WorldWideScience
 
 
1

A 3D-1D substitution matrix for protein fold recognition that includes predicted secondary structure of the sequence.  

Science.gov (United States)

In protein fold recognition, a probe amino acid sequence is compared to a library of representative folds of known structure to identify a structural homolog. In cases where the probe and its homolog have clear sequence similarity, traditional residue substitution matrices have been used to predict the structural similarity. In cases where the probe is sequentially distant from its homolog, we have developed a (7 x 3 x 2 x 7 x 3) 3D-1D substitution matrix (called H3P2), calculated from a database of 119 structural pairs. Members of each pair share a similar fold, but have sequence identity less than 30%. Each probe sequence position is defined by one of seven residue classes and three secondary structure classes. Each homologous fold position is defined by one of seven residue classes, three secondary structure classes, and two burial classes. Thus the matrix is five-dimensional and contains 7 x 3 x 2 x 7 x 3 = 882 elements or 3D-1D scores. The first step in assigning a probe sequence to its homologous fold is the prediction of the three-state (helix, strand, coil) secondary structure of the probe; here we use the profile based neural network prediction of secondary structure (PHD) program. Then a dynamic programming algorithm uses the H3P2 matrix to align the probe sequence with structures in a representative fold library. To test the effectiveness of the H3P2 matrix a challenging, fold class diverse, and cross-validated benchmark assessment is used to compare the H3P2 matrix to the GONNET, PAM250, BLOSUM62 and a secondary structure only substitution matrix. For distantly related sequences the H3P2 matrix detects more homologous structures at higher reliabilities than do these other substitution matrices, based on sensitivity versus specificity plots (or SENS-SPEC plots). The added efficacy of the H3P2 matrix arises from its information on the statistical preferences for various sequence-structure environment combinations from very distantly related proteins. It introduces the predicted secondary structure information from a sequence into fold recognition in a statistical way that normalizes the inherent correlations between residue type, secondary structure and solvent accessibility. PMID:9135128

Rice, D W; Eisenberg, D

1997-04-11

2

SSViewer: Sequence Structure Viewer  

Directory of Open Access Journals (Sweden)

Full Text Available An important aspect of bioinformatics is sequence. Sequence is a discrete function which contains the combinations of amino acids in proteins and nucleotides in Dna. Important functions of Amino Acids are to serve as the building blocks of proteins, which are linear chains of amino acids. Amino acids can be linked together in varying sequences to form a vast variety of proteins. Twenty-two amino acids are naturally incorporated into polypeptides and are called protein-o-genic or standard amino acids. Of these, 20 are encoded by the universal genetic code. In the case of the DNA sequence A, T, G, C is used to represent DNA. This sequence information is analysed to determine genes that encode polypeptides (proteins, RNA, genes, regulatory sequences, structural motifs, repetitive sequences and DNA sequences can be accurately analysed using computational techniques like BLAST, FASTA which is not possible manually. In the present study we developed a tool to visualize the 3D structure for a given sequence by using programming language Java and HTML.

Shyam Perugu,

2013-09-01

3

Structural complexity of DNA sequence.  

Science.gov (United States)

In modern bioinformatics, finding an efficient way to allocate sequence fragments with biological functions is an important issue. This paper presents a structural approach based on context-free grammars extracted from original DNA or protein sequences. This approach is radically different from all those statistical methods. Furthermore, this approach is compared with a topological entropy-based method for consistency and difference of the complexity results. PMID:23662161

Liou, Cheng-Yuan; Tseng, Shen-Han; Cheng, Wei-Chen; Tsai, Huai-Ying

2013-01-01

4

Structural Complexity of DNA Sequence  

Digital Repository Infrastructure Vision for European Research (DRIVER)

In modern bioinformatics, finding an efficient way to allocate sequence fragments with biological functions is an important issue. This paper presents a structural approach based on context-free grammars extracted from original DNA or protein sequences. This approach is radically different from all those statistical methods. Furthermore, this approach is compared with a topological entropy-based method for consistency and difference of the complexity results.

Liou, Cheng-yuan; Tseng, Shen-han; Cheng, Wei-chen; Tsai, Huai-ying

2013-01-01

5

[Chemical structural features and anti-complementary activity of polysaccharide HPS1-D from Hedysarum polybotrys].  

Science.gov (United States)

HPS1-D, an active polysaccharide,was isolated and purified from Hedysarum polybotrys. HPS1-D was obtained after treated with Savage method and H2O2, and purified with DEAE-cellulose 52 and Sephadex G-100 gel filtration chromatography. Then physicochemical property analysis, GC, methylation, partial acid hydrolysis, and NMR method were used to study chemical structural of HPS1-D. The conformation was primarily analyzed with GPC-MALLS method and Congo red reaction. The anti-complementary activity of HPS1-D was evaluated with the hemolysis assay. HPS1-D was a heteropolysaccharide and consisted of D-glucose, L-arabinose, (7.2:1.3). HPS1-D proved to be a neutral sugar, with 1, 4-and 1, 4, 6-alpha-D-glucopyranosyl residues in backbone ,and 1, 5-and 1, 3, 5-alpha-L-arabinofuranosyl residues in branches. HPS1-D has a random coil state conformation with monodisperse mass distribution in 0.9% NaCl solution. And HPS1-D had triple-helix conformation in concentrate of NaOH solution. Anti-complementary activity of HPS1-D was closed to its positive control heparin. PMID:24754175

Yang, Tao; Guo, Long; Li, Can; Yang, Ying-Lai; Feng, Shi-Lan

2014-01-01

6

Comments on the Bifurcation Structure of 1D Maps  

DEFF Research Database (Denmark)

The paper presents a complementary view on some of the phenomena related to the bifurcation structure of unimodal maps. An approximate renormalization theory for the period-doubling cascade is developed, and a mapping procedure is established that accounts directly for the box-within-a-box structure of the total bifurcation set. This presents a picture in which the homoclinic orbit bifurcations act as a skeleton for the bifurcational set. At the same time, experimental results on continued subharmonic generation for piezoelectrically amplified sound waves, predating the Feigenbaum theory, are called into attention.

Belykh, V.N.; Mosekilde, Erik

1997-01-01

7

Protein Structure Predicted from Sequence  

CERN Document Server

The evolutionary trajectory of a protein through sequence space is constrained by function and three-dimensional (3D) structure. Residues in spatial proximity tend to co-evolve, yet attempts to invert the evolutionary record to identify these constraints and use them to computationally fold proteins have so far been unsuccessful. Here, we show that co-variation of residue pairs, observed in a large protein family, provides sufficient information to determine 3D protein structure. Using a data-constrained maximum entropy model of the multiple sequence alignment, we identify pairs of statistically coupled residue positions which are expected to be close in the protein fold, termed contacts inferred from evolutionary information (EICs). To assess the amount of information about the protein fold contained in these coupled pairs, we evaluate the accuracy of predicted 3D structures for proteins of 50-260 residues, from 15 diverse protein families, including a G-protein coupled receptor. These structure predictions ...

Marks, Debora S; Sheridan, Robert; Hopf, Thomas A; Pagnani, Andrea; Zecchina, Riccardo; Sander, Chris

2011-01-01

8

Optical reflectance and omnidirectional bandgaps in Fibonacci quasicrystals type 1-D multilayer structures containing exponentially graded material  

Science.gov (United States)

A theoretical study of optical reflectance and reflection bands of 1-D photonic quasi-crystals (Fibonacci type arrangement) composed of exponentially graded material is presented. The proposed structures consist of two different layers, one of them is of constant refractive index (L) and the other one is of exponentially graded refractive index (S) dielectric materials. Four different generations (2nd, 3rd, 4th and 5th) of the Fibonacci sequence for 10 periods in one dimension (1-D) are considered and compared in view of their optical reflectance and bandgaps for both TE and TM polarisations. Also, we proposed some heterostructures made by the combination of different Fibonacci generations and their periods to obtain suitable omnidirectional reflection band. We used the transfer matrix method (TMM) to obtain the reflectance, bandgaps and omnidirectional reflectional bandgaps (ODR) of such structures in near infrared spectrum (800-2200 nm) at different angles of incidence. We show that ODR exists in these types of structures. The number of ODRs and total bandgap depend on the Fibonacci generations. Extraordinary ODR bandgaps are obtained in the case of heterostructures formed by the combination of different generations of the Fibonacci sequence. The ODR for these structures is similar to the ODR of photonic crystals containing left-handed materials. This work would be useful to study the Fibonacci type photonic crystals having graded index materials and also it will open new window to design several photonic crystal devices like sensors, reflectors, etc. in the infrared region.

Singh, Bipin K.; Thapa, Khem B.; Pandey, Praveen C.

2013-06-01

9

A First Measurement of the Tensor-Polarized Structure Function b1d  

International Nuclear Information System (INIS)

The Hermes experiment studies the spin structure of the nucleon using the 27.6 GeV longitudinally polarized positron beam of HERA and an internal target of pure gases. In addition to the well-known spin structure function g1, measured precisely with longitudinally polarized proton and deuteron targets, the use of a tensor-polarized deuteron target provides access to the tensor polarized structure function b1d. The latter, measured with an unpolarized beam, quantifies the dependence of the parton momentum distribution on the nucleon spin. Hermes had a 1-month dedicated run with a tensor polarized deuterium target during the 2000 data taking period. Here preliminary results on the tensor-polarized structure function b1d are presented for the kinematic range 0.002 < x < 0.85 and 0.1 GeV2 < Q2 < 20 GeV2

10

A First Measurement of the Tensor-Polarized Structure Function b1d  

CERN Document Server

The Hermes experiment studies the spin structure of the nucleon using the 27.6 GeV longitudinally polarized positron beam of HERA and an internal target of pure gases. In addition to the well-known spin structure function g_1, measured precisely with longitudinally polarized proton and deuteron targets, the use of a tensor-polarized deuteron target provides access to the tensor polarized structure function b1d. The latter, measured with an unpolarized beam, quantifies the dependence of the parton momentum distribution on the nucleon spin. Hermes had a 1-month dedicated run with a tensor polarized deuterium target during the 2000 data taking period. Here preliminary results on the tensor-polarized structure function b1d are presented for the kinematic range 0.002

Contalbrigo, M

2002-01-01

11

Identifying sequence-structure pairs undetected by sequence alignments.  

Science.gov (United States)

We examine how effectively simple potential functions previously developed can identify compatibilities between sequences and structures of proteins for database searches. The potential function consists of pairwise contact energies, repulsive packing potentials of residues for overly dense arrangement and short-range potentials for secondary structures, all of which were estimated from statistical preferences observed in known protein structures. Each potential energy term was modified to represent compatibilities between sequences and structures for globular proteins. Pairwise contact interactions in a sequence-structure alignment are evaluated in a mean field approximation on the basis of probabilities of site pairs to be aligned. Gap penalties are assumed to be proportional to the number of contacts at each residue position, and as a result gaps will be more frequently placed on protein surfaces than in cores. In addition to minimum energy alignments, we use probability alignments made by successively aligning site pairs in order by pairwise alignment probabilities. The results show that the present energy function and alignment method can detect well both folds compatible with a given sequence and, inversely, sequences compatible with a given fold, and yield mostly similar alignments for these two types of sequence and structure pairs. Probability alignments consisting of most reliable site pairs only can yield extremely small root mean square deviations, and including less reliable pairs increases the deviations. Also, it is observed that secondary structure potentials are usefully complementary to yield improved alignments with this method. Remarkably, by this method some individual sequence-structure pairs are detected having only 5-20% sequence identity. PMID:10906342

Miyazawa, S; Jernigan, R L

2000-07-01

12

Ground-state spin structure of strongly interacting disordered 1D Hubbard model  

International Nuclear Information System (INIS)

We study the influence of on-site disorder on the magnetic properties of the ground state of the infinite-U one-dimensional (1D) Hubbard model. We find that the ground state is not ferromagnetic. This is analysed in terms of the algebraic structure of the spin dependence of the Hamiltonian. A simple explanation is derived for the 1/N periodicity in the persistent current for this model. (author)

13

Structure and localization of the human SULT1B1 gene: neighborhood to SULT1E1 and a SULT1D pseudogene.  

Science.gov (United States)

The soluble sulfotransferases are involved in the elimination of xenobiotics, the activation of procarcinogens, and the regulation of hormones. They comprise a gene superfamily (SULT). The structure and chromosomal location of nine human SULT genes are known. We have characterized a further gene, SULT1B1. Its structure is similar to that of other SULT1 genes. However, the total length of its eight exons and the introns (33.6 kb) is larger than that of other human SULT1 genes (4 to 21 kb). The SULT1B1 gene sequence is part of a sequence entry in the unfinished High-Throughput Genomic Sequences (HTGS) division of GenBank. However, the order and orientation of the SULT1B1 exons are not correct in this entry. SULT1B1 is located on chromosome 4q13.1, nearly 100 kb downstream of SULT1E1 on the same strand. The intervening sequence contains a SULT-like structure showing substantial homology to the mouse SULT1D1 cDNA recently described. However, in humans this structure represents a pseudogene (SULT1D1P) because of mutated splice donors/acceptors and in-frame stop codons in the sequence corresponding to exon II. This SULT gene cluster is located on the minus strand of chromosome 4 with SULT1B1 being closest to the centromer. PMID:11688987

Meinl, W; Glatt, H

2001-11-01

14

Resistivity structure of Sumatran Fault (Aceh segment) derived from 1-D magnetotelluric modeling  

Science.gov (United States)

Sumatran Fault Zone is the most active fault in Indonesia as a result of strike-slip component of Indo-Australian oblique convergence. With the length of 1900 km, Sumatran fault was divided into 20 segments starting from the southernmost Sumatra Island having small slip rate and increasing to the north end of Sumatra Island. There are several geophysical methods to analyze fault structure depending on physical parameter used in these methods, such as seismology, geodesy and electromagnetic. Magnetotelluric method which is one of geophysical methods has been widely used in mapping and sounding resistivity distribution because it does not only has the ability for detecting contras resistivity but also has a penetration range up to hundreds of kilometers. Magnetotelluric survey was carried out in Aceh region with the 12 total sites crossing Sumatran Fault on Aceh and Seulimeum segments. Two components of electric and magnetic fields were recorded during 10 hours in average with the frequency range from 320 Hz to 0,01 Hz. Analysis of the pseudosection of phase and apparent resistivity exhibit vertical low phase flanked on the west and east by high phase describing the existence of resistivity contras in this region. Having rotated the data to N45°E direction, interpretation of the result has been performed using three different methods of 1D MT modeling i.e. Bostick inversion, 1D MT inversion of TM data, and 1D MT inversion of the impedance determinant. By comparison, we concluded that the use of TM data only and the impedance determinant in 1D inversion yield the more reliable resistivity structure of the fault compare to other methods. Based on this result, it has been shown clearly that Sumatra Fault is characterized by vertical contras resistivity indicating the existence of Aceh and Seulimeum faults which has a good agreement with the geological data.

Nurhasan, Sutarno, D.; Bachtiar, H.; Sugiyanto, D.; Ogawa, Y.; Kimata, F.; Fitriani, D.

2012-06-01

15

Computational Study and Analysis of Structural Imperfections in 1D and 2D Photonic Crystals  

Energy Technology Data Exchange (ETDEWEB)

Dielectric reflectors that are periodic in one or two dimensions, also known as 1D and 2D photonic crystals, have been widely studied for many potential applications due to the presence of wavelength-tunable photonic bandgaps. However, the unique optical behavior of photonic crystals is based on theoretical models of perfect analogues. Little is known about the practical effects of dielectric imperfections on their technologically useful optical properties. In order to address this issue, a finite-difference time-domain (FDTD) code is employed to study the effect of three specific dielectric imperfections in 1D and 2D photonic crystals. The first imperfection investigated is dielectric interfacial roughness in quarter-wave tuned 1D photonic crystals at normal incidence. This study reveals that the reflectivity of some roughened photonic crystal configurations can change up to 50% at the center of the bandgap for RMS roughness values around 20% of the characteristic periodicity of the crystal. However, this reflectivity change can be mitigated by increasing the index contrast and/or the number of bilayers in the crystal. In order to explain these results, the homogenization approximation, which is usually applied to single rough surfaces, is applied to the quarter-wave stacks. The results of the homogenization approximation match the FDTD results extremely well, suggesting that the main role of the roughness features is to grade the refractive index profile of the interfaces in the photonic crystal rather than diffusely scatter the incoming light. This result also implies that the amount of incoherent reflection from the roughened quarterwave stacks is extremely small. This is confirmed through direct extraction of the amount of incoherent power from the FDTD calculations. Further FDTD studies are done on the entire normal incidence bandgap of roughened 1D photonic crystals. These results reveal a narrowing and red-shifting of the normal incidence bandgap with increasing RMS roughness. Again, the homogenization approximation is able to predict these results. The problem of surface scratches on 1D photonic crystals is also addressed. Although the reflectivity decreases are lower in this study, up to a 15% change in reflectivity is observed in certain scratched photonic crystal structures. However, this reflectivity change can be significantly decreased by adding a low index protective coating to the surface of the photonic crystal. Again, application of homogenization theory to these structures confirms its predictive power for this type of imperfection as well. Additionally, the problem of a circular pores in 2D photonic crystals is investigated, showing that almost a 50% change in reflectivity can occur for some structures. Furthermore, this study reveals trends that are consistent with the 1D simulations: parameter changes that increase the absolute reflectivity of the photonic crystal will also increase its tolerance to structural imperfections. Finally, experimental reflectance spectra from roughened 1D photonic crystals are compared to the results predicted computationally in this thesis. Both the computed and experimental spectra correlate favorably, validating the findings presented herein.

K.R. Maskaly

2005-06-01

16

Study of phase transformation and crystal structure for 1D carbon-modified titania ribbons  

International Nuclear Information System (INIS)

One-dimensional hydrogen titanate ribbons were successfully prepared with hydrothermal reaction in a highly basic solution. A series of one-dimensional carbon-modified TiO2 ribbons were prepared via calcination of the mixture of hydrogen titanate ribbons and sucrose solution under N2 flow at different temperatures. The phase transformation process of hydrogen titanate ribbons was investigated by in-situ X-ray diffraction at various temperatures. Besides, one-dimensional carbon-modified TiO2 ribbons calcined at different temperatures were characterized by X-ray diffraction, scanning electron microscopy, transmission electron microscopy, nitrogen adsorption isotherms, diffuse reflectance ultraviolet–visible spectroscopy, and so on. Carbon-modified TiO2 ribbons showed one-dimensional ribbon crystal structure and various crystal phases of TiO2. After being modified with carbon, a layer of uniform carbon film was coated on the surface of TiO2 ribbons, which improved their adsorption capacity for methyl orange as a model organic pollutant. One-dimensional carbon-modified TiO2 ribbons also exhibited enhanced visible-light absorbance with the increase of calcination temperatures. - Highlights: • The synthesis of 1D carbon-modified TiO2 ribbons. • The phase transformation of 1D carbon-modified TiO2 ribbons. • 1D carbon-modified TiO2 exhibites enhanced visible-light absorbance

17

Study of phase transformation and crystal structure for 1D carbon-modified titania ribbons  

Energy Technology Data Exchange (ETDEWEB)

One-dimensional hydrogen titanate ribbons were successfully prepared with hydrothermal reaction in a highly basic solution. A series of one-dimensional carbon-modified TiO{sub 2} ribbons were prepared via calcination of the mixture of hydrogen titanate ribbons and sucrose solution under N{sub 2} flow at different temperatures. The phase transformation process of hydrogen titanate ribbons was investigated by in-situ X-ray diffraction at various temperatures. Besides, one-dimensional carbon-modified TiO{sub 2} ribbons calcined at different temperatures were characterized by X-ray diffraction, scanning electron microscopy, transmission electron microscopy, nitrogen adsorption isotherms, diffuse reflectance ultraviolet–visible spectroscopy, and so on. Carbon-modified TiO{sub 2} ribbons showed one-dimensional ribbon crystal structure and various crystal phases of TiO{sub 2}. After being modified with carbon, a layer of uniform carbon film was coated on the surface of TiO{sub 2} ribbons, which improved their adsorption capacity for methyl orange as a model organic pollutant. One-dimensional carbon-modified TiO{sub 2} ribbons also exhibited enhanced visible-light absorbance with the increase of calcination temperatures. - Highlights: • The synthesis of 1D carbon-modified TiO{sub 2} ribbons. • The phase transformation of 1D carbon-modified TiO{sub 2} ribbons. • 1D carbon-modified TiO{sub 2} exhibites enhanced visible-light absorbance.

Zhou, Lihui, E-mail: lhzhou@ecust.edu.cn; Zhang, Fang; Li, Jinxia

2014-02-15

18

Reversible interconversion of a divalent vanadium bronze between ? and ? quasi-1D structures.  

Science.gov (United States)

Charge fluctuations along the quasi-1D frameworks of M(x)V(2)O(5) bronzes have evinced much recent interest owing to the manifestation of colossal metal-insulator transitions and superconductivity. Depending upon the nature of the intercalating cation (M), distinctive geometries of the V(2)O(5) framework are accessible. Herein, we demonstrate an unprecedented reversible transformation between double-layered (?) and tunnel (?) quasi-1D geometries for nanowires of a divalent vanadium bronze, Ca(x)V(2)O(5) (x ? 0.23), upon annealing-induced dehydration and hydrothermally induced hydration. Such a facile hydration/dehydration-induced interconversion between two prominent quasi-1D structures (accompanied by a change in charge-ordering motifs) has not been observed in the bulk and is posited to result from the ease of propagation of crystallographic slip processes across the confined nanowire widths for the ? ? ? conversion and the facile diffusion of water molecules within the tunnel geometries for the ? ? ? reversion. PMID:22506534

Marley, Peter M; Banerjee, Sarbajit

2012-05-01

19

Constructing structure in number sequences  

Digital Repository Infrastructure Vision for European Research (DRIVER)

This paper reports on a design experiment in the domain of number sequences conducted in the course of the WebLabs project1. In this study, we designed and tested a set of activities in which 13-14 year old students use the ToonTalk programming environment to construct models of sequences and series, and then use the WebReports web-based collaboration system to share these models and their observations about them. We utilise a design pattern (programming method) called "Streams" which enables...

Mor, Yishay; Noss, Richard; Kahn, Ken; Hoyles, Celia; Simpson, Gordon

2005-01-01

20

????????????????????? Fabrication of Si-Based 1D,2D Ordered Nano Structure by Nanoimprint Lithography  

Directory of Open Access Journals (Sweden)

Full Text Available ????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????AFM????????????????????????????????The dimension of the microelectronic devices is reduced year by year as the development of the modern microelectronic technology. So, the research of the fabrication of nanometer structures becomes one of the most interesting topics. Nanoimprint lithography (NIL is a more promising technology. In this paper, the process of nanoimprint lithography was introduced. And, 1-D and 2-D quartz grating molds with the period 2 µm was transferred to Si substrate by NIL. The resolution is only related to the size and the template pattern without the limitation of optical lithography exposure wavelength. AFM measurement showed the perfect fidelity of the imprint process.

??

2011-11-01

 
 
 
 
21

MATLAB DESIGN & ANALYSIS OF 1D PHOTONIC BAND STRUCTURES USING TRANSFER MATRIX METHOD  

Directory of Open Access Journals (Sweden)

Full Text Available Presently, the propagation of electromagnetic waves in photonic crystals has become the subject of extensive research due to its remarkable properties. Photonic crystal is an artificial dielectric structure in which the nature of the photons is the same as that of electrons in a semiconductor crystals and it has inspired a lot of fundamental research on light–matter interaction. The tailoring of photonic band gap with designing parameters is a key for the designing of advanced photonic devices with desired properties. In this paper, MATLAB simulation of 1D photonic crystal using transfer matrix method (TMM is presented and important results are discussed.

S. SARAVANAN, R. S. DUBEY, S. KALAINATHAN

2013-11-01

22

Crystal Structures of Human TBC1D1 and TBC1D4 (AS160) RabGTPase-activating Protein (RabGAP) Domains Reveal Critical Elements for GLUT4 Translocation*  

Digital Repository Infrastructure Vision for European Research (DRIVER)

We have solved the x-ray crystal structures of the RabGAP domains of human TBC1D1 and human TBC1D4 (AS160), at 2.2 and 3.5 Å resolution, respectively. Like the yeast Gyp1p RabGAP domain, whose structure was solved previously in complex with mouse Rab33B, the human TBC1D1 and TBC1D4 domains both have 16 ?-helices and no ?-sheet elements. We expected the yeast Gyp1p RabGAP/mouse Rab33B structure to predict the corresponding interfaces between cognate mammalian RabGAPs and Rabs, but found tha...

Park, Sang-youn; Jin, Wanzhu; Woo, Ju Rang; Shoelson, Steven E.

2011-01-01

23

Use of residue pairs in protein sequence-sequence and sequence-structure alignments.  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Two new sets of scoring matrices are introduced: H2 for the protein sequence comparison and T2 for the protein sequence-structure correlation. Each element of H2 or T2 measures the frequency with which a pair of amino acid types in one protein, k-residues apart in the sequence, is aligned with another pair of residues, of given amino acid types (for H2) or in given structural states (for T2), in other structurally homologous proteins. There are four types, corresponding to the k-values of 1 t...

Jung, J.; Lee, B.

2000-01-01

24

Role of potential structure in the collisional excitation of metastable O(1D) atoms  

International Nuclear Information System (INIS)

This paper considers the collisional excitation of O(1D) modeled by the crossing of two valence 1 3?g curves dissociating to O(3P)+O(3P) [V11(R)] and O(3P)+O(1D) [V22(R)] which in turn are further crossed by the 3?g Rydberg curve dissociating to O(3P)+O(5S) [V33(R)]. The role of structure in the potential curves and coupling matrix elements is quantitatively probed by the first-order functional-sensitivity densities ? ln?12(E)/? lnVij(R) of the excitation cross section ?12(E) obtained from close-coupling calculations. The results reveal that, in spite of the well-separated nature of the crossing between the two valence curves from their crossings with the Rydberg potential curve, the excitation cross section ?12 displays considerable sensitivity to the Rydberg curve V33(R) at all energies in the range 3.0--9.0 eV. For relative collisional energies corresponding to the higher closely spaced vibrational energy levels of the Rydberg state, the excitation cross section is found to be much more sensitive to the Rydberg state than to the two valence states themselves

25

Inherent structures and non-equilibrium dynamics of 1D constrained kinetic models a comparison study  

CERN Document Server

e discuss the relevance of the Stillinger and Weber approach to the glass transition investigating the non-equilibrium behavior of models with non-trivial dynamics, but with simple equilibrium properties. We consider a family of 1D constrained kinetic models, which interpolates between the asymmetric chain introduced by Eisinger and J\\"ackle [Z. Phys. {\\bf B84}, 115 (1991)] and the symmetric chain introduced by Fredrickson and Andersen [Phys. Rev. Lett {\\bf 53}, 1244 (1984)], and the 1D version of the Backgammon model [Phys. Rev. Lett. {\\bf 75}, 1190 (1995)]. We show that the configurational entropy obtained from the inherent structures is the same for all models irrespective of their different microscopic dynamics. We present a detailed study of the coarsening behavior of these models, including the relation between fluctuations and response. Our results suggest that any approach to the glass transition inspired by mean-field ideas and resting on the definition of a configurational entropy must rely on the a...

Crisanti, A; Rocco, A; Sellitto, M

2000-01-01

26

Hydrothermal synthesis and structural characterization of two 1-D and 2-D Dawson-based phosphotungstates  

International Nuclear Information System (INIS)

Two new Dawson-based phosphotungstates (H2en)0.5H[Cu(en)2(H2O)]2{[Cu(en)2](?1-P2W17CuO61)}.8H2O (1) (en=ethylenediamine) and [4,4'-H2bpy]2{[Cu(4,4'-bpy)3][Cu(4,4'-bpy)4(H2O)2]2[Cu(4,4'-bpy)] [?-P2W18O62]2}.6H2O (2) (4,4'-bpy=4,4'-bipyridine) have been hydrothermally synthesized and structurally characterized. 1 crystallizes in the triclinic space group P-1 with a=11.7626(17), b=13.246(2), c=29.350(5) A, ?=87.355(5), ?=79.583(5), ?=66.993(3)o, V=4138.3(11) A3, Z=2, GOF=1.089, R1=0.0563 and wR2=0.1505, whereas 2 belongs to the orthorhombic space group Iba2 with a=22.277(8), b=47.04(2), c=22.153(8) A, V=23215(17) A3, Z=4, GOF=1.051, R1=0.0627 and wR2=0.1477. 1 consists of a 1-D linear chain structure constructed from monocopperII-substituted Dawson polyoxoanions, while 2 represents the first 2-D sheet-like structure with a (4,4)-connected topological net built up from plenary Dawson-type polyoxoanions and CuII-4,4'-bpy complex cations in polyoxometalate chemistry. - Graphical abstract: Two Dawson-based phosphotungstates (H2en)0.5H[Cu(en)2(H2O)]2{[Cu(en)2](O)]2{[Cu(en)2](?1-P2W17CuO61)}.8H2O (1) and [4,4'-H2bpy]2{[Cu(4,4'-bpy)3] [Cu(4,4'-bpy)4(H2O)2]2[Cu(4,4'-bpy)][?-P2W18O62]2}.6H2O (2) have been hydrothermally synthesized and structurally characterized. 1 consists of a 1-D linear chain structure constructed from monocopper-substituted Dawson polyoxoanions, while 2 represents the first 2-D sheet-like structure with a (4,4)-connected topological net built up from saturated Dawson-type polyoxoanions and CuII-4,4'-bpy complex cations in polyoxometalate chemistry.

27

Quadruplex DNA: sequence, topology and structure  

Digital Repository Infrastructure Vision for European Research (DRIVER)

G-quadruplexes are higher-order DNA and RNA structures formed from G-rich sequences that are built around tetrads of hydrogen-bonded guanine bases. Potential quadruplex sequences have been identified in G-rich eukaryotic telomeres, and more recently in non-telomeric genomic DNA, e.g. in nuclease-hypersensitive promoter regions. The natural role and biological validation of these structures is starting to be explored, and there is particular interest in them as targets for therapeutic interven...

Burge, S.; Parkinson, G. N.; Hazel, P.; Todd, A. K.; Neidle, S.

2006-01-01

28

Permittivity and Permeability for Floquet-Bloch Space Harmonics in Infinite 1D Magneto-Dielectric Periodic Structures  

DEFF Research Database (Denmark)

For an infinite 1D periodic structure with unit cells consisting of two planar slabs of magnetodielectric materials, the electric field – as well as magnetic field, electric flux density, magnetic flux density, polarization, and magnetization – can be expressed as infinite series of Floquet-Bloch space harmonics. We discuss how space harmonic permittivity and permeability can be expressed in seemingly different though equivalent forms, and we investigate these parameters of the zeroeth order space harmonic for a particular 1D periodic structure that is based on a previously reported 3D periodic structure with unit cells containing a magneto-dielectric sphere.

Breinbjerg, Olav; Yaghjian, Arthur D.

2014-01-01

29

Multiplet structure of the defect modes in 1D helical photonic crystals with twist defects  

International Nuclear Information System (INIS)

We theoretically analyse the defect modes generated by equispaced twist defects in 1D helical (cholesteric-like) structures within their frequency gap which is such that only the first two of the four eigenwaves 1±, 2± are exponentially attenuated. n0 identical defects generate n0 different defect modes, each one represented by a linear combination of the four eigenwaves. The components 1+ and 1- are by far the dominant ones and they are localized near the defect planes. We give exact analytic expressions for the elements of the transfer and scattering matrices of the defect planes, for the functions defining the defect mode when n0 = 1, and for the defect frequencies when n0 = 1, 2, 3. In the particular case n0 = 2 and twist angle ? = ?/2, the difference between the two defect wavelengths ?d2, ?d1 depends exponentially on the distance z1 between the defect planes, going to zero for z1 ? ? and becoming as large as the entire frequency gap for z1 ? 0

30

Crystal Structures of Human TBC1D1 and TBC1D4 (AS160) RabGTPase-activating Protein (RabGAP) Domains Reveal Critical Elements for GLUT4 Translocation  

Energy Technology Data Exchange (ETDEWEB)

We have solved the x-ray crystal structures of the RabGAP domains of human TBC1D1 and human TBC1D4 (AS160), at 2.2 and 3.5 {angstrom} resolution, respectively. Like the yeast Gyp1p RabGAP domain, whose structure was solved previously in complex with mouse Rab33B, the human TBC1D1 and TBC1D4 domains both have 16 {alpha}-helices and no {beta}-sheet elements. We expected the yeast Gyp1p RabGAP/mouse Rab33B structure to predict the corresponding interfaces between cognate mammalian RabGAPs and Rabs, but found that residues were poorly conserved. We further tested the relevance of this model by Ala-scanning mutagenesis, but only one of five substitutions within the inferred binding site of the TBC1D1 RabGAP significantly perturbed catalytic efficiency. In addition, substitution of TBC1D1 residues with corresponding residues from Gyp1p did not enhance catalytic efficiency. We hypothesized that biologically relevant RabGAP/Rab partners utilize additional contacts not described in the yeast Gyp1p/mouse Rab33B structure, which we predicted using our two new human TBC1D1 and TBC1D4 structures. Ala substitution of TBC1D1 Met{sup 930}, corresponding to a residue outside of the Gyp1p/Rab33B contact, substantially reduced catalytic activity. GLUT4 translocation assays confirmed the biological relevance of our findings. Substitutions with lowest RabGAP activity, including catalytically dead RK and Met{sup 930} and Leu{sup 1019} predicted to perturb Rab binding, confirmed that biological activity requires contacts between cognate RabGAPs and Rabs beyond those in the yeast Gyp1p RabGAP/mouse Rab33B structure.

S Park; W Jin; S Shoelson

2011-12-31

31

Entangling strings of neutral atoms in 1D atomic pipeline structures  

CERN Document Server

We study a string of neutral atoms with nearest neighbor interaction in a 1D beam splitter configuration, where the longitudinal motion is controlled by a moving optical lattice potential. The dynamics of the atoms crossing the beam splitter maps to a 1D spin model with controllable time dependent parameters, which allows the creation of maximally entangled states of atoms by crossing a quantum phase transition. Furthermore, we show that this system realizes protected quantum memory, and we discuss the implementation of one- and two-qubit gates in this setup.

Dorner, U; Jaksch, D; Lewenstein, M; Zoller, P

2002-01-01

32

Entangling strings of neutral atoms in 1D atomic pipeline structures.  

Science.gov (United States)

We study a string of neutral atoms with nearest neighbor interaction in a 1D beam splitter configuration, where the longitudinal motion is controlled by a moving optical lattice potential. The dynamics of the atoms crossing the beam splitter maps to a 1D spin model with controllable time dependent parameters, which allows the creation of maximally entangled states of atoms by crossing a quantum phase transition. Furthermore, we show that this system realizes protected quantum memory, and we discuss the implementation of one- and two-qubit gates in this setup. PMID:12935017

Dorner, U; Fedichev, P; Jaksch, D; Lewenstein, M; Zoller, P

2003-08-15

33

Structural protein descriptors in 1-dimension and their sequence-based predictions.  

Science.gov (United States)

The last few decades observed an increasing interest in development and application of 1-dimensional (1D) descriptors of protein structure. These descriptors project 3D structural features onto 1D strings of residue-wise structural assignments. They cover a wide-range of structural aspects including conformation of the backbone, burying depth/solvent exposure and flexibility of residues, and inter-chain residue-residue contacts. We perform first-of-its-kind comprehensive comparative review of the existing 1D structural descriptors. We define, review and categorize ten structural descriptors and we also describe, summarize and contrast over eighty computational models that are used to predict these descriptors from the protein sequences. We show that the majority of the recent sequence-based predictors utilize machine learning models, with the most popular being neural networks, support vector machines, hidden Markov models, and support vector and linear regressions. These methods provide high-throughput predictions and most of them are accessible to a non-expert user via web servers and/or stand-alone software packages. We empirically evaluate several recent sequence-based predictors of secondary structure, disorder, and solvent accessibility descriptors using a benchmark set based on CASP8 targets. Our analysis shows that the secondary structure can be predicted with over 80% accuracy and segment overlap (SOV), disorder with over 0.9 AUC, 0.6 Matthews Correlation Coefficient (MCC), and 75% SOV, and relative solvent accessibility with PCC of 0.7 and MCC of 0.6 (0.86 when homology is used). We demonstrate that the secondary structure predicted from sequence without the use of homology modeling is as good as the structure extracted from the 3D folds predicted by top-performing template-based methods. PMID:21787299

Kurgan, Lukasz; Disfani, Fatemeh Miri

2011-09-01

34

Inhibition of Human Steroid 5-Reductase (AKR1D1) by Finasteride and Structure of the Enzyme-Inhibitor Complex  

Energy Technology Data Exchange (ETDEWEB)

The {Delta}{sup 4}-3-ketosteroid functionality is present in nearly all steroid hormones apart from estrogens. The first step in functionalization of the A-ring is mediated in humans by steroid 5{alpha}- or 5{beta}-reductase. Finasteride is a mechanism-based inactivator of 5{alpha}-reductase type 2 with subnanomolar affinity and is widely used as a therapeutic for the treatment of benign prostatic hyperplasia. It is also used for androgen deprivation in hormone-dependent prostate carcinoma, and it has been examined as a chemopreventive agent in prostate cancer. The effect of finasteride on steroid 5{beta}-reductase (AKR1D1) has not been previously reported. We show that finasteride competitively inhibits AKR1D1 with low micromolar affinity but does not act as a mechanism-based inactivator. The structure of the AKR1D1 {center_dot} NADP{sup +} {center_dot} finasteride complex determined at 1.7 {angstrom} resolution shows that it is not possible for NADPH to reduce the {Delta}{sup 1-2}-ene of finasteride because the cofactor and steroid are not proximal to each other. The C3-ketone of finasteride accepts hydrogen bonds from the catalytic residues Tyr-58 and Glu-120 in the active site of AKR1D1, providing an explanation for the competitive inhibition observed. This is the first reported structure of finasteride bound to an enzyme involved in steroid hormone metabolism.

Drury, J.; Di Costanzo, L; Penning, T; Christianson, D

2009-01-01

35

Protein homorepeats sequences, structures, evolution, and functions.  

Science.gov (United States)

The vast majority of protein sequences are aperiodic; they do not have any strong bias in the amino acid composition, and they use a subtle mixture of all or most of the 20 amino acid residues to code a great number of various structures and functions. In this context, homorepeats, runs of a single amino acid residue, represent unusual, eye-catching motifs in proteins. Despite the sequence simplicity and relatively small size, the homorepeat runs have a strong potential for molecular interactions due to the excessively high local concentration of a certain physico-chemical property. Appearance of such runs within proteins may give them new structural and functional features. An increasing number of studies demonstrate the abundance of these motifs in proteins, their important roles in biological processes, and their link to a number of hereditary and age-related diseases. In this chapter, we summarize data on the distribution of homorepeats in proteomes and on their structural properties, evolution, and functions. PMID:20621281

Jorda, Julien; Kajava, Andrey V

2010-01-01

36

A revised 1-D electrical conductivity reference structure beneath North Pacific obtained by semi-global induction study  

International Nuclear Information System (INIS)

Complete text of publication follows. One dimensional (1-D) electrical conductivity structure in the mid-mantle beneath the northern Pacific is revised in order to discuss the mean state of the mantle and to obtain a credible starting model for 3-D inversions. Semi-global geomagnetic depth sounding (GDS) responses obtained at 13 stations and submarine cable magnetotelluric (MT) responses for 8 cables in the period range 1.7 to 113 days were used to obtain the revised structure. We employed an iterative scheme combining surface layer correction to remove the effect of ocean-land heterogeneity in the responses and 1-D inversion to obtain the revised structure. The validity of the scheme is examined by making synthetic tests: We confirmed that the structure obtained using this scheme not only represents the model which explains the corrected response the best but also reflects the actual mean conductivity structure in the mid-mantle depths. The obtained 1-D conductivity in the transition zone by supposing jumps at 400 and 650 km depths (2-jump model) is higher than that of dry Wadsleyite and Ringwoodite measured experimentally by Yoshino et al. (2008). If the high conductivity is entirely due to the effect of water in the transition zone, the region contains 0.5 wt% of water. However, if an additional discontinuity of electrical conductivity is allowed at 500 km depth in the 1-D inversion, the obtained model has lower conductivity than the 2-jump model in the upper 100 ky than the 2-jump model in the upper 100 km of the transition zone. In this case, the conductivity in the layer is rather close to that of dry Wadsleyite.

37

Synthesis, crystal structure, and properties of a 1-D terbium-substituted monolacunary Keggin-type polyoxotungstate.  

Science.gov (United States)

A new 1-D linear chainlike terbium-substituted polyoxometalate [Tb(H2O)2(?-PW11O39)](4-) (1) has been synthesized in aqueous solution and characterized by elemental analysis, inductively coupled plasma atomic emission spectrometry (ICP-AES), X-ray powder diffraction (XRPD), IR spectrum, thermal analysis, electrospray ionization mass spectrometry (ESI-MS), and X-ray single-crystal diffraction. X-ray structural analysis reveals that 1 displays a 1-D linear chain containing [Tb(H2O)2(?-PW11O39)](4-) moieties. The Tb(III) cation incorporated into the monolacunary Keggin-type [?-PW11O39](7-) unit resides in a distorted monocapped triangular prismatic geometry and acts as a linker to join two adjacent [?-PW11O39](7-) units to form a 1-D chain structure. Solid-state photoluminescent property of 1 has been investigated at room temperature and the photoluminescent emission mainly results from the synergistic effect of the Tb(III) cation and the Na7[?-PW11O39] precursor. The ESI-MS spectrum of 1 confirms that the polyanion [Tb(H2O)(HPW11O39)](3-) is stable in aqueous solution. PMID:25541394

Ma, Pengtao; Si, Yanan; Wan, Rong; Zhang, Shaowei; Wang, Jingping; Niu, Jingyang

2015-03-01

38

The ASTRAL compendium for protein structure and sequence analysis  

Digital Repository Infrastructure Vision for European Research (DRIVER)

The ASTRAL compendium provides several databases and tools to aid in the analysis of protein structures, particularly through the use of their sequences. The SPACI scores included in the system summarize the overall characteristics of a protein structure. A structural alignments database indicates residue equivalencies in superimposed protein domain structures. The PDB sequence-map files provide a linkage between the amino acid sequence of the molecule studied (SEQRES records in a database en...

Brenner, Steven E.; Koehl, Patrice; Levitt, Michael

2000-01-01

39

Measurement of the Deuteron Spin Structure Function g1d(x) for 1 (GeV/c)2 2 2  

International Nuclear Information System (INIS)

New measurements are reported on the deuteron spin structure function g1d. These results were obtained from deep inelastic scattering of 48.3 GeV electrons on polarized deuterons in the kinematic range 0.01 2 2. These are the first high dose electron scattering data obtained using lithium deuteride (6Li2H) as the target material. Extrapolations of the data were performed to obtain moments of g1d, including ?1d, and the net quark polarization ? ?

40

Development of input structure software for MARS 1D-3D graphic user interface  

International Nuclear Information System (INIS)

A user-friendly Input Software for MARS 1D-3D GUI called MARA (MARS Adjunct Reactor Assembler) has been developed. Extension of the current MARA to the overall input system for MARS will result in an integrated commercial GUI comparable to those for computational analysis codes ANSYS, ABAQUS, FLUENT and CFX. MARA will help accelerate marketing of MARS and other potential system analysis codes to developing countries in Southeast Asia planning to put nuclear power in their electrical grids. MARS code and associated developmental technology are in the process of being disseminated to twenty-two organizations spanning the industry, academia and laboratories across the country. MARA will find its way to practical applications in a variety of engineering problems

 
 
 
 
41

Histone and histone fold sequences and structures: a database.  

Digital Repository Infrastructure Vision for European Research (DRIVER)

A database of aligned histone protein sequences has been constructed based on the results of homology searches of the major public sequence databases. In addition, sequences of proteins identified as containing the histone fold motif and structures of all known histone and histone fold proteins have been included in the current release. Database resources include information on conflicts between similar sequence entries in different source databases, multiple sequence alignments, and links to...

Baxevanis, A. D.; Landsman, D.

1997-01-01

42

Use of a structural alphabet to find compatible folds for amino acid sequences.  

Science.gov (United States)

The structural annotation of proteins with no detectable homologs of known 3D structure identified using sequence-search methods is a major challenge today. We propose an original method that computes the conditional probabilities for the amino-acid sequence of a protein to fit to known protein 3D structures using a structural alphabet, known as "Protein Blocks" (PBs). PBs constitute a library of 16 local structural prototypes that approximate every part of protein backbone structures. It is used to encode 3D protein structures into 1D PB sequences and to capture sequence to structure relationships. Our method relies on amino acid occurrence matrices, one for each PB, to score global and local threading of query amino acid sequences to protein folds encoded into PB sequences. It does not use any information from residue contacts or sequence-search methods or explicit incorporation of hydrophobic effect. The performance of the method was assessed with independent test datasets derived from SCOP 1.75A. With a Z-score cutoff that achieved 95% specificity (i.e., less than 5% false positives), global and local threading showed sensitivity of 64.1% and 34.2%, respectively. We further tested its performance on 57 difficult CASP10 targets that had no known homologs in PDB: 38 compatible templates were identified by our approach and 66% of these hits yielded correctly predicted structures. This method scales-up well and offers promising perspectives for structural annotations at genomic level. It has been implemented in the form of a web-server that is freely available at http://www.bo-protscience.fr/forsa. PMID:25297700

Mahajan, Swapnil; de Brevern, Alexandre G; Sanejouand, Yves-Henri; Srinivasan, Narayanaswamy; Offmann, Bernard

2015-01-01

43

Structure elucidation of two new unusual monoterpene glycosides from Euphorbia decipiens, by 1D and 2D NMR experiments.  

Science.gov (United States)

Two new unusual monoterpene glycosides, (Z)-3,6-dimethyl-3-(?-D-O-glucosylmethylene)cyclohept-4-ene-1-one (1) and 3,6-dimethyl-3-(?-D-O-glucosylmethylene)cycloheptanone (2) have been isolated along with five known compounds, 3-hydroxy-4-methoxybenzoic acid, 6,7-dihydroxycoumarin, luteolin, apigenin 5-O-?l-L-rhamnoside, and pinocembrin-7-O-rutinoside from ethyl acetate extract of Euphorbia decipiens. The structures of the isolated compounds were elucidated by extensive 1D- and 2D-NMR, and mass spectroscopic analyses. PMID:21898586

Demirkiran, Ozlem; Topcu, Gulacti; Hussain, Javid; Ahmad, Viqar Uddin; Choudhary, M Iqbal

2011-10-01

44

Genetic heterogeneity of Indian field isolates of foot-and-mouth disease virus serotype O as revealed by partial sequencing of 1D gene.  

Science.gov (United States)

The sequence of 165 nucleotides at the 3' end of the 1D gene, determined from RT PCR amplified cDNA fragments, of 25 type O strains isolated from different parts/regions of India during 1987 1995 and the vaccine strain (R2/75) currently in use in India were subjected to phylogenetic analysis. One isolate from the neighbouring country Nepal was also included in the study. The virus/ field strains showed high degree of genetic heterogeneity among themselves with % divergence in nucleotide sequence ranging from 1.2 to 19.4%. The Indian strains were much away (13.3 20.6%) from the exotic type O strains of O1BFS, O1K, and O1Campos. The type O strains analyzed were classified into three genotypes basing on level of divergence observed in nucleotide sequence. The type O vaccine virus (R2/75) was > 71% divergent (7.3-15.2%) from the field strains which revealed significant ( > 5%) genetic heterogeneity between the two. The phylogenetic analysis identified three distinct lineages, viz., (i) lineage 1 represented by the exotic strains, (ii) lineage 2 represented by 25 of the field strains which clustered into seven subgroups/sublines (2a-2g), and (iii) lineage 3 represented by a unique field isolate which shared the branching/origin with the vaccine strain. The lineage 2 which comprised of 25 of the 26 type O field strains analyzed, was placed almost at equidistance from the lineages 1 and 3 in the phylogenetic tree. The vaccine strain was closer to the viruses in lineage 2. Though there was no specific distribution pattern of sequences in different geographical regions of India, the viruses/ sequences in subgroup 2f appeared to be restricted to the southern states. Comparison of deduced amino acid sequence in the immunodominant regions 133-160 and 200-208 of the 1D gene product (VP1) showed that the two viruses in lineage 3 had unique amino acid residues at the positions 138 (D), 139 (G), 144 (I), and 158 (A) compared to rest of the strains including the exotic ones. Comparison of amino acid residues at critical positions 144, 148, 149, 151, 153, 154, and 208 revealed similarity between the type O strains analyzed. The virus strains showed variation (V/L/I) at position 144. One field strain showed replacement from Q149-->E and another from P208-->L. Thus, the study revealed that the type O FMD virus populations circulating in India and causing disease outbreaks are genetically much heterogeneous but related at the immunodominant region of VP1 polypeptide, and there are more than one genetically distinct virus populations in almost every region of the country which is possible due to unrestricted animal movement in the country. The involvement of vaccine virus in disease outbreaks was ruled out as the field strains (excluding the one in lineage 3) were phylogenetically distinct from it. PMID:9725665

Pattnaik, B; Venkataramanan, R; Tosh, C; Sanyal, A; Hemadri, D; Samuel, A R; Knowles, N J; Kitching, R P

1998-06-01

45

Computational methods in sequence and structure prediction  

Science.gov (United States)

This dissertation is organized into two parts. In the first part, we will discuss three computational methods for cis-regulatory element recognition in three different gene regulatory networks as the following: (a) Using a comprehensive "Phylogenetic Footprinting Comparison" method, we will investigate the promoter sequence structures of three enzymes (PAL, CHS and DFR) that catalyze sequential steps in the pathway from phenylalanine to anthocyanins in plants. Our result shows there exists a putative cis-regulatory element "AC(C/G)TAC(C)" in the upstream of these enzyme genes. We propose this cis-regulatory element to be responsible for the genetic regulation of these three enzymes and this element, might also be the binding site for MYB class transcription factor PAP1. (b) We will investigate the role of the Arabidopsis gene glutamate receptor 1.1 (AtGLR1.1) in C and N metabolism by utilizing the microarray data we obtained from AtGLR1.1 deficient lines (antiAtGLR1.1). We focus our investigation on the putatively co-regulated transcript profile of 876 genes we have collected in antiAtGLR1.1 lines. By (a) scanning the occurrence of several groups of known abscisic acid (ABA) related cisregulatory elements in the upstream regions of 876 Arabidopsis genes; and (b) exhaustive scanning of all possible 6-10 bps motif occurrence in the upstream regions of the same set of genes, we are able to make a quantative estimation on the enrichment level of each of the cis-regulatory element candidates. We finally conclude that one specific cis-regulatory element group, called "ABRE" elements, are statistically highly enriched within the 876-gene group as compared to their occurrence within the genome. (c) We will introduce a new general purpose algorithm, called "fuzzy REDUCE1", which we have developed recently for automated cis-regulatory element identification. In the second part, we will discuss our newly devised protein design framework. With this framework we have developed a software package which is capable of designing novel protein structures at the atomic resolution. This software package allows us to perform protein structure design with a flexible backbone. The backbone flexibility includes loop region relaxation as well as a secondary structure collective mode relaxation scheme. (Abstract shortened by UMI.)

Lang, Caiyi

46

Structure and relaxation processes of an anisotropic molecular fluid confined into 1D nanochannels  

CERN Document Server

Structural order parameters of a smectic liquid crystal confined into the columnar form of porous silicon are studied using neutron scattering and optical spectroscopic techniques. It is shown that both the translational and orientational anisotropic properties of the confined phase strongly couple to the one-dimensional character of the porous silicon matrix. The influence of this confinement induced anisotropic local structure on the molecular reorientations occuring in the picosecond timescale is discussed.

Lefort, R; Guégan, R; Alain, M; Ecolivet, C; Guendouz, M; Lefort, Ronan; Morineau, Denis; Alain, Mor\\'{e}ac; Ecolivet, Claude; Guendouz, Mohammed

2006-01-01

47

Structure and relaxation processes of an anisotropic molecular fluid confined into 1D nanochannels  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Abstract Structural order parameters of a smectic liquid crystal confined into the columnar form of porous silicon are studied using neutron scattering and optical spectroscopic techniques. It is shown that both the translational and orientational anisotropic properties of the confined phase strongly couple to the one-dimensional character of the porous silicon matrix. The influence of this confinement induced anisotropic local structure on the molecular reorientations occuring in ...

Lefort, Ronan; Morineau, Denis; Gue?gan, Re?gis; Alain, More?ac; Ecolivet, Claude; Guendouz, Mohammed

2007-01-01

48

Properties of Floquet-Bloch space harmonics in 1D periodic magneto-dielectric structures  

DEFF Research Database (Denmark)

Recent years have witnessed a significant research interest in Floquet-Bloch analysis for determining the homogenized permittivity and permeability of metamaterials consisting of periodic structures. This work investigates fundamental properties of the Floquet-Bloch space harmonics in a 1-dimensional magneto-dielectric lossless structure supporting a transverse-electric-magnetic Floquet-Bloch wave; in particular, the space harmonic permittivity and permeability, as well as the space harmonic Poynting vector.

Breinbjerg, O.

2012-01-01

49

SAAS: Short Amino Acid Sequence - A Promising Protein Secondary Structure Prediction Method of Single Sequence  

Directory of Open Access Journals (Sweden)

Full Text Available In statistical methods of predicting protein secondary structure, many researchers focus on single amino acid frequencies in ?-helices, ?-sheets, and so on, or the impact near amino acids on an amino acid forming a secondary structure. But the paper considers a short sequence of amino acids (3, 4, 5 or 6 amino acids as integer, and statistics short sequence's probability forming secondary structure. Also, many researchers select low homologous sequences as statistical database. But this paper select whole PDB database. In this paper we propose a strategy to predict protein secondary structure using simple statistical method. Numerical computation shows that, short amino acids sequence as integer to statistics, which can easy see trend of short sequence forming secondary structure, and it will work well to select large statistical database (whole PDB database without considering homologous, and Q3 accuracy is ca. 74% using this paper proposed simple statistical method, but accuracy of others statistical methods is less than 70%.

Zhou Yuan Wu

2013-07-01

50

Improving protein secondary structure prediction with aligned homologous sequences.  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Most recent protein secondary structure prediction methods use sequence alignments to improve the prediction quality. We investigate the relationship between the location of secondary structural elements, gaps, and variable residue positions in multiple sequence alignments. We further investigate how these relationships compare with those found in structurally aligned protein families. We show how such associations may be used to improve the quality of prediction of the secondary structure el...

Di Francesco, V.; Garnier, J.; Munson, P. J.

