface while straight ones are preferred in the core. Interfaces display a mixture of local conformations either preferred in core or surface. The analysis of the structural letters transition occurring between protein-bound and unbound conformations shows that the deformation of secondary structure is tightly linked to the compartment preference of the local conformations. Conclusion The conformation of secondary structures can be further analysed and detailed thanks to a structural alphabet which allows a better description of protein surface, core and interface in terms of secondary structures' shape and deformation. Induced-fit modification tendencies described here should be valuable information to identify and characterize regions under strong structural constraints for functional reasons.

  3. Toward the solution structure of human insulin: Sequential 2D 1H NMR assignment of a des-pentapeptide analogue and comparison with crystal structure

    International Nuclear Information System (INIS)

    2D 1H NMR studies are presented of des-pentapeptide-insulin, an analogue of human insulin lacking the C-terminal five residues of the B chain. Removal of these residues, which are not required for function, is shown to reduce conformational broadening previously described in the spectrum of intact insulin. This difference presumably reflects more rapid internal motions in the fragment, which lead to more complete averaging of chemical shifts on the NMR time scale. Sequential 1H NMR assignment and preliminary structural analysis demonstrate retention in solution of the three α-helices observed in the crystal state and the relative orientation of the receptor-binding surfaces. These studies provide a foundation for determining the solution structure of insulin

  4. Toward the solution structure of human insulin: Sequential 2D sup 1 H NMR assignment of a des-pentapeptide analogue and comparison with crystal structure

    Energy Technology Data Exchange (ETDEWEB)

    Hua, Q.; Weiss, M.A. (Harvard Medical School, Boston, MA (USA) Massachusetts Institute of Technology, Cambridge (USA))

    1990-11-01

    2D {sup 1}H NMR studies are presented of des-pentapeptide-insulin, an analogue of human insulin lacking the C-terminal five residues of the B chain. Removal of these residues, which are not required for function, is shown to reduce conformational broadening previously described in the spectrum of intact insulin. This difference presumably reflects more rapid internal motions in the fragment, which lead to more complete averaging of chemical shifts on the NMR time scale. Sequential {sup 1}H NMR assignment and preliminary structural analysis demonstrate retention in solution of the three {alpha}-helices observed in the crystal state and the relative orientation of the receptor-binding surfaces. These studies provide a foundation for determining the solution structure of insulin.

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

    Directory of Open Access Journals (Sweden)

    Sudha Sharma

    2011-01-01

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

  6. Amino acid distance matrices and classifications for different protein secondary structure

    CERN Document Server

    Zhang, L; Guan, S; Zheng, W M; Zhang, Li-mei; Liu, Xin; Guan, Shan; Zheng, Wei-Mou

    2003-01-01

    The property of an amino acid is different according to the variation of protein secondary structure. Each central amino acid corresponds to a position specific amino acid distribution around it. Based on the probability distribution for the central amino acid, we get amino acid distance matrices and classifications for helix, sheet, coil and turn. It is observed that evident discrepancy exists in amino acid distance for different protein secondary structure. Some obvious difference between the distance matrices and blocks substitution matrix(BLOSUM) is found which can tell the difference of amino acid property between in certain protein secondary structure and the whole protein database. The classification of amino acid alphabets for specific protein secondary structure provide a clue for observing these difference.

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

    Directory of Open Access Journals (Sweden)

    Won Kyoung-Jae

    2007-09-01

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

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

    DEFF Research Database (Denmark)

    Swenson, M Shel; Anderson, Joshua; Ash, Andrew; Gaurav, Prashant; Sükösd, Zsuzsanna; Bader, David A; Harvey, Stephen C; Heitsch, Christine E

    2012-01-01

    Accurate and efficient RNA secondary structure prediction remains an important open problem in computational molecular biology. Historically, advances in computing technology have enabled faster and more accurate RNA secondary structure predictions. Previous parallelized prediction programs...... achieved significant improvements in runtime, but their implementations were not portable from niche high-performance computers or easily accessible to most RNA researchers. With the increasing prevalence of multi-core desktop machines, a new parallel prediction program is needed to take full advantage of...

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

    OpenAIRE

    Griebenow, K; Klibanov, A M

    1995-01-01

    Changes in the secondary structure of some dozen different proteins upon lyophilization of their aqueous solutions have been investigated by means of Fourier-transform infrared spectroscopy in the amide III band region. Dehydration markedly (but reversibly) alters the secondary structure of all the proteins studied, as revealed by both the quantitative analysis of the second derivative spectra and the Gaussian curve fitting of the original infrared spectra. Lyophilization substantially increa...

  10. TMPyP4, a Stabilizer of Nucleic Acid Secondary Structure, Is a Novel Acetylcholinesterase Inhibitor

    OpenAIRE

    Fujiwara, Nana; Mazzola, Michael; Cai, Elizabeth; Wang, Meng; Cave, John W.

    2015-01-01

    The porphyrin compound, TMPyP4 (5,10,15,20-Tetrakis-(N-methyl-4-pyridyl)porphine), is widely used as a photosensitizer and a modulator of nucleic acid secondary structure stability. Our group recently showed in cultured cells and forebrain slice cultures that this compound can also down regulate expression of Tyrosine hydroxylase (Th), which encodes the rate-limiting enzyme in catecholamine biosynthesis, by stabilizing DNA secondary structures in the Th proximal promoter. The current study so...

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

    OpenAIRE

    2012-01-01

    Background Prediction of ribonucleic acid (RNA) secondary structure remains one of the most important research areas in bioinformatics. The Zuker algorithm is one of the most popular methods of free energy minimization for RNA secondary structure prediction. Thus far, few studies have been reported on the acceleration of the Zuker algorithm on general-purpose processors or on extra accelerators such as Field Programmable Gate-Array (FPGA) and Graphics Processing Units (GPU). To the best of ou...

  12. Secondary Structure as a Functional Feature in the Downstream Region of Mammalian Polyadenylation Signals

    OpenAIRE

    Wu, Chunxiao; Alwine, James C.

    2004-01-01

    Secondary structure within the downstream region of mammalian polyadenylation signals has been proposed to perform important functions. The simian virus 40 late polyadenylation signal (SVLPA) forms alternate secondary structures in equilibrium. Their formation correlates with cleavage-polyadenylation efficiency (H. Hans and J. C. Alwine, Mol. Cell. Biol. 20:2926-2932, 2000; M. I. Zarudnaya, I. M. Kolomiets, A. L. Potyahaylo, and D. M. Hovorun, Nucleic Acids Res. 3:1375-1386, 2003), and oligon...

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

    Science.gov (United States)

    Gwynne, Darryl T.

    2002-03-01

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

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

    OpenAIRE

    Hoang, Trinh Xuan; Cieplak, Marek

    1999-01-01

    We consider six different secondary structures of proteins and construct two types of Go-type off-lattice models: with the steric constraints and without. The basic aminoacid-aminoacid potential is Lennard Jones for the native contacts and a soft repulsion for the non-native contacts. The interactions are chosen to make the target secondary structure be the native state of the system. We provide a thorough equilibrium and kinetic characterization of the sequences through the molecular dynamic...

  15. 4SALE – A tool for synchronous RNA sequence and secondary structure alignment and editing

    Directory of Open Access Journals (Sweden)

    Schultz Jörg

    2006-11-01

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

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

    OpenAIRE

    Aydın, Zafer; AYDIN, Zafer; Altunbaşak, Yücel; Altunbasak, Yucel; Pakatcı, Kemal İsa; Pakatci, Kemal Isa; Erdoğan, Hakan; Erdogan, Hakan

    2007-01-01

    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 prof...

  17. GC content around splice sites affects splicing through pre-mRNA secondary structures

    Directory of Open Access Journals (Sweden)

    Chen Liang

    2011-01-01

    Full Text Available Abstract Background Alternative splicing increases protein diversity by generating multiple transcript isoforms from a single gene through different combinations of exons or through different selections of splice sites. It has been reported that RNA secondary structures are involved in alternative splicing. Here we perform a genomic study of RNA secondary structures around splice sites in humans (Homo sapiens, mice (Mus musculus, fruit flies (Drosophila melanogaster, and nematodes (Caenorhabditis elegans to further investigate this phenomenon. Results We observe that GC content around splice sites is closely associated with the splice site usage in multiple species. RNA secondary structure is the possible explanation, because the structural stability difference among alternative splice sites, constitutive splice sites, and skipped splice sites can be explained by the GC content difference. Alternative splice sites tend to be GC-enriched and exhibit more stable RNA secondary structures in all of the considered species. In humans and mice, splice sites of first exons and long exons tend to be GC-enriched and hence form more stable structures, indicating the special role of RNA secondary structures in promoter proximal splicing events and the splicing of long exons. In addition, GC-enriched exon-intron junctions tend to be overrepresented in tissue-specific alternative splice sites, indicating the functional consequence of the GC effect. Compared with regions far from splice sites and decoy splice sites, real splice sites are GC-enriched. We also found that the GC-content effect is much stronger than the nucleotide-order effect to form stable secondary structures. Conclusion All of these results indicate that GC content is related to splice site usage and it may mediate the splicing process through RNA secondary structures.

  18. Secondary systems modeled as fuzzy sub-structures

    DEFF Research Database (Denmark)

    Tarp-Johansen, Niels Jacob; Ditlevsen, Ove Dalager; Lin, Y.K.

    1998-01-01

    the simplest case be modeled by attaching random single degree of freedom oscillators, called fuzzies, to the master structure at randomly distributed points of the structure. Each of these fuzzies are characterized by a random triplet of mass, eigenfrequency, and damping ratio. This characterization...... can be combined with a model of the random distribution of the fuzzies over the structure by letting the entire system of fuzzies be characterized as a triplet of random fields over the structure. Two specific examples, a Poisson point pulse field and a Poisson square wave field, of such a triplet...... determine the probabilistic properties of the impulse response function, say, or of the nonergodic steady state response to stationary excitation, say. The study prepares for a finite element model of a flexible master structure with a fuzzy subsystem attached to it....

  19. STUDY ON THE SEQUENCE STRUCTURE OF SBR BY 13C- NMR METHOD Ⅱ . PEAK ASSIGNMENT FOR ALIPHATIC CARBONS SPECTRA

    Institute of Scientific and Technical Information of China (English)

    JIAO Shuke; CHEN Xiaonong; HU Liping; YAN Baozhen

    1990-01-01

    The study on 13C-NMR spectra of aliphatic carbon region of emulsion-processed and solution-processed ( by lithium catalyst ) SBR was carried out. The assignments for more than thirty odd peaks observed experimentally were made by using " corresponding analysis " method, combined with the empirical parameters reported in literature. The peak intensities were calculated based on Bernoullian statistic assumption.

  20. Balanced input-output assignment

    Science.gov (United States)

    Gawronski, W.; Hadaegh, F. Y.

    1989-01-01

    Actuator/sensor locations and balanced representations of linear systems are considered for a given set of controllability and observability grammians. The case of equally controlled and observed states is given special attention. The assignability of grammians is examined, and the conditions for their existence are presented, along with several algorithms for their determination. Although an arbitrary positive semidefinite matrix is not always assignable, the identity grammian is shown to be always assignable. The results are extended to the case of flexible structures.

  1. Inflatable Habitat with Integrated Primary and Secondary Structure Project

    Data.gov (United States)

    National Aeronautics and Space Administration — Paragon Space Development Corp (Paragon) and Thin Red Line Aerospace (TRLA) proposes to explore the utilization of inflatable structures by designing a habitation...

  2. RNA-PAIRS: RNA probabilistic assignment of imino resonance shifts

    Energy Technology Data Exchange (ETDEWEB)

    Bahrami, Arash; Clos, Lawrence J.; Markley, John L.; Butcher, Samuel E. [National Magnetic Resonance Facility at Madison (United States); Eghbalnia, Hamid R., E-mail: eghbalhd@uc.edu [University of Cincinnati, Department of Molecular and Cellular Physiology (United States)

    2012-04-15

    The significant biological role of RNA has further highlighted the need for improving the accuracy, efficiency and the reach of methods for investigating RNA structure and function. Nuclear magnetic resonance (NMR) spectroscopy is vital to furthering the goals of RNA structural biology because of its distinctive capabilities. However, the dispersion pattern in the NMR spectra of RNA makes automated resonance assignment, a key step in NMR investigation of biomolecules, remarkably challenging. Herein we present RNA Probabilistic Assignment of Imino Resonance Shifts (RNA-PAIRS), a method for the automated assignment of RNA imino resonances with synchronized verification and correction of predicted secondary structure. RNA-PAIRS represents an advance in modeling the assignment paradigm because it seeds the probabilistic network for assignment with experimental NMR data, and predicted RNA secondary structure, simultaneously and from the start. Subsequently, RNA-PAIRS sets in motion a dynamic network that reverberates between predictions and experimental evidence in order to reconcile and rectify resonance assignments and secondary structure information. The procedure is halted when assignments and base-parings are deemed to be most consistent with observed crosspeaks. The current implementation of RNA-PAIRS uses an initial peak list derived from proton-nitrogen heteronuclear multiple quantum correlation ({sup 1}H-{sup 15}N 2D HMQC) and proton-proton nuclear Overhauser enhancement spectroscopy ({sup 1}H-{sup 1}H 2D NOESY) experiments. We have evaluated the performance of RNA-PAIRS by using it to analyze NMR datasets from 26 previously studied RNAs, including a 111-nucleotide complex. For moderately sized RNA molecules, and over a range of comparatively complex structural motifs, the average assignment accuracy exceeds 90%, while the average base pair prediction accuracy exceeded 93%. RNA-PAIRS yielded accurate assignments and base pairings consistent with imino

  3. Evolutionary rate variation and RNA secondary structure prediction

    DEFF Research Database (Denmark)

    Knudsen, B; Andersen, E S; Damgaard, Christian Kroun;

    2004-01-01

    regions. In addition we obtained an alignment of the 5' HIV-1 region that is more consistent with the structure than that currently in the database. We added randomized noise to the original values of the rates to investigate the stability of predictions to rate matrix deviations. We find that changes...... by applying rates derived from tRNA and rRNA to the prediction of the much more rapidly evolving 5'-region of HIV-1. We find that the HIV-1 prediction is in agreement with experimental data, even though the relative evolutionary rate between A and G is significantly increased, both in stem and loop...... of approach. Determining these rates can be hard to do reliably without a large and accurate initial alignment, which ideally also has structural annotation. Hence, one must often apply rates extracted from other RNA families with trusted alignments and structures. Here, we investigate this problem...

  4. Analysis of an optimal hidden Markov model for secondary structure prediction

    Directory of Open Access Journals (Sweden)

    Gibrat Jean-François

    2006-12-01

    Full Text Available Abstract Background Secondary structure prediction is a useful first step toward 3D structure prediction. A number of successful secondary structure prediction methods use neural networks, but unfortunately, neural networks are not intuitively interpretable. On the contrary, hidden Markov models are graphical interpretable models. Moreover, they have been successfully used in many bioinformatic applications. Because they offer a strong statistical background and allow model interpretation, we propose a method based on hidden Markov models. Results Our HMM is designed without prior knowledge. It is chosen within a collection of models of increasing size, using statistical and accuracy criteria. The resulting model has 36 hidden states: 15 that model α-helices, 12 that model coil and 9 that model β-strands. Connections between hidden states and state emission probabilities reflect the organization of protein structures into secondary structure segments. We start by analyzing the model features and see how it offers a new vision of local structures. We then use it for secondary structure prediction. Our model appears to be very efficient on single sequences, with a Q3 score of 68.8%, more than one point above PSIPRED prediction on single sequences. A straightforward extension of the method allows the use of multiple sequence alignments, rising the Q3 score to 75.5%. Conclusion The hidden Markov model presented here achieves valuable prediction results using only a limited number of parameters. It provides an interpretable framework for protein secondary structure architecture. Furthermore, it can be used as a tool for generating protein sequences with a given secondary structure content.

  5. POPULATION STRUCTURE OF Ocotea puberula IN A SECONDARY AND A PRIMARY MIXED FOREST IN MISIONES

    Directory of Open Access Journals (Sweden)

    Silvana Lucia Caldato

    2010-08-01

    Full Text Available The aim of this work was to study the population structure of Ocotea puberula (Nees et Mart. Nees (Lauraceae, in a secondary and a primary forests Northeast of Misiones in Argentina, at 26º 15¢ S and 54º 15¢ W. Two permanent sampling plots of 3 hectares each were installed in the secondary and primary forest, respectively. Each sampling plot was divided into 75 subplots of 20 x 20 m. In each subplot all individuals of Ocotea puberula equal or greater than 20 cm of height were measured. The structure of size and spatial distribution was surveyed. Ocotea puberula was a secondary species, with a high number of individuals of natural regeneration in the secondary forest, and only adult trees in the primary forest. The species presented a clustered pattern of spatial distribution in both forests.

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

    OpenAIRE

    Byun, Yanga; Han, Kyungsook

    2006-01-01

    Visualizing RNA secondary structures and pseudoknot structures is essential to bioinformatics systems that deal with RNA structures. However, many bioinformatics systems use heterogeneous data structures and incompatible software components, so integration of software components (including a visualization component) into a system can be hindered by incompatibilities between the components of the system. This paper presents an XML web service and web application program for visualizing RNA sec...

  7. FTIR Analysis of Protein Secondary Structure in Cheddar Cheese during Ripening

    Institute of Scientific and Technical Information of China (English)

    WANG Fang; LIU Ai-ping; REN Fa-zheng; ZHANG Xiao-ying; Stephanie Clark; ZHANG Lu-da; GUO Hui-yuan

    2011-01-01

    Proteolysis is one of the most important biochemical reactions during cheese ripening. Studies on the secondary structure of proteins during ripening would be helpful for characterizing protein changes for assessing cheese quality. Fourier transform infrared spectroscopy (FTIR), with self-deconvolution, second derivative analysis and band curve-fitting, was used to characterize the secondary structure of proteins in Cheddar cheese during ripening. The spectra of the amide I region showed great similarity, while the relative contents of the secondary structures underwent a series of changes. As ripening progressed, the α-helix content decreased and the β-sheet content increased. This structural shift was attributed to the strengthening of hydrogen bonds that resulted from hydrolysis of caseins. In summary, FTIR could provide the basis for rapid characterization of cheese that is undergoing ripening.

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

    OpenAIRE

    Jacques, J P; Susskind, M M

    1991-01-01

    Natural antisense RNAs have stem-loop (hairpin) secondary structures that are important for their function. The sar antisense RNA of phage P22 is unusual: the 3' half of the molecule forms an extensive stem-loop, but potential structures for the 5' half are not predicted to be thermodynamically stable. We devised a novel method to determine the secondary structure of sar RNA by examining the electrophoretic mobility on non-denaturing gels of numerous sar mutants. The results show that the wil...

  9. Use of secondary structural information and C-C distance restraints to model protein structures with MODELLER

    Indian Academy of Sciences (India)

    Boojala V B Reddy; Yiannis N Kaznessis

    2007-08-01

    Protein secondary structure predictions and amino acid long range contact map predictions from primary sequence of proteins have been explored to aid in modelling protein tertiary structures. In order to evaluate the usefulness of secondary structure and 3D-residue contact prediction methods to model protein structures we have used the known Q3 (alpha-helix, beta-strands and irregular turns/loops) secondary structure information, along with residue-residue contact information as restraints for MODELLER. We present here results of our modelling studies on 30 best resolved single domain protein structures of varied lengths. The results shows that it is very difficult to obtain useful models even with 100% accurate secondary structure predictions and accurate residue contact predictions for up to 30% of residues in a sequence. The best models that we obtained for proteins of lengths 37, 70, 118, 136 and 193 amino acid residues are of RMSDs 4.17, 5.27, 9.12, 7.89 and 9.69, respectively. The results show that one can obtain better models for the proteins which have high percent of alpha-helix content. This analysis further shows that MODELLER restrain optimization program can be useful only if we have truly homologous structure(s) as a template where it derives numerous restraints, almost identical to the templates used. This analysis also clearly indicates that even if we satisfy several true residue-residue contact distances, up to 30% of their sequence length with fully known secondary structural information, we end up predicting model structures much distant from their corresponding native structures.

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

    Science.gov (United States)

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

    2011-10-01

    Methods for predicting protein secondary structures provide information that is useful both in ab initio structure prediction and as additional restraints for fold recognition algorithms. Secondary structure predictions may also be used to guide the design of site directed mutagenesis studies, and to locate potential functionally important residues. In this article, we propose a multi-modal back propagation neural network (MMBP) method for predicting protein secondary structures. Using a Knowledge Discovery Theory based on Inner Cognitive Mechanism (KDTICM) method, we have constructed a compound pyramid model (CPM), which is composed of three layers of intelligent interface that integrate multi-modal back propagation neural network (MMBP), mixed-modal SVM (MMS), modified Knowledge Discovery in Databases (KDD(⁎)) process and so on. The CPM method is both an integrated web server and a standalone application that exploits recent advancements in knowledge discovery and machine learning to perform very accurate protein secondary structure predictions. Using a non-redundant test dataset of 256 proteins from RCASP256, the CPM method achieves an average Q(3) score of 86.13% (SOV99=84.66%). Extensive testing indicates that this is significantly better than any other method currently available. Assessments using RS126 and CB513 datasets indicate that the CPM method can achieve average Q(3) score approaching 83.99% (SOV99=80.25%) and 85.58% (SOV99=81.15%). By using both sequence and structure databases and by exploiting the latest techniques in machine learning it is possible to routinely predict protein secondary structure with an accuracy well above 80%. A program and web server, called CPM, which performs these secondary structure predictions, is accessible at http://kdd.ustb.edu.cn/protein_Web/. PMID:21880310

  11. FTIR Characterization of the Secondary Structure of Insulin Encapsulated within Liposome

    Institute of Scientific and Technical Information of China (English)

    ZHANGXuan; HUANGLi-xin; NIESong-qing; QIXian-rong; ZHANGQiang

    2003-01-01

    Aim:To determine the secondary structure of insulin encapsulated within liposome.Methods:The secondary structure of native insulin,mixture of insulin with liposome(sample I) and insulin encapsulated within liposome(sample Ⅱ) were determined by FTIR(Fourier Transform Infrared) spectroscopy.Results:The secondary structure of insulin encspsulated within liposome(Ⅱ) are similar with the secondary structure of native insulin.The difference existed in the amount of α-helices (from 36% of insulin to 31% of sample Ⅱ)and β-sheet(from 48% of insulin to 51% of sample Ⅱ).The content of α-helices and β-sheet of insulin in sample I was found to be very close to that of sample Ⅱ.The results revealed that the insulin encapsulated within liposome possibly spread on the surface of liposome,without inserting into the liposome membrane.Coclusion:The secondary structure of insulin encapsulated within liposome is similar with the native insulin.

  12. Secondary structure in the target as a confounding factor in synthetic oligomer microarray design

    Directory of Open Access Journals (Sweden)

    Gibas Cynthia J

    2005-03-01

    Full Text Available Abstract Background Secondary structure in the target is a property not usually considered in software applications for design of optimal custom oligonucleotide probes. It is frequently assumed that eliminating self-complementarity, or screening for secondary structure in the probe, is sufficient to avoid interference with hybridization by stable secondary structures in the probe binding site. Prediction and thermodynamic analysis of secondary structure formation in a genome-wide set of transcripts from Brucella suis 1330 demonstrates that the properties of the target molecule have the potential to strongly influence the rate and extent of hybridization between transcript and tethered oligonucleotide probe in a microarray experiment. Results Despite the relatively high hybridization temperatures and 1M monovalent salt imposed in the modeling process to approximate hybridization conditions used in the laboratory, we find that parts of the target molecules are likely to be inaccessible to intermolecular hybridization due to the formation of stable intramolecular secondary structure. For example, at 65°C, 28 ± 7% of the average cDNA target sequence is predicted to be inaccessible to hybridization. We also analyzed the specific binding sites of a set of 70mer probes previously designed for Brucella using a freely available oligo design software package. 21 ± 13% of the nucleotides in each probe binding site are within a double-stranded structure in over half of the folds predicted for the cDNA target at 65°C. The intramolecular structures formed are more stable and extensive when an RNA target is modeled rather than cDNA. When random shearing of the target is modeled for fragments of 200, 100 and 50 nt, an overall destabilization of secondary structure is predicted, but shearing does not eliminate secondary structure. Conclusion Secondary structure in the target is pervasive, and a significant fraction of the target is found in double stranded

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

    Directory of Open Access Journals (Sweden)

    Tahi Fariza

    2007-11-01

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

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

    International Nuclear Information System (INIS)

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

  15. Structuring Free-text Microbiology Culture Reports For Secondary Use

    Science.gov (United States)

    Yim, Wen-wai; Evans, Heather L.; Yetisgen, Meliha

    2015-01-01

    Microbiology lab culture reports are a frequently used diagnostic tool for clinical providers. However, their incorporation into clinical surveillance applications and evidence-based medicine can be severely hindered by the free-text nature of these reports. In this work, we (1) created a microbiology culture template to structure free-text microbiology reports, (2) generated an annotated microbiology report corpus, and (3) built a microbiology information extraction system. Specifically, we combined rule-based, hybrid, and statistical techniques to extract microbiology entities and fill templates for structuring data. System performances were favorable, with entity f1-score 0.889 and relation f1-score 0.795. We plan to incorporate these extractions as features for our ongoing ventilator-associated pneumonia surveillance project, though this tool can be used as an upstream process in other applications. Our newly created corpus includes 1442 unique gram stain and culture microbiology reports generated from a cohort of 715 patients at the University of Washington Medical Facilities. PMID:26306288

  16. Structural class prediction of protein using novel feature extraction method from chaos game representation of predicted secondary structure.

    Science.gov (United States)

    Zhang, Lichao; Kong, Liang; Han, Xiaodong; Lv, Jinfeng

    2016-07-01

    Protein structural class prediction plays an important role in protein structure and function analysis, drug design and many other biological applications. Extracting good representation from protein sequence is fundamental for this prediction task. In recent years, although several secondary structure based feature extraction strategies have been specially proposed for low-similarity protein sequences, the prediction accuracy still remains limited. To explore the potential of secondary structure information, this study proposed a novel feature extraction method from the chaos game representation of predicted secondary structure to mainly capture sequence order information and secondary structure segments distribution information in a given protein sequence. Several kinds of prediction accuracies obtained by the jackknife test are reported on three widely used low-similarity benchmark datasets (25PDB, 1189 and 640). Compared with the state-of-the-art prediction methods, the proposed method achieves the highest overall accuracies on all the three datasets. The experimental results confirm that the proposed feature extraction method is effective for accurate prediction of protein structural class. Moreover, it is anticipated that the proposed method could be extended to other graphical representations of protein sequence and be helpful in future research. PMID:27084358

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

    Science.gov (United States)

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

    2003-01-01

    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 β-turn and random coil increase rapidly and the percentages of α-helix and anti-parallel β-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.

  18. Dynamics of beta and proliferating cell nuclear antigen sliding clamps in traversing DNA secondary structure.

    Science.gov (United States)

    Yao, N; Hurwitz, J; O'Donnell, M

    2000-01-14

    Chromosomal replicases of cellular organisms utilize a ring shaped protein that encircles DNA as a mobile tether for high processivity in DNA synthesis. These "sliding clamps" have sufficiently large linear diameters to encircle duplex DNA and are perhaps even large enough to slide over certain DNA secondary structural elements. This report examines the Escherichia coli beta and human proliferating cell nuclear antigen clamps for their ability to slide over various DNA secondary structures. The results show that these clamps are capable of traversing a 13-nucleotide ssDNA loop, a 4-base pair stem-loop, a 4-nucleotide 5' tail, and a 15-mer bubble within the duplex. However, upon increasing the size of these structures (20-nucleotide loop, 12-base pair stem-loop, 28-nucleotide 5' tail, and 20-nucleotide bubble) the sliding motion of the beta and proliferating cell nuclear antigen over these elements is halted. Studies of the E. coli replicase, DNA polymerase III holoenzyme, in chain elongation with the beta clamp demonstrate that upon encounter with an oligonucleotide annealed in its path, it traverses the duplex and resumes synthesis on the 3' terminus of the oligonucleotide. This sliding and resumption of synthesis occurs even when the oligonucleotide contains a secondary structure element, provided the beta clamp can traverse the structure. However, upon encounter with a downstream oligonucleotide containing a large internal secondary structure, the holoenzyme clears the obstacle by strand displacing the oligonucleotide from the template. Implications of these protein dynamics to DNA transactions are discussed. PMID:10625694

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

    OpenAIRE

    Puton, T.; Kozlowski, L. P.; Rother, K. M.; Bujnicki, J. M.

    2013-01-01

    We present a continuous benchmarking approach for the assessment of RNA secondary structure prediction methods implemented in the CompaRNA web server. As of 3 October 2012, the performance of 28 single-sequence and 13 comparative methods has been evaluated on RNA sequences/structures released weekly by the Protein Data Bank. We also provide a static benchmark generated on RNA 2D structures derived from the RNAstrand database. Benchmarks on both data sets offer insight into the relative perfor...

  20. Secondary Structural Change Can Occur Diffusely and Not Modularly during Protein Folding and Unfolding Reactions.

    Science.gov (United States)

    Malhotra, Pooja; Udgaonkar, Jayant B

    2016-05-11

    A major goal of protein folding studies is to understand the structural basis of the coupling between stabilizing interactions, which leads to cooperative conformational change. The goal is challenging because of the difficulty in simultaneously measuring global cooperativity by determining population distributions of the conformations present, and the structures of these conformations. Here, hydrogen exchange (HX) into the small protein monellin was carried out under conditions where structure-opening is rate limiting for most backbone amide sites. Detection by mass spectrometry allowed characterization of not only segment-specific structure-opening rates but also the cooperativity of unfolding of the different secondary structural segments of the protein. The segment-specific pattern of HX reveals that the backbone hydrogen-bonding network disassembles in a structurally diffuse, asynchronous manner. A comparison of the site-specific transient opening rates of secondary and tertiary structure in the protein provides a structural rationale for the observation that unfolding is hierarchical and describable by exponential kinetics, despite being diffuse. Since unfolding was studied in native conditions, the sequence of events during folding in the same conditions will be the reverse of the sequence of events observed during unfolding. Hence, the formation of secondary structural units during folding would also occur in a non-cooperative, diffuse, and asynchronous manner. PMID:27093885

  1. FASTR: A novel data format for concomitant representation of RNA sequence and secondary structure information

    Indian Academy of Sciences (India)

    Tungadri Bose; Anirban Dutta; Mohammed Mh; Hemang Gandhi; Sharmila S Mande

    2015-09-01

    Given the importance of RNA secondary structures in defining their biological role, it would be convenient for researchers seeking RNA data if both sequence and structural information pertaining to RNA molecules are made available together. Current nucleotide data repositories archive only RNA sequence data. Furthermore, storage formats which can frugally represent RNA sequence as well as structure data in a single file, are currently unavailable. This article proposes a novel storage format, `FASTR’, for concomitant representation of RNA sequence and structure. The storage efficiency of the proposed FASTR format has been evaluated using RNA data from various microorganisms. Results indicate that the size of FASTR formatted files (containing both RNA sequence as well as structure information) are equivalent to that of FASTA-format files, which contain only RNA sequence information. RNA secondary structure is typically represented using a combination of a string of nucleotide characters along with the corresponding dot-bracket notation indicating structural attributes. `FASTR’ – the novel storage format proposed in the present study enables a frugal representation of both RNA sequence and structural information in the form of a single string. In spite of having a relatively smaller storage footprint, the resultant `fastr’ string(s) retain all sequence as well as secondary structural information that could be stored using a dot-bracket notation. An implementation of the `FASTR’ methodology is available for download at http://metagenomics.atc.tcs.com/compression/fastr.

  2. Study of angiotensin-(1-7) vasoactive peptide and its beta-cyclodextrin inclusion complexes: complete sequence-specific NMR assignments and structural studies.

    Science.gov (United States)

    Lula, Ivana; Denadai, Angelo L; Resende, Jarbas M; de Sousa, Frederico B; de Lima, Guilherme F; Pilo-Veloso, Dorila; Heine, Thomas; Duarte, Hélio A; Santos, Robson A S; Sinisterra, Rubén D

    2007-11-01

    We report the complete sequence-specific hydrogen NMR assignments of vasoactive peptide angiotensin-(1-7) (Ang-(1-7)). Assignments of the majority of the resonances were accomplished by COSY, TOCSY, and ROESY peak coordinates at 400MHz and 600MHz. Long-side-chain amino acid spin system identification was facilitated by long-range coherence transfer experiments (TOCSY). Problems with overlapped resonance signals were solved by analysis of heteronuclear 2D experiments (HSQC and HMBC). Nuclear Overhauser effects (NOE) results were used to probe peptide conformation. We show that the inclusion of the angiotensin-(1-7) tyrosine residue is favored in inclusion complexes with beta-cyclodextrin. QM/MM simulations at the DFTB/UFF level confirm the experimental NMR findings and provide detailed structural information on these compounds in aqueous solution. PMID:17904691

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

    Directory of Open Access Journals (Sweden)

    Chen Chun

    2008-03-01

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

  4. Active control of structural vibration with on-line secondary path modeling

    Institute of Scientific and Technical Information of China (English)

    YANG Tiejun; GU Zhongquan

    2004-01-01

    An active control strategy with on-line secondary path modeling is proposed and applied in active control of helicopter structural vibration. Computer simulations of the secondary path modeling performance demonstrate the superiorities of the active control strategy. A 2-input 4-output active control simulation for a helicopter model is performed and great reduction of structural vibration is achieved. 2-input 2-output and 2-input 4-output experimental studies of structural vibration control for a free-free beam are also carried out in laboratory to simulate a flying helicopter. The experimental results also show better reduction of the structural vibration, which verifies that the proposed method is effective and practical in structural vibration reduction.

  5. The internal transcribed spacer 2 exhibits a common secondary structure in green algae and flowering plants.

    Science.gov (United States)

    Mai, J C; Coleman, A W

    1997-03-01

    Sequences of the Internal Transcribed Spacer 2 (ITS-2) regions of the nuclear rDNA repeats from 111 organisms of the family Volvocaceae (Chlorophyta) and unicellular organisms of the Volvocales, including Chlamydomonas reinhardtii, were determined. The use of thermodynamic energy optimization to generate secondary structures and phylogenetic comparative analysis of the spacer regions revealed a common secondary structure that is conserved despite wide intra- and interfamilial primary sequence divergence. The existence of this conserved higher-order structure is supported by the presence of numerous compensating basepair changes as well as by an evolutionary history of insertions and deletions that nevertheless maintains major aspects of the overall structure. Furthermore, this general structure is preserved across broad phylogenetic lines, as it is observed in the ITS-2s of other chlorophytes, including flowering plants; previous reports of common ITS-2 secondary structures in other eukaryotes were restricted to the order level. The reported ITS-2 structure possesses important conserved structural motifs which may help to mediate cleavages in the ITS-2 that occur during rRNA transcript processing. Their recognition can guide further studies of eukaryotic rRNA processing, and their application to sequence alignments may contribute significantly to the value of ITS-2 sequences in phylogenetic analyses at several taxonomic levels, but particularly in characterizing populations and species. PMID:9060392

  6. Combining sequence-based prediction methods and circular dichroism and infrared spectroscopic data to improve protein secondary structure determinations

    OpenAIRE

    Lees Jonathan G; Janes Robert W

    2008-01-01

    Abstract Background A number of sequence-based methods exist for protein secondary structure prediction. Protein secondary structures can also be determined experimentally from circular dichroism, and infrared spectroscopic data using empirical analysis methods. It has been proposed that comparable accuracy can be obtained from sequence-based predictions as from these biophysical measurements. Here we have examined the secondary structure determination accuracies of sequence prediction method...

  7. Two-dimensional NMR and photo-CIDNP studies of the insulin monomer: Assignment of aromatic resonances with application to protein folding, structure, and dynamics

    International Nuclear Information System (INIS)

    The aromatic 1H NMR resonances of the insulin monomer are assigned at 500 MHz by comparative studies of chemically modified and genetically altered variants, including a mutant insulin (PheB25 → Leu) associated with diabetes mellitus. The two histidines, three phenylalanines, and four tyrosines are observed to be in distinct local environments; their assignment provides sensitive markers for studies of tertiary structure, protein dynamics, and protein folding. The environments of the tyrosine residues have also been investigated by photochemically induced dynamic nuclear polarization (photo-CIDNP) and analyzed in relation to packing constrains in the crystal structures of insulin. Dimerization involving specific B-chain interactions is observed with increasing protein concentration and is shown to depend on temperature, pH, and solvent composition. The differences between proinsulin and mini-proinsulin suggest a structural mechanism for the observation that the fully reduced B29-A1 analogue folds more efficiently than proinsulin to form the correct pattern of disulfide bonds. These results are discussed in relation to molecular mechanics calculations of insulin based on the available crystal structures

  8. Two-dimensional NMR and photo-CIDNP studies of the insulin monomer: Assignment of aromatic resonances with application to protein folding, structure, and dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Weiss, M.A.; Shoelson, S.E. (Harvard Medical School, Boston, MA (USA) Massachusetts General Hospital, Boston (USA)); Nguyen, D.T.; O' Shea, E.; Karplus, M. (Harvard Univ., Cambridge, MA (USA)); Khait, I.; Neuringer, L.J. (Massachusetts Institute of Technology, Cambridge (USA)); Inouye, K. (Shionogi and Co., Ltd., Osaka (Japan)); Frank, B.H.; Beckage, M. (Eli Lilly and Co., Indianapolis, IN (USA))

    1989-12-12

    The aromatic {sup 1}H NMR resonances of the insulin monomer are assigned at 500 MHz by comparative studies of chemically modified and genetically altered variants, including a mutant insulin (PheB25 {yields} Leu) associated with diabetes mellitus. The two histidines, three phenylalanines, and four tyrosines are observed to be in distinct local environments; their assignment provides sensitive markers for studies of tertiary structure, protein dynamics, and protein folding. The environments of the tyrosine residues have also been investigated by photochemically induced dynamic nuclear polarization (photo-CIDNP) and analyzed in relation to packing constrains in the crystal structures of insulin. Dimerization involving specific B-chain interactions is observed with increasing protein concentration and is shown to depend on temperature, pH, and solvent composition. The differences between proinsulin and mini-proinsulin suggest a structural mechanism for the observation that the fully reduced B29-A1 analogue folds more efficiently than proinsulin to form the correct pattern of disulfide bonds. These results are discussed in relation to molecular mechanics calculations of insulin based on the available crystal structures.