1996-01-01

51

Dicopper(II) Schiff base aminobenzoates with discrete molecular and 1D-chain polymeric structures  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Dicopper(II) complexes $[Cu_2L(O_2CC_6H_4-o-NH_2)]$ (1) and $[Cu_2L(O_2CC_6H_4-p-NH_2)]$ (2) are prepared from a reaction of $[Cu_2-L(O_2CMe)]$ with the corresponding aminobenzoic acid and a base in MeOH, where L is a trianionic pentadentate Schiff base ligand N,N'-(2-hydroxypropane-1,3-diyl)bis(salicylaidimine). The complexes are structurally characterized by X-ray crystallography. The crystal structures show the presence of an asymmetrically dibridged ${Cu^{II}_2(\\mu-OR)(\\mu-O_2CR)}$ core w...

Mukherjee, Arindam; Saha, Manas K.; Nethaji, Munirathinam; Chakravarty, Akhil R.

2004-01-01

52

Integrability of and differential–algebraic structures for spatially 1D hydrodynamical systems of Riemann type  

International Nuclear Information System (INIS)

Highlights: • A new differential–algebraic–geometric approach for testing integrability is described. • The approach is applied to a generalized Riemann type hydrodynamic system. • The approach is applied to a generalized Ostrovsky–Vakhnenko system. • The approach is applied to a new two-component Burgers type hydrodynamic system. -- Abstract: A differential–algebraic approach to studying the Lax integrability of a generalized Riemann type hydrodynamic hierarchy is revisited and a new Lax representation is constructed. The related bi-Hamiltonian integrability and compatible Poissonian structures of this hierarchy are also investigated using gradient-holonomic and geometric methods. The complete integrability of a new generalized Riemann hydrodynamic system is studied via a novel combination of symplectic and differential–algebraic tools. A compatible pair of polynomial Poissonian structures, a Lax representation and a related infinite hierarchy of conservation laws are obtained. In addition, the differential–algebraic approach is used to prove the complete Lax integrability of the generalized Ostrovsky–Vakhnenko and a new Burgers type system, and special cases are studied using symplectic and gradient-holonomic tools. Compatible pairs of polynomial Poissonian structures, matrix Lax representations and infinite hierarchies of conservation laws are derived

53

Ultrasound-induced modulations of tetrapeptide hierarchical 1-D self-assembly and underlying molecular structures via sonocrystallization.  

Science.gov (United States)

Herein, we report the ultrasound-induced modulations of the morphologies and underlying molecular structures of tetrapeptide 1-D self-assembly. The self-assembly of the tetrapeptide (TTR108-111) precipitating out of the 1:1 mixed methanol/water is modulated from microtapes into nanotapes, nanofibers, and then bundles of nanorods when subjected to sonication for a period. The sonication-treated and untreated self-assemblies all give a set of equatorial pattern and a series of meridional pattern, indications of a typical "cross-beta-structure" as the core structural motif. FTIR data indicate that all the assemblies contain a mixed pattern of beta-sheets (dominant) and unstructured conformations (minor), and the relative proportion of unbound structures to beta-sheets is as a function of sonication time, suggesting an ultrasound-induced modulation of beta-sheet interactions. Accordingly, a possible model regarding a dynamic equilibrium between re-dissolution and re-assembling processes, e.g., a typical sonocrystallization process was proposed for such ultrasound-induced modulations of morphologies and underlying molecular structures. PMID:19527909

Ke, Damei; Zhan, Chuanlang; Li, Xiao; Wang, Xi; Zeng, Yi; Yao, Jiannian

2009-09-01

54

Filovirus Glycoprotein Sequence, Structure and Virulence  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Leading Ebola subtypes exhibit a wide mortality range, here explained at the molecular level by using fractal hydropathic scaling of amino acid sequences based on protein self-organized criticality. Specific hydrophobic features in the hydrophilic mucin-like domain suffice to account for the wide mortality range. Significance statement: Ebola virus is spreading rapidly in Africa. The connection between protein amino acid sequence and mortality is identified here.

Phillips, J. C.

2014-01-01

55

3D mechanical measurements with an atomic force microscope on 1D structures.  

DEFF Research Database (Denmark)

We have developed a simple method to characterize the mechanical properties of three dimensional nanostructures, such as nanorods standing up from a substrate. With an atomic force microscope the cantilever probe is used to deflect a horizontally aligned nanorod at different positions along the nanorod, using the apex of the cantilever itself rather than the tip normally used for probing surfaces. This enables accurate determination of nanostructures' spring constant. From these measurements, Young's modulus is found on many individual nanorods with different geometrical and material structures in a short time. Based on this method Young's modulus of carbon nanofibers and epitaxial grown III-V nanowires has been determined.

KallesØe, Christian; Larsen, Martin Benjamin Barbour Spanget

2012-01-01

56

Structure elucidation of organic compounds from natural sources using 1D and 2D NMR techniques  

Science.gov (United States)

In our continuing studies on Lamiaceae family plants including Salvia, Teucrium, Ajuga, Sideritis, Nepeta and Lavandula growing in Anatolia, many terpenoids, consisting of over 50 distinct triterpenoids and steroids, and over 200 diterpenoids, several sesterterpenoids and sesquiterpenoids along with many flavonoids and other phenolic compounds have been isolated. For Salvia species abietanes, for Teucrium and Ajuga species neo-clerodanes for Sideritis species ent-kaurane diterpenes are characteristic while nepetalactones are specific for Nepeta species. In this review article, only some interesting and different type of skeleton having constituents, namely rearranged, nor- or rare diterpenes, isolated from these species will be presented. For structure elucidation of these natural diterpenoids intensive one- and two-dimensional NMR techniques ( 1H, 13C, APT, DEPT, NOE/NOESY, 1H- 1H COSY, HETCOR, COLOC, HMQC/HSQC, HMBC, SINEPT) were used besides mass and some other spectroscopic methods.

Topcu, Gulacti; Ulubelen, Ayhan

2007-05-01

57

Novel copper(II) sulfonate-arsonates with discrete cluster, 1D chain and layered structures  

Science.gov (United States)

Hydrothermal reactions of copper(II) salts with o-sulfophenylarsonic acid ( o-HO 3S-C 6H 4-AsO 3H 2, H 3L) led to a layered compound, Cu 2.5(L)(OH) 2 ( 1). Introduction of the auxiliary chelating ligands such as 2,2'-bipyridine (bipy) or 1,10-phenanthroline (phen) and 2,2':6',2''-terpyridine (terpy) led to three new copper(II) sulfonate-arsonates with lower dimensional structures, namely, mononuclear Cu(HL)(bipy)(H 2O)·2H 2O ( 2), dinuclear [Cu(HL)(phen)] 2·4H 2O ( 3) and one-dimensional Cu(HL)(terpy)·2H 2O ( 4). Magnetic property measurements indicate that 1 exhibits ordinary antiferromagnetic feature, without the geometric spin frustration as expected. 2 shows a typical paramagnetic behavior. There exists antiferromagnetic interactions between the magnetic centers in dimeric 3. 4 displays an antiferromagnetic magnetic exchange interaction propagated via O sbnd S sbnd O bridges.

Yi, Fei-Yan; Lin, Qi-Pu; Zhou, Tian-Hua; Mao, Jiang-Gao

2010-12-01

58

Combining Sequence and Structural Profiles for Protein Solvent Accessibility Prediction  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Solvent accessibility is an important structural feature for a protein. We propose a new method for solvent accessibility prediction that uses known structure and sequence information more efficiently. We first estimate the relative solvent accessibility of the query protein using fuzzy mean operator from the solvent accessibilities of known structure fragments that have similar sequences to the query protein. We then integrate the estimated solvent accessibility and the position specific sco...

Bondugula, Rajkumar; Xu, Dong

2008-01-01

59

Progressive structure-based alignment of homologous proteins: Adopting sequence comparison strategies.  

Science.gov (United States)

Comparison of multiple protein structures has a broad range of applications in the analysis of protein structure, function and evolution. Multiple structure alignment tools (MSTAs) are necessary to obtain a simultaneous comparison of a family of related folds. In this study, we have developed a method for multiple structure comparison largely based on sequence alignment techniques. A widely used Structural Alphabet named Protein Blocks (PBs) was used to transform the information on 3D protein backbone conformation as a 1D sequence string. A progressive alignment strategy similar to CLUSTALW was adopted for multiple PB sequence alignment (mulPBA). Highly similar stretches identified by the pairwise alignments are given higher weights during the alignment. The residue equivalences from PB based alignments are used to obtain a three dimensional fit of the structures followed by an iterative refinement of the structural superposition. Systematic comparisons using benchmark datasets of MSTAs underlines that the alignment quality is better than MULTIPROT, MUSTANG and the alignments in HOMSTRAD, in more than 85% of the cases. Comparison with other rigid-body and flexible MSTAs also indicate that mulPBA alignments are superior to most of the rigid-body MSTAs and highly comparable to the flexible alignment methods. PMID:22676903

Joseph, Agnel Praveen; Srinivasan, Narayanaswamy; de Brevern, Alexandre G

2012-09-01

60

Radial 1-D seismic structures in the deep mantle in mantle convection simulations with self-consistently calculated mineralogy  

Science.gov (United States)

Numerical thermo-chemical mantle convection simulations in a spherical annulus geometry with self-consistently calculated mineralogy and mineral physics are used to predict detailed deep mantle seismic structures, particularly local radial profiles of shear wave velocity (Vs) and bulk sound velocity (Vb). The predicted structures are compared to seismological observations and used to guide the interpretation of seismic observations and to test the model. The mantle composition is described as a mixture of MORB (Mid-Oceanic-Ridge-Basalt) and harzburgitic end-members in the Na2O-CaO-FeO-MgO-Al2O3-SiO2system. To assess the influence of chemical variability, four different sets of end-member compositions are evaluated. Results confirm that the post-perovskite (pPv) phase causes anti-correlated S wave and bulk sound velocities in the deep mantle, due to pPv being fast in Vs but slow in bulk sound velocity. Local 1-D seismic profiles display great lateral variability, and often have multiple discontinuities in the deep mantle due to MORB layers in folded slabs, with a positive Vs anomaly and negative bulk sound anomaly, or the perovskite-pPv phase transition. The pPv transition is not visible inside piles of segregated MORB because of the high temperature and small velocity contrast of pPv in MORB. Piles of segregated MORB are seismically slow in both Vs and bulk sound despite being expected to be fast in Vs, because they are hotter than the surrounding material. Anelasticity has a significant influence on profiles of Vs only in the lower thermal boundary layer, which corresponds to below 2600 to 2800 km depth depending on region, where temperatures are higher than the extrapolated adiabat. These results indicate the importance of using a joint geodynamical-mineralogical approach to predict and aid in the interpretation of deep mantle seismic structure, because interpretations based on seismology and mineral physics alone may be misleading and do not capture the strong lateral variability in 1-D structure obtained here: for example, multiple reflections arising from folded slabs and the precise balance between thermal and compositional influences on seismic structure.

Nakagawa, Takashi; Tackley, Paul J.; Deschamps, FréDéRic; Connolly, James A. D.

2012-11-01

 
 
 
 
61

Syntheses, structures, and photoluminescence of d 10 coordination architectures: From 1D to 3D complexes based on mixed ligands  

Science.gov (United States)

Six new compounds, namely, {[Cd 3(Himpy) 3(tda) 2]·3H 2O} n ( 1), {[Zn 3(bipy) 2(tda) 2(H 2O) 2]·4H 2O} n ( 2), {[Cd 3(bipy) 3(tda) 2]·4H 2O} n ( 3), {[Cd 3(tda) 2(H 2O) 3Cl]·H 2O} n ( 4), {[Zn 2(tz)(tda)(H 2O) 2]·H 2O} n ( 5) and {[Cd 7(pz)(tda) 4(OAc)(H 2O) 7]·3H 2O} n ( 6) [H 3tda = 1H-1,2,3-triazole-4,5-dicarboxylic acid, Himpy = 2-(1H-imidazol-2-yl)pyridine, bipy = 2,2'-bipyridine, Htz = 1H-1,2,4-triazole, H 2pz = piperazine] have been prepared under hydrothermal condition and characterized by elemental analyses, infrared spectroscopy, powder X-ray diffraction and single-crystal X-ray diffraction analyses. Compound 1 is a 1D column-like structure and displays a 3D supramolecular network via the ?···? stacking interaction. The compounds 2 and 3 exhibit similar 2D layer-like structure, which further extend to 3D supermolecular structure by the ?···? stacking interaction. All of compounds 4- 6 display 3D framework with diverse topology constructed from the tda 3- ligands in different coordination modes and secondary ligands (or bridging atom) connecting metal ions. Furthermore, the thermal stabilities and photoluminescent properties of compounds 1- 6 were studied.

Yuan, Gang; Shao, Kui-Zhan; Du, Dong-Ying; Wang, Xin-Long; Su, Zhong-Min

2011-05-01

62

Structure and biosynthesis of the signal-sequence receptor  

Digital Repository Infrastructure Vision for European Research (DRIVER)

The signal-sequence receptor (SSR) has previously been shown to be a component of the environment which nascent polypeptides meet on passage through the endoplasmic reticulum (ER) membrane. We report here on the primary structure of the SSR as deduced from cDNA clones and from direct protein sequencing. The glycoprotein is synthesized with a cleavable amino-terminal signal sequence and contains only one classical membrane-spanning segment. Its insertion into the ER membrane during biosynthesi...

Prehn, Siegfried; Herz, Joachim; Hartmann, Enno; Kurzchalia, Teymuras V.; Frank, Rainer; Ro?misch, Karin; Dobberstein, Bernhard; Rapoport, Tom A.

1990-01-01

63

Sequence and structure of the yeast galactose transporter.  

Digital Repository Infrastructure Vision for European Research (DRIVER)

The previously cloned GAL2 gene of the Saccharomyces cerevisiae galactose transporter has been sequenced. The nucleotide sequence predicts a protein with 574 amino acids (Mr, 63,789). Hydropathy plots suggest that there are 12 membrane-spanning segments. The galactose transporter shows both sequence and structural homology with a superfamily of sugar transporters which includes the human HepG2-erythrocyte and fetal muscle glucose transporters, the rat brain and liver glucose transporters, the...

Szkutnicka, K.; Tschopp, J. F.; Andrews, L.; Cirillo, V. P.

1989-01-01

64

X-ray diffraction and Raman scattering studies on large-area array and nanobranched structure of 1D MoO{sub 2} nanorods  

Energy Technology Data Exchange (ETDEWEB)

One-dimensional (1D) MoO{sub 2} nanorods in the form of a large-area array and nanobranched structure were prepared by hot-filament metal-oxide vapour deposition at low and high pressures in atmospheric argon flows respectively. The x-ray diffraction (XRD) patterns of both as-synthesized samples show that the 1D MoO{sub 2} nanorods are monoclinic crystals in space group P 2{sub 1}/c. The Raman spectrum of the large-area array of 1D MoO{sub 2} nanorods appears to be the same as that of a two-dimensional (2D) MoO{sub 2} thin film. The Raman spectrum of the nanobranched structure of 1D MoO{sub 2} nanorods showed a downshift and asymmetric broadening of the Raman first-order TO peak when compared with the bulk (q = 0) mode. The Raman shift and broadening were attributed to phonon confinement effect in the 1D nanorods. The in situ Raman spectra of laser-induced oxidation of the nanobranched structure of 1D MoO{sub 2} nanorods demonstrate that they can be oxidized easily and more strongly than the 3D bulk MoO{sub 2} powder.

Kumari, Latha [Department of Physics, National Dong Hwa University, Hualien 974, Taiwan (China); Ma, Y-R [Department of Physics, National Dong Hwa University, Hualien 974, Taiwan (China); Tsai, C-C [Department of Physics, National Dong Hwa University, Hualien 974, Taiwan (China); Lin, Y-W [Department of Physics, National Dong Hwa University, Hualien 974, Taiwan (China); Wu, S Y [Department of Physics, National Dong Hwa University, Hualien 974, Taiwan (China); Cheng, K-W [Institute of Physics, Academia Sinica, Taipei 1159, Taiwan (China); Liou Yung [Institute of Physics, Academia Sinica, Taipei 1159, Taiwan (China)

2007-03-21

65

Spatial structure and dispersion of drift mirror waves coupled with Alfvén waves in a 1-D inhomogeneous plasma  

Directory of Open Access Journals (Sweden)

Full Text Available The paper employs the frame of a 1-D inhomogeneous model of space plasma,to examine the spatial structure and growth rate of drift mirror modes, often suggested for interpreting some oscillation types in space plasma. Owing to its coupling with the Alfvén mode, the drift mirror mode attains dispersion across magnetic shells (dependence of the frequency on the wave-vector's radial component, kr. The spatial structure of a mode confined across magnetic shells is studied. The scale of spatial localization of the wave is shown to be determined by the plasma inhomogeneity scale and by the azimuthal component of the wave vector. The wave propagates across magnetic shells, its amplitude modulated along the radial coordinate by the Gauss function. Coupling with the Alfvén mode strongly influences the growth rate of the drift mirror instability. The mirror mode can only exist in a narrow range of parameters. In the general case, the mode represents an Alfvén wave modified by plasma inhomogeneity.

D. Yu. Klimushkin

2006-09-01

66

HOTCFGM-1D: A Coupled Higher-Order Theory for Cylindrical Structural Components with Through-Thickness Functionally Graded Microstructures  

Science.gov (United States)

The objective of this three-year project was to develop and deliver to NASA Lewis one-dimensional and two-dimensional higher-order theories, and related computer codes, for the analysis, optimization and design of cylindrical functionally graded materials/structural components for use in advanced aircraft engines (e.g., combustor linings, rotor disks, heat shields, blisk blades). To satisfy this objective, a quasi one-dimensional version of the higher-order theory, HOTCFGM-1D, and four computer codes based on this theory, for the analysis, design and optimization of cylindrical structural components functionally graded in the radial direction were developed. The theory is applicable to thin multi-phased composite shell/cylinders subjected to macroscopically axisymmetric thermomechanical and inertial loading applied uniformly along the axial direction such that the overall deformation is characterized by a constant average axial strain. The reinforcement phases are uniformly distributed in the axial and circumferential directions, and arbitrarily distributed in the radial direction, thereby allowing functional grading of the internal reinforcement in this direction.

Pindera, Marek-Jerzy; Aboudi, Jacob

1998-01-01

67

Occurrence of protein structure elements in conserved sequence regions  

Directory of Open Access Journals (Sweden)

Full Text Available Abstract Background Conserved protein sequence regions are extremely useful for identifying and studying functionally and structurally important regions. By means of an integrated analysis of large-scale protein structure and sequence data, structural features of conserved protein sequence regions were identified. Results Helices and turns were found to be underrepresented in conserved regions, while strands were found to be overrepresented. Similar numbers of loops were found in conserved and random regions. Conclusion These results can be understood in light of the structural constraints on different secondary structure elements, and their role in protein structural stabilization and topology. Strands can tolerate fewer sequence changes and nonetheless keep their specific shape and function. They thus tend to be more conserved than helices, which can keep their shape and function with more changes. Loop behavior can be explained by the presence of both constrained and freely changing loops in proteins. Our detailed statistical analysis of diverse proteins links protein evolution to the biophysics of protein thermodynamic stability and folding. The basic structural features of conserved sequence regions are also important determinants of protein structure motifs and their function.

Pietrokovski Shmuel

2007-01-01

68

Sequence-Structure Relationship in Proteins: a Computational Analysis of Proteins that Differ in Sequence but Share the Same Fold  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Mapping between sequence and structure is currently an open problem in structural biology. Despite many experimental and computational efforts it is not clear yet how the structure is encoded in the sequence. Answering this question may pave the way for predicting a protein fold given its sequence. My doctoral studies have focused on a particular phenomenon relevant to the protein sequence-structure relationship. It has been observed that many proteins having apparently di...

Friedberg, Iddo

2013-01-01

69

On maximal eigenfrequency separation in two-material structures: the 1D and 2D scalar cases  

DEFF Research Database (Denmark)

We present a method to maximize the separation of two adjacent eigenfrequencies in structures with two material components. The method is based on finite element analysis and topology optimization in which an iterative algorithm is used to find the optimal distribution of the materials. Results are presented for eigenvalue problems based on the 1D and 2D scalar wave equations. Two different objectives are used in the optimization, the difference between two adjacent eigenfrequencies and the ratio between the squared eigenfrequencies. In the ID case, we use simple interpolation of material parameters but in the 2D case the use of a more involved interpolation is needed, and results obtained with a new interpolation function are shown. In the 2D case, the objective is reformulated into a double-bound formulation due to the complication from multiple eigenfrequencies. It is shown that some general conclusions can be drawn that relate the material parameters to the obtainable objective values and the optimized designs.

Jensen, Jakob SØndergaard; Pedersen, Niels Leergaard

2006-01-01

70

Pairwise local structural alignment of RNA sequences with sequence similarity less than 40%  

DEFF Research Database (Denmark)

Motivation: Searching for non-coding RNA (ncRNA) genes and structural RNA elements (eleRNA) are major challenges in gene finding todya as these often are conserved in structure rather than in sequence. Even though the number of available methods is growing, it is still of interest to pairwise detect two genes with low sequence similarity, where the genes are part of a larger genomic region. Results: Here we present such an approach for pairwise local alignment which is based on FILDALIGN and the Sankoff algorithm for simultaneous structural alignment of multiple sequences. We include the ability to conduct mutual scans of two sequences of arbitrary length while searching for common local structural motifs of some maximum length. This drastically reduces the complexity of the algorithm. The scoring scheme includes structural parameters corresponding to those available for free energy as well as for substitution matrices similar to RIBOSUM. The new FOLDALIGN implementation is tested on a dataset where the ncRNAs and eleRNAs have sequence similarity <40% and where the ncRNAs and eleRNAs are energetically indistinguishable from the surrounding genomic sequence context. The method is tested in two ways: (1) its ability to find the common structure between the genes only and (2) its ability to locate ncRNAs and eleRNAs in a genomic context. In case (1), it makes sense to compare with methods like Dynalign, and the performances are very similar, but FOLDALIGN is substantially faster. The structure prediction performance for a family is typically around 0.7 using Matthews correlation coefficient. In case (2), the algorithm is successful at locating RNA families with an average sensitivity of 0.8 and a positive predictive value of 0.9 using a BLAST-like hit selection scheme. Availability: The program is available online at http://foldalign.kvl.dk Contact: gorodkin@bioinf.kvl.dk

Havgaard, Jakob Hull; LyngsØ, Rune B.

2005-01-01

71

A fast structural multiple alignment method for long RNA sequences  

Directory of Open Access Journals (Sweden)

Full Text Available Abstract Background Aligning multiple RNA sequences is essential for analyzing non-coding RNAs. Although many alignment methods for non-coding RNAs, including Sankoff's algorithm for strict structural alignments, have been proposed, they are either inaccurate or computationally too expensive. Faster methods with reasonable accuracies are required for genome-scale analyses. Results We propose a fast algorithm for multiple structural alignments of RNA sequences that is an extension of our pairwise structural alignment method (implemented in SCARNA. The accuracies of the implemented software, MXSCARNA, are at least as favorable as those of state-of-art algorithms that are computationally much more expensive in time and memory. Conclusion The proposed method for structural alignment of multiple RNA sequences is fast enough for large-scale analyses with accuracies at least comparable to those of existing algorithms. The source code of MXSCARNA and its web server are available at http://mxscarna.ncrna.org.

Kin Taishin

2008-01-01

72

Topological characterization of crystalline ice structures from coordination sequences  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Topological properties of crystalline ice structures are studied by considering ring statistics, coordination sequences, and topological density of different ice phases. The coordination sequences (number of sites at topological distance k from a reference site) have been obtained by direct enumeration until at least 40 coordination spheres for different ice polymorphs. This allows us to study the asymptotic behavior of the mean number of sites in the k-th shell, Mk, for high values of k: Mk ...

Herrero, C. P.; Rami?rez, Rafael

2013-01-01

73

Structure-activity relationships of human AKR-type oxidoreductases involved in bile acid synthesis: AKR1D1 and AKR1C4.  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Two members of the human aldo-keto reductase (AKR) superfamily participate in the biosynthesis of bile acids by catalyzing the NADP(H) dependent reduction of 3-keto groups (AKR1C4) and Delta4 double bonds (AKR1D1) of oxysterol precursors. Structure determination of human AKR1C4 and homology modelling of AKR1D1 followed by docking experiments were used to explore active site geometries. Substrate docking resulted in ligand poses satisfying catalytic constraints, and indicates a critical role f...

Lee, Wen Hwa; Lukacik, Petra; Guo, Kunde; Ugochukwu, Emilie; Kavanagh, Kathryn L.; Marsden, Brian; Oppermann, Udo

2009-01-01

74

Evolutionarily consistent families in SCOP: sequence, structure and function  

Directory of Open Access Journals (Sweden)

Full Text Available Abstract Background SCOP is a hierarchical domain classification system for proteins of known structure. The superfamily level has a clear definition: Protein domains belong to the same superfamily if there is structural, functional and sequence evidence for a common evolutionary ancestor. Superfamilies are sub-classified into families, however, there is not such a clear basis for the family level groupings. Do SCOP families group together domains with sequence similarity, do they group domains with similar structure or by common function? It is these questions we answer, but most importantly, whether each family represents a distinct phylogenetic group within a superfamily. Results Several phylogenetic trees were generated for each superfamily: one derived from a multiple sequence alignment, one based on structural distances, and the final two from presence/absence of GO terms or EC numbers assigned to domains. The topologies of the resulting trees and confidence values were compared to the SCOP family classification. Conclusions We show that SCOP family groupings are evolutionarily consistent to a very high degree with respect to classical sequence phylogenetics. The trees built from (automatically generated structural distances correlate well, but are not always consistent with SCOP (hand annotated groupings. Trees derived from functional data are less consistent with the family level than those from structure or sequence, though the majority still agree. Much of GO and EC annotation applies directly to one family or subset of the family; relatively few terms apply at the superfamily level. Maximum sequence diversity within a family is on average 22% but close to zero for superfamilies.

Pethica Ralph B

2012-10-01

75

Modeling of Subject Arterial Segments Using 3D Fluid Structure Interaction and 1D-0D Arterial Tree Network Boundary Condition  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Modeling of Subject Specific Arterial Segments Using 3D Fluid Structure Interaction and a 1D-0D Arterial Tree Network Boundary Condition   Magnus Andersson, Jonas Lantz , Matts Karlsson   Department of Management and Engineering, Linköping University, SE-581 83 Linköping, Sweden   Introduction In recent years it has been possible to simulate 3D blood flow through CFD including the dilatation effect in elastic arteries using Fluid-Structure Interaction (FSI) to better match in vivo data. ...

Andersson, Magnus; Lantz, Jonas; Karlsson, Matts

2011-01-01

76

Massively Parallel Interrogation of Aptamer Sequence, Structure and Function  

Energy Technology Data Exchange (ETDEWEB)

Optimization of high affinity reagents is a significant bottleneck in medicine and the life sciences. The ability to synthetically create thousands of permutations of a lead high-affinity reagent and survey the properties of individual permutations in parallel could potentially relieve this bottleneck. Aptamers are single stranded oligonucleotides affinity reagents isolated by in vitro selection processes and as a class have been shown to bind a wide variety of target molecules. Methodology/Principal Findings. High density DNA microarray technology was used to synthesize, in situ, arrays of approximately 3,900 aptamer sequence permutations in triplicate. These sequences were interrogated on-chip for their ability to bind the fluorescently-labeled cognate target, immunoglobulin E, resulting in the parallel execution of thousands of experiments. Fluorescence intensity at each array feature was well resolved and shown to be a function of the sequence present. The data demonstrated high intra- and interchip correlation between the same features as well as among the sequence triplicates within a single array. Consistent with aptamer mediated IgE binding, fluorescence intensity correlated strongly with specific aptamer sequences and the concentration of IgE applied to the array. The massively parallel sequence-function analyses provided by this approach confirmed the importance of a consensus sequence found in all 21 of the original IgE aptamer sequences and support a common stem:loop structure as being the secondary structure underlying IgE binding. The microarray application, data and results presented illustrate an efficient, high information content approach to optimizing aptamer function. It also provides a foundation from which to better understand and manipulate this important class of high affinity biomolecules.

Fischer, N O; Tok, J B; Tarasow, T M

2008-02-08

77

Draft Genome Sequence of the Cyanobacterium Aphanizomenon flos-aquae Strain 2012/KM1/D3, Isolated from the Curonian Lagoon (Baltic Sea).  

Science.gov (United States)

We report here the de novo genome assembly of a cyanobacterium, Aphanizomenon flos-aquae strain 2012/KM1/D3, a harmful bloom-forming species in temperate aquatic ecosystems. The genome is 5.7 Mb with a G+C content of 38.2%, and it is enriched mostly with genes involved in amino acid and carbohydrate metabolism. PMID:25593252

Šul?ius, Sigitas; Alzbutas, Gediminas; Kvederavi?i?t?, Kotryna; Koreivien?, Judita; Zakrys, Linas; Lubys, Arvydas; Paškauskas, Ri?ardas

2015-01-01

78

Detecting DNA-binding helix–turn–helix structural motifs using sequence and structure information  

Digital Repository Infrastructure Vision for European Research (DRIVER)

In this work, we analyse the potential for using structural knowledge to improve the detection of the DNA-binding helix–turn–helix (HTH) motif from sequence. Starting from a set of DNA-binding protein structures that include a functional HTH motif and have no apparent sequence similarity to each other, two different libraries of hidden Markov models (HMMs) were built. One library included sequence models of whole DNA-binding domains, which incorporate the HTH motif, the second library inc...

Pellegrini-calace, Marialuisa; Thornton, Janet M.

2005-01-01

79

Inhibition of human steroid 5beta-reductase (AKR1D1) by finasteride and structure of the enzyme-inhibitor complex.  

Science.gov (United States)

The Delta(4)-3-ketosteroid functionality is present in nearly all steroid hormones apart from estrogens. The first step in functionalization of the A-ring is mediated in humans by steroid 5alpha- or 5beta-reductase. Finasteride is a mechanism-based inactivator of 5alpha-reductase type 2 with subnanomolar affinity and is widely used as a therapeutic for the treatment of benign prostatic hyperplasia. It is also used for androgen deprivation in hormone-dependent prostate carcinoma, and it has been examined as a chemopreventive agent in prostate cancer. The effect of finasteride on steroid 5beta-reductase (AKR1D1) has not been previously reported. We show that finasteride competitively inhibits AKR1D1 with low micromolar affinity but does not act as a mechanism-based inactivator. The structure of the AKR1D1.NADP(+)*finasteride complex determined at 1.7 A resolution shows that it is not possible for NADPH to reduce the Delta(1-2)-ene of finasteride because the cofactor and steroid are not proximal to each other. The C3-ketone of finasteride accepts hydrogen bonds from the catalytic residues Tyr-58 and Glu-120 in the active site of AKR1D1, providing an explanation for the competitive inhibition observed. This is the first reported structure of finasteride bound to an enzyme involved in steroid hormone metabolism. PMID:19515843

Drury, Jason E; Di Costanzo, Luigi; Penning, Trevor M; Christianson, David W

2009-07-24

80

Quantifying sequence and structural features of protein-RNA interactions.  

Science.gov (United States)

Increasing awareness of the importance of protein-RNA interactions has motivated many approaches to predict residue-level RNA binding sites in proteins based on sequence or structural characteristics. Sequence-based predictors are usually high in sensitivity but low in specificity; conversely structure-based predictors tend to have high specificity, but lower sensitivity. Here we quantified the contribution of both sequence- and structure-based features as indicators of RNA-binding propensity using a machine-learning approach. In order to capture structural information for proteins without a known structure, we used homology modeling to extract the relevant structural features. Several novel and modified features enhanced the accuracy of residue-level RNA-binding propensity beyond what has been reported previously, including by meta-prediction servers. These features include: hidden Markov model-based evolutionary conservation, surface deformations based on the Laplacian norm formalism, and relative solvent accessibility partitioned into backbone and side chain contributions. We constructed a web server called aaRNA that implements the proposed method and demonstrate its use in identifying putative RNA binding sites. PMID:25063293

Li, Songling; Yamashita, Kazuo; Amada, Karlou Mar; Standley, Daron M

2014-01-01

 
 
 
 
81

Designing polymorphic ISSR primers in order to study gene sequences x and y types glutenin subunits in 1D locus controlling favourable baking quality in elite mutant lines of bread wheat  

International Nuclear Information System (INIS)

Baking quality is one of important traits in qualitative improvement of bread wheat. Gluten prolamins determine wheat flour quality for different technological process such as bread making. Between gluten proteins, High Molecular Glutenin (HMW) group and specially, d allele in 1D locus with x-type and y-type subunits are very valuable in baking quality. In this study, amino acid sequences of x-type subunits (2.1, 2.2, 2.2*, 5) and y-type subunits (10, 12) related to 1D locus were searched, found and compared together using Genedoc software. After amino acid sequences alignment of y-type subunits and x-type subunits, it was characterized that deletion, insertion (duplication) and point mutations in these subunits involved in biological function of proteins. most important insertion and deletion mutations were 185 amino acids sequence insertion of 2.2* subunit and 102 amino acids sequence insertion of x2.2 subunit in position 486 of amino acid sequence and six amino acid sequence deletion IGQGQQ in position 203 of y10 subunit. From important point mutations can be pointed to conversion of serine to cysteine in position 118 of x 5 subunit and substitution of glutamine to histidine in position 626 of x5 subunit. Finally, polymorph ISSR primers in repetitive domains were designed on similarities and differences in subunits of x and y-types. These primers show good banding polymorphisms in elite mutant lines, standard commercial cultivars and F2 populations from tivars and F2 populations from crosses. (author)

82

HSP: evolved and conserved proteins, structure and sequence studies  

Directory of Open Access Journals (Sweden)

Full Text Available Heat shock proteins (HSPs are the proteins which are present normally in the cell but theirexpression level increases under stress condition and are mainly divided into five groups, low molecularweight HSP (LMW HSP, HSP 60, HSP 70, HSP 90 and high molecular weight HSP (HMW HSP. All theseclasses of HSPs are highly conserved and ubiquitous in nature and hence serve as a good model forphylogenetic analysis. For the first time in this study,the sequence and structural analysis has been carriedout to predict evolution of HSPs. The results obtained clearly show higher degree of sequence and structuralconservation. HSP 60 and HSP 70 are highly conserved in terms of both sequence and structure alignmentin comparison to HSP 90. The minimum amino acid identity that has been observed between all thehomologous sequences is 32.46%, 38%, 23.60% for HSP 60, HSP 70 and HSP 90 respectively, indicatingHSP 70 as the most conserved protein family followed by HSP 60 and HSP 90 family. The structuralanalysis of these proteins showed dominance of beta sheets in HSP70 and helices in HSP 90. The detailedanalysis of all the HSP homologues revealed high conservation of glycine residues and ATP binding pockets.Thus this study has revealed that HSPs are highly structurally and functionally conserved proteins andwarrants further detailed analysis at organism level.

Desai N.S.

2010-06-01

83

Improving protein secondary structure prediction with aligned homologous sequences.  

Science.gov (United States)

Most recent protein secondary structure prediction methods use sequence alignments to improve the prediction quality. We investigate the relationship between the location of secondary structural elements, gaps, and variable residue positions in multiple sequence alignments. We further investigate how these relationships compare with those found in structurally aligned protein families. We show how such associations may be used to improve the quality of prediction of the secondary structure elements, using the Quadratic-Logistic method with profiles. Furthermore, we analyze the extent to which the number of homologous sequences influences the quality of prediction. The analysis of variable residue positions shows that surprisingly, helical regions exhibit greater variability than do coil regions, which are generally thought to be the most common secondary structure elements in loops. However, the correlation between variability and the presence of helices does not significantly improve prediction quality. Gaps are a distinct signal for coil regions. Increasing the coil propensity for those residues occurring in gap regions enhances the overall prediction quality. Prediction accuracy increases initially with the number of homologues, but changes negligibly as the number of homologues exceeds about 14. The alignment quality affects the prediction more than other factors, hence a careful selection and alignment of even a small number of homologues can lead to significant improvements in prediction accuracy. PMID:8771202

Di Francesco, V; Garnier, J; Munson, P J

1996-01-01

84

Sequence-structure relationships in DNA oligomers: a computational approach.  

Science.gov (United States)

A collective-variable model for DNA structure is used to predict the conformation of a set of 30 octamer, decamer, and dodecamer oligomers for which high-resolution crystal structures are available. The model combines an all-atom base pair representation with an empirical backbone, emphasizing the role of base stacking in fixing sequence-dependent structure. We are able to reproduce trends in roll and twist to within 5 degrees across a large database of both A- and B-DNA oligomers. A genetic algorithm approach is used to search for global minimum structures and this is augmented by a grid search to identify local minimums. We find that the number of local minimums is highly sequence dependent, with certain sequences having a set of minimums that span the entire range between canonical A- and B-DNA conformations. Although the global minimum does not always agree with the crystal structure, for 24 of the 30 oligomers, we find low-energy local minimums that match the experimental step parameters. Discrepancies throw some light on the role of crystal packing in determining the solid-state conformation of double-helical DNA. PMID:11472171

Packer, M J; Hunter, C A

2001-08-01

85

Sequence, structure, function, immunity: structural genomics of costimulation  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Costimulatory receptors and ligands trigger the signaling pathways that are responsible for modulating the strength, course and duration of an immune response. High-resolution structures have provided invaluable mechanistic insights by defining the chemical and physical features underlying costimulatory receptor/ligand specificity, affinity, oligomeric state, and valency. Furthermore, these structures revealed general architectural features that are important for the integration of these inte...

Chattopadhyay, Kausik; Lazar-molnar, Eszter; Yan, Qingrong; Rubinstein, Rotem; Zhan, Chenyang; Vigdorovich, Vladimir; Ramagopal, Udupi A.; Bonanno, Jeffrey; Nathenson, Stanley G.; Almo, Steven C.

2009-01-01

86

Structural changes in quasi- 1D many-electron systems: from linear to zig-zag and beyond  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Many-electron systems confined to a quasi-1D geometry by a cylindrical distribution of positive charge have been investigated by density functional computations in the unrestricted local spin density approximation. Our investigations have been focused on the low density regime, in which electrons are localised. The results reveal a wide variety of different charge and spin configurations, including linear and zig-zag chains, single and double-strand helices, and twisted chai...

Ballone, R. Cortes-huerto M. Paternostro P.

2010-01-01

87

From the 2D graphene honeycomb lattice to 1D nanoribbons: dimensional crossover signals in the structural thermal fluctuations  

Digital Repository Infrastructure Vision for European Research (DRIVER)

We study the dimensional crossover from 2D to 1D type behavior, which takes place in the thermal excited rippling of a graphene honeycomb lattice, when one of the dimensions of the layer is reduced. Through a joint study, by Monte Carlo (MC) atomistic simulations using a quasi-harmonic potential and analytical calculations, we find that the normal-normal correlation function does not change its power law behavior in the long wavelength limit. However the system size dependen...

Costamagna, S.; Dobry, A.

2011-01-01

88

EURDYN-1D: a computer code for the one-dimensional non-linear dynamic analysis of structural systems. Description and users' manual (release 1)  

International Nuclear Information System (INIS)

The goal of the present report is to provide for a comprehensive users' manual describing the capabilities of the computer code EURDYN-1D. It includes information and examples about the type of problems which can be solved with the code and explanation on how to prepare input data and, how to interpret output results. The field of applications of EURDYN-1D is the one dimensional dynamic analysis of general structural systems and the code is particularly suited for fast transient events involving propagation of longitudinal mechanical waves (subsonic) in structures. Both geometrical and physical non-linearities can be taken into account. Typical examples are impact problems, fast dynamic loading due the explosions or sudden release for initial loads due to failures, etc. To these classes belong many problems encountered in the reactor safety field as well as in more common and general technological applications

89

Inferring gene structures in genomic sequences using pattern recognition and expressed sequence tags  

Energy Technology Data Exchange (ETDEWEB)

Computational methods for gene identification in genomic sequences typically have two phases: coding region prediction and gene parsing. While there are many effective methods for predicting coding regions (exons), parsing the predicted exons into proper gene structures, to a large extent, remains an unsolved problem. This paper presents an algorithm for inferring gene structures from predicted exon candidates, based on Expressed Sequence Tags (ESTs) and biological intuition/rules. The algorithm first finds all the related ESTs in the EST database (dbEST) for each predicted exon, and infers the boundaries of one or a series of genes based on the available EST information and biological rules. Then it constructs gene models within each pair of gene boundaries, that are most consistent with the EST information. By exploiting EST information and biological rules, the algorithm can (1) model complicated multiple gene structures, including embedded genes, (2) identify falsely-predicted exons and locate missed exons, and (3) make more accurate exon boundary predictions. The algorithm has been implemented and tested on long genomic sequences with a number of genes. Test results show that very accurate (predicted) gene models can be expected when related ESTs exist for the predicted exons.

Xu, Y.; Mural, R.; Uberbacher, E.

1997-02-01

90

Biophysical and structural considerations for protein sequence evolution  

Directory of Open Access Journals (Sweden)

Full Text Available Abstract Background Protein sequence evolution is constrained by the biophysics of folding and function, causing interdependence between interacting sites in the sequence. However, current site-independent models of sequence evolutions do not take this into account. Recent attempts to integrate the influence of structure and biophysics into phylogenetic models via statistical/informational approaches have not resulted in expected improvements in model performance. This suggests that further innovations are needed for progress in this field. Results Here we develop a coarse-grained physics-based model of protein folding and binding function, and compare it to a popular informational model. We find that both models violate the assumption of the native sequence being close to a thermodynamic optimum, causing directional selection away from the native state. Sampling and simulation show that the physics-based model is more specific for fold-defining interactions that vary less among residue type. The informational model diffuses further in sequence space with fewer barriers and tends to provide less support for an invariant sites model, although amino acid substitutions are generally conservative. Both approaches produce sequences with natural features like dN/dS Conclusions Simple coarse-grained models of protein folding can describe some natural features of evolving proteins but are currently not accurate enough to use in evolutionary inference. This is partly due to improper packing of the hydrophobic core. We suggest possible improvements on the representation of structure, folding energy, and binding function, as regards both native and non-native conformations, and describe a large number of possible applications for such a model.

Grahnen Johan A

2011-12-01

91

Metal-binding loop length and not sequence dictates structure.  

Science.gov (United States)

The C-terminal copper-binding loop in the beta-barrel fold of the cupredoxin azurin has been replaced with a range of sequences containing alanine, glycine, and valine residues to assess the importance of amino acid composition and the length of this region. The introduction of 2 and 4 alanines between the coordinating Cys, His, and Met results in loop structures matching those in naturally occurring proteins with the same loop lengths. A loop with 4 alanines between the Cys and His and 3 between the His and Met ligands has a structure identical to that of the WT protein, whose loop is the same length. Loop structure is dictated by length and not sequence allowing the properties of the main surface patch for interactions with partners, to which the loop is a major contributor, to be optimized. Loops with 2 amino acids between the ligands using glycine, alanine, and valine residues have been compared. An empirical relationship is found between copper site protection by the loop and reduction potential. A loop adorned with 4 methyl groups is sufficient to protect the copper ion, enabling most sequences to adequately perform this task. The mutant with 3 alanine residues between the ligands forms a strand-swapped dimer in the crystal structure, an arrangement that has not, to our knowledge, been seen previously for this family of proteins. Cupredoxins function as redox shuttles and are required to be monomeric; therefore, none have evolved with a metal-binding loop of this length. PMID:19299503

Sato, Katsuko; Li, Chan; Salard, Isabelle; Thompson, Andrew J; Banfield, Mark J; Dennison, Christopher

2009-04-01

92

Early-Stage Folding in Proteins (In Silico Sequence-to-Structure Relation  

Directory of Open Access Journals (Sweden)

Full Text Available A sequence-to-structure library has been created based on the complete PDB database. The tetrapeptide was selected as a unit representing a well-defined structural motif. Seven structural forms were introduced for structure classification. The early-stage folding conformations were used as the objects for structure analysis and classification. The degree of determinability was estimated for the sequence-to-structure and structure-to-sequence relations. Probability calculus and informational entropy were applied for quantitative estimation of the mutual relation between them. The structural motifs representing different forms of loops and bends were found to favor particular sequences in structure-to-sequence analysis.

Brylinski Micha?

2005-01-01

93

A case of Beauveria bassiana keratitis confirmed by internal transcribed spacer and LSU rDNA D1-D2 sequencing.  

Science.gov (United States)

We describe a case of fungal keratitis due to Beauveria bassiana in a farmer with Fuchs' dystrophy, treated with amphotericin B. Surgery with penetrating keratoplasty was necessary to resolve the lesions. Susceptibility testing and molecular sequencing permitted the identification and treatment of this rare aetiological agent of invasive fungal disease. PMID:25356350

Ligozzi, M; Maccacaro, L; Passilongo, M; Pedrotti, E; Marchini, G; Koncan, R; Cornaglia, G; Centonze, A R; Lo Cascio, G

2014-05-01

94

A case of Beauveria bassiana keratitis confirmed by internal transcribed spacer and LSU rDNA D1D2 sequencing  

Digital Repository Infrastructure Vision for European Research (DRIVER)

We describe a case of fungal keratitis due to Beauveria bassiana in a farmer with Fuchs' dystrophy, treated with amphotericin B. Surgery with penetrating keratoplasty was necessary to resolve the lesions. Susceptibility testing and molecular sequencing permitted the identification and treatment of this rare aetiological agent of invasive fungal disease.

Ligozzi, M.; Maccacaro, L.; Passilongo, M.; Pedrotti, E.; Marchini, G.; Koncan, R.; Cornaglia, G.; Centonze, A. R.; Lo Cascio, G.

2014-01-01

95

A case of Beauveria bassiana keratitis confirmed by internal transcribed spacer and LSU rDNA D1D2 sequencing  

Science.gov (United States)

We describe a case of fungal keratitis due to Beauveria bassiana in a farmer with Fuchs' dystrophy, treated with amphotericin B. Surgery with penetrating keratoplasty was necessary to resolve the lesions. Susceptibility testing and molecular sequencing permitted the identification and treatment of this rare aetiological agent of invasive fungal disease. PMID:25356350

Ligozzi, M; Maccacaro, L; Passilongo, M; Pedrotti, E; Marchini, G; Koncan, R; Cornaglia, G; Centonze, A R; Lo Cascio, G

2014-01-01

96

Sequence analysis of the cDNA for the human casein kinase I delta (CSNK1D) gene and its chromosomal localization.  

Science.gov (United States)

A cDNA clone coding for human casein kinase I (CK1) has been isolated and sequenced. The insert of 1911 bp contained an open reading frame of 415 amino acids. The entire amino acid sequence of human CK1 was 97% homologous to that of rat CK1 delta, and their sequences in the kinase domain (284 amino acid residues) were completely identical, predicting that the obtained cDNA is for a human homolog of the CK1 delta isoform (CSNKID). The considerable similarity in the amino acid sequence of the kinase domain of human CK1 delta to the Saccharomyces cerevisiae CK1, HRR25 (66%), and to the Saccharomyces pombe CK1, HHP1 (78%), which are involved in the repair of DNA strand break, supports the speculation that human CK1 delta might also act in DNA metabolism through excision and recombinational repair. The human CK1 delta gene was mapped to chromosome 17q25.2-q25.3 by fluorescence in situ hybridization and polymerase chain reaction analysis of the human/rodent hybrid cell panels. PMID:8786104

Kusuda, J; Hidari, N; Hirai, M; Hashimoto, K

1996-02-15

97

Geometric structure of N = 1, D = 10 and N = 4, D = 4 super Yang-Mills theory  

International Nuclear Information System (INIS)

In this paper we present the group manifold formulation of N = 1, D = 10 and N = 4, D = 4 super Yang-Mills theory. Our result is an off-shell, first-order action in superspace without central charges. Analysis of the Bianchi identities based on a general group theoretical technique described in a previous publication shows that no constraint can be imposed on the curvatures without implying propagation equations. This suggests that our first-order action is probably the only off-shell one: no second-order, off-shell formulation seems to exist. (orig.)

98

Intraspecies diversity of the industrial yeast strains Saccharomyces cerevisiae and Saccharomyces pastorianus based on analysis of the sequences of the internal transcribed spacer (ITS) regions and the D1/D2 region of 26S rDNA.  

Science.gov (United States)

We divided industrial yeast strains of Saccharomyces cerevisiae into three groups based on the sequences of their internal transcribed spacer (ITS) regions. One group contained sake yeasts, shochu yeasts, and one bakery yeast, another group contained wine yeasts, and the third group contained beer and whisky yeasts, including seven bakery yeasts. The three groups were distinguished by polymorphisms at two positions, designated positions B and C, corresponding to nucleotide numbers 279 and 301 respectively in the S288C strain. The yeasts in the Japanese group had one thymine at position B and one thymine at position C. The wine yeasts had one thymine at position B and one cytosine at position C. And the beer and whisky yeasts had two thymines at position B and one cytosine at position C. Strains of S. pastorianus were divided into three groups based on the sequences of their 26S rDNA D1/D2 and ITS regions. PMID:17617725

Kawahata, Miho; Fujii, Tsutomu; Iefuji, Haruyuki

2007-07-01

99

Chromatin structure characteristics of pre-miRNA genomic sequences  

Directory of Open Access Journals (Sweden)

Full Text Available Abstract Background MicroRNAs (miRNAs are non-coding RNAs with important roles in regulating gene expression. Recent studies indicate that transcription and cleavage of miRNA are coupled, and that chromatin structure may influence miRNA transcription. However, little is known about the relationship between the chromatin structure and cleavage of pre-miRNA from pri-miRNA. Results By analysis of genome-wide nucleosome positioning data sets from human and Caenorhabditis elegans (C. elegans, we found an enrichment of positioned nucleosome on pre-miRNA genomic sequences, which is highly correlated with GC content within pre-miRNA. In addition, obvious enrichments of three histone modifications (H2BK5me1, H3K36me3 and H4K20me1 as well as RNA Polymerase II (RNAPII were observed on pre-miRNA genomic sequences corresponding to the active-promoter miRNAs and expressed miRNAs. Conclusion Our results revealed the chromatin structure characteristics of pre-miRNA genomic sequences, and implied potential mechanisms that can recognize these characteristics, thus improving pre-miRNA cleavage.

Teng Mingxiang

2011-06-01

100

Coalescence phenomena in 1D silver nanostructures  

International Nuclear Information System (INIS)

Different coalescence processes on 1D silver nanostructures synthesized by a PVP assisted reaction in ethylene glycol at 160 deg. C were studied experimentally and theoretically. Analysis by TEM and HRTEM shows different defects found on the body of these materials, suggesting that they were induced by previous coalescence processes in the synthesis stage. TEM observations showed that irradiation with the electron beam eliminates the boundaries formed near the edges of the structures, suggesting that this process can be carried out by the application of other means of energy (i.e. thermal). These results were also confirmed by theoretical calculations by Monte Carlo simulations using a Sutton-Chen potential. A theoretical study by molecular dynamics simulation of the different coalescence processes on 1D silver nanostructures is presented, showing a surface energy driven sequence followed to form the final coalesced structure. Calculations were made at 1000-1300 K, which is near the melting temperature of silver (1234 K). Based on these results, it is proposed that 1D nanostructures can grow through a secondary mechanism based on coalescence, without losing their dimensionality.

 
 
 
 
101

Syntheses, crystal structures and properties of two 1-D cadmium(II) coordination polymers based on 1,1'-(1,3-propanediyl)bis-1H-benzimidazole  

International Nuclear Information System (INIS)

The combination of framework-builders 1,1'-(1,3-propanediyl)bis-1H-benzimidazole (pbbm), Cd(II) ion and framework-regulator ClO4- or SO42- provides two new coordination polymers [Cd(pbbm)2(ClO4)2]n(1) and {[Cd(pbbm)SO4(H2O)2].CH3OH}n(2). Both of them display 1-D chain framework, but their detailed structures are clearly different from each other. 1 displays a 1-D ribbon of rings framework, 2 features an interesting infinite 1-D looped chain structure composed of two kinds of rings, the smaller 8-membered ring and the larger 20-membered ring. The antimicrobial activities of the two polymers were tested by the agar diffusion method and the results indicated that they exhibited antimicrobial activities against bacterial strands. The measurement of the non-isothermal kinetics of the thermal decomposition of 2 reveals that there are at least three steps that occur in its decomposition process. - Graphical abstract: Two new Cd(II)-containing complexes have been synthesized and characterized by single-crystal X-ray diffraction. The antimicrobial activity and the non-isothermal kinetics of the thermal decomposition of the polymers were also investigated. Display Omitted

102

Syntheses, crystal structures and luminescent properties of two new 1D d 1 coordination polymers constructed from 2,2'-bibenzimidazole and 1,4-benzenedicarboxylate  

International Nuclear Information System (INIS)

Two novel interesting d 1 metal coordination polymers, [Zn(H2bibzim)(BDC)] n (1) and [Cd(H2bibzim)(BDC)] n (2) [H2bibzim=2,2'-bibenzimidazole, BDC=1,4-benzenedicarboxylate] have been synthesized under solvothermal conditions and structurally characterized. Both 1 and 2 are constructed from infinite neutral zigzag-like one-dimensional (1D) chains. The ?-? interactions and interchain hydrogen-bonding interactions further extend the 1D arrangement to generate a 3D supramolecular architecture for 1 and 2. Both complexes have high thermal stability and display strong blue fluorescent emissions in the solid state upon photo-excitation at 365 nm at room temperature. They are the first two examples that 2,2'-bibenzimidazole has been introduced into the d 1 coordination polymeric framework

103

Syntheses, crystal structures and luminescent properties of two new 1D d10 coordination polymers constructed from 2,2?-bibenzimidazole and 1,4-benzenedicarboxylate  

Science.gov (United States)

Two novel interesting d10 metal coordination polymers, [Zn(H 2bibzim)(BDC)] n ( 1) and [Cd(H 2bibzim)(BDC)] n ( 2) [H 2bibzim=2,2'-bibenzimidazole, BDC=1,4-benzenedicarboxylate] have been synthesized under solvothermal conditions and structurally characterized. Both 1 and 2 are constructed from infinite neutral zigzag-like one-dimensional (1D) chains. The ?- ? interactions and interchain hydrogen-bonding interactions further extend the 1D arrangement to generate a 3D supramolecular architecture for 1 and 2. Both complexes have high thermal stability and display strong blue fluorescent emissions in the solid state upon photo-excitation at 365 nm at room temperature. They are the first two examples that 2,2'-bibenzimidazole has been introduced into the d10 coordination polymeric framework.

Wen, Lili; Li, Yizhi; Dang, Dongbin; Tian, Zhengfang; Ni, Zhaoping; Meng, Qingjin

2005-11-01

104

Metastable Se6 as a ligand for Ag+: from isolated molecular to polymeric 1D and 2D structures.  