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

    Science.gov (United States)

    Palla, Marina; Potari, Despina; Spyrou, Panagiotis

    2012-01-01

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

  10. Radiation damage of proteins in the solid state: changes of β-lactoglobulin secondary structure

    International Nuclear Information System (INIS)

    β-Lactoglobulin has been irradiated with 100 keV electrons simulating the environmental conditions of electron microscopy. Attenuated total reflection-infrared spectroscopy reveals that in the dose range between 60 and 200e-/nm2, which is far below that required for high resolution imaging of isolated proteins, their secondary structure is completely randomized

  11. Molecular systematics of Barbatosphaeria (Sordariomycetes): multigene phylogeny and secondary ITS structure

    Czech Academy of Sciences Publication Activity Database

    Réblová, Martina; Réblová, K.; Štěpánek, Václav

    2015-01-01

    Roč. 35, December 2015 (2015), s. 21-38. ISSN 0031-5850 R&D Projects: GA ČR GAP506/12/0038 Institutional support: RVO:67985939 ; RVO:61388971 Keywords : Barbatosphaeria * molecular systematic * ITS secondary structures Subject RIV: EF - Botanics; EE - Microbiology, Virology (MBU-M) Impact factor: 5.300, year: 2014

  12. Two-dimensional dynamics of a free molecular chain with a secondary structure

    DEFF Research Database (Denmark)

    Zolotaryuk, Alexander; Christiansen, Peter Leth; Savin, A.V.

    1996-01-01

    A simple two-dimensional (2D) model of an isolated (free) molecular chain with primary and secondary structures has been suggested and investigated both analytically and numerically. This model can be considered as the simplest generalization of the well-known Fermi-Pasta-Ulam model of an anharmo...

  13. Derivation of the Secondary Structure of the ITS-1 Transcript in Volvocales and its Taxonomic Correlations.

    Science.gov (United States)

    Coleman, A W; Maria Preparata, R; Mehrotra, B; Mai, J C

    1998-05-01

    Knowledge of secondary structure, formed by the gene spacer regions of the primary transcript of nuclear rDNA cistrons, is lacking for most phyla of eukaryotes. We have sequenced the first internal transcribed spacer region (ITS-1) of multiple representatives of the Volvocales, and from comparisons of these, derived a secondary structure common to the entire group. The secondary structure model is supported by numerous compensating base pair changes located within the paired regions of the stem-loops. Within the morphological species, such as those of Astrephomene and Gonium, the three basal nucleotide pairs of helices are highly conserved in primary sequence, and the single stranded region rich in CCAA is identical in sequence, even when isolates come from all continents of the earth. In other Volvocacean species known to include many pairs of mating types, this same level of conservation is found to correlate with the mating subgroups of the species. Thus a comparable degree of sequence similarity appears to characterize all isolates of a "biological" species; this is valid for taxonomic species only where the biological and taxonomic species levels coincide. In addition, the ITS-1 contains information useful for population analyses, and spacer secondary structure may have additional phylogenetic utility at the level of class or subclass when that information becomes available for other protistan groups. PMID:23196163

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

    DEFF Research Database (Denmark)

    Weile, Christian; Gardner, Paul P; Hedegaard, Mads M;

    2007-01-01

    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...

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

    Science.gov (United States)

    Pikaart, Michael

    2011-01-01

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

  16. Tropical rain-forest matrix quality affects bat assemblage structure in secondary forest patches

    NARCIS (Netherlands)

    Vleut, I.; Levy-Tacher, I.; Galindo-Gonzalez, J.; Boer, de W.F.; Ramirez-Marcial, N.

    2012-01-01

    We studied Phyllostomidae bat assemblage structure in patches of secondary forest dominated by the pioneer tree Ochroma pyramidale, largely (.85%) or partially (,35%) surrounded by a matrix of tropical rain forest, to test 3 hypotheses: the highest bat diversity and richness is observed in the matri

  17. Secondary flow structure in a model curved artery: 3D morphology and circulation budget analysis

    Science.gov (United States)

    Bulusu, Kartik V.; Plesniak, Michael W.

    2015-11-01

    In this study, we examined the rate of change of circulation within control regions encompassing the large-scale vortical structures associated with secondary flows, i.e. deformed Dean-, Lyne- and Wall-type (D-L-W) vortices at planar cross-sections in a 180° curved artery model (curvature ratio, 1/7). Magnetic resonance velocimetry (MRV) and particle image velocimetry (PIV) experiments were performed independently, under the same physiological inflow conditions (Womersley number, 4.2) and using Newtonian blood-analog fluids. The MRV-technique performed at Stanford University produced phase-averaged, three-dimensional velocity fields. Secondary flow field comparisons of MRV-data to PIV-data at various cross-sectional planes and inflow phases were made. A wavelet-decomposition-based approach was implemented to characterize various secondary flow morphologies. We hypothesize that the persistence and decay of arterial secondary flow vortices is intrinsically related to the influence of the out-of-plane flow, tilting, in-plane convection and diffusion-related factors within the control regions. Evaluation of these factors will elucidate secondary flow structures in arterial hemodynamics. Supported by the National Science Foundation under Grant Number CBET-0828903, and GW Center for Biomimetics and Bioinspired Engineering (COBRE). The MRV data were acquired at Stanford University in collaboration with Christopher Elkins and John Eaton.

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

    OpenAIRE

    Banks, Jennifer D.; Linial, Maxine L.

    2000-01-01

    We previously identified a 160-nucleotide packaging signal, MΨ, from the 5′ end of the Rous sarcoma virus genome. In this study, we determine the secondary structure of MΨ by using phylogenetic analysis with computer modeling and heterologous packaging assays of point mutants. The results of the in vivo studies are in good agreement with the computer model. Additionally, the packaging studies indicate several structures which are important for efficient packaging, including a single-stranded ...

  19. Analysis of energy-based algorithms for RNA secondary structure prediction

    OpenAIRE

    Hajiaghayi Monir; Condon Anne; Hoos Holger H

    2012-01-01

    Abstract Background RNA molecules play critical roles in the cells of organisms, including roles in gene regulation, catalysis, and synthesis of proteins. Since RNA function depends in large part on its folded structures, much effort has been invested in developing accurate methods for prediction of RNA secondary structure from the base sequence. Minimum free energy (MFE) predictions are widely used, based on nearest neighbor thermodynamic parameters of Mathews, Turner et al. or those of Andr...

  20. Minimum-Free-Energy Distribution of RNA Secondary Structures: Entropic and Thermodynamic Properties of Rare Events

    OpenAIRE

    Wolfsheimer, S; Hartmann, A. K.

    2008-01-01

    We study the distribution of the minimum free energy (MFE) for the Turner model of pseudoknot free RNA secondary structures over ensembles of random RNA sequences. In particular, we are interested in those rare and intermediate events of unexpected low MFEs. Generalized ensemble Markov-chain Monte Carlo methods allow us to explore the rare-event tail of the MFE distribution down to probabilities like $10^{-70}$ and to study the relationship between the sequence entropy and structural properti...

  1. Louse (Insecta : Phthiraptera) mitochondrial 12S rRNA secondary structure is highly variable

    OpenAIRE

    Page, R.D.M.; Cruickshank, R.; Johnson, K P

    2002-01-01

    Lice are ectoparasitic insects hosted by birds and mammals. Mitochondrial 12S rRNA sequences obtained from lice show considerable length variation and are very difficult to align. We show that the louse 12S rRNA domain III secondary structure displays considerable variation compared to other insects, in both the shape and number of stems and loops. Phylogenetic trees constructed from tree edit distances between louse 12S rRNA structures do not closely resemble trees constructed from sequence ...

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

    OpenAIRE

    Spencer, Matt; Eickholt, Jesse; Cheng, Jianlin

    2014-01-01

    Ab initio protein secondary structure (SS) predictions are utilized to generate tertiary structure predictions, which are increasingly demanded due to the rapid discovery of proteins. Although recent developments have slightly exceeded previous methods of SS prediction, accuracy has stagnated around 80% and many wonder if prediction cannot be advanced beyond this ceiling. Disciplines that have traditionally employed neural networks are experimenting with novel deep learning techniques in atte...

  3. A permutation based simulated annealing algorithm to predict pseudoknotted RNA secondary structures.

    Science.gov (United States)

    Tsang, Herbert H; Wiese, Kay C

    2015-01-01

    Pseudoknots are RNA tertiary structures which perform essential biological functions. This paper discusses SARNA-Predict-pk, a RNA pseudoknotted secondary structure prediction algorithm based on Simulated Annealing (SA). The research presented here extends previous work of SARNA-Predict and further examines the effect of the new algorithm to include prediction of RNA secondary structure with pseudoknots. An evaluation of the performance of SARNA-Predict-pk in terms of prediction accuracy is made via comparison with several state-of-the-art prediction algorithms using 20 individual known structures from seven RNA classes. We measured the sensitivity and specificity of nine prediction algorithms. Three of these are dynamic programming algorithms: Pseudoknot (pknotsRE), NUPACK, and pknotsRG-mfe. One is using the statistical clustering approach: Sfold and the other five are heuristic algorithms: SARNA-Predict-pk, ILM, STAR, IPknot and HotKnots algorithms. The results presented in this paper demonstrate that SARNA-Predict-pk can out-perform other state-of-the-art algorithms in terms of prediction accuracy. This supports the use of the proposed method on pseudoknotted RNA secondary structure prediction of other known structures. PMID:26558299

  4. Variability in automated assignment of NOESY spectra and three-dimensional structure determination: A test case on three small disulfide-bonded proteins

    Energy Technology Data Exchange (ETDEWEB)

    Savarin, Philippe; Zinn-Justin, Sophie; Gilquin, Bernard [CEA-Saclay, Departement d' Ingenierie et d' Etudes des Proteines (Bat. 152) (France)

    2001-01-15

    Three independent runs of automatic assignment and structure calculations were performed on three small proteins, calcicludine from the venom of the green mamba Dendroaspis angusticeps, {kappa}-conotoxin PVIIA from the purple cone Conus purpurascens and HsTX1, a short scorpion toxin from the venom of Heterometrus spinnifer. At the end of all the runs, the number of cross peaks which remained unassigned (0.6%, 1.4% and 2% for calcicludine, {kappa}-conotoxin and HsTX1, respectively), as well as the number of constraints which were rejected as producing systematic violations (2.7%, 1.0%, and 1.4% for calcicludine, {kappa}-conotoxin and HsTX1, respectively) were low. The conformation of the initial model used in the procedure (linear model or constructed by homology) has no influence on the final structures. Mainly two parameters control the procedure: the chemical shift tolerance and the cut-off distance. Independent runs of structure calculations, using the same parameters, yield structures for which the rmsd between averaged structures and the rmsd around each averaged structure were of the same order of magnitude. A different cut-off distance and a different chemical shift tolerance yield rmsd values on final average structures which did not differ more than 0.5 A compared to the rmsd obtained around the averaged structure for each calculation. These results show that the procedure is robust when applied to such a small disulfide-bonded protein.

  5. Variability in automated assignment of NOESY spectra and three-dimensional structure determination: A test case on three small disulfide-bonded proteins

    International Nuclear Information System (INIS)

    Three independent runs of automatic assignment and structure calculations were performed on three small proteins, calcicludine from the venom of the green mamba Dendroaspis angusticeps, κ-conotoxin PVIIA from the purple cone Conus purpurascens and HsTX1, a short scorpion toxin from the venom of Heterometrus spinnifer. At the end of all the runs, the number of cross peaks which remained unassigned (0.6%, 1.4% and 2% for calcicludine, κ-conotoxin and HsTX1, respectively), as well as the number of constraints which were rejected as producing systematic violations (2.7%, 1.0%, and 1.4% for calcicludine, κ-conotoxin and HsTX1, respectively) were low. The conformation of the initial model used in the procedure (linear model or constructed by homology) has no influence on the final structures. Mainly two parameters control the procedure: the chemical shift tolerance and the cut-off distance. Independent runs of structure calculations, using the same parameters, yield structures for which the rmsd between averaged structures and the rmsd around each averaged structure were of the same order of magnitude. A different cut-off distance and a different chemical shift tolerance yield rmsd values on final average structures which did not differ more than 0.5 A compared to the rmsd obtained around the averaged structure for each calculation. These results show that the procedure is robust when applied to such a small disulfide-bonded protein

  6. A contribution to understanding the structure of amphivasal secondary bundles in monocotyledons

    Directory of Open Access Journals (Sweden)

    Joanna Jura-Morawiec

    2014-04-01

    Full Text Available Secondary growth of monocotyledonous plants is connected with the activity of the monocot cambium that accumulates most of the derivatives inner to the cambial cylinder. These derivatives differentiate into (a secondary bundles with the amphivasal arrangement, i.e. xylem composed of tracheids surrounds the phloem cells and (b the parenchymatous secondary conjunctive tissue in which the bundles are embedded. The amphivasal secondary bundles differ in the arrangement of xylem cells as visible on single cross sections through the secondary body of the monocots. Apart from the bundles with typical ring of tracheids also the bundles where tracheids do not quite surround the phloem are present. We aimed to elucidate the cross sectional anatomy of the amphivasal secondary bundles with the use of the serial sectioning method which allowed us to follow very precisely the bundle structure along its length. The studies were carried out with the samples of secondary tissues collected from the stem of Dracaena draco L. growing in the greenhouses of the Polish Academy of Sciences Botanical Garden – CBDC in Powsin and the Adam Mickiewicz University Botanical Garden. The material was fixed in a mixture of glycerol and ethanol (1:1; v/v, dehydrated stepwise with graded ethanol series and finally embedded in epon resin. Afterwards, the material was sectioned with microtome into continuous series of thin (3 μm sections, stained with PAS/toluidine blue and examined under the light microscope. The results, described in details in Jura‑Morawiec & Wiland-Szymańska (2014, revealed novel facts about tracheids arrangement. Each amphivasal bundle is composed of sectors where tracheids form a ring as well as of such where tracheids are separated by vascular parenchyma cells. We hypothesize that strands of vascular parenchyma cells locally separating the tracheids enable radial transport of assimilates from sieve elements of the bundle towards the sink tissues, e

  7. ATR-FTIR investigations of secondary structure of lyophilized proteins in water and deuterated water

    International Nuclear Information System (INIS)

    The conformational and structural changes due to lyophilization of bovine hemoglobin, casein and trypsin of neutral pH value have been studied by FT-IR spectrometry using an Attenuated Total Reflectance (ATR) accessory (Bruker EQUINOX 55 spectrometer). Lyophilization induced significant structural alterations in proteins, characterized by a decrease in the α-helix and a significant increase in the β-sheet content. The proteins were lyophilized from twice-distilled water solution and deuterated water solution. The secondary structure was quantitatively determined using the second derivative of the protein spectra and curve fitting procedures to resolve the overlapping components under the amide I contour. The band of amide I, is due to the in-plane C=O stretching vibration, weakly coupled with C-N stretching and in-plane N-H bending. Each type of secondary structure (i.e. α-helix, β-sheet, β-turn and disordered) gives rise to different C-O stretching frequencies, hence, results in characteristic band positions which are designated by wavenumber (cm-1). In the Fourier domain derivative, the second-derivative analysis of infrared spectra allows direct quantitative analysis of the secondary structural components of proteins. Thus, the areas corresponding to the different types of secondary structure are quantitatively and qualitatively evaluated by integration and curve fitting. The second derivatives of all spectra were calculated using the spectrometer software OPUS. Before starting the fitting procedure, the obtained depths of the minima in the second derivative spectrum and, subsequently, the calculated maximum intensities were corrected for the interference of all neighboring peaks. The curve fitting is performed by stepwise iterative adjustment towards a minimum root-mean-square error of the different parameters determining the shape and position of the absorption peaks. (author)

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

    Science.gov (United States)

    Waldispühl, J; Clote, P

    2007-03-01

    An RNA secondary structure is saturated if no base pairs can be added without violating the definition of secondary structure. Here we describe a new algorithm, RNAsat, which for a given RNA sequence a, an integral temperature 0 web server for RNAsat is under construction at bioinformatics.bc.edu/clotelab/RNAsat/. PMID:17456015

  9. Isolation, Structure Elucidation, Biosynthesis, and Synthesis of Antalid, a Secondary Metabolite from Polyangium species.

    Science.gov (United States)

    Tautz, Thomas; Hoffmann, Judith; Hoffmann, Thomas; Steinmetz, Heinrich; Washausen, Peter; Kunze, Brigitte; Huch, Volker; Kitsche, Andreas; Reichenbach, Hans; Höfle, Gerhard; Müller, Rolf; Kalesse, Markus

    2016-06-01

    The isolation, structure elucidation, and synthesis of antalid (1), a novel secondary metabolite from Polyangium sp., is described herein. The structure elucidation of 1 was performed with the aid of mass spectrometry, high field NMR experiments, and crystal structure analysis. The absolute configuration of antalid was confirmed through the Mosher ester method and ultimately by total synthesis. In addition, the biosynthetic origin of this hybrid PKS-NRPS natural product was unraveled by the in silico analysis of its biosynthetic gene cluster. PMID:27220069

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

    Science.gov (United States)

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

    2013-01-01

    Peptide mimics that display amino acid side-chains on semi-rigid scaffolds (not peptide polyamides) can be referred to as minimalist mimics. Accessible conformations of these scaffolds may overlay with secondary structures giving, for example, “minimalist helical mimics”. It is difficult for researchers who want to apply minimalist mimics to decide which one to use because there is no widely accepted protocol for calibrating how closely these compounds mimic secondary structures. Moreover, it is also difficult for potential practitioners to evaluate which ideal minimalist helical mimics are preferred for a particular set of side-chains. For instance, what mimic presents i, i+4, i+7 side-chains in orientations that best resemble an ideal α-helix, and is a different mimic required for a i, i+3, i+7 helical combination? This article describes a protocol for fitting each member of an array of accessible scaffold conformations on secondary structures. The protocol involves: (i) use quenched molecular dynamics (QMD) to generate an ensemble consisting of hundreds of accessible, low energy conformers of the mimics; (ii) representation of each of these as a set of Cα and Cβ coordinates corresponding to three amino acid side-chains displayed by the scaffolds;(iii) similar representation of each combination of three side-chains in each ideal secondary structure as a set of Cα and Cβ coordinates corresponding to three amino acid side-chains displayed by the scaffolds; and, (iv) overlay Cα and Cβ coordinates of all the conformers on all the sets of side-chain “triads” in the ideal secondary structures and express the goodness of fit in terms of root mean squared deviation (RMSD, Å) for each overlay. We refer to this process as Exploring Key Orientations on Secondary structures (EKOS). Application of this procedure reveals the relative bias of a scaffold to overlay on different secondary structures, the “side-chain correspondences” (eg i, i+4, i+7 or i, i+3

  11. Computational Approaches for determination of Most Probable RNA Secondary Structure Using Different Thermodynamics Parameters

    Directory of Open Access Journals (Sweden)

    Binod Kumar,

    2010-03-01

    Full Text Available Many bioinformatics studies require the analysis of RNA structures. More specifically, extensive work is done to elaborate efficient algorithms able to predict the 2-D folding structures of RNA. The core of RNA structure is a dynamic programming algorithm to predict RNA secondary structures from sequence based on the principle of minimizing free energy. In this paper the thermodynamic data have been used for RNA predictions. In this paper the free energy inimization and the partition function code has been used to predictinternal loops of any size in O (N3 time. The free energy table for multibranch loops has been used by Dynalign. Base pair probabilities have been determined by the partition function calculation. Parameters controlling the prediction of suboptimal structures are Max % Energy Difference and Max Number of Structures. The foldmodule provides the basic implementation of RNA secondary structure prediction. A Dynalign dot plot, a separate dot plot is generated foreach of the two sequences involved. OligoScreen calculates the unimolecular and bimolecular folding free energies for a set of RNA oligonucleotides.

  12. On the structure and dynamics of secondary n-alkyl cations

    Science.gov (United States)

    East, Allan L. L.; Bučko, Tomáš; Hafner, Jürgen

    2009-09-01

    A variety of computational studies was undertaken to examine and establish the relative importance of open versus closed structures for unbranched secondary n-alkyl cations. First, the PW91 level of density functional theory was used to optimize over 20 minimum-energy structures of sec-pentyl, sec-hexyl, and sec-heptyl ions, demonstrating that closed structures are more stable than open ones on the potential energy surface (PES). Second, PW91 was used with a theoretical Andersen thermostat to perform a molecular dynamics simulation (150 ps) of C9H19+ at a typical catalytic temperature of 800 K, demonstrating that the structure preference is inverted on the free-energy surface. Third, both quantum (rigid-rotor/harmonic oscillator) and classical partition functions were used to demonstrate that the simulated structure-opening at catalytic temperatures is due to the floppiness of the open forms, which improves its free energy by both lowering its zero-point vibrational energy and increasing its molecular entropy. The particular conformer of the preferred open form (at 800 K) is dependent on length of alkyl ion, with pentyl ions preferring syn/anti structures but longer ions preferring open-clinal ones. These results, plus an additional set of PES optimized structures from an alternative level of theory (MP2/6-31G(d,p)), are used to discuss the likely nature of secondary n-alkyl ions.

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

    Directory of Open Access Journals (Sweden)

    Sharma Gaurav

    2011-04-01

    Full Text Available Abstract Background The prediction of secondary structure, i.e. the set of canonical base pairs between nucleotides, is a first step in developing an understanding of the function of an RNA sequence. The most accurate computational methods predict conserved structures for a set of homologous RNA sequences. These methods usually suffer from high computational complexity. In this paper, TurboFold, a novel and efficient method for secondary structure prediction for multiple RNA sequences, is presented. Results TurboFold takes, as input, a set of homologous RNA sequences and outputs estimates of the base pairing probabilities for each sequence. The base pairing probabilities for a sequence are estimated by combining intrinsic information, derived from the sequence itself via the nearest neighbor thermodynamic model, with extrinsic information, derived from the other sequences in the input set. For a given sequence, the extrinsic information is computed by using pairwise-sequence-alignment-based probabilities for co-incidence with each of the other sequences, along with estimated base pairing probabilities, from the previous iteration, for the other sequences. The extrinsic information is introduced as free energy modifications for base pairing in a partition function computation based on the nearest neighbor thermodynamic model. This process yields updated estimates of base pairing probability. The updated base pairing probabilities in turn are used to recompute extrinsic information, resulting in the overall iterative estimation procedure that defines TurboFold. TurboFold is benchmarked on a number of ncRNA datasets and compared against alternative secondary structure prediction methods. The iterative procedure in TurboFold is shown to improve estimates of base pairing probability with each iteration, though only small gains are obtained beyond three iterations. Secondary structures composed of base pairs with estimated probabilities higher than a

  14. 13C direct detected COCO-TOCSY: A tool for sequence specific assignment and structure determination in protonless NMR experiments

    Science.gov (United States)

    Balayssac, Stéphane; Jiménez, Beatriz; Piccioli, Mario

    2006-10-01

    A novel experiment is proposed to provide inter-residue sequential correlations among carbonyl spins in 13C detected, protonless NMR experiments. The COCO-TOCSY experiment connects, in proteins, two carbonyls separated from each other by three, four or even five bonds. The quantitative analysis provides structural information on backbone dihedral angles ϕ as well as on the side chain dihedral angles of Asx and Glx residues. This is the first dihedral angle constraint that can be obtained via a protonless approach. About 75% of backbone carbonyls in Calbindin D 9K, a 75 aminoacid dicalcium protein, could be sequentially connected via a COCO-TOCSY spectrum. 49 3J values were measured and related to backbone ϕ angles. Structural information can be extended to the side chain orientation of aminoacids containing carbonyl groups. Additionally, long range homonuclear coupling constants, 4JCC and 5JCC, could be measured. This constitutes an unprecedented case for proteins of medium and small size.

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

    CERN Document Server

    Wilke, C O; Adami, C; Wilke, Claus O; Lenski, Richard E; Adami, Christoph

    2003-01-01

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

  16. TMPyP4, a Stabilizer of Nucleic Acid Secondary Structure, Is a Novel Acetylcholinesterase Inhibitor.

    Directory of Open Access Journals (Sweden)

    Nana Fujiwara

    Full Text Available The porphyrin compound, TMPyP4 (5,10,15,20-Tetrakis-(N-methyl-4-pyridylporphine, is widely used as a photosensitizer and a modulator of nucleic acid secondary structure stability. Our group recently showed in cultured cells and forebrain slice cultures that this compound can also down regulate expression of Tyrosine hydroxylase (Th, which encodes the rate-limiting enzyme in catecholamine biosynthesis, by stabilizing DNA secondary structures in the Th proximal promoter. The current study sought to establish whether treatment with TMPyP4 could modify mouse Th expression levels in vivo. Intraperitoneal administration of low TMPyP4 doses (10mg/kg, similar to those used for photosensitization, did not significantly reduce Th transcript levels in several catecholaminergic regions. Administration of a high dose (40 mg/kg, similar to those used for tumor xenograph reduction, unexpectedly induced flaccid paralysis in an age and sex-dependent manner. In vitro analyses revealed that TMPyP4, but not putative metabolites, inhibited Acetylcholinesterase activity and pre-treatment of TMPyP4 with Hemeoxygenase-2 (HO-2 rescued Acetylcholinesterase function. Age-dependent differences in HO-2 expression levels may account for some of the variable in vivo effects of high TMPyP4 doses. Together, these studies indicate that only low doses of TMPyP4, such as those typically used for photosensitization, are well tolerated in vivo. Thus, despite its widespread use in vitro, TMPyP4 is not ideal for modifying neuronal gene expression in vivo by manipulating nucleic acid secondary structure stability, which highlights the need to identify more clinically suitable compounds that can modulate nucleic acid secondary structure and gene expression.

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

    OpenAIRE

    Borodovsky Mark; Altunbasak Yucel; Aydin Zafer

    2006-01-01

    Abstract 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 could make an important contribution...

  18. A generalized threading model using integer programming that allows for secondary structure element deletion.

    Science.gov (United States)

    Ellrott, Kyle; Guo, Jun-tao; Olman, Victor; Xu, Ying

    2006-01-01

    Integer programming is a combinatorial optimization method that has been successfully applied to the protein threading problem. We seek to expand the model optimized by this technique to allow for a more accurate description of protein threading. We have developed and implemented an expanded model of integer programming that has the capability to model secondary structure element deletion, which was not possible in previous version of integer programming based optimization. PMID:17503397

  19. BTEC Integrative Assignments.

    Science.gov (United States)

    Foot, G. E.

    1992-01-01

    To equip electrical engineering students with common and transferable work skills, a program of integrative assignments was created to develop communication and teamwork skills. Discusses assignment components; the log book, a personal account of each assignment; assessment; conversion of "common skills" to competence statements, and performance…

  20. On correlation between protein secondary structure, backbone bond angles, and side-chain orientations

    CERN Document Server

    Lundgren, Martin

    2012-01-01

    We investigate the fine structure of the sp3 hybridized covalent bond geometry that governs the tetrahedral architecture around the central C$_\\alpha$ carbon of a protein backbone, and for this we develop new visualization techniques to analyze high resolution X-ray structures in 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$_\\beta$ carbon orientations. The energy function can model the side-chain geometry with a sub-atomic precision. As an example we construct the C$_\\alpha$-C$_\\beta$ structure of HP35 chicken villin headpiece. We obtain a configuration that deviates less than 0.4 \\.A in root-mean-square distance from the experimental X-ray structure.

  1. Assignment of near-edge x-ray absorption fine structure spectra of metalloporphyrins by means of time-dependent density-functional calculations

    Science.gov (United States)

    Schmidt, Norman; Fink, Rainer; Hieringer, Wolfgang

    2010-08-01

    The C 1s and N 1s near-edge x-ray absorption fine structure (NEXAFS) spectra of three prototype tetraphenyl porphyrin (TPP) molecules are discussed in the framework of a combined experimental and theoretical study. We employ time-dependent density-functional theory (TDDFT) to compute the NEXAFS spectra of the open- and closed-shell metalloporphyrins CoTPP and ZnTPP as well as the free-base 2HTPP in realistic nonplanar conformations. Using Becke's well-known half-and-half hybrid functional, the computed core excitation spectra are mostly in good agreement with the experimental data in the low-energy region below the appropriate ionization threshold. To make these calculations feasible, we apply a new, simple scheme based on TDDFT using a modified single-particle input spectrum. This scheme is very easy to implement in standard codes and allows one to compute core excitation spectra at a similar cost as ordinary UV/vis spectra even for larger molecules. We employ these calculations for a detailed assignment of the NEXAFS spectra including subtle shifts in certain peaks of the N 1s spectra, which depend on the central coordination of the TPP ligand. We furthermore assign the observed NEXAFS resonances to the individual molecular subunits of the investigated TPP molecules.

  2. 3'-Terminal RNA secondary structures are important for accumulation of tomato bushy stunt virus DI RNAs

    International Nuclear Information System (INIS)

    The plus-strand RNA genome of tomato bushy stunt virus (TBSV) contains a 351-nucleotide (nt)-long 3'-untranslated region. We investigated the role of the 3'-proximal 130 nt of this sequence in viral RNA accumulation within the context of a TBSV defective interfering (DI) RNA. Sequence comparisons between different tombusviruses revealed that the 3' portion of the 130-nt sequence is highly conserved and deletion analysis confirmed that this segment is required for accumulation of DI RNAs in protoplasts. Computer-aided sequence analysis and in vitro solution structure probing indicated that the conserved sequence consists of three stem-loop (SL) structures (5'-SL3-SL2-SL1-3'). The existence of SLs 1 and 3 was also supported by comparative secondary structure analysis of sequenced tombusvirus genomes. Formation of the stem regions in all three SLs was found to be very important, and modification of the terminal loop sequences of SL1 and SL2, but not SL3, decreased DI RNA accumulation in vivo. For SL3, alterations to an internal loop resulted in significantly reduced DI RNA levels. Collectively, these data indicate that all three SLs are functionally relevant and contribute substantially to DI RNA accumulation. In addition, secondary structure analysis of other tombusvirus replicons and related virus genera revealed that a TBSV satellite RNA and members of the closely related genus Aureusvirus (family Tombusviridae) share fundamental elements of this general structural arrangement. Thus, this secondary structure model appears to extend beyond tombusvirus genomes. These conserved 3'-terminal RNA elements likely function in vivo by promoting and/or regulating minus-strand synthesis

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

    Directory of Open Access Journals (Sweden)

    Borodovsky Mark

    2006-03-01

    Full Text Available Abstract 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 could make an important contribution to studies of proteins with no detected homologs, however the accuracy of protein secondary structure prediction from a single-sequence is not as high as when the additional evolutionary information is present. Results In this paper, we further refine and extend the hidden semi-Markov model (HSMM initially considered in the BSPSS algorithm. We introduce an improved residue dependency model by considering the patterns of statistically significant amino acid correlation at structural segment borders. We also derive models that specialize on different sections of the dependency structure and incorporate them into HSMM. In addition, we implement an iterative training method to refine estimates of HSMM parameters. The three-state-per-residue accuracy and other accuracy measures of the new method, IPSSP, are shown to be comparable or better than ones for BSPSS as well as for PSIPRED, tested under the single-sequence condition. Conclusions We have shown that new dependency models and training methods bring further improvements to single-sequence protein secondary structure prediction. The results are obtained under cross-validation conditions using a dataset with no pair of sequences having significant sequence similarity. As new sequences are added to the database it is possible to augment the dependency structure and obtain even higher accuracy. Current and future advances should contribute to the improvement of function prediction for orphan proteins inscrutable

  4. Sheath structure in plasma with two species of positive ions and secondary electrons

    Science.gov (United States)

    Xiao-Yun, Zhao; Nong, Xiang; Jing, Ou; De-Hui, Li; Bin-Bin, Lin

    2016-02-01

    The properties of a collisionless plasma sheath are investigated by using a fluid model in which two species of positive ions and secondary electrons are taken into account. It is shown that the positive ion speeds at the sheath edge increase with secondary electron emission (SEE) coefficient, and the sheath structure is affected by the interplay between the two species of positive ions and secondary electrons. The critical SEE coefficients and the sheath widths depend strongly on the positive ion charge number, mass and concentration in the cases with and without SEE. In addition, ion kinetic energy flux to the wall and the impact of positive ion species on secondary electron density at the sheath edge are also discussed. Project supported by the National Natural Science Foundation of China (Grant Nos. 11475220 and 11405208), the Program of Fusion Reactor Physics and Digital Tokamak with the CAS “One-Three-Five” Strategic Planning, the National ITER Program of China (Grant No. 2015GB101003), and the Higher Education Natural Science Research Project of Anhui Province, China (Grant No. 2015KJ009).

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

    Science.gov (United States)

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

    2013-06-01

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

  6. Prediction of Spontaneous Protein Deamidation from Sequence-Derived Secondary Structure and Intrinsic Disorder.

    Directory of Open Access Journals (Sweden)

    J Ramiro Lorenzo

    Full Text Available Asparagine residues in proteins undergo spontaneous deamidation, a post-translational modification that may act as a molecular clock for the regulation of protein function and turnover. Asparagine deamidation is modulated by protein local sequence, secondary structure and hydrogen bonding. We present NGOME, an algorithm able to predict non-enzymatic deamidation of internal asparagine residues in proteins in the absence of structural data, using sequence-based predictions of secondary structure and intrinsic disorder. Compared to previous algorithms, NGOME does not require three-dimensional structures yet yields better predictions than available sequence-only methods. Four case studies of specific proteins show how NGOME may help the user identify deamidation-prone asparagine residues, often related to protein gain of function, protein degradation or protein misfolding in pathological processes. A fifth case study applies NGOME at a proteomic scale and unveils a correlation between asparagine deamidation and protein degradation in yeast. NGOME is freely available as a webserver at the National EMBnet node Argentina, URL: http://www.embnet.qb.fcen.uba.ar/ in the subpage "Protein and nucleic acid structure and sequence analysis".

  7. Vibrational assignments and structure of bis(3-amino-1- phenyl-2-buten-1-onato)copper(II) complex

    Science.gov (United States)

    Tayyari, Sayyed Faramarz; Jamialahmadi, Mina; Ghafari, Maliheh; Moosavi-Tekieh, Zainab

    2016-05-01

    The bis(3-amino-1-phenyl-2-buten-1-onato)copper(II) complex, Cu(APBO)2, has been characterized by ab initio calculations and vibrational spectroscopic techniques. The geometry optimization are performed at the UB3LYP level using 6-311G(d) and 6-311+G(d,p) basis sets. The vibrational frequencies were calculated at the UB3LYP/6-311+G(d,p) level. Furthermore, to include the relativistic effects on the core electrons of Cu atom, the optimization and vibrational frequencies were recalculated at the UB3LYP level with 6-311G(d,p) basis set for all atoms but the Cu atom, whose basis set was LanL2DZ and CEP-31G, with their corresponding pseudopotential. The scaled theoretical frequencies and the structural parameters are in excellent agreement with the experimental data. HOMO-LUMO energies and natural charges over chelated ring atoms of Cu(APBO)2 and Cu(APO)2 are also compared.

  8. Molecular structure and vibrational and chemical shift assignments of 3‧-chloro-4-dimethylamino azobenzene by DFT calculations

    Science.gov (United States)

    Toy, Mehmet; Tanak, Hasan

    2016-01-01

    In the present work, a combined experimental and theoretical study on ground state molecular structure, spectroscopic and nonlinear optical properties of azo compound 3‧-chloro-4-dimethlamino azobenzene are reported. The molecular geometry, vibrational wavenumbers and the first order hyperpolarizability of the title compound were calculated with the help of density functional theory computations. The optimized geometric parameters obtained by using DFT (B3LYP/6-311++G(d,p)) show good agreement with the experimental data. The vibrational transitions were identified based on the recorded FT-IR spectra in the range of 4000-400 cm-1 for solid state. The 1H isotropic chemical shifts with respect to TMS were also calculated using the gauge independent atomic orbital (GIAO) method and compared with the experimental data. Using the TD-DFT method, electronic absorption spectra of the title compound have been predicted, and good agreement is determined with the experimental ones. To investigate the NLO properties of the title compound, the polarizability and the first hyperpolarizability were calculated using the density functional B3LYP method with the 6-311++G(d,p) basis set. According to results, the title compound exhibits non-zero first hyperpolarizability value revealing second order NLO behavior. In addition, DFT calculations of the title compound, molecular electrostatic potential and frontier molecular orbitals were also performed at 6-311++G(d,p) level of theory.

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

    CERN Document Server

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

    2014-01-01

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

  10. Teaching the foundations of quantum mechanics in secondary school: a proposed conceptual structure

    Directory of Open Access Journals (Sweden)

    Maria de los Angeles Fanaro

    2009-03-01

    Full Text Available This paper is part of a doctoral thesis that investigates Basic Quantum Mechanics (QM teaching in high school. A Conceptual Structure of Reference (CSR based on the Path Integral Method of Feynman (1965 was rebuilt and a Proposed Conceptual Structure for Teaching (PCST (Otero, 2006, 2007 the basics of Quantum Mechanics at secondary school was designed, analysed and carried out. This PCST does not follow the historical route and it is complementary to the canonical formalism. The concepts: probability distribution, quantum system, x(t alternative, amplitude of probability, sum of probability amplitude, action, Planck's constant, and classic-quantum transition were rebuilt with the students. Mathematical formalism was avoided by using simulation software assistance. The Proposed Conceptual Structure for Teaching (PCST is described and some results from the test carried out by the class group are discussed. This information allows the analysis of the Conceptual Structure Effectively Reconstructed (CSER to be initiated with the students.

  11. An Algorithm for Finding Conserved Secondary Structure Motifs in Unaligned RNA Sequences

    Institute of Scientific and Technical Information of China (English)

    Giulio Pavesi; Giancarlo Mauri; Graziano Pesole

    2004-01-01

    Several experiments and observations have revealed the fact that small local distinct structural features in RNA molecules are correlated with their biological function, for example, in post-transcriptional regulation of gene expression. Thus, finding similar structural features in a set of RNA sequences known to play the same biological function could provide substantial information concerning which parts of the sequences are responsible for the function itself. Unfortunately, finding common structural elements in RNA molecules is a very challenging task, even if limited to secondary structure. The main difficulty lies in the fact that in nearly all the cases the structure of the molecules is unknown, has to be somehow predicted, and that sequences with little or no similarity can fold into similar structures. Although they differ in some details, the approaches proposed so far are usually based on the preliminary alignment of the sequences and attempt to predict common structures (either local or global, or for some selected regions) for the aligned sequences. These methods give good results when sequence and structure similarity are very high, but function less well when similarity is limited to small and local elements, like single stem-loop motifs. Instead of aligning the sequences, the algorithm we present directly searches for regions of the sequences that can fold into similar structures, where the degree of similarity can be defined by the user. Any information concerning sequence similarity in the motifs can be used either as a search constraint, or a posteriori, by post-processing the output. The search for the regions sharing structural similarity is implemented with the affix tree, a novel text-indexing structure that significantly accelerates the search for patterns having a symmetric layout, such as those forming stem-loop structures. Tests based on experimentally known structures have shown that the algorithm is able to identify functional motifs in

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

    Science.gov (United States)

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

    2012-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Samuel Bleckley

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

  14. An evaluation of chemical shift index-based secondary structure determination in proteins: Influence of random coil chemical shifts

    Energy Technology Data Exchange (ETDEWEB)

    Mielke, S.P.; Krishnan, V.V. [Biophysics Graduate Group, University of California, Davis (United States)], E-mail: krish@llnl.gov

    2004-10-15

    Random coil chemical shifts are commonly used to detect protein secondary structural elements in chemical shift index (CSI) calculations. Though this technique is widely used and seems reliable for folded proteins, the choice of reference random coil chemical shift values can significantly alter the outcome of secondary structure estimation. In order to evaluate these effects, we present a comparison of secondary structure content calculated using CSI, based on five different reference random coil chemical shift value sets, to that derived from three-dimensional structures. Our results show that none of the reference random coil data sets chosen for evaluation fully reproduces the actual secondary structures. Among the reference values generally available to date, most tend to be good estimators only of helices. Based on our evaluation, we recommend the experimental values measured by Schwarzinger et al. (2000), and statistical values obtained by Lukin et al. (1997), as good estimators of both helical and sheet content.

  15. Structural effects of liana presence in secondary tropical dry forests using ground LiDAR

    Science.gov (United States)

    Sánchez-Azofeifa, A.; Portillo-Quintero, C.; Durán, S. M.

    2015-10-01

    Lianas, woody vines, are a key component of tropical forest because they may reduce carbon storage potential. Lianas are increasing in density and biomass in tropical forests, but it is unknown what the potential consequences of these increases are for forest dynamics. Lianas may proliferate in disturbed areas, such as regenerating forests, but little is known about the role of lianas in secondary succession. In this study, we evaluated the potential of the ground LiDAR to detect differences in the vertical structure of stands of different ages with and without lianas in tropical dry forests. Specifically, we used a terrestrial laser scanner called VEGNET to assess whether liana presence influences the vertical signature of stands of different ages, and whether successional trajectories as detected by the VEGNET could be altered by liana presence. We deployed the VEGNET ground LiDAR system in 15 secondary forests of different ages early (21 years old since land abandonment), intermediate (32-35 years old) and late stages (> 80 years old) with and without lianas. We compared laser-derived vegetation components such as Plant Area Index (PAI), plant area volume density (PAVD), and the radius of gyration (RG) across forest stands between liana and no-liana treatments. In general forest stands without lianas show a clearer distinction of vertical strata and the vertical height of accumulated PAVD. A significant increase of PAI was found from intermediate to late stages in stands without lianas, but in stands where lianas were present there was not a significant trend. This suggests that lianas may be influencing successional trajectories in secondary forests, and these effects can be captured by terrestrial laser scanners such as the VEGNET. This research contributes to estimate the potential effects of lianas in secondary dry forests and highlight the role of ground LiDAR to monitor structural changes in tropical forests due to liana presence.

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

    Science.gov (United States)

    Ellerbrock, Cheryl R.; Kiefer, Sarah M.

    2013-01-01

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

  17. Effective stiffness and formation of secondary structures in a protein-like model.

    Science.gov (United States)

    Škrbić, Tatjana; Hoang, Trinh X; Giacometti, Achille

    2016-08-28

    We use Wang-Landau and replica exchange techniques to study the effect of an increasing stiffness on the formation of secondary structures in protein-like systems. Two possible models are considered. In both models, a polymer chain is formed by tethered beads where non-consecutive backbone beads attract each other via a square-well potential representing the tendency of the chain to fold. In addition, smaller hard spheres are attached to each non-terminal backbone bead along the direction normal to the chain to mimic the steric hindrance of side chains in real proteins. The two models, however, differ in the way bending rigidity is enforced. In the first model, partial overlap between consecutive beads is allowed. This reduces the possible bending angle between consecutive bonds thus producing an effective entropic stiffness that competes with a short-range attraction, and leads to the formation of secondary structures characteristic of proteins. We discuss the low-temperature phase diagram as a function of increasing interpenetration and find a transition from a planar, beta-like structure, to helical shape. In the second model, an energetic stiffness is explicitly introduced by imposing an infinitely large energy penalty for bending above a critical angle between consecutive bonds, and no penalty below it. The low-temperature phase of this model does not show any sign of protein-like secondary structures. At intermediate temperatures, however, where the chain is still in the coil conformation but stiffness is significant, we find the two models to predict a quite similar dependence of the persistence length as a function of the stiffness. This behaviour is rationalized in terms of a simple geometrical mapping between the two models. Finally, we discuss the effect of shrinking side chains to zero and find the above mapping to still hold true. PMID:27586943

  18. Discrete state model and accurate estimation of loop entropy of RNA secondary structures.

    Science.gov (United States)

    Zhang, Jian; Lin, Ming; Chen, Rong; Wang, Wei; Liang, Jie

    2008-03-28

    Conformational entropy makes important contribution to the stability and folding of RNA molecule, but it is challenging to either measure or compute conformational entropy associated with long loops. We develop optimized discrete k-state models of RNA backbone based on known RNA structures for computing entropy of loops, which are modeled as self-avoiding walks. To estimate entropy of hairpin, bulge, internal loop, and multibranch loop of long length (up to 50), we develop an efficient sampling method based on the sequential Monte Carlo principle. Our method considers excluded volume effect. It is general and can be applied to calculating entropy of loops with longer length and arbitrary complexity. For loops of short length, our results are in good agreement with a recent theoretical model and experimental measurement. For long loops, our estimated entropy of hairpin loops is in excellent agreement with the Jacobson-Stockmayer extrapolation model. However, for bulge loops and more complex secondary structures such as internal and multibranch loops, we find that the Jacobson-Stockmayer extrapolation model has large errors. Based on estimated entropy, we have developed empirical formulae for accurate calculation of entropy of long loops in different secondary structures. Our study on the effect of asymmetric size of loops suggest that loop entropy of internal loops is largely determined by the total loop length, and is only marginally affected by the asymmetric size of the two loops. Our finding suggests that the significant asymmetric effects of loop length in internal loops measured by experiments are likely to be partially enthalpic. Our method can be applied to develop improved energy parameters important for studying RNA stability and folding, and for predicting RNA secondary and tertiary structures. The discrete model and the program used to calculate loop entropy can be downloaded at http://gila.bioengr.uic.edu/resources/RNA.html. PMID:18376982

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

    International Nuclear Information System (INIS)

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

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

    International Nuclear Information System (INIS)

    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

  1. Protein secondary structure appears to be robust under in silico evolution while protein disorder appears not to be.

    KAUST Repository

    Schaefer, Christian

    2010-01-16

    MOTIVATION: The mutation of amino acids often impacts protein function and structure. Mutations without negative effect sustain evolutionary pressure. We study a particular aspect of structural robustness with respect to mutations: regular protein secondary structure and natively unstructured (intrinsically disordered) regions. Is the formation of regular secondary structure an intrinsic feature of amino acid sequences, or is it a feature that is lost upon mutation and is maintained by evolution against the odds? Similarly, is disorder an intrinsic sequence feature or is it difficult to maintain? To tackle these questions, we in silico mutated native protein sequences into random sequence-like ensembles and monitored the change in predicted secondary structure and disorder. RESULTS: We established that by our coarse-grained measures for change, predictions and observations were similar, suggesting that our results were not biased by prediction mistakes. Changes in secondary structure and disorder predictions were linearly proportional to the change in sequence. Surprisingly, neither the content nor the length distribution for the predicted secondary structure changed substantially. Regions with long disorder behaved differently in that significantly fewer such regions were predicted after a few mutation steps. Our findings suggest that the formation of regular secondary structure is an intrinsic feature of random amino acid sequences, while the formation of long-disordered regions is not an intrinsic feature of proteins with disordered regions. Put differently, helices and strands appear to be maintained easily by evolution, whereas maintaining disordered regions appears difficult. Neutral mutations with respect to disorder are therefore very unlikely.

  2. Analyzing Tenant Assignment Policies

    OpenAIRE

    Kaplan, Edward H.

    1987-01-01

    This paper discusses two popular policies used by housing authorities to assign applicants to housing projects: first available unit and priority assignment policies. The policies are compared according to their abilities to integrate housing projects, applicant assignment probabilities, and mean waiting times. Our results show that priority policies can successfully integrate public housing projects while first available unit policies can exacerbate segregation. These results support the rep...

  3. Nuclear resonance vibrational spectroscopy applied to [Fe(OEP)(NO)] : the vibrational assignments of five-coordinate ferrous heme-nitrosyls and implications for electronic structure.

    Energy Technology Data Exchange (ETDEWEB)

    Lehnert, N.; Galinato, M. I.; Paulat, F.; Richter-Addo, G. B.; Sturhahn, W.; Xu, N.; Zhao, J. (X-Ray Science Division); (Univ. of Michigan); (Univ. of Oklahoma)

    2010-01-01

    This study presents Nuclear Resonance Vibrational Spectroscopy (NRVS) data on the five-coordinate (5C) ferrous heme-nitrosyl complex [Fe(OEP)(NO)] (1, OEP{sup 2-} = octaethylporphyrinato dianion) and the corresponding {sup 15}N{sup 18}O labeled complex. The obtained spectra identify two isotope sensitive features at 522 and 388 cm{sup -1}, which shift to 508 and 381 cm{sup -1}, respectively, upon isotope labeling. These features are assigned to the Fe-NO stretch v(Fe-NO) and the in-plane Fe-N-O bending mode {delta}{sub ip}(Fe-N-O), the latter has been unambiguously assigned for the first time for 1. The obtained NRVS data were simulated using our quantum chemistry centered normal coordinate analysis (QCC-NCA). Since complex 1 can potentially exist in 12 different conformations involving the FeNO and peripheral ethyl orientations, extended density functional theory (DFT) calculations and QCC-NCA simulations were performed to determine how these conformations affect the NRVS properties of [Fe(OEP)NO]. These results show that the properties and force constants of the FeNO unit are hardly affected by the conformational changes involving the ethyl substituents. On the other hand, the NRVS-active porphyrin-based vibrations around 340-360, 300-320, and 250-270 cm{sup -1} are sensitive to the conformational changes. The spectroscopic changes observed in these regions are due to selective mechanical couplings of one component of Eu-type (in ideal D4h symmetry) porphyrin-based vibrations with the in-plane Fe-N-O bending mode. This leads to the observed variations in Fe(OEP) core mode energies and NRVS intensities without affecting the properties of the FeNO unit. The QCC-NCA simulated NRVS spectra of 1 show excellent agreement with experiment, and indicate that conformer F is likely present in the samples of this complex investigated here. The observed porphyrin-based vibrations in the NRVS spectra of 1 are also assigned based on the QCC-NCA results. The obtained force

  4. A Novel Framework Based on ACO and PSO for RNA Secondary Structure Prediction

    Directory of Open Access Journals (Sweden)

    Gang Wang

    2013-01-01

    Full Text Available Prediction of RNA structure is a useful process for creating new drugs and understanding genetic diseases. In this paper, we proposed a particle swarm optimization (PSO and ant colony optimization (ACO based framework (PAF for RNA secondary structure prediction. PAF consists of crucial stem searching (CSS and global sequence building (GSB. In CSS, a modified ACO (MACO is used to search the crucial stems, and then a set of stems are generated. In GSB, we used a modified PSO (MPSO to construct all the stems in one sequence. We evaluated the performance of PAF on ten sequences, which have length from 122 to 1494. We also compared the performance of PAF with the results obtained from six existing well-known methods, SARNA-Predict, RnaPredict, ACRNA, PSOfold, IPSO, and mfold. The comparison results show that PAF could not only predict structures with higher accuracy rate but also find crucial stems.

  5. Effects of high hydrostatic pressure on secondary structure and emulsifying behavior of sweet potato protein

    Science.gov (United States)

    Mehmood Khan, Nasir; Mu, Tai-Hua; Sun, Hong-Nan; Zhang, Miao; Chen, Jing-Wang

    2015-04-01

    In this study, secondary structures of sweet potato protein (SPP) after high hydrostatic pressure (HHP) treatment (200-600 MPa) were evaluated and emulsifying properties of emulsions with HHP-treated SPP solutions in different pH values (3, 6, and 9) were investigated. Circular dichroism analysis confirmed the modification of the SPP secondary structure. Surface hydrophobicity increased at pH 3 and decreased at 6 and 9. Emulsifying activity index at pH 6 increased with an increase in pressure, whereas emulsifying stability index increased at pH 6 and 9. Oil droplet sizes decreased, while volume frequency distribution of the smaller droplets increased at pH 3 and 6 with the HHP treatment. Emulsion viscosity increased at pH 6 and 9 and pseudo-plastic flow behaviors were not altered for all emulsions produced with HHP-treated SPP. These results suggested that HHP could modify the SPP structure for better emulsifying properties, which could increase the use of SPP emulsion in the food industry.

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

    Directory of Open Access Journals (Sweden)

    Vijay Kumar

    2014-01-01

    Full Text Available β-D-Galactosidases (EC 3.2.1.23 hydrolyze the terminal nonreducing β-D-galactose residues in β-D-galactosides and are ubiquitously present in all life forms including extremophiles. Eighteen microbial β-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 β-galactosidases whereas valine, glutamine, glutamic acid, phenylalanine, threonine, and tyrosine are found to be statistically preferred by thermophilic β-galactosidases. Cold active β-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 β-galactosidases have higher percentage of α-helix region responsible for temperature tolerance while cold loving β-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 β-galactosidase. Coil region of cold active β-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 β-galactosidase.

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

    International Nuclear Information System (INIS)

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

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

    Science.gov (United States)

    Wang, Ting; Zhou, Tong; Saadat, Laleh; Garcia, Joe G N

    2015-06-01

    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. PMID:25271083

  9. Secondary Structure Preferences of Mn2+ Binding Sites in Bacterial Proteins

    Directory of Open Access Journals (Sweden)

    Tatyana Aleksandrovna Khrustaleva

    2014-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Zou Yue

    2006-03-01

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

  11. Structure of the secondary xylem of Aniba Aubl. species from the Brazilian Amazon

    Directory of Open Access Journals (Sweden)

    Cláudia Viana Urbinati

    2014-09-01

    Full Text Available The aim of this study was to characterize the wood of Aniba species from the Brazilian Amazon, on the basis of specimens in the wood collection of the Herbarium of the Museu Paraense Emílio Goeldi, in the city of Belém, Brazil. The species were found to present a homogeneous structure in the secondary xylem, as defined by the location of oil cells; the presence of tyloses and crystals; and singularities of the radial and axial parenchyma.

  12. 5-Azacytidine and RNA secondary structure increase the retrovirus mutation rate.

    OpenAIRE

    Pathak, V K; Temin, H M

    1992-01-01

    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 substitut...

  13. Altered features in the secondary structure of Vicia faba 5.8s rRNA.

    OpenAIRE

    Nazar, R N; Wildeman, A G

    1981-01-01

    We have re-examined the nucleotide sequence of Vicia faba (broad bean) 5.8S rRNA using partial chemical degradation and a new approach to high temperature (65-80 degrees C) sequencing gels. The results indicate that the secondary structure was not completely disrupted in previous studies (Tanaka, Y., Dyer, T.A. and Brownlee, G.G. (1980) Nucleic Acid Res. 8, 1259-1272) and explain ambiguities between the nucleotide sequence and T1 ribonuclease digests. Despite this revision, estimates in the s...

  14. Secondary structure and phylogeny of Staphylococcus and Micrococcus 5S rRNAs.

    OpenAIRE

    Dekio, S; Yamasaki, R; Jidoi, J; Hori, H.; Osawa, S

    1984-01-01

    Nucleotide sequences of 5S rRNAs from four bacteria, Staphylococcus aureus Smith (diffuse), Staphylococcus epidermidis ATCC 14990, Micrococcus luteus ATCC 9341 and Micrococcus luteus ATCC 4698, were determined. The secondary structural models of S. aureus and S. epidermidis sequences showed characteristics of the gram-positive bacterial 5S rRNA (116-N type [H. Hori and S. Osawa, Proc. Natl. Acad. Sci. U.S.A. 76:381-385, 1979]). Those of M. luteus ATCC 9341 and M. luteus ATCC 4698 together wit...

  15. Estimation of protein secondary structure from synchrotron radiation circular dichroism (SRCD) spectroscopy with five methods

    International Nuclear Information System (INIS)

    To study the nanosafety issues, we integrate several different techniques including nuclear techniques such as nuclear analytical method, synchrotron radiation analyses, biological techniques, and nanotechniques, etc., applying to explore interactions of nanoparticles on the protein and DNA. Circular dichroism (CD) is a measure of the difference in absorption of left- and right- polarized light as it passes through an optically active or chiral sample. Optical activity arises due to the influence of neighbouring groups on the electronic structure of a chromophore involved in an electronic transition. Electronic transitions span a large wavelength range, including the near UV (from 300 to 250 nm), the far UV (from 250 to 190 nm) and the VUV (from 190 to 178 nm). CD has found its principal application in studies of protein secondary structures (α-helical, β-strand, β-turn, and Unordered) because the shape of a CD spectrum is related to the geometry of the polypeptide backbone. The data in the region around 190 nm are potentially very valuable as they can provide information on sheet and aperiodic structures, and helix effects dominate the higher-wavelength data. Generally, conventional CD (CCD) instruments can detect transitions in the 300-200 nm, but the signals in the VUV region go beyond the CCD research. Using the synchrotron radiation circular dichroisrn (SRCD) with a vacuum environment instrument, the data in the VUV region can be obtained. Five methods (CONTINLL, SELCON3, CDSSTR, VARSLC, and K2D) based on deferent arithmetic, models and reference protein. databases are used to analyze the circular dichroism spectra. CONTINLL, SELCON3, CDSSTR, and VARSLC methods are the development of SVD algorithm in different sides; otherwise K2D is one of a few neural network programmes. In order to establish perfect experiment and data-analysis system for circular dichroism spectraphotometer of Beijing Synchrotron Radiation Facility (BEPC), comparison and estimation of

  16. SSpro/ACCpro 5: almost perfect prediction of protein secondary structure and relative solvent accessibility using profiles, machine learning and structural similarity

    OpenAIRE

    Magnan, Christophe N.; Baldi, Pierre

    2014-01-01

    Motivation: Accurately predicting protein secondary structure and relative solvent accessibility is important for the study of protein evolution, structure and function and as a component of protein 3D structure prediction pipelines. Most predictors use a combination of machine learning and profiles, and thus must be retrained and assessed periodically as the number of available protein sequences and structures continues to grow.

  17. Secondary Airflow Structure around Clustered Shrubs and Its Significance for Vegetated Dune Evolution

    Science.gov (United States)

    Luo, Wanyin; Dong, Zhibao; Qian, Guangqiang; Lu, Junfeng

    2016-04-01

    Shrubs have an important significance in aeolian processes due to their disturbance of the local airflow. In the formation of vegetated dunes, there is an iterative interaction between shrub geometry, the structure of the secondary airflow, and the interaction between neighboring shrubs. Understanding the dynamics of vegetated dunes thus requires an insight into the airflow fields around shrubs. Based on aerodynamic and aeolian sand physics theory, this project measured the complex secondary flow field and aeolian sand deposition pattern around single and cluster shrubs with varied densities (i.e., 0.05, 0.08, 0.15, 0.20) and gap ratios (the ratio of the gap spacing between the shrub models to the center-to-center distance for the shrub models, ranged from 1.1 to 1.8 with side-by-side arrangement and 1.2 to 4.3 with tandem arrangement) using the particle image velocimetry system through wind tunnle simulation. The relationship between the secondary airflow structure and the shrub's porosity and arrangement was analyzed quantitatively. Research results revealed that porosity (density) is the key parameter to affect the flow patterns around single shrub. Compared to solid obstacles, bleed flow through the shrubs has great influence on the secondary airflow patterns around itself. Under cluster modes, the distance between two adjacent shrubs has great influence on flow field structures around them. The flow patterns around two side-by-side arranged shrubs can be classified into three kinds of modes, that is: single-bluff-body, biased flow pattern and parallel vortex streets. The flow patterns around two tandem arranged shrubs can be classified into three regimes, that is: the extended body regime, reattachment regime and co-shedding regime. The "shadow zone" with low velocity in the lee of shrubs is the optimal position for sand deposition, but its form, size and orientation would varied with the shrub porosity and gap ratio between them. With the increase of the gap

  18. Secondary structural analysis of the carboxyl-terminal domain from different connexin isoforms.

    Science.gov (United States)

    Spagnol, Gaëlle; Al-Mugotir, Mona; Kopanic, Jennifer L; Zach, Sydney; Li, Hanjun; Trease, Andrew J; Stauch, Kelly L; Grosely, Rosslyn; Cervantes, Matthew; Sorgen, Paul L

    2016-03-01

    The connexin carboxyl-terminal (CxCT) domain plays a role in the trafficking, localization, and turnover of gap junction channels, as well as the level of gap junction intercellular communication via numerous post-translational modifications and protein-protein interactions. As a key player in the regulation of gap junctions, the CT presents itself as a target for manipulation intended to modify function. Specific to intrinsically disordered proteins, identifying residues whose secondary structure can be manipulated will be critical toward unlocking the therapeutic potential of the CxCT domain. To accomplish this goal, we used biophysical methods to characterize CxCT domains attached to their fourth transmembrane domain (TM4). Circular dichroism and nuclear magnetic resonance were complementary in demonstrating the connexin isoforms that form the greatest amount of α-helical structure in their CT domain (Cx45 > Cx43 > Cx32 > Cx50 > Cx37 ≈ Cx40 ≈ Cx26). Studies compared the influence of 2,2,2-trifluoroethanol, pH, phosphorylation, and mutations (Cx32, X-linked Charcot-Marie Tooth disease; Cx26, hearing loss) on the TM4-CxCT structure. While pH modestly influences the CT structure, a major structural change was associated with phosphomimetic substitutions. Since most connexin CT domains are phosphorylated throughout their life cycle, studies of phospho-TM4-CxCT isoforms will be critical toward understanding the role that structure plays in regulating gap junction function. PMID:26542351

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

    Directory of Open Access Journals (Sweden)

    Adami Christoph

    2003-02-01

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

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

    Science.gov (United States)

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

    2013-01-01

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

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

    Science.gov (United States)

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

    2010-02-01

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

  2. Transcriptome-wide interrogation of RNA secondary structure in living cells with icSHAPE.

    Science.gov (United States)

    Flynn, Ryan A; Zhang, Qiangfeng Cliff; Spitale, Robert C; Lee, Byron; Mumbach, Maxwell R; Chang, Howard Y

    2016-02-01

    icSHAPE (in vivo click selective 2-hydroxyl acylation and profiling experiment) captures RNA secondary structure at a transcriptome-wide level by measuring nucleotide flexibility at base resolution. Living cells are treated with the icSHAPE chemical NAI-N3 followed by selective chemical enrichment of NAI-N3-modified RNA, which provides an improved signal-to-noise ratio compared with similar methods leveraging deep sequencing. Purified RNA is then reverse-transcribed to produce cDNA, with SHAPE-modified bases leading to truncated cDNA. After deep sequencing of cDNA, computational analysis yields flexibility scores for every base across the starting RNA population. The entire experimental procedure can be completed in ∼5 d, and the sequencing and bioinformatics data analysis take an additional 4-5 d with no extensive computational skills required. Comparing in vivo and in vitro icSHAPE measurements can reveal in vivo RNA-binding protein imprints or facilitate the dissection of RNA post-transcriptional modifications. icSHAPE reactivities can additionally be used to constrain and improve RNA secondary structure prediction models. PMID:26766114

  3. Evolutionary conservation of sequence and secondary structures inCRISPR repeats

    Energy Technology Data Exchange (ETDEWEB)

    Kunin, Victor; Sorek, Rotem; Hugenholtz, Philip

    2006-09-01

    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.

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

    Science.gov (United States)

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

    2011-07-01

    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(α) 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

  5. Water-in-oil micro-emulsion enhances the secondary structure of a protein by confinement.

    Science.gov (United States)

    Shipovskov, Stepan; Oliveira, Cristiano L P; Hoffmann, Søren Vrønning; Schauser, Leif; Sutherland, Duncan S; Besenbacher, Flemming; Pedersen, Jan Skov

    2012-09-17

    A scheme is presented in which an organic solvent environment in combination with surfactants is used to confine a natively unfolded protein inside an inverse microemulsion droplet. This type of confinement allows a study that provides unique insight into the dynamic structure of an unfolded, flexible protein which is still solvated and thus under near-physiological conditions. In a model system, the protein osteopontin (OPN) is used. It is a highly phosphorylated glycoprotein that is expressed in a wide range of cells and tissues for which limited structural analysis exists due to the high degree of flexibility and large number of post-translational modifications. OPN is implicated in tissue functions, such as inflammation and mineralisation. It also has a key function in tumour metastasis and progression. Circular dichroism measurements show that confinement enhances the secondary structural features of the protein. Small-angle X-ray scattering and dynamic light scattering show that OPN changes from being a flexible protein in aqueous solution to adopting a less flexible and more compact structure inside the microemulsion droplets. This novel approach for confining proteins while they are still hydrated may aid in studying the structure of a wide range of natively unfolded proteins. PMID:22730383

  6. Secondary Structure Prediction of Protein Constructs Using Random Incremental Truncation and Vacuum-Ultraviolet CD Spectroscopy

    Science.gov (United States)

    Pukáncsik, Mária; Orbán, Ágnes; Nagy, Kinga; Matsuo, Koichi; Gekko, Kunihiko; Maurin, Damien; Hart, Darren; Kézsmárki, István; Vertessy, Beata G.

    2016-01-01

    A novel uracil-DNA degrading protein factor (termed UDE) was identified in Drosophila melanogaster with no significant structural and functional homology to other uracil-DNA binding or processing factors. Determination of the 3D structure of UDE is excepted to provide key information on the description of the molecular mechanism of action of UDE catalysis, as well as in general uracil-recognition and nuclease action. Towards this long-term aim, the random library ESPRIT technology was applied to the novel protein UDE to overcome problems in identifying soluble expressing constructs given the absence of precise information on domain content and arrangement. Nine constructs of UDE were chosen to decipher structural and functional relationships. Vacuum ultraviolet circular dichroism (VUVCD) spectroscopy was performed to define the secondary structure content and location within UDE and its truncated variants. The quantitative analysis demonstrated exclusive α-helical content for the full-length protein, which is preserved in the truncated constructs. Arrangement of α-helical bundles within the truncated protein segments suggested new domain boundaries which differ from the conserved motifs determined by sequence-based alignment of UDE homologues. Here we demonstrate that the combination of ESPRIT and VUVCD spectroscopy provides a new structural description of UDE and confirms that the truncated constructs are useful for further detailed functional studies. PMID:27273007

  7. Short Oligonucleotides Aligned in Stretched Humid Matrix: Secondary DNA Structure in Poly(vinyl alcohol) Environment

    KAUST Repository

    Hanczyc, Piotr

    2012-04-24

    We report that short, synthetic, double- as well as single-stranded DNA can be aligned in stretched humid poly(vinyl alcohol) (PVA) matrix, and the secondary structure (nucleobase orientation) can be characterized with linear dichroism (LD) spectroscopy. Oligonucleotides of lengths varying between 10 (3.4 nm) and 60 bases (20.4 nm) were investigated with respect to structural properties in the gel-like polymer environment. The DNA conformation as a function of relative humidity reveals a strong dependence of helical structure of DNA on PVA hydration level, results of relevance for nanotechnical studies of DNA-based supramolecular systems. Also, the PVA gel could provide possibilities to test models for nucleic acid interactions and distribution in cell contexts, including structural stability of genetic material in the cell and PVA-packaging for gene delivery. A method by which duplex oligonucleotides, with sequences designed to provide specific binding sites, become amenable to polarized-light spectroscopy opens up new possibilities for studying structure in DNA complexes with small adduct molecules as well as proteins. © 2012 American Chemical Society.

  8. Predicting protein folding pathways at the mesoscopic level based on native interactions between secondary structure elements

    Directory of Open Access Journals (Sweden)

    Sze Sing-Hoi

    2008-07-01

    Full Text Available Abstract Background Since experimental determination of protein folding pathways remains difficult, computational techniques are often used to simulate protein folding. Most current techniques to predict protein folding pathways are computationally intensive and are suitable only for small proteins. Results By assuming that the native structure of a protein is known and representing each intermediate conformation as a collection of fully folded structures in which each of them contains a set of interacting secondary structure elements, we show that it is possible to significantly reduce the conformation space while still being able to predict the most energetically favorable folding pathway of large proteins with hundreds of residues at the mesoscopic level, including the pig muscle phosphoglycerate kinase with 416 residues. The model is detailed enough to distinguish between different folding pathways of structurally very similar proteins, including the streptococcal protein G and the peptostreptococcal protein L. The model is also able to recognize the differences between the folding pathways of protein G and its two structurally similar variants NuG1 and NuG2, which are even harder to distinguish. We show that this strategy can produce accurate predictions on many other proteins with experimentally determined intermediate folding states. Conclusion Our technique is efficient enough to predict folding pathways for both large and small proteins at the mesoscopic level. Such a strategy is often the only feasible choice for large proteins. A software program implementing this strategy (SSFold is available at http://faculty.cs.tamu.edu/shsze/ssfold.

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

    DEFF Research Database (Denmark)

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

    2007-01-01

    Therefore, we have developed a method for evolving the structure of HMMs automatically, using Genetic Algorithms (GAs). RESULTS: In the GA procedure, populations of HMMs are assembled from biologically meaningful building blocks. Mutation and crossover operators were designed to explore the space...... evolved HMM also calculates the probabilities associated with the predictions. We carefully examined the performance of the HMM based predictor, both under the multiple- and single-sequence...

  10. 5-Azacytidine and RNA secondary structure increase the retrovirus mutation rate.

    Science.gov (United States)

    Pathak, V K; Temin, H M

    1992-01-01

    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

  11. Combining sequence-based prediction methods and circular dichroism and infrared spectroscopic data to improve protein secondary structure determinations

    Directory of Open Access Journals (Sweden)

    Lees Jonathan G

    2008-01-01

    Full Text Available Abstract Background A number of sequence-based methods exist for protein secondary structure prediction. Protein secondary structures can also be determined experimentally from circular dichroism, and infrared spectroscopic data using empirical analysis methods. It has been proposed that comparable accuracy can be obtained from sequence-based predictions as from these biophysical measurements. Here we have examined the secondary structure determination accuracies of sequence prediction methods with the empirically determined values from the spectroscopic data on datasets of proteins for which both crystal structures and spectroscopic data are available. Results In this study we show that the sequence prediction methods have accuracies nearly comparable to those of spectroscopic methods. However, we also demonstrate that combining the spectroscopic and sequences techniques produces significant overall improvements in secondary structure determinations. In addition, combining the extra information content available from synchrotron radiation circular dichroism data with sequence methods also shows improvements. Conclusion Combining sequence prediction with experimentally determined spectroscopic methods for protein secondary structure content significantly enhances the accuracy of the overall results obtained.

  12. Historical WBAN ID Assignments

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — 4"x6" index cards represent the first written assignments of Weather Bureau Army Navy (WBAN) station identifier numbers by the National Climatic Data Center....

  13. Relationship between protein structure and geometrical constraints

    DEFF Research Database (Denmark)

    Lund, Ole; Hansen, Jan; Brunak, Søren; Bohr, Jakob

    1996-01-01

    We evaluate to what extent the structure of proteins can be deduced from incomplete knowledge of disulfide bridges, surface assignments, secondary structure assignments, and additional distance constraints. A cost function taking such constraints into account was used to obtain protein structures...... using a simple minimization algorithm. For small proteins, the approximate structure could be obtained using one additional distance constraint for each amino acid in the protein. We also studied the effect of using predicted secondary structure and surface assignments. The constraints used in this...... approach typically may be obtained from low-resolution experimental data. When using a cost function based on distances, half of the resulting structures will be mirrored, because the resulting structure and its mirror image will have the same cost. The secondary structure assignments were therefore...

  14. Relationship between protein structure and geometrical constrains

    DEFF Research Database (Denmark)

    Lund, Ole; Hansen, Jan; Brunak, Søren; Bohr, Jakob

    1996-01-01

    We evaluate to what extent the structure of proteins can be deduced from incomplete knowledge of disulfide bridges, surface assignments, secondary structure assignments, and additional distance constraints. A cost function taking such constraints into account was used to obtain protein structures...... using a simple minimization algorithm. For small proteins, the approximate structure could be obtained using one additional distance constraint for each amino acid in the protein. We also studied the effect of using predicted secondary structure and surface assignments. The constraints used in this...... approach typically may be obtained from low-resolution experimental data. When using a cost function based on distances, half of the resulting structures will be mirrored, because the resulting structure and its mirror image will have the same cost. The secondary structure assignments were therefore...

  15. Factors that Affect Mathematics-Science (MS) Scores in the Secondary Education Institutional Exam: An Application of Structural Equation Modeling

    Science.gov (United States)

    Yavuz, Mustafa

    2009-01-01

    Discovering what determines students' success in the Secondary Education Institutional Exam is very important to parents and it is also critical for students, teachers, directors, and researchers. Research was carried out by studying the related literature and structural equation modeling techniques. A structural model was created that consisted…

  16. Molecular and crystal structure of the antibiotic enniatin B, a secondary microbial metabolite

    International Nuclear Information System (INIS)

    Single crystals of the secondary microbial metabolite C33H57N3O9·1(2/3)H2O with the known molecular weight were studied by the method of X-ray diffraction analysis, where a=b=15.102(3) A, c=14.548(3) A, sp. gr.R3, R=0.057. In the course of the structure determination, it was established that the substance is a natural antibiotic, namely, enniatin B. The conformation of its molecule is similar to that of the known synthetic antibiotic. The main difference between the natural and synthesized forms reduces to the different numbers of water molecules and their arrangement in the cavity of the antibiotic molecule

  17. Effect of Secondary Cooling Conditions on Solidification Structure and Central Macrosegregation in Continuously Cast High-Carbon Rectangular Billet

    Science.gov (United States)

    Zeng, Jie; Chen, Weiqing

    2015-10-01

    Solidification structures of high carbon rectangular billet with a size of 180 mm × 240 mm in different secondary cooling conditions were simulated using cellular automaton-finite element (CAFE) coupling model. The adequacy of the model was compared with the simulated and the actual macrostructures of 82B steel. Effects of the secondary cooling water intensity on solidification structures including the equiaxed grain ratio and the equiaxed grain compactness were discussed. It was shown that the equiaxed grain ratio and the equiaxed grain compactness changed in the opposite direction at different secondary cooling water intensities. Increasing the secondary cooling water intensity from 0.9 or 1.1 to 1.3 L/kg could improve the equiaxed grain compactness and decrease the equiaxed grain ratio. Besides, the industrial test was conducted to investigate the effect of different secondary cooling water intensities on the center carbon macrosegregation of 82B steel. The optimum secondary cooling water intensity was 0.9 L/kg, while the center carbon segregation degree was 1.10. The relationship between solidification structure and center carbon segregation was discussed based on the simulation results and the industrial test.

  18. The secondary structure of echistatin from 1H-NMR, circular-dichroism and Raman spectroscopy.

    Science.gov (United States)

    Saudek, V; Atkinson, R A; Lepage, P; Pelton, J T

    1991-12-01

    Detailed biophysical studies have been carried out on echistatin, a member of the disintegrin family of small, cysteine-rich, RGD-containing proteins, isolated from the venom of the saw-scaled viper Echis carinatus. Analysis of circular-dichroism spectra indicates that, at 20 degrees C, echistatin contains no alpha-helix but contains mostly beta-turns and beta-sheet. Two isobestic points are observed as the temperature is raised, the conformational changes associated with that observed between 40 degrees C and 72 degrees C being irreversible. Raman spectra also indicate considerable beta-turn and beta-sheet (20%) structure and an absence of alpha-helical structure. Three of the four disulphide bridges are shown to be in an all-gauche conformation, while the fourth adopts a trans-gauche-gauche conformation. The 1H-NMR spectrum of echistatin has been almost fully assigned. A single conformation was observed at 27 degrees C with the four proline residues adopting only the trans conformation. A large number of backbone amide protons were found to exchange slowly, but no segments of the backbone were found to be in either alpha-helical or beta-sheet conformation. A number of turns could be characterised. An irregular beta-hairpin contains the RGD sequence in a mobile loop at its tip. Two of the four disulphide cross-links have been identified from the NMR spectra. The data presented in this paper will serve to define the structure of echistatin more closely in subsequent studies. PMID:1761037

  19. Interaction Of Calcium Phosphate Nanoparticles With Human Chorionic Gonadotropin Modifies Secondary And Tertiary Protein Structure

    Directory of Open Access Journals (Sweden)

    Al-Hakeim Hussein K

    2015-12-01

    Full Text Available Calcium phosphate nanoparticles (CaPNP have good biocompatibility and bioactivity inside human body. In this study, the interaction between CaPNP and human chorionic gonadotropin (hCG was analyzed to determine the changes in the protein structure in the presence of CaPNP and the quantity of protein adsorbed on the CaPNP surface. The results showed a significant adsorption of hCG on the CaPNP nanoparticle surface. The optimal fit was achieved using the Sips isotherm equation with a maximum adsorption capacity of 68.23 µg/mg. The thermodynamic parameters, including ∆H° and ∆G°, of the adsorption process are positive, whereas ∆S° is negative. The circular dichroism results of the adsorption of hCG on CaPNP showed the changes in its secondary structure; such changes include the decomposition of α-helix strand and the increase in β-pleated sheet and random coil percentages. Fluorescence study indicated minimal changes in the tertiary structure near the microenvironment of the aromatic amino acids such as tyrosine and phenyl alanine caused by the interaction forces between the CaPNP and hCG protein. The desorption process showed that the quantity of the hCG desorbed significantly increases as temperature increases, which indicates the weak forces between hCG and the surface.

  20. Resolving detailed molecular structures in complex organic mixtures and modeling their secondary organic aerosol formation

    Science.gov (United States)

    Goodman-Rendall, Kevin A. S.; Zhuang, Yang R.; Amirav, Aviv; Chan, Arthur W. H.

    2016-03-01

    Characterization of unresolved complex mixtures (UCMs) remains an ongoing challenge towards developing detailed and accurate inputs for modeling secondary organic aerosol (SOA) formation. Traditional techniques based on gas chromatography/electron impact-mass spectrometry induce excessive fragmentation, making it difficult to speciate and quantify isomers precisely. The goal of this study is to identify individual organic isomers by gas chromatography/mass spectrometry with supersonic molecular beam (SMB-GC/MS, also known as GC/MS with Cold EI) and to incorporate speciated isomers into an SOA model that accounts for the specific structures elucidated. Two samples containing atmospherically relevant UCMs are analyzed. The relative isomer distributions exhibit remarkably consistent trends across a wide range of carbon numbers. Constitutional isomers of different alkanes are speciated and individually quantified as linear, branched - for the first time by position of branching - multiply branched, or unsaturated - by degree of ring substitution and number of rings. Relative amounts of exact molecular structures are used as input parameters in an SOA box model to study the effects of molecular structures on SOA yields and volatility evolution. Highly substituted cyclic, mono-substituted cyclic, and linear species have the highest SOA yields while branched alkanes formed the least SOA. The rate of functionalization of a representative UCM is found to be in agreement with current volatility basis set (VBS) parameterizations based on detailed knowledge of composition and known oxidation mechanisms, confirming the validity of VBS parameters currently used in air quality models.