Science.gov (United States)

Attempts to prepare the hitherto unknown Se(6)(2+) cation by the reaction of elemental selenium and Ag[A] ([A](-) = [Sb(OTeF(5))(6)](-), [Al(OC(CF(3))(3))(4)](-)) in SO(2) led to the formation of [(OSO)Ag(Se(6))Ag(OSO)][Sb(OTeF(5))(6)](2)1 and [(OSO)(2)Ag(Se(6))Ag(OSO)(2)][Al(OC(CF(3))(3))(4)](2)2a. 1 could only be prepared by using bromine as co-oxidant, however, bulk 2b (2a with loss of SO(2)) was accessible from Ag[Al(OC(CF(3))(3))(4)] and grey Se in SO(2) (chem. analysis). The reactions of Ag[MF(6)] (M = As, Sb) and elemental selenium led to crystals of 1/?{[Ag(Se(6))](?)[Ag(2)(SbF(6))(3)](?)} 3 and {1/?[Ag(Se(6))Ag](?)}[AsF(6)](2)4. Pure bulk 4 was best prepared by the reaction of Se(4)[AsF(6)](2), silver metal and elemental selenium. Attempts to prepare bulk 1 and 3 were unsuccessful. 1-4 were characterized by single-crystal X-ray structure determinations, 2b and 4 additionally by chemical analysis and 4 also by X-ray powder diffraction, FT-Raman and FT-IR spectroscopy. Application of the PRESTO III sequence allowed for the first time (109)Ag MAS NMR investigations of 4 as well as AgF, AgF(2), AgMF(6) and {1/?[Ag(I(2))](?)}[MF(6)] (M = As, Sb). Compounds 1 and 2a/b, with the very large counter ions, contain isolated [Ag(Se(6))Ag](2+) heterocubane units consisting of a Se(6) molecule bicapped by two silver cations (local D(3d) sym). 3 and 4, with the smaller anions, contain close packed stacked arrays of Se(6) rings with Ag(+) residing in octahedral holes. Each Ag(+) ion coordinates to three selenium atoms of each adjacent Se(6) ring. 4 contains [Ag(Se(6))(+)](?) stacks additionally linked by Ag(2)(+) into a two dimensional network. 3 features a remarkable 3-dimensional [Ag(2)(SbF(6))(3)](-) anion held together by strong Sb-FAg contacts between the component Ag(+) and [SbF(6)](-) ions. The hexagonal channels formed by the [Ag(2)(SbF(6))(3)](-) anions are filled by stacks of [Ag(Se(6))(+)](?) cations. Overall 1-4 are new members of the rare class of metal complexes of neutral main group elemental clusters, in which the main group element is positively polarized due to coordination to a metal ion. Notably, 1 to 4 include the commonly metastable Se(6) molecule as a ligand. The structure, bonding and thermodynamics of 1 to 4 were investigated with the help of quantum chemical calculations (PBE0/TZVPP and (RI-)MP2/TZVPP, in part including COSMO solvation) and Born-Fajans-Haber-cycle calculations. From an analysis of all the available data it appears that the formation of the usually metastable Se(6) molecule from grey selenium is thermodynamically driven by the coordination to the Ag(+) ions. PMID:21552624

Aris, Damian; Beck, Johannes; Decken, Andreas; Dionne, Isabelle; Schmedt auf der Günne, Jörn; Hoffbauer, Wilfried; Köchner, Tobias; Krossing, Ingo; Passmore, Jack; Rivard, Eric; Steden, Folker; Wang, Xinping

2011-06-14

105

Quadtree-structured linear prediction models for image sequence processing  

Energy Technology Data Exchange (ETDEWEB)

Image sequences capture not only static, but also dynamic aspects of a recorded scene. The evaluation or coding of image sequences therefore requires algorithms for extraction and interpretation of dynamic relations between successive frames in an image sequence, such as velocity and shape of moving brightness patterns, as well as, changes in illumination. The authors present the embedding of the described linear prediction models in an adaptive quadtree segmentation structure which helps to handle spatial nonstationaries. In this concept, two segmentation rules are discussed. This is, first, a simple minimum variance detector and, second they extended the well-known generalized likelihood ratio (GLR) detector of Willsky and Jones to the problem of change detection and spatial segmentation. A constrained joint process model is used for modeling of the relationships between subsequent images in a scene. The authors present several approaches on the important problem of segmenting the interframe formation into stationary regions of uniform size and shape utilizing a quadtree segmentation structure. They discuss two applications of the theoretical results obtained in the earlier sections.

Strobach, P. (SIEMENS AG, Zentralbereich Forschung und Technik, D-8000 Munchen 83 (DE))

1989-07-01

106

3-D imaging of large scale buried structure by 1-D inversion of very early time electromagnetic (VETEM) data  

Science.gov (United States)

A simple and efficient method for large scale three-dimensional (3-D) subsurface imaging of inhomogeneous background is presented. One-dimensional (1-D) multifrequency distorted Born iterative method (DBIM) is employed in the inversion. Simulation results utilizing synthetic scattering data are given. Calibration of the very early time electromagnetic (VETEM) experimental waveforms is detailed along with major problems encountered in practice and their solutions. This discussion is followed by the results of a large scale application of the method to the experimental data provided by the VETEM system of the U.S. Geological Survey. The method is shown to have a computational complexity that is promising for on-site inversion.

Aydmer, A.A.; Chew, W.C.; Cui, T.J.; Wright, D.L.; Smith, D.V.; Abraham, J.D.

2001-01-01

107

Sequence and structural analysis of BTB domain proteins  

Science.gov (United States)

Background The BTB domain (also known as the POZ domain) is a versatile protein-protein interaction motif that participates in a wide range of cellular functions, including transcriptional regulation, cytoskeleton dynamics, ion channel assembly and gating, and targeting proteins for ubiquitination. Several BTB domain structures have been experimentally determined, revealing a highly conserved core structure. Results We surveyed the protein architecture, genomic distribution and sequence conservation of BTB domain proteins in 17 fully sequenced eukaryotes. The BTB domain is typically found as a single copy in proteins that contain only one or two other types of domain, and this defines the BTB-zinc finger (BTB-ZF), BTB-BACK-kelch (BBK), voltage-gated potassium channel T1 (T1-Kv), MATH-BTB, BTB-NPH3 and BTB-BACK-PHR (BBP) families of proteins, among others. In contrast, the Skp1 and ElonginC proteins consist almost exclusively of the core BTB fold. There are numerous lineage-specific expansions of BTB proteins, as seen by the relatively large number of BTB-ZF and BBK proteins in vertebrates, MATH-BTB proteins in Caenorhabditis elegans, and BTB-NPH3 proteins in Arabidopsis thaliana. Using the structural homology between Skp1 and the PLZF BTB homodimer, we present a model of a BTB-Cul3 SCF-like E3 ubiquitin ligase complex that shows that the BTB dimer or the T1 tetramer is compatible in this complex. Conclusion Despite widely divergent sequences, the BTB fold is structurally well conserved. The fold has adapted to several different modes of self-association and interactions with non-BTB proteins. PMID:16207353

Stogios, Peter J; Downs, Gregory S; Jauhal, Jimmy JS; Nandra, Sukhjeen K; Privé, Gilbert G

2005-01-01

108

Fast and low-cost structured light pattern sequence projection.  

Science.gov (United States)

We present a high-speed and low-cost approach for structured light pattern sequence projection. Using a fast rotating binary spatial light modulator, our method is potentially capable of projection frequencies in the kHz domain, while enabling pattern rasterization as low as 2 ?m pixel size and inherently linear grayscale reproduction quantized at 12 bits/pixel or better. Due to the circular arrangement of the projected fringe patterns, we extend the widely used ray-plane triangulation method to ray-cone triangulation and provide a detailed description of the optical calibration procedure. Using the proposed projection concept in conjunction with the recently published coded phase shift (CPS) pattern sequence, we demonstrate high accuracy 3-D measurement at 200 Hz projection frequency and 20 Hz 3-D reconstruction rate. PMID:22109494

Wissmann, Patrick; Forster, Frank; Schmitt, Robert

2011-11-21

109

Structural Approaches to Sequence Evolution Molecules, Networks, Populations  

CERN Document Server

Structural requirements constrain the evolution of biological entities at all levels, from macromolecules to their networks, right up to populations of biological organisms. Classical models of molecular evolution, however, are focused at the level of the symbols - the biological sequence - rather than that of their resulting structure. Now recent advances in understanding the thermodynamics of macromolecules, the topological properties of gene networks, the organization and mutation capabilities of genomes, and the structure of populations make it possible to incorporate these key elements into a broader and deeply interdisciplinary view of molecular evolution. This book gives an account of such a new approach, through clear tutorial contributions by leading scientists specializing in the different fields involved.

Bastolla, Ugo; Roman, H. Eduardo; Vendruscolo, Michele

2007-01-01

110

Hinge Atlas: relating protein sequence to sites of structural flexibility  

Directory of Open Access Journals (Sweden)

Full Text Available Abstract Background Relating features of protein sequences to structural hinges is important for identifying domain boundaries, understanding structure-function relationships, and designing flexibility into proteins. Efforts in this field have been hampered by the lack of a proper dataset for studying characteristics of hinges. Results Using the Molecular Motions Database we have created a Hinge Atlas of manually annotated hinges and a statistical formalism for calculating the enrichment of various types of residues in these hinges. Conclusion We found various correlations between hinges and sequence features. Some of these are expected; for instance, we found that hinges tend to occur on the surface and in coils and turns and to be enriched with small and hydrophilic residues. Others are less obvious and intuitive. In particular, we found that hinges tend to coincide with active sites, but unlike the latter they are not at all conserved in evolution. We evaluate the potential for hinge prediction based on sequence. Motions play an important role in catalysis and protein-ligand interactions. Hinge bending motions comprise the largest class of known motions. Therefore it is important to relate the hinge location to sequence features such as residue type, physicochemical class, secondary structure, solvent exposure, evolutionary conservation, and proximity to active sites. To do this, we first generated the Hinge Atlas, a set of protein motions with the hinge locations manually annotated, and then studied the coincidence of these features with the hinge location. We found that all of the features have bearing on the hinge location. Most interestingly, we found that hinges tend to occur at or near active sites and yet unlike the latter are not conserved. Less surprisingly, we found that hinge residues tend to be small, not hydrophobic or aliphatic, and occur in turns and random coils on the surface. A functional sequence based hinge predictor was made which uses some of the data generated in this study. The Hinge Atlas is made available to the community for further flexibility studies.

Yang Julie

2007-05-01

111

Effective connectivity profile: a structural representation that evidences the relationship between protein structures and sequences.  

Science.gov (United States)

The complexity of protein structures calls for simplified representations of their topology. The simplest possible mathematical description of a protein structure is a one-dimensional profile representing, for instance, buriedness or secondary structure. This kind of representation has been introduced for studying the sequence to structure relationship, with applications to fold recognition. Here we define the effective connectivity profile (EC), a network theoretical profile that self-consistently represents the network structure of the protein contact matrix. The EC profile makes mathematically explicit the relationship between protein structure and protein sequence, because it allows predicting the average hydrophobicity profile (HP) and the distributions of amino acids at each site for families of homologous proteins sharing the same structure. In this sense, the EC provides an analytic solution to the statistical inverse folding problem, which consists in finding the statistical properties of the set of sequences compatible with a given structure. We tested these predictions with simulations of the structurally constrained neutral (SCN) model of protein evolution with structure conservation, for single- and multi-domain proteins, and for a wide range of mutation processes, the latter producing sequences with very different hydrophobicity profiles, finding that the EC-based predictions are accurate even when only one sequence of the family is known. The EC profile is very significantly correlated with the HP for sequence-structure pairs in the PDB as well. The EC profile generalizes the properties of previously introduced structural profiles to modular proteins such as multidomain chains, and its correlation with the sequence profile is substantially improved with respect to the previously defined profiles, particularly for long proteins. Furthermore, the EC profile has a dynamic interpretation, since the EC components are strongly inversely related with the temperature factors measured in X-ray experiments, meaning that positions with large EC component are more strongly constrained in their equilibrium dynamics. Last, the EC profile allows to define a natural measure of modularity that correlates with the number of domains composing the protein, suggesting its application for domain decomposition. Finally, we show that structurally similar proteins have similar EC profiles, so that the similarity between aligned EC profiles can be used as a structure similarity measure, a property that we have recently applied for protein structure alignment. The code for computing the EC profile is available upon request writing to ubastolla@cbm.uam.es, and the structural profiles discussed in this article can be downloaded from the SLOTH webserver http://www.fkp.tu-darmstadt.de/SLOTH/. PMID:18536008

Bastolla, Ugo; Ortíz, Angel R; Porto, Markus; Teichert, Florian

2008-12-01

112

Modulation of DNA radiolysis by sequence, structure and ligands  

International Nuclear Information System (INIS)

DNA structure, topology and interactions with ligands are continuously changing during the cell cycle, through phenomena such as replication or transcription. Until recently, it was considered that ionizing radiations break DNA strands with the same probability at all nucleotide sites. Using restriction fragments and synthetic oligonucleotides, we have shown that DNA is heterogeneously radiosensitive. The breakage probability at a given nucleotide site depends on nucleotide type and sequence, presence of ligands (metal ions, proteins, polyamines) and structural parameters (strandedness, handedness, minor groove depth, topological stress). We have observed that in 'naked'(without ligands) dna, the bent 5'-AATT regions that present a narrow minor groove are less sensitive than 'random DNA'. In a (GC)n sequence, all G sites are more radiosensitive, and all C sites are more radioresistant in a negatively super-coiling-induced left-handed Z-DNA than in the right-handed B-DNA. Some G's located in particular regions of single stranded DNA are more radiosensitive than in double stranded DNA. We have also shown that several natural ligands, such as Cu2+, polyamines or DNA-binding proteins modify DNA radiosensitivity directly of via the structural modifications that they induce in DNA. (authors)

113

Syllable and phrase structure effects on consonant sequence timing  

Science.gov (United States)

Both syllable and phrasal structure are known to influence articulatory timing in consonant sequences. For example, onset clusters have been reported as less overlapped and more stable in their intergestural timing than coda clusters [e.g., Byrd, J. Phonetics (1996)]. Also, consonants spanning a phrasal boundary have been observed to be less overlapped than those spanning only a word boundary [Byrd et al., LabPhon (2003)]. However, interactions between these two types of structure are less well understood; for example, it is unclear whether the intergestural timing of word-onset clusters will be perturbed at phrase boundaries, though such perturbations have been predicted [Byrd and Saltzman (2003)]. An articulatory (EMA) investigation of /s/+stop sequences produced by three speakers in a variety of syllable and phrasal positions will present kinematic data on these structural influences. Preliminary data from one speaker indicate that word-onset consonant clusters are more sensitive to prosodic context than segmentally identical coda clusters, having less overlap at successively larger boundaries. Further, while coda and onset clusters do not show a mean difference in overlap for this speaker, onset clusters do exhibit more timing stability within each phrasal context compared to corresponding coda clusters. [Work supported by NIH.

Byrd, Dani; Choi, Susie

2005-09-01

114

Topological characterization of crystalline ice structures from coordination sequences  

CERN Document Server

Topological properties of crystalline ice structures are studied by considering ring statistics, coordination sequences, and topological density of different ice phases. The coordination sequences (number of sites at topological distance k from a reference site) have been obtained by direct enumeration until at least 40 coordination spheres for different ice polymorphs. This allows us to study the asymptotic behavior of the mean number of sites in the k-th shell, M_k, for high values of k: M_k ~ a k^2, a being a structure-dependent parameter. Small departures from a strict parabolic dependence have been studied by considering first and second differences of the series {M_k} for each structure. The parameter a ranges from 2.00 for ice VI to 4.27 for ice XII, and is used to define a topological density for these solid phases of water. Correlations between such topological density and the actual volume of ice phases are discussed. Ices Ih and Ic are found to depart from the general trend in this correlation due ...

Herrero, Carlos P

2013-01-01

115

A structural basis for selection and cross-species reactivity of the semi-invariant NKT cell receptor in CD1d/glycolipid recognition  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Little is known regarding the basis for selection of the semi-invariant ?? T cell receptor (TCR) expressed by natural killer T (NKT) cells or how this mediates recognition of CD1d–glycolipid complexes. We have determined the structures of two human NKT TCRs that differ in their CDR3? composition and length. Both TCRs contain a conserved, positively charged pocket at the ligand interface that is lined by residues from the invariant TCR ?- and semi-invariant ?-chains. The cavity is centr...

Kjer-nielsen, Lars; Borg, Natalie A.; Pellicci, Daniel G.; Beddoe, Travis; Kostenko, Lyudmila; Clements, Craig S.; Williamson, Nicholas A.; Smyth, Mark J.; Besra, Gurdyal S.; Reid, Hugh H.; Bharadwaj, Mandvi; Godfrey, Dale I.; Rossjohn, Jamie; Mccluskey, James

2006-01-01

116

Metal-binding loop length and not sequence dictates structure  

Digital Repository Infrastructure Vision for European Research (DRIVER)

The C-terminal copper-binding loop in the ?-barrel fold of the cupredoxin azurin has been replaced with a range of sequences containing alanine, glycine, and valine residues to assess the importance of amino acid composition and the length of this region. The introduction of 2 and 4 alanines between the coordinating Cys, His, and Met results in loop structures matching those in naturally occurring proteins with the same loop lengths. A loop with 4 alanines between the Cys and His and 3 betwe...

Sato, Katsuko; Li, Chan; Salard, Isabelle; Thompson, Andrew J.; Banfield, Mark J.; Dennison, Christopher

2009-01-01

117

Age-structured Trait Substitution Sequence Process and Canonical Equation  

CERN Document Server

We are interested in a stochastic model of trait and age-structured population undergoing mutation and selection. We start with a continuous time, discrete individual-centered population process. Taking the large population and rare mutations limits under a well-chosen time-scale separation condition, we obtain a jump process that generalizes the Trait Substitution Sequence process describing Adaptive Dynamics for populations without age structure. Under the additional assumption of small mutations, we derive an age-dependent ordinary differential equation that extends the Canonical Equation. These evolutionary approximations have never been introduced to our knowledge. They are based on ecological phenomena represented by PDEs that generalize the Gurtin-McCamy equation in Demography. Another particularity is that they involve a fitness function, describing the probability of invasion of the resident population by the mutant one, that can not always be computed explicitly. Examples illustrate how adding an ag...

Méléard, Sylvie

2007-01-01

118

Knowledge of sequence structure prevents auditory distraction: an ERP study.  

Science.gov (United States)

Infrequent, salient stimuli often capture attention despite their task-irrelevancy, and disrupt on-going goal-directed behavior. A number of studies show that presenting cues signaling forthcoming deviants reduces distraction, which may be a "by-product" of cue-processing interference or the result of direct preparatory processes for the forthcoming distracter. In the present study, instead of "bursts" of cue information, information on the temporal structure of the stimulus sequence was provided. Young adults performed a spatial discrimination task where complex tones moving left or right were presented. In the predictable condition, every 7th tone was a pitch-deviant, while in the random condition the position of deviants was random with a probability of 1/7. Whereas the early event-related potential correlates of deviance-processing (N1 and MMN) were unaffected by predictability, P3a amplitude was significantly reduced in the predictable condition, indicating that prevention of distraction was based on the knowledge about the temporal structure of the stimulus sequence. PMID:24657900

Volosin, Márta; Horváth, János

2014-06-01

119

Application of 1D- and 2D-NMR techniques for the structural studies of glycoprotein-derived carbohydrates  

International Nuclear Information System (INIS)

The first part of this thesis (Chapters 1 to 4) describe the determination of the primary structure for a large number of oligosaccharide-alditols obtained from bronchial sputum of cystic fibrosis patients suffering from chronic bronchitis. The second part (Chapters 5 to 8) is devoted to the application of two-dimensional NMR methods for the structural analysis of oligosaccharides. (H.W.). 163 refs.; 50 figs.; 25 tabs

120

Wurst: a protein threading server with a structural scoring function, sequence profiles and optimized substitution matrices.  

Science.gov (United States)

Wurst is a protein threading program with an emphasis on high quality sequence to structure alignments (http://www.zbh.uni-hamburg.de/wurst). Submitted sequences are aligned to each of about 3000 templates with a conventional dynamic programming algorithm, but using a score function with sophisticated structure and sequence terms. The structure terms are a log-odds probability of sequence to structure fragment compatibility, obtained from a Bayesian classification procedure. A simplex optimization was used to optimize the sequence-based terms for the goal of alignment and model quality and to balance the sequence and structural contributions against each other. Both sequence and structural terms operate with sequence profiles. PMID:15215443

Torda, Andrew E; Procter, James B; Huber, Thomas

2004-07-01

 
 
 
 
121

Structator: fast index-based search for RNA sequence-structure patterns  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Abstract Background The secondary structure of RNA molecules is intimately related to their function and often more conserved than the sequence. Hence, the important task of searching databases for RNAs requires to match sequence-structure patterns. Unfortunately, current tools for this task have, in the best case, a running time that is only linear in the size of sequence databases. Furthermore, established index data structures for fast sequence matching, like suffix trees ...

Will Sebastian; Backofen Rolf; Kurtz Stefan; Meyer Fernando; Beckstette Michael

2011-01-01

122

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

Digital Repository Infrastructure Vision for European Research (DRIVER)

Although secondary structure predictions of an individual RNA sequence have been widely used in a number of sequence analyses of RNAs, accuracy is still limited. Recently, we proposed a method (called ‘CentroidHomfold’), which includes information about homologous sequences into the prediction of the secondary structure of the target sequence, and showed that it substantially improved the performance of secondary structure predictions. CentroidHomfold, however, forces users to prepare hom...

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

2011-01-01

123

Two extensions of 1D Toda hierarchy  

CERN Document Server

The extended Toda hierarchy of Carlet, Dubrovin and Zhang is reconsidered in the light of a 2+1D extension of the 1D Toda hierarchy constructed by Ogawa. These two extensions of the 1D Toda hierarchy turn out to have a very similar structure, and the former may be thought of as a kind of dimensional reduction of the latter. In particular, this explains an origin of the mysterious structure of the bilinear formalism proposed by Milanov.

Takasaki, Kanehisa

2010-01-01

124

Two extensions of 1D Toda hierarchy  

International Nuclear Information System (INIS)

The extended Toda hierarchy of Carlet, Dubrovin and Zhang is reconsidered in light of a 2 + 1D extension of the 1D Toda hierarchy constructed by Ogawa. These two extensions of the 1D Toda hierarchy turn out to have a very similar structure, and the former may be thought of as a kind of dimensional reduction of the latter. In particular, this explains an origin of the mysterious structure of the bilinear formalism proposed by Milanov.

125

Crystal structure of a promoter sequence in the B-raf gene reveals an intertwined dimer quadruplex.  

Science.gov (United States)

The sequence d(GGGCGGGGAGGGGGAAGGGA) occurs in the promoter region of the B-raf gene. An X-ray crystallographic study has found that this forms an unprecedented dimeric quadruplex arrangement, with a core of seven consecutive G-quartets and an uninterrupted run of six potassium ions in the central channel of the quadruplex. Analogy with previously reported promoter quadruplexes had initially suggested that in common with these a monomeric quadruplex was to be expected. The structure has a distorted G·C·G·C base quartet at one end and four flipped-out adenosine nucleosides at the other. The only loops in the structure are formed by the cytosine and by the three adenosines within the sequence, with all of the guanosines participating in G-quartet formation. Solution UV and circular dichroism data are in accord with a stable quadruple arrangement being formed. 1D NMR data, together with gel electrophoresis measurements, are consistent with a dimer being the dominant species in potassium solution. A single-chain intramolecular quadruplex has been straightforwardly constructed using molecular modeling, by means of a six-nucleotide sequence joining 3' and 5' ends of each strand in the dimer. A human genomic database search has revealed a number of sequences containing eight or more consecutive short G-tracts, suggesting that such intramolecular quadruplexes could be formed within the human genome. PMID:24295054

Wei, Dengguo; Todd, Alan K; Zloh, Mire; Gunaratnam, Mekala; Parkinson, Gary N; Neidle, Stephen

2013-12-26

126

The influence of a power law distribution of cluster size on the light transmission of disordered 1D photonic structures  

CERN Document Server

A better understanding of the optical properties of random photonic structures is beneficial for many applications, such as random lasing, optical imaging and photovoltaics. Here we investigated the light transmission properties of disordered photonic structures in which the high refractive index layers are aggregated in clusters. We sorted the size of the clusters from a power law distribution tuning the exponent a of the distribution function. The sorted high refractive layer clusters are randomly distributed within the low refractive index layers. We studied the total light transmission, within the photonic band gap of the corresponding periodic crystal, as a function of the exponent in the distribution. We observed that, for a within the interval [0,3.5], the trend can be fitted with a sigmoidal function.

Bellingeri, Michele

2014-01-01

127

Excitation of defect modes from the extended photonic band-gap structures of 1D photonic lattices  

International Nuclear Information System (INIS)

This paper stuides numerically the model equation in a one dimensional defective photonic lattice by modifying the potential function to a periodic function. It is found that defect modes (DMs) can be regarded as Bloch modes which are excited from the extended photonic band-gap structure at Bloch wave-numbers with kx = 0. The DMs for both positive and negative defects are considered in this method. (classical areas of phenomenology)

128

3D versus 1D quantum confinement in coherently strained CdS/ZnS quantum structures  

DEFF Research Database (Denmark)

Monolayer fluctuations in ultrathin, coherently strained CdS/ZnS quantum structures result in a very strong localization of excitons. The deepest localized excitons can be considered as individual, decoupled and three-dimensionally confined. Consequently, fingerprints of zero-dimensionality are found in the optical spectra like single, ultranarrow luminescence lines in micro-photoluminescence and spectrally broad optical gain in the deep blue spectral range. The exchange splitting is proven and a strong enhancement over the bulk value is observed.

Woggon, U.; Gindele, F.

1998-01-01

129

Functional region prediction with a set of appropriate homologous sequences-an index for sequence selection by integrating structure and sequence information with spatial statistics  

Science.gov (United States)

Background The detection of conserved residue clusters on a protein structure is one of the effective strategies for the prediction of functional protein regions. Various methods, such as Evolutionary Trace, have been developed based on this strategy. In such approaches, the conserved residues are identified through comparisons of homologous amino acid sequences. Therefore, the selection of homologous sequences is a critical step. It is empirically known that a certain degree of sequence divergence in the set of homologous sequences is required for the identification of conserved residues. However, the development of a method to select homologous sequences appropriate for the identification of conserved residues has not been sufficiently addressed. An objective and general method to select appropriate homologous sequences is desired for the efficient prediction of functional regions. Results We have developed a novel index to select the sequences appropriate for the identification of conserved residues, and implemented the index within our method to predict the functional regions of a protein. The implementation of the index improved the performance of the functional region prediction. The index represents the degree of conserved residue clustering on the tertiary structure of the protein. For this purpose, the structure and sequence information were integrated within the index by the application of spatial statistics. Spatial statistics is a field of statistics in which not only the attributes but also the geometrical coordinates of the data are considered simultaneously. Higher degrees of clustering generate larger index scores. We adopted the set of homologous sequences with the highest index score, under the assumption that the best prediction accuracy is obtained when the degree of clustering is the maximum. The set of sequences selected by the index led to higher functional region prediction performance than the sets of sequences selected by other sequence-based methods. Conclusions Appropriate homologous sequences are selected automatically and objectively by the index. Such sequence selection improved the performance of functional region prediction. As far as we know, this is the first approach in which spatial statistics have been applied to protein analyses. Such integration of structure and sequence information would be useful for other bioinformatics problems. PMID:22643026

2012-01-01

130

Infinite sequence of Poincare group extensions: structure and dynamics  

International Nuclear Information System (INIS)

We study the structure and dynamics of the infinite sequence of extensions of the Poincare algebra whose method of construction was described in a previous paper (Bonanos and Gomis J. Phys. A: Math. Theor. 42 (2009) 145206 (arXiv:hep-th/0808.2243)). We give explicitly the Maurer-Cartan (MC) 1-forms of the extended Lie algebras up to level 3. Using these forms and introducing a corresponding set of new dynamical couplings, we construct an invariant Lagrangian, which describes the dynamics of a distribution of charged particles in an external electromagnetic field. At each extension, the distribution is approximated by a set of moments about the world line of its center of mass and the field by its Taylor series expansion about the same line. The equations of motion after the second extensions contain back-reaction terms of the moments on the world line.

131

Syntheses, crystal structures, and characterization of three 1D, 2D and 3D complexes based on mixed multidentate N- and O-donor ligands  

Science.gov (United States)

Three new 1D to 3D complexes, namely, {[Ni(btec)(Himb)2(H2O)2]·6H2O}n (1), {[Cd(btec)0.5(imb)(H2O)]·1.5H2O}n (2), and {[Zn(btec)0.5(imb)]·H2O}n (3) (H4btec=1,2,4,5-benzenetetracarboxylic acid, imb=2-(1H-imidazol-1-methyl)-1H-benzimidazole) have been synthesized by adjusting the central metal ions. Single-crystal X-ray diffraction analyses reveal that complex 1 possesses a 1D chain structure which is further extended into the 3D supramolecular architecture via hydrogen bonds. Complex 2 features a 2D network with Schla¨fli symbol (53·62·7)(52·64). Complex 3 presents a 3D framework with a point symbol of (4·64·8)(42·62·82). Moreover, their IR spectra, PXRD patterns, thermogravimetric curves, and luminescent emissions were studied at room temperature.

Yang, Huai-Xia; Liang, Zhen; Hao, Bao-Lian; Meng, Xiang-Ru

2014-10-01

132

2D-1D crossover from quantum well to quantum wire behaviour in GaAs v-groove structures  

Digital Repository Infrastructure Vision for European Research (DRIVER)

he distribution of electron current in GaAs AlGaAs v-groove quantum wire structures with groove widths varying from 1 to 25 mum has been studied using far- and near-field spectroscopy techniques. We find clear evidence of the formation of 'corner' quantum wires in wide grooves which coalesce to form single wires in grooves with widths narrower than similar to 5 mum. Spatially resolved photoluminescence measurements in the presence of an applied voltage provide information about the distributi...

Roshan, R.; Cade, Ni; Maciel, Ac; Ryan, Jf; Schwarz, A.; Schapers, T.; Luth, H.

2002-01-01

133

Tails of the dynamical structure factor of 1D spinless fermions beyond the Tomonaga-Luttinger approximation  

International Nuclear Information System (INIS)

We consider one-dimensional interacting spinless fermions with a non-linear spectrum in a clean quantum wire (non-linear bosonization). We compute diagrammatically the one-dimensional dynamical structure factor, S(?, q), beyond the Tomonaga-Luttinger approximation focusing on its tails, i.e. vertical bar ? vertical bar >> vq. We provide a re-derivation, through diagrammatics, of the result of Pustilnik, Mishchenko, Glazman, and Andreev. We also extend their results to finite temperatures and long-range interactions. As applications we determine curvature and interaction corrections to the small- momentum, high-frequency conductivity and the electron-electron scattering rate. (author)

134

EPR study of a triple fine structure in a 1d alternating system: Cs2(TCNQ)3  

International Nuclear Information System (INIS)

The cesium salt of tetracyanoquinodimethan Cs2(TCNQ)3 exhibits a EPR spectrum showing a fine structure consisting of two doublets of equal magnitude. A theoretical interpretation is given using the alternating Heisenberg model characterized by two exchange integrals J and ?J with ?J <= h?sub(e) << J. The distance d between the lines of the triplets and the linewidth ??sub(I) are theoretically determined for two behaviours of the four spin correlation function psi(t). Measurements of the angular dependence of d and the temperature and angular dependence of ??sub(I), at 9600 and 35000 MHz, imply that psi(t) = exp (-?sub(E)t). Various theoretical parameters can also be calculated. Using the values obtained the theoretical and experimental angular dependence of the linewidth are compared at room temperature. The deviation from axial symmetry is also evaluated. (author)

135

Identification of similar regions of protein structures using integrated sequence and structure analysis tools  

Directory of Open Access Journals (Sweden)

Full Text Available Abstract Background Understanding protein function from its structure is a challenging problem. Sequence based approaches for finding homology have broad use for annotation of both structure and function. 3D structural information of protein domains and their interactions provide a complementary view to structure function relationships to sequence information. We have developed a web site http://www.sblest.org/ and an API of web services that enables users to submit protein structures and identify statistically significant neighbors and the underlying structural environments that make that match using a suite of sequence and structure analysis tools. To do this, we have integrated S-BLEST, PSI-BLAST and HMMer based superfamily predictions to give a unique integrated view to prediction of SCOP superfamilies, EC number, and GO term, as well as identification of the protein structural environments that are associated with that prediction. Additionally, we have extended UCSF Chimera and PyMOL to support our web services, so that users can characterize their own proteins of interest. Results Users are able to submit their own queries or use a structure already in the PDB. Currently the databases that a user can query include the popular structural datasets ASTRAL 40 v1.69, ASTRAL 95 v1.69, CLUSTER50, CLUSTER70 and CLUSTER90 and PDBSELECT25. The results can be downloaded directly from the site and include function prediction, analysis of the most conserved environments and automated annotation of query proteins. These results reflect both the hits found with PSI-BLAST, HMMer and with S-BLEST. We have evaluated how well annotation transfer can be performed on SCOP ID's, Gene Ontology (GO ID's and EC Numbers. The method is very efficient and totally automated, generally taking around fifteen minutes for a 400 residue protein. Conclusion With structural genomics initiatives determining structures with little, if any, functional characterization, development of protein structure and function analysis tools are a necessary endeavor. We have developed a useful application towards a solution to this problem using common structural and sequence based analysis tools. These approaches are able to find statistically significant environments in a database of protein structure, and the method is able to quantify how closely associated each environment is to a predicted functional annotation.

Heiland Randy

2006-03-01

136

Structure Elucidation Of Flavonoid Compound from the Leaves of Coleus Atropurpureus Benth using 1d- And 2d-NMR Techniques  

International Nuclear Information System (INIS)

Isolation of flavonoid compound from ethylacetate extract of the leaves of Coleus atropurpureus Benth using column chromatography have been carried out. Structure elucidation of the isolated compounds was done by one-and two-dimensional NMR (1H, 13C, DEPT, COSY, HMQC and HMBC). Analysis of 1D-NMR spectra (1H-NMR showed signals at ? 6-8 ppm for the aromatic region of the flavonoid aglycone and 13C-NMR showed signals for three carbon atoms of the flavonoid ring C at ? 182.8 ppm (C-4), 103.9 ppm (C-3), 166.4 ppm (C-2) and DEPT showed the presence of CH and CH2 group). Analysis of 2D- NMR spectra (COSY showed correlation of proton at ? 7.86 and 6.92 ppm and HMBC showed correlation between proton at ? 6.61 with 166.4 ppm and 6.92 with 123.3 ppm). (author)

137

Structural properties of replication origins in yeast DNA sequences  

International Nuclear Information System (INIS)

Sequence-dependent DNA flexibility is an important structural property originating from the DNA 3D structure. In this paper, we investigate the DNA flexibility of the budding yeast (S. Cerevisiae) replication origins on a genome-wide scale using flexibility parameters from two different models, the trinucleotide and the tetranucleotide models. Based on analyzing average flexibility profiles of 270 replication origins, we find that yeast replication origins are significantly rigid compared with their surrounding genomic regions. To further understand the highly distinctive property of replication origins, we compare the flexibility patterns between yeast replication origins and promoters, and find that they both contain significantly rigid DNAs. Our results suggest that DNA flexibility is an important factor that helps proteins recognize and bind the target sites in order to initiate DNA replication. Inspired by the role of the rigid region in promoters, we speculate that the rigid replication origins may facilitate binding of proteins, including the origin recognition complex (ORC), Cdc6, Cdt1 and the MCM2-7 complex

138

Reversible switching of electronic ground state in a pentacoordinated Cu(II) 1D cationic polymer and structural diversity.  

Science.gov (United States)

Two copper(II) polymeric complexes {[Cu(HPymat)(MeOH)](NO3)}n (1) and {[Cu4(Pymab)4(H2O)4](NO3)4} (2) were synthesized with the carboxylate-containing Schiff-base ligands HPymat(-) and Pymab(-) [H2Pymat = (E)-2-(1-(pyridin-2-yl)methyleneamino)terephthalic acid, HPymab = (E)-2-((pyridine-2-yl)methyleneamino)benzoic acid]. Complex 1 is a one-dimensional Cu(II) cationic polymeric complex containing free protonated carboxylic groups and nitrate anions as counterions. Complex 2 is a zero-dimensional tetranuclear cationic Cu(II) complex containing nitrate anions as counterions. Complex 1 shows rhombic electron paramagnetic resonance (EPR) spectra in the solid state at room temperature (RT) and 77 K and tetragonal EPR spectra in dimethyl sulfoxide (DMSO) and dimethylformamide (DMF) and "inverse" EPR spectrum in CH3CN. Complex 2 shows rhombic EPR spectra in the solid state at RT and 77 K. But complex 2 shows tetragonal spectra in DMSO, DMF, and CH3CN. Thermogravimetric analysis was also performed for both complexes 1 and 2. Mean-square displacement amplitude analysis was carried out to detect librational disorder along the metal-ligand bonds in crystal structures. PMID:24911032

Sasmal, Ashok; Garribba, Eugenio; Rizzoli, Corrado; Mitra, Samiran

2014-07-01

139

A Comparison of Long-Period SKS Datasets And What They Reveal About 1D Outer Core Structure  

Science.gov (United States)

Seismology is the most direct tool for documenting the presences or absence of outer core stratification. The outermost core is most effectively sampled by SKS, S2KS, S3KS, S4KS, etc.) which have bottoming depths at the top of the outermost core. In order to incorporate modern data sets (e.g., USArray, Europe, China, etc), we need to sift through massive amounts of seismic data to identify the smaller portion of quality signals in a time-efficient manner. We evaluate the application of a cluster analysis technique (Houser et al., 2008) toward identifying and evaluating the SKS phases that traverse the outer core. Cluster analysis is a semi-automated method for interrogating large datasets by processing all the data for an earthquake while allowing the user to graphically interact with the data to remove low quality records. The Houser et al. (2008) cluster analysis method has already been applied to diffracted S waves (Manners et al., 2004), and here we will expand the cluster analysis to the radial component core phases. These newly measured SKS arrival times will be compared with SKS arrival time measurements used in previous mantle tomographic models, namely, S20RTS (Ritsema and van Heist, 2002) using a purely automated method and TXBW (Grand, 2002) using a purely manual method. We find that the arrival times collected by the three methods (automated, clustered, and manual) during overlapping time frames are in agreement within the measurement error bars. Therefore, the SKS data from these studies can be combined to constrain the radial structure of the outermost core. Thus, cluster analysis is an ideal tool for developing a large compilation of SKS arrival times from modern global seismic data, while simultaneously providing a measure of data quality.

Houser, C. T.; Ritsema, J. E.; Grand, S.

2010-12-01

140

Genomic structure and sequence analysis of human HOXA-9.  

Science.gov (United States)

In order to understand the regulatory mechanisms establishing and maintaining HOXA-9 gene expression, structural information about the gene is a prerequisite. Therefore, we sequenced the 7.2-kb region of the human HOXA-9 gene and mapped the positions of two partial cDNAs consisting of one of two 5' exons, AB (358 bp) or CD (568 bp), and a common 3' exon (exon II), which are separated by 5.4- and 1.0-kb introns, respectively. When the amino acid sequence homologies were compared with those of other Hox genes belonging to the same paralogous group, exon CD exhibited the strongest homology: 73% of 91 aa residues exactly matched those of chicken Hoxa-9. An intermediate exon (90 bp) was detected within exon CD. It was surrounded by a splice acceptor and a donor at both the 5' and 3' ends, and one branchpoint site was found near the splice-acceptor site. Nucleotide sequence analysis along this region revealed two TATA boxes, one CAAT box, one GC box, and one each of the following binding sites--engrailed, eve-stripe2-hb3, and Krox20--just upstream of exon CD. A CpG island and two RARE repeats were detected within intron I. Northern blot analysis showed that at least four main transcripts were generated along this region: all fetal tissues tested (brain, lung, liver, and kidney) produced a 1.8-kb homeobox-containing transcript (HA-9A); a 2.2- and a 3.3-kb transcript were generated from exon CD and exon II (HA-9B), especially in fetal and adult kidneys as well as in adult skeletal muscle; the 1.0-kb transcript was likely to be generated by the intermediate exon in all adult and fetal tissues. Several weak bands without tissue specificity were likely to be contributed by the hybrid transcripts between HOXA-9 and the other HOXA gene(s). Together, these results may account for the unique degree of conservation of the HOX cluster in general. PMID:9628584

Kim, M H; Chang, H H; Shin, C; Cho, M; Park, D; Park, H W

1998-05-01

 
 
 
 
141

Structural characterization of genomes by large scale sequence-structure threading  

Directory of Open Access Journals (Sweden)

Full Text Available Abstract Background Using sequence-structure threading we have conducted structural characterization of complete proteomes of 37 archaeal, bacterial and eukaryotic organisms (including worm, fly, mouse and human totaling 167,888 genes. Results The reported data represent first rather general evaluation of performance of full sequence-structure threading on multiple genomes providing opportunity to evaluate its general applicability for large scale studies. According to the estimated results the sequence-structure threading has assigned protein folds to more then 60% of eukaryotic, 68% of archaeal and 70% of bacterial proteomes. The repertoires of protein classes, architectures, topologies and homologous superfamilies (according to the CATH 2.4 classification have been established for distant organisms and superkingdoms. It has been found that the average abundance of CATH classes decreases from "alpha and beta" to "mainly beta", followed by "mainly alpha" and "few secondary structures". 3-Layer (aba Sandwich has been characterized as the most abundant protein architecture and Rossman fold as the most common topology. Conclusion The analysis of genomic occurrences of CATH 2.4 protein homologous superfamilies and topologies has revealed the power-law character of their distributions. The corresponding double logarithmic "frequency – genomic occurrence" dependences characteristic of scale-free systems have been established for individual organisms and for three superkingdoms. Supplementary materials to this works are available at 1.

Cherkasov Artem

2004-04-01

142

The Holliday junction in an inverted repeat DNA sequence: Sequence effects on the structure of four-way junctions  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Holliday junctions are important structural intermediates in recombination, viral integration, and DNA repair. We present here the single-crystal structure of the inverted repeat sequence d(CCGGTACCGG) as a Holliday junction at the nominal resolution of 2.1 ?. Unlike the previous crystal structures, this DNA junction has B-DNA arms with all standard Watson–Crick base pairs; it therefore represents the intermediate proposed by Holliday as being involved in homologous recombination. The jun...

Eichman, Brandt F.; Vargason, Jeffrey M.; Mooers, Blaine H. M.; Ho, P. Shing

2000-01-01

143

Mononuclear, dinuclear and 1-D polymeric complexes of Cd(II) of a pyridyl pyrazole ligand: Syntheses, crystal structures and photoluminescence studies  

Science.gov (United States)

The syntheses, crystal structures and photoluminescence properties of four new Cd(II) complexes are reported using strongly coordinating ligand 3,5-dimethyl-1-(2'-pyridyl) pyrazole (L) in presence of anionic ancillary bridging ligands as nitrite, chloride and dicyanamide. Among the complexes two (1 and 2) are monomeric, 3 is ?2 - chloro bridged dimer and the last one (4) is a mixed alternate chloro - end to end (EE) dicyanamide bridged 1D polymer. All the four complexes have been X-ray crystallographically characterized. The ligand L behaves as a potent bidentate neutral N, N donor. Geometrical diversity of Cd(II) complexes is due to no loss or gain of crystal field stability with the variation of geometry. Consequently the stability of a structure depends on steric requirements. The ligand L shows considerable fluorescence and all four complexes in methanol exhibit interesting photoluminescence properties with different emission intensities. The band maxima and fluorescence efficiency (in methanol) are found to be dependent on the coordination chromophore and structural rigidity induced by the incorporated Cd(II) ion. Among the synthesized complexes 1 exhibits the highest fluorescence intensity in methanol.

Das, Kinsuk; Konar, Saugata; Jana, Atanu; Barik, Anil Kumar; Roy, Sangita; Kar, Susanta Kumar

2013-03-01

144

Two novel 1-D helical chains Zn(II)/Cd(II) polymers based on tetrazolate-1-acetic acid: Crystal structures, solid state fluorescence and thermal behaviors  

Science.gov (United States)

Two new d10 metal complexes with tetrazolate-1-acetic acid, [Zn(1-tza)(Cl)(H2O)] (1) and [Cd(1-tza)(phen)(NO3)] (2) (1-Htza = tetrazole-1-acetic acid, phen = 1,10-phenanthroline), have been prepared, and their structures have been characterized by single-crystal X-ray diffraction. The flexibilities of 1-tza ligands result in 1-D helical chained structures of the two obtained complexes, in which the 1-tza ligands adopt different coordination mode: 1 with ?2-kO1: kN4 and 2 with ?2-kO1, O2: kN3. Compounds 1 exhibits a nonracemic enantiopure topology while compound 2 reveals to be mesomeric structures. The crystal packing in 1 and 2 is controlled mainly by hydrogen bonds and face-to-face ?-? stacking interactions, respectively. Photoluminescence studies show that 1 and 2 exhibit strong luminescence. Moreover, compound 1 exhibits a second-order nonlinear optical coefficient equal to that of potassium dihydrogen phosphate (KDP). The thermal stability of the two complexes has also been investigated.

Lu, Ying-Bing; Jin, Shuang; Jian, Fang-Mei; Xie, Yong-Rong; Luo, Guo-Tian

2014-03-01

145

Polycatenation-driven self-assembly of nanoporous frameworks based on a 1D ribbon of rings: regular structural evolution, interpenetration transformation, and photochemical modification.  

Science.gov (United States)

A series of nanoporous frameworks constructed by a polycatenated isoreticular 1D?ribbon of rings have been developed. The orientation of catenated ribbons can be fine tuned by varying counter anions, which allows both pore size and shape to be systematically adjusted in a pre-synthetic process. Distinct from conventional pore construction modes in which the organic linkers are alternately connected by metal nodes into a 3D periodic arrangement, the present polycatenation approach represents an alternative for constructing soft porous materials with tunable pore metrics and functions. Furthermore, these porous structures can interconvert into each other based on an anion-exchange process, accompanied by the transformation of the interpenetrating structures in different dimensional networks, which is unusual in porous frameworks. In addition, such a porous framework can be post-synthetically modified by a photoinduced [2+2] cycloaddition reaction, which not only achieves the surface modification (from conjugated to non-conjugated inner surface), but also triggers the structural transformation from low dimension to high dimension. Such a post-modification process reinforces the pore architecture through a covalent locking effect and has a great impact on the adsorption properties. PMID:24478056

Sun, Jian-Ke; Tan, Bin; Cai, Li-Xuan; Chen, Rui-Ping; Zhang, Jian; Zhang, Jie

2014-02-24

146

Studies on structure-based sequence alignment and phylogenies of beta-lactamases  

Digital Repository Infrastructure Vision for European Research (DRIVER)

The ?-lactamases enzymes cleave the amide bond in ?-lactam ring, rendering ?-lactam antibiotics harmless to bacteria. In this communication we have studied structure-function relationship and phylogenies of class A, B and D beta-lactamases using structure-based sequence alignment and phylip programs respectively. The data of structure-based sequence alignment suggests that in different isolates of TEM-1, mutations did not occur at or near sequence motifs. Since deletions are repor...

Salahuddin, Parveen; Khan, Asad U.

2014-01-01

147

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

Science.gov (United States)

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

Ki, Jang-Seu; Han, Myung-Soo

2007-02-01

148

Adipose pyruvate carboxylase: amino acid sequence and domain structure deduced from cDNA sequencing.  

Digital Repository Infrastructure Vision for European Research (DRIVER)

The complete amino acid sequence of 3T3-L1 adipocyte pyruvate carboxylase (PC) [pyruvate:carbon-dioxide ligase (ADP-forming), EC 6.4.1.1] has been deduced from sequencing overlapping cDNA clones obtained from an adipocyte cDNA library constructed in the lambda Zap vector. The encoding mRNA for PC promoter contains 4067 nt, including a 3534-nt coding sequence and noncoding regions of 100 and 433 nt at the 5' and 3' ends, respectively. The biotinylated lysine of the encoded PC promoter (1178 am...

Zhang, J.; Xia, W. L.; Brew, K.; Ahmad, F.

1993-01-01

149

How the structure of an adenine tract depends on sequence context: a new model for the structure of TnAn DNA sequences.  

Science.gov (United States)

We present a new model to explain the bending and local structural properties of TnAn sequences in DNA. Current models suggest that an adenine tract has the same unusual structure when found in a TnAn sequence as it has when surrounded by mixed-sequence B-DNA. On the basis of hydroxyl radical cleavage patterns of several TnAn sequences, we instead propose that the T2A2 or T3A3 core of such sequences is B-DNA-like but that adenines and thymines outside of this core, if sufficient in number, can form the unusual structure adopted by adenine tracts surrounded by mixed sequence DNA. We pursued further the structure of T7A7N7, a molecule which exhibits reduced electrophoretic mobility on native polyacrylamide gels and is therefore presumed to be bent. We attempted to mimic the structure of T7A7N7 that was predicted by our model by designing two new sequences, one in which the T3A3 core of T7A7N7 is substituted by six nucleotides of mixed sequence (N6) and the other in which the T2A2 core is replaced by N4. Hydroxyl radical cleavage patterns of all three molecules are nearly indistinguishable. All three molecules run anomalously slowly on a native polyacrylamide gel, with the mobility of T4N6A4N7 > T7A7N7 approximately T5N4A5N7. Analysis of the hydroxyl radical cutting pattern of T7A7N7 by Fourier transformation reveals the occurrence of an unusual structure at intervals of approximately 10 bp, a periodicity which is not evident in the sequence of the DNA. PMID:8380329

Price, M A; Tullius, T D

1993-01-12

150

Designing to See and Share Structure in Number Sequences  

Science.gov (United States)

This paper reports on a design experiment in the domain of number sequences conducted in the course of the "WebLabs" project. We iteratively designed and tested a set of activities and tools in which 10-14 year old students used the "ToonTalk" programming environment to construct models of sequences and series, and then shared their models and…

Mor, Yishay; Noss, Richard; Hoyles, Celia; Kahn, Ken; Simpson, Gordon

2006-01-01

151

Using the T-Coffee package to build multiple sequence alignments of protein, RNA, DNA sequences and 3D structures.  

Science.gov (United States)

T-Coffee (Tree-based consistency objective function for alignment evaluation) is a versatile multiple sequence alignment (MSA) method suitable for aligning most types of biological sequences. The main strength of T-Coffee is its ability to combine third party aligners and to integrate structural (or homology) information when building MSAs. The series of protocols presented here show how the package can be used to multiply align proteins, RNA and DNA sequences. The protein section shows how users can select the most suitable T-Coffee mode for their data set. Detailed protocols include T-Coffee, the default mode, M-Coffee, a meta version able to combine several third party aligners into one, PSI (position-specific iterated)-Coffee, the homology extended mode suitable for remote homologs and Expresso, the structure-based multiple aligner. We then also show how the T-RMSD (tree based on root mean square deviation) option can be used to produce a functionally informative structure-based clustering. RNA alignment procedures are described for using R-Coffee, a mode able to use predicted RNA secondary structures when aligning RNA sequences. DNA alignments are illustrated with Pro-Coffee, a multiple aligner specific of promoter regions. We also present some of the many reformatting utilities bundled with T-Coffee. The package is an open-source freeware available from http://www.tcoffee.org/. PMID:21979275

Taly, Jean-Francois; Magis, Cedrik; Bussotti, Giovanni; Chang, Jia-Ming; Di Tommaso, Paolo; Erb, Ionas; Espinosa-Carrasco, Jose; Kemena, Carsten; Notredame, Cedric

2011-11-01

152

Structural features of B family chorion sequences in the silkmoth Bombyx mori, and their evolutionary implications.  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Partial protein sequences, and DNA sequences of corresponding cDNA and genomic clones were obtained and analyzed to reveal the primary structural features of major, developmentally middle or late components of the B chorion multigene family in Bombyx mori. Comparisons with other types of sequences confirm and clarify the tripartite domain structure of chorion proteins. Glycine-, leucine- and tyrosine-containing, tandemly repetitive peptides form the bulk of the amino-terminal and carboxy-term...

Tsitilou, S. G.; Rodakis, G. C.; Alexopoulou, M.; Kafatos, F. C.; Ito, K.; Iatrou, K.

1983-01-01

153

Structural basis for sequence-dependent DNA cleavage by nonspecific endonucleases  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Nonspecific endonucleases hydrolyze DNA without sequence specificity but with sequence preference, however the structural basis for cleavage preference remains elusive. We show here that the nonspecific endonuclease ColE7 cleaves DNA with a preference for making nicks after (at 3?O-side) thymine bases but the periplasmic nuclease Vvn cleaves DNA more evenly with little sequence preference. The crystal structure of the ‘preferred complex’ of the nuclease domain of ColE7 bound to an 18 bp...

Wang, Yi-ting; Yang, Wei-jen; Li, Chia-lung; Doudeva, Lyudmila G.; Yuan, Hanna S.

2006-01-01

154

Polymorphisms in CD1d affect antigen presentation and the activation of CD1d-restricted T cells  

Digital Repository Infrastructure Vision for European Research (DRIVER)

CD1 proteins constitute a distinct lineage of antigen-presenting molecules specialized for the presentation of lipid antigens to T cells. In contrast to the extensive sequence polymorphism characteristic of classical MHC molecules, CD1 proteins exhibit limited sequence diversity. Here, we describe the identification and characterization of CD1d alleles in wild-derived mouse strains. We demonstrate that polymorphisms in CD1d affect the presentation of endogenous and exogenous ligands to CD1d-r...

Zimmer, Michael I.; Nguyen, Hanh P.; Wang, Bin; Xu, Honglin; Colmone, Angela; Felio, Kyrie; Choi, Hak-jong; Zhou, Ping; Alegre, Maria-luisa; Wang, Chyung-ru

2009-01-01

155

Structural (and sequence-based) analysis of transcriptional regulation  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Most computational approaches to transcriptional regulation use sequence-based methodologies, that aim to discover regulatory motifs in genomic segments. Here we argue that the current content of the Protein Data Bank (PDB) can provide invaluable data that drive the prediction of regulatory interactions within genomes. First, we dissect protein-DNA interfaces and find atomic interactions that contribute to sequence-specific recognition, mainly hydrogen bonds and Van derWaals contacts. Thes...

Contreras-moreira, Bruno; Lozada-cha?vez, Irma; Espinosa Angarica, Vladimir

2008-01-01

156

3-D structure of the Rio Grande Rift from 1-D constrained joint inversion of receiver functions and surface wave dispersion  

Science.gov (United States)

The Southern terminus of the Rio Grande Rift region has been poorly defined in the geologic record, with few seismic studies that provide information on the deeper Rift structure. In consequence, important questions related to tectonic and lithospheric activity of the Rio Grande Rift remain unresolved. To address some of these geological questions, we collect and analyze seismic data from 147 EarthScope Transportable Array (USArray) and other seismic stations in the region, to develop a 3-D crust and upper mantle velocity model. We apply a constrained optimization approach for joint inversion of surface wave and receiver functions using seismic S wave velocities as a model parameter. In particular, we compute receiver functions stacks based on ray parameter, and invert them jointly with collected surface wave group velocity dispersion observations. The inversions estimate 1-D seismic S-wave velocity profiles to 300 km depth, which are then interpolated to a 3-D velocity model using a Bayesian kriging scheme. Our 3-D models show a thin lower velocity crust anomaly along the southeastern Rio Grande Rift, a persistent low velocity anomaly underneath the Colorado Plateau and Basin and Range province, and another one at depth beneath the Jemez lineament, and the southern RGR.