  1. The secondary and aggregation structural changes of BSA induced by trivalent chromium: A biophysical study

    International Nuclear Information System (INIS)

    Trivalent chromium Cr(III), which was originally considered to be innocuous as a nutriment, has been suspected to induce some abnormalities in human body recently. In the present work, the effects of Cr(III) on the structural state of BSA were comprehensively investigated through a series of appropriate methods in combination, including X-ray photoelectron spectroscopy (XPS), fourier transform infrared spectroscopy (FTIR), circular dichroism (CD), UV–vis absorption, synchronous fluorescence, fluorescence lifetime analysis, resonance light scattering (RLS), dynamic light scattering (DLS) and excitation–emission matrix spectroscopy (EEMS) methods. XPS accurately described the binding activity of Cr(III) with protein C, N and O atoms. The structural analysis according to FTIR and CD methods showed that the Cr(III) binding altered BSA conformation with a major reduction of α-helix. RLS and DLS analyses demonstrated that the presence of Cr(III) with low concentration could induce the aggregation structural changes of BSA. UV–vis absorption, EEMS and synchronous fluorescence suggested that the interaction between Cr(III) and BSA induced a slight unfolding of the polypeptide backbone and altered the microenvironments of Trp and Tyr residues in BSA. This research is helpful for understanding the structure-function relationship involved in metal ion-protein bioconjugate process. - Highlights: • The effect of Cr(III) on the conformational state of BSA was comprehensively studied. • XPS described the binding activity of Cr(III) with protein C, N and O atoms. • FTIR and CD data revealed secondary structural alteration in BSA. • Cr(III) complexation induced microenvironmental changes of Trp and Tyr. • RLS, DLS and EEMS presented the aggregational states of Cr(III)–BSA complex

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

    Science.gov (United States)

    Aguilar, Catalina; Sánchez, Juan Armando

    2007-06-01

    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 molecular morphometrics for 24 octocorals mostly from the Atlantic. ITS2 exhibited the six-helicoidal ring-model structure found in eukaryotes, and provided 38 parsimony-informative characters. The proposed phylogenies, though differing between sequence- and structure-base results, provided consistent support for several clades. Genera considered part of the polyphyletic genus Leptogorgia, such as Filigorgia, were distantly related to the former in all phylogenetic hypotheses. Main differences among the hypotheses consisted in the placement of Muriceopsis (previously considered from the Plexauridae family) and Filigorgia. Excluding Muriceopsis and an undescribed octocoral from Tobago, Plexaurella and Pterogorgia grouped together as a sister branch of Pinnigorgia spp. but long-branch attraction was evident for the grouping of Plexaurella nutans (another plexaurid) and Pterogorgia citrina. Unexpected results were the divergence between Caribbean genera, Gorgonia and Pseudopterogorgia, which were placed basal respect to Pacifigorgia and Leptogorgia (=Lophogorgia). ITS2 provided support to corroborate observations based on sclerite morphology: species with "capstan sclerites" (e.g., Pacifigorgia and Leptogorgia) were characterized by a long helix IV with one internal loop and a helix V with four internal loops; "scaphoid sclerites" had a predominantly long helix V if compared to helix IV; "asymmetric spiny sclerites" (Muriceopsis, Pinnigorgia and the undescribed octocoral) exhibited one or two lateral bulges in the V helix. Remarkably, Muriceopsis

  3. Pentacyclic triterpenoids of Mentha villosa: structural identification and {sup 1}H and {sup 13}C resonance assignments; Triterpenoides pentaciclicos de Mentha villosa: identificacao estrutural e atribuicao dos deslocamentos quimicos dos atomos de hidrogenio e carbono

    Energy Technology Data Exchange (ETDEWEB)

    Monte, Francisco J. Queiroz; Oliveira, Eliete F. de [Ceara Univ., Fortaleza, CE (Brazil). Dept. de Quimica Organica e Inorganica; Braz Filho, Raimundo [Universidade Estadual do Norte Fluminense, Campos dos Goytacazes, RJ (Brazil). Setor de Quimica de Produtos Naturais

    2001-08-01

    The structures of seven oleanene and ursene triterpenoids (1-7) isolated from aerial parts of Mentha villosa were identified. In addition, the complete {sup 1} H and {sup 13} C resonance assignments of these triterpenoids were accomplished using 1D and 2D NMR spectroscopic experiments. (author)

  4. 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.

    Science.gov (United States)

    Koenig, B.

    1977-01-01

    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.

  5. Protein-associated water and secondary structure effect removal of blood proteins from metallic substrates.

    Science.gov (United States)

    Anand, Gaurav; Zhang, Fuming; Linhardt, Robert J; Belfort, Georges

    2011-03-01

    Removing adsorbed protein from metals has significant health and industrial consequences. There are numerous protein-adsorption studies using model self-assembled monolayers or polymeric substrates but hardly any high-resolution measurements of adsorption and removal of proteins on industrially relevant transition metals. Surgeons and ship owners desire clean metal surfaces to reduce transmission of disease via surgical instruments and minimize surface fouling (to reduce friction and corrosion), respectively. A major finding of this work is that, besides hydrophobic interaction adhesion energy, water content in an adsorbed protein layer and secondary structure of proteins determined the access and hence ability to remove adsorbed proteins from metal surfaces with a strong alkaline-surfactant solution (NaOH and 5 mg/mL SDS in PBS at pH 11). This is demonstrated with three blood proteins (bovine serum albumin, immunoglobulin, and fibrinogen) and four transition metal substrates and stainless steel (platinum (Pt), gold (Au), tungsten (W), titanium (Ti), and 316 grade stainless steel (SS)). All the metallic substrates were checked for chemical contaminations like carbon and sulfur and were characterized using X-ray photoelectron spectroscopy (XPS). While Pt and Au surfaces were oxide-free (fairly inert elements), W, Ti, and SS substrates were associated with native oxide. Difference measurements between a quartz crystal microbalance with dissipation (QCM-D) and surface plasmon resonance spectroscopy (SPR) provided a measure of the water content in the protein-adsorbed layers. Hydrophobic adhesion forces, obtained with atomic force microscopy, between the proteins and the metals correlated with the amount of the adsorbed protein-water complex. Thus, the amount of protein adsorbed decreased with Pt, Au, W, Ti and SS, in this order. Neither sessile contact angle nor surface roughness of the metal substrates was useful as predictors here. All three globular proteins

  6. RNAspa: a shortest path approach for comparative prediction of the secondary structure of ncRNA molecules

    OpenAIRE

    Michaeli Shulamit; Doniger Tirza; Horesh Yair; Unger Ron

    2007-01-01

    Abstract Background In recent years, RNA molecules that are not translated into proteins (ncRNAs) have drawn a great deal of attention, as they were shown to be involved in many cellular functions. One of the most important computational problems regarding ncRNA is to predict the secondary structure of a molecule from its sequence. In particular, we attempted to predict the secondary structure for a set of unaligned ncRNA molecules that are taken from the same family, and thus presumably have...

  7. Prediction of protein secondary structure based on residue pair types and conformational states using dynamic programming algorithm.

    Science.gov (United States)

    Sadeghi, Mehdi; Parto, Sahar; Arab, Shahriar; Ranjbar, Bijan

    2005-06-20

    We have used a statistical approach for protein secondary structure prediction based on information theory and simultaneously taking into consideration pairwise residue types and conformational states. Since the prediction of residue secondary structure by one residue window sliding make ambiguity in state prediction, we used a dynamic programming algorithm to find the path with maximum score. A score system for residue pairs in particular conformations is derived for adjacent neighbors up to ten residue apart in sequence. The three state overall per-residue accuracy, Q3, of this method in a jackknife test with dataset created from PDBSELECT is more than 70%. PMID:15936021

  8. Upper mantle velocity structure beneath Italy from direct and secondary P-wave teleseismic tomography

    Directory of Open Access Journals (Sweden)

    P. De Gori

    1997-06-01

    Full Text Available High-quality teleseismic data digitally recorded by the National Seismic Network during 1988-1995 have been analysed to tomographically reconstruct the aspherical velocity structure of the upper mantle beneath the Italian region. To improve the quality and the reliability of the tomographic images, both direct (P, PKPdf and secondary (pP,sP,PcP,PP,PKPbc,PKPab travel-time data were used in the inversion. Over 7000 relative residuals were computed with respect to the IASP91 Earth velocity model and inverted using a modified version of the ACH technique. Incorporation of data of secondary phases resulted in a significant improvement of the sampling of the target volume and of the spatial resolution of the heterogeneous zones. The tomographic images show that most of the lateral variations in the velocity field are confined in the first ~250 km of depth. Strong low velocity anomalies are found beneath the Po plain, Tuscany and Eastern Sicily in the depth range between 35 and 85 km. High velocity anomalies dominate the upper mantle beneath the Central-Western Alps, Northern-Central Apennines and Southern Tyrrhenian sea at lithospheric depths between 85 and 150 km. At greater depth, positive anomalies are still observed below the northernmost part of the Apenninic chain and Southern Tyrrhenian sea. Deeper anomalies present in the 3D velocity model computed by inverting only the first arrivals dataset, generally appear less pronounced in the new tomographic reconstructions. We interpret this as the result of the ray sampling improvement on the reduction of the vertical smearing effects.

  9. Content-Related Knowledge of Biology Teachers from Secondary Schools: Structure and learning opportunities

    Science.gov (United States)

    Großschedl, Jörg; Mahler, Daniela; Kleickmann, Thilo; Harms, Ute

    2014-09-01

    Teachers' content-related knowledge is a key factor influencing the learning progress of students. Different models of content-related knowledge have been proposed by educational researchers; most of them take into account three categories: content knowledge, pedagogical content knowledge, and curricular knowledge. As there is no consensus about the empirical separability (i.e. empirical structure) of content-related knowledge yet, a total of 134 biology teachers from secondary schools completed three tests which were to capture each of the three categories of content-related knowledge. The empirical structure of content-related knowledge was analyzed by Rasch analysis, which suggests content-related knowledge to be composed of (1) content knowledge, (2) pedagogical content knowledge, and (3) curricular knowledge. Pedagogical content knowledge and curricular knowledge are highly related (rlatent = .70). The latent correlations between content knowledge and pedagogical content knowledge (rlatent = .48)-and curricular knowledge, respectively (rlatent = .35)-are moderate to low (all ps pedagogical content knowledge, and curricular knowledge acquisition. Our results show that an in-depth training in teacher education, professional development, and teacher self-study are positively related to particular categories of content-related knowledge. Furthermore, our results indicate that teaching experience is negatively related to curricular knowledge, compared to no significant relationship with content knowledge and pedagogical content knowledge.

  10. The Secondary Structure of Heated Whey Protein and Its Hydrolysates Antigenicity

    Institute of Scientific and Technical Information of China (English)

    PANGZhi-hua; ZHU Jun; WU Wei-jing; WANG Fang; RENFa-zheng; ZHANG Lu-daa; GUOHui-yuan

    2011-01-01

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

  11. Synthesis and characterization of nitroaromatic peptoids: fine tuning peptoid secondary structure through monomer position and functionality.

    Science.gov (United States)

    Fowler, Sarah A; Luechapanichkul, Rinrada; Blackwell, Helen E

    2009-02-20

    N-substituted glycine oligomers, or peptoids, have emerged as an important class of foldamers for the study of biomolecular interactions and for potential use as therapeutic agents. However, the design of peptoids with well-defined conformations a priori remains a formidable challenge. New approaches are required to address this problem, and the systematic study of the role of individual monomer units in the global peptoid folding process represents one strategy. Here, we report our efforts toward this approach through the design, synthesis, and characterization of peptoids containing nitroaromatic monomer units. This work required the synthesis of a new chiral amine building block, (S)-1-(2-nitrophenyl)ethanamine (s2ne), which could be readily installed into peptoids using standard solid-phase peptoid synthesis techniques. We designed a series of peptoid nonamers that allowed us to probe the effects of this relatively electron-deficient and sterically encumbered alpha-chiral side chain on peptoid structure, namely, the peptoid threaded loop and helix. Circular dichroism spectroscopy of the peptoids revealed that the nitroaromatic monomer has a significant effect on peptoid secondary structure. Specifically, the threaded loop structure was disrupted in a nonamer containing alternating N-(S)-1-phenylethylglycine (Nspe) and Ns2ne monomers, and the major conformation was helical instead. Indeed, placement of a single Ns2ne at the N-terminal position of (Nspe)(9) resulted in a destabilized form of the threaded loop structure relative to the homononamer (Nspe)(9). Conversely, we observed that incorporation of N-(S)-1-(4-nitrophenyl)ethylglycine (Nsnp, a p-nitro monomer) at the N-terminal position stabilized the threaded loop structure relative to (Nspe)(9). Additional experiments revealed that nitroaromatic side chains can influence peptoid nonamer folding by modulating the strength of key intramolecular hydrogen bonds in the peptoid threaded loop structure. Steric

  12. Insight into the secondary structure of chloramphenicol acetyltransferase type I — computer analysis and FT-IR spectroscopic characterization of the protein structure

    Science.gov (United States)

    Andreeva, A. E.; Karamancheva, I. R.

    2001-05-01

    The secondary structure of chloramphenicol O-acetyltransferase type I (CAT I) and an N-terminal deleted mutant has been studied by Fourier transform infrared spectroscopy. The analysis of the amide I band of different samples (KBr, hydrated films and buffer solution) by Fourier self-deconvolution followed by a curve fitting was performed. The spectroscopic data have been utilized to determine the α-helix and β-structure % contents, which depend strongly on the protein sample preparation. Furthermore, the secondary structure of the enzyme-inhibitor Crystal Violet complex was analyzed. The observed difference in the secondary structural contents suggests that some conformational changes of the enzyme are induced by the inhibitor after binding.

  13. Imaging the 3D structure of secondary osteons in human cortical bone using phase-retrieval tomography

    Energy Technology Data Exchange (ETDEWEB)

    Arhatari, B D; Peele, A G [Department of Physics, La Trobe University, Victoria 3086 (Australia); Cooper, D M L [Department of Anatomy and Cell Biology, University of Saskatchewan, Saskatoon (Canada); Thomas, C D L; Clement, J G [Melbourne Dental School, University of Melbourne, Victoria 3010 (Australia)

    2011-08-21

    By applying a phase-retrieval step before carrying out standard filtered back-projection reconstructions in tomographic imaging, we were able to resolve structures with small differences in density within a densely absorbing sample. This phase-retrieval tomography is particularly suited for the three-dimensional segmentation of secondary osteons (roughly cylindrical structures) which are superimposed upon an existing cortical bone structure through the process of turnover known as remodelling. The resulting images make possible the analysis of the secondary osteon structure and the relationship between an osteon and the surrounding tissue. Our observations have revealed many different and complex 3D structures of osteons that could not be studied using previous methods. This work was carried out using a laboratory-based x-ray source, which makes obtaining these sorts of images readily accessible.

  14. My Favorite Assignment.

    Science.gov (United States)

    Hebert, Margaret; And Others

    1991-01-01

    Contains seven brief articles which offer assignments designed to help students perform job searches, write job application letters, answer difficult questions, write letters of resignation, alleviate fears of public speaking, use the interview effectively in the business communication, and develop listening skills. (PRA)

  15. Secondary structure and phylogenetic utility of the ribosomal large subunit (28S) in monogeneans of the genus Thaparocleidus and Bifurcohaptor (Monogenea: Dactylogyridae)

    OpenAIRE

    Chaudhary, Anshu; SINGH, HRIDAYA SHANKER

    2012-01-01

    Present communication deals with secondary structure of 28S rDNA of two already known species of monogeneans viz., Bifurcohaptor indicus and Thaparocleidus parvulus parasitizing gill filaments of a freshwater fish, Mystus vittatus for phylogenetic inference. Secondary structure data are best used as accessory taxonomic characters as their phylogenetic resolving power and confidence in validity. Secondary structure of the 28S rDNA transcript could provide information for identifying homologous...

  16. Protein side-chain resonance assignment and NOE assignment using RDC-defined backbones without TOCSY data

    Energy Technology Data Exchange (ETDEWEB)

    Zeng Jianyang [Duke University, Department of Computer Science (United States); Zhou Pei [Duke University Medical Center, Department of Biochemistry (United States); Donald, Bruce Randall [Duke University, Department of Computer Science (United States)

    2011-08-15

    One bottleneck in NMR structure determination lies in the laborious and time-consuming process of side-chain resonance and NOE assignments. Compared to the well-studied backbone resonance assignment problem, automated side-chain resonance and NOE assignments are relatively less explored. Most NOE assignment algorithms require nearly complete side-chain resonance assignments from a series of through-bond experiments such as HCCH-TOCSY or HCCCONH. Unfortunately, these TOCSY experiments perform poorly on large proteins. To overcome this deficiency, we present a novel algorithm, called Nasca (NOE Assignment and Side-Chain Assignment), to automate both side-chain resonance and NOE assignments and to perform high-resolution protein structure determination in the absence of any explicit through-bond experiment to facilitate side-chain resonance assignment, such as HCCH-TOCSY. After casting the assignment problem into a Markov Random Field (MRF), Nasca extends and applies combinatorial protein design algorithms to compute optimal assignments that best interpret the NMR data. The MRF captures the contact map information of the protein derived from NOESY spectra, exploits the backbone structural information determined by RDCs, and considers all possible side-chain rotamers. The complexity of the combinatorial search is reduced by using a dead-end elimination (DEE) algorithm, which prunes side-chain resonance assignments that are provably not part of the optimal solution. Then an A* search algorithm is employed to find a set of optimal side-chain resonance assignments that best fit the NMR data. These side-chain resonance assignments are then used to resolve the NOE assignment ambiguity and compute high-resolution protein structures. Tests on five proteins show that Nasca assigns resonances for more than 90% of side-chain protons, and achieves about 80% correct assignments. The final structures computed using the NOE distance restraints assigned by Nasca have backbone RMSD 0

  17. Maximizing Expected Base Pair Accuracy in RNA Secondary Structure Prediction by Joining Stochastic Context-Free Grammars Method

    Directory of Open Access Journals (Sweden)

    Shahira M. Habashy

    2012-03-01

    Full Text Available The identification of RNA secondary structures has been among the most exciting recent developments in biology and medical science. Prediction of RNA secondary structure is a fundamental problem in computational structural biology. For several decades, free energy minimization has been the most popular method for prediction from a single sequence. It is based on a set of empirical free energy change parameters derived from experiments using a nearest-neighbor model. Accurate prediction of RNA secondary structure from the base sequence is an unsolved computational challenge. The accuracy of predictions made by free energy minimization is limited by the quality of the energy parameters in the underlying free energy model. More recently, stochastic context-free grammars (SCFGs have emerged as an alternative probabilistic methodology for modeling RNA structure. Unlike physics-based methods, which rely on thousands of experimentally -measured thermodynamic parameters, SCFGs use fully-automated statistical learning algorithms to derive model parameters. This paper proposes a new algorithm that computes base pairing pattern for RNA molecule. Complex internal structures in RNA are fully taken into account. It supports the calculation of stochastic context-free grammars (SCFGs, and equilibrium concentrations of duplex structures. This new algorithm is compared with dynamic programming benchmark mfold and algorithms (Tfold, and MaxExpect. The results showed that the proposed algorithm achieved better performance with respect to sensitivity and positive predictive value.

  18. Variation in secondary structure of the 16S rRNA molecule in cyanobacteria with implications for phylogenetic analysis

    Czech Academy of Sciences Publication Activity Database

    Řeháková, Klára; Johansen, J. R.; Bowen, M.B.; Martin, M.P.; Sheil, C.A.

    2014-01-01

    Roč. 14, č. 2 (2014), s. 161-178. ISSN 1802-5439 Institutional support: RVO:60077344 Keywords : 16S rRNA secondary structure * cyanobacteria * phylogeny Subject RIV: EE - Microbiology, Virology Impact factor: 1.930, year: 2014

  19. Effect of Programmed Instruction on Students' Attitude towards Structure of the Atom and the Periodic Table among Kenyan Secondary Schools

    Science.gov (United States)

    Wangila, M. J.; Martin, W.; Ronald, M.

    2015-01-01

    This study examined the effect of Programmed Instruction on students' attitude towards Structure of the Atom and the Periodic Table (SAPT) among mixed (co-educational) secondary schools of Butere district, Kakamega county, Kenya. The quasi-experimental research design was adopted, using the nonrandomized Solomon four-group as a model. The sample…

  20. Novel evolutionary lineages revealed in the Chaetothyriales (Fungi) based on multigene phylogenetic analyses and comparison of ITS secondary structure

    Czech Academy of Sciences Publication Activity Database

    Réblová, Martina; Untereiner, W. A.; Réblová, K.

    2013-01-01

    Roč. 8, č. 5 (2013), e63547. E-ISSN 1932-6203 R&D Projects: GA ČR GAP506/12/0038 Institutional support: RVO:67985939 Keywords : Cyphelophora * Phialophora * secondary structure Subject RIV: EF - Botanics Impact factor: 3.534, year: 2013

  1. Secondary dislocation structures in a Ni-TiN system from the GMS and O-lattice theory

    Science.gov (United States)

    Tang, Yiru; Dai, Fuzhi; Gu, Xinfu; Wang, Zhongchang; Zhang, Wenzheng

    2016-03-01

    The preferred state in an interface is the key to evaluating misfit strain, especially for the interphase interfaces in secondary preferred state. The structure of good matching site (GMS) in a GMS clusters offers a guidance for the preferred state, especially for identifying the coincidence site lattice in two dimension for secondary preferred state and the Burgers vectors in a large misfit system. Here, we combine the GMS with O-lattice theory to calculate the secondary dislocation structure in the habit planes of the type II and III TiN precipitates in a Ni-TiN system. We find that under a slight elastic strain, the type III habit plane contains a single set of secondary dislocations, consistent with the experimental observation. The type II habit plane contains three sets of secondary dislocations, two of which can be relaxed to be nearly parallel and another of which may be invisible in diffraction contrast due to its short Burgers vector. The present study provides a reasonable interpretation to the observed interfacial dislocations, and also suggests Burgers vectors for the dislocations that are not determined experimentally.

  2. Effect of boundary layer thickness on secondary structures in a short inlet curved duct

    International Nuclear Information System (INIS)

    Highlights: • Studied the flow field of a short inlet curved duct. • Flow field is asymmetric due to two opposing flow mechanisms. • Manipulation of the incoming boundary layers modified the secondary flow structures, resulting in a symmetric flow field. - Abstract: The flow pattern in short inlet ducts with aggressive curvature has been shown to lead, in some cases, to an asymmetric flow field at the aerodynamic interface plane. In the present work, a two-dimensional honeycomb mesh was added upstream of the curved duct to create a pressure drop across it, and therefore to an increased velocity deficit in the boundary layer. This velocity deficit led to a stronger streamwise separation, overcoming the instability that can result in an asymmetric flow field at the aerodynamic interface plane. Experiments were conducted at Mach numbers of M = 0.2, 0.44 and 0.58 in an expanding aggressive duct with rectangle to a square cross section with area ratio of 1.27. Steady and unsteady pressure measurements, together with Particle Image Velocimetry (PIV), were used to explore the effect of the honeycomb on the symmetry of the flow field. The effect of inserting a honeycomb was tested by increasing its height from 0 to 2.2 times the boundary layer thickness of the baseline flow upstream of the curve. Using the honeycomb, flow symmetry was achieved for the specific geometrical configuration tested with a negligible decrease of the pressure recovery

  3. Line-Based Object Recognition using Hausdorff Distance: From Range Images to Molecular Secondary Structure

    Energy Technology Data Exchange (ETDEWEB)

    Guerra, C; Pascucci, V

    2004-12-13

    Object recognition algorithms are fundamental tools in automatic matching of geometric shapes within a background scene. Many approaches have been proposed in the past to solve the object recognition problem. Two of the key aspects that distinguish them in terms of their practical usability are: (i) the type of input model description and (ii) the comparison criteria used. In this paper we introduce a novel scheme for 3D object recognition based on line segment representation of the input shapes and comparison using the Hausdor distance. This choice of model representation provides the flexibility to apply the scheme in different application areas. We define several variants of the Hausdor distance to compare the models within the framework of well defined metric spaces. We present a matching algorithm that efficiently finds a pattern in a 3D scene. The algorithm approximates a minimization procedure of the Hausdor distance. The output error due to the approximation is guaranteed to be within a known constant bound. Practical results are presented for two classes of objects: (i) polyhedral shapes extracted from segmented range images and (ii) secondary structures of large molecules. In both cases the use of our approximate algorithm allows to match correctly the pattern in the background while achieving the efficiency necessary for practical use of the scheme. In particular the performance is improved substantially with minor degradation of the quality of the matching.

  4. Investigation of surface of structural alloys after chemical treatment by secondary-ion mass spectrometry

    International Nuclear Information System (INIS)

    By the method of secondary-ion mass spectrometry the changes of composition of surface layers of some structural alloys (steel 12Kh18N10T, 2Kh13, VT-1) after successive redose treatment for the purpose of decontamination of the NPP first cirquit equipment are studied. It is shown that in acid oxidizing solutions (9% HNO3 + 0.25% KMnO4 + 0.25% K2Cr2O7) on the surface of chromium-containing steels the iron depleted layer, while in alkaline (3% NaOH + 0.5% KMnO4) - chromium depleted and nickel enriched layers. In the course of reduction treatment in the oxalate solution the chromium depleted layers dissolve completely and the iron depleted layers are not almost dissolved, on the surface of stainless and chromium steels oxalate depositions arise in proportion with the chromium depletion degree of initial surface. It is shown that on alkaline permanganate treatment of the model oxide layers of 12Kh18N10T, 48TS, 22K the chromium component of oxide is dissolved and after the treatment in oxalate solution and in a number of other acids - Fe and Ni components

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

    Directory of Open Access Journals (Sweden)

    Song Jun

    2008-06-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

    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

    2013-01-24

    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.

  7. Spatial structure of neuronal receptive field in awake monkey secondary visual cortex (V2).

    Science.gov (United States)

    Liu, Lu; She, Liang; Chen, Ming; Liu, Tianyi; Lu, Haidong D; Dan, Yang; Poo, Mu-ming

    2016-02-16

    Visual processing depends critically on the receptive field (RF) properties of visual neurons. However, comprehensive characterization of RFs beyond the primary visual cortex (V1) remains a challenge. Here we report fine RF structures in secondary visual cortex (V2) of awake macaque monkeys, identified through a projection pursuit regression analysis of neuronal responses to natural images. We found that V2 RFs could be broadly classified as V1-like (typical Gabor-shaped subunits), ultralong (subunits with high aspect ratios), or complex-shaped (subunits with multiple oriented components). Furthermore, single-unit recordings from functional domains identified by intrinsic optical imaging showed that neurons with ultralong RFs were primarily localized within pale stripes, whereas neurons with complex-shaped RFs were more concentrated in thin stripes. Thus, by combining single-unit recording with optical imaging and a computational approach, we identified RF subunits underlying spatial feature selectivity of V2 neurons and demonstrated the functional organization of these RF properties. PMID:26839410

  8. Identification of WD40 repeats by secondary structure-aided profile-profile alignment.

    Science.gov (United States)

    Wang, Chuan; Dong, Xiaobao; Han, Lei; Su, Xiao-Dong; Zhang, Ziding; Li, Jinyan; Song, Jiangning

    2016-06-01

    A WD40 protein typically contains four or more repeats of ~40 residues ended with the Trp-Asp dipeptide, which folds into β-propellers with four β strands in each repeat. They often function as scaffolds for protein-protein interactions and are involved in numerous fundamental biological processes. Despite their important functional role, the "velcro" closure of WD40 propellers and the diversity of WD40 repeats make their identification a difficult task. Here we develop a new WD40 Repeat Recognition method (WDRR), which uses predicted secondary structure information to generate candidate repeat segments, and further employs a profile-profile alignment to identify the correct WD40 repeats from candidate segments. In particular, we design a novel alignment scoring function that combines dot product and BLOSUM62, thereby achieving a great balance of sensitivity and accuracy. Taking advantage of these strategies, WDRR could effectively reduce the false positive rate and accurately identify more remote homologous WD40 repeats with precise repeat boundaries. We further use WDRR to re-annotate the Pfam families in the β-propeller clan (CL0186) and identify a number of WD40 repeat proteins with high confidence across nine model organisms. The WDRR web server and the datasets are available at http://protein.cau.edu.cn/wdrr/. PMID:27021623

  9. The Structure of Educational Costs: Multiproduct Cost Functions for Primary and Secondary Schools in Latin America.

    Science.gov (United States)

    Jimenez, Emmanuel

    1986-01-01

    Relying heavily on equations and tabular data, this paper analyzes the educational cost functions of primary and secondary schooling levels in Latin America. Economies of scale are found for both levels in Bolivian and Paraguayan urban schools; schools combining primary and secondary school services are shown to be less cost effective. (23…

  10. Ebola virus RNA editing depends on the primary editing site sequence and an upstream secondary structure.

    Science.gov (United States)

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

    2013-01-01

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

  11. Ebola virus RNA editing depends on the primary editing site sequence and an upstream secondary structure.

    Directory of Open Access Journals (Sweden)

    Masfique Mehedi

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

  12. Identification and suppression of secondary structures formed from deoxy-oligonucleotides during electrophoresis in denaturing polyacrylamide-gels.

    OpenAIRE

    Frank, R; Müller, D.; Wolff, C.

    1981-01-01

    Nature and stability of secondary structures formed from DNA-fragments during electrophoresis in urea containing polyacrylamide-gels were investigated. Duplices and especially hairpin loops were found to be surprisingly stable. Polyacrylamide-gels containing high concentrations of formamide effectively melt these structures. Such gels will improve nucleotide sequence analysis in regions of dyad symmetry that often cause 'band compressions' under standard electrophoresis conditions.

  13. RNAspa: a shortest path approach for comparative prediction of the secondary structure of ncRNA molecules

    Directory of Open Access Journals (Sweden)

    Michaeli Shulamit

    2007-10-01

    Full Text Available Abstract Background In recent years, RNA molecules that are not translated into proteins (ncRNAs have drawn a great deal of attention, as they were shown to be involved in many cellular functions. One of the most important computational problems regarding ncRNA is to predict the secondary structure of a molecule from its sequence. In particular, we attempted to predict the secondary structure for a set of unaligned ncRNA molecules that are taken from the same family, and thus presumably have a similar structure. Results We developed the RNAspa program, which comparatively predicts the secondary structure for a set of ncRNA molecules in linear time in the number of molecules. We observed that in a list of several hundred suboptimal minimal free energy (MFE predictions, as provided by the RNAsubopt program of the Vienna package, it is likely that at least one suggested structure would be similar to the true, correct one. The suboptimal solutions of each molecule are represented as a layer of vertices in a graph. The shortest path in this graph is the basis for structural predictions for the molecule. We also show that RNA secondary structures can be compared very rapidly by a simple string Edit-Distance algorithm with a minimal loss of accuracy. We show that this approach allows us to more deeply explore the suboptimal structure space. Conclusion The algorithm was tested on three datasets which include several ncRNA families taken from the Rfam database. These datasets allowed for comparison of the algorithm with other methods. In these tests, RNAspa performed better than four other programs.

  14. Neural Network Based on GA-BP Algorithm and its Application in the Protein Secondary Structure Prediction

    Institute of Scientific and Technical Information of China (English)

    YANG Yang; LI Kai-yang

    2006-01-01

    The advantages and disadvantages of genetic algorithm and BP algorithm are introduced. A neural network based on GA-BP algorithm is proposed and applied in the prediction of protein secondary structure, which combines the advantages of BP and GA. The prediction and training on the neural network are made respectively based on 4 structure classifications of protein so as to get higher rate of predication-the highest prediction rate 75.65%, the average prediction rate 65.04%.

  15. Fold classification based on secondary structure – how much is gained by including loop topology?

    Directory of Open Access Journals (Sweden)

    Przytycka Teresa

    2006-03-01

    Full Text Available Abstract Background It has been proposed that secondary structure information can be used to classify (to some extend protein folds. Since this method utilizes very limited information about the protein structure, it is not surprising that it has a higher error rate than the approaches that use full 3D fold description. On the other hand, the comparing of 3D protein structures is computing intensive. This raises the question to what extend the error rate can be decreased with each new source of information, especially if the new information can still be used with simple alignment algorithms. We consider the question whether the information about closed loops can improve the accuracy of this approach. While the answer appears to be obvious, we had to overcome two challenges. First, how to code and to compare topological information in such a way that local alignment of strings will properly identify similar structures. Second, how to properly measure the effect of new information in a large data sample. We investigate alternative ways of computing and presenting this information. Results We used the set of beta proteins with at most 30% pairwise identity to test the approach; local alignment scores were used to build a tree of clusters which was evaluated using a new log-odd cluster scoring function. In particular, we derive a closed formula for the probability of obtaining a given score by chance.Parameters of local alignment function were optimized using a genetic algorithm. Of 81 folds that had more than one representative in our data set, log-odds scores registered significantly better clustering in 27 cases and significantly worse in 6 cases, and small differences in the remaining cases. Various notions of the significant change or average change were considered and tried, and the results were all pointing in the same direction. Conclusion We found that, on average, properly presented information about the loop topology improves noticeably

  16. Probing secondary structures of end-capped tripeptide, BOC–Phe–Aib–Leu–OMe by combined study of infrared spectroscopy and quantum chemistry calculation

    International Nuclear Information System (INIS)

    Graphical abstract: Our analysis reveals two secondary structures of BOC–Phe–Aib–Leu–OMe in CCl4 solution, which are largely different from that present in solid crystal of the tripeptide. The figure shows the curve fitting of the amide-I spectral profile of the tripeptide in 0.006 M CCl4 solution at room temperature by voigt band shapes (right). Set 1 (green) corresponds to the amide-I transitions of secondary structure-1, and Set 2 (blue) corresponds to similar transitions of secondary structure-2. Highlights: ► Probed secondary structures of BOC–Phe–Aib–Leu–OMe in CCl4 solution and solid state. ► FTIR spectroscopy and quantum chemistry computations are used in the study. ► Study reveals largely different secondary structures in solid and solution phases. ► A β-turn structure in solid crystal, whereas the solution contains γ-turns. - Abstract: We report conformational analysis of an end-protected tripeptide, BOC–Phe–Aib–Leu–OMe in CCl4 solution and solid crystal at room temperature by infrared spectroscopy and quantum chemistry calculation. The measured spectra in those physical conditions appear different, which has been attributed to different secondary structures of the peptide in the two phases. Our analysis reveals that the peptide has only one secondary structure in the crystal, but in the solution there are two different secondary structures. While the spectrum in solution shows excellent correspondence with the superposition of predicted spectra of the two most favored gas-phase secondary structures, the spectrum of crystal shows best correspondence with the predicted spectrum of a relatively higher energy (∼6 kcal/mol) secondary structure. However, the latter in crystal can gain maximum stability by intermolecular hydrogen bonding. The secondary structure of the peptide in crystal that we have deduced agrees nicely with the one suggested by X-ray crystallographic study.

  17. Analysis of energy-based algorithms for RNA secondary structure prediction

    Directory of Open Access Journals (Sweden)

    Hajiaghayi Monir

    2012-02-01

    Full Text Available Abstract Background RNA molecules play critical roles in the cells of organisms, including roles in gene regulation, catalysis, and synthesis of proteins. Since RNA function depends in large part on its folded structures, much effort has been invested in developing accurate methods for prediction of RNA secondary structure from the base sequence. Minimum free energy (MFE predictions are widely used, based on nearest neighbor thermodynamic parameters of Mathews, Turner et al. or those of Andronescu et al. Some recently proposed alternatives that leverage partition function calculations find the structure with maximum expected accuracy (MEA or pseudo-expected accuracy (pseudo-MEA methods. Advances in prediction methods are typically benchmarked using sensitivity, positive predictive value and their harmonic mean, namely F-measure, on datasets of known reference structures. Since such benchmarks document progress in improving accuracy of computational prediction methods, it is important to understand how measures of accuracy vary as a function of the reference datasets and whether advances in algorithms or thermodynamic parameters yield statistically significant improvements. Our work advances such understanding for the MFE and (pseudo-MEA-based methods, with respect to the latest datasets and energy parameters. Results We present three main findings. First, using the bootstrap percentile method, we show that the average F-measure accuracy of the MFE and (pseudo-MEA-based algorithms, as measured on our largest datasets with over 2000 RNAs from diverse families, is a reliable estimate (within a 2% range with high confidence of the accuracy of a population of RNA molecules represented by this set. However, average accuracy on smaller classes of RNAs such as a class of 89 Group I introns used previously in benchmarking algorithm accuracy is not reliable enough to draw meaningful conclusions about the relative merits of the MFE and MEA-based algorithms

  18. Prediction of beta-turns at over 80% accuracy based on an ensemble of predicted secondary structures and multiple alignments

    Directory of Open Access Journals (Sweden)

    Kurgan Lukasz

    2008-10-01

    Full Text Available Abstract Background β-turn is a secondary protein structure type that plays significant role in protein folding, stability, and molecular recognition. To date, several methods for prediction of β-turns from protein sequences were developed, but they are characterized by relatively poor prediction quality. The novelty of the proposed sequence-based β-turn predictor stems from the usage of a window based information extracted from four predicted three-state secondary structures, which together with a selected set of position specific scoring matrix (PSSM values serve as an input to the support vector machine (SVM predictor. Results We show that (1 all four predicted secondary structures are useful; (2 the most useful information extracted from the predicted secondary structure includes the structure of the predicted residue, secondary structure content in a window around the predicted residue, and features that indicate whether the predicted residue is inside a secondary structure segment; (3 the PSSM values of Asn, Asp, Gly, Ile, Leu, Met, Pro, and Val were among the top ranked features, which corroborates with recent studies. The Asn, Asp, Gly, and Pro indicate potential β-turns, while the remaining four amino acids are useful to predict non-β-turns. Empirical evaluation using three nonredundant datasets shows favorable Qtotal, Qpredicted and MCC values when compared with over a dozen of modern competing methods. Our method is the first to break the 80% Qtotal barrier and achieves Qtotal = 80.9%, MCC = 0.47, and Qpredicted higher by over 6% when compared with the second best method. We use feature selection to reduce the dimensionality of the feature vector used as the input for the proposed prediction method. The applied feature set is smaller by 86, 62 and 37% when compared with the second and two third-best (with respect to MCC competing methods, respectively. Conclusion Experiments show that the proposed method constitutes an

  19. On the control of secondary carbanion structure utilising ligand effects during directed metallation

    Directory of Open Access Journals (Sweden)

    Andrew E. H. Wheatley

    2012-01-01

    Full Text Available N,N-Diisopropyl-2-propylbenzamide 6-H undergoes lateral deprotonation by t-BuLi in the presence of the Lewis base PMDTA (N,N,N′,N″,N″-pentamethyldiethylenetriamine to give a benzyllithium 6-Lil·PMDTA that incorporates a trigonal planar secondary carbanion. In the solid state, the amide directing group and the PMDTA additive work together to abstract the metal ion from the deprotonated α-C of the propyl group (4.107(4 Å. A short distance of 1.376(3 Å is observed between the deprotonated carbon centre and a planar aromatic system that shows a pattern of bond lengths which contrasts with that reported for related tertiary carbanion systems. Analogous benzylic deprotonation is seen if 6-H is treated with t-BuLi in the presence of diglyme to give 6-Lil·DGME. X-ray crystallography now shows that the metal ion more closely approaches the tertiary carbanion (2.418(6 Å but that the planarity of the deprotonated carbon centre and the bonding pattern in the organic anion seen in the PMDTA complex are retained. DFT analysis corroborates both the short distance between aromatic ring and carbanion centre and the unperturbed nature of aromaticity in 6-Lil·L (L = Lewis base. The observation of two structure-types for the carbanion in solution is explained theoretically and by NMR spectroscopy in terms of cis and trans isomerism imparted by partial double bond character in the arene–(α-C bond.