Sosa, Anibal; Thompson, Lennox; Velasco, Aaron A.; Romero, Rodrigo; Herrmann, Robert B.

2014-09-01

157

Learning hierarchically structured action sequences is unaffected by prefrontal-cortex lesion.  

Science.gov (United States)

This study tested the impact of prefrontal-cortex lesion on learning hierarchically structured action sequences. Using a visual-manual serial reaction time task, we had subjects first perform five blocks of trials with a hierarchically structured 14-element action sequence and then tested for sequence-specific learning by introducing a pseudo-random transfer sequence. Relative to control subjects (N = 39), we found that both lateral frontal (N = 16) and medial frontal (N = 18) patients showed reduced overall performance benefits across the training phase. In contrast, the negative transfer test showed significantly increased reaction times in all patient groups, indicating robust sequence-specific learning. This learning was not significantly different from that of the control group. Taken together, the data suggest that learning hierarchically structured action sequences is unimpaired in patients with prefrontal-cortex lesion. PMID:16835794

Koch, Iring; Reverberi, Carlo; Rumiati, Raffaella I

2006-11-01

158

Structure of a Functional Amyloid Protein Subunit Computed Using Sequence Variation  

DEFF Research Database (Denmark)

Functional amyloid fibers, called curli, play a critical role in adhesion and invasion of many bacteria. Unlike pathological amyloids, curli structures are formed by polypeptide sequences whose amyloid structure has been selected for during evolution. This important distinction provides us with an opportunity to obtain structural insights from an unexpected source: the covariation of amino acids in sequences of different curli proteins. We used recently developed methods to extract amino acid contacts from a multiple sequence alignment of homologues of the curli subunit protein, CsgA. Together with an efficient force field, these contacts allow us to determine structural models of CsgA. We find that CsgA forms a ?-helical structure, where each turn corresponds to previously identified repeat sequences in CsgA. The proposed structure is validated by previously measured solid-state NMR, electron microscopy and X-ray diffraction data, and agrees with an earlier proposed model derived by complementary means.

Tian, Pengfei; Boomsma, Wouter

2014-01-01

159

The chemical structure of DNA sequence signals for RNA transcription  

Science.gov (United States)

The proposed recognition sites for RNA transcription for E. coli NRA polymerase, bacteriophage T7 RNA polymerase, and eukaryotic RNA polymerase Pol II are evaluated in the light of the requirements for efficient recognition. It is shown that although there is good experimental evidence that specific nucleic acid sequence patterns are involved in transcriptional regulation in bacteria and bacterial viruses, among the sequences now available, only in the case of the promoters recognized by bacteriophage T7 polymerase does it seem likely that the pattern is sufficient. It is concluded that the eukaryotic pattern that is investigated is not restrictive enough to serve as a recognition site.

George, D. G.; Dayhoff, M. O.

1982-01-01

160

Designing to see and share structure in number sequences  

Digital Repository Infrastructure Vision for European Research (DRIVER)

This paper reports on a design experiment in the domain of number sequences conducted in the course of the WebLabs project. We iteratively designed and tested a set of activities and tools in which 10-14 year old students used the ToonTalk programming environment to construct models of sequences and series, and then shared their models and their observations about them utilising a webbased collaboration system. We report on the evolution of a design pattern (programming method) called ‘Stre...

Mor, Yishay; Noss, Richard; Hoyles, Celia; Kahn, Ken; Simpson, Gordon

2006-01-01

 
 
 
 
161

Structator: fast index-based search for RNA sequence-structure patterns  

Directory of Open Access Journals (Sweden)

Full Text Available Abstract Background The secondary structure of RNA molecules is intimately related to their function and often more conserved than the sequence. Hence, the important task of searching databases for RNAs requires to match sequence-structure patterns. Unfortunately, current tools for this task have, in the best case, a running time that is only linear in the size of sequence databases. Furthermore, established index data structures for fast sequence matching, like suffix trees or arrays, cannot benefit from the complementarity constraints introduced by the secondary structure of RNAs. Results We present a novel method and readily applicable software for time efficient matching of RNA sequence-structure patterns in sequence databases. Our approach is based on affix arrays, a recently introduced index data structure, preprocessed from the target database. Affix arrays support bidirectional pattern search, which is required for efficiently handling the structural constraints of the pattern. Structural patterns like stem-loops can be matched inside out, such that the loop region is matched first and then the pairing bases on the boundaries are matched consecutively. This allows to exploit base pairing information for search space reduction and leads to an expected running time that is sublinear in the size of the sequence database. The incorporation of a new chaining approach in the search of RNA sequence-structure patterns enables the description of molecules folding into complex secondary structures with multiple ordered patterns. The chaining approach removes spurious matches from the set of intermediate results, in particular of patterns with little specificity. In benchmark experiments on the Rfam database, our method runs up to two orders of magnitude faster than previous methods. Conclusions The presented method's sublinear expected running time makes it well suited for RNA sequence-structure pattern matching in large sequence databases. RNA molecules containing several stem-loop substructures can be described by multiple sequence-structure patterns and their matches are efficiently handled by a novel chaining method. Beyond our algorithmic contributions, we provide with Structator a complete and robust open-source software solution for index-based search of RNA sequence-structure patterns. The Structator software is available at http://www.zbh.uni-hamburg.de/Structator.

Will Sebastian

2011-05-01

162

Compression of structured high-throughput sequencing data.  

Science.gov (United States)

Large biological datasets are being produced at a rapid pace and create substantial storage challenges, particularly in the domain of high-throughput sequencing (HTS). Most approaches currently used to store HTS data are either unable to quickly adapt to the requirements of new sequencing or analysis methods (because they do not support schema evolution), or fail to provide state of the art compression of the datasets. We have devised new approaches to store HTS data that support seamless data schema evolution and compress datasets substantially better than existing approaches. Building on these new approaches, we discuss and demonstrate how a multi-tier data organization can dramatically reduce the storage, computational and network burden of collecting, analyzing, and archiving large sequencing datasets. For instance, we show that spliced RNA-Seq alignments can be stored in less than 4% the size of a BAM file with perfect data fidelity. Compared to the previous compression state of the art, these methods reduce dataset size more than 40% when storing exome, gene expression or DNA methylation datasets. The approaches have been integrated in a comprehensive suite of software tools (http://goby.campagnelab.org) that support common analyses for a range of high-throughput sequencing assays. PMID:24260313

Campagne, Fabien; Dorff, Kevin C; Chambwe, Nyasha; Robinson, James T; Mesirov, Jill P

2013-01-01

163

Effects of external interactions on protein sequence-structure relations of beta-trefoil fold.  

Science.gov (United States)

Proteins with symmetric structures are ideal models to investigate the sequence-structure relations. We investigate proteins with beta-trefoil fold and find they have different degrees of sequence symmetries although they show similar symmetric structures. To understand this, we calculate the strength of interactions of the beta-trefoil folds with surrounding environments and find the low degrees of sequence symmetries are often correlated with large external interactions. Our results give an additional confirmation of Anfinsen's thermodynamic hypothesis that protein structures are not only determined by their sequences but also by their surrounding environments. We suggest the external interactions should be considered additionally in protein structure prediction through ab initio folding. PMID:18320584

Li, Mingfeng; Huang, Yanzhao; Xiao, Yi

2008-09-01

164

Allelic Diversity and Population Structure of Bacillus sphaericus as Revealed by Multilocus Sequence Typing ? †  

Digital Repository Infrastructure Vision for European Research (DRIVER)

The genetic diversity of 35 Bacillus sphaericus strains was analyzed by a newly developed multilocus sequence typing (MLST) scheme, toxin gene pool survey, and mosquito bioassay. The results demonstrated that strains assigned to the same sequence type (ST) had the same occurrence of toxin genes. Further sequence analysis revealed that toxic strains presented a nearly clonal population structure, whereas nontoxic strains had a high level of heterogeneity and were significantly distinct from to...

Ge, Yong; Hu, Xiaomin; Zheng, Dasheng; Wu, Yiming; Yuan, Zhiming

2011-01-01

165

Structural analysis of DNA sequence: evidence for lateral gene transfer in Thermotoga maritima  

DEFF Research Database (Denmark)

The recently published complete DNA sequence of the bacterium Thermotoga maritima provides evidence, based on protein sequence conservation, for lateral gene transfer between Archaea and Bacteria. We introduce a new method of periodicity analysis of DNA sequences, based on structural parameters, which brings independent evidence for the lateral gene transfer in the genome of T.maritima, The structural analysis relates the Archaea-like DNA sequences to the genome of Pyrococcus horikoshii. Analysis of 24 complete genomic DNA sequences shows different periodicity patterns for organisms of different origin, The typical genomic periodicity for Bacteria is 11 bp whilst it is 10 bp for Archaea, Eukaryotes have more complex spectra but the dominant period in the yeast Saccharomyces cerevisiae is 10.2 bp. These periodicities are most likely reflective of differences in chromatin structure.

Worning, Peder; Jensen, Lars Juhl

2000-01-01

166

Structure, sequence and expression of the hepatitis delta (?) viral genome  

Science.gov (United States)

Biochemical and electron microscopic data indicate that the human hepatitis ? viral agent contains a covalently closed circular and single-stranded RNA genome that has certain similarities with viroid-like agents from plants. The sequence of the viral genome (1,678 nucleotides) has been determined and an open reading frame within the complementary strand has been shown to encode an antigen that binds specifically to antisera from patients with chronic hepatitis ? viral infections.

Wang, Kang-Sheng; Choo, Qui-Lim; Weiner, Amy J.; Ou, Jing-Hsiung; Najarian, Richard C.; Thayer, Richard M.; Mullenbach, Guy T.; Denniston, Katherine J.; Gerin, John L.; Houghton, Michael

1986-10-01

167

The sexual inducer of Volvox carteri. Primary structure deduced from cDNA sequence  

Digital Repository Infrastructure Vision for European Research (DRIVER)

The primary structure of the sexual inducer of Volvox carteri f. nagariensis has been deduced by cloning and sequence analysis of cDNA. The sexual inducer contains 208 amino acids including a signal sequence. A total of six potential N-glycosylation sites are found within the polypeptide chain. At the genomic level, the sexual inducer protein is encoded in five exons.

Mages, H. W.; Tschochner, H.; Sumper, Manfred

1988-01-01

168

Crystal structure of V?1 T cell receptor in complex with CD1d-sulfatide shows MHC-like recognition of a self-lipid by human ?? T cells.  

Science.gov (United States)

The nature of the antigens recognized by ?? T cells and their potential recognition of major histocompatibility complex (MHC)-like molecules has remained unclear. Members of the CD1 family of lipid-presenting molecules are suggested ligands for V?1 TCR-expressing ?? T cells, the major ?? lymphocyte population in epithelial tissues. We crystallized a V?1 TCR in complex with CD1d and the self-lipid sulfatide, revealing the unusual recognition of CD1d by germline V?1 residues spanning all complementarity-determining region (CDR) loops, as well as sulfatide recognition separately encoded by nongermline CDR3? residues. Binding and functional analysis showed that CD1d presenting self-lipids, including sulfatide, was widely recognized by gut V?1+ ?? T cells. These findings provide structural demonstration of MHC-like recognition of a self-lipid by ?? T cells and reveal the prevalence of lipid recognition by innate-like T cell populations. PMID:24239091

Luoma, Adrienne M; Castro, Caitlin D; Mayassi, Toufic; Bembinster, Leslie A; Bai, Li; Picard, Damien; Anderson, Brian; Scharf, Louise; Kung, Jennifer E; Sibener, Leah V; Savage, Paul B; Jabri, Bana; Bendelac, Albert; Adams, Erin J

2013-12-12

169

Molecular characterization of pouched amphistome parasites (Trematoda: Gastrothylacidae) using ribosomal ITS2 sequence and secondary structures.  

Science.gov (United States)

Members of the family Gastrothylacidae (Trematoda: Digenea: Paramphistomata) are parasitic in ruminants throughout Africa and Asia. In north-east India, five species of pouched amphistomes, namely Fischoederius cobboldi, F. elongatus, Gastrothylax crumenifer, Carmyerius spatiosus and Velasquezotrema tripurensis, belonging to this family have been reported so far. In the present study, the molecular phylogeny of these five gastrothylacid species is derived using the second internal transcribed spacer (ITS2) sequence and secondary structure analyses. ITS2 sequence analysis was carried out to see the occurrence of interspecific variations among the species. Phylogenetic analyses were performed for primary sequence data alone as well as the combined sequence-structure information using neighbour-joining and Bayesian approaches. The sequence analysis revealed that there exist considerable interspecific variations among the various gastrothylacid fluke species. In contrast, the inferred secondary structures for the five species using minimum free energy modelling showed structural identities, in conformity with the core four-helix domain structure that has been recently identified as common to almost all eukaryotic taxa. The phylogenetic tree reconstructed using combined sequence-structure data showed a better resolution, as compared to the one using sequence data alone, with the gastrothylacid species forming a monophyletic group that is well separated from members of the other family, Paramphistomidae, of the amphistomid flukes group. The study provides the molecular characterization based on primary sequence data of the rDNA ITS2 region of the gastrothylacid amphistome flukes. Results also demonstrate the phylogenetic utility of the ITS2 sequence-secondary structure data for inferences at higher taxonomic levels. PMID:21473796

Ghatani, S; Shylla, J A; Tandon, V; Chatterjee, A; Roy, B

2012-03-01

170

Protein sequence-structure alignment based on site-alignment probabilities.  

Science.gov (United States)

A protein sequence-structure alignment method for database searches is examined on how effectively this method together with a simple scoring function previously developed can identify compatibilities between sequences and structures of proteins. The scoring function consists of pairwise contact energies, repulsive packing potentials of residues for overly dense arrangement and short-range potentials for secondary structures. Pairwise contact interactions in a sequence-structure alignment are evaluated in a mean field approximation on the basis of probabilities of site pairs to be aligned. Gap penalties are assumed to be proportional to the number of contacts at each residue position, and as a result gaps will be more frequently placed on protein surfaces than in cores. In addition to minimum energy alignments, we use probability alignments made by successively aligning site pairs in order by pairwise alignment probabilities. Results show that the present energy function and alignment method can detect well both folds compatible with a given sequence and, inversely, sequences compatible with a given fold. Probability alignments consisting of most reliable site pairs only can yield small root mean square deviations, and including less reliable pairs increases the deviations. Remarkably, by this method some individual sequence-structure pairs are detected having only 5-20% sequence identity. PMID:11700595

Miyazawa, S

2000-01-01

171

Random Amino Acid Mutations and Protein Misfolding Lead to Shannon Limit in Sequence-Structure Communication  

Digital Repository Infrastructure Vision for European Research (DRIVER)

The transmission of genomic information from coding sequence to protein structure during protein synthesis is subject to stochastic errors. To analyze transmission limits in the presence of spurious errors, Shannon's noisy channel theorem is applied to a communication channel between amino acid sequences and their structures established from a large-scale statistical analysis of protein atomic coordinates. While Shannon's theorem confirms that in close to native conformations information is t...

Lisewski, Andreas Martin

2008-01-01

172

Sequence- and structural-selective nucleic acid binding revealed by the melting of mixtures  

Digital Repository Infrastructure Vision for European Research (DRIVER)

A simple method for the detection of sequence- and structural-selective ligand binding to nucleic acids is described. The method is based on the commonly used thermal denaturation method in which ligand binding is registered as an elevation in the nucleic acid melting temperature (Tm). The method can be extended to yield a new, higher -throughput, assay by the simple expediency of melting designed mixtures of polynucleotides (or oligonucleotides) with different sequences or structures of inte...

Shi, Xiaochun; Chaires, Jonathan B.

2006-01-01

173

The Holliday junction in an inverted repeat DNA sequence: sequence effects on the structure of four-way junctions.  

Science.gov (United States)

Holliday junctions are important structural intermediates in recombination, viral integration, and DNA repair. We present here the single-crystal structure of the inverted repeat sequence d(CCGGTACCGG) as a Holliday junction at the nominal resolution of 2. 1 A. Unlike the previous crystal structures, this DNA junction has B-DNA arms with all standard Watson-Crick base pairs; it therefore represents the intermediate proposed by Holliday as being involved in homologous recombination. The junction is in the stacked-X conformation, with two interconnected duplexes formed by coaxially stacked arms, and is crossed at an angle of 41.4 degrees as a right-handed X. A sequence comparison with previous B-DNA and junction crystal structures shows that an ACC trinucleotide forms the core of a stable junction in this system. The 3'-C x G base pair of this ACC core forms direct and water-mediated hydrogen bonds to the phosphates at the crossover strands. Interactions within this core define the conformation of the Holliday junction, including the angle relating the stacked duplexes and how the base pairs are stacked in the stable form of the junction. PMID:10760268

Eichman, B F; Vargason, J M; Mooers, B H; Ho, P S

2000-04-11

174

Determining 3-D motion and structure from image sequences  

Science.gov (United States)

A method of determining three-dimensional motion and structure from two image frames is presented. The method requires eight point correspondences between the two frames, from which motion and structure parameters are determined by solving a set of eight linear equations and a singular value decomposition of a 3x3 matrix. It is shown that the solution thus obtained is unique.

Huang, T. S.

1982-01-01

175

In silico structural study of random amino acid sequence proteins not present in nature.  

Science.gov (United States)

The three-dimensional structures of a set of 'never born proteins' (NBP, random amino acid sequence proteins with no significant homology with known proteins) were predicted using two methods: Rosetta and the one based on the 'fuzzy-oil-drop' (FOD) model. More than 3000 different random amino acid sequences have been generated, filtered against the non redundant protein sequence data base, to remove sequences with significant homology with known proteins, and subjected to three-dimensional structure prediction. Comparison between Rosetta and FOD predictions allowed to select the ten top (highest structural similarity) and the ten bottom (the lowest structural similarity) structures from the ranking list organized according to the RMS-D value. The selected structures were taken for detailed analysis to define the scale of structural accordance and discrepancy between the two methods. The structural similarity measurements revealed discrepancies between structures generated on the basis of the two methods. Their potential biological function appeared to be quite different as well. The ten bottom structures appeared to be 'unfoldable' for the FOD model. Some aspects of the general characteristics of the NBPs are also discussed. The calculations were performed on the EUChinaGRID grid platform to test the performance of this infrastructure for massive protein structure predictions. PMID:20020465

Prymula, Katarzyna; Piwowar, Monika; Kochanczyk, Marek; Flis, Lukasz; Malawski, Maciej; Szepieniec, Tomasz; Evangelista, Giovanni; Minervini, Giuseppe; Polticelli, Fabio; Wi?niowski, Zdzis?aw; Sa?apa, Kinga; Matczy?ska, Ewa; Roterman, Irena

2009-12-01

176

A novel 1D-AF hybrid organic-inorganic chromium(II) methyl phosphonate dihydrate: synthesis, X-ray crystal and molecular structure, and magnetic properties.  

Science.gov (United States)

Light-blue crystals of chromium(II) methyl phosphonate dihydrate, [Cr(CH(3)PO(3))(H(2)O)].H(2)O, were obtained in water by mixing filtered solutions of methylphosphonic acid and chromium(II) chloride in the presence of urea in an inert atmosphere. The compound was characterized by elemental analysis, TGA-DSC, X-ray crystallography, magnetic measurements, and UV-visible and FT-IR spectroscopies. The crystal and molecular structures (orthorhombic Pnma (no. 62): a = 4.4714(5) A, b = 6.8762(7) A, c = 19.180(2) A, Z = 4) have been solved using single-crystal X-ray diffraction. The chromium(II) ion is six-coordinated by oxygens (4 + 2) to form an elongated octahedron, with the four equatorial oxygen atoms belonging to [-PO(3)](2-) phosphonate groups. This stereochemistry of the Cr(II) ion (high-spin d(4) electronic configuration) is ascribed to the Jahn-Teller effect. The [CrO(6)] chromophore, the [CH(3)PO(3)](2-) anions, and the water molecules build a novel one-dimensional (1D) metal(II) oxide chain, anchored to each other within the ab plane by two oxygens of the phosphonate ligand. Within the chain, each Cr(2+) ion is connected through double oxygen bridges to its two neighbors, forming edge-sharing octahedra running along the b axis. The chains are further connected with the adjacent chains by phosphonate [-PO(3)](2-) groups of the ligand, forming an inorganic layer that alternates along the c axis of the unit cell with bilayers, consisting of methyl groups and water of crystallization. The thermal variation of the magnetic susceptibility follows the Curie-Weiss law, with a large negative Weiss constant, theta = -60 K, indicating the presence of antiferromagnetic AF exchange interactions between neighboring Cr(II) ions. The magnetic behavior and the magnetic dimensionality have been analyzed in terms of Fisher's classical limiting form of the Heisenberg chain theory, and a value of J = -9.3 cm(-1) was found. The negative value of the intra-chain exchange constant coupling J confirms the presence of an AF coupling. No sign of long-range magnetic ordering down to 2 K (the lowest measured temperature) is observed, in agreement with the predominant one-dimensional character of the exchange interactions. PMID:20690756

Bauer, Elvira M; Bellitto, Carlo; Imperatori, Patrizia; Righini, Guido; Colapietro, Marcello; Portalone, Gustavo; Gómez-García, Carlos J

2010-08-16

177

Primary structure similarity analysis of proteins sequences by a new graphical representation.  

Science.gov (United States)

A new graphical description of the primary structure of protein sequences is introduced. First, a three-dimensional space discrete point set of a protein sequence is created based on the three main physicochemical properties of the amino acids. Secondly, a continuous cubic B-spline curve interpolating the amino acid points is constructed to represent the shape of the protein sequence. Then the geometric properties (curvature and torsion) of the continuous curve are extracted for the purpose of analyzing the similarity between protein sequences. Finally, an improved Canberra distance comparison is introduced for the similarity analysis of protein sequences with different lengths. Experimental results show that our method is effective for the similarity comparison of protein sequences. PMID:25242152

Xu, S C; Li, Z; Zhang, S P; Hu, J L

2014-01-01

178

Crystal structure of Z-DNA without an alternating purine-pyrimidine sequence.  

Science.gov (United States)

In left-handed Z-DNA, consecutive nucleotides along the chain alternate in the syn and anti conformations. Purine residues form the syn conformation readily and up to now all Z-DNA crystal structures have sequences of alternating purines and pyrimidines. However, we find that d(C-G-A-T-C-G) with the cytosines brominated or methylated on C-5 crystallizes as Z-DNA. The structure reveals thymines in syn and adenines in anti conformations. This suggests that Z-DNA may occur in sequences other than those with alternating purine-pyrimidine sequence. PMID:3858839

Wang, A H; Gessner, R V; van der Marel, G A; van Boom, J H; Rich, A

1985-06-01

179

Implicit Structured Sequence Learning: An FMRI Study of the Structural Mere-Exposure Effect  

Directory of Open Access Journals (Sweden)

Full Text Available In this event-related FMRI study we investigated the effect of five days of implicit acquisition on preference classification by means of an artificial grammar learning (AGL paradigm based on the structural mere-exposure effect and preference classification using a simple right-linear unification grammar. This allowed us to investigate implicit AGL in a proper learning design by including baseline measurements prior to grammar exposure. After 5 days of implicit acquisition, the FMRI results showed activations in a network of brain regions including the inferior frontal (centered on BA 44/45 and the medial prefrontal regions (centered on BA 8/32. Importantly, and central to this study, the inclusion of a naive preference FMRI baseline measurement allowed us to conclude that these FMRI findings were the intrinsic outcomes of the learning process itself and not a reflection of a preexisting functionality recruited during classification, independent of acquisition. Support for the implicit nature of the knowledge utilized during preference classification on day 5 come from the fact that the basal ganglia, associated with implicit procedural learning, were activated during classification, while the medial temporal lobe system, associated with explicit declarative memory, was consistently deactivated. Thus, preference classification in combination with structural mere-exposure can be used to investigate structural sequence processing (syntax in unsupervised AGL paradigms with proper learning designs.

Karl MagnusPetersson

2014-02-01

180

Structural polymorphism of homopurine--homopyrimidine sequences: the secondary DNA structure adopted by a d(GA.CT)22 sequence in the presence of zinc ions.  

Digital Repository Infrastructure Vision for European Research (DRIVER)

In this paper, we have analysed the conformational behaviour shown by the homopurine--homopyrimidine alternating d(GA.CT)22 sequence cloned into SV40. Our results show that, in the presence of zinc ions, the d(GA.CT)22 sequence adopts an altered secondary DNA structure (*H-DNA) which differs from either B-DNA or H-DNA. Formation of *H-DNA is facilitated by negative supercoiling and does not appear to require base protonation, since it is induced at neutral pH by approximately 0.4 mM ZnCl2. Th...

Bernue?s, J.; Beltra?n, R.; Casasnovas, J. M.; Azori?n, F.

1989-01-01

 
 
 
 
181

Comprehensive characterization of complex structural variations in cancer by directly comparing genome sequence reads.  

Science.gov (United States)

The development of high-throughput sequencing technologies has advanced our understanding of cancer. However, characterizing somatic structural variants in tumor genomes is still challenging because current strategies depend on the initial alignment of reads to a reference genome. Here, we describe SMUFIN (somatic mutation finder), a single program that directly compares sequence reads from normal and tumor genomes to accurately identify and characterize a range of somatic sequence variation, from single-nucleotide variants (SNV) to large structural variants at base pair resolution. Performance tests on modeled tumor genomes showed average sensitivity of 92% and 74% for SNVs and structural variants, with specificities of 95% and 91%, respectively. Analyses of aggressive forms of solid and hematological tumors revealed that SMUFIN identifies breakpoints associated with chromothripsis and chromoplexy with high specificity. SMUFIN provides an integrated solution for the accurate, fast and comprehensive characterization of somatic sequence variation in cancer. PMID:25344728

Moncunill, Valentí; Gonzalez, Santi; Beà, Sílvia; Andrieux, Lise O; Salaverria, Itziar; Royo, Cristina; Martinez, Laura; Puiggròs, Montserrat; Segura-Wang, Maia; Stütz, Adrian M; Navarro, Alba; Royo, Romina; Gelpí, Josep L; Gut, Ivo G; López-Otín, Carlos; Orozco, Modesto; Korbel, Jan O; Campo, Elias; Puente, Xose S; Torrents, David

2014-11-01

182

Sequence- and structure-based prediction of eukaryotic proteinphosphorylation sites  

DEFF Research Database (Denmark)

Protein phosphorylation at serine, threonine or tyrosine residues affects a multitude of cellular signaling processes. Howis specificity in substrate recognition and phosphorylation by protein kinases achieved? Here, we present an artificialneural network method that predicts phosphorylation sites in independent sequences with a sensitivity in the range from69 % to 96 %. As an example, we predict novel phosphorylation sites in the p300/CBP protein that may regulateinteraction with transcription factors and histone acetyltransferase activity. In addition, serine and threonine residues inp300/CBP that can be modified by O-linked glycosylation with N-acetylglucosamine are identified. Glycosylation mayprevent phosphorylation at these sites, a mechanism named yin-yang regulation. The prediction server is available on theInternet at http://www.cbs.dtu.dk/services/NetPhos/or via e-mail to NetPhos@cbs. dtu.dk. Copyright 1999 AcademicPress.

Blom, Nikolaj; Gammeltoft, Steen

1999-01-01

183

Investigation of the protein osteocalcin of Camelops hesternus: Sequence, structure and phylogenetic implications  

Science.gov (United States)

Ancient DNA sequences offer an extraordinary opportunity to unravel the evolutionary history of ancient organisms. Protein sequences offer another reservoir of genetic information that has recently become tractable through the application of mass spectrometric techniques. The extent to which ancient protein sequences resolve phylogenetic relationships, however, has not been explored. We determined the osteocalcin amino acid sequence from the bone of an extinct Camelid (21 ka, Camelops hesternus) excavated from Isleta Cave, New Mexico and three bones of extant camelids: bactrian camel ( Camelus bactrianus); dromedary camel ( Camelus dromedarius) and guanaco ( Llama guanacoe) for a diagenetic and phylogenetic assessment. There was no difference in sequence among the four taxa. Structural attributes observed in both modern and ancient osteocalcin include a post-translation modification, Hyp 9, deamidation of Gln 35 and Gln 39, and oxidation of Met 36. Carbamylation of the N-terminus in ancient osteocalcin may result in blockage and explain previous difficulties in sequencing ancient proteins via Edman degradation. A phylogenetic analysis using osteocalcin sequences of 25 vertebrate taxa was conducted to explore osteocalcin protein evolution and the utility of osteocalcin sequences for delineating phylogenetic relationships. The maximum likelihood tree closely reflected generally recognized taxonomic relationships. For example, maximum likelihood analysis recovered rodents, birds and, within hominins, the Homo-Pan-Gorilla trichotomy. Within Artiodactyla, character state analysis showed that a substitution of Pro 4 for His 4 defines the Capra-Ovis clade within Artiodactyla. Homoplasy in our analysis indicated that osteocalcin evolution is not a perfect indicator of species evolution. Limited sequence availability prevented assigning functional significance to sequence changes. Our preliminary analysis of osteocalcin evolution represents an initial step towards a complete character analysis aimed at determining the evolutionary history of this functionally significant protein. We emphasize that ancient protein sequencing and phylogenetic analyses using amino acid sequences must pay close attention to post-translational modifications, amino acid substitutions due to diagenetic alteration and the impacts of isobaric amino acids on mass shifts and sequence alignments.

Humpula, James F.; Ostrom, Peggy H.; Gandhi, Hasand; Strahler, John R.; Walker, Angela K.; Stafford, Thomas W.; Smith, James J.; Voorhies, Michael R.; George Corner, R.; Andrews, Phillip C.

2007-12-01

184

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

Directory of Open Access Journals (Sweden)

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 to current similarity search methods.

Borodovsky Mark

2006-03-01

185

CATH: comprehensive structural and functional annotations for genome sequences.  

Science.gov (United States)

The latest version of the CATH-Gene3D protein structure classification database (4.0, http://www.cathdb.info) provides annotations for over 235 000 protein domain structures and includes 25 million domain predictions. This article provides an update on the major developments in the 2 years since the last publication in this journal including: significant improvements to the predictive power of our functional families (FunFams); the release of our 'current' putative domain assignments (CATH-B); a new, strictly non-redundant data set of CATH domains suitable for homology benchmarking experiments (CATH-40) and a number of improvements to the web pages. PMID:25348408

Sillitoe, Ian; Lewis, Tony E; Cuff, Alison; Das, Sayoni; Ashford, Paul; Dawson, Natalie L; Furnham, Nicholas; Laskowski, Roman A; Lee, David; Lees, Jonathan G; Lehtinen, Sonja; Studer, Romain A; Thornton, Janet; Orengo, Christine A

2015-01-28

186

Structural organization of the human glutathione reductase gene: determination of correct cDNA sequence and identification of a mitochondrial leader sequence.  

Science.gov (United States)

The primary structure of human glutathione reductase gene (GSR) was determined by genomic cloning. The gene structure of human GSR spans 50 kb, consists of 13 exons, and was found to be highly similar to the mouse GSR gene. The coding sequence of human GSR resides on all 13 exons. An N-terminal arginine-rich mitochondrial leader sequence was present, with high homology to the murine leader sequence, between two in-frame start codons in the first exon. The 5' and 3' intron/exon splice junctions, with one exception, followed the general consensus sequences for intron spliced donor and acceptance sites. PMID:10708558

Kelner, M J; Montoya, M A

2000-03-16

187

Sequence Analysis of the Protein Structure Homology Modeling of Growth Hormone Gene from Salmo trutta caspius  

Directory of Open Access Journals (Sweden)

Full Text Available In view of the growth hormone protein investigated and characterized from Salmo trutta caspius. Growth hormone gene in the Salmo trutta caspius have six exons in the full length that is translated into a Molecular Weight (kDa: ssDNA: 64.98 and dsDNA: 129.6. There are also 210 amino acid residue. The assembled full length of DNA contains open reading frame of growth hormone gene that contains 15 sequences in the full length. The average GC content is 47% and AT content is 53%. This protein multiple alignment has shown that this peptide is 100% identical to the corresponding homologous protein in the growth hormone protein which including Salmo salar (Accession number: AAA49558.1 and Rainbow trout (Salmo trutta (Accession number: AAA49555.1" sequences. The sequence of protein had deposited in Gene Bank, Accession number: AEK70940. Also we were analyzed second and third structure between sequences reported in Gene Bank Network system. The results are shown, there are homology between second structure in three sequences including: Salmo trutta caspius, Salmo salar and Rainbow trout. Regarding third structure, Salmo trutta caspius and Salmo salar are same type, but Rainbow trout has different homology with Salmo trutta caspius and Salmo salar. However, the sequences were observed three parallel " helix and in second structure there were almost same percent ? sheet.

Abolhasan Rezaei

2012-03-01

188

Structure and Dynamics of DNA-dendrimer complexation: Role of counterions, water and base pair sequence  

Digital Repository Infrastructure Vision for European Research (DRIVER)

We study sequence dependent complexation between oligonucleotides (single strand DNA) and various generation ethylene diamine (EDA) cored poly amido amide (PAMAM) dendrimers through atomistic molecular dynamics simulations accompanied by free energy calculations and inherent structure determination. Simulations reveal formation of a stable complex and provide a detailed molecular level understanding of the structure and dynamics of such a complexation. The reaction free ener...

Maiti, Prabal K.; Bagchi, Biman

2006-01-01

189

A coleopteran triosephosphate isomerase: X-ray structure and phylogenetic impact of insect sequences.  

Science.gov (United States)

A coleopteran triosephosphate isomerase (TIM) from Tenebrio molitor (yellow mealworm beetle) was recombinantly expressed in Escherichia coli and characterized with respect to thermal stability, kinetic parameters and oligomeric state. The enzyme was successfully crystallized and the structure determined by X-ray analysis to 2.0 A resolution. This is the first example of an invertebrate TIM. We compare structural features with known structures of TIMs from microorganisms, plants and vertebrates, and discuss the utility of the Tenebrio TIM sequence, together with several newly sequenced insect TIMs, for molecular phylogenetic analysis. PMID:19849721

Knobeloch, D; Schmidt, A; Scheerer, P; Krauss, N; Wessner, H; Scholz, Ch; Küttner, G; von Rintelen, T; Wessel, A; Höhne, W

2010-02-01

190

On the internal structure of main-sequence stars  

International Nuclear Information System (INIS)

The authors present the main results of a study of the observed internal structure constants, k2, for a wide set of eclipsing binaries. From the analysis of the variations in relative positions of the eclipses and the comparison with different theoretical models, they could deduce that the discrepancy, previously reported by several authors between theory and observations, is no longer supported. Moreover, a strong correlation has been found between the evolution of the parameter k2 and the gravity at the surface of the star, g. (Auth.)

191

Chicken intestinal 28-kilodalton calbindin-D: complete amino acid sequence and structural considerations.  

Digital Repository Infrastructure Vision for European Research (DRIVER)

The complete primary structure of the cholecalciferol-induced chicken intestinal 28-kDa calbindin-D is reported. It is a single-chain polypeptide consisting of 261 amino acid residues (computed Mr = 30,042) and is blocked at the amino terminus. Tryptic digestion of the S-pyridylethylated protein followed by HPLC peptide mapping and automated sequence determination provided the bulk of the sequence information. Subsequent chymotryptic and Staphylococcus aureus V8 protease cleavages yielded the...

Fullmer, C. S.; Wasserman, R. H.

1987-01-01

192

Multilocus Sequence Typing Analysis of Staphylococcus lugdunensis Implies a Clonal Population Structure  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Staphylococcus lugdunensis is recognized as one of the major pathogenic species within the genus Staphylococcus, even though it belongs to the coagulase-negative group. A multilocus sequence typing (MLST) scheme was developed to study the genetic relationships and population structure of 87 S. lugdunensis isolates from various clinical and geographic sources by DNA sequence analysis of seven housekeeping genes (aroE, dat, ddl, gmk, ldh, recA, and yqiL). The number of alleles ranged from four ...

Chassain, Benoi?t; Leme?e, Ludovic; Didi, Jennifer; Thiberge, Jean-michel; Brisse, Sylvain; Pons, Jean-louis; Pestel-caron, Martine

2012-01-01

193

A Java applet for multiple linked visualization of protein structure and sequence.  

Science.gov (United States)

The amount of biological data available from experimental techniques is huge, and rapidly expanding. The ability to make sense of this vast amount of data requires that we make correlations between distinct biological disciplines using visualization techniques to highlight the critical information. This article describes the visualization techniques of dynamic data brushing, view context maintenance, fisheye sequence view, and a magic lens that have been developed to display protein structure and sequence information. PMID:15562987

Oldfield, Thomas J

2004-04-01

194

Using Sequence-Specific Chemical and Structural Properties of DNA to Predict Transcription Factor Binding Sites  

Digital Repository Infrastructure Vision for European Research (DRIVER)

An important step in understanding gene regulation is to identify the DNA binding sites recognized by each transcription factor (TF). Conventional approaches to prediction of TF binding sites involve the definition of consensus sequences or position-specific weight matrices and rely on statistical analysis of DNA sequences of known binding sites. Here, we present a method called SiteSleuth in which DNA structure prediction, computational chemistry, and machine learning are applied to develop ...

Bauer, Amy L.; Hlavacek, William S.; Unkefer, Pat J.; Mu, Fangping

2010-01-01

195

Assignment of segments of the bacteriorhodopsin sequence to positions in the structural map.  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Specific amino acid sequence segments have been assigned to locations in the structural map of bacteriorhodopsin using two-dimensional neutron diffraction data and a model building analysis. Models are constructed computationally by building specific regions of the amino acid sequence as alpha helices and then positioning the helices on axes indicated by the density map of Henderson and Unwin (Nature [Lond.]. 1975, 257:28-32). Neutron diffraction data were collected from samples of stacked, o...

Trewhella, J.; Anderson, S.; Fox, R.; Gogol, E.; Khan, S.; Engelman, D.; Zaccai, G.

1983-01-01

196

Structural evolution of the High Himalayan Gneiss sequence, Langtang Valley, Nepal  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Within the High Himalayan Crystalline Sequence (HHCS) of the Langtang Valley of central Nepal, four different lithotectonic units have been identified in the field. The structurally lowest unit, immediately in the hanging wall of the Main Central Thrust (MCT) records an inverted metamorphic sequence with kyanite-grade rocks overlain by rocks containing sillimanite. Pressure-temperature-deformation histories of the different units since Himalayan collision 50 Ma ago, in combination with geoche...

Reddy, Sm; Searle, Mp; Massey, Ja

1993-01-01

197

Comparative analysis of MR sequences to detect structural brain lesions in tuberous sclerosis  

Energy Technology Data Exchange (ETDEWEB)

Tuberous sclerosis (TS) is a neurocutaneous genetically inherited disease with variable penetrance characterized by dysplasias and hamartomas affecting multiple organs. MR is the imaging method of choice to demonstrate structural brain lesions in TS. To compare MR sequences and determine which is most useful for the demonstration of each type of brain lesion in TS patients. We reviewed MR scans of 18 TS patients for the presence of cortical tubers, white matter lesions (radial bands), subependymal nodules, and subependymal giant cell astrocytoma (SGCA) on the following sequences: (1) T1-weighted spin-echo (T1 SE) images before and after gadolinium (Gd) injection; (2) nonenhanced T1 SE sequence with an additional magnetization transfer contrast medium pulse on resonance (T1 SE/MTC); and (3) fluid-attenuated inversion recovery (FLAIR) sequence. Cortical tubers were found in significantly (P<0.05) larger numbers and more conspicuously in FLAIR and T1 SE/MTC sequences. The T1 SE/MTC sequence was far superior to other methods in detecting white matter lesions (P<0.01). There was no significant difference between the T1 SE/MTC and T1 SE (before and after Gd injection) sequences in the detection of subependymal nodules; FLAIR sequence showed less sensitivity than the others in identifying the nodules. T1 SE sequences after Gd injection demonstrated better the limits of the SGCA. We demonstrated the importance of appropriate MRI sequences for diagnosis of the most frequent brain lesions in TS. Our study reinforces the fact that each sequence has a particular application according to the type of TS lesion. Gd injection might be useful in detecting SGCA; however, the parameters of size and location are also important for a presumptive diagnosis of these tumors. (orig.)

Pinto Gama, Hugo Pereira; Campos Meirelles, Rogerio Goncalves de; Mendonca do Rego, Jose Iram [Santa Casa de Misericordia de Sao Paulo, Section of Radiology, Sao Paulo (Brazil); Rocha, Antonio Jose da; Silva, Carlos Jorge da [Santa Casa de Misericordia de Sao Paulo, Section of Radiology, Centro de Medicina Diagnostica Fleury, Sao Paulo (Brazil); Braga, Flavio Tulio [Federal University of Sao Paulo, Escola Paulista de Medicina, Section of Radiology, Centro de Medicina Diagnostica Fleury, Santa Casa de Misericordia de Sao Paulo, Department of Diagnostic Imaging, Sao Paulo (Brazil); Martins Maia, Antonio Carlos [Federal University of Sao Paulo, Escola Paulista de Medicina, Section of Radiology, Centro de Medicina Diagnostica Fleury, Department of Neurology, Sao Paulo (Brazil); Lederman, Henrique Manoel [Federal University of Sao Paulo, Escola Paulista de Medicina, Division of Diagnostic Imaging in Pediatrics, Department of Diagnostic Imaging, Sao Paulo (Brazil)

2006-02-01

198

The PETfold and PETcofold web servers for intra- and intermolecular structures of multiple RNA sequences  

Digital Repository Infrastructure Vision for European Research (DRIVER)

The function of non-coding RNA genes largely depends on their secondary structure and the interaction with other molecules. Thus, an accurate prediction of secondary structure and RNA–RNA interaction is essential for the understanding of biological roles and pathways associated with a specific RNA gene. We present web servers to analyze multiple RNA sequences for common RNA structure and for RNA interaction sites. The web servers are based on the recent PET (Probabilistic Evolutionary and T...

Seemann, Stefan E.; Menzel, Peter; Backofen, Rolf; Gorodkin, Jan

2011-01-01

199

Biological Sequence Analysis with Multivariate String Kernels.  

Science.gov (United States)

String kernel-based machine learning methods have yielded great success in practical tasks of structured/sequential data analysis. They often exhibit state-of-the-art performance on many practical tasks of sequence analysis such as biological sequence classification, remote homology detection, or protein superfamily and fold prediction. However, typical string kernel methods rely on analysis of discrete one-dimensional (1D) string data (e.g., DNA or amino acid sequences). In this work we address the multi-class biological sequence classification problems using multivariate representations in the form of sequences of features vectors (as in biological sequence profiles, or sequences of individual amino acid physico-chemical descriptors) and a class of multivariate string kernels that exploit these representations. On a number of protein sequence classification tasks proposed multivariate representations and kernels show significant 15-20\\% improvements compared to existing state-of-the-art sequence classification methods. PMID:23509193

Kuksa, Pavel P

2013-03-01

200

Biological sequence classification with multivariate string kernels.  

Science.gov (United States)

String kernel-based machine learning methods have yielded great success in practical tasks of structured/sequential data analysis. They often exhibit state-of-the-art performance on many practical tasks of sequence analysis such as biological sequence classification, remote homology detection, or protein superfamily and fold prediction. However, typical string kernel methods rely on the analysis of discrete 1D string data (e.g., DNA or amino acid sequences). In this paper, we address the multiclass biological sequence classification problems using multivariate representations in the form of sequences of features vectors (as in biological sequence profiles, or sequences of individual amino acid physicochemical descriptors) and a class of multivariate string kernels that exploit these representations. On three protein sequence classification tasks, the proposed multivariate representations and kernels show significant 15-20 percent improvements compared to existing state-of-the-art sequence classification methods. PMID:24384708

Kuksa, Pavel P

2013-01-01

 
 
 
 
201

Collecting, Comparing, and Computing Sequences: The Making of Margaret O. Dayhoff’s Atlas of Protein Sequence and Structure, 1954–1965  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Collecting, comparing, and computing molecular sequences are among the most prevalent practices in contemporary biological research. They represent a specific way of producing knowledge. This paper explores the historical development of these practices, focusing on the work of Margaret O. Dayhoff, Richard V. Eck, and Robert S. Ledley, who produced the first computer-based collection of protein sequences, published in book format in 1965 as the Atlas of Protein Sequence and Structure. While th...

Strasser, Bruno

2010-01-01

202

The influence of 1D, meso- and crystal structures on charge transport and recombination in solid-state dye-sensitized solar cells  

Digital Repository Infrastructure Vision for European Research (DRIVER)

We have prepared single crystalline SnO2 and ZnO nanowires and polycrystalline TiO2 nanotubes (1D networks) as well as nanoparticle-based films (3D networks) from the same materials to be used as photoanodes for solid-state dye-sensitized solar cells. In general, superior photovoltaic performance can be achieved from devices based on 3-dimensional networks, mostly due to their higher short circuit currents. To further characterize the fabricated devices, the electronic properties of the diffe...

Docampo, P.; Aruna, I.; Gunning, R.; Diefenbach, S.; Kirkpatrick, J.; Palumbiny, Cm; Sivaram, V.; Geaney, H.; Schmidt-mende, L.; Welland, Me; Snaith, Hj

2013-01-01

203

Online homology modelling as a means of bridging the sequence-structure gap.  

Science.gov (United States)

For even the best-studied species, there is a large gap in their representation in the protein databank (PDB) compared to within sequence databases. Typically, less than 2% of sequences are represented in the PDB. This is partly due to the considerable experimental challenge and manual inputs required to solve three dimensional structures by methods such as X-ray diffraction and multi-dimensional nuclear magnetic resonance (NMR) spectroscopy in comparison to high-throughput sequencing. This gap is made even wider by the high level of redundancy within the PDB and under-representation of some protein categories such as membrane-associated proteins which comprise approximately 25% of proteins encoded in genomes. A traditional route to closing the sequence-structure gap is offered by homology modelling whereby the sequence of a target protein is modelled on a template represented in the PDB using in silico energy minimisation approaches. More recently, online homology servers have become available which automatically generate models from proffered sequences. However, many online servers give little indication of the structural plausibility of the generated model. In this paper, the online homology server Geno3D will be described. This server uses similar software to that used in modelling structures during structure determination and thus generates data allowing determination of the structural plausibility of models. For illustration, modelling of a chemotaxis protein (CheY) from Pseudomononas entomophila L48 (accession YP_609298) on a template (PDB id. 1mvo), the phosphorylation domain of an outer membrane protein PhoP from Bacillus subtilis, will be described. PMID:22064508

Sheehan, David; O'Sullivan, Siobhán

2011-01-01

204

Comparative genomics beyond sequence-based alignments : RNA structures in the ENCODE regions  

DEFF Research Database (Denmark)

Recent computational scans for non-coding RNAs (ncRNAs) in multiple organisms have relied on existing multiple sequence alignments. However, as sequence similarity drops, a key signal of RNA structure--frequent compensating base changes--is increasingly likely to cause sequence-based alignment methods to misalign, or even refuse to align, homologous ncRNAs, consequently obscuring that structural signal. We have used CMfinder, a structure-oriented local alignment tool, to search the ENCODE regions of vertebrate multiple alignments. In agreement with other studies, we find a large number of potential RNA structures in the ENCODE regions. We report 6587 candidate regions with an estimated false-positive rate of 50%. More intriguingly, many of these candidates may be better represented by alignments taking the RNA secondary structure into account than those based on primary sequence alone, often quite dramatically. For example, approximately one-quarter of our predicted motifs show revisions in >50% of their aligned positions. Furthermore, our results are strongly complementary to those discovered by sequence-alignment-based approaches--84% of our candidates are not covered by Washietl et al., increasing the number of ncRNA candidates in the ENCODE region by 32%. In a group of 11 ncRNA candidates that were tested by RT-PCR, 10 were confirmed to be present as RNA transcripts in human tissue, and most show evidence of significant differential expression across tissues. Our results broadly suggest caution in any analysis relying on multiple sequence alignments in less well-conserved regions, clearly support growing appreciation for the biological significance of ncRNAs, and strongly support the argument for considering RNA structure directly in any searches for these elements.

Þórarinsson, Elfar; Yao, Zizhen

2008-01-01

205

Crystal structure of Z-DNA without an alternating purine-pyrimidine sequence.  

Digital Repository Infrastructure Vision for European Research (DRIVER)

In left-handed Z-DNA, consecutive nucleotides along the chain alternate in the syn and anti conformations. Purine residues form the syn conformation readily and up to now all Z-DNA crystal structures have sequences of alternating purines and pyrimidines. However, we find that d(C-G-A-T-C-G) with the cytosines brominated or methylated on C-5 crystallizes as Z-DNA. The structure reveals thymines in syn and adenines in anti conformations. This suggests that Z-DNA may occur in sequences other tha...

Wang, A. H.; Gessner, R. V.; Marel, G. A.; Boom, J. H.; Rich, A.

1985-01-01

206

Independent premotor encoding of the sequence and structure of birdsong in avian cortex.  

Science.gov (United States)

How the brain coordinates rapid sequences of learned behavior, such as human speech, remains a fundamental problem in neuroscience. Birdsong is a model of such behavior, which is learned and controlled by a neural circuit that spans avian cortex, basal ganglia, and thalamus. The songs of adult male zebra finches (Taeniopygia guttata), produced as rapid sequences of vocal gestures (syllables), are encoded by the cortical premotor region HVC (proper name). While the motor encoding of song within HVC has traditionally been viewed as unitary and distributed, we used an ablation technique to ask whether the sequence and structure of song are processed independently within HVC. Results revealed a functional topography across the medial-lateral axis of HVC. Bilateral ablation of medial HVC induced a positive disruption of song (increase in atypical syllable sequences), whereas bilateral ablation of lateral HVC induced a negative disruption (omission of individual syllables). Bilateral ablation of central HVC either had no effect on song or induced syllable omission, similar to lateral HVC ablation. We then investigated HVC connectivity and found parallel afferent and efferent pathways that transit medial and lateral HVC and converge at vocal motor cortex. In light of recent evidence that syntactic and lexical components of human speech are processed independently by neighboring regions of cortex (Menenti et al., 2012), our demonstration of anatomically distinct pathways that differentially process the sequence and structure of birdsong in parallel suggests that the vertebrate brain relies on a common approach to encode rapid sequences of vocal gestures. PMID:25505334

Basista, Mark J; Elliott, Kevin C; Wu, Wei; Hyson, Richard L; Bertram, Richard; Johnson, Frank

2014-12-10

207

Elemental mapping of multilayered structures: A method to reconstruct 2D chemical maps from a set of 1D line scans  

International Nuclear Information System (INIS)

We introduce a method to characterize the chemical distribution in nanostructures using STEM and affiliated spectroscopy techniques. The method is applicable to any nanostructure where the continuous layers of arbitrary geometry and dimensions can be identified. The key feature of the suggested approach is digital warping of the original STEM image into the quasi-1D image. The chemical profiles of high resolution and high signal-to-noise ratio can be extracted from the minimal set of the STEM spectroscopy data while minimizing material damage during acquisitions. Finally, the 2D chemical maps of the area of interest are reconstructed. -- Highlights: ? Layered nanostructure is mapped with applying minimal electron dose. ? Spectroscopic data are aligned and accumulated using digital warping of the STEM image. ? Chemical maps are reconstructed by reverse warping.

208

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

Digital Repository Infrastructure Vision for European Research (DRIVER)

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 ...

Lees Jonathan G; Janes Robert W

2008-01-01

209

Sequence divergence of Entamoeba histolytica tubulin is responsible for its altered tertiary structure  

International Nuclear Information System (INIS)

Atypical microtubular structures of the protozoan parasite Entamoeba histolytica (Eh) have been attributed to amino acid sequence divergence of Eh tubulin. To investigate if this sequence divergence leads to significant differences in the tertiary structure of the Eh ??-tubulin heterodimer, we have modeled ??-tubulin heterodimer of Eh based on the crystal structure of mammalian tubulin. The predicted 3D homology model exhibits an overall resemblance with the known crystal structure of mammalian tubulin except for the 16 residue long carboxy terminal region of Eh ?-tubulin. We propose that this C-terminal region may provide steric hindrance in the polymerization of Eh ??-tubulin for microtubule formation. Using docking studies, we have identified the binding sites for different microtubule specific drugs on Eh ?-tubulin. Our model provides a rational framework, both for understanding the contribution of Eh?-tubulin C-terminal region to ??-tubulin polymerization and design of new anti-protozoan drugs in order to control amoebiasis

210

Structural and Sequence Stratigraphic Analysis of the Onshore Nile Delta, Egypt.  

Science.gov (United States)

The Nile Delta is considered the earliest known delta in the world. It was already described by Herodotus in the 5th Century AC. Nowadays; the Nile Delta is an emerging giant gas province in the Middle East with proven gas reserves which have more than doubled in size in the last years. The Nile Delta basin contains a thick sedimentary sequence inferred to extend from Jurassic to recent time. Structural styles and depositional environments varied during this period. Facies architecture and sequence stratigraphy of the Nile Delta are resolved using seismic stratigraphy based on (2D seismic lines) including synthetic seismograms and tying in well log data. Synthetic seismograms were constructed using sonic and density logs. The combination of structural interpretation and sequence stratigraphy of the development of the basin was resolved. Seven chrono-stratigraphic boundaries have been identified and correlated on seismic and well log data. Several unconformity boundaries also identified on seismic lines range from angular to disconformity type. Furthermore, time structure maps, velocity maps, depth structure maps as well as Isopach maps were constructed using seismic lines and log data. Several structural features were identified: normal faults, growth faults, listric faults, secondary antithetic faults and large rotated fault blocks of manly Miocene age. In some cases minor rollover structures could be identified. Sedimentary features such as paleo-channels were distinctively recognized. Typical Sequence stratigraphic features such as incised valley, clinoforms, topsets, offlaps and onlaps are identified and traced on the seismic lines allowing a good insight into sequence stratigraphic history of the Nile Delta most especially in the Miocene to Pliocene clastic sedimentary succession.

Barakat, Moataz; Dominik, Wilhelm

2010-05-01

211

What Makes Reforms Likely? Timing and Sequencing of Structural Reforms in Latin America  

Digital Repository Infrastructure Vision for European Research (DRIVER)

The wave of structural reforms in Latin America and elsewhere has stimulated the development of a wide body of theoretical literature on the political economy of reform, i. e. , the study of the political constraints that condition the timing, speed and sequencing of reforms. This paper tests some of the hypotheses associated with these theoretical models, using a set of structural reform indicators for approximately twenty Latin American countries for the period 1985-1995. Although there is ...