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

    Science.gov (United States)

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

    2003-12-01

    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

  1. Reduced Dimensionality (4,3)D-hnCOCANH Experiment: An Efficient Backbone Assignment tool for NMR studies of Proteins

    CERN Document Server

    Kumar, Dinesh

    2013-01-01

    Sequence specific resonance assignment and secondary structure determination of proteins form the basis for variety of structural and functional proteomics studies by NMR. In this context, an efficient standalone method for rapid assignment of backbone (1H, 15N, 13Ca and 13C') resonances and secondary structure determination of proteins has been presented here. Compared to currently available strategies used for the purpose, the method employs only a single reduced dimensionality (RD) experiment -(4,3)D-hnCOCANH and exploits the linear combinations of backbone (13Ca and 13C') chemical shifts to achieve a dispersion relatively better compared to those of individual chemical shifts (see the text) for efficient and rapid data analysis. Further, the experiment leads to the spectrum with direct distinction of self (intra-residue) and sequential (inter-residue) carbon correlation peaks; these appear opposite in signs and therefore can easily be discriminated without using an additional complementary experiment. On ...

  2. The Response of Greek Key Proteins to Changes in Connectivity Depends on the Nature of Their Secondary Structure

    Science.gov (United States)

    Kemplen, Katherine R.; De Sancho, David; Clarke, Jane

    2015-01-01

    What governs the balance between connectivity and topology in regulating the mechanism of protein folding? We use circular permutation to vary the order of the helices in the all-α Greek key protein FADD (Fas-associated death domain) to investigate this question. Unlike all-β Greek key proteins, where changes in the order of secondary structure cause a shift in the folding nucleus, the position of the nucleus in FADD is unchanged, even when permutation reduces the complexity significantly. We suggest that this is because local helical contacts are so dominant that permutation has little effect on the entropic cost of forming the folding nucleus whereas, in all-β Greek key proteins, all interactions in the nucleus are long range. Thus, the type of secondary structure modulates the sensitivity of proteins to changes in connectivity. PMID:25861761

  3. Kohonen map as a visualization tool for the analysis of protein sequences: multiple alignments, domains and segments of secondary structures.

    Science.gov (United States)

    Hanke, J; Reich, J G

    1996-12-01

    The method of Kohonen maps, a special form of neural networks, was applied as a visualization tool for the analysis of protein sequence similarity. The procedure converts sequence (domains, aligned sequences, segments of secondary structure) into a characteristic signal matrix. This conversion depends on the property or replacement score vector selected by the user. Similar sequences have small distance in the signal space. The trained Kohonen network is functionally equivalent to an unsupervised non-linear cluster analyzer. Protein families, or aligned sequences, or segments of similar secondary structure, aggregate as clusters, and their proximity may be inspected on a color screen or on paper. Pull-down menus permit access to background information in the established text-oriented way. PMID:9021261

  4. Intrusive growth of primary and secondary phloem fibres in hemp stem determines fibre-bundle formation and structure.

    Science.gov (United States)

    Snegireva, Anastasia; Chernova, Tatyana; Ageeva, Marina; Lev-Yadun, Simcha; Gorshkova, Tatyana

    2015-01-01

    Plant fibres-cells with important mechanical functions and a widely used raw material-are usually identified in microscopic sections only after reaching a significant length or after developing a thickened cell wall. We characterized the early developmental stages of hemp (Cannabis sativa) stem phloem fibres, both primary (originating from the procambium) and secondary (originating in the cambium), when they still had only a primary cell wall. We gave a major emphasis to the role of intrusive elongation, the specific type of plant cell growth by which fibres commonly attain large cell length. We could identify primary phloem fibres at a distance of only 1.2-1.5 mm from the shoot apical meristem when they grew symplastically with the surrounding tissues. Half a millimeter further downwards along the stem, fibres began their intrusive elongation, which led to a sharp increase in fibre numbers visible within the stem cross-sections. The intrusive elongation of primary phloem fibres was completed within the several distal centimetres of the growing stem, before the onset of their secondary cell wall formation. The formation of secondary phloem fibres started long after the beginning of secondary xylem formation. Our data indicate that only a small portion of the fusiform cambial initials (<10 %) give rise directly or via their derivatives to secondary phloem fibres. The key determinant of final bundle structure, both for primary and secondary phloem fibres, is intrusive growth. Through bi-directional elongation, fibres join other fibres initiated individually in other stem levels, thus forming the bundles. Our results provide the specific developmental basis for further biochemical and molecular-genetic studies of phloem fibre development in hemp, but may be applied to many other species. PMID:26019229

  5. Conservation of RNA secondary structures in two intron families including mitochondrial-, chloroplast- and nuclear-encoded members.

    OpenAIRE

    Michel, F; Dujon, B

    1983-01-01

    Two families of fungal mitochondrial introns that include all known sequences have been recognized. These families are now extended to incorporate a plant mitochondrial intron and several introns in chloroplast- and nuclear-encoded rRNA and tRNA precursors. Members of the same family share distinctive sequence stretches and a number of potential RNA secondary structures that would bring these stretches and the intron-exon junctions into relatively close proximity. Using several of these intro...

  6. Forest structure and species diversity of secondary forest after cultivation in relation to various sources at lower northern Thailand

    OpenAIRE

    C. Podong; R. Poolsiri

    2013-01-01

    The purpose of this study was to explore the characteristic of structure, species composition and species diversity in secondary mixed deciduous forest at Thung Salaeng Luang National Park, Lower North of Thailand. This vertical stratification of the tree canopy can affect the growth of young trees on the ground surface, especially that of saplings and seedlings. Ground species can establish themselves very quickly when the light intensity is high enough and especially when the light can pene...

  7. INFLUENCE OF MOLECULAR STRUCTURES OF SECONDARY AMINE TERMINATED POLY(ESTER-AMINE)S ON THE CURING PERFORMANCE WITH EPOXY RESIN

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    Five secondary amine terminated poly(ester-amine)s (defined as PEA) with controlled molecular structures were synthesized through reacting excessive piperazine with phthalicdiglycol diacrylate (PDDA) and 1,1,1-trimethylolpropane triacrylate (TMPTA) at a constant secondary amine/acrylate group ratio of 1.5/1 and at different PDDA/TMPTA molar ratios.Both IR and 1H-NMR spectra indicated that all acrylate groups were consumed in the reaction, based on which the structural parameters were calculated from the 1H-NMR spectra. With decreasing PDDA/TMPTA ratio, the content of secondary amine, degree of branching, molecular weight, Tg and Td increased accordingly. These polymers were further used as both crosslinkers and flexibilizers for a linear epoxy resin E51 to form cured films under ambient condition, The gel content,relative hardness and Tg of the resulting films increased as PEA molecules changed from linear to highly branching structures. Due to the flexibility of PEA molecules, all the films possessed excellent mechanical performance.

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

    Science.gov (United States)

    Zhao, Jian-Hua; Liu, Hsuan-Liang

    2006-03-01

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

  9. Depletion of phosphatidylglycerol head-group induces changes in oxygen evolution and protein secondary structures of photosystemⅡ

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    The techniques of oxygen electrode polarography and Fourier transform infrared (FT-IR) spectroscopy were employed to explore the roles of polar head-group of phosphatidylglycerol (PG) molecules in the functional and structural aspects of photosystemⅡ(PSⅡ) through enzymatic approach. It was shown that the depletion of PG by treatment of phospholipase C (PLC) on PSⅡ particles caused the inhibition of oxygen evolving activity in PSⅡ. This effect also gave rise to changes in the protein secondary structures of PSⅡ, that is, an increase in α-helical conformation which is compensated by the loss of β-strand structures. It revealed that the head-group of PG molecules plays an important structural role in the maintenance of normal structure of PSⅡ proteins, which is required to maintain the appropriate physiological activity of the PSⅡ complex such as the oxygen evolving activity. It is suggested that there most probably exist hydrogen-bonding interactions between PG molecules and PSⅡ proteins.

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

    Czech Academy of Sciences Publication Activity Database

    Uhlík, O.; Musilová, L.; Rídl, Jakub; Hroudová, Miluše; Vlček, Čestmír; Koubek, J.; Holečková, M.; Mackova, M.; Macek, T.

    2013-01-01

    Roč. 97, č. 20 (2013), s. 9245-9256. ISSN 0175-7598 Grant ostatní: EK(XE) 265946; GA MŠk(CZ) ME10041 Institutional support: RVO:68378050 Keywords : plant secondary metabolites (PSM) * bacterial community * metabolic activity * bioremediation * pyrosequencing Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 3.811, year: 2013

  11. Primary and secondary structure of 5.8S rRNA from the silkgland of Bombyx mori.

    OpenAIRE

    Fujiwara, H.; Kawata, Y.; H. Ishikawa

    1982-01-01

    Nucleotide sequence of 5.8S rRNA of the silkworm, Bombyx mori has been determined by gel sequencing methods. The 5.8S rRNA was the longest so far reported, with the 5'-terminal sequence several nucleotides longer than those of the other organisms. Upon constructing the secondary structure in accordance with the "burp gun" model (12), the Bombyx 5.8S rRNA formed a wide-open "muzzle" due to several unpaired bases at the ends. The overall structure also appeared less stable with less G . C pairs...

  12. Simulation of unsteady state performance of a secondary air system by the 1D-3D-Structure coupled method

    Science.gov (United States)

    Wu, Hong; Li, Peng; Li, Yulong

    2016-02-01

    This paper describes the calculation method for unsteady state conditions in the secondary air systems in gas turbines. The 1D-3D-Structure coupled method was applied. A 1D code was used to model the standard components that have typical geometric characteristics. Their flow and heat transfer were described by empirical correlations based on experimental data or CFD calculations. A 3D code was used to model the non-standard components that cannot be described by typical geometric languages, while a finite element analysis was carried out to compute the structural deformation and heat conduction at certain important positions. These codes were coupled through their interfaces. Thus, the changes in heat transfer and structure and their interactions caused by exterior disturbances can be reflected. The results of the coupling method in an unsteady state showed an apparent deviation from the existing data, while the results in the steady state were highly consistent with the existing data. The difference in the results in the unsteady state was caused primarily by structural deformation that cannot be predicted by the 1D method. Thus, in order to obtain the unsteady state performance of a secondary air system more accurately and efficiently, the 1D-3D-Structure coupled method should be used.

  13. Determining the Secondary Structure of Membrane Proteins and Peptides Via Electron Spin Echo Envelope Modulation (ESEEM) Spectroscopy.

    Science.gov (United States)

    Liu, Lishan; Mayo, Daniel J; Sahu, Indra D; Zhou, Andy; Zhang, Rongfu; McCarrick, Robert M; Lorigan, Gary A

    2015-01-01

    Revealing detailed structural and dynamic information of membrane embedded or associated proteins is challenging due to their hydrophobic nature which makes NMR and X-ray crystallographic studies challenging or impossible. Electron paramagnetic resonance (EPR) has emerged as a powerful technique to provide essential structural and dynamic information for membrane proteins with no size limitations in membrane systems which mimic their natural lipid bilayer environment. Therefore, tremendous efforts have been devoted toward the development and application of EPR spectroscopic techniques to study the structure of biological systems such as membrane proteins and peptides. This chapter introduces a novel approach established and developed in the Lorigan lab to investigate membrane protein and peptide local secondary structures utilizing the pulsed EPR technique electron spin echo envelope modulation (ESEEM) spectroscopy. Detailed sample preparation strategies in model membrane protein systems and the experimental setup are described. Also, the ability of this approach to identify local secondary structure of membrane proteins and peptides with unprecedented efficiency is demonstrated in model systems. Finally, applications and further developments of this ESEEM approach for probing larger size membrane proteins produced by overexpression systems are discussed. PMID:26477255

  14. Interactive Assignments for Online Students

    Directory of Open Access Journals (Sweden)

    Pam Lowry

    2009-04-01

    Full Text Available Students can experience first hand through interactive assignments what is involved in teaching an online course. Most students develop a whole new appreciation for the student learning process. Faculty are beginning to realize that online instruction is more than a series of readings posted to a course management system. This paper summarizes the faculty member's instructional strategies involved when creating student interaction assignments. The paper also summarizes the assignments, discussion board, and trends in education from the student's perspective. In summary, it concludes with the faculty's overall perspective concerning these assignments and how the assignments could be more effective for the student.

  15. Comparison of and limits of accuracy for statistical analyses of vibrational and electronic circular dichroism spectra in terms of correlations to and predictions of protein secondary structure.

    OpenAIRE

    Pancoska, P.; Bitto, E.; Janota, V.; Urbanova, M.; Gupta, V P; Keiderling, T A

    1995-01-01

    This work provides a systematic comparison of vibrational CD (VCD) and electronic CD (ECD) methods for spectral prediction of secondary structure. The VCD and ECD data are simplified to a small set of spectral parameters using the principal component method of factor analysis (PC/FA). Regression fits of these parameters are made to the X-ray-determined fractional components (FC) of secondary structure. Predictive capability is determined by computing structures for proteins sequentially left ...

  16. A new online secondary path modeling method for adaptive active structure vibration control

    International Nuclear Information System (INIS)

    This paper proposes a new variable step size FXLMS algorithm with an auxiliary noise power scheduling strategy for online secondary path modeling. The step size for the secondary path modeling filter and the gain of auxiliary noise are varied in accordance with the parameters available directly. The proposed method has a low computational complexity. Computer simulations show that an active vibration control system with the proposed method gives much better vibration attenuation and modeling accuracy at a faster convergence rate than existing methods. National Instruments’ CompactRIO is used as an embedded processor to control simply supported beam vibration. Experimental results indicate that the vibration of the beam has been effectively attenuated. (papers)

  17. Structural effects of liana presence in secondary tropical dry forests using ground LiDAR

    OpenAIRE

    Sánchez-Azofeifa, A.; Portillo-Quintero, C.; Durán, S. M.

    2015-01-01

    Lianas, woody vines, are a key component of tropical forest because they may reduce carbon storage potential. Lianas are increasing in density and biomass in tropical forests, but it is unknown what the potential consequences of these increases are for forest dynamics. Lianas may proliferate in disturbed areas, such as regenerating forests, but little is known about the role of lianas in secondary succession. In this study, we evaluated the potential of the ground LiDAR to d...

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

    Directory of Open Access Journals (Sweden)

    Jane C. Quinn

    2014-01-01

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

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

    OpenAIRE

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

    2014-01-01

    Photosensitivity in animals is defined as a severe dermatitis that results from a heightened reactivity of skin cells and associated dermal tissues upon their exposure to sunlight, following ingestion or contact with UV reactive secondary plant products. Photosensitivity occurs in animal cells as a reaction that is mediated by a light absorbing molecule, specifically in this case a plant-produced metabolite that is heterocyclic or polyphenolic. In sensitive animals, this reaction is most seve...

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

    Science.gov (United States)

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

    2014-01-01

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

  1. Spectral editing of two-dimensional magic-angle-spinning solid-state NMR spectra for protein resonance assignment and structure determination

    International Nuclear Information System (INIS)

    Several techniques for spectral editing of 2D 13C–13C correlation NMR of proteins are introduced. They greatly reduce the spectral overlap for five common amino acid types, thus simplifying spectral assignment and conformational analysis. The carboxyl (COO) signals of glutamate and aspartate are selected by suppressing the overlapping amide N–CO peaks through 13C–15N dipolar dephasing. The sidechain methine (CH) signals of valine, lecuine, and isoleucine are separated from the overlapping methylene (CH2) signals of long-chain amino acids using a multiple-quantum dipolar transfer technique. Both the COO and CH selection methods take advantage of improved dipolar dephasing by asymmetric rotational-echo double resonance (REDOR), where every other π-pulse is shifted from the center of a rotor period tr by about 0.15 tr. This asymmetry produces a deeper minimum in the REDOR dephasing curve and enables complete suppression of the undesired signals of immobile segments. Residual signals of mobile sidechains are positively identified by dynamics editing using recoupled 13C–1H dipolar dephasing. In all three experiments, the signals of carbons within a three-bond distance from the selected carbons are detected in the second spectral dimension via 13C spin exchange. The efficiencies of these spectral editing techniques range from 60 % for the COO and dynamic selection experiments to 25 % for the CH selection experiment, and are demonstrated on well-characterized model proteins GB1 and ubiquitin.

  2. Spectral editing of two-dimensional magic-angle-spinning solid-state NMR spectra for protein resonance assignment and structure determination

    Energy Technology Data Exchange (ETDEWEB)

    Schmidt-Rohr, K.; Fritzsching, K. J.; Liao, S. Y.; Hong Mei, E-mail: mhong@iastate.edu [Iowa State University, Department of Chemistry and Ames Laboratory (United States)

    2012-12-15

    Several techniques for spectral editing of 2D {sup 13}C-{sup 13}C correlation NMR of proteins are introduced. They greatly reduce the spectral overlap for five common amino acid types, thus simplifying spectral assignment and conformational analysis. The carboxyl (COO) signals of glutamate and aspartate are selected by suppressing the overlapping amide N-CO peaks through {sup 13}C-{sup 15}N dipolar dephasing. The sidechain methine (CH) signals of valine, lecuine, and isoleucine are separated from the overlapping methylene (CH{sub 2}) signals of long-chain amino acids using a multiple-quantum dipolar transfer technique. Both the COO and CH selection methods take advantage of improved dipolar dephasing by asymmetric rotational-echo double resonance (REDOR), where every other {pi}-pulse is shifted from the center of a rotor period t{sub r} by about 0.15 t{sub r}. This asymmetry produces a deeper minimum in the REDOR dephasing curve and enables complete suppression of the undesired signals of immobile segments. Residual signals of mobile sidechains are positively identified by dynamics editing using recoupled {sup 13}C-{sup 1}H dipolar dephasing. In all three experiments, the signals of carbons within a three-bond distance from the selected carbons are detected in the second spectral dimension via {sup 13}C spin exchange. The efficiencies of these spectral editing techniques range from 60 % for the COO and dynamic selection experiments to 25 % for the CH selection experiment, and are demonstrated on well-characterized model proteins GB1 and ubiquitin.

  3. Synonymous codon usage in different protein secondary structural classes of human genes: Implication for increased non-randomness of GC3 rich genes towards protein stability

    Indian Academy of Sciences (India)

    Pamela Mukhopadhyay; Surajit Basak; Tapash Chandra Ghosh

    2007-08-01

    The relationship between the synonymous codon usage and different protein secondary structural classes were investigated using 401 Homo sapiens proteins extracted from Protein Data Bank (PDB). A simple Chi-square test was used to assess the significance of deviation of the observed and expected frequencies of 59 codons at the level of individual synonymous families in the four different protein secondary structural classes. It was observed that synonymous codon families show non-randomness in codon usage in four different secondary structural classes. However, when the genes were classified according to their GC3 levels there was an increase in non-randomness in high GC3 group of genes. The non-randomness in codon usage was further tested among the same protein secondary structures belonging to four different protein folding classes of high GC3 group of genes. The results show that in each of the protein secondary structural unit there exist some synonymous family that shows class specific codonusage pattern. Moreover, there is an increased non-random behaviour of synonymous codons in sheet structure of all secondary structural classes in high GC3 group of genes. Biological implications of these results have been discussed.

  4. New recombinant cyclohexylamine oxidase variants for deracemization of secondary amines by orthogonally assaying designed mutants with structurally diverse substrates

    Science.gov (United States)

    Li, Guangyue; Yao, Peiyuan; Cong, Peiqian; Ren, Jie; Wang, Lei; Feng, Jinhui; Lau, Peter C. K.; Wu, Qiaqing; Zhu, Dunming

    2016-05-01

    To further expand the substrate range of the cyclohexylamine oxidase (CHAO) from Brevibacterium oxydans, a library of diverse mutants was created and assayed toward a group of structurally diverse substrates. Among them, mutants T198A and M226A exhibited enhanced activity relative to wt CHAO for most (S)-enantiomers of primary amines and some secondary amines. While mutants T198I, L199I, L199F, M226I and M226T were more active than wt CHAO toward the primary amines, mutants T198F, L199T, Y321A, Y321T, Y321I and Y321F enhanced the enzyme activity toward the secondary amines. In particular, mutant Y321I displayed an enhanced catalytic efficiency toward 1-(4-methoxybenzyl)-1, 2, 3, 4, 5, 6, 7, 8-octahydroisoquinoline (13). Whereas a double mutant, Y321I/M226T, acted on (S)-N-(prop-2-yn-1-yl)-2, 3-dihydro-1H-inden-1-amine [(S)-8]. Since (R)-8 is an irreversible inhibitor of monoamine oxidase and (S)-13 is an intermediate of dextromethorphan, a cough suppressant drug, deracemizations of 8 and 13 were carried out with crude enzyme extracts of the respective mutants. This resulted in 51% and 78% isolated yields of (R)-8 and (S)-13, respectively, each with high enantiomeric excess (93% and 99% ee). The results demonstrated the application potential of the evolved CHAO mutants in drug synthesis requiring chiral secondary amines.

  5. Electronic Structures and Alloying Behaviors of Ferrite Phases in High Co-Ni Secondary Hardened Martensitic Steels

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    @@The electronic structure of ferrite (tempered martensite phase) in high Co-Ni secondary hardened martensitic steel has been investigated. The local density of states (LDOS) of alloying elements in the steel displays the relationship between solid solubility and the shape of the LDOS. The bond order integral (BOI) between atoms in the steel shows that the directional bonding of the p orbital of Si or C leads to the brittleness of the steel. At last, ∑BOI between atoms demonstrate that C, Co, Mn, Cr, Mo, Si strengthen the alloyed steel through solid-solution effects.

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

    Directory of Open Access Journals (Sweden)

    Wolf Matthias

    2009-12-01

    Full Text Available Abstract 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

  7. Forest structure and species diversity of secondary forest after cultivation in relation to various sources at lower northern Thailand

    Directory of Open Access Journals (Sweden)

    C. Podong

    2013-09-01

    Full Text Available The purpose of this study was to explore the characteristic of structure, species composition and species diversity in secondary mixed deciduous forest at Thung Salaeng Luang National Park, Lower North of Thailand. This vertical stratification of the tree canopy can affect the growth of young trees on the ground surface, especially that of saplings and seedlings. Ground species can establish themselves very quickly when the light intensity is high enough and especially when the light can penetrate directly to the ground during gap formation. The data of tree individuals have served to give insight into the stand density, basal area, and frequency number of DBH class ranges. There were a large number of DBH class ranges but there were low DBH values. The species composition of secondary mixed deciduous forest is low rich and diversity but that is high density. The comparison between secondary mixed deciduous forest at Thung Salaeng Luang National Park and other forest is tree density higher than other forest but number of species is similarity or lower. The dominant species of trees were Haldina cordifolia, Albizia odoratissima and Lagerstroemia duperreana. The IVI values of trees were 132.91, 17.78 and 14.22, respectively. Species diversity compared to other forests,The Fisher's, Shannon-Wiener's index and Simpson's index in these studies are found to be lower than other forests. The size class distribution of trees in secondary mixed deciduous forest is shown to be on L-shape curve, which is high abundance of small trees.

  8. Evolving Networks with Nonlinear Assignment of Weight

    Institute of Scientific and Technical Information of China (English)

    TANG Chao; TANG Yi

    2006-01-01

    We propose a weighted evolving network model in which the underlying topological structure is still driven by the degree according to the preferential attachment rule while the weight assigned to the newly established edges is dependent on the degree in a nonlinear form. By varying the parameter α that controls the function determining the assignment of weight, a wide variety of power-law behaviours of the total weight distributions as well as the diversity of the weight distributions of edges are displayed. Variation of correlation and heterogeneity in the network is illustrated as well.

  9. Laser spectroscopy of UO: Characterization and assignment of states in the 0- to 3-eV range, with a comparison to the electronic structure of ThO

    International Nuclear Information System (INIS)

    Wavelength-resolved fluorescence excitation techniques have been used to record 33 electronic transitions of UO at a resolution of 0.03 cm-1. Nine low-lying electronic states that correlated with either U2+(5 line-integral 37s)O2- or U2+(5 line-integral 27s2)O2- were characterized. With few exceptions, Ω assignments were unambiguously determined from observations of the first lines in at least two rotational branches. Accurate term energies and rotational constants are reported. Deperturbed constants of ωe = 846.5 cm-1 and Re = 1.8383 angstrom have been determined for the ground state of the 5 line-integral 37s configuration, and ωe = 934.9 cm1 and Re = 1.7932 angstrom for states of the 5 line-integral 27s2 configuration. Ligand field theory models were used to analyze the low-energy electronic structure of UO. Ligand field theory calculations were also used in an attempt to provide configurational assignments for the excited states of UO and ThO. Experimentally derived values for ΔB00(nl/n'l') parameters were used to predict the electronic structures of UO and UO+. The energies of 23 electronic configurations of UO, and 19 electronic configurations of UO+, have been calculated. The density distribution of the bound state of UO and UO+ up to their ionization limits were also calculated

  10. Scaffolding students’ assignments

    DEFF Research Database (Denmark)

    Slot, Marie Falkesgaard

    2013-01-01

    learning goals) can help students structure their argumentative and communica-tive learning processes, and how various multimodal representations can give more open-ended learning possibilities for collaboration. The article presents a short introduction of the skills for 21st century learning and defines...

  11. Evaluation of the suitability of free-energy minimization using nearest-neighbor energy parameters for RNA secondary structure prediction

    Directory of Open Access Journals (Sweden)

    Cobaugh Christian W

    2004-08-01

    Full Text Available Abstract Background A detailed understanding of an RNA's correct secondary and tertiary structure is crucial to understanding its function and mechanism in the cell. Free energy minimization with energy parameters based on the nearest-neighbor model and comparative analysis are the primary methods for predicting an RNA's secondary structure from its sequence. Version 3.1 of Mfold has been available since 1999. This version contains an expanded sequence dependence of energy parameters and the ability to incorporate coaxial stacking into free energy calculations. We test Mfold 3.1 by performing the largest and most phylogenetically diverse comparison of rRNA and tRNA structures predicted by comparative analysis and Mfold, and we use the results of our tests on 16S and 23S rRNA sequences to assess the improvement between Mfold 2.3 and Mfold 3.1. Results The average prediction accuracy for a 16S or 23S rRNA sequence with Mfold 3.1 is 41%, while the prediction accuracies for the majority of 16S and 23S rRNA structures tested are between 20% and 60%, with some having less than 20% prediction accuracy. The average prediction accuracy was 71% for 5S rRNA and 69% for tRNA. The majority of the 5S rRNA and tRNA sequences have prediction accuracies greater than 60%. The prediction accuracy of 16S rRNA base-pairs decreases exponentially as the number of nucleotides intervening between the 5' and 3' halves of the base-pair increases. Conclusion Our analysis indicates that the current set of nearest-neighbor energy parameters in conjunction with the Mfold folding algorithm are unable to consistently and reliably predict an RNA's correct secondary structure. For 16S or 23S rRNA structure prediction, Mfold 3.1 offers little improvement over Mfold 2.3. However, the nearest-neighbor energy parameters do work well for shorter RNA sequences such as tRNA or 5S rRNA, or for larger rRNAs when the contact distance between the base-pairs is less than 100 nucleotides.

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

    Directory of Open Access Journals (Sweden)

    Meyer-Lucht Yvonne

    2008-05-01

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

  13. Carbon Policy and Technical Change: Market Structure, Increasing Returns, and Secondary Benefits. Final Report

    Energy Technology Data Exchange (ETDEWEB)

    Peretto, P.; Smith, V. K.

    2001-11-19

    An economic evaluation of the impact of policies intended to control emissions of CO{sub 2} and other ''greenhouse gases'' (GHGS) depends on the net costs of these controls and their distribution throughout the production sectors of developed and developing economics. The answers derived from appraisals of these net costs, in turn, stem from what is assumed about the timing of the controls, the pace of technological change, and any short-term secondary benefits from their control. There have only been a few serious attempts to estimate the economic benefits from the policies associated with such long run outcomes. All of the approaches to date have made fairly strong assumptions or relied on contingent valuation estimates of hypothetical situations.

  14. Mineral Association Changes the Secondary Structure and Dynamics of Murine Amelogenin

    Energy Technology Data Exchange (ETDEWEB)

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

    2013-10-15

    Biomineralization proteins, present during the formation of hard tissues including bones, teeth, egg shells and nacre, result in the exquisite structures and properties of the resulting materials.[1] The structure of these proteins is often implicated in the control of the mineral properties, however very little structural data is available for the bulk of these proteins due to the difficulty in determining structures of immobilized proteins. Solid-state NMR is uniquely suited to the study of the structure of proteins bound to surfaces, demonstrated with the structural and orientation insights provided for the hydroxyapatite mineralization proteins statherin and the amelogenin, LRAP.[2] While these data are some of the only structural data available for this important class of protein, the experiments are often expensive and time consuming, due to the need to prepare and measure samples with isolated spin pairs, and are limited to a size of ~60 residues. In this work, we utilized a combination of 1D and recent 2D[3] solid-state NMR techniques along with a sparsely labelled sample to characterize the structure and dynamics of potential HAP binding residues of the 180 residue enamel protein, amelogenin. Amelogenin nanospheres and mineral bound amelogenin were investigated and a shift from unstructured to β-sheet structure was observed, along with a decrease in protein flexibility. This work provides the first molecular level structure and dynamic information of full-length amelogenin on the surface of hydroxyapatite (HAP) and within nanospheres, and demonstrates the ability to evaluate structural characteristics of large biomineralization proteins bound to their physiologically relevant surface. The research was performed at the Pacific Northwest National Laboratory (PNNL), a facility operated by Battelle for the U.S. Department of Energy, with a portion of it performed at the W.R. Wiley Environmental Molecular Sciences Laboratory (EMSL), a national scientific user

  15. 76 FR 55880 - Recording Assignments

    Science.gov (United States)

    2011-09-09

    ..., depending on the date they were recorded. The public may also search patent and trademark assignment... United States Patent and Trademark Office Recording Assignments ACTION: Proposed collection; comment request. SUMMARY: The United States Patent and Trademark Office (USPTO), as part of its continuing...

  16. Community structure, life histories and secondary production of stoneflies in two small mountain streams with different degree of forest cover

    Directory of Open Access Journals (Sweden)

    Pavel Beracko

    2015-10-01

    Full Text Available Our study examines community structure and nymphal biology (life cycles and secondary production of stoneflies in two adjacent mountain streams with different degree of forest cover in the Prosiečanka River Basin (Chočské Vrchy Mts., West Carpathians. One of the streams has non-forested catchment, converted to meadows and pastures, while the other one has catchment with 60% covered by spruce forest. Differences in forest cover and in thermal regime of the streams were reflected by the difference of stonefly communities at their structural and functional level. Species Nemoura cinerea and Leuctra aurita created stonefly assemblage in non-forested stream, whereas Nemoura cinerea also occurred in naturally forested stream together with species Leuctra armata, Leuctra nigra, Leuctra prima, Siphonoperla neglecta and Arcynopteryx dichroa. All examined species had maximally annual life cycle and in eudominant species Nemoura cinerea one month shift was found in nymphal hatching and adult emergence between streams. Total secondary production of stoneflies in undisturbed stream (126.46 mg DW m-2 y-1 was more than two times higher than the production in non-forested stream (47.39 mg DW m-2 y-1. 

  17. Dopamine agonist suppression of rapid-eye-movement sleep is secondary to sleep suppression mediated via limbic structures

    International Nuclear Information System (INIS)

    The effects of pergolide, a direct dopamine receptor agonist, on sleep and wakefulness, motor behavior and 3H-spiperone specific binding in limbic structures and striatum in rats was studied. The results show that pergolide induced a biphasic dose effect, with high doses increasing wakefulness and suppressing sleep while low dose decreased wakefulness, but increased sleep. It was shown that pergolide-induced sleep suppression was blocked by α-glupenthixol and pimozide, two dopamine receptor antagonists. It was further shown that pergolide merely delayed the rebound resulting from rapid-eye-movement (REM) sleep deprivation, that dopamine receptors stimulation had no direct effect on the period, phase or amplitude of the circadian rhythm of REM sleep propensity and that there was no alteration in the coupling of REM sleep episodes with S2 episodes. Rapid-eye-movement sleep deprivation resulted in increased sensitivity to the pergolide-induced wakefulness stimulation and sleep suppression and pergolide-induced motor behaviors of locomotion and head bobbing. 3H-spiperone specific binding to dopamine receptors was shown to be altered by REM sleep deprivation in the subcortical limbic structures. It is concluded that the REM sleep suppressing action of dopamine receptor stimulation is secondary to sleep suppression per se and not secondary to a unique effect on the REM sleep. Further, it is suggested that the wakefulness stimulating action of dopamine receptor agonists is mediated by activation of the dopamine receptors in the terminal areas of the mesolimbocortical dopamine projection system

  18. RNAsnp: efficient detection of local RNA secondary structure changes induced by SNPs

    DEFF Research Database (Denmark)

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

    2013-01-01

    Structural characteristics are essential for the functioning of many noncoding RNAs and cis-regulatory elements of mRNAs. SNPs may disrupt these structures, interfere with their molecular function, and hence cause a phenotypic effect. RNA folding algorithms can provide detailed insights into stru...

  19. Optimal Estimation Retrievals of the Atmospheric Structure and Composition of HD 189733b from Secondary Eclipse Spectroscopy

    CERN Document Server

    Lee, Jae-Min; Irwin, Patrick G J

    2011-01-01

    Recent spectroscopic observations of transiting hot Jupiters have permitted the derivation of the thermal structure and molecular abundances of H2O, CO2, CO, and CH4 in these extreme atmospheres. Here, for the first time, we apply the technique of optimal estimation to determine the thermal structure and composition of an exoplanet by solving the inverse problem. The development of a suite of radiative transfer and retrieval tools for exoplanet atmospheres is described, building upon a retrieval algorithm which is extensively used in the study of our own solar system. First, we discuss the plausibility of detection of different molecules in the dayside atmosphere of HD 189733b and the best-fitting spectrum retrieved from all publicly available sets of secondary eclipse observations between 1.45 and 24 {\\mu}m. Additionally, we use contribution functions to assess the vertical sensitivity of the emission spectrum to temperatures and molecular composition. Over the altitudes probed by the contribution functions,...

  20. Optimizations of force-field parameters for protein systems with the secondary-structure stability and instability

    CERN Document Server

    Sakae, Yoshitake

    2013-01-01

    We propose a novel method for refining force-field parameters of protein systems. In this method, the agreement of the secondary-structure stability and instability between the protein conformations obtained by experiments and those obtained by molecular dynamics simulations is used as a criterion for the optimization of force-field parameters. As an example of the applications of the present method, we refined the force-field parameter set of the AMBER ff99SB force field by searching the torsion-energy parameter spaces of $\\psi$ (N-C$^{\\alpha}$-C-N) and $\\zeta$ (C$^{\\beta}$-C$^{\\alpha}$-C-N) of the backbone dihedral angles. We then performed folding simulations of $\\alpha$-helical and $\\beta$-hairpin peptides, using the optimized force field. The results showed that the new force-field parameters gave structures more consistent with the experimental implications than the original AMBER ff99SB force field.

  1. Peripheral vagus nerve stimulation significantly affects lipid composition and protein secondary structure within dopamine-related brain regions in rats.

    Science.gov (United States)

    Surowka, Artur Dawid; Krygowska-Wajs, Anna; Ziomber, Agata; Thor, Piotr; Chrobak, Adrian Andrzej; Szczerbowska-Boruchowska, Magdalena

    2015-06-01

    Recent immunohistochemical studies point to the dorsal motor nucleus of the vagus nerve as the point of departure of initial changes which are related to the gradual pathological developments in the dopaminergic system. In the light of current investigations, it is likely that biochemical changes within the peripheral nervous system may influence the physiology of the dopaminergic system, suggesting a putative role for it in the development of neurodegenerative disorders. By using Fourier transform infrared microspectroscopy, coupled with statistical analysis, we examined the effect of chronic, unilateral electrical vagus nerve stimulation on changes in lipid composition and in protein secondary structure within dopamine-related brain structures in rats. It was found that the chronic vagal nerve stimulation strongly affects the chain length of fatty acids within the ventral tegmental area, nucleus accumbens, substantia nigra, striatum, dorsal motor nucleus of vagus and the motor cortex. In particular, the level of lipid unsaturation was found significantly increasing in the ventral tegmental area, substantia nigra and motor cortex as a result of vagal nerve stimulation. When it comes to changes in protein secondary structure, we could see that the mesolimbic, mesocortical and nigrostriatal dopaminergic pathways are particularly affected by vagus nerve stimulation. This is due to the co-occurrence of statistically significant changes in the content of non-ordered structure components, alpha helices, beta sheets, and the total area of Amide I. Macromolecular changes caused by peripheral vagus nerve stimulation may highlight a potential connection between the gastrointestinal system and the central nervous system in rat during the development of neurodegenerative disorders. PMID:25893743

  2. Fast collapse but slow formation of secondary structure elements in the refolding transition of E. coli adenylate kinase.