Lora, Eduardo

2000-01-01

212

Telomeric DNA sequence and structure following de novo telomere synthesis in Euplotes crassus.  

Digital Repository Infrastructure Vision for European Research (DRIVER)

To learn more about the mechanism of de novo telomere synthesis, we have characterized the sequence and structure of newly synthesized telomeres from Euplotes crassus. E. crassus is a particularly useful organism for studying telomere synthesis because millions of telomeres are made in each cell at a well-defined time during the sexual stage of the life cycle. These newly synthesized telomeres are approximately 50 bp longer than mature macronuclear telomeres. We have investigated the structur...

Vermeesch, J. R.; Price, C. M.

1994-01-01

213

Genotyping by sequencing resolves shallow population structure to inform conservation of Chinook salmon (Oncorhynchus tshawytscha)  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Recent advances in population genomics have made it possible to detect previously unidentified structure, obtain more accurate estimates of demographic parameters, and explore adaptive divergence, potentially revolutionizing the way genetic data are used to manage wild populations. Here, we identified 10 944 single-nucleotide polymorphisms using restriction-site-associated DNA (RAD) sequencing to explore population structure, demography, and adaptive divergence in five populations of Chinook...

Larson, Wesley A.; Seeb, Lisa W.; Everett, Meredith V.; Waples, Ryan K.; Templin, William D.; Seeb, James E.

2014-01-01

214

Three-dimensional hydrogel structures as optical sensor arrays, for the detection of specific DNA sequences.  

Science.gov (United States)

The fabrication and characterization of surface-attached PEG-diacrylate hydrogel structures and their application as sensing platforms for the detection of specific target sequences are reported. Hydrogel structures were formed by a photopolymerization process, using substrate-bound Eosin Y molecules for the production of free radicals. We have demonstrated that this fabrication process allows for control over hydrogel growth down to the micrometer scale. Confocal imaging revealed relatively large pore structures for 25% (v/v) PEG-diacrylate hydrogels, which appear to lie in tightly packed layers. Our data suggest that these pore structures decrease in size for hydrogels with increasing levels of PEG-diacrylate. Surface coverage values calculated for hydrogels immobilized with 21-mer DNA probe sequences were significantly higher compared to those previously reported for 2- and 3-dimensional sensing platforms, on the order of 10(16)molecules cm(-2). Used as sensing platforms in DNA hybridization assays, a detection limit of 3.9 nM was achieved for hybridization reactions between 21-mer probe and target sequences. The ability of these hydrogel sensing platforms to discriminate between wild-type and mutant allele sequences was also demonstrated, down to target concentrations of 1-2 nM. A reduction in the hybridization time down to a period of 15 min was also achieved, while still maintaining confident results, demonstrating the potential for future integration of these sensing platforms within Lab-on-Chip or diagnostic devices. PMID:22079487

Kivlehan, Francine; Paolucci, Marta; Brennan, Des; Ragoussis, Ioannis; Galvin, Paul

2012-02-01

215

Multiple Sequence Alignments as Tools for Protein Structure and Function Prediction  

Directory of Open Access Journals (Sweden)

Full Text Available Multiple sequence alignments have much to offer to the understanding of protein structure, evolution and function. We are developing approaches to use this information in predicting protein-binding specificity, intra-protein and protein-protein interactions, and in reconstructing protein interaction networks.

Alfonso Valencia

2006-04-01

216

8-NH2-boldine, an antagonist of alpha1A and alpha1B adrenoceptors without affinity for the alpha1D subtype: structural requirements for aporphines at alpha1-adrenoceptor subtypes.  

Science.gov (United States)

Structure-activity analysis of 21 aporphine derivatives was performed by examining their affinities for cloned human alpha (1A), alpha (1B) and alpha (1D) adrenoceptors (AR) using membranes prepared from rat-1 fibroblasts stably expressing each alpha (1)-AR subtype. All the compounds tested competed for [ (125)I]-HEAT binding with steep and monophasic curves. The most interesting compound was 8-NH (2)-boldine, which retains the selective affinity for alpha(1A)-AR (pKi = 6.37 +/- 0.21) vs. alpha(1B)-AR (pKi = 5.53 +/- 0.11) exhibited by 1,2,9,10-tetraoxygenated aporphines, but shows low affinity for alpha(1D)-AR (pKi boldine for cloned alpha (1D)-AR and its potency as an inhibitor of noradrenaline-induced contraction or inositol phosphate accumulation in rat aorta, which confirms that a heterogeneous population of alpha (1)-AR mediates the adrenergic response in this vessel. PMID:16254819

Ivorra, M Dolores; Valiente, Miguel; Martínez, Sonia; Madrero, Yolanda; Noguera, M Antonia; Cassels, Bruce K; Sobarzo, Eduardo M; D'Ocon, Pilar

2005-10-01

217

WebScipio: An online tool for the determination of gene structures using protein sequences  

Directory of Open Access Journals (Sweden)

Full Text Available Abstract Background Obtaining the gene structure for a given protein encoding gene is an important step in many analyses. A software suited for this task should be readily accessible, accurate, easy to handle and should provide the user with a coherent representation of the most probable gene structure. It should be rigorous enough to optimise features on the level of single bases and at the same time flexible enough to allow for cross-species searches. Results WebScipio, a web interface to the Scipio software, allows a user to obtain the corresponding coding sequence structure of a here given a query protein sequence that belongs to an already assembled eukaryotic genome. The resulting gene structure is presented in various human readable formats like a schematic representation, and a detailed alignment of the query and the target sequence highlighting any discrepancies. WebScipio can also be used to identify and characterise the gene structures of homologs in related organisms. In addition, it offers a web service for integration with other programs. Conclusion WebScipio is a tool that allows users to get a high-quality gene structure prediction from a protein query. It offers more than 250 eukaryotic genomes that can be searched and produces predictions that are close to what can be achieved by manual annotation, for in-species and cross-species searches alike. WebScipio is freely accessible at http://www.webscipio.org.

Waack Stephan

2008-09-01

218

Role of sequence and structural polymorphism on the mechanical properties of amyloid fibrils.  

Science.gov (United States)

Amyloid fibrils playing a critical role in disease expression, have recently been found to exhibit the excellent mechanical properties such as elastic modulus in the order of 10 GPa, which is comparable to that of other mechanical proteins such as microtubule, actin filament, and spider silk. These remarkable mechanical properties of amyloid fibrils are correlated with their functional role in disease expression. This suggests the importance in understanding how these excellent mechanical properties are originated through self-assembly process that may depend on the amino acid sequence. However, the sequence-structure-property relationship of amyloid fibrils has not been fully understood yet. In this work, we characterize the mechanical properties of human islet amyloid polypeptide (hIAPP) fibrils with respect to their molecular structures as well as their amino acid sequence by using all-atom explicit water molecular dynamics (MD) simulation. The simulation result suggests that the remarkable bending rigidity of amyloid fibrils can be achieved through a specific self-aggregation pattern such as antiparallel stacking of ? strands (peptide chain). Moreover, we have shown that a single point mutation of hIAPP chain constituting a hIAPP fibril significantly affects the thermodynamic stability of hIAPP fibril formed by parallel stacking of peptide chain, and that a single point mutation results in a significant change in the bending rigidity of hIAPP fibrils formed by antiparallel stacking of ? strands. This clearly elucidates the role of amino acid sequence on not only the equilibrium conformations of amyloid fibrils but also their mechanical properties. Our study sheds light on sequence-structure-property relationships of amyloid fibrils, which suggests that the mechanical properties of amyloid fibrils are encoded in their sequence-dependent molecular architecture. PMID:24551113

Yoon, Gwonchan; Lee, Myeongsang; Kim, Jae In; Na, Sungsoo; Eom, Kilho

2014-01-01

219

Sequence and structural analysis of two designed proteins with 88% identity adopting different folds.  

Science.gov (United States)

Protein folding is a natural phenomenon by which a sequence of amino acids folds into a unique functional three-dimensional structure. Although the sequence code that governs folding remains a mystery, one can identify key inter-residue contacts responsible for a given topology. In nature, there are many pairs of proteins of a given length that share little or no sequence identity. Similarly, there are many proteins that share a common topology but lack significant evidence of homology. In order to tackle this problem, protein engineering studies have been used to determine the minimal number of amino acid residues that codes for a particular fold. In recent years, the coupling of theoretical models and experiments in the study of protein folding has resulted in providing some fruitful clues. He et al. have designed two proteins with 88% sequence identity, which adopt different folds and functions. In this work, we have systematically analysed these two proteins by performing pentapeptide search, secondary structure predictions, variation in inter-residue interactions and residue-residue pair preferences, surrounding hydrophobicity computations, conformational switching and energy computations. We conclude that the local secondary structural preference of the two designed proteins at the Nand C-terminal ends to adopt either coil or strand conformation may be a crucial factor in adopting the different folds. Early on during the process of folding, both proteins may choose different energetically favourable pathways to attain the different folds. PMID:20952437

Saravanan, K Mani; Balasubramanian, Harihar; Nallusamy, Saranya; Samuel, Selvaraj

2010-12-01

220

Genomic structure and sequence analysis of Lucilia cuprina HSP90 gene.  

Science.gov (United States)

The HSP90 family is one of the highly conserved chaperone families, varying between eubacteria to higher vertebrates. The HSP90 protein has been assigned different functions including thermal protection, but having major role in development. The present study is a detailed analysis of the structural characteristics of hsp90 gene (lchsp90) of sheep blowfly, Lucilia cuprina. The gene isolated by PCR revealed absence of intron. The nucleic acid and amino acid comparison revealed significant level of sequence similarity among species of various taxa. Significantly, the analysis of the amino acid sequence revealed that the HSP90 of L. cuprina belongs to hsp90? class. PMID:21366970

Janardhan Reddy, P V; Tiwari, P K

2011-01-01

 
 
 
 
221

SARA-Coffee web server, a tool for the computation of RNA sequence and structure multiple alignments.  

Science.gov (United States)

This article introduces the SARA-Coffee web server; a service allowing the online computation of 3D structure based multiple RNA sequence alignments. The server makes it possible to combine sequences with and without known 3D structures. Given a set of sequences SARA-Coffee outputs a multiple sequence alignment along with a reliability index for every sequence, column and aligned residue. SARA-Coffee combines SARA, a pairwise structural RNA aligner with the R-Coffee multiple RNA aligner in a way that has been shown to improve alignment accuracy over most sequence aligners when enough structural data is available. The server can be accessed from http://tcoffee.crg.cat/apps/tcoffee/do:saracoffee. PMID:24972831

Di Tommaso, Paolo; Bussotti, Giovanni; Kemena, Carsten; Capriotti, Emidio; Chatzou, Maria; Prieto, Pablo; Notredame, Cedric

2014-07-01

222

Multi-scale coding of genomic information: From DNA sequence to genome structure and function  

International Nuclear Information System (INIS)

Understanding how chromatin is spatially and dynamically organized in the nucleus of eukaryotic cells and how this affects genome functions is one of the main challenges of cell biology. Since the different orders of packaging in the hierarchical organization of DNA condition the accessibility of DNA sequence elements to trans-acting factors that control the transcription and replication processes, there is actually a wealth of structural and dynamical information to learn in the primary DNA sequence. In this review, we show that when using concepts, methodologies, numerical and experimental techniques coming from statistical mechanics and nonlinear physics combined with wavelet-based multi-scale signal processing, we are able to decipher the multi-scale sequence encoding of chromatin condensation-decondensation mechanisms that play a fundamental role in regulating many molecular processes involved in nuclear functions.

223

A structural study for the optimisation of functional motifs encoded in protein sequences  

Directory of Open Access Journals (Sweden)

Full Text Available Abstract Background A large number of PROSITE patterns select false positives and/or miss known true positives. It is possible that – at least in some cases – the weak specificity and/or sensitivity of a pattern is due to the fact that one, or maybe more, functional and/or structural key residues are not represented in the pattern. Multiple sequence alignments are commonly used to build functional sequence patterns. If residues structurally conserved in proteins sharing a function cannot be aligned in a multiple sequence alignment, they are likely to be missed in a standard pattern construction procedure. Results Here we present a new procedure aimed at improving the sensitivity and/ or specificity of poorly-performing patterns. The procedure can be summarised as follows: 1. residues structurally conserved in different proteins, that are true positives for a pattern, are identified by means of a computational technique and by visual inspection. 2. the sequence positions of the structurally conserved residues falling outside the pattern are used to build extended sequence patterns. 3. the extended patterns are optimised on the SWISS-PROT database for their sensitivity and specificity. The method was applied to eight PROSITE patterns. Whenever structurally conserved residues are found in the surface region close to the pattern (seven out of eight cases, the addition of information inferred from structural analysis is shown to improve pattern selectivity and in some cases selectivity and sensitivity as well. In some of the cases considered the procedure allowed the identification of functionally interesting residues, whose biological role is also discussed. Conclusion Our method can be applied to any type of functional motif or pattern (not only PROSITE ones which is not able to select all and only the true positive hits and for which at least two true positive structures are available. The computational technique for the identification of structurally conserved residues is already available on request and will be soon accessible on our web server. The procedure is intended for the use of pattern database curators and of scientists interested in a specific protein family for which no specific or selective patterns are yet available.

Helmer-Citterich Manuela

2004-04-01

224

Structure determination of salisomide and salisoflavan, two new secondary metabolites from Salsola imbricata, by 1D and 2D NMR spectroscopy.  

Science.gov (United States)

Chromatographic analysis of the alcoholic extract from Salsola imbricata yielded two new secondary metabolites, salisomide (1) and salisoflavan (2). Their structures were established with the help of spectroscopic techniques including COSY, HMQC and HMBC NMR experiments. PMID:19009575

Saleem, Muhammad; Akhter, Naseem; Shaiq Ali, Muhammad; Nazir, Mamona; Riaz, Naheed; Moazzam, Muhammad; Arshad, Muhammad; Jabbar, Abdul

2009-03-01

225

Parallel and antiparallel G-DNA structures from a complex telomeric sequence.  

Science.gov (United States)

We investigated the formation in vitro of higher order structures by a DNA oligomer containing the terminal motif TGTG3TGTGTGTG3, derived from the Saccharomyces telomeric consensus, in order to (a) understand why certain cations favor the formation of parallel-stranded (G4 and G8) G-DNA structures, while others favor foldback, antiparallel structures (G'2) and (b) probe the structures of G-DNAs formed by this telomeric sequence, which is more complex than its well-studied counterparts from the protozoans oxytricha and tetrahymena. We find that dramatic switches in the formation of G4 versus G'2 structures occur in solutions of not only the group Ia cations, Li(+)-Cs+, but also in those of the group IIa cations, Mg(2+)-Ba2+. These data and the temperature-dependent formation and destruction of the different structures lend support to the kinetic scheme of Sen and Gilbert (1990), by which rapidly forming G'2 structures accumulate in highly stabilizing potassium (and strontium) solutions at the expense of the thermodynamically more stable G4 structures. Both the G4 and the G'2 complexes formed by the Saccharomyces sequence show novel structural features. Protection and interference experiments with dimethyl sulfate and potassium permanganate reveal that the core of alternating thymines and guanines within the telomeric motif plays a critical role in the stabilization of the parallel G4 structure, but not of the antiparallel G'2. Very likely, in the G4 complex, this GT core forms a novel higher order arrangement of alternating G and T quartets, the latter possibly comparable to the U quartets described by Cheong and Moore (1992) in their NMR study of the higher order structure formed by rUG4U. PMID:8512932

Venczel, E A; Sen, D

1993-06-22

226

High-resolution NMR structure of an AT-rich DNA sequence  

International Nuclear Information System (INIS)

We have determined, by proton NMR and complete relaxation matrix methods, the high-resolution structure of a DNA oligonucleotide in solution with nine contiguous AT base pairs. The stretch of AT pairs, TAATTATAA.TTATAATTA, is imbedded in a 27-nucleotide stem-and-loop construct, which is stabilized by terminal GC base pairs and an extraordinarily stable DNA loop GAA (Hirao et al., 1994, Nucleic Acids Res.22, 576-582). The AT-rich sequence has three repeated TAA.TTA motifs, one in the reverse orientation. Comparison of the local conformations of the three motifs shows that the sequence context has a minor effect here: atomic RMSD between the three TAA.TTA fragments is 0.4-0.5 A, while each fragment is defined within the RMSD of 0.3-0.4 A. The AT-rich stem also contains a consensus sequence for the Pribnow box, TATAAT. The TpA, ApT, and TpT.ApA steps have characteristic local conformations, a combination of which determines a unique sequence-dependent pattern of minor groove width variation. All three TpA steps are locally bent in the direction compressing the major groove of DNA. These bends, however, compensate each other, because of their relative position in the sequence, so that the overall helical axis is essentially straight

227

Multifractal properties of the structure factor of a class of substitutional sequences  

International Nuclear Information System (INIS)

We show how to estimate the multifractal generating functional of the structure factor of a class of substitutional sequences. These sequences are sequences of two elements, a and b, and are generated by the repetitive application of the rules a??1(a,b) and b??2(a,b), with the ?'s consisting of strings of a's and b's. We restrict ourselves to the case in which ?1 and ?2 each contain R elements. This set includes the case of the Thue-Morse sequence. Subject to a technical assumption, we present a systematic approximation scheme for the multifractal generating functional, in which the lowest-order approximation is the generating functional of an R-scale Cantor set. As a by-product of our analysis, we demonstrate the existence of a discontinuity in the multifractal spectrum of the Thue-Morse sequence, and explain the origin of that discontinuity. We present explicit results for two examples, including the Thue-Morse case, and compare the results of our approximations for the Thue-Morse system with numerical simulations

228

Genomic structure and nucleotide sequence of the p55 gene of the puffer fish Fugu rubripes  

Energy Technology Data Exchange (ETDEWEB)

The p55 gene, which codes for a 55-kDa erythrocyte membrane protein, has been cloned and sequenced from the genome of the Japanese puffer fish Fugu rubripes (Fugu). This organism has the smallest recorded vertebrate genome and therefore provides an efficient way to sequence genes at the genomic level. The gene encoding p55 covers 5.5 kb from the beginning to the end of the coding sequence, four to six times smaller than the estimated size of the human gene, and is encoded by 12 exons. The structure of this gene has not been previously elucidated, but from this and other data we would predict a similar or identical structure in mammals. The predicted amino acid sequence of this gene in Fugu, coding for a polypeptide of 467 amino acids, is very similar to that of the human gene with the exception of the first two exons, which differ considerably. The predicted Fugu protein has a molecular weight (52.6 kDa compared with 52.3 kDa) and an isoelectric point very similar to those of human p55. In human, the p55 gene lies in the gene-dense Xq28 region, just 30 kb 3{prime} to the Factor VIII gene, and is estimated to cover 20-30 kb. Its 5{prime} end is associated with a CpG island, although there is no evidence that this is the case in Fugu. The small size of genes in Fugu and the high coding homology that they share with their mammalian equivalents, both in structure and sequence, make this compact vertebrate genome an ideal model for genomic studies. 23 refs., 3 figs.

Elgar, G.; Rattray, F.; Greystrong, J.; Brenner, S. [Univ. of Cambridge (United Kingdom)

1995-06-10

229

Using sequence-specific chemical and structural properties of DNA to predict transcription factor binding sites.  

Science.gov (United States)

An important step in understanding gene regulation is to identify the DNA binding sites recognized by each transcription factor (TF). Conventional approaches to prediction of TF binding sites involve the definition of consensus sequences or position-specific weight matrices and rely on statistical analysis of DNA sequences of known binding sites. Here, we present a method called SiteSleuth in which DNA structure prediction, computational chemistry, and machine learning are applied to develop models for TF binding sites. In this approach, binary classifiers are trained to discriminate between true and false binding sites based on the sequence-specific chemical and structural features of DNA. These features are determined via molecular dynamics calculations in which we consider each base in different local neighborhoods. For each of 54 TFs in Escherichia coli, for which at least five DNA binding sites are documented in RegulonDB, the TF binding sites and portions of the non-coding genome sequence are mapped to feature vectors and used in training. According to cross-validation analysis and a comparison of computational predictions against ChIP-chip data available for the TF Fis, SiteSleuth outperforms three conventional approaches: Match, MATRIX SEARCH, and the method of Berg and von Hippel. SiteSleuth also outperforms QPMEME, a method similar to SiteSleuth in that it involves a learning algorithm. The main advantage of SiteSleuth is a lower false positive rate. PMID:21124945

Bauer, Amy L; Hlavacek, William S; Unkefer, Pat J; Mu, Fangping

2010-01-01

230

MultiSeq: unifying sequence and structure data for evolutionary analysis  

Directory of Open Access Journals (Sweden)

Full Text Available Abstract Background Since the publication of the first draft of the human genome in 2000, bioinformatic data have been accumulating at an overwhelming pace. Currently, more than 3 million sequences and 35 thousand structures of proteins and nucleic acids are available in public databases. Finding correlations in and between these data to answer critical research questions is extremely challenging. This problem needs to be approached from several directions: information science to organize and search the data; information visualization to assist in recognizing correlations; mathematics to formulate statistical inferences; and biology to analyze chemical and physical properties in terms of sequence and structure changes. Results Here we present MultiSeq, a unified bioinformatics analysis environment that allows one to organize, display, align and analyze both sequence and structure data for proteins and nucleic acids. While special emphasis is placed on analyzing the data within the framework of evolutionary biology, the environment is also flexible enough to accommodate other usage patterns. The evolutionary approach is supported by the use of predefined metadata, adherence to standard ontological mappings, and the ability for the user to adjust these classifications using an electronic notebook. MultiSeq contains a new algorithm to generate complete evolutionary profiles that represent the topology of the molecular phylogenetic tree of a homologous group of distantly related proteins. The method, based on the multidimensional QR factorization of multiple sequence and structure alignments, removes redundancy from the alignments and orders the protein sequences by increasing linear dependence, resulting in the identification of a minimal basis set of sequences that spans the evolutionary space of the homologous group of proteins. Conclusion MultiSeq is a major extension of the Multiple Alignment tool that is provided as part of VMD, a structural visualization program for analyzing molecular dynamics simulations. Both are freely distributed by the NIH Resource for Macromolecular Modeling and Bioinformatics and MultiSeq is included with VMD starting with version 1.8.5. The MultiSeq website has details on how to download and use the software: http://www.scs.uiuc.edu/~schulten/multiseq/

Wright Dan

2006-08-01

231

FeatureMap3D - a tool to map protein features and sequence conservation onto homologous structures in the PDB  

DEFF Research Database (Denmark)

FeatureMap3D is a web-based tool that maps protein features onto 3D structures. The user provides sequences annotated with any feature of interest, such as post-translational modifications, protease cleavage sites or exonic structure and FeatureMap3D will then search the Protein Data Bank (PDB) for structures of homologous proteins. The results are displayed both as an annotated sequence alignment, where the user-provided annotations as well as the sequence conservation between the query and the target sequence are displayed, and also as a publication-quality image of the 3D protein structure with the selected features and sequence conservation enhanced. The results are also returned in a readily parsable text format as well as a PyMol (http://pymol.sourceforge.net/) script file, which allows the user to easily modify the protein structure image to suit a specific purpose. FeatureMap3D can also be used without sequence annotation, to evaluate the quality of the alignment of the input sequences to the most homologous structures in the PDB, through the sequence conservation colored 3D structure visualization tool. FeatureMap3D is available at: http://www.cbs.dtu.dk/services/FeatureMap3D/.

Wernersson, Rasmus; Rapacki, Kristoffer

2006-01-01

232

De novo prediction of structured RNAs from genomic sequences  

DEFF Research Database (Denmark)

Growing recognition of the numerous, diverse and important roles played by non-coding RNA in all organisms motivates better elucidation of these cellular components. Comparative genomics is a powerful tool for this task and is arguably preferable to any high-throughput experimental technology currently available, because evolutionary conservation highlights functionally important regions. Conserved secondary structure, rather than primary sequence, is the hallmark of many functionally important RNAs, because compensatory substitutions in base-paired regions preserve structure. Unfortunately, such substitutions also obscure sequence identity and confound alignment algorithms, which complicates analysis greatly. This paper surveys recent computational advances in this difficult arena, which have enabled genome-scale prediction of cross-species conserved RNA elements. These predictions suggest that a wealth of these elements indeed exist

Gorodkin, Jan; Hofacker, Ivo L.

2010-01-01

233

Comparative mapping of sequence-based and structure-based protein domains  

Directory of Open Access Journals (Sweden)

Full Text Available Abstract Background Protein domains have long been an ill-defined concept in biology. They are generally described as autonomous folding units with evolutionary and functional independence. Both structure-based and sequence-based domain definitions have been widely used. But whether these types of models alone can capture all essential features of domains is still an open question. Methods Here we provide insight on domain definitions through comparative mapping of two domain classification databases, one sequence-based (Pfam and the other structure-based (SCOP. A mapping score is defined to indicate the significance of the mapping, and the properties of the mapping matrices are studied. Results The mapping results show a general agreement between the two databases, as well as many interesting areas of disagreement. In the cases of disagreement, the functional and evolutionary characteristics of the domains are examined to determine which domain definition is biologically more informative.

Chandonia John-Marc

2005-03-01

234

Sequence and structural characterization of Trx-Grx type of monothiol glutaredoxins from Ashbya gossypii.  

Science.gov (United States)

Glutaredoxins are enzymatic antioxidants which are small, ubiquitous, glutathione dependent and essentially classified under thioredoxin-fold superfamily. Glutaredoxins are classified into two types: dithiol and monothiol. Monothiol glutaredoxins which carry the signature "CGFS" as a redox active motif is known for its role in oxidative stress, inside the cell. In the present analysis, the 138 amino acid long monothiol glutaredoxin, AgGRX1 from Ashbya gossypii was identified and has been used for the analysis. The multiple sequence alignment of the AgGRX1 protein sequence revealed the characteristic motif of typical monothiol glutaredoxin as observed in various other organisms. The proposed structure of the AgGRX1 protein was used to analyze signature folds related to the thioredoxin superfamily. Further, the study highlighted the structural features pertaining to the complex mechanism of glutathione docking and interacting residues. PMID:23515490

Yadav, Saurabh; Kumari, Pragati; Kushwaha, Hemant Ritturaj

2013-01-01

235

Structure and Dynamics of DNA-dendrimer complexation: Role of counterions, water and base pair sequence  

CERN Document Server

We study sequence dependent complexation between oligonucleotides (single strand DNA) and various generation ethylene diamine (EDA) cored poly amido amide (PAMAM) dendrimers through atomistic molecular dynamics simulations accompanied by free energy calculations and inherent structure determination. Simulations reveal formation of a stable complex and provide a detailed molecular level understanding of the structure and dynamics of such a complexation. The reaction free energy surface in the initial stage is found to be funnel-like with a significant barrier arising in the late stage due to the occurrence of misfolded states of DNA. Complexation shows surprisingly strong sensitivity to the ssDNA sequence which is found to arise from a competition between enthalpic versus entropic rigidity of ssDNA.

Maiti, P K; Maiti, Prabal K.; Bagchi, Biman

2006-01-01

236

Genomic Sequence Diversity and Population Structure of Saccharomyces cerevisiae Assessed by RAD-seq  

Digital Repository Infrastructure Vision for European Research (DRIVER)

The budding yeast Saccharomyces cerevisiae is important for human food production and as a model organism for biological research. The genetic diversity contained in the global population of yeast strains represents a valuable resource for a number of fields, including genetics, bioengineering, and studies of evolution and population structure. Here, we apply a multiplexed, reduced genome sequencing strategy (known as RAD-seq) to genotype a large collection of S. cerevisiae ...

Cromie, Gareth A.; Hyma, Katie E.; Ludlow, Catherine L.; Garmendia-torres, Cecilia; Gilbert, Teresa L.; May, Patrick; Huang, Angela A.; Dudley, Aime?e M.; Fay, Justin C.

2013-01-01

237

Possible sequence of structures in Nb4H3 hydride appearing at temperature change  

International Nuclear Information System (INIS)

The behaviour of the impurity subsystem in the interstitial solution is investigated in that particular case when impurity atoms in high temperature region can occupy lattice point in six interstitial sublattices and in low temperature region the superstructure is formed only in one sublattice. The results obtained are applied for describing possible sequence of structures appearing at temperature change in the single-phase hydride close by composition to Nb4H3

238

Predicting Function of Genes and Proteins from Sequence, Structure and Expression Data  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Functional genomics refers to the task of determining gene and protein function for whole genomes, and requires computational analysis of large amounts of biological data including DNA and protein sequences, protein structures and gene expressions. Machine learning methods provide a powerful tool to this end by first inducing general models from such data and already characterized genes or proteins and then by providing hypotheses on the functions of the remaining, uncharacterized cases. This...

Hvidsten, Torgeir R.

2004-01-01

239

A molecular phylogeny of Hypnales (Bryophyta) inferred from ITS2 sequence-structure data  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Abstract Background Hypnales comprise over 50% of all pleurocarpous mosses. They provide a young radiation complicating phylogenetic analyses. To resolve the hypnalean phylogeny, it is necessary to use a phylogenetic marker providing highly variable features to resolve species on the one hand and conserved features enabling a backbone analysis on the other. Therefore we used highly variable internal transcribed spacer 2 (ITS2) sequences and conserved secondary structures, as ...

Wolf Matthias; Merget Benjamin

2010-01-01

240

Sequencing and Analyses of All Known Human Rhinovirus Genomes Reveal Structure and Evolution  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Infection by human rhinovirus (HRV) is a major cause of upper and lower respiratory tract disease worldwide and displays considerable phenotypic variation. We examined diversity by completing the genome sequences for all known serotypes (n = 99). Superimposition of capsid crystal structure and optimal-energy RNA configurations established alignments and phylogeny. These revealed conserved motifs; clade-specific diversity, including a potential newly identified species (HRV-D); mutations in fi...

Palmenberg, Ann C.; Spiro, David; Kuzmickas, Ryan; Wang, Shiliang; Djikeng, Appolinaire; Rathe, Jennifer A.; Fraser-liggett, Claire M.; Liggett, Stephen B.

2009-01-01

 
 
 
 
241

MultiSeq: unifying sequence and structure data for evolutionary analysis  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Abstract Background Since the publication of the first draft of the human genome in 2000, bioinformatic data have been accumulating at an overwhelming pace. Currently, more than 3 million sequences and 35 thousand structures of proteins and nucleic acids are available in public databases. Finding correlations in and between these data to answer critical research questions is extremely challenging. This problem needs to be approached from several directions: information scienc...

Wright Dan; Eargle John; Roberts Elijah; Luthey-Schulten Zaida

2006-01-01

242

A human serotonin 1D receptor variant (5HT1D beta) encoded by an intronless gene on chromosome 6.  

Digital Repository Infrastructure Vision for European Research (DRIVER)

An intronless gene encoding a serotonin receptor (5HT1D beta) has been cloned and functionally expressed in mammalian fibroblast cultures. Based on the deduced amino acid sequence, the gene encodes a 390-amino acid protein displaying considerable homology, within putative transmembrane domains (approximately 75% identity) to the canine and human 5HT1D receptors. Membranes prepared from CHO cells stably expressing the receptor bound [3H]serotonin with high affinity (Kd 4 nM) and displayed a ph...

Demchyshyn, L.; Sunahara, R. K.; Miller, K.; Teitler, M.; Hoffman, B. J.; Kennedy, J. L.; Seeman, P.; Tol, H. H.; Niznik, H. B.

1992-01-01

243

Structural determination of kochiosides A-C, new steroidal glucosides from Kochia prostrata, by 1D and 2D NMR spectroscopy.  

Science.gov (United States)

Kochiosides A-C, three new steroidal glucosides, have been isolated from the ethyl acetate fraction of Kochia prostrata and their structures assigned from its (1)H and (13)C NMR spectra, DEPT and by 2D COSY, NOESY, HMQC and HMBC experiments. PMID:17640023

Imran, Muhammad; Ahmed, Ejaz; Malik, Abdul

2007-09-01

244

Structural studies of an arabinan from the stems of Ephedra sinica by methylation analysis and 1D and 2D NMR spectroscopy.  

Science.gov (United States)

Plant arabinan has important biological activity. In this study, a water-soluble arabinan (Mw?6.15kDa) isolated from the stems of Ephedra sinica was found to consist of (1?5)-Araƒ, (1?3,5)-Araƒ, T-Araƒ, (1?3)-Araƒ and (1?2,5)-Araƒ residues at proportions of 10:2:3:2:1. A tentative structure was proposed by methylation analysis, nuclear magnetic resonance (NMR) spectroscopy ((1)H NMR, (13)C NMR, DEPT-135, (1)H-(1)H COSY, HSQC, HMBC and ROESY) and literature. The structure proposed includes a branched (1?5)-?-Araf backbone where branching occurs at the O-2 and O-3 positions of the residues with 7.7% and 15.4% of the 1,5-linked ?-Araf substituted at the O-2 and O-3 positions. The presence of a branched structure was further observed by atomic force microscopy. This polymer was characterized as having a much longer linear (1?5)-?-Araf backbone as a repeating unit. In particular, the presence of ?-Araf?3)-?-Araf-(1?3)-?-Araf-(1? attached at the O-2 is a new finding. This study may facilitate a deeper understanding of structure-activity relationships of biological polysaccharides from the stems of E. sinica. PMID:25659720

Xia, Yong-Gang; Liang, Jun; Yang, Bing-You; Wang, Qiu-Hong; Kuang, Hai-Xue

2015-05-01

245

Revised Mimivirus major capsid protein sequence reveals intron-containing gene structure and extra domain  

Directory of Open Access Journals (Sweden)

Full Text Available Abstract Background Acanthamoebae polyphaga Mimivirus (APM is the largest known dsDNA virus. The viral particle has a nearly icosahedral structure with an internal capsid shell surrounded with a dense layer of fibrils. A Capsid protein sequence, D13L, was deduced from the APM L425 coding gene and was shown to be the most abundant protein found within the viral particle. However this protein remained poorly characterised until now. A revised protein sequence deposited in a database suggested an additional N-terminal stretch of 142 amino acids missing from the original deduced sequence. This result led us to investigate the L425 gene structure and the biochemical properties of the complete APM major Capsid protein. Results This study describes the full length 3430 bp Capsid coding gene and characterises the 593 amino acids long corresponding Capsid protein 1. The recombinant full length protein allowed the production of a specific monoclonal antibody able to detect the Capsid protein 1 within the viral particle. This protein appeared to be post-translationnally modified by glycosylation and phosphorylation. We proposed a secondary structure prediction of APM Capsid protein 1 compared to the Capsid protein structure of Paramecium Bursaria Chlorella Virus 1, another member of the Nucleo-Cytoplasmic Large DNA virus family. Conclusion The characterisation of the full length L425 Capsid coding gene of Acanthamoebae polyphaga Mimivirus provides new insights into the structure of the main Capsid protein. The production of a full length recombinant protein will be useful for further structural studies.

Suzan-Monti Marie

2009-05-01

246

Vector quantization kernels for the classification of protein sequences and structures.  

Science.gov (United States)

We propose a new kernel-based method for the classification of protein sequences and structures. We first represent each protein as a set of time series data using several structural, physicochemical, and predicted properties such as a sequence of consecutive dihedral angles, hydrophobicity indices, or predictions of disordered regions. A kernel function is then computed for pairs of proteins, exploiting the principles of vector quantization and subsequently used with support vector machines for protein classification. Although our method requires a significant pre-processing step, it is fast in the training and prediction stages owing to the linear complexity of kernel computation with the length of protein sequences. We evaluate our approach on two protein classification tasks involving the prediction of SCOP structural classes and catalytic activity according to the Gene Ontology. We provide evidence that the method is competitive when compared to string kernels, and useful for a range of protein classification tasks. Furthermore, the applicability of our approach extends beyond computational biology to any classification of time series data. PMID:24297558

Clark, Wyatt T; Radivojac, Predrag

2014-01-01

247

Fifty Years Later: The Sequence, Structure and Function of Lacewing Cross-beta Silk  

Energy Technology Data Exchange (ETDEWEB)

Classic studies of protein structure in the 1950s and 1960s demonstrated that green lacewing egg stalk silk possesses a rare native cross-beta sheet conformation. We have identified and sequenced the silk genes expressed by adult females of a green lacewing species. The two encoded silk proteins are 109 and 67 kDa in size and rich in serine, glycine and alanine. Over 70% of each protein sequence consists of highly repetitive regions with 16-residue periodicity. The repetitive sequences can be fitted to an elegant cross-beta sheet structural model with protein chains folded into regular 8-residue long beta strands. This model is supported by wide-angle X-ray scattering data and tensile testing from both our work and the original papers. We suggest that the silk proteins assemble into stacked beta sheet crystallites bound together by a network of cystine cross-links. This hierarchical structure gives the lacewing silk high lateral stiffness nearly threefold that of silkworm silk, enabling the egg stalks to effectively suspend eggs and protect them from predators.

Weisman, Sarah; Okada, Shoko; Mudie, Stephen T.; Huson, Mickey G.; Trueman, Holly E.; Sriskantha, Alagacone; Haritos, Victoria S.; Sutherland, Tara D.; (CSIRO/MSE); (CSIRO)

2009-12-01

248

Interpolation on a fixed interval discrete-valued sequence with random structure  

Directory of Open Access Journals (Sweden)

Full Text Available Discrete-valued sequences with random structure are widely used to describe electronic systems that operate under a priori uncertainty. An optimal interpolation algorithm on a fixed interval discrete-valued sequence with random structure have been obtained considering the Markov property of an extended process, which includes the value of a discrete-type sequence and its structure. This algorithm is recursive, and describes the evolution of the joint interpolation probability of the extended process in reverse time. Analysis of the optimal interpolation algorithm on a fixed interval was implemented by the example of decoding of a convolutional code by means of statistical computer modeling. For this example interpolation algorithm reduces the bit error probability to 3-4 times compared with the algorithm of filtering due to the fact that it takes into account all the received observations. The increase of statistical dependence between input symbols leads to a decrease in bit error rate in filtration and interpolation algorithms.

D. H. Ilyasova

2011-06-01

249

Fast computational methods for predicting protein structure from primary amino acid sequence  

Science.gov (United States)

The present invention provides a method utilizing primary amino acid sequence of a protein, energy minimization, molecular dynamics and protein vibrational modes to predict three-dimensional structure of a protein. The present invention also determines possible intermediates in the protein folding pathway. The present invention has important applications to the design of novel drugs as well as protein engineering. The present invention predicts the three-dimensional structure of a protein independent of size of the protein, overcoming a significant limitation in the prior art.

Agarwal, Pratul Kumar (Knoxville, TN)

2011-07-19

250

Population genetic structure and historical demography of Oratosquilla oratoria revealed by mitochondrial DNA sequences.  

Science.gov (United States)

Genetic diversity, population genetic structure and molecular phylogeographic pattern of mantis shrimp Oratosquilla oratoria in Bohai Sea and South China Sea were analyzed by mitochondrial DNA sequences. Nucleotide and haplotype diversities were 0.00409-0.00669 and 0.894-0.953 respectively. Neighbor-Joining phylogenetic tree clustered two distinct lineages. Both phylogenetic tree and median-joining network showed the consistent genetic structure corresponding to geographical distribution. Mismatch distributions, negative neutral test and "star-like" network supported a sudden population expansion event. And the time was estimated about 44000 and 50000 years ago. PMID:23516902

Zhang, D; Ding, Ge; Ge, B; Zhang, H; Tang, B

2012-12-01

251

Pattern matching through Chaos Game Representation: bridging numerical and discrete data structures for biological sequence analysis  

Directory of Open Access Journals (Sweden)

Full Text Available Abstract Background Chaos Game Representation (CGR is an iterated function that bijectively maps discrete sequences into a continuous domain. As a result, discrete sequences can be object of statistical and topological analyses otherwise reserved to numerical systems. Characteristically, CGR coordinates of substrings sharing an L-long suffix will be located within 2-L distance of each other. In the two decades since its original proposal, CGR has been generalized beyond its original focus on genomic sequences and has been successfully applied to a wide range of problems in bioinformatics. This report explores the possibility that it can be further extended to approach algorithms that rely on discrete, graph-based representations. Results The exploratory analysis described here consisted of selecting foundational string problems and refactoring them using CGR-based algorithms. We found that CGR can take the role of suffix trees and emulate sophisticated string algorithms, efficiently solving exact and approximate string matching problems such as finding all palindromes and tandem repeats, and matching with mismatches. The common feature of these problems is that they use longest common extension (LCE queries as subtasks of their procedures, which we show to have a constant time solution with CGR. Additionally, we show that CGR can be used as a rolling hash function within the Rabin-Karp algorithm. Conclusions The analysis of biological sequences relies on algorithmic foundations facing mounting challenges, both logistic (performance and analytical (lack of unifying mathematical framework. CGR is found to provide the latter and to promise the former: graph-based data structures for sequence analysis operations are entailed by numerical-based data structures produced by CGR maps, providing a unifying analytical framework for a diversity of pattern matching problems.

Vinga Susana

2012-05-01

252

Posttranslational modifications and subcellular localization signals: indicators of sequence regions without inherent 3D structure?  

Science.gov (United States)

Given the huge number of sequences of otherwise uncharacterized protein sequences, computer-aided prediction of posttranslational modifications (PTMs) and translocation signals from amino acid sequence becomes a necessity. We have contributed to this multi-faceted, worldwide effort with the development of predictors for GPI lipid anchor sites, for N-terminal N-myristoylation sites, for farnesyl and geranylgeranyl anchor attachment as well as for the PTS1 peroxisomal signal. Although the substrate protein sequence signals for various PTMs or translocation systems vary dramatically, we found that their principal architecture is similar for all the cases studied. Typically, a small stretch of the amino acid residues is buried in the catalytic cleft of the protein-modifying enzyme (or the binding site of the transporter). This piece most intensely interacts with the enzyme and its sequence variability is most restricted. This stretch is surrounded by linker segments that connect the part bound by the enzyme with the rest of the substrate protein. These residues are, as a trend, small with a flexible backbone and polar. Due to the mechanistic requirements of binding to the enzyme, we suggest that most PTM sites are necessarily embedded into intrinsically disordered regions (except for cases of autocatalytic PTMs, PTMs executed in the unfolded state or non-enzymatic PTMs) and this issue requires consideration in structural studies of proteins with complex architecture. Surprisingly, some proteins carry sequence signals for posttranslational modification or translocation that remain hidden in the normal biological context but can become fully functional in certain conditions. PMID:17430201

Eisenhaber, Birgit; Eisenhaber, Frank

2007-04-01

253

Correlations Between Amino Acids at Different Sites in Local Sequences of Protein Fragments with Given Structural Patterns  

Science.gov (United States)

Ample evidence suggests that the local structures of peptide fragments in native proteins are to some extent encoded by their local sequences. Detecting such local correlations is important but it is still an open question what would be the most appropriate method. This is partly because conventional sequence analyses treat amino acid preferences at each site of a protein sequence independently, while it is often the inter-site interactions that bring about local sequence-structure correlations. Here a new scheme is introduced to capture the correlation between amino acid preferences at different sites for different local structure types. A library of nine-residue fragments is constructed, and the fragments are divided into clusters based on their local structures. For each local structure cluster or type, chi-square tests are used to identify correlated preferences of amino acid combinations at pairs of sites. A score function is constructed including both the single site amino acid preferences and the dual-site amino acid combination preferences, which can be used to identify whether a sequence fragment would have a strong tendency to form a particular local structure in native proteins. The results show that, given a local structure pattern, dual-site amino acid combinations contain different information from single site amino acid preferences. Representative examples show that many of the statistically identified correlations agree with previously-proposed heuristic rules about local sequence-structure correlations, or are consistent with physical-chemical interactions required to stabilize particular local structures. Results also show that such dual-site correlations in the score function significantly improves the Z-score matching a sequence fragment to its native local structure relative to non-native local structures, and certain local structure types are highly predictable from the local sequence alone if inter-site correlations are considered.

Lu, Wen; Liu, Hai-yan

2007-02-01

254

Genomic sequence diversity and population structure of Saccharomyces cerevisiae assessed by RAD-seq.  

Science.gov (United States)

The budding yeast Saccharomyces cerevisiae is important for human food production and as a model organism for biological research. The genetic diversity contained in the global population of yeast strains represents a valuable resource for a number of fields, including genetics, bioengineering, and studies of evolution and population structure. Here, we apply a multiplexed, reduced genome sequencing strategy (restriction site-associated sequencing or RAD-seq) to genotype a large collection of S. cerevisiae strains isolated from a wide range of geographical locations and environmental niches. The method permits the sequencing of the same 1% of all genomes, producing a multiple sequence alignment of 116,880 bases across 262 strains. We find diversity among these strains is principally organized by geography, with European, North American, Asian, and African/S. E. Asian populations defining the major axes of genetic variation. At a finer scale, small groups of strains from cacao, olives, and sake are defined by unique variants not present in other strains. One population, containing strains from a variety of fermentations, exhibits high levels of heterozygosity and a mixture of alleles from European and Asian populations, indicating an admixed origin for this group. We propose a model of geographic differentiation followed by human-associated admixture, primarily between European and Asian populations and more recently between European and North American populations. The large collection of genotyped yeast strains characterized here will provide a useful resource for the broad community of yeast researchers. PMID:24122055

Cromie, Gareth A; Hyma, Katie E; Ludlow, Catherine L; Garmendia-Torres, Cecilia; Gilbert, Teresa L; May, Patrick; Huang, Angela A; Dudley, Aimée M; Fay, Justin C

2013-12-01

255

Assembling Metal Ions Induced Cyanide-Bridged Heterometallic 1D and Ion-Pair Complexes: Synthesis, Crystal Structures and Magnetic Properties  

Energy Technology Data Exchange (ETDEWEB)

We obtained a heterobimetallic one-dimensional cyanide-bridged Mn(II)-Ni(II) complex and an Co(III)-Ni(II) ion-pair complex with [Ni(CN){sub 4}]{sup 2-} as building block and M(II)-phenanthroline (M = Mn, Co) compounds as assembling segment. The different structural types of complexes 1 and 2 indicate that the property of the metal ions the assembling segment contained have obvious influence on the structure of the cyanide-bridged complex. Investigation over the magnetic properties of complex 1 reveals an overall weak antiferromagnetic coupling between the adjacent Mn(II) ions bridged by the antiferromagnetic [-NC-Ni-CN-] unit. Among of all the molecular magnetism systems, for the well known reasons, cyanide-containing complexes have been widely employed as bridges to assemble homo/hetero-metallic molecular magnetic materials by using the cyanide bridge transferring magnetic coupling between the neighboring paramagnetic ions, in whichsome showed interesting magnetic properties, such as high-Tc magnets, spin crossover materials, single-molecule magnets (SMMs) and single-chain magnets (SCMs)

Kong, Lingqian [Liaocheng Univ., Liaocheng (China); Zhao, Zengdian; Chen, Kexun; Wang, Ping; Zhang, Daopeng [Shandong Univ. of Technology, Zibo (China)

2013-07-15

256

Evolutionary conservation of sequence and secondary structures inCRISPR repeats  

Energy Technology Data Exchange (ETDEWEB)

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

Kunin, Victor; Sorek, Rotem; Hugenholtz, Philip

2006-09-01

257

Structure and Active Stie Residues of Pg1D, an N-Acetyltransferase from the Bacillosamine Synthetic Pathway Required for N-Glycan Synthesis in Campylobacter jejuni  

Energy Technology Data Exchange (ETDEWEB)

Campylobacter jejuni is highly unusual among bacteria in forming N-linked glycoproteins. The heptasaccharide produced by its pgl system is attached to protein Asn through its terminal 2, 4-diacetamido-2, 4,6-trideoxy-d-Glc (QuiNAc4NAc or N, N'-diacetylbacillosamine) moiety. The crucial, last part of this sugar's synthesis is the acetylation of UDP-2-acetamido-4-amino-2, 4,6-trideoxy-d-Glc by the enzyme PglD, with acetyl-CoA as a cosubstrate. We have determined the crystal structures of PglD in CoA-bound and unbound forms, refined to 1.8 and 1.75 Angstroms resolution, respectively. PglD is a trimer of subunits each comprised of two domains, an N-terminal {alpha}/{beta}-domain and a C-terminal left-handed {beta}-helix. Few structural differences accompany CoA binding, except in the C-terminal region following the {beta}-helix (residues 189-195), which adopts an extended structure in the unbound form and folds to extend the {beta}-helix upon binding CoA. Computational molecular docking suggests a different mode of nucleotide-sugar binding with respect to the acetyl-CoA donor, with the molecules arranged in an 'L-shape', compared with the 'in-line' orientation in related enzymes. Modeling indicates that the oxyanion intermediate would be stabilized by the NH group of Gly143', with His125' the most likely residue to function as a general base, removing H+ from the amino group prior to nucleophilic attack at the carbonyl carbon of acetyl-CoA. Site-specific mutations of active site residues confirmed the importance of His125', Glu124', and Asn118. We conclude that Asn118 exerts its function by stabilizing the intricate hydrogen bonding network within the active site and that Glu124' may function to increase the pKa of the putative general base, His125'.

Rangarajan,E.; Ruane, K.; Sulea, T.; Watson, D.; Proteau, A.; Leclerc, S.; Cygler, M.; Matte, A.; Young, N.

2008-01-01

258

Genetic structure of Florida green turtle rookeries as indicated by mitochondrial DNA control region sequences  

Science.gov (United States)

Green turtle (Chelonia mydas) nesting has increased dramatically in Florida over the past two decades, ranking the Florida nesting aggregation among the largest in the Greater Caribbean region. Individual beaches that comprise several hundred kilometers of Florida’s east coast and Keys support tens to thousands of nests annually. These beaches encompass natural to highly developed habitats, and the degree of demographic partitioning among rookeries was previously unresolved. We characterized the genetic structure of ten Florida rookeries from Cape Canaveral to the Dry Tortugas through analysis of 817 base pair mitochondrial DNA (mtDNA) control region sequences from 485 nesting turtles. Two common haplotypes, CM-A1.1 and CM-A3.1, accounted for 87 % of samples, and the haplotype frequencies were strongly partitioned by latitude along Florida’s Atlantic coast. Most genetic structure occurred between rookeries on either side of an apparent genetic break in the vicinity of the St. Lucie Inlet that separates Hutchinson Island and Jupiter Island, representing the finest scale at which mtDNA structure has been documented in marine turtle rookeries. Florida and Caribbean scale analyses of population structure support recognition of at least two management units: central eastern Florida and southern Florida. More thorough sampling and deeper sequencing are necessary to better characterize connectivity among Florida green turtle rookeries as well as between the Florida nesting aggregation and others in the Greater Caribbean region.

Shamblin, Brian M.; Bagley, Dean A.; Ehrhart, Llewellyn M.; Desjardin, Nicole A.; Martin, R. Erik; Hart, Kristen M.; Naro-Maciel, Eugenia; Rusenko, Kirt; Stiner, John C.; Sobel, Debra; Johnson, Chris; Wilmers, Thomas; Wright, Laura J.; Nairn, Campbell J.

2014-01-01

259

Comparative Analysis of Structure and Sequences of Oryza sativa Superoxide Dismutase  

Directory of Open Access Journals (Sweden)

Full Text Available One of the major classes of antioxidant enzymes, which protect the cellular and subcellular components against harmful reactive oxygen species (ROS, is superoxide dismutase (SOD. SODs play pivotal role in scavenging highly reactive free oxygen radicals and protecting cells from toxic effects. In Oryza sativa three types of SODs are available based on their metal content viz. Cu-Zn SOD, Mn SOD and Fe SOD. In the present study attempts were made to critically assess the structure and phylogenetic relationship among Oryza sativa SODs. The sequence similarity search using local BLAST shows that Mn SODs and Fe SODs have greater degree of similarity compared with that of Cu-Zn SODs. The multiple alignment reveals that seven amino acids were found to be totally conserved. The secondary structure shows that Mn SODs and Fe SODs have similar helixes, sheets, turns and coils compared with that of Cu-Zn SODs. The comparative analysis also displayed greater resemblance in primary, secondary and tertiary structures of Fe SODs and Mn SODs. Comparison between the structure and sequence analysis reveals that Mn SOD and Fe SOD are found to be closely related whereas Cu-Zn SOD evolves independently.

Aiyar Balasubramanian

2012-09-01

260

Combining classifiers for improved classification of proteins from sequence or structure  

Directory of Open Access Journals (Sweden)

Full Text Available Abstract Background Predicting a protein's structural or functional class from its amino acid sequence or structure is a fundamental problem in computational biology. Recently, there has been considerable interest in using discriminative learning algorithms, in particular support vector machines (SVMs, for classification of proteins. However, because sufficiently many positive examples are required to train such classifiers, all SVM-based methods are hampered by limited coverage. Results In this study, we develop a hybrid machine learning approach for classifying proteins, and we apply the method to the problem of assigning proteins to structural categories based on their sequences or their 3D structures. The method combines a full-coverage but lower accuracy nearest neighbor method with higher accuracy but reduced coverage multiclass SVMs to produce a full coverage classifier with overall improved accuracy. The hybrid approach is based on the simple idea of "punting" from one method to another using a learned threshold. Conclusion In cross-validated experiments on the SCOP hierarchy, the hybrid methods consistently outperform the individual component methods at all levels of coverage. Code and data sets are available at http://noble.gs.washington.edu/proj/sabretooth

Leslie Christina S

2008-09-01

 
 
 
 
261

Identification of microRNA precursors with new sequence-structure features  

Directory of Open Access Journals (Sweden)

Full Text Available MicroRNAs are an important subclass of non-coding RNAs (ncRNA, and serve as main players into RNA interference (RNAi. Mature microRNA derived from stem-loop structure called precursor. Identification of precursor microRNA (pre-miRNA is essential step to target microRNA in whole genome. The present work proposed 25 novel local features for identifying stem- loop structure of pre-miRNAs, which captures characteristics on both the sequence and structure. Firstly, we pulled the stem of hairpins and aligned the bases in bulges and internal loops used ‘?’, and then counted 24 base-pairs (‘AA’, ‘AU’, …, ‘?G’, except ‘??’ in pulled stem (formalized by length of pulled stem as features vector of Support Vector Machine (SVM. Performances of three classifiers with our features and different kernels trained on human data were all superior to Triplet-SVM-classifier’s in po- sitive and negative testing data sets. Moreover, we achieved higher prediction accuracy through combining 7 global sequence-structure. The result indicates validity of novel local features.

Ying-Jie Zhao

2009-12-01

262

Synthesis and crystal structure of 1D polyoxometalate-based composite compound, [{Gd(NMP) 6}(PMo 12O 40)] n (NMP= N-methyl-2-pyrrolidone)  

Science.gov (United States)

A novel compound, [{Gd(NMP) 6}(PMo 12O 40)] n, has been synthesized and characterized by IR, and UV spectroscopy, and single crystal X-ray structural analysis. It forms an unprecedented one-dimensional zigzag chain built from alternating polyanions and cationic units through Mo-O t-Gd-O t-Mo links in the crystal. In the compound, Gd 3+ is eight-coordinated with a bicapped trigonal prism geometry environment of oxygen atoms. The results of the single crystal X-ray diffraction analyses and IR are agreement and both show the metal cation units are coordinately bonded to the Keggin cluster. The UV spectrum of the title compound suggests that the compound is entirely dissociated in dilute solution.

Niu, Jing-Yang; Wei, Mei-Lin; Wang, Jing-Ping; Dang, Dong-Bin

2003-07-01

263

Three new 2-D metal-organic frameworks containing 1-D metal chains bridged by N-benzesulfonyl-glutamic acid: Syntheses, crystal structures and properties  

International Nuclear Information System (INIS)

To explore the possibility of obtaining the metal-organic frameworks (MOFs) bearing the bsgluH2 ligand, two new Cd(II) and one Cu(II) coordination polymers, [Cd(bsglu)(bipy)] n (1), [Cd(bsglu).(H2O)] n (2) and {[Cu2(bsglu)2(bipy)2].4H2O} n (3) (bsglu=N-benzesulfonyl-glutamic acid bianion, bipy=2,2'-bipyridine) were synthesized and characterized by IR, elemental analysis and X-ray diffraction analysis. Compounds 1 and 3 exhibit one-dimensional coordination chains, which are further connected to form two-dimensional supramolecular networks through ?-? aromatic stacking interactions in a novel zipper-like way. Compound 2 presents a two-dimensional layer structure. To the best of our knowledge, 2 is the first two-dimensional complex formed from transition metal and bsgluH2 ligand. Interestingly, the bsglu anion exhibits remarkable versatile coordination modes in these complexes. Fluorescent analyses show that 1 exhibits photoluminescence in the solid state. Magnetic measurements for 3 revealed that the Cu(II) chain exhibit a weak antiferromagnetic behavior with a J value of -0.606 cm-1. - Graphical abstract: Three new complexes, [Cd(bsglu)(bipy)] n (1), [Cd(bsglu).(H2O)] n (2) and {[Cu2(bsglu)2(bipy)2].4H2O} n (3), constructed from Cd(II) or Cu(II) salt with N-benzd from Cd(II) or Cu(II) salt with N-benzesulfonyl-glutamic acid were synthesized and characterized. Compounds 1 and 3 exhibit one-dimensional chains which are further connected to form two-dimensional supramolecular networks through ?-? aromatic stacking interactions in a novel zipper-like way. Compound 2 presents a two-dimensional layer structure. Luminescence of 1 and magnetic properties of 3 are also investigated

264

Synthesis, structure and luminescence of novel 1D chain coordination polymers [Ln(isophth)(Hisophth)(H 2O) 4·4H 2O] n (Ln=Sm, Dy)  

Science.gov (United States)

In this paper, we place emphasis on the structure and luminescent properties of novel [Ln(isophth)(Hisophth)(H 2O) 4·4H 2O] n (Ln=Sm, Dy; H 2isophth=isophthalic acid) coordination polymers, which was characterized by elementary analysis, IR, UV, and especially the X-rays single-crystal diffraction. The two complexes are an isostructural series which crystallize in the monoclinic system with P21/ c space group. The samarium compound, isomorphous with dysprosium one were determined as a one-dimensional (1D) chain-like configuration by one of the two isophthalic acid ligands in bidentate chelated pattern, while the other isophthalic acid ligands only offer a single carboxylic acid group to bond which is abbreviated as 'Hisophth'. Fluorescence excitation and emission spectra show that the isophthalic acid is suitable for the sensitization on the luminescence of both Sm(III) and Dy(III).

Yan, Bing; Bai, Yingying; Chen, Zhenxia

2005-05-01

265

Loss of quaternary structure is associated with rapid sequence divergence in the OSBS family.  

Science.gov (United States)

The rate of protein evolution is determined by a combination of selective pressure on protein function and biophysical constraints on protein folding and structure. Determining the relative contributions of these properties is an unsolved problem in molecular evolution with broad implications for protein engineering and function prediction. As a case study, we examined the structural divergence of the rapidly evolving o-succinylbenzoate synthase (OSBS) family, which catalyzes a step in menaquinone synthesis in diverse microorganisms and plants. On average, the OSBS family is much more divergent than other protein families from the same set of species, with the most divergent family members sharing <15% sequence identity. Comparing 11 representative structures revealed that loss of quaternary structure and large deletions or insertions are associated with the family's rapid evolution. Neither of these properties has been investigated in previous studies to identify factors that affect the rate of protein evolution. Intriguingly, one subfamily retained a multimeric quaternary structure and has small insertions and deletions compared with related enzymes that catalyze diverse reactions. Many proteins in this subfamily catalyze both OSBS and N-succinylamino acid racemization (NSAR). Retention of ancestral structural characteristics in the NSAR/OSBS subfamily suggests that the rate of protein evolution is not proportional to the capacity to evolve new protein functions. Instead, structural features that are conserved among proteins with diverse functions might contribute to the evolution of new functions. PMID:24872444

Odokonyero, Denis; Sakai, Ayano; Patskovsky, Yury; Malashkevich, Vladimir N; Fedorov, Alexander A; Bonanno, Jeffrey B; Fedorov, Elena V; Toro, Rafael; Agarwal, Rakhi; Wang, Chenxi; Ozerova, Nicole D S; Yew, Wen Shan; Sauder, J Michael; Swaminathan, Subramanyam; Burley, Stephen K; Almo, Steven C; Glasner, Margaret E

2014-06-10

266

Loss of quaternary structure is associated with rapid sequence divergence in the OSBS family  

Science.gov (United States)

The rate of protein evolution is determined by a combination of selective pressure on protein function and biophysical constraints on protein folding and structure. Determining the relative contributions of these properties is an unsolved problem in molecular evolution with broad implications for protein engineering and function prediction. As a case study, we examined the structural divergence of the rapidly evolving o-succinylbenzoate synthase (OSBS) family, which catalyzes a step in menaquinone synthesis in diverse microorganisms and plants. On average, the OSBS family is much more divergent than other protein families from the same set of species, with the most divergent family members sharing <15% sequence identity. Comparing 11 representative structures revealed that loss of quaternary structure and large deletions or insertions are associated with the family’s rapid evolution. Neither of these properties has been investigated in previous studies to identify factors that affect the rate of protein evolution. Intriguingly, one subfamily retained a multimeric quaternary structure and has small insertions and deletions compared with related enzymes that catalyze diverse reactions. Many proteins in this subfamily catalyze both OSBS and N-succinylamino acid racemization (NSAR). Retention of ancestral structural characteristics in the NSAR/OSBS subfamily suggests that the rate of protein evolution is not proportional to the capacity to evolve new protein functions. Instead, structural features that are conserved among proteins with diverse functions might contribute to the evolution of new functions. PMID:24872444

Odokonyero, Denis; Sakai, Ayano; Patskovsky, Yury; Malashkevich, Vladimir N.; Fedorov, Alexander A.; Bonanno, Jeffrey B.; Fedorov, Elena V.; Toro, Rafael; Agarwal, Rakhi; Wang, Chenxi; Ozerova, Nicole D. S.; Yew, Wen Shan; Sauder, J. Michael; Swaminathan, Subramanyam; Burley, Stephen K.; Almo, Steven C.; Glasner, Margaret E.

2014-01-01

267

Moments of the Spin Structure Functions g_1^p and g_1^d for 0.05 < Q^2 < 3.0 GeV^2  

CERN Document Server

The spin structure functions g_1 for the proton and the deuteron have been measured over a wide kinematic range in x and Q2 using 1.6 and 5.7 GeV longitudinally polarized electrons incident upon polarized NH_3 and ND_3 targets at Jefferson Lab. Scattered electrons were detected in the CEBAF Large Acceptance Spectrometer, for 0.05 < Q^2 < 5 GeV^2 and W < 3 GeV. The first moments of g_1 for the proton and deuteron are presented -- both have a negative slope at low Q2, as predicted by the extended Gerasimov-Drell-Hearn sum rule. The first result for the generalized forward spin polarizability of the proton gamma_0^p is also reported, and shows evidence of scaling above Q^2 = 1.5 GeV^2. Although the first moments of g_1 are consistent with Chiral Perturbation Theory (ChPT) calculations up to approximately Q^2 = 0.06 GeV^2, a significant discrepancy is observed between the \\gamma_0^p data and ChPT for gamma_0^p,even at the lowest Q2.

Prok, Y; Burkert, V D; Deur, A; Dharmawardane, K V; Dodge, G E; Griffioen, K A; Kuhn, S E; Minehart, R; Adams, G; Amaryan, M J; Anghinolfi, M; Asryan, G; Audit, G; Avakian, H; Bagdasaryan, H; Baillie, N; Ball, J P; Baltzell, N A; Barrow, S; Battaglieri, M; Beard, K; Bedlinskiy, I; Bektasoglu, M; Bellis, M; Benmouna, N; Berman, B L; Biselli, A S; Blaszczyk, L; Boiarinov, S; Bonner, B E; Bouchigny, S; Bradford, R; Branford, D; Briscoe, W J; Brooks, W K; Bültmann, S; Butuceanu, C; Calarco, J R; Careccia, S L; Carman, D S; Casey, L; Cazes, A; Chen, S; Cheng, L; Cole, P L; Collins, P; Coltharp, P; Cords, D; Corvisiero, P; Crabb, D; Credé, V; Cummings, J P; Dale, D; Dashyan, N; De Masi, R; De Vita, R; De Sanctis, E; Degtyarenko, P V; Denizli, H; Dennis, L; Dhuga, K S; Dickson, R; Djalali, C; Doughty, D; Dugger, M; Dytman, S; Dzyubak, O P; Egiyan, H; Egiyan, K S; El Fassi, L; Elouadrhiri, L; Eugenio, P; Fatemi, R; Fedotov, G; Feldman, G; Fersh, R G; Feuerbach, R J; Forest, T A; Fradi, A; Funsten, H; Garçon, M; Gavalian, G; Gevorgyan, N; Gilfoyle, G P; Giovanetti, K L; Girod, F X; Goetz, J T; Golovatch, E; Gothe, R W; Guidal, M; Guillo, M; Guler, N; Guo, L; Gyurjyan, V; Hadjidakis, C; Hafidi, K; Hakobyan, H; Hanretty, C; Hardie, J; Hassall, N; Heddle, D; Hersman, F W; Hicks, K; Hleiqawi, I; Holtrop, M; Huertas, M; Hyde-Wright, C E; Ilieva, Y; Ireland, D G; Ishkhanov, B S; Isupov, E L; Ito, M M; Jenkins, D; Jo, H S; Johnstone, J R; Joo, K; Jüngst, H G; Kalantarians, N; Keith, C D; Kellie, J D; Khandaker, M; Kim, K Y; Kim, K; Kim, W; Klein, A; Klein, F J; Klusman, M; Kossov, M; Krahn, Z; Kramer, L H; Kubarovski, V; Kühn, J; Kuleshov, S V; Kuznetsov, V; Lachniet, J; Laget, J M; Langheinrich, J; Lawrence, D; Ji Li; Lima, A C S; Livingston, K; Lu, H Y; Lukashin, K; MacCormick, M; Marchand, C; Markov, N; Mattione, P; McAleer, S; McKinnon, B; McNabb, J W C; Mecking, B A; Mestayer, M D; Meyer, C A; Mibe, T; Mikhailov, K; Mirazita, M; Miskimen, R; Mokeev, V; Morand, L; Moreno, B; Moriya, K; Morrow, S A; Moteabbed, M; Müller, J; Munevar, E; Mutchler, G S; Nadel-Turonski, P; Nasseripour, R; Niccolai, S; Niculescu, G; Niculescu, I; Niczyporuk, B B; Niroula, M R; Niyazov, R A; Nozar, M; O'Rielly, G V; Osipenko, M; Ostrovidov, A I; Park, K; Pasyuk, E; Paterson, C; Anefalos Pereira, S; Philips, S A; Pierce, J; Pivnyuk, N; Pocanic, D; Pogorelko, O; Popa, I; Pozdniakov, S; Preedom, B M; Price, J W; Procureur, S; Protopopescu, D; Qin, L M; Raue, B A; Riccardi, G; Ricco, G; Ripani, M; Ritchie, B G; Rosner, G; Rossi, P; Rowntree, D; Rubin, P D; Sabati, F; Salamanca, J; Salgado, C; Santoro, e J P; Sapunenko, V; Schumacher, R A; Seely, M L; Serov, V S; Sharabyan, Yu G; Sharov, D; Shaw, J; Shvedunov, N V; Skabelin, A V; Smith, E S; Smith, L C; Sober, D I; Sokhan, D; Stavinsky, A; Stepanyan, S S; Stepanyan, S; Stokes, B E; Stoler, P; Strakovsky, I I; Strauch, S; Suleiman, R; Taiuti, M; Tedeschi, D J; Tkabladze, A; Tkachenko, S; Todor, L; Ungaro, M; Vineyard, M F; Vlassov, A V; Watts, D P; Weinstein, L B; Weygand, D P; Williams, M; Wolin, E; Wood, M H; Yegneswaran, A; Yun, J; Zana, L; Zhang, J; Zhao, B; Zhao, Z W

2008-01-01

268

Moments of the Spin Structure Functions g1p and g1d for 0.05 < Q2 < 3.0 GeV2  

Energy Technology Data Exchange (ETDEWEB)

The spin structure functions $g_1$ for the proton and the deuteron have been measured over a wide kinematic range in $x$ and \\Q2 using 1.6 and 5.7 GeV longitudinally polarized electrons incident upon polarized NH$_3$ and ND$_3$ targets at Jefferson Lab. Scattered electrons were detected in the CEBAF Large Acceptance Spectrometer, for $0.05 < Q^2 < 5 $\\ GeV$^2$ and $W < 3$ GeV. The first moments of $g_1$ for the proton and deuteron are presented -- both have a negative slope at low \\Q2, as predicted by the extended Gerasimov-Drell-Hearn sum rule. The first result for the generalized forward spin polarizability of the proton $\\gamma_0^p$ is also reported, and shows evidence of scaling above $Q^2$ = 1.5 GeV$^2$. Although the first moments of $g_1$ are consistent with Chiral Perturbation Theory (\\ChPT) calculations up to approximately $Q^2 = 0.06$ GeV$^2$, a significant discrepancy is observed between the $\\gamma_0^p$ data and \\ChPT\\ for $\\gamma_0^p$,even at the lowest \\Q2.

Prok, Yelena; Bosted, Peter; Burkert, Volker; Deur, Alexandre; Dharmawardane, Kahanawita; Dodge, Gail; Griffioen, Keith; Kuhn, Sebastian; Minehart, Ralph; Adams, Gary; Amaryan, Moscov; Amaryan, Moskov; Anghinolfi, Marco; Asryan, G.; Audit, Gerard; Avagyan, Harutyun; Baghdasaryan, Hovhannes; Baillie, Nathan; Ball, J.P.; Ball, Jacques; Baltzell, Nathan; Barrow, Steve; Battaglieri, Marco; Beard, Kevin; Bedlinskiy, Ivan; Bektasoglu, Mehmet; Bellis, Matthew; Benmouna, Nawal; Berman, Barry; Biselli, Angela; Blaszczyk, Lukasz; Boyarinov, Sergey; Bonner, Billy; Bouchigny, Sylvain; Bradford, Robert; Branford, Derek; Briscoe, William; Brooks, William; Bultmann, S.; Bueltmann, Stephen; Butuceanu, Cornel; Calarco, John; Careccia, Sharon; Carman, Daniel; Casey, Liam; Cazes, Antoine; Chen, Shifeng; Cheng, Lu; Cole, Philip; Collins, Patrick; Coltharp, Philip; Cords, Dieter; Corvisiero, Pietro; Crabb, Donald; Crede, Volker; Cummings, John; Dale, Daniel; Dashyan, Natalya; De Masi, Rita; De Vita, Raffaella; De Sanctis, Enzo; Degtiarenko, Pavel; Denizli, Haluk; Dennis, Lawrence; Dhuga, Kalvir; Dickson, Richard; Djalali, Chaden; Doughty, David; Dugger, Michael; Dytman, Steven; Dzyubak, Oleksandr; Egiyan, Hovanes; Egiyan, Kim; Elfassi, Lamiaa; Elouadrhiri, Latifa; Eugenio, Paul; Fatemi, Renee; Fedotov, Gleb; Feldman, Gerald; Fersch, Robert; Feuerbach, Robert; Forest, Tony; Fradi, Ahmed; Funsten, Herbert; Garcon, Michel; Gavalian, Gagik; Gevorgyan, Nerses; Gilfoyle, Gerard; Giovanetti, Kevin; Girod, Francois-Xavier; Goetz, John; Golovach, Evgeny; Gothe, Ralf; Guidal, Michel; Guillo, Matthieu; Guler, Nevzat; Guo, Lei; Gyurjyan, Vardan; Hadjidakis, Cynthia; Hafidi, Kawtar; Hakobyan, Hayk; Hanretty, Charles; Hardie, John; Hassall, Neil; Heddle, David; Hersman, F.; Hicks, Kenneth; Hleiqawi, Ishaq; Holtrop, Maurik; Huertas, Marco; Hyde, Charles; Ilieva, Yordanka; Ireland, David; Ishkhanov, Boris; Isupov, Evgeny; Ito, Mark; Jenkins, David; Jo, Hyon-Suk; Johnstone, John; Joo, Kyungseon; Juengst, Henry; Kalantarians, Narbe; Keith, Christopher; Kellie, James; Khandaker, Mahbubul; Kim, Kui; Kim, Kyungmo; Kim, Wooyoung; Klein, Andreas; Klein, Franz; Klusman, Mike; Kossov, Mikhail; Krahn, Zebulun; Kramer, Laird; Kubarovsky, Valery; Kuhn, Joachim; Kuleshov, Sergey; Kuznetsov, Viacheslav; Lachniet, Jeff; Laget, Jean; Langheinrich, Jorn; Lawrence, Dave; Lima, Ana; Livingston, Kenneth; Lu, Haiyun; Lukashin, K.; MacCormick, Marion; Marchand, Claude; Markov, Nikolai; Mattione, Paul; McAleer, Simeon; McKinnon, Bryan; McNabb, John; Mecking, Bernhard; Mestayer, Mac; Meyer, Curtis; Mibe, Tsutomu; Mikhaylov, Konstantin; Mirazita, Marco; Miskimen, Rory; Mokeev, Viktor; Morand, Ludyvine; Moreno, Brahim; Moriya, Kei; Morrow, Steven; Moteabbed, Maryam; Mueller, James; Munevar Espitia, Edwin; Mutchler, Gordon; Nadel-Turonski, Pawel; Nasseripour, Rakhsha; Niccolai, Silvia; Niculescu, Gabriel; Niculescu, Maria-Ioana; Niczyporuk, Bogdan; Niroula, Megh; Niyazov, Rustam; Nozar, Mina; O' Rielly, Grant; Osipenko, Mikhail; Ostrovidov, Alexander; Park, Kijun; Pasyuk, Evgueni; Paterson, Craig; Anefalos Pereira, S.; Philips, Sasha; Pierce, J.; Pivnyuk, Nikolay; Pocanic, Dinko; Pogorelko, Oleg; Popa, Iulian; Pozdnyakov, Sergey; Preedom, Barry; Price, John; Procureur, Sebastien; Protopopescu, Dan; Qin, Liming; Raue, Brian; Riccardi, Gregory; Ricco, Giovanni; Ripani, Marco; Ritchie, Barry; Rosner, Guenther; Rossi, Patrizia; Rowntree, David; Rubin, Philip; Sabatie, Franck; Salamanca, Julian; Salgado, Carlos; Santoro, Joseph; Sapunenko, Vladimir; Schumacher, Reinhard; Seely, Mikell; Serov, Vladimir; Sharabian, Youri; Sharov, Dmitri; Shaw, Jeffrey; Shvedunov, Nikolay; Skabelin, Alexander; Smith, Elton; Smith, Lee; Sober, Daniel; Sokhan, Daria; Stavinskiy, Aleksey; Stepanyan, Samuel; Stepanyan, Stepan; Stokes, Burnham; Stoler, Paul; Strakovski, Igor; Strauch, Steffen; Suleiman, Riad; Taiuti, Mauro; Tedeschi, David; Tkabladze, Avtandil; Tkachenko, Svyatoslav; Todor, Luminita; Ungaro, Maurizio; V

2009-02-01

269

1D and 2D end-to-end azide-bridged cobalt(II) complexes: syntheses, crystal structures, and magnetic properties.  

Science.gov (United States)

Two new polynuclear azido-bridged Co(II) compounds with formulas catena-[Co(mu1,3-N3)(N3)(py)2(H2O)]n (1) and [Co(mu1,3-N3)2(4-acpy)2]n (2) (py=pyridine, 4-acpy=4-acetylpyridine) have been structurally and magnetically characterized. Compound 1 crystallizes in the orthorhombic system Fddd space group and consists of a single end-to-end azido-bridged chain with the Co(II) atoms in a CoN5O slightly distorted octahedron. Compound 2 crystallizes in the monoclinic system P21/a space group and shows 2D sheets built up through end-to-end azido bridges with the Co(II) atoms in a CoN6 environment. The magnetic properties of 1 and 2 are reported. In the high-temperature region, the plots of chiM or chiMT vs T for 1 and 2 compounds can be fitted by using the Curie-Weiss law, and the best-fit values are -69.1 and -22.6 K, respectively. For 2 magnetic ordering and spontaneous magnetization is achieved below Tc=25 K. PMID:17461574

Abu-Youssef, Morsy A M; Mautner, Franz A; Vicente, Ramon

2007-05-28

270

Sequence composition and environment effects on residue fluctuations in protein structures  

CERN Document Server

The spectrum and scale of fluctuations in protein structures affect the range of cell phenomena, including stability of protein structures or their fragments, allosteric transitions and energy transfer. The study presents a statistical-thermodynamic analysis of relationship between the sequence composition and the distribution of residue fluctuations in protein-protein complexes. A one-node-per residue elastic network model accounting for the nonhomogeneous protein mass distribution and the inter-atomic interactions through the renormalized inter-residue potential is developed. Two factors, a protein mass distribution and a residue environment, were found to determine the scale of residue fluctuations. Surface residues undergo larger fluctuations than core residues, showing agreement with experimental observations. Ranking residues over the normalized scale of fluctuations yields a distinct classification of amino acids into three groups. The structural instability in proteins possibly relates to the high con...

Ruvinsky, Anatoly M

2009-01-01

271

Main: 1D6R [RPSD[Archive  

Full Text Available 1D6R ?? Soybean Glycine max (L.) Merrill Bowman-Birk Type Proteinase Inhibitor Precursor Glyci ... Warkentin, G.Wenzl, P.Flecker Crystal Structure Of Cancer ... Chemopreventive Bowman-Birk Inhibitor In Ternary C ...

272

Complete sequence of the genome of the human isolate of Andes virus CHI-7913: comparative sequence and protein structure analysis  

Digital Repository Infrastructure Vision for European Research (DRIVER)

We report here the complete genomic sequence of the Chilean human isolate of Andes virus CHI-7913. The S, M, and L genome segment sequences of this isolate are 1,802, 3,641 and 6,466 bases in length, with an overall GC content of 38.7%. These genome segments code for a nucleocapsid protein of 428 amino acids, a glycoprotein precursor protein of 1,138 amino acids and a RNA-dependent RNA polymerase of 2,152 amino acids. In addition, the genome also has other ORFs coding for putative proteins of...

Tischler, Nicole D.; JORGE FERNÁNDEZ; ILSE MÜLLER; RODRIGO MARTÍNEZ; HÉCTOR GALENO; ELIECER VILLAGRA; JUDITH MORA; EUGENIO RAMÍREZ; MARIO ROSEMBLATT; Valenzuela, Pablo D. T.

2003-01-01

273

Protein fold recognition using sequence-derived predictions.  

Science.gov (United States)

In protein fold recognition, one assigns a probe amino acid sequence of unknown structure to one of a library of target 3D structures. Correct assignment depends on effective scoring of the probe sequence for its compatibility with each of the target structures. Here we show that, in addition to the amino acid sequence of the probe, sequence-derived properties of the probe sequence (such as the predicted secondary structure) are useful in fold assignment. The additional measure of compatibility between probe and target is the level of agreement between the predicted secondary structure of the probe and the known secondary structure of the target fold. That is, we recommend a sequence-structure compatibility function that combines previously developed compatibility functions (such as the 3D-1D scores of Bowie et al. [1991] or sequence-sequence replacement tables) with the predicted secondary structure of the probe sequence. The effect on fold assignment of adding predicted secondary structure is evaluated here by using a benchmark set of proteins (Fischer et al., 1996a). The 3D structures of the probe sequences of the benchmark are actually known, but are ignored by our method. The results show that the inclusion of the predicted secondary structure improves fold assignment by about 25%. The results also show that, if the true secondary structure of the probe were known, correct fold assignment would increase by an additional 8-32%. We conclude that incorporating sequence-derived predictions significantly improves assignment of sequences to known 3D folds. Finally, we apply the new method to assign folds to sequences in the SWISSPROT database; six fold assignments are given that are not detectable by standard sequence-sequence comparison methods; for two of these, the fold is known from X-ray crystallography and the fold assignment is correct. PMID:8732766

Fischer, D; Eisenberg, D

1996-05-01

274

Statistical significance of hierarchical multi-body potentials based on Delaunay tessellation and their application in sequence-structure alignment.  

Science.gov (United States)

Statistical potentials based on pairwise interactions between C alpha atoms are commonly used in protein threading/fold-recognition attempts. Inclusion of higher order interaction is a possible means of improving the specificity of these potentials. Delaunay tessellation of the C alpha-atom representation of protein structure has been suggested as a means of defining multi-body interactions. A large number of parameters are required to define all four-body interactions of 20 amino acid types (20(4) = 160,000). Assuming that residue order within a four-body contact is irrelevant reduces this to a manageable 8,855 parameters, using a nonredundant dataset of 608 protein structures. Three lines of evidence support the significance and utility of the four-body potential for sequence-structure matching. First, compared to the four-body model, all lower-order interaction models (three-body, two-body, one-body) are found statistically inadequate to explain the frequency distribution of residue contacts. Second, coherent patterns of interaction are seen in a graphic presentation of the four-body potential. Many patterns have plausible biophysical explanations and are consistent across sets of residues sharing certain properties (e.g., size, hydrophobicity, or charge). Third, the utility of the multi-body potential is tested on a test set of 12 same-length pairs of proteins of known structure for two protocols: Sequence-recognizes-structure, where a query sequence is threaded (without gap) through the native and a non-native structure; and structure-recognizes-sequence, where a query structure is threaded by its native and another non-native sequence. Using cross-validated training, protein sequences correctly recognized their native structure in all 24 cases. Conversely, structures recognized the native sequence in 23 of 24 cases. Further, the score differences between correct and decoy structures increased significantly using the three- or four-body potential compared to potentials of lower order. PMID:9232648

Munson, P J; Singh, R K

1997-07-01

275

Predicting Secondary Structures, Contact Numbers, and Residue-wise Contact Orders of Native Protein Structure from Amino Acid Sequence by Critical Random Networks  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Prediction of one-dimensional protein structures such as secondary structures and contact numbers is useful for the three-dimensional structure prediction and important for the understanding of sequence-structure relationship. Here we present a new machine-learning method, critical random networks (CRNs), for predicting one-dimensional structures, and apply it, with position-specific scoring matrices, to the prediction of secondary structures (SS), contact numbers (CN), and ...

Kinjo, Akira R.; Nishikawa, Ken

2005-01-01

276

PAIRpred: partner-specific prediction of interacting residues from sequence and structure.  

Science.gov (United States)

We present a novel partner-specific protein-protein interaction site prediction method called PAIRpred. Unlike most existing machine learning binding site prediction methods, PAIRpred uses information from both proteins in a protein complex to predict pairs of interacting residues from the two proteins. PAIRpred captures sequence and structure information about residue pairs through pairwise kernels that are used for training a support vector machine classifier. As a result, PAIRpred presents a more detailed model of protein binding, and offers state of the art accuracy in predicting binding sites at the protein level as well as inter-protein residue contacts at the complex level. We demonstrate PAIRpred's performance on Docking Benchmark 4.0 and recent CAPRI targets. We present a detailed performance analysis outlining the contribution of different sequence and structure features, together with a comparison to a variety of existing interface prediction techniques. We have also studied the impact of binding-associated conformational change on prediction accuracy and found PAIRpred to be more robust to such structural changes than existing schemes. As an illustration of the potential applications of PAIRpred, we provide a case study in which PAIRpred is used to analyze the nature and specificity of the interface in the interaction of human ISG15 protein with NS1 protein from influenza A virus. Python code for PAIRpred is available at http://combi.cs.colostate.edu/supplements/pairpred/. PMID:24243399

Minhas, Fayyaz ul Amir Afsar; Geiss, Brian J; Ben-Hur, Asa

2014-07-01

277

The post-Triassic sedimentary cover of Tunisia: Seismic sequences and structure  

Science.gov (United States)

A series of geological cross sections based on data from the new geological map of Tunisia coupled with stratigraphic and structural studies indicate that a folded, post-Triassic sedimentary cover was separated from the basement by a decollement zone located in Triassic evaporitic deposits. Four depositional basins were formed during the Triassic and Liassic in an extensional regime, on a presumably thinned continental crust. Geological fieldwork, studies of metamorphic grade and gravimetric and magnetic surveys indicate that their depocentres shifted with time from basin to basin, finally resulting in today's Tellian and Tunisian troughs to the north, Gafsa Trough to the west of Gabes and the Tuniso-Libyan Trough to the east. Subsidence in the latter trough commenced at the end of the Cretaceous and is still continuing today. There are four well-defined seismic stratigraphic sequences comprising Mesozoic and Cenozoic sedimentary rocks, each with distinctive lithoseismic characteristics. We display the distribution and structure of these seismic sequences in a series of cross sections. In addition, we note that the regional tectonic style of Tunisia has been greatly influenced by a conjugate strike-slip fault system. The role of wrench faulting has been well-documented in the Kasserine and other areas by detailed structural studies.

Bobier, C.; Viguier, C.; Chaari, A.; Chine, A.

1991-09-01

278

Magnetic exchange interactions in 1D and 2D cuprates  

International Nuclear Information System (INIS)

In many copper oxygen networks, especially for Cu-O bond angles close to 90 , ferromagnetic (FM) interactions play an important role in addition to the well known superexchange J ? t2/U. We present a systematic study of the electronic structure and the exchange integrals J for different types of 1D and 2D spin 1/2 cuprates: edge shared (Li2CuO2) and corner shared (A2CuO3 [A=Sr,Ca]) single-chains, double-chains (SrCuO2), and planar (CaCuO2, Sr2CuO2Cl2, R2CuO4 [R=La,Nd,Sm]) arrangements. Based on full potential LDA and LDA+U band structure calculations and subsequent tight-binding (TB) models we estimate sign and magnitude of the most relevant J's. We compare the results of total energy calculations with those of TB models from one-band and multi-band approaches. The FM contributions can be estimated from the difference between the TB and the total energy results. We investigate the effect of the inter-plaquette geometry (edge shared vs. corner shared CuO2 plaquettes) and the intra-plaquette geometry under pressure on the coupling strength. In excellent agreement with various experiments, our calculations result in; (i) dominant FM nearest neighbor (NN) coupling J1?-17 meV in Li2CuO2, (ii) strongly enhanced AFM NN J1?180 meV for the 1D corner shared chains compared to (iii) Jared chains compared to (iii) J1?110..150 meV for the 2D compounds where we observe a sequence of J's (with respect to the cations) in agreement with the experimental data. (orig.)

279

Chromatic dispersion compensation and coherent Direct-Sequence OCDMA operation on a single super structured FBG  

Digital Repository Infrastructure Vision for European Research (DRIVER)

We have proposed, fabricated and demonstrated experimentally a set of Coherent Direct Sequence-OCDMA en/decoders based on Super Structured Fiber Bragg Gratings (SSFBGs) which are able to compensate the fiber chromatic dispersion at the same time that they perform the en/decoding task. The proposed devices avoid the use of additional dispersion compensation stages reducing system complexity and losses. This performance was evaluated for 5.4, 11.4 and 16.8 km of SSMF. The twofold performance wa...

Ban?os Lo?pez, Roci?o; Pastor Abella?n, Daniel; Amaya Ocampo, Waldimar Alexander; Garci?a Mun?oz, Vi?ctor

2012-01-01

280

Nucleotide sequence of pilA, the gene encoding the structural component of type 1 pili in Escherichia coli.  

Digital Repository Infrastructure Vision for European Research (DRIVER)

The pilA gene of Escherichia coli J96 encoding pilin, the structural component of type 1 pili, was sequenced and found to specify a polypeptide 159 amino acids long preceded by a 23-amino-acid signal peptide. As determined from the DNA sequence, the mature peptide lacked tryptophane and methionine, two amino acids previously shown to be lacking in type 1 pili from E. coli. Also, the amino-terminal sequence of amino acids inferred from the DNA sequence corresponded to earlier 20-amino-acid ami...

Orndorff, P. E.; Falkow, S.

1985-01-01

 
 
 
 
281

ZnO1-x nanorod arrays/ZnO thin film bilayer structure: from homojunction diode and high-performance memristor to complementary 1D1R application.  

Science.gov (United States)

We present a ZnO(1-x) nanorod array (NR)/ZnO thin film (TF) bilayer structure synthesized at a low temperature, exhibiting a uniquely rectifying characteristic as a homojunction diode and a resistive switching behavior as memory at different biases. The homojunction diode is due to asymmetric Schottky barriers at interfaces of the Pt/ZnO NRs and the ZnO TF/Pt, respectively. The ZnO(1-x) NRs/ZnO TF bilayer structure also shows an excellent resistive switching behavior, including a reduced operation power and enhanced performances resulting from supplements of confined oxygen vacancies by the ZnO(1-x) NRs for rupture and recovery of conducting filaments inside the ZnO TF layer. A hydrophobic behavior with a contact angle of ~125° can be found on the ZnO(1-x) NRs/ZnO TF bilayer structure, demonstrating a self-cleaning effect. Finally, a successful demonstration of complementary 1D1R configurations can be achieved by simply connecting two identical devices back to back in series, realizing the possibility of a low-temperature all-ZnO-based memory system. PMID:22900519

Huang, Chi-Hsin; Huang, Jian-Shiou; Lin, Shih-Ming; Chang, Wen-Yuan; He, Jr-Hau; Chueh, Yu-Lun

2012-09-25

282

Structural organization of glycophorin A and B genes: Glycophorin B gene evolved by homologous recombination at Alu repeat sequences  

International Nuclear Information System (INIS)

Glycophorins A (GPA) and B (GPB) are two major sialoglycoproteins of the human erythrocyte membrane. Here the authors present a comparison of the genomic structures of GPA and GPB developed by analyzing DNA clones isolated from a K562 genomic library. Nucleotide sequences of exon-intron junctions and 5' and 3' flanking sequences revealed that the GPA and GPB genes consist of 7 and 5 exons, respectively, and both genes have >95% identical sequence from the 5' flanking region to the region ? 1 kilobase downstream from the exon encoding the transmembrane regions. In this homologous part of the genes, GPB lacks one exon due to a point mutation at the 5' splicing site of the third intron, which inactivates the 5' cleavage event of splicing and leads to ligation of the second to the fourth exon. Following these very homologous sequences, the genomic sequences for GPA and GPB diverge significantly and no homology can be detected in their 3' end sequences. The analysis of the Alu sequences and their flanking direct repeat sequences suggest that an ancestral genomic structure has been maintained in the GPA gene, whereas the GPB gene has arisen from the acquisition of 3' sequences different from those of the GPA gene by homologous recombination at the Alu repeats during or after gene duplication

283

Sequence-structure based phylogeny of GPCR Class A Rhodopsin receptors.  

Science.gov (United States)

Current methods of G protein coupled receptors (GPCRs) phylogenetic classification are sequence based and therefore inappropriate for highly divergent sequences, sharing low sequence identity. In this study, sequence structure profile based alignment generated by PROMALS3D was used to understand the GPCR Class A Rhodopsin superfamily evolution using the MEGA 5 software. Phylogenetic analysis included a combination of Neighbor-Joining method and Maximum Likelihood method, with 1000 bootstrap replicates. Our study was able to identify potential ligand association for Class A Orphans and putative/unclassified Class A receptors with no cognate ligand information: GPR21 and GPR52 with fatty acids; GPR75 with Neuropeptide Y; GPR82, GPR18, GPR141 with N-arachidonylglycine; GPR176 with Free fatty acids, GPR10 with Tachykinin & Neuropeptide Y; GPR85 with ATP, ADP & UDP glucose; GPR151 with Galanin; GPR153 and GPR162 with Adrenalin, Noradrenalin; GPR146, GPR139, GPR142 with Neuromedin, Ghrelin, Neuromedin U-25 & Thyrotropin-releasing hormone; GPR171 with ATP, ADP & UDP Glucose; GPR88, GPR135, GPR161, GPR101with 11-cis-retinal; GPR83 with Tackykinin; GPR148 with Prostanoids, GPR109b, GPR81, GPR31with ATP & UTP and GPR150 with GnRH I & GnRHII. Furthermore, we suggest that this study would prove useful in re-classification of receptors, selecting templates for homology modeling and identifying ligands which may show cross reactivity with other GPCRs as signaling via multiple ligands play a significant role in disease modulation. PMID:24503482

Kakarala, Kavita Kumari; Jamil, Kaiser

2014-05-01

284

Structure and thermodynamic properties of (C5H12N)CuBr3: a new weakly coupled antiferromagnetic spin-1/2 chain complex lying in the 1D-3D dimensional cross-over regime.  

Science.gov (United States)

Single crystals of a metal organic complex (C5H12N)CuBr3 (C5H12N = piperidinium, pipH for short) have been synthesized, and the structure was determined by single-crystal X-ray diffraction. (pipH)CuBr3 crystallizes in the monoclinic group C2/c. Edging-sharing CuBr5 units link to form zigzag chains along the c axis, and the neighboring Cu(II) ions with spin-1/2 are bridged by bibromide ions. Magnetic susceptibility data down to 1.8 K can be well fitted by the Bonner-Fisher formula for the antiferromagnetic spin-1/2 chain, giving the intrachain magnetic coupling constant J ? -17 K. At zero field, (pipH)CuBr3 shows three-dimensional (3D) order below TN = 1.68 K. Calculated by the mean-field theory, the interchain coupling constant J' = -0.91 K is obtained and the ordered magnetic moment m0 is about 0.23 ?B. This value of m0 makes (pipH)CuBr3 a rare compound suitable to study the 1D-3D dimensional cross-over problem in magnetism, since both 3D order and one-dimensional (1D) quantum fluctuations are prominent. In addition, specific heat measurements reveal two successive magnetic transitions with lowering temperature when external field ?0H ? 3 T is applied along the a' axis. The ?0H-T phase diagram of (pipH)CuBr3 is roughly constructed. PMID:24617285

Pan, Bingying; Wang, Yang; Zhang, Lijuan; Li, Shiyan

2014-04-01

285

Metallochaperones and metal-transporting ATPases: a comparative analysis of sequences and structures.  

Science.gov (United States)

A comparative structural genomic analysis of a new class of metal-trafficking proteins can provide insights into the intracellular chemistry of reactive cofactors such as copper and zinc. Starting from the sequences of the metallochaperone Atx1 and from the first soluble domain of the copper-transporting ATPase Ccc2, both from yeast, a search on the available genomes was performed using a homology criterion and a metal-binding motif x'-x"-C-x'''-x''''-C. By limiting ourselves to 20% identity with any of the proteins found, several soluble copper-transport proteins were identified, as well as soluble domains of membrane-bound ATPases. Structural models were calculated using high-resolution solution structures as templates, and the models were validated using statistical and energy criteria. Residue conservation and substitution have been interpreted and discussed in terms of structure-function relationship. The potential energy surfaces have been analyzed in terms of protein-protein interactions. We find that metallochaperones and their physiological partner ATPases from several phylogenetic kingdoms recognize one another, via an interplay of electrostatics, hydrogen bonding, and hydrophobic interactions, in a manner that precisely orients the metal-binding side chains for rapid metal transfer between otherwise tight binding sites. Finally, other putative metal-transport proteins are mentioned that have low homology and/or a different metal-binding consensus motif and that appear to use similar structures for recognition and transfer. This analysis highlights the wealth and the complexity of the field. PMID:11827945

Arnesano, Fabio; Banci, Lucia; Bertini, Ivano; Ciofi-Baffoni, Simone; Molteni, Elena; Huffman, David L; O'Halloran, Thomas V

2002-02-01

286

Complete sequence of the genome of the human isolate of Andes virus CHI-7913: comparative sequence and protein structure analysis  

Scientific Electronic Library Online (English)

Full Text Available SciELO Chile | Language: English Abstract in english We report here the complete genomic sequence of the Chilean human isolate of Andes virus CHI-7913. The S, M, and L genome segment sequences of this isolate are 1,802, 3,641 and 6,466 bases in length, with an overall GC content of 38.7%. These genome segments code for a nucleocapsid protein of 428 am [...] ino acids, a glycoprotein precursor protein of 1,138 amino acids and a RNA-dependent RNA polymerase of 2,152 amino acids. In addition, the genome also has other ORFs coding for putative proteins of 34 to 103 amino acids. The encoded proteins have greater than 98% overall similarity with the proteins of Andes virus isolates AH-1 and Chile R123. Among other sequenced Hantavirus, CHI-7913 is more closely related to Sin Nombre virus, with an overall protein similarity of 92%. The characteristics of the encoded proteins of this isolate, such as hydrophobic domains, glycosylation sites, and conserved amino acid motifs shared with other Hantavirus and other members of the Bunyaviridae family, are identified and discussed.

NICOLE D, TISCHLER; JORGE, FERNÁNDEZ; ILSE, MÜLLER; RODRIGO, MARTÍNEZ; HÉCTOR, GALENO; ELIECER, VILLAGRA; JUDITH, MORA; EUGENIO, RAMÍREZ; MARIO, ROSEMBLATT; PABLO D.T., VALENZUELA.

287

Exome sequencing improves genetic diagnosis of structural fetal abnormalities revealed by ultrasound.  

Science.gov (United States)

The genetic etiology of non-aneuploid fetal structural abnormalities is typically investigated by karyotyping and array-based detection of microscopically detectable rearrangements, and submicroscopic copy-number variants (CNVs), which collectively yield a pathogenic finding in up to 10% of cases. We propose that exome sequencing may substantially increase the identification of underlying etiologies. We performed exome sequencing on a cohort of 30 non-aneuploid fetuses and neonates (along with their parents) with diverse structural abnormalities first identified by prenatal ultrasound. We identified candidate pathogenic variants with a range of inheritance models, and evaluated these in the context of detailed phenotypic information. We identified 35 de novo single-nucleotide variants (SNVs), small indels, deletions or duplications, of which three (accounting for 10% of the cohort) are highly likely to be causative. These are de novo missense variants in FGFR3 and COL2A1, and a de novo 16.8 kb deletion that includes most of OFD1. In five further cases (17%) we identified de novo or inherited recessive or X-linked variants in plausible candidate genes, which require additional validation to determine pathogenicity. Our diagnostic yield of 10% is comparable to, and supplementary to, the diagnostic yield of existing microarray testing for large chromosomal rearrangements and targeted CNV detection. The de novo nature of these events could enable couples to be counseled as to their low recurrence risk. This study outlines the way for a substantial improvement in the diagnostic yield of prenatal genetic abnormalities through the application of next-generation sequencing. PMID:24476948

Carss, Keren J; Hillman, Sarah C; Parthiban, Vijaya; McMullan, Dominic J; Maher, Eamonn R; Kilby, Mark D; Hurles, Matthew E

2014-06-15

288

Cloning, Sequencing, Purification, and Crystal Structure of Grenache (Vitis vinifera) Polyphenol Oxidase  

Energy Technology Data Exchange (ETDEWEB)

The full-length cDNA sequence (P93622{_}VITVI) of polyphenol oxidase (PPO) cDNA from grape Vitis vinifera L., cv Grenache, was found to encode a translated protein of 607 amino acids with an expected molecular weight of ca. 67 kDa and a predicted pI of 6.83. The translated amino acid sequence was 99%, identical to that of a white grape berry PPO (1) (5 out of 607 amino acid potential sequence differences). The protein was purified from Grenache grape berries by using traditional methods, and it was crystallized with ammonium acetate by the hanging-drop vapor diffusion method. The crystals were orthorhombic, space group C2221. The structure was obtained at 2.2 {angstrom} resolution using synchrotron radiation using the 39 kDa isozyme of sweet potato PPO (PDB code: 1BT1) as a phase donor. The basic symmetry of the cell parameters (a, b, and c and {alpha}, {beta}, and {gamma}) as well as in the number of asymmetric units in the unit cell of the crystals of PPO, differed between the two proteins. The structures of the two enzymes are quite similar in overall fold, the location of the helix bundles at the core, and the active site in which three histidines bind each of the two catalytic copper ions, and one of the histidines is engaged in a thioether linkage with a cysteine residue. The possibility that the formation of the Cys-His thioether linkage constitutes the activation step is proposed. No evidence of phosphorylation or glycoslyation was found in the electron density map. The mass of the crystallized protein appears to be only 38.4 kDa, and the processing that occurs in the grape berry that leads to this smaller size is discussed.

Virador, V.; Reyes Grajeda, J; Blanco-Labra, A; Mendiola-Olaya, E; Smith, G; Moreno, A; Whitaker, J

2010-01-01

289

Modelling the effect of structure and base sequence on DNA molecular electronics  

International Nuclear Information System (INIS)

DNA is a material that has the potential to be used in nanoelectronic devices as an active component. However, the electronic properties of DNA responsible for its conducting behaviour remain controversial. Here we use a self-consistent quantum molecular dynamics method to study the effect of DNA structure and base sequence on the energy involved when electrons are added or removed from isolated molecules and the transfer of the injected charge along the molecular axis when an electric field is applied. Our results show that the addition or removal of an electron from DNA molecules is most exothermic for poly(dC)-poly(dG) in its B-form and poly(dA)-poly(dT) in its A-form, and least exothermic in its Z-form. Additionally, when an electric field is applied to a charged DNA molecule along its axis, there is electron transfer through the molecule, regardless of the number and sign of the injected charge, the molecular structure and the base sequence. Results from these simulations provide useful information that is hard to obtain from experiments and needs to be considered for further modelling aiming to improve charge transport efficiency in nanoelectronic devices based on DNA

290

Reduced false positives in PDZ binding prediction using sequence and structural descriptors.  

Science.gov (United States)

Abstract—Identifying the binding partners of proteins is a problem of fundamental importance in computational biology. The PDZ is one of the most common and well-studied protein binding domains, hence it is a perfect model system for designing protein binding predictors. The standard approach to identifying the binding partners of PDZ domains uses multiple sequence alignments to infer the set of contact residues that are used in a predictive model. We expand on the sequence alignment approach by incorporating structural information to generate descriptors of the binding site geometry. Furthermore, we generate a real-value score for binary predictions by applying a filter based on models that predict the probability distributions of contact residues at each of the canonical PDZ ligand binding positions. Under training cross validation, our model produced an order of magnitude more predictions at a false positive proportion (FPP) of 10 percent than our benchmark model chosen from the literature. Evaluated using an independent cross validation, with computationally predicted structures, our model was able to make five times as many predictions as the benchmark model, with a Matthews' correlation coefficient (MCC) of 0.33. In addition, our model achieved a false positive proportion of 0.14, while the benchmark model had a 0.25 false positive proportion. PMID:22508908

Hawkins, John C; Zhu, Hongbo; Teyra, Joan; Pisabarro, M Teresa

2012-01-01

291

Comparison of SIV and HIV-1 genomic RNA structures reveals impact of sequence evolution on conserved and non-conserved structural motifs.  

Science.gov (United States)

RNA secondary structure plays a central role in the replication and metabolism of all RNA viruses, including retroviruses like HIV-1. However, structures with known function represent only a fraction of the secondary structure reported for HIV-1(NL4-3). One tool to assess the importance of RNA structures is to examine their conservation over evolutionary time. To this end, we used SHAPE to model the secondary structure of a second primate lentiviral genome, SIVmac239, which shares only 50% sequence identity at the nucleotide level with HIV-1NL4-3. Only about half of the paired nucleotides are paired in both genomic RNAs and, across the genome, just 71 base pairs form with the same pairing partner in both genomes. On average the RNA secondary structure is thus evolving at a much faster rate than the sequence. Structure at the Gag-Pro-Pol frameshift site is maintained but in a significantly altered form, while the impact of selection for maintaining a protein binding interaction can be seen in the conservation of pairing partners in the small RRE stems where Rev binds. Structures that are conserved between SIVmac239 and HIV-1(NL4-3) also occur at the 5' polyadenylation sequence, in the plus strand primer sites, PPT and cPPT, and in the stem-loop structure that includes the first splice acceptor site. The two genomes are adenosine-rich and cytidine-poor. The structured regions are enriched in guanosines, while unpaired regions are enriched in adenosines, and functionaly important structures have stronger base pairing than nonconserved structures. We conclude that much of the secondary structure is the result of fortuitous pairing in a metastable state that reforms during sequence evolution. However, secondary structure elements with important function are stabilized by higher guanosine content that allows regions of structure to persist as sequence evolution proceeds, and, within the confines of selective pressure, allows structures to evolve. PMID:23593004

Pollom, Elizabeth; Dang, Kristen K; Potter, E Lake; Gorelick, Robert J; Burch, Christina L; Weeks, Kevin M; Swanstrom, Ronald

2013-01-01

292

The synthesis and structure of a chiral 1D aluminophosphate chain compound: d-Co(en) 3[AlP 2O 8]·6.5H 2O  

Science.gov (United States)

A new chiral one-dimensional (1D) aluminophosphate chain compound [ d-Co(en) 3][AlP 2O 8]·6.5H 2O (designated AlPO-CJ22) has been hydrothermally synthesized by using the optically pure d-Co(en) 3I 3 complex as the template. Single-crystal structural analysis reveals that its structure is built up from alternating connection of AlO 4 and PO 2(=O 2) tetrahedra to form corner-shared Al 2P 2 four-membered ring (4-MR) chains. The d-Co(en) 33+ complex cations extended along the 2 1 screw axis interact with the inorganic chains through hydrogen-bonds of N⋯O atoms in a helical fashion. Optical rotation measurement shows that AlPO-CJ22 is chiral as with d-Co(en) 33+ complex cations. Crystal data: orthorhombic, I2 12 12 1, a=8.5573(8) Å, b=22.613(2) Å, c=22.605(2) Å, Z=8, R1=0.067, wR2=0.1291, and Flack parameter: -0.02(3). CCDC number: 254179.

Chen, Peng; Li, Jiyang; Yu, Jihong; Wang, Yu; Pan, Qinhe; Xu, Ruren

2005-06-01

293

The synthesis and structure of a chiral 1D aluminophosphate chain compound: d-Co(en)3[AlP2O8].6.5H2O  

International Nuclear Information System (INIS)

A new chiral one-dimensional (1D) aluminophosphate chain compound [d-Co(en)3][AlP2O8].6.5H2O (designated AlPO-CJ22) has been hydrothermally synthesized by using the optically pure d-Co(en)3I3 complex as the template. Single-crystal structural analysis reveals that its structure is built up from alternating connection of AlO4 and PO2(=O2) tetrahedra to form corner-shared Al2P2 four-membered ring (4-MR) chains. The d-Co(en)33+ complex cations extended along the 21 screw axis interact with the inorganic chains through hydrogen-bonds of N...O atoms in a helical fashion. Optical rotation measurement shows that AlPO-CJ22 is chiral as with d-Co(en)33+ complex cations. Crystal data: orthorhombic, I212121, a=8.5573(8)A, b=22.613(2)A, c=22.605(2)A, Z=8, R1=0.067, wR2=0.1291, and Flack parameter: -0.02(3). CCDC number: 254179. -0.02(3). CCDC number: 254179

294

Structural identification of paramagnetic iron porphyrins from Colorado coal with the use of 1D and 2D [sup 1]H NMR spectroscopy: geochemical implications on their origin from heme  

Energy Technology Data Exchange (ETDEWEB)

A fraction of iron porphyrins from Colorado coal constituting one major and one minor C28 isomer was analysed with the use of 1D and 2D[sup 1]H nuclear magnetic resonance spectroscopy. 2D[sup 1]H COSY and NOESY experiments in a low viscosity solvent (CD[sub 3]OD) led to the structural identification of the major component. Assignment of the hyperfine shifted resonances, of all the peripheral substituents on the porphyrin macrocycle, resulted in an unambiguous identification of iron (III)2,7,12,18-tetramethyl-13,17-diethyl porphyrin. Reliability of the 2D [sup 1]H NMR method used was confirmed by analyzing a related structure, i.e. deuteroheme-IX in the same way. The minor constituent of the analysed fraction was identified by reproducing the [sup 1]H NMR spectrum with its synthetic counterpart: low-spin iron (III) 2,7,12,18-tetramethyl-3,8-diethyl porphyrin. Both identified coal iron porphyrins represent products derived from a common protoheme-IX related precursor, selectively degraded via different routes during coal diagenesis. 50 refs., 6 figs.

Czechowski, F.; Latos-Grazynski, L.; Wolowiec, S. (Technical University of Wroclaw, Wroclaw (Poland). Institute of Chemistry and Technology of Petroleum and Coal)

295

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

Directory of Open Access Journals (Sweden)

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

Akutsu Tatsuya

2009-01-01

296

Influence of loading sequence and stress ratio on Fatigue damage accumulation of a structural component  

Scientific Electronic Library Online (English)

Full Text Available SciELO Portugal | Language: English Abstract in portuguese Este artigo apresenta resultados experimentais relativos à acumulação de dano de fadiga de um componente estrutural de aço P355NL1. O componente estrutural é uma placa rectangular com duplo entalhe. Foram aplicadas sequências de dois e múltiplos blocos de carga de amplitude constante, para várias co [...] mbinações de razões de tensão remotas, nomeadamente R=0, R=0.15 e R=0.3. Também foram analisados os efeitos da aplicação de blocos de amplitude variável, aplicados de acordo com um espectro de carga predefinido. Este estudo foi complementado com resultados de ensaios realizados em amplitude constante, os quais serviram para os cálculos de acumulação de dano. Em geral, o carregamento por blocos demonstra que o dano provocado por fadiga apresenta uma evolução não linear com o número de ciclos de carga, sendo esta evolução de dano função da sequência de carga, do nível de tensão e da razão de tensões. Geralmente, a aplicação de carregamentos de amplitude variável indicia um importante efeito da razão de tensões na acumulação de dano por fadiga. Particularmente, é observado um efeito claro da sequência de carga nos carregamentos compostos por dois blocos de carga, com razão de tensões nula. Para as outras razões de tensões (altas), os efeitos da sequência de carga são praticamente desprezáveis; contudo a evolução de dano continua a ser não linear. Abstract in english This paper presents experimental results about the fatigue damage accumulation behaviour of a structural component made of P355NL1 steel. The structural component is a rectangular double notched plate. Two and multiple alternated constant amplitude block sequences were applied for various combinatio [...] ns of remote stress ranges. Three stress ratios were investigated, namely R=0, R=0.15 and R=0.3. Variable amplitude blocks were also investigated according predefined stress spectra. Constant amplitude data was also generated which is applied for damage calculation purposes. In general, the block loading demonstrates that fatigue damage evolves nonlinearly with the number of loading cycles, function of the load sequence, stress level and stress ratios. Generally, the application of variable amplitude loading suggests an important stress ratio effect on fatigue damage accumulation. In particular, a clear load sequence effect is verified for the two block loading, with null stress ratio. For the other (higher) stress ratios, the load sequence effects are almost negligible; however the damage evolution still is non-linear.