    Science.gov (United States)

    Ratner, V; Amir, D; Kahana, E; Haas, E

    2005-09-23

    The various models proposed for protein folding transition differ in their order of appearance of the basic steps during this process. In this study, steady state and time-resolved dynamic non-radiative excitation energy transfer (FRET and trFRET) combined with site specific labeling experiments were applied in order to characterize the initial transient ensemble of Escherichia coli adenylate kinase (AK) molecules upon shifting conditions from those favoring denaturation to refolding and from folding to denaturing. Three sets of labeled AK mutants were prepared, which were designed to probe the equilibrium and transient distributions of intramolecular segmental end-to-end distances. A 176 residue section (residues 28-203), which spans most of the 214 residue molecule, and two short secondary structure chain segments including an alpha-helix (residues 169-188) and a predominantly beta-strand region (residues 188-203), were labeled. Upon fast change of conditions from denaturing to folding, the end-to-end distance of the 176 residue chain section showed an immediate collapse to a mean value of 26 A. Under the same conditions, the two short secondary structure elements did not respond to this shift within the first ten milliseconds, and retained the characteristics of a fully unfolded state. Within the first 10 ms after changes of the solvent from folding to denaturing, only minor changes were observed at the local environments of residues 203 and 169. The response of these same local environments to the shift of conditions from denaturing to folding occurred within the dead time of the mixing device. Thus, the response of the CORE domain of AK to fast transfer from folding to unfolding conditions is slow at all three conformational levels that were probed, and for at least a few milliseconds the ensemble of folded molecules is maintained under unfolding conditions. A different order of the changes was observed upon initiation of refolding. The AK molecules undergo

  3. Extending DFT-based genetic algorithms by atom-to-place re-assignment via perturbation theory: A systematic and unbiased approach to structures of mixed-metallic clusters

    International Nuclear Information System (INIS)

    Energy surfaces of metal clusters usually show a large variety of local minima. For homo-metallic species the energetically lowest can be found reliably with genetic algorithms, in combination with density functional theory without system-specific parameters. For mixed-metallic clusters this is much more difficult, as for a given arrangement of nuclei one has to find additionally the best of many possibilities of assigning different metal types to the individual positions. In the framework of electronic structure methods this second issue is treatable at comparably low cost at least for elements with similar atomic number by means of first-order perturbation theory, as shown previously [F. Weigend, C. Schrodt, and R. Ahlrichs, J. Chem. Phys. 121, 10380 (2004)]. In the present contribution the extension of a genetic algorithm with the re-assignment of atom types to atom sites is proposed and tested for the search of the global minima of PtHf12 and [LaPb7Bi7]4−. For both cases the (putative) global minimum is reliably found with the extended technique, which is not the case for the “pure” genetic algorithm

  4. Extending DFT-based genetic algorithms by atom-to-place re-assignment via perturbation theory: A systematic and unbiased approach to structures of mixed-metallic clusters

    Science.gov (United States)

    Weigend, Florian

    2014-10-01

    Energy surfaces of metal clusters usually show a large variety of local minima. For homo-metallic species the energetically lowest can be found reliably with genetic algorithms, in combination with density functional theory without system-specific parameters. For mixed-metallic clusters this is much more difficult, as for a given arrangement of nuclei one has to find additionally the best of many possibilities of assigning different metal types to the individual positions. In the framework of electronic structure methods this second issue is treatable at comparably low cost at least for elements with similar atomic number by means of first-order perturbation theory, as shown previously [F. Weigend, C. Schrodt, and R. Ahlrichs, J. Chem. Phys. 121, 10380 (2004)]. In the present contribution the extension of a genetic algorithm with the re-assignment of atom types to atom sites is proposed and tested for the search of the global minima of PtHf12 and [LaPb7Bi7]4-. For both cases the (putative) global minimum is reliably found with the extended technique, which is not the case for the "pure" genetic algorithm.

  5. Teaching through Interactions in Secondary School Classrooms: Revisiting the Factor Structure and Practical Application of the Classroom Assessment Scoring System-­-Secondary

    Science.gov (United States)

    Hafen, Christopher A.; Hamre, Bridget K.; Allen, Joseph P.; Bell, Courtney A.; Gitomer, Drew H.; Pianta, Robert C.

    2014-01-01

    Valid measurement of how students' experiences in secondary school classrooms lead to gains in learning requires a developmental approach to conceptualizing classroom processes. This article presents a potentially useful theoretical model, the Teaching Through Interactions framework, which posits teacher-student interactions as a central driver…

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

    Directory of Open Access Journals (Sweden)

    Ul-Haq Zaheer

    2012-11-01

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

  7. Molecular evolution of rDNA in early diverging Metazoa: First comparative analysis and phylogenetic application of complete SSU rRNA secondary structures in Porifera

    Directory of Open Access Journals (Sweden)

    Wörheide Gert

    2008-02-01

    Full Text Available Abstract Background The cytoplasmic ribosomal small subunit (SSU, 18S ribosomal RNA (rRNA is the most frequently-used gene for molecular phylogenetic studies. However, information regarding its secondary structure is neglected in most phylogenetic analyses. Incorporation of this information is essential in order to apply specific rRNA evolutionary models to overcome the problem of co-evolution of paired sites, which violates the basic assumption of the independent evolution of sites made by most phylogenetic methods. Information about secondary structure also supports the process of aligning rRNA sequences across taxa. Both aspects have been shown to increase the accuracy of phylogenetic reconstructions within various taxa. Here, we explore SSU rRNA secondary structures from the three extant classes of Phylum Porifera (Grant, 1836, a pivotal, but largely unresolved taxon of early branching Metazoa. This is the first phylogenetic study of poriferan SSU rRNA data to date that includes detailed comparative secondary structure information for all three sponge classes. Results We found base compositional and structural differences in SSU rRNA among Demospongiae, Hexactinellida (glass sponges and Calcarea (calcareous sponges. We showed that analyses of primary rRNA sequences, including secondary structure-specific evolutionary models, in combination with reconstruction of the evolution of unusual structural features, reveal a substantial amount of additional information. Of special note was the finding that the gene tree topologies of marine haplosclerid demosponges, which are inconsistent with the current morphology-based classification, are supported by our reconstructed evolution of secondary structure features. Therefore, these features can provide alternative support for sequence-based topologies and give insights into the evolution of the molecule itself. To encourage and facilitate the application of rRNA models in phylogenetics of early

  8. Molecular evolution of rDNA in early diverging Metazoa: First comparative analysis and phylogenetic application of complete SSU rRNA secondary structures in Porifera

    Science.gov (United States)

    2008-01-01

    Background The cytoplasmic ribosomal small subunit (SSU, 18S) ribosomal RNA (rRNA) is the most frequently-used gene for molecular phylogenetic studies. However, information regarding its secondary structure is neglected in most phylogenetic analyses. Incorporation of this information is essential in order to apply specific rRNA evolutionary models to overcome the problem of co-evolution of paired sites, which violates the basic assumption of the independent evolution of sites made by most phylogenetic methods. Information about secondary structure also supports the process of aligning rRNA sequences across taxa. Both aspects have been shown to increase the accuracy of phylogenetic reconstructions within various taxa. Here, we explore SSU rRNA secondary structures from the three extant classes of Phylum Porifera (Grant, 1836), a pivotal, but largely unresolved taxon of early branching Metazoa. This is the first phylogenetic study of poriferan SSU rRNA data to date that includes detailed comparative secondary structure information for all three sponge classes. Results We found base compositional and structural differences in SSU rRNA among Demospongiae, Hexactinellida (glass sponges) and Calcarea (calcareous sponges). We showed that analyses of primary rRNA sequences, including secondary structure-specific evolutionary models, in combination with reconstruction of the evolution of unusual structural features, reveal a substantial amount of additional information. Of special note was the finding that the gene tree topologies of marine haplosclerid demosponges, which are inconsistent with the current morphology-based classification, are supported by our reconstructed evolution of secondary structure features. Therefore, these features can provide alternative support for sequence-based topologies and give insights into the evolution of the molecule itself. To encourage and facilitate the application of rRNA models in phylogenetics of early metazoans, we present 52 SSU r

  9. Comprehensive secondary structure elucidation of four genera of the family Pospiviroidae.

    Science.gov (United States)

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

    2014-01-01

    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

  10. Comprehensive secondary structure elucidation of four genera of the family Pospiviroidae.

    Directory of Open Access Journals (Sweden)

    Tamara Giguère

    Full Text Available 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.

  11. Sources of Information for Stress Assignment in Reading Greek

    Science.gov (United States)

    Protopapas, Athanassios; Gerakaki, Svetlana; Alexandri, Stella

    2007-01-01

    To assign lexical stress when reading, the Greek reader can potentially rely on lexical information (knowledge of the word), visual-orthographic information (processing of the written diacritic), or a default metrical strategy (penultimate stress pattern). Previous studies with secondary education children have shown strong lexical effects on…

  12. Membrane interaction and secondary structure of de novo designed arginine-and tryptophan peptides with dual function

    KAUST Repository

    Rydberg, Hanna A.

    2012-10-01

    Cell-penetrating peptides and antimicrobial peptides are two classes of positively charged membrane active peptides with several properties in common. The challenge is to combine knowledge about the membrane interaction mechanisms and structural properties of the two classes to design peptides with membrane-specific actions, useful either as transporters of cargo or as antibacterial substances. Membrane active peptides are commonly rich in arginine and tryptophan. We have previously designed a series of arg/trp peptides and investigated how the position and number of tryptophans affect cellular uptake. Here we explore the antimicrobial properties and the interaction with lipid model membranes of these peptides, using minimal inhibitory concentrations assay (MIC), circular dichroism (CD) and linear dichroism (LD). The results show that the arg/trp peptides inhibit the growth of the two gram positive strains Staphylococcus aureus and Staphylococcus pyogenes, with some individual variations depending on the position of the tryptophans. No inhibition of the gram negative strains Proteus mirabilis or Pseudomonas aeruginosa was noticed. CD indicated that when bound to lipid vesicles one of the peptides forms an α-helical like structure, whereas the other five exhibited rather random coiled structures. LD indicated that all six peptides were somehow aligned parallel with the membrane surface. Our results do not reveal any obvious connection between membrane interaction and antimicrobial effect for the studied peptides. By contrast cell-penetrating properties can be coupled to both the secondary structure and the degree of order of the peptides. © 2012 Elsevier Inc.

  13. Novel sequence variations in LAMA2 and SGCG genes modulating cis-acting regulatory elements and RNA secondary structure

    Directory of Open Access Journals (Sweden)

    Olfa Siala

    2010-01-01

    Full Text Available In this study, we detected new sequence variations in LAMA2 and SGCG genes in 5 ethnic populations, and analysed their effect on enhancer composition and mRNA structure. PCR amplification and DNA sequencing were performed and followed by bioinformatics analyses using ESEfinder as well as MFOLD software. We found 3 novel sequence variations in the LAMA2 (c.3174+22_23insAT and c.6085 +12delA and SGCG (c.*102A/C genes. These variations were present in 210 tested healthy controls from Tunisian, Moroccan, Algerian, Lebanese and French populations suggesting that they represent novel polymorphisms within LAMA2 and SGCG genes sequences. ESEfinder showed that the c.*102A/C substitution created a new exon splicing enhancer in the 3'UTR of SGCG genes, whereas the c.6085 +12delA deletion was situated in the base pairing region between LAMA2 mRNA and the U1snRNA spliceosomal components. The RNA structure analyses showed that both variations modulated RNA secondary structure. Our results are suggestive of correlations between mRNA folding and the recruitment of spliceosomal components mediating splicing, including SR proteins. The contribution of common sequence variations to mRNA structural and functional diversity will contribute to a better study of gene expression.

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

    Directory of Open Access Journals (Sweden)

    Shenkar Noa

    2009-08-01

    Full Text Available Abstract 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

  15. Feasibility Study on Nano-structured Coatings to Mitigate Flow-accelerated Corrosion in Secondary System of Nuclear Power Plants

    International Nuclear Information System (INIS)

    There have been many efforts to mitigate FAC through the adoption of the advanced and modified water chemistries such as optimized dissolved oxygen (DO) concentration and temperature. However, these mitigation techniques pose certain challenges relating to the compatibility of new water chemistries with the steam generator, the thermal efficiency of the secondary side, etc. In this context, nano-particle reinforced electroless nickel plating (NP ENP) could help solve the FAC issues in secondary pipe systems. This does not require modification of water chemistry or structural materials, and hence, its application is reasonable and time-saving compared to previous FAC mitigation techniques. The main parameters of FAC are known as electrochemical reaction at the interface, dissolution of magnetite and ferrous ions due to concentration gradient between carbon steels and water and wear due to a fast-flowing fluid. High-temperature corrosion characteristics of the both coatings have potential as FAC barrier for carbon steel. Feasibility study will be carried out with FAC simulation experiments

  16. Effects of Secondary Plant Metabolites on Microbial Populations: Changes in Community Structure and Metabolic Activity in Contaminated Environments.

    Science.gov (United States)

    Musilova, Lucie; Ridl, Jakub; Polivkova, Marketa; Macek, Tomas; Uhlik, Ondrej

    2016-01-01

    Secondary plant metabolites (SPMEs) play an important role in plant survival in the environment and serve to establish ecological relationships between plants and other organisms. Communication between plants and microorganisms via SPMEs contained in root exudates or derived from litter decomposition is an example of this phenomenon. In this review, the general aspects of rhizodeposition together with the significance of terpenes and phenolic compounds are discussed in detail. We focus specifically on the effect of SPMEs on microbial community structure and metabolic activity in environments contaminated by polychlorinated biphenyls (PCBs) and polyaromatic hydrocarbons (PAHs). Furthermore, a section is devoted to a complex effect of plants and/or their metabolites contained in litter on bioremediation of contaminated sites. New insights are introduced from a study evaluating the effects of SPMEs derived during decomposition of grapefruit peel, lemon peel, and pears on bacterial communities and their ability to degrade PCBs in a long-term contaminated soil. The presented review supports the "secondary compound hypothesis" and demonstrates the potential of SPMEs for increasing the effectiveness of bioremediation processes. PMID:27483244

  17. Secondary structure of prokaryotic 5S ribosomal ribonucleic acids: a study with ribonucleases

    DEFF Research Database (Denmark)

    Douthwaite, S; Garrett, R A

    1981-01-01

    The structures of 5S ribosomal RNAs from Escherichia coli and Bacillus stearothermophilus were examined by using ribonucleases A, T1, and T2 and a double helix specific cobra venom ribonuclease. By using both 5' and 3'-32P-end labeling methods and selecting for digested but intact 5S RNA molecule...

  18. An RNA secondary structure bias for non-homologous reverse transcriptase-mediated deletions in vivo

    DEFF Research Database (Denmark)

    Duch, Mogens; Carrasco, Maria L; Jespersen, Thomas;

    2004-01-01

    result from template switching during first-strand cDNA synthesis and that the choice of acceptor sites for non-homologous recombination are guided by non-paired regions. Our results may have implications for recombination events taking place within structured regions of retroviral RNA genomes......, especially in the absence of longer stretches of sequence similarity....

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

    Science.gov (United States)

    Parker, Gay E.

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

  20. Ner protein of phage Mu: Assignments using {sup 13}C/{sup 15}N-labeled protein

    Energy Technology Data Exchange (ETDEWEB)

    Strzelecka, T.; Gronenborn, A.M.; Clore, G.M. [National Institutes of Health, Bethesda, MD (United States)

    1994-12-01

    The Ner protein is a small (74-amino acid) DNA-binding protein that regulates a switch between the lysogenic and lytic stages of phage Mu. It inhibits expression of the C repressor gene and down-regulates its own expression. Two-dimensional NMR experiments on uniformly {sup 15}N-labeled protein provided most of the backbone and some of the sidechain proton assignments. The secondary structure determination using two-dimensional NOESY experiments showed that Ner consists of five {alpha}-helices. However, because most of the sidechain protons could not be assigned, the full structure was not determined. Using uniformly {sup 13}C/{sup 15}N-labeled Ner and a set of three-dimensional experiments, we were able to assign all of the backbone and 98% of the sidechain protons. In particular, the CBCANH and CBCA(CO)NH experiments were used to sequentially assign the C{alpha} and C{beta} resonances; the HCCH-CTOCSY and HCCH-COSY were used to assign sidechain carbon and proton resonances.

  1. Secondary structure and phylogenetic utility of the ribosomal large subunit (28S) in monogeneans of the genus Thaparocleidus and Bifurcohaptor (Monogenea: Dactylogyridae).

    Science.gov (United States)

    Chaudhary, Anshu; Singh, Hridaya Shanker

    2013-04-01

    Present communication deals with secondary structure of 28S rDNA of two already known species of monogeneans viz., Bifurcohaptor indicus and Thaparocleidus parvulus parasitizing gill filaments of a freshwater fish, Mystus vittatus for phylogenetic inference. Secondary structure data are best used as accessory taxonomic characters as their phylogenetic resolving power and confidence in validity. Secondary structure of the 28S rDNA transcript could provide information for identifying homologous nucleotide characters, useful for cladistic inference of relationships. Such structure data could be used as taxonomic character. The study supports that species-level sequence variability renders 28S sequence as a unique window for examining the behavior of fast evolving, non-coding DNA sequences. Apart from this it also confirms that molecular similarity present in various species could be host-induced. PMID:24431545

  2. Membrane Topology of the Sodium Ion-dependent Citrate Carrier of Klebsiella pneumoniae. Evidence for a New Structural Class of Secondary Transporters

    OpenAIRE

    Geest, Marleen van; Lolkema, Juke S.

    1996-01-01

    The predicted secondary structure model of the sodium ion-dependent citrate carrier of Klebsiella pneumoniae (CitS) presents the 12-transmembrane helix motif observed for many secondary transporters. Biochemical evidence presented in this paper is not consistent with this model. N-terminal and C-terminal fusions of CitS with the biotin acceptor domain of the oxaloacetate decarboxylase of K. pneumoniae catalyze citrate transport, showing the correct folding of the CitS part of the fusion prote...

  3. Job Assignment with Multivariate Skills

    OpenAIRE

    Brilon, Stefanie

    2010-01-01

    This paper analyzes the job assignment problem faced by a firm when workers' skills are distributed along several dimensions and jobs require different skills to varying extent. I derive optimal assignment rules with and without slot constraints, and show that under certain circumstances workers may get promoted although in their new job they are expected to be less productive than in their old job. This can be interpreted as a version of the Peter Principle which states that workers get prom...

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

    Science.gov (United States)

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

    2014-01-01

    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…

  5. The most important structures utilizing primary and secondary hydroenergetic potential for electric energy production

    International Nuclear Information System (INIS)

    In this paper the construction, technological parameters and operation of Gabcikovo (primary hydro energy power) and Cierny Vah (secondary hydro energy power) are described. Construction of the hydroelectric power plant (HPP) Gabcikovo started in 1978 as a part of a system of hydro power projects Gabcikovo-Nagymaros. Basic technical data are: installed capacity 8 x 90 MW, production in an average aqueous year 2.650 GWh, number of hydroelectric generating sets (HGS) 8, turbine flow 8 x 413-636 m3/s, head 12.9-24 m.The Gabcikovo plant produced 9.163 GWh of electricity from the beginning of its operation till the end of 1966. The construction of the pumped storage plant (PSP) Cierny Vah started in 1976 and it was put into operation at the end of 1980. The main goal of the PSP Cierny Vah is to meet the control functions of an electrification system of the Slovak Republic, a substitute function in the cases of unexpected power outages and a planned electricity production from re-pumping. Technological parts are: six re-pumping vertical HGS in a three machine arrangement - a motor-generator, a turbine, a pump - are located in three double-blocks. Basic technical data: installed capacity 6 x 122.4 MW + 0.768 MW, yearly production 1,281 GWh, number of HGS 6, number of domestic hydroelectric generating sets 1, turbine flow 3 x 30 m/s, pump flow 6 x 22 m3/s, upper reservoir volume 3.7 mil. m3, max. head 434 m, peak time 5.71 hour, pumping time 7.78 hour, re-pumping cycle efficiency 74.36%. From putting the PSP into operation till the end of 1996, the HGS in operation 145,269 hours in total, including 53,332 hours in a turbine mode of operation, 70,293 hours in a pumping mode operation and 21,644 hours in a compensation mode operation. Whereas they supplied 5,346 GWh in the mains and the consumed 6,933 GWh of electricity for pumping. Hydroenergetic potential is a primary source of energy which is recyclable, i.e. unexhaustible and also ecologically the most tolerable. No

  6. Structure of Velocity Distribution of Sheath-Accelerated Secondary Electrons in Asymmetric RF-DC Discharge

    CERN Document Server

    Khrabrov, Alexander V; Ventzek, Peter L G; Ranjan, Alok; Chen, Lee

    2015-01-01

    The ballistic population is thought to be responsible for alleviating the electron shading effect and the notching of the photoresist layer. We have performed test-particle simulations where the features in the EVDF of electrons impacting the RF electrode are fully resolved at all energies. An analytic model has been developed to predict existence of peaked and step-like structures in the EVDF.

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

    OpenAIRE

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

    2013-01-01

    Ebolavirus (EBOV), the causative agent of a severe hemorrhagic fever and a biosafety level 4 pathogen, increases its genome coding capacity by producing multiple transcripts encoding for structural and nonstructural glycoproteins from a single gene. This is achieved through RNA editing, during which non-template adenosine residues are incorporated into the EBOV mRNAs at an editing site encoding for 7 adenosine residues. However, the mechanism of EBOV RNA editing is currently not understood. I...

  8. Secondary-Structure Analysis of Denatured Proteins by Vacuum-Ultraviolet Circular Dichroism Spectroscopy

    OpenAIRE

    Matsuo, Koichi; Sakurada, Yoshie; Yonehara, Ryuta; Kataoka, Mikio; Gekko, Kunihiko

    2007-01-01

    To elucidate the structure of denatured proteins, we measured the vacuum-ultraviolet circular dichroism (VUVCD) spectra from 260 to 172 nm of three proteins (metmyoglobin, staphylococcal nuclease, and thioredoxin) in the native and the acid-, cold-, and heat-denatured states, using a synchrotron-radiation VUVCD spectrophotometer. The circular dichroism spectra of proteins fully unfolded by guanidine hydrochloride (GdnHCl) were also measured down to 197 nm for comparison. These denatured prote...

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

    OpenAIRE

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

    2007-01-01

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

  10. Formation of secondary phases during deep geological final disposal of research reactor fuel elements. Structure and phase analysis

    International Nuclear Information System (INIS)

    For the assessment of a confident und sustainable final disposal of high level radioactive waste - fuel elements of german research reactors also account for such waste - in suitable, deep geological facilities, processes of the alteration of the disposed of waste and therefore the formation of the corrosion products, i. e. secondary phases must be well understood considering an accident scenario of a potential water inflow. In order to obtain secondary phases non-irradiated research reactor fuel elements (FR-BE) consisting of UAlx-Al were subjected to magnesium chloride rich brine (brine 2, salt repository) and to clay pore solution, respectively and furthermore of the type U3Si2-Al were solely subjected to magnesium chloride rich brine. Considering environmental aspects of final repositories the test conditions of the corrosion experiments were adjusted in a way that the temperature was kept constant at 90 C and a reducing anaerobic environment was ensured. As major objective of this research secondary phases, obtained from the autoclave experiments after appropriate processing and grain size separation have been identified and quantified. Powder X-ray diffraction (PXRD) and the application of Rietveld refinement methods allowed the identification of the corrosion products and a quantitative assessment of crystalline and amorphous contents. Scanning and transmission electron microscopy were additionally applied as a complementary method for the characterisation of the secondary phases. The qualitative phase analysis of the preprocessed secondary phases of the systems UAlx-Al and U3Si2-Al in brine 2 shows many similarities. Lesukite - an aluminium chloro hydrate - was observed for the first time considering the given experimental conditions. Further on different layered structures of the LDH type, iron oxyhydroxide and possibly iron chlorides, uncorroded residues of nuclear fuel and elementary iron were identified as well. Depending on preceding preparation

  11. Effect of principal and secondary ligands on the electronic structures and spectra of a series of ruthenium(II complexes

    Directory of Open Access Journals (Sweden)

    Zhang Yanli

    2016-01-01

    Full Text Available A DFT(density functional theory/TDDFT(time-dependent density functional theory investigation is performed to study the ground-state geometries, electronic structures, and absorption spectra of twelve ruthenium(II thiosemicarbazone complexes [Ru(CO(C(Ln], where Ln=derivatives of dibasic tetradentate Schiff-base ligand and X=AsPh3/PPh3/Py. The ground-state geometries are optimized at the B3LYP/6-31G(d-LANL2DZ level, and the spectra are simulated by means of TD-B3LYP/6-31G(d-LANL2DZ method on the basis of the optimized geometries. The influence of principal and secondary ligands (Ln and X on transition characters and absorption peak positions is evaluated.

  12. Effect of low energy N+ ion beam implantation on the secondary structure and activity of α-amylase

    International Nuclear Information System (INIS)

    Samples of the α-amylase were treated with 1015-1016 ions/cm2 of 20 keV N+. The secondary structure of the ion-implanted α-amylase was studied by circular dichroism, and activity change of the α-amylase was analyzed. The results showed that in the dose range under investigation, the N+ implantation affected the relative contents of α-helix, β-sheet, β-turn and random coil of the α-amylase, but no significant differences were found between the samples implanted to different doses. The activity of the N+-implanted α-amylase changed, with a relationship between the activity increase and the conformation change. (authors)

  13. Optimal State Assignment for Finite State Machines

    OpenAIRE

    Micheli, Giovanni De; Brayton, Robert K.; Sangiovanni-Vincentelli, Alberto

    1985-01-01

    Computer-Aided synthesis of sequential functions of VLSI systems, such as microprocessor control units, must include design optimization procedures to yield area-effective circuits. We model sequential functions as deterministic synchronous Finite State Machines (FSM's), and we consider a regular and structured implementation by means of Programmable Logic Arrays (PLA's) and feedback registers. State assignment, i.e., binary encoding of the internal states of the finite state machine, affects...

  14. First-principles investigation of the structural characteristics of LiMO2 cathode materials for lithium secondary batteries

    Science.gov (United States)

    Kim, Yongseon

    2015-11-01

    The structural features related to the defects of LiMO2 (M = Ni, Co, Mn) cathode materials for lithium secondary batteries were investigated by a simulation of phase diagrams based on first-principle calculations. Crystal models with various types of point defects were designed and dealt with as independent phases, which enabled an examination of the thermodynamic stability of the defects. A perfect phase without defects appeared to be the most stable for LiCoO2, whereas the formation of Li vacancies, O vacancies, and antisites between Li and Ni was thermodynamically unavoidable for LiNiO2. The introduction of both Co and Mn in LiNiO2 was effective in reducing the formation of point defects, but increasing the relative amount of Mn was undesirable because the antisite defect remained stable with Mn doping. The simulation showed good agreement with the experimental data and previous reports. Therefore, the method and the results of this study are expected to be useful for examining the synthesis, structure and related properties of layer-structured cathode materials.

  15. Secondary School Students' LLL Competencies, and Their Relation with Classroom Structure and Achievement.

    Science.gov (United States)

    Klug, Julia; Lüftenegger, Marko; Bergsmann, Evelyn; Spiel, Christiane; Schober, Barbara

    2016-01-01

    There is a strong urge to foster lifelong learning (LLL) competencies with its key components - motivation and self-regulated learning - from early on in the education system. School in general is presently not considered to be successful in systematically imparting motivation and self-regulated learning strategies. There is strong evidence that decisive motivational determinants decrease the longer students stay in school. At present, the central sources of information about the situation in Austria are international monitoring studies, which only examine selected aspects of specific target groups, and their interpretability concerning mean values is constricted due to cultural differences. Thus, it is important to conduct additional and more differentiated national surveys of the actual state. This is why this study aimed at answering the following questions: (1) how well are Austrian students equipped for the future, in terms of their lifelong learning competencies, (2) can perceived classroom structure predict students' LLL, and (3) is there a correlation of students' LLL with their achievement in the school subjects math and German language. 5366 students (52.1% female) from 36 Austrian schools took part in the online-questionnaire (mean age 15.35 years, SD = 2.45), which measured their perceived LLL competencies in the subjects math and German language, their perceived classroom structure and their achievement. Results showed that the great majority of Austrian students - independent from domain and sex - know and are able to apply cognitive as well as metacognitive learning strategies. With regard to motivation the picture is less satisfactory: whilst students' self-efficacy is not the problem, there is a lack of interest in the school subjects and they often report to follow performance approach goals. Classroom structure positively predicted students' goals, interest, self-efficacy and learning strategies. Self-efficacy, performance approach goals, meta

  16. Secondary School Students’ LLL Competencies, and Their Relation with Classroom Structure and Achievement

    Science.gov (United States)

    Klug, Julia; Lüftenegger, Marko; Bergsmann, Evelyn; Spiel, Christiane; Schober, Barbara

    2016-01-01

    There is a strong urge to foster lifelong learning (LLL) competencies with its key components – motivation and self-regulated learning – from early on in the education system. School in general is presently not considered to be successful in systematically imparting motivation and self-regulated learning strategies. There is strong evidence that decisive motivational determinants decrease the longer students stay in school. At present, the central sources of information about the situation in Austria are international monitoring studies, which only examine selected aspects of specific target groups, and their interpretability concerning mean values is constricted due to cultural differences. Thus, it is important to conduct additional and more differentiated national surveys of the actual state. This is why this study aimed at answering the following questions: (1) how well are Austrian students equipped for the future, in terms of their lifelong learning competencies, (2) can perceived classroom structure predict students’ LLL, and (3) is there a correlation of students’ LLL with their achievement in the school subjects math and German language. 5366 students (52.1% female) from 36 Austrian schools took part in the online-questionnaire (mean age 15.35 years, SD = 2.45), which measured their perceived LLL competencies in the subjects math and German language, their perceived classroom structure and their achievement. Results showed that the great majority of Austrian students – independent from domain and sex – know and are able to apply cognitive as well as metacognitive learning strategies. With regard to motivation the picture is less satisfactory: whilst students’ self-efficacy is not the problem, there is a lack of interest in the school subjects and they often report to follow performance approach goals. Classroom structure positively predicted students’ goals, interest, self-efficacy and learning strategies. Self-efficacy, performance

  17. An automated system designed for large scale NMR data deposition and annotation: application to over 600 assigned chemical shift data entries to the BioMagResBank from the Riken Structural Genomics/Proteomics Initiative internal database

    International Nuclear Information System (INIS)

    Biomolecular NMR chemical shift data are key information for the functional analysis of biomolecules and the development of new techniques for NMR studies utilizing chemical shift statistical information. Structural genomics projects are major contributors to the accumulation of protein chemical shift information. The management of the large quantities of NMR data generated by each project in a local database and the transfer of the data to the public databases are still formidable tasks because of the complicated nature of NMR data. Here we report an automated and efficient system developed for the deposition and annotation of a large number of data sets including 1H, 13C and 15N resonance assignments used for the structure determination of proteins. We have demonstrated the feasibility of our system by applying it to over 600 entries from the internal database generated by the RIKEN Structural Genomics/Proteomics Initiative (RSGI) to the public database, BioMagResBank (BMRB). We have assessed the quality of the deposited chemical shifts by comparing them with those predicted from the PDB coordinate entry for the corresponding protein. The same comparison for other matched BMRB/PDB entries deposited from 2001–2011 has been carried out and the results suggest that the RSGI entries greatly improved the quality of the BMRB database. Since the entries include chemical shifts acquired under strikingly similar experimental conditions, these NMR data can be expected to be a promising resource to improve current technologies as well as to develop new NMR methods for protein studies.

  18. The effect of Berberine on the secondary structure of human serum albumin

    Science.gov (United States)

    Li, Ying; He, WenYing; Tian, Jianniao; Tang, Jianghong; Hu, Zhide; Chen, Xingguo

    2005-05-01

    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 α-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).

  19. Study of bioengineered zebra fish olfactory receptor 131-2: receptor purification and secondary structure analysis.

    Directory of Open Access Journals (Sweden)

    Kwong-Joo Leck

    Full Text Available How fishes are able to detect trace molecules in large bodies of water is not understood. It is plausible that they use olfactory receptors to detect water-soluble compounds. How the zebra fish Danio Rerio, an organism with only 98 functional olfactory receptors, is able to selectively detect and recognize numerous compounds in water remains a puzzling phenomenon. We are interested in studying the biochemical and molecular mechanisms of olfaction in fish. Here, we report on the study of a bioengineered zebra fish olfactory receptor OR131-2, affinity-purified from a HEK293S tetracycline-inducible system. This receptor was expressed and translocated to the cell plasma membrane as revealed by confocal microscopy. Circular dichroism spectroscopy showed that the purified zebra fish receptor folded into an α-helical structure, as observed for other G-protein coupled receptors (GPCRs. Our study shows that it is possible to produce viable quantities of the zebra fish olfactory receptor. This will not only enable detailed structural and functional analyses, but also aid in the design of biosensor devices in order to detect water-soluble metabolites or its intermediates, which are associated with human health.

  20. Isolation and structural elucidation of secondary metabolites of plants of the families asteraceae and urticaceae

    International Nuclear Information System (INIS)

    A phytochemistry study of plant's species of the Asteraceae and Urticaceae family is proposed in order to isolate and to elucidate the structure of active principles; due to the fact that several studies have found that some of these families have compounds with anti-inflammatory activity, mainly lactonas sesquiterpenicas . The phytochemistry study was carried out through the application of chromatography techniques, for the separation and purification of the compounds. Includes chromatography of column, fine and liquid layer of high resolution. On the other hand, spectroscopic techniques were used for the elucidation, mainly of nuclear magnetic resonance (RMN) as much of one as of two dimensions. In this way, it was possible to isolate 14 compounds in Decachaeta thieleana and 10 in Phenax mexicanus, from which 6 correspond compounds of innovative structure. The comparison of the results obtained in Decachaeta thieleana (with previous studies) evidences that specimens, orphologically identical (the same species, but different locations), possess totally different compounds. This suggests that the studied specimens do not correspond to the same species. However, the determination of such a cause not only evade the objectives of this work but also the area of study of Chemistry

  1. Discovery of Novel ncRNA Sequences in Multiple Genome Alignments on the Basis of Conserved and Stable Secondary Structures.

    Directory of Open Access Journals (Sweden)

    Yinghan Fu

    Full Text Available Recently, non-coding RNAs (ncRNAs have been discovered with novel functions, and it has been appreciated that there is pervasive transcription of genomes. Moreover, many novel ncRNAs are not conserved on the primary sequence level. Therefore, de novo computational ncRNA detection that is accurate and efficient is desirable. The purpose of this study is to develop a ncRNA detection method based on conservation of structure in more than two genomes. A new method called Multifind, using Multilign, was developed. Multilign predicts the common secondary structure for multiple input sequences. Multifind then uses measures of structure conservation to estimate the probability that the input sequences are a conserved ncRNA using a classification support vector machine. Multilign is based on Dynalign, which folds and aligns two sequences simultaneously using a scoring scheme that does not include sequence identity; its structure prediction quality is therefore not affected by input sequence diversity. Additionally, ensemble defect was introduced to Multifind as an additional discriminating feature that quantifies the compactness of the folding space for a sequence. Benchmarks showed Multifind performs better than RNAz and LocARNATE+RNAz, a method that uses RNAz on structure alignments generated by LocARNATE, on testing sequences extracted from the Rfam database. For de novo ncRNA discovery in three genomes, Multifind and LocARNATE+RNAz had an advantage over RNAz in low similarity regions of genome alignments. Additionally, Multifind and LocARNATE+RNAz found different subsets of known ncRNA sequences, suggesting the two approaches are complementary.

  2. Secondary structure of double-stranded DNA under stretching: elucidation of the stretched form.

    Science.gov (United States)

    Maaloum, M; Beker, A-F; Muller, P

    2011-03-01

    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 λ-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 of 18 nm. PMID:21517521

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

    International Nuclear Information System (INIS)

    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 λ-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.

  4. RNA Secondary Structure Modulates FMRP's Bi-Functional Role in the MicroRNA Pathway.

    Science.gov (United States)

    Kenny, Phillip; Ceman, Stephanie

    2016-01-01

    MicroRNAs act by post-transcriptionally regulating the gene expression of 30%-60% of mammalian genomes. MicroRNAs are key regulators in all cellular processes, though the mechanism by which the cell activates or represses microRNA-mediated translational regulation is poorly understood. In this review, we discuss the RNA binding protein Fragile X Mental Retardation Protein (FMRP) and its role in microRNA-mediated translational regulation. Historically, FMRP is known to function as a translational suppressor. However, emerging data suggests that FMRP has both an agonistic and antagonistic role in regulating microRNA-mediated translational suppression. This bi-functional role is dependent on FMRP's interaction with the RNA helicase Moloney leukemia virus 10 (MOV10), which modifies the structural landscape of bound mRNA, therefore facilitating or inhibiting its association with the RNA-Induced Silencing Complex. PMID:27338369

  5. A novel Multi-Agent Ada-Boost algorithm for predicting protein structural class with the information of protein secondary structure.

    Science.gov (United States)

    Fan, Ming; Zheng, Bin; Li, Lihua

    2015-10-01

    Knowledge of the structural class of a given protein is important for understanding its folding patterns. Although a lot of efforts have been made, it still remains a challenging problem for prediction of protein structural class solely from protein sequences. The feature extraction and classification of proteins are the main problems in prediction. In this research, we extended our earlier work regarding these two aspects. In protein feature extraction, we proposed a scheme by calculating the word frequency and word position from sequences of amino acid, reduced amino acid, and secondary structure. For an accurate classification of the structural class of protein, we developed a novel Multi-Agent Ada-Boost (MA-Ada) method by integrating the features of Multi-Agent system into Ada-Boost algorithm. Extensive experiments were taken to test and compare the proposed method using four benchmark datasets in low homology. The results showed classification accuracies of 88.5%, 96.0%, 88.4%, and 85.5%, respectively, which are much better compared with the existing methods. The source code and dataset are available on request. PMID:26350693

  6. Osmolality and non-structural carbohydrate composition in the secondary phloem of trees across a latitudinal gradient in Europe

    Directory of Open Access Journals (Sweden)

    Anna eLintunen

    2016-06-01

    Full Text Available Phloem osmolality and its components are involved in basic cell metabolism, cell growth, and in various physiological processes including the ability of living cells to withstand drought and frost. Osmolality and sugar composition responses to environmental stresses have been extensively studied for leaves, but less for the secondary phloem of plant stems and branches. Leaf osmotic concentration and the share of pinitol and raffinose among soluble sugars increase with increasing drought or cold stress, and osmotic concentration is adjusted with osmoregulation. We hypothesize that similar responses occur in the secondary phloem of branches. We collected living bark samples from branches of adult Pinus sylvestris, Picea abies, Betula pendula and Populus tremula trees across Europe, from boreal Northern Finland to Mediterranean Portugal. In all studied species, the observed variation in phloem osmolality was mainly driven by variation in phloem water content, while tissue solute content was rather constant across regions. Osmoregulation, in which osmolality is controlled by variable tissue solute content, was stronger for Betula and Populus in comparison to the evergreen conifers. Osmolality was lowest in mid-latitude region, and from there increased by 37% towards northern Europe and 38% towards southern Europe due to low phloem water content in these regions. The ratio of raffinose to all soluble sugars was negligible at mid-latitudes and increased towards north and south, reflecting its role in cold and drought tolerance. For pinitol, another sugar known for contributing to stress tolerance, no such latitudinal pattern was observed. The proportion of sucrose was remarkably low and that of hexoses (i.e. glucose and fructose high at mid-latitudes. The ratio of starch to all non-structural carbohydrates increased towards the northern latitudes in agreement with the build-up of osmotically inactive C reservoir that can be converted into soluble

  7. Toward non-Newtonian effects on secondary flow structures in a 180 degree bent tube model for curved arteries

    Science.gov (United States)

    van Wyk, Stevin; Prahl Wittberg, Lisa; Fuchs, Laszlo; Bulusu, Kartik V.; Plesniak, Michael W.