Hélder F. S. G., Pereira; Abílio M.P. de, Jesus; Alfredo S., Ribeiro; António A., Fernandes.

2008-01-01

297

Genome sequencing of disease and carriage isolates of nontypeable Haemophilus influenzae identifies discrete population structure  

Science.gov (United States)

One of the main hurdles for the development of an effective and broadly protective vaccine against nonencapsulated isolates of Haemophilus influenzae (NTHi) lies in the genetic diversity of the species, which renders extremely difficult the identification of cross-protective candidate antigens. To assess whether a population structure of NTHi could be defined, we performed genome sequencing of a collection of diverse clinical isolates representative of both carriage and disease and of the diversity of the natural population. Analysis of the distribution of polymorphic sites in the core genome and of the composition of the accessory genome defined distinct evolutionary clades and supported a predominantly clonal evolution of NTHi, with the majority of genetic information transmitted vertically within lineages. A correlation between the population structure and the presence of selected surface-associated proteins and lipooligosaccharide structure, known to contribute to virulence, was found. This high-resolution, genome-based population structure of NTHi provides the foundation to obtain a better understanding, of NTHi adaptation to the host as well as its commensal and virulence behavior, that could facilitate intervention strategies against disease caused by this important human pathogen. PMID:24706866

De Chiara, Matteo; Hood, Derek; Muzzi, Alessandro; Pickard, Derek J.; Perkins, Tim; Pizza, Mariagrazia; Dougan, Gordon; Rappuoli, Rino; Moxon, E. Richard; Soriani, Marco; Donati, Claudio

2014-01-01

298

Genome sequencing of disease and carriage isolates of nontypeable Haemophilus influenzae identifies discrete population structure.  

Science.gov (United States)

One of the main hurdles for the development of an effective and broadly protective vaccine against nonencapsulated isolates of Haemophilus influenzae (NTHi) lies in the genetic diversity of the species, which renders extremely difficult the identification of cross-protective candidate antigens. To assess whether a population structure of NTHi could be defined, we performed genome sequencing of a collection of diverse clinical isolates representative of both carriage and disease and of the diversity of the natural population. Analysis of the distribution of polymorphic sites in the core genome and of the composition of the accessory genome defined distinct evolutionary clades and supported a predominantly clonal evolution of NTHi, with the majority of genetic information transmitted vertically within lineages. A correlation between the population structure and the presence of selected surface-associated proteins and lipooligosaccharide structure, known to contribute to virulence, was found. This high-resolution, genome-based population structure of NTHi provides the foundation to obtain a better understanding, of NTHi adaptation to the host as well as its commensal and virulence behavior, that could facilitate intervention strategies against disease caused by this important human pathogen. PMID:24706866

De Chiara, Matteo; Hood, Derek; Muzzi, Alessandro; Pickard, Derek J; Perkins, Tim; Pizza, Mariagrazia; Dougan, Gordon; Rappuoli, Rino; Moxon, E Richard; Soriani, Marco; Donati, Claudio

2014-04-01

299

DNA sequence similarity search through content-based retrieval technique  

Science.gov (United States)

Deoxyribonucleic acid (DNA) sequences are difficult to analyze similarity due to their length and complexity. The challenge lies in being able to use digital signal processing (DSP) to solve highly relevant problems in DNA sequences. Here, we transfer a one-dimensional (1D) DNA sequence into a two-dimensional (2D) pattern by using the Peano scan algorithm. Four complex values are assigned to the characters "A", "C", "T", and "G", respectively. Then, Fourier transform is employed to obtain far-field amplitude distribution of the 2D pattern. Hereto, a 1D DNA sequence becomes a 2D image pattern. Features are extracted from the 2D image pattern with the Principle Component Analysis (PCA) method. Therefore, the DNA sequence database can be established. Unfortunately, comparing features may take a long time when the database is large since multi-dimensional features are often available. This problem is solved by building indexing structure like a filter to filter-out non-relevant items and select a subset of candidate DNA sequences. Clustering algorithms can organize the multi-dimensional feature data into the indexing structure for effective retrieval. Accordingly, the query sequence can be only compared against candidate ones rather than all sequences in database. In fact, our algorithm provides a pre-processing method to accelerate the DNA sequence search process. Finally, experimental results further demonstrate the efficiency of our proposed algorithm for DNA sequences similarity retrieval.

Yeh, Chia Hung; Sung, Po Yi; Chang, Hsuan T.; Kuo, Chung J.

2003-08-01

300

Sequence homology and structural analysis of plasmepsin 4 isolated from Indian Plasmodium vivax isolates.  

Science.gov (United States)

Plasmodium vivax malaria is a globally widespread disease responsible for 50% of human malaria cases in Central and South America, South East Asia and Indian subcontinent. The rising severity of the disease and emerging resistance of the parasite has emphasized the need for the search of novel therapeutic targets to combat P. vivax malaria. Plasmepsin 4 (PM4) a food vacuole aspartic protease is essential in parasite functions and viability such as initiating hemoglobin digestion and processing of proteins and is being looked upon as potential drug target. Although the plasmepsins of Plasmodium falciparum have been extensively studied, the plasmepsins of P. vivax are not well characterized. This is the first report detailing complete PM4 gene analysis from Indian P. vivax isolates. Blast results of sequences of P. vivax plasmepsin 4 (PvPM4) shows 100% homology among isolates of P. vivax collected from different geographical regions of India. All of the seven Indian isolates did not contain intron within the coding region. Interestingly, PvPM4 sequence analysis showed a very high degree of homology with all other sequences of Plasmodium species available in the genebank. Our results strongly suggest that PvPM4 are highly conserved except a small number of amino acid substitutions that did not modify key motifs at active site formation for the function or the structure of the enzymes. Furthermore, our study shows that PvPM4 occupies unique phylogenetic status within Plasmodium group and sufficiently differ from the most closely related human aspartic protease, cathepsin D. The analysis of 3D model of PM4 showed a typical aspartic protease structure with bi-lobed, compact and distinct peptide binding cleft in both P. vivax and P. falciparum. In order to validate appropriate use of PM4 as potential anti-malarial drug target, studies on genetic and structural variations among P. vivax plasmepsins (PvPMs) from different geographical regions are of utmost importance for drugs and vaccine designs for anti-malarial strategies. PMID:21382523

Rawat, Manmeet; Vijay, Sonam; Gupta, Yash; Dixit, Rajnikant; Tiwari, P K; Sharma, Arun

2011-07-01

 
 
 
 
301

Use of Endogenous Retroviral Sequences (ERVs and structural markers for retroviral phylogenetic inference and taxonomy  

Directory of Open Access Journals (Sweden)

Full Text Available Abstract Background Endogenous retroviral sequences (ERVs are integral parts of most eukaryotic genomes and vastly outnumber exogenous retroviruses (XRVs. ERVs with a relatively complete structure were retrieved from the genetic archives of humans and chickens, diametrically opposite representatives of vertebrate retroviruses (over 3300 proviruses, and analyzed, using a bioinformatic program, RetroTector©, developed by us. This rich source of proviral information, accumulated in a local database, and a collection of XRV sequences from the literature, allowed the reconstruction of a Pol based phylogenetic tree, more extensive than previously possible. The aim was to find traits useful for classification and evolutionary studies of retroviruses. Some of these traits have been used by others, but they are here tested in a wider context than before. Results In the ERV collection we found sequences similar to the XRV-based genera: alpha-, beta-, gamma-, epsilon- and spumaretroviruses. However, the occurrence of intermediates between them indicated an evolutionary continuum and suggested that taxonomic changes eventually will be necessary. No delta or lentivirus representatives were found among ERVs. Classification based on Pol similarity is congruent with a number of structural traits. Acquisition of dUTPase occurred three times in retroviral evolution. Loss of one or two NC zinc fingers appears to have occurred several times during evolution. Nucleotide biases have been described earlier for lenti-, delta- and betaretroviruses and were here confirmed in a larger context. Conclusion Pol similarities and other structural traits contribute to a better understanding of retroviral phylogeny. "Global" genomic properties useful in phylogenies are i. translational strategy, ii. number of Gag NC zinc finger motifs, iii. presence of Pro N-terminal dUTPase (dUTPasePro, iv. presence of Pro C-terminal G-patch and v. presence of a GPY/F motif in the Pol integrase (IN C-terminal domain. "Local" retroviral genomic properties useful for delineation of lower level taxa are i. host species range, ii. nucleotide compositional bias and iii. LTR lengths.

Sperber Göran O

2005-08-01

302

Lanthanide complexes in hybrid halometallate materials: interconversion between a novel 2D microporous framework and a 1D zigzag chain structure of iodoargentates templated by octakis-solvated terbium(III) cation.  

Science.gov (United States)

Octakis solvated terbium iodide complexes [Tb(DMSO)(8)]I(3) (1) and [Tb(DMF)(8)]I(3) (2) (DMSO = dimethylsulfoxide; DMF = dimethylformamide) were used as synthons to construct novel iodoargentate fabrics. Reaction of 1 with 6 equivalents of AgI in the presence of NH(4)I produced a novel framework compound [Tb(DMSO)(8)](2)[Ag(2)(mu-I)(3)I(2)][Ag(5)(mu(3)-I)(4)(mu-I)(4)](2infinity) (3) involving alternate layers of discrete [Tb(DMSO)(8)](3+) cation, [Ag(2)I(5)](3-) anion and a 2D microporous sheet of the composition [Ag(5)I(8)](3-), whereas similar reaction of 2 yielded [Tb(DMF)(8)][Ag(6)(mu(4)-I)(2)(mu(3)-I)(2)(mu-I)(5)](1infinity) (4) with a 1D zigzag structure. The two structural forms are completely inter-convertible on mutual exchange of DMSO and DMF ligands, the partial substitution of the former ligand in 3 yielding a mixed-ligand complex [Tb(DMF)(6.7)(DMSO)(1.3)][Ag(6)(mu(4)-I)(2)(mu(3)-I)(2)(mu-I)(5)](1infinity) (5). Single crystal X-ray structures are reported for all the complexes. Thermo-gravimetric analyses of these complexes show that thermal stability decreases in the order 4 > 2 > 3 > 1, whereas the diffuse reflectance spectra of 3 and 4 exhibit an optical band gap of about 3.7 eV, thus revealing the insulator nature of these hybrid iodoargentates. Compared to solvated terbium iodide complexes 1 and 2, the high energy transitions in the excitation spectra of the iodoargentate complexes 3 and 4 are quenched by a process which can best be attributed to the auto-ionization of the carriers in the above materials. PMID:19662287

Mishra, Shashank; Jeanneau, Erwann; Ledoux, Gilles; Daniele, Stéphane

2009-07-01

303

A transposon-like structure in the 5' flanking sequence of a legumin gene from Pisum sativum.  

Science.gov (United States)

The legumin storage proteins of Pisum sativum are coded for by a multigene family. An insertion element (Pis1) has been found integrated into the 5' flanking sequence of the legC legumin seed storage protein gene. This element contains all the sequence features of the CACTA family of insertion elements, has perfect 12 bp inverted repeats at its termini, and generates a target host site duplication upon integration. An 8 bp sequence within the left arm of the insertion element shows perfect homology to a sequence in the legC flanking region. Three stem-loop structures which can be formed within the element have the same stem sequence. PMID:2836701

Shirsat, A H

1988-04-01

304

Structure analysis of 16S rDNA sequences from strains of Acidithiobacillus ferrooxidans.  

Science.gov (United States)

Four strains of Acidithiobacillus ferrooxidans with different iron oxidation capacity were isolated from different mine drainage stations. The 16S rRNA gene of these strains were cloned and sequenced. Based on our sequences analysis on the four strain and the data on the other strains deposited in Genbank, all A. ferrooxidans may be classified into three phylogenetic groups. The analysis data showed that nucleotide variables (signature sites) were detected in 21 positions, and most of them were found in the first 800 bp from 5' terminal except position 970 and 1375. Interestingly, the first 13 signature sites were located in two main regions: the first region (position 175-234) located in V2 while the second region (position 390-439) were detected in constant region between V2 and V3. Furthermore, the secondary structure and minimal free energy were determined in two regions among strains of three groups. These results may be useful in characterizing the microevolutionary mechanisms of species formation and monitoring in biohydrometallurgical application. PMID:16584633

Peng, Hong; Yang, Yu; Li, Xuan; Qiu, Guanzhou; Liu, Xueduan; Huang, Jufang; Hu, Yuehua

2006-03-31

305

Cluster Segmentation of Thermal Image Sequences Using kd-Tree Structure  

Science.gov (United States)

This paper presents optimization methods for the K-means segmentation algorithm for a sequence of thermal images. Images of the sample response in the frequency domain to the thermal stimulation with a known spectrum were subjected to cluster segmentation, grouping pixels with similar frequency characteristics. Compared were all pixel characteristics in the function of the frame number and grouped using the minimal sum of deviations of the pixels from their segment mean for all the frames of the processed image sequence. A new initialization method for the K-means algorithm, using density information, was used. A K-means algorithm with a kd-tree structure C# implementation was tested for speed and accuracy. This algorithm divides the set of pixels to the subspaces in the hierarchy of a binary tree. This allows skipping the calculation of distances of pixels to some centroids and pruning a set of centroid clusters through the hierarchy tree. Results of the segmentation were compared with the K-means and FCM algorithm MATLAB implementations.

?wita, R.; Suszy?ski, Z.

2014-12-01

306

Population structure of the Yersinia pseudotuberculosis complex according to multilocus sequence typing.  

Science.gov (United States)

Multilocus sequence analysis of 417 strains of Yersinia pseudotuberculosis revealed that it is a complex of four populations, three of which have been previously assigned species status [Y.?pseudotuberculosis sensu stricto (s.s.), Yersinia pestis and Yersinia similis] and a fourth population, which we refer to as the Korean group, which may be in the process of speciation. We detected clear signs of recombination within Y.?pseudotuberculosis s.s. as well as imports from Y.?similis and the Korean group. The sources of genetic diversification within Y.?pseudotuberculosis s.s. were approximately equally divided between recombination and mutation, whereas recombination has not yet been demonstrated in Y.?pestis, which is also much more genetically monomorphic than is Y.?pseudotuberculosis s.s. Most Y.?pseudotuberculosis s.s. belong to a diffuse group of sequence types lacking clear population structure, although this species contains a melibiose-negative clade that is present globally in domesticated animals. Yersinia? similis corresponds to the previously identified Y.?pseudotuberculosis genetic type G4, which is probably not pathogenic because it lacks the virulence factors that are typical for Y.?pseudotuberculosis s.s. In contrast, Y.?pseudotuberculosis s.s., the Korean group and Y.?pestis can all cause disease in humans. PMID:21951486

Laukkanen-Ninios, Riikka; Didelot, Xavier; Jolley, Keith A; Morelli, Giovanna; Sangal, Vartul; Kristo, Paula; Brehony, Carina; Imori, Priscilla F M; Fukushima, Hiroshi; Siitonen, Anja; Tseneva, Galina; Voskressenskaya, Ekaterina; Falcao, Juliana P; Korkeala, Hannu; Maiden, Martin C J; Mazzoni, Camila; Carniel, Elisabeth; Skurnik, Mikael; Achtman, Mark

2011-12-01

307

H-1 and P-31 NMR studies of oligonucleotides directed towards investigating the sequence-dependent structural nature of DNA  

International Nuclear Information System (INIS)

Assignments of the 31P resonances of a series of six sequence-related tetradecamer and two dodecamer DNA duplexes were determined by either site-specific 17O labelling of the phosphoryl groups or by two-dimensional 1H-31P heteronuclear NMR methods. Comparisons of the 31P resonances of these sequences have allowed greater insight of various factors responsible for 31p chemical shifts in oligonucleotides. Common patterns of the 31P shift variation along the DNA duplex are shown to be sequence-dependent. The observed variation is largely a function of the purine-pyrimidine base step arrangement of the sequence. An accumulation of the 31P shift values from these sequences, as well as others presented in the literature allowed the formation of 31P shift rules, which can be used to predict the 31P NMR spectrum of other oligonucleotide sequences. Comparison of the 31P shift variation to variations in DNA helical geometry obtained from crystallographic studies of oligonucleotides in the literature indicates a sequence-dependent structural relationship exists. The 31P shifts correlate well with some geometric helical parameters, as predicted by the Dickerson/Calladine sum function rules. These correlations are consistent with the hypothesis that the structural variation is responsible for perturbing the deoxyribose phosphate backbone, which responoxyribose phosphate backbone, which responds to changes in local helical structure. The variation of the 31P chemical shift, and the degree of this variation from one base step to the next is proposed as a potential probe of local helical conformation within the DNA double helix. Inter- and intra- nucleotide 1H-1H distances were determined for four sequence-related tetradecamer sequences using a series of time-developed nuclear Overhauser enhancement measurements

308

An MML classification of protein structure that knows about angles and sequence.  

Science.gov (United States)

The MML classification program, Snob, deals with mixture modelling (or clustering) of circular data. It has recently been extended to do Markov modelling of the serial correlation between clusters such as modelling the fact that a Helix cluster favours being followed by another Helix cluster. Such a model is better known as a Hidden Markov Model. The search for the most appropriate secondary structure classification of protein data is of significant importance and was addressed by Hunter and States (1992) using the Bayesian classifier, AutoClass, on Cartesian co-ordinate data of protein residues. Dowe et al. (1996) improved upon this earlier work by using Snob to cluster dihedral angle data, with the advantage that 3 x 3 = 9 Cartesian co-ordinates can be represented by the 2 orientation-invariant angles, phi and psi. The Hidden Markov Model used here is shown to be a more appropriate way again of modelling protein data and results in the selection of a simpler class model with 17 structure classes. We report on this classification, including the class transition matrix, and relate it back to the amino-acid sequence and the simple Helix, Beta, Turn classification. We find 3 types of Helix, 2 types of Beta and many types of Turn. The msot numerous Turn class defines a continuous flexible structure that is negatively correlated to all the other classes. PMID:9697214

Edgoose, T; Allison, L; Dowe, D L

1998-01-01

309

Fine-scale population structure and the era of next-generation sequencing.  

Science.gov (United States)

Fine-scale population structure characterizes most continents and is especially pronounced in non-cosmopolitan populations. Roughly half of the world's population remains non-cosmopolitan and even populations within cities often assort along ethnic and linguistic categories. Barriers to random mating can be ecologically extreme, such as the Sahara Desert, or cultural, such as the Indian caste system. In either case, subpopulations accumulate genetic differences if the barrier is maintained over multiple generations. Genome-wide polymorphism data, initially with only a few hundred autosomal microsatellites, have clearly established differences in allele frequency not only among continental regions, but also within continents and within countries. We review recent evidence from the analysis of genome-wide polymorphism data for genetic boundaries delineating human population structure and the main demographic and genomic processes shaping variation, and discuss the implications of population structure for the distribution and discovery of disease-causing genetic variants, in the light of the imminent availability of sequencing data for a multitude of diverse human genomes. PMID:20876616

Henn, Brenna M; Gravel, Simon; Moreno-Estrada, Andres; Acevedo-Acevedo, Suehelay; Bustamante, Carlos D

2010-10-15

310

CPHmodels-3.0—remote homology modeling using structure-guided sequence profiles  

Science.gov (United States)

CPHmodels-3.0 is a web server predicting protein 3D structure by use of single template homology modeling. The server employs a hybrid of the scoring functions of CPHmodels-2.0 and a novel remote homology-modeling algorithm. A query sequence is first attempted modeled using the fast CPHmodels-2.0 profile–profile scoring function suitable for close homology modeling. The new computational costly remote homology-modeling algorithm is only engaged provided that no suitable PDB template is identified in the initial search. CPHmodels-3.0 was benchmarked in the CASP8 competition and produced models for 94% of the targets (117 out of 128), 74% were predicted as high reliability models (87 out of 117). These achieved an average RMSD of 4.6?Å when superimposed to the 3D structure. The remaining 26% low reliably models (30 out of 117) could superimpose to the true 3D structure with an average RMSD of 9.3?Å. These performance values place the CPHmodels-3.0 method in the group of high performing 3D prediction tools. Beside its accuracy, one of the important features of the method is its speed. For most queries, the response time of the server is <20?min. The web server is available at http://www.cbs.dtu.dk/services/CPHmodels/. PMID:20542909

Nielsen, Morten; Lundegaard, Claus; Lund, Ole; Petersen, Thomas Nordahl

2010-01-01

311

CPHmodels-3.0--remote homology modeling using structure-guided sequence profiles  

DEFF Research Database (Denmark)

CPHmodels-3.0 is a web server predicting protein 3D structure by use of single template homology modeling. The server employs a hybrid of the scoring functions of CPHmodels-2.0 and a novel remote homology-modeling algorithm. A query sequence is first attempted modeled using the fast CPHmodels-2.0 profile-profile scoring function suitable for close homology modeling. The new computational costly remote homology-modeling algorithm is only engaged provided that no suitable PDB template is identified in the initial search. CPHmodels-3.0 was benchmarked in the CASP8 competition and produced models for 94% of the targets (117 out of 128), 74% were predicted as high reliability models (87 out of 117). These achieved an average RMSD of 4.6 A when superimposed to the 3D structure. The remaining 26% low reliably models (30 out of 117) could superimpose to the true 3D structure with an average RMSD of 9.3 A. These performance values place the CPHmodels-3.0 method in the group of high performing 3D prediction tools. Beside its accuracy, one of the important features of the method is its speed. For most queries, the response time of the server is

Nielsen, Morten; Lundegaard, Claus

2010-01-01

312

Chromatic dispersion compensation and Coherent Direct-Sequence OCDMA operation on a single super structured FBG.  

Science.gov (United States)

We have proposed, fabricated and demonstrated experimentally a set of Coherent Direct Sequence-OCDMA en/decoders based on Super Structured Fiber Bragg Gratings (SSFBGs) which are able to compensate the fiber chromatic dispersion at the same time that they perform the en/decoding task. The proposed devices avoid the use of additional dispersion compensation stages reducing system complexity and losses. This performance was evaluated for 5.4, 11.4 and 16.8 km of SSMF. The twofold performance was verified in Low Reflectivity regime employing only one GVD compensating device at decoder or sharing out the function between encoder and decoder devices. Shared functionality requires shorter SSFBGs designs and also provides added flexibility to the optical network design. Moreover, dispersion compensated en/decoders were also designed into the High Reflectivity regime employing synthesis methods achieving more than 9 dB reduction of insertion loss for each device. PMID:22714462

Baños, Rocío; Pastor, Daniel; Amaya, Waldimar; Garcia-Munoz, Victor

2012-06-18

313

Mitogenomic sequences better resolve stock structure of southern Greater Caribbean green turtle rookeries.  

Science.gov (United States)

Analyses of mitochondrial control region polymorphisms have supported the presence of several demographically independent green turtle (Chelonia mydas) rookeries in the Greater Caribbean region. However, extensive sharing of common haplotypes based on 490-bp control region sequences confounds assessment of the scale of natal homing and population structure among regional rookeries. We screened the majority of the mitochondrial genomes of 20 green turtles carrying the common haplotype CM-A5 and representing the rookeries of Buck Island, St. Croix, United States Virgin Islands (USVI); Aves Island, Venezuela; Galibi, Suriname; and Tortuguero, Costa Rica. Five single-nucleotide polymorphisms (SNPs) were identified that subdivided CM-A5 among regions. Mitogenomic pairwise ?(ST) values of eastern Caribbean rookery comparisons were markedly lower than the respective pairwise F(ST) values. This discrepancy results from the presence of haplotypes representing two divergent lineages in each rookery, highlighting the importance of choosing the appropriate test statistic for addressing the study question. Haplotype frequency differentiation supports demographic independence of Aves Island and Suriname, emphasizing the need to recognize the smaller Aves rookery as a distinct management unit. Aves Island and Buck Island rookeries shared mitogenomic haplotypes; however, frequency divergence suggests that the Buck Island rookery is sufficiently demographically isolated to warrant management unit status for the USVI rookeries. Given that haplotype sharing among rookeries is common in marine turtles with cosmopolitan distributions, mitogenomic sequencing may enhance inferences of population structure and phylogeography, as well as improve the resolution of mixed stock analyses aimed at estimating natal origins of foraging turtles. PMID:22432442

Shamblin, Brian M; Bjorndal, Karen A; Bolten, Alan B; Hillis-Starr, Zandy M; Lundgren, Ian; Naro-Maciel, Eugenia; Nairn, Campbell J

2012-05-01

314

Predicting deleterious nsSNPs: an analysis of sequence and structural attributes  

Directory of Open Access Journals (Sweden)

Full Text Available Abstract Background There has been an explosion in the number of single nucleotide polymorphisms (SNPs within public databases. In this study we focused on non-synonymous protein coding single nucleotide polymorphisms (nsSNPs, some associated with disease and others which are thought to be neutral. We describe the distribution of both types of nsSNPs using structural and sequence based features and assess the relative value of these attributes as predictors of function using machine learning methods. We also address the common problem of balance within machine learning methods and show the effect of imbalance on nsSNP function prediction. We show that nsSNP function prediction can be significantly improved by 100% undersampling of the majority class. The learnt rules were then applied to make predictions of function on all nsSNPs within Ensembl. Results The measure of prediction success is greatly affected by the level of imbalance in the training dataset. We found the balanced dataset that included all attributes produced the best prediction. The performance as measured by the Matthews correlation coefficient (MCC varied between 0.49 and 0.25 depending on the imbalance. As previously observed, the degree of sequence conservation at the nsSNP position is the single most useful attribute. In addition to conservation, structural predictions made using a balanced dataset can be of value. Conclusion The predictions for all nsSNPs within Ensembl, based on a balanced dataset using all attributes, are available as a DAS annotation. Instructions for adding the track to Ensembl are at http://www.brightstudy.ac.uk/das_help.html

Saqi Mansoor AS

2006-04-01

315

Involvement of interstitial telomeric sequences in two new cases of mosaicism for autosomal structural rearrangements.  

Science.gov (United States)

Mosaicism for an autosomal structural rearrangement that does not involve ring or marker chromosomes is rare. The mechanisms responsible for genome instability have not always been explained. Several studies have shown that interstitial telomeric sequences (ITSs), involved in some mosaic constitutional anomalies, are potent sources of genomic instability. Here we describe two cases of mosaicism for uncommon constitutional autosomal rearrangements, involving ITSs, identified by karyotyping and characterized by FISH and SNP-array analysis. The first patient, a boy with global developmental delay, had a rare type of pure distal 1q inverted duplication (1q32-qter), attached to the end of the short arm of the same chromosome 1, in approximately 35% of his cells. The second patient, a phenotypically normal man, was diagnosed as having mosaic for a balanced non-reciprocal translocation of the distal segment of 7q (7q33qter), onto the terminal region of the short arm of a whole chromosome 12, in approximately 80% of his cells. The remaining 20% of the cells showed an unbalanced state of the translocation, with only the der(7) chromosome. He was ascertained through his malformed fetus carrying a non-mosaic partial monosomy 7q, identified at prenatal diagnosis. We show that pan-telomeric and subtelomeric sequences were observed at the interstitial junction point of the inv dup(1q) and of the der(12)t(7;12), respectively. The present cases and review of the literature suggest that the presence of ITSs at internal sites of the chromosomes may explain mechanisms of the patients's mosaic structural rearrangements. © 2014 Wiley Periodicals, Inc. PMID:25428228

Lévy, Jonathan; Receveur, Aline; Jedraszak, Guillaume; Chantot-Bastaraud, Sandra; Renaldo, Florence; Gondry, Jean; Andrieux, Joris; Copin, Henri; Siffroi, Jean-Pierre; Portnoï, Marie-France

2015-02-01

316

Novel sequence variations in LAMA2 andSGCG genes modulating cis-acting regulatory elements and RNA secondary structure  

Digital Repository Infrastructure Vision for European Research (DRIVER)

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 Tunisia...

Siala, Olfa; Salem, Ikhlass Hadj; Tlili, Abdelaziz; Ammar, Imen; Belguith, Hanen; Fakhfakh, Faiza

2010-01-01

317

Novel sequence variations in LAMA2 and SGCG genes modulating cis-acting regulatory elements and RNA secondary structure  

Digital Repository Infrastructure Vision for European Research (DRIVER)

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,...

Olfa Siala; Ikhlass Hadj Salem; Abdelaziz Tlili; Imen Ammar; Hanen Belguith; Faiza Fakhfakh

2010-01-01

318

Spatio-temporal structure extraction and denoising of geophysical fluid image sequences using 3D curvelet transforms  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Since several decades many satellites have been launched for the observation of the Earth for a better knowledge of the atmosphere and of the ocean. The sequences of images that such satellites provide show the evolution of some large scale structures such as vortices and fronts. It is obvious that the dynamic of these structures may have a strong predictive potential. Extracting these structures and tracking their evolution automatically is then essential for future forecast systems. In this...

Ma, Jianwei; Titaud, Olivier; Vidard, Arthur; Le Dimet, Franc?ois-xavier

2008-01-01

319

Nucleotide sequence of the 3'-terminal tRNA-like structure in barley stripe mosaic virus genome.  

Science.gov (United States)

This paper describes the sequence of 257 nucleotides from the 3' end of RNA 2 of barley stripe mosaic virus ( BSMV , strain Argentina Mild) including an internal oligo (A) tract localized at a distance of 236 nucleotides from the 3' end, and the 3' terminal tRNA-like structure accepting tyrosine. This sequence is shown to be the same with RNAs 1,2 and 3 of another BSMV strain, Norwich , for at least the first 106 nucleotides from the 3' end. The 3' extremity of BSMV RNA bears some resemblance to tRNATyr from yeast in its primary structure. The possible secondary structures of the tRNA-like sequence in BSMV genome are discussed. PMID:6328450

Kozlov YuV; Rupasov, V V; Adyshev, D M; Belgelarskaya, S N; Agranovsky, A A; Mankin, A S; Morozov SYu; Dolja, V V; Atabekov, J G

1984-05-11

320

The investigation of the secondary structures of various peptide sequences of ?-casein by the multicanonical simulation method  

Science.gov (United States)

The structural properties of Arginine-Glutamic acid-Leucine-Glutamic acid-Glutamic acid-Leucine-Asparagine-Valine-Proline-Glycine (RELEELNVPG, in one letter code), Glutamic acid-Glutamic acid-Glutamine-Glutamine-Glutamine-Threonine-Glutamic acid (EEQQQTE) and Glutamic acid-Aspartic acid-Glutamic acid-Leucine-Glutamine-Aspartic acid-Lysine-Isoleucine (EDELQDKI) peptide sequences of ?-casein were studied by three-dimensional molecular modeling. In this work, the three-dimensional conformations of each peptide from their primary sequences were obtained by multicanonical simulations. With using major advantage of this simulation technique, Ramachandran plots were prepared and analysed to predict the relative occurrence probabilities of ?-turn, ?-turn and helical structures. Structural predictions of these sequences of ?-casein molecule indicate the presence of high level of helical structures and ?III-turns. The occurrence probabilities of inverse and classical ?-turns were low. The probability of helical structure of each sequence significantly decreased when the temperature increased. Our results show these peptides have highly helical structure and better agreement with the results of spectroscopic techniques and other prediction methods.

Ya?ar, F.; Çelik, S.; Köksel, H.

2006-05-01

 
 
 
 
321

Novel sequence variations in LAMA2 andSGCG genes modulating cis-acting regulatory elements and RNA secondary structure.  

Science.gov (United States)

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. PMID:21637626

Siala, Olfa; Salem, Ikhlass Hadj; Tlili, Abdelaziz; Ammar, Imen; Belguith, Hanen; Fakhfakh, Faiza

2010-01-01

322

Novel sequence variations in LAMA2 and SGCG genes modulating cis-acting regulatory elements and RNA secondary structure  

Directory of Open Access Journals (Sweden)

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.

Olfa Siala

2010-01-01

323

Novel sequence variations in LAMA2 and SGCG genes modulating cis-acting regulatory elements and RNA secondary structure  

Scientific Electronic Library Online (English)

Full Text Available SciELO Brazil | Language: English Abstract in english 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 softw [...] are. 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.

Olfa, Siala; Ikhlass Hadj, Salem; Abdelaziz, Tlili; Imen, Ammar; Hanen, Belguith; Faiza, Fakhfakh.

324

Comparative analysis of ribonuclease P RNA using gene sequences from natural microbial populations reveals tertiary structural elements  

Energy Technology Data Exchange (ETDEWEB)

PCR amplification of template DNAs extracted from mixed, naturally occurring microbial populations, using oligonucleotide primers complementary to highly conserved sequences, was used to obtain a large collection of diverse RNase P RNA-encoding genes. An alignment of these sequences was used in a comparative analysis of RNase P RNA secondary and tertiary structure. The new sequences confirm the secondary structure model based on sequences rom cultivated organisms (with minor alterations in helices P12 and P18), providing additional support for nearly every base pair. Analysis of sequence covariation using the entire RNase P RNA data set reveals elements of tertiary structure in the RNA; the third nucleotides (underlined) of the GNRA tetraloops L14 and L18 are seen to interact with adjacent Watson-Crick base pairs in helix P8, forming A:G/C or G:A/U base triples. These experiments demonstrate one way in which the enormous diversity of natural microbial populations can be used to elucidate molecular structure through comparative analysis. 32 refs., 4 figs., 1 tab.

Brown, J.W.; Haas, E.S. [North Carolina State Univ., Raleigh, NC (United States); Nolan, J.M.; Rubio, M.T. [Indiana Univ., Bloomington, IN (United States)] [and others

1996-04-02

325

A sequence-based survey of the complex structural organization of tumor genomes  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Tumors and cancer cell lines were surveyed with end-sequencing profiling, yielding the largest available collection of sequence-ready tumor genome breakpoints and providing evidence that some rearrangements may be recurrent.

Raphael, Benjamin J.; Volik, Stanislav; Yu, Peng; Wu, Chunxiao; Huang, Guiqing; Linardopoulou, Elena V.; Trask, Barbara J.; Waldman, Frederic; Costello, Joseph; Pienta, Kenneth J.; Mills, Gordon B.; Bajsarowicz, Krystyna; Kobayashi, Yasuko; Sridharan, Shivaranjani; Paris, Pamela L.

2008-01-01

326

Super resolution and spectral properties for 1D multilayer systems  

Digital Repository Infrastructure Vision for European Research (DRIVER)

We investigate the spectral properties of one-dimensional multilayer structures for the two polarizations TE and TM. We give a physical explanation for the large spatial transmission band that can be obtained with this kind of system, and the correlated super resolution effect. We also suggest a designing approach to build 1D metal-dielectric multilayer structures that have super resolution.

Mandatori, A.; Bertolotti, M.

2009-01-01

327

How Does Sequence Structure Affect the Judgment of Time? Exploring a Weighted Sum of Segments Model  

Science.gov (United States)

This paper examines the judgment of segmented temporal intervals, using short tone sequences as a convenient test case. In four experiments, we investigate how the relative lengths, arrangement, and pitches of the tones in a sequence affect judgments of sequence duration, and ask whether the data can be described by a simple weighted sum of…

Matthews, William J.

2013-01-01

328

Compression-based classification of biological sequences and structures via the Universal Similarity Metric: experimental assessment  

Directory of Open Access Journals (Sweden)

Full Text Available Abstract Background Similarity of sequences is a key mathematical notion for Classification and Phylogenetic studies in Biology. It is currently primarily handled using alignments. However, the alignment methods seem inadequate for post-genomic studies since they do not scale well with data set size and they seem to be confined only to genomic and proteomic sequences. Therefore, alignment-free similarity measures are actively pursued. Among those, USM (Universal Similarity Metric has gained prominence. It is based on the deep theory of Kolmogorov Complexity and universality is its most novel striking feature. Since it can only be approximated via data compression, USM is a methodology rather than a formula quantifying the similarity of two strings. Three approximations of USM are available, namely UCD (Universal Compression Dissimilarity, NCD (Normalized Compression Dissimilarity and CD (Compression Dissimilarity. Their applicability and robustness is tested on various data sets yielding a first massive quantitative estimate that the USM methodology and its approximations are of value. Despite the rich theory developed around USM, its experimental assessment has limitations: only a few data compressors have been tested in conjunction with USM and mostly at a qualitative level, no comparison among UCD, NCD and CD is available and no comparison of USM with existing methods, both based on alignments and not, seems to be available. Results We experimentally test the USM methodology by using 25 compressors, all three of its known approximations and six data sets of relevance to Molecular Biology. This offers the first systematic and quantitative experimental assessment of this methodology, that naturally complements the many theoretical and the preliminary experimental results available. Moreover, we compare the USM methodology both with methods based on alignments and not. We may group our experiments into two sets. The first one, performed via ROC (Receiver Operating Curve analysis, aims at assessing the intrinsic ability of the methodology to discriminate and classify biological sequences and structures. A second set of experiments aims at assessing how well two commonly available classification algorithms, UPGMA (Unweighted Pair Group Method with Arithmetic Mean and NJ (Neighbor Joining, can use the methodology to perform their task, their performance being evaluated against gold standards and with the use of well known statistical indexes, i.e., the F-measure and the partition distance. Based on the experiments, several conclusions can be drawn and, from them, novel valuable guidelines for the use of USM on biological data. The main ones are reported next. Conclusion UCD and NCD are indistinguishable, i.e., they yield nearly the same values of the statistical indexes we have used, accross experiments and data sets, while CD is almost always worse than both. UPGMA seems to yield better classification results with respect to NJ, i.e., better values of the statistical indexes (10% difference or above, on a substantial fraction of experiments, compressors and USM approximation choices. The compression program PPMd, based on PPM (Prediction by Partial Matching, for generic data and Gencompress for DNA, are the best performers among the compression algorithms we have used, although the difference in performance, as measured by statistical indexes, between them and the other algorithms depends critically on the data set and may not be as large as expected. PPMd used with UCD or NCD and UPGMA, on sequence data is very close, although worse, in performance with the alignment methods (less than 2% difference on the F-measure. Yet, it scales well with data set size and it can work on data other than sequences. In summary, our quantitative analysis naturally complements the rich theory behind USM and supports the conclusion that the methodology is worth using because of its robustness, flexibility, scalability, and competitiveness with existing techniques. In particular, the methodology applies to all biological

Manzini Giovanni

2007-07-01

329

Structural characterization of genomes by large scale sequence-structure threading: application of reliability analysis in structural genomics  

Directory of Open Access Journals (Sweden)

Full Text Available Abstract Background We establish that the occurrence of protein folds among genomes can be accurately described with a Weibull function. Systems which exhibit Weibull character can be interpreted with reliability theory commonly used in engineering analysis. For instance, Weibull distributions are widely used in reliability, maintainability and safety work to model time-to-failure of mechanical devices, mechanisms, building constructions and equipment. Results We have found that the Weibull function describes protein fold distribution within and among genomes more accurately than conventional power functions which have been used in a number of structural genomic studies reported to date. It has also been found that the Weibull reliability parameter ? for protein fold distributions varies between genomes and may reflect differences in rates of gene duplication in evolutionary history of organisms. Conclusions The results of this work demonstrate that reliability analysis can provide useful insights and testable predictions in the fields of comparative and structural genomics.

Brunham Robert C

2004-07-01

330

IMPROVEMENTS OF RIVER MODELING 1D DATA PREPARATION  

Directory of Open Access Journals (Sweden)

Full Text Available Improvements of river modeling 1D data preparation. The importance of hydrographical networks data and the need for detailed studies do generate an increase of projects in this specialized area and a diversification of river mathematical modeling software. River mathematical modeling can be done in two ways, namely; the "2D mode" and the “1D mode”. The “2D mode” is where a digital terrain model of a full hydrographical basin must be produced and "1D mode" is where only cross sections, long sections and structures elevations needs to be presented in a graphical environment and in a specific formats for the mathematical modeling software. This paper will show the principle of a custom built GIS, specially created to help the preparation of 1D river modeling data. The benefits are; elimination of human errors, automated processing, increasing productivity, flexible output and cost reduction.

ION-MARIAN MOISOIU

2012-11-01

331

The HIVToolbox 2 web system integrates sequence, structure, function and mutation analysis.  

Science.gov (United States)

There is enormous interest in studying HIV pathogenesis for improving the treatment of patients with HIV infection. HIV infection has become one of the best-studied systems for understanding how a virus can hijack a cell. To help facilitate discovery, we previously built HIVToolbox, a web system for visual data mining. The original HIVToolbox integrated information for HIV protein sequence, structure, functional sites, and sequence conservation. This web system has been used for almost 40,000 searches. We report improvements to HIVToolbox including new functions and workflows, data updates, and updates for ease of use. HIVToolbox2, is an improvement over HIVToolbox with new functions. HIVToolbox2 has new functionalities focused on HIV pathogenesis including drug-binding sites, drug-resistance mutations, and immune epitopes. The integrated, interactive view enables visual mining to generate hypotheses that are not readily revealed by other approaches. Most HIV proteins form multimers, and there are posttranslational modification and protein-protein interaction sites at many of these multimerization interfaces. Analysis of protease drug binding sites reveals an anatomy of drug resistance with different types of drug-resistance mutations regionally localized on the surface of protease. Some of these drug-resistance mutations have a high prevalence in specific HIV-1 M subtypes. Finally, consolidation of Tat functional sites reveals a hotspot region where there appear to be 30 interactions or posttranslational modifications. A cursory analysis with HIVToolbox2 has helped to identify several global patterns for HIV proteins. An initial analysis with this tool identifies homomultimerization of almost all HIV proteins, functional sites that overlap with multimerization sites, a global drug resistance anatomy for HIV protease, and specific distributions of some DRMs in specific HIV M subtypes. HIVToolbox2 is an open-access web application available at [http://hivtoolbox2.bio-toolkit.com]. PMID:24886930

Sargeant, David P; Deverasetty, Sandeep; Strong, Christy L; Alaniz, Izua J; Bartlett, Alexandria; Brandon, Nicholas R; Brooks, Steven B; Brown, Frederick A; Bufi, Flaviona; Chakarova, Monika; David, Roxanne P; Dobritch, Karlyn M; Guerra, Horacio P; Hedden, Michael W; Kumra, Rma; Levitt, Kelvy S; Mathew, Kiran R; Matti, Ray; Maza, Dorothea Q; Mistry, Sabyasachy; Novakovic, Nemanja; Pomerantz, Austin; Portillo, Josue; Rafalski, Timothy F; Rathnayake, Viraj R; Rezapour, Noura; Songao, Sarah; Tuggle, Sean L; Yousif, Sandy; Dorsky, David I; Schiller, Martin R

2014-01-01

332

Analysis of the Population Structure of Anaplasma phagocytophilum Using Multilocus Sequence Typing  

Science.gov (United States)

Anaplasma phagocytophilum is a Gram-negative obligate intracellular bacterium that replicates in neutrophils. It is transmitted via tick-bite and causes febrile disease in humans and animals. Human granulocytic anaplasmosis is regarded as an emerging infectious disease in North America, Europe and Asia. However, although increasingly detected, it is still rare in Europe. Clinically apparent A. phagocytophilum infections in animals are mainly found in horses, dogs, cats, sheep and cattle. Evidence from cross-infection experiments that A. phagocytophilum isolates of distinct host origin are not uniformly infectious for heterologous hosts has led to several approaches of molecular strain characterization. Unfortunately, the results of these studies are not always easily comparable, because different gene regions and fragment lengths were investigated. Multilocus sequence typing is a widely accepted method for molecular characterization of bacteria. We here provide for the first time a universal typing method that is easily transferable between different laboratories. We validated our approach on an unprecedented large data set of almost 400 A. phagocytophilum strains from humans and animals mostly from Europe. The typability was 74% (284/383). One major clonal complex containing 177 strains was detected. However, 54% (49/90) of the sequence types were not part of a clonal complex indicating that the population structure of A. phagocytophilum is probably semiclonal. All strains from humans, dogs and horses from Europe belonged to the same clonal complex. As canine and equine granulocytic anaplasmosis occurs frequently in Europe, human granulocytic anaplasmosis is likely to be underdiagnosed in Europe. Further, wild boars and hedgehogs may serve as reservoir hosts of the disease in humans and domestic animals in Europe, because their strains belonged to the same clonal complex. In contrast, as they were only distantly related, roe deer, voles and shrews are unlikely to harbor A. phagocytophilum strains infectious for humans, domestic or farm animals. PMID:24699849

Huhn, Christian; Winter, Christina; Wolfsperger, Timo; Wüppenhorst, Nicole; Strašek Smrdel, Katja; Skuballa, Jasmin; Pfäffle, Miriam; Petney, Trevor; Silaghi, Cornelia; Dyachenko, Viktor; Pantchev, Nikola; Straubinger, Reinhard K.; Schaarschmidt-Kiener, Daniel; Ganter, Martin; Aardema, Matthew L.; von Loewenich, Friederike D.

2014-01-01

333

Structure and recognition of sheared tandem G x A base pairs associated with human centromere DNA sequence at atomic resolution.  

Science.gov (United States)

G x A mismatched base pairs are frequently found in nucleic acids. Human centromere DNA sequences contain unusual repeating motifs, e.g. , (GAATG)n x (CATTC)n found in the human chromosome. The purine-rich strand of this repeating pentamer sequence forms duplex and hairpin structures with unusual stability. The high stability of these structures is contributed by the "sheared" G x A base pairs which present a novel recognition surface for ligands and proteins. We have solved the crystal structure, by the multiple-wavelength anomalous diffraction (MAD) method of d(CCGAATGAGG) in which the centromere core sequence motif GAATG is embedded. Three crystal forms were refined to near-atomic resolution. The structures reveal the detailed conformation of tandem G x A base pairs whose unique hydrogen-bonding surface has interesting interactions with bases, hydrated magnesium ions, cobalt(III)hexaammine, spermine, and water molecules. The results are relevant in understanding the structure associated with human centromere sequence in particular and G x A base pairs in nucleic acids (including RNA, like ribozyme) in general. PMID:10600106

Gao, Y G; Robinson, H; Sanishvili, R; Joachimiak, A; Wang, A H

1999-12-14

334

Correlation property of length sequences based on global structure of complete genome  

CERN Document Server

This paper considers three kinds of length sequences of the complete genome. Detrended fluctuation analysis, spectral analysis, and the mean distance spanned within time $L$ are used to discuss the correlation property of these sequences. Through comparing the appropriate exponents of the three methods, it is found that the exponent related to the mean distance is the best scale to characterise the correlation property of the time series. The values of the exponents of these three kinds of length sequences of bacteria indicate that the increments of the sequences are uncorrelated ($\\gamma =1.0\\pm 0.03$). It is also found that these sequences exhibit $1/f$ noise in some interval of frequency ($f>1$). The length of this interval of frequency depends on the length of the sequence. The shape of the periodogram in $f>1$ exhibits some periodicity. The period seems to depend on the length and the complexity of the length sequence.

Yu, Z G; Wang, B; Wang, Bin

2001-01-01

335

SFAPS: an R package for structure/function analysis of protein sequences based on informational spectrum method.  

Science.gov (United States)

The R package SFAPS has been developed for structure/function analysis of protein sequences based on information spectrum method. The informational spectrum method employs the electron-ion interaction potential parameter as the numerical representation for the protein sequence, and obtains the characteristic frequency of a particular protein interaction after computing the Discrete Fourier Transform for protein sequences. The informational spectrum method is often used to analyze protein sequences, so we developed this software tool, which is implemented as an add-on package to the freely available and widely used statistical language R. Our package is distributed as open source code for Linux, Unix and Microsoft Windows. It is released under the GNU General Public License. The R package along with its source code and additional material are freely available at http://mlsbl.tongji.edu.cn/DBdownload.asp. PMID:25132640

Deng, Su-Ping; Huang, De-Shuang

2014-10-01

336

Structure and sequence of mutations induced by ionizing radiation at selectable loci in Chinese hamster ovary cells  

International Nuclear Information System (INIS)

The spectrum of mutations induced by ionizing radiation at two non-essential genetic loci varies markedly. Those at the adenine phosphoribosyl transferase (aprt) locus predominantly have no detectable alterations of gene structure on Southern blots, while those at the hypoxanthine guanine phosphoribosyl transferase (hprt) locus are largely massive deletions eliminating all coding sequence. Insertion mutations were detected at both loci. To characterize the sequence alterations producing the minor changes at the aprt locus, two mutant genes were cloned from lambda genomic libraries and sequenced. One of these mutants proved to be a 20 base-pair deletion formed between two short (3 base-pair) direct repeat sequences, while the second was the result of a 58 base-pair insertion accompanied by a 13 base-pair deletion. (author)

337

Insight into G-DNA structural polymorphism and folding from sequence and loop connectivity through free energy analysis.  

Science.gov (United States)

The lengths of G-tracts and their connecting loop sequences determine G-quadruplex folding and stability. Complete understanding of the sequence-structure relationships remains elusive. Here, single-loop G-quadruplexes were investigated using explicit solvent molecular dynamics (MD) simulations to characterize the effect of loop length, loop sequence, and G-tract length on the folding topologies and stability of G-quadruplexes. Eight loop types, including different variants of lateral, diagonal, and propeller loops, and six different loop sequences [d0 (i.e., no intervening residues in the loop), dT, dT(2), dT(3), dTTA, and dT(4)] were considered through MD simulation and free energy analysis. In most cases the free energetic estimates agree well with the experimental observations. The work also provides new insight into G-quadruplex folding and stability. This includes reporting the observed instability of the left propeller loop, which extends the rules for G-quadruplex folding. We also suggest a plausible explanation why human telomere sequences predominantly form hybrid-I and hybrid-II type structures in K(+) solution. Overall, our calculation results indicate that short loops generally are less stable than longer loops, and we hypothesize that the extreme stability of sequences with very short loops could possibly derive from the formation of parallel multimers. The results suggest that free energy differences, estimated from MD and free energy analysis with current force fields and simulation protocols, are able to complement experiment and to help dissect and explain loop sequence, loop length, and G-tract length and orientation influences on G-quadruplex structure. PMID:21761922

Cang, Xiaohui; Šponer, Ji?í; Cheatham, Thomas E

2011-09-14

338

Developing JSequitur to Study the Hierarchical Structure of Biological Sequences in a Grammatical Inference Framework of String Compression Algorithms.  

Science.gov (United States)

Grammatical inference methods are expected to find grammatical structures hidden in biological sequences. One hopes that studies of grammar serve as an appropriate tool for theory formation. Thus, we have developed JSequitur for automatically generating the grammatical structure of biological sequences in an inference framework of string compression algorithms. Our original motivation was to find any grammatical traits of several cancer genes that can be detected by string compression algorithms. Through this research, we could not find any meaningful unique traits of the cancer genes yet, but we could observe some interesting traits in regards to the relationship among gene length, similarity of sequences, the patterns of the generated grammar, and compression rate. PMID:23346041

Galbadrakh, Bulgan; Lee, Kyung-Eun; Park, Hyun-Seok

2012-12-01

339

The performance of several multiple-sequence alignment programs in relation to secondary-structure features for an rRNA sequence.  

Science.gov (United States)

The performances of five global multiple-sequence alignment programs (CLUSTAL W, Divide and Conquer, Malign, PileUp, and TreeAlign) were evaluated using part of the animal mitochondrial small subunit (12S) rRNA molecule. Conserved sequence motifs derived from an alignment based on secondary structural information were used to score how well each program aligned a data set of five vertebrate and five invertebrate taxa over a range of parameter values. All of the programs could align the motifs with reasonable accuracy for at least one set of parameter conditions, although if the whole sequence was considered, similarity to the structural alignment was only 25%-34%. Use of small gap costs generally gave more accurate results, although Malign and TreeAlign generated longer alignments when gap costs were low. The programs differed in the consistency of the alignments when gap cost was varied; CLUSTAL W, Divide and Conquer, and TreeAlign were the most accurate and robust, while PileUp performed poorly as gap cost values increased, and the accuracy of Malign fluctuated. Default settings for the programs did not give the best results, and attempting to select similar parameter values in different programs did not always result in more similar alignments. Poor alignment of even well-conserved motifs can occur if these are near sites with insertions or deletions. Since there is no a priori way to determine gap costs and because such costs can vary over the gene, alignment of rRNA sequences, particularly the less well conserved regions, should be treated carefully and aided by secondary structure and conserved motifs. Some motifs are single bases and so are often invisible to alignment programs. Our tests involved the most conserved regions of the 12S rRNA gene, and alignment of less well conserved regions will be more problematical. None of the alignments we examined produced a fully resolved phylogeny for the data set, indicating that this portion of 12S rRNA is insufficient for resolution of distant evolutionary relationships. PMID:10742045

Hickson, R E; Simon, C; Perrey, S W

2000-04-01

340

AdoMet radical proteins—from structure to evolution—alignment of divergent protein sequences reveals strong secondary structure element conservation  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Eighteen subclasses of S-adenosyl-l-methionine (AdoMet) radical proteins have been aligned in the first bioinformatics study of the AdoMet radical superfamily to utilize crystallographic information. The recently resolved X-ray structure of biotin synthase (BioB) was used to guide the multiple sequence alignment, and the recently resolved X-ray structure of coproporphyrinogen III oxidase (HemN) was used as the control. Despite the low 9% sequence identity between BioB and HemN, the multiple s...

Nicolet, Yvain; Drennan, Catherine L.

2004-01-01

 
 
 
 
341

Influence of the sequence on the ab initio band structures of single and double stranded DNA models  

Science.gov (United States)

The solid state physical approach is widely used for the characterization of electronic properties of DNA. In the simplest case the helical symmetry is explicitly utilized with a repeat unit containing only a single nucleotide or nucleotide pair. This model provides a band structure that is easily interpretable and reflects the main characteristic features of the single nucleotide or a nucleotide pair chain, respectively. The chemical variability of the different DNA chains is, however, almost completely neglected in this way. In the present work we have investigated the effect of the different sequences on the band structure of periodic DNA models. For this purpose we have applied the Hartree-Fock crystal orbital method for single and double stranded DNA chains with two different subsequent nucleotides in the repeat unit of former and two different nucleotide pairs in the latter case, respectively. These results are compared to simple helical models with uniform sequences. The valence and conduction bands related to the stacked nucleotide bases of single stranded DNA built up only from guanidine as well as of double stranded DNA built up only from guanidine-cytidine pairs showed special properties different from the other cases. Namely, they had higher conduction and lower valence band positions and this way larger band gaps and smaller widths of these bands. With the introduction of non-uniform guanidine containing sequences band structures became more similar to each other and to the band structures of other sequences without guanidine. The maximal bandwidths of the non-uniform sequences are considerably smaller than in the case of uniform sequences implying smaller charge carrier mobilities both in the conduction and valence bands.