    2013-11-01

    The purpose of this study is to investigate the development of vortical flow structures of blood like fluids in a 180 degree tube bend, analogous to the aortic arch. Cardiovascular diseases are localized to regions of curvature in the arterial tree. The pathology of atherogenesis is widely considered an inflammatory response, hypothesized to be modulated by the interplay between Wall Shear Stress (WSS) variations and particulate transport mechanisms from the bulk fluid core to the near wall. The WSS is determined by the local flow characteristics as well as the rheological properties of the blood, which in turn are dependent on the bulk secondary flows. In this work, the time dependent fluid flow under various physiological flow conditions are investigated both experimentally and numerically. A Newtonian blood analog fluid model is considered in both studies to validate both methods and thereby study flow structure development during steady as well as pulsatile conditions. Particle image velocimetry (2C - 2D PIV) is used to acquire velocity field data from an acrylic tube bend. The numerical study is extended to consider the non-Newtonian properties of blood according to an empirical model to identify the relative importance of the non-Newtonian behavior. The studies show complex Dean and Lyne vortex interaction that are enhanced with increasing peak Reynolds numbers.

  8. The influence of secondary processing on the structural relaxation dynamics of fluticasone propionate.

    Science.gov (United States)

    Depasquale, Roberto; Lee, Sau L; Saluja, Bhawana; Shur, Jagdeep; Price, Robert

    2015-06-01

    This study investigated the structural relaxation of micronized fluticasone propionate (FP) under different lagering conditions and its influence on aerodynamic particle size distribution (APSD) of binary and tertiary carrier-based dry powder inhaler (DPI) formulations. Micronized FP was lagered under low humidity (LH 25 C, 33% RH [relative humidity]), high humidity (HH 25°C, 75% RH) for 30, 60, and 90 days, respectively, and high temperature (HT 60°C, 44% RH) for 14 days. Physicochemical, surface interfacial properties via cohesive-adhesive balance (CAB) measurements and amorphous disorder levels of the FP samples were characterized. Particle size, surface area, and rugosity suggested minimal morphological changes of the lagered FP samples, with the exception of the 90-day HH (HH90) sample. HH90 FP samples appeared to undergo surface reconstruction with a reduction in surface rugosity. LH and HH lagering reduced the levels of amorphous content over 90-day exposure, which influenced the CAB measurements with lactose monohydrate and salmeterol xinafoate (SX). CAB analysis suggested that LH and HH lagering led to different interfacial interactions with lactose monohydrate but an increasing adhesive affinity with SX. HT lagering led to no detectable levels of the amorphous disorder, resulting in an increase in the adhesive interaction with lactose monohydrate. APSD analysis suggested that the fine particle mass of FP and SX was affected by the lagering of the FP. In conclusion, environmental conditions during the lagering of FP may have a profound effect on physicochemical and interfacial properties as well as product performance of binary and tertiary carrier-based DPI formulations. PMID:25398478

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

    Energy Technology Data Exchange (ETDEWEB)

    Yu,P.

    2007-01-01

    Studying the secondary structure of proteins leads to an understanding of the components that make up a whole protein, and such an understanding of the structure of the whole protein is often vital to understanding its digestive behaviour and nutritive value in animals. The main protein secondary structures are the {alpha}-helix and {beta}-sheet. The percentage of these two structures in protein secondary structures influences protein nutritive value, quality and digestive behaviour. A high percentage of {beta}-sheet structure may partly cause a low access to gastrointestinal digestive enzymes, which results in a low protein value. The objectives of the present study were to use advanced synchrotron-based Fourier transform IR (S-FTIR) microspectroscopy as a new approach to reveal the molecular chemistry of the protein secondary structures of feed tissues affected by heat-processing within intact tissue at a cellular level, and to quantify protein secondary structures using multicomponent peak modelling Gaussian and Lorentzian methods, in relation to protein digestive behaviours and nutritive value in the rumen, which was determined using the Cornell Net Carbohydrate Protein System. The synchrotron-based molecular chemistry research experiment was performed at the National Synchrotron Light Source at Brookhaven National Laboratory, US Department of Energy. The results showed that, with S-FTIR microspectroscopy, the molecular chemistry, ultrastructural chemical make-up and nutritive characteristics could be revealed at a high ultraspatial resolution ({approx}10 {mu}m). S-FTIR microspectroscopy revealed that the secondary structure of protein differed between raw and roasted golden flaxseeds in terms of the percentages and ratio of {alpha}-helixes and {beta}-sheets in the mid-IR range at the cellular level. By using multicomponent peak modelling, the results show that the roasting reduced (P <0.05) the percentage of {alpha}-helixes (from 47.1% to 36.1%: S

  10. Protein Secondary Structures (α-helix and β-sheet) at a Cellular Level and Protein Fractions in Relation to Rumen Degradation Behaviours of Protein: A New Approach

    International Nuclear Information System (INIS)

    Studying the secondary structure of proteins leads to an understanding of the components that make up a whole protein, and such an understanding of the structure of the whole protein is often vital to understanding its digestive behaviour and nutritive value in animals. The main protein secondary structures are the α-helix and β-sheet. The percentage of these two structures in protein secondary structures influences protein nutritive value, quality and digestive behaviour. A high percentage of β-sheet structure may partly cause a low access to gastrointestinal digestive enzymes, which results in a low protein value. The objectives of the present study were to use advanced synchrotron-based Fourier transform IR (S-FTIR) microspectroscopy as a new approach to reveal the molecular chemistry of the protein secondary structures of feed tissues affected by heat-processing within intact tissue at a cellular level, and to quantify protein secondary structures using multicomponent peak modelling Gaussian and Lorentzian methods, in relation to protein digestive behaviours and nutritive value in the rumen, which was determined using the Cornell Net Carbohydrate Protein System. The synchrotron-based molecular chemistry research experiment was performed at the National Synchrotron Light Source at Brookhaven National Laboratory, US Department of Energy. The results showed that, with S-FTIR microspectroscopy, the molecular chemistry, ultrastructural chemical make-up and nutritive characteristics could be revealed at a high ultraspatial resolution (∼10 μm). S-FTIR microspectroscopy revealed that the secondary structure of protein differed between raw and roasted golden flaxseeds in terms of the percentages and ratio of α-helixes and β-sheets in the mid-IR range at the cellular level. By using multicomponent peak modelling, the results show that the roasting reduced (P <0.05) the percentage of α-helixes (from 47.1% to 36.1%: S-FTIR absorption intensity), increased the

  11. ¹H, ¹³C and ¹⁵N resonance assignment of the soluble form of the lipid-modified Azurin from Neisseria gonorrhoeae.

    Science.gov (United States)

    Nóbrega, Cláudia S; Matzapetakis, Manolis; Pauleta, Sofia R

    2013-10-01

    Lipid-modified azurin (Laz) from Neisseria gonorrhoeae is a type 1 copper protein proposed to be the electron donor to several enzymes involved in the resistance mechanism to reactive oxygen and nitrogen species. Here we report the backbone and side-chain resonance assignment of Laz in the reduced form, which has been complete at 97%. The predicted secondary structure indicates that this protein belongs to the azurin subfamily of type 1 copper proteins. PMID:23070845

  12. Cationized bovine serum albumin as gene carrier: Influence of specific secondary structure on DNA complexibility and gene transfection.

    Science.gov (United States)

    Du, Jianwei; Li, Bangbang; Zhang, Peng; Wang, Youxiang

    2016-07-01

    In this research, BSA, one of the natural rigid globular proteins with ca. 51% of α-helix secondary structure, was utilized to prepare cationized BSA (cBSA) as gene carrier. Tetraethylenepentamine (TEPA) or polyethylenimine (PEI1800) was grafted to BSA with different grafting levels. Based on the circular dichoism (CD) spectra, all cBSA remained α-helical structure to some degree. This was exciting to endow cBSA with quite different DNA complexibility and cellular biology behavior from the random coiled and flexible polycations such as PEI and poly-l-lysine (PLL). Strangely, the DNA condensability decreased with the increment of TEPA or PEI1800 grafting level. Also, the cBSA could condense DNA effectively to form irregular nanoparticles around 50-200nm above N/P ratio of 10. On account of the excellent hydration of BSA, the cBSA/DNA complexes revealed good colloidal stability under physiological salt condition. Cell culture experiments indicated this BSA-based gene carrier possessed good cellular compatibility. Surprisingly, cBSA/DNA complexes could be uptaken excellently by up to 90% cells. This might be owing to the agitation effect of α-helical structure and the positive potential of these complexes. BSA-PEI1800/DNA complexes with quick endosome escape even had transfection efficiency as high as PEI25k/DNA complexes. Overall, this paper provided us the potential of cBSA as gene carrier and might have some instructions in the design of protein-based gene delivery system. PMID:26998865

  13. Structure of the velocity distribution of sheath-accelerated secondary electrons in an asymmetric RF-dc discharge

    Science.gov (United States)

    Khrabrov, Alexander V.; Kaganovich, Igor D.; Ventzek, Peter L. G.; Ranjan, Alok; Chen, Lee

    2015-10-01

    Low-pressure capacitively-coupled discharges with additional dc bias applied to a separate electrode are utilized in plasma-assisted etching for semiconductor device manufacturing. Measurements of the electron velocity distribution function (EVDF) of the flux impinging on the wafer, as well as in the plasma bulk, show a thermal population and additional peaks within a broad range of energies. That range extends from the thermal level up to the value for the ‘ballistic’ peak, corresponding to the bias potential. The non-thermal electron flux has been correlated to alleviating the electron shading effect and providing etch-resistance properties to masking photoresist layers. ‘Middle-energy peak electrons’ at energies of several hundred eV may provide an additional sustaining mechanism for the discharge. These features in the electron velocity (or energy) distribution functions are possibly caused by secondary electrons emitted from the electrodes and interacting with two high-voltage sheaths: a stationary sheath at the dc electrode and an oscillating self-biased sheath at the powered electrode. Since at those energies the mean free path for large-angle scattering (momentum relaxation length) is comparable to, or exceeds the size of the discharge gap, these ‘ballistic’ electrons will not be fully scattered by the background gas as they traverse the inter-electrode space. We have performed test-particle simulations in which the features in the EVDF of electrons impacting the RF electrode are fully resolved at all energies. An analytical model has been developed to predict existence of peaked and step-like structures in the EVDF. Those features can be explained by analyzing the kinematics of electron trajectories in the discharge gap. Step-like structures in the EVDF near the powered electrode appear due to accumulation of electrons emitted from the dc electrode within a portion of the RF cycle, and their subsequent release. Trapping occurs when the RF

  14. Who Benefits from Homework Assignments?

    Science.gov (United States)

    Ronning, Marte

    2011-01-01

    Using Dutch data on pupils in elementary school this paper is the first empirical study to analyze whether assigning homework has a heterogeneous impact on pupil achievement. Addressing potential biases by using a difference-in-difference approach, I find that the test score gap is larger in classes where everybody gets homework than in classes…

  15. Assigning agents to a line

    DEFF Research Database (Denmark)

    Hougaard, Jens Leth; Moreno-Ternero, Juan D.; Østerdal, Lars Peter Raahave

    2014-01-01

    minimizing modification of the classic random priority method to solve this class of problems. We also provide some logical relations in our setting among standard axioms in the literature on assignment problems, and explore the robustness of our results to several extensions of our setting....

  16. Probabilistic analysis of power assignments

    NARCIS (Netherlands)

    Graaf, de Maurits; Manthey, Bodo

    2014-01-01

    A fundamental problem for wireless ad hoc networks is the assignment of suitable transmission powers to the wireless devices such that the resulting communication graph is connected. The goal is to minimize the total transmit power in order to maximize the life-time of the network. Our aim is a prob

  17. Preparation, Purification, and Secondary Structure Determination of Bacillus Circulans Xylanase. A Molecular Laboratory Incorporating Aspects of Molecular Biology, Biochemistry, and Biophysical Chemistry

    Science.gov (United States)

    Russo, Sal; Gentile, Lisa

    2006-01-01

    A project module designed for biochemistry or cellular and molecular biology student which involves determining the secondary structure of Bacillus circulans xylanase (BCX) by circular dichroism (CD) spectroscopy under conditions that compromise its stabilizing intramolecular forces is described. The lab model enhanced students knowledge of the…

  18. Prediction of the secondary structure of the mitochondrial tRNASer (UCN) of Lutzomyia hartmanni (Diptera: Psychodidae)

    International Nuclear Information System (INIS)

    Lutzomyia (Helcocyrtomyia) hartmanni is a sand fly that has been implicated in the transmission of Leishmania (Viannia) colombiensis, an etiologic agent of cutaneous Leishmaniasis in Colombia. The objective of this work was to explore the potential usefulness of the mitochondrial serine transfer RNA (UCN) (tRNASer) in the taxonomic determination of L. hartmanni. Mitochondrial DNA was extracted, amplified and sequenced from entomological material collected in Envigado, Antioquia, Colombia. The tRNASer gene length was 68 nucleotide pairs, with an average adenine-thymine content of 80.9%. The studied tRNASer differs from other sand fly tRNASer known to date, on the basis of its primary and secondary structure. The observed number of intrachain base pairing was 7 in the acceptor arm, 3 in the dihydrouridine (DHU) arm, 5 in the anticodon arm, and 5 in the ribothymidine-pseudouridine-cytosine (TC) arm. The size of the DHU, anticodon, variable and TC loops was estimated to be 5, 7, 4, and 8 nucleotides, respectively. The notorious absence of non-Watson-Crick base pairs in the four arms of the tRNASer distinguishes that of L. hartmanni from others Lutzomyia spp.

  19. Structural Incorporation of Uranium into Iron Oxides: A Competitive Secondary Sequestration Pathway Mediated by Fe(II)

    Science.gov (United States)

    Massey, M. S.; Lezama-Pacheco, J. S.; Nico, P. S.; Bargar, J.; Fendorf, S.

    2011-12-01

    Uranium retention and sequestration pathways determine the long-term fate of this important contaminant in soils and sediments. Direct, enzymatic U reduction and subsequent precipitation of UO2 is one potential sequestration pathway, but indirect U transformations can also occur as a result of reactions with microbially-generated Fe(II). Here we explored uranium retention mechanisms active during abiotic reduction of U(VI) by aqueous Fe(II), in the presence of ferrihydrite, in Ca and carbonate-bearing solutions. Ferrihydrite transformation and U reduction were studied in batch incubations containing Ca (0 and 4 mM), carbonate (3.8 mM), ferrihydrite (~180 mg/L), Fe(II) (0.3 mM), and a range of concentrations of uranyl (1 to 170 μM). Uranium retention pathways were differentiated using extended x-ray absorption fine structure (EXAFS) spectroscopy and synchrotron X-ray powder diffraction. At U concentrations >50 μM, U(VI) reduction to U(IV) and subsequent precipitation of UO2 was a dominant sequestration pathway. At lower U concentrations (1-10 μM), UO2 precipitation was not observed and incorporation into goethite, the secondary transformation product of ferrihydrite, was dominant. For groundwaters having micromolar U(VI) concentrations, U incorporation into ferrihydrite transformation products via microbially-produced Fe(II) may be an important sequestration process.

  20. Isolation and structure elucidation of secondary metabolites in Central and South American Calea species and their biochemical systematic implications

    International Nuclear Information System (INIS)

    Fourteen species of the genus Calea (Family Compositae, Tribe Heliantheae) from Central and northern South America, including the type species for the genus, were investigated chemically to determine their secondary metabolites. The taxa studied were C. leptocephala Blake, C. megacephala Rob, and Greenm., and C. trichotoma B. Smith from Mexico, C. prunifolia Kunth (syn. C. pittieri) from Costa Rica, C. prunifolia Kunth from Panama, C. jamaicensis L. from Jamaica, and the Venezuelan species C. berteriana DC., C. divaricata Benthem, C. oliverii Rob. and Greenm., C. prunifolia Kunth, C. septuplinervia Hieron., C. solidaginea Kunth, and C. subcordata Kunth. The chemical investigation of these Calea species, undertaken as part of biochemical systematic study, has resulted in the isolation of 83 compounds, of which 38 are new natural products. The isolated compounds were represented by a dioxin derivative, 3 benzofuranes, 5 chromenes, 12 flavones, and 62 sesquiterpene lactones. The structures of the new compounds were established by chemical and spectroscopic methods. These methods included MS, IR, UV, and CD, 1H NMR, 13C NMR, and single crystal x-ray diffraction analysis

  1. Structure and functional characterization of a bile acid 7α dehydratase BaiE in secondary bile acid synthesis.

    Science.gov (United States)

    Bhowmik, Shiva; Chiu, Hsien-Po; Jones, David H; Chiu, Hsiu-Ju; Miller, Mitchell D; Xu, Qingping; Farr, Carol L; Ridlon, Jason M; Wells, James E; Elsliger, Marc-André; Wilson, Ian A; Hylemon, Phillip B; Lesley, Scott A

    2016-03-01

    Conversion of the primary bile acids cholic acid (CA) and chenodeoxycholic acid (CDCA) to the secondary bile acids deoxycholic acid (DCA) and lithocholic acid (LCA) is performed by a few species of intestinal bacteria in the genus Clostridium through a multistep biochemical pathway that removes a 7α-hydroxyl group. The rate-determining enzyme in this pathway is bile acid 7α-dehydratase (baiE). In this study, crystal structures of apo-BaiE and its putative product-bound [3-oxo-Δ(4,6) -lithocholyl-Coenzyme A (CoA)] complex are reported. BaiE is a trimer with a twisted α + β barrel fold with similarity to the Nuclear Transport Factor 2 (NTF2) superfamily. Tyr30, Asp35, and His83 form a catalytic triad that is conserved across this family. Site-directed mutagenesis of BaiE from Clostridium scindens VPI 12708 confirm that these residues are essential for catalysis and also the importance of other conserved residues, Tyr54 and Arg146, which are involved in substrate binding and affect catalytic turnover. Steady-state kinetic studies reveal that the BaiE homologs are able to turn over 3-oxo-Δ(4) -bile acid and CoA-conjugated 3-oxo-Δ(4) -bile acid substrates with comparable efficiency questioning the role of CoA-conjugation in the bile acid metabolism pathway. PMID:26650892

  2. Investigation of an Immunoassay with Broad Specificity to Quinolone Drugs by Genetic Algorithm with Linear Assignment of Hypermolecular Alignment of Data Sets and Advanced Quantitative Structure-Activity Relationship Analysis.

    Science.gov (United States)

    Chen, Jiahong; Lu, Ning; Shen, Xing; Tang, Qiushi; Zhang, Chijian; Xu, Jun; Sun, Yuanming; Huang, Xin-An; Xu, Zhenlin; Lei, Hongtao

    2016-04-01

    A polyclonal antibody against the quinolone drug pazufloxacin (PAZ) but with surprisingly broad specificity was raised to simultaneously detect 24 quinolones (QNs). The developed competitive indirect enzyme-linked immunosorbent assay (ciELISA) exhibited limits of detection (LODs) for the 24 QNs ranging from 0.45 to 15.16 ng/mL, below the maximum residue levels (MRLs). To better understand the obtained broad specificity, a genetic algorithm with linear assignment of hypermolecular alignment of data sets (GALAHAD) was used to generate the desired pharmacophore model and superimpose the QNs, and then advanced comparative molecular field analysis (CoMFA) and advanced comparative molecular similarity indices analysis (CoMSIA) models were employed to study the three-dimensional quantitative structure-activity relationship (3D QSAR) between QNs and the antibody. It was found that the QNs could interact with the antibody with different binding poses, and cross-reactivity was mainly positively correlated with the bulky substructure containing electronegative atom at the 7-position, while it was negatively associated with the large bulky substructure at the 1-position of QNs. PMID:26982746

  3. MicroRNA prediction using a fixed-order Markov model based on the secondary structure pattern.

    Directory of Open Access Journals (Sweden)

    Wei Shen

    Full Text Available Predicting miRNAs is an arduous task, due to the diversity of the precursors and complexity of enzyme processes. Although several prediction approaches have reached impressive performances, few of them could achieve a full-function recognition of mature miRNA directly from the candidate hairpins across species. Therefore, researchers continue to seek a more powerful model close to biological recognition to miRNA structure. In this report, we describe a novel miRNA prediction algorithm, known as FOMmiR, using a fixed-order Markov model based on the secondary structural pattern. For a training dataset containing 809 human pre-miRNAs and 6441 human pseudo-miRNA hairpins, the model's parameters were defined and evaluated. The results showed that FOMmiR reached 91% accuracy on the human dataset through 5-fold cross-validation. Moreover, for the independent test datasets, the FOMmiR presented an outstanding prediction in human and other species including vertebrates, Drosophila, worms and viruses, even plants, in contrast to the well-known algorithms and models. Especially, the FOMmiR was not only able to distinguish the miRNA precursors from the hairpins, but also locate the position and strand of the mature miRNA. Therefore, this study provides a new generation of miRNA prediction algorithm, which successfully realizes a full-function recognition of the mature miRNAs directly from the hairpin sequences. And it presents a new understanding of the biological recognition based on the strongest signal's location detected by FOMmiR, which might be closely associated with the enzyme cleavage mechanism during the miRNA maturation.

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

    Science.gov (United States)

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

    2015-03-01

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

  5. Fleet Assignment Using Collective Intelligence

    Science.gov (United States)

    Antoine, Nicolas E.; Bieniawski, Stefan R.; Kroo, Ilan M.; Wolpert, David H.

    2004-01-01

    Product distribution theory is a new collective intelligence-based framework for analyzing and controlling distributed systems. Its usefulness in distributed stochastic optimization is illustrated here through an airline fleet assignment problem. This problem involves the allocation of aircraft to a set of flights legs in order to meet passenger demand, while satisfying a variety of linear and non-linear constraints. Over the course of the day, the routing of each aircraft is determined in order to minimize the number of required flights for a given fleet. The associated flow continuity and aircraft count constraints have led researchers to focus on obtaining quasi-optimal solutions, especially at larger scales. In this paper, the authors propose the application of this new stochastic optimization algorithm to a non-linear objective cold start fleet assignment problem. Results show that the optimizer can successfully solve such highly-constrained problems (130 variables, 184 constraints).

  6. Who benefits from homework assignments?

    OpenAIRE

    Rønning, Marte

    2008-01-01

    Abstract: Using Dutch data on pupils in elementary school this paper is the first empirical study that analyzes whether assigning homework has an heterogeneous impact on pupil achievement. Addressing potential biases that arise from unobserved school quality, pupil selection by exploiting different methods, I find that the test score gap is larger in classes where everybody gets homework than in classes where nobody gets homework. More precisely pupils belonging to the upper part of the so...

  7. Relevant Explanations: Allowing Disjunctive Assignments

    OpenAIRE

    Shimony, Solomon Eyal

    2013-01-01

    Relevance-based explanation is a scheme in which partial assignments to Bayesian belief network variables are explanations (abductive conclusions). We allow variables to remain unassigned in explanations as long as they are irrelevant to the explanation, where irrelevance is defined in terms of statistical independence. When multiple-valued variables exist in the system, especially when subsets of values correspond to natural types of events, the over specification problem, alleviated by inde...

  8. Application of secondary and residual stresses to the assessment of the structural integrity of nuclear power-generating plant

    International Nuclear Information System (INIS)

    Magnox nuclear power stations were built in the 1960s to design codes that, in general, required weldments to be subject to a post-weld heat treatment to remove residual stresses. Implicit in this was the assumption that the heat treatment reduced the stresses significantly such that as stated in the codes 'stresses caused by fabrication and welding are practically annulled'. However, it has since been realised that the stresses remaining, although small, could still be significant when incorporated into the subsequently developed failure avoidance methodologies such as R6. Moreover, either at the time of construction or during the operating life, repairs are undertaken to remove manufacturing or service-induced defects. These repairs can be put into service with or without a post-weld heat treatment. As a consequence of a paucity of data for the two- and three-dimensional distribution of the magnitude of these stresses, extremely conservative values of stresses have been adopted to ensure that the plant is secure against the design intent throughout the service life. In this paper, the requirements of the failure-avoidance methodology R6 Revision 4 are briefly reviewed with respect to the categorisation of secondary and residual stresses and the application of the three approaches for determining the as-welded residual stress distribution at room temperature. These three levels comprise, Level 1, simple estimates, Level 2, bounding profiles, and Level 3, detailed evaluation. Examples are presented where knowledge of the residual stresses has been an important component of the overall integrity assessment. The first relates to multi-pass weldments in superheater headers fabricated from a ferritic steel and the second to the weldments in the standpipes, both at Magnox power stations with concrete pressure vessels. Although in these cases the weldments had been subject to a post-weld heat treatment, the remaining residual stresses presented a significant challenge to

  9. Detection of non-coding RNAs on the basis of predicted secondary structure formation free energy change

    Directory of Open Access Journals (Sweden)

    Uzilov Andrew V

    2006-03-01

    Full Text Available Abstract Background Non-coding RNAs (ncRNAs have a multitude of roles in the cell, many of which remain to be discovered. However, it is difficult to detect novel ncRNAs in biochemical screens. To advance biological knowledge, computational methods that can accurately detect ncRNAs in sequenced genomes are therefore desirable. The increasing number of genomic sequences provides a rich dataset for computational comparative sequence analysis and detection of novel ncRNAs. Results Here, Dynalign, a program for predicting secondary structures common to two RNA sequences on the basis of minimizing folding free energy change, is utilized as a computational ncRNA detection tool. The Dynalign-computed optimal total free energy change, which scores the structural alignment and the free energy change of folding into a common structure for two RNA sequences, is shown to be an effective measure for distinguishing ncRNA from randomized sequences. To make the classification as a ncRNA, the total free energy change of an input sequence pair can either be compared with the total free energy changes of a set of control sequence pairs, or be used in combination with sequence length and nucleotide frequencies as input to a classification support vector machine. The latter method is much faster, but slightly less sensitive at a given specificity. Additionally, the classification support vector machine method is shown to be sensitive and specific on genomic ncRNA screens of two different Escherichia coli and Salmonella typhi genome alignments, in which many ncRNAs are known. The Dynalign computational experiments are also compared with two other ncRNA detection programs, RNAz and QRNA. Conclusion The Dynalign-based support vector machine method is more sensitive for known ncRNAs in the test genomic screens than RNAz and QRNA. Additionally, both Dynalign-based methods are more sensitive than RNAz and QRNA at low sequence pair identities. Dynalign can be used as a

  10. A New Approach to Pointer Analysis for Assignments

    Institute of Scientific and Technical Information of China (English)

    HUANG Bo; ZANG Binyu; LI Jing; ZHU Chuanqi

    2001-01-01

    Pointer analysis is a technique to identify at compile-time the po tential values of the pointer expressions in a program, which promises significant benefits for optimizing and parallelizing compilers. In this paper, a new approach to pointer analysis for assignments is presented. In this approach, assignments are clas sified into three categories: pointer assignments, structure (union) assignments and normal assignments which don't affect the point-to information. Pointer analyses for these three kinds of assignments respectively make up the integrated algorithm. When analyzing a pointer assignment, a new method called expression expansion is used to calculate both the left targets and the right targets. The integration of recursive data structure analysis into pointer analysis is a significant originality of this paper, which uniforms the pointer analysis for heap variables and the pointer analysis for stack variables. This algorithm is implemented in Agassiz, an analyzing tool for C programs developed by Institute of Parallel Processing, Fudan University. Its accuracy and effectiveness are illustrated by experimental data.

  11. Secondary parkinsonism

    Science.gov (United States)

    Parkinsonism - secondary; Atypical Parkinson disease ... to be less responsive to medical therapy than Parkinson disease. ... Unlike Parkinson disease, some types of secondary parkinsonism may stabilize or even improve if the underlying cause is treated. ...

  12. NMR assignments of the N-terminal domain of Ogataea polymorpha telomerase reverse transcriptase.

    Science.gov (United States)

    Polshakov, Vladimir I; Petrova, Olga A; Parfenova, Yulia Yu; Efimov, Sergey V; Klochkov, Vladimir V; Zvereva, Maria I; Dontsova, Olga A

    2016-04-01

    Telomerase is a ribonucleoprotein enzyme that adds telomeric DNA fragments to the ends of chromosomes. This enzyme is the focus of substantial attention, both because its structure and mechanism of action are still poorly studied, and because of its pivotal roles in aging and cellular proliferation. The use of telomerase as a potential target for the design of new anticancer drugs is also of great interest. The catalytic protein subunit of telomerase (TERT) contains an N-terminal domain (TEN) that is essential for activity and processivity. Elucidation of the structure and dynamics of TEN in solution is important for understanding the molecular mechanism of telomerase activity and for the design of new telomerase inhibitors. To approach this problem, in this study we report the (1)H, (13)C, and (15)N chemical shift assignments of TEN from Ogataea polymorpha. Analysis of the assigned chemical shifts allowed us to identify secondary structures and protein regions potentially involved in interaction with other participants of the telomerase catalytic cycle. PMID:26721464

  13. A Statistical Programme Assignment Model

    DEFF Research Database (Denmark)

    Rosholm, Michael; Staghøj, Jonas; Svarer, Michael

    When treatment effects of active labour market programmes are heterogeneous in an observable way  across the population, the allocation of the unemployed into different programmes becomes a particularly  important issue. In this paper, we present a statistical model designed to improve the present...... duration of unemployment spells may result if a statistical programme assignment model is introduced. We discuss several issues regarding the  plementation of such a system, especially the interplay between the statistical model and  case workers....

  14. Triterpenóides pentacíclicos de Mentha villosa: identificação estrutural e atribuição dos deslocamentos químicos dos átomos de hidrogênio e carbono Pentacyclic triterpenoids of Mentha villosa: structural identification and ¹H and 13C resonance assignments

    OpenAIRE

    Francisco J. Queiroz Monte; Eliete F. de Oliveira; Raimundo Braz Filho

    2001-01-01

    The structures of seven oleanene and ursene triterpenoids (1-7) isolated from aerial parts of Mentha villosa were identified. In addition, the complete ¹H and 13C resonance assignments of these triterpenoids were accomplished using 1D and 2D NMR spectroscopic experiments.

  15. Influence of high-molecular-weight glutenin subunit composition at Glu-B1 locus on secondary and micro structures of gluten in wheat (Triticum aestivum L.).

    Science.gov (United States)

    Gao, Xin; Liu, Tianhong; Yu, Jing; Li, Liqun; Feng, Yi; Li, Xuejun

    2016-04-15

    Glutenin is one of the critical gluten proteins that affect the processing quality of wheat dough. High-molecular-weight glutenin subunits (HMW-GS) affect rheological behavior of wheat dough. This research demonstrated the effects of four variations of HMW-GS composition at the Glu-B1 locus on secondary and micro structures of gluten and rheological properties of wheat dough, using the bread wheat Xinong 1330 and its three near-isogenic lines (NILs). Results indicated that the Amide I bands of the four wheat lines shifted slightly, but the secondary structure, such as content of α-helices, β-sheets, disulfide bands, tryptophan bands and tyrosine bands, differed significantly among the four NILs. The micro structure of gluten in NIL 2 (Bx14+By15) and NIL 3 (Bx17+By18) showed more cross linkage, with two contrasting patterns. Correlation analysis demonstrated that the content of β-sheets and disulfide bonds has a significant relationship with dough stability, which suggests that the secondary structures could be used as predictors of wheat quality. PMID:26675856

  16. An efficient method for the prediction of deleterious multiple-point mutations in the secondary structure of RNAs using suboptimal folding solutions

    Directory of Open Access Journals (Sweden)

    Barash Danny

    2008-04-01

    Full Text Available Abstract Background RNAmute is an interactive Java application which, given an RNA sequence, calculates the secondary structure of all single point mutations and organizes them into categories according to their similarity to the predicted structure of the wild type. The secondary structure predictions are performed using the Vienna RNA package. A more efficient implementation of RNAmute is needed, however, to extend from the case of single point mutations to the general case of multiple point mutations, which may often be desired for computational predictions alongside mutagenesis experiments. But analyzing multiple point mutations, a process that requires traversing all possible mutations, becomes highly expensive since the running time is O(nm for a sequence of length n with m-point mutations. Using Vienna's RNAsubopt, we present a method that selects only those mutations, based on stability considerations, which are likely to be conformational rearranging. The approach is best examined using the dot plot representation for RNA secondary structure. Results Using RNAsubopt, the suboptimal solutions for a given wild-type sequence are calculated once. Then, specific mutations are selected that are most likely to cause a conformational rearrangement. For an RNA sequence of about 100 nts and 3-point mutations (n = 100, m = 3, for example, the proposed method reduces the running time from several hours or even days to several minutes, thus enabling the practical application of RNAmute to the analysis of multiple-point mutations. Conclusion A highly efficient addition to RNAmute that is as user friendly as the original application but that facilitates the practical analysis of multiple-point mutations is presented. Such an extension can now be exploited prior to site-directed mutagenesis experiments by virologists, for example, who investigate the change of function in an RNA virus via mutations that disrupt important motifs in its secondary

  17. Moving beyond "Bookish Knowledge": Using Film-Based Assignments to Promote Deep Learning

    Science.gov (United States)

    Olson, Joann S.; Autry, Linda; Moe, Jeffry

    2016-01-01

    This article investigates the effectiveness of a film-based assignment given to adult learners in a graduate-level group counseling class. Semi-structured interviews were conducted with four students; data analysis suggested film-based assignments may promote deep approaches to learning (DALs). Participants indicated the assignment helped them…

  18. Waste management - textbook for secondary schools

    International Nuclear Information System (INIS)

    This text-book consist of five parts: (I) Waste management; (II) Solid waste management; (III) Recovery and recycling of secondary raw materials; (IV) Radioactive waste management; Examples of verification knowledge and testing of the secondary students through the worksheet. (V) Suggestions for leisure time activities. This text-book is assigned for high school students.

  19. Molecular evolution of rDNA in early diverging Metazoa: First comparative analysis and phylogenetic application of complete SSU rRNA secondary structures in Porifera

    OpenAIRE

    Wörheide Gert; Erpenbeck Dirk; Voigt Oliver

    2008-01-01

    Abstract Background The cytoplasmic ribosomal small subunit (SSU, 18S) ribosomal RNA (rRNA) is the most frequently-used gene for molecular phylogenetic studies. However, information regarding its secondary structure is neglected in most phylogenetic analyses. Incorporation of this information is essential in order to apply specific rRNA evolutionary models to overcome the problem of co-evolution of paired sites, which violates the basic assumption of the independent evolution of sites made by...

  20. Secondary structure and feature of mitochondrial tRNA genes of the Ussurian tube-nosed bat Murina ussuriensis (Chiroptera: Vespertilionidae)

    OpenAIRE

    Kwang Bae Yoon; Yung Chul Park

    2015-01-01

    The complete mitogenome (NC_021119) of the Ussurian tube-nosed bat Murina ussuriensis (Chiroptera: Vespertilionidae) was annotated and characterized in our recent publication (http://www.ncbi.nlm.nih.gov/nuccore/NC_021119). Here we provide additional information on methods in detail for obtaining the complete sequence of M. ussuriensis mitogenome. In addition, we describe characteristics of 22 tRNA genes and secondary structure and feature of 22 tRNAs of M. ussuriensis mitogenome.

  1. Chemical composition, molecular weight distribution, secondary structure and effect of NaCl on functional properties of walnut (Juglans regia L) protein isolates and concentrates

    OpenAIRE

    Mao, Xiao-Ying; Hua, Yu-Fei

    2012-01-01

    Chemical composition, molecular weight distribution, secondary structure and effect of sodium chloride concentration on functional properties of walnut protein isolates, concentrates and defatted walnut flour were study. Compared with walnut protein concentrates (75.6%) and defatted walnut flour (52.5%), walnut protein isolates contain a relatively high amount of protein (90.5%). The yield of walnut protein isolates and concentrates was 43.2% and 76.6%, respectively. In molecular weight distr...

  2. Secondary structure and feature of mitochondrial tRNA genes of the Ussurian tube-nosed bat Murina ussuriensis (Chiroptera: Vespertilionidae

    Directory of Open Access Journals (Sweden)

    Kwang Bae Yoon

    2015-09-01

    Full Text Available The complete mitogenome (NC_021119 of the Ussurian tube-nosed bat Murina ussuriensis (Chiroptera: Vespertilionidae was annotated and characterized in our recent publication (http://www.ncbi.nlm.nih.gov/nuccore/NC_021119. Here we provide additional information on methods in detail for obtaining the complete sequence of M. ussuriensis mitogenome. In addition, we describe characteristics of 22 tRNA genes and secondary structure and feature of 22 tRNAs of M. ussuriensis mitogenome.

  3. Fiber-Optic-Based Pressure and Residual Strain Monitoring in CFRP Bonding Process: Toward Realization of Secondary Bonding in CFRP Aircraft Structures

    OpenAIRE

    Minakuchi, Shu; Uhira, Keigo; TERADA, Yutaka; Takeda, Nobuo; Saito, Nozomi; Shimizu, Takayuki

    2014-01-01

    Applying secondary bonding to places where carbon fiber reinforced plastic (CFRP) structures are conventionally bolted leads to significant cost and weight saving. However, it has yet to be utilized due to difficulties in quality control. Lack of local pressure in bonding process has detrimental influence on the quality of the cured adhesive layer. Pressure detection is hence a key for controlling bonding quality, and a new quality assurance technique is urgently needed. This study establishe...

  4. Assignment Choice, Effort, and Assignment Completion: Does Work Ethic Predict Those Who Choose Higher-Effort Assignments?

    Science.gov (United States)

    Parkhurst, John T.; Fleisher, Matthew S.; Skinner, Christopher H.; Woehr, David J.; Hawthorn-Embree, Meredith L.