Bogár, Ferenc; Bende, Attila; Ladik, János

2014-06-01

342

Slump folds and gravity slide structures in a Lower Palaeozoic marginal basin sequence (the Skiddaw Group) N.W. England  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Major folds with associated thrust faults and a major olistostrome are described from the Skiddaw Group, a Lower Ordovician turbidite sequence in the Lake District of NW England. The style and geometry of the structures are shown to be compatible with their generation as submarine slumps or slide masses although they are much larger than any slump structures hitherto described from Britain. The predominant strain is shown to be simple shear. Spatial and temporal variations in strain permit a ...

Webb, B. C.; Cooper, A. H.

1988-01-01

343

Three-dimensional simulations of near-surface convection in main-sequence stars - I. Overall structure  

Digital Repository Infrastructure Vision for European Research (DRIVER)

The near-surface layers of cool main-sequence stars are structured by convective flows, which are overshooting into the atmosphere. The flows and the associated spatio-temporal variations of density and temperature affect spectral line profiles and thus have an impact on estimates of stellar properties such as effective temperature, gravitational acceleration, and abundances. We aim at identifying distinctive properties of the thermodynamic structure of the atmospheres of di...

Beeck, Benjamin; Cameron, Robert H.; Reiners, Ansgar; Schu?ssler, Manfred

2013-01-01

344

STING Millennium: a web-based suite of programs for comprehensive and simultaneous analysis of protein structure and sequence  

Science.gov (United States)

STING Millennium Suite (SMS) is a new web-based suite of programs and databases providing visualization and a complex analysis of molecular sequence and structure for the data deposited at the Protein Data Bank (PDB). SMS operates with a collection of both publicly available data (PDB, HSSP, Prosite) and its own data (contacts, interface contacts, surface accessibility). Biologists find SMS useful because it provides a variety of algorithms and validated data, wrapped-up in a user friendly web interface. Using SMS it is now possible to analyze sequence to structure relationships, the quality of the structure, nature and volume of atomic contacts of intra and inter chain type, relative conservation of amino acids at the specific sequence position based on multiple sequence alignment, indications of folding essential residue (FER) based on the relationship of the residue conservation to the intra-chain contacts and C?–C? and C?–C? distance geometry. Specific emphasis in SMS is given to interface forming residues (IFR)—amino acids that define the interactive portion of the protein surfaces. SMS may simultaneously display and analyze previously superimposed structures. PDB updates trigger SMS updates in a synchronized fashion. SMS is freely accessible for public data at http://www.cbi.cnptia.embrapa.br, http://mirrors.rcsb.org/SMS and http://trantor.bioc.columbia.edu/SMS. PMID:12824333

Neshich, Goran; Togawa, Roberto C.; Mancini, Adauto L.; Kuser, Paula R.; Yamagishi, Michel E. B.; Pappas, Georgios; Torres, Wellington V.; Campos, Tharsis Fonseca e; Ferreira, Leonardo L.; Luna, Fabio M.; Oliveira, Adilton G.; Miura, Ronald T.; Inoue, Marcus K.; Horita, Luiz G.; de Souza, Dimas F.; Dominiquini, Fabiana; Álvaro, Alexandre; Lima, Cleber S.; Ogawa, Fabio O.; Gomes, Gabriel B.; Palandrani, Juliana F.; dos Santos, Gabriela F.; de Freitas, Esther M.; Mattiuz, Amanda R.; Costa, Ivan C.; de Almeida, Celso L.; Souza, Savio; Baudet, Christian; Higa, Roberto H.

2003-01-01

345

An Introductory Bioinformatics Exercise to Reinforce Gene Structure and Expression and Analyze the Relationship between Gene and Protein Sequences  

Science.gov (United States)

We have developed an introductory bioinformatics exercise for sophomore biology and biochemistry students that reinforces the understanding of the structure of a gene and the principles and events involved in its expression. In addition, the activity illustrates the severe effect mutations in a gene sequence can have on the protein product.…

Almeida, Craig A.; Tardiff, Daniel F.; De Luca, Jane P.

2004-01-01

346

?-Glutamyl transpeptidase architecture: Effect of extra sequence deletion on autoprocessing, structure and stability of the protein from Bacillus licheniformis.  

Science.gov (United States)

?-Glutamyl transpeptidases (?-GTs, EC 2.3.2.2) are a class of ubiquitous enzymes which initiate the cleavage of extracellular glutathione (?-Glu-Cys-Gly, GSH) into its constituent glutamate, cysteine, and glycine and catalyze the transfer of its ?-glutamyl group to water (hydrolysis), amino acids or small peptides (transpeptidation). These proteins utilize a conserved Thr residue to process their chains into a large and a small subunit that then form the catalytically competent enzyme. Multiple sequence alignments have shown that some bacterial ?-GTs, including that from Bacillus licheniformis (BlGT), possess an extra sequence at the C-terminal tail of the large subunit, whose role is unknown. Here, autoprocessing, structure, catalytic activity and stability against both temperature and the chemical denaturant guanidinium hydrochloride of six BlGT extra-sequence deletion mutants have been characterized by SDS-PAGE, circular dichroism, intrinsic fluorescence and homology modeling. Data suggest that the extra sequence has a crucial role in enzyme activation and structural stability. Our results assist in the development of a structure-based interpretation of the autoprocessing reaction of ?-GTs and are helpful to unveil the molecular bases of their structural stability. PMID:25218521

Chi, Meng-Chun; Lo, Yi-Hui; Chen, Yi-Yu; Lin, Long-Liu; Merlino, Antonello

2014-09-10

347

Improved Bevirimat resistance prediction by combination of structural and sequence-based classifiers  

Directory of Open Access Journals (Sweden)

Full Text Available Abstract Background Maturation inhibitors such as Bevirimat are a new class of antiretroviral drugs that hamper the cleavage of HIV-1 proteins into their functional active forms. They bind to these preproteins and inhibit their cleavage by the HIV-1 protease, resulting in non-functional virus particles. Nevertheless, there exist mutations in this region leading to resistance against Bevirimat. Highly specific and accurate tools to predict resistance to maturation inhibitors can help to identify patients, who might benefit from the usage of these new drugs. Results We tested several methods to improve Bevirimat resistance prediction in HIV-1. It turned out that combining structural and sequence-based information in classifier ensembles led to accurate and reliable predictions. Moreover, we were able to identify the most crucial regions for Bevirimat resistance computationally, which are in line with experimental results from other studies. Conclusions Our analysis demonstrated the use of machine learning techniques to predict HIV-1 resistance against maturation inhibitors such as Bevirimat. New maturation inhibitors are already under development and might enlarge the arsenal of antiretroviral drugs in the future. Thus, accurate prediction tools are very useful to enable a personalized therapy.

Dybowski J Nikolaj

2011-11-01

348

Mining featured patterns of MiRNA interaction based on sequence and structure similarity.  

Science.gov (United States)

MicroRNA (miRNA) is an endogenous small noncoding RNA that plays an important role in gene expression through the post-transcriptional gene regulation pathways. There are many literature works focusing on predicting miRNA targets and exploring gene regulatory networks of miRNA families. We suggest, however, the study to identify the interaction between miRNAs is insufficient. This paper presents a framework to identify relationships between miRNAs using joint entropy, to investigate the regulatory features of miRNAs. Both the sequence and secondary structure are taken into consideration to make our method more relevant from the biological viewpoint. Further, joint entropy is applied to identify correlated miRNAs, which are more desirable from the perspective of the gene regulatory network. A data set including Drosophila melanogaster and Anopheles gambiae is used in the experiment. The results demonstrate that our approach is able to identify known miRNA interaction and uncover novel patterns of miRNA regulatory network. PMID:23929865

Chen, Qingfeng; Lan, Wei; Wang, Jianxin

2013-01-01

349

BEID: database for sequence-structure-function information on antigen-antibody interactions.  

Science.gov (United States)

The B-cell Epitope Interaction Database (BEID; http://datam.i2r.a-star.edu.sg/BEID) is an open-access database describing sequence-structure-function information on immunoglobulin (Ig)-antigen interactions. The current version of the database contains 164 antigens, 126 Ig and 189 Ig-antigen complexes extracted from the Protein Data Bank (PDB). Each entry is manually verified, classified, and analyzed for intermolecular interactions between antigens and the corresponding bound Ig molecules. Ig-antigen interaction information that is stored in BEID includes solvent accessibility, hydrogen bonds, non-hydrogen bonds, gap volume, gap index, interface area and contact residues. The database can be searched with a user-friendly search tool and schematic diagrams for Ig-antigen interactions are available for download in PDF format. The ultimate purpose of BEID is to enhance the understanding of the rules of engagement between antigen and the corresponding bound Ig molecules. It is also a precious data source for developing computational predictors for B-cell epitopes. PMID:19238231

Tong, Joo Chuan; Song, Chun Meng; Tan, Paul Thiam Joo; Ren, Ee Chee; Sinha, Animesh A

2008-01-01

350

Improved Bevirimat resistance prediction by combination of structural and sequence-based classifiers  

Science.gov (United States)

Background Maturation inhibitors such as Bevirimat are a new class of antiretroviral drugs that hamper the cleavage of HIV-1 proteins into their functional active forms. They bind to these preproteins and inhibit their cleavage by the HIV-1 protease, resulting in non-functional virus particles. Nevertheless, there exist mutations in this region leading to resistance against Bevirimat. Highly specific and accurate tools to predict resistance to maturation inhibitors can help to identify patients, who might benefit from the usage of these new drugs. Results We tested several methods to improve Bevirimat resistance prediction in HIV-1. It turned out that combining structural and sequence-based information in classifier ensembles led to accurate and reliable predictions. Moreover, we were able to identify the most crucial regions for Bevirimat resistance computationally, which are in line with experimental results from other studies. Conclusions Our analysis demonstrated the use of machine learning techniques to predict HIV-1 resistance against maturation inhibitors such as Bevirimat. New maturation inhibitors are already under development and might enlarge the arsenal of antiretroviral drugs in the future. Thus, accurate prediction tools are very useful to enable a personalized therapy. PMID:22082002

2011-01-01

351

Structure of a sequence of two zone polytropic stellar models with indices 0 and 1  

International Nuclear Information System (INIS)

The structure and physical properties of a sequence of two zone polytropic stellar models, based on E-type composite analytical solutions of the Lane-Emden equation for indices n = 0 and 1, have been determined. The resulting models are characterized by an inner zone of constant density, corresponding to the n = 0 component, and a relatively small envelope with a steep polytropic density gradient and index n = 1. At the surface of these near uniform density composite configurations the physically significant condition p = 0 is always satisfied, a condition which is not fulfilled by the complete polytrope of index n = 0. In each model the surface corresponds to the first zero of the associated composite function, which in turn is given by one of the higher order zeros of the E solution of the Lane-Emden equation for n = 1. The radial pulsational properties of these low central condensation type models have also been investigated with the relative amplitudes of radial displacement and density variation given as a function of radial distance for the first six modes of some selected models. Overall, these results establish that the radial displacement amplitudes are only significant in the n = 1 outer layer and accordingly the pulsations can be classified as essentially surface phenomena

352

EbEST: An Automated Tool Using Expressed Sequence Tags to Delineate Gene?Structure  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Large numbers of expressed sequence tags (ESTs) continue to fill public and private databases with partial cDNA sequences. However, using this huge amount of ESTs to facilitate gene finding in genomic sequence imposes a challenge, especially to wet-lab scientists who often have limited computing resources. In an effort to consolidate the information hidden in the vast number of ESTs into a readable and manageable format, we have developed EbEST—a program that automates the process of using ...

Jiang, Jian; Jacob, Howard J.

1998-01-01

353

Insilico structural analysis of parasporin 2 protein sequences of non-toxic bacillus thuringiensis  

Directory of Open Access Journals (Sweden)

Full Text Available The unusual and remarkable property of parasporin 2 of non-insecticidal Bacillus thuringiensis is specifically recognizing and selectively targeting human leukemic cell lines. The 37-kDa inactive nascent protein is proteolytically cleaved to the 30-kDa active form that loses both the N-terminal and the C-terminal segments. Accumulated cytological and biochemical observations on parasporin-2 imply that the protein is a pore-forming toxin. To confirm the hypothesis, insilico analysis was performed using homology modeling. The resulting model of parasporin 2 protein is unusually elongated and mainly comprises long ?-strands aligned with its long axis. It is similar to aerolysin-type ?-pore-forming toxins, which strongly reinforce the pore-forming hypothesis. The molecule can be divided into three domains. Domain 1, comprising a small ?-sheet sandwiched by short ?-helices, is probably the target-binding module. Two other domains are both ?-sandwiches and thought to be involved in oligomerization and pore formation. Domain 2 has a putative channel-forming ?-hairpin characteristic of aerolysin-type toxins. The surface of the protein has an extensive track of exposed side chains of serine and threonine residues. The track might orient the molecule on the cell membrane when domain 1 binds to the target until oligomerization and pore formation are initiated. The ?-hairpin has such a tight structure that it seems unlikely to reform as postulated in a recent model of pore formation developed for aerolysin-type toxins. Parasporin 2 (Accession no: BAD35170 protein sequence analysis indicated two different domains namely, aerolysin toxin and clostridium toxin domain based on different database searches (CDD and Pfam. It showed a close similarity with the available PDB template (PDB id: 2ZTB of parasporin which has cytocidal activity against MOLT-4, HL60 and Jurkat cell lines. Based on the PSI Blast analysis, 3D structures of the domains were predicted by using Swiss model server. Accuracy of the prediction of 3D structure of different domains of parasporin protein was further validated by Ramachandran plot and PROCHECK (G-value. The structure is dominated by ?-strands (67%, S1-12, most of which are remarkably extensive, running all or most of the longer axis of the molecule. This study helped to elucidate the 3D structure of parasporin 2 (Acc. No. BAD35170 which might enable to probe further its specific mechanism of action. Though the similarity is observed in the domain architecture, there is variation in the regions of the domains even among the same group of parasporin 2. Docking of this model structure and experimental structure with specific receptors of the cancer cells will facilitate to explore mechanism of parasporin 2 action and also provide information about its evolutionary relationship with toxic Cry proteins.

Ayyasamy Mahalakshmi

2010-04-01

354

A Revised Parallel-Sequence Morphological Classification of Galaxies: Structure and Formation of S0 and Spheroidal Galaxies  

CERN Document Server

We update van den Bergh's parallel sequence galaxy classification in which S0 galaxies form a sequence S0a-S0b-S0c that parallels the sequence Sa-Sb-Sc of spiral galaxies. The ratio B/T of bulge to total light defines the position of a galaxy in each sequence. Our classification makes one improvement. We extend the S0a-S0b-S0c sequence to spheroidal ("Sph'") galaxies that are positioned in parallel to irregular galaxies in a similarly extended Sa-Sb-Sc-Im sequence. This provides a natural "home" for spheroidals, which previously were omitted from galaxy classifications. To motivate our juxtaposition of Sph and irregular galaxies, we present photometry and bulge-disk decompositions of Virgo S0s, including late-type S0s that bridge the gap between S0b and Sph galaxies. NGC 4762 is a SB0bc with B/T = 0.13. NGC 4452 is a SB0c galaxy with an even tinier pseudobulge. VCC 2048 and NGC 4638 have properties of both S0cs and Sphs. We update the structural parameter correlations Sphs, irregulars, bulges, and disks. We s...

Kormendy, John

2011-01-01

355

Characterization of bud emergence 46 (BEM46) protein: Sequence, structural, phylogenetic and subcellular localization analyses  

Energy Technology Data Exchange (ETDEWEB)

Highlights: •All eukaryotes have at least a single copy of a bem46 ortholog. •The catalytic triad of BEM46 is illustrated using sequence and structural analysis. •We identified indels in the conserved domain of BEM46 protein. •Localization studies of BEM46 protein were carried out using GFP-fusion tagging. -- Abstract: The bud emergence 46 (BEM46) protein from Neurospora crassa belongs to the ?/?-hydrolase superfamily. Recently, we have reported that the BEM46 protein is localized in the perinuclear ER and also forms spots close by the plasma membrane. The protein appears to be required for cell type-specific polarity formation in N. crassa. Furthermore, initial studies suggested that the BEM46 amino acid sequence is conserved in eukaryotes and is considered to be one of the widespread conserved “known unknown” eukaryotic genes. This warrants for a comprehensive phylogenetic analysis of this superfamily to unravel origin and molecular evolution of these genes in different eukaryotes. Herein, we observe that all eukaryotes have at least a single copy of a bem46 ortholog. Upon scanning of these proteins in various genomes, we find that there are expansions leading into several paralogs in vertebrates. Usingcomparative genomic analyses, we identified insertion/deletions (indels) in the conserved domain of BEM46 protein, which allow to differentiate fungal classes such as ascomycetes from basidiomycetes. We also find that exonic indels are able to differentiate BEM46 homologs of different eukaryotic lineage. Furthermore, we unravel that BEM46 protein from N. crassa possess a novel endoplasmic-retention signal (PEKK) using GFP-fusion tagging experiments. We propose that three residues namely a serine 188S, a histidine 292H and an aspartic acid 262D are most critical residues, forming a catalytic triad in BEM46 protein from N. crassa. We carried out a comprehensive study on bem46 genes from a molecular evolution perspective with combination of functional analyses. The evolutionary history of BEM46 proteins is characterized by exonic indels in lineage specific manner.

Kumar, Abhishek; Kollath-Leiß, Krisztina; Kempken, Frank, E-mail: fkempken@bot.uni-kiel.de

2013-08-30

356

Characterization of bud emergence 46 (BEM46) protein: Sequence, structural, phylogenetic and subcellular localization analyses  

International Nuclear Information System (INIS)

Highlights: •All eukaryotes have at least a single copy of a bem46 ortholog. •The catalytic triad of BEM46 is illustrated using sequence and structural analysis. •We identified indels in the conserved domain of BEM46 protein. •Localization studies of BEM46 protein were carried out using GFP-fusion tagging. -- Abstract: The bud emergence 46 (BEM46) protein from Neurospora crassa belongs to the ?/?-hydrolase superfamily. Recently, we have reported that the BEM46 protein is localized in the perinuclear ER and also forms spots close by the plasma membrane. The protein appears to be required for cell type-specific polarity formation in N. crassa. Furthermore, initial studies suggested that the BEM46 amino acid sequence is conserved in eukaryotes and is considered to be one of the widespread conserved “known unknown” eukaryotic genes. This warrants for a comprehensive phylogenetic analysis of this superfamily to unravel origin and molecular evolution of these genes in different eukaryotes. Herein, we observe that all eukaryotes have at least a single copy of a bem46 ortholog. Upon scanning of these proteins in various genomes, we find that there are expansions leading into several paralogs in vertebrates. Usingcomparative genomic analyses, we identified insertion/deletions (indels) in the conserved domain of BEM46 protein, which allow to differentiate fungal classes such as ascomycetes from basidiomycetes. We also find that exonic indels are able to differentiate BEM46 homologs of different eukaryotic lineage. Furthermore, we unravel that BEM46 protein from N. crassa possess a novel endoplasmic-retention signal (PEKK) using GFP-fusion tagging experiments. We propose that three residues namely a serine 188S, a histidine 292H and an aspartic acid 262D are most critical residues, forming a catalytic triad in BEM46 protein from N. crassa. We carried out a comprehensive study on bem46 genes from a molecular evolution perspective with combination of functional analyses. The evolutionary history of BEM46 proteins is characterized by exonic indels in lineage specific manner

357

Structure of the axial-vector meson $D_{s1}(2460)$ and the strong coupling constant $g_{D_{s1} D^* K}$ with the light-cone QCD sum rules  

Digital Repository Infrastructure Vision for European Research (DRIVER)

In this article, we take the point of view that the charmed axial-vector meson $D_{s1}(2460)$ is the conventional $c\\bar{s}$ meson and calculate the strong coupling constant $g_{D_{s1} D^* K}$ in the framework of the light-cone QCD sum rules approach. The numerical values of strong coupling constants $g_{D_{s1} D^* K}$ and $g_{D_{s0} D K}$ are very large, and support the hadronic dressing mechanism. Just like the scalar mesons $f_0(980)$ and $a_0(980)$, the scalar meson $D_{...

Wang, Z. G.

2006-01-01

358

An extended Escherichia coli "selenocysteine insertion sequence" (SECIS) as a multifunctional RNA structure.  

Science.gov (United States)

The genetic code, once thought to be rigid, has been found to permit several alternatives in its reading. Interesting alternative relates to the function of the UGA codon. Usually, it acts as a stop codon, but it can also direct the incorporation of the amino acid selenocysteine into a polypeptide. UGA-directed selenocysteine incorporation requires a cis-acting mRNA element called the "selenocysteine insertion sequence" (SECIS) that can form a stem-loop RNA structure. Here we discuss our investigation on the E. coli SECIS. This includes the follows: 1) The nature of the minimal E. coli SECIS. We found that in E. coli only the upper-stem and loop of 17 nucleotides of the SECIS is necessary for selenocysteine incorporation on the condition that it is located in the proper distance from the UGA [34]; 2) The upper stem and loop structure carries a bulged U residue that is required for selenocysteine incorporation [34] because of its interaction with SelB; and 3) We described an extended fdhF SECIS that includes the information for an additional function: The prevention of UGA readthrough under conditions of selenium deficiency [35]. This information is contained in a short mRNA region consisting of a single C residue adjacent to the UGA on its downstream side, and an additional segment consisting of the six nucleotides immediately upstream from it. These two regions act independently and additively and probably through different mechanisms. The single C residue acts as itself; the upstream region acts at the level of the two amino acids, arginine and valine, for which it codes. These two codons at the 5' side of the UGA correspond to the ribosomal E and P sites. Finally, we present a model for the E. coli fdhF SECIS as a multifunctional RNA structure containing three functional elements. Depending on the availability of selenium the SECIS enables one of two alternatives for the translational machinery: Either selenocysteine incorporation into a polypeptide or termination of the polypeptide chain. PMID:11568441

Engelberg-Kulka, H; Liu, Z; Li, C; Reches, M

2001-01-01

359

Structure-guided approach for detecting large domain inserts in protein sequences as illustrated using the haloacid dehalogenase superfamily.  

Science.gov (United States)

In multi-domain proteins, the domains typically run end-to-end, that is, one domain follows the C-terminus of another domain. However, approximately 10% of multi-domain proteins are formed by insertion of one domain sequence into that of another domain. Detecting such insertions within protein sequences is a fundamental challenge in structural biology. The haloacid dehalogenase superfamily (HADSF) serves as a challenging model system wherein a variable cap domain (?5-200 residues in length) accessorizes the ubiquitous Rossmann-fold core domain, with variations in insertion site and topology corresponding to different classes of cap types. Herein, we describe a comprehensive computational strategy, CapPredictor, for determining large, variable domain insertions in protein sequences. Using a novel sequence-alignment algorithm in conjunction with a structure-guided sequence profile from 154 core-domain-only structures, more than 40,000 HADSF member sequences were assigned cap types. The resulting data set afforded insight into HADSF evolution. Notably, a similar distribution of cap-type classes across different phyla was observed, indicating that all cap types existed in the last universal common ancestor. In addition, comparative analyses of the predicted cap-type and functional assignments showed that different cap types carry out similar chemistries. Thus, while cap domains play a role in substrate recognition and chemical reactivity, cap-type does not strictly define functional class. Through this example, we have shown that CapPredictor is an effective new tool for the study of form and function in protein families where domain insertion occurs. PMID:24577717

Pandya, Chetanya; Dunaway-Mariano, Debra; Xia, Yu; Allen, Karen N

2014-09-01

360

Structural gene for the phosphate-repressible phosphate-binding protein of Escherichia coli has its own promoter: complete nucleotide sequence of the phoS gene.  

Digital Repository Infrastructure Vision for European Research (DRIVER)

The complete nucleotide sequence of the phoS gene, the structural gene for the phosphate-repressible, periplasmic phosphate-binding protein Escherichia coli K-12, was determined. The phosphate-binding protein is synthesized in a precursor form which includes an additional N-terminal segment containing 25 amino acid residues, with the general characteristics of a signal sequence. The amino acid sequence derived from the nucleotide sequence shows the mature protein to be composed of 321 amino a...

Surin, B. P.; Jans, D. A.; Fimmel, A. L.; Shaw, D. C.; Cox, G. B.; Rosenberg, H.

1984-01-01

 
 
 
 
361

THE INTERIOR STRUCTURE CONSTANTS AS AN AGE DIAGNOSTIC FOR LOW-MASS, PRE-MAIN-SEQUENCE DETACHED ECLIPSING BINARY STARS  

Energy Technology Data Exchange (ETDEWEB)

We propose a novel method for determining the ages of low-mass, pre-main-sequence stellar systems using the apsidal motion of low-mass detached eclipsing binaries. The apsidal motion of a binary system with an eccentric orbit provides information regarding the interior structure constants of the individual stars. These constants are related to the normalized stellar interior density distribution and can be extracted from the predictions of stellar evolution models. We demonstrate that low-mass, pre-main-sequence stars undergoing radiative core contraction display rapidly changing interior structure constants (greater than 5% per 10 Myr) that, when combined with observational determinations of the interior structure constants (with 5%-10% precision), allow for a robust age estimate. This age estimate, unlike those based on surface quantities, is largely insensitive to the surface layer where effects of magnetic activity are likely to be most pronounced. On the main sequence, where age sensitivity is minimal, the interior structure constants provide a valuable test of the physics used in stellar structure models of low-mass stars. There are currently no known systems where this technique is applicable. Nevertheless, the emphasis on time domain astronomy with current missions, such as Kepler, and future missions, such as LSST, has the potential to discover systems where the proposed method will be observationally feasible.

Feiden, Gregory A. [Department of Physics and Astronomy, Dartmouth College, 6127 Wilder Laboratory, Hanover, NH 03755 (United States); Dotter, Aaron, E-mail: Gregory.A.Feiden.GR@Dartmouth.edu, E-mail: aaron.dotter@gmail.com [Research School of Astronomy and Astrophysics, Australian National University, Weston, ACT 2611 (Australia)

2013-03-10

362

THE INTERIOR STRUCTURE CONSTANTS AS AN AGE DIAGNOSTIC FOR LOW-MASS, PRE-MAIN-SEQUENCE DETACHED ECLIPSING BINARY STARS  

International Nuclear Information System (INIS)

We propose a novel method for determining the ages of low-mass, pre-main-sequence stellar systems using the apsidal motion of low-mass detached eclipsing binaries. The apsidal motion of a binary system with an eccentric orbit provides information regarding the interior structure constants of the individual stars. These constants are related to the normalized stellar interior density distribution and can be extracted from the predictions of stellar evolution models. We demonstrate that low-mass, pre-main-sequence stars undergoing radiative core contraction display rapidly changing interior structure constants (greater than 5% per 10 Myr) that, when combined with observational determinations of the interior structure constants (with 5%-10% precision), allow for a robust age estimate. This age estimate, unlike those based on surface quantities, is largely insensitive to the surface layer where effects of magnetic activity are likely to be most pronounced. On the main sequence, where age sensitivity is minimal, the interior structure constants provide a valuable test of the physics used in stellar structure models of low-mass stars. There are currently no known systems where this technique is applicable. Nevertheless, the emphasis on time domain astronomy with current missions, such as Kepler, and future missions, such as LSST, has the potential to discover systems where the proposed method will be observationally feasible.

363

Two-dimensional deterministic photonic band gap structures based on the quasiperiodic sequences at millimeter wave frequencies  

Directory of Open Access Journals (Sweden)

Full Text Available Two-dimensional quasi-periodic band gap structures were investigated theoretically in microwave frequency range. Quasiperiodic photonic crystal based on the square range, arranged in a quasi-periodical fashion which follows Thue Morse or Fibonaci period substitutional sequences were obtained by the inflation rules emerging from the quasi-periodic sequence. The introduction of 2D quasi-periodicity distribution like Thue Morse or Fibonacci order and deterministic aperiodicity give some interesting microwave properties and offers amultitude of adjacent pseudo-band gap in different frequency range. The potential of photonic structures are explored by varying the structural parameters. The photonic band gap formation was explored as function of geometries of the structures such as pillar radius and parameters of quasi-periodical sequences. The electromagnetic field distribution can be described as a quasi-localized state varied by some defect carried by Thue Morse order. These structures provide interesting properties, which could be used to design novelmicrowave devices.

Y. Trabelsi

2011-08-01

364

Nucleotide sequence of the phoS gene, the structural gene for the phosphate-binding protein of Escherichia coli.  

Digital Repository Infrastructure Vision for European Research (DRIVER)

phoS is the structural gene for the phosphate-binding protein, which is localized in periplasm and involved in active transport of phosphate in Escherichia coli. It is also a negative regulatory gene for the pho regulon, and the gene expression is inducible by phosphate starvation. The complete nucleotide sequence of the phoS gene was determined by the method of Maxam and Gilbert (A. M. Maxam and W. Gilbert, Methods Enzymol. 65:499-560, 1980). The amino acid sequences at the amino termini of ...

Magota, K.; Otsuji, N.; Miki, T.; Horiuchi, T.; Tsunasawa, S.; Kondo, J.; Sakiyama, F.; Amemura, M.; Morita, T.; Shinagawa, H.

1984-01-01

365

Malakite: an automatic tool for characterisation of structure of reliable blocks in multiple alignments of protein sequences.  

Science.gov (United States)

It makes sense to speak of alignment of protein sequences only within the regions, where the sequences are related to each other. This simple consideration is often disregarded by programs of multiple alignment construction. A package for alignment analysis MAlAKiTE (Multiple Alignment Automatic Kinship Tiling Engine) is introduced. It aims to find the blocks of reliable alignment, which contain related regions only, within the whole alignment and allows for dealing with them. The validity of the detection of reliable blocks' was verified by comparison with structural data. PMID:20556859

Burkov, Boris; Nagaev, Boris; Spirin, Sergei; Alexeevski, Andrei

2010-06-01

366

Phosphorylation-dependent PIH1D1 interactions define substrate specificity of the R2TP cochaperone complex.  

Science.gov (United States)

The R2TP cochaperone complex plays a critical role in the assembly of multisubunit machines, including small nucleolar ribonucleoproteins (snoRNPs), RNA polymerase II, and the mTORC1 and SMG1 kinase complexes, but the molecular basis of substrate recognition remains unclear. Here, we describe a phosphopeptide binding domain (PIH-N) in the PIH1D1 subunit of the R2TP complex that preferentially binds to highly acidic phosphorylated proteins. A cocrystal structure of a PIH-N domain/TEL2 phosphopeptide complex reveals a highly specific phosphopeptide recognition mechanism in which Lys57 and 64 in PIH1D1, along with a conserved DpSDD phosphopeptide motif within TEL2, are essential and sufficient for binding. Proteomic analysis of PIH1D1 interactors identified R2TP complex substrates that are recruited by the PIH-N domain in a sequence-specific and phosphorylation-dependent manner suggestive of a common mechanism of substrate recognition. We propose that protein complexes assembled by the R2TP complex are defined by phosphorylation of a specific motif and recognition by the PIH1D1 subunit. PMID:24656813

Ho?ejší, Zuzana; Stach, Lasse; Flower, Thomas G; Joshi, Dhira; Flynn, Helen; Skehel, J Mark; O'Reilly, Nicola J; Ogrodowicz, Roksana W; Smerdon, Stephen J; Boulton, Simon J

2014-04-10

367

Phosphorylation-Dependent PIH1D1 Interactions Define Substrate Specificity of the R2TP Cochaperone Complex  

Directory of Open Access Journals (Sweden)

Full Text Available The R2TP cochaperone complex plays a critical role in the assembly of multisubunit machines, including small nucleolar ribonucleoproteins (snoRNPs, RNA polymerase II, and the mTORC1 and SMG1 kinase complexes, but the molecular basis of substrate recognition remains unclear. Here, we describe a phosphopeptide binding domain (PIH-N in the PIH1D1 subunit of the R2TP complex that preferentially binds to highly acidic phosphorylated proteins. A cocrystal structure of a PIH-N domain/TEL2 phosphopeptide complex reveals a highly specific phosphopeptide recognition mechanism in which Lys57 and 64 in PIH1D1, along with a conserved DpSDD phosphopeptide motif within TEL2, are essential and sufficient for binding. Proteomic analysis of PIH1D1 interactors identified R2TP complex substrates that are recruited by the PIH-N domain in a sequence-specific and phosphorylation-dependent manner suggestive of a common mechanism of substrate recognition. We propose that protein complexes assembled by the R2TP complex are defined by phosphorylation of a specific motif and recognition by the PIH1D1 subunit.

Zuzana Ho?ejší

2014-04-01

368

Uncovering the Pseudo-Subclonal Structure of Tumor Sample With Copy Number Variation Analysis of Next-Generation Sequencing Data - Yi Qiao, TCGA Scientific Symposium 2011  

Science.gov (United States)

Home News and Events Multimedia Library Videos Uncovering the Pseudo-Subclonal Structure of Tumor Samples - Yi Qiao Uncovering the Pseudo-Subclonal Structure of Tumor Sample With Copy Number Variation Analysis of Next-Generation Sequencing Data -

369

The effect of disease associated point mutations on 5?-reductase (AKR1D1) enzyme function.  

Science.gov (United States)

The stereospecific 5?-reduction of ?(4)-3-ketosterols is very difficult to achieve chemically and introduces a 90° bend between ring A and B of the planar steroid. In mammals, the reaction is catalyzed by steroid 5?-reductase, a member of the aldo-keto reductase (AKR) family. The human enzyme, AKR1D1, plays an essential role in bile-acid biosynthesis since the 5?-configuration is required for the emulsifying properties of bile. Deficient 5?-reductase activity can lead to cholestasis and neo-natal liver failure and is often lethal if it remains untreated. In five patients with 5?-reductase deficiency, sequencing revealed individual, non-synonymous point mutations in the AKR1D1 gene: L106F, P133R, G223E, P198L and R261C. However, mapping these mutations to the AKR1D1 crystal structure failed to reveal any obvious involvement in substrate or cofactor binding or catalytic mechanism, and it remained unclear whether these mutations could be causal for the observed disease. We analyzed the positions of the reported mutations and found that they reside in highly conserved portions of AKR1D1 and hypothesized that they would likely lead to changes in protein folding, and hence enzyme activity. Attempts to purify the mutant enzymes for further characterization by over-expression in Escherichia coli yielded sufficient amounts of only one mutant (P133R). This enzyme exhibited reduced K(m) and k(cat) values with the bile acid intermediate ?(4)-cholesten-7?-ol-3-one as substrate reminiscent of uncompetitive inhibition. In addition, P133R displayed no change in cofactor affinity but was more thermolabile as judged by CD-spectroscopy. When all AKR1D1 mutants were expressed in HEK 293 cells, protein expression levels and enzyme activity were dramatically reduced. Furthermore, cycloheximide treatment revealed decreased stability of several of the mutants compared to wild type. Our data show, that all five mutations identified in patients with functional bile acid deficiency strongly affected AKR1D1 enzyme functionality and therefore may be causal for this disease. PMID:21185810

Mindnich, Rebekka; Drury, Jason E; Penning, Trevor M

2011-05-30

370

Statistical aspects of discerning indel-type structural variation via DNA sequence alignment  

Directory of Open Access Journals (Sweden)

Full Text Available Abstract Background Structural variations in the form of DNA insertions and deletions are an important aspect of human genetics and especially relevant to medical disorders. Investigations have shown that such events can be detected via tell-tale discrepancies in the aligned lengths of paired-end DNA sequencing reads. Quantitative aspects underlying this method remain poorly understood, despite its importance and conceptual simplicity. We report the statistical theory characterizing the length-discrepancy scheme for Gaussian libraries, including coverage-related effects that preceding models are unable to account for. Results Deletion and insertion statistics both depend heavily on physical coverage, but otherwise differ dramatically, refuting a commonly held doctrine of symmetry. Specifically, coverage restrictions render insertions much more difficult to capture. Increased read length has the counterintuitive effect of worsening insertion detection characteristics of short inserts. Variance in library insert length is also a critical factor here and should be minimized to the greatest degree possible. Conversely, no significant improvement would be realized in lowering fosmid variances beyond current levels. Detection power is examined under a straightforward alternative hypothesis and found to be generally acceptable. We also consider the proposition of characterizing variation over the entire spectrum of variant sizes under constant risk of false-positive errors. At 1% risk, many designs will leave a significant gap in the 100 to 200 bp neighborhood, requiring unacceptably high redundancies to compensate. We show that a few modifications largely close this gap and we give a few examples of feasible spectrum-covering designs. Conclusion The theory resolves several outstanding issues and furnishes a general methodology for designing future projects from the standpoint of a spectrum-wide constant risk.

Wilson Richard K

2009-08-01

371

Complete sequence and structure of the gene for human adenosine deaminase.  

Science.gov (United States)

The nucleotide sequence of the human adenosine deaminase gene was determined. The gene was isolated in a series of overlapping lambda phage clones containing human germ line DNA. A total of 36,741 base pairs were sequenced, including 32,040 base pairs from the transcription initiation site to the polyadenylation site, 3935 base pairs of 5'-flanking DNA, and 766 base pairs of 3'-flanking DNA. The gene contains 12 exons separated by 11 introns. The exons range in size from 62 to 325 base pairs while the introns are 76-15 166 base pairs in size. The area sequenced contains 23 copies of Alu repetitive DNA and a single copy of an "O" family repeat. All but one of these repeat sequences are located in the first three introns or the 5'-flanking region. The apparent promoter region of the gene lacks the "TATA" and "CAAT" sequences often found in eucaryotic promoters and is extremely G/C rich. Contained within this region are areas homologous to other G/C-rich promoters, including six decanucleotide sequences that are highly homologous to sequences identified as functional binding sites for transcription factor Sp1. PMID:3028473

Wiginton, D A; Kaplan, D J; States, J C; Akeson, A L; Perme, C M; Bilyk, I J; Vaughn, A J; Lattier, D L; Hutton, J J

1986-12-16

372

Simulation of Organic Solar Cells Using AMPS-1D Program  

Directory of Open Access Journals (Sweden)

Full Text Available The analysis of microelectronic and photonic structure in one dimension program [AMPS-1D] program has been successfully used to study inorganic solar cells. In this work the program has been used to optimize the performance of the organic solar cells. The cells considered consist of poly(2-methoxy-5-(3,7- dimethyloctyloxy-1,4-phenylenevinylene [MDMO-PPV

Samah G. Babiker

2012-03-01

373

Prediction of guide strand of microRNAs from its sequence and secondary structure  

Directory of Open Access Journals (Sweden)

Full Text Available Abstract Background MicroRNAs (miRNAs are produced by the sequential processing of a long hairpin RNA transcript by Drosha and Dicer, an RNase III enzymes, and form transitory small RNA duplexes. One strand of the duplex, which incorporates into RNA-induced silencing complex (RISC and silences the gene expression is called guide strand, or miRNA; while the other strand of duplex is degraded and called the passenger strand, or miRNA*. Predicting the guide strand of miRNA is important for better understanding the RNA interference pathways. Results This paper describes support vector machine (SVM models developed for predicting the guide strands of miRNAs. All models were trained and tested on a dataset consisting of 329 miRNA and 329 miRNA* pairs using five fold cross validation technique. Firstly, models were developed using mono-, di-, and tri-nucleotide composition of miRNA strands and achieved the highest accuracies of 0.588, 0.638 and 0.596 respectively. Secondly, models were developed using split nucleotide composition and achieved maximum accuracies of 0.553, 0.641 and 0.602 for mono-, di-, and tri-nucleotide respectively. Thirdly, models were developed using binary pattern and achieved the highest accuracy of 0.708. Furthermore, when integrating the secondary structure features with binary pattern, an accuracy of 0.719 was seen. Finally, hybrid models were developed by combining various features and achieved maximum accuracy of 0.799 with sensitivity 0.781 and specificity 0.818. Moreover, the performance of this model was tested on an independent dataset that achieved an accuracy of 0.80. In addition, we also compared the performance of our method with various siRNA-designing methods on miRNA and siRNA datasets. Conclusion In this study, first time a method has been developed to predict guide miRNA strands, of miRNA duplex. This study demonstrates that guide and passenger strand of miRNA precursors can be distinguished using their nucleotide sequence and secondary structure. This method will be useful in understanding microRNA processing and can be implemented in RNA silencing technology to improve the biological and clinical research. A web server has been developed based on SVM models described in this study http://crdd.osdd.net:8081/RISCbinder/.

Ahmed Firoz

2009-04-01

374

A Study of Sequence Clustering on Protein’s Primary Structure using a Statistical Method  

Directory of Open Access Journals (Sweden)

Full Text Available The clustering of biological sequences into biologically meaningful classesdenotes two computationally complex challenges: the choice of a biologically pertinent andcomputable criterion to evaluate the clusters homogenity, and the optimal exploration ofthe solution space. Here we are analysing the clustering potential of a new method ofsequence similarity based on statistical sequence content evaluation. Applying on the samedata the popular CLUSTAL W method for sequence similarity we contrasted the results.The analysis, computational efficiency and high accuracy of the results from the newmethod is encouraging for further development that could make it an appealing alternativeto the existent methods.

Alina Bogan-Marta

2006-07-01

375

Genomic structure analysis of promoter sequence of a mouse mu opioid receptor gene.  

Digital Repository Infrastructure Vision for European Research (DRIVER)

We have isolated mouse mu opioid receptor genomic clones (termed MOR) containing the entire amino acid coding sequence corresponding to rat MOR-1 cDNA, including additional 5' flanking sequence. The mouse MOR gene is > 53 kb long, and the coding sequence is divided by three introns, with exon junctions in codons 95 and 213 and between codons 386 and 387. The first intron is > 26 kb, the second is 0.8 kb, and the third is > 12 kb. Multiple transcription initiation sites were observed, with fou...

Min, B. H.; Augustin, L. B.; Felsheim, R. F.; Fuchs, J. A.; Loh, H. H.

1994-01-01

376

Crystal structure of importin-? complexed with a classic nuclear localization sequence obtained by oriented peptide library screening  

International Nuclear Information System (INIS)

Full text: Importin-? (Imp?) plays a role in the classical nuclear import pathway, binding to cargo proteins with activities in the nucleus. Different Imp? paralogs responsible for specific cargos can be found in a single organism. The cargos contain nuclear localization sequences (NLSs), which are characterized by one or two clusters of basic amino acids (monopartite and bipartite NLSs, respectively). In this work we present the crystal structure of Imp? from M. musculus (residues 70-529, lacking the auto inhibitory domain) bound to a NLS peptide (pepTM). The peptide corresponds to the optimal sequence obtained by an oriented peptide library experiment designed to probe the specificity of the major NLS binding site. The peptide library used five degenerate positions and identified the sequence KKKRR as the optimal sequence for binding to this site for mouse Imp? (70-529). The protein was obtained using an E. coli expression system and purified by affinity chromatography followed by an ion exchange chromatography. A single crystal of Imp? -pepTM complex was grown by the hanging drop method. The data were collected using the Synchrotron Radiation Source LNLS, Brazil and processed to 2.3. Molecular replacement techniques were used to determine the crystal structure. Electron density corresponding to the peptide was present in both major and minor binding sites The peptide is bound to Imp? similar as the simian virus 40 (SV40) large tumour (T)-antigen NLS. Binding assays confirmed that the peptide bound to Imp? with low nM affinities. This is the first time that structural information has been linked to an oriented peptide library screening approach for importin-?; the results will contribute to understanding of the sequence determinants of classical NLSs, and may help identify as yet unidentified classical NLSs in novel proteins. (author)

377

Sequence dependent structure and thermodynamics of DNA oligonucleotides and polynucleotides: uv melting and NMR (nuclear magnetic resonance) studies  

International Nuclear Information System (INIS)

Thermodynamic parameters for double strand formation have been measured for the twenty-five DNA double helices made by mixing deoxyoligonucleotides of the sequence dCA3XA3G with the complement dCT3YT3G. Each of the bases A, C, G, T, and I (I = hypoxanthine) have been substituted at the positions labeled X and Y. The results are analyzed in terms of nearest neighbors. At higher temperatures the sequences containing a G/center dot/C base pair become more stable than those containing only A/center dot/T. All molecules containing mismatcher are destabilized with respect to those with only Watson-Crick pairing, but there is a wide range of destabilization. Large neighboring base effects upon stability were observed. For example, when (X, Y) = (I, A), the duplex is eightfold more stable than when (X, Y) = (A, I). Independent of sequence effects the order of stabilities is: I/center dot/C /succ/ I/center dot/ A/succ/ I/center dot/T ? I/center dot/G. All of these results are discussed within the context of models for sequence dependent DNA secondary structure, replication fidelity and mechanisms of mismatch repair, and implications for probe design. The duplex deoxyoligonucleotide d(GGATGGGAG)/center dot/d(CTCCCATCC) is a portion of the gene recognition sequence of the protein transcription factor IIIA. The crystal structure of this oligonucleotide was shown to be A-form The present study employs Nuclear Magnetic Resonance, optical, chemical and enzymatic techniques to investigate the solution structure of this DNA 9-mer. (157 refs., 19 figs., 10 tabs.)

378

Sequence dependent structure and thermodynamics of DNA oligonucleotides and polynucleotides: uv melting and NMR (nuclear magnetic resonance) studies  

Energy Technology Data Exchange (ETDEWEB)

Thermodynamic parameters for double strand formation have been measured for the twenty-five DNA double helices made by mixing deoxyoligonucleotides of the sequence dCA/sub 3/XA/sub 3/G with the complement dCT/sub 3/YT/sub 3/G. Each of the bases A, C, G, T, and I (I = hypoxanthine) have been substituted at the positions labeled X and Y. The results are analyzed in terms of nearest neighbors. At higher temperatures the sequences containing a G)centerreverse arrowdot)C base pair become more stable than those containing only A)centerreverse arrowdot)T. All molecules containing mismatcher are destabilized with respect to those with only Watson-Crick pairing, but there is a wide range of destabilization. Large neighboring base effects upon stability were observed. For example, when (X, Y) = (I, A), the duplex is eightfold more stable than when (X, Y) = (A, I). Independent of sequence effects the order of stabilities is: I)centerreverse arrowdot)C )succ) I)centerreverse arrowdot) A)succ) I)centerreverse arrowdot)T approx. I)centerreverse arrowdot)G. All of these results are discussed within the context of models for sequence dependent DNA secondary structure, replication fidelity and mechanisms of mismatch repair, and implications for probe design. The duplex deoxyoligonucleotide d(GGATGGGAG))centerreverse arrowdot)d(CTCCCATCC) is a portion of the gene recognition sequence of the protein transcription factor IIIA. The crystal structure of this oligonucleotide was shown to be A-form The present study employs Nuclear Magnetic Resonance, optical, chemical and enzymatic techniques to investigate the solution structure of this DNA 9-mer. (157 refs., 19 figs., 10 tabs.

Aboul-ela, F.M.

1987-12-01

379

Crystal structure of importin-{alpha} complexed with a classic nuclear localization sequence obtained by oriented peptide library screening  

Energy Technology Data Exchange (ETDEWEB)

Full text: Importin-{alpha} (Imp{alpha}) plays a role in the classical nuclear import pathway, binding to cargo proteins with activities in the nucleus. Different Imp{alpha} paralogs responsible for specific cargos can be found in a single organism. The cargos contain nuclear localization sequences (NLSs), which are characterized by one or two clusters of basic amino acids (monopartite and bipartite NLSs, respectively). In this work we present the crystal structure of Imp{alpha} from M. musculus (residues 70-529, lacking the auto inhibitory domain) bound to a NLS peptide (pepTM). The peptide corresponds to the optimal sequence obtained by an oriented peptide library experiment designed to probe the specificity of the major NLS binding site. The peptide library used five degenerate positions and identified the sequence KKKRR as the optimal sequence for binding to this site for mouse Imp{alpha} (70-529). The protein was obtained using an E. coli expression system and purified by affinity chromatography followed by an ion exchange chromatography. A single crystal of Imp{alpha} -pepTM complex was grown by the hanging drop method. The data were collected using the Synchrotron Radiation Source LNLS, Brazil and processed to 2.3. Molecular replacement techniques were used to determine the crystal structure. Electron density corresponding to the peptide was present in both major and minor binding sites The peptide is bound to Imp{alpha} similar as the simian virus 40 (SV40) large tumour (T)-antigen NLS. Binding assays confirmed that the peptide bound to Imp{alpha} with low nM affinities. This is the first time that structural information has been linked to an oriented peptide library screening approach for importin-{alpha}; the results will contribute to understanding of the sequence determinants of classical NLSs, and may help identify as yet unidentified classical NLSs in novel proteins. (author)

Takeda, A.A.S.; Fontes, M.R.M. [UNESP, Universidade Estadual Paulista, Botucatu, SP (Brazil); Yang, S.N.Y. [University of Melbourne, Melbourne (Australia); Harris, J.M. [Queensland University of Technology, Brisbane (Australia); Jans, D.A. [Monash University, Clayton (Australia); Kobe, B. [University of Queensland, Brisbane, QU (Australia)

2012-07-01

380

The nucleotide sequence of cDNA coding for the structural proteins of foot-and-mouth disease virus.  

Science.gov (United States)

The complete nucleotide sequence of cDNA coding for the structural capsid polypeptides of foot-and-mouth disease virus (FMDV) (strain A(10)61) has been determined. Portions of the flanking sequence coding for the nonstructural proteins p20a and p52 are also provided. The three larger structural polypeptides VP1, VP2 and VP3 have unmodified Mrs of 23248, 24649 and 24213, respectively. The size of the smaller polypeptide, VP4, can only be estimated at 7360 because the 5'-limit of its coding region is not yet known with certainty. The sequence data for VP1 (the major immunising antigen) and the amino-terminal quarter of p52 are compared with the data of Kurz et al. (Nucl. Acids Res. 9 (1981) 1919-1931) for a different serotype (O1K). This shows that variation is much greater in the region coding for VP1 than in that coding for p52. This is reflected in the level of amino acid sequence variation predicted for the two proteins. Analysis of relative codon usage reveals a strong bias in favour of C and G over U and A in the third base position. The dinucleotide frequencies show a bias against A-U and U-A, and for A-C and C-A. PMID:6282711

Boothroyd, J C; Harris, T J; Rowlands, D J; Lowe, P A

1982-02-01

 
 
 
 
381

Cyanobacterial community structure as seen from RNA polymerase gene sequence analysis.  

Digital Repository Infrastructure Vision for European Research (DRIVER)

PCR was used to amplify DNA-dependent RNA polymerase gene sequences specifically from the cyanobacterial population in a seawater sample from the Sargasso Sea. Sequencing and analysis of the cloned fragments suggest that the population in the sample consisted of two distinct clusters of Prochlorococcus-like cyanobacteria and four clusters of Synechococcus-like cyanobacteria. The diversity within these clusters was significantly different, however. Clones within each Synechococcus-like cluster...

Palenik, B.

1994-01-01

382

Divergent N-Terminal Sequences Target an Inducible Testis Deubiquitinating Enzyme to Distinct Subcellular Structures  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Ubiquitin-specific processing proteases (UBPs) presently form the largest enzyme family in the ubiquitin system, characterized by a core region containing conserved motifs surrounded by divergent sequences, most commonly at the N-terminal end. The functions of these divergent sequences remain unclear. We identified two isoforms of a novel testis-specific UBP, UBP-t1 and UBP-t2, which contain identical core regions but distinct N termini, thereby permitting dissection of the functions of these...

Lin, Haijiang; Keriel, Anne; Morales, Carlos R.; Bedard, Nathalie; Zhao, Qing; Hingamp, Pascal; Lefranc?ois, Stephanie; Combaret, Lydie; Wing, Simon S.

2000-01-01

383

Structural Analysis of a Repetitive Protein Sequence Motif in Strepsirrhine Primate Amelogenin  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Strepsirrhines are members of a primate suborder that has a distinctive set of features associated with the development of the dentition. Amelogenin (AMEL), the better known of the enamel matrix proteins, forms 90% of the secreted organic matrix during amelogenesis. Although AMEL has been sequenced in numerous mammalian lineages, the only reported strepsirrhine AMEL sequences are those of the ring-tailed lemur and galago, which contain a set of additional proline-rich tandem repeats absent in...

Lacruz, Rodrigo S.; Lakshminarayanan, Rajamani; Bromley, Keith M.; Hacia, Joseph G.; Bromage, Timothy G.; Snead, Malcolm L.; Moradian-oldak, Janet; Paine, Michael L.

2011-01-01

384

Cellular immunostimulation by CpG-sequence-coated DNA origami structures  

Digital Repository Infrastructure Vision for European Research (DRIVER)

To investigate the potential of DNA origami constructs as programmable and noncytotoxic immunostimulants, we tested the immune responses induced by hollow 30-helix DNA origami tubes covered with up to 62 cytosine-phosphate-guanine (CpG) sequences in freshly isolated spleen cells. Unmethylated CpG sequences that are highly specific for bacterial DNA are recognized by a specialized receptor of the innate immune system localized in the endosome, the Toll-like receptor 9 (TLR9). When incubated wi...

Schu?ller, Verena J.; Heidegger, Simon; Sandholzer, Nadja; Nickels, Philipp C.; Suhartha, Nina A.; Endres, Stefan; Bourquin, Carole; Liedl, Tim

2012-01-01

385

Manganese-dependent peroxidase from Phanerochaete chrysosporium. Primary structure deduced from cDNA sequence.  

Science.gov (United States)

A cDNA clone encoding a manganese-dependent peroxidase from the filamentous fungus Phanerochaete chrysosporium was isolated and characterized. The clone, lambda MP-1, was isolated by screening a lambda gt11 expression library with polyclonal antibodies raised against a purified manganese-dependent peroxidase (isozyme H4, pI 4.5). The lambda MP-1 cDNA sequence predicts a mature protein containing 358 amino acids with a molecular weight of 37,711 preceded by a leader peptide of 24 amino acid residues. The N-terminal amino acid sequence of a purified manganese-dependent peroxidase (H4) corresponds to the sequence deduced from the cDNA. Some homology (58% in nucleotide sequence and 65% in amino acid sequence) is observed between the manganese-dependent peroxidase and lignin peroxidase isozyme H8. The highest degree of similarity is observed near the enzyme active site. Residues essential for peroxidase activity, the distal and proximal histidines, can be identified in the amino acid sequence. Near these residues, homology is also observed with several other peroxidases. Northern blot analysis of poly(A)+ RNA from nitrogen-limited P. chrysosporium cultures indicates that the level of messenger RNA correlates with expression of the enzyme and its activity. This is consistent with the regulation of the enzyme being at the level of transcription. PMID:2760033

Pease, E A; Andrawis, A; Tien, M

1989-08-15

386