    2011-01-01

    After completing the Multidimensional Work-Ethic Profile (MWEP), 98 college students were given a 20-problem math computation assignment and instructed to stop working on the assignment after completing 10 problems. Next, they were allowed to choose to finish either the partially completed assignment that had 10 problems remaining or a new…

  5. Signs of Selection in Synonymous Sites of the Mitochondrial Cytochrome b Gene of Baikal Oilfish (Comephoridae by mRNA Secondary Structure Alterations

    Directory of Open Access Journals (Sweden)

    Veronika I. Teterina

    2015-01-01

    Full Text Available Studies over the past decade have shown a significant role of synonymous mutations in posttranscriptional regulation of gene expression, which is particularly associated with messenger RNA (mRNA secondary structure alterations. Most studies focused on prokaryote genomes and the nuclear genomes of eukaryotes while little is known about the regulation of mitochondrial DNA (mtDNA gene expression. This paper reveals signs of selection in synonymous sites of the mitochondrial cytochrome b gene (Cytb of Baikal oilfish or golomyankas (Comephoridae directed towards altering the secondary structure of the mRNA and probably altering the character of mtDNA gene expression. Our findings are based on comparisons of intraspecific genetic variation patterns of small golomyanka (Comephorus dybowski and two genetic groups of big golomyanka (Comephorus dybowskii. Two approaches were used: (i analysis of the distribution of synonymous mutations between weak-AT (W and strong-GC (S nucleotides within species and groups in accordance with mutation directions from central to peripheral haplotypes and (ii approaches based on the predicted mRNA secondary structure.

  6. Amyloid-β-Secondary Structure Distribution in Cerebrospinal Fluid and Blood Measured by an Immuno-Infrared-Sensor: A Biomarker Candidate for Alzheimer's Disease.

    Science.gov (United States)

    Nabers, Andreas; Ollesch, Julian; Schartner, Jonas; Kötting, Carsten; Genius, Just; Hafermann, Henning; Klafki, Hans; Gerwert, Klaus; Wiltfang, Jens

    2016-03-01

    The misfolding of the Amyloid-beta (Aβ) peptide into β-sheet enriched conformations was proposed as an early event in Alzheimer's Disease (AD). Here, the Aβ peptide secondary structure distribution in cerebrospinal fluid (CSF) and blood plasma of 141 patients was measured with an immuno-infrared-sensor. The sensor detected the amide I band, which reflects the overall secondary structure distribution of all Aβ peptides extracted from the body fluid. We observed a significant downshift of the amide I band frequency of Aβ peptides in Dementia Alzheimer type (DAT) patients, which indicated an overall shift to β-sheet. The secondary structure distribution of all Aβ peptides provides a better marker for DAT detection than a single Aβ misfold or the concentration of a specific oligomer. The discrimination between DAT and disease control patients according to the amide I frequency was in excellent agreement with the clinical diagnosis (accuracy 90% for CSF and 84% for blood). The amide I band maximum above or below the decisive marker frequency appears as a novel spectral biomarker candidate of AD. Additionally, a preliminary proof-of-concept study indicated an amide I band shift below the marker band already in patients with mild cognitive impairment due to AD. The presented immuno-IR-sensor method represents a promising, simple, robust, and label-free diagnostic tool for CSF and blood analysis. PMID:26828829

  7. Secondary structure analyses of the nuclear rRNA internal transcribed spacers and assessment of its phylogenetic utility across the Brassicaceae (mustards).

    Science.gov (United States)

    Edger, Patrick P; Tang, Michelle; Bird, Kevin A; Mayfield, Dustin R; Conant, Gavin; Mummenhoff, Klaus; Koch, Marcus A; Pires, J Chris

    2014-01-01

    The internal transcribed spacers of the nuclear ribosomal RNA gene cluster, termed ITS1 and ITS2, are the most frequently used nuclear markers for phylogenetic analyses across many eukaryotic groups including most plant families. The reasons for the popularity of these markers include: 1.) Ease of amplification due to high copy number of the gene clusters, 2.) Available cost-effective methods and highly conserved primers, 3.) Rapidly evolving markers (i.e. variable between closely related species), and 4.) The assumption (and/or treatment) that these sequences are non-functional, neutrally evolving phylogenetic markers. Here, our analyses of ITS1 and ITS2 for 50 species suggest that both sequences are instead under selective constraints to preserve proper secondary structure, likely to maintain complete self-splicing functions, and thus are not neutrally-evolving phylogenetic markers. Our results indicate the majority of sequence sites are co-evolving with other positions to form proper secondary structure, which has implications for phylogenetic inference. We also found that the lowest energy state and total number of possible alternate secondary structures are highly significantly different between ITS regions and random sequences with an identical overall length and Guanine-Cytosine (GC) content. Lastly, we review recent evidence highlighting some additional problematic issues with using these regions as the sole markers for phylogenetic studies, and thus strongly recommend additional markers and cost-effective approaches for future studies to estimate phylogenetic relationships. PMID:24984034

  8. Secondary structure analyses of the nuclear rRNA internal transcribed spacers and assessment of its phylogenetic utility across the Brassicaceae (mustards.

    Directory of Open Access Journals (Sweden)

    Patrick P Edger

    Full Text Available The internal transcribed spacers of the nuclear ribosomal RNA gene cluster, termed ITS1 and ITS2, are the most frequently used nuclear markers for phylogenetic analyses across many eukaryotic groups including most plant families. The reasons for the popularity of these markers include: 1. Ease of amplification due to high copy number of the gene clusters, 2. Available cost-effective methods and highly conserved primers, 3. Rapidly evolving markers (i.e. variable between closely related species, and 4. The assumption (and/or treatment that these sequences are non-functional, neutrally evolving phylogenetic markers. Here, our analyses of ITS1 and ITS2 for 50 species suggest that both sequences are instead under selective constraints to preserve proper secondary structure, likely to maintain complete self-splicing functions, and thus are not neutrally-evolving phylogenetic markers. Our results indicate the majority of sequence sites are co-evolving with other positions to form proper secondary structure, which has implications for phylogenetic inference. We also found that the lowest energy state and total number of possible alternate secondary structures are highly significantly different between ITS regions and random sequences with an identical overall length and Guanine-Cytosine (GC content. Lastly, we review recent evidence highlighting some additional problematic issues with using these regions as the sole markers for phylogenetic studies, and thus strongly recommend additional markers and cost-effective approaches for future studies to estimate phylogenetic relationships.

  9. Performance of a neural-network-based determination of amino acid class and secondary structure from 1H-15N NMR data

    International Nuclear Information System (INIS)

    A neural network which can determine both amino acid class and secondary structure using NMR data from 15N-labeled proteins is described. We have included nitrogen chemical shifts,3JHNHα coupling constants, α-proton chemical shifts, and side-chain proton chemical shifts as input to a three-layer feed-forward network. The network was trained with 456 spin systems from several proteins containing various types of secondary structure, and tested on human ubiquitin, which has no sequence homology with any of the proteins in the training set. A very limited set of data,representative of those from a TOCSY-HSQC and HNHA experiment, was used.Nevertheless, in 60% of the spin systems the correct amino acid class was among the top two choices given by the network, while in 96% of the spin systems the secondary structure was correctly identified. The performance of this network clearly shows the potential of the neural network algorithm in the automation of NMR spectral analysis

  10. Extensive de novo solid-state NMR assignments of the 33 kDa C-terminal domain of the Ure2 prion

    International Nuclear Information System (INIS)

    We present the de novo resonance assignments for the crystalline 33 kDa C-terminal domain of the Ure2 prion using an optimized set of five 3D solid-state NMR spectra. We obtained, using a single uniformly 13C, 15N labeled protein sample, sequential chemical-shift information for 74% of the N, Cα, Cβ triples, and for 80% of further side-chain resonances for these spin systems. We describe the procedures and protocols devised, and discuss possibilities and limitations of the assignment of this largest protein assigned today by solid-state NMR, and for which no solution-state NMR shifts were available. A comparison of the NMR chemical shifts with crystallographic data reveals that regions with high crystallographic B-factors are particularly difficult to assign. While the secondary structure elements derived from the chemical shift data correspond mainly to those present in the X-ray crystal structure, we detect an additional helical element and structural variability in the protein crystal, most probably originating from the different molecules in the asymmetric unit, with the observation of doubled resonances in several parts, including entire stretches, of the protein. Our results provide the point of departure towards an atomic-resolution structural analysis of the C-terminal Ure2p domain in the context of the full-length prion fibrils.

  11. Extensive de novo solid-state NMR assignments of the 33 kDa C-terminal domain of the Ure2 prion

    Energy Technology Data Exchange (ETDEWEB)

    Habenstein, Birgit [UMR 5086 CNRS/Universite de Lyon 1, Institut de Biologie et Chimie des Proteines (France); Wasmer, Christian [Harvard Medical School (United States); Bousset, Luc; Sourigues, Yannick [UPR 3082 CNRS, Laboratoire d' Enzymologie et Biochimie Structurales (France); Schuetz, Anne [ETH Zurich, Physical Chemistry (Switzerland); Loquet, Antoine [Max Planck Institute for Biophysical Chemistry (Germany); Meier, Beat H., E-mail: beme@ethz.ch [ETH Zurich, Physical Chemistry (Switzerland); Melki, Ronald, E-mail: melki@lebs.cnrs-gif.fr [UPR 3082 CNRS, Laboratoire d' Enzymologie et Biochimie Structurales (France); Boeckmann, Anja, E-mail: a.bockmann@ibcp.fr [UMR 5086 CNRS/Universite de Lyon 1, Institut de Biologie et Chimie des Proteines (France)

    2011-11-15

    We present the de novo resonance assignments for the crystalline 33 kDa C-terminal domain of the Ure2 prion using an optimized set of five 3D solid-state NMR spectra. We obtained, using a single uniformly {sup 13}C, {sup 15}N labeled protein sample, sequential chemical-shift information for 74% of the N, C{alpha}, C{beta} triples, and for 80% of further side-chain resonances for these spin systems. We describe the procedures and protocols devised, and discuss possibilities and limitations of the assignment of this largest protein assigned today by solid-state NMR, and for which no solution-state NMR shifts were available. A comparison of the NMR chemical shifts with crystallographic data reveals that regions with high crystallographic B-factors are particularly difficult to assign. While the secondary structure elements derived from the chemical shift data correspond mainly to those present in the X-ray crystal structure, we detect an additional helical element and structural variability in the protein crystal, most probably originating from the different molecules in the asymmetric unit, with the observation of doubled resonances in several parts, including entire stretches, of the protein. Our results provide the point of departure towards an atomic-resolution structural analysis of the C-terminal Ure2p domain in the context of the full-length prion fibrils.

  12. [Secondary hypertension].

    Science.gov (United States)

    Yoshida, Yuichi; Shibata, Hirotaka

    2015-11-01

    Hypertension is a common disease and a crucial predisposing factor of cardiovascular diseases. Approximately 10% of hypertensive patients are secondary hypertension, a pathogenetic factor of which can be identified. Secondary hypertension consists of endocrine, renal, and other diseases. Primary aldosteronism, Cushing's syndrome, pheochromocytoma, hyperthyroidism, and hypothyroidism result in endocrine hypertension. Renal parenchymal hypertension and renovascular hypertension result in renal hypertension. Other diseases such as obstructive sleep apnea syndrome are also very prevalent in secondary hypertension. It is very crucial to find and treat secondary hypertension at earlier stages since most secondary hypertension is curable or can be dramatically improved by specific treatment. One should keep in mind that screening of secondary hypertension should be done at least once in a daily clinical practice. PMID:26619670

  13. DNATCO: assignment of DNA conformers at dnatco.org.

    Science.gov (United States)

    Černý, Jiří; Božíková, Paulína; Schneider, Bohdan

    2016-07-01

    The web service DNATCO (dnatco.org) classifies local conformations of DNA molecules beyond their traditional sorting to A, B and Z DNA forms. DNATCO provides an interface to robust algorithms assigning conformation classes called NTC: to dinucleotides extracted from DNA-containing structures uploaded in PDB format version 3.1 or above. The assigned dinucleotide NTC: classes are further grouped into DNA structural alphabet NTA: , to the best of our knowledge the first DNA structural alphabet. The results are presented at two levels: in the form of user friendly visualization and analysis of the assignment, and in the form of a downloadable, more detailed table for further analysis offline. The website is free and open to all users and there is no login requirement. PMID:27150812

  14. Solving multiconstraint assignment problems using learning automata.

    Science.gov (United States)

    Horn, Geir; Oommen, B John

    2010-02-01

    This paper considers the NP-hard problem of object assignment with respect to multiple constraints: assigning a set of elements (or objects) into mutually exclusive classes (or groups), where the elements which are "similar" to each other are hopefully located in the same class. The literature reports solutions in which the similarity constraint consists of a single index that is inappropriate for the type of multiconstraint problems considered here and where the constraints could simultaneously be contradictory. This feature, where we permit possibly contradictory constraints, distinguishes this paper from the state of the art. Indeed, we are aware of no learning automata (or other heuristic) solutions which solve this problem in its most general setting. Such a scenario is illustrated with the static mapping problem, which consists of distributing the processes of a parallel application onto a set of computing nodes. This is a classical and yet very important problem within the areas of parallel computing, grid computing, and cloud computing. We have developed four learning-automata (LA)-based algorithms to solve this problem: First, a fixed-structure stochastic automata algorithm is presented, where the processes try to form pairs to go onto the same node. This algorithm solves the problem, although it requires some centralized coordination. As it is desirable to avoid centralized control, we subsequently present three different variable-structure stochastic automata (VSSA) algorithms, which have superior partitioning properties in certain settings, although they forfeit some of the scalability features of the fixed-structure algorithm. All three VSSA algorithms model the processes as automata having first the hosting nodes as possible actions; second, the processes as possible actions; and, third, attempting to estimate the process communication digraph prior to probabilistically mapping the processes. This paper, which, we believe, comprehensively reports the

  15. Burnout: Testing for the Validity, Replication, and Invariance of Causal Structure across Elementary, Intermediate, and Secondary Teachers.

    Science.gov (United States)

    Byrne, Barbara M.

    1994-01-01

    This study investigated the impact of organizational and personality factors on three factors of teacher burnout: emotional exhaustion, depersonalization, and reduced personal accomplishment. Results with 3,044 elementary, intermediate, and secondary teachers demonstrate that teacher burnout is not a unidimensional construct. (SLD)

  16. Cellular biopolymers and molecular structure of a secondary pulp and paper mill sludge verified by spectroscopy and chemical extraction techniques.

    Science.gov (United States)

    Edalatmanesh, Maryam; Sain, Mohini; Liss, Steven N

    2010-01-01

    For proper treatment, recycling, or disposal of the pulp and paper mill secondary sludge qualitative and quantitative determination of its characteristics are necessary. Chemical extraction, quantitative characterization, and spectroscopic experiments have been performed to determine the molecular composition and chemical functionality of a pulp and paper mill secondary sludge. In order to extract the low-molecular-weight substances, soxhlet extraction with polar and non-polar solvents was performed where most of the target substances (17±1.3%.) were extracted after 2 hours. Over time, this extraction followed a first-order kinetics. Fiber analyses have shown 12±3% lignin, 28±3% cellulose, and 12±4% hemicelluloses content. The ash content was about 17±0.5%. In this work, 7 and 16% intra- and extracellular polymeric substances, respectively, were extracted from the secondary sludge. EPS and mixture of intra- and extracellular biopolymers have shown similar chemical functionalities. These analyses confirmed that the paper secondary sludge consisted mainly of wood fiber, i.e. lignocellulosic substances, along with proteins and polysaccharides originated from microorganisms. PMID:21123914

  17. 7 CFR 1437.104 - Assigned production.

    Science.gov (United States)

    2010-01-01

    ... 7 Agriculture 10 2010-01-01 2010-01-01 false Assigned production. 1437.104 Section 1437.104... Determining Yield Coverage Using Actual Production History § 1437.104 Assigned production. (a) When determining losses under this section, assigned production will be used to offset the loss of production...

  18. Lexical Stress Assignment in Italian Developmental Dyslexia

    Science.gov (United States)

    Paizi, Despina; Zoccolotti, Pierluigi; Burani, Cristina

    2011-01-01

    Stress assignment to Italian polysyllabic words is unpredictable, because stress is neither marked nor predicted by rule. Stress assignment, especially to low frequency words, has been reported to be a function of stress dominance and stress neighbourhood. Two experiments investigate stress assignment in sixth-grade, skilled and dyslexic, readers.…

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

    Directory of Open Access Journals (Sweden)

    Sánchez Juan A

    2007-06-01

    Full Text Available Abstract 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 "morphological" information. Despite the number of recent molecular studies on octocorals, there is no consensus opinion about a region that carries enough phylogenetic resolution to solve intrageneric or close species relationships. Moreover, intrageneric morphological information by itself does not always produce accurate phylogenies; intra-species comparisons can reveal greater differences than intra-generic ones. The search for new phylogenetic approaches, such as by RNA secondary structure analysis, is therefore a priority in octocoral research. Results Initially, twelve predicted RNA secondary structures were reconstructed to provide the basic information for phylogenetic analyses; they accorded with the 6 helicoidal ring model, also present in other groups of corals and eukaryotes. We obtained three similar topologies for nine species of the Caribbean gorgonian genus Eunicea (candelabrum corals with two sister taxa as outgroups (genera Plexaura and Pseudoplexaura on the basis of molecular morphometrics of ITS2 RNA secondary structures only, traditional primary sequence analyses and maximum likelihood, and a Bayesian analysis of the combined data. The latter approach allowed us to include both primary sequence and RNA molecular morphometrics; each data partition was allowed to have a different evolution rate. In addition, each helix was partitioned as if it had evolved at a distinct rate. Plexaura flexuosa was found to group within Eunicea; this was best supported by both the molecular morphometrics and combined analyses. We suggest Eunicea flexuosa (Lamouroux, 1821 comb. nov., and we present a new species description including Scanning Electron Microscopy (SEM images of

  20. Sequential backbone resonance assignments of the E. coli dihydrofolate reductase Gly67Val mutant: folate complex.

    Science.gov (United States)

    Puthenpurackal Narayanan, Sunilkumar; Maeno, Akihiro; Wada, Yuji; Tate, Shin-Ichi; Akasaka, Kazuyuki

    2016-04-01

    Occasionally, a mutation in an exposed loop region causes a significant change in protein function and/or stability. A single mutation Gly67Val of E. coli dihydrofolate reductase (DHFR) in the exposed CD loop is such an example. We have carried out the chemical shift assignments for H(N), N(H), C(α) and C(β) atoms of the Gly67Val mutant of E. coli DHFR complexed with folate at pH 7.0, 35 °C, and then evaluated the H(N), N(H), C(α) and C(β) chemical shift changes caused by the mutation. The result indicates that, while the overall secondary structure remains the same, the single mutation Gly67Val causes site-specific conformational changes of the polypeptide backbone restricted around the adenosine-binding subdomain (residues 38-88) and not in the distant catalytic domain. PMID:26482924

  1. Effects of essential oil treatments on the secondary protein structure of Vicia faba: A mid-infrared spectroscopic study supported by two-dimensional correlation analysis

    Science.gov (United States)

    Mecozzi, Mauro; Sturchio, Elena

    2015-02-01

    In this study we investigated the effects of essential oil treatments on the secondary protein structure of the Vicia faba roots, a bioindicator plant, in order to obtain information for the potential allelopathic uses of these oils as alternative to the use of pesticides in agriculture. We tested two mixtures of essential oils consisting of Tween 20-emulsions of tea tree oil (TTO) and Tween 20-emulsion of Clove and Rosemary (GARROM) essential oils respectively at three different oil concentrations each. The molecular modifications caused in Vicia faba by exposure to oil emulsions were investigated by FTIR spectroscopy in diffuse reflectance (DRIFT) mode. We considered the specific Amide I, Amide II and Amide VI bands by ordinary and second derivative spectroscopy and the results showed that both Tween 20-emulsion of GARROM and Tween 20-emulsion of TTO oils cause transitions among the secondary (α-helix, β-sheet and β-turn) structures with in addition the appearance of random coil structures in exposed samples. The Amide VI bands, placed between 500 and 600 cm-1, confirmed the structural transitions observed for the Amide I bands. In addition we observed the presence of a protein oxidation effect for TTO treated samples, oxidation which resulted negligible instead for the GARROM oil samples. At last, FTIR spectra were also submitted to two-dimensional correlation analysis (2DCORR) and double two-dimensional correlation analysis (D2DCORR); the results confirmed the different effects caused by the two typologies of essential oils on the secondary protein structures of Vicia faba roots.

  2. ITS1, 5.8S and ITS2 secondary structure modelling for intra-specific differentiation among species of the Colletotrichum gloeosporioides sensu lato species complex.

    Science.gov (United States)

    Rampersad, Sephra N

    2014-01-01

    The Colletotrichum gloeosporioides species complex is among the most destructive fungal plant pathogens in the world, however, identification of member species which are of quarantine importance is impacted by a number of factors that negatively affect species identification. Structural information of the rRNA marker may be considered to be a conserved marker which can be used as supplementary information for possible species identification. The difficulty in using ITS rDNA sequences for identification lies in the low level of sequence variation at the intra-specific level and the generation of artificially-induced sequence variation due to errors in polymerization of the ITS array during DNA replication. Type and query ITS sequences were subjected to sequence analyses prior to generation of predicted consensus secondary structures, including the pattern of nucleotide polymorphisms and number of indel haplotypes, GC content, and detection of artificially-induced sequence variation. Data pertaining to structure stability, the presence of conserved motifs in secondary structures and mapping of all sequences onto the consensus C. gloeosporioides sensu stricto secondary structure for ITS1, 5.8S and ITS2 markers was then carried out. Motifs that are evolutionarily conserved among eukaryotes were found for all ITS1, 5.8S and ITS2 sequences. The sequences exhibited conserved features typical of functional rRNAs. Generally, polymorphisms occurred within less conserved regions and were seen as bulges, internal and terminal loops or non-canonical G-U base-pairs within regions of the double stranded helices. Importantly, there were also taxonomic motifs and base changes that were unique to specific taxa and which may be used to support intra-specific identification of members of the C. gloeosporioides sensu lato species complex. PMID:25512885

  3. 低同源性蛋白质结构预测%Low Homologous Protein Structure Prediction

    Institute of Scientific and Technical Information of China (English)

    倪立生; 毛凤楼; 韩玉真; 来鲁华

    2001-01-01

    The development of human genome project calls for more rapid and accurate protein structure prediction method to assign the structure and function of gene products. Threading has been proved to be successful in protein fold assignment,although difficulties remain for low homologous sequences. We have developed a method for solving the sequence rearrangement problem in threading. By reshuffling secondary elements,protein structures with the same spatial arrangement of secondary structures but different connections can be predicted. This method has been proved to be useful in fold recognition for proteins of different evolutionary origin and converge to the same fold.

  4. Computational Assignment of Chemical Shifts for Protein Residues

    CERN Document Server

    Bratholm, Lars A

    2013-01-01

    Fast and accurate protein structure prediction is one of the major challenges in structural biology, biotechnology and molecular biomedicine. These fields require 3D protein structures for rational design of proteins with improved or novel properties. X-ray crystallography is the most common approach even with its low success rate, but lately NMR based approaches have gained popularity. The general approach involves a set of distance restraints used to guide a structure prediction, but simple NMR triple-resonance experiments often provide enough structural information to predict the structure of small proteins. Previous protein folding simulations that have utilised experimental data have weighted the experimental data and physical force field terms more or less arbitrarily, and the method is thus not generally applicable to new proteins. Furthermore a complete and near error-free assignment of chemical shifts obtained by the NMR experiments is needed, due to the static, or deterministic, assignment. In this ...

  5. Primary and secondary interactions between CK2alpha and CK2beta lead to ring-like structures in the crystals of the CK2 holoenzyme

    DEFF Research Database (Denmark)

    Niefind, Karsten; Issinger, Olaf-Georg

    Protein kinase CK2 predominantly exists as a heterotetrameric holoenyzme consisting of two catalytic subunits (CK2alpha) and two non-catalytic subunits (CK2beta). Early investigations which we review here had revealed the presence of two types of contacts between CK2alpha and CK2beta: a primary...... interaction responsible for the stability of the CK2 holoenzyme and stimulatory for the catalytic activity, and a secondary interaction which is inhibitory and in which the acidic loop of CK2beta associates with the basic stretch and the (p+1)-loop of CK2alpha. At the end of the last decade both types of...... distinct aggregation propensity of CK2. We demonstrate here that in the CK2 holoenzyme crystals contacts between different CK2 tetramers exists which provide structural details of the secondary CK2alpha/CK2beta interactions. These mainly ionic interactions lead to trimeric rings of CK2 holoenzymes in the...

  6. Relating the variation of secondary structure of gelatin at fish oil-water interface to adsorption kinetics, dynamic interfacial tension and emulsion stability.

    Science.gov (United States)

    Liu, Huihua; Wang, Bo; Barrow, Colin J; Adhikari, Benu

    2014-01-15

    The objectives of this study were to quantify the relationship between secondary structure of gelatin and its adsorption at the fish-oil/water interface and to quantify the implication of the adsorption on the dynamic interfacial tension (DST) and emulsion stability. The surface hydrophobicity of the gelatin solutions decreased when the pH increased from 4.0 to 6.0, while opposite tend was observed in the viscosity of the solution. The DST values decreased as the pH increased from 4.0 to 6.0, indicating that higher positive charges (measured trough zeta potential) in the gelatin solution tended to result in higher DST values. The adsorption kinetics of the gelatin solution was examined through the calculated diffusion coefficients (Deff). The addition of acid promoted the random coil and β-turn structures at the expense of α-helical structure. The addition of NaOH decreased the β-turn and increased the α-helix and random coil. The decrease in the random coil and triple helix structures in the gelatin solution resulted into increased Deff values. The highest diffusion coefficients, the highest emulsion stability and the lowest amount of random coil and triple helix structures were observed at pH=4.8. The lowest amount of random coil and triple helix structures in the interfacial protein layer correlated with the highest stability of the emulsion (highest ESI value). The lower amount of random coil and triple helix structures allowed higher coverage of the oil-water interface by relatively highly ordered secondary structure of gelatin. PMID:24054271

  7. Proteolytically-induced changes of secondary structural protein conformation of bovine serum albumin monitored by Fourier transform infrared (FT-IR) and UV-circular dichroism spectroscopy

    Science.gov (United States)

    Güler, Günnur; Vorob'ev, Mikhail M.; Vogel, Vitali; Mäntele, Werner

    2016-05-01

    Enzymatically-induced degradation of bovine serum albumin (BSA) by serine proteases (trypsin and α-chymotrypsin) in various concentrations was monitored by means of Fourier transform infrared (FT-IR) and ultraviolet circular dichroism (UV-CD) spectroscopy. In this study, the applicability of both spectroscopies to monitor the proteolysis process in real time has been proven, by tracking the spectral changes together with secondary structure analysis of BSA as proteolysis proceeds. On the basis of the FTIR spectra and the changes in the amide I band region, we suggest the progression of proteolysis process via conversion of α-helices (1654 cm- 1) into unordered structures and an increase in the concentration of free carboxylates (absorption of 1593 and 1402 cm- 1). For the first time, the correlation between the degree of hydrolysis and the concentration of carboxylic groups measured by FTIR spectroscopy was revealed as well. The far UV-CD spectra together with their secondary structure analysis suggest that the α-helical content decreases concomitant with an increase in the unordered structure. Both spectroscopic techniques also demonstrate that there are similar but less spectral changes of BSA for the trypsin attack than for α-chymotrypsin although the substrate/enzyme ratio is taken the same.

  8. Effect of thermal treatment on secondary structure and conformational change of mushroom polyphenol oxidase (PPO) as food quality related enzyme: A FTIR study.

    Science.gov (United States)

    Baltacıoğlu, Hande; Bayındırlı, Alev; Severcan, Mete; Severcan, Feride

    2015-11-15

    In order to understand the conformational changes of polyphenol oxidase (PPO), which is a food quality related enzyme, after thermal treatment, secondary structure changes of the enzyme were analyzed by using Fourier Transform Infrared (FTIR) spectroscopy and compared with the change in enzyme activity in the temperature range of 25-80 °C. Fourier self-deconvolution, neural network (NN) and curve-fitting analysis were applied to the amide I band of FTIR spectra for detail analysis of secondary structure elements. FTIR analysis indicated that PPO is an α-helix dominating enzyme. Detail analysis revealed that, as temperature increased, α-helix and β-sheet decreased, but aggregated β-sheet, turns and random coil increased. The marked changes were noted at 40 °C with the occurrence of new bands due to aggregated β-sheet structures, all of which indicate protein denaturation. These aggregation bands were still observed when the temperature was reduced back to 25 °C, from 70 °C, demonstrating an irreversible change in the structure. PMID:25977025

  9. An Investigation of the Partial-Assignment Completion Effect on Students' Assignment Choice Behavior

    Science.gov (United States)

    Hawthorn-Embree, Meredith L.; Skinner, Christopher H.; Parkhurst, John; Conley, Elisha

    2011-01-01

    This study was designed to investigate the partial assignment completion effect. Seventh-grade students were given a math assignment. After working for 5 min, they were interrupted and their partially completed assignments were collected. About 20 min later, students were given their partially completed assignment and a new, control assignment…

  10. Further exploration of the conformational space of α-synuclein fibrils: solid-state NMR assignment of a high-pH polymorph.

    Science.gov (United States)

    Verasdonck, Joeri; Bousset, Luc; Gath, Julia; Melki, Ronald; Böckmann, Anja; Meier, Beat H

    2016-04-01

    Polymorphism is a common and important phenomenon for protein fibrils which has been linked to the appearance of strains in prion and other neurodegenerative diseases. Parkinson disease is a frequently occurring neurodegenerative pathology, tightly associated with the formation of Lewy bodies. These deposits mainly consist of α-synuclein in fibrillar, β-sheet-rich form. α-synuclein is known to form numerous different polymorphs, which show distinct structural features. Here, we describe the chemical shift assignments, and derive the secondary structure, of a polymorph that was fibrillized at higher-than-physiological pH conditions. The fibrillar core contains residues 40-95, with both the C- and N-terminus not showing any ordered, rigid parts. The chemical shifts are similar to those recorded previously for an assigned polymorph that was fibrillized at neutral pH. PMID:26318307

  11. THE FACTOR STRUCTURE OF MOTOR SKILLS AND KNOWLEDGE OF THE FEMALE STUDENTS OF THE FIRST YEAR OF SECONDARY SCHOOL

    OpenAIRE

    Said Hasanbegovic; Mirela Osmanovic

    2012-01-01

    The aim of this research is to determine the latent space of motor skills and knowledge of the female students of the first year of secondary school. This study included 120 girls, and it was conducted at the end of the school year, after the realization of the regular physical education classes. According to nine tests aimed to evaluate motor skills and 16 more to assess motor knowledge, factors that define the latent space of motor skills of the test group were isolated by factor analysis, ...

  12. Peritonitis - secondary

    Science.gov (United States)

    ... of the abdominal organs. It is called the peritoneum. Secondary means it is due to another condition. ... has several major causes. Bacteria may enter the peritoneum through a hole (perforation) in the gastrointestinal tract. ...

  13. Secondary structure in solution of two anti-HIV-1 hammerhead ribozymes as investigated by two-dimensional 1H 500 MHz NMR spectroscopy in water

    Science.gov (United States)

    Sarma, R. H.; Sarma, M. H.; Rein, R.; Shibata, M.; Setlik, R. S.; Ornstein, R. L.; Kazim, A. L.; Cairo, A.; Tomasi, T. B.

    1995-01-01

    Two hammerhead chimeric RNA/DNA ribozymes (HRz) were synthesized in pure form. Both were 30 nucleotides long, and the sequences were such that they could be targeted to cleave the HIV-1 gag RNA. Named HRz-W and HRz-M, the former had its invariable core region conserved, the latter had a uridine in the invariable region replaced by a guanine. Their secodary structures were determined by 2D NOESY 1H 500 MHz NMR spectroscopy in 90% water and 10% D2(0), following the imino protons. The data show that both HRz-M and HRz-W form identical secondary structures with stem regions consisting of continuous stacks of AT and GT pairs. An energy minimized computer model of this stem region is provided. The results suggest that the loss of catalytic activity that is known to result when an invariant core residue is replaced is not related to the secondary structure of the ribozymes in the absence of substrate.

  14. Design and commission of an experimental test rig to apply a full-scale pressure load on composite sandwich panels representative of an aircraft secondary structure

    International Nuclear Information System (INIS)

    This paper describes the design of a test rig, which is used to apply a representative pressure load to a full-scale composite sandwich secondary aircraft structure. A generic panel was designed with features to represent those in the composite sandwich secondary aircraft structure. To provide full-field strain data from the panels, the test rig was designed for use with optical measurement techniques such as thermoelastic stress analysis (TSA) and digital image correlation (DIC). TSA requires a cyclic load to be applied to a structure for the measurement of the strain state; therefore, the test rig has been designed to be mounted on a standard servo-hydraulic test machine. As both TSA and DIC require an uninterrupted view of the surface of the test panel, an important consideration in the design is facilitating the optical access for the two techniques. To aid the test rig design a finite element (FE) model was produced. The model provides information on the deflections that must be accommodated by the test rig, and ensures that the stress and strain levels developed in the panel when loaded in the test rig would be sufficient for measurement using TSA and DIC. Finally, initial tests using the test rig have shown it to be capable of achieving the required pressure and maintaining a cyclic load. It was also demonstrated that both TSA and DIC data can be collected from the panels under load, which are used to validate the stress and deflection derived from the FE model

  15. Analysis on secondary stress of primary member of UHV transmission tower structure%特高压输电钢管塔主材次应力分析

    Institute of Scientific and Technical Information of China (English)

    帅群; 邓洪洲; 李琳; 施菁华

    2012-01-01

    In order to study the secondary stress of the primary member of UHV transmission tower structure,the course of 1 000 kV UHV transmission tower full-scale test was carried out,and the secondary stress was measured by test.Based on methods of finite element numerical analysis,the distribution of secondary stress and the influences on tower-SZ2U behavior of total structure were analyzed.Both of the finite beam-link elements considering and not considering the stiffness of the gusset plate were established.The difference of the two calculations was compared,and the analytical results were compared with the full-scale test.The accurate finite element model of the tower leg joint was established in order to investigate the force transfer mechanism and the performance and failure pattern under the secondary moment.The result indicates: it is the tower leg member that is influenced by the secondary stress most.The maximum secondary stress ratio measured by test is 45%.The result of calculation model considering the stiffness of the gusset plate is in better agreement with the experiment result.The secondary effect of the towers’ leg not only has relation with slenderness ratio,but also has relation with the angles of primary members and auxiliary members.The failure pattern of the tower leg joint under the secondary moment is local bucking at the pressure side above the ring plate.%为了研究特高压输电钢管塔的主材次应力问题,对1 000 kV特高压输电钢管塔SZ2U进行真型试验,实测主材次应力;通过有限元分析,得出主材次应力的分布规律及影响因素;分别建立考虑有无节点板刚度的有限元梁杆单元模型,并与实测结果进行比较;对塔脚节点建立精细化有限元模型,考察次弯矩作用下节点的受力性能和破坏模式。研究结果表明:对SZ2U塔次应力影响最大的位置在塔脚主材处,实测最大次应力比(弯曲应力占轴力应力的百分比)达到45%;采用考虑

  16. Prediction and characterization of noncoding RNAs in C. elegans by integrating conservation, secondary structure, and high-throughput sequencing and array data

    OpenAIRE

    Lu, Zhi John; Yip, Kevin Y.; Wang, Guilin; Shou, Chong; Hillier, LaDeana W.; Khurana, Ekta; Agarwal, Ashish; Auerbach, Raymond; Rozowsky, Joel; Cheng, Chao; Kato, Masaomi; Miller, David M.; Slack, Frank; Snyder, Michael; Waterston, Robert H.

    2011-01-01

    We present an integrative machine learning method, incRNA, for whole-genome identification of noncoding RNAs (ncRNAs). It combines a large amount of expression data, RNA secondary-structure stability, and evolutionary conservation at the protein and nucleic-acid level. Using the incRNA model and data from the modENCODE consortium, we are able to separate known C. elegans ncRNAs from coding sequences and other genomic elements with a high level of accuracy (97% AUC on an independent validation...

  17. The Mechanism Design Approach to Student Assignment

    OpenAIRE

    Pathak, Parag A.

    2011-01-01

    The mechanism design approach to student assignment involves the theoretical, empirical, and experimental study of systems used to allocate students into schools around the world. Recent practical experience designing systems for student assignment has raised new theoretical questions for the theory of matching and assignment. This article reviews some of this recent literature, highlighting how issues from the field motivated theoretical developments and emphasizing how the dialogue may be a...

  18. Job Assignments, Intrinsic Motivation and Explicit Incentives

    OpenAIRE

    Nafziger, Julia

    2008-01-01

    This paper considers the interplay of job assignments with the intrinsic and extrinsic motivation of an agent. Job assignments influence the self confidence of the agent, and thereby his intrinsic motivation. Monetary reward allow the principal to complement intrinsic motivation with extrinsic incentives. The main result is that the principal chooses an inefficient job assignment rule to enhance the agent's intrinsic motivation even though she can motivate him with monetary rewards. This show...

  19. Assigning proctors to exams with scatter search

    OpenAIRE

    Ramalhinho-Louren??o, Helena; Mart??, Rafael; Laguna, Manuel

    2001-01-01

    In this paper we present an algorithm to assign proctors to exams. This NP-hard problem is related to the generalized assignment problem with multiple objectives. The problem consists of assigning teaching assistants to proctor final exams at a university. We formulate this problem as a multiobjective integer program (IP) with a preference function and a workload-fairness function. We then consider also a weighted objective that combines both functions. We develop a scatter ...

  20. Non-universal spectra of ultra-high energy cosmic ray primaries and secondaries in a structured universe

    International Nuclear Information System (INIS)

    Analytical calculations of extra-galactic cosmic ray spectra above ∼ 1017 eV are often performed assuming continuous source distributions, giving rise to spectra that depend little on the propagation mode, be it rectilinear or diffusive. We perform trajectory simulations for proton primaries in the probably more realistic case of discrete sources with a density of ∼ 10-5 Mpc-3. We find two considerable non-universal effects that depend on source distributions and magnetic fields: First, the primary extra-galactic cosmic ray flux can become strongly suppressed below a few 1018 eV due to partial confinement in magnetic fields surrounding sources. Second, the secondary photon to primary cosmic ray flux ratio between ≅ 3 x 1018 eV and ≅ 1020 eV decreases with decreasing source density and increasing magnetization. As a consequence, in acceleration scenarios for the origin of highest energy cosmic rays the fraction of secondary photons may be difficult to detect even for experiments such as Pierre Auger. The cosmogenic neutrino flux does not significantly depend on source density and magnetization. (author)